Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013672.1 Kokia drynarioides strain JFW-HI SEQ_128700, 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: 100403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:2518 original size:13 final size:13
Alignment explanation
Indices: 2500--2524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2490 GATAACAACA
2500 CCTACAATTATTG
1 CCTACAATTATTG
2513 CCTACAATTATT
1 CCTACAATTATT
2525 CGGGGTTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (13 bp):
CCTACAATTATTG
Found at i:5540 original size:199 final size:199
Alignment explanation
Indices: 5196--5591 Score: 684
Period size: 199 Copynumber: 2.0 Consensus size: 199
5186 ATGGGAATCC
* * *
5196 CTGAAATTGGCCATCTGGAATTTTAAACATCCAAGTGAACTTAATGCTCAGGGTCAGGAGCTGCT
1 CTGAAATTGGCCATCTGCAATTTTAAACACCCAAGTGAACGTAATGCTCAGGGTCAGGAGCTGCT
* *
5261 TAAGAACCAGAAAGTGAAGTTGCTTCTGTAAAAGAAACAACATGCCCTTCTCAAGACACTACCAT
66 TAAGAAACAGAAAGTGAAGATGCTTCTGTAAAAGAAACAACATGCCCTTCTCAAGACACTACCAT
5326 TTAAGTAAGCATTTAACTAGGATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAGCTTTT
131 TTAAGTAAGCATTTAACTAGGATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAGCTTTT
5391 ATCA
196 ATCA
* * *
5395 CTGAAATTGGCCATCTGCAGTTTTAAACACCCAAGTGCAGGTAATGCTCAGGGTCAGGAGCTGCT
1 CTGAAATTGGCCATCTGCAATTTTAAACACCCAAGTGAACGTAATGCTCAGGGTCAGGAGCTGCT
* *
5460 TAAGAAACAGCAAGTGAAGATGCTTCTGTAAAAGAACCAACATGCCCTTCTCAAGACACTACCAT
66 TAAGAAACAGAAAGTGAAGATGCTTCTGTAAAAGAAACAACATGCCCTTCTCAAGACACTACCAT
* *
5525 TTAAGTAATCATTTAACTAGTATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAGCTTTT
131 TTAAGTAAGCATTTAACTAGGATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAGCTTTT
5590 AT
196 AT
5592 AATCTAAATA
Statistics
Matches: 185, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
199 185 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (199 bp):
CTGAAATTGGCCATCTGCAATTTTAAACACCCAAGTGAACGTAATGCTCAGGGTCAGGAGCTGCT
TAAGAAACAGAAAGTGAAGATGCTTCTGTAAAAGAAACAACATGCCCTTCTCAAGACACTACCAT
TTAAGTAAGCATTTAACTAGGATGCAAGTTTTGGTGTACTCAAATGCTAGAATTAAATAGCTTTT
ATCA
Found at i:21324 original size:23 final size:23
Alignment explanation
Indices: 21251--21422 Score: 154
Period size: 23 Copynumber: 7.5 Consensus size: 23
21241 TATACGGAAC
* *
21251 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
21273 -AACAGAGAGCACA-TAAGTTCT
1 AAACAGAGAGCACACAAAGTGCT
* *
21294 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
21320 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
21343 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
21366 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
21389 GATCAGAGGGCACGA-AACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
21412 AAACAGAGAGC
1 AAACAGAGAGC
21423 GTTAGTGTTC
Statistics
Matches: 124, Mismatches: 19, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
21 17 0.14
23 88 0.71
24 1 0.01
25 13 0.10
26 5 0.04
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:21396 original size:69 final size:66
Alignment explanation
Indices: 21251--21388 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 66
21241 TATACGGAAC
* * *
21251 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTTCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACAAAG
21316 TGCT
63 TGCT
21320 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACAAA
21384 GTGCT
62 GTGCT
21389 GATCAGAGGG
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
68 2 0.03
69 32 0.52
70 11 0.18
71 11 0.18
72 6 0.10
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACAAAGTGC
T
Found at i:25147 original size:32 final size:33
Alignment explanation
Indices: 25101--25167 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
25091 CACTAGACAC
25101 TTAACTTTTTTTAATG-TTTTTAGAATTTTCTT
1 TTAACTTTTTTTAATGTTTTTTAGAATTTTCTT
*
25133 TTAAGTTTTTTTAATGTTTTTTAGAATTTTCTT
1 TTAACTTTTTTTAATGTTTTTTAGAATTTTCTT
25166 TT
1 TT
25168 CATCTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.45
33 18 0.55
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.67
Consensus pattern (33 bp):
TTAACTTTTTTTAATGTTTTTTAGAATTTTCTT
Found at i:25153 original size:11 final size:11
Alignment explanation
Indices: 25106--25154 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
25096 GACACTTAAC
25106 TTTTTTTAATG
1 TTTTTTTAATG
**
25117 TTTTTAGAAT-
1 TTTTTTTAATG
25127 TTTCTTTTAA-G
1 TTT-TTTTAATG
25138 TTTTTTTAATG
1 TTTTTTTAATG
25149 TTTTTT
1 TTTTTT
25155 AGAATTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.71
Consensus pattern (11 bp):
TTTTTTTAATG
Found at i:27454 original size:23 final size:25
Alignment explanation
Indices: 27404--27456 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
27394 TAAATATTTT
* * *
27404 ATTTTAAATATAAATATTTTATATA
1 ATTTAAAATATAAATATTATATAAA
27429 ATTTAAAATA-AAATATTATA-AAA
1 ATTTAAAATATAAATATTATATAAA
27452 ATTTA
1 ATTTA
27457 CTTATACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAAAATATAAATATTATATAAA
Found at i:38328 original size:6 final size:6
Alignment explanation
Indices: 38317--38341 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38307 TAACTAAGCC
38317 AAACCA AAACCA AAACCA AAACCA A
1 AAACCA AAACCA AAACCA AAACCA A
38342 GCCCAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCA
Found at i:40784 original size:31 final size:31
Alignment explanation
Indices: 40730--40789 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
40720 AGAACCCAAT
* * *
40730 GACTTAAATAAAATCTGTTGAATAGTTCAAC
1 GACTTAAATAAAATATGTCGAATAATTCAAC
40761 GACTTAAATGAAAATAT-TCGAATAATTCA
1 GACTTAAAT-AAAATATGTCGAATAATTCA
40790 GTGAGACAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (31 bp):
GACTTAAATAAAATATGTCGAATAATTCAAC
Found at i:43668 original size:6 final size:6
Alignment explanation
Indices: 43657--43690 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
43647 CACCTCATTG
*
43657 TCTCTT TCTCTT TCTCTT TCTCTT CCTCTT TCTC
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTC
43691 ACTAATTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
TCTCTT
Found at i:47377 original size:38 final size:37
Alignment explanation
Indices: 47325--47397 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
47315 TCTTATCGAT
* *
47325 GTAAAAAAATATGAGTTCGAGCTATTTATGGGTTGGG
1 GTAAAAAAACATGAGTTCGAACTATTTATGGGTTGGG
47362 GTAAAAAAAGCATGAGTTCGAACTATTTATGGGTTG
1 GTAAAAAAA-CATGAGTTCGAACTATTTATGGGTTG
47398 AGGAAGGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 9 0.27
38 24 0.73
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (37 bp):
GTAAAAAAACATGAGTTCGAACTATTTATGGGTTGGG
Found at i:48220 original size:18 final size:16
Alignment explanation
Indices: 48177--48237 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
48167 AATACCCACC
*
48177 TATATTAATATA-AAT
1 TATATTAAAATATAAT
* * *
48192 GATTATGAAAATATTAT
1 TA-TATTAAAATATAAT
48209 ATACTATTAAAATATAAT
1 -TA-TATTAAAATATAAT
48227 TATATTAAAAT
1 TATATTAAAAT
48238 TTAAAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 17 0.49
17 4 0.11
18 13 0.37
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (16 bp):
TATATTAAAATATAAT
Found at i:48234 original size:16 final size:17
Alignment explanation
Indices: 48199--48237 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
48189 AATGATTATG
*
48199 AAAATATTATATACTATT
1 AAAATATAAT-TACTATT
48217 AAAATATAATTA-TATT
1 AAAATATAATTACTATT
48233 AAAAT
1 AAAAT
48238 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 9 0.45
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATAATTACTATT
Found at i:49537 original size:30 final size:31
Alignment explanation
Indices: 49498--49559 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
49488 AAGTATCGAC
* *
49498 TTAAAAAAAGA-GTCAATTTTAAGTACCAAA
1 TTAAAAAAAGATGTCAAGTTCAAGTACCAAA
* *
49528 TTAAGAAAAGATGTCAAGTTCAAGTACTAAA
1 TTAAAAAAAGATGTCAAGTTCAAGTACCAAA
49559 T
1 T
49560 GTTATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (31 bp):
TTAAAAAAAGATGTCAAGTTCAAGTACCAAA
Found at i:75214 original size:115 final size:115
Alignment explanation
Indices: 75007--75236 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 115
74997 CTTGTTTATG
* *
75007 AAAATTGTCTGCGTGTGGCCTGGCCGAGATGGCCTCATGGCCTTATTTTGGGAACCACAGAGTTT
1 AAAAGTGTCTGCGTGTGGCCCGGCCGAGATGGCCTCATGGCCTTATTTTGGGAACCACAGAGTTT
75072 GAGTAATGTGGTTTTCAAATCCAATTGATTAAAAATATTAAGGGATAGTA
66 GAGTAATGTGGTTTTCAAATCCAATTGATTAAAAATATTAAGGGATAGTA
75122 AAAAGTGTCTGCGTGTGGCCCGGCCGAGATGGCCTCATGGCCTTATTTTGGGAACCACAGAGTTT
1 AAAAGTGTCTGCGTGTGGCCCGGCCGAGATGGCCTCATGGCCTTATTTTGGGAACCACAGAGTTT
75187 GAGTAATGTGGTTTTCAAATCCAATTGATTAAAAATATTAAGGGATAGTA
66 GAGTAATGTGGTTTTCAAATCCAATTGATTAAAAATATTAAGGGATAGTA
75237 TTTTGATGCG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (115 bp):
AAAAGTGTCTGCGTGTGGCCCGGCCGAGATGGCCTCATGGCCTTATTTTGGGAACCACAGAGTTT
GAGTAATGTGGTTTTCAAATCCAATTGATTAAAAATATTAAGGGATAGTA
Found at i:81160 original size:2 final size:2
Alignment explanation
Indices: 81153--81178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
81143 TGTTGGAACG
81153 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
81179 GGAAATGAAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:85609 original size:16 final size:18
Alignment explanation
Indices: 85583--85616 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
85573 TTAGAATTGG
85583 ATTGAAAAAATT-ATTTA
1 ATTGAAAAAATTAATTTA
85600 ATTG-AAAAATTAATTTA
1 ATTGAAAAAATTAATTTA
85617 GTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTGAAAAAATTAATTTA
Found at i:85642 original size:9 final size:9
Alignment explanation
Indices: 85606--85645 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
85596 TTTAATTGAA
85606 AAATTAATT
1 AAATTAATT
* *
85615 TAGTTAATT
1 AAATTAATT
*
85624 TAATTAATT
1 AAATTAATT
85633 AAATTAATT
1 AAATTAATT
85642 AAAT
1 AAAT
85646 AATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
AAATTAATT
Found at i:87156 original size:14 final size:14
Alignment explanation
Indices: 87139--87170 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
87129 AATTTAGAAG
87139 GAGAAAGAGAGAGA
1 GAGAAAGAGAGAGA
87153 GAGAAAGAGAGAGA
1 GAGAAAGAGAGAGA
87167 GAGA
1 GAGA
87171 TCTTAGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (14 bp):
GAGAAAGAGAGAGA
Found at i:88190 original size:58 final size:58
Alignment explanation
Indices: 88069--88198 Score: 145
Period size: 58 Copynumber: 2.2 Consensus size: 58
88059 ATCCGGGGGC
* * * * * * **
88069 AAAATGGTAATTTTAGATTCTCGAGGGTAAAATGGTAATTTTGGGAAAATTTGGGGTTT
1 AAAATGG-AATTTTAGAATCTCAAGGGTAAAATGGTAATTTTGAGAAAAATCGGGATAA
*
88128 AAAATGGAATTTTAGACATC-CAAGGGTAAAATGGTAATTTTTAGAAAAATCGGGATAA
1 AAAATGGAATTTTAGA-ATCTCAAGGGTAAAATGGTAATTTTGAGAAAAATCGGGATAA
*
88186 AAAATAGAATTTT
1 AAAATGGAATTTT
88199 TGGACATTCG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
58 51 0.85
59 9 0.15
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTAGAATCTCAAGGGTAAAATGGTAATTTTGAGAAAAATCGGGATAA
Found at i:88217 original size:30 final size:29
Alignment explanation
Indices: 88185--88474 Score: 280
Period size: 30 Copynumber: 9.8 Consensus size: 29
88175 AATCGGGATA
*
88185 AAAAATAGAATTTTTGGACA-TTCGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGT
* *
88214 AAAAATGGAGTTCTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
88243 AAAAATGGAATTTTTGGAAGTTTCGGGAGT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT
* * * * *
88273 AAATATGTAATTTTTAGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGGT
* ** *
88303 AAAAATGGAATTTTTTGAAGTTTTGAGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
88332 CAAAAATGGAATTTTTGGAAGTTCGGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTC-GGGGGT
* *
88363 AAAAAAT-GATTTTTTAGAAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGGGGGT
** **
88392 AAAAAATGTG-ATTTTTAAAAGTTTTGGGGT
1 -AAAAATG-GAATTTTTGGAAGTTCGGGGGT
*
88422 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
88452 AAAAATGTAATTTTTGGACAGTT
1 AAAAATGGAATTTTTGGA-AGTT
88475 TAAGGACCTC
Statistics
Matches: 217, Mismatches: 36, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.00
29 79 0.36
30 126 0.58
31 11 0.05
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:88350 original size:90 final size:88
Alignment explanation
Indices: 88208--88475 Score: 310
Period size: 90 Copynumber: 3.0 Consensus size: 88
88198 TTGGACATTC
* * * **
88208 GGGGG-TAAAAATGGAGTTCTTGGAAGTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGA
1 GGGGGTTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG-TTCGGG-
*
88271 GTAAATATGTAATTTTTAGAAGTTT
64 GTAAAAATGTAATTTTTAGAAGTTT
* * *
88296 TGGGGTTAAAAATGGAATTTTTTGAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGG
1 GGGGGTTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTC--GGG
* *
88361 GTAAAAAATG-ATTTTTTAGAAGTTC
64 GT-AAAAATGTAATTTTTAGAAGTTT
* *
88386 GGGGGTAAAAAATGTG-ATTTTTAAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGG
1 GGGGGTTAAAAATG-GAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCG-GG
*
88450 GTAAAAATGTAATTTTTGGACAGTTT
64 GTAAAAATGTAATTTTTAGA-AGTTT
88476 AAGGACCTCC
Statistics
Matches: 153, Mismatches: 18, Indels: 16
0.82 0.10 0.09
Matches are distributed among these distances:
88 12 0.08
89 39 0.25
90 92 0.60
91 10 0.07
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (88 bp):
GGGGGTTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGGGGT
AAAAATGTAATTTTTAGAAGTTT
Found at i:90266 original size:17 final size:17
Alignment explanation
Indices: 90240--90338 Score: 76
Period size: 17 Copynumber: 5.8 Consensus size: 17
90230 CTTTTTAATT
* *
90240 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAGTA
90257 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
* ** *
90274 AAATTAAACTCAAAAGTG
1 AATTTAAA-TTTAAAGTA
*
90292 AATTTAAATTTAGAA-CA
1 AATTTAAATTTA-AAGTA
* *
90309 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAGTA
*
90326 AA-TTAAAGTTAAA
1 AATTTAAATTTAAA
90339 ATTTGGACTC
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
16 11 0.17
17 37 0.59
18 15 0.24
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:91037 original size:206 final size:206
Alignment explanation
Indices: 90672--91205 Score: 680
Period size: 206 Copynumber: 2.6 Consensus size: 206
90662 TCTGGTTTCA
* * * * * * *
90672 TTGACTTGGCCTTCTTCTCAGTATCGT-ATCGGGAAGATGTCCGCATCACTTGTTTT-GATCCAC
1 TTGATTTGGCTTTCTTCTCAGTATC-TCATCAGGAAGATGACCGCGTCA-TTTTTTTCAATCCAC
* * * * * ** * *
90735 TTCTTTGTGTTTCATCAGGAAGATGGATTAGGTTTACTTCTCCGTATCTCATCAGGAAGCTAACC
64 TTCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACC
* * * *
90800 ACTTTATTCCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTAGGGTTTGAAGATTTGTTCAC
129 ACTTTATTCCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCAC
*
90865 ATCGAGCGTGGGT
194 ATCGAGCGTAGGT
* * *
90878 TTGATTTGGCTTTCTTCTCTGTGTCTCATCAGGAAGATGACCGCGTCATTTTTTTCAATCCATTT
1 TTGATTTGGCTTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTTTTTCAATCCACTT
*
90943 CTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCAT
66 CTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCAC
* * *
91008 TTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTCCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
91073 CGAGCGTAGGT
196 CGAGCGTAGGT
* * * * **
91084 TTGATTTGG-TCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAATCTGCT
1 TTGATTTGGCT-TTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTTTTTCAATCCACT
* *
91148 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCA-TCTCTCAGTATCTCATTAGGAAG
65 TCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACT-TCTCAGTATCTCATTAGGAAG
91206 ATGACCGTGT
Statistics
Matches: 285, Mismatches: 39, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
205 9 0.03
206 276 0.97
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (206 bp):
TTGATTTGGCTTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTTTTTCAATCCACTT
CTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCAC
TTTATTCCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACAT
CGAGCGTAGGT
Found at i:91235 original size:86 final size:86
Alignment explanation
Indices: 91087--91291 Score: 340
Period size: 86 Copynumber: 2.4 Consensus size: 86
91077 CGTAGGTTTG
** * *
91087 ATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAATCTGCTTCTC
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCTC
91152 TGTATCTCATCAAGAAGACGA
66 TGTATCTCATCAAGAAGACGA
*
91173 ATTTGGTCCA-TCTCTCAGTATCTCATTAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCT
1 ATTTGGTCCACT-TCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCT
*
91237 CTGTATCTCATCAGGAAGACGA
65 CTGTATCTCATCAAGAAGACGA
91259 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
91292 CTAACCATTT
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
85 1 0.01
86 108 0.98
87 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (86 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCTC
TGTATCTCATCAAGAAGACGA
Found at i:91385 original size:206 final size:206
Alignment explanation
Indices: 91173--91575 Score: 675
Period size: 206 Copynumber: 2.0 Consensus size: 206
91163 AAGAAGACGA
*
91173 ATTTGGTCCATC-TCTCAGTATCTCATTAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCT
1 ATTTGGT-CATCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCT
91237 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
65 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
* * * * *
91302 TATTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGG-TTCGAAGATTTGCTCATATC
130 CATCGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCT-GGGATTCGAAGATTTGCTCACATC
91366 GAGCTTGAGTTTG
194 GAGCTTGAGTTTG
* * *
91379 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGTGTTGTTTGTTTCAATCCGCTTCTC
1 ATTTGGTCATCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCTC
*
91444 TGTATCTCATCAGGAAGACGAATTTTGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTC
66 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTC
*
91509 ATCGCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGA
131 ATCGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGA
91574 GC
196 GC
91576 CCTGAGTTAG
Statistics
Matches: 184, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
205 6 0.03
206 178 0.97
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (206 bp):
ATTTGGTCATCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCTC
TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTC
ATCGCTTCAACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGA
GCTTGAGTTTG
Found at i:91432 original size:292 final size:292
Alignment explanation
Indices: 90891--91497 Score: 984
Period size: 292 Copynumber: 2.1 Consensus size: 292
90881 ATTTGGCTTT
* * * * *
90891 CTTCTCTGTGTCTCATCAGGAAGATGACCGCGTCATTTTTTTCAATCCATTTCTTTGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTCAT
* **
90956 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTTGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAA
*
91021 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTAGGTTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTAGGTTT
*
91086 GATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAATCTGCTTCT
196 GATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCT
91151 CTGTATCTCATCAAGAAGACGAATTTGGTCCA
261 CTGTATCTCATCAAGAAGACGAATTTGGTCCA
* * * *
91183 -TCTCTCAGTATCTCATTAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCA
1 CT-TCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTCA
91247 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCA
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCA
* * *
91312 ACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCATATCGAGC-TTGAGT
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTAG-GT
* * *
91376 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGTGTTGTTTGTTTCAATCCGCTT
194 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAATCCGCTT
* *
91441 CTCTGTATCTCATCAGGAAGACGAATTTTGTCCA
259 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCA
91475 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
91498 CTAACCATTT
Statistics
Matches: 289, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
291 3 0.01
292 285 0.99
293 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (292 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAA
CCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTAGGTTT
GATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAATCCGCTTCT
CTGTATCTCATCAAGAAGACGAATTTGGTCCA
Found at i:91701 original size:39 final size:39
Alignment explanation
Indices: 91658--91827 Score: 155
Period size: 39 Copynumber: 4.4 Consensus size: 39
91648 TGCCTCGTGA
* * * *
91658 TCGGGGTAGGAGTTTGGTTGACGATGATTTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
* *** * * **
91697 TCGGGGTAAGAGATCGAACGACTG-TAATTTACCCCTGGC
1 TCGGGGTAAGAGATTGGTTGAC-GATGATCTACCCCAAGC
* * *
91736 TCGGGGTAAGAGATTGGTTAACGATGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
*
91775 TCGGGGTAAAAGATTGGTTGATC-ATGATCTACCCCAAGC
1 TCGGGGTAAGAGATTGGTTGA-CGATGATCTACCCCAAGC
*
91814 TCGGGGTAAAAGAT
1 TCGGGGTAAGAGAT
91828 AAAATGGCTT
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
38 1 0.01
39 102 0.97
40 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
Found at i:91808 original size:78 final size:77
Alignment explanation
Indices: 91658--91827 Score: 180
Period size: 78 Copynumber: 2.2 Consensus size: 77
91648 TGCCTCGTGA
* * * * *
91658 TCGGGGTAGGAGTTTGGTTGACGATGATTTGCCCCAAGCTCGGGGTAAGAGATCGAACGACTGTA
1 TCGGGGTAAGAGATTGGTTAACGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAACGACTG-A
* **
91723 ATTTACCCCTGGC
65 ATCTACCCCAAGC
* * ***
91736 TCGGGGTAAGAGATTGGTTAACGATGATCTGCCCCAGGCTCGGGGTAAAAGATTGGTTGATCATG
1 TCGGGGTAAGAGATTGGTTAACGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAACGA-C-TG
91801 -ATCTACCCCAAGC
64 AATCTACCCCAAGC
*
91814 TCGGGGTAAAAGAT
1 TCGGGGTAAGAGAT
91828 AAAATGGCTT
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 73 0.96
79 1 0.01
80 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (77 bp):
TCGGGGTAAGAGATTGGTTAACGATGATCTGCCCCAAGCTCGGGGTAAAAGATCGAACGACTGAA
TCTACCCCAAGC
Found at i:92046 original size:101 final size:101
Alignment explanation
Indices: 91933--92130 Score: 272
Period size: 101 Copynumber: 2.0 Consensus size: 101
91923 GCTGCTGTAG
* ** * * * * *
91933 TTTTATTCCAACTTTGTTGCAACTTCAGGAAGATAGGATTTGATGTTGAAA-CTTCATCTTGCTC
1 TTTTAATCCAACTTTACTGCAACTTCAAGAAGATAGAAATTGACGTT-AAAGCTTCATATTGCTC
*
91997 TTACTACAAGTTCAAAGAGATAAAGACTTGCTATTGT
65 TTACTACAACTTCAAAGAGATAAAGACTTGCTATTGT
*
92034 TTTTAATCCAACTTTACTGCAACTTCAAGAGGATAGAAATTGACGTTAAAGCTTCATATTGCTCT
1 TTTTAATCCAACTTTACTGCAACTTCAAGAAGATAGAAATTGACGTTAAAGCTTCATATTGCTCT
* *
92099 TACTGCAACTTCAGAGAGATAAAGACTTGCTA
66 TACTACAACTTCAAAGAGATAAAGACTTGCTA
92131 CAGTAGTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 3 0.04
101 81 0.96
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (101 bp):
TTTTAATCCAACTTTACTGCAACTTCAAGAAGATAGAAATTGACGTTAAAGCTTCATATTGCTCT
TACTACAACTTCAAAGAGATAAAGACTTGCTATTGT
Found at i:92588 original size:139 final size:139
Alignment explanation
Indices: 92260--92605 Score: 442
Period size: 145 Copynumber: 2.4 Consensus size: 139
92250 TTCAAATCTT
* * * * * * *
92260 TGGTACTGGATTCGCCGTTACTGCTTAAATCTTTCCCTTATTATCTTCTGAGGTACATGGTCTGC
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTAAGGTACACGGTCTGC
* * *
92325 CATTGCAACTTAAACTTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCGGTATTAGA
66 CATTGCAACTTAAACTTTTCCCTTTTGTATCTTTGTGATACTAGATCTACCATTGCGGTATTAG-
92390 TCTTTCATGTCTTCA
130 ----T-ATGTCTTCA
* * *
92405 TGGTACTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCTTGTCTTCTAAGGTACACGGTCTGC
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTAAGGTACACGGTCTGC
* * * * *
92470 CGTTGCGACTTAGACTTTTTCCTTTTTGTATCTTTGTGATACTAGATCTACCATTGCGGTCTTAG
66 CATTGCAACTTAAAC-TTTTCCCTTTTGTATCTTTGTGATACTAGATCTACCATTGCGGTATTAG
*
92535 -ATGTCTTTA
130 TATGTCTTCA
*
92544 TGGTATTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTAAGGTACACGGTC
1 TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTAAGGTACACGGTC
92606 CGCCCCTTTT
Statistics
Matches: 179, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
139 66 0.37
145 69 0.39
146 44 0.25
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (139 bp):
TGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTAAGGTACACGGTCTGC
CATTGCAACTTAAACTTTTCCCTTTTGTATCTTTGTGATACTAGATCTACCATTGCGGTATTAGT
ATGTCTTCA
Found at i:92685 original size:50 final size:51
Alignment explanation
Indices: 92625--92832 Score: 169
Period size: 49 Copynumber: 4.2 Consensus size: 51
92615 TGTATCTTTG
92625 TGGTACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTCATGTATTC-A
1 TGGTACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTCATGTATTCTA
* * * * *
92675 TGTTACTGGATTCGCCGTTGTGG-CTTAAATCTTTCCC-TCTTGTCTTCTA
1 TGGTACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTCATGTATTCTA
* * * * * ** *
92724 AGGTACACGG-TCCGCCGTTG-CGACTTAGACCTTTCCCTTTTTGTA-TCTT
1 TGGTAC-TGGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTCATGTATTCTA
* * * * * *
92773 TGTGATACTGGATCTGCTGTTGCGGTATTAGATCTTTCCTTTCATGTCTTC-A
1 TG-G-TACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTCATGTATTCTA
92825 TGGTACTG
1 TGGTACTG
92833 AGACCTGTAG
Statistics
Matches: 121, Mismatches: 28, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
48 9 0.07
49 43 0.36
50 36 0.30
51 12 0.10
52 19 0.16
53 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (51 bp):
TGGTACTGGATCCGCCGTTGTGGTCTTAGATCTTTCCCTTCATGTATTCTA
Found at i:94059 original size:6 final size:6
Alignment explanation
Indices: 94025--94082 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
94015 TTTTTTCTAT
* * * *
94025 TTTTTG TTTTTC TTCTTG TTTTTGC -TTTTC TTTTT- TTTTTC TTTCTC
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC
94072 TTTTT- TTTTTC
1 TTTTTC TTTTTC
94083 ATTGTATCCG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
5 11 0.27
6 30 0.73
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:94064 original size:18 final size:18
Alignment explanation
Indices: 94024--94081 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
94014 TTTTTTTCTA
* *
94024 TTTTTTGTTTTTCTTCTT
1 TTTTTTGCTTTTCTTTTT
*
94042 GTTTTTGCTTTTC-TTTT
1 TTTTTTGCTTTTCTTTTT
94059 TTTTTT-CTTTCTCTTTTT
1 TTTTTTGCTTT-TCTTTTT
94077 TTTTT
1 TTTTT
94082 CATTGTATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.12
17 10 0.29
18 20 0.59
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (18 bp):
TTTTTTGCTTTTCTTTTT
Found at i:94080 original size:33 final size:33
Alignment explanation
Indices: 94017--94079 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
94007 TTCTCCCTTT
94017 TTTTCTATTTTTTGTTTTTCTTCTTGTTTTTGC
1 TTTTCTATTTTTTGTTTTTCTTCTTGTTTTTGC
* *
94050 TTTTCT-TTTTTTTTTCTTTC-TCTTTTTTTT
1 TTTTCTATTTTTTGTT-TTTCTTCTTGTTTTT
94080 TTCATTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.81
Consensus pattern (33 bp):
TTTTCTATTTTTTGTTTTTCTTCTTGTTTTTGC
Found at i:94082 original size:17 final size:16
Alignment explanation
Indices: 94017--94082 Score: 71
Period size: 17 Copynumber: 4.0 Consensus size: 16
94007 TTCTCCCTTT
* *
94017 TTTTCTATTTTTTGT-
1 TTTTCTTTTTTTTTTC
*
94032 TTTTCTTCTTGTTTTTGC
1 TTTTCTT-TT-TTTTTTC
94050 TTTTCTTTTTTTTTTC
1 TTTTCTTTTTTTTTTC
94066 TTTCTCTTTTTTTTTTC
1 TTT-TCTTTTTTTTTTC
94083 ATTGTATCCG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
15 6 0.14
16 11 0.26
17 19 0.44
18 7 0.16
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTC
Found at i:99386 original size:28 final size:28
Alignment explanation
Indices: 99356--99416 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
99346 AAATGAGACT
*
99356 TTTTGGATAC-CGGGGGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGGTAA
* *
99383 TTTTGGATTCTCGAGTGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGGTAA
*
99411 ATTTGG
1 TTTTGG
99417 GAAAATTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGGTAA
Found at i:99521 original size:30 final size:29
Alignment explanation
Indices: 99489--99743 Score: 212
Period size: 29 Copynumber: 8.6 Consensus size: 29
99479 AATCGGGATA
* *
99489 AAAAATAGAATTTTTGGACA-TTCAGGGGT
1 AAAAATGGAATTTTTGGA-ATTTTAGGGGT
*
99518 AAAAATGGAATTTTTGGAAGTTTTAAGGGT
1 AAAAATGGAATTTTTGGAA-TTTTAGGGGT
* * *
99548 -AAAATGTAATTTTTAGAATTTTTAGGGTT
1 AAAAATGGAATTTTTGGAA-TTTTAGGGGT
*
99577 AAAAATGGAATTTTTAGAAATTTTAGGGGTT
1 AAAAATGGAATTTTT-GGAATTTTAGGGG-T
* *
99608 AAAAATGGAATTTTTTGAAAGTTTAGGGGT
1 AAAAATGGAA-TTTTTGGAATTTTAGGGGT
*
99638 AAAAAATGGAATTTTTGGAAGTTTA-GGGT
1 -AAAAATGGAATTTTTGGAATTTTAGGGGT
*** * * *
99667 AAAAATGTG-ATTTTCAAAAGTTTCGAGGT
1 AAAAATG-GAATTTTTGGAATTTTAGGGGT
* * **
99696 GAAAAATGGAATTTTTGGTAGTTCGGGGGT
1 -AAAAATGGAATTTTTGGAATTTTAGGGGT
*
99726 AAAAATGTAATTTTTGGA
1 AAAAATGGAATTTTTGGA
99744 CAGTTTAAGG
Statistics
Matches: 187, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 19 0.10
29 66 0.35
30 62 0.33
31 35 0.19
32 5 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAATTTTAGGGGT
Done.