Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014230.1 Kokia drynarioides strain JFW-HI SEQ_129263, 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: 620973
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 39 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:252608 original size:56 final size:56
Alignment explanation
Indices: 252522--252763 Score: 326
Period size: 56 Copynumber: 4.3 Consensus size: 56
252512 CCAAATGGAA
** * *
252522 GGCTCGGGTAGAGCGAAATTCTTAATCTTGCTCGGGTAGAGCATTATTCTACTTTT
1 GGCTCGGGTAGAGCGTTATACTGAATCTTGCTCGGGTAGAGCATTATTCTACTTTT
*
252578 GGCTCGGGTAGAGCGTTATACTGAATCTTGCTCGGGTAGAGCATTAATCTACTTTT
1 GGCTCGGGTAGAGCGTTATACTGAATCTTGCTCGGGTAGAGCATTATTCTACTTTT
* * * *
252634 AGCTTGGGT-GAAGCGTTATACTGAATCTTGTTGGGGTAGAGCATTATTCTACTTTT
1 GGCTCGGGTAG-AGCGTTATACTGAATCTTGCTCGGGTAGAGCATTATTCTACTTTT
* * * *
252690 GGCTCGGGTAGAGCGTTATACTAAATCTTGCTCAGGTAGAGCATTATTATGC-TTT
1 GGCTCGGGTAGAGCGTTATACTGAATCTTGCTCGGGTAGAGCATTATTCTACTTTT
* *
252745 GGCTTGGGTAGAGCATTAT
1 GGCTCGGGTAGAGCGTTAT
252764 CTTGATTCTG
Statistics
Matches: 164, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
55 21 0.13
56 142 0.87
57 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (56 bp):
GGCTCGGGTAGAGCGTTATACTGAATCTTGCTCGGGTAGAGCATTATTCTACTTTT
Found at i:252736 original size:28 final size:27
Alignment explanation
Indices: 252544--252736 Score: 165
Period size: 28 Copynumber: 6.9 Consensus size: 27
252534 GCGAAATTCT
*
252544 TAATCTTGCTCGGGTAGAGCATTATTC
1 TAATCTTGCTCGGGTAGAGCATTATAC
* * *
252571 TACTTTTGGCTCGGGTAGAGCGTTATAC
1 TAATCTT-GCTCGGGTAGAGCATTATAC
252599 TGAATCTTGCTCGGGTAGAGCATTA-ATC
1 T-AATCTTGCTCGGGTAGAGCATTATA-C
* * * *
252627 TACTTTTAGCTTGGGT-GAAGCGTTATAC
1 TAATCTT-GCTCGGGTAG-AGCATTATAC
* * *
252655 TGAATCTTGTTGGGGTAGAGCATTATTC
1 T-AATCTTGCTCGGGTAGAGCATTATAC
* * *
252683 TACTTTTGGCTCGGGTAGAGCGTTATAC
1 TAATCTT-GCTCGGGTAGAGCATTATAC
*
252711 TAAATCTTGCTCAGGTAGAGCATTAT
1 T-AATCTTGCTCGGGTAGAGCATTAT
252737 TATGCTTTGG
Statistics
Matches: 129, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
27 15 0.12
28 100 0.78
29 14 0.11
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (27 bp):
TAATCTTGCTCGGGTAGAGCATTATAC
Found at i:257373 original size:11 final size:11
Alignment explanation
Indices: 257335--257364 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
257325 TCTACATTAA
257335 ATAATTTATAT
1 ATAATTTATAT
257346 ATAATTTATAT
1 ATAATTTATAT
257357 ATAATTTA
1 ATAATTTA
257365 AATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATAATTTATAT
Found at i:259413 original size:6 final size:6
Alignment explanation
Indices: 259402--259440 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
259392 TGATCAAAAT
* * *
259402 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
259441 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:259644 original size:37 final size:38
Alignment explanation
Indices: 259544--259646 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
259534 GACCTTGAGT
* **
259544 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** * ** *
259585 CGATGAGGTACTGAGTACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
259622 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
259647 TTACTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 14 0.29
41 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:260115 original size:36 final size:36
Alignment explanation
Indices: 260068--260137 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
260058 CGCGTTTATT
*
260068 TCAACACGTAGGTATAAGACCTTCGAGAAGTTAAGG
1 TCAACACGTAGGTATAAGACCTCCGAGAAGTTAAGG
*
260104 TCAACGCGTAGGTATAAGACCTCCGAGAAGTTAA
1 TCAACACGTAGGTATAAGACCTCCGAGAAGTTAA
260138 AGTTGGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (36 bp):
TCAACACGTAGGTATAAGACCTCCGAGAAGTTAAGG
Found at i:261195 original size:15 final size:16
Alignment explanation
Indices: 261175--261212 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
261165 TTTTTTTTAC
*
261175 AAAACCCAAA-ATTAA
1 AAAACCCAAACACTAA
*
261190 AAAACCTAAACACTAA
1 AAAACCCAAACACTAA
261206 AAAACCC
1 AAAACCC
261213 TAGCTTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.63, C:0.26, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAACCCAAACACTAA
Found at i:262137 original size:32 final size:31
Alignment explanation
Indices: 262101--262160 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
262091 CCTTTTTGTA
262101 TTTTTAAGGGATTTTAATTTAGTCCTTTTGCT
1 TTTTTAAGGGATTTTAATTTAG-CCTTTTGCT
* ***
262133 TTTTTTATTTATTTTAATTTAGCCTTTT
1 TTTTTAAGGGATTTTAATTTAGCCTTTT
262161 AATTTTAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 6 0.25
32 18 0.75
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.63
Consensus pattern (31 bp):
TTTTTAAGGGATTTTAATTTAGCCTTTTGCT
Found at i:262538 original size:12 final size:12
Alignment explanation
Indices: 262523--262575 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
262513 TTTTATTTAA
262523 TTTTATGTATTT
1 TTTTATGTATTT
262535 TTTTATGTATTT
1 TTTTATGTATTT
* * *
262547 TATGTATTTGTTAT
1 T-TTTATGTATT-T
262561 TTTTATGCTATTT
1 TTTTATG-TATTT
262574 TT
1 TT
262576 ATTTTTGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
12 13 0.41
13 14 0.44
14 5 0.16
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (12 bp):
TTTTATGTATTT
Found at i:262546 original size:21 final size:22
Alignment explanation
Indices: 262513--262555 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
262503 ACATTTTTGC
*
262513 TTTTATTTAATTTTATGTATTT
1 TTTTATGTAATTTTATGTATTT
262535 TTTTATGT-ATTTTATGTATTT
1 TTTTATGTAATTTTATGTATTT
262556 GTTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTATGTAATTTTATGTATTT
Found at i:262566 original size:17 final size:17
Alignment explanation
Indices: 262544--262581 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
262534 TTTTTATGTA
262544 TTTTATG-TATTTGTTAT
1 TTTTATGCTATTT-TTAT
262561 TTTTATGCTATTTTTAT
1 TTTTATGCTATTTTTAT
262578 TTTT
1 TTTT
262582 GCCTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATGCTATTTTTAT
Found at i:264165 original size:2 final size:2
Alignment explanation
Indices: 264158--264186 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
264148 GTGATTGCAC
264158 AT AT 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 AT AT A
264187 GATTATACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:274212 original size:14 final size:14
Alignment explanation
Indices: 274195--274228 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
274185 AAATTTGAAC
274195 AATAAAATTAATTT
1 AATAAAATTAATTT
274209 AATAAAATTAATTT
1 AATAAAATTAATTT
*
274223 ACTAAA
1 AATAAA
274229 TTTCACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAAATTAATTT
Found at i:277936 original size:16 final size:16
Alignment explanation
Indices: 277915--277945 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
277905 ATAATGTGAA
277915 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
277931 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
277946 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:286894 original size:59 final size:59
Alignment explanation
Indices: 286802--287382 Score: 543
Period size: 59 Copynumber: 9.8 Consensus size: 59
286792 TTCAGGGGTG
* * * * * *
286802 AAATGGTAATTTTGGGAAAATTT-GAGGTTAAAAATAGAATTTTTGGATGTTCGAGCGTAA
1 AAATGG-AATTTTTGG-AAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
* * *
286862 AAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
* * * *
286921 AAATAGAATTTTTAGAAGTTTCGGGGTTAAAAATGGGATTTTTAGG-AGTT-TAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTT-GGAAGTTCGA-GGGTAA
* * * * * *
286980 AAACGGAATTTTTTGGAAGTTTTGTGGTT-AAAATGGGATTTTTGGTATTTCAAGGGTAA
1 AAATGGAA-TTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
* * * * **
287039 AAATGGAATTTTTTGAAGTTTTGGGGTTAAAAATGGGATTTTTGGTAGTTTAAGGGT-A
1 AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
* *
287097 AAATGGAATTTTTGGAAGTTTCGGGGTTGAAAATGGGATTTTTGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
** * * * *
287156 AAATGGAATTTTTAAAAGTGTC-AGGGTCAAAATTGGGATTTTGGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGA-GGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
** * * * * **
287215 AAATAAAATTTTTAGAAGTTTCGGGGTTAAAAATGGAATTTTTAGAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT-AA
* * * * * *
287275 AAATGGGATTTTTGGAAGTTT-GAGGGTACAAATGGAATTTTTGAAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAG-TTCGAGGGTAA
* * * *
287334 AAAT-GAGATTTTTAGG-AG-TTCGAGGGTAAAAATAGAATTTTTGAAAGTT
1 AAATGGA-ATTTTT-GGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTT
287383 TAGGGACCTT
Statistics
Matches: 438, Mismatches: 68, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
58 82 0.19
59 303 0.69
60 53 0.12
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (59 bp):
AAATGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
Found at i:287070 original size:89 final size:88
Alignment explanation
Indices: 286771--287383 Score: 491
Period size: 89 Copynumber: 6.9 Consensus size: 88
286761 ACTTGAGGGC
* * **
286771 AAAATGGTAATTTTTTGAAGTTTCAGGGG-T-GAAATGGTAATTTTGGGAAAATTTGAGGTTAAA
1 AAAATGG-AATTTTTTGAAGTTTC-GGGGTTAAAAATGG-AATTTTTGGAAGTTTTG-GGTT-AA
* * *
286834 AATAGAATTTTTGGATG-TTCGAGCGTA
61 AATGGAATTTTTGGAAGTTTCGAGGGTA
* * * * * * *
286861 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATA
1 AAAATGGAATTTTTTGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT-TGGGTTAAAATG
*
286926 GAATTTTTAGAAGTTTCG-GGGTTA
65 GAATTTTTGGAAGTTTCGAGGG-TA
* * * * *
286950 AAAATGGGATTTTTAGGAGTTTAGGGG-TAAAAACGGAATTTTTTGGAAGTTTTGTGGTTAAAAT
1 AAAATGGAATTTTTTGAAGTTTCGGGGTTAAAAATGGAA-TTTTTGGAAGTTTTG-GGTTAAAAT
* * *
287014 GGGATTTTTGGTA-TTTCAAGGGTA
64 GGAATTTTTGGAAGTTTCGAGGGTA
* * * *
287038 AAAATGGAATTTTTTGAAGTTTTGGGGTTAAAAATGGGATTTTTGGTAGTTTAAGGG-TAAAATG
1 AAAATGGAATTTTTTGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT-TGGGTTAAAATG
*
287102 GAATTTTTGGAAGTTTCG-GGGTTG
65 GAATTTTTGGAAGTTTCGAGGG-TA
* * ** ** *
287126 AAAATGGGATTTTTGGAAG-TTCGAGGG-TAAAAATGGAATTTTTAAAAGTGTCAGGGTCAAAAT
1 AAAATGGAATTTTTTGAAGTTTCG-GGGTTAAAAATGGAATTTTTGGAAGT-TTTGGGTTAAAA-
* *
287189 TGGGATTTTGGGAAG-TTCGAGGGTA
63 TGGAATTTTTGGAAGTTTCGAGGGTA
** * * *
287214 AAAATAAAATTTTTAGAAGTTTCGGGGTTAAAAATGGAATTTTTAGAAGTTTTAGGGTCAAAAAT
1 AAAATGGAATTTTTTGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTTT-GGGT-TAAAAT
*
287279 GGGATTTTTGGAAGTTT-GAGGGTA
64 GGAATTTTTGGAAGTTTCGAGGGTA
* * ** *
287303 CAAATGGAA-TTTTTGAAAGTTTCGAGGTTAAAAAT-GAGATTTTTAGG-AGTTCGAGGGTAAAA
1 AAAATGGAATTTTTTG-AAGTTTCGGGGTTAAAAATGGA-ATTTTT-GGAAGTT-TTGGGTTAAA
* *
287365 ATAGAATTTTTGAAAGTTT
62 ATGGAATTTTTGGAAGTTT
287384 AGGGACCTTT
Statistics
Matches: 425, Mismatches: 72, Indels: 54
0.77 0.13 0.10
Matches are distributed among these distances:
87 45 0.11
88 155 0.36
89 204 0.48
90 21 0.05
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (88 bp):
AAAATGGAATTTTTTGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTTTGGGTTAAAATGG
AATTTTTGGAAGTTTCGAGGGTA
Found at i:287382 original size:29 final size:29
Alignment explanation
Indices: 286771--287382 Score: 451
Period size: 30 Copynumber: 20.7 Consensus size: 29
286761 ACTTGAGGGC
*
286771 AAAATGGTAATTTTTTGAAGTTTC-AGGGGT-
1 AAAATGG-AATTTTTGGAAG-TTCGA-GGGTA
* * * * *
286801 GAAATGGTAATTTTGGGAAAATTTGAGGTTA
1 AAAATGG-AATTTTTGG-AAGTTCGAGGGTA
* * *
286832 AAAATAGAATTTTTGGATGTTCGAGCGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
286861 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* * *
286891 AAAATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
286920 AAAATAGAATTTTTAGAAGTTTCG-GGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGG-TA
* *
286950 AAAATGGGATTTTTAGG-AGTT-TAGGGGTA
1 AAAATGGAATTTTT-GGAAGTTCGA-GGGTA
* * * *
286979 AAAACGGAATTTTTTGGAAGTTTTG-TGGTT
1 AAAATGGAA-TTTTTGGAAG-TTCGAGGGTA
* * * *
287009 AAAATGGGATTTTTGGTATTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
287038 AAAATGGAATTTTTTGAAGTTTTG-GGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGG-TA
* * **
287068 AAAATGGGATTTTTGGTAGTTTAAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
287096 AAAATGGAATTTTTGGAAGTTTCG-GGGTTG
1 AAAATGGAATTTTTGGAAG-TTCGAGGG-TA
*
287126 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
**
287155 AAAATGGAATTTTTAAAAGTGTC-AGGGTCA
1 AAAATGGAATTTTTGGAAGT-TCGAGGGT-A
* * *
287185 AAATTGGGATTTTGGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
** *
287214 AAAATAAAATTTTTAGAAGTTTCG-GGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGG-TA
* **
287244 AAAATGGAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
* *
287274 AAAATGGGATTTTTGGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
287303 CAAATGGAATTTTTGAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
287333 AAAAT-GAGATTTTTAGG-AGTTCGAGGGTA
1 AAAATGGA-ATTTTT-GGAAGTTCGAGGGTA
* *
287362 AAAATAGAATTTTTGAAAGTT
1 AAAATGGAATTTTTGGAAGTT
287383 TAGGGACCTT
Statistics
Matches: 460, Mismatches: 87, Indels: 71
0.74 0.14 0.11
Matches are distributed among these distances:
28 23 0.05
29 191 0.42
30 234 0.51
31 12 0.03
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:289045 original size:6 final size:6
Alignment explanation
Indices: 289034--289117 Score: 54
Period size: 6 Copynumber: 14.7 Consensus size: 6
289024 TTAAATGAAT
* *
289034 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
289080 TTTAGAA --TAAA CTTAAT TTTAAA -ATAAA TTTAAG TTTA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
289118 TTGGGCCCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
4 4 0.07
5 11 0.18
6 41 0.68
7 4 0.07
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:289056 original size:17 final size:17
Alignment explanation
Indices: 289036--289118 Score: 96
Period size: 17 Copynumber: 4.9 Consensus size: 17
289026 AAATGAATTT
289036 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
*
289053 TAAATTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
*
289070 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
289087 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
289104 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
289119 TGGGCCCAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 1 0.02
17 54 0.96
18 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:289074 original size:34 final size:34
Alignment explanation
Indices: 289036--289118 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
289026 AAATGAATTT
* * *
289036 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
* *
289070 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
289104 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
289119 TGGGCCCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:327126 original size:52 final size:52
Alignment explanation
Indices: 327039--327176 Score: 186
Period size: 52 Copynumber: 2.7 Consensus size: 52
327029 AAATGAAAAG
* * *
327039 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTCTACGGATTATAA
* * *
327091 GGTCCGATAACTATCTGTCATCGTGAGTATATGAATCCTCTACGGATTATAA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTCTACGGATTATAA
* * * *
327143 GTTCTGGTGACTAAGTGTCATCGTGAGTGTATGA
1 GGTCTGATGACTATGTGTCATCGTGAGTATATGA
327177 TTCAGGTTGA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTCTACGGATTATAA
Found at i:337931 original size:9 final size:9
Alignment explanation
Indices: 337917--337952 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
337907 ATAATATAGT
337917 TTTATTCGA
1 TTTATTCGA
*
337926 TTTATTCAA
1 TTTATTCGA
337935 TTTATTCGA
1 TTTATTCGA
*
337944 GTTATTCGA
1 TTTATTCGA
337953 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (9 bp):
TTTATTCGA
Found at i:337940 original size:18 final size:19
Alignment explanation
Indices: 337917--337955 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
337907 ATAATATAGT
*
337917 TTTATTCGATTTATTC-AA
1 TTTATTCGAGTTATTCGAA
337935 TTTATTCGAGTTATTCGAA
1 TTTATTCGAGTTATTCGAA
337954 TT
1 TT
337956 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTATTCGAGTTATTCGAA
Found at i:342508 original size:21 final size:20
Alignment explanation
Indices: 342482--342525 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
342472 TATTATAATC
342482 TATAATA-TAATAACATTTATA
1 TATAATAGTAAT-ACA-TTATA
*
342503 TATAATAGTAGTACATTATA
1 TATAATAGTAATACATTATA
342523 TAT
1 TAT
342526 TAATTATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 10 0.48
22 3 0.14
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
TATAATAGTAATACATTATA
Found at i:343757 original size:31 final size:31
Alignment explanation
Indices: 343722--343805 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
343712 AAAAATTCAA
* * *
343722 AATTTGAAAAGTGCAATGACTAAAATTGACC
1 AATTTAAAAAGTACAAAGACTAAAATTGACC
* *
343753 AATTTAAAAAGTACAAAGATTAAAATTGATC
1 AATTTAAAAAGTACAAAGACTAAAATTGACC
* *
343784 AAATT--AAAGTATAAAGACTAAA
1 AATTTAAAAAGTACAAAGACTAAA
343806 CCTATAATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 15 0.33
31 30 0.67
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.26
Consensus pattern (31 bp):
AATTTAAAAAGTACAAAGACTAAAATTGACC
Found at i:344303 original size:19 final size:20
Alignment explanation
Indices: 344279--344316 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
344269 AAATTTATAT
344279 TTTTAAAAAAT-TATAAAAA
1 TTTTAAAAAATATATAAAAA
*
344298 TTTTAAAGAATATATAAAA
1 TTTTAAAAAATATATAAAA
344317 GAAAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
TTTTAAAAAATATATAAAAA
Found at i:344343 original size:17 final size:17
Alignment explanation
Indices: 344323--344355 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
344313 AAAAGAAAGT
344323 TAAAATTAA-AAATTTTC
1 TAAAA-TAATAAATTTTC
344340 TAAAATAATAAATTTT
1 TAAAATAATAAATTTT
344356 GGACCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATAATAAATTTTC
Found at i:347629 original size:18 final size:19
Alignment explanation
Indices: 347593--347640 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
347583 TTATGAAGAG
347593 AAAATGTATTAAAGATAAA
1 AAAATGTATTAAAGATAAA
* *
347612 AAAATGTATTCAA-TTAAA
1 AAAATGTATTAAAGATAAA
347630 AAAATAGTATT
1 AAAAT-GTATT
347641 TCAAGCACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.31
Consensus pattern (19 bp):
AAAATGTATTAAAGATAAA
Found at i:358274 original size:21 final size:22
Alignment explanation
Indices: 358239--358283 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
358229 TGGCCCATCC
*
358239 TTATTTTTTATTATTCTAATTA
1 TTATTTTTTATTATTATAATTA
*
358261 TTATTTTTTA-TATTATTATTA
1 TTATTTTTTATTATTATAATTA
358282 TT
1 TT
358284 GTAGTTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTTTTTATTATTATAATTA
Found at i:358291 original size:15 final size:15
Alignment explanation
Indices: 358246--358283 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
358236 TCCTTATTTT
358246 TTATTATTCTAATTA
1 TTATTATTCTAATTA
*
358261 TTATT-TTTTATATTA
1 TTATTATTCTA-ATTA
358276 TTATTATT
1 TTATTATT
358284 GTAGTTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 14 0.70
16 2 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTATTCTAATTA
Found at i:365375 original size:17 final size:18
Alignment explanation
Indices: 365353--365393 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
365343 ATATCATTCC
365353 AAAAATCCA-AAAAA-AAA
1 AAAAAT-CAGAAAAAGAAA
*
365370 AAAAATGAGAAAAAGAAA
1 AAAAATCAGAAAAAGAAA
365388 AAAAAT
1 AAAAAT
365394 TAAAAACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.52
18 9 0.43
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAATCAGAAAAAGAAA
Found at i:367644 original size:30 final size:30
Alignment explanation
Indices: 367610--367670 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
367600 TTTAATAGAA
367610 AAACAATCGTTTAGTTGAACTAAGAGAGAG
1 AAACAATCGTTTAGTTGAACTAAGAGAGAG
367640 AAACAATCGTTTAGTTGAACTAAGAGAGAG
1 AAACAATCGTTTAGTTGAACTAAGAGAGAG
367670 A
1 A
367671 GAGGGGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (30 bp):
AAACAATCGTTTAGTTGAACTAAGAGAGAG
Found at i:368182 original size:10 final size:10
Alignment explanation
Indices: 368167--368211 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
368157 CTCTCTCAAC
368167 AAAAAAATTT
1 AAAAAAATTT
368177 AAAAAAATTT
1 AAAAAAATTT
*
368187 AAAAATA-TT
1 AAAAAAATTT
368196 AATAAAAATTT
1 AA-AAAAATTT
368207 CAAAA
1 -AAAA
368212 TTTATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 4 0.13
10 20 0.67
11 4 0.13
12 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:368202 original size:20 final size:18
Alignment explanation
Indices: 368169--368215 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
368159 CTCTCAACAA
368169 AAAAATTTAAAAAAATTT
1 AAAAATTTAAAAAAATTT
368187 AAAAATATTAATAAAAATTT
1 AAAAAT-TTAA-AAAAATTT
*
368207 CAAAATTTA
1 AAAAATTTA
368216 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 7 0.27
20 13 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTTAAAAAAATTT
Found at i:372290 original size:20 final size:20
Alignment explanation
Indices: 372252--372295 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
372242 GAGTTTTGAA
*
372252 TAAAAAATTTATTCAATTAT
1 TAAAAAATTTATTCAATTAC
*
372272 TAAAAAGTTTATT-ACATTAC
1 TAAAAAATTTATTCA-ATTAC
372292 TAAA
1 TAAA
372296 CTTGAAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAAAAATTTATTCAATTAC
Found at i:379783 original size:21 final size:20
Alignment explanation
Indices: 379745--379783 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
379735 ATTATATGTA
379745 TATATAACTAAATATGCTTT
1 TATATAACTAAATATGCTTT
379765 TATATGAA-TAAAGTATGCT
1 TATAT-AACTAAA-TATGCT
379784 GAAAACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (20 bp):
TATATAACTAAATATGCTTT
Found at i:384083 original size:22 final size:21
Alignment explanation
Indices: 384057--384101 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
384047 CTTTCAATAG
* *
384057 AAAATTTTCAAAAGAACTTTA
1 AAAAATTTCAAAAGAAATTTA
*
384078 AAAAATTTCAAAATAAATTTA
1 AAAAATTTCAAAAGAAATTTA
384099 AAA
1 AAA
384102 TATTAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAATTTCAAAAGAAATTTA
Found at i:385446 original size:20 final size:21
Alignment explanation
Indices: 385394--385446 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
385384 CTGTCTCAAC
*
385394 AAAAA-ATCAAAATAATTTTT
1 AAAAATATCAAAATAATTTAT
* *
385414 AAAAATTTTAAAAT-ATTTAT
1 AAAAATATCAAAATAATTTAT
385434 AAAAATATCAAAA
1 AAAAATATCAAAA
385447 ATTATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATATCAAAATAATTTAT
Found at i:385476 original size:17 final size:19
Alignment explanation
Indices: 385456--385491 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
385446 AATTATATTT
385456 TTTTAAA-AA-ATATAAAA
1 TTTTAAAGAATATATAAAA
385473 TTTTAAAGAATATATAAAA
1 TTTTAAAGAATATATAAAA
385492 GAAAGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TTTTAAAGAATATATAAAA
Found at i:386601 original size:23 final size:23
Alignment explanation
Indices: 386570--386624 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
386560 ACATTGACAC
*
386570 ATGTTATAAATGACATCATAGTG
1 ATGTCATAAATGACATCATAGTG
386593 ATGTCATAAATGACATCATAGTG
1 ATGTCATAAATGACATCATAGTG
*
386616 ACGTCATAA
1 ATGTCATAA
386625 TATAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (23 bp):
ATGTCATAAATGACATCATAGTG
Found at i:390756 original size:23 final size:23
Alignment explanation
Indices: 390724--391348 Score: 782
Period size: 23 Copynumber: 27.2 Consensus size: 23
390714 TAATTCTTTG
*
390724 AGCACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * *
390747 ATCATAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* *
390770 AGCATAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
* * *
390793 AGCGCAAATAATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* *
390816 AGCATAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
* *
390839 AGCACAAATCATATTAATATTTG
1 AGCACAAATCACATTAATATTTA
*
390862 AGCACAAATCACATTAATATTTG
1 AGCACAAATCACATTAATATTTA
* *
390885 ACCACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
390908 AGCACAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
*
390931 AGCACAAATCACAATAATATTTA
1 AGCACAAATCACATTAATATTTA
* *
390954 AGCATAAATCACATTAATATTAA
1 AGCACAAATCACATTAATATTTA
* * * *
390977 AACATAAATCACATTAGTATTTG
1 AGCACAAATCACATTAATATTTA
*
391000 AGTACAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * *
391023 AGTATAAATCACATTAATACTTA
1 AGCACAAATCACATTAATATTTA
*
391046 AGCACAAATCACATTAATATTTT
1 AGCACAAATCACATTAATATTTA
* * *
391069 ATCATAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
391092 AGCACAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* *
391115 AGCATAAATCACATTAATACTTA
1 AGCACAAATCACATTAATATTTA
* *
391138 AGCACAAATAACATTTATATTTA
1 AGCACAAATCACATTAATATTTA
* * *
391161 ATCATAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
391184 AGCACAAATCACATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* ** *
391207 AGCATAAATCACAACAATATTTG
1 AGCACAAATCACATTAATATTTA
*
391230 AGCACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* *
391253 AGCACAAATCATATTAATATTTG
1 AGCACAAATCACATTAATATTTA
*
391276 AGCACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
* * **
391299 AGCATAAATCAAATTAATACCTA
1 AGCACAAATCACATTAATATTTA
* *
391322 AGTACAAATCATATTAATATTTA
1 AGCACAAATCACATTAATATTTA
391345 AGCA
1 AGCA
391349 TAGATATAAG
Statistics
Matches: 518, Mismatches: 84, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 518 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (23 bp):
AGCACAAATCACATTAATATTTA
Found at i:393667 original size:25 final size:27
Alignment explanation
Indices: 393613--393667 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
393603 GCTAATGTCA
* **
393613 TTTTTGTTGATTGATTTTTTAAAGTCT
1 TTTTTGTTGATTGATTTTTCAAAGGAT
393640 TTTTTGTTG-TTGA-TTTTCAAAGGAT
1 TTTTTGTTGATTGATTTTTCAAAGGAT
393665 TTT
1 TTT
393668 CTCGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.48
26 4 0.16
27 9 0.36
ACGTcount: A:0.18, C:0.04, G:0.16, T:0.62
Consensus pattern (27 bp):
TTTTTGTTGATTGATTTTTCAAAGGAT
Found at i:394978 original size:27 final size:27
Alignment explanation
Indices: 394947--394999 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
394937 CAAAAGCAAT
394947 CATTGCTATTCCCTTAGCACTTTCTAG
1 CATTGCTATTCCCTTAGCACTTTCTAG
** *
394974 CATTGCTATTTTCTTAGCATTTTCTA
1 CATTGCTATTCCCTTAGCACTTTCTA
395000 TATTAAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.47
Consensus pattern (27 bp):
CATTGCTATTCCCTTAGCACTTTCTAG
Found at i:395264 original size:14 final size:14
Alignment explanation
Indices: 395245--395284 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
395235 ACAAAGTAAG
*
395245 TCATTTTCCAGAAA
1 TCATTTTACAGAAA
*
395259 TCATTTTACGGAAA
1 TCATTTTACAGAAA
395273 TCATTTTA-AGAA
1 TCATTTTACAGAA
395285 TTATATAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (14 bp):
TCATTTTACAGAAA
Found at i:412962 original size:78 final size:77
Alignment explanation
Indices: 412833--413026 Score: 239
Period size: 78 Copynumber: 2.5 Consensus size: 77
412823 TACTATTTAA
* *
412833 TCATCGGCTCGAAGCCTGCTAATTATTCACCGGCTCGAGGACTACTATTTATTCACCAGCTCAAG
1 TCATCGGCTC-AAGCCTGCTATTTATTCACCGGCTCAAGGACTACTATTTATTCACCAGCTCAAG
*
412898 GCCTATTATATTT
65 GCCTACTATATTT
* * * *
412911 TCATCGGCTCAAGGCCTGTTATTTATTCACCGGCTCAAGG-CATGCTATTTATTCATCGGCTCAA
1 TCATCGGCTCAA-GCCTGCTATTTATTCACCGGCTCAAGGAC-TACTATTTATTCACCAGCTCAA
*
412975 GGCCTGCTATATTT
64 GGCCTACTATATTT
* *
412989 TCACCGGCTCAAAGCCTGCTATATT-TTCACCGACTCAA
1 TCATCGGCTC-AAGCCTGCTAT-TTATTCACCGGCTCAA
413027 AGCTTACTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.03
78 94 0.93
79 4 0.04
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (77 bp):
TCATCGGCTCAAGCCTGCTATTTATTCACCGGCTCAAGGACTACTATTTATTCACCAGCTCAAGG
CCTACTATATTT
Found at i:413029 original size:26 final size:27
Alignment explanation
Indices: 412837--413026 Score: 207
Period size: 26 Copynumber: 7.3 Consensus size: 27
412827 ATTTAATCAT
412837 CGGCTCGAA-GCCTGCTA-ATTATTCAC
1 CGGCTC-AAGGCCTGCTATATTATTCAC
* * *
412863 CGGCTCGAGGACTACTAT-TTATTCAC
1 CGGCTCAAGGCCTGCTATATTATTCAC
* ** *
412889 CAGCTCAAGGCCTATTATATT-TTCAT
1 CGGCTCAAGGCCTGCTATATTATTCAC
*
412915 CGGCTCAAGGCCTGTTAT-TTATTCAC
1 CGGCTCAAGGCCTGCTATATTATTCAC
* *
412941 CGGCTCAAGGCATGCTAT-TTATTCAT
1 CGGCTCAAGGCCTGCTATATTATTCAC
412967 CGGCTCAAGGCCTGCTATATT-TTCAC
1 CGGCTCAAGGCCTGCTATATTATTCAC
*
412993 CGGCTCAAAGCCTGCTATATT-TTCAC
1 CGGCTCAAGGCCTGCTATATTATTCAC
*
413019 CGACTCAA
1 CGGCTCAA
413027 AGCTTACTAT
Statistics
Matches: 141, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
25 3 0.02
26 134 0.95
27 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (27 bp):
CGGCTCAAGGCCTGCTATATTATTCAC
Found at i:413038 original size:52 final size:53
Alignment explanation
Indices: 412821--413036 Score: 217
Period size: 52 Copynumber: 4.2 Consensus size: 53
412811 CGGCACGAAA
* * * *
412821 CCTACTATTTAATCATCGGCTCGAAGCCTGCTA-ATTATTCACCGGCTCGAGG
1 CCTACTATTTATTCACCGGCTCAAAGCCTGCTATATTATTCACCGGCTCAAGG
* * * ** *
412873 ACTACTATTTATTCACCAGCTCAAGGCCTATTATATT-TTCATCGGCTCAAGG
1 CCTACTATTTATTCACCGGCTCAAAGCCTGCTATATTATTCACCGGCTCAAGG
** * * *
412925 CCTGTTATTTATTCACCGGCTCAAGGCATGCTAT-TTATTCATCGGCTCAAGG
1 CCTACTATTTATTCACCGGCTCAAAGCCTGCTATATTATTCACCGGCTCAAGG
* * *
412977 CCTGCTATATT-TTCACCGGCTCAAAGCCTGCTATATT-TTCACCGACTCAAAG
1 CCTACTAT-TTATTCACCGGCTCAAAGCCTGCTATATTATTCACCGGCTCAAGG
*
413029 CTTACTAT
1 CCTACTAT
413037 ATAATTGTTT
Statistics
Matches: 135, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
51 2 0.01
52 126 0.93
53 7 0.05
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (53 bp):
CCTACTATTTATTCACCGGCTCAAAGCCTGCTATATTATTCACCGGCTCAAGG
Found at i:416287 original size:510 final size:509
Alignment explanation
Indices: 415329--416333 Score: 1672
Period size: 510 Copynumber: 2.0 Consensus size: 509
415319 TGACTTGTTG
* *
415329 GCAAATCAAACATTTTGATGTATACTCCACAATTTCTCTCTTCATACCGGGCCACCAAAACAATT
1 GCAAATCAAACATTTGGATATATACTCCACAATTTCTCTCTTCATACCGGGCCACCAAAACAATT
* *
415394 GTTTCAAGTCATTATACATTTTATTTCTCCCCTATGCATAGAAAAACTACTATCATGAGCTTCCT
66 ATTTCAAGTCATTATACATTTTATTACTCCCCTATGCATAGAAAAACTACTATCATGAGCTTCCT
*
415459 GTAAAATCTTCTATTTAATCTCTGAATTTTTCGAGACACAATGTCTGTTCCTGAAATACAATCCC
131 GTAAAATCTTCTATTTAATCTCTGAATTTTTCGAGACACAATGTCTATTCCTGAAATACAATCCC
* * * *
415524 CCATCCATACCAACTTGAAATTTTGACTCAATTGATTATCCTAATTGTTTCTTCTTATTCTTTAA
196 CCATCCATACCAACTTGAAATTTTGACTCAATTGATTATCCTAACTATTCCTTCTTATTCTCTAA
* * * *
415589 ATCTACATTATTCTCTTAAGCCTTGCAAATCTGTTGGAAGAATATCGGTTTAGCTTTTAATTTAG
261 ATCTACATCATTCTCTTAAGCCTTGCAAATCTCTTGGAAGAATACCGGTTTAGCTTTTAATTAAG
*
415654 CCAAAATAGAACCATCATCACCAATGCTAATCGGGCATTCATAGCTCTCAGGGCAAATAAATATT
326 CCAAAATAGAACCATCATCACCAATGCTAATCGGGCATTCATAGCTCTCAGGGCAAATAAAAATT
* *
415719 TTCAACTCAATGCATCCGCAACAATGTTAACCTTACCTTGGTGATAGTCAATGATTAAATCATAA
391 TTCAACTCAACGCATCCGCAACAATGTTAACCTTACCTGGGTGATAGTCAATGATTAAATCATAA
415784 TAATTTATCAGTTCTAACCATCTTCGTTGCCTCAAATTAAACTCCCCAATTTGA
456 TAATTTATCAGTTCTAACCATCTTCGTTGCCTCAAATTAAACTCCCCAATTTGA
*
415838 GCAAATCAAACATTTGGATATATACTCC-CTAATTTCTCTCTTCATACCGGGCCACCAAAATAAT
1 GCAAATCAAACATTTGGATATATACTCCAC-AATTTCTCTCTTCATACCGGGCCACCAAAACAAT
* *
415902 TATTTCAAGTCATTATAGATTTTATTACTCCCCGTATGCATAGAGAAACTACTATCATGAGCTTC
65 TATTTCAAGTCATTATACATTTTATTACTCCCC-TATGCATAGAAAAACTACTATCATGAGCTTC
* *
415967 CTGTAAAATCTTCTATTTAATCTTTGAATTTTTCGAGACACAATTTCTATTCCTGAAATACAATC
129 CTGTAAAATCTTCTATTTAATCTCTGAATTTTTCGAGACACAATGTCTATTCCTGAAATACAATC
* * * *
416032 CCCCATCCGTACCAACTTGAAATTTTGACTTAATTGCTTCTCCTAACTATTCCTTCTTATTCTCT
194 CCCCATCCATACCAACTTGAAATTTTGACTCAATTGATTATCCTAACTATTCCTTCTTATTCTCT
*
416097 AAATCTACATCATTCTCTTGAGCCTTGCAAATCTCTTGGAAGAATACCGGTTTAGCTTTTAATTA
259 AAATCTACATCATTCTCTTAAGCCTTGCAAATCTCTTGGAAGAATACCGGTTTAGCTTTTAATTA
*
416162 AGCCAAAATAGAACCATCGTCTACCAAT-CTAATCGGGCATTCATAGCTCTCAGGGCAAATAAAA
324 AGCCAAAATAGAACCATCATC-ACCAATGCTAATCGGGCATTCATAGCTCTCAGGGCAAATAAAA
* * **
416226 ATTTTCGACTCAACGCATCCGTAACAATGTTGGCCTTACCTGGGTGATAGTCAATGATTAAATCA
388 ATTTTCAACTCAACGCATCCGCAACAATGTTAACCTTACCTGGGTGATAGTCAATGATTAAATCA
* *
416291 TAATATTTTATCAGTTCTAACCATCTTCGTTGTCTCAAATTAA
453 TAATAATTTATCAGTTCTAACCATCTTCGTTGCCTCAAATTAA
416334 GCTCTTTTTA
Statistics
Matches: 460, Mismatches: 33, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
508 1 0.00
509 89 0.19
510 364 0.79
511 6 0.01
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (509 bp):
GCAAATCAAACATTTGGATATATACTCCACAATTTCTCTCTTCATACCGGGCCACCAAAACAATT
ATTTCAAGTCATTATACATTTTATTACTCCCCTATGCATAGAAAAACTACTATCATGAGCTTCCT
GTAAAATCTTCTATTTAATCTCTGAATTTTTCGAGACACAATGTCTATTCCTGAAATACAATCCC
CCATCCATACCAACTTGAAATTTTGACTCAATTGATTATCCTAACTATTCCTTCTTATTCTCTAA
ATCTACATCATTCTCTTAAGCCTTGCAAATCTCTTGGAAGAATACCGGTTTAGCTTTTAATTAAG
CCAAAATAGAACCATCATCACCAATGCTAATCGGGCATTCATAGCTCTCAGGGCAAATAAAAATT
TTCAACTCAACGCATCCGCAACAATGTTAACCTTACCTGGGTGATAGTCAATGATTAAATCATAA
TAATTTATCAGTTCTAACCATCTTCGTTGCCTCAAATTAAACTCCCCAATTTGA
Found at i:421499 original size:26 final size:26
Alignment explanation
Indices: 421472--421685 Score: 209
Period size: 26 Copynumber: 8.2 Consensus size: 26
421462 CCGGCACGAA
* *
421472 GCCTGCTATTTAATCACCGGCTCAAA
1 GCCTGCTATTTATTCACCGGCTCAAG
* *
421498 GCCTGCTAATTATTCACCGGCTCGAG
1 GCCTGCTATTTATTCACCGGCTCAAG
* *
421524 GCCTGCTATTTATTCAACAGCTCAAG
1 GCCTGCTATTTATTCACCGGCTCAAG
*
421550 GCCTGTTATATT-TTCACCGGCTCAAG
1 GCCTGCTAT-TTATTCACCGGCTCAAG
* * *
421576 TCCTGTTATTTATCCACCGGCTCAAG
1 GCCTGCTATTTATTCACCGGCTCAAG
* * *
421602 GCATGCTATTTATTCATCAGCTCAAG
1 GCCTGCTATTTATTCACCGGCTCAAG
* * *
421628 GCCTGCTATATT-TTCAACAGCTCGAG
1 GCCTGCTAT-TTATTCACCGGCTCAAG
* **
421654 GCCTGCTATATT-TCCACCAACTCAAG
1 GCCTGCTAT-TTATTCACCGGCTCAAG
421680 GCCTGC
1 GCCTGC
421686 AATATAATTG
Statistics
Matches: 159, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
25 2 0.01
26 153 0.96
27 4 0.03
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.30
Consensus pattern (26 bp):
GCCTGCTATTTATTCACCGGCTCAAG
Found at i:421609 original size:78 final size:78
Alignment explanation
Indices: 421472--421681 Score: 246
Period size: 78 Copynumber: 2.7 Consensus size: 78
421462 CCGGCACGAA
* * * *
421472 GCCTGCTAT-TTAATCACCGGCTCAAAGCCTGCTAATTATTCACCGGCTCGAGGCCTGCTATTTA
1 GCCTGCTATATT-TTCACCGGCTCAAAGCCTGCTAATTATCCACCGGCTCAAGGCATGCTATTTA
421536 TTCAACAGCTCAAG
65 TTCAACAGCTCAAG
* * *
421550 GCCTGTTATATTTTCACCGGCTC-AAGTCCTGTTATTTATCCACCGGCTCAAGGCATGCTATTTA
1 GCCTGCTATATTTTCACCGGCTCAAAG-CCTGCTAATTATCCACCGGCTCAAGGCATGCTATTTA
*
421614 TTCATCAGCTCAAG
65 TTCAACAGCTCAAG
* * * * **
421628 GCCTGCTATATTTTCAACAGCTCGAGGCCTGCTATATT-TCCACCAACTCAAGGC
1 GCCTGCTATATTTTCACCGGCTCAAAGCCTGCTA-ATTATCCACCGGCTCAAGGC
421682 CTGCAATATA
Statistics
Matches: 112, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
77 3 0.03
78 103 0.92
79 6 0.05
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.30
Consensus pattern (78 bp):
GCCTGCTATATTTTCACCGGCTCAAAGCCTGCTAATTATCCACCGGCTCAAGGCATGCTATTTAT
TCAACAGCTCAAG
Found at i:430108 original size:15 final size:16
Alignment explanation
Indices: 430077--430109 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
430067 ATATATAAAA
430077 TTAAAATTAAAAATTT
1 TTAAAATTAAAAATTT
*
430093 TTAAAA-TAATAATTT
1 TTAAAATTAAAAATTT
430108 TT
1 TT
430110 GAGATCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATTAAAAATTT
Found at i:438758 original size:24 final size:24
Alignment explanation
Indices: 438699--438759 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
438689 GACTAATAAT
* * *
438699 AGTTTGACTCAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAACAG
* *
438723 AGTTTAATTGAAACAATTAAACAG
1 AGTTTAACTGAAACAAATAAACAG
438747 AGTTTAACTGAAA
1 AGTTTAACTGAAA
438760 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAG
Found at i:440686 original size:24 final size:24
Alignment explanation
Indices: 440658--440744 Score: 111
Period size: 24 Copynumber: 3.6 Consensus size: 24
440648 TAGACTAATA
* *
440658 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTAAAACAAATAAAC
*
440682 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTAAAACAAATAAAC
* * *
440706 AGATTTTAATTAAAACAATTAAAC
1 AGAGTTTAACTAAAACAAATAAAC
*
440730 AAAGTTTAACTAAAA
1 AGAGTTTAACTAAAA
440745 GATTATTTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTAAAACAAATAAAC
Found at i:443937 original size:17 final size:19
Alignment explanation
Indices: 443912--443950 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
443902 TCAATTAATT
443912 AATTGATAATTT-TAAAAA
1 AATTGATAATTTGTAAAAA
443930 AATT-ATAATTTGGTAAAAA
1 AATTGATAATTT-GTAAAAA
443949 AA
1 AA
443951 ACAAGCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (19 bp):
AATTGATAATTTGTAAAAA
Found at i:445141 original size:19 final size:20
Alignment explanation
Indices: 445113--445150 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
445103 TTTATTTTGA
445113 TTTTCACTCTCAAATTTTTT
1 TTTTCACTCTCAAATTTTTT
*
445133 TTTTC-CTCTCCAATTTTT
1 TTTTCACTCTCAAATTTTT
445151 CAAACGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTCACTCTCAAATTTTTT
Found at i:447969 original size:34 final size:35
Alignment explanation
Indices: 447931--447999 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
447921 AATTTTTAAC
* *
447931 TTTTAAAATATTAATAAAAA-TTTCAA-AATATATA
1 TTTTAAAAAATT-ATAAAAAGTTTAAAGAATATATA
447965 TTTTAAAAAATTATAAAAAGTTTAAAGAATATATA
1 TTTTAAAAAATTATAAAAAGTTTAAAGAATATATA
448000 AAAAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 7 0.23
34 16 0.52
35 8 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (35 bp):
TTTTAAAAAATTATAAAAAGTTTAAAGAATATATA
Found at i:447990 original size:19 final size:20
Alignment explanation
Indices: 447966--448003 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
447956 AAATATATAT
447966 TTTAAAAAAT-TATAAAAAG
1 TTTAAAAAATATATAAAAAG
*
447985 TTTAAAGAATATATAAAAA
1 TTTAAAAAATATATAAAAA
448004 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TTTAAAAAATATATAAAAAG
Found at i:448009 original size:20 final size:19
Alignment explanation
Indices: 447967--448012 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
447957 AATATATATT
**
447967 TTAAAAAATTATAAAAAGT
1 TTAAAAAATTATAAAAAAA
*
447986 TTAAAGAATATATAAAAAAA
1 TTAAAAAAT-TATAAAAAAA
448006 TTAAAAA
1 TTAAAAA
448013 TTTTCTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TTAAAAAATTATAAAAAAA
Found at i:448620 original size:14 final size:14
Alignment explanation
Indices: 448601--448631 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
448591 CCTTTATTTG
448601 TTTTGTTCTAATAT
1 TTTTGTTCTAATAT
*
448615 TTTTGTTGTAATAT
1 TTTTGTTCTAATAT
448629 TTT
1 TTT
448632 AGTTTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68
Consensus pattern (14 bp):
TTTTGTTCTAATAT
Found at i:456923 original size:22 final size:22
Alignment explanation
Indices: 456898--456939 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
456888 AAGCAACATA
456898 TTAGTTAGTAAATGACTAAACC
1 TTAGTTAGTAAATGACTAAACC
456920 TTAGTTAGTAAATGACTAAA
1 TTAGTTAGTAAATGACTAAA
456940 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
TTAGTTAGTAAATGACTAAACC
Found at i:457359 original size:25 final size:24
Alignment explanation
Indices: 457313--457365 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
457303 CCAACTTTTG
457313 TTTTCTCTCATAAACTTGTTCTTGT
1 TTTTCTCTCATAAACTTGTTC-TGT
457338 TTTTCTCTCA-AATAC-TGCTTCTGT
1 TTTTCTCTCATAA-ACTTG-TTCTGT
457362 TTTT
1 TTTT
457366 GGTTATAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTTCTCTCATAAACTTGTTCTGT
Found at i:458735 original size:16 final size:17
Alignment explanation
Indices: 458699--458737 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
458689 AATAACACCG
458699 GCACAAAGCCTACTACA
1 GCACAAAGCCTACTACA
458716 -CACAAAGCCTACTA-A
1 GCACAAAGCCTACTACA
458731 GCACAAA
1 GCACAAA
458738 TCTTGATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.10
Consensus pattern (17 bp):
GCACAAAGCCTACTACA
Found at i:458756 original size:37 final size:37
Alignment explanation
Indices: 458715--458850 Score: 209
Period size: 37 Copynumber: 3.7 Consensus size: 37
458705 AGCCTACTAC
* *
458715 ACACAAAGCCTACTAAGCACAAATCTTGATAACACCG
1 ACACAAAGCCTACTAGGCACAAAGCTTGATAACACCG
* *
458752 ACACAAAGCCTACTAGGCGCAAAGCTTGATAACACTG
1 ACACAAAGCCTACTAGGCACAAAGCTTGATAACACCG
*
458789 ACACAAAGCCTACTAGGCACAAAGCCTGATAACACCG
1 ACACAAAGCCTACTAGGCACAAAGCTTGATAACACCG
* *
458826 GCACAAAGCCTACTAGGCACGAAGC
1 ACACAAAGCCTACTAGGCACAAAGC
458851 CTGAATTTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 90 1.00
ACGTcount: A:0.40, C:0.30, G:0.17, T:0.13
Consensus pattern (37 bp):
ACACAAAGCCTACTAGGCACAAAGCTTGATAACACCG
Found at i:458776 original size:53 final size:53
Alignment explanation
Indices: 458666--458766 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
458656 TCACTAGCAT
* * *
458666 AAAGCCTATTAGGCACAAAGCCTAATAACACCGGCACAAAGCCTACTACACAC
1 AAAGCCTACTAAGCACAAAGCCTAATAACACCGACACAAAGCCTACTACACAC
* * *
458719 AAAGCCTACTAAGCACAAATCTTGATAACACCGACACAAAGCCTACTA
1 AAAGCCTACTAAGCACAAAGCCTAATAACACCGACACAAAGCCTACTA
458767 GGCGCAAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.43, C:0.31, G:0.12, T:0.15
Consensus pattern (53 bp):
AAAGCCTACTAAGCACAAAGCCTAATAACACCGACACAAAGCCTACTACACAC
Found at i:458811 original size:16 final size:16
Alignment explanation
Indices: 458790--458852 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 16
458780 ATAACACTGA
458790 CACAAAGCCTACTAGG
1 CACAAAGCCTACTAGG
458806 CACAAAGCCTGA-TAACACCGG
1 CACAAAGCCT-ACT---A--GG
458827 CACAAAGCCTACTAGG
1 CACAAAGCCTACTAGG
*
458843 CACGAAGCCT
1 CACAAAGCCT
458853 GAATTTGTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
16 22 0.56
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 13 0.33
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.11
Consensus pattern (16 bp):
CACAAAGCCTACTAGG
Found at i:463015 original size:37 final size:37
Alignment explanation
Indices: 462961--463159 Score: 317
Period size: 37 Copynumber: 5.4 Consensus size: 37
462951 TTGGATCACT
*
462961 GGCACAAAGCCTAATAACACCGGCACAAAGCCTACTA
1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA
*
462998 GGCACAAAGCCTGATAACACCGACACAAAGCCTACTA
1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA
* *
463035 GGCACAAAGCTTTATAACACCGGCACAAAGCCTACTA
1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA
* **
463072 GGCACAAATCCTGATAACATTGGCACAAAGCCTACTA
1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA
* *
463109 GGCACAAAGCCTTATAACACCAGCACAAAGCCTACTA
1 GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA
463146 GGCACAAAGCCTGA
1 GGCACAAAGCCTGA
463160 ATTTGTATAA
Statistics
Matches: 146, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 146 1.00
ACGTcount: A:0.39, C:0.31, G:0.17, T:0.14
Consensus pattern (37 bp):
GGCACAAAGCCTGATAACACCGGCACAAAGCCTACTA
Found at i:463594 original size:2 final size:2
Alignment explanation
Indices: 463587--463615 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
463577 AACAACAACA
463587 AT AT 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 AT AT A
463616 AAATCCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:464115 original size:3 final size:3
Alignment explanation
Indices: 464107--464149 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
464097 ACTTATAAAT
464107 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
464150 ACTCTTACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:471601 original size:23 final size:23
Alignment explanation
Indices: 471570--471899 Score: 293
Period size: 23 Copynumber: 14.3 Consensus size: 23
471560 CTTATATCCG
*
471570 TGCTTAAATATTTATATGATTTA
1 TGCTTAAATATTAATATGATTTA
* * *
471593 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
* * *
471616 CGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTA
*
471639 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTA
* * * *
471662 TGCTGAAATAATAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
* * * *
471685 TGCTCAAATATTAATTTAATTTG
1 TGCTTAAATATTAATATGATTTA
* * *
471708 TGCTCAAATATTAATGTAATTTA
1 TGCTTAAATATTAATATGATTTA
* * * *
471731 TGTTTATATATTAATGTGATTTT
1 TGCTTAAATATTAATATGATTTA
* *
471754 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
* * * * *
471777 TACTGAAATAATAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
* * *
471800 TGCTTAAATGTTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
*
471823 TGCTTAAATATTAACT-TGATTTG
1 TGCTTAAATATTAA-TATGATTTA
* *
471846 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTA
* * *
471869 TGCTGAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTA
471892 TGCTTAAA
1 TGCTTAAA
471900 GAATTAAGAT
Statistics
Matches: 263, Mismatches: 42, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
22 1 0.00
23 261 0.99
24 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTA
Found at i:471638 original size:46 final size:46
Alignment explanation
Indices: 471569--471899 Score: 421
Period size: 46 Copynumber: 7.2 Consensus size: 46
471559 TCTTATATCC
* * *
471569 GTGCTTAAATATTTATATGATTTATGATTAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
* * *
471615 GCGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATATGATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
* * * * * *
471661 GTGCTGAAATAATAATGTGATTTGTGCTCAAATATTAATTTAATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
* * * *
471707 GTGCTCAAATATTAATGTAATTTATGTTTATATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
* * * * *
471753 TTGCTTAAATATTAATGTGATTTGTACTGAAATAATAATGTGATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
* *
471799 GTGCTTAAATGTTAATGTGATTTGTGCTTAAATATTAACT-TGATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAA-TGTGATTT
* *
471845 GTGCTCAAATATTAATGTGATTTATGCTGAAATATTAATGTGATTT
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
471891 GTGCTTAAA
1 GTGCTTAAA
471900 GAATTAAGAT
Statistics
Matches: 241, Mismatches: 42, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
45 1 0.00
46 239 0.99
47 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (46 bp):
GTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
Found at i:471656 original size:69 final size:69
Alignment explanation
Indices: 471569--471899 Score: 421
Period size: 69 Copynumber: 4.8 Consensus size: 69
471559 TCTTATATCC
* * * * * *
471569 GTGCTTAAATATTTATATGATTTATGATTAAATATTAATGTGATTTGCGCTTAAGTATTAATGTG
1 GTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
471634 ATTT
66 ATTT
* * * * * * * * *
471638 ATGCTTAAATATTAATATGATTTGTGCTGAAATAATAATGTGATTTGTGCTCAAATATTAATTTA
1 GTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
471703 ATTT
66 ATTT
* * * *
471707 GTGCTCAAATATTAATGTAATTTATGTTTATATATTAATGTGATTTTTGCTTAAATATTAATGTG
1 GTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
471772 ATTT
66 ATTT
* * * * *
471776 GTACTGAAATAATAATGTGATTTGTGCTTAAATGTTAATGTGATTTGTGCTTAAATATTAACT-T
1 GTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAA-TGT
471840 GATTT
65 GATTT
*
471845 GTGCTCAAATATTAATGTGATTTATGCTGAAATATTAATGTGATTTGTGCTTAAA
1 GTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAA
471900 GAATTAAGAT
Statistics
Matches: 222, Mismatches: 39, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
69 221 1.00
70 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (69 bp):
GTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
ATTT
Found at i:472009 original size:36 final size:36
Alignment explanation
Indices: 471969--472076 Score: 100
Period size: 36 Copynumber: 3.1 Consensus size: 36
471959 TGACGACCGT
** * *
471969 TGTGAAAGTGAATATGTGTGTATGATCTTCATGCCA
1 TGTGAAAGAAAATACGTGGGTATGATCTTCATGCCA
* *
472005 TGTGACAGAAAATACGTGGGTATG---TTC-T-TCA
1 TGTGAAAGAAAATACGTGGGTATGATCTTCATGCCA
* * *
472036 TGTGACAGAAAATATGTGGGTATGATCTTCATGTCA
1 TGTGAAAGAAAATACGTGGGTATGATCTTCATGCCA
472072 TGTGA
1 TGTGA
472077 CTGATTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
31 25 0.42
32 1 0.02
33 3 0.05
34 3 0.05
35 1 0.02
36 27 0.45
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (36 bp):
TGTGAAAGAAAATACGTGGGTATGATCTTCATGCCA
Found at i:472041 original size:31 final size:31
Alignment explanation
Indices: 472003--472069 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
471993 ATCTTCATGC
*
472003 CATGTGACAGAAAATACGTGGGTATGTTCTT
1 CATGTGACAGAAAATACGTGGGTATGATCTT
*
472034 CATGTGACAGAAAATATGTGGGTATGATCTT
1 CATGTGACAGAAAATACGTGGGTATGATCTT
472065 CATGT
1 CATGT
472070 CATGTGACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (31 bp):
CATGTGACAGAAAATACGTGGGTATGATCTT
Found at i:494036 original size:8 final size:8
Alignment explanation
Indices: 494023--494049 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
494013 AATTAAAATA
494023 AAAACATT
1 AAAACATT
494031 AAAACATT
1 AAAACATT
494039 AAAACATT
1 AAAACATT
494047 AAA
1 AAA
494050 TTTACACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAACATT
Found at i:497720 original size:21 final size:21
Alignment explanation
Indices: 497691--497730 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
497681 TGTATTTATC
*
497691 AAGTGGATATCGTGATACCCA
1 AAGTGGATATCGCGATACCCA
* *
497712 AAGTTGATATTGCGATACC
1 AAGTGGATATCGCGATACC
497731 ACTAAAGGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (21 bp):
AAGTGGATATCGCGATACCCA
Found at i:499365 original size:21 final size:21
Alignment explanation
Indices: 499336--499380 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
499326 CTCTCAATAG
*
499336 AAAAGTTTCAAAATAACTTTA
1 AAAAATTTCAAAATAACTTTA
*
499357 AAAAATTTCAAAATAATTTTA
1 AAAAATTTCAAAATAACTTTA
499378 AAA
1 AAA
499381 TATTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATTTCAAAATAACTTTA
Found at i:499374 original size:11 final size:11
Alignment explanation
Indices: 499341--499382 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
499331 AATAGAAAAG
499341 TTTCAAAATAA
1 TTTCAAAATAA
499352 CTTT-AAAA-AA
1 -TTTCAAAATAA
499362 TTTCAAAATAA
1 TTTCAAAATAA
*
499373 TTTTAAAATA
1 TTTCAAAATA
499383 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.11
10 6 0.22
11 15 0.56
12 3 0.11
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (11 bp):
TTTCAAAATAA
Found at i:501197 original size:19 final size:20
Alignment explanation
Indices: 501168--501207 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
501158 CATCAAGATT
501168 AATCTCATTTCCTTTTATCA
1 AATCTCATTTCCTTTTATCA
*
501188 AATC-CATTTCTTTTTATCA
1 AATCTCATTTCCTTTTATCA
501207 A
1 A
501208 GTAATTGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.50
Consensus pattern (20 bp):
AATCTCATTTCCTTTTATCA
Found at i:519980 original size:24 final size:24
Alignment explanation
Indices: 519919--519981 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
519909 TAGACTAATA
* *
519919 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
*
519943 AGAGTTTAATTGAAACAAATTAAAT
1 AGAGTTTAACTGAAACAAA-TAAAT
519968 AGAG-TTAACTGAAA
1 AGAGTTTAACTGAAA
519982 GATTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 25 0.74
25 9 0.26
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:521944 original size:24 final size:25
Alignment explanation
Indices: 521917--521968 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
521907 AGTTTGACTC
*
521917 AAAC-AAATAAACAGAGATTAATTG
1 AAACGAAATAAACAGAGATTAACTG
* * *
521941 AAACGAATTAAATAGAGTTTAACTG
1 AAACGAAATAAACAGAGATTAACTG
521966 AAA
1 AAA
521969 TATTATTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.56, C:0.08, G:0.13, T:0.23
Consensus pattern (25 bp):
AAACGAAATAAACAGAGATTAACTG
Found at i:525781 original size:3 final size:3
Alignment explanation
Indices: 525773--525823 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
525763 TATACTTTGG
*
525773 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
525821 ATT
1 ATT
525824 TATTGGGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:531751 original size:13 final size:13
Alignment explanation
Indices: 531721--531759 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
531711 CTGTTAACCG
*
531721 TTGATTGTTGACCA
1 TTGATCGTTGA-CA
531735 TTGATCGTTGACA
1 TTGATCGTTGACA
*
531748 TTGACCGTTGAC
1 TTGATCGTTGAC
531760 TTTTTTCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGATCGTTGACA
Found at i:537842 original size:13 final size:13
Alignment explanation
Indices: 537812--537850 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
537802 CTGTTAACCG
*
537812 TTGATTGTTGACCA
1 TTGATCGTTGA-CA
537826 TTGATCGTTGACA
1 TTGATCGTTGACA
*
537839 TTGACCGTTGAC
1 TTGATCGTTGAC
537851 TTTTTTCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGATCGTTGACA
Found at i:540020 original size:27 final size:27
Alignment explanation
Indices: 540001--540068 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
539991 GGAAACTAAA
*
540001 GAAGAGAAGGAAGAAGAGGATAAAAGT
1 GAAGAGAAGGAAGAAGAGGAGAAAAGT
540028 GAAGAGAAGGAAGAAGAGGAGAAAAGT
1 GAAGAGAAGGAAGAAGAGGAGAAAAGT
540055 GAAGAGAAGGAAGA
1 GAAGAGAAGGAAGA
540069 TGCCCCGACA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (27 bp):
GAAGAGAAGGAAGAAGAGGAGAAAAGT
Found at i:540049 original size:15 final size:15
Alignment explanation
Indices: 539999--540068 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 15
539989 AAGGAAACTA
539999 AAGAAGAGAAGGAAG
1 AAGAAGAGAAGGAAG
* *
540014 AAGAGGATAA--AAG
1 AAGAAGAGAAGGAAG
*
540027 -TGAAGAGAAGGAAG
1 AAGAAGAGAAGGAAG
*
540041 AAGAGGAGAA--AAG
1 AAGAAGAGAAGGAAG
*
540054 -TGAAGAGAAGGAAG
1 AAGAAGAGAAGGAAG
540068 A
1 A
540069 TGCCCCGACA
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
12 13 0.32
13 6 0.15
14 6 0.15
15 15 0.38
ACGTcount: A:0.57, C:0.00, G:0.39, T:0.04
Consensus pattern (15 bp):
AAGAAGAGAAGGAAG
Found at i:540345 original size:21 final size:21
Alignment explanation
Indices: 540316--540355 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
540306 GGTTGACTTC
*
540316 AAGGAAAAAAAGAGAAAGAGG
1 AAGGAAAAAAAGAAAAAGAGG
*
540337 AAGGGAAAAAAGAAAAAGA
1 AAGGAAAAAAAGAAAAAGA
540356 AGCACAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
AAGGAAAAAAAGAAAAAGAGG
Found at i:540491 original size:18 final size:17
Alignment explanation
Indices: 540465--540508 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
540455 ATGCATCTCA
* *
540465 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
*
540483 TTTATTTGTCACTGGAT
1 TTTATTTGTCACTGCAT
540500 TTTATTTGT
1 TTTATTTGT
540509 TAGTACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:541934 original size:30 final size:30
Alignment explanation
Indices: 541899--542095 Score: 159
Period size: 30 Copynumber: 6.6 Consensus size: 30
541889 ATTTGAGGTG
*
541899 AAAATGTAATTTTGGAAAAATTCAAGGGTC
1 AAAATGTAATTTTGGAAAAATTTAAGGGTC
* * * * *
541929 AAAATGTGATTTTGG-GAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAATTTAAGGGTC
* * ** * *
541958 AAAATGTGATTTTGG-GAGGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAATTTAAGGGTC
*
541987 AAACTGTAATTTT-GAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAA-TTTAAGGGTC
* *
542017 AAAATGTAATTTTGGAAAAGTTTAAAGGTC
1 AAAATGTAATTTTGGAAAAATTTAAGGGTC
* * * *
542047 AAAATATAATTTT-AAAAAAGTTAAGGGGTT
1 AAAATGTAATTTTGGAAAAATTTAA-GGGTC
* *
542077 AAAATGAAATTTTAGAAAA
1 AAAATGTAATTTTGGAAAA
542096 GTTTGAGCTT
Statistics
Matches: 136, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
28 1 0.01
29 57 0.42
30 69 0.51
31 9 0.07
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAATTTAAGGGTC
Found at i:542064 original size:59 final size:60
Alignment explanation
Indices: 541899--542099 Score: 201
Period size: 60 Copynumber: 3.4 Consensus size: 60
541889 ATTTGAGGTG
* * * *** *
541899 AAAATGTAATTTTGGAAAAATTCAAGGGTCAAAATGTGATTTT-GGGAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAAAAAAGTTTAAGGGTT
* * * * * * * *
541958 AAAATGTGATTTTGG-GAGGTTTGAGGGTTAAACTGTAATTTTGAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAAAAAAGTTTAAGGGTT
* *
542017 AAAATGTAATTTTGGAAAAGTTTAAAGGTCAAAATATAATTTTAAAAAAG-TTAAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAAAAAAGTTTAA-GGGTT
* *
542077 AAAATGAAATTTTAGAAAAGTTT
1 AAAATGTAATTTTGGAAAAGTTT
542100 GAGCTTCAAA
Statistics
Matches: 113, Mismatches: 26, Indels: 5
0.78 0.18 0.03
Matches are distributed among these distances:
58 19 0.17
59 43 0.38
60 51 0.45
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.34
Consensus pattern (60 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTAAAAAAGTTTAAGGGTT
Found at i:553307 original size:16 final size:16
Alignment explanation
Indices: 553286--553321 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
553276 AAATAATCCC
*
553286 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
553302 AAAATTAAAAGTCTCA
1 AAAATTAAAAGTCTCA
553318 AAAA
1 AAAA
553322 CACTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:556106 original size:25 final size:25
Alignment explanation
Indices: 556052--556107 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
556042 GAAAATAGCG
*
556052 AAAGAAAGGATTTTTTTAGGTTTTC
1 AAAGGAAGGATTTTTTTAGGTTTTC
556077 AAAGGAAGGATTTTTTTAGGTTTTC
1 AAAGGAAGGATTTTTTTAGGTTTTC
556102 AAAGGA
1 AAAGGA
556108 TTTTTGTGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (25 bp):
AAAGGAAGGATTTTTTTAGGTTTTC
Found at i:559849 original size:23 final size:23
Alignment explanation
Indices: 559819--560374 Score: 709
Period size: 23 Copynumber: 24.2 Consensus size: 23
559809 GATTAATGAC
*
559819 TAAATATT-ATAGTGATTTGCGCT
1 TAAATATTAAT-GTGATTTGTGCT
* *
559842 TAAGTATTAATGTGATTTATGCT
1 TAAATATTAATGTGATTTGTGCT
* *
559865 TAAATATTAATATGATTTGTGAT
1 TAAATATTAATGTGATTTGTGCT
* *
559888 CAAATATTAATGTGATATGTGCT
1 TAAATATTAATGTGATTTGTGCT
*
559911 CAAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
*
559934 TAAATATTAATATGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
* * **
559957 CAAATATTAAAGTGATTTAAGCT
1 TAAATATTAATGTGATTTGTGCT
* *
559980 TAAATATTAATATGATTTGTGTT
1 TAAATATTAATGTGATTTGTGCT
* * *
560003 TAGATATTAATGTGGTTTATGCT
1 TAAATATTAATGTGATTTGTGCT
*
560026 TAAATATTAATATGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
*
560049 CAAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
* *
560072 TAAATATTAATATGATTTGGGCT
1 TAAATATTAATGTGATTTGTGCT
* * *
560095 GAAATATTAATTTGATTTGTGAT
1 TAAATATTAATGTGATTTGTGCT
**
560118 TAAATATTAACATGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
* * *
560141 AAAATATTAATGAGATTTATGCT
1 TAAATATTAATGTGATTTGTGCT
*
560164 TAAATATTAATATGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
* ** *
560187 CAAATATTAATGTGATTTAAGTT
1 TAAATATTAATGTGATTTGTGCT
*
560210 TAAATATTAATGTTATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
560233 TAAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
*
560256 TAAATAATAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
560279 TAAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
560302 TAAATATTAATGTGATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
* * * *
560325 CAAATATTAATATGATTTATGAT
1 TAAATATTAATGTGATTTGTGCT
* *
560348 TAAATATTAATTTCATTTGTGCT
1 TAAATATTAATGTGATTTGTGCT
560371 TAAA
1 TAAA
560375 GAATTAAGAT
Statistics
Matches: 454, Mismatches: 78, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
23 452 1.00
24 2 0.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
TAAATATTAATGTGATTTGTGCT
Found at i:570051 original size:46 final size:46
Alignment explanation
Indices: 569984--570078 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
569974 AACCTATTCA
569984 AAATTAGCTTACAACCAGCAATAGAATGCCTAGAAACATGCAAAGG
1 AAATTAGCTTACAACCAGCAATAGAATGCCTAGAAACATGCAAAGG
570030 AAATTAGCTTACAACCAGCAATAGAATGCCTAGAAACATGCAAAGG
1 AAATTAGCTTACAACCAGCAATAGAATGCCTAGAAACATGCAAAGG
570076 AAA
1 AAA
570079 CCATAACAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.17
Consensus pattern (46 bp):
AAATTAGCTTACAACCAGCAATAGAATGCCTAGAAACATGCAAAGG
Found at i:570072 original size:22 final size:22
Alignment explanation
Indices: 570001--570072 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
569991 CTTACAACCA
570001 GCAATAGAATGCCTAGAAACAT
1 GCAATAGAATGCCTAGAAACAT
* * *
570023 GCAA-AGGAAATTAGCTTACAACCA-
1 GCAATA-G-AA-T-GCCTAGAAACAT
570047 GCAATAGAATGCCTAGAAACAT
1 GCAATAGAATGCCTAGAAACAT
570069 GCAA
1 GCAA
570073 AGGAAACCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 9 0.24
22 10 0.26
23 4 0.11
24 6 0.16
25 9 0.24
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.17
Consensus pattern (22 bp):
GCAATAGAATGCCTAGAAACAT
Found at i:571044 original size:31 final size:31
Alignment explanation
Indices: 571008--571084 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
570998 CATCCAATGT
571008 AATCATCACTTGATGATTGGTGTATTATCCA
1 AATCATCACTTGATGATTGGTGTATTATCCA
571039 AATCATCACTTGATGATTGGTGTATTATCCA
1 AATCATCACTTGATGATTGGTGTATTATCCA
571070 AATCATCACTTGATG
1 AATCATCACTTGATG
571085 CTAAAGTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (31 bp):
AATCATCACTTGATGATTGGTGTATTATCCA
Found at i:575216 original size:18 final size:16
Alignment explanation
Indices: 575193--575228 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
575183 GTTTAAAATT
575193 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
575211 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
575227 TT
1 TT
575229 CTCATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:579877 original size:21 final size:20
Alignment explanation
Indices: 579852--579896 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
579842 AGTCTCAACA
*
579852 AAAAATTCCAAAATAGTTTT
1 AAAAATTCCAAAATAATTTT
**
579872 CAAAAATTTTAAAATAATTTT
1 -AAAAATTCCAAAATAATTTT
579893 AAAA
1 AAAA
579897 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTCCAAAATAATTTT
Found at i:579914 original size:19 final size:19
Alignment explanation
Indices: 579874--579915 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
579864 ATAGTTTTCA
*
579874 AAAATTTTAAAATAATTTT
1 AAAATTTTAAAATAATTAT
579893 AAAATTTTAAAAT-ATTAAT
1 AAAATTTTAAAATAATT-AT
579912 AAAA
1 AAAA
579916 ATTGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTTTAAAATAATTAT
Found at i:609163 original size:17 final size:17
Alignment explanation
Indices: 609132--609189 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
609122 TAATTGTCCA
* *
609132 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
609149 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
609166 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
609183 TGCATTT
1 TGCATTT
609190 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:609170 original size:34 final size:34
Alignment explanation
Indices: 609124--609189 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
609114 GTGTAGTATA
*
609124 ATTGTCCATGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCATGCATCTA-CAATGTCATTGCATTTTT
*
609158 ATTGTCGC-TGCATCTACATTGTCATTGCATTT
1 ATTGTC-CATGCATCTACAATGTCATTGCATTT
609190 CCATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCATGCATCTACAATGTCATTGCATTTTT
Found at i:618506 original size:25 final size:23
Alignment explanation
Indices: 618473--618519 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
618463 TTAATAGATT
*
618473 AAAAGAAATAAACTAAAAGTAAAG
1 AAAAGAAATAAAATAAAA-TAAAG
618497 AAAATGAAATAAAATAAAATAAA
1 AAAA-GAAATAAAATAAAATAAA
618520 ATTGTATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (23 bp):
AAAAGAAATAAAATAAAATAAAG
Done.