Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 179 of 193
Found at i:55974563 original size:15 final size:14
Alignment explanation
Indices: 55974545--55974574 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
55974535 CTATTGCCTC
55974545 TCTCTCTT-TCTTT
1 TCTCTCTTATCTTT
55974558 TCTCTCTTATCTTT
1 TCTCTCTTATCTTT
55974572 TCT
1 TCT
55974575 TGTATACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTCTCTTATCTTT
Found at i:55976657 original size:24 final size:25
Alignment explanation
Indices: 55976628--55976681 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
55976618 TTAAATTTCT
*
55976628 GTTTTTGGGTGCCTTCTAGAAACTA
1 GTTTTTGGGCGCCTTCTAGAAACTA
55976653 GTTTTTGGGCGCCTTCTAGAAACTA
1 GTTTTTGGGCGCCTTCTAGAAACTA
55976678 GTTT
1 GTTT
55976682 ATTTAACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (25 bp):
GTTTTTGGGCGCCTTCTAGAAACTA
Found at i:55981282 original size:19 final size:18
Alignment explanation
Indices: 55981255--55981310 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
55981245 TACAACAAAA
* *
55981255 AAAAATTAAAATAATTTTT
1 AAAATTTAAAAT-ATTTAT
55981274 AAAATTTAAAATATTTAT
1 AAAATTTAAAATATTTAT
*
55981292 AAAGATTTTAAA-ATTTAT
1 AAA-ATTTAAAATATTTAT
55981310 A
1 A
55981311 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAATTTAAAATATTTAT
Found at i:55981307 original size:18 final size:17
Alignment explanation
Indices: 55981256--55981310 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
55981246 ACAACAAAAA
* *
55981256 AAAATTAAAATAATTTTT
1 AAAATTTAAA-AATTTAT
55981274 AAAATTTAAAATATTTAT
1 AAAATTTAAAA-ATTTAT
*
55981292 AAAGATTTTAAAATTTAT
1 AAA-ATTTAAAAATTTAT
55981310 A
1 A
55981311 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 1 0.03
18 24 0.75
19 7 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AAAATTTAAAAATTTAT
Found at i:55985200 original size:59 final size:58
Alignment explanation
Indices: 55985130--55985597 Score: 443
Period size: 59 Copynumber: 7.9 Consensus size: 58
55985120 CCCGGGGATG
*
55985130 AAATGGTAATTTTTAGTGAA-ATCGGGGTTAAAAATGAGATTTTGGAAAGTTCAGGGGTA
1 AAATGGTAATTTTT-G-GAAGATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGGTA
* * * **
55985189 ATATAGTAATTTTTGGTGAA-ATCGAGGTT-AAAATGAGATTTTGGAAAGTTCGGGGGTA
1 AAATGGTAATTTTT-G-GAAGATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGGTA
* ** * * * *
55985247 AAAT-GTAATTTTTGGTGAA-ATCGAGGTTAAAAGCGGGATTTTAGAGAGTTTGGGGGTA
1 AAATGGTAATTTTT-G-GAAGATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGGTA
* *
55985305 AAATGGTAATTTTTAGTGAA-ATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAA
1 AAATGGTAATTTTT-G-GAAGATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGGT-A
* *
55985365 AAATGGTAATTTTTGGAAGTTTCGAGGGTTAAAAATG-GAATTTTGGGAAGTTT-GGGGTA
1 AAATGGTAATTTTTGGAAG-ATCG-GGGTTAAAAATGAG-ATTTTGGAAAGTTTAGGGGTA
* * * * *
55985424 AAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTGGGAAGTTTAGGGGTA
1 AAATGGTAATTTTTGGAAG-ATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGGTA
* * * * * *
55985483 AAATGGTTATTTTTGGAAGTTTTGGGGTCAAAAATG-GAAGTTTGGGAAGTTTAGGGGTA
1 AAATGGTAATTTTTGGAAG-ATCGGGGTTAAAAATGAG-ATTTTGGAAAGTTTAGGGGTA
* *
55985542 AAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAAT-AGAATTTTGGAAAGTTTAGGG
1 AAATGGTAATTTTTGGAAG-ATCGGGGTTAAAAATGAG-ATTTTGGAAAGTTTAGGG
55985598 ACTAGAGAGC
Statistics
Matches: 367, Mismatches: 31, Indels: 22
0.87 0.07 0.05
Matches are distributed among these distances:
57 24 0.07
58 87 0.24
59 208 0.57
60 24 0.07
61 24 0.07
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (58 bp):
AAATGGTAATTTTTGGAAGATCGGGGTTAAAAATGAGATTTTGGAAAGTTTAGGGGTA
Found at i:55985232 original size:28 final size:29
Alignment explanation
Indices: 55985194--55985278 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 29
55985184 GGGTAATATA
55985194 GTAATTTTTGGTGAAATCGAGGTTAAAAT
1 GTAATTTTTGGTGAAATCGAGGTTAAAAT
* *
55985223 G-AGA-TTTT-G-GAAAGTTCGGGGGTAAAAT
1 GTA-ATTTTTGGTGAAA--TCGAGGTTAAAAT
55985251 GTAATTTTTGGTGAAATCGAGGTTAAAA
1 GTAATTTTTGGTGAAATCGAGGTTAAAA
55985279 GCGGGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 18 0.40
29 17 0.38
30 1 0.02
31 4 0.09
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GTAATTTTTGGTGAAATCGAGGTTAAAAT
Found at i:55985316 original size:116 final size:116
Alignment explanation
Indices: 55985130--55985557 Score: 386
Period size: 116 Copynumber: 3.6 Consensus size: 116
55985120 CCCGGGGATG
* * * * * *
55985130 AAATGGTAATTTTTAGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTCAGGGGTAATATAG
1 AAATGGTAATTTTT-GTGAAATCGAGGTTAAAAATGGGATTTT-GAGAGTT-TGGGGTAAAATGG
*
55985195 TAATTTTTGGTGAAATCGAGGTT-AAAATGAGATTTTGGAAAGTTCGGGGGT-A
63 TAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCAGGGGTAA
**
55985247 AAAT-GTAATTTTTGGTGAAATCGAGGTTAAAAGCGGGATTTTAGAGAGTTTGGGGGTAAAATGG
1 AAATGGTAATTTTT-GTGAAATCGAGGTTAAAAATGGGATTTT-GAGAGTTT-GGGGTAAAATGG
* * *
55985311 TAATTTTTAGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAA
63 TAATTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCAGGGGTAA
* * *
55985365 AAATGGTAATTTTTG-GAAGTTTCGAGGGTTAAAAATGGAATTTTGGGAAGTTTGGGGTAAAATG
1 AAATGGTAATTTTTGTGAA--ATCGA-GGTTAAAAATGGGATTTTGAG-AGTTTGGGGTAAAATG
* * * * * * *
55985429 GTAATTTTT-G-GAAGTTTTGGGGTCAAAAATGGGATTTTGGGAAGTTTAGGGGT-A
62 GTAATTTTTGGTGAA--ATCGAGGTTAAAAATGAGATTTTGGAAAGTTCAGGGGTAA
* * * * * * * *
55985483 AAATGGTTATTTTTG-GAAGTTTTGGGGTCAAAAATGGAAGTTTGGGAAGTTTAGGGGTAAAATG
1 AAATGGTAATTTTTGTGAA--ATCGAGGTTAAAAATGGGATTTTGAG-AGTTT-GGGGTAAAATG
55985547 GTAATTTTTGG
62 GTAATTTTTGG
55985558 AAGTTTCGGG
Statistics
Matches: 270, Mismatches: 29, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
116 70 0.26
117 61 0.23
118 50 0.19
119 69 0.26
120 20 0.07
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (116 bp):
AAATGGTAATTTTTGTGAAATCGAGGTTAAAAATGGGATTTTGAGAGTTTGGGGTAAAATGGTAA
TTTTTGGTGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTCAGGGGTAA
Found at i:55985438 original size:29 final size:31
Alignment explanation
Indices: 55985293--55985597 Score: 256
Period size: 29 Copynumber: 10.3 Consensus size: 31
55985283 GATTTTAGAG
* *
55985293 AGTTTGGGGGT-AAAATGGTAATTTTTAGTGA
1 AGTTTAGGGGTAAAAATGGTAATTTTT-GGGA
* * * *
55985324 A--ATCGGGGTTAAAAATGG-GA-TTTTGGAA
1 AGTTTAGGGG-TAAAAATGGTAATTTTTGGGA
*
55985352 AGTTCAGGGGTAAAAATGGTAATTTTT-GGA
1 AGTTTAGGGGTAAAAATGGTAATTTTTGGGA
*
55985382 AGTTTCGAGGGTTAAAAATGG-AA-TTTTGGGA
1 AGTTT--AGGGGTAAAAATGGTAATTTTTGGGA
55985413 AGTTT-GGGGT-AAAATGGTAATTTTT-GGA
1 AGTTTAGGGGTAAAAATGGTAATTTTTGGGA
* *
55985441 AGTTTTGGGGTCAAAAATGG-GA-TTTTGGGA
1 AGTTTAGGGGT-AAAAATGGTAATTTTTGGGA
*
55985471 AGTTTAGGGGT-AAAATGGTTATTTTT-GGA
1 AGTTTAGGGGTAAAAATGGTAATTTTTGGGA
* *
55985500 AGTTTTGGGGTCAAAAATGG-AA-GTTTGGGA
1 AGTTTAGGGGT-AAAAATGGTAATTTTTGGGA
55985530 AGTTTAGGGGT-AAAATGGTAATTTTT-GGA
1 AGTTTAGGGGTAAAAATGGTAATTTTTGGGA
* * *
55985559 AGTTTCGGGGTCAAAAATAG-AA-TTTTGGAA
1 AGTTTAGGGGT-AAAAATGGTAATTTTTGGGA
55985589 AGTTTAGGG
1 AGTTTAGGG
55985598 ACTAGAGAGC
Statistics
Matches: 224, Mismatches: 25, Indels: 51
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.03
28 31 0.14
29 67 0.30
30 64 0.29
31 42 0.19
32 13 0.06
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.34
Consensus pattern (31 bp):
AGTTTAGGGGTAAAAATGGTAATTTTTGGGA
Found at i:55987328 original size:17 final size:16
Alignment explanation
Indices: 55987310--55987395 Score: 79
Period size: 17 Copynumber: 5.4 Consensus size: 16
55987300 TTAATACTAT
*
55987310 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
*
55987326 TTTAAACTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
55987343 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
* * *
55987360 TTTAAA-ATCAAT--T
1 TTTAAATTTAAATAAA
55987373 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
55987390 TTTAAA
1 TTTAAA
55987396 ATCAATTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
13 6 0.11
14 1 0.02
15 6 0.11
16 11 0.20
17 28 0.51
18 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:55987330 original size:6 final size:6
Alignment explanation
Indices: 55987310--55987395 Score: 65
Period size: 6 Copynumber: 15.0 Consensus size: 6
55987300 TTAATACTAT
* *
55987310 TTTAAA TTT-AA -TTAAA TTTAAA CTTAAA -GTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
55987355 -ATAAA TTTAAA ATCAATT TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
55987396 ATCAATTTAA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
4 2 0.03
5 16 0.26
6 40 0.66
7 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:55987347 original size:11 final size:11
Alignment explanation
Indices: 55987345--55987406 Score: 76
Period size: 11 Copynumber: 5.9 Consensus size: 11
55987335 AAAGTAAATT
55987345 TAAATTTAAAA
1 TAAATTTAAAA
55987356 TAAATTTAAAA
1 TAAATTTAAAA
* *
55987367 TCAATTT---T
1 TAAATTTAAAA
55987375 TAAATTTAAAA
1 TAAATTTAAAA
55987386 TAAATTTAAAA
1 TAAATTTAAAA
*
55987397 TCAATTTAAA
1 TAAATTTAAA
55987407 CCTCAATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.14
11 37 0.86
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:55987379 original size:30 final size:30
Alignment explanation
Indices: 55987343--55987403 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
55987333 TTAAAGTAAA
55987343 TTTAAATTTAAAATAAATTTAAAATCAATT
1 TTTAAATTTAAAATAAATTTAAAATCAATT
55987373 TTTAAATTTAAAATAAATTTAAAATCAATT
1 TTTAAATTTAAAATAAATTTAAAATCAATT
55987403 T
1 T
55987404 AAACCTCAAT
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:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAAATAAATTTAAAATCAATT
Found at i:55987380 original size:19 final size:19
Alignment explanation
Indices: 55987356--55987392 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55987346 AAATTTAAAA
*
55987356 TAAATTTAAAATCAATTTT
1 TAAATTTAAAATAAATTTT
55987375 TAAATTTAAAATAAATTT
1 TAAATTTAAAATAAATTT
55987393 AAAATCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTTAAAATAAATTTT
Found at i:55987414 original size:12 final size:11
Alignment explanation
Indices: 55987347--55987422 Score: 70
Period size: 11 Copynumber: 7.2 Consensus size: 11
55987337 AGTAAATTTA
*
55987347 AATTTAAAATA
1 AATTTAAAATC
55987358 AATTTAAAATC
1 AATTTAAAATC
* *
55987369 AATTT---TTA
1 AATTTAAAATC
*
55987377 AATTTAAAATA
1 AATTTAAAATC
55987388 AATTTAAAATC
1 AATTTAAAATC
*
55987399 AATTTAAACCTC
1 AATTTAAA-ATC
55987411 AA-TTAAAATC
1 AATTTAAAATC
55987421 AA
1 AA
55987423 AAGTTCAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
8 6 0.11
10 4 0.07
11 40 0.74
12 4 0.07
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTTAAAATC
Found at i:55990102 original size:16 final size:17
Alignment explanation
Indices: 55990072--55990106 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
55990062 AAATAAATTT
55990072 AATTAATTAAAATTTTA
1 AATTAATTAAAATTTTA
*
55990089 AATTAATT-ACATTTTA
1 AATTAATTAAAATTTTA
55990105 AA
1 AA
55990107 CTGAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAATTAAAATTTTA
Found at i:56000321 original size:28 final size:28
Alignment explanation
Indices: 56000286--56000345 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
56000276 TGAGGGTCCA
*
56000286 AAATTTTTTTATTAACTTTTAAA-AGACCT
1 AAATTTTTTT-TCAACTTTTAAAGA-ACCT
56000315 AAATTTTTTTTCAACTTTTAAAGAACCT
1 AAATTTTTTTTCAACTTTTAAAGAACCT
56000343 AAA
1 AAA
56000346 ACCTCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (28 bp):
AAATTTTTTTTCAACTTTTAAAGAACCT
Found at i:56007159 original size:55 final size:55
Alignment explanation
Indices: 56007071--56007177 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 55
56007061 GAAGCTAATA
* * * *
56007071 AAGCAAAACCAAAACCAAAAATACTAATTATAATTGATACGTTTCCGATCAACAT
1 AAGCAAAACCAAAAACAAAAATACTAATGATAATAGATACGTTTCAGATCAACAT
** * *
56007126 AAGCAAAACCAAAAACATGAATAC-AAGTGATAATAGATGCTTTTCAGATCAA
1 AAGCAAAACCAAAAACAAAAATACTAA-TGATAATAGATACGTTTCAGATCAA
56007178 AGAACCAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 2 0.05
55 41 0.95
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (55 bp):
AAGCAAAACCAAAAACAAAAATACTAATGATAATAGATACGTTTCAGATCAACAT
Found at i:56009543 original size:24 final size:26
Alignment explanation
Indices: 56009514--56009569 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
56009504 ATAAAAAATT
*
56009514 ATAAAAACAGT-TAAA-G-ATTATAAA
1 ATAAAAA-AGTATAAATGAATTACAAA
56009538 ATAAAAAAGTATAAATGAATTACAAA
1 ATAAAAAAGTATAAATGAATTACAAA
56009564 A-AAAAA
1 ATAAAAA
56009570 TGTTAGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 11 0.39
25 6 0.21
26 8 0.29
ACGTcount: A:0.68, C:0.04, G:0.07, T:0.21
Consensus pattern (26 bp):
ATAAAAAAGTATAAATGAATTACAAA
Found at i:56014265 original size:18 final size:17
Alignment explanation
Indices: 56014236--56014279 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
56014226 TGATTTAAAT
*
56014236 ATGAAATGAAATTG-AA
1 ATGAAATGAAAATGAAA
56014252 ATGATAATGAAAATGAAA
1 ATGA-AATGAAAATGAAA
56014270 ATGAGAATGA
1 ATGA-AATGA
56014280 TATGAAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 9 0.38
18 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (17 bp):
ATGAAATGAAAATGAAA
Found at i:56014267 original size:23 final size:23
Alignment explanation
Indices: 56014234--56014286 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
56014224 TATGATTTAA
*
56014234 ATATG-AAATGAAATTGA-AATG
1 ATATGAAAATGAAAATGAGAATG
56014255 ATAATGAAAATGAAAATGAGAATG
1 AT-ATGAAAATGAAAATGAGAATG
56014279 ATATGAAA
1 ATATGAAA
56014287 TGGATGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 3 0.11
23 17 0.61
24 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.25
Consensus pattern (23 bp):
ATATGAAAATGAAAATGAGAATG
Found at i:56028156 original size:8 final size:8
Alignment explanation
Indices: 56028143--56028168 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
56028133 TTAAAAGTAA
56028143 TTTTTTAT
1 TTTTTTAT
56028151 TTTTTTAT
1 TTTTTTAT
56028159 TTTTTTAT
1 TTTTTTAT
56028167 TT
1 TT
56028169 AAAAATCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:56030341 original size:25 final size:25
Alignment explanation
Indices: 56030271--56030343 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
56030261 GAATTTTCTC
* * * *
56030271 AAAATTTTATTGGGGTTTAAATCGTT
1 AAAATTTTATT-AGGATAAAATCGTA
** *
56030297 AAAATTTTACCAAGGGTAAAATCGTA
1 AAAATTTTA-TTAGGATAAAATCGTA
56030323 AAAATTTTATTAGGATAAAAT
1 AAAATTTTATTAGGATAAAAT
56030344 TGGGATGAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
25 9 0.24
26 28 0.76
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (25 bp):
AAAATTTTATTAGGATAAAATCGTA
Found at i:56035362 original size:18 final size:18
Alignment explanation
Indices: 56035340--56035376 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56035330 ATGCAAAAAA
*
56035340 AAAAACTAAAACTAAAATT
1 AAAAA-TAAAAATAAAATT
56035359 AAAAATAAAAATAAAATT
1 AAAAATAAAAATAAAATT
56035377 GGGTTGCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAATAAAAATAAAATT
Found at i:56048705 original size:16 final size:17
Alignment explanation
Indices: 56048671--56048709 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
56048661 TACCTTTAGT
*
56048671 TTTTTTTAATAGTTTTTA
1 TTTTTTTAATA-TTATTA
56048689 TTTTTTTAAT-TTATTA
1 TTTTTTTAATATTATTA
56048705 TTTTT
1 TTTTT
56048710 AATATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
18 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTAATATTATTA
Found at i:56048710 original size:14 final size:14
Alignment explanation
Indices: 56048685--56048719 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
56048675 TTTAATAGTT
56048685 TTTATT-TTTTTAA
1 TTTATTATTTTTAA
56048698 TTTATTATTTTTAA
1 TTTATTATTTTTAA
*
56048712 TATATTAT
1 TTTATTAT
56048720 CTACTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTATTTTTAA
Found at i:56052089 original size:29 final size:30
Alignment explanation
Indices: 56052035--56052098 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
56052025 AATACCAAAT
56052035 TATACATGAACTATAATTTAATGTGCAATTG
1 TATACATGAACTATAATTT-ATGTGCAATTG
* * *
56052066 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTATAATTTATGTGCAATTG
56052095 TATA
1 TATA
56052099 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (30 bp):
TATACATGAACTATAATTTATGTGCAATTG
Found at i:56052363 original size:61 final size:58
Alignment explanation
Indices: 56052251--56052364 Score: 133
Period size: 61 Copynumber: 1.9 Consensus size: 58
56052241 TAAATCTTAA
* *
56052251 AATTATACATGAATTTTAATTTAATATGCAATTGTATACATGAACTTTAATTTGATGC
1 AATTATACATGAATTTTAATTTAATATGCAAATGTATACATGAACTCTAATTTGATGC
* *
56052309 AATTATACACGTGAAATTTTAATTGTGAT-T-CAAATGTATACTTGAAACTCTAATTT
1 AATTATACA--TG-AATTTTAATT-TAATATGCAAATGTATACATG-AACTCTAATTT
56052365 TGATTTGATC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
58 9 0.19
60 14 0.30
61 21 0.45
62 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (58 bp):
AATTATACATGAATTTTAATTTAATATGCAAATGTATACATGAACTCTAATTTGATGC
Found at i:56061255 original size:2 final size:2
Alignment explanation
Indices: 56061248--56061298 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
56061238 ACAAATCTAC
56061248 AT AT AT AT AT AT 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 AT AT AT AT AT AT
56061290 AT AT AT AT A
1 AT AT AT AT A
56061299 AAAGCACGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56061515 original size:17 final size:18
Alignment explanation
Indices: 56061483--56061516 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56061473 AAAAATTTTG
56061483 ATAATTACATATTTAAAA
1 ATAATTACATATTTAAAA
*
56061501 ATAATTAGA-ATTTAAA
1 ATAATTACATATTTAAA
56061517 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATTACATATTTAAAA
Found at i:56072103 original size:6 final size:6
Alignment explanation
Indices: 56072092--56072124 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
56072082 AGAATTCAGA
56072092 TTTCTC TTTCTC TTTCTC TTTCTC TTTCT- TTTC
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTTC
56072125 CTCACTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTC
Found at i:56072367 original size:16 final size:16
Alignment explanation
Indices: 56072338--56072387 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
56072328 GCACCCTTAT
*
56072338 TTTATATAACAAATATA
1 TTTA-ATAAAAAATATA
56072355 TTTAATAAAAAATA-A
1 TTTAATAAAAAATATA
* *
56072370 TGTAA-AAAAATTATA
1 TTTAATAAAAAATATA
56072385 TTT
1 TTT
56072388 TAATTGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
16 9 0.32
17 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TTTAATAAAAAATATA
Found at i:56078134 original size:6 final size:6
Alignment explanation
Indices: 56078123--56078150 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
56078113 AAAAGGGAAA
56078123 AAGATG AAGATG AAGATG AAGATG AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGA
56078151 ATAGAGGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.32, T:0.14
Consensus pattern (6 bp):
AAGATG
Found at i:56078426 original size:13 final size:13
Alignment explanation
Indices: 56078408--56078433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56078398 GCCCGAGACA
56078408 AACAAAAGTGACT
1 AACAAAAGTGACT
56078421 AACAAAAGTGACT
1 AACAAAAGTGACT
56078434 GTTTTTATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AACAAAAGTGACT
Found at i:56084325 original size:11 final size:11
Alignment explanation
Indices: 56084294--56084335 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
56084284 CCCAACTTGG
56084294 ATTTTAAATTA
1 ATTTTAAATTA
* *
56084305 AGTTTGAATTA
1 ATTTTAAATTA
*
56084316 ATTTTAAATTT
1 ATTTTAAATTA
56084327 A-TTTAAATT
1 ATTTTAAATT
56084336 TAAAGTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:56084335 original size:17 final size:16
Alignment explanation
Indices: 56084313--56084357 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
56084303 TAAGTTTGAA
*
56084313 TTAATTTTAAATT-TAT
1 TTAAATTTAAATTGT-T
56084329 TTAAATTTAAAGTTGTT
1 TTAAATTTAAA-TTGTT
56084346 TTAAATTTAAAT
1 TTAAATTTAAAT
56084358 ACATTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.42
17 14 0.54
18 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
TTAAATTTAAATTGTT
Found at i:56084338 original size:22 final size:22
Alignment explanation
Indices: 56084294--56084335 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56084284 CCCAACTTGG
*
56084294 ATTTTAAATTAAGTTTGAATTA
1 ATTTTAAATTAAGTTTAAATTA
*
56084316 ATTTTAAATTTA-TTTAAATT
1 ATTTTAAATTAAGTTTAAATT
56084336 TAAAGTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTAAATTAAGTTTAAATTA
Found at i:56084366 original size:16 final size:16
Alignment explanation
Indices: 56084313--56084366 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
56084303 TAAGTTTGAA
* *
56084313 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
56084329 TTAAATTTAAAGTTGTT
1 TTAAATTTAAA-TTCAT
*
56084346 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
56084362 TTAAA
1 TTAAA
56084367 ATAATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:56085152 original size:12 final size:12
Alignment explanation
Indices: 56085132--56085172 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
56085122 TAACCTTTTA
*
56085132 AATATTATTAAT
1 AATAATATTAAT
*
56085144 AATAATATTAGT
1 AATAATATTAAT
*
56085156 AATAATAATAAT
1 AATAATATTAAT
56085168 AATAA
1 AATAA
56085173 ATTTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:56085152 original size:15 final size:15
Alignment explanation
Indices: 56085132--56085165 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
56085122 TAACCTTTTA
*
56085132 AATATTATTAATAAT
1 AATATTAGTAATAAT
56085147 AATATTAGTAATAAT
1 AATATTAGTAATAAT
56085162 AATA
1 AATA
56085166 ATAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATATTAGTAATAAT
Found at i:56085187 original size:20 final size:21
Alignment explanation
Indices: 56085162--56085200 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
56085152 TAGTAATAAT
56085162 AATAATAATAAAT-TTTTTTA
1 AATAATAATAAATGTTTTTTA
56085182 AATAATAATAAATGTTTTT
1 AATAATAATAAATGTTTTT
56085201 GGTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
AATAATAATAAATGTTTTTTA
Found at i:56086242 original size:30 final size:30
Alignment explanation
Indices: 56086208--56086490 Score: 131
Period size: 30 Copynumber: 9.5 Consensus size: 30
56086198 CCCAAACTTT
56086208 CCAAAATT-CCATTTTTGACCCCGATTTCAC
1 CCAAAATTACCATTTTT-ACCCCGATTTCAC
*
56086238 CCAAAATTACCA-TTTTACCCCTAAACTTT---
1 CCAAAATTACCATTTTTACCCC--GA-TTTCAC
* *
56086267 TCAAAATT-CCATTTTTAACCTCGATTTCAC
1 CCAAAATTACCATTTTT-ACCCCGATTTCAC
*
56086297 CCAAAATTACCA-TTTTACCCCTAAACTTT---
1 CCAAAATTACCATTTTTACCCC--GA-TTTCAC
**
56086326 CCAAAATT-CCATTTTTAACCTTGATTTCAC
1 CCAAAATTACCATTTTT-ACCCCGATTTCAC
*
56086356 CCAAAATTACCA-TTTTACCCCTAAACTTT---
1 CCAAAATTACCATTTTTACCCC--GA-TTTCAC
* * * *
56086385 CTAAGATT-CCATTTTTAACCCTGATTTTAC
1 CCAAAATTACCATTTTT-ACCCCGATTTCAC
*
56086415 CCAAAATTACCA-TTTTACCCCCAAACTTT---
1 CCAAAATTACCATTTTTA-CCCC-GA-TTTCAC
*
56086444 CCAAAATT-CTATTTTTTAACCCCGATTTCAC
1 CCAAAATTACCA-TTTTT-ACCCCGATTTCAC
*
56086475 CAAAAATTACCATTTT
1 CCAAAATTACCATTTT
56086491 AGCCTCAAAC
Statistics
Matches: 190, Mismatches: 25, Indels: 75
0.66 0.09 0.26
Matches are distributed among these distances:
27 9 0.05
28 17 0.09
29 55 0.29
30 67 0.35
31 28 0.15
32 14 0.07
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (30 bp):
CCAAAATTACCATTTTTACCCCGATTTCAC
Found at i:56086293 original size:59 final size:59
Alignment explanation
Indices: 56086196--56086524 Score: 482
Period size: 59 Copynumber: 5.6 Consensus size: 59
56086186 TGCTCGCTAG
* *
56086196 CCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCACCCAAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
* *
56086255 CCCCTAAACTTTTCAAAATTCCATTTTTAACCTCGATTTCACCCAAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
**
56086314 CCCCTAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
* * * *
56086373 CCCCTAAACTTTCTAAGATTCCATTTTTAACCCTGATTTTACCCAAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
* * *
56086432 CCCCCAAACTTTCCAAAATTCTATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAATTCCA-TTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
* * *
56086492 -GCCTCAAACTTTCTAAAATTCTA-TTTTAACCCC
1 CCCCT-AAACTTTCCAAAATTCCATTTTTAACCCC
56086525 AAATTTTCTC
Statistics
Matches: 248, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
58 10 0.04
59 188 0.76
60 50 0.20
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.36
Consensus pattern (59 bp):
CCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTA
Found at i:56086519 original size:28 final size:30
Alignment explanation
Indices: 56086197--56086547 Score: 158
Period size: 29 Copynumber: 11.9 Consensus size: 30
56086187 GCTCGCTAGC
*
56086197 CCCCAAACTTTC-CAAAATT-CCATTTTTGA
1 CCCCAAACTTTCTCAAAATTACCA-TTTTAA
* *
56086226 CCCC-GA-TTTCACCCAAAATTACCATTTT-A
1 CCCCAAACTTT--CTCAAAATTACCATTTTAA
56086255 CCCCTAAACTTT-TCAAAATT-CCATTTTTAA
1 CCCC-AAACTTTCTCAAAATTACCA-TTTTAA
* * *
56086285 CCTC-GA-TTTCACCCAAAATTACCATTTT-A
1 CCCCAAACTTT--CTCAAAATTACCATTTTAA
56086314 CCCCTAAACTTTC-CAAAATT-CCATTTTTAA
1 CCCC-AAACTTTCTCAAAATTACCA-TTTTAA
*** *
56086344 -CCTTGA-TTTCACCCAAAATTACCATTTT-A
1 CCCCAAACTTT--CTCAAAATTACCATTTTAA
*
56086373 CCCCTAAACTTTCT-AAGATT-CCATTTTTAA
1 CCCC-AAACTTTCTCAAAATTACCA-TTTTAA
** * * *
56086403 -CCCTGATTTTACCCAAAATTACCATTTTAC
1 CCCCAAACTTT-CTCAAAATTACCATTTTAA
*
56086433 CCCCAAACTTTC-CAAAATT-CTATTTTTTAA
1 CCCCAAACTTTCTCAAAATTACCA--TTTTAA
* * *
56086463 CCCC-GA-TTTCACCAAAAATTACCATTTTAG
1 CCCCAAACTTTC-TC-AAAATTACCATTTTAA
* *
56086493 CCTCAAACTTTCT-AAAATT-CTATTTTAA
1 CCCCAAACTTTCTCAAAATTACCATTTTAA
*
56086521 CCCCAAATTTTCTCAAAATTA-CATTTT
1 CCCCAAACTTTCTCAAAATTACCATTTT
56086548 TGCCCCCGAT
Statistics
Matches: 243, Mismatches: 38, Indels: 82
0.67 0.10 0.23
Matches are distributed among these distances:
27 9 0.04
28 40 0.16
29 78 0.32
30 72 0.30
31 29 0.12
32 15 0.06
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.37
Consensus pattern (30 bp):
CCCCAAACTTTCTCAAAATTACCATTTTAA
Found at i:56091038 original size:15 final size:15
Alignment explanation
Indices: 56090999--56091038 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
56090989 GCTCCTGTAT
* * *
56090999 ATTTTTTTAAATTTA
1 ATTTTTATACATTGA
56091014 ATTTTTATACATTGA
1 ATTTTTATACATTGA
56091029 ATTTTTATAC
1 ATTTTTATAC
56091039 TTTTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTTATACATTGA
Found at i:56093775 original size:3 final size:3
Alignment explanation
Indices: 56093767--56093804 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
56093757 ACACTTCATA
56093767 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56093805 CTGTTGTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56096540 original size:19 final size:19
Alignment explanation
Indices: 56096518--56096562 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
56096508 TTATATTAGG
56096518 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATAT
* *
56096537 ATTTATTATTTAAATTTAT
1 ATTTAATATTTAAATATAT
56096556 ATTTAAT
1 ATTTAAT
56096563 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATAT
Found at i:56099329 original size:24 final size:24
Alignment explanation
Indices: 56099287--56099332 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
56099277 TTCTTGTAAT
*
56099287 TATTATGTGATGTGCATGCAATTA
1 TATTATGTGATGAGCATGCAATTA
56099311 TATTATGTGATGAAG-ATGCAAT
1 TATTATGTGATG-AGCATGCAAT
56099333 CTTCCAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.39
Consensus pattern (24 bp):
TATTATGTGATGAGCATGCAATTA
Found at i:56105712 original size:127 final size:131
Alignment explanation
Indices: 56105552--56105789 Score: 297
Period size: 127 Copynumber: 1.8 Consensus size: 131
56105542 GGTTTGTCAG
* * *
56105552 GAAAAAAATTTCAAAATTTTGGGGTGTTGGCCAT-CAAATGGCCGACACTCCCTATT-TC-AAAA
1 GAAAAAAATTTCAAAATTTTGGGGTGTTGGCCATGC-AATGACAGACACCCCCTATTCTCGAAAA
* * ***
56105614 AAAATT-ACA-TTTTTGGGTGTTGGCCATTGCATGGCCGACACCCCCTAACACCCTCTATTTATC
65 AAAATTCAAATTTTTTGGGTGTTAGCCATCAAATGGCCGACACCCCCTAACACCCTCTATTTATC
56105677 GA
130 GA
* * **
56105679 GAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATGCAATGACAGACACCCCCTATTCTCGAGAAA
1 GAAAAAAATTTCAAAATTTTGGGGTGTTGGCCATGCAATGACAGACACCCCCTATTCTC--GAAA
*
56105744 AAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCC
64 AAAAATTCAAATTTTTTGGGTGTTAGCCATCAAATGGCCGACACCC
56105790 TCTGTTCTGG
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
127 47 0.52
128 3 0.03
131 10 0.11
132 2 0.02
133 29 0.32
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (131 bp):
GAAAAAAATTTCAAAATTTTGGGGTGTTGGCCATGCAATGACAGACACCCCCTATTCTCGAAAAA
AAATTCAAATTTTTTGGGTGTTAGCCATCAAATGGCCGACACCCCCTAACACCCTCTATTTATCG
A
Found at i:56105830 original size:122 final size:122
Alignment explanation
Indices: 56105677--56105910 Score: 334
Period size: 122 Copynumber: 1.9 Consensus size: 122
56105667 TCTATTTATC
*
56105677 GAGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATGC-AAT-GACAGACACCCCCTATTCTCGA
1 GAGAAAAAAATATTAAATTTTTTTGGTGTTGGCCAT-CAAATGGAC-GACA-CCCCTATTCTCGA
56105740 GA-AAAAAAA-TTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCTCTGTTCTG
63 -ATAAAAAAATTTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCTCTGTTCTG
* * *
56105799 GAGAAAAAAA-ATTAAATTTTTTTGGGTGTTGGCCATCAAATGGTCGACACCCTTTTTCTCGAAT
1 GAGAAAAAAATATTAAATTTTTTT-GGTGTTGGCCATCAAATGGACGACACCCCTATTCTCGAAT
* *
56105863 AAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCTGACACC
65 AAAAAAATTTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACC
56105911 AACTTCTCCT
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
120 1 0.01
121 31 0.31
122 67 0.66
123 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (122 bp):
GAGAAAAAAATATTAAATTTTTTTGGTGTTGGCCATCAAATGGACGACACCCCTATTCTCGAATA
AAAAAATTTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCGACACCCTCTGTTCTG
Found at i:56105918 original size:60 final size:60
Alignment explanation
Indices: 56105661--56105910 Score: 301
Period size: 61 Copynumber: 4.1 Consensus size: 60
56105651 ACACCCCCTA
* * * * *
56105661 ACACCCTCTATTTATCGAGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATGC-AATGACAG
1 ACACCCTC--TTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCAT-CAAATGGCTG
* * *
56105723 ACACCCCCTATTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTAGCCATCAAATGGCCG
1 ACACCCTCT-TTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCTG
*
56105784 ACACCCTCTGTTCTGGAGAAAAAAAATT-AAATTTTTTTGGGTGTTGGCCATCAAATGG-TCG
1 ACACCCTCT-TTCTCGAGAAAAAAAATTCAAATTTTTTT-GGTGTTGGCCATCAAATGGCT-G
*
56105845 ACACCCTTTTTCTCGA-ATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCTG
1 ACACCCTCTTTCTCGAGA-AAAAAAA-TTCAAATTTTTTTGGTGTTGGCCATCAAATGGCTG
56105906 ACACC
1 ACACC
56105911 AACTTCTCCT
Statistics
Matches: 166, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
59 1 0.01
60 25 0.15
61 122 0.73
62 18 0.11
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (60 bp):
ACACCCTCTTTCTCGAGAAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCTG
Found at i:56106646 original size:19 final size:20
Alignment explanation
Indices: 56106609--56106648 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
56106599 GTTAAGGAAT
56106609 AAATATTATCTACAAATTAA
1 AAATATTATCTACAAATTAA
56106629 AAATATTAAT-TA-AAATTAA
1 AAATATT-ATCTACAAATTAA
56106648 A
1 A
56106649 TTTACGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTATCTACAAATTAA
Found at i:56108511 original size:11 final size:11
Alignment explanation
Indices: 56108495--56108526 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
56108485 TAAGGCGATC
56108495 GGAGGTTCCGT
1 GGAGGTTCCGT
56108506 GGAGGTTCCGT
1 GGAGGTTCCGT
56108517 GGAGG-TCCGT
1 GGAGGTTCCGT
56108527 TTATTGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.09, C:0.19, G:0.47, T:0.25
Consensus pattern (11 bp):
GGAGGTTCCGT
Found at i:56109594 original size:12 final size:12
Alignment explanation
Indices: 56109577--56109603 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56109567 TATATTTGTG
56109577 TAAAAATTAATT
1 TAAAAATTAATT
56109589 TAAAAATTAATT
1 TAAAAATTAATT
56109601 TAA
1 TAA
56109604 GTTGAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAAATTAATT
Found at i:56110208 original size:80 final size:80
Alignment explanation
Indices: 56109760--56110349 Score: 821
Period size: 80 Copynumber: 7.3 Consensus size: 80
56109750 AAAATAGTTA
* * * * * *
56109760 TTATATTACAATTTATATCAAATATTGTATTAATTTGACAATACATTATTTATCAAATTTTCATA
1 TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-TAATTTT-ATA
56109825 --TTTAAAGTACAAATTATTATT
64 TCTTTAAA-T--AAA-T-TT-TT
* * *
56109846 ATTATATTACAATTTTTATCATATAATATGTTGATTTGACAATACAATATTTATTAATTTTATAC
1 -TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATAT
*
56109911 CTTTAAATAATTTTTTT
65 CTTTAAATAA-ATTTTT
* * *
56109928 TTATATTACAATTTTTATCATATAATATCTTAATTTGACAATACATTATTTATTAATTTTATATC
1 TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATC
*
56109993 TTTAAATAAAAATTTT
66 TTTAAAT-AAATTTTT
*
56110009 TTATATTACAATTTTTATCATATAATGTGTTGATTTGGCAATACATTATTTATTAATTTTATATC
1 TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATC
****
56110074 TTTAAATAAA-AAAA
66 TTTAAATAAATTTTT
*
56110088 TTATATTACAATTTTTATCATATAATGTGTTTG-TTTGACAATATATTATTTATTAATTTTATAT
1 TTATATTACAATTTTTATCATATAATGTG-TTGATTTGACAATACATTATTTATTAATTTTATAT
56110152 CTTTAAATAAATTTTT
65 CTTTAAATAAATTTTT
* *
56110168 TTATATTACAATTTTTATCATATAATGTCTTGATTTGACAATATATTATTTATTAATTTTATATC
1 TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATC
56110233 TTTAAATAAATTTTT
66 TTTAAATAAATTTTT
*
56110248 TTATATTACAATTTTTATCATATAATGTGTTGATTTGATAATACATTATTTATTAATTTTATATC
1 TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATC
*
56110313 TTTAAAT-AATATTT
66 TTTAAATAAATTTTT
56110327 TTATATTACAATTTTTATCATAT
1 TTATATTACAATTTTTATCATAT
56110350 TTTATATTTA
Statistics
Matches: 462, Mismatches: 34, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
79 101 0.22
80 150 0.32
81 140 0.30
82 4 0.01
83 2 0.00
84 3 0.01
85 3 0.01
86 7 0.02
87 52 0.11
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (80 bp):
TTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTATATC
TTTAAATAAATTTTT
Found at i:56110537 original size:20 final size:20
Alignment explanation
Indices: 56110512--56110569 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
56110502 CGTCCCGAGA
*
56110512 CCGTCGTTGACCTACTTTGT
1 CCGTCGTTGACCGACTTTGT
*
56110532 CCGTCGTTGACCGACTTTTT
1 CCGTCGTTGACCGACTTTGT
* * *
56110552 CTGCCGTTGATCGACTTT
1 CCGTCGTTGACCGACTTT
56110570 CATCCTTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.10, C:0.29, G:0.21, T:0.40
Consensus pattern (20 bp):
CCGTCGTTGACCGACTTTGT
Found at i:56112279 original size:24 final size:24
Alignment explanation
Indices: 56112228--56112281 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
56112218 TCAGATTCTA
*
56112228 AGCCCGAGGATGAGCCCAATGTCG
1 AGCCCGAGGATGAGCCCAATGTCC
* *
56112252 AGCCCGCGGATGAGGCCAAT-TACC
1 AGCCCGAGGATGAGCCCAATGT-CC
56112276 AGCCCG
1 AGCCCG
56112282 GTTATGAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.24, C:0.33, G:0.31, T:0.11
Consensus pattern (24 bp):
AGCCCGAGGATGAGCCCAATGTCC
Found at i:56113275 original size:43 final size:41
Alignment explanation
Indices: 56113158--56113277 Score: 107
Period size: 43 Copynumber: 2.9 Consensus size: 41
56113148 TAGAATAAAG
* * ** * *
56113158 TCTTTAGCGGCGCTTTTCACACAAACGTCACTAAAAAATGG
1 TCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAAAATGA
* * * * *
56113199 TCTTTAACAACACTTTTTCCACAAA-AGCTGCTAAAGAACATGA
1 TCTTTAGCGACGCTTTTCCCACAAACA-CCGCTAAA-AA-ATGA
56113242 TCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAA
1 TCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAA
56113278 TTAACAAATT
Statistics
Matches: 59, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
41 24 0.41
42 3 0.05
43 31 0.53
44 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (41 bp):
TCTTTAGCGACGCTTTTCCCACAAACACCGCTAAAAAATGA
Found at i:56122693 original size:19 final size:20
Alignment explanation
Indices: 56122669--56122708 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
56122659 TTGAAATATT
56122669 ATCAATTTAAAGTTA-AAAA
1 ATCAATTTAAAGTTAGAAAA
56122688 ATCAATTTAAAGTTAGAAAA
1 ATCAATTTAAAGTTAGAAAA
56122708 A
1 A
56122709 AACCATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (20 bp):
ATCAATTTAAAGTTAGAAAA
Found at i:56126181 original size:19 final size:19
Alignment explanation
Indices: 56126157--56126229 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
56126147 TTTATACTTC
56126157 ATAAAAATTTAAAAAATTA
1 ATAAAAATTTAAAAAATTA
* *
56126176 ATAAAAAAATT-AAAAGTTCA
1 AT-AAAAATTTAAAAAATT-A
* *
56126196 AT--AAATTTCAAAAAGTTC
1 ATAAAAATTT-AAAAAATTA
*
56126214 ATGAAAATTTAAAAAA
1 ATAAAAATTTAAAAAA
56126230 ATATATATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
17 5 0.12
18 2 0.05
19 20 0.47
20 16 0.37
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAAAAATTTAAAAAATTA
Found at i:56127636 original size:32 final size:33
Alignment explanation
Indices: 56127562--56127638 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
56127552 CAAAATATCT
* *
56127562 ATAACCCAAAATGACTTGAATCTCGAACTCGAA
1 ATAACCCAAAATGAATTGAATCTCGAACTCAAA
*
56127595 ATAATCCAAACATGAAATT-AA-CTCG-ACTCAAA
1 ATAACCCAAA-ATG-AATTGAATCTCGAACTCAAA
56127627 ATAACCCAAAAT
1 ATAACCCAAAAT
56127639 TTTGAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 2 0.05
32 15 0.39
33 13 0.34
34 5 0.13
35 3 0.08
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.21
Consensus pattern (33 bp):
ATAACCCAAAATGAATTGAATCTCGAACTCAAA
Found at i:56128493 original size:32 final size:32
Alignment explanation
Indices: 56128457--56128520 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
56128447 GCTATTATTA
56128457 GGATTTGAATTTAACCAACAATATTGCAGATG
1 GGATTTGAATTTAACCAACAATATTGCAGATG
56128489 GGATTTGAATTTAACCAACAATATTGCAGATG
1 GGATTTGAATTTAACCAACAATATTGCAGATG
56128521 AGTCCTCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (32 bp):
GGATTTGAATTTAACCAACAATATTGCAGATG
Found at i:56131493 original size:21 final size:22
Alignment explanation
Indices: 56131453--56131494 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
56131443 ATATTTTATT
* *
56131453 TTCAAAAAATTTAATGATTAAA
1 TTCAAAAAATTGAATAATTAAA
56131475 TTCAAAAAA-TGAATAATTAA
1 TTCAAAAAATTGAATAATTAA
56131495 CAAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (22 bp):
TTCAAAAAATTGAATAATTAAA
Found at i:56132962 original size:12 final size:12
Alignment explanation
Indices: 56132871--56132975 Score: 61
Period size: 12 Copynumber: 8.9 Consensus size: 12
56132861 ATAACATTTA
*
56132871 AACAACTAAAAT
1 AACAACAAAAAT
*
56132883 AACAACCAAAAT
1 AACAACAAAAAT
* **
56132895 AGCAGTAAAAAT
1 AACAACAAAAAT
* *
56132907 AATAAAAAAAAT
1 AACAACAAAAAT
* **
56132919 AGCAAC-AAAGC
1 AACAACAAAAAT
* **
56132930 AGCAGTAAAAAT
1 AACAACAAAAAT
*
56132942 AATAA-AAAAAT
1 AACAACAAAAAT
56132953 AACAACAAAAAT
1 AACAACAAAAAT
*
56132965 AACAATAAAAA
1 AACAACAAAAA
56132976 CAGCACCAAA
Statistics
Matches: 68, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
11 17 0.25
12 51 0.75
ACGTcount: A:0.70, C:0.12, G:0.06, T:0.12
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:56132975 original size:35 final size:35
Alignment explanation
Indices: 56132878--56132962 Score: 127
Period size: 35 Copynumber: 2.4 Consensus size: 35
56132868 TTAAACAACT
56132878 AAAATAACAACCAAAATAGCAGTAAAAATAATAAAA
1 AAAATAACAA-CAAAATAGCAGTAAAAATAATAAAA
* **
56132914 AAAATAGCAACAAAGCAGCAGTAAAAATAAT-AAA
1 AAAATAACAACAAAATAGCAGTAAAAATAATAAAA
56132948 AAAATAACAACAAAA
1 AAAATAACAACAAAA
56132963 ATAACAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 16 0.36
35 19 0.43
36 9 0.20
ACGTcount: A:0.69, C:0.12, G:0.07, T:0.12
Consensus pattern (35 bp):
AAAATAACAACAAAATAGCAGTAAAAATAATAAAA
Found at i:56143514 original size:99 final size:97
Alignment explanation
Indices: 56143358--56143535 Score: 225
Period size: 99 Copynumber: 1.8 Consensus size: 97
56143348 CTTCAAACTA
* * * *
56143358 TTTAAAAAAAAAAAACAATTAAGCCCTTCTTTGTTTTTGCACTCAATTAAGCACTTGAACTTTTA
1 TTTAAAAAAAAAAAACAACTAAGCCCTACTTTGTTTTTCCACTCAATTAAGCACTTGAACTTTCA
56143423 AAATGTATCAAAAAGACCCTCAAACTTTTTTT
66 AAATGTATCAAAAAGACCCTCAAACTTTTTTT
** *
56143455 TTTAAAAAAAAAAGCAA-AACTAAGCTCCTACTTT-TTTTTCCTACTCAATTGGGTACTTGAACT
1 TTTAAAAAAAAAA--AACAACTAAGC-CCTACTTTGTTTTTCC-ACTCAATTAAGCACTTGAACT
* *
56143518 TTCAAAATTTTTCAAAAA
62 TTCAAAATGTATCAAAAA
56143536 AGCAATTAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 13 0.19
98 13 0.19
99 42 0.62
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (97 bp):
TTTAAAAAAAAAAAACAACTAAGCCCTACTTTGTTTTTCCACTCAATTAAGCACTTGAACTTTCA
AAATGTATCAAAAAGACCCTCAAACTTTTTTT
Found at i:56143685 original size:8 final size:9
Alignment explanation
Indices: 56143650--56143683 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
56143640 TTAATTTTTT
56143650 TTGTAAAAA
1 TTGTAAAAA
56143659 TTGTAAAAA
1 TTGTAAAAA
*
56143668 ATG-AAAAA
1 TTGTAAAAA
56143676 TTGTAAAA
1 TTGTAAAA
56143684 TTTTATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (9 bp):
TTGTAAAAA
Found at i:56143886 original size:28 final size:26
Alignment explanation
Indices: 56143846--56143924 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 26
56143836 ATTTCTTTAC
*
56143846 ATTTTGTATATTTTTTAGGACTTTATAAA
1 ATTTTATA-ATTTTTTA-GA-TTTATAAA
* * *
56143875 ATTTTATAATTTTTTTATATTTTTATAT
1 ATTTTATAA-TTTTTTAGATTTATA-AA
56143903 ATTTTATAATTTTTTACGATTT
1 ATTTTATAATTTTTTA-GATTT
56143925 TTATAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.29
28 16 0.38
29 14 0.33
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTATAATTTTTTAGATTTATAAA
Found at i:56143907 original size:57 final size:55
Alignment explanation
Indices: 56143831--56143955 Score: 137
Period size: 56 Copynumber: 2.2 Consensus size: 55
56143821 AATTACAAAA
* * **
56143831 TTTATATTTCTTTACATTTTGTATATTTTTTAGGA-CTTTAT-AAAATTTTATAATTTT
1 TTTATATTT-TTTACATTTTATA-ATTTTTTACGATCTTTATAAAAAAATTAT-A-TTT
* *
56143888 TTTATATTTTTATATATTTTATAATTTTTTACGATTTTTATAAAAAAATTATATTT
1 TTTATATTTTT-TACATTTTATAATTTTTTACGATCTTTATAAAAAAATTATATTT
56143944 TTTATATTTTTT
1 TTTATATTTTTT
56143956 CTATAATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
55 1 0.02
56 26 0.44
57 24 0.41
58 8 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (55 bp):
TTTATATTTTTTACATTTTATAATTTTTTACGATCTTTATAAAAAAATTATATTT
Found at i:56143925 original size:28 final size:28
Alignment explanation
Indices: 56143875--56143929 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
56143865 ACTTTATAAA
*
56143875 ATTTTATAATTTTTTTATATTTTTATAT
1 ATTTTATAATTTTTTTAGATTTTTATAT
56143903 ATTTTATAA-TTTTTTACGATTTTTATA
1 ATTTTATAATTTTTTTA-GATTTTTATA
56143930 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (28 bp):
ATTTTATAATTTTTTTAGATTTTTATAT
Found at i:56144161 original size:90 final size:92
Alignment explanation
Indices: 56144042--56144296 Score: 277
Period size: 90 Copynumber: 2.8 Consensus size: 92
56144032 TAAAAAATTT
* *
56144042 TCAAACTTTTTCAAAAAATAAAAAGCAATTAAGCCTCTGCTTTTATTTTGCACTCACTTGGATAC
1 TCAAACTTTTTC--AAAA-AAAAAGCAATTAAGCCTCTGTTTTTATTTTGCACTCAATTGGATAC
* * **
56144107 TTAAATTTTCAAAATGCATCAAAAAGGC-C
63 TTAAACTTTCAAAATGCATAAAAAAAACAC
** * * * *
56144136 TTCAAA-TTTTT-TTAGAAAAAGCAATTAAGCACT-TGTTTTTATTTTACACTCAAATGGGTACT
1 -TCAAACTTTTTCAAAAAAAAAGCAATTAAGC-CTCTGTTTTTATTTTGCACTCAATTGGATACT
56144198 TAAACTTTCAAAATGCATAAAAAAAACAC
64 TAAACTTTCAAAATGCATAAAAAAAACAC
* *
56144227 TCAAACTTTTTCAAAAAAAAAACAATTAAGCC-CTTGATTTTTTTTTTGCACTCAATTGGATACT
1 TCAAACTTTTTCAAAAAAAAAGCAATTAAGCCTC-TG-TTTTTATTTTGCACTCAATTGGATACT
*
56144291 TGAACT
64 TAAACT
56144297 GTCCCTAACT
Statistics
Matches: 132, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
90 67 0.51
91 10 0.08
92 17 0.13
93 28 0.21
94 5 0.04
95 5 0.04
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (92 bp):
TCAAACTTTTTCAAAAAAAAAGCAATTAAGCCTCTGTTTTTATTTTGCACTCAATTGGATACTTA
AACTTTCAAAATGCATAAAAAAAACAC
Found at i:56144447 original size:16 final size:15
Alignment explanation
Indices: 56144387--56144455 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
56144377 TTTTTTATGC
56144387 ATTTTCTATTTTT-TA
1 ATTTT-TATTTTTATA
* *
56144402 TATTTTT-TTATTAAA
1 -ATTTTTATTTTTATA
*
56144417 ATTTAATAGTTTTTATTA
1 ATTT-TTA-TTTTTA-TA
56144435 ATTTTTATTTTTATA
1 ATTTTTATTTTTATA
56144450 ATTTTT
1 ATTTTT
56144456 TTGCCACATG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 8 0.19
15 11 0.26
16 11 0.26
17 7 0.17
18 5 0.12
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (15 bp):
ATTTTTATTTTTATA
Found at i:56144456 original size:16 final size:16
Alignment explanation
Indices: 56144426--56144455 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56144416 AATTTAATAG
56144426 TTTTTATTAATTTTTA
1 TTTTTATTAATTTTTA
56144442 TTTTTA-TAATTTTT
1 TTTTTATTAATTTTT
56144456 TTGCCACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTATTAATTTTTA
Found at i:56144831 original size:89 final size:85
Alignment explanation
Indices: 56144603--56144838 Score: 213
Period size: 89 Copynumber: 2.7 Consensus size: 85
56144593 TATTCAATTG
* * * * *
56144603 AGTGCAAAAAAAATTGGGGGTTTAATTGCTGTTTTTTGAAAAAACTAAGGGCATTTTTATGCATT
1 AGTGCAAAAAAAAGTAGGGGTTTAATTGCT-TTTTTTG-AAAAATTGAGGAC-TTTTTATGCATT
* * * *
56144668 TTAAAAGTTCAAGTATCCAATTG
63 TTAAAAGTTAAAATATCCAAGTA
* ** * ***
56144691 AGTGCAAAATAAAAGCAGGGCCTTAATTGTTTTTTTTTTCTTAAATTGAGGATCTTTTTGATGCA
1 AGTGCAAAA-AAAAGTAGGGGTTTAATTG--CTTTTTTTGAAAAATTGAGGA-CTTTTT-ATGCA
*
56144756 TTTTGAAAGTTAAAAT-TCCCAAGTA
61 TTTTAAAAGTTAAAATAT-CCAAGTA
56144781 AGTGCAAAAAAAAGTAGGGGTTTAATTGCTTTTTTTGAAAAAGTTTGAGGACTTTTTA
1 AGTGCAAAAAAAAGTAGGGGTTTAATTGCTTTTTTTGAAAAA--TTGAGGACTTTTTA
56144839 CACCCTTAAA
Statistics
Matches: 116, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
87 11 0.09
88 15 0.13
89 50 0.43
90 39 0.34
91 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (85 bp):
AGTGCAAAAAAAAGTAGGGGTTTAATTGCTTTTTTTGAAAAATTGAGGACTTTTTATGCATTTTA
AAAGTTAAAATATCCAAGTA
Found at i:56149417 original size:27 final size:26
Alignment explanation
Indices: 56149361--56149418 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
56149351 ACAAATATGA
*
56149361 AACATT-T-ATTTTATAATTGAAAAT
1 AACATTATCATTTAATAATTGAAAAT
*
56149385 AACATTATCATTTAATACATTGATAAT
1 AACATTATCATTTAATA-ATTGAAAAT
*
56149412 ATCATTA
1 AACATTA
56149419 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 1 0.04
26 7 0.25
27 14 0.50
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (26 bp):
AACATTATCATTTAATAATTGAAAAT
Found at i:56149782 original size:15 final size:16
Alignment explanation
Indices: 56149757--56149790 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
56149747 AAAATGTAAT
56149757 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
56149773 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
56149788 TTT
1 TTT
56149791 TTGAAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:56149821 original size:30 final size:29
Alignment explanation
Indices: 56149780--56149847 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
56149770 TAATTTATAT
* *
56149780 TTTTATAATTTTTGAAGA-ATTAAATTAAAA
1 TTTTATCATTTTT--AGATATTAAAATAAAA
*
56149810 TTTTATCA-TTTTAGATATTAAAATATAA
1 TTTTATCATTTTTAGATATTAAAATAAAA
56149838 TTTTATCATT
1 TTTTATCATT
56149848 AAATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 3 0.09
28 18 0.55
29 5 0.15
30 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (29 bp):
TTTTATCATTTTTAGATATTAAAATAAAA
Found at i:56149860 original size:28 final size:27
Alignment explanation
Indices: 56149798--56149865 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
56149788 TTTTTGAAGA
* * *
56149798 ATTAAATTAAAATTTTATCATTTTAGAT
1 ATTAAAATATAATTTTATCA-TTTAAAT
56149826 ATTAAAATATAATTTTATCA-TTAAAT
1 ATTAAAATATAATTTTATCATTTAAAT
56149852 ATTTAAAAATATAA
1 A-TT-AAAATATAA
56149866 AGAATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.17
27 2 0.06
28 27 0.77
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (27 bp):
ATTAAAATATAATTTTATCATTTAAAT
Found at i:56155184 original size:18 final size:18
Alignment explanation
Indices: 56155148--56155184 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56155138 TTAATAGTAA
*
56155148 TAATAATAATAAATGTTT
1 TAATAATAATAAATATTT
*
56155166 TAATAATAATAGATATTT
1 TAATAATAATAAATATTT
56155184 T
1 T
56155185 GGTAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TAATAATAATAAATATTT
Found at i:56156327 original size:29 final size:29
Alignment explanation
Indices: 56156295--56156388 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
56156285 CCCAAACTTT
* *
56156295 CCAAAATCCCATTTTTAACCTCGATGTCA
1 CCAAAATCCCATTTTTAACCCCGATCTCA
* * * **
56156324 CCAAAAATTACCA-TTTTACCCCCGAACTTT
1 CC-AAAA-TCCCATTTTTAACCCCGATCTCA
*
56156354 CCAAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAATCCCATTTTTAACCCCGATCTCA
56156383 CCAAAA
1 CCAAAA
56156389 ATTACCATTT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 4 0.08
29 24 0.49
30 17 0.35
31 4 0.08
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (29 bp):
CCAAAATCCCATTTTTAACCCCGATCTCA
Found at i:56156341 original size:59 final size:59
Alignment explanation
Indices: 56156278--56156427 Score: 246
Period size: 59 Copynumber: 2.5 Consensus size: 59
56156268 AAAATTATAT
* * *
56156278 TTTTACTCCCAAACTTTCCAAAATCCCATTTTTAACCTCGATGTCACCAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATGTCACCAAAAATTACCA
*
56156337 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATGTCACCAAAAATTACCA
* *
56156396 TTTTGCCCCCGAACATTCCAAAATCCCATTTT
1 TTTTACCCCCGAACTTTCCAAAATCCCATTTT
56156428 CGATCCCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 85 1.00
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.32
Consensus pattern (59 bp):
TTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATGTCACCAAAAATTACCA
Found at i:56156404 original size:29 final size:30
Alignment explanation
Indices: 56156307--56156399 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 30
56156297 AAAATCCCAT
* *
56156307 TTTTAACCTCGATGTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACCAAAAATTACCA
* *
56156337 TTTTACCCCCGAACTTT--CC-AAAA-TCCCA
1 TTTTAACCCCG-A-TTTCACCAAAAATTACCA
56156365 TTTTTAACCCCGATTTCACCAAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAAATTACCA
56156396 TTTT
1 TTTT
56156400 GCCCCCGAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 16 0.32
30 19 0.38
31 5 0.10
32 2 0.04
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
TTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:56156417 original size:30 final size:30
Alignment explanation
Indices: 56156324--56156418 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
56156314 CTCGATGTCA
56156324 CCAAAAATTACCATTTTACCCCCGAACTTT
1 CCAAAAATTACCATTTTACCCCCGAACTTT
* *
56156354 CC-AAAA-TCCCATTTTTAACCCCG-A-TTT
1 CCAAAAATTACCA-TTTTACCCCCGAACTTT
* *
56156381 CACCAAAAATTACCATTTTGCCCCCGAACATT
1 --CCAAAAATTACCATTTTACCCCCGAACTTT
56156413 CCAAAA
1 CCAAAA
56156419 TCCCATTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 16 0.31
30 21 0.40
31 5 0.10
32 2 0.04
ACGTcount: A:0.35, C:0.34, G:0.04, T:0.27
Consensus pattern (30 bp):
CCAAAAATTACCATTTTACCCCCGAACTTT
Found at i:56156419 original size:29 final size:28
Alignment explanation
Indices: 56156327--56156427 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 28
56156317 GATGTCACCA
56156327 AAAATTACCATTTTACCCCCGAACTTTCC
1 AAAA-TACCATTTTACCCCCGAACTTTCC
* *
56156356 AAAATCCCATTTTTAACCCCG-A-TTTCACC
1 AAAATACCA-TTTTACCCCCGAACTTT--CC
* *
56156385 AAAAATTACCATTTTGCCCCCGAACATTCC
1 -AAAA-TACCATTTTACCCCCGAACTTTCC
*
56156415 AAAATCCCATTTT
1 AAAATACCATTTT
56156428 CGATCCCGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
27 3 0.05
28 13 0.22
29 20 0.34
30 15 0.26
31 5 0.09
32 2 0.03
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATACCATTTTACCCCCGAACTTTCC
Found at i:56167602 original size:19 final size:20
Alignment explanation
Indices: 56167558--56167604 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
56167548 TTGACATGAG
56167558 ACTA-ATTTTTAAAATATTT
1 ACTATATTTTTAAAATATTT
* *
56167577 A-TTTATTTTTAATAT-TTT
1 ACTATATTTTTAAAATATTT
56167595 ACTATATTTT
1 ACTATATTTT
56167605 AAAGAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
ACTATATTTTTAAAATATTT
Found at i:56168279 original size:18 final size:19
Alignment explanation
Indices: 56168238--56168287 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
56168228 TTATAAAAAC
56168238 TTTTAATTATTA-AATATA
1 TTTTAATTATTATAATATA
* *
56168256 TATTAATTATTATAGTAT-
1 TTTTAATTATTATAATATA
*
56168274 TTTTAATCATTATA
1 TTTTAATTATTATA
56168288 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTAATTATTATAATATA
Found at i:56168616 original size:26 final size:25
Alignment explanation
Indices: 56168578--56168633 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
56168568 TTTAAAAGCT
* * *
56168578 TTTTTAACCATAATTTTTCTCACAAC
1 TTTTTAAACATAA-CTTTCTAACAAC
* *
56168604 TTTTTAAATATAACTTTCTAACAAT
1 TTTTTAAACATAACTTTCTAACAAC
56168629 TTTTT
1 TTTTT
56168634 TTTTATATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTTAAACATAACTTTCTAACAAC
Found at i:56173568 original size:17 final size:20
Alignment explanation
Indices: 56173526--56173563 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
56173516 TAAATTCTAA
*
56173526 AATTGTTAATATTTATTTAT
1 AATTGTTAATAATTATTTAT
56173546 AATTGTT-ATAATTATTTA
1 AATTGTTAATAATTATTTA
56173564 ATTGTGTTTA
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:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTGTTAATAATTATTTAT
Found at i:56180886 original size:96 final size:96
Alignment explanation
Indices: 56180722--56180915 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
56180712 GGTGGCAAAC
56180722 TCGGGCGGTGTTTGCTCCCGGTGGTGATGCGTGGCATCCTGAAAACAGAAAAGTAAAGATGTCTG
1 TCGGGCGGTGTTTGCTCCCGGTGGTGATGCGTGGCATCCTGAAAACAGAAAAGTAAAGATGTCTG
56180787 TTACAGTGAAGGAGCTCGGGCTTTCAAAGCA
66 TTACAGTGAAGGAGCTCGGGCTTTCAAAGCA
56180818 TCGGGCGGTGTTTGCTCCCGGTGGTGATGCGTGGCATCCTGAAAACAGAAAAGTAAAGATGTCTG
1 TCGGGCGGTGTTTGCTCCCGGTGGTGATGCGTGGCATCCTGAAAACAGAAAAGTAAAGATGTCTG
56180883 TTACAGTGAAGGAGCTCGGGCTTTCAAAGCA
66 TTACAGTGAAGGAGCTCGGGCTTTCAAAGCA
56180914 TC
1 TC
56180916 AATTCCGCCG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (96 bp):
TCGGGCGGTGTTTGCTCCCGGTGGTGATGCGTGGCATCCTGAAAACAGAAAAGTAAAGATGTCTG
TTACAGTGAAGGAGCTCGGGCTTTCAAAGCA
Found at i:56181506 original size:21 final size:21
Alignment explanation
Indices: 56181474--56181513 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
56181464 TCATAAAACT
56181474 TATTTATATTTTAATTAATCA
1 TATTTATATTTTAATTAATCA
56181495 TATTT-TAGTTTTAATTAAT
1 TATTTATA-TTTTAATTAAT
56181514 TTTAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
TATTTATATTTTAATTAATCA
Found at i:56181522 original size:21 final size:21
Alignment explanation
Indices: 56181482--56181522 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56181472 CTTATTTATA
*
56181482 TTTTAATTAATCATATTTTAG
1 TTTTAATTAATCATAATTTAG
**
56181503 TTTTAATTAATTTTAATTTA
1 TTTTAATTAATCATAATTTA
56181523 CTAAATTAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTAATTAATCATAATTTAG
Found at i:56189297 original size:139 final size:139
Alignment explanation
Indices: 56189028--56189446 Score: 752
Period size: 139 Copynumber: 3.0 Consensus size: 139
56189018 GTCATCATCC
*
56189028 ATTGCCATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
** *
56189093 T-GTTGTACAAATATTATGTTGCTTCCAATTTTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
56189157 GACCCAAAT
131 GACCCAAAT
*
56189166 ATTGACATTCGGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTA-GAGGGTTCAATGTGTTG
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGA-GGTTCAATGTGTTG
56189230 CTGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTG
65 CTGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTG
*
56189295 AGACCTAAAT
130 AGACCCAAAT
56189305 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
1 ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
*
56189370 TGGTTGTACAAATATTATGTTACTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
66 TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
56189435 GACCCAAAT
131 GACCCAAAT
56189444 ATT
1 ATT
56189447 AAGTGTTGCT
Statistics
Matches: 269, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
137 2 0.01
138 61 0.23
139 204 0.76
140 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (139 bp):
ATTGACATTCTGTTAGGATACTTTGTTGATTCTGTTATTTTGTTCTAGGAGGTTCAATGTGTTGC
TGGTTGTACAAATATTATGTTGCTTCTGATTCTGCACAACCATGTTTGCAGAAACTGTGTTTTGA
GACCCAAAT
Found at i:56190306 original size:25 final size:25
Alignment explanation
Indices: 56190272--56190320 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
56190262 AAAGTATATT
56190272 AGTTTAGGATTAAGAAATAAGACTC
1 AGTTTAGGATTAAGAAATAAGACTC
56190297 AGTTTAGGATTAAGAAATAAGACT
1 AGTTTAGGATTAAGAAATAAGACT
56190321 ACAAGTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (25 bp):
AGTTTAGGATTAAGAAATAAGACTC
Found at i:56194066 original size:26 final size:26
Alignment explanation
Indices: 56193988--56194129 Score: 88
Period size: 26 Copynumber: 5.0 Consensus size: 26
56193978 TAATTCATAT
*
56193988 TTTAATAATAATTATATTAAAAATATTA
1 TTTAATAATAATTATATT--AAATTTTA
* *
56194016 TTAAATTATATATTATTTTATTAAATTTTA
1 TTTAA-TA-ATA--ATTATATTAAATTTTA
56194046 TTTAATAATAATTATATTAAAATATAATTAA
1 TTTAATAATAATTATATT-AAAT-T--TT-A
* * * *
56194077 ATTAATTAATATTTTTATTAAATTATA
1 TTTAA-TAATAATTATATTAAATTTTA
*
56194104 TTTAATAATAATCT-TATTAAAATTTA
1 TTTAATAATAAT-TATATTAAATTTTA
56194130 ATAAGAATAA
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
26 23 0.26
27 10 0.11
28 9 0.10
29 4 0.04
30 17 0.19
31 9 0.10
32 18 0.20
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAATAATAATTATATTAAATTTTA
Found at i:56194096 original size:32 final size:31
Alignment explanation
Indices: 56193989--56194115 Score: 99
Period size: 32 Copynumber: 4.3 Consensus size: 31
56193979 AATTCATATT
*
56193989 TTAATAATAATTATATTAAAAATATTATTAAA
1 TTAATAATAATTATATT-AAAATATAATTAAA
* * *
56194021 TT-ATATATTATTTTATT-AAAT-T--TT-AT
1 TTAATA-ATAATTATATTAAAATATAATTAAA
56194047 TTAATAATAATTATATTAAAATATAATTAAA
1 TTAATAATAATTATATTAAAATATAATTAAA
* * * *
56194078 TTAATTAATATTTTTATTAAATTAT-ATTTAA
1 TTAA-TAATAATTATATTAAAATATAATTAAA
56194109 -TAATAAT
1 TTAATAAT
56194116 CTTATTAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
26 12 0.16
27 9 0.12
28 1 0.01
29 5 0.06
30 9 0.12
31 13 0.17
32 28 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATAATAATTATATTAAAATATAATTAAA
Found at i:56194126 original size:58 final size:58
Alignment explanation
Indices: 56193961--56194131 Score: 206
Period size: 58 Copynumber: 2.9 Consensus size: 58
56193951 TCTAATATTA
* * *
56193961 TATATTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAAT
1 TATATAAT-ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAAT
* *
56194022 TATATATTA-TTTTATTAAATTTTATTTAATAATAATTATATTAAAATATAATTAAAT
1 TATATAATATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
*
56194079 TA-ATTAATATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TATA-TAATATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
56194132 AAGAATAATC
Statistics
Matches: 98, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
56 1 0.01
57 20 0.20
58 57 0.58
59 9 0.09
60 5 0.05
61 6 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (58 bp):
TATATAATATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:56194308 original size:16 final size:16
Alignment explanation
Indices: 56194287--56194358 Score: 126
Period size: 16 Copynumber: 4.5 Consensus size: 16
56194277 TGAATTACTG
56194287 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
56194303 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
56194319 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
*
56194335 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
56194351 ATTACAGC
1 ATTACAGC
56194359 GAACCAAACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:56195458 original size:42 final size:42
Alignment explanation
Indices: 56195399--56195486 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
56195389 AATGACGTTT
*
56195399 TTTCCACTTTTACATTCTATCTAGTTCCCACCTCTTCAACAA
1 TTTCCACTTTTACATTCTATCTAGTTCCCAACTCTTCAACAA
56195441 TTTCCACTTTTACATTCTATCTAGTTCCCAACTCTTCAACAA
1 TTTCCACTTTTACATTCTATCTAGTTCCCAACTCTTCAACAA
56195483 TTTC
1 TTTC
56195487 AAGAAATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (42 bp):
TTTCCACTTTTACATTCTATCTAGTTCCCAACTCTTCAACAA
Found at i:56200478 original size:30 final size:30
Alignment explanation
Indices: 56200386--56200478 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
56200376 AGGGGGGACC
*
56200386 ATTTACTAAAATGGTACAAAATATATATTT
1 ATTTACTAAAATGGTACAAAATAAATATTT
* * * * * * **
56200416 ATATACCAAAATTGTATCCACA-CACCA-TT
1 ATTTACTAAAATGGTA-CAAAATAAATATTT
56200445 ATTTACTAAAATGGTACAAAATAAATATTT
1 ATTTACTAAAATGGTACAAAATAAATATTT
56200475 ATTT
1 ATTT
56200479 TATACCATTT
Statistics
Matches: 43, Mismatches: 17, Indels: 6
0.65 0.26 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 20 0.47
31 3 0.07
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (30 bp):
ATTTACTAAAATGGTACAAAATAAATATTT
Found at i:56200532 original size:16 final size:16
Alignment explanation
Indices: 56200511--56200560 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
56200501 TGATGAGGAT
56200511 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
56200527 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
56200542 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
56200557 ATTA
1 ATTA
56200561 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:56201293 original size:17 final size:17
Alignment explanation
Indices: 56201266--56201309 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
56201256 TTTTTATGTG
*
56201266 AATTCTTTTAA-ACAAAA
1 AATTATTTTAATA-AAAA
*
56201283 TATTATTTTAATAAAAA
1 AATTATTTTAATAAAAA
56201300 AATTATTTTA
1 AATTATTTTA
56201310 GCAGGATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATTTTAATAAAAA
Found at i:56203046 original size:18 final size:18
Alignment explanation
Indices: 56203023--56203059 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56203013 ACAATTCATA
56203023 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
56203041 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
56203059 T
1 T
56203060 TGTTCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:56210250 original size:16 final size:17
Alignment explanation
Indices: 56210215--56210255 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
56210205 AAAATCTATC
* *
56210215 TGAAAAATAAGAGAATT
1 TGAAAAATAAGAAAACT
56210232 TGAAAAATAA-AAAACT
1 TGAAAAATAAGAAAACT
56210248 TGAAAAAT
1 TGAAAAAT
56210256 GAACTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (17 bp):
TGAAAAATAAGAAAACT
Found at i:56215508 original size:16 final size:17
Alignment explanation
Indices: 56215479--56215511 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56215469 ATATATTTTC
56215479 TTATAAAATAATTTATT
1 TTATAAAATAATTTATT
56215496 TTATAAAAT-ATTTATT
1 TTATAAAATAATTTATT
56215512 ATAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATAAAATAATTTATT
Found at i:56215679 original size:17 final size:17
Alignment explanation
Indices: 56215657--56215692 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
56215647 TTAAAATACA
56215657 TTTTAATATTAGGTACT
1 TTTTAATATTAGGTACT
*
56215674 TTTTAATATTAGTTACT
1 TTTTAATATTAGGTACT
56215691 TT
1 TT
56215693 AATTTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTAATATTAGGTACT
Found at i:56220334 original size:2 final size:2
Alignment explanation
Indices: 56220327--56220357 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
56220317 GCTAAAAGCA
56220327 AT 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 AT A
56220358 GGGAAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56222963 original size:30 final size:30
Alignment explanation
Indices: 56222927--56222991 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
56222917 TAATGCCTAC
56222927 AGAAAGCCTATCATGCATGGATAGAAGTAA
1 AGAAAGCCTATCATGCATGGATAGAAGTAA
* *
56222957 AGAAAGCCTATTATGCGTGGATAGAAGTAA
1 AGAAAGCCTATCATGCATGGATAGAAGTAA
56222987 AGAAA
1 AGAAA
56222992 TGAATACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.20
Consensus pattern (30 bp):
AGAAAGCCTATCATGCATGGATAGAAGTAA
Found at i:56227372 original size:19 final size:19
Alignment explanation
Indices: 56227348--56227390 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
56227338 TTTTTTTATG
*
56227348 TTTATTTCAT-GAAAAGTAA
1 TTTATTTAATAGAAAA-TAA
56227367 TTTATTTAATAGAAAATAA
1 TTTATTTAATAGAAAATAA
56227386 TTTAT
1 TTTAT
56227391 CAACGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (19 bp):
TTTATTTAATAGAAAATAA
Found at i:56229539 original size:16 final size:18
Alignment explanation
Indices: 56229518--56229554 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
56229508 GTTGTGGTGT
56229518 TATTGG-TTTCAT-TCAA
1 TATTGGATTTCATATCAA
*
56229534 TATTGGATTTTATATCAA
1 TATTGGATTTCATATCAA
56229552 TAT
1 TAT
56229555 ACAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTGGATTTCATATCAA
Found at i:56237683 original size:22 final size:21
Alignment explanation
Indices: 56237655--56237695 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
56237645 CCAATAAACT
56237655 TAAAAAA-TGTAATAAAAAAAGC
1 TAAAAAAGTG-AA-AAAAAAAGC
56237677 TAAAAAAGTGAAAAAAAAA
1 TAAAAAAGTGAAAAAAAAA
56237696 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (21 bp):
TAAAAAAGTGAAAAAAAAAGC
Found at i:56237692 original size:21 final size:22
Alignment explanation
Indices: 56237655--56237695 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
56237645 CCAATAAACT
56237655 TAAAAAATGTAATAAAAAAAGC
1 TAAAAAATGTAATAAAAAAAGC
56237677 TAAAAAA-GTGAA-AAAAAAA
1 TAAAAAATGT-AATAAAAAAA
56237696 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
TAAAAAATGTAATAAAAAAAGC
Found at i:56239210 original size:19 final size:19
Alignment explanation
Indices: 56239186--56239246 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
56239176 ATTAATTTTA
56239186 ATTTAATATTTGATTTGAT
1 ATTTAATATTTGATTTGAT
* *
56239205 ATTTAAT-TTT--TTTAAA
1 ATTTAATATTTGATTTGAT
*
56239221 ATTTAATATTTGTACTTGAT
1 ATTTAATATTTG-ATTTGAT
56239241 -TTTAAT
1 ATTTAAT
56239247 GTTCAGTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 11 0.33
17 3 0.09
18 3 0.09
19 13 0.39
20 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (19 bp):
ATTTAATATTTGATTTGAT
Found at i:56244572 original size:14 final size:14
Alignment explanation
Indices: 56244537--56244586 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
56244527 TCAGAAAAAG
*
56244537 TCAACGGTCAACGA
1 TCAACAGTCAACGA
* *
56244551 TCAA-AGTCAATGG
1 TCAACAGTCAACGA
56244564 TCAACAGTCAACGA
1 TCAACAGTCAACGA
56244578 TCAACAGTC
1 TCAACAGTC
56244587 GGTCAACAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (14 bp):
TCAACAGTCAACGA
Found at i:56248477 original size:14 final size:14
Alignment explanation
Indices: 56248460--56248486 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56248450 AATACTTTTA
56248460 TTCAAATTCTTTCT
1 TTCAAATTCTTTCT
56248474 TTCAAATTCTTTC
1 TTCAAATTCTTTC
56248487 AAATTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (14 bp):
TTCAAATTCTTTCT
Found at i:56250703 original size:31 final size:28
Alignment explanation
Indices: 56250633--56250704 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
56250623 GATCAAATAA
56250633 AAATTCATGTATAAAATTGCACAAAATC
1 AAATTCATGTATAAAATTGCACAAAATC
* *
56250661 AAAGTCATGTATACAATTGCACATTAAATC
1 AAATTCATGTATAAAATTGCACA--AAATC
56250691 ATAATTCATGTATA
1 A-AATTCATGTATA
56250705 GTTTTGGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.55
30 6 0.16
31 11 0.29
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (28 bp):
AAATTCATGTATAAAATTGCACAAAATC
Found at i:56250885 original size:22 final size:22
Alignment explanation
Indices: 56250828--56250903 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 22
56250818 TGTAGTAGTG
** * *
56250828 AAATAGTAGCAAAATAGAGAGA
1 AAATAGTAAAAAAATAGAAAAA
* * * *
56250850 AAACAATAAGAAAATAGAAACA
1 AAATAGTAAAAAAATAGAAAAA
*
56250872 AAATAGTAAAAAAAAGTAAAAAAA
1 AAATAGT-AAAAAAA-TAGAAAAA
56250896 AAATAGTA
1 AAATAGTA
56250904 GTTTCTTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
22 21 0.51
23 7 0.17
24 13 0.32
ACGTcount: A:0.70, C:0.04, G:0.13, T:0.13
Consensus pattern (22 bp):
AAATAGTAAAAAAATAGAAAAA
Found at i:56251483 original size:27 final size:27
Alignment explanation
Indices: 56251436--56251529 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 27
56251426 CACAAAAGTC
** *
56251436 ATTCTTTCATGA-TTCGTCACAAAGGCT
1 ATTCTTTCAT-ATTTCACCACAAAGACT
* *
56251463 ATTCTTTCATATTTCCCCACAAAGATT
1 ATTCTTTCATATTTCACCACAAAGACT
*
56251490 ATTCTTTCATATTTCACGACAAAGACT
1 ATTCTTTCATATTTCACCACAAAGACT
*
56251517 ATTCTTTCCTATT
1 ATTCTTTCATATT
56251530 CTTTCGTGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 1 0.02
27 57 0.98
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.41
Consensus pattern (27 bp):
ATTCTTTCATATTTCACCACAAAGACT
Found at i:56266260 original size:25 final size:24
Alignment explanation
Indices: 56266218--56266289 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 24
56266208 AATCTAAAAT
**
56266218 TTACTTGTTAAAAAAAAATTATA-G
1 TTACTT-TTAAATTAAAATTATATG
*
56266242 TTACAATTTTAAATTAAAACCTATATG
1 TTAC--TTTTAAATTAAAA-TTATATG
56266269 TTACTTTTAAATTACAAATTA
1 TTACTTTTAAATTA-AAATTA
56266290 GTTTTAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 4 0.10
25 21 0.54
26 9 0.23
27 5 0.13
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (24 bp):
TTACTTTTAAATTAAAATTATATG
Found at i:56267112 original size:20 final size:18
Alignment explanation
Indices: 56267087--56267123 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
56267077 ATTAATGTAT
56267087 ATAAATGACGTTGTAACTTG
1 ATAAATGA-GTTG-AACTTG
56267107 ATAAATGAGTTGAACTT
1 ATAAATGAGTTGAACTT
56267124 ACCCTTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (18 bp):
ATAAATGAGTTGAACTTG
Found at i:56270487 original size:30 final size:31
Alignment explanation
Indices: 56270446--56270533 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 31
56270436 AAAATTTAAA
56270446 TTAAAAA--AATAAAATTATATTTTAATTTT
1 TTAAAAATTAATAAAATTATATTTTAATTTT
*
56270475 TT-AAAATTAATAAAAATT-TAATTTAATTTT
1 TTAAAAATTAAT-AAAATTATATTTTAATTTT
56270505 TTAAAAATT-ATAAAGATATATATTATTAA
1 TTAAAAATTAATAAA-AT-TATATT-TTAA
56270534 AAATTATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
28 4 0.08
29 5 0.10
30 20 0.41
31 13 0.27
32 3 0.06
33 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TTAAAAATTAATAAAATTATATTTTAATTTT
Found at i:56270491 original size:31 final size:31
Alignment explanation
Indices: 56270456--56270533 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
56270446 TTAAAAAAAT
56270456 AAAATTATATTTTAATTTTTT-AAAATTAATA
1 AAAATTATATTTTAATTTTTTAAAAATT-ATA
*
56270487 AAAATT-TAATTTAATTTTTTAAAAATTATA
1 AAAATTATATTTTAATTTTTTAAAAATTATA
*
56270517 AAGATATATATTATTAA
1 AAAAT-TATATT-TTAA
56270534 AAATTATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 20 0.50
31 13 0.32
32 3 0.08
33 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
AAAATTATATTTTAATTTTTTAAAAATTATA
Done.