Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000260.1 Hibiscus syriacus cultivar Beakdansim tig00000477_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: 5583615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 26
Found at i:2471709 original size:15 final size:16
Alignment explanation
Indices: 2471689--2471727 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2471679 TGGCCATGGC
2471689 TCAACTTTTTC-TTTT
1 TCAACTTTTTCATTTT
2471704 TCAAC-TTTTCATTTT
1 TCAACTTTTTCATTTT
2471719 TCAA-TTTTT
1 TCAACTTTTT
2471728 TTGACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (16 bp):
TCAACTTTTTCATTTT
Found at i:2475259 original size:14 final size:14
Alignment explanation
Indices: 2475228--2475273 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
2475218 TTCTCTTAAA
*
2475228 CTCTCTATCCCTTCT
1 CTCTCTTTCCC-TCT
2475243 CTCTCTTTCCCTCT
1 CTCTCTTTCCCTCT
2475257 CTCTCTTTCCCTCT
1 CTCTCTTTCCCTCT
2475271 CTC
1 CTC
2475274 ATGCAAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (14 bp):
CTCTCTTTCCCTCT
Found at i:2475601 original size:24 final size:24
Alignment explanation
Indices: 2475565--2475625 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2475555 CTTTCTTTTT
*
2475565 TATTTAT-TTTATTTAATCTA-ATA
1 TATTTATATATATTTAAT-TATATA
*
2475588 TATTTATATATATTTTATTATATA
1 TATTTATATATATTTAATTATATA
*
2475612 TATATATATATATT
1 TATTTATATATATT
2475626 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTATATATATTTAATTATATA
Found at i:2475617 original size:22 final size:22
Alignment explanation
Indices: 2475585--2475628 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2475575 ATTTAATCTA
* *
2475585 ATATATTTATATATATTTTATT
1 ATATATATATATATATATTATT
2475607 ATATATATATATATATATTATT
1 ATATATATATATATATATTATT
2475629 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATATATATATATATATTATT
Found at i:2475638 original size:24 final size:24
Alignment explanation
Indices: 2475573--2475662 Score: 71
Period size: 26 Copynumber: 3.7 Consensus size: 24
2475563 TTTATTTATT
* *
2475573 TTATTTAATCTAATATATTTATATA
1 TTATTT-ATTTAATATATATATATA
2475598 -TATTTTATTATATATATATATATATA
1 TTA-TTTATT-TA-ATATATATATATA
2475624 TTATTTATTTAATAT-TA-ATATTA
1 TTATTTATTTAATATATATATA-TA
**
2475647 AGATTTATTT-ATATAT
1 TTATTTATTTAATATAT
2475663 TTTTATTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
22 7 0.13
23 13 0.24
24 8 0.15
25 7 0.13
26 18 0.33
27 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (24 bp):
TTATTTATTTAATATATATATATA
Found at i:2475722 original size:2 final size:2
Alignment explanation
Indices: 2475715--2475763 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
2475705 ATTTTTCATT
2475715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
2475757 AA TA TA T
1 TA TA TA T
2475764 TTTCGTGGGC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2477654 original size:21 final size:21
Alignment explanation
Indices: 2477601--2477656 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
2477591 GTATTTAATA
2477601 TATATATAATTAGTTAATTTATT
1 TATATAT-ATTAG-TAATTTATT
*
2477624 TA-ATAAATTAGT-ATTTATT
1 TATATATATTAGTAATTTATT
2477643 TATTATATATTAGT
1 TA-TATATATTAGT
2477657 CATAACTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 9 0.31
20 1 0.03
21 14 0.48
22 3 0.10
23 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TATATATATTAGTAATTTATT
Found at i:2487536 original size:24 final size:24
Alignment explanation
Indices: 2487494--2487550 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2487484 GTCATTTGGG
* *
2487494 ACAAA-TCTATGTGGCACTTCGGT
1 ACAAATTCTATATGGAACTTCGGT
* * *
2487517 GCATATTCTATATGGAACTTTGGT
1 ACAAATTCTATATGGAACTTCGGT
2487541 ACAAATTCTA
1 ACAAATTCTA
2487551 CGCGACAGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (24 bp):
ACAAATTCTATATGGAACTTCGGT
Found at i:2488811 original size:18 final size:18
Alignment explanation
Indices: 2488788--2488822 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2488778 TATACAAAGT
*
2488788 AGTATCGGTACCCTTTTG
1 AGTATCGGTACCATTTTG
2488806 AGTATCGGTACCATTTT
1 AGTATCGGTACCATTTT
2488823 TACATTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (18 bp):
AGTATCGGTACCATTTTG
Found at i:2502813 original size:23 final size:23
Alignment explanation
Indices: 2502751--2502816 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
2502741 GAGTCGAGGG
**
2502751 TTCTATGCGGTCCTTTTGGATAA
1 TTCTATGCGGTCCTTCGGGATAA
** **
2502774 TTCTATGTAGTAATTCGGGATAA
1 TTCTATGCGGTCCTTCGGGATAA
2502797 TTCTATGCGGTCCTTCGGGA
1 TTCTATGCGGTCCTTCGGGA
2502817 CAAATCTGTG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGATAA
Found at i:2504505 original size:19 final size:19
Alignment explanation
Indices: 2504481--2504521 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2504471 ATGTTTTAAG
*
2504481 TAACTAGATGAAAGAAAGT
1 TAACTAAATGAAAGAAAGT
*
2504500 TAACTAAATGAAGGAAAGT
1 TAACTAAATGAAAGAAAGT
2504519 TAA
1 TAA
2504522 TATGGTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.22
Consensus pattern (19 bp):
TAACTAAATGAAAGAAAGT
Found at i:2505296 original size:46 final size:46
Alignment explanation
Indices: 2505230--2505353 Score: 187
Period size: 46 Copynumber: 2.7 Consensus size: 46
2505220 TGCTCTAAAT
2505230 CGAA-TCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA
1 CGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA
* * *
2505275 CGAATTCCATAATTTAAATGCATGAAAGAATGCATTAGGGCATGAA
1 CGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA
* * *
2505321 AGGATGCCATAATTAAAATGCATGAAAGGATGC
1 CGAATTCCATAATTAAAATGCATGAAAGGATGC
2505354 CATAATTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 4 0.06
46 66 0.94
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
CGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA
Found at i:2505377 original size:118 final size:118
Alignment explanation
Indices: 2505235--2505467 Score: 376
Period size: 118 Copynumber: 2.0 Consensus size: 118
2505225 TAAATCGAAT
** * *
2505235 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGAATTCCATAATTTAAATGCATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGAAAGCCATAATTAAAATACATGA
* * *
2505300 AAGAATGCATTAGGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
66 AAGAATACATTAAGGCACGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
**
2505353 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGCCCGAAAGCCATAATTAAAATACATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGAAAGCCATAATTAAAATACATGA
*
2505418 AAGGATACATTAAGGCACGAAAGGATGCCATAATTAAAATGCATGAAAGG
66 AAGAATACATTAAGGCACGAAAGGATGCCATAATTAAAATGCATGAAAGG
2505468 TTTCATTAAG
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (118 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGAAAGCCATAATTAAAATACATGA
AAGAATACATTAAGGCACGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
Found at i:2505390 original size:46 final size:46
Alignment explanation
Indices: 2505340--2505608 Score: 353
Period size: 46 Copynumber: 5.8 Consensus size: 46
2505330 TAATTAAAAT
*
2505340 GCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATACATGAAAGGATGCATTAAG
*** * * *
2505386 GCATGCCCGAAAGCCATAATTAAAATACATGAAAGGATACATTAAG
1 GCATGAAAGGATGCCATAATTAAAATACATGAAAGGATGCATTAAG
* * * *
2505432 GCACGAAAGGATGCCATAATTAAAATGCATGAAAGGTTTCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATACATGAAAGGATGCATTAAG
*
2505478 GCATGAACA-GATGCCATAATTAAAATACATGAAACGATGCATTAAG
1 GCATGAA-AGGATGCCATAATTAAAATACATGAAAGGATGCATTAAG
* * *
2505524 GCATGAAACGATGTCATAATTAAAATACATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATACATGAAAGGATGCATTAAG
* *
2505570 GCATGAAAGGAAGCCATAATTAAAATGCAT-AAACGGATG
1 GCATGAAAGGATGCCATAATTAAAATACATGAAA-GGATG
2505609 TGGTAATGCG
Statistics
Matches: 192, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 4 0.02
46 187 0.97
47 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAATTAAAATACATGAAAGGATGCATTAAG
Found at i:2505484 original size:138 final size:138
Alignment explanation
Indices: 2505340--2505599 Score: 398
Period size: 138 Copynumber: 1.9 Consensus size: 138
2505330 TAATTAAAAT
* * **
2505340 GCATGAA-AGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG-CCCGAAAGCCAT
1 GCATGAACA-GATGCCATAATTAAAATACATGAAACGATGCATTAAGGCATGAAACG-AAGCCAT
* *
2505403 AATTAAAATACATGAAAGGATACATTAAGGCACGAAAGGATGCCATAATTAAAATGCATGAAAGG
64 AATTAAAATACATGAAAAGATACATTAAGGCACGAAAGGAAGCCATAATTAAAATGCATGAAAGG
2505468 TTTCATTAAG
129 TTTCATTAAG
* *
2505478 GCATGAACAGATGCCATAATTAAAATACATGAAACGATGCATTAAGGCATGAAACGATGTCATAA
1 GCATGAACAGATGCCATAATTAAAATACATGAAACGATGCATTAAGGCATGAAACGAAGCCATAA
* *
2505543 TTAAAATACATGAAAAGATGCATTAAGGCATGAAAGGAAGCCATAATTAAAATGCAT
66 TTAAAATACATGAAAAGATACATTAAGGCACGAAAGGAAGCCATAATTAAAATGCAT
2505600 AAACGGATGT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
138 107 0.97
139 3 0.03
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (138 bp):
GCATGAACAGATGCCATAATTAAAATACATGAAACGATGCATTAAGGCATGAAACGAAGCCATAA
TTAAAATACATGAAAAGATACATTAAGGCACGAAAGGAAGCCATAATTAAAATGCATGAAAGGTT
TCATTAAG
Found at i:2505530 original size:20 final size:20
Alignment explanation
Indices: 2505505--2505577 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 20
2505495 AATTAAAATA
2505505 CATGAAACGATGCATTAAGG
1 CATGAAACGATGCATTAAGG
**
2505525 CATGAAACGATGTCATAATTAAAATA
1 CATGAAACGATG-C---ATT--AAGG
*
2505551 CATGAAAAGATGCATTAAGG
1 CATGAAACGATGCATTAAGG
2505571 CATGAAA
1 CATGAAA
2505578 GGAAGCCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 21 0.50
21 1 0.02
22 3 0.07
24 3 0.07
25 1 0.02
26 13 0.31
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (20 bp):
CATGAAACGATGCATTAAGG
Found at i:2505555 original size:72 final size:71
Alignment explanation
Indices: 2505281--2505563 Score: 205
Period size: 72 Copynumber: 4.0 Consensus size: 71
2505271 TGAACGAATT
* * * * *
2505281 CCATAATTTAAATGCATGAAAGAATGCATTAGGGCATGAAAGGATGCCATAATTAAAATGCATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAACGATGCCATAATTAAAATACATGA
2505346 AAGGATG
66 AA-GATG
** *
2505353 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG-CCCGAAAGCCATAATTAAAATACATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAACG-ATGCCATAATTAAAATACATG
2505417 AAAG--G
65 AAAGATG
* * * ** *
2505422 --ATACATT--AAGGCACGAAAGGATGCCATAATTAAAATGCATGAAA-G--G-TTTCATT--AA
1 CCATA-ATTAAAATGCATGAAAGGATG-C---ATT--AAGGCATGAAACGATGCCATAATTAAAA
**
2505477 GGCATGAACAGATG
59 TACATGAA-AGATG
* * *
2505491 CCATAATTAAAATACATGAAACGATGCATTAAGGCATGAAACGATGTCATAATTAAAATACATGA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAACGATGCCATAATTAAAATACATG-
2505556 AAAGATG
65 AAAGATG
2505563 C
1 C
2505564 ATTAAGGCAT
Statistics
Matches: 160, Mismatches: 28, Indels: 46
0.68 0.12 0.20
Matches are distributed among these distances:
66 32 0.20
67 7 0.04
68 10 0.06
69 4 0.03
70 10 0.06
71 6 0.04
72 89 0.56
73 2 0.01
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (71 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAACGATGCCATAATTAAAATACATGA
AAGATG
Found at i:2511812 original size:22 final size:20
Alignment explanation
Indices: 2511760--2511829 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 20
2511750 ATGCAAAAAT
*
2511760 GGTATCGATACCATAG-CAG
1 GGTATCGATACCATAGTAAG
* *
2511779 GGTATTGGTACCATAGTAAG
1 GGTATCGATACCATAGTAAG
*
2511799 GTAGTATCGATACCATAGTAGG
1 G--GTATCGATACCATAGTAAG
2511821 GGTATCGAT
1 GGTATCGAT
2511830 GCCGAGGTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 14 0.33
20 11 0.26
22 17 0.40
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:2512301 original size:46 final size:46
Alignment explanation
Indices: 2512225--2512657 Score: 638
Period size: 46 Copynumber: 9.5 Consensus size: 46
2512215 TAAATCGAAT
*
2512225 CCATAATTAAAATGCATGAAAGGATGCATTAAAGCATGAACGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
* * * * * **
2512271 CCAAAATTAAAATGCATGAAATGATACATTAAGGAATTAAAAGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
* * * * *
2512317 TCATAATTAAAATGCGTGAAATGATGCAATAAGGAATGAACGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
*
2512363 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
* * **
2512409 CCATAATTAAAATGCATGAAATGATGCATTAAGACATGAACAAATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
*
2512455 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAA---AGG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
* *
2512498 CCATAATTAAAATGCATGAAAGGAAGCATTAAGGCATAAACGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
* *
2512544 CCATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
2512590 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
2512636 CCATAATTAAAATGCATGAAAG
1 CCATAATTAAAATGCATGAAAG
2512658 AATTCCATAA
Statistics
Matches: 345, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
43 40 0.12
46 305 0.88
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATG
Found at i:2512752 original size:96 final size:96
Alignment explanation
Indices: 2512647--2512820 Score: 294
Period size: 96 Copynumber: 1.8 Consensus size: 96
2512637 CATAATTAAA
* * * *
2512647 ATGCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGTATTAAGGGATGAACGAATTCCAT
1 ATGCATGAAAGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATTCCAT
2512712 AATTAAAATGCATGAAAGGACGCATTAAGGC
66 AATTAAAATGCATGAAAGGACGCATTAAGGC
* *
2512743 ATGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCAT
1 ATGCATGAAAGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATTCCAT
2512808 AATTAAAATGCAT
66 AATTAAAATGCAT
2512821 AATGGATGCG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (96 bp):
ATGCATGAAAGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATTCCAT
AATTAAAATGCATGAAAGGACGCATTAAGGC
Found at i:2512758 original size:12 final size:12
Alignment explanation
Indices: 2512719--2512786 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
2512709 CATAATTAAA
2512719 ATGCATGAAAGG
1 ATGCATGAAAGG
* *
2512731 ACGCAT-TAAGG
1 ATGCATGAAAGG
2512742 CATGCATGAAAGG
1 -ATGCATGAAAGG
**
2512755 ATGCCAT-AATTAAA
1 ATG-CATGAA--AGG
2512769 ATGCATGAAAGG
1 ATGCATGAAAGG
2512781 ATGCAT
1 ATGCAT
2512787 TAAGGCATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
11 4 0.10
12 22 0.52
13 10 0.24
14 6 0.14
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (12 bp):
ATGCATGAAAGG
Found at i:2512772 original size:50 final size:47
Alignment explanation
Indices: 2512649--2512829 Score: 251
Period size: 46 Copynumber: 3.9 Consensus size: 47
2512639 TAATTAAAAT
*
2512649 GCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGTATTAAGG
1 GCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGG
* *
2512696 G-ATGAACGAATTCCATAATTAAAATGCATGAAAGGACGCATTAAGG
1 GCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGG
* *
2512742 CATGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAA-G
1 ---GCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGG
* *
2512791 GCATGAAAGGATTCCATAATTAAAATGCAT-AATGGATGC
1 GCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGC
2512830 GGTAATGCGT
Statistics
Matches: 121, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
45 8 0.07
46 71 0.59
47 1 0.01
49 2 0.02
50 39 0.32
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.24
Consensus pattern (47 bp):
GCATGAAAGAATTCCATAATTAAAATGCATGAAAGGATGCATTAAGG
Found at i:2515049 original size:26 final size:27
Alignment explanation
Indices: 2515012--2515077 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 27
2515002 ATTTTACCTG
2515012 AAGAAAAA-AAAAGAGA-AGGAAAAAAT
1 AAGAAAAAGAAAAGAGAGA-GAAAAAAT
*
2515038 -AGAAAAAGAAAA-AGAGAGACAAAAT
1 AAGAAAAAGAAAAGAGAGAGAAAAAAT
2515063 AAGAAAAAGAAAAGA
1 AAGAAAAAGAAAAGA
2515078 AATAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 17 0.49
26 17 0.49
27 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.03
Consensus pattern (27 bp):
AAGAAAAAGAAAAGAGAGAGAAAAAAT
Found at i:2515049 original size:27 final size:26
Alignment explanation
Indices: 2515015--2515075 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
2515005 TTACCTGAAG
2515015 AAAA-AAAAAGAGAAGGAAAAAAT-AGA
1 AAAAGAAAAAGAG-A-GAAAAAATAAGA
*
2515041 AAAAGAAAAAGAGAGACAAAATAAGA
1 AAAAGAAAAAGAGAGAAAAAATAAGA
2515067 AAAAGAAAA
1 AAAAGAAAA
2515076 GAAATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 7 0.22
26 17 0.53
27 8 0.25
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAAGAAAAAGAGAGAAAAAATAAGA
Found at i:2515088 original size:27 final size:26
Alignment explanation
Indices: 2515012--2515091 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
2515002 ATTTTACCTG
*
2515012 AAGAAAAA-AAAAGAGAAGGAAAAAAT
1 AAGAAAAAGAAAAGA-AAGAAAAAAAT
* *
2515038 -AGAAAAAGAAAA-AGAGAGACAAAAT
1 AAGAAAAAGAAAAGAAAGA-AAAAAAT
*
2515063 AAGAAAAAGAAAAGAAATAAATAAAAT
1 AAGAAAAAGAAAAGAAAGAAA-AAAAT
2515090 AA
1 AA
2515092 ATAAAAGGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
24 2 0.05
25 14 0.33
26 17 0.40
27 10 0.23
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (26 bp):
AAGAAAAAGAAAAGAAAGAAAAAAAT
Found at i:2516472 original size:134 final size:134
Alignment explanation
Indices: 2516290--2516897 Score: 593
Period size: 134 Copynumber: 4.5 Consensus size: 134
2516280 ATTCTAAACC
* * * *
2516290 TTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGAAAATCAAGTTTGATTCAATCTTCCCTAAAGAG
1 TTCAGATTTGGTCTTCTTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAG
* * * * * * *
2516355 TAG-CAATGTGGAACAAAGTTTTCCCGAGTCTAATCTCCCCTAAAGAGAAGTGGAGCATATTCTT
66 CAGTGAA-GTGGAACAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGAAGTAGAGCAGATTCTT
2516419 CTTCT
130 CTTCT
** * *
2516424 TTCAGATTTGGTCTTCTTGAAGAGTGGCGAAGCAAATCAAGTTCGATTCAATATTCCCTGAAGAT
1 TTCAGATTTGGTCTTCTTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAG
* * * * * * * * * ** *
2516489 CAGTAAAAT-GAATTAAAGTATTCTTGAGTCTGATCTCCCCTAAATAGTAGAAGAATATATTCTT
66 CAGTGAAGTGGAA-CAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGAAGTAGAGCAGATTCTT
*
2516553 CCTCT
130 CTTCT
* * *
2516558 TTCAGATTTTGTATTCTTGAAGAGCAGCGAAGCAAATCAAG-TCTGATTTAATCTTCCCTGAAGA
1 TTCAGATTTGGTCTTCTTGAAGAGCAGCGAAGCAAATCAAGTTC-GATTCAATCTTCCCTGAAGA
* * *
2516622 GCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAA-CAGAGCAGATTAT
65 GCAGTGAAGTGGAACAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAG-AAGTAGAGCAGATTCT
2516686 TCTTCT
129 TCTTCT
* ** * * ** * * *
2516692 TTGATCTTTGGTCTTCCTGAAAAGCAATGAAGTAAATCAAGCTCGATTAAATCTTCCCTGAAGAG
1 TTCAGATTTGGTCTTCTTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAG
* * * *
2516757 CAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCT-CCCTAAAGAGTAGTGGAGTAGATTCTTC
66 CAGTGAAGTGGAACAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGAAGTAGAGCAGATTCTTC
2516821 TTC-
131 TTCT
* * * * * * *
2516824 TTCTAGAATTAGTATT-TCTAAAGAGC-GACGAAGCAAATCAAGTTTGGTTCAATATTCCCTGAA
1 TTC-AGATTTGGTCTTCT-TGAAGAGCAG-CGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
*
2516887 GTGCAGTGAAG
63 GAGCAGTGAAG
2516898 GAAATTGATT
Statistics
Matches: 385, Mismatches: 79, Indels: 21
0.79 0.16 0.04
Matches are distributed among these distances:
132 3 0.01
133 80 0.21
134 295 0.77
135 7 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (134 bp):
TTCAGATTTGGTCTTCTTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAG
CAGTGAAGTGGAACAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGAAGTAGAGCAGATTCTTC
TTCT
Found at i:2516788 original size:268 final size:266
Alignment explanation
Indices: 2516289--2516897 Score: 677
Period size: 268 Copynumber: 2.3 Consensus size: 266
2516279 GATTCTAAAC
* * * * *
2516289 CTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGAAAATCAAGTTTGATTCAATCTTCCCTAAAGA
1 CTTCAGATTTAGTATTCTTGAAGAGCAGCGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGA
* * * ** * *
2516354 GTAG-CAATGTGGAACAAAGTTTTCCCGAGTCTAATCTCCCCTAAAGAGAAGTGGAGCATATTCT
66 GCAGTGAA-GTGGAACAAAATTTTCCCGAGTCTAATCTCCCCTAAAGAGAAGCAGAGCAGATTAT
* * *** * *
2516418 TCTTCTTTCAGATTTGGTCTTCTTGAAGAGTGGCGAAGCAAATCAAGTTCGATTCAATATTCCCT
130 TCTTCTTTCAGATTTGGTCTTCCTGAAAAGCAACGAAGCAAATCAAGCTCGATTAAATATTCCCT
* * * * * *
2516483 GAAGATCAGTAAAATGAATTAAAGTATTCTTGAGTCTGATCTCCCCTAAATAGTAGAAGAATATA
195 GAAGAGCAGTAAAATGAATCAAAATATTCTCGAGTCTGATCT-CCCTAAAGAGTAGAAGAATAGA
2516548 TTCTTCCT
259 TTCTTCCT
* * *
2516556 CTTTCAGATTTTGTATTCTTGAAGAGCAGCGAAGCAAATCAAGTCTGATTTAATCTTCCCTGAAG
1 C-TTCAGATTTAGTATTCTTGAAGAGCAGCGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAG
* * *
2516621 AGCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAGAGTAA-CAGAGCAGATTA
65 AGCAGTGAAGTGGAACAAAATTTTCCCGAGTCTAATCTCCCCTAAAGAG-AAGCAGAGCAGATTA
* ** * * *
2516685 TTCTTCTTTGATCTTTGGTCTTCCTGAAAAGCAATGAAGTAAATCAAGCTCGATTAAATCTTCCC
129 TTCTTCTTTCAGATTTGGTCTTCCTGAAAAGCAACGAAGCAAATCAAGCTCGATTAAATATTCCC
* * * * ** *
2516750 TGAAGAGCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCTAAAGAGTAGTGGAGTAGA
194 TGAAGAGCAGTAAAATGAATCAAAATATTCTCGAGTCTGATCTCCCTAAAGAGTAGAAGAATAGA
*
2516815 TTCTTCTT
259 TTCTTCCT
* * * *
2516823 CTTCTAGAATTAGTATT-TCTAAAGAGC-GACGAAGCAAATCAAGTTTGGTTCAATATTCCCTGA
1 CTTC-AGATTTAGTATTCT-TGAAGAGCAG-CGAAGCAAATCAAGTTTGATTCAATCTTCCCTGA
*
2516886 AGTGCAGTGAAG
63 AGAGCAGTGAAG
2516898 GAAATTGATT
Statistics
Matches: 284, Mismatches: 52, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
266 5 0.02
267 84 0.30
268 191 0.67
269 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (266 bp):
CTTCAGATTTAGTATTCTTGAAGAGCAGCGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGA
GCAGTGAAGTGGAACAAAATTTTCCCGAGTCTAATCTCCCCTAAAGAGAAGCAGAGCAGATTATT
CTTCTTTCAGATTTGGTCTTCCTGAAAAGCAACGAAGCAAATCAAGCTCGATTAAATATTCCCTG
AAGAGCAGTAAAATGAATCAAAATATTCTCGAGTCTGATCTCCCTAAAGAGTAGAAGAATAGATT
CTTCCT
Found at i:2519295 original size:34 final size:34
Alignment explanation
Indices: 2519220--2519308 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
2519210 AAAAAAATAG
*
2519220 CAGCAACATGTTCAAATTTACTTACAAAAGATGA
1 CAGCAACATGTTTAAATTTACTTACAAAAGATGA
* * *
2519254 CATCAACATGTTTAAGTTTACTTATAAAA-ATTGGA
1 CAGCAACATGTTTAAATTTACTTACAAAAGA-T-GA
*
2519289 -AGCAACATGTCTAAATTTAC
1 CAGCAACATGTTTAAATTTAC
2519309 AAAACATGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
33 1 0.02
34 43 0.93
35 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (34 bp):
CAGCAACATGTTTAAATTTACTTACAAAAGATGA
Found at i:2521213 original size:2 final size:2
Alignment explanation
Indices: 2521206--2521234 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2521196 TGTCGTAAAT
2521206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2521235 TGTAGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2536355 original size:21 final size:21
Alignment explanation
Indices: 2536331--2536371 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2536321 GTGGAATGAA
2536331 ATGAAAATGTAGTAGAAGGAC
1 ATGAAAATGTAGTAGAAGGAC
2536352 ATGAAAATGTAGTAGAAGGA
1 ATGAAAATGTAGTAGAAGGA
2536372 AGTTTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.29, T:0.20
Consensus pattern (21 bp):
ATGAAAATGTAGTAGAAGGAC
Found at i:2538373 original size:29 final size:29
Alignment explanation
Indices: 2538331--2538395 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
2538321 AGAATCATAT
*
2538331 ATTCATTTTTGTGGCTTAGACTTTAATAA
1 ATTCATTTTTGTGGCTTAGACTTCAATAA
*
2538360 ATTCATTTTTGTGGCTTAGACTTCCATAA
1 ATTCATTTTTGTGGCTTAGACTTCAATAA
2538389 ATTCATT
1 ATTCATT
2538396 GTCAAACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (29 bp):
ATTCATTTTTGTGGCTTAGACTTCAATAA
Found at i:2546461 original size:11 final size:11
Alignment explanation
Indices: 2546421--2546454 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2546411 ACATGTTTAA
*
2546421 ATTATTACTTTA
1 ATTATTA-TTTT
2546433 ATTATTATTTT
1 ATTATTATTTT
2546444 ATTATTATTTT
1 ATTATTATTTT
2546455 CATATTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:2546478 original size:2 final size:2
Alignment explanation
Indices: 2546465--2546509 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2546455 CATATTAGTC
*
2546465 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2546506 AT AT
1 AT AT
2546510 TGTTTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2546626 original size:147 final size:148
Alignment explanation
Indices: 2546466--2546755 Score: 336
Period size: 147 Copynumber: 2.0 Consensus size: 148
2546456 ATATTAGTCA
* * ** *
2546466 TATAAATATATATATATAT-ATATATATATATATATATATTATATTGTTTA-AATAATAATATTT
1 TATAAATAAATATATATATGATATA-ATAT-TATATAAATTATATTAATCATAATAATAATATTT
* *
2546529 ATTTATTTTTAAATATTAAGAAAGGACAATCTTAATATAATTAGATGTCATATTCTGGTATTTTA
64 ATTTATTTTTAAATATTAAGAAAGGACAATCTTAAAATAACTAGATGTCATATTCTGGTATTTTA
2546594 AAA-ATAATAAATATCATGTT
129 AAATA-AATAAATATCATGTT
* * * * * * **
2546614 TATAAA-AAATATATATTTGCTTTAATCTTATATAAATTATTTTAATCATATTTTTAATATTTAT
1 TATAAATAAATATATATATGATATAATATTATATAAATTATATTAATCATAATAATAATATTTAT
* * * * * *
2546678 TTATTTTTTAATATTAAGAAAGGGCAGTCTTAAAATAACTAGATGTCATTTTCTGTTATTTTTAA
66 TTATTTTTAAATATTAAGAAAGGACAATCTTAAAATAACTAGATGTCATATTCTGGTATTTTAAA
2546743 ATAAATAAATATC
131 ATAAATAAATATC
2546756 CTACTTTTAT
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
146 15 0.13
147 93 0.79
148 10 0.08
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (148 bp):
TATAAATAAATATATATATGATATAATATTATATAAATTATATTAATCATAATAATAATATTTAT
TTATTTTTAAATATTAAGAAAGGACAATCTTAAAATAACTAGATGTCATATTCTGGTATTTTAAA
ATAAATAAATATCATGTT
Found at i:2546942 original size:24 final size:23
Alignment explanation
Indices: 2546910--2546956 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2546900 AAGTAAATAA
2546910 ATATCTTATAAAAATATATATATAT
1 ATATCTTATAAAAAT-TA-ATATAT
2546935 ATAT-TTATAAAAATTAATATAT
1 ATATCTTATAAAAATTAATATAT
2546957 TTTCTTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
24 10 0.45
25 4 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATCTTATAAAAATTAATATAT
Found at i:2547612 original size:64 final size:64
Alignment explanation
Indices: 2547539--2547725 Score: 162
Period size: 64 Copynumber: 2.9 Consensus size: 64
2547529 GCATCAATCC
* *
2547539 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTAGAATAAATTAAAACATCGAATGCATTTCATGCACCGATGCACTCTC
2547602 T
64 T
** ** *** *
2547603 ATGCATCGATGCACTTAGGTTTTATTAAAACATCGAATGCATTTCATGCACCGATGCACAAGCA
1 ATGCATCGATGCACTTAGAATAAATTAAAACATCGAATGCATTTCATGCACCGATGCACTCTCT
* * ** ** * * * *
2547667 ATGCACCGATGCACTCAGGCTATTTTCAAACACCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACTTAGAATAAATTAAAACATCGAATGCATTTCATGCACCGATGCAC
2547726 ACTTGGTGCA
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 94 0.92
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACTTAGAATAAATTAAAACATCGAATGCATTTCATGCACCGATGCACTCTCT
Found at i:2547726 original size:64 final size:64
Alignment explanation
Indices: 2547567--2547726 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 64
2547557 GAATAAATTG
*** * * * *
2547567 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTAGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGTATTATTAA
* *
2547631 AACATCGAATGCATTTCATGCACCGATGCACAAGCAATGCACCGATGCACTCAGGCTATT-TTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGG-TATTATTAA
* *
2547695 AACACCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
2547727 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 80 0.96
65 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTCAGGTATTATTAA
Found at i:2547736 original size:64 final size:63
Alignment explanation
Indices: 2547567--2547745 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 63
2547557 GAATAAATTG
* * * *
2547567 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTAGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTCAGGTATTATTAA
* * *
2547631 AACATCGAATGCATTTCATGCACCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACTCAGG-TATTATTA
2547694 A
63 A
* * * *
2547695 AACACCGAATGCATTTTATGCATCGATGCACACTTGGTGCACTGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACT
2547746 AAGTGTTCCA
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 91 0.94
65 3 0.03
66 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTCAGGTATTATTAA
Found at i:2555195 original size:21 final size:21
Alignment explanation
Indices: 2555153--2555196 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2555143 ACTCCGGGAG
* *
2555153 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
2555174 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
2555195 CT
1 CT
2555197 CCTCCTCCTC
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:2555197 original size:3 final size:3
Alignment explanation
Indices: 2555189--2555213 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2555179 TCCTCTCGTG
2555189 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
2555214 GGCTCCGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:2555915 original size:19 final size:20
Alignment explanation
Indices: 2555891--2555930 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2555881 GAGAAGTGTA
*
2555891 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
2555910 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
2555931 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:2556482 original size:64 final size:63
Alignment explanation
Indices: 2556313--2556492 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 63
2556303 GAATAAATTG
* * * * *
2556313 AACATCGAATGCATTTCATGCATCGATGCACTCTATATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* * * *
2556377 AACATCGAAAGAATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
2556440 A
63 A
* *
2556441 AACATCGAATGCATTTAATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
2556493 AGTGTTCCAA
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 88 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:2559731 original size:14 final size:14
Alignment explanation
Indices: 2559712--2559747 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2559702 TATGTTTTCT
2559712 TTTGCATTGCACAA
1 TTTGCATTGCACAA
2559726 TTTGCATTGCACAA
1 TTTGCATTGCACAA
*
2559740 TTTTCATT
1 TTTGCATT
2559748 CTTATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (14 bp):
TTTGCATTGCACAA
Found at i:2559771 original size:14 final size:14
Alignment explanation
Indices: 2559754--2559803 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2559744 CATTCTTATT
*
2559754 TTTGCATTTACATA
1 TTTGCATTTGCATA
2559768 TTTGCATTTGC--A
1 TTTGCATTTGCATA
*
2559780 TTTGCATTTTGCATC
1 TTTGCA-TTTGCATA
2559795 TTTGCATTT
1 TTTGCATTT
2559804 TTACGTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 7 0.23
13 5 0.16
14 13 0.42
15 6 0.19
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.54
Consensus pattern (14 bp):
TTTGCATTTGCATA
Found at i:2559800 original size:8 final size:7
Alignment explanation
Indices: 2559753--2559804 Score: 56
Period size: 6 Copynumber: 7.6 Consensus size: 7
2559743 TCATTCTTAT
2559753 TTTTGCA
1 TTTTGCA
*
2559760 -TTTACA
1 TTTTGCA
2559766 TATTTGCA
1 T-TTTGCA
2559774 -TTTGCA
1 TTTTGCA
2559780 -TTTGCA
1 TTTTGCA
2559786 TTTTGCA
1 TTTTGCA
2559793 TCTTTGCA
1 T-TTTGCA
2559801 TTTT
1 TTTT
2559805 TACGTTTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 17 0.44
7 10 0.26
8 12 0.31
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (7 bp):
TTTTGCA
Found at i:2564842 original size:54 final size:54
Alignment explanation
Indices: 2564777--2564938 Score: 270
Period size: 54 Copynumber: 3.0 Consensus size: 54
2564767 CTAACCAGAA
* *
2564777 ATCTGAGCAGAAACCACATGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
1 ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
2564831 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
1 ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
*
2564885 ATCTGAGCAGAAGCCACATGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
2564939 CAACGATTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:2566032 original size:45 final size:45
Alignment explanation
Indices: 2565968--2566905 Score: 1626
Period size: 45 Copynumber: 20.7 Consensus size: 45
2565958 GGGACCTTTT
*
2565968 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGAGCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* * *
2566013 TGATGTTTTCAAAACCTTCGGGTTATTTATAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
2566058 TGATATTTTCAAAACCATCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
2566103 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* * *
2566148 TGATGTTTTCAAAACCATCGGGCCATCTGTAAGACCTTCAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
2566193 TGATGTTTTCAAAACCATCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
2566238 TGATGTTTTCAAAACCTTCGGGTCATCTGTACGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
2566283 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566328 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
2566373 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGATCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566419 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566464 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566509 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566554 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
2566599 TGATATTTTCAAAATCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566644 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566690 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566736 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* **
2566782 TGATGTTTTCAAAACCTTCGGGTCATCTATTGGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
2566827 TGATGTTTTCAAAAACCTTTGGGTCATCTGTAAGACATTCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
2566873 TGATGTTTTCAAAGA-CTTCGGGTCATCTGTAAG
1 TGATGTTTTCAAA-ACCTTCGGGTCATCTGTAAG
2566906 TCTTCCGAGC
Statistics
Matches: 851, Mismatches: 38, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
45 630 0.74
46 221 0.26
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:2566661 original size:26 final size:26
Alignment explanation
Indices: 2566632--2566755 Score: 78
Period size: 26 Copynumber: 5.2 Consensus size: 26
2566622 CATCTGTAAG
2566632 ACCTTCAGTGCATGATGTTTTCAAAA
1 ACCTTCAGTGCATGATGTTTTCAAAA
* * *
2566658 ACCTTC-GGGTCAT-CTG---T--AAG
1 ACCTTCAGTG-CATGATGTTTTCAAAA
2566678 ACCTTCAGTGCATGATGTTTTCAAAA
1 ACCTTCAGTGCATGATGTTTTCAAAA
* * *
2566704 ACCTTC-GGGTCAT-CTG---T--AAG
1 ACCTTCAGTG-CATGATGTTTTCAAAA
2566724 ACCTTCAGTGCATGATGTTTTCAAAA
1 ACCTTCAGTGCATGATGTTTTCAAAA
2566750 ACCTTC
1 ACCTTC
2566756 GGGTCATCTG
Statistics
Matches: 70, Mismatches: 12, Indels: 32
0.61 0.11 0.28
Matches are distributed among these distances:
20 22 0.31
21 8 0.11
22 2 0.03
24 2 0.03
25 8 0.11
26 28 0.40
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (26 bp):
ACCTTCAGTGCATGATGTTTTCAAAA
Found at i:2567104 original size:3 final size:3
Alignment explanation
Indices: 2567096--2567156 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
2567086 CATTTTACTT
*
2567096 TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
2567142 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2567157 AATAAAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 53 0.96
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2568487 original size:11 final size:11
Alignment explanation
Indices: 2568447--2568480 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2568437 ATATGTTTAA
*
2568447 ATTATTACTTTA
1 ATTATTA-TTTT
2568459 ATTATTATTTT
1 ATTATTATTTT
2568470 ATTATTATTTT
1 ATTATTATTTT
2568481 CATATTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:2568812 original size:149 final size:149
Alignment explanation
Indices: 2568523--2568801 Score: 323
Period size: 149 Copynumber: 1.9 Consensus size: 149
2568513 ATTTAAATAA
* * * *
2568523 TAATATTTATTTATTTTTAAATATTAAGAAAGGGCAGTCTTAATATAACTAAATGTCATATTCTG
1 TAATATTTATTTATTTTTAAATATTAAGAAAAGACAATCTTAAAATAACTAAATGTCATATTCTG
* * ** * *
2568588 GTATTTTAAAAATAATAAATATCATGTTTATAAAAAATATATATATTTGCTTTAATCTTATATAA
66 CTATTTTAAAAATAATAAATATCATCTTTATAAAAAATATATATATTTGAATTAATCTTAGAGAA
2568653 ATTATTTTAATCATATTTT
131 ATTATTTTAATCATATTTT
* * * *
2568672 TAATATTTATTTATTTTTTAATATTAAGAAAAGATAATCTTAAAATAACTAGATGTCATTTTCTG
1 TAATATTTATTTATTTTTAAATATTAAGAAAAGACAATCTTAAAATAACTAAATGTCATATTCTG
* * * * * * *
2568737 CTATTTT-TAAATAAATAAATATCCTACTTT-T-ATAAAT-TATATTTTTTAATTATTTTTAGAG
66 CTATTTTAAAAAT-AATAAATATCAT-CTTTATAAAAAATATATATATTTGAATTAATCTTAGAG
2568798 AAAT
129 AAAT
2568802 GTTTTATTAA
Statistics
Matches: 107, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
147 20 0.19
148 9 0.08
149 75 0.70
150 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (149 bp):
TAATATTTATTTATTTTTAAATATTAAGAAAAGACAATCTTAAAATAACTAAATGTCATATTCTG
CTATTTTAAAAATAATAAATATCATCTTTATAAAAAATATATATATTTGAATTAATCTTAGAGAA
ATTATTTTAATCATATTTT
Found at i:2568913 original size:17 final size:18
Alignment explanation
Indices: 2568887--2568932 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2568877 ATTTCTAAGT
2568887 AAATAAATAT-CTTATAA
1 AAATAAATATACTTATAA
* *
2568904 AAATATATATATTTATAA
1 AAATAAATATACTTATAA
*
2568922 AAATTAATATA
1 AAATAAATATA
2568933 TTTTCTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAAATATACTTATAA
Found at i:2568921 original size:18 final size:18
Alignment explanation
Indices: 2568893--2568935 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
2568883 AAGTAAATAA
2568893 ATATCTTATAAAAA-TATAT
1 ATAT-TTATAAAAATTA-AT
2568912 ATATTTATAAAAATTAAT
1 ATATTTATAAAAATTAAT
2568930 ATATTT
1 ATATTT
2568936 TCTTAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTATAAAAATTAAT
Found at i:2577636 original size:22 final size:22
Alignment explanation
Indices: 2577594--2577650 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2577584 GCCATATGAT
* *
2577594 CGAGCCGATCGAGCTGTGTGAC
1 CGAGCCGACCGAGCAGTGTGAC
2577616 CGAGCCGACCGAGCCAG-GTGAC
1 CGAGCCGACCGAG-CAGTGTGAC
* *
2577638 CTAGTCGACCGAG
1 CGAGCCGACCGAG
2577651 ACGATTAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.21, C:0.32, G:0.35, T:0.12
Consensus pattern (22 bp):
CGAGCCGACCGAGCAGTGTGAC
Found at i:2588019 original size:24 final size:24
Alignment explanation
Indices: 2587979--2588038 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 24
2587969 TAACAAAAAG
2587979 GGGGAGAAATGTTAAAGTGTTTTAAA
1 GGGGAG-AA-GTTAAAGTGTTTTAAA
*
2588005 GGGGATAAGTTAAAGTGTTTTAAA
1 GGGGAGAAGTTAAAGTGTTTTAAA
2588029 GGGGAGAAGT
1 GGGGAGAAGT
2588039 GTTAGAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 25 0.78
25 2 0.06
26 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.28
Consensus pattern (24 bp):
GGGGAGAAGTTAAAGTGTTTTAAA
Found at i:2591854 original size:14 final size:14
Alignment explanation
Indices: 2591835--2591865 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2591825 AACGAACGTA
2591835 AACGAACACAAACG
1 AACGAACACAAACG
*
2591849 AACGAACATAAACG
1 AACGAACACAAACG
2591863 AAC
1 AAC
2591866 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:2602201 original size:28 final size:28
Alignment explanation
Indices: 2602168--2602226 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
2602158 CGTATGTTTT
*
2602168 ATGGTACACTTTGATAGTTCGTAAATGC
1 ATGGTACACATTGATAGTTCGTAAATGC
*
2602196 ATGGTACACATTGATAGTTGGTAAATGC
1 ATGGTACACATTGATAGTTCGTAAATGC
2602224 ATG
1 ATG
2602227 AATAAGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (28 bp):
ATGGTACACATTGATAGTTCGTAAATGC
Found at i:2604118 original size:3 final size:3
Alignment explanation
Indices: 2604112--2604219 Score: 162
Period size: 3 Copynumber: 35.7 Consensus size: 3
2604102 TCATTTAAAT
** *
2604112 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2604160 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
2604209 TTA TTA TTA TT
1 TTA TTA TTA TT
2604220 TAATAAATAA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 91 0.97
4 3 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2604986 original size:13 final size:13
Alignment explanation
Indices: 2604970--2605010 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2604960 CGCCGTATAT
*
2604970 GGTAGCCGGCGGC
1 GGTAGCTGGCGGC
*
2604983 GGTAGCTGGTGGC
1 GGTAGCTGGCGGC
*
2604996 GGTGGCTGGCGGC
1 GGTAGCTGGCGGC
2605009 GG
1 GG
2605011 AGTACGGTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.05, C:0.22, G:0.59, T:0.15
Consensus pattern (13 bp):
GGTAGCTGGCGGC
Found at i:2605111 original size:7 final size:7
Alignment explanation
Indices: 2605099--2605198 Score: 170
Period size: 7 Copynumber: 14.7 Consensus size: 7
2605089 GTTTGAGAGA
2605099 GAGAAGG
1 GAGAAGG
2605106 GAGAAGG
1 GAGAAGG
2605113 GAGAAGG
1 GAGAAGG
2605120 GAGAAGG
1 GAGAAGG
2605127 GAGAA-G
1 GAGAAGG
2605133 G-G-AGG
1 GAGAAGG
2605138 GAGAAGG
1 GAGAAGG
2605145 GAGAAGG
1 GAGAAGG
2605152 GAGAAGG
1 GAGAAGG
2605159 GAGAAGG
1 GAGAAGG
2605166 GAGAAGG
1 GAGAAGG
2605173 GAGAAGG
1 GAGAAGG
2605180 GAGAAGG
1 GAGAAGG
*
2605187 GAGAAAG
1 GAGAAGG
2605194 GAGAA
1 GAGAA
2605199 TGAGAGAGCT
Statistics
Matches: 89, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
4 1 0.01
5 3 0.03
6 3 0.03
7 82 0.92
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GAGAAGG
Found at i:2611150 original size:13 final size:13
Alignment explanation
Indices: 2611132--2611170 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2611122 GCAAAGAAAG
2611132 AAGAAAAGAAAAT
1 AAGAAAAGAAAAT
2611145 AAGAAAAGAAAA-
1 AAGAAAAGAAAAT
*
2611157 AAAAAAAGGAAAAT
1 AAGAAAA-GAAAAT
2611171 TGAATCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (13 bp):
AAGAAAAGAAAAT
Found at i:2611168 original size:18 final size:18
Alignment explanation
Indices: 2611132--2611169 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2611122 GCAAAGAAAG
*
2611132 AAGAAAAGAAAATAAGAA
1 AAGAAAAGAAAAAAAGAA
2611150 AAGAAAA-AAAAAAAGGAA
1 AAGAAAAGAAAAAAA-GAA
2611168 AA
1 AA
2611170 TTGAATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AAGAAAAGAAAAAAAGAA
Found at i:2613615 original size:83 final size:82
Alignment explanation
Indices: 2613384--2613625 Score: 448
Period size: 82 Copynumber: 2.9 Consensus size: 82
2613374 ATATCCTAGT
*
2613384 CCAATCATTGAATTGGAAGATGAATATGCTCATAGCGTCTTCTGGAAGTGTTCTTTGAGTTATCT
1 CCAATCATTGAATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
2613449 GATCTGGTTTGGCAGAA
66 GATCTGGTTTGGCAGAA
2613466 CCAATCATTGAATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
1 CCAATCATTGAATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
2613531 GATCTGGTTTGGCAGAA
66 GATCTGGTTTGGCAGAA
* *
2613548 CCAATTATTGAAATTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTG-AATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
2613613 TGATCTGGTTTGG
65 TGATCTGGTTTGG
2613626 TATGAACCCC
Statistics
Matches: 156, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
82 90 0.58
83 66 0.42
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (82 bp):
CCAATCATTGAATTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
GATCTGGTTTGGCAGAA
Found at i:2613777 original size:114 final size:114
Alignment explanation
Indices: 2613577--2613892 Score: 530
Period size: 114 Copynumber: 2.8 Consensus size: 114
2613567 GATGAATTTG
2613577 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAACC
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAACC
2613642 AATCATTGAATTTAAAAGATGAATTTGCTCATAGTAAAAATAAGGAGAC
66 AATCATTGAATTTAAAAGATGAATTTGCTCATAGTAAAAATAAGGAGAC
2613691 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAACC
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAACC
2613756 AATCATTGAATTTAAAAGATGAATTTGCTCATAGTAAAAATAAGGAGAC
66 AATCATTGAATTTAAAAGATGAATTTGCTCATAGTAAAAATAAGGAGAC
* * * *
2613805 C-CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCC-AGAA
1 CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA-AA
* *
2613868 CCGATCATTGGAA-TTGAAAGATGAA
64 CCAATCATT-GAATTTAAAAGATGAA
2613893 CTGCATGATC
Statistics
Matches: 193, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
113 2 0.01
114 188 0.97
115 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (114 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGAAACC
AATCATTGAATTTAAAAGATGAATTTGCTCATAGTAAAAATAAGGAGAC
Found at i:2617309 original size:76 final size:76
Alignment explanation
Indices: 2617210--2618006 Score: 1488
Period size: 76 Copynumber: 10.5 Consensus size: 76
2617200 CTATTTCCCA
*
2617210 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617275 AGCCTTCGGGT
66 AGCCTTCGGGT
2617286 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617351 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2617362 CATCTGTAAGTCCTTCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617427 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2617438 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617503 AGCCTTCGGGT
66 AGCCTTCGGGT
2617514 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617579 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2617590 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617654 AGCCTTCGGGT
66 AGCCTTCGGGT
2617665 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617730 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2617741 CATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2617806 AGCCTTCGGGT
66 AGCCTTCGGGT
2617817 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2617882 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
2617893 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
2617958 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
2617970 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
2618007 TTTCCATCCT
Statistics
Matches: 704, Mismatches: 15, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
75 74 0.11
76 583 0.83
77 47 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2617914 original size:379 final size:381
Alignment explanation
Indices: 2617210--2618006 Score: 1508
Period size: 379 Copynumber: 2.1 Consensus size: 381
2617200 CTATTTCCCA
2617210 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
2617275 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
2617340 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCTAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTC
2617405 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
*
2617470 AAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGC
261 AAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGC
* *
2617535 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AAAGCCTTCGGGT
326 ATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
2617590 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
2617654 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
2617719 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTC
2617784 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
* *
2617849 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTACAGTGC
261 AAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGC
2617914 ATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
326 ATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
*
2617970 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
2618007 TTTCCATCCT
Statistics
Matches: 408, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
379 311 0.76
380 97 0.24
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (381 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
AAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGC
ATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
Found at i:2618135 original size:3 final size:3
Alignment explanation
Indices: 2618129--2618236 Score: 128
Period size: 3 Copynumber: 35.0 Consensus size: 3
2618119 TTTCATTTAA
**
2618129 ATT ATT ATT ATT ATT AAA ATT ATT ATT A-T ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
* * *
2618174 ATA ATAT ATT ATT ATT ATT ATT ATT ATTT ATT ATT AAT ATT AAT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
2618221 ATAT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT
2618237 TAATAAATAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.02
3 77 0.86
4 11 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2618191 original size:22 final size:22
Alignment explanation
Indices: 2618134--2618236 Score: 116
Period size: 22 Copynumber: 4.6 Consensus size: 22
2618124 TTTAAATTAT
** *
2618134 TATTATTATTAAAATTATTATTA
1 TATTATTATTATTATTA-TAATA
2618157 TATTATTTATTATTATTATAATA
1 TATTA-TTATTATTATTATAATA
* *
2618180 TATTATTATTATTATTATTATT
1 TATTATTATTATTATTATAATA
* * *
2618202 TATTATTAATATTAATATTATA
1 TATTATTATTATTATTATAATA
2618224 TATTATTATTATT
1 TATTATTATTATT
2618237 TAATAAATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
22 46 0.66
23 14 0.20
24 10 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTATTATTATAATA
Found at i:2625545 original size:16 final size:16
Alignment explanation
Indices: 2625515--2625557 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2625505 CAATGAGTCT
2625515 AAATC-AAAT-AAGGA
1 AAATCAAAATAAAGGA
* *
2625529 AAGTTAAAATAAAGGA
1 AAATCAAAATAAAGGA
2625545 AAATCAAAATAAA
1 AAATCAAAATAAA
2625558 TAAAGTCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 3 0.13
15 4 0.17
16 16 0.70
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (16 bp):
AAATCAAAATAAAGGA
Found at i:2626175 original size:18 final size:18
Alignment explanation
Indices: 2626152--2626196 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2626142 TTACATTCCA
*
2626152 GTAATCTTATTCCCATAG
1 GTAATCTTATTCCCAGAG
2626170 GTAATCTTATTCCCAGAG
1 GTAATCTTATTCCCAGAG
2626188 GTAATCTTA
1 GTAATCTTA
2626197 CATTTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (18 bp):
GTAATCTTATTCCCAGAG
Found at i:2628008 original size:31 final size:31
Alignment explanation
Indices: 2627956--2628018 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
2627946 AAATATAATG
* * * *
2627956 TTTGGTCATTTTCGTTTTTATTTGATTAAGA
1 TTTGATCACTTTCATTTTTATTTAATTAAGA
2627987 TTTGATCACTTTCATTTTTATTTAATTAAGA
1 TTTGATCACTTTCATTTTTATTTAATTAAGA
2628018 T
1 T
2628019 GCGGTCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (31 bp):
TTTGATCACTTTCATTTTTATTTAATTAAGA
Found at i:2629441 original size:22 final size:20
Alignment explanation
Indices: 2629390--2629442 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
2629380 GAATACAAAG
* *
2629390 AATAAGATTAAGACAATAAA
1 AATAAGAATAAGACAAGAAA
* *
2629410 GATAAAAATAGAGACAAGGAAA
1 AATAAGAATA-AGACAA-GAAA
2629432 AATAAGAATAA
1 AATAAGAATAA
2629443 TAATAGGATA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 11 0.44
ACGTcount: A:0.66, C:0.04, G:0.15, T:0.15
Consensus pattern (20 bp):
AATAAGAATAAGACAAGAAA
Found at i:2650943 original size:338 final size:334
Alignment explanation
Indices: 2650298--2650963 Score: 929
Period size: 335 Copynumber: 2.0 Consensus size: 334
2650288 ATTTTCTACA
* * **
2650298 ATTATGTAGTACGTGTCACCACCTATGAGGATAAAATAAAACAAATCATTTTTGCTACTAGCATA
1 ATTAGGTAGTACGTGTCACCACCTATGAGGATAAAATAAAACAAATAATTCCTGCTACTAGCATA
* * * * **
2650363 AATTAGACCTTAGCCTCTTGCATAAGATGCAAGACATTCAACCATTAAGATAAACTAGTTGTTTA
66 AATTAGACCTAAGCCTCTTGCATAAAATGCAAGACACTCAACAATTAAGATAAACTAGTCATTTA
* * * *
2650428 GGTTAATTTCACCATATTTTATATCTAACTCATATAACATATCACCATAAATTAATTTTTTCGAT
131 GGTTAAGTTCACCATATTTTATATCAAACTCATATAACATATCACCATAAATTAATTTTTCCAAT
* * * *
2650493 GATTATAAAATTCGAATATGTGACACTTTAAATTAATGACCCAAAACTTAGCCACTCAGTTATAT
196 GATTATAAAATTCGAATAGGCGACACTTTAAATTAATGAACCAAAACTTAGCCACTCAATTATAT
* *
2650558 TGCGAACCTATTTTTATTATATTGAACTTAATACTTACTTATATCATTATTAAGTTAAAGAACAA
261 TACGAACCTATTTTTATTATATTGAACTTAATACTTACTTATATCATTATTAAGTAAAAGAACAA
2650623 TTTCAATCT
326 TTTCAATCT
* * *
2650632 ATTAGGTAGTAACGTGTCACTACCTATGAGGATAAAATAAAAGAAATAATTCCTGCTACTTGCAT
1 ATTAGGTAGT-ACGTGTCACCACCTATGAGGATAAAATAAAACAAATAATTCCTGCTACTAGCAT
* ** * **
2650697 GAATT-GAACCTAAGCCTCTTGCATAAAATGCAAGGTACTCAACAATTAAGCTAGGCTAGTCATT
65 AAATTAG-ACCTAAGCCTCTTGCATAAAATGCAAGACACTCAACAATTAAGATAAACTAGTCATT
* * * *
2650761 TAGGTTAGGTTCACCATATTTTGTATCAAACTTATATAACAATATCGCCATAAAATTAATATTTT
129 TAGGTTAAGTTCACCATATTTTATATCAAACTCATATAAC-ATATCACCAT-AAATTAAT-TTTT
* * * *
2650826 CCAATGATTATAAAATTTGAATAGGCGATACTTTAAATTAATGAACGAAAGCTTAGCCACTCAAT
191 CCAATGATTATAAAATTCGAATAGGCGACACTTTAAATTAATGAACCAAAACTTAGCCACTCAAT
*
2650891 TATATTACGAACTTATTTTTATTATATTGAACTTAATACTTACTTATATCATTATTAAGTAAAAG
256 TATATTACGAACCTATTTTTATTATATTGAACTTAATACTTACTTATATCATTATTAAGTAAAAG
*
2650956 AATAATTT
321 AACAATTT
2650964 TTCATTTTCT
Statistics
Matches: 288, Mismatches: 39, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
334 10 0.03
335 133 0.46
336 9 0.03
337 8 0.03
338 128 0.44
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (334 bp):
ATTAGGTAGTACGTGTCACCACCTATGAGGATAAAATAAAACAAATAATTCCTGCTACTAGCATA
AATTAGACCTAAGCCTCTTGCATAAAATGCAAGACACTCAACAATTAAGATAAACTAGTCATTTA
GGTTAAGTTCACCATATTTTATATCAAACTCATATAACATATCACCATAAATTAATTTTTCCAAT
GATTATAAAATTCGAATAGGCGACACTTTAAATTAATGAACCAAAACTTAGCCACTCAATTATAT
TACGAACCTATTTTTATTATATTGAACTTAATACTTACTTATATCATTATTAAGTAAAAGAACAA
TTTCAATCT
Found at i:2651655 original size:20 final size:22
Alignment explanation
Indices: 2651632--2651671 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2651622 AATTAAATAT
2651632 ATATT-TAAA-ATATTTTTATA
1 ATATTATAAACATATTTTTATA
2651652 ATATTATAAACATATTTTTA
1 ATATTATAAACATATTTTTA
2651672 GAATGATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTATAAACATATTTTTATA
Found at i:2653767 original size:28 final size:27
Alignment explanation
Indices: 2653736--2653810 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
2653726 ATATTTAAAA
* *
2653736 TTAATATAATTTTAGTATTTTTATATTT
1 TTAATATAATTTTAATATTTTT-TATGT
*
2653764 TTAA-ATTAAATTTAATATTTTTTATGT
1 TTAATA-TAATTTTAATATTTTTTATGT
*
2653791 TTAATA-AATTATATATATTT
1 TTAATATAATTTTA-ATATTT
2653811 AAATCATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.13
27 15 0.38
28 19 0.49
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (27 bp):
TTAATATAATTTTAATATTTTTTATGT
Found at i:2654686 original size:20 final size:20
Alignment explanation
Indices: 2654640--2654688 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2654630 AACGTACTGC
* *
2654640 ATGAATAGTATTGATACTGT
1 ATGAATAGTATCGATAATGT
*
2654660 ATAAATAGTATCGATAATGT
1 ATGAATAGTATCGATAATGT
*
2654680 GTGAATAGT
1 ATGAATAGT
2654689 GGTATCGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (20 bp):
ATGAATAGTATCGATAATGT
Found at i:2655471 original size:20 final size:20
Alignment explanation
Indices: 2655446--2655496 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2655436 TAATGTACTA
2655446 TATGAATAGTACCAATAATG
1 TATGAATAGTACCAATAATG
* *
2655466 TATGAATAGTACTAATACTG
1 TATGAATAGTACCAATAATG
* *
2655486 TGTGAACAGTA
1 TATGAATAGTA
2655497 GTATCGATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
TATGAATAGTACCAATAATG
Found at i:2655514 original size:21 final size:21
Alignment explanation
Indices: 2655488--2655559 Score: 135
Period size: 21 Copynumber: 3.4 Consensus size: 21
2655478 TAATACTGTG
2655488 TGAACAGTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
2655509 TGAACAGTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
*
2655530 TGAATAGTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
2655551 TGAACAGTA
1 TGAACAGTA
2655560 CCGATGCTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (21 bp):
TGAACAGTAGTATCGATACCA
Found at i:2655637 original size:21 final size:21
Alignment explanation
Indices: 2655608--2655663 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
2655598 ATGCTGATAT
*
2655608 AGTATTATTGATACAATGAAC
1 AGTAATATTGATACAATGAAC
* * * *
2655629 ATTAATATTCATACCATGAAT
1 AGTAATATTGATACAATGAAC
*
2655650 AGTAGTATTGATAC
1 AGTAATATTGATAC
2655664 TATCAAGCCC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (21 bp):
AGTAATATTGATACAATGAAC
Found at i:2659047 original size:21 final size:22
Alignment explanation
Indices: 2659021--2659069 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2659011 CGATGTTGTG
2659021 TGAACAGA-AGTATCGATACCA
1 TGAACAGATAGTATCGATACCA
* *
2659042 TGAACA-ATTGTCTCGATACCA
1 TGAACAGATAGTATCGATACCA
2659063 TGAACAG
1 TGAACAG
2659070 TACCGATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (22 bp):
TGAACAGATAGTATCGATACCA
Found at i:2659142 original size:21 final size:21
Alignment explanation
Indices: 2659118--2659178 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
2659108 CAATACTACT
*
2659118 ACAGTAGTATCTATACCATGA
1 ACAGTAGTATCGATACCATGA
*
2659139 ACAGTAGTATCGATACCGTGA
1 ACAGTAGTATCGATACCATGA
2659160 ACAGTAGTATCGATACCAT
1 ACAGTAGTATCGATACCAT
2659179 TTAATTTGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (21 bp):
ACAGTAGTATCGATACCATGA
Found at i:2659253 original size:20 final size:20
Alignment explanation
Indices: 2659224--2659266 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2659214 ACTAGCGTAT
*
2659224 TGTATTAATAGTACCAATAA
1 TGTATAAATAGTACCAATAA
* *
2659244 TGTATAAATAGTATCGATAA
1 TGTATAAATAGTACCAATAA
2659264 TGT
1 TGT
2659267 GTGAACAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (20 bp):
TGTATAAATAGTACCAATAA
Found at i:2664217 original size:15 final size:15
Alignment explanation
Indices: 2664197--2664232 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
2664187 ATATGGATTG
2664197 ATTTATTTTTAAATA
1 ATTTATTTTTAAATA
2664212 ATTTA-TTTTAAATA
1 ATTTATTTTTAAATA
2664226 ATTTATT
1 ATTTATT
2664233 AGTATGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATTTTTAAATA
Found at i:2664251 original size:22 final size:22
Alignment explanation
Indices: 2664233--2664277 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2664223 ATAATTTATT
2664233 AGTATGAATTGATTTATTTTAA
1 AGTATGAATTGATTTATTTTAA
2664255 AGTATGAATTGATTTATTTTAA
1 AGTATGAATTGATTTATTTTAA
2664277 A
1 A
2664278 TAATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
AGTATGAATTGATTTATTTTAA
Found at i:2664251 original size:32 final size:32
Alignment explanation
Indices: 2664212--2664309 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 32
2664202 TTTTTAAATA
2664212 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
2664244 ATTTA-TTT---T-A---A--AGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
2664266 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
2664298 ATTTATTTTAAA
1 ATTTATTTTAAA
2664310 ATATGGATTG
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
22 16 0.29
23 3 0.05
24 1 0.02
26 1 0.02
27 2 0.04
28 1 0.02
30 1 0.02
31 3 0.05
32 27 0.49
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:2664277 original size:54 final size:54
Alignment explanation
Indices: 2664212--2665113 Score: 879
Period size: 54 Copynumber: 16.4 Consensus size: 54
2664202 TTTTTAAATA
* * *
2664212 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2664266 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* **
2664320 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * *
2664369 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
* *
2664432 ATTTATTTTAAATGATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2664486 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTG
2664544 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--A-AA---A----TATGGATTG
*
2664608 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2664662 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
2664710 ATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAATTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2664764 ATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2664818 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2664872 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2664926 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * ***
2664976 ATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* *
2665038 ATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2665092 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
2665114 TTGTAGTTGT
Statistics
Matches: 715, Mismatches: 65, Indels: 136
0.78 0.07 0.15
Matches are distributed among these distances:
47 4 0.01
48 84 0.12
49 10 0.01
50 27 0.04
51 1 0.00
52 13 0.02
53 8 0.01
54 371 0.52
55 8 0.01
56 5 0.01
57 5 0.01
58 30 0.04
59 5 0.01
60 8 0.01
61 5 0.01
62 25 0.03
63 17 0.02
64 89 0.12
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2664377 original size:32 final size:32
Alignment explanation
Indices: 2664336--2664475 Score: 183
Period size: 32 Copynumber: 4.7 Consensus size: 32
2664326 TATTGTAGTT
2664336 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664368 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664391 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* * *
2664422 GTATGAATTGATTTATTTTAAATGATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664454 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2664476 ATATGGATTG
Statistics
Matches: 94, Mismatches: 4, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
22 14 0.15
23 4 0.04
25 1 0.01
26 3 0.03
28 3 0.03
29 1 0.01
31 4 0.04
32 64 0.68
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2664394 original size:22 final size:22
Alignment explanation
Indices: 2664369--2664411 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2664359 AATTTATTAG
2664369 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2664391 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2664412 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2664419 original size:14 final size:14
Alignment explanation
Indices: 2664398--2664453 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
2664388 AAATATGGAT
2664398 TGATTTATTTTAAA
1 TGATTTATTTTAAA
* *
2664412 TAATTTATTAGTATGAAT
1 TGATTTATT--T-T-AAA
2664430 TGATTTATTTTAAA
1 TGATTTATTTTAAA
2664444 TGATTTATTT
1 TGATTTATTT
2664454 GTATGGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.59
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (14 bp):
TGATTTATTTTAAA
Found at i:2664486 original size:166 final size:166
Alignment explanation
Indices: 2664255--2664969 Score: 782
Period size: 166 Copynumber: 4.3 Consensus size: 166
2664245 TTTATTTTAA
2664255 AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2664320 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
66 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
2664385 TTAAAATATGGATTGATTTATTTTAAATAATTTATT
131 TTAAAATATGGATTGATTTATTTTAAATAATTTATT
* *
2664421 AGTATGAATTGATTTATTTTAAATGATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2664486 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
66 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T
2664551 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATT
130 TT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATT
* * *
2664597 TGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
** ** * **
2664662 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATA
66 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTA
* * * *
2664724 ATTTATTAGTATGGACTGATTTA-TTT---TAA---ATT
129 TTTTA-AAATATGGATTGATTTATTTTAAATAATTTATT
*
2664756 A-TA-G-ATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTG
1 AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* ** **
2664818 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAA-ATATGAATT-G-ATTTATT
66 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-T
* ** * * *
2664879 TTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T
122 TGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATT
2664920 -G---G-ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
2664970 TAATTTATTT
Statistics
Matches: 500, Mismatches: 24, Indels: 54
0.87 0.04 0.09
Matches are distributed among these distances:
156 62 0.12
157 1 0.00
158 4 0.01
159 3 0.01
160 2 0.00
161 2 0.00
162 121 0.24
163 3 0.01
164 3 0.01
165 4 0.01
166 139 0.28
167 3 0.01
169 1 0.00
170 3 0.01
171 2 0.00
173 1 0.00
174 5 0.01
175 8 0.02
176 133 0.27
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (166 bp):
AGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
TTAAAATATGGATTGATTTATTTTAAATAATTTATT
Found at i:2664543 original size:32 final size:32
Alignment explanation
Indices: 2664502--2665001 Score: 490
Period size: 32 Copynumber: 16.7 Consensus size: 32
2664492 TATTGTAGTT
2664502 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664534 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
2664566 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664598 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
2664630 GTATAGATTGATTTATTTTAAAATATGGATTGATTTA
1 GTATGGATTGATTTATTTT-AAATA---ATTTA-TTA
* * ** * ** * *
2664667 TTATTGTAGTTGTATGGA-TTGATTTATTTTA-AA
1 GTA-TGGA-TTG-ATTTATTTTAAATAATTTATTA
*
2664700 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
2664732 GTATGGACTGATTTA-TTT---TAA---ATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664757 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
2664786 GTATTGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664809 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664840 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664866 G-A---ATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664894 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664917 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
2664948 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
2664980 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2665002 ATATGGATTG
Statistics
Matches: 389, Mismatches: 29, Indels: 100
0.75 0.06 0.19
Matches are distributed among these distances:
22 49 0.13
23 13 0.03
24 4 0.01
25 7 0.02
26 12 0.03
27 2 0.01
28 12 0.03
29 7 0.02
30 7 0.02
31 25 0.06
32 218 0.56
33 8 0.02
35 3 0.01
36 4 0.01
37 5 0.01
38 5 0.01
39 5 0.01
40 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2664660 original size:22 final size:22
Alignment explanation
Indices: 2664635--2664721 Score: 111
Period size: 22 Copynumber: 3.8 Consensus size: 22
2664625 TATTAGTATA
2664635 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
***
2664657 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTA-T-TT-TA-AAATATG
2664683 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
2664705 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
2664722 TAATTTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
22 31 0.56
23 3 0.05
24 4 0.07
25 3 0.05
26 14 0.25
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:2664765 original size:22 final size:22
Alignment explanation
Indices: 2664740--2664830 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 22
2664730 TAGTATGGAC
2664740 TGATTTATTTTAAATTATAGAT
1 TGATTTATTTTAAATTATAGAT
2664762 TGATTTATTTTAAATAATTTATTAGTAT
1 TGATTTATTTT--A-AA-TTA-TAG-AT
* *
2664790 TGATTGATTTATTTTAAAATATGGAT
1 TGA-T---TTATTTTAAATTATAGAT
2664816 TGATTTATTTTAAAT
1 TGATTTATTTTAAAT
2664831 AATTTATTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
22 21 0.38
24 1 0.02
25 3 0.05
26 8 0.14
27 5 0.09
28 7 0.12
29 3 0.05
30 1 0.02
32 7 0.12
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (22 bp):
TGATTTATTTTAAATTATAGAT
Found at i:2664866 original size:22 final size:22
Alignment explanation
Indices: 2664841--2664883 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2664831 AATTTATTAG
*
2664841 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
2664863 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2664884 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2664920 original size:22 final size:22
Alignment explanation
Indices: 2664895--2664937 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2664885 AATTTATTAG
2664895 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2664917 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2664938 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2665086 original size:22 final size:22
Alignment explanation
Indices: 2665061--2665103 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2665051 AATTTATTAG
2665061 TATGAATTAATTTATTTTAAAA
1 TATGAATTAATTTATTTTAAAA
* *
2665083 TATGGATTGATTTATTTTAAA
1 TATGAATTAATTTATTTTAAA
2665104 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGAATTAATTTATTTTAAAA
Found at i:2665163 original size:31 final size:31
Alignment explanation
Indices: 2665128--2665186 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2665118 AGTTGTATGG
* *
2665128 ATTATTTAAATTTCACTATTGTAAAACTAAA
1 ATTATTTAAATCTCACTATTGCAAAACTAAA
*
2665159 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCACTATTGCAAAACT
2665187 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCACTATTGCAAAACTAAA
Found at i:2667978 original size:20 final size:19
Alignment explanation
Indices: 2667937--2667979 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2667927 AATGATATTC
* *
2667937 TTTTGAAAGCAAAATTAGA
1 TTTTGAAAGCAAAATGAAA
*
2667956 TTTTGAAAATCAAAATGAAA
1 TTTTG-AAAGCAAAATGAAA
2667976 TTTT
1 TTTT
2667980 AAGAAAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (19 bp):
TTTTGAAAGCAAAATGAAA
Found at i:2670931 original size:17 final size:17
Alignment explanation
Indices: 2670909--2670979 Score: 81
Period size: 17 Copynumber: 4.1 Consensus size: 17
2670899 AATTAAGAGT
*
2670909 TAGTTTAATAAATGAAC
1 TAGTTTAATTAATGAAC
*
2670926 TAGTTTGATTAATGAAC
1 TAGTTTAATTAATGAAC
*
2670943 TAGTTTAGTTAATGAAC
1 TAGTTTAATTAATGAAC
*
2670960 TA-TCTTTATTCAATGAAC
1 TAGT-TTAATT-AATGAAC
2670978 TA
1 TA
2670980 AATGCATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 1 0.02
17 36 0.78
18 9 0.20
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2670947 original size:34 final size:35
Alignment explanation
Indices: 2670909--2670979 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
2670899 AATTAAGAGT
2670909 TAGTTTAATAAATGAACTAGT-TTGATT-AATGAAC
1 TAGTTTAATAAATGAACTA-TCTTGATTCAATGAAC
* * *
2670943 TAGTTTAGTTAATGAACTATCTTTATTCAATGAAC
1 TAGTTTAATAAATGAACTATCTTGATTCAATGAAC
2670978 TA
1 TA
2670980 AATGCATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 1 0.03
34 22 0.69
35 9 0.28
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTATCTTGATTCAATGAAC
Found at i:2672769 original size:16 final size:15
Alignment explanation
Indices: 2672742--2672779 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
2672732 AAAATTGAAG
2672742 GCATAAAATTAAATA
1 GCATAAAATTAAATA
2672757 GCATAATAATTAAATA
1 GCATAA-AATTAAATA
*
2672773 ACATAAA
1 GCATAAA
2672780 TAAAAGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (15 bp):
GCATAAAATTAAATA
Found at i:2672939 original size:16 final size:16
Alignment explanation
Indices: 2672920--2672959 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2672910 GTGGTTAGAA
*
2672920 GTTAGAAAAATTAGTT
1 GTTAGAAAAATTAATT
*
2672936 GTTAGAAAAGTTAATT
1 GTTAGAAAAATTAATT
2672952 GTTAGAAA
1 GTTAGAAA
2672960 TTAATTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (16 bp):
GTTAGAAAAATTAATT
Found at i:2672965 original size:14 final size:15
Alignment explanation
Indices: 2672920--2672965 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
2672910 GTGGTTAGAA
*
2672920 GTTAGAAAAATTAGTT
1 GTTAG-AAAATTAATT
2672936 GTTAGAAAAGTTAATT
1 GTTAGAAAA-TTAATT
2672952 GTTAG-AAATTAATT
1 GTTAGAAAATTAATT
2672966 AGGTTCGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 7 0.25
16 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.39
Consensus pattern (15 bp):
GTTAGAAAATTAATT
Found at i:2677828 original size:21 final size:21
Alignment explanation
Indices: 2677803--2677842 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2677793 ATAAGACTAT
2677803 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
2677824 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
2677843 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:2681488 original size:18 final size:18
Alignment explanation
Indices: 2681465--2681530 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2681455 GTGTAATACC
*
2681465 AGATTGAAGCTAAAAACT
1 AGATTGAAGCAAAAAACT
*
2681483 AGATTGAAGCAAAAAAAT
1 AGATTGAAGCAAAAAACT
* *
2681501 AGA-TGAATGACCAAAAACC
1 AGATTGAA-G-CAAAAAACT
2681520 AGATTGAAGCA
1 AGATTGAAGCA
2681531 GAAGCCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.10
18 21 0.54
19 10 0.26
20 4 0.10
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.17
Consensus pattern (18 bp):
AGATTGAAGCAAAAAACT
Found at i:2683006 original size:17 final size:18
Alignment explanation
Indices: 2682979--2683012 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2682969 AGTACAATGA
2682979 TTTATTTAAATTTAATTG
1 TTTATTTAAATTTAATTG
2682997 TTTA-TTAAATTTAATT
1 TTTATTTAAATTTAATT
2683013 TTAACATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTTAAATTTAATTG
Found at i:2689442 original size:188 final size:190
Alignment explanation
Indices: 2689125--2689503 Score: 744
Period size: 188 Copynumber: 2.0 Consensus size: 190
2689115 ACTTTAGAGG
2689125 TCTCATACCTATCATGAAGTGCTTACCCTTCATATATTTCCTTAAGATTTTGAATCATCTCATAT
1 TCTCATACCTATCATGAAGTGCTTACCCTTCATATATTTCCTTAAGATTTTGAATCATCTCATAT
2689190 GCAACCATGTCCTTATGTTGCTTCTGAAGCTCGGGAGTCACGGTGGCAAGTATTAGACATCCAAC
66 GCAACCATGTCCTTATGTTGCTTCTGAAGCTCGGGAGTCACGGTGGCAAGTATTAGACATCCAAC
2689255 ATCTAACATATCATCCATA-GTTTCTTAAATTTTTCTTTGTCAGATCT-AAAGCATTAGC
131 ATCTAACATATCATCCATATGTTTCTTAAATTTTTCTTTGTCAGATCTAAAAGCATTAGC
2689313 TCTCATACCTATCATGAAGTGCTTACCCTTCATATATTTCCTTAAGATTTTGAATCATCTCATAT
1 TCTCATACCTATCATGAAGTGCTTACCCTTCATATATTTCCTTAAGATTTTGAATCATCTCATAT
2689378 GCAACCATGTCCTTATGTTGCTTCTGAAGCTCGGGAGTCACGGTGGCAAGTATTAGACATCCAAC
66 GCAACCATGTCCTTATGTTGCTTCTGAAGCTCGGGAGTCACGGTGGCAAGTATTAGACATCCAAC
2689443 ATCTAACATATCATCCATATGTTTCTTAAATTTTTCTTTGTCAGATCTAAAAGCATTAGC
131 ATCTAACATATCATCCATATGTTTCTTAAATTTTTCTTTGTCAGATCTAAAAGCATTAGC
2689503 T
1 T
2689504 ATTGGTTCAT
Statistics
Matches: 189, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
188 149 0.79
189 28 0.15
190 12 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (190 bp):
TCTCATACCTATCATGAAGTGCTTACCCTTCATATATTTCCTTAAGATTTTGAATCATCTCATAT
GCAACCATGTCCTTATGTTGCTTCTGAAGCTCGGGAGTCACGGTGGCAAGTATTAGACATCCAAC
ATCTAACATATCATCCATATGTTTCTTAAATTTTTCTTTGTCAGATCTAAAAGCATTAGC
Found at i:2692954 original size:20 final size:20
Alignment explanation
Indices: 2692917--2692956 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2692907 CTCTAAAAAA
*
2692917 ATATAATTTAATTATAATTT
1 ATATAATTTAAATATAATTT
2692937 ATATAATTTATAAT-TAATTT
1 ATATAATTTA-AATATAATTT
2692957 TTAATAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATAATTTAAATATAATTT
Found at i:2692970 original size:18 final size:18
Alignment explanation
Indices: 2692949--2692983 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2692939 ATAATTTATA
*
2692949 ATTAATTTTTAATAAATG
1 ATTAATTTTAAATAAATG
2692967 ATTAATTTTAAATAAAT
1 ATTAATTTTAAATAAAT
2692984 CCTTATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAATTTTAAATAAATG
Found at i:2694532 original size:15 final size:17
Alignment explanation
Indices: 2694494--2694537 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
2694484 AAATATATGG
2694494 TAAATCAA-ATATCAGA
1 TAAATCAATATATCAGA
2694510 TAAA-CAATAT-TCAGA
1 TAAATCAATATATCAGA
2694525 -AAATCAAT-TATCA
1 TAAATCAATATATCA
2694538 TGTCGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.27
Consensus pattern (17 bp):
TAAATCAATATATCAGA
Found at i:2699010 original size:23 final size:23
Alignment explanation
Indices: 2698980--2699028 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
2698970 ATACCTGACC
*
2698980 CGGACATTATGACCAAATCTAGG
1 CGGACATTATAACCAAATCTAGG
2699003 CGGACATTATAACCAAATCTAGG
1 CGGACATTATAACCAAATCTAGG
2699026 CGG
1 CGG
2699029 TCACATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
CGGACATTATAACCAAATCTAGG
Found at i:2699143 original size:2 final size:2
Alignment explanation
Indices: 2699130--2699292 Score: 308
Period size: 2 Copynumber: 81.5 Consensus size: 2
2699120 CATACGATAA
* *
2699130 AC AC AA AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2699172 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2699214 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2699256 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2699293 TATATATATA
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 157 1.00
ACGTcount: A:0.51, C:0.48, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:2699370 original size:2 final size:2
Alignment explanation
Indices: 2699292--2699354 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
2699282 ACACACACAC
2699292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2699334 AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2699355 CAGAAATTCG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2701952 original size:15 final size:14
Alignment explanation
Indices: 2701934--2701963 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2701924 GCGGGTTTTG
2701934 ACGGTGCGGGCGTAA
1 ACGGTGCGGGC-TAA
2701949 ACGGTGCGGGCTAA
1 ACGGTGCGGGCTAA
2701963 A
1 A
2701964 AAGCCCGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.23, C:0.20, G:0.43, T:0.13
Consensus pattern (14 bp):
ACGGTGCGGGCTAA
Found at i:2705448 original size:13 final size:13
Alignment explanation
Indices: 2705430--2705454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2705420 CAGCTTCCCC
2705430 AAAATTTTTCTTG
1 AAAATTTTTCTTG
2705443 AAAATTTTTCTT
1 AAAATTTTTCTT
2705455 TTATTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
AAAATTTTTCTTG
Found at i:2708187 original size:16 final size:15
Alignment explanation
Indices: 2708174--2708240 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 15
2708164 TAAAAAAATA
2708174 AAAAGAAGAGAAAAAG
1 AAAA-AAGAGAAAAAG
2708190 AGAAAAAGAGAAAAAG
1 A-AAAAAGAGAAAAAG
2708206 AGAAAAAGAAGAAAATAG
1 A-AAAAAG-AGAAAA-AG
2708224 AAAAAAG-G-AAAAG
1 AAAAAAGAGAAAAAG
2708237 AAAA
1 AAAA
2708241 GAAAACATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.12
14 3 0.06
15 1 0.02
16 20 0.42
17 15 0.31
18 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (15 bp):
AAAAAAGAGAAAAAG
Found at i:2708187 original size:19 final size:19
Alignment explanation
Indices: 2708159--2708217 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 19
2708149 AAATCAAGGC
* *
2708159 GAAGATAAAAAAATAAAAA
1 GAAGAGAAAAAAAGAAAAA
*
2708178 GAAGAG--AAAAAGAGAAA
1 GAAGAGAAAAAAAGAAAAA
*
2708195 -AAGAGAAAAAGAGAAAAA
1 GAAGAGAAAAAAAGAAAAA
2708213 GAAGA
1 GAAGA
2708218 AAATAGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 5 0.16
17 9 0.28
18 9 0.28
19 9 0.28
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (19 bp):
GAAGAGAAAAAAAGAAAAA
Found at i:2708190 original size:8 final size:8
Alignment explanation
Indices: 2708179--2708235 Score: 82
Period size: 8 Copynumber: 7.1 Consensus size: 8
2708169 AAATAAAAAG
2708179 AAGAGAAA
1 AAGAGAAA
2708187 AAGAGAAA
1 AAGAGAAA
2708195 AAGAGAAA
1 AAGAGAAA
2708203 AAGAGAAA
1 AAGAGAAA
2708211 AAGAAGAAA
1 AAG-AGAAA
2708220 ATAGA-AAA
1 A-AGAGAAA
2708228 AAG-GAAA
1 AAGAGAAA
2708235 A
1 A
2708236 GAAAAGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
7 6 0.13
8 31 0.67
9 7 0.15
10 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (8 bp):
AAGAGAAA
Found at i:2708206 original size:24 final size:25
Alignment explanation
Indices: 2708168--2708245 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
2708158 CGAAGATAAA
2708168 AAAATA-AAAAGAAGAGAAAAAG-AG
1 AAAATAGAAAA-AAGAGAAAAAGAAG
2708192 AAAA-AGAGAAAAAGAGAAAAAGAAG
1 AAAATAGA-AAAAAGAGAAAAAGAAG
*
2708217 AAAATAGAAAAAAG-GAAAAGAAAAG
1 AAAATAGAAAAAAGAGAAAA-AGAAG
2708242 AAAA
1 AAAA
2708246 CATATCAAGC
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
23 1 0.02
24 21 0.44
25 23 0.48
26 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (25 bp):
AAAATAGAAAAAAGAGAAAAAGAAG
Found at i:2708243 original size:18 final size:17
Alignment explanation
Indices: 2708159--2708245 Score: 72
Period size: 18 Copynumber: 4.9 Consensus size: 17
2708149 AAATCAAGGC
*
2708159 GAAGATAAAAAAATAAAAA
1 GAAGA-AAAAAGA-AAAAA
2708178 GAAGAGAAAAAGAGAAAAA
1 GAAGA-AAAAAGA-AAAAA
2708197 G-AG-AAAAAGAGAAAAA
1 GAAGAAAAAAGA-AAAAA
*
2708213 GAAGAAAATAGAAAAAA
1 GAAGAAAAAAGAAAAAA
2708230 GGAA-AAGAAAAGAAAA
1 -GAAGAA-AAAAGAAAA
2708246 CATATCAAGC
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
16 14 0.24
17 9 0.15
18 19 0.32
19 17 0.29
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
GAAGAAAAAAGAAAAAA
Done.