Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 5 of 172
Found at i:1369642 original size:12 final size:12
Alignment explanation
Indices: 1369625--1369672 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
1369615 AGAGAATCCA
1369625 ACCATCATCATC
1 ACCATCATCATC
* *
1369637 ACCATCACCACC
1 ACCATCATCATC
1369649 ACCATCATCATC
1 ACCATCATCATC
1369661 ACCATCATCATC
1 ACCATCATCATC
1369673 CTCTCACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (12 bp):
ACCATCATCATC
Found at i:1372359 original size:42 final size:43
Alignment explanation
Indices: 1372211--1372384 Score: 235
Period size: 43 Copynumber: 4.1 Consensus size: 43
1372201 TTATTTCTAT
* **
1372211 AAACGCTGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTCCCAC
***
1372254 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTAATCAC
1 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTCCCAC
*
1372297 AAACGCCGCTAAAGAACATGAATTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTCCCAC
** *
1372339 AAACGTTGCTATAA-ATCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTA-AAGAACATGACTTTTAGCGGCGCTTTTCCCAC
1372382 AAA
1 AAA
1372385 TGCCATTATT
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 32 0.28
43 83 0.72
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACTTTTAGCGGCGCTTTTCCCAC
Found at i:1372374 original size:85 final size:86
Alignment explanation
Indices: 1372211--1372375 Score: 244
Period size: 85 Copynumber: 1.9 Consensus size: 86
1372201 TTATTTCTAT
* ** *
1372211 AAACGCTGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGAC
1 AAACGCCGCTAAAGAACATGAATTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGAC
1372276 TTTTAGCGGCGCTTTAATCAC
66 TTTTAGCGGCGCTTTAATCAC
** *
1372297 AAACGCCGCTAAAGAACATGAATTTTAGCGGCGC-TTTCCCACAAACGTTGCTATAA-ATCATGA
1 AAACGCCGCTAAAGAACATGAATTTTAGCGGCGCTTTTCCCACAAACGCCGCTA-AAGAACATGA
1372360 CTTTTAGCGGCGCTTT
65 CTTTTAGCGGCGCTTT
1372376 TCCCACAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
85 39 0.55
86 32 0.45
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGAATTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGAC
TTTTAGCGGCGCTTTAATCAC
Found at i:1378263 original size:9 final size:9
Alignment explanation
Indices: 1378249--1378581 Score: 207
Period size: 9 Copynumber: 38.4 Consensus size: 9
1378239 TTTTTATGTA
1378249 TTATGTAAG
1 TTATGTAAG
1378258 TTATGTACTAAG
1 TTATG---TAAG
*
1378270 TTGTGT-A-
1 TTATGTAAG
*
1378277 TTATGTGAG
1 TTATGTAAG
1378286 TTATGTAAG
1 TTATGTAAG
*
1378295 TTGTGT-A-
1 TTATGTAAG
1378302 TTATGTAAG
1 TTATGTAAG
1378311 TTATGT-A-
1 TTATGTAAG
*
1378318 TTATGTATG
1 TTATGTAAG
1378327 TTATGTAAG
1 TTATGTAAG
1378336 TTATGT-A-
1 TTATGTAAG
*
1378343 -TATTGTATG
1 TTA-TGTAAG
1378352 TTATGTAAG
1 TTATGTAAG
1378361 TTATGTAAG
1 TTATGTAAG
1378370 TTATGT-A-
1 TTATGTAAG
*
1378377 TTATGTATG
1 TTATGTAAG
1378386 TTATGTAAG
1 TTATGTAAG
1378395 TTATGT-A-
1 TTATGTAAG
1378402 TTATGT-A-
1 TTATGTAAG
1378409 TTATGTAAG
1 TTATGTAAG
1378418 -TACTGTAAG
1 TTA-TGTAAG
1378427 TTATGTAAG
1 TTATGTAAG
*
1378436 TAATGT-A-
1 TTATGTAAG
1378443 TTATGTAAG
1 TTATGTAAG
* *
1378452 TTGTGTATGATA
1 TTATGTA--A-G
1378464 TTAAT-TAAG
1 TT-ATGTAAG
*
1378473 TTATATAAG
1 TTATGTAAG
1378482 TTATGTAAG
1 TTATGTAAG
*
1378491 TAATGT-A-
1 TTATGTAAG
1378498 TTATGTAAG
1 TTATGTAAG
* *
1378507 TTGTGTATGATA
1 TTATGTA--A-G
1378519 TTAAT-TAAG
1 TT-ATGTAAG
1378528 TTATGTAAG
1 TTATGTAAG
*
1378537 TTGTGT-A-
1 TTATGTAAG
*
1378544 TAATGTAAG
1 TTATGTAAG
*
1378553 TTA-GGAAGG
1 TTATGTAA-G
1378562 TTATGT-A-
1 TTATGTAAG
1378569 TTATGTAAG
1 TTATGTAAG
1378578 TTAT
1 TTAT
1378582 TATGTTATTA
Statistics
Matches: 255, Mismatches: 30, Indels: 78
0.70 0.08 0.21
Matches are distributed among these distances:
6 2 0.01
7 58 0.23
8 25 0.10
9 143 0.56
10 7 0.03
11 2 0.01
12 16 0.06
13 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1378263 original size:16 final size:16
Alignment explanation
Indices: 1378242--1378555 Score: 185
Period size: 16 Copynumber: 19.2 Consensus size: 16
1378232 TGATATATTT
1378242 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
1378258 TTATGTACTAAGTTGTGTA-
1 TTATGTA-TTA--TGT-AAG
1378277 TTATGTGAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
1378295 TTGTGTATTATGTAAG
1 TTATGTATTATGTAAG
1378311 TTATGTATTA--T--G
1 TTATGTATTATGTAAG
1378323 -TATG--TTATGTAAG
1 TTATGTATTATGTAAG
*
1378336 TTATGTA-TATTGTATG
1 TTATGTATTA-TGTAAG
1378352 TTATGTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
1378370 TTATGTATTATGTATG
1 TTATGTATTATGTAAG
1378386 TTATGTAAGTTATGT-A-
1 TTATGT-A-TTATGTAAG
1378402 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
1378418 -TACTGTAAGTTATGTAAG
1 TTA-TGT-A-TTATGTAAG
*
1378436 TAATGTATTATGTAAGTTG
1 TTATGTATTATGTAA---G
1378455 TGTATGATATTAAT-TAAG
1 T-TATG-TATT-ATGTAAG
*
1378473 TTATATAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
1378491 TAATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
1378507 TTGTGTATGATAT-TAA-
1 TTATGTAT--TATGTAAG
*
1378523 TTAAG--TTATGTAAG
1 TTATGTATTATGTAAG
* *
1378537 TTGTGTATAATGTAAG
1 TTATGTATTATGTAAG
1378553 TTA
1 TTA
1378556 GGAAGGTTAT
Statistics
Matches: 234, Mismatches: 24, Indels: 80
0.69 0.07 0.24
Matches are distributed among these distances:
9 3 0.01
11 5 0.02
12 4 0.02
13 4 0.02
14 15 0.06
15 6 0.03
16 96 0.41
17 19 0.08
18 52 0.22
19 14 0.06
20 7 0.03
21 7 0.03
22 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:1378300 original size:25 final size:25
Alignment explanation
Indices: 1378242--1378608 Score: 276
Period size: 25 Copynumber: 15.1 Consensus size: 25
1378232 TGATATATTT
1378242 TTATGTATTATGTAAGTTATGTACTAAG
1 TTATGTATTATGTAAGTTATG---TAAG
* *
1378270 TTGTGTATTATGTGAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
1378295 TTGTGTATTATGTAAGTTATGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
*
1378318 TTATGTATGTTATGTAAGTTATGTATAT
1 TTATGTA--TTATGTAAGTTATGTA-AG
1378346 TGTATG--TTATGTAAGTTATGTAAG
1 T-TATGTATTATGTAAGTTATGTAAG
*
1378370 TTATGTATTATGTATGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
1378395 TTATGTATTATGT-A-TTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
1378418 -TACTGTAAGTTATGTAAGTAATGT-A-
1 TTA-TGT-A-TTATGTAAGTTATGTAAG
* * *
1378443 TTATGTAAGTTGTGTATGATAT-TAA-
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
1378468 TTAAG--TTATATAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* * *
1378491 TAATGTATTATGTAAGTTGTGTATG
1 TTATGTATTATGTAAGTTATGTAAG
*
1378516 ATAT-TA--AT-TAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* * *
1378537 TTGTGTATAATGTAAGTTA-GGAAGG
1 TTATGTATTATGTAAGTTATGTAA-G
*
1378562 TTATGTATTATGTAAGTTAT-TATG
1 TTATGTATTATGTAAGTTATGTAAG
*
1378586 TTAT-TA-TA--TAAGTTATGGAAG
1 TTATGTATTATGTAAGTTATGTAAG
1378607 TT
1 TT
1378609 TATATATAAG
Statistics
Matches: 278, Mismatches: 35, Indels: 59
0.75 0.09 0.16
Matches are distributed among these distances:
20 8 0.03
21 26 0.09
22 11 0.04
23 27 0.10
24 17 0.06
25 155 0.56
26 4 0.01
27 6 0.02
28 20 0.07
29 4 0.01
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:1378321 original size:41 final size:41
Alignment explanation
Indices: 1378266--1378458 Score: 202
Period size: 41 Copynumber: 4.6 Consensus size: 41
1378256 AGTTATGTAC
* *
1378266 TAAGTTGTGTATTATGTGAGTTATGTAAGTTGTGTA-TTATG
1 TAAGTTATGTATTATGT-AGTTATGTAAGTTATGTAGTTATG
1378307 TAAGTTATGTATTATGTATGTTATGTAAGTTATGTA--TATTG
1 TAAGTTATGTATTATGTA-GTTATGTAAGTTATGTAGTTA-TG
*
1378348 TATGTTATGTAAGTTATGTAAGTTATGT-A-TTATGTATGTTATG
1 TAAGTTATGT-A-TTATGT-AGTTATGTAAGTTATGTA-GTTATG
1378391 TAAGTTATGTATTATGTA-TTATGTAAG-TACTGTAAGTTATG
1 TAAGTTATGTATTATGTAGTTATGTAAGTTA-TGT-AGTTATG
* *
1378432 TAAGTAATGTATTATGTAAGTTGTGTA
1 TAAGTTATGTATTATGT-AGTTATGTA
1378459 TGATATTAAT
Statistics
Matches: 132, Mismatches: 6, Indels: 26
0.80 0.04 0.16
Matches are distributed among these distances:
39 6 0.05
40 7 0.05
41 81 0.61
42 5 0.04
43 30 0.23
44 3 0.02
ACGTcount: A:0.29, C:0.01, G:0.22, T:0.49
Consensus pattern (41 bp):
TAAGTTATGTATTATGTAGTTATGTAAGTTATGTAGTTATG
Found at i:1378534 original size:30 final size:30
Alignment explanation
Indices: 1378443--1378544 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 30
1378433 AAGTAATGTA
1378443 TTATGTAAGTTGTGTATGATATTAATTAAG
1 TTATGTAAGTTGTGTATGATATTAATTAAG
* * *
1378473 TTATATAAGTTATG--T-A-AGTAATGT-A-
1 TTATGTAAGTTGTGTATGATATTAAT-TAAG
1378498 TTATGTAAGTTGTGTATGATATTAATTAAG
1 TTATGTAAGTTGTGTATGATATTAATTAAG
1378528 TTATGTAAGTTGTGTAT
1 TTATGTAAGTTGTGTAT
1378545 AATGTAAGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
25 12 0.20
26 6 0.10
27 3 0.05
28 3 0.05
29 6 0.10
30 29 0.49
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (30 bp):
TTATGTAAGTTGTGTATGATATTAATTAAG
Found at i:1378569 original size:55 final size:55
Alignment explanation
Indices: 1378302--1378550 Score: 246
Period size: 55 Copynumber: 4.5 Consensus size: 55
1378292 AAGTTGTGTA
* *
1378302 TTATGTAAGTTATGT-A-TTATGTATGTTATGTAAGTTATGTAT-ATTGTATGTTATGTAAG
1 TTATGTAAGTTATGTAAGTAATGTA--TTATGTAAGTTATGTATGA---TAT-TAAT-TAAG
* *
1378361 TTATGTAAGTTATGT-A-TTATGTATGTTATGTAAGTTATGTATTATGTATT-ATGTAAG
1 TTATGTAAGTTATGTAAGTAATGTA--TTATGTAAGTTATGTATGA--TATTAAT-TAAG
*
1378418 -TACTGTAAGTTATGTAAGTAATGTATTATGTAAGTTGTGTATGATATTAATTAAG
1 TTA-TGTAAGTTATGTAAGTAATGTATTATGTAAGTTATGTATGATATTAATTAAG
* *
1378473 TTATATAAGTTATGTAAGTAATGTATTATGTAAGTTGTGTATGATATTAATTAAG
1 TTATGTAAGTTATGTAAGTAATGTATTATGTAAGTTATGTATGATATTAATTAAG
*
1378528 TTATGTAAGTTGTGT-A-TAATGTA
1 TTATGTAAGTTATGTAAGTAATGTA
1378551 AGTTAGGAAG
Statistics
Matches: 178, Mismatches: 6, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
53 7 0.04
54 1 0.01
55 72 0.40
56 6 0.03
57 36 0.20
58 2 0.01
59 53 0.30
60 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (55 bp):
TTATGTAAGTTATGTAAGTAATGTATTATGTAAGTTATGTATGATATTAATTAAG
Found at i:1378592 original size:20 final size:19
Alignment explanation
Indices: 1378562--1378601 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1378552 GTTAGGAAGG
*
1378562 TTATGTATTATGTAAGTTA
1 TTATGTATTATATAAGTTA
1378581 TTATGTTATTATATAAGTTA
1 TTATG-TATTATATAAGTTA
1378601 T
1 T
1378602 GGAAGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TTATGTATTATATAAGTTA
Found at i:1378651 original size:16 final size:16
Alignment explanation
Indices: 1378627--1378667 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1378617 AGTTTATATA
*
1378627 TTATATATTATTTAAG
1 TTATATATTATGTAAG
*
1378643 TTATGTATTATGTAAG
1 TTATATATTATGTAAG
1378659 TTTATATAT
1 -TTATATAT
1378668 AAGTTATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (16 bp):
TTATATATTATGTAAG
Found at i:1378679 original size:12 final size:12
Alignment explanation
Indices: 1378604--1378672 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
1378594 TAAGTTATGG
1378604 AAGTTTATATAT
1 AAGTTTATATAT
1378616 AAGTTTATATAT
1 AAGTTTATATAT
* * *
1378628 TA-TATATTATTT
1 AAGTTTA-TATAT
*
1378640 AAGTTATGTATTATGT
1 AAG-T-T-TA-TATAT
1378656 AAGTTTATATAT
1 AAGTTTATATAT
1378668 AAGTT
1 AAGTT
1378673 ATGATATGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.07
12 27 0.60
13 2 0.04
14 2 0.04
15 1 0.02
16 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (12 bp):
AAGTTTATATAT
Found at i:1378755 original size:17 final size:18
Alignment explanation
Indices: 1378719--1378756 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1378709 GATATGATTG
1378719 ATAAATTTTGAAAAAAAT
1 ATAAATTTTGAAAAAAAT
*
1378737 ATAAATTTT-AAAAATAT
1 ATAAATTTTGAAAAAAAT
1378754 ATA
1 ATA
1378757 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
ATAAATTTTGAAAAAAAT
Found at i:1378771 original size:15 final size:15
Alignment explanation
Indices: 1378731--1378773 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1378721 AAATTTTGAA
* *
1378731 AAAAATATAAATTTT
1 AAAAATATATATATT
1378746 AAAAATATATATATT
1 AAAAATATATATATT
*
1378761 AAAAATGTATATA
1 AAAAATATATATA
1378774 AATATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAAATATATATATT
Found at i:1379150 original size:21 final size:21
Alignment explanation
Indices: 1379124--1379164 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1379114 CCCAAATTGA
1379124 TTGCGTTTTTTGCACGAATGG
1 TTGCGTTTTTTGCACGAATGG
1379145 TTGCGTTTTTTGCACGAATG
1 TTGCGTTTTTTGCACGAATG
1379165 TAGCAAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (21 bp):
TTGCGTTTTTTGCACGAATGG
Found at i:1379255 original size:21 final size:21
Alignment explanation
Indices: 1379226--1379266 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1379216 CCCAAATTGA
*
1379226 TTGCTTTTTTTGCACGAATGG
1 TTGCGTTTTTTGCACGAATGG
1379247 TTGCGTTTTTTGCACGAATG
1 TTGCGTTTTTTGCACGAATG
1379267 TAGCAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (21 bp):
TTGCGTTTTTTGCACGAATGG
Found at i:1379255 original size:102 final size:103
Alignment explanation
Indices: 1379070--1379275 Score: 387
Period size: 102 Copynumber: 2.0 Consensus size: 103
1379060 TGTTATATAT
1379070 TAAAAAGTTTTTGTCTTATAATATTTGAGTTATAATATTTATGTCCCAAATTGATTGCGTTTTTT
1 TAAAAAG-TTTTGTCTTATAATATTTGAGTTATAATATTTATGTCCCAAATTGATTGCGTTTTTT
1379135 GCACGAATGGTTGCGTTTTTTGCACGAATGTAGCAAACC
65 GCACGAATGGTTGCGTTTTTTGCACGAATGTAGCAAACC
*
1379174 TAAAAAG-TTTGTCTTATAATATTTGAGTTATAATATTTATGTCCCAAATTGATTGCTTTTTTTG
1 TAAAAAGTTTTGTCTTATAATATTTGAGTTATAATATTTATGTCCCAAATTGATTGCGTTTTTTG
1379238 CACGAATGGTTGCGTTTTTTGCACGAATGTAGCAAACC
66 CACGAATGGTTGCGTTTTTTGCACGAATGTAGCAAACC
1379276 ATATTCCTTT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
102 94 0.93
104 7 0.07
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (103 bp):
TAAAAAGTTTTGTCTTATAATATTTGAGTTATAATATTTATGTCCCAAATTGATTGCGTTTTTTG
CACGAATGGTTGCGTTTTTTGCACGAATGTAGCAAACC
Found at i:1381429 original size:47 final size:47
Alignment explanation
Indices: 1381339--1381429 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
1381329 AAATTTGATT
* * *
1381339 TATAGTGCTTGTATTTTTCTTAAAATTTATAGTAGGAACTTAATCCG
1 TATAGTGCTTGTATTTTTCTTAAAATTCAAAGTAGAAACTTAATCCG
* * *
1381386 TATAGTGTTTGTATTTTTC-TAAAACTTCAAATTAGAAATTTAAT
1 TATAGTGCTTGTATTTTTCTTAAAA-TTCAAAGTAGAAACTTAAT
1381430 TCTATGAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
46 5 0.14
47 32 0.86
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (47 bp):
TATAGTGCTTGTATTTTTCTTAAAATTCAAAGTAGAAACTTAATCCG
Found at i:1381552 original size:7 final size:7
Alignment explanation
Indices: 1381542--1381611 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
1381532 CACTAGATCA
1381542 TAAACCC
1 TAAACCC
1381549 TAAACCC
1 TAAACCC
**
1381556 TTAAACAT
1 -TAAACCC
1381564 TAAACCC
1 TAAACCC
*
1381571 ACAAACCC
1 -TAAACCC
**
1381579 TAAACAA
1 TAAACCC
1381586 T-AACCC
1 TAAACCC
*
1381592 ATAAACCT
1 -TAAACCC
1381600 TAAACCC
1 TAAACCC
1381607 TAAAC
1 TAAAC
1381612 TTTGAGCCCT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
6 3 0.06
7 29 0.62
8 15 0.32
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:1381570 original size:22 final size:23
Alignment explanation
Indices: 1381541--1381604 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 23
1381531 ACACTAGATC
1381541 ATAAACCC-TAAACCCTTAAACA
1 ATAAACCCATAAACCCTTAAACA
* *
1381563 TTAAACCCACAAACCC-TAAACA
1 ATAAACCCATAAACCCTTAAACA
1381585 AT-AACCCATAAA-CCTTAAAC
1 ATAAACCCATAAACCCTTAAAC
1381605 CCTAAACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.06
21 14 0.39
22 14 0.39
23 6 0.17
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (23 bp):
ATAAACCCATAAACCCTTAAACA
Found at i:1381690 original size:21 final size:21
Alignment explanation
Indices: 1381666--1381706 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1381656 ATCATAAATC
*
1381666 CCTAACCCTTAACCCCTAACA
1 CCTAAACCTTAACCCCTAACA
*
1381687 CCTAAACCTTAAGCCCTAAC
1 CCTAAACCTTAACCCCTAAC
1381707 CTCAAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.44, G:0.02, T:0.20
Consensus pattern (21 bp):
CCTAAACCTTAACCCCTAACA
Found at i:1381809 original size:15 final size:15
Alignment explanation
Indices: 1381788--1381829 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1381778 CATTAACTAT
1381788 AAACCCTTAAACCCC
1 AAACCCTTAAACCCC
*
1381803 TAACCCTT-AACCCC
1 AAACCCTTAAACCCC
1381817 AAACACC-TAAACC
1 AAAC-CCTTAAACC
1381830 TTAAATCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACCCTTAAACCCC
Found at i:1381938 original size:21 final size:21
Alignment explanation
Indices: 1381905--1381944 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1381895 TAAAACATAT
*
1381905 ATAAACCTCAACCCTTAAACA
1 ATAAACCTCAACCCCTAAACA
1381926 ATAAACCAT-AACCCCTAAA
1 ATAAACC-TCAACCCCTAAA
1381945 TCCATAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
ATAAACCTCAACCCCTAAACA
Found at i:1381949 original size:15 final size:14
Alignment explanation
Indices: 1381927--1381960 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1381917 CCTTAAACAA
1381927 TAAACCATAACCCC
1 TAAACCATAACCCC
*
1381941 TAAATCCATAATCCC
1 TAAA-CCATAACCCC
1381956 TAAAC
1 TAAAC
1381961 TGCCAATGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAACCCC
Found at i:1382237 original size:114 final size:116
Alignment explanation
Indices: 1382106--1382632 Score: 273
Period size: 115 Copynumber: 4.6 Consensus size: 116
1382096 AATAAAACAT
* * *
1382106 TGTCATTTGCTTAAAAACTTTTGCGGTGCTATTG-TGAAAGCGCCA-CTAATTCTTGCCTTTTGC
1 TGTCGTTTGCTTAAAAACTTTTGCGGTGCTATTGAT-AAAGCG-CAGCTAATGCTTGACTTTTGC
* *
1382169 GGCGTTTTTAGGAATGCGCCACTAATATCTCCAAAGCTGAAAAAG-AAAACG-C
64 GGCATTTTTAGGAAAGCGCCACTAATATCTCCAAAGCT-AAAAAGAAAAACGAC
* * ** * *
1382221 TGTCGTTTGCTT-AAAACTATTGTGACGCTTTTGATAAAGTGCAGCTAATGCTTGACTTTTGCGG
1 TGTCGTTTGCTTAAAAACTTTTGCGGTGCTATTGATAAAGCGCAGCTAATGCTTGACTTTTGCGG
* * * * * *
1382285 CATTTTTTGTAAAGCGCCACTAATGTCTCTAAAGCTCAACAGAAAAACGAC
66 CATTTTTAGGAAAGCGCCACTAATATCTCCAAAGCTAAAAAGAAAAACGAC
* * * * * * * * *
1382336 -GCCGTTTGCTTAAAAATTTTTGCCGTGCT-TCCCG-TAAAGCGCCGCTAATGATTGACATCTGT
1 TGTCGTTTGCTTAAAAACTTTTGCGGTGCTAT--TGATAAAGCGCAGCTAATGCTTGACTTTTGC
*** ** * * * * *
1382398 GGCATTTTTCCTAAAATGCCACTAATGTGTCTAAAGCTCAACAA-TAAAACGAC
64 GGCATTTTTAGGAAAGCGCCACTAATATCTCCAAAGCT-AAAAAGAAAAACGAC
* * * * * * * *
1382451 -GTCGTTTG-ATAAAAACTTTTGTGGCGCT-TTGGAGAAAGTGCCGCTAATACATGATCTTTTGC
1 TGTCGTTTGCTTAAAAACTTTTGCGGTGCTATT-GATAAAGCGCAGCTAATGCTTGA-CTTTTGC
* * * * * * *
1382513 GGCGTTTCTT--GATAAACACCACTACTGTCTCTAAATCT-AAAAG-AAAACGA-
64 GGCATTT-TTAGGA-AAGCGCCACTAATATCTCCAAAGCTAAAAAGAAAAACGAC
* * * * * * * * *
1382563 TGTCGTCTACTT-AACAGTTTTGTGGCGCTTTTG-TAAAAGCGCCGCTAATGTTTGACTTTTGCG
1 TGTCGTTTGCTTAAAAACTTTTGCGGTGCTATTGAT-AAAGCGCAGCTAATGCTTGACTTTTGCG
*
1382626 GCGTTTT
65 GCATTTT
1382633 GTTTAAAGTG
Statistics
Matches: 321, Mismatches: 73, Indels: 40
0.74 0.17 0.09
Matches are distributed among these distances:
111 1 0.00
112 14 0.04
113 55 0.17
114 122 0.38
115 124 0.39
116 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (116 bp):
TGTCGTTTGCTTAAAAACTTTTGCGGTGCTATTGATAAAGCGCAGCTAATGCTTGACTTTTGCGG
CATTTTTAGGAAAGCGCCACTAATATCTCCAAAGCTAAAAAGAAAAACGAC
Found at i:1382422 original size:115 final size:114
Alignment explanation
Indices: 1382255--1382471 Score: 283
Period size: 115 Copynumber: 1.9 Consensus size: 114
1382245 ACGCTTTTGA
* * * * ** *
1382255 TAAAGTGCAGCTAATGCTTGACTTTTGCGGCATTTTTTGTAAAGCGCCACTAATGTCTCTAAAGC
1 TAAAGCGCAGCTAATGATTGACATCTGCGGCATTTTTCCTAAAACGCCACTAATGTCTCTAAAGC
* *
1382320 TCAACAGA-AAAACGACGCCGTTTGCTTAAAAATTTTTGCCGTGCTTCCCG
66 TCAACA-ATAAAACGACGCCGTTTG-ATAAAAACTTTTGCCGTGCTTCCCG
* * * *
1382370 TAAAGCGCCGCTAATGATTGACATCTGTGGCATTTTTCCTAAAATGCCACTAATGTGTCTAAAGC
1 TAAAGCGCAGCTAATGATTGACATCTGCGGCATTTTTCCTAAAACGCCACTAATGTCTCTAAAGC
*
1382435 TCAACAATAAAACGACGTCGTTTGATAAAAACTTTTG
66 TCAACAATAAAACGACGCCGTTTGATAAAAACTTTTG
1382472 TGGCGCTTTG
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
114 12 0.14
115 75 0.86
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (114 bp):
TAAAGCGCAGCTAATGATTGACATCTGCGGCATTTTTCCTAAAACGCCACTAATGTCTCTAAAGC
TCAACAATAAAACGACGCCGTTTGATAAAAACTTTTGCCGTGCTTCCCG
Found at i:1386649 original size:16 final size:16
Alignment explanation
Indices: 1386628--1386663 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1386618 TTTGGTTCGC
1386628 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1386644 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1386660 TGTA
1 TGTA
1386664 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1387037 original size:16 final size:16
Alignment explanation
Indices: 1386993--1387039 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1386983 TACTATAAAA
*
1386993 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
1387009 TATTATT-AAATATAT
1 TATAATTAAAATATAT
1387024 TATAATTAAAATATAT
1 TATAATTAAAATATAT
1387040 AATTTAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:1387111 original size:120 final size:121
Alignment explanation
Indices: 1386877--1387413 Score: 868
Period size: 120 Copynumber: 4.5 Consensus size: 121
1386867 ATTTAATTAT
* * *
1386877 ATTTAAACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
1386942 ATCAATA-TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* * *
1386997 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAGTAAAATTCTTAAAA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
1387061 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
1387117 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
1387181 ATCAAAATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* * *
1387237 ATTTGAA-GTAATTAATATTAAAAATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
*
1387301 ATCAACATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
* * * *
1387357 ATTTGAA-GTAATTAATATTAAAAATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
1387414 TAAAATAATT
Statistics
Matches: 398, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
119 63 0.16
120 333 0.84
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
ATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
Found at i:1387159 original size:18 final size:17
Alignment explanation
Indices: 1387138--1387172 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1387128 TTATTATTAA
*
1387138 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1387156 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1387173 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1387189 original size:16 final size:15
Alignment explanation
Indices: 1387164--1387193 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1387154 ATATATAATT
1387164 TAATAAAATTCTTAA
1 TAATAAAATTCTTAA
1387179 TAATCAAAATTCTTA
1 TAAT-AAAATTCTTA
1387194 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAAATTCTTAA
Found at i:1387412 original size:59 final size:59
Alignment explanation
Indices: 1387214--1387402 Score: 174
Period size: 59 Copynumber: 3.2 Consensus size: 59
1387204 CTAAAATCAT
1387214 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
* * * * * ** * *
1387273 AATATAT-A-A-T-T-TAATAAAATTCTTAA-TAATCAACATTCTTATATGAATTTACTAAAATC
1 AATATATGATACTATAAAATATAATT-TGAAGTAATTAATATT-AAAAAT--ATTT--T--AATT
*
1387332 AT
58 AA
1387334 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
1387393 AATATATGAT
1 AATATATGAT
1387403 TTAATAAAAT
Statistics
Matches: 96, Mismatches: 20, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
54 17 0.18
55 7 0.07
56 1 0.01
57 5 0.05
58 1 0.01
59 22 0.23
61 12 0.12
62 1 0.01
63 5 0.05
64 1 0.01
65 7 0.07
66 17 0.18
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (59 bp):
AATATATGATACTATAAAATATAATTTGAAGTAATTAATATTAAAAATATTTTAATTAA
Found at i:1387464 original size:47 final size:46
Alignment explanation
Indices: 1387395--1387562 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
1387385 TTAATTAAAA
*
1387395 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * *
1387442 TATATGAATTTGTATAATTTAAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
1387487 TA-AT-AATAATATATAATTTCATAA-AATTCGTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
1387533 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
1387563 ATATTAAATA
Statistics
Matches: 95, Mismatches: 14, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.23
45 9 0.09
46 8 0.08
47 46 0.48
48 7 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:1387471 original size:101 final size:92
Alignment explanation
Indices: 1387410--1387586 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 92
1387400 GATTTAATAA
* *
1387410 AATTT-AAAATAATT-ATAACTAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTAT
1 AATTTCAAAA-AATTCATAA-TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAA
1387473 TATTAAATATAATTTAA-TAATAATATAT
64 TATTAAATATAATTTAATTAATAATATAT
* * * *
1387501 AATTTCATAAAATTCGTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATA
1 AATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
1387566 TTAAATATAATTTAA-TAATAA
66 TTAAATATAATTTAATTAATAA
1387587 AATGTTCTTA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
91 73 0.94
92 5 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (92 bp):
AATTTCAAAAAATTCATAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATA
TTAAATATAATTTAATTAATAATATAT
Found at i:1387582 original size:17 final size:15
Alignment explanation
Indices: 1387551--1387589 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1387541 TTTATACAAT
1387551 TTAAAATAATTAATA
1 TTAAAATAATTAATA
1387566 TTAAATATAATTTAATA
1 TTAAA-ATAA-TTAATA
*
1387583 ATAAAAT
1 TTAAAAT
1387590 GTTCTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:1400437 original size:108 final size:108
Alignment explanation
Indices: 1400301--1400520 Score: 395
Period size: 108 Copynumber: 2.0 Consensus size: 108
1400291 ATATATTGCG
* * *
1400301 TGTAGATATGGCCAACATGATAGATCTCATGTTGTAAACAACTTGGTAGGTCTAGGTTAAAATTT
1 TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGATAGGTCTAGGTTAAAATTT
*
1400366 TCTATTAGTCCTTGTATTTTTCTAAAATTATAGATTTAGTCCA
66 TCTATTAGTCCTTGAATTTTTCTAAAATTATAGATTTAGTCCA
1400409 TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGATAGGTCTAGGTTAAAATTT
1 TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGATAGGTCTAGGTTAAAATTT
*
1400474 TCTATTAGTCCTTGAATTTTTCTAAAGTTATAGATTTAGTCCA
66 TCTATTAGTCCTTGAATTTTTCTAAAATTATAGATTTAGTCCA
1400517 TGTA
1 TGTA
1400521 CTTTAATTTG
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.39
Consensus pattern (108 bp):
TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGATAGGTCTAGGTTAAAATTT
TCTATTAGTCCTTGAATTTTTCTAAAATTATAGATTTAGTCCA
Found at i:1401577 original size:18 final size:16
Alignment explanation
Indices: 1401554--1401596 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
1401544 ATGTAATTAT
1401554 GTAAAACAAATTAACTCA
1 GTAAAACAAATT--CTCA
1401572 GTAAAA-AAATTCTCA
1 GTAAAACAAATTCTCA
1401587 GT-AAACAAAT
1 GTAAAACAAAT
1401597 GTATGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
17 5 0.21
18 6 0.25
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (16 bp):
GTAAAACAAATTCTCA
Found at i:1404863 original size:25 final size:24
Alignment explanation
Indices: 1404827--1404873 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1404817 TTTCAAAAGG
*
1404827 TTTTAAAATATTATTTTGTTTTAC
1 TTTTAAAATATTATTTTATTTTAC
1404851 TTTTAAAAATATTATTTTATTTT
1 TTTT-AAAATATTATTTTATTTT
1404874 TATTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTAAAATATTATTTTATTTTAC
Found at i:1404885 original size:25 final size:24
Alignment explanation
Indices: 1404831--1404891 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
1404821 AAAAGGTTTT
1404831 AAAATATTATTTTGTTTTACTTTTA
1 AAAATATTATTTTGTTTTAC-TTTA
*
1404856 AAAATATTATTTTATTTTTA-TTTA
1 AAAATATTATTTT-GTTTTACTTTA
*
1404880 ATAA-ATTATTTT
1 AAAATATTATTTT
1404892 CATCAAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 13 0.39
26 5 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
AAAATATTATTTTGTTTTACTTTA
Found at i:1406153 original size:38 final size:38
Alignment explanation
Indices: 1406102--1406178 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
1406092 AATTGCCCCT
*
1406102 TTCTGTTAAAAATT-ACATTCATTTCTACTATTAAAAAC
1 TTCTGTTAAAAATTCA-ATTCACTTCTACTATTAAAAAC
1406140 TTCTGTTAAAAATTCAATTCACTTCTACTATTAAAAAC
1 TTCTGTTAAAAATTCAATTCACTTCTACTATTAAAAAC
1406178 T
1 T
1406179 GGCATAACTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 36 0.97
39 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42
Consensus pattern (38 bp):
TTCTGTTAAAAATTCAATTCACTTCTACTATTAAAAAC
Found at i:1424946 original size:24 final size:25
Alignment explanation
Indices: 1424914--1424966 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
1424904 AATATTTTCA
*
1424914 AAAATTAAATAT-TTAATTAATAAT
1 AAAATTAAATATGATAATTAATAAT
*
1424938 AAAATTAAATATGATAATTAATATT
1 AAAATTAAATATGATAATTAATAAT
1424963 AAAA
1 AAAA
1424967 ATAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATTAAATATGATAATTAATAAT
Found at i:1424965 original size:19 final size:18
Alignment explanation
Indices: 1424933--1424984 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 18
1424923 TATTTAATTA
1424933 ATAATAAAATTAAATATG
1 ATAATAAAATTAAATATG
*
1424951 ATAATTAATATTAAA-A--
1 ATAA-TAAAATTAAATATG
1424967 ATAATAAAATTAAATATG
1 ATAATAAAATTAAATATG
1424985 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
18 5 0.18
19 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
ATAATAAAATTAAATATG
Found at i:1431240 original size:24 final size:24
Alignment explanation
Indices: 1431212--1431263 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1431202 TTAGTAGGTC
* *
1431212 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1431236 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1431260 AAAT
1 AAAT
1431264 CTTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1441161 original size:6 final size:6
Alignment explanation
Indices: 1441152--1441176 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1441142 AATTCTGTTC
1441152 CTTTTA CTTTTA CTTTTA CTTTTA C
1 CTTTTA CTTTTA CTTTTA CTTTTA C
1441177 ACATTGTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
CTTTTA
Found at i:1444157 original size:3 final size:3
Alignment explanation
Indices: 1444151--1444178 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1444141 TTCTTCTTCA
1444151 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1444179 GTAACAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1444663 original size:3 final size:3
Alignment explanation
Indices: 1444655--1444686 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1444645 TGAGAAGCCA
1444655 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1444687 AGTGGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1471039 original size:22 final size:22
Alignment explanation
Indices: 1471007--1471057 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1470997 ATTCTCATAC
* *
1471007 CACGAATTGCTTCGAGTATGGG
1 CACGAACTGCTTCGAGTATAGG
1471029 CACGAACTGCTTCGAGTATAGG
1 CACGAACTGCTTCGAGTATAGG
*
1471051 CTCGAAC
1 CACGAAC
1471058 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (22 bp):
CACGAACTGCTTCGAGTATAGG
Found at i:1473447 original size:41 final size:42
Alignment explanation
Indices: 1473402--1473502 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
1473392 TAAAGGTCAT
*
1473402 GACCTTTAGCGGCGCTTTGA-AAAAACGCCACTAAAGAACAG
1 GACCTTTAGCGGCGCTTTGATAAAAACACCACTAAAGAACAG
* * *
1473443 GACCTTTAGCGGCGCTTTTATTAAAACATCACTAAAGAACAG
1 GACCTTTAGCGGCGCTTTGATAAAAACACCACTAAAGAACAG
1473485 GACCTTTAGCGGCGCTTT
1 GACCTTTAGCGGCGCTTT
1473503 ACCCAAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
41 19 0.35
42 36 0.65
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (42 bp):
GACCTTTAGCGGCGCTTTGATAAAAACACCACTAAAGAACAG
Found at i:1477606 original size:38 final size:39
Alignment explanation
Indices: 1477554--1477659 Score: 142
Period size: 38 Copynumber: 2.7 Consensus size: 39
1477544 TATTTTTAGC
* *
1477554 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTTACCATTA
1 GGCGCTTTTTCAAAAACGCCGCTAAAGCCCCTACCATTA
*
1477593 -GCGCTTTTTCAAAAACGCCACTAAAGCCCCTACCATTA
1 GGCGCTTTTTCAAAAACGCCGCTAAAGCCCCTACCATTA
*
1477631 GCGGCGCTTTTTCTAAAAATGCCGCTAAA
1 --GGCGCTTTTTC-AAAAACGCCGCTAAA
1477660 AACTAGGCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
38 35 0.60
41 10 0.17
42 13 0.22
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (39 bp):
GGCGCTTTTTCAAAAACGCCGCTAAAGCCCCTACCATTA
Found at i:1477782 original size:41 final size:41
Alignment explanation
Indices: 1477549--1477782 Score: 262
Period size: 41 Copynumber: 5.8 Consensus size: 41
1477539 TAAAATATTT
* ***
1477549 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTTACCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGGGCA
* * * **
1477590 TTA---GCGCTTTTTCAAAAACGCCACTAAAGCCCCT-ACCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG-ACCTGGGCA
* * * *
1477628 TTAGCGGCGCTTTTTCTAAAAATGCCGCTAAA-AACTAGGCA
1 TTAGCGGCGC-TTTTCCAAAAACGCCGCTAAAGACCTGGGCA
* *
1477669 TTAGCGGCGCTTTTCCAAAAACGCTGCTAAAGACATGGGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGGGCA
* *
1477710 TTAGCGGCGCTTTTCTAAAAACGTCGCTAAAGACCTGGGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGGGCA
1477751 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
1477783 CCACGAAAGG
Statistics
Matches: 164, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
38 31 0.19
39 4 0.02
40 20 0.12
41 92 0.56
42 17 0.10
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGGGCA
Found at i:1477858 original size:41 final size:39
Alignment explanation
Indices: 1477820--1477895 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1477810 TGGGCTTATG
* *
1477820 TTTTTCGCAGCGTTTTTAAAAAAACGCCGCTAATGCTTA
1 TTTTTAGCAGCGTTTTTAAAAAAACGCCACTAATGCTTA
* **
1477859 TTTTTAGCGGCGTTTTTTGAAAAACGCCACTAATGCT
1 TTTTTAGCAGCGTTTTTAAAAAAACGCCACTAATGCT
1477896 CAATCTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (39 bp):
TTTTTAGCAGCGTTTTTAAAAAAACGCCACTAATGCTTA
Found at i:1477872 original size:39 final size:39
Alignment explanation
Indices: 1477820--1477955 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 39
1477810 TGGGCTTATG
* *
1477820 TTTTTCGCAGCGTTTTTAAAAAAACGCCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCTTA
** * *
1477859 TTTTTAGCGGCGTTTTTTGAAAAACGCCACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCT-TA
* * * ** * * *
1477899 TCTTTAGTGGCGATTTCCATAAAGCGTCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCTT-A
*
1477939 TTTTTACCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
1477956 TGTCCAAACG
Statistics
Matches: 73, Mismatches: 22, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
39 32 0.44
40 41 0.56
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTAAAAAAACGCCGCTAATGCTTA
Found at i:1477905 original size:40 final size:39
Alignment explanation
Indices: 1477829--1477910 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
1477819 GTTTTTCGCA
* * *
1477829 GCGTTTTTAAAAAAACGCCGCTAATGCTTATTTTTAGCG
1 GCGTTTTTAAAAAAACGCCACTAATGCTAATCTTTAGCG
** *
1477868 GCGTTTTTTGAAAAACGCCACTAATGCTCAATCTTTAGTG
1 GCGTTTTTAAAAAAACGCCACTAATGCT-AATCTTTAGCG
1477908 GCG
1 GCG
1477911 ATTTCCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 25 0.69
40 11 0.31
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (39 bp):
GCGTTTTTAAAAAAACGCCACTAATGCTAATCTTTAGCG
Found at i:1487845 original size:60 final size:60
Alignment explanation
Indices: 1487741--1488002 Score: 272
Period size: 60 Copynumber: 4.3 Consensus size: 60
1487731 GGCCTTACAT
** * * * * *
1487741 AGAGTTTTGCCACAAAGGCATCCTTTACATTGAGTGCTCACCACAAAGGTTTTCCTGTCT
1 AGAGTTTTGCCACAAAGGCATCCTTTACATCCAATACTCGCCACAAAGGCTTTCCTGTCC
* * * *
1487801 AGAGCTTTGCTACAAAGGCATCCTTTACATCCAATACTTGCCACAAAGGCTTTCCTGTCA
1 AGAGTTTTGCCACAAAGGCATCCTTTACATCCAATACTCGCCACAAAGGCTTTCCTGTCC
* ** * * * *
1487861 AGAGTTTTGCCAGAAAGGTGGTCCTTTACATCCAATAGTCGCTACATAGGCTTTCTTGTCC
1 AGAGTTTTGCCACAAAGG-CATCCTTTACATCCAATACTCGCCACAAAGGCTTTCCTGTCC
* * ** * * *
1487922 AGAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCACAAAGGCTTTCATGTCC
1 AGAGTTTTGCC-ACAAAGG-CATCCTTTACATCCAATACTCGCCACAAAGGCTTTCCTGTCC
1487984 AGAGTTTTGCCACAAAGGC
1 AGAGTTTTGCCACAAAGGC
1488003 TTTCCTGTCC
Statistics
Matches: 167, Mismatches: 33, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
60 65 0.39
61 50 0.30
62 52 0.31
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (60 bp):
AGAGTTTTGCCACAAAGGCATCCTTTACATCCAATACTCGCCACAAAGGCTTTCCTGTCC
Found at i:1487959 original size:62 final size:62
Alignment explanation
Indices: 1487824--1487995 Score: 229
Period size: 62 Copynumber: 2.8 Consensus size: 62
1487814 AAAGGCATCC
* * * * *
1487824 TTTACATCCAATACTTGCCACAAAGGCTTTCCTGTCAAGAGTTTTGCC-AGAAAGGTGGTCC
1 TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGGTGGTCA
* * * * * *
1487885 TTTACATCCAATAGTCGCTACATAGGCTTTCTTGTCCAGAGTTATGCCAAAAAAGGTTGTCA
1 TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGGTGGTCA
*
1487947 TTTACATCCAATACTCCCCACAAAGGCTTTCATGTCCAGAGTTTTGCCA
1 TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCA
1487996 CAAAGGCTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 41 0.44
62 53 0.56
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (62 bp):
TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGGTGGTCA
Found at i:1488058 original size:61 final size:60
Alignment explanation
Indices: 1487993--1488161 Score: 266
Period size: 61 Copynumber: 2.8 Consensus size: 60
1487983 CAGAGTTTTG
1487993 CCACAAAGGCTTTCCTGTCCAAAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTCA
1 CCACAAAGGCTTTCCTGT-CAAAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTCA
*
1488054 CCACAAAGGCTTTCATGTTCAAAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTCA
1 CCACAAAGGCTTTCCTG-TCAAAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTCA
* * * * *
1488115 CCACAAAGGCTTTCCTATCATAGTTGTGCTACAAAGGCTGTCCTTTA
1 CCACAAAGGCTTTCCTGTCAAAGTTGTGCCACAAAGGTTGTCATTTA
1488162 ACTGGTGTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
60 26 0.26
61 73 0.73
62 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (60 bp):
CCACAAAGGCTTTCCTGTCAAAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTCA
Found at i:1488059 original size:32 final size:32
Alignment explanation
Indices: 1488022--1488123 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
1488012 CAAAGTTGTG
1488022 CCACAAAGGTTGTCATTTACATCCAATACTCA
1 CCACAAAGGTTGTCATTTACATCCAATACTCA
** *
1488054 CCACAAAGGCTT-TCATGTT-CA---AAGTTGT-G
1 CCACAAAGG-TTGTCAT-TTACATCCAA-TACTCA
1488083 CCACAAAGGTTGTCATTTACATCCAATACTCA
1 CCACAAAGGTTGTCATTTACATCCAATACTCA
1488115 CCACAAAGG
1 CCACAAAGG
1488124 CTTTCCTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
28 4 0.07
29 17 0.31
30 2 0.04
31 2 0.04
32 26 0.47
33 4 0.07
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (32 bp):
CCACAAAGGTTGTCATTTACATCCAATACTCA
Found at i:1488062 original size:90 final size:91
Alignment explanation
Indices: 1487908--1488091 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 91
1487898 GTCGCTACAT
* * *
1487908 AGGCTTTCTTGTCCAGAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCACAAAGG
1 AGGCTTTCCTGTCCAAAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCACCACAAAGG
* *
1487973 CTTTCATGTCCAGAGTTTTGCCACAA
66 CTTTCATGTCCAAAGTTGTGCCACAA
* *
1487999 AGGCTTTCCTGTCCAAAGTTGTGCC-ACAAAGGTTGTCATTTACATCCAATACTCACCACAAAGG
1 AGGCTTTCCTGTCCAAAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCACCACAAAGG
*
1488063 CTTTCATGTTCAAAGTTGTGCCACAA
66 CTTTCATGTCCAAAGTTGTGCCACAA
1488089 AGG
1 AGG
1488092 TTGTCATTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 63 0.74
91 22 0.26
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (91 bp):
AGGCTTTCCTGTCCAAAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCACCACAAAGG
CTTTCATGTCCAAAGTTGTGCCACAA
Found at i:1488098 original size:29 final size:29
Alignment explanation
Indices: 1487964--1488091 Score: 116
Period size: 29 Copynumber: 4.3 Consensus size: 29
1487954 CCAATACTCC
* *
1487964 CCACAAAGGCTTTCATGTCCAGAGTTTTG
1 CCACAAAGGCTTTCATGTCCAAAGTTGTG
*
1487993 CCACAAAGGCTTTCCTGTCCAAAGTTGTG
1 CCACAAAGGCTTTCATGTCCAAAGTTGTG
* * ** *
1488022 CCACAAAGG-TTGTCATTTACATCCAA-TACTCA
1 CCACAAAGGCTT-TCATGT-C--CAAAGTTGT-G
*
1488054 CCACAAAGGCTTTCATGTTCAAAGTTGTG
1 CCACAAAGGCTTTCATGTCCAAAGTTGTG
1488083 CCACAAAGG
1 CCACAAAGG
1488092 TTGTCATTTA
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
28 2 0.03
29 51 0.66
30 3 0.04
31 2 0.03
32 17 0.22
33 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (29 bp):
CCACAAAGGCTTTCATGTCCAAAGTTGTG
Found at i:1496451 original size:12 final size:13
Alignment explanation
Indices: 1496428--1496452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1496418 GGTTATTTAT
1496428 TTCAATTTTTTTC
1 TTCAATTTTTTTC
1496441 TTCAATTTTTTT
1 TTCAATTTTTTT
1496453 ATTTGACTTG
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCAATTTTTTTC
Found at i:1497154 original size:20 final size:21
Alignment explanation
Indices: 1497103--1497155 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1497093 CGGAAACCCA
*
1497103 AGGTATAGGAACATAGATATG
1 AGGTATAAGAACATAGATATG
1497124 AGGTATAAGAACATA-AGTATG
1 AGGTATAAGAACATAGA-TATG
*
1497145 -GGTATCAGAAC
1 AGGTATAAGAAC
1497156 CTAGGCCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.43, C:0.08, G:0.26, T:0.23
Consensus pattern (21 bp):
AGGTATAAGAACATAGATATG
Found at i:1500173 original size:17 final size:18
Alignment explanation
Indices: 1500131--1500174 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1500121 CAATAATGCC
*
1500131 CAGGCACAAACCAATAAA
1 CAGGCCCAAACCAATAAA
* *
1500149 CGGGCCCAAACCAGT-AA
1 CAGGCCCAAACCAATAAA
1500166 CAGGCCCAA
1 CAGGCCCAA
1500175 CAACTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.43, C:0.34, G:0.18, T:0.05
Consensus pattern (18 bp):
CAGGCCCAAACCAATAAA
Found at i:1502887 original size:30 final size:30
Alignment explanation
Indices: 1502852--1502912 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1502842 AAGATTTTAT
* *
1502852 GTGTCATTTAATTATTTTAATAATGGAAGG
1 GTGTCATTTAATTATTTCAATAATGAAAGG
*
1502882 GTGTCATTTAATTATTTCAATACTGAAAGG
1 GTGTCATTTAATTATTTCAATAATGAAAGG
1502912 G
1 G
1502913 CCTAATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (30 bp):
GTGTCATTTAATTATTTCAATAATGAAAGG
Found at i:1514923 original size:53 final size:53
Alignment explanation
Indices: 1514864--1514970 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
1514854 TTTTCTATTA
* * *
1514864 AAAATTAATATGATTAACGAAATAATTAGATATGATTAAAAAGTAAACTGTAC
1 AAAATTAATACGATTAACGAAATAATTAGATATGATTAAAAAGCAAACTATAC
* *
1514917 AAAATTAATACGATTAATGGAATAATTAGATATGATTAAAAAGCAAACTATAC
1 AAAATTAATACGATTAACGAAATAATTAGATATGATTAAAAAGCAAACTATAC
1514970 A
1 A
1514971 CGTTTCATGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (53 bp):
AAAATTAATACGATTAACGAAATAATTAGATATGATTAAAAAGCAAACTATAC
Found at i:1515670 original size:18 final size:19
Alignment explanation
Indices: 1515622--1515672 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1515612 AAACATCATT
*
1515622 AAAATTTATAAAAATATTA
1 AAAATTAATAAAAATATTA
1515641 AATAA--AATTAAAAA-ATTA
1 AA-AATTAA-TAAAAATATTA
1515659 AAAATTAATAAAAA
1 AAAATTAATAAAAA
1515673 CCATTTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
17 2 0.07
18 13 0.48
19 10 0.37
20 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTAATAAAAATATTA
Found at i:1515989 original size:35 final size:36
Alignment explanation
Indices: 1515943--1516013 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
1515933 TTATTTAAAC
1515943 GTGTATCAATTATTTTATT-ATGTGTAGCCTAAAAG
1 GTGTATCAATTATTTTATTAATGTGTAGCCTAAAAG
* *
1515978 GTGTATCAATTATTTTCTTACATGTGTTGCCTAAAA
1 GTGTATCAATTATTTTATTA-ATGTGTAGCCTAAAA
1516014 AGTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 18 0.56
37 14 0.44
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (36 bp):
GTGTATCAATTATTTTATTAATGTGTAGCCTAAAAG
Found at i:1516368 original size:21 final size:21
Alignment explanation
Indices: 1516329--1516367 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1516319 GAAATTTATT
1516329 TAATATTTTTATAAATTTTAA
1 TAATATTTTTATAAATTTTAA
1516350 TAATATTTTTA-AAATTTT
1 TAATATTTTTATAAATTTT
1516368 TTTTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATTTTTATAAATTTTAA
Found at i:1520862 original size:26 final size:26
Alignment explanation
Indices: 1520825--1520880 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
1520815 CCAAATTAAA
*
1520825 TATATGTGAAAATAT-AAT-ATATTGT
1 TATAAGTGAAAAT-TGAATAATATTGT
1520850 TATAAGTGTAAAATTGAATCAATATTGT
1 TATAAGTG-AAAATTGAAT-AATATTGT
1520878 TAT
1 TAT
1520881 GAAATATGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 8 0.31
26 8 0.31
28 10 0.38
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (26 bp):
TATAAGTGAAAATTGAATAATATTGT
Found at i:1538262 original size:4 final size:4
Alignment explanation
Indices: 1538253--1538294 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
1538243 GTAATCAACA
1538253 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1538295 AAGAAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1538520 original size:26 final size:21
Alignment explanation
Indices: 1538480--1538544 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 21
1538470 AAAATTATAT
1538480 AATA-ATATA-AAAAGAAATCAA
1 AATATATATATAAAAGAAAT--A
1538501 AATAATAGTATATAATAAGATAATA
1 AAT-ATA-TATATAA-AAGA-AATA
1538526 AATATATATATAAAAGAAA
1 AATATATATATAAAAGAAA
1538545 AAAGTAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
21 5 0.13
22 5 0.13
23 8 0.21
24 7 0.18
25 6 0.16
26 4 0.11
27 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (21 bp):
AATATATATATAAAAGAAATA
Found at i:1538592 original size:15 final size:15
Alignment explanation
Indices: 1538569--1538605 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1538559 ATAACCAAAT
* *
1538569 ATAACAATATCAATA
1 ATAATAATAGCAATA
1538584 ATAATAATAGCAATA
1 ATAATAATAGCAATA
1538599 ATAATAA
1 ATAATAA
1538606 ATTAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (15 bp):
ATAATAATAGCAATA
Found at i:1548187 original size:11 final size:11
Alignment explanation
Indices: 1548173--1548197 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1548163 ATATAAATAT
1548173 TATATATTTAA
1 TATATATTTAA
1548184 TATATATTTAA
1 TATATATTTAA
1548195 TAT
1 TAT
1548198 GGGCTGGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATTTAA
Found at i:1554621 original size:40 final size:40
Alignment explanation
Indices: 1554564--1554641 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
1554554 AAATAATTAA
1554564 AAATAGGGATTTAAGAGAAATTT-GAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGGA-AGCAAATTGAGATT
* * *
1554604 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTGGAAGCAAATTGAGA
1554642 GATAATTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.27, T:0.27
Consensus pattern (40 bp):
AAATAGGGATTTAAGAGAAATTTGGAAGCAAATTGAGATT
Found at i:1564296 original size:20 final size:20
Alignment explanation
Indices: 1564255--1564298 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1564245 AAACATATAA
*
1564255 TTTTAAATTTCTTTTGTAAT
1 TTTTAAATTTCTTTAGTAAT
*
1564275 TTTTAAATATT-TTTAGTGAT
1 TTTTAAAT-TTCTTTAGTAAT
1564295 TTTT
1 TTTT
1564299 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTAAATTTCTTTAGTAAT
Found at i:1565356 original size:20 final size:20
Alignment explanation
Indices: 1565328--1565374 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1565318 GGCCTTCTGC
*
1565328 CACCGCCGCCAACGTCACGT
1 CACCACCGCCAACGTCACGT
**
1565348 CACCACCGCCATGGTCACGT
1 CACCACCGCCAACGTCACGT
1565368 CACCACC
1 CACCACC
1565375 ACCACTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.51, G:0.17, T:0.11
Consensus pattern (20 bp):
CACCACCGCCAACGTCACGT
Found at i:1566244 original size:3 final size:3
Alignment explanation
Indices: 1566236--1566266 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1566226 CTTGGCAATT
1566236 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1566267 CTACTTATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1570806 original size:19 final size:19
Alignment explanation
Indices: 1570766--1570808 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1570756 ATCTCTTTAG
* *
1570766 GCATTCATTTCATGCATGT
1 GCATTCATTGCATGCATAT
1570785 GCATTGCATTGCAT-CATAT
1 GCATT-CATTGCATGCATAT
1570804 GCATT
1 GCATT
1570809 AGATTTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (19 bp):
GCATTCATTGCATGCATAT
Found at i:1573181 original size:104 final size:104
Alignment explanation
Indices: 1573001--1573224 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
1572991 TGTATATAAA
** * *
1573001 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
1573066 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
1573105 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
1573169 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1573209 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
1573225 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:1573289 original size:26 final size:26
Alignment explanation
Indices: 1573254--1573305 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1573244 AAATGAAAAG
* *
1573254 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
1573280 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
1573306 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:1573292 original size:70 final size:72
Alignment explanation
Indices: 1573143--1573293 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 72
1573133 TCATTGGTGG
* *
1573143 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
1573208 GAGGGGT
66 GAGGGGT
***
1573215 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
1573278 GAGGGGT
66 GAGGGGT
1573285 TGCTAAGTG
1 TGCTAAGTG
1573294 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 20 0.27
71 24 0.32
72 30 0.41
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:1580724 original size:104 final size:106
Alignment explanation
Indices: 1580558--1580783 Score: 368
Period size: 105 Copynumber: 2.2 Consensus size: 106
1580548 TTGTATATAA
** * *
1580558 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGCTGGTGCTATGTGCGTGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGCTGGTGCTAAGTGCGTGATCCACCATATCT
1580623 TTGAAATGTGAAAGGGGGTTGCTATGTG-CTGATTCCCCCG
66 TTGAAATGTGAAAGGGGGTTGCTATGTGTCTGATTCCCCCG
* *
1580663 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGG-TGGTGCTAAGTGCGAT-ATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGCTGGTGCTAAGTGCG-TGATCCACCATATC
1580726 TTTGAAATGTGAAAGGGGGTTGCTATGTGTCTGATTCCCCCG
65 TTTGAAATGTGAAAGGGGGTTGCTATGTGTCTGATTCCCCCG
1580768 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
1580784 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
104 54 0.48
105 59 0.52
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.31
Consensus pattern (106 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGCTGGTGCTAAGTGCGTGATCCACCATATCT
TTGAAATGTGAAAGGGGGTTGCTATGTGTCTGATTCCCCCG
Found at i:1580848 original size:71 final size:73
Alignment explanation
Indices: 1580701--1580853 Score: 247
Period size: 73 Copynumber: 2.1 Consensus size: 73
1580691 TCATTGGTGG
* *
1580701 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGTCTGATTCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGTCTGATTCCCC
1580766 CGAGGGGT
66 CGAGGGGT
***
1580774 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTG-CTGATTCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGTCTGATTCCCC
1580837 CGAGGGGT
66 CGAGGGGT
1580845 TGCTAAGTG
1 TGCTAAGTG
1580854 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
71 27 0.36
72 18 0.24
73 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (73 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGTCTGATTCCCC
CGAGGGGT
Found at i:1584045 original size:26 final size:26
Alignment explanation
Indices: 1584010--1584059 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1584000 AATGTGAAAG
*
1584010 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
1584036 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
1584060 AGTTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.24, G:0.34, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:1584147 original size:26 final size:26
Alignment explanation
Indices: 1584112--1584161 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1584102 AAATAAAAAG
*
1584112 GGGGTTGCTATGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
1584138 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
1584162 GATTAAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:1584173 original size:102 final size:103
Alignment explanation
Indices: 1583931--1584194 Score: 415
Period size: 102 Copynumber: 2.6 Consensus size: 103
1583921 GTTGTACATA
** *
1583931 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
1583996 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
*
1584034 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1584098 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
* * *
1584136 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
1584195 AATAACGGTT
Statistics
Matches: 148, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
102 82 0.55
103 66 0.45
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
Found at i:1586022 original size:24 final size:22
Alignment explanation
Indices: 1585995--1586054 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
1585985 AAGAATTTTC
1585995 AAAAAAAAAAGAAGAAGAAGAAGA
1 AAAAAAAAAAGAAGAA-AAGAA-A
*
1586019 AAAAGAAAAAGAAAGAAAAGAAA
1 AAAAAAAAAAG-AAGAAAAGAAA
*
1586042 AAAAAGAAAAGAA
1 AAAAAAAAAAGAA
1586055 AATGAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 10 0.31
24 15 0.47
25 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAGAAGAAAAGAAA
Found at i:1586030 original size:15 final size:14
Alignment explanation
Indices: 1585995--1586066 Score: 76
Period size: 15 Copynumber: 5.0 Consensus size: 14
1585985 AAGAATTTTC
1585995 AAAAA-AAAAAGAAG
1 AAAAAGAAAAA-AAG
*
1586009 AAGAAGAAGAAAAAG
1 AAAAAGAA-AAAAAG
1586024 AAAAAGAAAGAAAAG
1 AAAAAGAAA-AAAAG
1586039 AAAAA-AAAGAAAAG
1 AAAAAGAAA-AAAAG
*
1586053 AAAATGAAAAAAAG
1 AAAAAGAAAAAAAG
1586067 GAGAGGCAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
14 23 0.45
15 25 0.49
16 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:1586061 original size:6 final size:5
Alignment explanation
Indices: 1585996--1586062 Score: 66
Period size: 5 Copynumber: 12.8 Consensus size: 5
1585986 AGAATTTTCA
*
1585996 AAAAA AAAAG AAGAAG AAGAAG AAAAAG AAAA- AGAAAG AAAAG AAAA-
1 AAAAG AAAAG AA-AAG AA-AAG -AAAAG AAAAG A-AAAG AAAAG AAAAG
1586043 AAAAG AAAAG AAAATG AAAA
1 AAAAG AAAAG AAAA-G AAAA
1586063 AAAGGAGAGG
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
4 5 0.09
5 30 0.55
6 18 0.33
7 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:1586065 original size:9 final size:8
Alignment explanation
Indices: 1585998--1586066 Score: 52
Period size: 9 Copynumber: 8.0 Consensus size: 8
1585988 AATTTTCAAA
1585998 AAAAAAAG
1 AAAAAAAG
*
1586006 AAGAAGAAG
1 AA-AAAAAG
1586015 AAGAAAAAG
1 AA-AAAAAG
1586024 --AAAAAG
1 AAAAAAAG
1586030 AAAGAAAAG
1 AAA-AAAAG
1586039 AAAAAAAAG
1 -AAAAAAAG
1586048 AAAAGAAAATG
1 -AAA-AAAA-G
1586059 AAAAAAAG
1 AAAAAAAG
1586067 GAGAGGCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 6 0.12
8 4 0.08
9 31 0.60
10 10 0.19
11 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1586066 original size:19 final size:18
Alignment explanation
Indices: 1586024--1586065 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
1586014 GAAGAAAAAG
1586024 AAAAAGAAAGAAAAGAAA
1 AAAAAGAAAGAAAAGAAA
1586042 AAAAAGAAAAGAAAATGAAA
1 AAAAAG-AAAGAAAA-GAAA
1586062 AAAA
1 AAAA
1586066 GGAGAGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 8 0.36
20 8 0.36
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAGAAAAGAAA
Found at i:1586302 original size:14 final size:14
Alignment explanation
Indices: 1586283--1586318 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1586273 AGGGTTTTCA
1586283 AGAAGCTCGTATAG
1 AGAAGCTCGTATAG
*
1586297 AGAAGCTCTTATAG
1 AGAAGCTCGTATAG
1586311 AGAAGCTC
1 AGAAGCTC
1586319 ATACTGCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (14 bp):
AGAAGCTCGTATAG
Found at i:1586529 original size:97 final size:97
Alignment explanation
Indices: 1586363--1586747 Score: 592
Period size: 97 Copynumber: 4.0 Consensus size: 97
1586353 ATTCATTTCG
* *
1586363 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTATGCTGTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
1586428 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
*
1586460 TATCTTAGCAGAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
1586525 CATCTTATCCATTGTGATAATCTTTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
* * * *
1586557 TATCTTAGCAGAATTTGCTATCTTGATTAATTTATTCATTTTGAGTTGTGCTCTGAATAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
* *
1586622 TATCTTATCCATTGTGATAATCATTTTCATCT
66 CATCTTATCCATTGTGATAATCTTTTTCATCT
** ** * * *
1586654 TATCTTAGCAAAATTTGCTATCTTGATTGGTTTATTTGTTTAGAGCTTTGCTCTCAACAAAATTT
1 TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
* *
1586719 CATTTTGTCCACTT-TGATAATCTTTTTCA
66 CATCTTATCCA-TTGTGATAATCTTTTTCA
1586748 AGCATTTTTC
Statistics
Matches: 265, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
97 263 0.99
98 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (97 bp):
TATCTTAGCAAAATTTGCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTT
CATCTTATCCATTGTGATAATCTTTTTCATCT
Found at i:1587436 original size:15 final size:16
Alignment explanation
Indices: 1587416--1587451 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1587406 TGACATTCTG
1587416 CATTC-ATGCAAATAT
1 CATTCAATGCAAATAT
1587431 CATTCAATGCAAATAT
1 CATTCAATGCAAATAT
1587447 CATTC
1 CATTC
1587452 CTACACACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (16 bp):
CATTCAATGCAAATAT
Found at i:1587717 original size:46 final size:46
Alignment explanation
Indices: 1587662--1588196 Score: 854
Period size: 46 Copynumber: 11.6 Consensus size: 46
1587652 GACTAGAAGC
*
1587662 AGCAGATCTTGTCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1587708 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAAAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * *
1587754 ATCAGATCTTATCTTCCTGTATTTGGCAGCAGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * *
1587800 AGCAGATCTTGTCTTCCTGCATTTGGCAGTGGATGAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
1587846 AGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAAGAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1587892 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * *
1587938 AGCAGATCTTGTCTTCCTATATTTGGCAGCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1587984 AGCAGATCTTGTCTTCCTGTATTTAGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1588030 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1588076 AGCAGATCTTGTCTTCCTGTATTTAGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
1588122 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
1588168 AGCAGATATTGTCTTCCTGTATCTGGCAG
1 AGCAGATCTTGTCTTCCTGTATTTGGCAG
1588197 TGAAGCAGAT
Statistics
Matches: 452, Mismatches: 37, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 452 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (46 bp):
AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
Found at i:1588464 original size:44 final size:42
Alignment explanation
Indices: 1588415--1588508 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
1588405 TAAGGTTGTG
** *
1588415 GTGGAGCAGGTTAAAGATATAAGTCTTATTTCCATGAAGTTGCA
1 GTGGAGCAGACTAAAG--ATAAGTCTCATTTCCATGAAGTTGCA
* * * *
1588459 GTGGAGTAGACTGAAGATGAGTCTCATTTCCTTGAAGTTGCA
1 GTGGAGCAGACTAAAGATAAGTCTCATTTCCATGAAGTTGCA
*
1588501 GAGGAGCA
1 GTGGAGCA
1588509 AACTGAAGCT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
42 29 0.71
44 12 0.29
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (42 bp):
GTGGAGCAGACTAAAGATAAGTCTCATTTCCATGAAGTTGCA
Found at i:1588469 original size:89 final size:89
Alignment explanation
Indices: 1588313--1588476 Score: 215
Period size: 89 Copynumber: 1.8 Consensus size: 89
1588303 AATCTCATCC
* * *
1588313 CCCTAAGGTTATAGTAGGGCAGGTTGAAGCTACAAGTCTTATCTCACTGAGGTTGCAGTAGAATA
1 CCCTAAGGTTATAGTAGGGCAGGTTAAAGATACAAGTCTTATCTCACTGAAGTTGCAGTAGAATA
1588378 GACTGAAGATAGCAAACCTTACCT
66 GACTGAAGATAGCAAACCTTACCT
* * * * * *
1588402 CCCTAAGGTTGTGGT-GGAGCAGGTTAAAGATATAAGTCTTATTTC-CATGAAGTTGCAGTGGAG
1 CCCTAAGGTTATAGTAGG-GCAGGTTAAAGATACAAGTCTTATCTCAC-TGAAGTTGCAGTAGAA
1588465 TAGACTGAAGAT
64 TAGACTGAAGAT
1588477 GAGTCTCATT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
88 3 0.05
89 61 0.95
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (89 bp):
CCCTAAGGTTATAGTAGGGCAGGTTAAAGATACAAGTCTTATCTCACTGAAGTTGCAGTAGAATA
GACTGAAGATAGCAAACCTTACCT
Found at i:1588489 original size:42 final size:42
Alignment explanation
Indices: 1588436--1588516 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
1588426 TAAAGATATA
* * * *
1588436 AGTCTTATTTCCATGAAGTTGCAGTGGAGTAGACTGAAGATG
1 AGTCTCATTTCCATGAAGTTGCAGAGGAGCAAACTGAAGATG
*
1588478 AGTCTCATTTCCTTGAAGTTGCAGAGGAGCAAACTGAAG
1 AGTCTCATTTCCATGAAGTTGCAGAGGAGCAAACTGAAG
1588517 CTACTAATCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
AGTCTCATTTCCATGAAGTTGCAGAGGAGCAAACTGAAGATG
Found at i:1589154 original size:20 final size:20
Alignment explanation
Indices: 1589116--1589154 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1589106 CGCTGCCAAT
* *
1589116 GTCACGTCGCCACCGCCACG
1 GTCACGTCACCACCACCACG
*
1589136 GTCACGTCACTACCACCAC
1 GTCACGTCACCACCACCAC
1589155 TTGTGCCATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.49, G:0.18, T:0.13
Consensus pattern (20 bp):
GTCACGTCACCACCACCACG
Found at i:1590023 original size:3 final size:3
Alignment explanation
Indices: 1590015--1590051 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1590005 CTTGGCAATT
1590015 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1590052 CTACTTATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1597003 original size:19 final size:20
Alignment explanation
Indices: 1596975--1597023 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1596965 TTGTTTCACA
* *
1596975 GAAAACAACTT-GGTCAACG
1 GAAAATAACTTAGATCAACG
1596994 GAAAATAACTTACAGATCAACG
1 GAAAATAACTT--AGATCAACG
1597016 GAAAATAA
1 GAAAATAA
1597024 GCCTTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (20 bp):
GAAAATAACTTAGATCAACG
Found at i:1604416 original size:46 final size:46
Alignment explanation
Indices: 1604349--1604533 Score: 325
Period size: 46 Copynumber: 4.0 Consensus size: 46
1604339 CATGGCAAAG
1604349 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1604395 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
* *
1604441 TATGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
* * *
1604487 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAGCCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1604533 T
1 T
1604534 ATAGCAATGT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
Found at i:1607656 original size:32 final size:30
Alignment explanation
Indices: 1607604--1607662 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
1607594 CAACCAAGTA
*
1607604 AATTAATTGATTTTTTAATTAAATAAATTT
1 AATTAATTGATTTTTAAATTAAATAAATTT
* *
1607634 AATTAGTTGAATTTTCTAAATTAATTAAA
1 AATTAATTG-ATTTT-TAAATTAAATAAA
1607663 GGAAAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 5 0.21
32 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
AATTAATTGATTTTTAAATTAAATAAATTT
Found at i:1609487 original size:25 final size:25
Alignment explanation
Indices: 1609458--1609526 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
1609448 TACCAATTTT
*
1609458 AGCTCTTATGAGCTTACCGATACTC
1 AGCTCGTATGAGCTTACCGATACTC
* * * *
1609483 AGCTCGTATGATCTTATCGTTATTC
1 AGCTCGTATGAGCTTACCGATACTC
*
1609508 AGCTCG-AAGAAGCTTACCG
1 AGCTCGTATG-AGCTTACCG
1609527 TTTACAGCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATACTC
Found at i:1609528 original size:25 final size:25
Alignment explanation
Indices: 1609458--1609536 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1609448 TACCAATTTT
* * * *
1609458 AGCTCTTATGAGCTTACCGATACTC
1 AGCTCGTAAGAGCTTACCGTTATTC
* * *
1609483 AGCTCGTATGATCTTATCGTTATTC
1 AGCTCGTAAGAGCTTACCGTTATTC
*
1609508 AGCTCG-AAGAAGCTTACCGTT-TAC
1 AGCTCGTAAG-AGCTTACCGTTATTC
1609532 AGCTC
1 AGCTC
1609537 ATATGAGCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
24 9 0.20
25 35 0.80
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (25 bp):
AGCTCGTAAGAGCTTACCGTTATTC
Found at i:1611818 original size:16 final size:17
Alignment explanation
Indices: 1611797--1611833 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1611787 AGAGATTATT
*
1611797 TAAATATA-AAAATAAA
1 TAAATATAGAAAAAAAA
1611813 TAAATATAGAAAAAAAA
1 TAAATATAGAAAAAAAA
1611830 TAAA
1 TAAA
1611834 GGAAGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
TAAATATAGAAAAAAAA
Found at i:1613673 original size:12 final size:12
Alignment explanation
Indices: 1613653--1613687 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1613643 TCACGAACAA
1613653 GCTCGTTTATTG
1 GCTCGTTTATTG
*
1613665 GCTCATTTATTG
1 GCTCGTTTATTG
*
1613677 ACTCGTTTATT
1 GCTCGTTTATT
1613688 TATTAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:1613973 original size:23 final size:23
Alignment explanation
Indices: 1613904--1613990 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
1613894 TTATTAACAT
*
1613904 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
**
1613928 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCAATTAA
**
1613951 TGTTTGTGAACATGTTCAATTAA
1 TGTTCATGAACATGTTCAATTAA
*
1613974 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
1613991 GTGAACATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.58
24 19 0.36
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:1615697 original size:26 final size:26
Alignment explanation
Indices: 1615647--1615698 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1615637 TTTAGTTTCA
*
1615647 TTAATTGTAGTTTCTTATTCCACAAG
1 TTAATTGTAGTTTCTTATGCCACAAG
*
1615673 TTAATTTTAGTTTCTTA-GCCTACAAG
1 TTAATTGTAGTTTCTTATGCC-ACAAG
1615699 AATAAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TTAATTGTAGTTTCTTATGCCACAAG
Found at i:1616786 original size:9 final size:9
Alignment explanation
Indices: 1616772--1616831 Score: 93
Period size: 9 Copynumber: 6.7 Consensus size: 9
1616762 TTTGGTTAAA
1616772 AATTAACCG
1 AATTAACCG
1616781 AATTAACCG
1 AATTAACCG
*
1616790 AATTAACCA
1 AATTAACCG
1616799 AATTAACCG
1 AATTAACCG
* *
1616808 GATTACCCG
1 AATTAACCG
1616817 AATTAACCG
1 AATTAACCG
1616826 AATTAA
1 AATTAA
1616832 ATCACTACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:1616960 original size:18 final size:18
Alignment explanation
Indices: 1616920--1616960 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1616910 AATTTTTATG
* *
1616920 ATTGGGTTGGGTTGAGTA
1 ATTGGATTGGGTTGAATA
1616938 ATTGGATTGGGTTGAATA
1 ATTGGATTGGGTTGAATA
*
1616956 CTTGG
1 ATTGG
1616961 GTTTAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (18 bp):
ATTGGATTGGGTTGAATA
Found at i:1617740 original size:14 final size:15
Alignment explanation
Indices: 1617721--1617750 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1617711 ATAAAAGCAC
1617721 TTAATT-TAGTTTCT
1 TTAATTATAGTTTCT
1617735 TTAATTATAGTTTCT
1 TTAATTATAGTTTCT
1617750 T
1 T
1617751 ATTCTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (15 bp):
TTAATTATAGTTTCT
Found at i:1617764 original size:26 final size:26
Alignment explanation
Indices: 1617735--1617786 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1617725 TTTAGTTTCT
*
1617735 TTAATTATAGTTTCTTATTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
*
1617761 TTAATTTTAGTTTCTTAGTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
1617787 AATAAAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (26 bp):
TTAATTATAGTTTCTTAGTCTACAAG
Found at i:1623666 original size:21 final size:20
Alignment explanation
Indices: 1623628--1623666 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1623618 AATATATAAT
* *
1623628 AATTTTTTAATTTTAATTAG
1 AATTTTTTAAATTAAATTAG
1623648 AATTTTTATAAATTAAATT
1 AATTTTT-TAAATTAAATT
1623667 TAAATAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTTTTAAATTAAATTAG
Found at i:1624310 original size:13 final size:13
Alignment explanation
Indices: 1624292--1624317 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1624282 AACATTATTA
1624292 ATTTTATAATTTT
1 ATTTTATAATTTT
1624305 ATTTTATAATTTT
1 ATTTTATAATTTT
1624318 TTTAGGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:1628450 original size:6 final size:6
Alignment explanation
Indices: 1628431--1628469 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
1628421 TGTAAATGAA
1628431 TTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TT
1628470 GAGAAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCATT
Found at i:1628581 original size:10 final size:10
Alignment explanation
Indices: 1628566--1628594 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1628556 ATTTCTCCAA
1628566 TTTTATTCAT
1 TTTTATTCAT
1628576 TTTTATTCAT
1 TTTTATTCAT
1628586 TTTTATTCA
1 TTTTATTCA
1628595 ACATGCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATTCAT
Found at i:1634222 original size:21 final size:21
Alignment explanation
Indices: 1634196--1634235 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1634186 CAAAACAATG
*
1634196 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTGACTTTTAACTTGA
1634217 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
1634236 TAGATAAGGT
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:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTGA
Found at i:1634585 original size:17 final size:18
Alignment explanation
Indices: 1634552--1634591 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1634542 TATTTTTTAG
**
1634552 ATTTTTTTAAATTTAT-A
1 ATTTTTTTAAAAATATAA
1634569 ATTTTTTTAAAAATATAA
1 ATTTTTTTAAAAATATAA
1634587 ATTTT
1 ATTTT
1634592 AGGATTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTTTAAAAATATAA
Found at i:1638840 original size:5 final size:5
Alignment explanation
Indices: 1638830--1638854 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1638820 AAACAAAAAC
1638830 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
1638855 GATAATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:1639179 original size:18 final size:17
Alignment explanation
Indices: 1639135--1639179 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1639125 TATAAGTTAA
1639135 AATTATAAATTTAGATAT
1 AATTAT-AATTTAGATAT
1639153 AATTATAATTTA-ATACT
1 AATTATAATTTAGATA-T
1639170 AAGTTATAAT
1 AA-TTATAAT
1639180 AATTGCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.12
17 9 0.36
18 13 0.52
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATTATAATTTAGATAT
Done.