Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015379.1 Kokia drynarioides strain JFW-HI SEQ_130426, 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: 289102
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 339 characters in sequence are not A, C, G, or T
Found at i:3469 original size:18 final size:18
Alignment explanation
Indices: 3384--3477 Score: 109
Period size: 18 Copynumber: 5.2 Consensus size: 18
3374 CAGGTTCTGC
* * *
3384 TCCAAGTTAACGTTGTGA
1 TCCAAGTTCACATTGTGT
* *
3402 ACCAAGCTT-ACATCGTGT
1 TCCAAG-TTCACATTGTGT
*
3420 TCCAAGTTCACATCGTGT
1 TCCAAGTTCACATTGTGT
3438 TCCAAGTTCACATTGTGT
1 TCCAAGTTCACATTGTGT
*
3456 TCCAAGTTCACATTGGGT
1 TCCAAGTTCACATTGTGT
3474 TCCA
1 TCCA
3478 TGTCCACGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
17 2 0.03
18 63 0.94
19 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (18 bp):
TCCAAGTTCACATTGTGT
Found at i:5351 original size:6 final size:7
Alignment explanation
Indices: 5320--5363 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
5310 TATATATTTC
5320 TTTTATT
1 TTTTATT
*
5327 TTTTGTT
1 TTTTATT
*
5334 TTTAAAATT
1 TTT--TATT
5343 TTTTATT
1 TTTTATT
5350 TTTTATT
1 TTTTATT
5357 TTTTATT
1 TTTTATT
5364 ACATGGCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 26 0.84
9 5 0.16
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTATT
Found at i:22168 original size:6 final size:6
Alignment explanation
Indices: 22159--22195 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
22149 TGTGGATTGT
22159 GATTAG GATTAG GATTAG GATTAG GATTAG GATTAG G
1 GATTAG GATTAG GATTAG GATTAG GATTAG GATTAG G
22196 CCATAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (6 bp):
GATTAG
Found at i:29325 original size:2 final size:2
Alignment explanation
Indices: 29318--29342 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29308 AGACATTATG
29318 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29343 AGGTTAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31776 original size:18 final size:17
Alignment explanation
Indices: 31748--31789 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 17
31738 TTGTTGGGTG
31748 AAAAATGAATTACTAAAAA
1 AAAAATGAATT--TAAAAA
31767 AAAAAT-AATTTAAAAA
1 AAAAATGAATTTAAAAA
31783 AAAAATG
1 AAAAATG
31790 GTAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.55
18 4 0.18
19 6 0.27
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAATGAATTTAAAAA
Found at i:48562 original size:6 final size:6
Alignment explanation
Indices: 48551--48581 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
48541 AGTTGTTCAT
48551 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG G
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG G
48582 ACCGAGTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (6 bp):
GGGTCG
Found at i:48864 original size:22 final size:22
Alignment explanation
Indices: 48839--48881 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
48829 TAATTGTTAT
48839 AAAACAAAGAGA-ATGAGAGAGC
1 AAAACAAAGAGAGA-GAGAGAGC
* *
48861 AAAAGAGAGAGAGAGAGAGAG
1 AAAACAAAGAGAGAGAGAGAG
48882 AGAGAACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.05, G:0.35, T:0.02
Consensus pattern (22 bp):
AAAACAAAGAGAGAGAGAGAGC
Found at i:60299 original size:20 final size:21
Alignment explanation
Indices: 60260--60300 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
60250 ATGAAGGTTA
*
60260 GTCTCGAGACCTGAAGACCTTT
1 GTCTCGAGACAT-AAGACCTTT
60282 GTCTCGAGACAT-AGACCTT
1 GTCTCGAGACATAAGACCTT
60301 AATGTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
GTCTCGAGACATAAGACCTTT
Found at i:62761 original size:26 final size:26
Alignment explanation
Indices: 62725--62794 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
62715 AAATAAACAA
* *
62725 TTAATAGAATCAGTTGGTTAGATCAG
1 TTAATAGAATCAATTGGTTAAATCAG
*
62751 TTAATAGAATCAATTGATTAAATCAG
1 TTAATAGAATCAATTGGTTAAATCAG
62777 TTAATAGAATCAATTGGT
1 TTAATAGAATCAATTGGT
62795 CAAACTAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (26 bp):
TTAATAGAATCAATTGGTTAAATCAG
Found at i:62762 original size:13 final size:13
Alignment explanation
Indices: 62725--62788 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
62715 AAATAAACAA
62725 TTAATAGAATCAG
1 TTAATAGAATCAG
**
62738 TTGGTTAG-ATCAG
1 TT-AATAGAATCAG
*
62751 TTAATAGAATCAA
1 TTAATAGAATCAG
*
62764 TTGATTA-AATCAG
1 TT-AATAGAATCAG
62777 TTAATAGAATCA
1 TTAATAGAATCA
62789 ATTGGTCAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
12 6 0.15
13 27 0.69
14 6 0.15
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (13 bp):
TTAATAGAATCAG
Found at i:68548 original size:24 final size:24
Alignment explanation
Indices: 68503--68548 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
68493 AATATTTTAG
*
68503 TAATTTATTTTATACGATTTTTGA
1 TAATTTATTTTATACGAATTTTGA
*
68527 TAATTT-TTTTATTCTGAATTTT
1 TAATTTATTTTATAC-GAATTTT
68549 AAACTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (24 bp):
TAATTTATTTTATACGAATTTTGA
Found at i:68567 original size:21 final size:20
Alignment explanation
Indices: 68543--68588 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
68533 TTTTATTCTG
68543 AATTTTAAACTTTGAATTTCA
1 AATTTTAAACTTTGAATTT-A
*
68564 AATTTTAAATTTTGAATTTA
1 AATTTTAAACTTTGAATTTA
68584 AATTT
1 AATTT
68589 ATTTAGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (20 bp):
AATTTTAAACTTTGAATTTA
Found at i:69296 original size:20 final size:21
Alignment explanation
Indices: 69271--69310 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
69261 GTATTTGATT
*
69271 AATTTA-ATGCAAAACTAAAC
1 AATTTACAAGCAAAACTAAAC
*
69291 AATTTACAAGCAACACTAAA
1 AATTTACAAGCAAAACTAAA
69311 TTTATTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.23
Consensus pattern (21 bp):
AATTTACAAGCAAAACTAAAC
Found at i:70266 original size:28 final size:30
Alignment explanation
Indices: 70224--70281 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
70214 GAATTTGATC
*
70224 AAATCAAAATTTCATG-ATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
70253 AAATCAAAA-TTCATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
70282 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.28
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:75713 original size:16 final size:17
Alignment explanation
Indices: 75694--75731 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
75684 GAAAATGGAG
75694 TTTATTT-AAATTTAAA
1 TTTATTTAAAATTTAAA
75710 TTTATTTAAAATTTAAA
1 TTTATTTAAAATTTAAA
*
75727 ATTAT
1 TTTAT
75732 AAAATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATTTAAAATTTAAA
Found at i:77509 original size:30 final size:30
Alignment explanation
Indices: 77460--77630 Score: 197
Period size: 29 Copynumber: 5.7 Consensus size: 30
77450 GAGGGTCCCT
77460 AAACTGTCCAAAAAT-CCATTTTTGACCCCG
1 AAACT-TCCAAAAATCCCATTTTTGACCCCG
77490 AAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATCCCATTTTTGACCCCG
**
77520 -AACTTCCAAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATCCCATTTTTGACCCCG
* *
77549 AAACTTCCAAAAATTCCATTTTT-AGCTCCG
1 AAACTTCCAAAAATCCCATTTTTGA-CCCCG
* * **
77579 -AACTTCCAAAAATTCCATTTTTGACACTA
1 AAACTTCCAAAAATCCCATTTTTGACCCCG
* *
77608 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAA-TCCCATTTT
77631 ACCCCTAAAT
Statistics
Matches: 124, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
29 61 0.49
30 55 0.44
31 8 0.06
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:77631 original size:59 final size:58
Alignment explanation
Indices: 77461--77631 Score: 211
Period size: 59 Copynumber: 2.9 Consensus size: 58
77451 AGGGTCCCTA
* * *
77461 AACTGTCCAAAAA-TCCATTTTTGACCCCGAAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACT-TCCAAAAATTCCATTTTTGA-CCTGAAACTTCCAAAAATTCCATTTTAGACCCCG
* *
77520 AACTTCCAAAAATCCCATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTTAG-CTCCG
1 AACTTCCAAAAATTCCATTTTTGACC-TGAAACTTCCAAAAATTCCA-TTTTAGACCCCG
* *
77579 AACTTCCAAAAATTCCATTTTTGACACTAAAACTTTCAAAAATTACCATTTTA
1 AACTTCCAAAAATTCCATTTTTGAC-CTGAAACTTCCAAAAATT-CCATTTTA
77632 CCCCTAAATG
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
58 10 0.10
59 80 0.81
60 9 0.09
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTGACCTGAAACTTCCAAAAATTCCATTTTAGACCCCG
Found at i:82219 original size:18 final size:18
Alignment explanation
Indices: 82197--82263 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
82187 GTTATAAATT
82197 TTTTTAATTTTTTAATGAA
1 TTTTTAATTTTTTAAT-AA
*
82216 TTTTTTATTTTTTACATAA
1 TTTTTAATTTTTTA-ATAA
* * *
82235 -TTATAGTTTTTTAAATAT
1 TTTTTAATTTTTT-AATAA
82253 TTTTATAATTT
1 TTTT-TAATTT
82264 CAGAAAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
18 12 0.32
19 18 0.49
20 7 0.19
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAATTTTTTAATAA
Found at i:94421 original size:25 final size:25
Alignment explanation
Indices: 94393--94440 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
94383 AAAAAAGTTC
*
94393 AAAAATACAAAATTAAATAATTAAA
1 AAAAACACAAAATTAAATAATTAAA
* * *
94418 AAAAACCCATAATTGAATAATTA
1 AAAAACACAAAATTAAATAATTA
94441 TTTTATAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAAACACAAAATTAAATAATTAAA
Found at i:102487 original size:376 final size:376
Alignment explanation
Indices: 101687--102631 Score: 1421
Period size: 376 Copynumber: 2.5 Consensus size: 376
101677 CCTAACCCCA
* * *
101687 TTCAAACCTAAATGTGCTCAACTCAAAACAACCAGAATTCAAACCCATAAGGTGAAGTAAAAATG
1 TTCAAACCTGAATGAGCTCAACTCAAAACAACCAGAATTCAAACCCATAAGTTGAAGTAAAAATG
* * * *
101752 ACCCAAACCCGAAATTAATCCAAAAATAACCCCCTCAATTGACAGGGCTAATTGCACTGCAATGA
66 A-CCAAACCCGAAATTAATCCAAAAATAATCCACTCAATTGACAGGCCTAATTGTACTGCAATGA
101817 ATTCACCATGCAAACAAATCAAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTCA
130 ATTCACCATGCAAACAAATCAAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTCA
*
101882 ACAAACATCATCCTAATGGATTGATGGTCAATGTCAACCAACATCATCCACAGTTACCAAGTACC
195 ACAAACATCATCCTAATGGATTGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTACC
*
101947 ATCCTCAACCATCGGCTTCTTCAACCCGAATTGGCTCAAACCAAAAGCAACCCGAACCCAAGATA
260 ATCCTCAACCATCGGCTTCTTCAACCCGAATTGGCTCAAACCAAAAGCAACCCAAACCCAAGATA
102012 CCATAACTCAAAACGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGC
325 CCATAACTCAAAACGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGC
*
102064 TTCAAACCTGAATGAGCTCAACTCAAAACAACCCGAATTCAAACCCATAAGTTGAAGTAAAAATG
1 TTCAAACCTGAATGAGCTCAACTCAAAACAACCAGAATTCAAACCCATAAGTTGAAGTAAAAATG
*
102129 ACCTAAACCCGAAATTAATCCAAAAATAATCCACTCAATTGACAGGCCTAATTGTATTGCAATGA
66 ACC-AAACCCGAAATTAATCCAAAAATAATCCACTCAATTGACAGGCCTAATTGTACTGCAATGA
* * *
102194 ATTTACCATGCAAACAAATCAAGTTAACAA-CTACCCTATAGAGAAACAAAGTTGAAGAATCTTC
130 ATTCACCATGCAAACAAATCAAATTAA-AAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTC
102258 AACAAACATCATCCTAATGGA-TGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTAC
194 AACAAACATCATCCTAATGGATTGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTAC
* * * *
102322 CATCCTTAACCATCGGCTTCTTCCACTCGAATTGGCTCAAGCCAAAAGCAACCCAAACCCAAGAT
259 CATCCTCAACCATCGGCTTCTTCAACCCGAATTGGCTCAAACCAAAAGCAACCCAAACCCAAGAT
* * *
102387 ACCATAACTCGAAATGATCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGC
324 ACCATAACTCAAAACGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGC
* * * * * **
102440 TTCAAACCTGGATGAGCTCAACTCGAAACAACCTGAATTCGAACCCATAACAAGTTAAAGCCAAA
1 TTCAAACCTGAATGAGCTCAACTCAAAACAACCAGAATTCAAACCCAT---AAGTTGAAGTAAAA
* * * ** *
102505 ATGACACAAACCCGAAATGAGTTCAACTGAAAGCATCCACTCAATTGACAGGTCTAATTGTACTG
63 ATGAC-CAAACCCGAAATTAATCCAA---AAATAATCCACTCAATTGACAGGCCTAATTGTACTG
* * *
102570 CAAT-AGATTCACCAAGCAAACAAATCAAATTAAAAGCTACTCC-ATATAGAAACAAAGATGAA
124 CAATGA-ATTCACCATGCAAACAAATCAAATTAAAAGCTAC-CCTATAAAGAAACAAAGTTGAA
102632 ATGTTACCAG
Statistics
Matches: 516, Mismatches: 40, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
376 198 0.38
377 197 0.38
378 2 0.00
379 32 0.06
380 1 0.00
381 3 0.01
382 81 0.16
383 2 0.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (376 bp):
TTCAAACCTGAATGAGCTCAACTCAAAACAACCAGAATTCAAACCCATAAGTTGAAGTAAAAATG
ACCAAACCCGAAATTAATCCAAAAATAATCCACTCAATTGACAGGCCTAATTGTACTGCAATGAA
TTCACCATGCAAACAAATCAAATTAAAAGCTACCCTATAAAGAAACAAAGTTGAAGAATCTTCAA
CAAACATCATCCTAATGGATTGATGATCAATGTCAACCAACATCATCCACAGTTACCAAGTACCA
TCCTCAACCATCGGCTTCTTCAACCCGAATTGGCTCAAACCAAAAGCAACCCAAACCCAAGATAC
CATAACTCAAAACGACCCCAACTCGTAATGTCCTAACCCAAAAAACTAAGC
Found at i:104186 original size:99 final size:98
Alignment explanation
Indices: 103998--104386 Score: 467
Period size: 99 Copynumber: 4.0 Consensus size: 98
103988 GAATTTTGCT
* *
103998 TTTAATTTGATGAATTTATTTTACTCTGAGTGAGCTAGCTGTTGTATTTGTGATGATACA-TAGT
1 TTTAATTTGATGAATTTA-TTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGT-GT
* * *
104062 TAATTGATTGGAGTTCAGTAATTGTTATGATTTTGA-
64 TAATTGATTTGAGTT-AGTATTTGTTA-GATTTTAAC
*
104098 TTTAATTTAATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTA
1 TTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTA
*
104163 ATTTATTTGAGATTAGTATTTGTTAG-TTTTAAC
66 ATTGATTTGAG-TTAGTATTTGTTAGATTTTAAC
* * *
104196 TTTTAATTTGACGAACTTT-TTTAATCGGAGTGAGCTAGCTGTTGTATTTGTGGTGATATAGTGT
1 -TTTAATTTGATGAA-TTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
* *
104260 T-ATTAATATT-TGTT-GTGA--T-TTA-ATTTTAAC
64 TAATTGAT-TTGAGTTAGT-ATTTGTTAGATTTTAAC
*
104290 TTTTACTTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTT
1 -TTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTT
*
104355 AATTGATTTCAGATTAGTATTTGTTATGATTT
65 AATTGATTTGAG-TTAGTATTTGTTA-GATTT
104387 AGTATTGATT
Statistics
Matches: 252, Mismatches: 19, Indels: 35
0.82 0.06 0.11
Matches are distributed among these distances:
93 3 0.01
94 69 0.27
95 7 0.03
96 5 0.02
97 10 0.04
98 8 0.03
99 123 0.49
100 23 0.09
101 4 0.02
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.49
Consensus pattern (98 bp):
TTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGTTA
ATTGATTTGAGTTAGTATTTGTTAGATTTTAAC
Found at i:107285 original size:3 final size:3
Alignment explanation
Indices: 107277--107301 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
107267 AGCAGCTGCA
107277 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
107302 GAGCTCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:112198 original size:26 final size:26
Alignment explanation
Indices: 112160--112210 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
112150 AAAGAGCAAG
*
112160 AACTACCAGTTAAACAACACCGAAAA
1 AACTACCAATTAAACAACACCGAAAA
* *
112186 AACTACCAATTAAAGAACACTGAAA
1 AACTACCAATTAAACAACACCGAAA
112211 TTTTCTGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.24, G:0.08, T:0.14
Consensus pattern (26 bp):
AACTACCAATTAAACAACACCGAAAA
Found at i:132671 original size:16 final size:16
Alignment explanation
Indices: 132650--132680 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
132640 TAAATTATTT
*
132650 TAAAAATTTATAAAAA
1 TAAAAAATTATAAAAA
132666 TAAAAAATTATAAAA
1 TAAAAAATTATAAAA
132681 TTTCTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAAATTATAAAAA
Found at i:133657 original size:40 final size:40
Alignment explanation
Indices: 133613--133690 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
133603 TTTTAAAATT
* *
133613 TTTGAATTTGACCATTACGGATTCGGATTATTTTGGGTTC
1 TTTGAATTTGACCATTACGGATTCGAATAATTTTGGGTTC
* *
133653 TTTGAGTTTGACCGTTACGGATTCGAATAATTTTGGGT
1 TTTGAATTTGACCATTACGGATTCGAATAATTTTGGGT
133691 CATTTGGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.44
Consensus pattern (40 bp):
TTTGAATTTGACCATTACGGATTCGAATAATTTTGGGTTC
Found at i:146557 original size:21 final size:21
Alignment explanation
Indices: 146533--146576 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
146523 ATAATAAATA
146533 AAATCCAAATTCAAATAATTG
1 AAATCCAAATTCAAATAATTG
* * **
146554 AAATTCATATTCTCATAATTG
1 AAATCCAAATTCAAATAATTG
146575 AA
1 AA
146577 TAACTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATCCAAATTCAAATAATTG
Found at i:163588 original size:2 final size:2
Alignment explanation
Indices: 163581--163606 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
163571 AAATGTTCCA
163581 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
163607 TGCATTGCCA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:175077 original size:62 final size:62
Alignment explanation
Indices: 174886--175085 Score: 260
Period size: 62 Copynumber: 3.2 Consensus size: 62
174876 ACATACATTG
* * * * *
174886 TTTGCCTTCAATTCAATAAATTCAATCAAAGAAGAGGGAACTTTAGGACATATTTACCCAACA
1 TTTGCCTTCAATTCCATAAATTCAAGCAAAAAAGAGGGAACTTTAGGTCA-ATTTAACCAACA
* *
174949 TTTGCCTTCAATTCCACAAATTCAAGCAAAAAAGA-GGAACCTTAGGTCAATTT-ACCTAACA
1 TTTGCCTTCAATTCCATAAATTCAAGCAAAAAAGAGGGAACTTTAGGTCAATTTAACC-AACA
* * * *
175010 ATTGCTTTCAATTCCATAAATTCAAGCAAAAAAGAGGGAGCTTTAGGTCAATTTAAGCAACA
1 TTTGCCTTCAATTCCATAAATTCAAGCAAAAAAGAGGGAACTTTAGGTCAATTTAACCAACA
*
175072 TTTGCTTTCAATTC
1 TTTGCCTTCAATTC
175086 AAAACCCGAC
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
60 2 0.02
61 40 0.33
62 45 0.38
63 33 0.28
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (62 bp):
TTTGCCTTCAATTCCATAAATTCAAGCAAAAAAGAGGGAACTTTAGGTCAATTTAACCAACA
Found at i:184716 original size:60 final size:61
Alignment explanation
Indices: 184583--184718 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 61
184573 TCGCTTCAAG
*
184583 ATTTAATTTGGTACTTAAAATTTTATTTTTGGTCCAATTAAGTAGTAGAACTTGGTTTTACT
1 ATTTAATTTGGTACTTAAAATTTTATTTTTGGTCCAATTAAGTACTAGAACTTGGTTTTA-T
* *
184645 ATTCAATTTGGTACTTAAAA-TTTA-TTTTGGTCCAATTAGGTACCT-GAACTTGGTTTCT-T
1 ATTTAATTTGGTACTTAAAATTTTATTTTTGGTCCAATTAAGTA-CTAGAACTTGGTTT-TAT
*
184704 AGTTTAAATTGGTAC
1 A-TTTAATTTGGTAC
184719 CTGAACTTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
59 2 0.03
60 39 0.59
61 6 0.09
62 19 0.29
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (61 bp):
ATTTAATTTGGTACTTAAAATTTTATTTTTGGTCCAATTAAGTACTAGAACTTGGTTTTAT
Found at i:186854 original size:2 final size:2
Alignment explanation
Indices: 186847--186876 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
186837 TCTATTTAAA
186847 AT 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 AT
186877 CAGAATTTTC
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187013 original size:23 final size:23
Alignment explanation
Indices: 186983--187028 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
186973 ATTAATTGGG
*
186983 TCAAATTACGTTTTTGTTCTTAT
1 TCAAATTACGATTTTGTTCTTAT
* *
187006 TCAAATTATGATTTTGTTGTTAT
1 TCAAATTACGATTTTGTTCTTAT
187029 ACTACATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.57
Consensus pattern (23 bp):
TCAAATTACGATTTTGTTCTTAT
Found at i:189312 original size:21 final size:22
Alignment explanation
Indices: 189280--189322 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
189270 GAATTAAAAA
*
189280 AAATAGATTTTT-ATCTATTTT
1 AAATAGATTTTTAATATATTTT
189301 AAATA-ATCTTTTAATATATTTT
1 AAATAGAT-TTTTAATATATTTT
189323 TAATTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 9 0.47
22 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
AAATAGATTTTTAATATATTTT
Found at i:197587 original size:49 final size:49
Alignment explanation
Indices: 197515--197611 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
197505 ATGCCTCATG
*
197515 AAACGTGGGTTAAAGATGAACTACATTATCTTCTTATATTTGAATTTTC
1 AAACGTAGGTTAAAGATGAACTACATTATCTTCTTATATTTGAATTTTC
*
197564 AAACGTAGGTTAAAGATGAACTACATTATCTTTTTATATTTGAATTTT
1 AAACGTAGGTTAAAGATGAACTACATTATCTTCTTATATTTGAATTTT
197612 TCATTCTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (49 bp):
AAACGTAGGTTAAAGATGAACTACATTATCTTCTTATATTTGAATTTTC
Found at i:200840 original size:13 final size:12
Alignment explanation
Indices: 200806--200855 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
200796 AAAACATCCA
*
200806 AACAACAAAAAT
1 AACAGCAAAAAT
*
200818 AACAACAAAAAT
1 AACAGCAAAAAT
*
200830 AGCAGCAAAAAT
1 AACAGCAAAAAT
200842 AACAGCAAACAAT
1 AACAGCAAA-AAT
200855 A
1 A
200856 TTAAAAACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (12 bp):
AACAGCAAAAAT
Found at i:200851 original size:43 final size:43
Alignment explanation
Indices: 200804--200888 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
200794 AAAAAACATC
* *
200804 CAAACAACA-AAAATAACAACAAAAATAGCAGCAAAAATAACAG
1 CAAACAACATAAAA-AACAACAAAAATAGCAACAAAAACAACAG
* *
200847 CAAACAATATTAAAAACAACAAAAATAGCAACAAAAACAACA
1 CAAACAACATAAAAAACAACAAAAATAGCAACAAAAACAACA
200889 CGAAAGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 34 0.92
44 3 0.08
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (43 bp):
CAAACAACATAAAAAACAACAAAAATAGCAACAAAAACAACAG
Found at i:200948 original size:22 final size:20
Alignment explanation
Indices: 200900--200969 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
200890 GAAAGTAATA
*
200900 ACCAAAATAGTAAAAAAAAC
1 ACCAAAATAGTAAAAAAAGC
* *
200920 ACAAAAATAGCAAAAAACAGC
1 ACCAAAATAGTAAAAAA-AGC
*
200941 AACCAAAATAATAAAAAAAAGC
1 -ACCAAAATAGT-AAAAAAAGC
200963 ACCAAAA
1 ACCAAAA
200970 CAATAATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 15 0.37
21 9 0.22
22 11 0.27
23 6 0.15
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.07
Consensus pattern (20 bp):
ACCAAAATAGTAAAAAAAGC
Found at i:200956 original size:21 final size:21
Alignment explanation
Indices: 200900--200975 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
200890 GAAAGTAATA
* *
200900 ACCAAAATAGTAAAAAAAA-C
1 ACCAAAACAATAAAAAAAAGC
* * ** *
200920 ACAAAAATAGCAAAAAACAGC
1 ACCAAAACAATAAAAAAAAGC
*
200941 AACCAAAATAATAAAAAAAAGC
1 -ACCAAAACAATAAAAAAAAGC
200963 ACCAAAACAATAA
1 ACCAAAACAATAA
200976 TATATTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.35
21 13 0.28
22 17 0.37
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (21 bp):
ACCAAAACAATAAAAAAAAGC
Found at i:201575 original size:110 final size:110
Alignment explanation
Indices: 201379--201584 Score: 324
Period size: 110 Copynumber: 1.9 Consensus size: 110
201369 ACCATGTATA
* * *
201379 CCAACAAATCAACAAATTAGCAAACCCTTTTATTAGGGTTAATAGTACCAAATTATATCAAATCA
1 CCAACAAATCAACAAATTAGCAAACACTTTTATCAGGGTGAATAGTACCAAATTATATCAAATCA
*
201444 AAATATAGAGATTAAATATATACCATATATATAGACGATTAAATC
66 AAATATAGAGATTAAAGATATACCATATATATAGACGATTAAATC
* * *
201489 CCAACAAATCAACAAATTAGTAGAA-ACTTTTATCAGGGTGAATAGTACCAAATTATATCAAGTT
1 CCAACAAATCAACAAATTAGCA-AACACTTTTATCAGGGTGAATAGTACCAAATTATATCAAATC
*
201553 AAAATATAGAGATTAAGGATATACCATATATA
65 AAAATATAGAGATTAAAGATATACCATATATA
201585 GTTCATGCAA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 85 0.98
111 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (110 bp):
CCAACAAATCAACAAATTAGCAAACACTTTTATCAGGGTGAATAGTACCAAATTATATCAAATCA
AAATATAGAGATTAAAGATATACCATATATATAGACGATTAAATC
Found at i:226685 original size:28 final size:28
Alignment explanation
Indices: 226624--226704 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
226614 CGGTTAATTT
*
226624 TTTAAAT-TAAAAATTACAAAAAAATAATA
1 TTTAAATATAAAAA-TA-AAAAAAAAAATA
* *
226653 ATTAAATATCAAAATAAAAAAAAAAATA
1 TTTAAATATAAAAATAAAAAAAAAAATA
*
226681 TTTAAATATTAAAATAAAAAAAAA
1 TTTAAATATAAAAATAAAAAAAAA
226705 CAAATATAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 33 0.72
29 8 0.17
30 5 0.11
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (28 bp):
TTTAAATATAAAAATAAAAAAAAAAATA
Found at i:229441 original size:17 final size:16
Alignment explanation
Indices: 229415--229477 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
229405 TGGACATGAC
229415 TTGA-TTAAATTCAAAA
1 TTGAGTTAAATT-AAAA
* *
229431 TCGAGTTAAATTTAATA
1 TTGAGTTAAA-TTAAAA
*
229448 TTGA-TTAAATTATAA
1 TTGAGTTAAATTAAAA
229463 TTGAGTTAAATTAAA
1 TTGAGTTAAATTAAA
229478 TGTTTTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.21
16 17 0.45
17 11 0.29
18 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (16 bp):
TTGAGTTAAATTAAAA
Found at i:229457 original size:16 final size:16
Alignment explanation
Indices: 229415--229463 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
229405 TGGACATGAC
* *
229415 TTGATTAAATTCAAAA
1 TTGATTAAATTTAATA
*
229431 TCGAGTTAAATTTAATA
1 TTGA-TTAAATTTAATA
229448 TTGATTAAATTATAAT
1 TTGATTAAATT-TAAT
229464 TGAGTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (16 bp):
TTGATTAAATTTAATA
Found at i:230243 original size:29 final size:30
Alignment explanation
Indices: 230209--230265 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
230199 TTTGAAAGAT
230209 AAATA-TAAAAAAATTACAAAT-AAATATCC
1 AAATATTAAAAAAATT-CAAATCAAATATCC
**
230238 AAATATTATCAAAATTCAAATCAAATAT
1 AAATATTAAAAAAATTCAAATCAAATAT
230266 TAAATTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (30 bp):
AAATATTAAAAAAATTCAAATCAAATATCC
Found at i:230245 original size:21 final size:22
Alignment explanation
Indices: 230207--230250 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
230197 AATTTGAAAG
230207 ATAAATATAAAAAAATTA-CAA
1 ATAAATATAAAAAAATTATCAA
** *
230228 ATAAATATCCAAATATTATCAA
1 ATAAATATAAAAAAATTATCAA
230250 A
1 A
230251 ATTCAAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAATATAAAAAAATTATCAA
Found at i:241418 original size:14 final size:14
Alignment explanation
Indices: 241401--241446 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
241391 ATTTTTTAAA
241401 AAATAATATAATTT
1 AAATAATATAATTT
**
241415 AAAT-AT-TTTTTT
1 AAATAATATAATTT
241427 AAAATAATATAATTT
1 -AAATAATATAATTT
241442 AAATA
1 AAATA
241447 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 11 0.44
15 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATAATATAATTT
Found at i:241431 original size:27 final size:27
Alignment explanation
Indices: 241377--241459 Score: 132
Period size: 27 Copynumber: 3.1 Consensus size: 27
241367 AACTTACAAA
*
241377 AATATAATATAAATATTTTTTAAAAAAT
1 AATATAATTTAAATATTTTTT-AAAAAT
*
241405 AATATAATTTAAATATTTTTTTAAAAT
1 AATATAATTTAAATATTTTTTAAAAAT
241432 AATATAATTTAAATA-TTTTTAAAAAT
1 AATATAATTTAAATATTTTTTAAAAAT
241458 AA
1 AA
241460 ACTTAAATTG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
26 12 0.23
27 20 0.38
28 20 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATAATTTAAATATTTTTTAAAAAT
Found at i:248747 original size:198 final size:197
Alignment explanation
Indices: 248402--249003 Score: 924
Period size: 198 Copynumber: 3.0 Consensus size: 197
248392 CCACTTCAAG
* *
248402 GTAAGTTTTAAAGAAAATTTAGGTCCCTTGGCAATTGAAAATAAAAGAAAATGTTTATATCCTTA
1 GTAATTTTTAAAGAAAATTTAGGTCCCTTGGCAATTGGAAATAAAAGAAAATGTTTATATCCTTA
*
248467 AGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGAAGATCAAAAAAGAAATTAA
66 AGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATC-AAAAAGAAATTAA
248532 CCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCCATTCTACACCTTACAAAGTGACAACCACTTT
130 CCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCCATTCTACACCTTACAAAGTGACAACCACTTT
248597 ATA
195 ATA
*
248600 GTAATTTTTAAATAAAATTTAGGTCCCTTGGCCAATTGGAAATAAAAGAAAATGTTTATATCCTT
1 GTAATTTTTAAAGAAAATTTAGGTCCCTTGG-CAATTGGAAATAAAAGAAAATGTTTATATCCTT
248665 AAGTGCCTAGCATGACCAGACAAT-ATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGAAATTA
65 AAGTGCCTAGCATGACCAGAC-ATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGAAATTA
* *
248729 ACCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACTCCTTACAAAGTGACAACCACTT
129 ACCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCCATTCTACACCTTACAAAGTGACAACCACTT
248794 TATA
194 TATA
* *
248798 GTAA-TTTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAATAAAACAAGAAAATGTTTATATCC
1 GTAATTTTTAAAGAAAATTTAGGTCCCTT-GGCAATTGGAA-ATAA-AAGAAAATGTTTATATCC
* * * * *
248862 TTAAGGAGCCTAGCAAGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCGATAAGATA-
63 TTAA-GTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGAAAT
* * * * * *
248926 TAGACCACCTTGGCAAAGTTGCCCATCCTTCAAATTCCAGTCTACATCTTACAGAGTGACAAACA
127 TA-ACCACCTCGGCAAAGTTGCCCAGCCTTCAAATTCCATTCTACACCTTACAAAGTGACAACCA
248991 -TTTATA
191 CTTTATA
*
248997 ATAATTT
1 GTAATTT
249004 GATAAAAACA
Statistics
Matches: 372, Mismatches: 23, Indels: 16
0.91 0.06 0.04
Matches are distributed among these distances:
197 31 0.08
198 117 0.31
199 115 0.31
200 109 0.29
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (197 bp):
GTAATTTTTAAAGAAAATTTAGGTCCCTTGGCAATTGGAAATAAAAGAAAATGTTTATATCCTTA
AGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATCAAAAAGAAATTAAC
CACCTCGGCAAAGTTGCCCAGCCTTCAAATTCCATTCTACACCTTACAAAGTGACAACCACTTTA
TA
Found at i:256271 original size:17 final size:17
Alignment explanation
Indices: 256245--256277 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
256235 AAATTAATCG
*
256245 AATTACCCAAATTAAAA
1 AATTAACCAAATTAAAA
256262 AATTAACCAAATTAAA
1 AATTAACCAAATTAAA
256278 GTATTGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
AATTAACCAAATTAAAA
Found at i:259246 original size:72 final size:73
Alignment explanation
Indices: 259129--259305 Score: 284
Period size: 72 Copynumber: 2.4 Consensus size: 73
259119 GTCCGAAGCT
259129 ATTTTAACGCAAGCCAGCCTACCACATAGCTACAGGCACGAGAAGGTCCAATT-CTAAGCTAAAA
1 ATTTTAACGCAAGCCAGCCTACCACATAGCTACAGGCACGAGAAGGTCCAATTCCTAAGCTAAAA
*
259193 TCTATGAG
66 TCCATGAG
* * *
259201 ATTTTAACACAAGCCTGCCTACCACATAGCTACAGGCACGAGAAGGTCCAATTCCTAAGCTAAAC
1 ATTTTAACGCAAGCCAGCCTACCACATAGCTACAGGCACGAGAAGGTCCAATTCCTAAGCTAAAA
259266 TCCATGAG
66 TCCATGAG
* **
259274 ATTTTCACGCAAGCCAGCCTACTGCATAGCTA
1 ATTTTAACGCAAGCCAGCCTACCACATAGCTA
259306 TATGCATAGG
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 51 0.54
73 44 0.46
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (73 bp):
ATTTTAACGCAAGCCAGCCTACCACATAGCTACAGGCACGAGAAGGTCCAATTCCTAAGCTAAAA
TCCATGAG
Found at i:262328 original size:18 final size:18
Alignment explanation
Indices: 262290--262344 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
262280 AATATTGCTA
*
262290 TTATTATGTTGTT-ATTAT
1 TTATTATATTGTTAATT-T
262308 TTA-TATATTGTATAATTT
1 TTATTATATTGT-TAATTT
*
262326 TTATTTTATTGTTAATTT
1 TTATTATATTGTTAATTT
262344 T
1 T
262345 GTTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 7 0.22
18 15 0.47
19 10 0.31
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
TTATTATATTGTTAATTT
Found at i:288099 original size:26 final size:26
Alignment explanation
Indices: 288063--288116 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
288053 TGATTACTTA
288063 TACACATATAATACTTACCTTTCATG
1 TACACATATAATACTTACCTTTCATG
288089 TACACATATAATACTTACCTTTCATG
1 TACACATATAATACTTACCTTTCATG
288115 TA
1 TA
288117 TTCAACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (26 bp):
TACACATATAATACTTACCTTTCATG
Found at i:288348 original size:23 final size:22
Alignment explanation
Indices: 288316--288395 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
288306 GCTGGGGAAA
* *
288316 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAATGCAAT
*
288338 CCAGTAGGCACACACAATACAAT
1 -CAGTAGGCACACACAATGCAAT
* * *
288361 CAGTAGGCGCACATAACGCTAAT
1 CAGTAGGCACACACAATGC-AAT
288384 CAGTAGGCACAC
1 CAGTAGGCACAC
288396 GATGTGCGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAATGCAAT
Found at i:288536 original size:24 final size:26
Alignment explanation
Indices: 288498--288545 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
288488 TCTACATGGG
288498 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
288524 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
288546 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.