Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold77
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1619719
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 197531 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:387109 original size:48 final size:47
Alignment explanation
Indices: 387038--387132 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 47
387028 ATAAGATGGA
387038 AACCATTGACATTGATTTATTGTAAGGAAATTAAGAATCAGCCTAAC
1 AACCATTGACATTGATTTATTGTAAGGAAATTAAGAATCAGCCTAAC
*
387085 NAACCATTGACATTGATTTATTGTAAGGAAATTAGGAATCAGCCTAAC
1 -AACCATTGACATTGATTTATTGTAAGGAAATTAAGAATCAGCCTAAC
387133 GTCATTTAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (47 bp):
AACCATTGACATTGATTTATTGTAAGGAAATTAAGAATCAGCCTAAC
Found at i:388950 original size:21 final size:20
Alignment explanation
Indices: 388886--388951 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
388876 ACATGTCCGT
* *
388886 TGTACAAGGGATGTTGTCCAC
1 TGTAC-AGGGAAGTTGTTCAC
** * *
388907 TGTACAAAGAATGTCGTTAAC
1 TGTACAGGGAA-GTTGTTCAC
388928 TGTACATGGGAAGTTGTTCAC
1 TGTACA-GGGAAGTTGTTCAC
388949 TGT
1 TGT
388952 GCACTTTATG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (20 bp):
TGTACAGGGAAGTTGTTCAC
Found at i:389093 original size:21 final size:21
Alignment explanation
Indices: 389064--389692 Score: 407
Period size: 21 Copynumber: 30.0 Consensus size: 21
389054 AATACAAAGT
* * *
389064 AAGTAGTCCACTGTACTCGGG
1 AAGTCGTCCACTGTACACAGG
* *
389085 AAGTCGTCCATTGTACACGGG
1 AAGTCGTCCACTGTACACAGG
** **
389106 ATA-TTTTCCACTTGTACACATT
1 A-AGTCGTCCAC-TGTACACAGG
* *
389128 ATGTCGTCCACTGTAGACAGG
1 AAGTCGTCCACTGTACACAGG
* * *
389149 ATGTCGTCCACTCTACACGGG
1 AAGTCGTCCACTGTACACAGG
* *
389170 ATGTCGTCCACTGTACAAAGG
1 AAGTCGTCCACTGTACACAGG
* *
389191 AAGTCGTCCACTGTCCAC-TG
1 AAGTCGTCCACTGTACACAGG
***
389211 -A-TC-T---CTGTACAATTG
1 AAGTCGTCCACTGTACACAGG
** * *
389226 ATCTCGTCCAATGTACACGGG
1 AAGTCGTCCACTGTACACAGG
* * * *
389247 ATGTTGTCCTCTGTACACGGG
1 AAGTCGTCCACTGTACACAGG
* *
389268 AATGTCGTCAACTGTATTA-AGG
1 AA-GTCGTCCACTGTA-CACAGG
*
389290 AAGTCGTCCACTGTACACAAG
1 AAGTCGTCCACTGTACACAGG
*
389311 AAGTCATCCACTGTACACAGG
1 AAGTCGTCCACTGTACACAGG
* *
389332 ATA-TCTTCCACTTGTACACGGG
1 A-AGTCGTCCAC-TGTACACAGG
** * * * *
389354 GTGTCATCCACGGTACTCGGG
1 AAGTCGTCCACTGTACACAGG
* * * *
389375 ATGTCCTCTAATGTACACAGG
1 AAGTCGTCCACTGTACACAGG
* * *
389396 AAATCGTCGACTGTACACGGG
1 AAGTCGTCCACTGTACACAGG
* *
389417 ATGTCGTCCACTGTACAAAGG
1 AAGTCGTCCACTGTACACAGG
**
389438 ATTTCGTCCACTGTACACAGG
1 AAGTCGTCCACTGTACACAGG
* * * *
389459 AAGTCGTCAATTGTATACGGG
1 AAGTCGTCCACTGTACACAGG
* * * *
389480 ATGTCTTCAACTTGTACTCAGG
1 AAGTCGTCCAC-TGTACACAGG
* *
389502 AAGTCGTCCACTATACACGGG
1 AAGTCGTCCACTGTACACAGG
*
389523 ATGTCGTCCACTGTACACAGG
1 AAGTCGTCCACTGTACACAGG
* * *
389544 AAATCGTCTACTTGTACACGGG
1 AAGTCGTCCAC-TGTACACAGG
*
389566 ATGTCGTCCACTGTACACAGG
1 AAGTCGTCCACTGTACACAGG
* *
389587 ATGTCGTCCACTGTACACAAG
1 AAGTCGTCCACTGTACACAGG
* * * *
389608 ATGTTGTCCACTGTTCACGGG
1 AAGTCGTCCACTGTACACAGG
* * *
389629 ATGTCGCCCACTGTACAAAGG
1 AAGTCGTCCACTGTACACAGG
*
389650 AAGTCGTCCACTGTACACTGG
1 AAGTCGTCCACTGTACACAGG
389671 AAGTCGTCCGA-TGTACACAGG
1 AAGTCGTCC-ACTGTACACAGG
389692 A
1 A
389693 TGTCATTCAC
Statistics
Matches: 471, Mismatches: 118, Indels: 38
0.75 0.19 0.06
Matches are distributed among these distances:
14 6 0.01
15 2 0.00
17 3 0.01
18 3 0.01
19 1 0.00
20 2 0.00
21 374 0.79
22 79 0.17
23 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (21 bp):
AAGTCGTCCACTGTACACAGG
Found at i:389178 original size:42 final size:42
Alignment explanation
Indices: 389069--389696 Score: 475
Period size: 42 Copynumber: 15.0 Consensus size: 42
389059 AAAGTAAGTA
* * * * * * *
389069 GTCCACTGTACTCGGGAAGTCGTCCATTGTACACGGGATATT
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* ** *
389111 TTCCACTTGTACACATTATGTCGTCCACTGTAGACAGGATGTC
1 GTCCAC-TGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* * * *
389154 GTCCACTCTACACGGGATGTCGTCCACTGTACAAAGGAAGTC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* * * *
389196 GTCCACTGTCCAC-TGA--TC-T---CTGTACA-ATTGATCTC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACA-GGATGTC
* * * * *
389231 GTCCAATGTACACGGGATGTTGTCCTCTGTACACGGGAATGTC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGG-ATGTC
* * * * *
389274 GTCAACTGTATTA-AGGAAGTCGTCCACTGTACACAAGAAGTC
1 GTCCACTGTA-CACAGGATGTCGTCCACTGTACACAGGATGTC
* * * * *
389316 ATCCACTGTACACAGGATATCTTCCACTTGTACACGGGGTGTC
1 GTCCACTGTACACAGGATGTCGTCCAC-TGTACACAGGATGTC
* * * * * * * **
389359 ATCCACGGTACTCGGGATGTCCTCTAATGTACACAGGAAATC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* * * *
389401 GTCGACTGTACACGGGATGTCGTCCACTGTACAAAGGATTTC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* * * * *
389443 GTCCACTGTACACAGGAAGTCGTCAATTGTATACGGGATGTC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* * * * * *
389485 TTCAACTTGTACTCAGGAAGTCGTCCACTATACACGGGATGTC
1 GTCCAC-TGTACACAGGATGTCGTCCACTGTACACAGGATGTC
** * *
389528 GTCCACTGTACACAGGAAATCGTCTACTTGTACACGGGATGTC
1 GTCCACTGTACACAGGATGTCGTCCAC-TGTACACAGGATGTC
* *
389571 GTCCACTGTACACAGGATGTCGTCCACTGTACACAAGATGTT
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* * * * *
389613 GTCCACTGTTCACGGGATGTCGCCCACTGTACAAAGGAAGTC
1 GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
* *
389655 GTCCACTGTACACTGGAAGTCGTCCGA-TGTACACAGGATGTC
1 GTCCACTGTACACAGGATGTCGTCC-ACTGTACACAGGATGTC
389697 ATTCACTTAA
Statistics
Matches: 455, Mismatches: 114, Indels: 34
0.75 0.19 0.06
Matches are distributed among these distances:
34 1 0.00
35 22 0.05
36 2 0.00
38 2 0.00
39 3 0.01
41 3 0.01
42 255 0.56
43 166 0.36
44 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (42 bp):
GTCCACTGTACACAGGATGTCGTCCACTGTACACAGGATGTC
Found at i:389591 original size:212 final size:212
Alignment explanation
Indices: 389258--389678 Score: 556
Period size: 212 Copynumber: 2.0 Consensus size: 212
389248 TGTTGTCCTC
* *
389258 TGTACACGGGAATGTCGTCAACTGTATTAAGGAAGTCGTCCACTGTACACAAGAAGTCATCCACT
1 TGTACACGGGAATGTCGTCAACTGTACTAAGGAAGTCGTCCACTATACACAAGAAGTCATCCACT
* * * * * *
389323 GTACACAGGATATCTTCCACTTGTACACGGGGTGTCATCCACGGTACTCGGGATGTCCTCTAATG
66 GTACACAGGAAATCGTCCACTTGTACACGGGATGTCATCCACGGTACACAGGATGTCCTCCAATG
* * * **
389388 TACACAGGAAATCGTCGACTGTACACGGGATGTCGTCCACTGTACAAAGGATTTCGTCCACTGTA
131 TACACAAGAAATCGTCCACTGTACACGGGATGTCGCCCACTGTACAAAGGAAGTCGTCCACTGTA
389453 CACAGGAAGTCGTCAAT
196 CACAGGAAGTCGTCAAT
* * * ** * *
389470 TGTATACGGG-ATGTCTTCAACTTGTACTCAGGAAGTCGTCCACTATACACGGGATGTCGTCCAC
1 TGTACACGGGAATGTCGTCAAC-TGTACTAAGGAAGTCGTCCACTATACACAAGAAGTCATCCAC
* * * * *
389534 TGTACACAGGAAATCGTCTACTTGTACACGGGATGTCGTCCACTGTACACAGGATGTCGTCCACT
65 TGTACACAGGAAATCGTCCACTTGTACACGGGATGTCATCCACGGTACACAGGATGTCCTCCAAT
** * *
389599 GTACACAAGATGTTGTCCACTGTTCACGGGATGTCGCCCACTGTACAAAGGAAGTCGTCCACTGT
130 GTACACAAGAAATCGTCCACTGTACACGGGATGTCGCCCACTGTACAAAGGAAGTCGTCCACTGT
*
389664 ACACTGGAAGTCGTC
195 ACACAGGAAGTCGTC
389679 CGATGTACAC
Statistics
Matches: 178, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
211 10 0.06
212 168 0.94
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (212 bp):
TGTACACGGGAATGTCGTCAACTGTACTAAGGAAGTCGTCCACTATACACAAGAAGTCATCCACT
GTACACAGGAAATCGTCCACTTGTACACGGGATGTCATCCACGGTACACAGGATGTCCTCCAATG
TACACAAGAAATCGTCCACTGTACACGGGATGTCGCCCACTGTACAAAGGAAGTCGTCCACTGTA
CACAGGAAGTCGTCAAT
Found at i:389696 original size:212 final size:210
Alignment explanation
Indices: 389215--389701 Score: 553
Period size: 212 Copynumber: 2.3 Consensus size: 210
389205 CCACTGATCT
** * * * * ** *
389215 CTGTACAATTGATCTCGTCCAATGTACACGGGATGTTGTCCTCTGTACACGGGAATGTCGTCAAC
1 CTGTACAAAGGATCTCGTCCACTGTACACAGGAAGTCGTCCAATGTACACGGG-ATGTCTTCAAC
* * ** * *
389280 TGTATTAAGGAAGTCGTCCACTGTACACAAGAAGTCATCCACTGTACACAGGATATCTTCCACTT
65 TGTACTCAGGAAGTCGTCCACTGTACACGGGATGTCATCCACTGTACACAGGATATCGTCCACTT
* * * * * * * * * *
389345 GTACACGGGGTGTCATCCACGGTACTCGGGATGTCCTCTAATGTACACAGGAAATCGTCGACTGT
130 GTACACGGGATGTCGTCCACTGTACACGGGATGTCGTCCACTGTACACAAGAAGTCGTCCACTGT
389410 ACACGGGATGTCGTCCA
195 ACACGGGATGTCG-CCA
* *
389427 CTGTACAAAGGATTTCGTCCACTGTACACAGGAAGTCGT-CAATTGTATACGGGATGTCTTCAAC
1 CTGTACAAAGGATCTCGTCCACTGTACACAGGAAGTCGTCCAA-TGTACACGGGATGTCTTCAAC
* * * *
389491 TTGTACTCAGGAAGTCGTCCACTATACACGGGATGTCGTCCACTGTACACAGGAAATCGTCTACT
65 -TGTACTCAGGAAGTCGTCCACTGTACACGGGATGTCATCCACTGTACACAGGATATCGTCCACT
* * *
389556 TGTACACGGGATGTCGTCCACTGTACACAGGATGTCGTCCACTGTACACAAGATGTTGTCCACTG
129 TGTACACGGGATGTCGTCCACTGTACACGGGATGTCGTCCACTGTACACAAGAAGTCGTCCACTG
*
389621 TTCACGGGATGTCGCCCA
194 TACACGGGATGTCG-CCA
** * * *
389639 CTGTACAAAGGAAGTCGTCCACTGTACACTGGAAGTCGTCCGATGTACACAGGATGTCATTCA
1 CTGTACAAAGGATCTCGTCCACTGTACACAGGAAGTCGTCCAATGTACACGGGATGTC-TTCA
389702 CTTAACACGG
Statistics
Matches: 229, Mismatches: 42, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
211 11 0.05
212 212 0.93
213 6 0.03
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (210 bp):
CTGTACAAAGGATCTCGTCCACTGTACACAGGAAGTCGTCCAATGTACACGGGATGTCTTCAACT
GTACTCAGGAAGTCGTCCACTGTACACGGGATGTCATCCACTGTACACAGGATATCGTCCACTTG
TACACGGGATGTCGTCCACTGTACACGGGATGTCGTCCACTGTACACAAGAAGTCGTCCACTGTA
CACGGGATGTCGCCA
Found at i:389724 original size:21 final size:21
Alignment explanation
Indices: 389685--389724 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
389675 CGTCCGATGT
*
389685 ACACAGGATGTCATTCACTTA
1 ACACAGGATGTCATCCACTTA
* *
389706 ACACGGGATGTTATCCACT
1 ACACAGGATGTCATCCACT
389725 ATACCCGGGA
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:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
ACACAGGATGTCATCCACTTA
Found at i:391513 original size:10 final size:10
Alignment explanation
Indices: 391498--391522 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
391488 CTTTTATGTT
391498 CTGAAGAAGA
1 CTGAAGAAGA
391508 CTGAAGAAGA
1 CTGAAGAAGA
391518 CTGAA
1 CTGAA
391523 CATTTAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.28, T:0.12
Consensus pattern (10 bp):
CTGAAGAAGA
Found at i:406876 original size:179 final size:179
Alignment explanation
Indices: 406572--407568 Score: 1421
Period size: 179 Copynumber: 5.6 Consensus size: 179
406562 GGCAATCGGT
* * * * *
406572 TTTTGGAACGCAGTTCGCTATTCAATATTTAGAATTCATATTTAGGGCCTGAAATTTTCAGGGTC
1 TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
*
406637 ATCTACAGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATAT-TTAAGGTTTATAG
66 ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATATATT-AGGTTTATAG
*
406701 ACTTGGG-CTCCACTCGTTAAACACCATTCGCAATTGAAAAGTGAACTGCG
130 ACTTGGGCCT-CACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCG
*
406751 TTTTGGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
1 TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
* *
406816 ATCTACTGGTGGTATACAATTACCACTGTGAAAATATCGTAATGGTCATATATTAGGTTTATAGA
66 ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGA
* * **
406881 CTCGGGCCTCACCCGTTAAACACTA-TCGCAATTGAAAAGTGAACTGAA
131 CTTGGGCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCG
* * * **
406929 TTCTAGGACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGAAGCCTGAAATTTTCAGGGTC
1 TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
* * * * *
406994 ATCTACTGGTGGTATACAATTACCACTGTGAAAATATGGTTATAGTCATATATCAGTTTTATAGA
66 ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGA
*
407059 CTTGGGCCTCACTCGTTAAACACTATTTGCAATTGAAAAGTGAACTGCG
131 CTTGGGCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCG
* * * * * * *
407108 TTCTAGAATGCAGTTCGCAATTCAAAATATAAAATTTATTTTTAGGACCTGAAATTTTCAGGGTC
1 TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
** *
407173 ATCTACTAATGGTATACCACTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGA
66 ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGA
* * * *
407238 CTTGGG-CTCCACTCGTCAATCACTATTTGCAATTGAAAAGTGAACTGTG
131 CTTGGGCCT-CACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCG
* * *
407287 TTCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCTGAAATGTTCAGGGTC
1 TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
* *
407352 ATCTACTGGTGGTATACGATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGT
66 ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGA
*
407417 CTTGGGCCTCACTCGTTAAACACTATTCGCAATGGAAAAGTGAACTGCG
131 CTTGGGCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCG
* * * * * *
407466 TTATAGAACGCAGTTCGCAATTCAAAATATAGAA-TAATACTTGGTGACTG-AATTTTTAGGGTC
1 TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
* * ** *
407529 ATCTACTAGTGATATACCATTACCACCATGTAAATATGGT
66 ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGT
407569 GAAAAGGTCA
Statistics
Matches: 732, Mismatches: 81, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
177 45 0.06
178 177 0.24
179 504 0.69
180 6 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (179 bp):
TTTTAGAACGCAGTTCGCAATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTC
ATCTACTGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGA
CTTGGGCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCG
Found at i:407425 original size:358 final size:357
Alignment explanation
Indices: 406577--407568 Score: 1483
Period size: 357 Copynumber: 2.8 Consensus size: 357
406567 TCGGTTTTTG
* * *
406577 GAACGCAGTTCGCTATTCAATATTTAGAATTCATATTTAGGGCCTGAAATTTTCAGGGTCATCTA
1 GAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTCATCTA
* *
406642 CAGGTGGTATACCATTACCACTGTGAAAATATGGTAATGGTCATAT-TTAAGGTTTATAGACTTG
66 CTGGTGGTATACAATTACCACTGTGAAAATATGGTAATGGTCATATATT-AGGTTTATAGACTTG
* * *
406706 GG-CTCCACTCGTTAAACACCATTCGCAATTGAAAAGTGAACTGCGTTTTGGAACGCAGTTCGCA
130 GGCCT-CACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCGTTATAGAACGCAGTTCGCA
* * * *
406770 ATTCAAAATATAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTCATCTACTGGTGGTATACAA
194 ATTCAAAATATAGAATTAATATTTGGGACCTGAAATTTTCAGGGTCATCTACTAGTGGTATACCA
* *
406835 TTACCACTGTGAAAATATCGTAATGGTCATATATTAGGTTTATAGACTCGGGCCTCACCCGTTAA
259 TTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTCGGGCCTCACCCGTCAA
406900 ACACTATCGCAATTGAAAAGTGAACTGAATTCTA
324 ACACTATCGCAATTGAAAAGTGAACTGAATTCTA
* **
406934 GGACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGAAGCCTGAAATTTTCAGGGTCATCTA
1 GAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTCATCTA
* * * *
406999 CTGGTGGTATACAATTACCACTGTGAAAATATGGTTATAGTCATATATCAGTTTTATAGACTTGG
66 CTGGTGGTATACAATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTTGG
* * *
407064 GCCTCACTCGTTAAACACTATTTGCAATTGAAAAGTGAACTGCGTTCTAGAATGCAGTTCGCAAT
131 GCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCGTTATAGAACGCAGTTCGCAAT
* * * * * *
407129 TCAAAATATAAAATTTATTTTTAGGACCTGAAATTTTCAGGGTCATCTACTAATGGTATACCACT
196 TCAAAATATAGAATTAATATTTGGGACCTGAAATTTTCAGGGTCATCTACTAGTGGTATACCATT
* * *
407194 ACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTTGGG-CTCCACTCGTCAAT
261 ACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTCGGGCCT-CACCCGTCAAA
* **
407258 CACTATTTGCAATTGAAAAGTGAACTGTGTTCTA
325 CACTA-TCGCAATTGAAAAGTGAACTGAATTCTA
*
407292 GAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCTGAAATGTTCAGGGTCATCTA
1 GAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTCATCTA
* *
407357 CTGGTGGTATACGATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGTCTTGG
66 CTGGTGGTATACAATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTTGG
*
407422 GCCTCACTCGTTAAACACTATTCGCAATGGAAAAGTGAACTGCGTTATAGAACGCAGTTCGCAAT
131 GCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCGTTATAGAACGCAGTTCGCAAT
* * *
407487 TCAAAATATAGAA-TAATACTTGGTGA-CTG-AATTTTTAGGGTCATCTACTAGTGATATACCAT
196 TCAAAATATAGAATTAATATTTGG-GACCTGAAATTTTCAGGGTCATCTACTAGTGGTATACCAT
** *
407549 TACCACCATGTAAATATGGT
260 TACCACTGTGAAAATATGGT
407569 GAAAAGGTCA
Statistics
Matches: 570, Mismatches: 60, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
356 48 0.08
357 299 0.52
358 223 0.39
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (357 bp):
GAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTTGGGGCCTGAAATTTTCAGGGTCATCTA
CTGGTGGTATACAATTACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTTGG
GCCTCACTCGTTAAACACTATTCGCAATTGAAAAGTGAACTGCGTTATAGAACGCAGTTCGCAAT
TCAAAATATAGAATTAATATTTGGGACCTGAAATTTTCAGGGTCATCTACTAGTGGTATACCATT
ACCACTGTGAAAATATGGTAATGGTCATATATTAGGTTTATAGACTCGGGCCTCACCCGTCAAAC
ACTATCGCAATTGAAAAGTGAACTGAATTCTA
Found at i:415985 original size:164 final size:162
Alignment explanation
Indices: 415662--416510 Score: 609
Period size: 164 Copynumber: 5.3 Consensus size: 162
415652 GTAATAGTGT
* * * * *
415662 ACCCTGAAAATTTCAAGCCCAAAATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCCAGAAT
1 ACCCTAAAAATTTCAGGCCC-CAATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAAC
* * * * *
415727 GCAGTTCACTTTTCAATT-CCAAATAAGCTCG-A-ATCTAAAACGTAGAGATAAGCACTTCAGCA
65 GCAGTTCACTTTTCAATTGCCAAA-AA-CCCGAATATTTAAAAC-TAGAGATGACCACTTCACCA
* * * * *
415789 TATTTTCAAGCTGGTAATGGTATGCGACTAGTAGACG
127 TATATTCAAG-TGGTAATGGTATACAACCAGTAGATG
* * * *
415826 CCCCTGAAAATTTCAGGCCCCAGATATGAATTCTAAATTTTGAATTGCAAACTGCTTTCCAGAAC
1 ACCCTAAAAATTTCAGGCCCCA-ATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAAC
** * * *
415891 GCAGTTCACTTTTCAATTGGGAAAAACCCGAATATTTTAAACTAGAGTTGACCATTTCACCATAT
65 GCAGTTCACTTTTCAATTGCCAAAAACCCGAATATTTAAAACTAGAGATGACCACTTCACCATAT
* * *
415956 ATTCAGAGTGGTAACGGTATACCACTAGTAGATG
130 ATTCA-AGTGGTAATGGTATACAACCAGTAGATG
* * * * * * *
415990 ATCCAAAAAATGTCAGGCTCCAA-AT--A---TGAATTTTGAATTGC-GA--G-ATTCTAGAACG
1 ACCCTAAAAATTTCAGGCCCCAATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAACG
* * * **
416045 CAGTTCACTTTTCAATTGCAAATAAACCGGAAT-CTTAAAAAGAGAGATGACCACTTCACCATAT
66 CAGTTCACTTTTCAATTGCCAA-AAACCCGAATATTTAAAACTAGAGATGACCACTTCACCATAT
* * * **
416109 CTTCAAGGTGGTAATGGTGTACTACCAAAAGATG
130 ATTCAA-GTGGTAATGGTATACAACCAGTAGATG
* * * * * *
416143 ACCCTAAAAATTTCA-G-ACCAA-A--AATTCGAAGTTTTGAATTGCGAATTGTGTTCTAGAACG
1 ACCCTAAAAATTTCAGGCCCCAATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAACG
* * * * * * *
416203 CACTTCA-TGTTTAAATGGCCATTAAACCAGAATA-ATAAAAGTAGAGATGACCACTTCA-C-TA
66 CAGTTCACT-TTTCAATTGCCA-AAAACCCGAATATTTAAAACTAGAGATGACCACTTCACCATA
* * *
416264 -ATTTAGAATGGTAATGATATACAACCAGTAGATG
129 TATTCA-AGTGGTAATGGTATACAACCAGTAGATG
*
416298 ACCCTTAAAATTTCAGGCCCCAAATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAAC
1 ACCCTAAAAATTTCAGGCCCC-AATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAAC
* * ** * ** *
416363 GCAATTCACTTTTCAATTG-CAAATAAGCCCGAATCTCAAAAAGTAGAGAT-ATCTTCATCACCA
65 GCAGTTCACTTTTCAATTGCCAAA-AA-CCCGAATATTTAAAACTAGAGATGA-CCACTTCACCA
* * * * ** *
416426 TATTTTCAAAGTAGCAGT-GTAATATGACTAGTAGATG
127 TATATTC-AAGTGGTAATGGT-ATACAACCAGTAGATG
* * * * *
416463 AACCTGAAAATTTCGGGCCCCAAATACGAATTATAAATTTTGAATTGC
1 ACCCTAAAAATTTCAGGCCCC-AATATGAATTCTAAATTTTGAATTGC
416511 GAAAAAGCCA
Statistics
Matches: 545, Mismatches: 105, Indels: 69
0.76 0.15 0.10
Matches are distributed among these distances:
151 6 0.01
152 2 0.00
153 91 0.17
154 22 0.04
155 39 0.07
156 5 0.01
157 19 0.03
158 57 0.10
159 2 0.00
160 5 0.01
161 53 0.10
162 20 0.04
163 6 0.01
164 142 0.26
165 75 0.14
166 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (162 bp):
ACCCTAAAAATTTCAGGCCCCAATATGAATTCTAAATTTTGAATTGCAAACTGCGTTCTAGAACG
CAGTTCACTTTTCAATTGCCAAAAACCCGAATATTTAAAACTAGAGATGACCACTTCACCATATA
TTCAAGTGGTAATGGTATACAACCAGTAGATG
Found at i:417005 original size:2 final size:2
Alignment explanation
Indices: 417000--417046 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
416990 TTTTCATATA
*
417000 TG TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
417042 TG TG T
1 TG TG T
417047 ACTTTTCTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
TG
Found at i:417422 original size:19 final size:19
Alignment explanation
Indices: 417398--417436 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
417388 AAATTTGAAT
*
417398 TTTAAAACCTTGATGTGCA
1 TTTAAAACCTAGATGTGCA
417417 TTTAAAACCTAGATGTGCA
1 TTTAAAACCTAGATGTGCA
417436 T
1 T
417437 AAGGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (19 bp):
TTTAAAACCTAGATGTGCA
Found at i:418215 original size:3 final size:3
Alignment explanation
Indices: 418175--418200 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
418165 TAGAGCGGGA
418175 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
418201 TACATGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:419165 original size:10 final size:10
Alignment explanation
Indices: 419150--419174 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
419140 GTTCTAATGG
419150 TTCAGTCTTC
1 TTCAGTCTTC
419160 TTCAGTCTTC
1 TTCAGTCTTC
419170 TTCAG
1 TTCAG
419175 AACATAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.28, G:0.12, T:0.48
Consensus pattern (10 bp):
TTCAGTCTTC
Found at i:422722 original size:63 final size:63
Alignment explanation
Indices: 422651--422924 Score: 242
Period size: 64 Copynumber: 4.3 Consensus size: 63
422641 TCGGACGACT
* *
422651 TCCAGTGTACAGTGGACGACTTCCTTTGTACAGTGGGCGACATCCCGTGAACAGTGGACAACA
1 TCCAGTGTACAGTGGACGACTTCCTGTGTACAGTGGACGACATCCCGTGAACAGTGGACAACA
** * * * * *
422714 TCCAGTGTACAGTGGACGACTTCCTGTGCGCAATGGACAACATCCTGTGTACAGTGGACGACA
1 TCCAGTGTACAGTGGACGACTTCCTGTGTACAGTGGACGACATCCCGTGAACAGTGGACAACA
* * * * * * * *
422777 TCCCGTGTACAAGTAGACGATTTCCTGTGTACAGTGGACGACATCCCGTGTATAGAGGACGACT
1 TCCAGTGTAC-AGTGGACGACTTCCTGTGTACAGTGGACGACATCCCGTGAACAGTGGACAACA
* * * * * * * * * * * * *
422841 TCCTGAGTACAAGTTGAAGACATCCCGTATACAATTGACGACTTCCTGTGTACAGTGGACGACA
1 TCCAGTGTAC-AGTGGACGACTTCCTGTGTACAGTGGACGACATCCCGTGAACAGTGGACAACA
**
422905 TCCTTTGTACAGTGGACGAC
1 TCCAGTGTACAGTGGACGAC
422925 ATCCCTTGTA
Statistics
Matches: 171, Mismatches: 39, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
63 71 0.42
64 100 0.58
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (63 bp):
TCCAGTGTACAGTGGACGACTTCCTGTGTACAGTGGACGACATCCCGTGAACAGTGGACAACA
Found at i:422915 original size:64 final size:64
Alignment explanation
Indices: 422624--422929 Score: 233
Period size: 64 Copynumber: 4.8 Consensus size: 64
422614 CTTTAAGTGA
* * * * * ** * *
422624 ACGACATCTTGTGTACA-TCGGACGACTTCCAGTGTAC-AGTGGACGACTTCCTTTGTACAGTGG
1 ACGACATCCTGTGTACAGT-GGACGACATCCTGTGTACAAGTAGACGACATCCCGTATACAATGG
* * * * * * * * ***
422687 GCGACATCCCGTGAACAGTGGACAACATCCAGTGTAC-AGTGGACGACTTCCTGTGCGCAATGG
1 ACGACATCCTGTGTACAGTGGACGACATCCTGTGTACAAGTAGACGACATCCCGTATACAATGG
* * ** * * *
422750 ACAACATCCTGTGTACAGTGGACGACATCCCGTGTACAAGTAGACGATTTCCTGTGTACAGTGG
1 ACGACATCCTGTGTACAGTGGACGACATCCTGTGTACAAGTAGACGACATCCCGTATACAATGG
* * * * * * * *
422814 ACGACATCCCGTGTATAGAGGACGACTTCCTGAGTACAAGTTGAAGACATCCCGTATACAATTG
1 ACGACATCCTGTGTACAGTGGACGACATCCTGTGTACAAGTAGACGACATCCCGTATACAATGG
* * *
422878 ACGACTTCCTGTGTACAGTGGACGACATCCTTTGTAC-AGTGGACGACATCCC
1 ACGACATCCTGTGTACAGTGGACGACATCCTGTGTACAAGTAGACGACATCCC
422930 TTGTACAACG
Statistics
Matches: 196, Mismatches: 45, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
63 95 0.48
64 101 0.52
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (64 bp):
ACGACATCCTGTGTACAGTGGACGACATCCTGTGTACAAGTAGACGACATCCCGTATACAATGG
Found at i:422922 original size:85 final size:84
Alignment explanation
Indices: 422633--422924 Score: 309
Period size: 85 Copynumber: 3.5 Consensus size: 84
422623 AACGACATCT
* * * *
422633 TGTGTACA-TCGGACGACTTCCAGTGTACAGTGGACGACTTCCTTTGTACAGTGGGCGACATCCC
1 TGTGTACAGT-GGACGACATCCTGTGTACAGTGGACGACTTCCTGTGTACAGTGGACGACATCCC
* * * *
422697 GTGA-ACAGTGGACAACATCC
65 GT-ATACAATAGACGACTTCC
* * ** * * *
422717 AGTGTACAGTGGACGACTTCCTGTGCGCAATGGACAACATCCTGTGTACAGTGGACGACATCCCG
1 TGTGTACAGTGGACGACATCCTGTGTACAGTGGACGACTTCCTGTGTACAGTGGACGACATCCCG
* *
422782 TGTACAAGTAGACGATTTCC
66 TATACAA-TAGACGACTTCC
* * * * * *
422802 TGTGTACAGTGGACGACATCCCGTGTATAGAGGACGACTTCCTGAGTACAAGTTGAAGACATCCC
1 TGTGTACAGTGGACGACATCCTGTGTACAGTGGACGACTTCCTGTGTAC-AGTGGACGACATCCC
*
422867 GTATACAATTGACGACTTCC
65 GTATACAATAGACGACTTCC
*
422887 TGTGTACAGTGGACGACATCCTTTGTACAGTGGACGAC
1 TGTGTACAGTGGACGACATCCTGTGTACAGTGGACGAC
422925 ATCCCTTGTA
Statistics
Matches: 169, Mismatches: 35, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
84 58 0.34
85 91 0.54
86 20 0.12
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (84 bp):
TGTGTACAGTGGACGACATCCTGTGTACAGTGGACGACTTCCTGTGTACAGTGGACGACATCCCG
TATACAATAGACGACTTCC
Found at i:422925 original size:21 final size:21
Alignment explanation
Indices: 422619--422936 Score: 289
Period size: 21 Copynumber: 15.0 Consensus size: 21
422609 TGCCCCTTTA
* *
422619 AGTGAACGACATCTTGTGTAC
1 AGTGGACGACATCCTGTGTAC
* *
422640 A-TCGGACGACTTCCAGTGTAC
1 AGT-GGACGACATCCTGTGTAC
* *
422661 AGTGGACGACTTCCTTTGTAC
1 AGTGGACGACATCCTGTGTAC
* * *
422682 AGTGGGCGACATCCCGTGAAC
1 AGTGGACGACATCCTGTGTAC
* *
422703 AGTGGACAACATCCAGTGTAC
1 AGTGGACGACATCCTGTGTAC
* **
422724 AGTGGACGACTTCCTGTGCGC
1 AGTGGACGACATCCTGTGTAC
* *
422745 AATGGACAACATCCTGTGTAC
1 AGTGGACGACATCCTGTGTAC
*
422766 AGTGGACGACATCCCGTGTAC
1 AGTGGACGACATCCTGTGTAC
* **
422787 AAGTAGACGATTTCCTGTGTAC
1 -AGTGGACGACATCCTGTGTAC
* *
422809 AGTGGACGACATCCCGTGTAT
1 AGTGGACGACATCCTGTGTAC
* * *
422830 AGAGGACGACTTCCTGAGTAC
1 AGTGGACGACATCCTGTGTAC
* * * *
422851 AAGTTGAAGACATCCCGTATAC
1 -AGTGGACGACATCCTGTGTAC
* * *
422873 AATTGACGACTTCCTGTGTAC
1 AGTGGACGACATCCTGTGTAC
*
422894 AGTGGACGACATCCTTTGTAC
1 AGTGGACGACATCCTGTGTAC
422915 AGTGGACGACATCCCT-TGTAC
1 AGTGGACGACAT-CCTGTGTAC
422936 A
1 A
422937 ACGGACATGT
Statistics
Matches: 234, Mismatches: 58, Indels: 10
0.77 0.19 0.03
Matches are distributed among these distances:
20 1 0.00
21 198 0.85
22 35 0.15
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
AGTGGACGACATCCTGTGTAC
Found at i:422942 original size:21 final size:21
Alignment explanation
Indices: 422897--422942 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
422887 TGTGTACAGT
* **
422897 GGACGACATCCTTTGTACAGT
1 GGACGACATCCCTTGTACAAC
422918 GGACGACATCCCTTGTACAAC
1 GGACGACATCCCTTGTACAAC
422939 GGAC
1 GGAC
422943 ATGTAAAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (21 bp):
GGACGACATCCCTTGTACAAC
Found at i:428522 original size:15 final size:15
Alignment explanation
Indices: 428502--428532 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
428492 ATATGTACCG
428502 TTATATATTACTATA
1 TTATATATTACTATA
*
428517 TTATATATTATTATA
1 TTATATATTACTATA
428532 T
1 T
428533 GTTACGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTACTATA
Found at i:464294 original size:4 final size:4
Alignment explanation
Indices: 464278--464321 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
464268 CTTTCCTCTG
* * * *
464278 CGTC CGTC AGTC CGTC CGTC TGTC CGTC TGTC TGTC CGTC CGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
464322 TGTCTGTCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.02, C:0.41, G:0.25, T:0.32
Consensus pattern (4 bp):
CGTC
Found at i:464295 original size:12 final size:12
Alignment explanation
Indices: 464278--464325 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
464268 CTTTCCTCTG
*
464278 CGTCCGTCAGTC
1 CGTCCGTCTGTC
464290 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
464302 CGTCTGTCTGTC
1 CGTCCGTCTGTC
464314 CGTCCGTCTGTC
1 CGTCCGTCTGTC
464326 TGTCTGTCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.40, G:0.25, T:0.33
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:464326 original size:4 final size:4
Alignment explanation
Indices: 464295--464333 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
464285 CAGTCCGTCC
* * *
464295 GTCT GTCC GTCT GTCT GTCC GTCC GTCT GTCT GTCT GTC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTC
464334 CCACTTCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41
Consensus pattern (4 bp):
GTCT
Found at i:464332 original size:8 final size:8
Alignment explanation
Indices: 464291--464334 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
464281 CCGTCAGTCC
464291 GTCCGTCT
1 GTCCGTCT
464299 GTCCGTCT
1 GTCCGTCT
* *
464307 GTCTGTCC
1 GTCCGTCT
464315 GTCCGTCT
1 GTCCGTCT
*
464323 GTCTGTCT
1 GTCCGTCT
464331 GTCC
1 GTCC
464335 CACTTCAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39
Consensus pattern (8 bp):
GTCCGTCT
Found at i:468618 original size:21 final size:21
Alignment explanation
Indices: 468592--468644 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
468582 TAATTAACAG
**
468592 CTGATGATAATGTACCAAAAC
1 CTGATGATAACATACCAAAAC
*
468613 CTGATGATAACATACCAACAC
1 CTGATGATAACATACCAAAAC
*
468634 CTGATAATAAC
1 CTGATGATAAC
468645 CAAAGACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (21 bp):
CTGATGATAACATACCAAAAC
Found at i:470330 original size:21 final size:21
Alignment explanation
Indices: 470288--470547 Score: 238
Period size: 21 Copynumber: 12.3 Consensus size: 21
470278 ATAGTGGATA
*
470288 ACATCCTGTGTTA-AGTGAACG
1 ACATCCTGTG-TACAGTGGACG
470309 ACATCCTGTGTACA-TCGGACG
1 ACATCCTGTGTACAGT-GGACG
* * *
470330 ACTTCCAGTGTACAGCGGACG
1 ACATCCTGTGTACAGTGGACG
* *
470351 ACTTCCTTTGTACAGTGGACG
1 ACATCCTGTGTACAGTGGACG
* * *
470372 ACATCCCGTGAACAGTGGACA
1 ACATCCTGTGTACAGTGGACG
*
470393 ACATCCAGTGTACAGTGGACG
1 ACATCCTGTGTACAGTGGACG
* * * * *
470414 ACTTACTGTGTGCAATGGACA
1 ACATCCTGTGTACAGTGGACG
470435 ACATCCTGTGTACAGTGGACG
1 ACATCCTGTGTACAGTGGACG
470456 ACATTCC-GTGTACAAGTGGACG
1 ACA-TCCTGTGTAC-AGTGGACG
**
470478 ATTTCCTGTGTACAGTGGACG
1 ACATCCTGTGTACAGTGGACG
* * *
470499 ACATCCCGCGTATAGTGGACG
1 ACATCCTGTGTACAGTGGACG
* * * *
470520 ACTTCCTGAGTACAAGTTGAAG
1 ACATCCTGTGTAC-AGTGGACG
470542 ACATCC
1 ACATCC
470548 CGTATACAAT
Statistics
Matches: 192, Mismatches: 40, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
20 3 0.02
21 160 0.83
22 29 0.15
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.24
Consensus pattern (21 bp):
ACATCCTGTGTACAGTGGACG
Found at i:470407 original size:63 final size:63
Alignment explanation
Indices: 470291--470521 Score: 270
Period size: 63 Copynumber: 3.7 Consensus size: 63
470281 GTGGATAACA
* * * *
470291 TCCTGTGTTA-AGTGAACGACATCCTGTGTACA-TCGGACGACTTCCAGTGTACAGCGGACGACT
1 TCCTGTG-TACAGTGGACGACATCCCGTGTACAGT-GGACGACATCCAGTGTACAGTGGACGACT
* * *
470354 TCCTTTGTACAGTGGACGACATCCCGTGAACAGTGGACAACATCCAGTGTACAGTGGACGACT
1 TCCTGTGTACAGTGGACGACATCCCGTGTACAGTGGACGACATCCAGTGTACAGTGGACGACT
* * * * * *
470417 TACTGTGTGCAATGGACAACATCCTGTGTACAGTGGACGACATTCC-GTGTACAAGTGGACGATT
1 TCCTGTGTACAGTGGACGACATCCCGTGTACAGTGGACGACA-TCCAGTGTAC-AGTGGACGACT
* *
470481 TCCTGTGTACAGTGGACGACATCCCGCGTATAGTGGACGAC
1 TCCTGTGTACAGTGGACGACATCCCGTGTACAGTGGACGAC
470522 TTCCTGAGTA
Statistics
Matches: 141, Mismatches: 23, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
62 2 0.01
63 91 0.65
64 48 0.34
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (63 bp):
TCCTGTGTACAGTGGACGACATCCCGTGTACAGTGGACGACATCCAGTGTACAGTGGACGACT
Found at i:499935 original size:2 final size:2
Alignment explanation
Indices: 499928--499960 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
499918 TATCATTATC
499928 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
499961 AAATCGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:527100 original size:38 final size:38
Alignment explanation
Indices: 527052--527650 Score: 997
Period size: 38 Copynumber: 15.8 Consensus size: 38
527042 CCCTGTGACA
*
527052 TGTTCATCGTATCTTCTGTATGCCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
* * *
527090 TGTCCATCGTATATTCTGTATACCCACTTGTAGTCATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
527128 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
*
527166 TGTTCATCGTATCTTCTGTATACCCACTTGCAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
* *
527204 TGTTCATCGTATATTCTGTATACCCACTTGTAGTCATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
*
527242 TGTTCATCTTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
* *
527280 TGTCCATCGTATAC-TCTGTATACCCACTTGTAGTCATG
1 TGTTCATCGTAT-CTTCTGTATACCCACTTGTAGACATG
*
527318 TGTTCATCTTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
*
527356 TGTTCATCGTATCTTCTGTATACCAACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
527394 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACAT-
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
527431 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
*
527469 TGTTCATCTTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
*
527507 TGTTCATCGTATCTTCTGTATACCCACTTGAAGACAT-
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
* *
527544 TGTTTATTGTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
527582 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
1 TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
* * *
527620 TGTTCATCGCATTTTTTGTATACCCACTTGT
1 TGTTCATCGTATCTTCTGTATACCCACTTGT
527651 GGACGTGTTA
Statistics
Matches: 523, Mismatches: 34, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
37 72 0.14
38 450 0.86
39 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (38 bp):
TGTTCATCGTATCTTCTGTATACCCACTTGTAGACATG
Found at i:534774 original size:14 final size:14
Alignment explanation
Indices: 534747--534781 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
534737 CCCTTTCATC
534747 AATATATTAAATCA
1 AATATATTAAATCA
* *
534761 AATATCTTATATCA
1 AATATATTAAATCA
534775 AATATAT
1 AATATAT
534782 CTCAAGTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATATTAAATCA
Found at i:541393 original size:27 final size:27
Alignment explanation
Indices: 541353--541434 Score: 146
Period size: 27 Copynumber: 3.0 Consensus size: 27
541343 TTCTTAAAAC
*
541353 CCTGATCCCAATATTATATACACTTTG
1 CCTGATCCCGATATTATATACACTTTG
*
541380 CCTGATCCCGATATTAAATACACTTTG
1 CCTGATCCCGATATTATATACACTTTG
541407 CCTGATCCCGATATTATATACACTTTG
1 CCTGATCCCGATATTATATACACTTTG
541434 C
1 C
541435 TAAAAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (27 bp):
CCTGATCCCGATATTATATACACTTTG
Found at i:556805 original size:2 final size:2
Alignment explanation
Indices: 556798--556844 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
556788 TTTCTTTCTT
556798 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
556840 TC TC T
1 TC TC T
556845 TTTTTTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:561395 original size:25 final size:25
Alignment explanation
Indices: 561367--561415 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
561357 ATGAAACAAT
* *
561367 ATTGAAGAATATTATATAATATTGC
1 ATTGAAGAATATGATAAAATATTGC
*
561392 ATTGAATAATATGATAAAATATTG
1 ATTGAAGAATATGATAAAATATTG
561416 ATATTGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (25 bp):
ATTGAAGAATATGATAAAATATTGC
Found at i:569964 original size:166 final size:166
Alignment explanation
Indices: 569563--570873 Score: 1509
Period size: 166 Copynumber: 7.9 Consensus size: 166
569553 AAAAACTTGT
* * * *
569563 GTGGAGGCATCATCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAG
1 GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
*
569628 GGGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
66 GGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
* *
569693 CTCCAAAAAACTATCAGGCCAGAAAATCTCAAATTATAA
131 CT-C-AAAAACTATTAGGCCAGAAAAGCTCAAATTA-AA
* * * * *
569732 -TGGGAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTGAAATCATGGTTCCCGGGGGTATGGTG
1 GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
* *
569796 GGGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAGAGAACATCTTTAAAAATCTTCTT
66 GGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
569861 CTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
131 CTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
* *
569897 ATGGAAGCATCCTCAGGA-AGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGT
1 GTGGAAGCATCCTCA-GATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGT
* * * * *
569961 GGGGGCACAATTTGGGGATCATGTTTTACATAGGAATATACAGAGAAAAATCTTTAAAATTCTTC
65 GGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAG-AAAATCTTTAAAAATCTTC
* * * * **
570026 TTCTCAAAAACTATCAGGCCTGGAAAGCTCAACTTTGA
129 TTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
* *
570064 GTGGAAGCATCCTTAGATAGTGTAGATTCAAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTG
1 GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
* * *
570129 GGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAAAGAAAATCTTTAAAAATCTTTTT
66 GGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
*
570194 CTAAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
131 CTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
* * * * *
570230 ATGGAAGCATCCTCAGATGGTGTAGATTCACGTTTGTTCAAATTATAGTCCCCGGGGGTAGGGTG
1 GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
* * * * * *
570295 GGGCAACAATTGGGGGATCAATTTTTACATAGGAATATAAATAGATAATCTTTAAGAATCTTCTT
66 GGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
* *
570360 CTCAAAAACTTTTAGGCCA-AGAAAGCTCAAATTTAA
131 CTCAAAAACTATTAGGCCAGA-AAAGCTCAAATTAAA
*
570396 GTGGAAGCATCCTCAGATAGTGTAGATTCAGGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGT-
1 GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
** * * ** *
570460 GGGCCACAATTATGGGATAAATTTTTTTATAGGAATATAAAGAGAAAATCTTTTAAAAAAT-TTC
66 GGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC-TTT-AAAAATCTTC
* * * ***
570524 TT-TTAAAAACTATTTGGCTA-AGAAAGCTCAAATTGGC
129 TTCTCAAAAACTATTAGGCCAGA-AAAGCTCAAATTAAA
* * * *
570561 GTGTAACCATCCTCAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGCG-
1 GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGG-GT
* * *
570625 GGACCGACCACAA-TGGGGGAT-ACA-TTTT---T---TATATATAGAG-AAATCTTTAAAAGTC
65 GG---GGCCACAATTGGGGGATCA-AGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATC
* **
570680 TTCTTCTC-AAAACTATTAGGCCAGGAAAG-TCCAAATTTGA
126 TTCTTCTCAAAAACTATTAGGCCAGAAAAGCT-CAAATTAAA
* * * * * * * * *
570720 GTGGAGGCATCCCCATATCA-TATAGATTCAAGTTTGTTTAAATAATAGT--CCAGGGGTGGGGT
1 GTGGAAGCATCCTCAGAT-AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGT
* * * * *
570782 GAGGCCACAA-TGGGGGATGAATTTTTACTTAGGAATATATAGAGAAAATCTTTCAAAATCTTCT
65 GGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCT
* * * * *
570846 TTTTAAAGACTATTTGGACAGAAAAGCT
130 TCTCAAAAACTATTAGGCCAGAAAAGCT
570874 TAAACTTGTG
Statistics
Matches: 987, Mismatches: 125, Indels: 65
0.84 0.11 0.06
Matches are distributed among these distances:
154 16 0.02
155 5 0.01
156 1 0.00
157 9 0.01
158 7 0.01
159 70 0.07
160 7 0.01
161 19 0.02
162 19 0.02
163 17 0.02
164 2 0.00
165 130 0.13
166 391 0.40
167 157 0.16
168 130 0.13
169 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (166 bp):
GTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
GGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
CTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA
Found at i:570188 original size:333 final size:330
Alignment explanation
Indices: 569564--570873 Score: 1518
Period size: 333 Copynumber: 4.0 Consensus size: 330
569554 AAAACTTGTG
* * * * *
569564 TGGAGGCATCATCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGG
1 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTGG
* *
569629 GGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTC
66 GGCCACAATTGGGGGATC-ATTTTTACATAGGAATATATAGAGAAAATCTTT-AAAATCTTCTTC
* * * * *
569694 TCCAAAAAACTATCAGGCCAGAAAATCTCAAATTAT-AATGGGAGCATCCTCAGGTAGTGTAGAT
129 T-C-AAAAACTATCAGGCCAGGAAAGCTCAAATT-TGAGTGGAAGCATCCTCAGATAGTGTAGAT
* * * **
569758 TCAAGTTTGTTGAAATCATGGTTCCCGGGGGTATGGTGGGGCCACAATTTGGGGATCAAGTTTTA
191 TCAAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTA
* * *
569823 CATAGGAATATATAGAGAACATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCT
256 CATAGGAATATATAAAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAAGCT
569888 CAAATTAAAA
321 CAAATTAAAA
569898 TGGAAGCATCCTCAGGA-AGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTG
1 TGGAAGCATCCTCA-GATAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTG
* * *
569962 GGGGCACAATTTGGGGATCATGTTTTACATAGGAATATACAGAGAAAAATCTTTAAAATTCTTCT
65 GGGCCACAATTGGGGGATCAT-TTTTACATAGGAATATATAGAG-AAAATCTTTAAAA-TCTTCT
* * *
570027 TCTCAAAAACTATCAGGCCTGGAAAGCTCAACTTTGAGTGGAAGCATCCTTAGATAGTGTAGATT
127 TCTCAAAAACTATCAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTAGATT
570092 CAAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTAC
192 CAAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTAC
* *
570157 ATAGGAATATATAAAGAAAATCTTTAAAAATCTTTTTCTAAAAAACTATTAGGCCAGAAAAGCTC
257 ATAGGAATATATAAAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAAGCTC
570222 AAATTAAAA
322 AAATTAAAA
* * *
570231 TGGAAGCATCCTCAGATGGTGTAGATTCACGTTTGTTCAAATTATA-GTCCCCGGGGGTAGGGTG
1 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCA-AGGTCCCCGGGGGTAGGGTG
* * * *
570295 GGGCAACAATTGGGGGATCAATTTTTACATAGGAATATAAATAGATAATCTTTAAGAATCTTCTT
65 GGGCCACAATTGGGGGATC-ATTTTTACATAGGAATATATAGAGAAAATCTTTAA-AATCTTCTT
* * * *
570360 CTCAAAAACTTTTAGGCCAAGAAAGCTCAAATTTAAGTGGAAGCATCCTCAGATAGTGTAGATTC
128 CTCAAAAACTATCAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTAGATTC
* * * * * **
570425 AGGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGT-GGGCCACAATTA-TGGGATAAATTTTTTT
193 AAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-TAGGGGGATCAAGTTTTAC
* *
570488 ATAGGAATATA-AAGAGAAAATCTTTTAAAAAAT-TTCTT-TTAAAAACTATTTGGCTA-AGAAA
257 ATAGGAATATATAA-AGAAAATC-TTT-AAAAATCTTCTTCTTAAAAACTATTAGGCCAGA-AAA
****
570549 GCTCAAATTGGCG
318 GCTCAAATTAAAA
* * * * *
570562 TGTAACCATCCTCAGATAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGCG-G
1 TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGG-GTG
*
570626 GACCGACCACAA-TGGGGGATACATTTTT---T----ATATATAGAG-AAATCTTTAAAAGTCTT
65 G---GGCCACAATTGGGGGAT-CATTTTTACATAGGAATATATAGAGAAAATCTTTAAAA-TCTT
* * * * *
570682 CTTCTC-AAAACTATTAGGCCAGGAAAG-TCCAAATTTGAGTGGAGGCATCCCCATATCA-TATA
125 CTTCTCAAAAACTATCAGGCCAGGAAAGCT-CAAATTTGAGTGGAAGCATCCTCAGAT-AGTGTA
* * * * * * * *
570744 GATTCAAGTTTGTTTAAATAATAGT--CCAGGGGTGGGGTGAGGCCACAAT-GGGGGATGAATTT
188 GATTCAAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTT
* * * * * * *
570806 TTACTTAGGAATATATAGAGAAAATCTTTCAAAATCTTCTTTTTAAAGACTATTTGGACAGAAAA
253 TTACATAGGAATATATAAAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAA
570871 GCT
318 GCT
570874 TAAACTTGTG
Statistics
Matches: 854, Mismatches: 93, Indels: 70
0.84 0.09 0.07
Matches are distributed among these distances:
320 5 0.01
321 8 0.01
322 63 0.07
323 11 0.01
324 68 0.08
325 20 0.02
326 8 0.01
330 4 0.00
331 120 0.14
332 121 0.14
333 296 0.35
334 111 0.13
335 19 0.02
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (330 bp):
TGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTGG
GGCCACAATTGGGGGATCATTTTTACATAGGAATATATAGAGAAAATCTTTAAAATCTTCTTCTC
AAAAACTATCAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGATAGTGTAGATTCAAG
TTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAG
GAATATATAAAGAAAATCTTTAAAAATCTTCTTCTTAAAAACTATTAGGCCAGAAAAGCTCAAAT
TAAAA
Found at i:570645 original size:499 final size:495
Alignment explanation
Indices: 569583--570873 Score: 1559
Period size: 499 Copynumber: 2.6 Consensus size: 495
569573 CATCAGGTAG
*
569583 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAATTTGGGGATCA
1 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAA-TGGGGGATCA
* *
569648 AGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCCAAAAAACTATCAGGCC
65 AGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTT-TT-TCTAAAAAACTATTAGGCC
* * * * * * *
569713 AGAAAATCTCAAATTATAATGGGAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTGAAATCATG
128 AGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATAATA
* * *
569778 GTTCCCGGGGGTATGGTGGGGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAGAGAAC
193 G-TCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAATTTTTACATAGGAATATATAGAGAA-
569843 ATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATC
256 ATCTTT-AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATC
*
569908 CTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTGGGGGCACAATT
320 CTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTGGGGCCACAATT
* * *
569973 TGGGGATCATGTTTTACATAGGAATATACAGAGAAAAATCTTTAAAATTCTTCTTCTCAAAAACT
385 TGGGGATAATGTTTTACATAGGAATATAAAGAGAAAAATCTTTAAAAATCTTCTTCTCAAAAACT
* * * * * *
570038 ATCAGGCCTGGAAAGCTCAACTTTGAGTGGAAGCATCCTTAGATAG
450 ATCAGGCCTAGAAAGCTCAAATTGGAGTGGAACCATCCTCAGATAA
* *
570084 TGTAGATTCAAGTTTGTTAAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATAGGGGGATCA
1 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAAT-GGGGGATCA
*
570149 AGTTTTACATAGGAATATATAAAGAAAATCTTTAAAAATCTTTTTCTAAAAAACTATTAGGCCAG
65 AGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTTTTCTAAAAAACTATTAGGCCAG
* * *
570214 AAAAGCTCAAATTAAAATGGAAGCATCCTCAGATGGTGTAGATTCACGTTTGTTCAAATTATAGT
130 AAAAGCTCAAATTAAAATGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATAATAGT
* * *
570279 CCCCGGGGGTAGGGTGGGGCAACAATTGGGGGATCAATTTTTACATAGGAATATAAATAGATAAT
195 -CCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAATTTTTACATAGGAATATATAGAGA-AAT
* * *
570344 CTTTAAGAATCTTCTTCTCAAAAACTTTTAGGCCA-AGAAAGCTCAAATTTAAGTGGAAGCATCC
258 CTTTAA-AATCTTCTTCTCAAAAACTATTAGGCCAGA-AAAGCTCAAATTAAAATGGAAGCATCC
* *
570408 TCA-GATAGTGTAGATTCAGGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGT-GGGCCACAATT
321 TCAGGA-AGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTGGGGCCACAATT
** *
570471 AT-GGGATAAAT-TTTTTTATAGGAATATAAAGAG-AAAATCTTTTAAAAAAT-TTCTT-TTAAA
385 -TGGGGAT-AATGTTTTACATAGGAATATAAAGAGAAAAATC-TTT-AAAAATCTTCTTCTCAAA
** * *
570531 AACTATTTGG-CTAAGAAAGCTCAAATTGGCGTGTAACCATCCTCAGATAA
446 AACTATCAGGCCT-AGAAAGCTCAAATTGGAGTGGAACCATCCTCAGATAA
* *
570581 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGCG-GGACCGACCACAATGGGGGA
1 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGG-GAGG---GGCCACAATGGGGGA
* * * *
570645 T-ACA-TTTT---T---TATATATAGAG-AAATCTTTAAAAGTCTTCTTCT-CAAAACTATTAGG
62 TCA-AGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTTTTCTAAAAAACTATTAGG
* ** * * * * * *
570700 CCAGGAAAG-TCCAAATTTGAGTGGAGGCATCCCCATATCA-TATAGATTCAAGTTTGTTTAAAT
126 CCAGAAAAGCT-CAAATTAAAATGGAAGCATCCTCAGAT-AGTGTAGATTCAAGTTTGTTCAAAT
* * * * *
570763 AATAGT-CCAGGGGTGGGGTGAGGCCACAA-TGGGGGATGAATTTTTACTTAGGAATATATAGAG
189 AATAGTCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAATTTTTACATAGGAATATATAGAG
* * * * *
570826 AAAATCTTTCAAAATCTTCTTTTTAAAGACTATTTGGACAGAAAAGCT
254 -AAATCTTT-AAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCT
570874 TAAACTTGTG
Statistics
Matches: 692, Mismatches: 77, Indels: 56
0.84 0.09 0.07
Matches are distributed among these distances:
487 65 0.09
488 23 0.03
489 1 0.00
490 66 0.10
491 20 0.03
492 9 0.01
495 1 0.00
496 2 0.00
497 89 0.13
498 54 0.08
499 249 0.36
500 12 0.02
501 101 0.15
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (495 bp):
TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAATGGGGGATCAA
GTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTTTTCTAAAAAACTATTAGGCCAGA
AAAGCTCAAATTAAAATGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATAATAGTC
CCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAATTTTTACATAGGAATATATAGAGAAATCTT
TAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
AAGTGTAGATTCAAGTTTGTTCAAATCAAGGTCCCCGGGGGTAGGGTGGGGCCACAATTTGGGGA
TAATGTTTTACATAGGAATATAAAGAGAAAAATCTTTAAAAATCTTCTTCTCAAAAACTATCAGG
CCTAGAAAGCTCAAATTGGAGTGGAACCATCCTCAGATAA
Found at i:582698 original size:14 final size:14
Alignment explanation
Indices: 582681--582725 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
582671 TTCATTCAAT
*
582681 ATTCAAAATTCGAG
1 ATTCGAAATTCGAG
*
582695 ATTCGAAATACGAG
1 ATTCGAAATTCGAG
582709 ATTCGAAATTCGAG
1 ATTCGAAATTCGAG
582723 ATT
1 ATT
582726 AAATATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (14 bp):
ATTCGAAATTCGAG
Found at i:604700 original size:170 final size:166
Alignment explanation
Indices: 604300--605112 Score: 933
Period size: 172 Copynumber: 4.8 Consensus size: 166
604290 CCCACATTTG
* * * *
604300 TGGGAGTAGAGAAGAATATTTTTTAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * * * * * * *
604365 CCCTAGATCCTGAACCCCTTATAAAGGGGTCATGAATTTCACAATTTTGGTAGAAGGCTTTATGG
66 CCCTAGAGCCTGAA-CCCTGACACAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGG
* * *
604430 ACATTATAACCAGGCATTTAGTTTTTAACAAATTTATA
130 ACATTATAATCATGCATTTAGTTTTTAAC-AATATATA
* *
604468 TGGGAGTAGAGAAGAAGATTCTT-TTA-ATTTAATACATTTTTACTATATGGCCATACTGGCCCC
1 TGGGAGTAGAGAAGAAGATT-TTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
* * * * *
604531 ACCCTAGACCCTGAA-CCTGACACTGGGGTCATGTATTTTACAATTTTAGTAGATGGCCTCATGG
65 ACCCTAGAGCCTGAACCCTGACACAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGG
* *
604595 ACATAATGGACATAATCATGCATTGAGTTTTTAACAA-ATGTA
130 ACAT--T----ATAATCATGCATTTAGTTTTTAACAATATATA
* *
604637 TGGGAGTAGAGAAGAAGATTTTCTCAGATTTAATACATTTTTACTATATGGCAATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
604702 CCCTAGAGCCTGAACCCCTGATC-CAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATG
66 CCCTAGAGCCTGAA-CCCTGA-CACAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATG
* *
604766 CACATCATAATCATGCATTTAGTTTTTAACACATATATA
129 GACATTATAATCATGCATTTAGTTTTTAACA-ATATATA
* * * **
604805 TTTGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTAACTATTTGGTTATATTGGTCG
1 --TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGG-C-
* * * * * * *
604870 GCCGCCTTATAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGTACAGGGCTT
62 CCCACCCTAGAGCCTGAA-CCCTGACACAGGGGTCATGAATTTCACAATTTTA-GTAGAGGGCCT
* * **
604934 CATGGGCATTATAATCATGCATATAAATTTTAACAAATATATA
125 CATGGACATTATAATCATGCATTTAGTTTTTAAC-AATATATA
*
604977 TGGGAGTAAAGAA-AA-ATATTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
1 TGGGAGTAGAGAAGAAGAT-TTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
* * *
605040 A-CCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATATTAGTAGAGGGCCGTTAT
65 ACCCTAGAGCCTGAA-CCCTGACACAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCC-TCAT
605104 GGACATTAT
128 GGACATTAT
605113 TACAATAAAA
Statistics
Matches: 555, Mismatches: 66, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
165 43 0.08
166 73 0.13
167 66 0.12
168 30 0.05
169 65 0.12
170 117 0.21
171 27 0.05
172 132 0.24
173 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (166 bp):
TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
CCCTAGAGCCTGAACCCTGACACAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGGA
CATTATAATCATGCATTTAGTTTTTAACAATATATA
Found at i:604888 original size:172 final size:168
Alignment explanation
Indices: 604300--605098 Score: 943
Period size: 170 Copynumber: 4.7 Consensus size: 168
604290 CCCACATTTG
* * * *
604300 TGGGAGTAGAGAAGAATATTTTTTAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * *** * * * * *
604365 CCCTAGATCCTGAACCCCTTATAAAGGGGTCATGAATTTCACAATTTTGGTAGAAGGCTTTATGG
66 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGC
* * * *
604430 ACATTATAACCAGGCATTTAGTTTTTAACAAATTTATA
131 ACATCATAATCATGCATTTAGTTTTTAACAAATATATA
* *
604468 TGGGAGTAGAGAAGAAGATTCTT-TTA-ATTTAATACATTTTTACTATATGGCCATACTGGCCCC
1 TGGGAGTAGAGAAGAAGATT-TTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
* * * * * *
604531 ACCCTAGACCCTGAA--CCTGACACTGGGGTCATGTATTTTACAATTTTAGTAGATGGCCTCATG
65 ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCAT-
* * *
604594 GACATAATGGACATAATCATGCATTGAGTTTTTAAC-AA-ATGTA
129 G-CA-CAT---CATAATCATGCATTTAGTTTTTAACAAATATATA
* *
604637 TGGGAGTAGAGAAGAAGATTTTCTCAGATTTAATACATTTTTACTATATGGCAATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
*
604702 CCCTAGAGCCTGAACCCCTGATCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGC
66 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGC
*
604767 ACATCATAATCATGCATTTAGTTTTTAACACATATATATT
131 ACATCATAATCATGCATTTAGTTTTTAACA-A-ATATATA
* * * ** *
604807 TGGGAGTAGAGAAGAAGATTTTCTAAGATTAAATACATTTTAACTATTTGGTTATATTGGTCGGC
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGG-C-CC
* * * * *
604872 CGCCTTATAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGTACAGGGCTTCA
64 CACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGGGCCTCA
** * * **
604936 TGGGCATTATAATCATGCATATAAATTTTAACAAATATATA
128 TGCACATCATAATCATGCATTTAGTTTTTAACAAATATATA
*
604977 TGGGAGTAAAGAA-AA-ATATTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
1 TGGGAGTAGAGAAGAAGAT-TTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC
*
605040 A-CCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATATTAGTAGAGGGCC
65 ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCC
605099 GTTATGGACA
Statistics
Matches: 540, Mismatches: 71, Indels: 42
0.83 0.11 0.06
Matches are distributed among these distances:
165 37 0.07
166 74 0.14
167 54 0.10
168 29 0.05
169 68 0.13
170 128 0.24
171 28 0.05
172 122 0.23
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (168 bp):
TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTAGTAGAGGGCCTCATGC
ACATCATAATCATGCATTTAGTTTTTAACAAATATATA
Found at i:608104 original size:75 final size:75
Alignment explanation
Indices: 607981--608132 Score: 241
Period size: 75 Copynumber: 2.0 Consensus size: 75
607971 GGTTGGCTGT
* *
607981 GAGACAGGTGGTGATGAGAGAGGGAGCACAGGCACTGCAGCCGACACAGATGGCATGGATGGCAT
1 GAGACAGGCGGTGATAAGAGAGGGAGCACAGGCACTGCAGCCGACACAGATGGCATGGATGGCAT
608046 GGCTGACTGG
66 GGCTGACTGG
* ** *
608056 GAGACAGGCGGTGATAAGAGAGGGAGTATGGGCACTGCAGCTGACACAGATGGCATGGATGGCAT
1 GAGACAGGCGGTGATAAGAGAGGGAGCACAGGCACTGCAGCCGACACAGATGGCATGGATGGCAT
*
608121 GGCTGGCTGG
66 GGCTGACTGG
608131 GA
1 GA
608133 CTTCTTGGGA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.26, C:0.17, G:0.42, T:0.14
Consensus pattern (75 bp):
GAGACAGGCGGTGATAAGAGAGGGAGCACAGGCACTGCAGCCGACACAGATGGCATGGATGGCAT
GGCTGACTGG
Found at i:609754 original size:47 final size:46
Alignment explanation
Indices: 609674--609801 Score: 143
Period size: 47 Copynumber: 2.8 Consensus size: 46
609664 TCAACCCTGG
** * *
609674 TGAGGGCCATAGACTGCACACCTCCGTCACCTCCCAACATCAGAAG-
1 TGAGGGCCATAGACTGTGCACATCCGTCACCTCCCAACACCA-AAGA
* * * *
609720 TGTGGGCCATAGA-TGGTGCACAATCCGTCTCCTCCCATCACCAATGA
1 TGAGGGCCATAGACT-GTGCAC-ATCCGTCACCTCCCAACACCAAAGA
609767 TGAGGGCCATAGACTGTGCACATCCGTCACCTCCC
1 TGAGGGCCATAGACTGTGCACATCCGTCACCTCCC
609802 TCCACCTGAC
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
45 1 0.01
46 31 0.46
47 35 0.51
48 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.21, T:0.20
Consensus pattern (46 bp):
TGAGGGCCATAGACTGTGCACATCCGTCACCTCCCAACACCAAAGA
Found at i:619011 original size:88 final size:88
Alignment explanation
Indices: 618862--619037 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
618852 GACTATGAAC
*
618862 ACGAGGCACGATTTTTACTGCGAAACTGAAAGGGTCAAATAAAACCACGTGGTCTAAAATTTAAA
1 ACGAGGCACGATTTTTAATGCGAAACTGAAAGGGTCAAATAAAACCACGTGGTCTAAAATTTAAA
*
618927 TGTCAATAACATTCGCAGGGGTG
66 TGACAATAACATTCGCAGGGGTG
*
618950 ACGAGGCACGATTTTTAATGCGAAACTGAAAGGGTCAAATAAAATCACGTGGTCTAAAATTTAAA
1 ACGAGGCACGATTTTTAATGCGAAACTGAAAGGGTCAAATAAAACCACGTGGTCTAAAATTTAAA
619015 TGACAATAACATTCGCAGGGGTG
66 TGACAATAACATTCGCAGGGGTG
619038 TATAAGGTTG
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (88 bp):
ACGAGGCACGATTTTTAATGCGAAACTGAAAGGGTCAAATAAAACCACGTGGTCTAAAATTTAAA
TGACAATAACATTCGCAGGGGTG
Found at i:621059 original size:146 final size:145
Alignment explanation
Indices: 620640--621107 Score: 564
Period size: 145 Copynumber: 3.2 Consensus size: 145
620630 CTCAATTGAT
* * * * * * *
620640 CTTGGGTCAAGGTCATGACACCCCCTCAGGTTATAAGCAATCTTTATGTGAATTAAGAACTTCCA
1 CTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTTTGAAGTAAGAACTTTCA
* * * * * * *
620705 ATATTTGTCCATAATAAAGATATGGA-CTGAACATGCATTTTGCAC-TTTTCTGCCAGTGCCCTT
66 ATGTTTCTCCATAAGAAAGATATGGACCAG-ACACG-AATTTGCACTTTTTCTGCCAGTGACCTT
620768 GACCTTGCCCGAATGAC
129 GACCTTGCCCGAATGAC
** * ** * * *
620785 CAAGGGTCAAGGTCATGACACACTCTTTTGTCATAAGCATTCTTTGTTTGAAGTGA-AACATTCA
1 CTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTTTGAAGTAAGAACTTTCA
* *
620849 ATGCTTCTCCATAAGAAAGATATGGACCGGACACGAATTTGGCACTTTTTCTGCCAGTGACCTTG
66 ATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTT-GCACTTTTTCTGCCAGTGACCTTG
**
620914 ACCTTGCCTAAATGAC
130 ACCTTGCCCGAATGAC
* *
620930 CTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTCGTTTGAAGTCAGAACTTTCA
1 CTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTTTGAAGTAAGAACTTTCA
* * *
620995 ATGTTTTTCCATAAGAAAAATATGGACCAGACACGAATTCTGCACTTTTTCTGCCAGTGGCCTTG
66 ATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATT-TGCACTTTTTCTGCCAGTGACCTTG
621060 ACCTTGCCCGAATGAC
130 ACCTTGCCCGAATGAC
* * * *
621076 CTTGGTTTAAGGTCATGATACACACTTAGGTC
1 CTTGGGTCAAGGTCATGACACACCCTTAGGTC
621108 TAAATCAACA
Statistics
Matches: 273, Mismatches: 45, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
143 4 0.01
144 36 0.13
145 125 0.46
146 107 0.39
147 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (145 bp):
CTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTTTGAAGTAAGAACTTTCA
ATGTTTCTCCATAAGAAAGATATGGACCAGACACGAATTTGCACTTTTTCTGCCAGTGACCTTGA
CCTTGCCCGAATGAC
Found at i:633862 original size:21 final size:21
Alignment explanation
Indices: 633838--633884 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
633828 AAGCTTCACC
*
633838 CGTAAACCAATCCCCAAACCG
1 CGTAAACCAATCCCAAAACCG
*
633859 CGTAAACCAATCCCAAAACCT
1 CGTAAACCAATCCCAAAACCG
633880 CGTAA
1 CGTAA
633885 GAATATAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.38, G:0.09, T:0.13
Consensus pattern (21 bp):
CGTAAACCAATCCCAAAACCG
Found at i:635815 original size:32 final size:31
Alignment explanation
Indices: 635771--635863 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
635761 AATGACCGGG
* *
635771 GGTCATTTTTCTACGTAGAATAATGACCCCC
1 GGTCATTATTCTACGTAGAAAAATGACCCCC
*
635802 TGGTCATTATTCTACGCAGAAAAATGACCCCC
1 -GGTCATTATTCTACGTAGAAAAATGACCCCC
635834 GGTCATTATTCTACGTAGAAAAATGACCCC
1 GGTCATTATTCTACGTAGAAAAATGACCCC
635864 TTTGCCTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 29 0.51
32 28 0.49
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (31 bp):
GGTCATTATTCTACGTAGAAAAATGACCCCC
Found at i:637136 original size:16 final size:16
Alignment explanation
Indices: 637117--637151 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
637107 TCACCGAGAC
637117 GAGGCATCACCTTTAT
1 GAGGCATCACCTTTAT
637133 GAGGCATCACCTTTAT
1 GAGGCATCACCTTTAT
637149 GAG
1 GAG
637152 ACCACCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (16 bp):
GAGGCATCACCTTTAT
Found at i:637159 original size:14 final size:16
Alignment explanation
Indices: 637117--637162 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
637107 TCACCGAGAC
*
637117 GAGGCATCACCTTTAT
1 GAGGCACCACCTTTAT
*
637133 GAGGCATCACCTTTAT
1 GAGGCACCACCTTTAT
637149 GA-G-ACCACCTTTAT
1 GAGGCACCACCTTTAT
637163 CATATTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 18 0.62
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (16 bp):
GAGGCACCACCTTTAT
Found at i:638740 original size:168 final size:164
Alignment explanation
Indices: 638433--638754 Score: 459
Period size: 168 Copynumber: 1.9 Consensus size: 164
638423 GAACTGCAAA
* * **
638433 TAACTGGAATTTTTTCTATGTCCAAGGGGTATAACTCTGTCGAAAATTGCTCGATCGTACCCAAT
1 TAACTAGAATTTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAAT
*
638498 ATCGTGACCTAGATACTATCATGATAAACCTGTATACACAATTTCATTCCAATATGTTTATCCTC
66 ATCGTGACCTAGATACTATCATGATAAACCTGTATACACAATTTCATTCCAATATGTTCATCCTC
* *
638563 TGTGAAGAAAAATGAGCGAAAACTGCAAATACATG
131 TGCGAAG-AAAATGAACGAAAACTGCAAATACATG
*
638598 TAACTAGAA-TTTTTCTACGTCCAAGGGCCATAGCTCTGTCGAAAATTGCTCGATCGTACCCAAT
1 TAACTAGAATTTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAAT
* **
638662 ATCGAACTTGACCTAGATATTATCATGATAAACCTGTATAC-CAAATTTCATTTGAATATGTTCA
66 ATCG----TGACCTAGATACTATCATGATAAACCTGTATACAC-AATTTCATTCCAATATGTTCA
* *
638726 TCTTCTGCGAAGAAAATGAACGGAAACTG
126 TCCTCTGCGAAGAAAATGAACGAAAACTG
638755 TTAGTGGGCA
Statistics
Matches: 139, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
164 55 0.40
165 8 0.06
167 16 0.12
168 60 0.43
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (164 bp):
TAACTAGAATTTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGCTCGATCGTACCCAAT
ATCGTGACCTAGATACTATCATGATAAACCTGTATACACAATTTCATTCCAATATGTTCATCCTC
TGCGAAGAAAATGAACGAAAACTGCAAATACATG
Found at i:639877 original size:176 final size:177
Alignment explanation
Indices: 639559--639888 Score: 439
Period size: 176 Copynumber: 1.9 Consensus size: 177
639549 CATTATCCAG
*
639559 CATCCGAAACCTATGGCTCAGACTCAGCATTCAAACCTGTCAAGTGCACCAGTATCATAAGACGC
1 CATCCGAAACCTATGGCTCAGACTCAGCATTCAAACCTGCCAAGTGCACCAGTATCATAAGACGC
** ** *
639624 ACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTGATAACTAAGAAATCATCATCAGAGGGCAC
66 ACCATCCATACAAGTCTAATGAAGTTAGGACAAGTGATAACTAAGAAATAATCATCAGAGGGCAC
***
639689 CTGTTTCAAAAACTTTAACCAGCTCTTAAAATCTTAACCTCCTCTAT
131 CTGCAACAAAAACTTTAACCAGCTCTTAAAATCTTAACCTCCTCTAT
* * * * ** * * *
639736 CATCCG-AACCTGTGGTTCAGATTCAGCATTTAGGCCTGCCAGGTGCATCGGTATCATAAGACGC
1 CATCCGAAACCTATGGCTCAGACTCAGCATTCAAACCTGCCAAGTGCACCAGTATCATAAGACGC
* * * *
639800 ACCATCCATACAAGTTTAATGAAGTTAGGACCAGT-AGTAACTAAGATATAATCATTAGAGGGCA
66 ACCATCCATACAAGTCTAATGAAGTTAGGACAAGTGA-TAACTAAGAAATAATCATCAGAGGGCA
639864 CCTGCAACAAAAACTTTAACCAGCT
130 CCTGCAACAAAAACTTTAACCAGCT
639889 TCAAAAACCT
Statistics
Matches: 130, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
175 1 0.01
176 123 0.95
177 6 0.05
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (177 bp):
CATCCGAAACCTATGGCTCAGACTCAGCATTCAAACCTGCCAAGTGCACCAGTATCATAAGACGC
ACCATCCATACAAGTCTAATGAAGTTAGGACAAGTGATAACTAAGAAATAATCATCAGAGGGCAC
CTGCAACAAAAACTTTAACCAGCTCTTAAAATCTTAACCTCCTCTAT
Found at i:640265 original size:22 final size:22
Alignment explanation
Indices: 640236--640289 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
640226 GGTGAGCTAA
640236 AAAGGCGAAAGCGCGAAGATT-C
1 AAAGGCGAAAGCGCGAA-ATTGC
* * *
640258 GAAGGCGAGAGTGCGAAATTGC
1 AAAGGCGAAAGCGCGAAATTGC
640280 AAAGGCGAAA
1 AAAGGCGAAA
640290 AAGCGATAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.41, C:0.15, G:0.35, T:0.09
Consensus pattern (22 bp):
AAAGGCGAAAGCGCGAAATTGC
Found at i:645683 original size:15 final size:15
Alignment explanation
Indices: 645663--645692 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
645653 AGTGGGGCCT
*
645663 CAGATATCCGGACGC
1 CAGATAACCGGACGC
645678 CAGATAACCGGACGC
1 CAGATAACCGGACGC
645693 TTCAGTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (15 bp):
CAGATAACCGGACGC
Found at i:647256 original size:17 final size:17
Alignment explanation
Indices: 647234--647266 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
647224 CTGGTACTGT
647234 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
647251 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
647267 ACTTAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:649894 original size:2 final size:2
Alignment explanation
Indices: 649887--649931 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
649877 TGATGAAAAG
649887 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
649929 TC T
1 TC T
649932 AATATTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:650559 original size:2 final size:2
Alignment explanation
Indices: 650544--650595 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
650534 GATAAAGGAT
* *
650544 GA GA GA GG GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
650586 GA GA GA GA GA
1 GA GA GA GA GA
650596 TGTCTCTGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.46, C:0.00, G:0.52, T:0.02
Consensus pattern (2 bp):
GA
Found at i:651142 original size:12 final size:12
Alignment explanation
Indices: 651125--651155 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
651115 TTTGTCCGTC
*
651125 GTCCGTCTGTCT
1 GTCCGTCTGACT
651137 GTCCGTCTGACT
1 GTCCGTCTGACT
651149 GTCCGTC
1 GTCCGTC
651156 AACTTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.35, G:0.26, T:0.35
Consensus pattern (12 bp):
GTCCGTCTGACT
Found at i:652155 original size:2 final size:2
Alignment explanation
Indices: 652140--652175 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
652130 GATAAAGGAT
* *
652140 GA GA GA GG GT GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
652176 TGTCTCTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.03
Consensus pattern (2 bp):
GA
Found at i:652721 original size:12 final size:12
Alignment explanation
Indices: 652704--652734 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
652694 TTTGTCCGTC
*
652704 GTCCGTCTGTCT
1 GTCCGTCTGACT
652716 GTCCGTCTGACT
1 GTCCGTCTGACT
652728 GTCCGTC
1 GTCCGTC
652735 AACTTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.35, G:0.26, T:0.35
Consensus pattern (12 bp):
GTCCGTCTGACT
Found at i:660953 original size:439 final size:432
Alignment explanation
Indices: 660229--661209 Score: 1077
Period size: 438 Copynumber: 2.3 Consensus size: 432
660219 TTTACAACCT
* * ** *
660229 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCTTTACAAAATCTTGATCGTTTTCCAGGT
1 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
* * * *
660294 ATGTGT-A-AGA--GA-C-T--CTTGGCCCCTAATTTAAGGGGGCAGCTCCTTTTTCTGGAGTTC
66 ATTTGTAATAGATTAAGCGTGCCTTGGCCCCT-ATTTAAGGGGCCAGCCCCTTTTTCTGGAGTTC
* * * *
660351 ATTCTAAAGGTCCCACGATTACTAACATTTTTTTCCTTACAACCATTTAAAATTGTTGTTCATTT
130 ATTCTAAAGGTCCCAAGAATACAAACATTTTTTTCCTTACAACCATTTAAAATTGTTGATCATTT
* * * * *
660416 TTTAGATACAAATGATTGAATGTTTTAGGGGCCAGCCCTGTAGATCATTCATTGGGACAGACATT
195 TTGAGATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTAGATCATTCAATGGGACAAACATT
* * *
660481 GGTGCTTTGATTGAGGGAATCGATTAGAATCATAAATACAGACATTTTCACTTCTGCAATG-CTT
260 CGTGCTTTGATTGAGGGAATCGATTAGAATCATAAATACAAACATTTTCACTTCTACAATGTC-T
* * *
660545 AACAAAATATGTCT-CATTTTCTAGATT-TATTGCGTCAAAGTTTAAGTACTTTGGCCCCTAGTA
324 AACAAAATATGTCTAC-TTCTCTAG-TTATATTG-GTCAAAGTTTAAGTACTTTGACCCCTAGAA
** * *
660608 GTCCCTAATTTGGTAATAAATGGGCGT-GCAATTGAT-CTTTTCTGATA
386 GTCCCTAATTACGTAATAAATGGGCGTGGCAA-TGATGC-TGTCTAATA
*
660655 GATATTGTTACGATTAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
1 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
* *
660720 ATTTGTAATAGATTTTAAGCGTGCCTTGGTCCCTATTTTTAAGGGGCCAGCCCCTTTTTTCTTGA
66 ATTTGTAATAGA--TTAAGCGTGCCTTGGCCCCTA--TTTAAGGGGCCAGCCCC-TTTTTCTGGA
** *
660785 -TTCATT-TGAAAAGGT-TTAAGAATACAAACATTTTTTTGTTCTTAC-ACTCATTTAAAATTGT
126 GTTCATTCT--AAAGGTCCCAAGAATACAAACA-TTTTTT-TCCTTACAAC-CATTTAAAATTGT
* ** *
660846 TGATCATTTTTGAGATACTAATGATTGAATATTTTAGGGGCCATTCCTCTAGATCCTT-AATGGG
186 TGATCATTTTTGAGATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTAGATCATTCAATGGG
** * * *
660910 A-AAACAAATTCGTTTTTTGATATG-TGGAATCGATTTA-AATCATAAATTCAAACATTTTCTCT
251 ACAAAC--ATTCGTGCTTTGAT-TGAGGGAATCGA-TTAGAATCATAAATACAAACATTTTCACT
* ** * * * *
660972 TTTATGATGTCTAACAAAATATTTCTACTTCTCTAGTTATATTGTTCAATGTTTTAGTACTTTGA
312 TCTACAATGTCTAACAAAATATGTCTACTTCTCTAGTTATATTGGTCAAAGTTTAAGTACTTTGA
* * *
661037 CCCCTTGAAGTGCCTTATTACGTAATAAATGGGCGTGGCAATGATGCTGTCTAATA
377 CCCCTAGAAGTCCCTAATTACGTAATAAATGGGCGTGGCAATGATGCTGTCTAATA
* *
661093 GATATTGGTACAATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
1 GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
* * *
661158 ATTTGTAATAGAGTTCACGAGTGCCTTGGCCCCTCATTTAAGGGGCTAGCCC
66 ATTTGTAATAGA-TT-AAGCGTGCCTTGGCCCCT-ATTTAAGGGGCCAGCCC
661210 TTTCACCCTT
Statistics
Matches: 465, Mismatches: 61, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
426 64 0.14
427 1 0.00
428 3 0.01
432 1 0.00
433 1 0.00
434 1 0.00
435 1 0.00
436 10 0.02
437 51 0.11
438 178 0.38
439 147 0.32
440 7 0.02
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (432 bp):
GATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
ATTTGTAATAGATTAAGCGTGCCTTGGCCCCTATTTAAGGGGCCAGCCCCTTTTTCTGGAGTTCA
TTCTAAAGGTCCCAAGAATACAAACATTTTTTTCCTTACAACCATTTAAAATTGTTGATCATTTT
TGAGATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTAGATCATTCAATGGGACAAACATTC
GTGCTTTGATTGAGGGAATCGATTAGAATCATAAATACAAACATTTTCACTTCTACAATGTCTAA
CAAAATATGTCTACTTCTCTAGTTATATTGGTCAAAGTTTAAGTACTTTGACCCCTAGAAGTCCC
TAATTACGTAATAAATGGGCGTGGCAATGATGCTGTCTAATA
Found at i:662973 original size:164 final size:165
Alignment explanation
Indices: 662609--662990 Score: 529
Period size: 164 Copynumber: 2.3 Consensus size: 165
662599 TTCCGTTGGA
* *
662609 AAGAAGATTTTTAAAGATTTTCTCTAAATATTCCTATGTAAAAATTCATCCCCCACTGTGGCCTC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTTATCCCCCACTGTGGCCTC
* *
662674 ACCCTTACCCCGGGGACTATGATATTAACAAACTTGAATCTATACTATCTAAAGATGCTTCCACT
66 ACCCTTACCCCAGGGACTATGA-ATTAACAAACTTGAATCTATACTATCTAAAGATGCTTCCACC
*
662739 CAAATGTTCAGCTTTCCTGGCCTAACAGCTTTTAAG
130 CAAATGTTCAGCTTCCCTGGCCTAACAGCTTTTAAG
*
662775 AAGAAGATTTTTAAAGATTTTCTCCATATATTCCTAATGTAAAAATTTATCCCCCACTGTGGCCT
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCT-ATGTAAAAATTTATCCCCCACTGTGGCCT
* * * * * *
662840 CACCC-TACCCTCAGGGACTATG-GTTAATAAACTTGAATCTTTACTTTCTGAGGATGCTTCCAC
65 CACCCTTACCC-CAGGGACTATGAATTAACAAACTTGAATCTATACTATCTAAAGATGCTTCCAC
** ** *
662903 CCAAAT-TTGGGCTTCCCTGGCCTAATGGTTTTTAAG
129 CCAAATGTTCAGCTTCCCTGGCCTAACAGCTTTTAAG
* *
662939 AAGAAGACTTTTAAAGATTTTCTCTATATATTCCT-TCATAAAAATTTATCCC
1 AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTAT-GTAAAAATTTATCCC
662991 TTCCCCCTAT
Statistics
Matches: 193, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
162 1 0.01
163 14 0.07
164 57 0.30
165 40 0.21
166 38 0.20
167 43 0.22
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.35
Consensus pattern (165 bp):
AAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATTTATCCCCCACTGTGGCCTC
ACCCTTACCCCAGGGACTATGAATTAACAAACTTGAATCTATACTATCTAAAGATGCTTCCACCC
AAATGTTCAGCTTCCCTGGCCTAACAGCTTTTAAG
Found at i:663798 original size:17 final size:17
Alignment explanation
Indices: 663754--663805 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
663744 TTCTTTGCAA
*
663754 AATTTCACGGTTATAACG
1 AATTT-ACGGATATAACG
663772 AA-TT-CGGATATAACG
1 AATTTACGGATATAACG
*
663787 AATTTACGGATATAGCG
1 AATTTACGGATATAACG
663804 AA
1 AA
663806 CTGATTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 12 0.40
16 2 0.07
17 14 0.47
18 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (17 bp):
AATTTACGGATATAACG
Found at i:666290 original size:19 final size:19
Alignment explanation
Indices: 666263--666299 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
666253 GAGGGCACCT
* *
666263 GCTCTAAAAACTTTAACCA
1 GCTCCAAAAACCTTAACCA
666282 GCTCCAAAAACCTTAACC
1 GCTCCAAAAACCTTAACC
666300 TCATACAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (19 bp):
GCTCCAAAAACCTTAACCA
Found at i:667680 original size:15 final size:15
Alignment explanation
Indices: 667657--667690 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
667647 ATCATAATAA
* *
667657 ATATTATACAGTATC
1 ATATGATACACTATC
667672 ATATGATACACTATC
1 ATATGATACACTATC
667687 ATAT
1 ATAT
667691 CACATAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (15 bp):
ATATGATACACTATC
Found at i:669142 original size:12 final size:12
Alignment explanation
Indices: 669125--669150 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
669115 ACATGTATTG
669125 TTTATCAGTGAT
1 TTTATCAGTGAT
669137 TTTATCAGTGAT
1 TTTATCAGTGAT
669149 TT
1 TT
669151 GGGTTAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (12 bp):
TTTATCAGTGAT
Found at i:669341 original size:29 final size:29
Alignment explanation
Indices: 669298--669367 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
669288 TTGATGATAA
* *
669298 ATAACTTCATAATGAACAAGCAAGGGAAG
1 ATAACTCCATTATGAACAAGCAAGGGAAG
* **
669327 ATAACTCTATTATGAGGAAGCAAGGGAAG
1 ATAACTCCATTATGAACAAGCAAGGGAAG
669356 ATAACTCCATTA
1 ATAACTCCATTA
669368 ACTGTCTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.21
Consensus pattern (29 bp):
ATAACTCCATTATGAACAAGCAAGGGAAG
Found at i:671529 original size:168 final size:166
Alignment explanation
Indices: 671270--671611 Score: 375
Period size: 168 Copynumber: 2.0 Consensus size: 166
671260 GAGGAAAGAG
* * **
671270 AAGATTTTCTACGATTTAATACATTTTCACCAAATGGCCATATTGGCCCCACCCTAGGGCCTAAA
1 AAGATTTTCTAAGATTGAATACATTTTCACCAAATGGCCATATTGGCCCCACCCTACAGCCTAAA
* * * *
671335 GCCCTGTCCCATGGGTAACAAATTTCAAAATTTAGGTAGAAGACTTCATGAACATCAT-TTCTAT
66 CCCCTGTCCCAGGGGCAACAAATTTCAAAATTTAGGTAGAAGACTTCATGAACATCATAATC-AT
*
671399 GCAATGAGTTTTTTTCTCACAAGTGTGAGAGTGGAGAAA
130 GCAATAAG-TTTTTTC-CACAAGTGTGAGAGTGGAGAAA
* * *
671438 AAGATTTTCTAAGATTGAATACAATTTT-ACTATATGGCCATATTGGCCCCACCCTACAGCCTGA
1 AAGATTTTCTAAGATTGAATAC-ATTTTCACCAAATGGCCATATTGGCCCCACCCTACAGCCTAA
* ** * * * ** *
671502 ACCCCTGAT-CCAGGGGCCATGAATTTCATAATTTTGGTAGAGGGTTTCATGGACATCATAATCA
65 ACCCCTG-TCCCAGGGGCAACAAATTTCAAAATTTAGGTAGAAGACTTCATGAACATCATAATCA
* * * * *
671566 TGCATTAAGTTTTTTCCTCAGGTGTGGGAGTGGAGAAG
129 TGCAATAAGTTTTTTCCACAAGTGTGAGAGTGGAGAAA
*
671604 AAGGTTTT
1 AAGATTTT
671612 TGAAAATTTG
Statistics
Matches: 144, Mismatches: 27, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
166 25 0.17
167 7 0.05
168 104 0.72
169 8 0.06
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (166 bp):
AAGATTTTCTAAGATTGAATACATTTTCACCAAATGGCCATATTGGCCCCACCCTACAGCCTAAA
CCCCTGTCCCAGGGGCAACAAATTTCAAAATTTAGGTAGAAGACTTCATGAACATCATAATCATG
CAATAAGTTTTTTCCACAAGTGTGAGAGTGGAGAAA
Found at i:672182 original size:15 final size:16
Alignment explanation
Indices: 672152--672200 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
672142 GATACAGCTT
* *
672152 ACTCCACTTATATTGA
1 ACTCCGCTTATTTTGA
672168 ACT-CGCTTATTTTGAA
1 ACTCCGCTTATTTTG-A
*
672184 ATTCCGCTTATTTTGA
1 ACTCCGCTTATTTTGA
672200 A
1 A
672201 ATAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 11 0.39
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (16 bp):
ACTCCGCTTATTTTGA
Found at i:681670 original size:16 final size:16
Alignment explanation
Indices: 681649--681692 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
681639 GAGAATGTCA
681649 GACACCTCGGCCCCAG
1 GACACCTCGGCCCCAG
681665 GACACCTCGGCCCCAG
1 GACACCTCGGCCCCAG
*
681681 GACTCCTCGGCC
1 GACACCTCGGCC
681693 AAGACGGGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.50, G:0.25, T:0.09
Consensus pattern (16 bp):
GACACCTCGGCCCCAG
Found at i:681741 original size:21 final size:21
Alignment explanation
Indices: 681716--681755 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
681706 CCAAATTTTG
681716 AGACACCCCGGCTCAAGCAAA
1 AGACACCCCGGCTCAAGCAAA
* *
681737 AGACATCTCGGCTCAAGCA
1 AGACACCCCGGCTCAAGCA
681756 GAATTAAAAT
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:0.35, C:0.35, G:0.20, T:0.10
Consensus pattern (21 bp):
AGACACCCCGGCTCAAGCAAA
Found at i:683261 original size:19 final size:19
Alignment explanation
Indices: 683214--683267 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
683204 GGACCAATCT
*
683214 CCCAAATGGGATATAATAG
1 CCCAAATGGGATATAACAG
* ***
683233 TCCGTTTGGGATATAACAG
1 CCCAAATGGGATATAACAG
683252 CCCAAATGGGATATAA
1 CCCAAATGGGATATAA
683268 TTTTAAAGTG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CCCAAATGGGATATAACAG
Found at i:683566 original size:19 final size:19
Alignment explanation
Indices: 683554--683591 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
683544 ATATCTCATT
683554 TGGGCTATTATATCCCAAA
1 TGGGCTATTATATCCCAAA
*
683573 TGGGCTATTACATCCCAAA
1 TGGGCTATTATATCCCAAA
683592 CGGGAGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (19 bp):
TGGGCTATTATATCCCAAA
Found at i:686877 original size:4 final size:4
Alignment explanation
Indices: 686868--686913 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
686858 GTTACTCTGT
* * * *
686868 TCCG TCCG TCCG TCCG TCCA TCCA TCCG TCTG TCCG TCCG TACG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
686914 TGTCACGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.07, C:0.46, G:0.20, T:0.28
Consensus pattern (4 bp):
TCCG
Found at i:687708 original size:21 final size:21
Alignment explanation
Indices: 687684--687723 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
687674 TTAAGTTCTC
687684 CTTAAAGATAGCTTAAAGATG
1 CTTAAAGATAGCTTAAAGATG
*
687705 CTTAAAGGTAGCTTAAAGA
1 CTTAAAGATAGCTTAAAGA
687724 CAATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
CTTAAAGATAGCTTAAAGATG
Found at i:687709 original size:10 final size:11
Alignment explanation
Indices: 687684--687723 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
687674 TTAAGTTCTC
687684 CTTAAAGATAG
1 CTTAAAGATAG
687695 CTTAAAGAT-G
1 CTTAAAGATAG
*
687705 CTTAAAGGTAG
1 CTTAAAGATAG
687716 CTTAAAGA
1 CTTAAAGA
687724 CAATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (11 bp):
CTTAAAGATAG
Found at i:687758 original size:11 final size:11
Alignment explanation
Indices: 687728--687759 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
687718 TAAAGACAAT
*
687728 CTTTAAGCCAC
1 CTTTAAGCTAC
687739 CTTTAAGCTAC
1 CTTTAAGCTAC
687750 CTTTAAGCTA
1 CTTTAAGCTA
687760 TATGTGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:687784 original size:11 final size:11
Alignment explanation
Indices: 687768--687808 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
687758 TATATGTGTT
687768 GCTTAAAGATG
1 GCTTAAAGATG
**
687779 GCTTAAAGAAA
1 GCTTAAAGATG
*
687790 GCGTAAAGATG
1 GCTTAAAGATG
687801 GCTTAAAG
1 GCTTAAAG
687809 GCAGCTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (11 bp):
GCTTAAAGATG
Found at i:687818 original size:22 final size:22
Alignment explanation
Indices: 687768--687820 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
687758 TATATGTGTT
687768 GCTTAAAGATGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
687790 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
687812 GCTTAAAGA
1 GCTTAAAGA
687821 CTATCTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:687841 original size:11 final size:11
Alignment explanation
Indices: 687825--687853 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
687815 TAAAGACTAT
687825 CTTTAAGCCAC
1 CTTTAAGCCAC
687836 CTTTAAGCCAC
1 CTTTAAGCCAC
687847 CTTTAAG
1 CTTTAAG
687854 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:687901 original size:11 final size:11
Alignment explanation
Indices: 687885--687938 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
687875 GTCCAAACTT
687885 CTTTAAGCCAC
1 CTTTAAGCCAC
687896 CTTTAAGCCAC
1 CTTTAAGCCAC
*
687907 CTTTAAGCTAC
1 CTTTAAGCCAC
687918 CTTTAAGCCAC
1 CTTTAAGCCAC
687929 CTTTAAGCCA
1 CTTTAAGCCA
687939 TTAAAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:689154 original size:112 final size:112
Alignment explanation
Indices: 688957--689179 Score: 410
Period size: 112 Copynumber: 2.0 Consensus size: 112
688947 AACCCTGACG
*
688957 TGCACCTGGGCACACGACACACCTGTTGTGTATATCGTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAACTGTTGTGTATATCGTGTATATTCTGTGTTAGTTCCAGGGGTT
* *
689022 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACA
66 TTCTTAAGTTGGACAAACAATAGACTCTAAATAGATATACACAAACA
*
689069 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAACTGTTGTGTATATCGTGTATATTCTGTGTTAGTTCCAGGGGTT
689134 TTCTTAAGTTGGACAAACAATAGACTCTAAATAGATATACACAAAC
66 TTCTTAAGTTGGACAAACAATAGACTCTAAATAGATATACACAAAC
689180 GAACAAAACT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 107 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (112 bp):
TGCACCTGGGCACACGACACAACTGTTGTGTATATCGTGTATATTCTGTGTTAGTTCCAGGGGTT
TTCTTAAGTTGGACAAACAATAGACTCTAAATAGATATACACAAACA
Found at i:689400 original size:2 final size:2
Alignment explanation
Indices: 689393--689459 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
689383 CTGGAGGAAC
689393 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
689435 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
689460 TTTTTTTCAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:689804 original size:22 final size:22
Alignment explanation
Indices: 689776--689836 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
689766 AATATTGACT
*
689776 TAAAGGCCACTTAAAGACAGTG
1 TAAAGGCCACTTAAAGACAGCG
* *
689798 TAAAGG-CAGTGTAAAGAGAGCG
1 TAAAGGCCACT-TAAAGACAGCG
*
689820 TAAATGCCACTTAAAGA
1 TAAAGGCCACTTAAAGA
689837 TGCTTAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 26 0.81
23 3 0.09
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.18
Consensus pattern (22 bp):
TAAAGGCCACTTAAAGACAGCG
Found at i:689852 original size:11 final size:11
Alignment explanation
Indices: 689829--689879 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
689819 GTAAATGCCA
689829 CTTAAAGAT-G
1 CTTAAAGATGG
689839 CTTAAAGATGG
1 CTTAAAGATGG
*
689850 CTTAAAGGTGG
1 CTTAAAGATGG
*
689861 CTTAAAGGTGG
1 CTTAAAGATGG
689872 CTTAAAGA
1 CTTAAAGA
689880 AGTTTGGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.27
Consensus pattern (11 bp):
CTTAAAGATGG
Found at i:689964 original size:10 final size:11
Alignment explanation
Indices: 689949--689988 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
689939 GGTTGTATAG
*
689949 CCTTTAAG-CT
1 CCTTTAAGCCA
*
689959 CCTTTAAGTCA
1 CCTTTAAGCCA
689970 CCTTTAAGCCA
1 CCTTTAAGCCA
689981 CCTTTAAG
1 CCTTTAAG
689989 GACTTGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:690685 original size:4 final size:4
Alignment explanation
Indices: 690668--690767 Score: 175
Period size: 4 Copynumber: 25.2 Consensus size: 4
690658 AGAAAACGAG
*
690668 TATC TATT TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
690716 TATC TATC TATC TATC TATC TATC TATC TATC TATC -ATC CATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
690763 TATC T
1 TATC T
690768 GCTTAATTCA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
3 3 0.03
4 89 0.97
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:700051 original size:7 final size:7
Alignment explanation
Indices: 700039--700105 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
700029 GAGAAGGATC
700039 ATTCGAG
1 ATTCGAG
700046 ATTCGAG
1 ATTCGAG
*
700053 ATTCGAA
1 ATTCGAG
*
700060 ATACGAG
1 ATTCGAG
*
700067 ATTCGAA
1 ATTCGAG
*
700074 ATACGAG
1 ATTCGAG
700081 ATTCGAG
1 ATTCGAG
*
700088 ATTCGAA
1 ATTCGAG
700095 ATTCGAG
1 ATTCGAG
700102 ATTC
1 ATTC
700106 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:704800 original size:4 final size:4
Alignment explanation
Indices: 704793--704819 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
704783 CTTTTTTTTC
704793 TCTG TCTG TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCTG TCT
704820 CTCTCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.22, T:0.52
Consensus pattern (4 bp):
TCTG
Found at i:704824 original size:2 final size:2
Alignment explanation
Indices: 704817--704852 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
704807 TGTCTGTCTG
*
704817 TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
704853 ATTACACTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:736231 original size:2 final size:2
Alignment explanation
Indices: 736224--736255 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
736214 TCTTCTGCTT
736224 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
736256 ATCTTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:739111 original size:17 final size:17
Alignment explanation
Indices: 739089--739208 Score: 186
Period size: 17 Copynumber: 7.1 Consensus size: 17
739079 CTTCCGAGTT
*
739089 TCTTTGTTACACCTGTA
1 TCTTTGTTATACCTGTA
739106 TCTTTGTTATACCTGTA
1 TCTTTGTTATACCTGTA
*
739123 TCTTTGTTACACCTGTA
1 TCTTTGTTATACCTGTA
*
739140 TCTTTGTTATACCTGTT
1 TCTTTGTTATACCTGTA
* *
739157 TCTTTGTTGTACCTGTT
1 TCTTTGTTATACCTGTA
*
739174 TCTTTGTTATACCTGTT
1 TCTTTGTTATACCTGTA
739191 TCTTTGTTATACCTGTA
1 TCTTTGTTATACCTGTA
739208 T
1 T
739209 AAACATCTAC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 96 1.00
ACGTcount: A:0.14, C:0.19, G:0.12, T:0.54
Consensus pattern (17 bp):
TCTTTGTTATACCTGTA
Found at i:747835 original size:13 final size:13
Alignment explanation
Indices: 747817--747841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
747807 TTTTCTCTGT
747817 TTTTGCGATCCTG
1 TTTTGCGATCCTG
747830 TTTTGCGATCCT
1 TTTTGCGATCCT
747842 ATCGATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.20, T:0.48
Consensus pattern (13 bp):
TTTTGCGATCCTG
Found at i:750359 original size:2 final size:2
Alignment explanation
Indices: 750352--750407 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
750342 ATTTAGATAA
750352 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
750394 CC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC
750408 ATACACTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:765070 original size:87 final size:87
Alignment explanation
Indices: 764972--765149 Score: 250
Period size: 87 Copynumber: 2.0 Consensus size: 87
764962 ACACACAGAC
* ** *
764972 AAGTACACAGTTTACATTTACATATTAGTTCAGTACTGCTAAAATGTTCTCTACAATAATACATT
1 AAGTACACAGTTTACATTTACATATTAGTCCAGTACTGCTAAAATGCACTATACAATAATACATT
765037 ATTCAACGGACACAT-ATGGCAA
66 ATTCAACGGACAC-TGATGGCAA
* * * * *
765059 AAGTATACAGTTTATATTTACATGTTAGTCCAGTGCTGCTCAAATGCACTATACAATAATACATT
1 AAGTACACAGTTTACATTTACATATTAGTCCAGTACTGCTAAAATGCACTATACAATAATACATT
*
765124 ATTCAGCGGACACTGATGGCAA
66 ATTCAACGGACACTGATGGCAA
765146 AAGT
1 AAGT
765150 GTTGACCTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 1 0.01
87 79 0.99
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (87 bp):
AAGTACACAGTTTACATTTACATATTAGTCCAGTACTGCTAAAATGCACTATACAATAATACATT
ATTCAACGGACACTGATGGCAA
Found at i:780603 original size:19 final size:19
Alignment explanation
Indices: 780556--780609 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
780546 GGACCACTCT
780556 CCCAATTGGGATATAATAG
1 CCCAATTGGGATATAATAG
***
780575 CCGGTTTGGGATATAATAG
1 CCCAATTGGGATATAATAG
*
780594 CCCAAATGGGATATAA
1 CCCAATTGGGATATAA
780610 ATTTTAAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (19 bp):
CCCAATTGGGATATAATAG
Found at i:784105 original size:13 final size:13
Alignment explanation
Indices: 784084--784121 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
784074 TTTCAGATAC
*
784084 ATATTTAAAAAAA
1 ATATATAAAAAAA
784097 ATATATAAAAAAA
1 ATATATAAAAAAA
*
784110 A-AAATAAAAAAA
1 ATATATAAAAAAA
784122 TTTAGCATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
ATATATAAAAAAA
Found at i:784987 original size:18 final size:18
Alignment explanation
Indices: 784955--784989 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
784945 ACAGAACCTA
**
784955 AAAAAAAAATTAAAAAAC
1 AAAAAAAAACAAAAAAAC
784973 AAAAAAAAACAAAAAAA
1 AAAAAAAAACAAAAAAA
784990 AACCCAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.89, C:0.06, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAAACAAAAAAAC
Found at i:784997 original size:12 final size:10
Alignment explanation
Indices: 784966--784992 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
784956 AAAAAAAATT
784966 AAAAAACAAA
1 AAAAAACAAA
784976 AAAAAACAAA
1 AAAAAACAAA
784986 AAAAAAC
1 AAAAAAC
784993 CCAAACAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:785016 original size:1 final size:1
Alignment explanation
Indices: 785010--785039 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
785000 AGCAAACAAA
*
785010 CCCCCCCCCCCTCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
785040 GTGATATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:785864 original size:16 final size:16
Alignment explanation
Indices: 785840--785871 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
785830 GAAAAACACA
*
785840 CATTTATTTATTTATT
1 CATTCATTTATTTATT
785856 CATTCATTTATTTATT
1 CATTCATTTATTTATT
785872 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (16 bp):
CATTCATTTATTTATT
Found at i:785962 original size:2 final size:2
Alignment explanation
Indices: 785955--785989 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
785945 GAACTGATAG
785955 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
785990 GTGCGTAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:786207 original size:19 final size:20
Alignment explanation
Indices: 786155--786201 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
786145 GTTAAATGAA
*
786155 ATAAATGTATATAAATAAAAC
1 ATAAAGGTA-ATAAATAAAAC
*
786176 ATCAAGGTAATAAATAAAAC
1 ATAAAGGTAATAAATAAAAC
786196 A-AAAGG
1 ATAAAGG
786202 AGATAACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 12 0.52
21 7 0.30
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (20 bp):
ATAAAGGTAATAAATAAAAC
Found at i:787358 original size:13 final size:13
Alignment explanation
Indices: 787340--787364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
787330 CGTTTAGACC
787340 CCCCCCCCCCCCT
1 CCCCCCCCCCCCT
787353 CCCCCCCCCCCC
1 CCCCCCCCCCCC
787365 CCGTTATAGN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.96, G:0.00, T:0.04
Consensus pattern (13 bp):
CCCCCCCCCCCCT
Found at i:787358 original size:14 final size:14
Alignment explanation
Indices: 787339--787365 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
787329 ACGTTTAGAC
787339 CCCCCCCCCCCCCT
1 CCCCCCCCCCCCCT
787353 CCCCCCCCCCCCC
1 CCCCCCCCCCCCC
787366 CGTTATAGNN
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:0.00, C:0.96, G:0.00, T:0.04
Consensus pattern (14 bp):
CCCCCCCCCCCCCT
Found at i:787358 original size:15 final size:15
Alignment explanation
Indices: 787338--787366 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
787328 TACGTTTAGA
787338 CCCCCCCCCCCCCCT
1 CCCCCCCCCCCCCCT
787353 CCCCCCCCCCCCCC
1 CCCCCCCCCCCCCC
787367 GTTATAGNNN
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (15 bp):
CCCCCCCCCCCCCCT
Found at i:791459 original size:13 final size:13
Alignment explanation
Indices: 791441--791465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
791431 CAGGGATGGG
791441 GTAATGGTAATTT
1 GTAATGGTAATTT
791454 GTAATGGTAATT
1 GTAATGGTAATT
791466 GAGTGTACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GTAATGGTAATTT
Found at i:793047 original size:165 final size:165
Alignment explanation
Indices: 792725--793051 Score: 523
Period size: 166 Copynumber: 2.0 Consensus size: 165
792715 TACCACCTTA
*
792725 ACAGACATCAAAGTTTGTACATTCATACCCCATATTGAGGACATATAAATTACCTATTTGTTGAA
1 ACAGACATCAAAGTTTGTACATTCATACCCCATATTGAGGACATATAAATAACCTATTTGTTGAA
*
792790 AGGTCACAAAAACAAAAGTTGAAGTGTCAAAATACTCTGGTCATTGACTTTATATCAAGAGATTT
66 AGGTCACAAAAACAAAAGTTGAAGTGTCAAAATACTCTGGTCATTGACTTTATATCAAGAGATTC
792855 CTGCTCAATATTTTGAGAAACCCTTTGCTTTATCT
131 CTGCTCAATATTTTGAGAAACCCTTTGCTTTATCT
* * * * *
792890 ACAGACATCTAATTTTGTACATTTATACCCCATATTGAGGACATGTAAATGAATTCTA-TTGTTG
1 ACAGACATCAAAGTTTGTACATTCATACCCCATATTGAGGACATATAAAT-AA-CCTATTTGTTG
* * *
792954 CAAGGTCACAAGAACAAAGGTTGAAGTGTCAAAATACTCTGGTCATTGACTTTATATCAAGAGAT
64 AAAGGTCACAAAAACAAAAGTTGAAGTGTCAAAATACTCTGGTCATTGACTTTATATCAAGAGAT
*
793019 TCCTGCTCAATATTTTGAG-AATCCTTTGCTTTA
129 TCCTGCTCAATATTTTGAGAAACCCTTTGCTTTA
793052 CAGACAACAA
Statistics
Matches: 149, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
165 59 0.40
166 87 0.58
167 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (165 bp):
ACAGACATCAAAGTTTGTACATTCATACCCCATATTGAGGACATATAAATAACCTATTTGTTGAA
AGGTCACAAAAACAAAAGTTGAAGTGTCAAAATACTCTGGTCATTGACTTTATATCAAGAGATTC
CTGCTCAATATTTTGAGAAACCCTTTGCTTTATCT
Found at i:803392 original size:15 final size:15
Alignment explanation
Indices: 803372--803400 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
803362 GCAACGTGCT
803372 TGAGAATACATTTCA
1 TGAGAATACATTTCA
803387 TGAGAATACATTTC
1 TGAGAATACATTTC
803401 TGATATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (15 bp):
TGAGAATACATTTCA
Found at i:804787 original size:39 final size:41
Alignment explanation
Indices: 804691--804788 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 41
804681 AATAGAGATT
* *
804691 GTTAACTTCATGTACTTTATTCAAAATACATGAACATGTAA
1 GTTAACTTCATGTACTTTATTCAAAATACATAAAAATGTAA
* *
804732 CTTAACTTCATGTACTTTCTTTCAAAAT-CA-AAAAAT-TAA
1 GTTAACTTCATGTACTTT-ATTCAAAATACATAAAAATGTAA
*
804771 GTTAACTTGATGTACTTT
1 GTTAACTTCATGTACTTT
804789 GTATGATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 19 0.38
40 4 0.08
41 19 0.38
42 8 0.16
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (41 bp):
GTTAACTTCATGTACTTTATTCAAAATACATAAAAATGTAA
Found at i:807213 original size:9 final size:10
Alignment explanation
Indices: 807191--807217 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
807181 GTATGAAAAT
807191 CCCCTGTCAC
1 CCCCTGTCAC
807201 CCCCTGTCAC
1 CCCCTGTCAC
807211 CCCCTGT
1 CCCCTGT
807218 GTTTTCACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.59, G:0.11, T:0.22
Consensus pattern (10 bp):
CCCCTGTCAC
Found at i:807258 original size:31 final size:31
Alignment explanation
Indices: 807194--807259 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
807184 TGAAAATCCC
**
807194 CTGTCACCCCCTGTCACCCCCTGTGTTTTCA
1 CTGTCACCCCCTGTCACCCCCTGTGTTGCCA
* *
807225 CTGTCATCCCCTGTACATCCCCTGTG-TGCCA
1 CTGTCACCCCCTGT-CACCCCCTGTGTTGCCA
807256 CTGT
1 CTGT
807260 ACAGAGCCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.11, C:0.42, G:0.15, T:0.32
Consensus pattern (31 bp):
CTGTCACCCCCTGTCACCCCCTGTGTTGCCA
Found at i:807313 original size:43 final size:43
Alignment explanation
Indices: 807233--807315 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
807223 CACTGTCATC
* * *
807233 CCCTGTACATCCCCTGTGTGCCACTGTACAGAGCCCCTGTATA
1 CCCTGTACATCCCCTGTGCGCCACTGTACACACCCCCTGTATA
*
807276 CCCTGT-CATCCCCTGTGCGCCCCTGTACACATCCCCCTGT
1 CCCTGTACATCCCCTGTGCGCCACTGTACACA-CCCCCTGT
807316 GTGCCACTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 22 0.63
43 13 0.37
ACGTcount: A:0.14, C:0.43, G:0.17, T:0.25
Consensus pattern (43 bp):
CCCTGTACATCCCCTGTGCGCCACTGTACACACCCCCTGTATA
Found at i:807345 original size:20 final size:20
Alignment explanation
Indices: 807322--807366 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
807312 CTGTGTGCCA
807322 CTGTAAGCCCCTGTCACCCC
1 CTGTAAGCCCCTGTCACCCC
* * *
807342 CTGTACGCCCCTGTTATCCC
1 CTGTAAGCCCCTGTCACCCC
807362 CTGTA
1 CTGTA
807367 GGCCACTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.44, G:0.16, T:0.27
Consensus pattern (20 bp):
CTGTAAGCCCCTGTCACCCC
Found at i:807375 original size:20 final size:20
Alignment explanation
Indices: 807339--807385 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
807329 CCCCTGTCAC
*
807339 CCCCTGTACGCCCCTGT-TA
1 CCCCTGTACGCCACTGTATA
*
807358 TCCCCTGTAGGCCACTGTATA
1 -CCCCTGTACGCCACTGTATA
807379 CCCCTGT
1 CCCCTGT
807386 GCATGCCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.13, C:0.43, G:0.17, T:0.28
Consensus pattern (20 bp):
CCCCTGTACGCCACTGTATA
Found at i:808329 original size:2 final size:2
Alignment explanation
Indices: 808322--808374 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
808312 AAATAGTCAT
808322 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
808364 GA GA GA GA GA G
1 GA GA GA GA GA G
808375 TTTGCATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:808574 original size:2 final size:2
Alignment explanation
Indices: 808567--808613 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
808557 GAGTTTATAC
808567 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
808609 AG AG A
1 AG AG A
808614 ATGCATTGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:809127 original size:141 final size:136
Alignment explanation
Indices: 808876--809158 Score: 372
Period size: 141 Copynumber: 2.0 Consensus size: 136
808866 ATTATTTCAC
*
808876 TCGGTCAGTGATTATATAATAGCTACTGTACACAGCCCTTCTTGACAATTTGCAGTTCACGGTAG
1 TCGGTCAGTGATTATATAATAGCTACTGTACACAGCCCTTCTTGACAATTTGCAGTGCACGGTAG
* * * *
808941 CGAGGTAGGGAAAAGACTTGATAGACACACGTGTACACGTATATATACACACACTTCCTCAGATC
66 CGAGCTAGGGAAAAGACGTGACAGACACACGTGTA-ACGTATATATACACACACGTCCTCAGATC
809006 TGAATGG
130 TGAATGG
*
809013 TCGGTCAGTGATTATATAATAGCTATATACTGTATACAGCCCTTCTTGACAATTTGCAGTGCACG
1 TCGGTCAGTGATTATATAATAGC----TACTGTACACAGCCCTTCTTGACAATTTGCAGTGCACG
* * *
809078 GTAGCGAGACT-GGGAACAATGAGGTGACAGACACACGTGT-ACTTGTATATACACACACGTCCT
62 GTAGCGAG-CTAGGGAA-AA-GACGTGACAGACACACGTGTAACGTATATATACACACACGTCCT
* * *
809141 CAGGTCTGGATGT
124 CAGATCTGAATGG
809154 TCGGT
1 TCGGT
809159 AATGCTACAC
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
137 23 0.18
141 84 0.66
142 3 0.02
143 17 0.13
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (136 bp):
TCGGTCAGTGATTATATAATAGCTACTGTACACAGCCCTTCTTGACAATTTGCAGTGCACGGTAG
CGAGCTAGGGAAAAGACGTGACAGACACACGTGTAACGTATATATACACACACGTCCTCAGATCT
GAATGG
Found at i:809311 original size:11 final size:10
Alignment explanation
Indices: 809295--809354 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 10
809285 ATTATTTGGC
809295 ACAGGGGATG
1 ACAGGGGATG
809305 TACAGGGGATG
1 -ACAGGGGATG
** **
809316 ACAGTGAAAAC
1 ACAG-GGGATG
809327 ACAGGGG-TG
1 ACAGGGGATG
*
809336 ACAGGGGAAG
1 ACAGGGGATG
809346 ACAGGGGAT
1 ACAGGGGAT
809355 TTTCATACGG
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
9 7 0.19
10 14 0.38
11 16 0.43
ACGTcount: A:0.35, C:0.12, G:0.43, T:0.10
Consensus pattern (10 bp):
ACAGGGGATG
Found at i:812117 original size:9 final size:9
Alignment explanation
Indices: 812103--812133 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
812093 TGCACAAATT
812103 AGAGCTATA
1 AGAGCTATA
812112 AGAGCTATA
1 AGAGCTATA
812121 AGAGCTATA
1 AGAGCTATA
812130 AGAG
1 AGAG
812134 GTGGTTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (9 bp):
AGAGCTATA
Found at i:818481 original size:2 final size:2
Alignment explanation
Indices: 818474--818515 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
818464 TTAAAAGCAT
818474 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
818516 CTTTGATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:821050 original size:437 final size:437
Alignment explanation
Indices: 820296--821226 Score: 1445
Period size: 437 Copynumber: 2.1 Consensus size: 437
820286 AGCCTTTCAA
* * * * * *
820296 GCCCCTAATTTGAGTGGTCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCTCGCTAATTTAAAC
1 GCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCTTGCAAATATAAAC
* * * * *
820361 ATATTTTGTTCTACAAGTGTTCACAAATTGTAAAACTTTATCGAGATATCTAAACAACTGTGTTT
66 ATATTTTGTTCAACAAGTGTTCACAAATTGTAAAACTCTATCAAGATATCTAAACAAATATGTTT
* * * * ** * * *
820426 TAGGGGCTGACCCTTTAACCCCTTATCGGGGCCACTGACAACAACATTTTTGGTATCATTTTGTT
131 TAGGGGCCGACCCTTAAACCCATTACCGGGGCCACCAACAACAACAATTTTAGTATCATATTGTT
*
820491 AAGAACATTATTTTGAACAACTTTTGTTCTACAGTGCTATTCAAAATATTTCTCCTTTTTCTGAT
196 AAGAACATTATTTTAAACAACTTTTGTTCTACAGTGCTATTCAAAATATTTCTCCTTTTTCTGAT
*
820556 ATTTATGATCAAATTTTTCAACTTCTGGCCCCTTGAAACCCCTAATTACGTAACATATGACTAAG
261 ATTAATGATCAAATTTTTCAACTTCTGGCCCCTTGAAACCCCTAATTACGTAACATATGACTAAG
* * * *
820621 GTATTGTACTGTATAGATAAACAGCTTTACAATGAGCATTTTTGCTTCTATAATTAATAACAAAA
326 GTATTGTACTGAATAGATAAACAGCTGTACAATAAACATTTTTGCTTCTATAATTAATAACAAAA
*
820686 TATTGTTCAGTAAAGAGTTATTGTTAGAATACTTTAGAGCCATCTTG
391 TATTGTTCAGTAAAGAGTTATTGTAAGAATACTTTAGAGCCATCTTG
820733 GCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCTTGCAAATATAAAC
1 GCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCTTGCAAATATAAAC
* ** * * * ** *
820798 ATATTTTGTTCAACAAGTGTTTAGGAATTGTTAACCTCTCTCAAGATATCTGTATAAATATGTTT
66 ATATTTTGTTCAACAAGTGTTCACAAATTGTAAAACTCTATCAAGATATCTAAACAAATATGTTT
*
820863 TAGGGGCCGACCCTTAAACTCCATT-CCGGGGCCACCAACAACAA-AATTTTAGTATTCGTATTG
131 TAGGGGCCGACCCTTAAAC-CCATTACCGGGGCCACCAACAACAACAATTTTAGTA-TCATATTG
*
820926 TTGAGAACATTATTTTAAACAACTTTTGTTCTACAGTGCTATTCAAAATATTTCTCCTTTTTCTG
194 TTAAGAACATTATTTTAAACAACTTTTGTTCTACAGTGCTATTCAAAATATTTCTCCTTTTTCTG
* *
820991 ATATTAATGATCAAATTTTTCAGCTTCTGGCCCCTTGAAACCCCTAATTATGTAACATATGACTA
259 ATATTAATGATCAAATTTTTCAACTTCTGGCCCCTTGAAACCCCTAATTACGTAACATATGACTA
*
821056 AGGTATTGTACTGAATAGATAAACAGCTGTACAGTAAACATTTTTGCTTCTATAATTAATAACAA
324 AGGTATTGTACTGAATAGATAAACAGCTGTACAATAAACATTTTTGCTTCTATAATTAATAACAA
821121 AATATTGTTCAGTAAAGAGTTATTGTAAGAATACTTTAGAGCCATCTTG
389 AATATTGTTCAGTAAAGAGTTATTGTAAGAATACTTTAGAGCCATCTTG
821170 GCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATTG-AAGGTCTTGCAA
1 GCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAA-TGAAAGGTCTTGCAA
821227 CTTTTGCATT
Statistics
Matches: 450, Mismatches: 41, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
436 8 0.02
437 436 0.97
438 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (437 bp):
GCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATGAAAGGTCTTGCAAATATAAAC
ATATTTTGTTCAACAAGTGTTCACAAATTGTAAAACTCTATCAAGATATCTAAACAAATATGTTT
TAGGGGCCGACCCTTAAACCCATTACCGGGGCCACCAACAACAACAATTTTAGTATCATATTGTT
AAGAACATTATTTTAAACAACTTTTGTTCTACAGTGCTATTCAAAATATTTCTCCTTTTTCTGAT
ATTAATGATCAAATTTTTCAACTTCTGGCCCCTTGAAACCCCTAATTACGTAACATATGACTAAG
GTATTGTACTGAATAGATAAACAGCTGTACAATAAACATTTTTGCTTCTATAATTAATAACAAAA
TATTGTTCAGTAAAGAGTTATTGTAAGAATACTTTAGAGCCATCTTG
Done.