Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008522.1 Hibiscus syriacus cultivar Beakdansim tig00111390_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1416293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1032488 original size:14 final size:14
Alignment explanation
Indices: 1032445--1032506 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 14
1032435 AGGGGGAGTA
1032445 ATTTTACAAAATTG
1 ATTTTACAAAATTG
* *
1032459 A-TTT-CAAAAGTA
1 ATTTTACAAAATTG
1032471 ATTTTACAAAATTG
1 ATTTTACAAAATTG
*
1032485 ATTTCA-AAAATT-
1 ATTTTACAAAATTG
*
1032497 ATTTTTCAAA
1 ATTTTACAAA
1032507 GAAAATCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
12 11 0.29
13 15 0.39
14 12 0.32
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (14 bp):
ATTTTACAAAATTG
Found at i:1032500 original size:26 final size:26
Alignment explanation
Indices: 1032443--1032506 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
1032433 TAAGGGGGAG
*
1032443 TAATTTTACAAAATTGATTTCAAAAG
1 TAATTTTACAAAATTGATTTCAAAAA
1032469 TAATTTTACAAAATTGATTTCAAAAA
1 TAATTTTACAAAATTGATTTCAAAAA
* *
1032495 TTATTTTTCAAA
1 TAATTTTACAAA
1032507 GAAAATCTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (26 bp):
TAATTTTACAAAATTGATTTCAAAAA
Found at i:1032949 original size:19 final size:19
Alignment explanation
Indices: 1032921--1032972 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1032911 AATGCATTTT
*
1032921 ATGCACCGATGCACATACC
1 ATGCATCGATGCACATACC
1032940 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1032959 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1032973 TCCTAGCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:1034504 original size:55 final size:55
Alignment explanation
Indices: 1034434--1034829 Score: 542
Period size: 55 Copynumber: 7.2 Consensus size: 55
1034424 CTATTTGTAC
* * ***
1034434 TATCGGCACTAAGTGTGCAAAACCACAGAATTTATAATATGTTTATGAACGATAA
1 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
* *
1034489 TATCGACATTAAGTGTGCAAAACCACATAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
* * * * * *
1034544 TATCTG-TATTAAGTGTACAAAACCACATAATTCATAAAATATTTATGAACGACCG
1 TATC-GACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
1034599 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
* * * *
1034654 TATCGACACTAAGTGTGCAAAACCACGGAATTAATAATGTGTTTAAGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
* * * * * *
1034709 TATCGGCACTAAGTGTGAAAAACTACGGAATTCATAATATGTTTATGAATGACTG
1 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
* *
1034764 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACAACCA
1 TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
*
1034819 TATTGACACTA
1 TATCGACACTA
1034830 CATGTACACC
Statistics
Matches: 301, Mismatches: 38, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
54 1 0.00
55 299 0.99
56 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (55 bp):
TATCGACACTAAGTGTGCAAAACCACAGAATTCATAATATGTTTATGAACGACCG
Found at i:1048393 original size:19 final size:20
Alignment explanation
Indices: 1048353--1048393 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1048343 AAGTTAGAGT
*
1048353 TTAGAGTTTATGGGTTAGGG
1 TTAGAGTTTATGGGTTAAGG
*
1048373 TTAGAG-TTATGGTTTAAGG
1 TTAGAGTTTATGGGTTAAGG
1048392 TT
1 TT
1048394 TAAGGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (20 bp):
TTAGAGTTTATGGGTTAAGG
Found at i:1048395 original size:7 final size:7
Alignment explanation
Indices: 1048383--1048443 Score: 95
Period size: 7 Copynumber: 8.7 Consensus size: 7
1048373 TTAGAGTTAT
1048383 GGTTTAA
1 GGTTTAA
1048390 GGTTTAA
1 GGTTTAA
1048397 GGTTTAA
1 GGTTTAA
1048404 GGTTTAA
1 GGTTTAA
1048411 GGTTTAA
1 GGTTTAA
*
1048418 GGTTTAG
1 GGTTTAA
1048425 GGTTTAA
1 GGTTTAA
* *
1048432 GATTTAG
1 GGTTTAA
1048439 GGTTT
1 GGTTT
1048444 TAAGTTAGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (7 bp):
GGTTTAA
Found at i:1050381 original size:3 final size:3
Alignment explanation
Indices: 1050373--1050407 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1050363 CGCCCGTTCT
1050373 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1050408 GTAATCACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1052364 original size:20 final size:20
Alignment explanation
Indices: 1052335--1052373 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1052325 ATAGCTCATA
*
1052335 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1052355 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1052374 ATGGCGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1054523 original size:54 final size:54
Alignment explanation
Indices: 1054458--1054744 Score: 351
Period size: 54 Copynumber: 5.3 Consensus size: 54
1054448 TGACCGAATG
* * *
1054458 GGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * * *
1054512 GGCACTGTGTGTGCAACTTAAAAAATTGATAATAATTTTATGAATTTCCTTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
1054566 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
1054620 GGCACTGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTACT
1 GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * * * * *
1054674 GACACTGTGTGTGCAACCCCACGTAATTCAGAATGAGTTTGTGAA-TTACAGTATT
1 GGCACTGTGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATT
* *
1054729 GACACTATGTGTGCAA
1 GGCACTGTGTGTGCAA
1054745 AACATAGAAT
Statistics
Matches: 203, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
54 162 0.80
55 41 0.20
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:1060359 original size:16 final size:16
Alignment explanation
Indices: 1060338--1060370 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1060328 TTTTATATGA
1060338 GATTTCATAAAATGGG
1 GATTTCATAAAATGGG
1060354 GATTTCATAAAATGGG
1 GATTTCATAAAATGGG
1060370 G
1 G
1060371 TTTTAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (16 bp):
GATTTCATAAAATGGG
Found at i:1061276 original size:54 final size:54
Alignment explanation
Indices: 1061227--1061664 Score: 601
Period size: 54 Copynumber: 8.1 Consensus size: 54
1061217 GGCATTATGC
* * *
1061227 GTGCAACTTAAGAAATTCATAATGAGTTTATAAATTTTTGTATTGGCATTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
* * * *
1061281 ATGCAACTTAAAAAATTCATAATAAGTTTATTAATTTTTGTATTGGCGCTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
* * * *
1061335 ATGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTCTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
* * *
1061389 GTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCGTTTTGGCACTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
* *
1061443 GTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCT-TATTGGCATTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTT-TGTATTGGCACTGTGT
* * *
1061497 GTGAAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCATTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
* **
1061551 GTGCAACTTTAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
* * * * *
1061605 -TGCAACCTAATAAATTCATAATAAGTTTATGAATTTCTATGTTGGCACTGTGT
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
*
1061658 GTACAAC
1 GTGCAAC
1061665 CCCACGTTAT
Statistics
Matches: 345, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
53 48 0.14
54 297 0.86
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (54 bp):
GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTGTGT
Found at i:1065695 original size:15 final size:15
Alignment explanation
Indices: 1065671--1065737 Score: 107
Period size: 15 Copynumber: 4.5 Consensus size: 15
1065661 CATTCCTGAT
1065671 AATGATAGACTGAAG
1 AATGATAGACTGAAG
*
1065686 AATAATAGACTGAAG
1 AATGATAGACTGAAG
1065701 AATGATAGACTGAAG
1 AATGATAGACTGAAG
*
1065716 AATGATAGCCTGAAG
1 AATGATAGACTGAAG
*
1065731 AAAGATA
1 AATGATA
1065738 TTCTTTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.49, C:0.07, G:0.24, T:0.19
Consensus pattern (15 bp):
AATGATAGACTGAAG
Found at i:1067986 original size:20 final size:22
Alignment explanation
Indices: 1067942--1067986 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1067932 GAAATATTGG
*
1067942 TACCATAGTATAGAAGTATCGA
1 TACCATAGTATAGAAGTACCGA
*
1067964 TACCATAG-A-AGAGGTACCGA
1 TACCATAGTATAGAAGTACCGA
1067984 TAC
1 TAC
1067987 TAAGCAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 1 0.05
22 8 0.38
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (22 bp):
TACCATAGTATAGAAGTACCGA
Found at i:1068374 original size:54 final size:54
Alignment explanation
Indices: 1068315--1068806 Score: 616
Period size: 54 Copynumber: 9.2 Consensus size: 54
1068305 ATGGGAAATA
* * * *
1068315 TGTGTGCAACTTAAGAAATTAATTATTAGTTTATGAATTTCCCTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* *
1068369 TGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCTTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* * *
1068423 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGTACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* * * * *
1068477 TGTGTACAACTTAAGAAATTCAAAATAAG--TCTGAATTTTCGTATTGGCACTT
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* * * **
1068529 TGTGTGCAACCTAAGAAATTAATAATGAG--TATGAATTTTTGTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* *
1068581 TGTGTGCAACTTAAGAAATTC-TCAATAAGTTTATGAATTTCTGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCAT-AATAAGTTTATGAATTTCCGTATTGGCACTG
1068635 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* * **
1068689 TGTGTGTAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGTGCTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
* * * * * * * * *
1068743 TGTGTGCTACTCCATGTAATTCATAATGAGTTTGTGAATTACCGTATTGCCACTA
1 TGTGTGCAACT-TAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
*
1068798 CGTGTGCAA
1 TGTGTGCAA
1068807 AACATATAAT
Statistics
Matches: 384, Mismatches: 49, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
51 1 0.00
52 88 0.23
54 254 0.66
55 41 0.11
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (54 bp):
TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTG
Found at i:1068691 original size:212 final size:214
Alignment explanation
Indices: 1068315--1068737 Score: 629
Period size: 212 Copynumber: 2.0 Consensus size: 214
1068305 ATGGGAAATA
* * *
1068315 TGTGTGCAACTTAAGAAATTAATTATTAGTTTATGAATTTCCCTATTGGCACTGTGTGTGCAACT
1 TGTGTGCAACCTAAGAAATTAATAATGAG-TTATGAATTTCCCTATTGGCACTGTGTGTGCAACT
* *
1068380 TAAGAAATTCATAATGAGTTTATGAATTTCCTTATTGGCACTGTGTGTGCAACCTAAGAAATTCA
65 TAAGAAATTCATAATAAGTTTATGAATTTCCTTATTGGCACTATGTGTGCAACCTAAGAAATTCA
* * * *
1068445 TAATAAGTTTATGAATTTTCGTATTGGTACTGTGTGTACAACTTAAGAAATTCAAAATAAG-TCT
130 TAATAAGTTTATGAATTTCCGTATTGGCACTGTGTGTACAACCTAAGAAATTCAAAATAAGTTAT
*
1068509 GAATTTTCGTATTGGCACTT
195 GAATTTCCGTATTGGCACTT
***
1068529 TGTGTGCAACCTAAGAAATTAATAATGAG-TATGAATTTTTGTATTGGCACTGTGTGTGCAACTT
1 TGTGTGCAACCTAAGAAATTAATAATGAGTTATGAATTTCCCTATTGGCACTGTGTGTGCAACTT
*
1068593 AAGAAATTC-TCAATAAGTTTATGAATTT-CTGTATTGGCACTATGTGTGCAACTTAAGAAATTC
66 AAGAAATTCAT-AATAAGTTTATGAATTTCCT-TATTGGCACTATGTGTGCAACCTAAGAAATTC
** *
1068656 ATAATAAGTTTATGAATTTCCGTATTGGCACTGTGTGTGTAACCTAAGAAATTCATAATAAGTTT
129 ATAATAAGTTTATGAATTTCCGTATTGGCACTGTGTGTACAACCTAAGAAATTCAAAATAAG-TT
1068721 ATGAATTTCCGTATTGG
193 ATGAATTTCCGTATTGG
1068738 TGCTGTGTGT
Statistics
Matches: 188, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
211 3 0.02
212 143 0.76
214 42 0.22
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (214 bp):
TGTGTGCAACCTAAGAAATTAATAATGAGTTATGAATTTCCCTATTGGCACTGTGTGTGCAACTT
AAGAAATTCATAATAAGTTTATGAATTTCCTTATTGGCACTATGTGTGCAACCTAAGAAATTCAT
AATAAGTTTATGAATTTCCGTATTGGCACTGTGTGTACAACCTAAGAAATTCAAAATAAGTTATG
AATTTCCGTATTGGCACTT
Found at i:1072532 original size:23 final size:23
Alignment explanation
Indices: 1072506--1072554 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1072496 GAATGACCAT
*
1072506 ATAGGTTTGCACCGAAGAGCCAC
1 ATAGGTTTACACCGAAGAGCCAC
* * *
1072529 ATAGGTTTATACTGAAGTGCCAC
1 ATAGGTTTACACCGAAGAGCCAC
1072552 ATA
1 ATA
1072555 TTTGTCCCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (23 bp):
ATAGGTTTACACCGAAGAGCCAC
Found at i:1072574 original size:21 final size:21
Alignment explanation
Indices: 1072481--1072596 Score: 76
Period size: 21 Copynumber: 5.3 Consensus size: 21
1072471 CATTGAAGTG
*
1072481 CCACATAATTGTCCCGAATGA
1 CCACATATTTGTCCCGAATGA
*
1072502 CCATATAGGTTTG-CACCGAA-GA
1 CCACATA--TTTGTC-CCGAATGA
* * *
1072524 GCCACATAGGTTTATACTGAAGTG-
1 -CCACATA--TTTGTCCCGAA-TGA
1072548 CCACATATTTGTCCCGAATGA
1 CCACATATTTGTCCCGAATGA
* * *
1072569 CCACATAATTATCCCGAAGGA
1 CCACATATTTGTCCCGAATGA
1072590 CCACATA
1 CCACATA
1072597 AAACCCTCGA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
20 2 0.03
21 39 0.52
22 3 0.04
23 30 0.40
25 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
CCACATATTTGTCCCGAATGA
Found at i:1073305 original size:20 final size:20
Alignment explanation
Indices: 1073289--1073338 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1073279 CATCCTTTAG
1073289 GTATCGATACTACCCTTATA
1 GTATCGATACTACCCTTATA
1073309 GTATCGATACTACCCTTATA
1 GTATCGATACTACCCTTATA
1073329 GTATCGATAC
1 GTATCGATAC
1073339 CTAATCAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (20 bp):
GTATCGATACTACCCTTATA
Found at i:1074253 original size:20 final size:20
Alignment explanation
Indices: 1074228--1074266 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1074218 GTATATAGCT
*
1074228 GTTGGGAATATTTTGGAGCA
1 GTTGGGAATATTTTAGAGCA
1074248 GTTGGGAATATTTTAGAGC
1 GTTGGGAATATTTTAGAGC
1074267 CGTTTGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.36
Consensus pattern (20 bp):
GTTGGGAATATTTTAGAGCA
Found at i:1079572 original size:21 final size:21
Alignment explanation
Indices: 1079548--1079597 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1079538 TACCAAAGTG
* *
1079548 CCACA-AATTTGTCCCGAAGGA
1 CCACATAATTT-TCCCAAAAGA
1079569 CCACATAATTTTCCCAAAAGA
1 CCACATAATTTTCCCAAAAGA
1079590 CCACATAA
1 CCACATAA
1079598 AACCCTCGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (21 bp):
CCACATAATTTTCCCAAAAGA
Found at i:1083158 original size:20 final size:20
Alignment explanation
Indices: 1083129--1083167 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1083119 TAAGAGCTCA
*
1083129 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1083149 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1083168 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1084988 original size:18 final size:19
Alignment explanation
Indices: 1084951--1084988 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1084941 CCAGCATTGA
*
1084951 TTGCATTTAATTTTCATTT
1 TTGCATTTAATTTCCATTT
1084970 TTGC-TTTAATTTCC-TTT
1 TTGCATTTAATTTCCATTT
1084987 TT
1 TT
1084989 ATTTGTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 9 0.50
19 4 0.22
ACGTcount: A:0.16, C:0.13, G:0.05, T:0.66
Consensus pattern (19 bp):
TTGCATTTAATTTCCATTT
Found at i:1089223 original size:202 final size:204
Alignment explanation
Indices: 1088877--1089282 Score: 798
Period size: 202 Copynumber: 2.0 Consensus size: 204
1088867 TGAAATAGGG
1088877 GTACAAGTTCCTGATAGCCCAAACGTCTTTGAAAATTTATTGAGATATGTGTCGAGGTTGCATGA
1 GTACAAGTTCCTGATAGCCCAAACGTCTTTGAAAATTTATTGAGATATGTGTCGAGGTTGCATGA
1088942 TGAGTTTGGAAGGAATGAAAGAGTCATCTATTATCTTAGCAAGAAGAATATTGATTGTGAGATAT
66 TGAGTTTGGAAGGAATGAAAGAGTCATCTATTATCTTAGCAAGAAGAATATTGATTGTGAGATAT
1089007 GATACCTGCCAATCCAAGACATATGATGTGC-TTGGTATGGGCTACCTGAAGGC-CAGGCAGTAC
131 GATACCTGCCAATCCAAGACATATGATGTGCTTTGGTATGGGCTACCTGAAGGCTCAGGCAGTAC
1089070 ATGTTATAC
196 ATGTTATAC
1089079 GTACAAGTTCCTGATAGCCCAAACGTCTTTGAAAATTTATTGAGATATGTGTCGAGGTTGCATGA
1 GTACAAGTTCCTGATAGCCCAAACGTCTTTGAAAATTTATTGAGATATGTGTCGAGGTTGCATGA
1089144 TGAGTTTGGAAGGAATGAAAGAGTCATCTATTATCTTAGCAAGAAGAATATTGATTGTGAGATAT
66 TGAGTTTGGAAGGAATGAAAGAGTCATCTATTATCTTAGCAAGAAGAATATTGATTGTGAGATAT
1089209 GATACCTGCCAATCCAAGACATATGATGTGCTTTGGTATGGGCTACCTGAAGGCTCAGGCAGTAC
131 GATACCTGCCAATCCAAGACATATGATGTGCTTTGGTATGGGCTACCTGAAGGCTCAGGCAGTAC
1089274 ATGTTATAC
196 ATGTTATAC
1089283 CATACTACTC
Statistics
Matches: 202, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
202 161 0.80
203 22 0.11
204 19 0.09
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (204 bp):
GTACAAGTTCCTGATAGCCCAAACGTCTTTGAAAATTTATTGAGATATGTGTCGAGGTTGCATGA
TGAGTTTGGAAGGAATGAAAGAGTCATCTATTATCTTAGCAAGAAGAATATTGATTGTGAGATAT
GATACCTGCCAATCCAAGACATATGATGTGCTTTGGTATGGGCTACCTGAAGGCTCAGGCAGTAC
ATGTTATAC
Found at i:1090183 original size:14 final size:14
Alignment explanation
Indices: 1090164--1090203 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1090154 ACTACACTCA
1090164 AAGAAAGGAAAAGG
1 AAGAAAGGAAAAGG
1090178 AAGAAAAGGAAAAGG
1 AAG-AAAGGAAAAGG
*
1090193 AA-AAATGAAAA
1 AAGAAAGGAAAA
1090204 ATGAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 3 0.12
15 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (14 bp):
AAGAAAGGAAAAGG
Found at i:1090232 original size:12 final size:11
Alignment explanation
Indices: 1090215--1090271 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
1090205 TGAAAAAATG
*
1090215 AAAAAATGAAA
1 AAAAAAAGAAA
1090226 AAAAAAAGAAGA
1 AAAAAAAGAA-A
*
1090238 AAAAGAAGAAA
1 AAAAAAAGAAA
1090249 AAAAGAAA-AAA
1 AAAA-AAAGAAA
* *
1090260 GAGAAAAGAAA
1 AAAAAAAGAAA
1090271 A
1 A
1090272 CTGAAATGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 3 0.08
11 22 0.59
12 12 0.32
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:1090240 original size:9 final size:9
Alignment explanation
Indices: 1090228--1090258 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1090218 AAATGAAAAA
1090228 AAAAAGAAG
1 AAAAAGAAG
1090237 AAAAAGAAG
1 AAAAAGAAG
1090246 AAAAA-AAG
1 AAAAAGAAG
1090254 AAAAA
1 AAAAA
1090259 AGAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:1090259 original size:7 final size:7
Alignment explanation
Indices: 1090167--1090271 Score: 77
Period size: 7 Copynumber: 14.1 Consensus size: 7
1090157 ACACTCAAAG
*
1090167 AAAGGAA
1 AAAGAAA
*
1090174 AAGGAAGA
1 AAAGAA-A
*
1090182 AAAGGAA
1 AAAGAAA
*
1090189 AAGGAAA
1 AAAGAAA
*
1090196 AATGAAA
1 AAAGAAA
*
1090203 AATGAAA
1 AAAGAAA
1090210 AAATGAAA
1 AAA-GAAA
1090218 AAATGAAA
1 AAA-GAAA
1090226 AAA-AAA
1 AAAGAAA
1090232 AGAAGAAAA
1 A-AAG-AAA
1090241 AGAAGAAAA
1 A-AAG-AAA
1090250 AAAGAAA
1 AAAGAAA
*
1090257 AAAGAGA
1 AAAGAAA
1090264 AAAGAAA
1 AAAGAAA
1090271 A
1 A
1090272 CTGAAATGAG
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
6 4 0.05
7 43 0.52
8 23 0.28
9 13 0.16
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:1090259 original size:9 final size:9
Alignment explanation
Indices: 1090207--1090271 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
1090197 ATGAAAAATG
*
1090207 AAAAAATGA
1 AAAAAAAGA
1090216 AAAAATGAA-A
1 AAAAA--AAGA
1090226 AAAAAAAGA
1 AAAAAAAGA
*
1090235 AGAAAAAGAA
1 AAAAAAAG-A
1090245 GAAAAAAAGA
1 -AAAAAAAGA
*
1090255 AAAAAGAGA
1 AAAAAAAGA
1090264 AAAGAAAA
1 AAA-AAAA
1090272 CTGAAATGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
8 2 0.04
9 24 0.53
10 11 0.24
11 8 0.18
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:1092211 original size:55 final size:55
Alignment explanation
Indices: 1092141--1092777 Score: 841
Period size: 55 Copynumber: 11.6 Consensus size: 55
1092131 AATAATTTTT
* * * * **
1092141 AGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATTATTTTTAAATGACCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * ** *
1092196 AGAAACTAAGTCTAATTTTCAGAAGTTTATTGAT-ATTTTTAAATGAAATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * *
1092250 AGAAGCTAAGTCCGATTTTCGGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * *
1092305 AGAAACTAAGTCTGATTTTCAAAAGCTTCTTGAT-ATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* *
1092359 AGAAATTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* *
1092414 AGAAACTAAGTATGATTTTCAGAAGTTTCTTGATGA-TTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
1092468 AGAAACTAAGTCTAATTTTCAGAAGTTTCTTAATGATTTTCAAATGAGTTTTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG---TTTTCAA
* *
1092526 AGAAAC-AAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
1092580 AGAAACTAATTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
** * *
1092635 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
1092690 AGAAACTAAATCTGATTTTCATAAGTTTATTGATGATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
*
1092745 AGAAACTAAGTCTGATTTCCAGAAGTTTCTTGA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
1092778 CATGATTATT
Statistics
Matches: 512, Mismatches: 63, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
54 156 0.30
55 306 0.60
57 37 0.07
58 13 0.03
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
Found at i:1092282 original size:109 final size:109
Alignment explanation
Indices: 1092141--1092831 Score: 860
Period size: 109 Copynumber: 6.3 Consensus size: 109
1092131 AATAATTTTT
* * * * *
1092141 AGAAACTAAGCCTAATTTTCAGGAGTTTCTTGATTATTTTTAAATGACCTTTCAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
* * ** *
1092206 TCTAATTTTCAGAAGTTTATTGATATTTTTAAATGAAATTTGAA
66 TCTGATTTTCAGAAGTTTCTTGATATTTTTAAATGAGTTTTTAA
* * * *
1092250 AGAAGCTAAGTCCGATTTTCGGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
* *
1092315 TCTGATTTTCAAAAGCTTCTTGATATTTTTAAATGAGTTTTTAA
66 TCTGATTTTCAGAAGTTTCTTGATATTTTTAAATGAGTTTTTAA
* * *
1092359 AGAAATTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTAAATGAGTTTTCAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
*
1092424 TATGATTTTCAGAAGTTTCTTGATGA-TTTTAAATGAGTTTTTAA
66 TCTGATTTTCAGAAGTTTCTTGAT-ATTTTTAAATGAGTTTTTAA
* * * * *
1092468 AGAAACTAAGTCTAATTTTCAGAAGTTTCTTAATGATTTTCAAATGAGTTTTTTTTAAAGAAAC-
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG---CTTTCAAAGAAACT
* * *
1092532 AAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAA
63 AAGTCTGATTTTCAGAAGTTTCTTGA-TATTTTTAAATGAGTTTTTAA
* * * * *
1092580 AGAAACTAATTCTGATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGTTTTTAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
* *
1092645 TCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGTTTTTAA
66 TCTGATTTTCAGAAGTTTCTTGA-TATTTTTAAATGAGTTTTTAA
* * *
1092690 AGAAACTAAATCTGATTTTCATAAGTTTATTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
* * **
1092755 TCTGATTTCCAGAAGTTTCTTGACATGATT--AT---TTTTTAA
66 TCTGATTTTCAGAAGTTTCTTGATATTTTTAAATGAGTTTTTAA
*
1092794 AGAAACTAAG-CATGATTTTCATG-GGTTTCTTGATGATT
1 AGAAACTAAGTC-TGATTTTCA-GAAGTTTCTTGATGATT
1092832 ATTTCCAATG
Statistics
Matches: 513, Mismatches: 60, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
103 1 0.00
104 38 0.07
107 2 0.00
109 251 0.49
110 125 0.24
111 26 0.05
112 70 0.14
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (109 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTCAAAGAAACTAAG
TCTGATTTTCAGAAGTTTCTTGATATTTTTAAATGAGTTTTTAA
Found at i:1092822 original size:49 final size:47
Alignment explanation
Indices: 1092743--1092835 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 47
1092733 ATGAGCTTTC
1092743 AAAGAAACTAAGTCTGATTTCCAGAAGTTTCTTGACATGATTATTTTTT
1 AAAGAAACTAAGTCTGATTTCCAGAAGTTTCTTG--ATGATTATTTTTT
* *
1092792 AAAGAAACTAAG-CATGATTTTCATG-GGTTTCTTGATGATTATTT
1 AAAGAAACTAAGTC-TGATTTCCA-GAAGTTTCTTGATGATTATTT
1092836 CCAATGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
47 10 0.25
48 1 0.03
49 28 0.70
50 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (47 bp):
AAAGAAACTAAGTCTGATTTCCAGAAGTTTCTTGATGATTATTTTTT
Found at i:1095378 original size:14 final size:14
Alignment explanation
Indices: 1095359--1095394 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1095349 TTTTTATTTA
*
1095359 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
1095373 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
1095387 TTTAATTT
1 TTTAATTT
1095395 TTTGTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:1096150 original size:2 final size:2
Alignment explanation
Indices: 1096145--1096237 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
1096135 TTTTCGTGTG
1096145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1096186 TA TA TA TA TA 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 TA TA TA TA TA
1096228 TA TA TA TA TA
1 TA TA TA TA TA
1096238 GATGTTTTAT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1097072 original size:21 final size:20
Alignment explanation
Indices: 1097040--1097087 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1097030 AATCTAAACC
*
1097040 AAATT-AACAAAAATCATTAA
1 AAATTAAACAAAAAT-AATAA
*
1097060 AAATTAAATAAAAATAATAA
1 AAATTAAACAAAAATAATAA
*
1097080 AAACTAAA
1 AAATTAAA
1097088 AGATCAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (20 bp):
AAATTAAACAAAAATAATAA
Found at i:1100661 original size:113 final size:113
Alignment explanation
Indices: 1100532--1100757 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
1100522 TTTAAAACAG
1100532 TAATTGAATGACCAAAACAAAAAATAATAATAATAAATAAGTGACTAAATAGATAATTTTGAGCC
1 TAATTGAATGACCAAAACAAAAAATAATAATAATAAATAAGTGACTAAATAGATAATTTTGAGCC
1100597 CTAGAAAGTTATATCCCTCCTACACAAACTCTGTTACAACACTTTATA
66 CTAGAAAGTTATATCCCTCCTACACAAACTCTGTTACAACACTTTATA
1100645 TAATTGAATGACCAAAACAAAAAATAATAATAATAAATAAGTGACTAAATAGATAATTTTGAGCC
1 TAATTGAATGACCAAAACAAAAAATAATAATAATAAATAAGTGACTAAATAGATAATTTTGAGCC
1100710 CTAGAAAGTTATATCCCTCCTACACAAACTCTGTTACAACACTTTATA
66 CTAGAAAGTTATATCCCTCCTACACAAACTCTGTTACAACACTTTATA
1100758 CATATAGTTA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (113 bp):
TAATTGAATGACCAAAACAAAAAATAATAATAATAAATAAGTGACTAAATAGATAATTTTGAGCC
CTAGAAAGTTATATCCCTCCTACACAAACTCTGTTACAACACTTTATA
Found at i:1106650 original size:2 final size:2
Alignment explanation
Indices: 1106639--1106683 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1106629 TAAAGACGAT
1106639 TA TA -A TA TA 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 TA TA TA TA TA
1106680 TA TA
1 TA TA
1106684 ATTCAGCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1107537 original size:32 final size:33
Alignment explanation
Indices: 1107495--1107562 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 33
1107485 TTACAAACTT
*
1107495 CCTAG-TTTTTACGGGCTAAACTAGAACCTTTC
1 CCTAGCTTTTAACGGGCTAAACTAGAACCTTTC
*
1107527 CCTAGCTTTTACACGGGCTAAGCTAGAACCTTTC
1 CCTAGCTTTTA-ACGGGCTAAACTAGAACCTTTC
1107561 CC
1 CC
1107563 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 5 0.16
33 4 0.12
34 23 0.72
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (33 bp):
CCTAGCTTTTAACGGGCTAAACTAGAACCTTTC
Found at i:1107977 original size:19 final size:20
Alignment explanation
Indices: 1107910--1107993 Score: 107
Period size: 21 Copynumber: 4.2 Consensus size: 20
1107900 TTGTTAGACA
1107910 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
1107930 GGGGGGAAATCGGTACCCCCT
1 GGGGGG-AATCGGTACCCCCT
* *
1107951 GGGGGGGAATCTGTATCCCCT
1 -GGGGGGAATCGGTACCCCCT
**
1107972 -GGGGGAATATGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
1107991 GGG
1 GGG
1107994 CAATCTGATT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
19 17 0.30
20 8 0.14
21 26 0.46
22 6 0.11
ACGTcount: A:0.17, C:0.26, G:0.39, T:0.18
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:1107988 original size:18 final size:19
Alignment explanation
Indices: 1107911--1107993 Score: 78
Period size: 19 Copynumber: 4.2 Consensus size: 19
1107901 TGTTAGACAG
**
1107911 GGGGGAATCGGTACCCCCT
1 GGGGGAATATGTACCCCCT
1107930 GGGGGGAA-ATCGGTACCCCCT
1 -GGGGGAATAT--GTACCCCCT
* *
1107951 GGGGGGGAATCTGTATCCCCT
1 --GGGGGAATATGTACCCCCT
1107972 GGGGGAATATGTACCCCCT
1 GGGGGAATATGTACCCCCT
1107991 GGG
1 GGG
1107994 CAATCTGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 20 0.38
20 7 0.13
21 17 0.32
22 8 0.15
23 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.39, T:0.18
Consensus pattern (19 bp):
GGGGGAATATGTACCCCCT
Found at i:1110761 original size:41 final size:41
Alignment explanation
Indices: 1110704--1110804 Score: 148
Period size: 41 Copynumber: 2.5 Consensus size: 41
1110694 CCGTTAGACA
* *
1110704 GGGGGAATCGCTACCCCCTAGGGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTAGGGGGGAATCGGTACCCCCTG
* * *
1110745 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTATCCCCTG
1 GGGGGAATCGGTACCCCCTAGGGGGGAATCGGTACCCCCTG
*
1110786 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
1110805 GGGCAATCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.19
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCCTAGGGGGGAATCGGTACCCCCTG
Found at i:1110805 original size:20 final size:20
Alignment explanation
Indices: 1110704--1110807 Score: 145
Period size: 20 Copynumber: 5.1 Consensus size: 20
1110694 CCGTTAGACA
*
1110704 GGGGGAATCGCTACCCCCTAG
1 GGGGGAATCGGTACCCCCT-G
*
1110725 GGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTG
1110745 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCT-G
* *
1110766 GGGGGAATCTGTATCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
1110786 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
1110806 GG
1 GG
1110808 CAATCTGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 41 0.54
21 35 0.46
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:1113500 original size:41 final size:41
Alignment explanation
Indices: 1113443--1113543 Score: 148
Period size: 41 Copynumber: 2.5 Consensus size: 41
1113433 CCGTTAGACA
* *
1113443 GGGGGAATCGCTACCCCCTAGGGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTAGGGGGGAATCGGTACCCCCTG
* * *
1113484 GGGGGAATCGGTACCCCCTGGGGGGGAATCTGTATCCCCTG
1 GGGGGAATCGGTACCCCCTAGGGGGGAATCGGTACCCCCTG
*
1113525 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
1113544 GGGCAATCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.19
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCCTAGGGGGGAATCGGTACCCCCTG
Found at i:1113544 original size:20 final size:20
Alignment explanation
Indices: 1113443--1113546 Score: 145
Period size: 20 Copynumber: 5.1 Consensus size: 20
1113433 CCGTTAGACA
*
1113443 GGGGGAATCGCTACCCCCTAG
1 GGGGGAATCGGTACCCCCT-G
*
1113464 GGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTG
1113484 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCT-G
* *
1113505 GGGGGAATCTGTATCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
1113525 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
1113545 GG
1 GG
1113547 CAATCTGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 41 0.54
21 35 0.46
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:1116251 original size:18 final size:18
Alignment explanation
Indices: 1116196--1116250 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
1116186 GATCATACCA
*
1116196 TGGGGGAATCGGTACCCC
1 TGGGGGAATCTGTACCCC
1116214 TGGGGGAATCTGTATCCCC
1 TGGGGGAATCTGTA-CCCC
1116233 TGGGGGGAATCTGTACCC
1 T-GGGGGAATCTGTACCC
1116251 TTTGAAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 13 0.38
19 8 0.24
20 13 0.38
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.22
Consensus pattern (18 bp):
TGGGGGAATCTGTACCCC
Found at i:1118565 original size:32 final size:34
Alignment explanation
Indices: 1118529--1118598 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1118519 CCTTACAAAC
*
1118529 TCCCTAG-TTTT-TCGGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTATAGGGGCTAAACTAGAACCTT
* *
1118561 TCCCTAGCTTTTATAGGGGCTAAGCTAGAATCTT
1 TCCCTAGCTTTTATAGGGGCTAAACTAGAACCTT
1118595 TCCC
1 TCCC
1118599 ATTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (34 bp):
TCCCTAGCTTTTATAGGGGCTAAACTAGAACCTT
Found at i:1118940 original size:43 final size:42
Alignment explanation
Indices: 1118873--1118957 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 42
1118863 ATAGCTTAGA
1118873 GCGTGGGGGAATCGGTACCGCCCTCATGGGGAATCGGGTTCCC
1 GCGTGGGGGAATCGGTACCGCCCTCATGGGGAATC-GGTTCCC
1118916 GCGTGGGGGGAATCGGTACC-CCCTCATGGGGAATCGGTTCCC
1 GCGT-GGGGGAATCGGTACCGCCCTCATGGGGAATCGGTTCCC
1118958 TAAGTGCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
42 7 0.17
43 19 0.46
44 15 0.37
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.19
Consensus pattern (42 bp):
GCGTGGGGGAATCGGTACCGCCCTCATGGGGAATCGGTTCCC
Found at i:1118948 original size:21 final size:21
Alignment explanation
Indices: 1118878--1118953 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 21
1118868 TTAGAGCGTG
1118878 GGGGAATCGGTACCGCCCTCAT
1 GGGGAATCGGTACC-CCCTCAT
* * **
1118900 GGGGAATCGGGTTCCCGCGT-GG
1 GGGGAATC-GGTACCC-CCTCAT
1118922 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
1118943 GGGGAATCGGT
1 GGGGAATCGGT
1118954 TCCCTAAGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.05
21 17 0.40
22 17 0.40
23 7 0.16
ACGTcount: A:0.16, C:0.26, G:0.39, T:0.18
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTCAT
Found at i:1119014 original size:21 final size:21
Alignment explanation
Indices: 1118988--1119027 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1118978 CCGTTAGATA
1118988 GGGGGAATCGGTACCCCCTAG
1 GGGGGAATCGGTACCCCCTAG
*
1119009 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
1119028 GGGCAATCTG
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:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTAG
Found at i:1120228 original size:23 final size:23
Alignment explanation
Indices: 1120196--1120251 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1120186 CAGCTCGTAT
* *
1120196 AATTACACCGAAGTGCCA-CGTAG
1 AATTGCACCGAAGTG-CAGCATAG
* *
1120219 AATTGTACCGGAGTGCAGCATAG
1 AATTGCACCGAAGTGCAGCATAG
1120242 AATTGCACCG
1 AATTGCACCG
1120252 TAGTACCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCAGCATAG
Found at i:1121096 original size:20 final size:19
Alignment explanation
Indices: 1121032--1121106 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
1121022 AATGAAGGTA
1121032 TGCATCGATGCACTATACTG
1 TGCATCGATGCACT-TACTG
* *
1121052 TGTATCGATGCATTCTTAACGG
1 TGCATCGATGCA--CTT-ACTG
1121074 TGCATCGATGCACTTACTTG
1 TGCATCGATGCACTTAC-TG
*
1121094 TGCATCGGTGCAC
1 TGCATCGATGCAC
1121107 AAAATACATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 1 0.02
22 16 0.35
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTTACTG
Found at i:1124305 original size:20 final size:20
Alignment explanation
Indices: 1124280--1124319 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1124270 CCGTTAGACA
*
1124280 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGATACCCCCTG
*
1124300 GGGGGAATCTATACCCCCTG
1 GGGGGAATCGATACCCCCTG
1124320 AGCAATCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCTG
Found at i:1125746 original size:58 final size:59
Alignment explanation
Indices: 1125596--1125805 Score: 230
Period size: 59 Copynumber: 3.6 Consensus size: 59
1125586 ATATGATATC
* * * * *
1125596 TTTAAAGAAACTAAGCCTCATTTTCATAGGTTTCTTGACATGGTGTTTTCAAATGCATT
1 TTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATATTTTCAAATGCATT
* * *
1125655 TTTAAAGAAACTAAGTCTGATTTTTAGAGGTTTCTTGACATTATATTTTCAAATGGA-T
1 TTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATATTTTCAAATGCATT
* * * ** * *
1125713 TTTAAAGAAGCTAAATCTGATTTTCAGAAGTTTCTTG--ATGAT-TTCCCCACATGAATT
1 TTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATATT-TTCAAATGCATT
* *
1125770 TTTAAAGAAGCTAAGTCTTATTTTCAGAGGTTTCTT
1 TTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTT
1125806 AACGATTACT
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
55 2 0.02
56 10 0.08
57 34 0.26
58 34 0.26
59 49 0.38
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (59 bp):
TTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATATTTTCAAATGCATT
Found at i:1126469 original size:240 final size:238
Alignment explanation
Indices: 1125870--1126475 Score: 772
Period size: 237 Copynumber: 2.5 Consensus size: 238
1125860 ATTTTCAAGG
**
1125870 GTTTCTTGA-TTAGTAAGTCCATT-GGGCCATCAGTAAGTCTTTCGATAATGATGCTTAAATCCT
1 GTTTCTT-ACTTAGTAAGT-CATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAT-CT
* * * *
1125933 TT-TGGTCATCTATAAGCCTTTCGAGCAAGATGATATGTCCTTCGGGCCATCCATAAGACCTTCA
63 TTCGGGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCA
* * * * **
1125997 GGTAGGATGTTTTCACATGATTTTCAAAAAACGAGAAAGTGATTTCCAAAGTTTTCATTTAAATA
128 GGCAAGATATTTTCACACGATTTTCAAAAAACGAGAAAGAAATTTCCAAAGTTTTCATTTAAATA
* *
1126062 TTTTATGAAAATTTATTTTTTTTAAAGTAAGAAAACGATTTCCAAC
193 TTTTATGAAAATTGATTTTTTTAAAAGTAAGAAAACGATTTCCAAC
** * *
1126108 GTTTCTTACTTAGTAA-TCCCTCGTGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTC
1 GTTTCTTACTTAGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTC
* * * * * * ** *
1126172 GGATCATCTATAAGCCTTTCAAGCGAGACGATAAATACTCCGGGTTATCTATAAGACCTTCGGGC
66 GGGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGC
* * *
1126237 AAGATATTTTCACACGA-TTTCAAAAAATGAGAAAGCAAATTTTCAAAGTTTCTCATTTAAATCT
131 AAGATATTTTCACACGATTTTCAAAAAACGAGAAAG-AAATTTCCAAAGTTT-TCATTTAAATAT
*
1126301 TTTATGAAAATTGATTTTTTTGAAAAGTAAGAAAATGATTTCCAAC
194 TTTATGAAAATTGATTTTTTT-AAAAGTAAGAAAACGATTTCCAAC
* * *
1126347 GTTTCTTACTTAATAAGTCATTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCCTAAATCTTTC
1 GTTTCTTACTTAGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTC
* * ** *
1126412 GGGTCATCTATAAGCCTTTTAAGCAATATGATAAGTCCTTCGACCCATCTGTAAGACCTTCAGG
66 GGGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGG
1126476 TACAATGTTT
Statistics
Matches: 309, Mismatches: 52, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
236 22 0.07
237 113 0.37
238 45 0.15
239 37 0.12
240 92 0.30
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (238 bp):
GTTTCTTACTTAGTAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTC
GGGTCATCTATAAGCCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGC
AAGATATTTTCACACGATTTTCAAAAAACGAGAAAGAAATTTCCAAAGTTTTCATTTAAATATTT
TATGAAAATTGATTTTTTTAAAAGTAAGAAAACGATTTCCAAC
Found at i:1126537 original size:33 final size:35
Alignment explanation
Indices: 1126500--1126566 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
1126490 ATGGTGTTTA
1126500 AAAATAT-ATAAAAAAAGAAAAAAG-AAAAAAAAC
1 AAAATATGATAAAAAAAGAAAAAAGCAAAAAAAAC
* * * *
1126533 AAAATATGCTAAAAAATGAGAAATGCAAAAAAAA
1 AAAATATGATAAAAAAAGAAAAAAGCAAAAAAAA
1126567 AATGAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.25
34 13 0.46
35 8 0.29
ACGTcount: A:0.75, C:0.04, G:0.09, T:0.12
Consensus pattern (35 bp):
AAAATATGATAAAAAAAGAAAAAAGCAAAAAAAAC
Found at i:1126576 original size:22 final size:20
Alignment explanation
Indices: 1126543--1126590 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
1126533 AAAATATGCT
*
1126543 AAAAAATGAGAAATGCAAAA
1 AAAAAATGAGAAATCCAAAA
*
1126563 AAAAAATGAAAGAAGTCCAAAA
1 AAAAAATG--AGAAATCCAAAA
1126585 GAAAAA
1 -AAAAA
1126591 GAAGAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
22 10 0.43
23 5 0.22
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAAAATGAGAAATCCAAAA
Found at i:1126595 original size:20 final size:22
Alignment explanation
Indices: 1126558--1126597 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1126548 ATGAGAAATG
1126558 CAAAAAAAAAATGAAAGAAGTC
1 CAAAAAAAAAATGAAAGAAGTC
*
1126580 CAAAAGAAAAA-G-AAGAAG
1 CAAAAAAAAAATGAAAGAAG
1126598 AATAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.05
Consensus pattern (22 bp):
CAAAAAAAAAATGAAAGAAGTC
Found at i:1130163 original size:20 final size:20
Alignment explanation
Indices: 1130138--1130182 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1130128 TTATCCCGAA
*
1130138 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
1130158 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
1130178 AAAAA
1 AAAAA
1130183 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:1132384 original size:27 final size:27
Alignment explanation
Indices: 1132353--1132406 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1132343 CCATGATAAG
1132353 TTGAAAGGTAAGGCATATGCTAAGAAA
1 TTGAAAGGTAAGGCATATGCTAAGAAA
*
1132380 TTGAAAGGTAAGGCATATGCTATGAAA
1 TTGAAAGGTAAGGCATATGCTAAGAAA
1132407 GAAAAGGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.26, T:0.24
Consensus pattern (27 bp):
TTGAAAGGTAAGGCATATGCTAAGAAA
Found at i:1134410 original size:56 final size:56
Alignment explanation
Indices: 1134324--1134432 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
1134314 TTATACCAAG
1134324 TGTTATAAGCTCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGACCCAT
1 TGTTATAAGCTCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGACCCAT
* * *
1134380 TGTTATAGGCTCTTTGCTGTCCCGTTTTTGTTGTTGAGCCGAATGTTTAGACC
1 TGTTATAAGCTCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGACC
1134433 ATTTTCATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (56 bp):
TGTTATAAGCTCTTTGCTGTCCAGTTTTTGTTGTCGAGCCGAATGTTTAGACCCAT
Found at i:1139657 original size:20 final size:20
Alignment explanation
Indices: 1139632--1139669 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1139622 AGCGAGTCGA
*
1139632 TTGTGAGTTTAACAATGTAC
1 TTGTGAATTTAACAATGTAC
1139652 TTGTGAATTTAACAATGT
1 TTGTGAATTTAACAATGT
1139670 TCGTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGTGAATTTAACAATGTAC
Found at i:1144239 original size:64 final size:64
Alignment explanation
Indices: 1144142--1144351 Score: 194
Period size: 65 Copynumber: 3.2 Consensus size: 64
1144132 ATTTCAAAGG
* * * * *
1144142 CATGCACCGATGCATCAATCCATGCATCGATGCACCATTGAATAAATT-GAACATCGAATGCATT
1 CATGCATCGATGCA-CAAGCAATGCATCGATGCACCATTG-ATATATTAAAACATCGAATGCATT
1144206 T
64 T
*** * * *
1144207 CATGCATCGATGCACTCTCTATGCATCGATGCA-C-TTGGGTTTTTATTAAAACATCGAATGCAT
1 CATGCATCGATGCACAAGCAATGCATCGATGCACCATT--G-ATATATTAAAACATCGAATGCAT
1144270 TT
63 TT
* * * *
1144272 CATGCATCGATGCACAAGCAATGCACCGATGCACTCA-TGCTATTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCAATGCATCGATGCAC-CATTGATATATTAAAACATCGAATGCATTT
*
1144336 TATGCATCGATGCACA
1 CATGCATCGATGCACA
1144352 CTTGGTGCAC
Statistics
Matches: 120, Mismatches: 19, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 57 0.47
65 58 0.48
67 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCAATGCATCGATGCACCATTGATATATTAAAACATCGAATGCATTT
Found at i:1144361 original size:64 final size:64
Alignment explanation
Indices: 1144191--1144370 Score: 211
Period size: 65 Copynumber: 2.8 Consensus size: 64
1144181 GAATAAATTG
* * ** * *
1144191 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTCAGGCTATTATTAA
* * *
1144256 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCATGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACTCAGGCTATTATTA
1144319 A
64 A
* *
1144320 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACT
1144371 AAGTGTTCCA
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 47 0.47
65 49 0.49
67 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTCAGGCTATTATTAA
Found at i:1150291 original size:18 final size:18
Alignment explanation
Indices: 1150270--1150305 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1150260 ATTCGTCCCT
*
1150270 CTCTCACTCTAAATCATC
1 CTCTCACTCAAAATCATC
*
1150288 CTCTTACTCAAAATCATC
1 CTCTCACTCAAAATCATC
1150306 GAAAAATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (18 bp):
CTCTCACTCAAAATCATC
Found at i:1151742 original size:21 final size:21
Alignment explanation
Indices: 1151700--1151743 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1151690 ACTCCGGGAG
* *
1151700 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1151721 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1151742 CT
1 CT
1151744 CCTCCGGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1180738 original size:76 final size:78
Alignment explanation
Indices: 1180655--1180799 Score: 181
Period size: 76 Copynumber: 1.9 Consensus size: 78
1180645 AATAAAATAA
* *
1180655 TATTTAATTAATT-TAAATTAAATAT-AGATT-AAGGACTTATAATCTAAATTACAAT-GTTTAA
1 TATTTAATT-ATTCCAAATTAAATATCA-ATTAAAAGACTTATAATCTAAATTACAATCGTTTAA
1180716 TGCTTATTTAAAACT
64 TGCTTATTTAAAACT
* * * * *
1180731 TATTTAATTATTCCAAATTATATATCAATTAAAAGAGTTGTAATCTAAATTACATTCTTTTAATG
1 TATTTAATTATTCCAAATTAAATATCAATTAAAAGACTTATAATCTAAATTACAATCGTTTAATG
1180796 CTTA
66 CTTA
1180800 CTTACTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 3 0.05
76 22 0.38
77 22 0.38
78 11 0.19
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (78 bp):
TATTTAATTATTCCAAATTAAATATCAATTAAAAGACTTATAATCTAAATTACAATCGTTTAATG
CTTATTTAAAACT
Found at i:1183882 original size:20 final size:20
Alignment explanation
Indices: 1183815--1183886 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1183805 GTGCACTTTG
* *
1183815 TATCGATACTACTCACATAA
1 TATCGATACTACTAACCTAA
*** *
1183835 TATCGATACTACTCTTGCTAGG
1 TATCGATACTACT-AACCTA-A
*
1183857 TATCGATACTACTAACCTAC
1 TATCGATACTACTAACCTAA
1183877 TATCGATACT
1 TATCGATACT
1183887 GTTCTTATTG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 23 0.56
21 5 0.12
22 13 0.32
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (20 bp):
TATCGATACTACTAACCTAA
Found at i:1187618 original size:12 final size:12
Alignment explanation
Indices: 1187601--1187626 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1187591 GAGATAAAAC
1187601 ATAATGGGTTCG
1 ATAATGGGTTCG
1187613 ATAATGGGTTCG
1 ATAATGGGTTCG
1187625 AT
1 AT
1187627 CAACTAAGAA
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:0.27, C:0.08, G:0.31, T:0.35
Consensus pattern (12 bp):
ATAATGGGTTCG
Found at i:1191359 original size:16 final size:17
Alignment explanation
Indices: 1191338--1191370 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1191328 AACCCCATTT
*
1191338 TTTTCTCTC-TTTTTCA
1 TTTTCTCCCATTTTTCA
1191354 TTTTCTCCCATTTTTCA
1 TTTTCTCCCATTTTTCA
1191371 AAAGTTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCTCCCATTTTTCA
Found at i:1192583 original size:43 final size:43
Alignment explanation
Indices: 1192519--1192736 Score: 208
Period size: 43 Copynumber: 5.1 Consensus size: 43
1192509 GAATAAAGGT
** *
1192519 CGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACGC
1 CGCAAAAGGTATAGATCTATAGCGGCGTTTTTGGAACAAACGC
* ** * * * * *
1192562 CGTAAAAGGTATAGATCTATAGCATCATTTTTTGAGCAAATGT
1 CGCAAAAGGTATAGATCTATAGCGGCGTTTTTGGAACAAACGC
* * *
1192605 CGCAAAAGGTCAT--ATCTATAGCAGCATTTTTGGAACAAACAC
1 CGCAAAAGGT-ATAGATCTATAGCGGCGTTTTTGGAACAAACGC
* *
1192647 CGCAAAAGTTCTAGATCTATAGCGGCGTTTTTGGATACAAACGC
1 CGCAAAAGGTATAGATCTATAGCGGCGTTTTTGGA-ACAAACGC
* * * *
1192691 CACAAAAGGT-CAGATCTATAGCGGTGTTTTTGTATACAAACGC
1 CGCAAAAGGTATAGATCTATAGCGGCGTTTTTGGA-ACAAACGC
1192734 CGC
1 CGC
1192737 TAATTACCTT
Statistics
Matches: 142, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 32 0.23
43 92 0.65
44 17 0.12
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (43 bp):
CGCAAAAGGTATAGATCTATAGCGGCGTTTTTGGAACAAACGC
Found at i:1192678 original size:85 final size:86
Alignment explanation
Indices: 1192517--1192712 Score: 241
Period size: 85 Copynumber: 2.3 Consensus size: 86
1192507 AAGAATAAAG
* * * *
1192517 GTCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAACAAACGCCGTAAAAGGTATAGATCTAT
1 GTCGCAAAAGGTC-ATATCTATAGCAGCATTTTTGGAACAAACACCGCAAAAGGTATAGATCTAT
* * * *
1192582 AGCATCATTTTTTGA-GCAAAT
65 AGCAGCATTTTTGGATACAAAC
* *
1192603 GTCGCAAAAGGTCATATCTATAGCAGCATTTTTGGAACAAACACCGCAAAAGTTCTAGATCTATA
1 GTCGCAAAAGGTCATATCTATAGCAGCATTTTTGGAACAAACACCGCAAAAGGTATAGATCTATA
* *
1192668 GCGGCGTTTTTGGATACAAAC
66 GCAGCATTTTTGGATACAAAC
* * *
1192689 GCCACAAAAGGTCAGATCTATAGC
1 GTCGCAAAAGGTCATATCTATAGC
1192713 GGTGTTTTTG
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
85 56 0.60
86 38 0.40
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (86 bp):
GTCGCAAAAGGTCATATCTATAGCAGCATTTTTGGAACAAACACCGCAAAAGGTATAGATCTATA
GCAGCATTTTTGGATACAAAC
Found at i:1195150 original size:82 final size:84
Alignment explanation
Indices: 1195054--1195348 Score: 234
Period size: 82 Copynumber: 3.6 Consensus size: 84
1195044 ACATACCAAA
*
1195054 CTATTGCGGTGTTTGTAAAAAAAATGATGCTAAAATACTACTCTGTTGC-G-GCATTTTTGAAAA
1 CTATTGCGGTGTTTGT-AAAAAAATGACGCTAAAATACTACTCTGTTGCAGCGCATTTTTGAAAA
*
1195117 AACA-CCACTATAGATGAA-G
65 AA-AGCCACTATAGATGAATC
* * * * **
1195136 CTATTACGGTGTTTGT-AAAAAATGCCGCTAAAGTACTACTTTGTTGCAGCGTTTTTTTGAAAAA
1 CTATTGCGGTGTTTGTAAAAAAATGACGCTAAAATACTACTCTGTTGCAGCGCATTTTTGAAAAA
*
1195200 AATGTCACTATAGATGAATC
66 AA-GCCACTATAGATGAATC
* * * * *
1195220 CTATTGCGGTGTTTGT-ATAAAA-CAC-CATTAAAGTACTACTGTATTGC-GCG--TTTGTTGAA
1 CTATTGCGGTGTTTGTAAAAAAATGACGC--TAAAATACTACTCTGTTGCAGCGCATTT-TTGAA
* * *
1195279 AAAACGCCACCATAGATTAATC
63 AAAAAGCCACTATAGATGAATC
* ** * * * * *
1195301 CTATTGTGGCATTTGTATAAAAACGCCGCTAAAGTATTACTCTGTTGC
1 CTATTGCGGTGTTTGTAAAAAAATGACGCTAAAATACTACTCTGTTGC
1195349 GGCGTTTGTT
Statistics
Matches: 173, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
80 27 0.16
81 32 0.18
82 58 0.34
83 18 0.10
84 38 0.22
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (84 bp):
CTATTGCGGTGTTTGTAAAAAAATGACGCTAAAATACTACTCTGTTGCAGCGCATTTTTGAAAAA
AAGCCACTATAGATGAATC
Found at i:1195316 original size:81 final size:83
Alignment explanation
Indices: 1195083--1195369 Score: 251
Period size: 83 Copynumber: 3.5 Consensus size: 83
1195073 AAAAATGATG
* * * * * * * *
1195083 CTAAAATACTACTCTGTTGCGGCATTT-TTGAAAAAACACCACTATAGATGAA-GCTATTACGGT
1 CTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAACGCCACCATAGATGAATCCTATTGCGGC
* ** *
1195146 GTTTGTA-AAAAATGCCG
66 ATTTGTATAAAAACACCA
* * * * *
1195163 CTAAAGTACTACTTTGTTGCAGCGTTTTTTTGAAAAAAATGTCACTATAGATGAATCCTATTGCG
1 CTAAAGTACTACTCTGTTGCAGCG-TTTGTTG-AAAAAACGCCACCATAGATGAATCCTATTGCG
**
1195228 GTGTTTGTAT-AAAACACCA
64 GCATTTGTATAAAAACACCA
* * * * *
1195247 TTAAAGTACTACTGTATTGC-GCGTTTGTTGAAAAAACGCCACCATAGATTAATCCTATTGTGGC
1 CTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAACGCCACCATAGATGAATCCTATTGCGGC
* *
1195311 ATTTGTATAAAAACGCCG
66 ATTTGTATAAAAACACCA
* * * *
1195329 CTAAAGTATTACTCTGTTGCGGCGTTTGTTCAACAAACGCC
1 CTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAACGCC
1195370 GCTAAAGTTA
Statistics
Matches: 169, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
80 20 0.12
81 38 0.22
82 32 0.19
83 40 0.24
84 39 0.23
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (83 bp):
CTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAAAAACGCCACCATAGATGAATCCTATTGCGGC
ATTTGTATAAAAACACCA
Found at i:1195335 original size:166 final size:165
Alignment explanation
Indices: 1195054--1195355 Score: 374
Period size: 166 Copynumber: 1.8 Consensus size: 165
1195044 ACATACCAAA
** *
1195054 CTATTGCGGTGTTTGTAAAAAAAATGATGCTAAAATACTACTCTGTTGCGGCATTTTTGAAAAAA
1 CTATTGCGGTGTTTGTAAAAAAAACCAT-CTAAAATACTACTCTATTGCGGCATTTTTGAAAAAA
* * ** * *
1195119 CACCACTATAGATGAAGCTATTACGGTGTTTGTAAAAAATGCCGCTAAAGTACTACTTTGTTGCA
65 CACCACCATAGATGAACCTATTACGGCATTTGTAAAAAACGCCGCTAAAGTACTACTCTGTTGCA
1195184 GCGTTTTTTTGAAAAAAATGTCACTATAGATGAATC
130 GCGTTTTTTTGAAAAAAATGTCACTATAGATGAATC
* * * * *
1195220 CTATTGCGGTGTTTGTATAAAACACCAT-TAAAGTACTACTGTATTGC-GCGTTTGTTGAAAAAA
1 CTATTGCGGTGTTTGTAAAAAAAACCATCTAAAATACTACTCTATTGCGGCATTT-TTGAAAAAA
* * ** *
1195283 CGCCACCATAGATTAATCCTATTGTGGCATTTGTATAAAAACGCCGCTAAAGTATTACTCTGTTG
65 CACCACCATAGATGAA-CCTATTACGGCATTTGTA-AAAAACGCCGCTAAAGTACTACTCTGTTG
*
1195348 CGGCGTTT
128 CAGCGTTT
1195356 GTTCAACAAA
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
163 5 0.04
164 38 0.34
165 13 0.12
166 57 0.50
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (165 bp):
CTATTGCGGTGTTTGTAAAAAAAACCATCTAAAATACTACTCTATTGCGGCATTTTTGAAAAAAC
ACCACCATAGATGAACCTATTACGGCATTTGTAAAAAACGCCGCTAAAGTACTACTCTGTTGCAG
CGTTTTTTTGAAAAAAATGTCACTATAGATGAATC
Found at i:1196282 original size:23 final size:23
Alignment explanation
Indices: 1196247--1196321 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1196237 CTAGTTGCAT
1196247 TAAAATGAA-AAAA-ATAGTGTG-
1 TAAAATGAACAAAATATA-TGTGC
*
1196268 TAAAAATGAACAAAATGTATGTGC
1 T-AAAATGAACAAAATATATGTGC
*
1196292 TAAAATGAACAAAATGTATGTGC
1 TAAAATGAACAAAATATATGTGC
1196315 TAAAATG
1 TAAAATG
1196322 TTTGTAATGC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
21 1 0.02
22 8 0.16
23 37 0.76
24 3 0.06
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.25
Consensus pattern (23 bp):
TAAAATGAACAAAATATATGTGC
Found at i:1196330 original size:23 final size:23
Alignment explanation
Indices: 1196270--1196321 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
1196260 ATAGTGTGTA
1196270 AAAATGAACAAAATGTATGTGCT
1 AAAATGAACAAAATGTATGTGCT
1196293 AAAATGAACAAAATGTATGTGCT
1 AAAATGAACAAAATGTATGTGCT
1196316 AAAATG
1 AAAATG
1196322 TTTGTAATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (23 bp):
AAAATGAACAAAATGTATGTGCT
Found at i:1199575 original size:14 final size:13
Alignment explanation
Indices: 1199533--1199575 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1199523 ATTGTATCTG
1199533 GTTCTTTTTTTTT
1 GTTCTTTTTTTTT
**
1199546 GCCCTTTTTTTTTT
1 GTTC-TTTTTTTTT
1199560 GTTCTTTTTTTCTT
1 GTTCTTTTTTT-TT
1199574 GT
1 GT
1199576 GTGTGATCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (13 bp):
GTTCTTTTTTTTT
Found at i:1200025 original size:55 final size:55
Alignment explanation
Indices: 1199949--1200327 Score: 446
Period size: 55 Copynumber: 6.9 Consensus size: 55
1199939 TGACGAGTCC
* * ** * *
1199949 GCTCCCTATTCTTTCAAGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTCT
1 GCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCATAAAATGGGTCT
* * * * *
1200004 GCTTCCTACTCATTCAGGGAGTATA-AGACTCGAACAATCTTCA-ACAAACGGGTTT
1 GCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCATA-AAATGGGTCT
1200059 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGT-T
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCT
** * * *
1200113 CGCTCCCTATTCGATCAAGGAGTATAGAACTTGAACAATCTTAATAAAATGGGT-T
1 -GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCT
* * * *
1200168 CGCTCCCTATTCTTTCAGGGAGTATAGAGCTCGAACAATCTTTATAAAATGGGTCC
1 -GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCT
* *
1200224 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCC
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCT
* *
1200279 GCTCCTTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTTC-TAAAAT
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATC-TTCATAAAAT
1200328 TAAATATGTT
Statistics
Matches: 290, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
54 1 0.00
55 284 0.98
56 5 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCT
Found at i:1200187 original size:165 final size:165
Alignment explanation
Indices: 1199945--1200319 Score: 499
Period size: 165 Copynumber: 2.3 Consensus size: 165
1199935 CGAATGACGA
* * * * *
1199945 GTCCGCTCCCTATTCTTTCAAGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTCTGCTTC
1 GTCCGCTCCCTATTCCTTCAAGGAGTATAGA-ACTCGAACAATCTTAAGAAAACGGGTCTGCTCC
**
1200009 CTACTCATTCAGGGAGTATA-AGACTCGAACAATCTTCA-ACAAACGGGTTTGCTCCCTATTCCT
65 CTACTCATTCAGGGAGTATAGAG-CTCGAACAATCTTCATA-AAACGGGTCCGCTCCCTATTCCT
*
1200072 TCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGG
128 TCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGG
* ** * * *
1200110 GTTCGCTCCCTATTCGATCAAGGAGTATAGAACTTGAACAATCTTAATAAAATGGGT-TCGCTCC
1 GTCCGCTCCCTATTCCTTCAAGGAGTATAGAACTCGAACAATCTTAAGAAAACGGGTCT-GCTCC
* * * *
1200174 CTATTCTTTCAGGGAGTATAGAGCTCGAACAATCTTTATAAAATGGGTCCGCTCCCTATTCCTTC
65 CTACTCATTCAGGGAGTATAGAGCTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTC
1200239 AGAGAGTATAGAACTCGAACAATCTTCATAAAATGG
130 AGAGAGTATAGAACTCGAACAATCTTCATAAAATGG
*
1200275 GTCCGCTCCTTATTCCTTC-AGAGAGTATAGAACTCGAACAATCTT
1 GTCCGCTCCCTATTCCTTCAAG-GAGTATAGAACTCGAACAATCTT
1200320 TCTAAAATTA
Statistics
Matches: 183, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
164 3 0.02
165 176 0.96
166 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (165 bp):
GTCCGCTCCCTATTCCTTCAAGGAGTATAGAACTCGAACAATCTTAAGAAAACGGGTCTGCTCCC
TACTCATTCAGGGAGTATAGAGCTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCA
GAGAGTATAGAACTCGAACAATCTTCATAAAATGG
Found at i:1200382 original size:36 final size:36
Alignment explanation
Indices: 1200342--1200498 Score: 242
Period size: 36 Copynumber: 4.3 Consensus size: 36
1200332 TATGTTTCAT
* * *
1200342 TGATTTGCTTTACTACTCTTCCATTAAGGCTTAAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
*
1200378 TGATTTGCTTCACTACTATTCCGTGAAGGCTTAAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
1200414 TTATTTGCTTCACTACTCTTTCGTGAAGGCTTAAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
*
1200450 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTT
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG-A
1200487 TGATTTGCTTCA
1 TGATTTGCTTCA
1200499 AAGATTGAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 98 0.89
37 12 0.11
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (36 bp):
TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:1201841 original size:14 final size:15
Alignment explanation
Indices: 1201816--1201845 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1201806 TCATTTTTTC
1201816 TTCTATTTTCCCATT
1 TTCTATTTTCCCATT
1201831 TTCTA-TTTCCCATT
1 TTCTATTTTCCCATT
1201845 T
1 T
1201846 CATTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (15 bp):
TTCTATTTTCCCATT
Found at i:1201868 original size:8 final size:8
Alignment explanation
Indices: 1201843--1201937 Score: 70
Period size: 8 Copynumber: 11.4 Consensus size: 8
1201833 CTATTTCCCA
1201843 TTTCATTT
1 TTTCATTT
1201851 TTCATCATTT
1 TT--TCATTT
1201861 TTTCATTT
1 TTTCATTT
1201869 TTTCATTT
1 TTTCATTT
1201877 TTTCATCGTT
1 TTTCAT--TT
1201887 CTTTCATTT
1 -TTTCATTT
1201896 TTT--TCTT
1 TTTCAT-TT
*
1201903 TTTCCTTT
1 TTTCATTT
* *
1201911 TTCCTTTT
1 TTTCATTT
*
1201919 TTTTA-TT
1 TTTCATTT
1201926 TTTCTATTT
1 TTTC-ATTT
1201935 TTT
1 TTT
1201938 TTTATCTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
6 1 0.01
7 10 0.14
8 36 0.51
9 8 0.11
10 10 0.14
11 6 0.08
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTCATTT
Found at i:1201891 original size:27 final size:26
Alignment explanation
Indices: 1201843--1201906 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
1201833 CTATTTCCCA
*
1201843 TTTCATTTTTCATCATTTTTTCATTT
1 TTTCATTTTTCATCATTCTTTCATTT
*
1201869 TTTCATTTTTTCATCGTTCTTTCATTTT
1 TTTCA-TTTTTCATCATTCTTTCA-TTT
1201897 TTTC-TTTTTC
1 TTTCATTTTTC
1201907 CTTTTTCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 11 0.32
27 16 0.47
28 7 0.21
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTCATTTTTCATCATTCTTTCATTT
Found at i:1201939 original size:19 final size:19
Alignment explanation
Indices: 1201915--1201953 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1201905 TCCTTTTTCC
1201915 TTTTTTT-TATTTTTCTATT
1 TTTTTTTATATTTTTC-ATT
*
1201934 TTTTTTTATCTTTTTCATT
1 TTTTTTTATATTTTTCATT
1201953 T
1 T
1201954 ATTCTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTATATTTTTCATT
Found at i:1211651 original size:45 final size:46
Alignment explanation
Indices: 1211593--1211680 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
1211583 AACATAAAAC
1211593 CCTAACCGCATGATATCTAATTCGCATGC-TTATGCGAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCATTATGCGAAAAATAAA
* *
1211638 CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGAAAAA
1 CCTAACCGCATGATATCTAATTCGCATGCA-TTATGCGAAAAA
1211681 CGAAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 28 0.72
47 11 0.28
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (46 bp):
CCTAACCGCATGATATCTAATTCGCATGCATTATGCGAAAAATAAA
Found at i:1214103 original size:24 final size:24
Alignment explanation
Indices: 1214071--1214142 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
1214061 GCAGGATATG
1214071 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
1214095 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
1214119 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
1214143 CTGGAAGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCAT
Found at i:1219863 original size:30 final size:30
Alignment explanation
Indices: 1219827--1219900 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
1219817 AAATGGATTT
* **
1219827 GTTTAGTGACCAAATTATAAA-TTTGGTAAA
1 GTTTAGTGACCAAACTATAAACTTT-AAAAA
1219857 GTTTAGTGACCAAACTATAAACTTTAAAAA
1 GTTTAGTGACCAAACTATAAACTTTAAAAA
*
1219887 GTTTAGGGACCAAA
1 GTTTAGTGACCAAA
1219901 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 36 0.92
31 3 0.08
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (30 bp):
GTTTAGTGACCAAACTATAAACTTTAAAAA
Found at i:1226201 original size:131 final size:130
Alignment explanation
Indices: 1225997--1226348 Score: 425
Period size: 131 Copynumber: 2.7 Consensus size: 130
1225987 CGAGAAGTAG
* * *
1225997 TGACCTCTCATGCCTTAAAGAAATCATTTGTTACTCCAATCAAAATAAAGAAATATTACTATTTC
1 TGACCTCTCATGCCTTAAA-AAATCATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTC
* * * * * * * *
1226062 CTTCTAAAATTTGATATTAATTCGAGAGGAAACGATAATATCCAATTATTTTCATTCGAGAACAA
65 ATCCTAAAATTAGATATTAATTCGAGAGAAAACGATAACAACCAATTATTTCCAATCGAGAACAA
1226127 A
130 A
* * * *
1226128 TGACCTCTCATGCCTTAAAACAACCATTTATTGCTCCAATCGAAATGAAGAGATATTACTTTTTC
1 TGACCTCTCATGCCTTAAAA-AATCATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTC
* * * * *
1226193 ATCCTAAAATTAAATATTAATCCAAGAGAAAATGATAACAACCAATTATTTCCAATCGAGAATAA
65 ATCCTAAAATTAGATATTAATTCGAGAGAAAACGATAACAACCAATTATTTCCAATCGAGAACAA
1226258 A
130 A
* * * * *
1226259 TGCCCTCTCATACCTTAAAGTAATCATTTATTACTCCAATCAAAATGAAAAGATATCACTATTTC
1 TGACCTCTCATGCCTTAAA-AAATCATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTC
* * *
1226324 ATCTTAAAATTCGATTTTAATTCGA
65 ATCCTAAAATTAGATATTAATTCGA
1226349 ATGTTTTTAT
Statistics
Matches: 184, Mismatches: 35, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
130 1 0.01
131 183 0.99
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (130 bp):
TGACCTCTCATGCCTTAAAAAATCATTTATTACTCCAATCAAAATGAAGAGATATTACTATTTCA
TCCTAAAATTAGATATTAATTCGAGAGAAAACGATAACAACCAATTATTTCCAATCGAGAACAAA
Found at i:1228232 original size:14 final size:14
Alignment explanation
Indices: 1228196--1228236 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1228186 TAAATATGAA
*
1228196 AATAATAATAGAAAT
1 AATAATAAT-TAAAT
1228211 AATAATAATTAAAT
1 AATAATAATTAAAT
1228225 AATAATAATTAA
1 AATAATAATTAA
1228237 TATTAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (14 bp):
AATAATAATTAAAT
Found at i:1228687 original size:133 final size:133
Alignment explanation
Indices: 1228458--1229075 Score: 632
Period size: 133 Copynumber: 4.7 Consensus size: 133
1228448 TCTGCTCCTC
* * * * * * * *
1228458 TGCTTCTTCAGGGCAGATCAGATCTGGAAATGTTAATTCATTCCACTATTCTTTAGTGTATATTG
1 TGCTTCTTCAGGGAAAATCAGATCTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAAATTG
* * * * * * * * *
1228523 AATCGAGGTAGCCTTATTCCACTGTTTCTCAGGGAAGATCAAATCTGGAAAGAGGGGATCTGTTT
66 AATCGAGGCAGACTTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGAATCTATTC
*
1228588 CGC
131 CGT
* * * *
1228591 T-CTTTCTTCACGGAAAATCAGATTTGGAGACGTTGATTCATTCCACTATTCTTCAGGGAAGATT
1 TGC-TTCTTCAGGGAAAATCAGATCTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAAATT
* * * *
1228655 GAATCGAGCCAGACTTGTTCGACTGCTACTCAGGGAAGATCAAATATGGAATGAGGGAATCTGTT
65 GAATCGAGGCAGACTTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGAATCTATT
*
1228720 CCGA
130 CCGT
* * * * * * * *
1228724 TGCTTCTTTAGGGAAAATTAGATTTGGAGACATTGATTAATTCCACTGTTCTTCAGGGAAGATTG
1 TGCTTCTTCAGGGAAAATCAGATCTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAAATTG
* ** * * * * * *
1228789 AATCGAGACAGTTTTATGCCGCTGCTACCCAGGTAAGATCAAATATGGAAAGATGGAATCTATTC
66 AATCGAGGCAGACTTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGAATCTATTC
1228854 CGT
131 CGT
* * * *
1228857 TGCTTCTTCAGAGAAAATCAGATATGGAAACGTTGATTCATTTCACTGTTCTTCAGGGAAAATTG
1 TGCTTCTTCAGGGAAAATCAGATCTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAAATTG
* * * * * * *
1228922 AATCAAGGTAAACTTGTTCCACTGCTTCTTCAGGGAAGATCAAATTTGGAAAGAGGGTATCCATT
66 AATCGAGGCAGACTTGTTCCACTGCTAC-TCAGGGAAGATCAAATATGGAAAGAGGGAATCTATT
1228987 CCGT
130 CCGT
* ** * *
1228991 TGC-T-TTCTGGGAAAATCAGATCTAAAAATGTTGATTCATTCCACTATT-TTCAGGAAAAATTG
1 TGCTTCTTCAGGGAAAATCAGATCTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAAATTG
* *
1229053 ATTCGAGGAAGACTTGTTCCACT
66 AATCGAGGCAGACTTGTTCCACT
1229076 ATTTCTTTTG
Statistics
Matches: 402, Mismatches: 80, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
131 32 0.08
132 37 0.09
133 295 0.73
134 38 0.09
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (133 bp):
TGCTTCTTCAGGGAAAATCAGATCTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAAATTG
AATCGAGGCAGACTTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGAATCTATTC
CGT
Found at i:1230408 original size:15 final size:16
Alignment explanation
Indices: 1230390--1230426 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1230380 TTATTTTCTT
1230390 TTTTTTTCA-TTTTCA
1 TTTTTTTCATTTTTCA
*
1230405 -TTTTTTCATTTTTCC
1 TTTTTTTCATTTTTCA
1230420 TTTTTTT
1 TTTTTTT
1230427 TTCCTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 5 0.26
16 6 0.32
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTCATTTTTCA
Found at i:1230426 original size:18 final size:17
Alignment explanation
Indices: 1230383--1230442 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
1230373 CTTTTATTTA
*
1230383 TTTT-CTTTTTTTTTCA
1 TTTTCCTTTTTTTTTCC
* **
1230399 TTTTCATTTTTTCAT--
1 TTTTCCTTTTTTTTTCC
1230414 TTTTCCTTTTTTTTTCC
1 TTTTCCTTTTTTTTTCC
1230431 TTTTCCTTTTTT
1 TTTTCCTTTTTT
1230443 CCTCTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.34
16 4 0.11
17 19 0.54
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCCTTTTTTTTTCC
Found at i:1230428 original size:32 final size:31
Alignment explanation
Indices: 1230383--1230461 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 31
1230373 CTTTTATTTA
1230383 TTTTCTTTTTTTTTCATTTTCATTTTTTCAT
1 TTTTCTTTTTTTTTCATTTTCATTTTTTCAT
* * *
1230414 TTTTCCTTTTTTTTTCCTTTTCCTTTTTTCCT
1 TTTT-CTTTTTTTTTCATTTTCATTTTTTCAT
* *
1230446 CTTTATTTTTTTTTCA
1 TTTTCTTTTTTTTTCA
1230462 AGTGAAGTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 14 0.34
32 27 0.66
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTCTTTTTTTTTCATTTTCATTTTTTCAT
Found at i:1230434 original size:25 final size:27
Alignment explanation
Indices: 1230406--1230455 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1230396 TCATTTTCAT
*
1230406 TTTTTCATTTTTCCT-TTT-TTTTTCC
1 TTTTCCATTTTTCCTCTTTATTTTTCC
*
1230431 TTTTCCTTTTTTCCTCTTTATTTTT
1 TTTTCCATTTTTCCTCTTTATTTTT
1230456 TTTTCAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 3 0.14
27 5 0.24
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTCCATTTTTCCTCTTTATTTTTCC
Found at i:1230459 original size:25 final size:25
Alignment explanation
Indices: 1230405--1230460 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1230395 TTCATTTTCA
1230405 TTTTTT-CATTTTTCCT-TTT-TTT
1 TTTTTTCCATTTTTCCTCTTTATTT
*
1230427 TTCCTTTTCCTTTTTTCCTCTTTATTT
1 TT--TTTTCCATTTTTCCTCTTTATTT
1230454 TTTTTTC
1 TTTTTTC
1230461 AAGTGAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.07
24 4 0.14
25 14 0.50
26 3 0.11
27 5 0.18
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTCCATTTTTCCTCTTTATTT
Found at i:1235748 original size:15 final size:14
Alignment explanation
Indices: 1235728--1235784 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
1235718 AATCGGGTAT
1235728 CGGGTACCCGATTCC
1 CGGGTACCCGATT-C
*
1235743 CGGGTACCCGCAAAATC
1 CGGGTACCCG---ATTC
1235760 CGGGTACCCGATTAC
1 CGGGTACCCGATT-C
1235775 CGGGTACCCG
1 CGGGTACCCG
1235785 TAACATCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 2 0.06
15 21 0.58
17 11 0.31
18 2 0.06
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGGTACCCGATTC
Found at i:1235769 original size:32 final size:32
Alignment explanation
Indices: 1235728--1235793 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
1235718 AATCGGGTAT
*
1235728 CGGGTACCCGATTCCCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
1235760 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1235792 CG
1 CG
1235794 AGTCGGGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:1243005 original size:2 final size:2
Alignment explanation
Indices: 1243000--1243032 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1242990 ACACACACAC
1243000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1243033 AAGTGTATTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1243222 original size:32 final size:32
Alignment explanation
Indices: 1243181--1243241 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1243171 CCGAAGGTCC
1243181 TGTCCATATGTCCCGAAGAACATAGGTAAGTT
1 TGTCCATATGTCCCGAAGAACATAGGTAAGTT
* *
1243213 TGTCTATATGTCCCGAAGGACATAGGTAA
1 TGTCCATATGTCCCGAAGAACATAGGTAA
1243242 CCCTCAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAGTT
Found at i:1248853 original size:314 final size:314
Alignment explanation
Indices: 1248284--1248910 Score: 1245
Period size: 314 Copynumber: 2.0 Consensus size: 314
1248274 ATGAAGTTTG
1248284 GTTACAAGCCTTAAACATAACACATATAGATCTGAGTTATCTCTCCTAATTGTTGCAGGTGCCCT
1 GTTACAAGCCTTAAACATAACACATATAGATCTGAGTTATCTCTCCTAATTGTTGCAGGTGCCCT
1248349 AGTAAATCCAAAATCCTCTGAGCTTTTTCAGTCTTGGTCTCCAATCTTTCGTTTACAACATCAGA
66 AGTAAATCCAAAATCCTCTGAGCTTTTTCAGTCTTGGTCTCCAATCTTTCGTTTACAACATCAGA
*
1248414 TTTATGTGATAAATCAACCAAGTACTGAGCCACTCCTTAGGCATGTTCCATGTAGCTTACGATAA
131 TTTATGTGATAAATCAACCAAGTACTGAGCCACTCCTTAGGCATGTTCCAGGTAGCTTACGATAA
1248479 GGTCATCCCTTTTCTTAACTCTCCACTGAGCATGTTCCCAATGATGGCTGATAACTCCATAAAAA
196 GGTCATCCCTTTTCTTAACTCTCCACTGAGCATGTTCCCAATGATGGCTGATAACTCCATAAAAA
1248544 TACTATGTTTTCTGTCTCTTTACTCAAGTTATTCTATGTCTAACAGCCAATTTA
261 TACTATGTTTTCTGTCTCTTTACTCAAGTTATTCTATGTCTAACAGCCAATTTA
1248598 GTTACAAGCCTTAAACATAACACATATAGATCTGAGTTATCTCTCCTAATTGTTGCAGGTGCCCT
1 GTTACAAGCCTTAAACATAACACATATAGATCTGAGTTATCTCTCCTAATTGTTGCAGGTGCCCT
1248663 AGTAAATCCAAAATCCTCTGAGCTTTTTCAGTCTTGGTCTCCAATCTTTCGTTTACAACATCAGA
66 AGTAAATCCAAAATCCTCTGAGCTTTTTCAGTCTTGGTCTCCAATCTTTCGTTTACAACATCAGA
1248728 TTTATGTGATAAATCAACCAAGTACTGAGCCACTCCTTAGGCATGTTCCAGGTAGCTTACGATAA
131 TTTATGTGATAAATCAACCAAGTACTGAGCCACTCCTTAGGCATGTTCCAGGTAGCTTACGATAA
1248793 GGTCATCCCTTTTCTTAACTCTCCACTGAGCATGTTCCCAATGATGGCTGATAACTCCATAAAAA
196 GGTCATCCCTTTTCTTAACTCTCCACTGAGCATGTTCCCAATGATGGCTGATAACTCCATAAAAA
1248858 TACTATGTTTTCTGTCTCTTTACTCAAGTTATTCTATGTCTAACAGCCAATTT
261 TACTATGTTTTCTGTCTCTTTACTCAAGTTATTCTATGTCTAACAGCCAATTT
1248911 CATAGCATTT
Statistics
Matches: 312, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
314 312 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (314 bp):
GTTACAAGCCTTAAACATAACACATATAGATCTGAGTTATCTCTCCTAATTGTTGCAGGTGCCCT
AGTAAATCCAAAATCCTCTGAGCTTTTTCAGTCTTGGTCTCCAATCTTTCGTTTACAACATCAGA
TTTATGTGATAAATCAACCAAGTACTGAGCCACTCCTTAGGCATGTTCCAGGTAGCTTACGATAA
GGTCATCCCTTTTCTTAACTCTCCACTGAGCATGTTCCCAATGATGGCTGATAACTCCATAAAAA
TACTATGTTTTCTGTCTCTTTACTCAAGTTATTCTATGTCTAACAGCCAATTTA
Found at i:1252046 original size:21 final size:20
Alignment explanation
Indices: 1252018--1252056 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1252008 CATTGTAGGA
1252018 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
**
1252038 ATTTCATGGTTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
1252057 GACCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:1256525 original size:15 final size:15
Alignment explanation
Indices: 1256505--1256559 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1256495 TGTATATAAA
1256505 TATTCTATATTATTT
1 TATTCTATATTATTT
* *
1256520 TATTCTATATGA-GT
1 TATTCTATATTATTT
*
1256534 TATT-TATTTTTATTT
1 TATTCTA-TATTATTT
*
1256549 TATTCTCTATT
1 TATTCTATATT
1256560 TTTGTTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
13 2 0.07
14 8 0.27
15 19 0.63
16 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (15 bp):
TATTCTATATTATTT
Found at i:1264772 original size:131 final size:131
Alignment explanation
Indices: 1264599--1264955 Score: 448
Period size: 131 Copynumber: 2.7 Consensus size: 131
1264589 TCTTTTATTA
* * * * *
1264599 AGAAGAAATGACCTCTCATGCCTCAAAGCAGTCATTTCTTACTCCAATCAAAATAAAGAAATATT
1 AGAACAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATAAAGAGATATT
* *
1264664 ACTATTTCCTTCTAAAATTTGATATTAATTCGAGATG-AAACGATAATAACCAATTTTTTCCAAT
66 ACTATTTCCTTCTAAAATTTGATATTAATTCGAGA-GAAAAAGATAATAACCAATTATTTCCAAT
1264728 AG
130 AG
* ** * *
1264730 AGAACAAATGACCTCTCATGCCTTAAAGAAACCATTTATTACTCCAATCGAAATGAAGAGACATT
1 AGAACAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATAAAGAGATATT
* * ** * * *
1264795 ATTATTT-CTTCCTAAACTTAAATATTAATCCGAGAGAAAAAGATAATATCCTATTATTTCCAAT
66 ACTATTTCCTT-CTAAAATTTGATATTAATTCGAGAGAAAAAGATAATAACCAATTATTTCCAAT
*
1264859 TG
130 AG
* * * *
1264861 AGAATAAATGAACTCTCATACCTTAAAGCAGTCATTTATTACTCCAATCGAAATTAAGAGATATT
1 AGAACAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATAAAGAGATATT
* *
1264926 ACTATTTCATCCTAAAATTTGATATTAATT
66 ACTATTTCCTTCTAAAATTTGATATTAATT
1264956 TGAATGTTTT
Statistics
Matches: 188, Mismatches: 35, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
130 4 0.02
131 183 0.97
132 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (131 bp):
AGAACAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATAAAGAGATATT
ACTATTTCCTTCTAAAATTTGATATTAATTCGAGAGAAAAAGATAATAACCAATTATTTCCAATA
G
Found at i:1267579 original size:133 final size:131
Alignment explanation
Indices: 1267202--1267642 Score: 438
Period size: 133 Copynumber: 3.3 Consensus size: 131
1267192 TCAAATGAGA
* * * * *
1267202 CTAGAAAGAGGGGATATGTTCCATTGTTTCTTCAGGGAAAATCAAATCTGGAGACATTGATTCAT
1 CTAGAAAGAGGGGATATGTTTCGTTGCTTCTTCAGGGAAAATCAGATCT-GAGACGTTGATTCAT
* * * * * * * *
1267267 TCCACTATTCTTAAGGAAGATTGAATCGAGGCAGACTCGTTCCATTACTACTCATGGAAGAGCAA
65 TCCACTGTTCTTCAGGAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAGGGAAGATCAA
1267332 AT
130 AT
* * * *
1267334 C-AGGAAAGAGGGGTTTTG-TTCTGTTGCTTCTTTAGGGAAAATCAGGTCTAGAGACGTTGATTC
1 CTA-GAAAGAGGGGATATGTTTC-GTTGCTTCTTCAGGGAAAATCAGATCT-GAGACGTTGATTC
* * *
1267397 ATTCCA-TCGTTCTTCAGGGAAGATTGAATCGAGGTAGACATATTCCACTGCTACCCAGGGAAGA
63 ATTCCACT-GTTCTTCA-GGAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAGGGAAGA
1267461 TCAAAT
126 TCAAAT
* * * * *
1267467 CTAGAAAGAGGGGATTTGTTTCGCTGCTTCTTCAAGGAAAATCAGATCTGCAAATGTTGATTCAT
1 CTAGAAAGAGGGGATATGTTTCGTTGCTTCTTCAGGGAAAATCAGATCTG-AGACGTTGATTCAT
* * * * * * *
1267532 TTCACTGTTCTTCAGAGAAAATTGAATCAAGGTACACTTGTTTCACTGCTTCATCAGGTAAGATC
65 TCCACTGTTCTTCAG-GAAGATTGAATCGAGGTAGACTTGTTCCACTGCTAC-TCAGGGAAGATC
1267597 AAAT
128 AAAT
* * * * * *
1267601 ATGGAAAAAAGAGATATGTTTCGTTACTTCTTCAGGGAAAAT
1 CTAGAAAGAGGGGATATGTTTCGTTGCTTCTTCAGGGAAAAT
1267643 TGAATCGAGG
Statistics
Matches: 252, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
131 4 0.02
132 62 0.25
133 134 0.53
134 52 0.21
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (131 bp):
CTAGAAAGAGGGGATATGTTTCGTTGCTTCTTCAGGGAAAATCAGATCTGAGACGTTGATTCATT
CCACTGTTCTTCAGGAAGATTGAATCGAGGTAGACTTGTTCCACTGCTACTCAGGGAAGATCAAA
T
Found at i:1267918 original size:3 final size:3
Alignment explanation
Indices: 1267910--1267955 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1267900 CCATTTTTAA
* *
1267910 TAT TAT TAT CAT TA- TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1267956 ATTAATACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1273740 original size:16 final size:16
Alignment explanation
Indices: 1273719--1273755 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1273709 ATCAACACCA
1273719 TGCATTGAATTTATAT
1 TGCATTGAATTTATAT
1273735 TGCATTGAATTTATAT
1 TGCATTGAATTTATAT
1273751 TGCAT
1 TGCAT
1273756 CTACATTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (16 bp):
TGCATTGAATTTATAT
Found at i:1277131 original size:19 final size:17
Alignment explanation
Indices: 1277088--1277153 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 17
1277078 TACCACACTC
*
1277088 GAAA-AAAGAAGAAAAA
1 GAAATAAAGAAAAAAAA
*
1277104 GATATAAAGAAATAAAAA
1 GAAATAAAGAAA-AAAAA
1277122 GAAATAAAAGAAAAATAAA
1 GAAAT-AAAGAAAAA-AAA
*
1277141 GAAAGAAAGAAAA
1 GAAATAAAGAAAA
1277154 GATAAATGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.07
17 6 0.14
18 19 0.45
19 14 0.33
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (17 bp):
GAAATAAAGAAAAAAAA
Found at i:1277148 original size:23 final size:22
Alignment explanation
Indices: 1277113--1277174 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1277103 AGATATAAAG
1277113 AAATAA-AAAGAAATAAAAGAA
1 AAATAAGAAAGAAATAAAAGAA
* *
1277134 AAATAAAGAAAGAAAGAAAAGAT
1 AAAT-AAGAAAGAAATAAAAGAA
*
1277157 AAATGAGAAAGAGAATAA
1 AAATAAGAAAGA-AATAA
1277175 GGAAAATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.12
22 9 0.26
23 21 0.62
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (22 bp):
AAATAAGAAAGAAATAAAAGAA
Found at i:1277867 original size:29 final size:29
Alignment explanation
Indices: 1277824--1277909 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
1277814 AATGATGGAG
* *
1277824 ATCTTAGAAGCTGTTAAGGCTTATTCTAC
1 ATCTTAGAAGATGTTGAGGCTTATTCTAC
*
1277853 ATCTTAGAAGATGTTGAGGCTTATTATAC
1 ATCTTAGAAGATGTTGAGGCTTATTCTAC
**
1277882 ATCTTAGAACTTGTTGAGGCTTATTCTA
1 ATCTTAGAAGATGTTGAGGCTTATTCTA
1277910 ACTAAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (29 bp):
ATCTTAGAAGATGTTGAGGCTTATTCTAC
Found at i:1279144 original size:134 final size:134
Alignment explanation
Indices: 1278967--1279632 Score: 807
Period size: 134 Copynumber: 5.0 Consensus size: 134
1278957 AGTGAATCAA
* * * *
1278967 ACTCAATTTAATCTTCCCTAAAGAATAGT-GAAATGAATCAACGTCCCCAGATCTGATTTTCCCT
1 ACTCGATTCAATCTTCCCTGAAGAACAGTAG-AATGAATCAACGTCCCCAGATCTGATTTTCCCT
* ** * * * * *
1279031 AAAGAAGAAGTGGAACAAATTCCACTCATTCAAAATTTGATATTCCCTCAGTAACAGTGGAACAA
65 CAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
1279096 GTCTA
130 GTCTG
* * *
1279101 ACTCGATTCAATCTTCTCTGAAGGACAGTAGAATGAATCAACGTCCCTAGATCTGATTTTCCCTC
1 ACTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTC
** * *
1279166 AAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGGTATTCTCTGAGTAACAGTGGAACAAG
66 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
1279231 TGTG
131 TCTG
* * * ** * *
1279235 CCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATATCCCAAGAGCTGATTTTCCCTC
1 ACTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTC
* * * * * ** *
1279300 AAGAAAAAGCAAAATATATCCCTCTCTTTCAAGATTTGGTATTCGATGAGTAACGGTGGAACAAG
66 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
1279365 TCTG
131 TCTG
* * *
1279369 CCTCGATTAAATCTTCCCTGAAGAACAG-ATGAATGAATCAACGT-CCCAGATCTAATTTTCCCT
1 ACTCGATTCAATCTTCCCTGAAGAACAGTA-GAATGAATCAACGTCCCCAGATCTGATTTTCCCT
* * * *
1279432 TAAGAAGAAGCAGAACAACTCCCTCTCTTTCAAGATTTGATATTCACTGAGTAACAGTAGAACAA
65 CAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1279497 GTCTG
130 GTCTG
* * * * ** *
1279502 ACTCGATTCAATCTTCCCTGAAGGACAGTAGAATAAATCAATGTTCTTAGATCTAATTTTCCCTC
1 ACTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTC
* * * *
1279567 AAGAAAAAGCATAACAAGTCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAG
66 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
1279632 T
131 T
1279633 TTTCCTCGAT
Statistics
Matches: 459, Mismatches: 69, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
133 112 0.24
134 346 0.75
135 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (134 bp):
ACTCGATTCAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTCCCCAGATCTGATTTTCCCTC
AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
TCTG
Found at i:1279521 original size:267 final size:267
Alignment explanation
Indices: 1278967--1279642 Score: 852
Period size: 267 Copynumber: 2.5 Consensus size: 267
1278957 AGTGAATCAA
* * * * * * *
1278967 ACTCAATTTAATCTTCCCTAAAGAATAGTGAAATGAATCAACGTCCCCAGATCTGATTTTCCCTA
1 ACTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATGTCCCAAGATCTGATTTTCCCTC
* *** * * * * *
1279032 AAGAAGAAGTGGAACAAATTCCACTCATTCAAAATTTGATATTCCCTCAGTAACAGTGGAACAAG
66 AAGAAAAAGCAAAAC-AATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
* * * * *
1279097 TCTAACTCGATTCAATCTTCTCTGAAGGACAGTAGAATGAATCAACGTCCCTAGATCTGATTTTC
130 TCTACCTCGATTAAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTCCCTAGATCTAATTTTC
** * * *
1279162 CCTCAAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGGTATTCTCTGAGTAACAGTGGAA
195 CCTCAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCACTGAGTAACAGTAGAA
*
1279227 CAAGTGTG
260 CAAGTCTG
* * *
1279235 CCTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATATCCCAAGAGCTGATTTTCCCTC
1 ACTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATGTCCCAAGATCTGATTTTCCCTC
* * ** *
1279300 AAGAAAAAGCAAAATATATCCCTCTCTTTCAAGATTTGGTATTCGATGAGTAACGGTGGAACAAG
66 AAGAAAAAGCAAAACA-ATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
1279365 TCTGCCTCGATTAAATCTTCCCTGAAGAACAG-ATGAATGAATCAACGTCCC-AGATCTAATTTT
130 TCTACCTCGATTAAATCTTCCCTGAAGAACAGTA-GAATGAATCAACGTCCCTAGATCTAATTTT
* *
1279428 CCCTTAAGAAGAAGCAGAACAACTCCCTCTCTTTCAAGATTTGATATTCACTGAGTAACAGTAGA
194 CCCTCAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCACTGAGTAACAGTAGA
1279493 ACAAGTCTG
259 ACAAGTCTG
* * * * * ** *
1279502 ACTCGATTCAATCTTCCCTGAAGGACAGTAGAATAAATCAATGTTCTTAGATCTAATTTTCCCTC
1 ACTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATGTCCCAAGATCTGATTTTCCCTC
* *
1279567 AAGAAAAAGCATAACAAGTCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAG
66 AAGAAAAAGCAAAACAA-TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
* *
1279632 TTTTCCTCGAT
130 TCTACCTCGAT
1279643 CTCATCTACC
Statistics
Matches: 347, Mismatches: 58, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
266 1 0.00
267 198 0.57
268 148 0.43
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (267 bp):
ACTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAATCAATGTCCCAAGATCTGATTTTCCCTC
AAGAAAAAGCAAAACAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTACCTCGATTAAATCTTCCCTGAAGAACAGTAGAATGAATCAACGTCCCTAGATCTAATTTTCC
CTCAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCACTGAGTAACAGTAGAAC
AAGTCTG
Found at i:1279825 original size:3 final size:3
Alignment explanation
Indices: 1279817--1279847 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1279807 GTTATCGTTA
1279817 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1279848 TAATATTTTT
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):
TAT
Found at i:1279932 original size:23 final size:23
Alignment explanation
Indices: 1279884--1279938 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1279874 ATTACATCAT
*
1279884 ACCCAAACCCAGAGCCAAGAAAG
1 ACCCAAACCCAGACCCAAGAAAG
* *
1279907 ACCCAAACCCAGATCCCAA-TAGG
1 ACCCAAACCCAGA-CCCAAGAAAG
1279930 ACCCAAACC
1 ACCCAAACC
1279939 TATTAGGGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.44, C:0.40, G:0.13, T:0.04
Consensus pattern (23 bp):
ACCCAAACCCAGACCCAAGAAAG
Found at i:1283169 original size:3 final size:3
Alignment explanation
Indices: 1283155--1283234 Score: 78
Period size: 3 Copynumber: 27.0 Consensus size: 3
1283145 GGCATACAGA
*
1283155 AAT AAA AAT AAT AAT AAT AAT -AT AA- ATAT AAT AAT AAT AAT AGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT
* *
1283199 AAT AAT AAT AAT AA- AAT AAT ATT AATT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
1283235 GAAATCAACA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.09
3 53 0.83
4 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1283185 original size:14 final size:14
Alignment explanation
Indices: 1283155--1283234 Score: 74
Period size: 14 Copynumber: 5.6 Consensus size: 14
1283145 GGCATACAGA
*
1283155 AATAAAAATAATAAT
1 AATAATAATAAT-AT
1283170 AATAAT-ATAAATAT
1 AATAATAAT-AATAT
*
1283184 AATAATAATAATAGA
1 AATAATAATAATA-T
*
1283199 AATAATAATAATAA
1 AATAATAATAATAT
*
1283213 AATAATATTAAT-T
1 AATAATAATAATAT
*
1283226 AATATTAAT
1 AATAATAAT
1283235 GAAATCAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.12
14 26 0.46
15 23 0.41
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (14 bp):
AATAATAATAATAT
Found at i:1287936 original size:54 final size:53
Alignment explanation
Indices: 1287839--1288394 Score: 521
Period size: 54 Copynumber: 10.4 Consensus size: 53
1287829 TACAGTTATT
* * * * * * *
1287839 ATCAAGAAATCCCT-AAAATGAGGCTTAACTCTTTAAAAATTCATTTGAAGAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAGCTTTTTAAAAATTCATTTAAAAAC
* * *
1287891 ATCAACAAACCCCTAAAAATCATGTTTAGCTCTTTTAAAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAGCT-TTTTAAAAATTCATTTAAAAAC
* * * * *
1287945 ATCAAGAAACCCCTAAAAATTAGGTTTAGTTTCTTTCAAAATTCATTTAAAAAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAGCTT-TTTAAAAATTCATTTAAAAAC
* * *
1287999 ATCAAGAAA-CCATTAAAATACA-GTCTTAGCTCCTTTAAAAATTCATTTAAAAAC
1 ATCAAGAAACCCCTAAAAAT-CATG-CTTAGCT-TTTTAAAAATTCATTTAAAAAC
* * * *
1288053 ATCAGGAAACCCCT-AAAATTATACTTAGCTTATTTAAAAATTCATTTAAAAAT
1 ATCAAGAAACCCCTAAAAATCATGCTTAGCTT-TTTAAAAATTCATTTAAAAAC
* * * * * * *
1288106 ATCAAGAAA-CTCTGAAAATCA-GAATTAGATCCTCTAAAAATTAATTTAAAAAC
1 ATCAAGAAACCCCTAAAAATCATG-CTTAGCT-TTTTAAAAATTCATTTAAAAAC
* * *
1288159 ATCAAGAAACCCCTAAAAAACTTGCTTAGCTTTTTTAAAAGTTCATTTAAAAAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAGC-TTTTTAAAAATTCATTTAAAAAC
* * * *
1288213 ATCAAGAAACACCTGAAAATCAGGCTTAGATTCTTTAAAAATTCATTTAAAAAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAGCTT-TTTAAAAATTCATTTAAAAAC
* * * *
1288267 ATCAAGAAACACCTAAAAATCATGCATAGCTTCTTTAAAAGTTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAGCTT-TTTAAAAATTCATTTAAAAAC
* * * * * * *
1288321 ATCAAGAAACCCTTGAAAATCAAGCTTAGTTTTTTTCAGAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATCATGCTTAG-CTTTTTAAAAATTCATTTAAAAAC
* *
1288375 ATCAAGAAATCCCTGAAAAT
1 ATCAAGAAACCCCTAAAAAT
1288395 TGGGCTCCTC
Statistics
Matches: 416, Mismatches: 71, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
52 15 0.04
53 98 0.24
54 296 0.71
55 7 0.02
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.30
Consensus pattern (53 bp):
ATCAAGAAACCCCTAAAAATCATGCTTAGCTTTTTAAAAATTCATTTAAAAAC
Found at i:1288160 original size:214 final size:216
Alignment explanation
Indices: 1287870--1288342 Score: 593
Period size: 214 Copynumber: 2.2 Consensus size: 216
1287860 GGCTTAACTC
* * * * * * * * *
1287870 TTTAAAAATTCATTTGAAGACATCAACAAACCCCTAAAAATCATG-TTTAGCTCTTTTAAAAATT
1 TTTAAAAATTCATTTAAAAACATCAAGAAACCCTTGAAAATCA-GAATTAGATCCTCTAAAAATT
* * *
1287934 CATTTGAAAACATCAAGAAACCCCT-AAAAA-TTAGGTTTAG-TTTCTTTCAAAA-TTCATTTAA
65 AATTTAAAAACATCAAGAAACCCCTAAAAAACTT--GCTTAGCTTT-TTT-AAAAGTTCATTTAA
* * * *
1287995 AAACATCAAGAAAC-CATTAAAATACAGTCTTAGCTCCTTTAAAAATTCATTTAAAAACATCAGG
126 AAACATCAAGAAACACATGAAAAT-CAGGCTTAGATCCTTTAAAAATTCATTTAAAAACATCAAG
* * *
1288059 AAACCCCT-AAAATTATACTTAGCTTA
190 AAACACCTAAAAATCATACATAGCTTA
* *
1288085 TTTAAAAATTCATTTAAAAATATCAAGAAACTC-TGAAAATCAGAATTAGATCCTCTAAAAATTA
1 TTTAAAAATTCATTTAAAAACATCAAGAAACCCTTGAAAATCAGAATTAGATCCTCTAAAAATTA
1288149 ATTTAAAAACATCAAGAAACCCCTAAAAAACTTGCTTAGCTTTTTTAAAAGTTCATTTAAAAACA
66 ATTTAAAAACATCAAGAAACCCCTAAAAAACTTGCTTAGCTTTTTTAAAAGTTCATTTAAAAACA
* *
1288214 TCAAGAAACACCTGAAAATCAGGCTTAGATTCTTTAAAAATTCATTTAAAAACATCAAGAAACAC
131 TCAAGAAACACATGAAAATCAGGCTTAGATCCTTTAAAAATTCATTTAAAAACATCAAGAAACAC
* *
1288279 CTAAAAATCATGCATAGCTTC
196 CTAAAAATCATACATAGCTTA
* *
1288300 TTTAAAAGTTCATTTGAAAACATCAAGAAACCCTTGAAAATCA
1 TTTAAAAATTCATTTAAAAACATCAAGAAACCCTTGAAAATCA
1288343 AGCTTAGTTT
Statistics
Matches: 222, Mismatches: 28, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
213 5 0.02
214 120 0.54
215 86 0.39
216 11 0.05
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (216 bp):
TTTAAAAATTCATTTAAAAACATCAAGAAACCCTTGAAAATCAGAATTAGATCCTCTAAAAATTA
ATTTAAAAACATCAAGAAACCCCTAAAAAACTTGCTTAGCTTTTTTAAAAGTTCATTTAAAAACA
TCAAGAAACACATGAAAATCAGGCTTAGATCCTTTAAAAATTCATTTAAAAACATCAAGAAACAC
CTAAAAATCATACATAGCTTA
Found at i:1289712 original size:26 final size:27
Alignment explanation
Indices: 1289646--1289713 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
1289636 GGGAAGATAG
* *
1289646 AGTGTTTCATGTTAATTTGGAGAGGTA
1 AGTGTTTCAGGTTGATTTGGAGAGGTA
*
1289673 ATGTGTTTCAGGTTGATTTGGGGAGGTA
1 A-GTGTTTCAGGTTGATTTGGAGAGGTA
1289701 A-TGTTTCAGGTTG
1 AGTGTTTCAGGTTG
1289714 GCTTCTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.32
27 1 0.03
28 24 0.65
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (27 bp):
AGTGTTTCAGGTTGATTTGGAGAGGTA
Found at i:1290488 original size:19 final size:20
Alignment explanation
Indices: 1290466--1290540 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
1290456 CTCTTCCTTC
* *
1290466 TTTTTTCTCTCTTTTTTAT-
1 TTTTCTCTCTTTTTTTTATA
1290485 TTTTCTCTTCTTTTTTTTATA
1 TTTTCTC-TCTTTTTTTTATA
1290506 TTTTCTCTTCTTTTTTTTATA
1 TTTTCTC-TCTTTTTTTTATA
1290527 TTTTCTCT-TTTTTT
1 TTTTCTCTCTTTTTT
1290541 CTATCTTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 12 0.23
20 12 0.23
21 28 0.54
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTCTCTTTTTTTTATA
Found at i:1290493 original size:15 final size:16
Alignment explanation
Indices: 1290444--1290547 Score: 73
Period size: 18 Copynumber: 6.0 Consensus size: 16
1290434 TTTTTTTTGC
1290444 CTTTTTTTCTCTCTCTT
1 CTTTTTTT-TCTCTCTT
1290461 CCTTCTTTTTTCTCTCTT
1 -CTT-TTTTTTCTCTCTT
*
1290479 TTTTATTTTTCTCTTCTT
1 CTTT-TTTTTCTC-TCTT
* *
1290497 TTTTTTATATTTTCTCTT
1 CTTTTT-T-TTCTCTCTT
* * *
1290515 CTTTTTTTTATATTTT
1 CTTTTTTTTCTCTCTT
*
1290531 CTCTTTTTTTCTATCTT
1 CT-TTTTTTTCTCTCTT
1290548 TGTTATCAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
16 9 0.12
17 25 0.35
18 29 0.40
19 9 0.12
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (16 bp):
CTTTTTTTTCTCTCTT
Found at i:1290509 original size:21 final size:21
Alignment explanation
Indices: 1290477--1290540 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
1290467 TTTTTCTCTC
1290477 TTTTTTAT-TTTTCTCTTCTT
1 TTTTTTATATTTTCTCTTCTT
1290497 TTTTTTATATTTTCTCTTCTT
1 TTTTTTATATTTTCTCTTCTT
1290518 TTTTTTATATTTTCTCTT-TT
1 TTTTTTATATTTTCTCTTCTT
1290538 TTT
1 TTT
1290541 CTATCTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.30
21 30 0.70
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTATATTTTCTCTTCTT
Done.