Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold409
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: 3905031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 22 of 25
Found at i:3369411 original size:50 final size:50
Alignment explanation
Indices: 3369351--3369614 Score: 456
Period size: 50 Copynumber: 5.3 Consensus size: 50
3369341 GCTTTTTTCA
*
3369351 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCGAATTGCAATTTTTATGC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
* * *
3369401 TTTCCCATGCATGCCTCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
3369451 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
* * *
3369501 TTTCCCATGCATGCCTCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
*
3369551 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATAC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
3369601 TTTCCCATGCATGC
1 TTTCCCATGCATGC
3369615 ATTTTCTATT
Statistics
Matches: 200, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 200 1.00
ACGTcount: A:0.16, C:0.26, G:0.15, T:0.44
Consensus pattern (50 bp):
TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGC
Found at i:3369645 original size:100 final size:100
Alignment explanation
Indices: 3369351--3369614 Score: 510
Period size: 100 Copynumber: 2.6 Consensus size: 100
3369341 GCTTTTTTCA
*
3369351 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCGAATTGCAATTTTTATGCTTTCCCATGCATGCC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCC
3369416 TCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
66 TCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
3369451 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCC
3369516 TCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
66 TCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
*
3369551 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATACTTTCCCATGCATGC
1 TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGC
3369615 ATTTTCTATT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 162 1.00
ACGTcount: A:0.16, C:0.26, G:0.15, T:0.44
Consensus pattern (100 bp):
TTTCCCATGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCC
TCCGCATGTTTTGTCTCCAATTGCAATTTTTGTGT
Found at i:3370421 original size:13 final size:13
Alignment explanation
Indices: 3370403--3370428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3370393 CAAGTTTTTG
3370403 TGTATCGATACAT
1 TGTATCGATACAT
3370416 TGTATCGATACAT
1 TGTATCGATACAT
3370429 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3370453 original size:19 final size:18
Alignment explanation
Indices: 3370383--3370453 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
3370373 TACAAGCCAA
*
3370383 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
3370403 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3370416 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3370435 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3370454 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3370951 original size:13 final size:13
Alignment explanation
Indices: 3370933--3370958 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3370923 TACACAAAGT
3370933 ATGTATCGATACA
1 ATGTATCGATACA
3370946 ATGTATCGATACA
1 ATGTATCGATACA
3370959 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3370956 original size:32 final size:33
Alignment explanation
Indices: 3370915--3370978 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3370905 TAGCCAAACT
**
3370915 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3370947 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3370979 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3376250 original size:13 final size:13
Alignment explanation
Indices: 3376232--3376257 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3376222 TACAGAAAGT
3376232 ATGTATCGATACA
1 ATGTATCGATACA
3376245 ATGTATCGATACA
1 ATGTATCGATACA
3376258 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3376255 original size:32 final size:33
Alignment explanation
Indices: 3376214--3376277 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3376204 TAGCCAAACT
* **
3376214 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3376246 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3376278 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3379581 original size:15 final size:15
Alignment explanation
Indices: 3379549--3379579 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3379539 CAACTTGCAA
3379549 TTCAATTATTTTCTT
1 TTCAATTATTTTCTT
3379564 TTCAATT-TTTTCTT
1 TTCAATTATTTTCTT
3379578 TT
1 TT
3379580 TCTTCCGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCAATTATTTTCTT
Found at i:3381775 original size:13 final size:13
Alignment explanation
Indices: 3381757--3381782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3381747 TACATTTTGG
3381757 ATGTATCGATACA
1 ATGTATCGATACA
3381770 ATGTATCGATACA
1 ATGTATCGATACA
3381783 TATTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3381778 original size:32 final size:32
Alignment explanation
Indices: 3381737--3381802 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
3381727 GTTACAAGCT
3381737 AATGTATCGATACAT-TT-TGGATGTATCGATAC
1 AATGTATCGATACATATTAT-G-TGTATCGATAC
3381769 AATGTATCGATACATATTATGTGTATCGATAC
1 AATGTATCGATACATATTATGTGTATCGATAC
3381801 AA
1 AA
3381803 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 28 0.88
33 3 0.09
34 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATATTATGTGTATCGATAC
Found at i:3384722 original size:18 final size:19
Alignment explanation
Indices: 3384699--3384735 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
3384689 ATCAATCATG
3384699 CCATTTTTTTT-CTTTTGC
1 CCATTTTTTTTCCTTTTGC
3384717 CCATTTTTTTTCCTTTTGC
1 CCATTTTTTTTCCTTTTGC
3384736 AGAGAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.65
Consensus pattern (19 bp):
CCATTTTTTTTCCTTTTGC
Found at i:3386607 original size:20 final size:20
Alignment explanation
Indices: 3386562--3386637 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
3386552 CTGCCAAGAA
***
3386562 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
3386583 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
3386603 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
3386623 GTGTATCGATACATT
1 ATGTATCGATACATT
3386638 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:3391194 original size:15 final size:15
Alignment explanation
Indices: 3391174--3391204 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3391164 ATTTCGTTTG
*
3391174 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3391189 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3391204 G
1 G
3391205 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3395289 original size:13 final size:13
Alignment explanation
Indices: 3395271--3395296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3395261 CAATTTTTTG
3395271 TGTATCGATACAT
1 TGTATCGATACAT
3395284 TGTATCGATACAT
1 TGTATCGATACAT
3395297 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3395380 original size:20 final size:20
Alignment explanation
Indices: 3395335--3395410 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
3395325 CTGCCAAGAA
***
3395335 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
3395356 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
3395376 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
3395396 GTGTATCGATACATT
1 ATGTATCGATACATT
3395411 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:3398131 original size:22 final size:21
Alignment explanation
Indices: 3398089--3398130 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3398079 GCAGATAGTG
*
3398089 TAAAAAAAATTATGAATAAAA
1 TAAAAAAAATTATGAAAAAAA
3398110 TAAAAAAAATT-TAGAAAAAAA
1 TAAAAAAAATTAT-GAAAAAAA
3398131 AAGGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (21 bp):
TAAAAAAAATTATGAAAAAAA
Found at i:3401491 original size:20 final size:20
Alignment explanation
Indices: 3401466--3401579 Score: 149
Period size: 20 Copynumber: 5.7 Consensus size: 20
3401456 TTTTAACAAG
3401466 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
3401486 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
*
3401506 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * * *
3401526 ATGTTTCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
3401546 ATGTATCGATACATT-AAAGA
1 ATGTATCGATACATTGAAA-A
*
3401566 ATGTATCAATACAT
1 ATGTATCGATACAT
3401580 CTAGGTAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
19 2 0.02
20 81 0.98
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:3401566 original size:60 final size:60
Alignment explanation
Indices: 3401466--3401579 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
3401456 TTTTAACAAG
* * *
3401466 ATGTATCGATACATTGAAAAATGTATCGATACATTGAAGAATGTATCGATACATTGAAGA
1 ATGTATCGATACATTCAAAAATGTATCGATACATTAAAGAATGTATCAATACATTGAAGA
* * *
3401526 ATGTTTCGATACATTCATACATGTATCGATACATTAAAGAATGTATCAATACAT
1 ATGTATCGATACATTCAAAAATGTATCGATACATTAAAGAATGTATCAATACAT
3401580 CTAGGTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (60 bp):
ATGTATCGATACATTCAAAAATGTATCGATACATTAAAGAATGTATCAATACATTGAAGA
Found at i:3402617 original size:28 final size:28
Alignment explanation
Indices: 3402520--3403088 Score: 744
Period size: 28 Copynumber: 20.0 Consensus size: 28
3402510 AAAAAAAAAA
*
3402520 GGTGCCATTAACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTAAC-T-TGTGGGCTTTG-AAAG
* * *
3402551 AGTTACCACTAGCTTGTGGGCTTTGAAAAG
1 -GGTGCCACTAACTTGTGGGCTTTG-AAAG
* *
3402581 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3402609 GGTGCCACTAACTTGTGGGTTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3402637 GGTACCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3402665 GATGCCACTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTAACTTGTGGGCTTTG-AAAG
* *
3402694 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
* * *
3402722 GGTGCCATTGACTTGTGGGCTTTGGAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
* * *
3402750 GATGCCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTAACTTGTGGGCTTTG-AAAG
* *
3402779 AGTGCCACTAACTTATGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3402807 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3402835 GAGTGCCACTGACTTGTGGGCTTTGAAAG
1 G-GTGCCACTAACTTGTGGGCTTTGAAAG
3402864 GGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
3402892 GGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3402920 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTAACTTGTGGGCTTTG-AAAG
* * * *
3402949 AGTGCCACTGAGTTGTGGGCTATGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
* *
3402977 GATGCCATTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTAACTTGTGGGCTTTG-AAAG
* * **
3403006 AGTGCCACTGACTTGTGGGCTTCAAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
3403034 GGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
*
3403062 GATGCCACTAACTTGTGGGCTTT-AAAG
1 GGTGCCACTAACTTGTGGGCTTTGAAAG
3403089 AGATGAACGT
Statistics
Matches: 478, Mismatches: 54, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.01
28 308 0.64
29 141 0.29
30 16 0.03
31 1 0.00
32 8 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
GGTGCCACTAACTTGTGGGCTTTGAAAG
Found at i:3402699 original size:85 final size:85
Alignment explanation
Indices: 3402516--3403093 Score: 806
Period size: 85 Copynumber: 6.8 Consensus size: 85
3402506 TTAAAAAAAA
* * * * *
3402516 AAAAG-GTGCCATTAACTTGTGTGGGCTTTGAAAAGAGTTACCACTAGCTTGTGGGCTTTGAAAA
1 AAAAGAGTGCCACTAAC-T-TGTGGGCTTTG-AAAG-GGTGCCACTAACTTGTGGGCTTTGAAAG
3402580 GAGTGCCACTGACTTGTGGGCTTTG
62 GA-TGCCACTGACTTGTGGGCTTTG
* * *
3402605 -AAAGGGTGCCACTAACTTGTGGGTTTTGAAAGGGTACCACTAACTTGTGGGCTTTGAAAGGATG
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
*
3402669 CCACTAACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* * * *
3402689 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGGAAGGATG
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
*
3402754 CCATTGACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* *
3402774 AAAAGAGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAGT
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGA-T
3402839 GCCACTGACTTGTGGGCTTTG
65 GCCACTGACTTGTGGGCTTTG
* *
3402860 -AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTG
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
3402924 CCACTGACTTGTGGGCTTTG
66 CCACTGACTTGTGGGCTTTG
* * * * * *
3402944 AAAAGAGTGCCACTGAGTTGTGGGCTATGAAAGGATGCCATTAACTTGTGGGCTTTGAAAAGAGT
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGA-T
*
3403009 GCCACTGACTTGTGGGC-TTC
65 GCCACTGACTTGTGGGCTTTG
* *
3403029 AAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT-AAAGAGAT
1 AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAG-GAT
3403093 G
65 G
3403094 AACGTTCTAG
Statistics
Matches: 444, Mismatches: 39, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
84 48 0.11
85 328 0.74
86 43 0.10
87 10 0.02
88 5 0.01
89 10 0.02
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (85 bp):
AAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATG
CCACTGACTTGTGGGCTTTG
Found at i:3407368 original size:52 final size:52
Alignment explanation
Indices: 3407290--3407418 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
3407280 CGAAATATGA
*
3407290 AAATTTGCCCGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
3407342 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
**
3407394 AAATTTGGTTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3407419 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:3407429 original size:52 final size:52
Alignment explanation
Indices: 3407290--3407438 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 52
3407280 CGAAATATGA
* **
3407290 AAATTTGCCCGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTAGGC
** *
3407342 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTAGGC
** *
3407394 AAATTTGGTTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATAACAT-AGTGTATCGATACA
3407439 ATGTATCAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTAGGC
Found at i:3407537 original size:32 final size:32
Alignment explanation
Indices: 3407496--3407566 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
3407486 AGCTTCGTAG
3407496 CGATACATTGTATCGATACAAAACTTATCTAT
1 CGATACATTGTATCGATACAAAACTTATCTAT
* *
3407528 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATCTAT
*
3407560 TGATACA
1 CGATACA
3407567 AATCGTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATCTAT
Found at i:3408326 original size:47 final size:47
Alignment explanation
Indices: 3408256--3408370 Score: 151
Period size: 47 Copynumber: 2.4 Consensus size: 47
3408246 AAAAGGATGT
* * *
3408256 CAATGTGCTGATTCACGGTCAGCG-TCATTAGACTTGAAGAAGAATGC
1 CAATGTGCTGATTCAAGGCCAGCGAT-ATTAGACTTAAAGAAGAATGC
* * *
3408303 CAATGAGCTGAGTCAAGGCCAGCGATATTGGACTTAAAGAAGAATGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGAAGAATGC
*
3408350 CAATGTGTTGATTCAAGGCCA
1 CAATGTGCTGATTCAAGGCCA
3408371 AGGCCAACGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 57 0.98
48 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (47 bp):
CAATGTGCTGATTCAAGGCCAGCGATATTAGACTTAAAGAAGAATGC
Found at i:3408484 original size:49 final size:49
Alignment explanation
Indices: 3408404--3409209 Score: 803
Period size: 49 Copynumber: 16.9 Consensus size: 49
3408394 AAATGAGAAG
* *
3408404 AAGGCGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * * * *
3408453 AAGGTGCCAATGTGCTGATTCAAGGCTAGCGAAATTAGTCTTAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---A
*
3408505 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---A
** * *
3408557 AAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * *
3408606 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * * * * *
3408655 AAGGTGCCAATGTGCTTATTCAAAGCCAGCGACATTGGTCTTAAGGATGAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--A
* *
3408706 GAAGGCGCTAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TA
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * * *
3408750 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
3408799 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * ** *
3408842 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * *
3408891 AAAGTGCCAATATGCTGATTCAAGGCTAGTGATATTGGAC-T-----TA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * * * *
3408934 AAGGTGCCAATGTGCTGATTCATGGCCAACGACATTGGTCTTAAAGAT-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * *
3408982 GAGGTGCCAATATGCTGATTTAAGGCCAGTGATATTGGAC-T-----TA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * *
3409025 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * * *
3409073 GAGGTGCCAATATGCTGATTTAAGGCTAGGGATATTGGAC-T-----TA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* * * *
3409116 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
* *
3409165 AAGGTGCCAAAATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
3409210 AGAAGATGCC
Statistics
Matches: 622, Mismatches: 97, Indels: 76
0.78 0.12 0.10
Matches are distributed among these distances:
42 2 0.00
43 172 0.28
44 6 0.01
46 1 0.00
47 2 0.00
48 67 0.11
49 245 0.39
51 1 0.00
52 126 0.20
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATA
Found at i:3408780 original size:43 final size:43
Alignment explanation
Indices: 3408715--3409209 Score: 495
Period size: 43 Copynumber: 10.9 Consensus size: 43
3408705 AGAAGGCGCT
3408715 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
* * *
3408758 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCC
3408807 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
* * **
3408850 AATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGAAAAAAGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG------GTGCC
* *
3408899 AATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
* * * * *
3408942 AATGTGCTGATTCATGGCCAACGACATTGGTCTTAAAGATGAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AGGTGCC
* *
3408990 AATATGCTGATTTAAGGCCAGTGATATTGGACTTAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
* * *
3409033 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AGGTGCC
* * *
3409081 AATATGCTGATTTAAGGCTAGGGATATTGGACTTAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
* * *
3409124 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCC
* *
3409173 AAAATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
3409210 AGAAGATGCC
Statistics
Matches: 373, Mismatches: 51, Indels: 56
0.78 0.11 0.12
Matches are distributed among these distances:
43 180 0.48
45 4 0.01
46 4 0.01
48 69 0.18
49 116 0.31
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (43 bp):
AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCC
Found at i:3408848 original size:92 final size:92
Alignment explanation
Indices: 3408563--3409209 Score: 931
Period size: 92 Copynumber: 7.0 Consensus size: 92
3408553 GACAAAGGCA
* * * * *
3408563 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-AATGAAGGTGCCAATGTGCTGATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAA-AAAGGTGCCAATATGCTGATTC
*
3408627 AAGGCCAGCGACATTGGACTTAAAGATGAAGGTG
65 AAGGCCAGCGATATTGGACTT----A--AAGGTG
* * * * *
3408661 CCAATGTGCTTATTCAAAGCCAGCGACATTGGTCTTAAGGATGAAGAAGGCGCTAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAA--A-GAAAAAGGTGCCAATATGCTGAT
3408726 TCAAGGCCAGCGATATTGGACTTAAAGGTG
63 TCAAGGCCAGCGATATTGGACTTAAAGGTG
3408756 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
3408821 AGGCCAGCGATATTGGACTTAAAGGTG
66 AGGCCAGCGATATTGGACTTAAAGGTG
* *
3408848 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGAAAAAAGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
* *
3408913 AGGCTAGTGATATTGGACTTAAAGGTG
66 AGGCCAGCGATATTGGACTTAAAGGTG
* * ** *
3408940 CCAATGTGCTGATTCATGGCCAACGACATTGGTCTTAAAG-ATGAGGTGCCAATATGCTGATTTA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
*
3409004 AGGCCAGTGATATTGGACTTAAAGGTG
66 AGGCCAGCGATATTGGACTTAAAGGTG
** *
3409031 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG-ATGAGGTGCCAATATGCTGATTTA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
* *
3409095 AGGCTAGGGATATTGGACTTAAAGGTG
66 AGGCCAGCGATATTGGACTTAAAGGTG
*
3409122 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAAAATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
*
3409187 AGGCCAGCGATATTGGGCTTAAA
66 AGGCCAGCGATATTGGACTTAAA
3409210 AGAAGATGCC
Statistics
Matches: 507, Mismatches: 37, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
91 173 0.34
92 215 0.42
93 1 0.00
95 42 0.08
97 1 0.00
98 33 0.07
100 1 0.00
101 39 0.08
102 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (92 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGTGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGGTG
Found at i:3409278 original size:33 final size:35
Alignment explanation
Indices: 3409237--3409378 Score: 149
Period size: 34 Copynumber: 4.3 Consensus size: 35
3409227 TGTGTGGGCT
*
3409237 TTTGAAAAGGAGAAAGATGCCACAGAA-TTGTGGAC
1 TTTGAAAAGGA-AAAGGTGCCACAGAAGTTGTGGAC
3409272 -TT-AAAAGGAACAAGGTGCCAC-GAAGTTGTGGAC
1 TTTGAAAAGGAA-AAGGTGCCACAGAAGTTGTGGAC
* *
3409305 TTTGAAAAGAAAAAGGTGCCACA-AAGTTGTGGGC
1 TTTGAAAAGGAAAAGGTGCCACAGAAGTTGTGGAC
* * *
3409339 TTTG-AAA--AAAAGATGCCACTG-AGTCGTGGAC
1 TTTGAAAAGGAAAAGGTGCCACAGAAGTTGTGGAC
3409370 TTTGAAAAG
1 TTTGAAAAG
3409379 AGATTGCCAC
Statistics
Matches: 92, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
31 23 0.25
32 7 0.08
33 27 0.29
34 28 0.30
35 7 0.08
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (35 bp):
TTTGAAAAGGAAAAGGTGCCACAGAAGTTGTGGAC
Found at i:3409356 original size:31 final size:31
Alignment explanation
Indices: 3409287--3409482 Score: 182
Period size: 31 Copynumber: 6.2 Consensus size: 31
3409277 AGGAACAAGG
* * *
3409287 TGCCACGAAGTTGTGGACTTTGAAAAGAAAAAGG
1 TGCCACTAAGTCGTGGACTTTG--AA-AAAAAGA
* * *
3409321 TGCCACAAAGTTGTGGGCTTTGAAAAAAAGA
1 TGCCACTAAGTCGTGGACTTTGAAAAAAAGA
* *
3409352 TGCCACTGAGTCGTGGACTTTG-AAAAGAGA
1 TGCCACTAAGTCGTGGACTTTGAAAAAAAGA
* *
3409382 TTGCCACTAAGTCGTGGACTTTG-AGACAAGA
1 -TGCCACTAAGTCGTGGACTTTGAAAAAAAGA
*
3409413 TGCCACTGAGTCGTGGACTTTGAAGAAAAGAGA
1 TGCCACTAAGTCGTGGACTTTGAA-AAAA-AGA
* * * *
3409446 TGCCACTGAGTCATGGACTTT-AGAAAGAGA
1 TGCCACTAAGTCGTGGACTTTGAAAAAAAGA
3409476 TGCCACT
1 TGCCACT
3409483 GACAAAATGA
Statistics
Matches: 140, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
30 38 0.27
31 54 0.39
32 5 0.04
33 23 0.16
34 20 0.14
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (31 bp):
TGCCACTAAGTCGTGGACTTTGAAAAAAAGA
Found at i:3409419 original size:30 final size:31
Alignment explanation
Indices: 3409333--3409484 Score: 202
Period size: 30 Copynumber: 4.9 Consensus size: 31
3409323 CCACAAAGTT
* * *
3409333 GTGGGCTTTGAAAAAAAGATGCCACTGAGTC
1 GTGGACTTTGAGAAAGAGATGCCACTGAGTC
*
3409364 GTGGACTTTGA-AAAGAGATTGCCACTAAGTC
1 GTGGACTTTGAGAAAGAGA-TGCCACTGAGTC
*
3409395 GTGGACTTTGAGACA-AGATGCCACTGAGTC
1 GTGGACTTTGAGAAAGAGATGCCACTGAGTC
3409425 GTGGACTTTGAAGAAAAGAGATGCCACTGAGTC
1 GTGGACTTTG-AG-AAAGAGATGCCACTGAGTC
*
3409458 ATGGACTTT-AGAAAGAGATGCCACTGA
1 GTGGACTTTGAGAAAGAGATGCCACTGA
3409485 CAAAATGAGG
Statistics
Matches: 109, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
30 43 0.39
31 39 0.36
32 4 0.04
33 23 0.21
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.23
Consensus pattern (31 bp):
GTGGACTTTGAGAAAGAGATGCCACTGAGTC
Found at i:3409424 original size:61 final size:60
Alignment explanation
Indices: 3409313--3409484 Score: 204
Period size: 63 Copynumber: 2.8 Consensus size: 60
3409303 ACTTTGAAAA
* * * * *
3409313 GAAAA-AGGTGCCACAAAGTTGTGGGCTTTGAAAAAAAGATGCCACTGAGTCGTGGACTTT
1 GAAAAGAGATGCCACTAAGTCGTGGACTTTG-AGAAAAGATGCCACTGAGTCGTGGACTTT
*
3409373 GAAAAGAGATTGCCACTAAGTCGTGGACTTTGAGACAAGATGCCACTGAGTCGTGGACTTT
1 GAAAAGAGA-TGCCACTAAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTT
* *
3409434 GAAGAAAAGAGATGCCACTGAGTCATGGACTTT-AGAAAGAGATGCCACTGA
1 ---GAAAAGAGATGCCACTAAGTCGTGGACTTTGAGAAA-AGATGCCACTGA
3409485 CAAAATGAGG
Statistics
Matches: 97, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
60 5 0.05
61 29 0.30
62 23 0.24
63 31 0.32
64 9 0.09
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (60 bp):
GAAAAGAGATGCCACTAAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTT
Found at i:3409663 original size:13 final size:13
Alignment explanation
Indices: 3409635--3409685 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
3409625 TTTTTTGCTA
*
3409635 TTTTTTTCTTGGT
1 TTTTTTTCTTTGT
*
3409648 TTTTTTT-TGTTTT
1 TTTTTTTCT-TTGT
* *
3409661 TTTTTTTTTTTGC
1 TTTTTTTCTTTGT
3409674 TTTTTTTCTTTG
1 TTTTTTTCTTTG
3409686 GTGCAAAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 1 0.03
13 29 0.94
14 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTTTGT
Found at i:3409666 original size:16 final size:17
Alignment explanation
Indices: 3409647--3409680 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3409637 TTTTTCTTGG
3409647 TTTTTTTTTG-TTTTTT
1 TTTTTTTTTGCTTTTTT
3409663 TTTTTTTTTGCTTTTTT
1 TTTTTTTTTGCTTTTTT
3409680 T
1 T
3409681 CTTTGGTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (17 bp):
TTTTTTTTTGCTTTTTT
Found at i:3409677 original size:10 final size:9
Alignment explanation
Indices: 3409616--3409684 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 9
3409606 CATCTGGACC
3409616 TTTTTCTATT
1 TTTTTCT-TT
3409626 TTTTTGCTATT
1 TTTTT-CT-TT
3409637 TTTTTCTTGGT
1 TTTTTCTT--T
*
3409648 TTTTTTTTGT
1 TTTTTCTT-T
*
3409658 TTTTTTTTT
1 TTTTTCTTT
3409667 TTTTTGC-TT
1 TTTTT-CTTT
3409676 TTTTTCTTT
1 TTTTTCTTT
3409685 GGTGCAAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
8 1 0.02
9 16 0.31
10 17 0.33
11 18 0.35
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3413857 original size:1 final size:1
Alignment explanation
Indices: 3413851--3413899 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
3413841 AAATCTTCAC
* * * *
3413851 TTTTTTTTTTTTTTTTTCTTTTTTTTTGTTTTGTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3413900 CCAATTGCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.04, G:0.04, T:0.92
Consensus pattern (1 bp):
T
Found at i:3427742 original size:12 final size:12
Alignment explanation
Indices: 3427725--3427751 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3427715 GATATTGTAT
3427725 TTGACAATTCAG
1 TTGACAATTCAG
3427737 TTGACAATTCAG
1 TTGACAATTCAG
3427749 TTG
1 TTG
3427752 CGTCTGGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (12 bp):
TTGACAATTCAG
Found at i:3435198 original size:20 final size:19
Alignment explanation
Indices: 3435174--3435248 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
3435164 ACACACCCAG
*
3435174 ATGTATCGATACATGCTACT
1 ATGTATCGATACATG-TACA
* *
3435194 TTGTATCGATACATGTTCA
1 ATGTATCGATACATGTACA
*
3435213 ATGTATCGATACATGGACAA
1 ATGTATCGATACATGTAC-A
3435233 ATTGTATCGATACATG
1 A-TGTATCGATACATG
3435249 AAATTGGCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.36
20 16 0.34
21 14 0.30
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATGTACA
Found at i:3441490 original size:13 final size:13
Alignment explanation
Indices: 3441472--3441500 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3441462 ACAACATTCC
3441472 TTGTATCGATACA
1 TTGTATCGATACA
3441485 TTGTATCGATACA
1 TTGTATCGATACA
3441498 TTG
1 TTG
3441501 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3443375 original size:18 final size:18
Alignment explanation
Indices: 3443325--3443382 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
3443315 ATAATTTTTT
3443325 TATAAAAAGGGGGAGAAGA
1 TATAAAAA-GGGGAGAAGA
*
3443344 TATTAAAAGAGGGAGAAGA
1 TATAAAAAG-GGGAGAAGA
*
3443363 TATAAAAAGGGGAAAAGA
1 TATAAAAAGGGGAGAAGA
3443381 TA
1 TA
3443383 ATCGTTTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.31
19 24 0.69
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (18 bp):
TATAAAAAGGGGAGAAGA
Found at i:3443411 original size:19 final size:18
Alignment explanation
Indices: 3443387--3443455 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
3443377 AAGATAATCG
*
3443387 TTTAAGGGGGAGAATTTTT
1 TTTAA-GGGGAGAATATTT
* **
3443406 TTTAAGAGGAG-ATAATCG
1 TTTAAGGGGAGAAT-ATTT
*
3443424 TTTAAGGGGGAAAATATTT
1 TTTAA-GGGGAGAATATTT
3443443 TTTAAGGGGAGAA
1 TTTAAGGGGAGAA
3443456 AAACGAAAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
17 2 0.05
18 18 0.47
19 16 0.42
20 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.30, T:0.33
Consensus pattern (18 bp):
TTTAAGGGGAGAATATTT
Found at i:3443421 original size:37 final size:37
Alignment explanation
Indices: 3443378--3443454 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
3443368 AAAGGGGAAA
* *
3443378 AGATAATCGTTTAAGGGGGAGAATTTTTTTTAAGAGG
1 AGATAATCGTTTAAGGGGGAAAATATTTTTTAAGAGG
*
3443415 AGATAATCGTTTAAGGGGGAAAATATTTTTTAAGGGG
1 AGATAATCGTTTAAGGGGGAAAATATTTTTTAAGAGG
3443452 AGA
1 AGA
3443455 AAAACGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (37 bp):
AGATAATCGTTTAAGGGGGAAAATATTTTTTAAGAGG
Found at i:3444035 original size:19 final size:21
Alignment explanation
Indices: 3444011--3444062 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3444001 CAATACATTA
**
3444011 TATCGATACATGTTC-AA-TG
1 TATCGATACATGGACAAATTG
3444030 TATCGATACATGGACAAATTG
1 TATCGATACATGGACAAATTG
3444051 TATCGATACATG
1 TATCGATACATG
3444063 AAATTGCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 2 0.07
21 14 0.48
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (21 bp):
TATCGATACATGGACAAATTG
Found at i:3445235 original size:19 final size:20
Alignment explanation
Indices: 3445211--3445262 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3445201 TGTATCTATA
* *
3445211 CATTGTATCGATAGATGC-T
1 CATTGTATCGATACATACTT
3445230 CATTGTATCGATACATACTT
1 CATTGTATCGATACATACTT
*
3445250 AATTGTATCGATA
1 CATTGTATCGATA
3445263 TATGAAACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
CATTGTATCGATACATACTT
Found at i:3448096 original size:20 final size:21
Alignment explanation
Indices: 3448071--3448125 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
3448061 CTGCCAAGGA
3448071 AATGTATCGATACATTAT-T-C
1 AATGTATCGATACATT-TCTAC
*
3448091 AATGTATCGATACATTTCTAG
1 AATGTATCGATACATTTCTAC
3448112 AATGTATCGATACA
1 AATGTATCGATACA
3448126 AGGTCCCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 17 0.53
21 14 0.44
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTCTAC
Found at i:3448960 original size:13 final size:13
Alignment explanation
Indices: 3448942--3448967 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3448932 CAATTTTTTG
3448942 TGTATCGATACAT
1 TGTATCGATACAT
3448955 TGTATCGATACAT
1 TGTATCGATACAT
3448968 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3452098 original size:21 final size:21
Alignment explanation
Indices: 3452069--3452113 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3452059 AAGTTTTTAT
*
3452069 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3452089 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3452111 TTT
1 TTT
3452114 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3454178 original size:14 final size:14
Alignment explanation
Indices: 3454159--3454194 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
3454149 TTGTAGCCGT
3454159 TGGAGTTTGATTAG
1 TGGAGTTTGATTAG
3454173 TGGAGTTTGATTAG
1 TGGAGTTTGATTAG
3454187 TGGAGTTT
1 TGGAGTTT
3454195 CTAGCCGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.44
Consensus pattern (14 bp):
TGGAGTTTGATTAG
Found at i:3454354 original size:13 final size:13
Alignment explanation
Indices: 3454336--3454361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3454326 CAATTTTTGG
3454336 TGTATCGATACAT
1 TGTATCGATACAT
3454349 TGTATCGATACAT
1 TGTATCGATACAT
3454362 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3454373 original size:32 final size:33
Alignment explanation
Indices: 3454316--3454379 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3454306 TACAAGCCAA
**
3454316 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
3454349 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
3454380 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3454386 original size:19 final size:18
Alignment explanation
Indices: 3454316--3454386 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
3454306 TACAAGCCAA
3454316 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
3454336 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3454349 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3454368 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3454387 CTACTGCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3455651 original size:20 final size:20
Alignment explanation
Indices: 3455626--3455770 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
3455616 TTTTAACTAG
3455626 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
3455646 ATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
*
3455677 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
3455697 ATGTATCGATACATT-AAAGA
1 ATGTATCGATACATTGAAA-A
* * * *
3455717 ATGTATTGATACATTCATAC
1 ATGTATCGATACATTGAAAA
3455737 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
3455757 ATGTATCAATACAT
1 ATGTATCGATACAT
3455771 CTGGGCAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.02
20 74 0.73
21 3 0.03
22 1 0.01
23 2 0.02
28 2 0.02
29 1 0.01
30 2 0.02
31 15 0.15
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:3455842 original size:47 final size:47
Alignment explanation
Indices: 3455737--3455878 Score: 169
Period size: 47 Copynumber: 2.9 Consensus size: 47
3455727 ACATTCATAC
* **
3455737 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGCAAAAGACAGA
1 ATGTATCGATAC--T-AAAAATGTATCGATACATCTGGTAAAAAGACAGA
3455787 ATGTATCGATAC-AAAAATGTATCGATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACTAAAAATGTATCGATACATCT-GGTAAAAAGACAGA
*
3455834 ATGTATCGATACATTAAAGAATGTATCGATACATTTCGGTAAAAA
1 ATGTATCGATAC--TAAA-AATGTATCGATACATCT-GGTAAAAA
3455879 TGTGACTTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
46 19 0.23
47 24 0.29
50 15 0.18
51 24 0.29
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (47 bp):
ATGTATCGATACTAAAAATGTATCGATACATCTGGTAAAAAGACAGA
Found at i:3455856 original size:20 final size:20
Alignment explanation
Indices: 3455831--3455868 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3455821 GTAAAAAGAC
3455831 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
3455851 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
3455869 TCGGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:3460489 original size:17 final size:17
Alignment explanation
Indices: 3460443--3460495 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
3460433 AACTTCATAT
*
3460443 TTATCTCAATAAATATTAT
1 TTATCT-AATAAATA-TAA
* *
3460462 TTTTTTAATAAATATAA
1 TTATCTAATAAATATAA
*
3460479 TTATCTAATAATTATAA
1 TTATCTAATAAATATAA
3460496 AACTAGATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 16 0.57
18 8 0.29
19 4 0.14
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATCTAATAAATATAA
Found at i:3461407 original size:13 final size:13
Alignment explanation
Indices: 3461389--3461413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3461379 ATATGGCTTA
3461389 GTATCGATACATT
1 GTATCGATACATT
3461402 GTATCGATACAT
1 GTATCGATACAT
3461414 GTTCTTGGTA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:3464145 original size:3 final size:3
Alignment explanation
Indices: 3464137--3464168 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3464127 TTCCTTCGTC
3464137 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
3464169 AACAATTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:3468445 original size:3 final size:3
Alignment explanation
Indices: 3468439--3468480 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3468429 TTTGGTATTG
3468439 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3468481 AGTAACTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3468663 original size:15 final size:15
Alignment explanation
Indices: 3468643--3468673 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3468633 ATGCGTATTG
3468643 AAATTTCATGATGAA
1 AAATTTCATGATGAA
*
3468658 AAATTTTATGATGAA
1 AAATTTCATGATGAA
3468673 A
1 A
3468674 TAAAATAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (15 bp):
AAATTTCATGATGAA
Found at i:3471524 original size:40 final size:41
Alignment explanation
Indices: 3471480--3471586 Score: 100
Period size: 40 Copynumber: 2.7 Consensus size: 41
3471470 TTTATATAAA
*
3471480 ATTTAATATGTTA-ATAAT-TTATATTTATATTTATGTTTG-T
1 ATTT-ATATGTTATATAATATTATATTT-TAATTATGTTTGAT
* * *
3471520 ATTTATTTTTTATATAATATTATATTTTAATTATTTTTGAT
1 ATTTATATGTTATATAATATTATATTTTAATTATGTTTGAT
*
3471561 A-TTATAT-TTATATTA-ATTATAATTTT
1 ATTTATATGTTATATAATATTAT-ATTTT
3471587 GTGTCCTATC
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
38 5 0.09
39 18 0.32
40 24 0.42
41 10 0.18
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.63
Consensus pattern (41 bp):
ATTTATATGTTATATAATATTATATTTTAATTATGTTTGAT
Found at i:3471572 original size:29 final size:30
Alignment explanation
Indices: 3471504--3471574 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 30
3471494 TAATTTATAT
* * *
3471504 TTATATTTATGTTTGTATTTATTTTTTATA
1 TTATATTTATATTTGTAATTATTTTTGATA
*
3471534 TAATA-TTATATTT-TAATTATTTTTGATA
1 TTATATTTATATTTGTAATTATTTTTGATA
3471562 TTATATTTATATT
1 TTATATTTATATT
3471575 AATTATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 17 0.49
29 14 0.40
30 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (30 bp):
TTATATTTATATTTGTAATTATTTTTGATA
Found at i:3471587 original size:29 final size:28
Alignment explanation
Indices: 3471522--3471580 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
3471512 ATGTTTGTAT
* *
3471522 TTATTTTTTATATAATATTATATTTTAA
1 TTATTTTTGATATAATATTATATATTAA
*
3471550 TTATTTTTGATATTATATT-TATATTAA
1 TTATTTTTGATATAATATTATATATTAA
3471577 TTAT
1 TTAT
3471581 AATTTTGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TTATTTTTGATATAATATTATATATTAA
Found at i:3472438 original size:18 final size:17
Alignment explanation
Indices: 3472405--3472438 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3472395 ATTAAGTTTA
*
3472405 TTTAATAAATAAATATT
1 TTTAATAAAAAAATATT
3472422 TTTAATAAGAAAAATAT
1 TTTAATAA-AAAAATAT
3472439 ATCTTAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAATAAAAAAATATT
Found at i:3473243 original size:89 final size:89
Alignment explanation
Indices: 3473134--3473306 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 89
3473124 ATTACTGAGG
* * * * * *
3473134 TTTTTTACTTTGTAAATTTTTT-TAAAAAAATTTTCTT-ACTTTTTAATTTTTAAAATTTATCAC
1 TTTTCTACTTCGTAAATTTTTTCGAAAAAAATTTTCTTGA-TTTTTAATTTTTAAAATTCATAAA
3473197 ATATTAGTTATTTAATTCATACGAAA
65 ATATTA-TTATTTAATTCATACGAAA
** ** *
3473223 TTTTCTACTTCGTAAATTTTTTCGGGAGGATTTTTCTTGATTTTTAATTTTTAAAATTCATAAAA
1 TTTTCTACTTCGTAAATTTTTTCGAAAAAAATTTTCTTGATTTTTAATTTTTAAAATTCATAAAA
*
3473288 TATTATTATTTATTTCATA
66 TATTATTATTTAATTCATA
3473307 TTAAATCAGT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
89 33 0.47
90 36 0.51
91 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (89 bp):
TTTTCTACTTCGTAAATTTTTTCGAAAAAAATTTTCTTGATTTTTAATTTTTAAAATTCATAAAA
TATTATTATTTAATTCATACGAAA
Found at i:3473455 original size:162 final size:163
Alignment explanation
Indices: 3473223--3473689 Score: 638
Period size: 162 Copynumber: 2.8 Consensus size: 163
3473213 TCATACGAAA
* * * *
3473223 TTTTCTACTTCGTAAATTTTTTCGGGAGGATTTTTCTTGATTTTTAATTTTTAAAATTCATAAAA
1 TTTTCTACTCCGTAAATTTTTTCAGG-GGATTTTTCTTGGTTTTTAATTTTT-TAATTCATAAAA
*
3473288 TATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTTCATTCA-TTTTTGAA
64 TATTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTCATTCATTTTCATT-AGTTTTTGAA
3473352 TTTTTTCTTGAAATTTCCTTGTTTT-CAA-AAGAGAG
128 TTTTTTCTTGAAATTTCCTTGTTTTCCAATAAG-GAG
*
3473387 TTTTTTACTCCGTAAATTTTTTCAGGGGATTTTTCTTGGTTTTTAATTTTTTAATTCATAAAATA
1 TTTTCTACTCCGTAAATTTTTTCAGGGGATTTTTCTTGGTTTTTAATTTTTTAATTCATAAAATA
* * * *
3473452 TTATTATTTATTTTATAATT-AATCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTAAATT
66 TTATTATTTATTTCAT-ATTAAATCAGTTTTAAAAAATTCATTCATTTTCATTAGTTTTTGAATT
* *
3473516 TTTTCCTTGAAATTTCTTTGTTTTCGCAATACGGAG
130 TTTT-CTTGAAATTTCCTTGTTTTC-CAATAAGGAG
* * * *
3473552 TTTCCTACTCCTTAATTTTTTTCAGGGAGATTTTTCTTCGTTTTTAATTTTTTAAATTCATAAAA
1 TTTTCTACTCCGTAAATTTTTTCAGGG-GATTTTTCTTGGTTTTTAATTTTTT-AATTCATAAAA
* * *
3473617 TATTATTATTTATTTCATATTAAATAATTTTTAAAAAAATTCCTTCATTTTCATTAGTTTTTG-A
64 TATTATTATTTATTTCATATTAAATCAGTTTT-AAAAAATTCATTCATTTTCATTAGTTTTTGAA
3473681 TTTTTTCTT
128 TTTTTTCTT
3473690 TTAAATTCCC
Statistics
Matches: 270, Mismatches: 23, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
161 1 0.00
162 71 0.26
163 45 0.17
164 23 0.09
165 29 0.11
166 32 0.12
167 43 0.16
168 26 0.10
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (163 bp):
TTTTCTACTCCGTAAATTTTTTCAGGGGATTTTTCTTGGTTTTTAATTTTTTAATTCATAAAATA
TTATTATTTATTTCATATTAAATCAGTTTTAAAAAATTCATTCATTTTCATTAGTTTTTGAATTT
TTTCTTGAAATTTCCTTGTTTTCCAATAAGGAG
Found at i:3473769 original size:166 final size:161
Alignment explanation
Indices: 3473223--3473774 Score: 573
Period size: 162 Copynumber: 3.4 Consensus size: 161
3473213 TCATACGAAA
* * *
3473223 TTTTCTACTTCGTAAATTTTTTC-GGGAGGATTTTTCTTGATTTTTAATTTTTAAAATTCATAAA
1 TTTTCTACTCCATAAATTTTTTCAGGGA-GATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAA
* *
3473287 ATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTTCATTCA-TTTTTGA
65 ATATTATTATTTATTTCATATTAAAT-AATTTTTAAAAATTCATTCATTTTCATT-AGTTTTTG-
*
3473351 ATTTTTTCTTGAAATTTCCTTGTTTTCAAAAGA--GAG
127 ATTTTTTCTTGAAA-TTCCTT-TTTT-AAAAAATCGAG
* * *
3473387 TTTTTTACTCCGTAAATTTTTTCAGGG-GATTTTTCTTGGTTTTTAATTTTT-TAATTCATAAAA
1 TTTTCTACTCCATAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAA
* * * *
3473450 TATTATTATTTATTTTATAATT-AATCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTAAA
66 TATTATTATTTATTTCAT-ATTAAAT-AATTTTTAAAAATTCATTCATTTTCATTAGTTTTT-GA
* ****
3473514 TTTTTTCCTTGAAATTTCTTTGTTTTCGCAATACGGAG
128 TTTTTT-CTTGAAATTCCTTT-TTTAAAAAAT-C-GAG
* * * * *
3473552 TTTCCTACTCCTTAATTTTTTTCAGGGAGATTTTTCTTCGTTTTTAATTTTTTAAATTCATAAAA
1 TTTTCTACTCCATAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAA
*
3473617 TATTATTATTTATTTCATATTAAATAATTTTTAAAAAAATTCCTTCATTTTCATTAGTTTTTGAT
66 TATTATTATTTATTTCATATTAAATAATTTTT--AAAAATTCATTCATTTTCATTAGTTTTTGAT
*
3473682 TTTTTCTTTTAAATTCCCATTTTTTAAAAAATCGAG
129 TTTTTC-TTGAAATT-CC-TTTTTTAAAAAATCGAG
* ** ***
3473718 TTTTCTATTCCATAAACATTTTC-GGGCAGA-TTTTCTTTGGTTCAAAATTTTTAAAAT
1 TTTTCTACTCCATAAATTTTTTCAGGG-AGATTTTTC-TTGGTTTTTAATTTTTAAAAT
3473775 GCATCTAATA
Statistics
Matches: 326, Mismatches: 42, Indels: 38
0.80 0.10 0.09
Matches are distributed among these distances:
161 3 0.01
162 78 0.24
163 33 0.10
164 21 0.06
165 37 0.11
166 72 0.22
167 46 0.14
168 33 0.10
169 3 0.01
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (161 bp):
TTTTCTACTCCATAAATTTTTTCAGGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAA
TATTATTATTTATTTCATATTAAATAATTTTTAAAAATTCATTCATTTTCATTAGTTTTTGATTT
TTTCTTGAAATTCCTTTTTTAAAAAATCGAG
Found at i:3474332 original size:9 final size:9
Alignment explanation
Indices: 3474320--3474364 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
3474310 AAGAAGAGAG
*
3474320 AGAAAGAAT
1 AGAAAAAAT
3474329 AGAAAAAAAT
1 AG-AAAAAAT
3474339 A-AAGAAAAT
1 AGAA-AAAAT
3474348 AGAAAAAAT
1 AGAAAAAAT
3474357 AGAAAAAA
1 AGAAAAAA
3474365 CTAAGCTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 2 0.06
9 21 0.66
10 9 0.28
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (9 bp):
AGAAAAAAT
Found at i:3475546 original size:159 final size:156
Alignment explanation
Indices: 3475257--3475568 Score: 448
Period size: 159 Copynumber: 2.0 Consensus size: 156
3475247 GTGATAAAAT
*
3475257 TAAATTTTAATTATTTCTTCTAATCTTTTATATTCCTATGGGCATCTCTAGGAGTATAAAAGATT
1 TAAATTTTAATTATTTCTTCTAA--TATTATATTCCTATGGGCATCTCTAGGAGTATAAAAGATT
* *
3475322 TTAAAAACGTTTCATATCCTTTTGGGCTTCCATTAGGGTACAAAATAGTATTTTCGAAAATAAAT
64 TAAAAAACATTTCATATCCTTTTGGGCTTCCATTAGGGTACAAAATAGTATTTTCGAAAATAAAT
3475387 AAAATAAAATTGAATTAATACTTTCAGGA
129 -AAATAAAATTGAATTAATACTTTCAGGA
* *
3475416 TAAATTTTAATTATTTTTTCTAA-ATTATATTCCTATGGGCAT-TCGTAGGGGTATAAAAGATTT
1 TAAATTTTAATTATTTCTTCTAATATTATATTCCTATGGGCATCTC-TAGGAGTATAAAAGATTT
* * * *
3475479 CAAAAAAAACATTTCGTATCCTTTTGGGCTTTCATTAGGGTACAAAATGGTGTTTTCGAAAATAA
65 ---AAAAAACATTTCATATCCTTTTGGGCTTCCATTAGGGTACAAAATAGTATTTTCGAAAATAA
* *
3475544 ATAAATTAAGTTGAATTAATACTTT
127 ATAAATAAAATTGAATTAATACTTT
3475569 TGAAATTTTT
Statistics
Matches: 138, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
155 2 0.01
156 35 0.25
158 21 0.15
159 80 0.58
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (156 bp):
TAAATTTTAATTATTTCTTCTAATATTATATTCCTATGGGCATCTCTAGGAGTATAAAAGATTTA
AAAAACATTTCATATCCTTTTGGGCTTCCATTAGGGTACAAAATAGTATTTTCGAAAATAAATAA
ATAAAATTGAATTAATACTTTCAGGA
Found at i:3477319 original size:47 final size:47
Alignment explanation
Indices: 3477247--3477337 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
3477237 TGTATTGAAT
* * * *
3477247 GGTTTGTAATTTTATCCGTATAAAAGTTACAAGTTAATTATAAGGAA
1 GGTTTGCAACTTTATCCCTACAAAAGTTACAAGTTAATTATAAGGAA
* **
3477294 GGTTTGCAACTTTATCCCTACAAAAGTTATAAGTTGTTTATAAG
1 GGTTTGCAACTTTATCCCTACAAAAGTTACAAGTTAATTATAAG
3477338 TATAGACACC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (47 bp):
GGTTTGCAACTTTATCCCTACAAAAGTTACAAGTTAATTATAAGGAA
Found at i:3479848 original size:300 final size:298
Alignment explanation
Indices: 3479293--3479882 Score: 753
Period size: 300 Copynumber: 2.0 Consensus size: 298
3479283 TTAAATAGTA
*
3479293 AAAAATAAAAAACTTTGTTTCAAGGCCTATCATGCTTTCCTAAATCACTTATAGACCTTTAGGAT
1 AAAAATAAAAAACTTTGTTTCAAGGCCTATCATGCTTGCCTAAATCACTTATAGACCTTTAGGAT
* * * *
3479358 GTCTTCCATGTGTATTTGGCATGTTTGAATATGATTCACTTATTTTTAACCTTTTTGGGGCTTTT
66 GCCTTCCATGTGTATTTGGCATGTTTGAAGATGATTCACTTATTTTTAACCTTTTTAGGGCTTAT
* * *
3479423 TTGTAATTTTTGAAAGTTTAAGAGTTTATTTCTAAATATTAAAAAATTCATCCTAAGGCCAAAGG
131 TTGTAATTTTTAAAAGTTTAAGAGTTTATTTATAAATATTAAAAAATTCATCCTAAGGCCAAAAG
* * * ** * *
3479488 TAGTTGGTCGAGCCTTTCTTGTAATTTTTGGATGTGATTTTTATGTTGATTTGGATATATTCGAT
196 TAGTTGGTCGAACCTTTCTTGTAATCTTTAGACCTAATTTTTATGCTGATTTGGATATATTCGAT
* *
3479553 GTTTAATTTTGTGCTTTAATTATATAGGGACTAAATTAT
261 GTTTAA-TTTGTACTTTAATTATATAAGGACTAAATTAT
* * *
3479592 AAAAATAAAAAAGTTTTGTTTCAAGGCCTATCATGCTTGGCC-GAATCACTTGTAGACCTTTAGA
1 AAAAATAAAAAA-CTTTGTTTCAAGGCCTATCATGCTT-GCCTAAATCACTTATAGACCTTTAG-
* * *
3479656 GGTGCCTTTCATGTGTATTCAT-G-ATGTTTGAAGGTGATTCACATT-TTTTTAACCTTTTTAGG
63 GATGCCTTCCATGTGTATT--TGGCATGTTTGAAGATGATTCAC-TTATTTTTAACCTTTTTAGG
* * * *
3479718 TC-TATTTGTAATTTTTAAAAGTTTAGGGGTTTATTTATAAATATTGAAAAAATT-ATCTTAAGG
125 GCTTATTTGTAATTTTTAAAAGTTTAAGAGTTTATTTATAAATATT-AAAAAATTCATCCTAAGG
* * * *
3479781 CTAAAAGTAGTTGGTTGAACC-TTCGTTGTAATCTTTAGACCTAATTTTTGTGCTGATTTTGATA
189 CCAAAAGTAGTTGGTCGAACCTTTC-TTGTAATCTTTAGACCTAATTTTTATGCTGATTTGGATA
* *
3479845 TATTTGATGTTTAATTTGTATTTTAATTATATAAGGAC
253 TATTCGATGTTTAATTTGTACTTTAATTATATAAGGAC
3479883 CAATTTACAA
Statistics
Matches: 250, Mismatches: 33, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
299 36 0.14
300 150 0.60
301 60 0.24
302 3 0.01
303 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (298 bp):
AAAAATAAAAAACTTTGTTTCAAGGCCTATCATGCTTGCCTAAATCACTTATAGACCTTTAGGAT
GCCTTCCATGTGTATTTGGCATGTTTGAAGATGATTCACTTATTTTTAACCTTTTTAGGGCTTAT
TTGTAATTTTTAAAAGTTTAAGAGTTTATTTATAAATATTAAAAAATTCATCCTAAGGCCAAAAG
TAGTTGGTCGAACCTTTCTTGTAATCTTTAGACCTAATTTTTATGCTGATTTGGATATATTCGAT
GTTTAATTTGTACTTTAATTATATAAGGACTAAATTAT
Found at i:3480887 original size:51 final size:51
Alignment explanation
Indices: 3480761--3480895 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 51
3480751 TTTTACTGTT
* *
3480761 TGTATCGATATATTATTCATTATATCGATACATTTTGGGTTTTTACCCAGA
1 TGTATCGATATATTATTCATTGTATCGATACATTATGGGTTTTTACCCAGA
* * ** * * *
3480812 TGAATCGATACATTCCTCATTGTATCGATATATTATGGGTTTTTACTCGGA
1 TGTATCGATATATTATTCATTGTATCGATACATTATGGGTTTTTACCCAGA
* *
3480863 TGTATCGATATATTATTCAATGTATCGACACAT
1 TGTATCGATATATTATTCATTGTATCGATACAT
3480896 ACAGGTAAAT
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (51 bp):
TGTATCGATATATTATTCATTGTATCGATACATTATGGGTTTTTACCCAGA
Found at i:3484609 original size:20 final size:20
Alignment explanation
Indices: 3484584--3484719 Score: 136
Period size: 20 Copynumber: 6.8 Consensus size: 20
3484574 TTTTCATAAT
3484584 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
3484604 TTGTATCGATACATTGTATACA
1 TTGTATCGATACATTGT-T-CA
* * * *
3484626 TTAT-TC-ATTATATCGATACA
1 TTGTATCGA-TACATTG-TTCA
*
3484646 TTGTATCGATACATT-CTCA
1 TTGTATCGATACATTGTTCA
*
3484665 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
3484685 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
3484705 ATGTATCGATACATT
1 TTGTATCGATACATT
3484720 CAGGATTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
19 18 0.19
20 58 0.60
21 14 0.14
22 7 0.07
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:3484634 original size:29 final size:30
Alignment explanation
Indices: 3484592--3484685 Score: 111
Period size: 29 Copynumber: 3.1 Consensus size: 30
3484582 ATTTGTATCG
3484592 ATACATTGTTCATTGTATCGATACATTG-T-
1 ATACATT-TTCATTGTATCGATACATTGATC
*
3484621 ATACATTATTCATTATATCGATACATTGTATC
1 ATACATT-TTCATTGTATCGATACATTG-ATC
* *
3484653 GATACATTCTCATTGTATCGATACATTGCTC
1 -ATACATTTTCATTGTATCGATACATTGATC
3484684 AT
1 AT
3484686 TGTATCGATA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
29 26 0.46
30 2 0.04
31 3 0.05
32 18 0.32
33 7 0.12
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (30 bp):
ATACATTTTCATTGTATCGATACATTGATC
Found at i:3484679 original size:13 final size:13
Alignment explanation
Indices: 3484602--3484660 Score: 66
Period size: 13 Copynumber: 4.3 Consensus size: 13
3484592 ATACATTGTT
3484602 CATTGTATCGATA
1 CATTGTATCGATA
3484615 CATTGTATAC-ATTA
1 CATTGTAT-CGA-TA
*
3484629 TTCATTATATCGATA
1 --CATTGTATCGATA
3484644 CATTGTATCGATA
1 CATTGTATCGATA
3484657 CATT
1 CATT
3484661 CTCATTGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 25 0.64
14 3 0.08
15 3 0.08
16 8 0.21
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3487169 original size:51 final size:51
Alignment explanation
Indices: 3487000--3487178 Score: 182
Period size: 51 Copynumber: 3.5 Consensus size: 51
3486990 AAATTTCTAT
* * *** * **
3487000 ATTTTTCAT-CTCGGGGATACTCCAA-TCCCGGTTCCGTTTCCAAAACGTCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAGCACCA
* * * *
3487050 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATCG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGCACCA
** **
3487101 ATTTACCGCAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGCACCA
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGCACCA
*
3487152 ATTTTTCATAATTGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
3487179 CCCGTTATTT
Statistics
Matches: 105, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
50 8 0.08
51 96 0.91
52 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGCACCA
Found at i:3487230 original size:56 final size:56
Alignment explanation
Indices: 3487165--3487294 Score: 217
Period size: 56 Copynumber: 2.3 Consensus size: 56
3487155 TTTCATAATT
* *
3487165 GGGGATACTCCAACCCCGTTATTTCATC-GGGATACTCCAACCCCTGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATGTCATCGGGGATACTCCAACCCC-GTTATTTCCGA
*
3487221 GGGGATACTCCAACCCCGTTATGTCATCGGGGATACTCCAATCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATGTCATCGGGGATACTCCAACCCCGTTATTTCCGA
3487277 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3487295 ATTTTATTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
56 55 0.79
57 15 0.21
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (56 bp):
GGGGATACTCCAACCCCGTTATGTCATCGGGGATACTCCAACCCCGTTATTTCCGA
Found at i:3487241 original size:28 final size:27
Alignment explanation
Indices: 3487164--3487294 Score: 167
Period size: 28 Copynumber: 4.7 Consensus size: 27
3487154 TTTTCATAAT
3487164 TGGGGATACTCCAACCCCGTTATTTCA
1 TGGGGATACTCCAACCCCGTTATTTCA
*
3487191 TCGGGATACTCCAACCCCTGTTATTTTCGA
1 TGGGGATACTCCAACCCC-GTTA-TTTC-A
*
3487221 -GGGGATACTCCAACCCCGTTATGTCA
1 TGGGGATACTCCAACCCCGTTATTTCA
*
3487247 TCGGGGATACTCCAATCCCGTTATTTCCGA
1 T-GGGGATACTCCAACCCCGTTATTT-C-A
3487277 -GGGGATACTCCAACCCCG
1 TGGGGATACTCCAACCCCG
3487295 ATTTTATTTC
Statistics
Matches: 91, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.01
27 20 0.22
28 47 0.52
29 21 0.23
30 2 0.02
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (27 bp):
TGGGGATACTCCAACCCCGTTATTTCA
Found at i:3487349 original size:51 final size:51
Alignment explanation
Indices: 3487277--3487393 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
3487267 TTATTTCCGA
* *
3487277 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
*
3487328 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* *
3487379 AGGGATACTCTAACC
1 GGGGATACTCCAACC
3487394 TTGTTATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:3488734 original size:155 final size:155
Alignment explanation
Indices: 3488457--3488737 Score: 404
Period size: 155 Copynumber: 1.8 Consensus size: 155
3488447 TAGTCATCAA
* * *
3488457 GATGCTTTTTCGCCAAATCTGTGCATTTAGGATAGGTTTGCCCTACTATGATTATTTTTGAGTCC
1 GATGCTTTTTCGCCAAAGCTATGCATTTAGGATAGGTTTGCCCTACTATGATCATTTTTGAGTCC
* * * * * ** *
3488522 TTTAAGGTTACTAGGATACTTTTATGTCAAAAGTATACCCTAATGGCATTTTGGTAATTTTCATA
66 TTTAAAGTCACCAGAATACTTTCATGTCAAAAGTATACCCTAATAACATTTTAGTAATTTTCATA
3488587 AAACTAAGTCCAATATAGTCACCGG
131 AAACTAAGTCCAATATAGTCACCGG
*
3488612 GATGCTTTTAT-GCCAAAGCTATGCATTTAGGATAGG-TTGACCCTTCTATGATCATTTTTGAGT
1 GATGCTTTT-TCGCCAAAGCTATGCATTTAGGATAGGTTTG-CCCTACTATGATCATTTTTGAGT
* *
3488675 CCTTTAAAGTCACCATAATACTTTCATGTTAAAAGTATACCCTAATAACATTTTAGTAATTTT
64 CCTTTAAAGTCACCAGAATACTTTCATGTCAAAAGTATACCCTAATAACATTTTAGTAATTTT
3488738 GTATTAGAAC
Statistics
Matches: 110, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
154 3 0.03
155 106 0.96
156 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (155 bp):
GATGCTTTTTCGCCAAAGCTATGCATTTAGGATAGGTTTGCCCTACTATGATCATTTTTGAGTCC
TTTAAAGTCACCAGAATACTTTCATGTCAAAAGTATACCCTAATAACATTTTAGTAATTTTCATA
AAACTAAGTCCAATATAGTCACCGG
Found at i:3489640 original size:29 final size:28
Alignment explanation
Indices: 3489581--3489640 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3489571 CCTAAAAATG
* * *
3489581 AAAAAAATATTAATAGTGATATGGCCCT
1 AAAAAAATATAAATAGTGATATGACCAT
3489609 AAAAAAATATAAAATAGTGATAT-ACCAAT
1 AAAAAAATAT-AAATAGTGATATGACC-AT
3489638 AAA
1 AAA
3489641 TATAGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (28 bp):
AAAAAAATATAAATAGTGATATGACCAT
Found at i:3496142 original size:20 final size:19
Alignment explanation
Indices: 3496121--3496187 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
3496111 AGAATATATT
* *
3496121 GATACATTGAAGAGTGTATT
1 GATACATTGAA-AATGTATC
* * *
3496141 GATATATTCATACATGTATC
1 GATACATTGA-AAATGTATC
3496161 GATACATTGAAAAATGTATC
1 GATACATTG-AAAATGTATC
3496181 GATACAT
1 GATACAT
3496188 CTGGGTACTT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 35 0.95
21 2 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (19 bp):
GATACATTGAAAATGTATC
Found at i:3497146 original size:28 final size:28
Alignment explanation
Indices: 3497048--3500324 Score: 3542
Period size: 28 Copynumber: 114.9 Consensus size: 28
3497038 TTTAAAAAAA
* *
3497048 GGTGCCACTAACTTGTGTGGGTTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* * *
3497079 AGTCGCCACCGACTCGTGTGGGCTTTAAAAAG
1 GGT-GCCACTGACT--TGTGGGCTTT-GAAAG
** *
3497111 AATGCCACCGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3497139 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3497167 GATGCCACTGACTTGTGGGCTTTGAAAAA
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3497196 AGTGCCGCTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3497224 GGTGTCGCTGACTTGTGGGCTTGGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* ** *
3497253 TGTTGCCACCAACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
** *
3497282 AATGCCACT-ATCTTGTGGGCTTTGAAAT
1 GGTGCCACTGA-CTTGTGGGCTTTGAAAG
* *
3497310 GATGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3497338 GGTGCCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3497367 AGTGCCACTAACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3497395 GATGCCATTAACTTATGGGCTTTGATAAG
1 GGTGCCACTGACTTGTGGGCTTTGA-AAG
* * *
3497424 AGTTGCCACCGACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3497453 GATGCCACTAACTTATGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3497481 GATGCCATTGACTTGTGGGATTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3497509 GGTGCCGCTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
3497538 GGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3497566 GATGCCACTAACTTATGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
3497595 AGTGCCACT-ACCTTGTGGGCTTTGAAAG
1 GGTGCCACTGA-CTTGTGGGCTTTGAAAG
* * *
3497623 GGTGCCACTAACTTATGAGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
** * * *
3497652 ACTTGCCCCCGACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3497681 AAGTGCCACCGCCTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* ** * *
3497710 GGGGCCACAAACTTATGGACTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3497738 GGTGCCACTGACTAGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3497766 GATGCAACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3497795 AGTGCTACTGACCTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* **
3497823 GGTGCCACTAACTTGTGAACTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * ** * * *
3497852 AGTTACCACCAACTCGTGGGCTTTAAAAA
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
** *
3497881 AATGCCACTGACTTGTGGGCTTCGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3497909 GGTGCCACTGACTTGTAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3497937 GGTGCCACTAACATGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3497966 AGTTGCCACCGACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3497995 GAGTGCCACCGACTTGTGGGTTTTGAAAG
1 G-GTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498024 GGTGCAACTGACTTGTAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* ** *
3498052 GGTGCCACTAACTTGTGCACTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498080 GATGCCACTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
3498109 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3498137 GGTGCCACTGACTTGTGGGCTTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAG
*
3498166 AGTTGCCA-TCGACTTGTGGGCTTTGAAAG
1 -GGTGCCACT-GACTTGTGGGCTTTGAAAG
* *
3498195 GATGCCACTGACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498223 GATGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3498251 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3498280 AGTGCCACTGATTTGTGTGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498308 GATGCCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3498337 AGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498365 GGTGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3498393 GATGCCATTGGCTTGTGGGCTTTTAAAAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
* *
3498422 AGTGCCACTGACTTGTGGGCTTTGAAAAAA
1 GGTGCCACTGACTTGTGGGCTTTG--AAAG
* * *
3498452 GTTGCCACCGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498480 AAGTGCCACCGACTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498509 GGTGCTACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3498537 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3498565 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3498594 AGTGCCACTGAGTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498622 GGTGCCATTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
3498651 AGTTGCCA-TCGACTTGTGGGCTTTGAAAG
1 -GGTGCCACT-GACTTGTGGGCTTTGAAAG
* *
3498680 GATGCCACTGACTTGTGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498708 GATGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3498736 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3498765 AGTGCCACTGATTTGTGTGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498793 GATGCCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3498822 AGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498850 GGTGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3498878 GATGCCA-TCGGCTTGTGGGCTTTTAAAAG
1 GGTGCCACT-GACTTGTGGGC-TTTGAAAG
*
3498907 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3498935 GATGCCATTGACTTGTGGGCTTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAG
* *
3498964 AGTGCCACCGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3498992 GGTGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499020 GATGCCACTGGCTTGTGGGTTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3499049 AGTGCCACTAACTTGTAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499077 AGTGCCACTGACTTATAGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * * *
3499106 AGTGCCACCGAATTGTGGGCTTTGAATG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499134 GATGCCATTGACTTGTGGGCTTCGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3499162 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499190 GGTGCCACTAACTTGTGGGCTTTGAAAAAA
1 GGTGCCACTGACTTGTGGGCTTTG--AAAG
* * *
3499220 GTTGCCACCGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499248 AAGTGCCACCGACTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499277 GGTGCTACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3499305 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
3499334 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499362 AGTGCCATTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3499391 AGTGCCACTAACTTGTGGGTTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3499420 AGTGCCACTGACTTATGGGCTTTGAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499448 GATGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3499476 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3499505 AGTGCCACTGATTTGTGTGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499533 GATGCCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3499562 AGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499590 GGTGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
3499618 GATGCCATTGGCTTGTGGGCTTTTAAAAA
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
*
3499647 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499675 GATGCCATTGACTTGTGGGCTTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAG
* * *
3499704 AGTGCCACCGACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499732 GGTGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499760 GATGCCACTGGCTTGTGGGTTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3499789 AGTGCCACTAACTTGTAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499817 AGTGCCACTGACTTATAGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * * *
3499846 AGTGCCACCGAATTGTGGGCTTTGAATG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499874 GATGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3499902 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
3499930 GGTGCCTCTAACTTGTGGGCTTTGAAAAAA
1 GGTGCCACTGACTTGTGGGCTTTG--AAAG
* * *
3499960 GTTGCCACCGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3499988 AAGTGCCACCGACTTGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3500017 GGTGCTACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
3500045 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3500073 GATGTCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3500101 GTTGCCACTGACTTATGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
3500130 AGTGCCACTAACTTGTGGGTTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3500159 AGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3500187 GGTACCGCTAACTTGTGGGCTTTGAAAAA
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3500216 AGTGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3500244 GGTGCCATTGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3500272 GATGCCACTGACTTGTGGG-TTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
3500299 TGTGCCACTGACTTGTGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
3500325 GAGATGAACG
Statistics
Matches: 2742, Mismatches: 440, Indels: 131
0.83 0.13 0.04
Matches are distributed among these distances:
27 26 0.01
28 1620 0.59
29 863 0.31
30 197 0.07
31 13 0.00
32 23 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:3497207 original size:57 final size:57
Alignment explanation
Indices: 3497045--3500324 Score: 3592
Period size: 57 Copynumber: 57.5 Consensus size: 57
3497035 TTTTTTAAAA
* * * *
3497045 AAAGG-TGCCACTAACTTGTGTGGGTTTTGAAAAGAGTCGCCACCGACTCGTGTGGGCTTTAA
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTGAAAAGAGT-GCCACTGACT--TGTGGGCTTT-G
* * *
3497107 AAAGAATGCCACCGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3497163 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCGCTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * * ** *
3497220 AAAGGGTGTCGCTGACTTGTGGGCTTGGAAAAGTGTTGCCACCAACTCGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * *
3497278 AAAGAATGCCACT-ATCTTGTGGGCTTTGAAATGA-TGCCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGA-CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3497334 AAAGGGTGCCATTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * * *
3497391 AAAGGATGCCATTAACTTATGGGCTTTGATAAGAGTTGCCACCGACTCGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * * * *
3497449 AAAGGATGCCACTAACTTATGGGCTTTGAAAAGA-TGCCATTGACTTGTGGGATTTA
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3497505 AAAGGGTGCCGCTAACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3497562 AAAGGATGCCACTAACTTATGGGCTTTGAAAAGAGTGCCACT-ACCTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGA-CTTGTGGGCTTTG
* * * * * * * *
3497619 AAAGGGTGCCACTAACTTATGAGCTTTGAAAAGACTTGCCCCCGACTCGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGA-GTGCCACTGACTTGTGGGCTTTG
* * * * * ** * *
3497677 AAAGAAGTGCCACCGCCTTGTGGGCTTTG-AAAGGGGGCCACAAACTTATGGACTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3497734 AAAGGGTGCCACTGACTAGTGGGCTTTGAAAGGA-TGCAACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * * **
3497790 AAAAGAGTGCTACTGACCTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGAACTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * ** * * * *
3497847 AAAAGAGTTACCACCAACTCGTGGGCTTT-AAAAAAATGCCACTGACTTGTGGGCTTCG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3497905 AAAGGGTGCCACTGACTTGTAGGCTTTG-AAAGGGTGCCACTAACATGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * * *
3497961 AAAAGAGTTGCCACCGACTCGTGGGCTTTGAAAGGAGTGCCACCGACTTGTGGGTTTTG
1 -AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * * **
3498020 AAAGGGTGCAACTGACTTGTAGGCTTTG-AAAGGGTGCCACTAACTTGTGCACTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3498076 AAAAGATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3498133 AAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGAGTTGCCA-TCGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACT-GACTTGTGGGCTTTG
* *
3498191 AAAGGATGCCACTGACTTGTGGGCTTTGAAATGA-TGCCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3498247 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGTGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3498304 AAAGGATGCCATTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3498361 AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA-TGCCATTGGCTTGTGGGCTTTT
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3498417 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAAAGTTGCCACCGACTCGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * * * *
3498476 AAAGAAGTGCCACCGACTTGTGGGCTTTG-AAAGGGTGCTACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3498533 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3498589 AAAAGAGTGCCACTGAGTTGTGGGCTTTG-AAAGGGTGCCATTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3498646 AAAAGAGTTGCCA-TCGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG
1 -AAAG-GATGCCACT-GACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3498704 AAATGATGCCATTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3498760 AAAAGAGTGCCACTGATTTGTGTGCTTTGAAAGGA-TGCCATTGACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3498817 AAAAGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3498874 AAAAGATGCCA-TCGGCTTGTGGGCTTTTAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACT-GACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3498931 AAAGGATGCCATTGACTTGTGGGCTTTAAAAAGAGTGCCACCGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3498988 AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA-TGCCACTGGCTTGTGGGTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3499044 AAAAGAGTGCCACTAACTTGTAGGCTTTG-AAAGAGTGCCACTGACTTATAGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * ** * *
3499101 AAAAGAGTGCCACCGAATTGTGGGCTTTGAATGGA-TGCCATTGACTTGTGGGCTTCG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3499158 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3499214 AAAAAAGTTGCCACCGACTCGTGGGCTTTG-AAAGAAGTGCCACCGACTTGTGGGCTTTG
1 --AAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-AGTGCCACTGACTTGTGGGCTTTG
* * * *
3499273 AAAGGGTGCTACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3499329 AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCATTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3499386 AAAAGAGTGCCACTAACTTGTGGGTTTTGAAAAGAGTGCCACTGACTTATGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3499444 AAATGATGCCATTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3499500 AAAAGAGTGCCACTGATTTGTGTGCTTTGAAAGGA-TGCCATTGACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3499557 AAAAGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3499614 AAAAGATGCCATTGGCTTGTGGGCTTTTAAAAAAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3499671 AAAGGATGCCATTGACTTGTGGGCTTTAAAAAGAGTGCCACCGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3499728 AAAAGG-TGCCACTAACTTGTGGGCTTTGAAAAGA-TGCCACTGGCTTGTGGGTTTTG
1 -AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3499784 AAAAGAGTGCCACTAACTTGTAGGCTTTG-AAAGAGTGCCACTGACTTATAGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * ** *
3499841 AAAAGAGTGCCACCGAATTGTGGGCTTTGAATGGA-TGCCATTGACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3499898 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCTCTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * *
3499954 AAAAAAGTTGCCACCGACTCGTGGGCTTTG-AAAGAAGTGCCACCGACTTGTGGGCTTTG
1 --AAAGGATGCCACTGACTTGTGGGCTTTGAAAAG-AGTGCCACTGACTTGTGGGCTTTG
* * * *
3500013 AAAGGGTGCTACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3500069 AAAGGATGTCACTGACTTGTGGGCTTTG-AAAG-GTTGCCACTGACTTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * * *
3500125 AAAAGAGTGCCACTAACTTGTGGGTTTTGAAAAGAGTGCCACTGACTTATGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * * * *
3500183 AAAGGGTACCGCTAACTTGTGGGCTTTGAAAAAAGTGCCATTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3500240 AAAGGGTGCCATTGACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGG-TTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3500295 AAAATG-TGCCACTGACTTGTGGGCTTTGAA
1 -AAAGGATGCCACTGACTTGTGGGCTTTGAA
3500325 GAGATGAACG
Statistics
Matches: 2717, Mismatches: 429, Indels: 151
0.82 0.13 0.05
Matches are distributed among these distances:
55 39 0.01
56 739 0.27
57 1359 0.50
58 412 0.15
59 139 0.05
60 6 0.00
61 10 0.00
62 5 0.00
63 8 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (57 bp):
AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
Found at i:3501484 original size:18 final size:18
Alignment explanation
Indices: 3501456--3501519 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 18
3501446 TTAAGATCAA
3501456 TTTTTTCTTGGTTTTTTTG
1 TTTTTT-TTGGTTTTTTTG
3501475 TTTTTTTTGGTTTTTTTTG
1 TTTTTTTTGG-TTTTTTTG
***
3501494 TTTTTTTAATTTTTTTTG
1 TTTTTTTTGGTTTTTTTG
3501512 TTTTTTTT
1 TTTTTTTT
3501520 TGGTATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 19 0.47
19 21 0.52
ACGTcount: A:0.03, C:0.02, G:0.11, T:0.84
Consensus pattern (18 bp):
TTTTTTTTGGTTTTTTTG
Found at i:3501521 original size:10 final size:9
Alignment explanation
Indices: 3501456--3501519 Score: 83
Period size: 9 Copynumber: 6.9 Consensus size: 9
3501446 TTAAGATCAA
3501456 TTTTTTCTTG
1 TTTTTT-TTG
*
3501466 GTTTTTTTG
1 TTTTTTTTG
3501475 TTTTTTTTGG
1 TTTTTTTT-G
3501485 TTTTTTTTG
1 TTTTTTTTG
**
3501494 TTTTTTTAA
1 TTTTTTTTG
3501503 TTTTTTTTG
1 TTTTTTTTG
3501512 TTTTTTTT
1 TTTTTTTT
3501520 TGGTATGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
9 33 0.70
10 14 0.30
ACGTcount: A:0.03, C:0.02, G:0.11, T:0.84
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3511200 original size:22 final size:22
Alignment explanation
Indices: 3511174--3511219 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3511164 AAAATAATGG
3511174 GAATG-ACTAGCAAGAAAAAAAA
1 GAATGAAC-AGCAAGAAAAAAAA
* *
3511196 GAATGAACATCAATAAAAAAAA
1 GAATGAACAGCAAGAAAAAAAA
3511218 GA
1 GA
3511220 GTGGCCCCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.65, C:0.09, G:0.15, T:0.11
Consensus pattern (22 bp):
GAATGAACAGCAAGAAAAAAAA
Found at i:3516596 original size:15 final size:15
Alignment explanation
Indices: 3516576--3516608 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3516566 TAATGATCAA
3516576 TGTTGAAAATAAGCT
1 TGTTGAAAATAAGCT
3516591 TGTTGAAAATAAGCT
1 TGTTGAAAATAAGCT
3516606 TGT
1 TGT
3516609 ACTCTCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (15 bp):
TGTTGAAAATAAGCT
Found at i:3517775 original size:166 final size:164
Alignment explanation
Indices: 3517436--3517907 Score: 498
Period size: 165 Copynumber: 2.8 Consensus size: 164
3517426 GGGTTTAAAA
* *
3517436 TTTTAAAATTCATTAAATATTATT-ATTTAACTCATATTAAATCGGTTTTCAAAAATTCATTCAT
1 TTTTAAAATTCA-TAAATATTATTGATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCAT
** * * * *
3517500 TTTCACAAATTTTTAAATTTTTTCCTTGAAACTCTCTTT-T-TTTTT-AAATATGAAATTTCCTA
65 TTTCATGAGTTTTTAAA-TTTTTCCTTGAAA-T-T-TTTCTATTTTTGAAATACGAAGTTTTCTA
*
3517562 CTTCGTAAATGTTTTTGAATGGATTTTTCTCAGTTTTAAT
126 -TTCGTAAATGTTTTTGAAGGGATTTTTCTCAGTTTTAAT
* *
3517602 TTTTAAAATTCATAAA-ATTATATGATTTAAGTTTAAATTAAATCAGTTTTCAAAAATTCATTCA
1 TTTTAAAATTCATAAATATTAT-TGATTTAA-TTCATATTAAATCAGTTTTCAAAAATTCATTCA
*
3517666 TCTTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTGAAATACGAAGTTTTCTATTC
64 TTTTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTGAAATACGAAGTTTTCTATTC
*
3517731 TGT-AAT-TTTTT-AAGGGGGATTTTTCTCAATTTTTAAT
129 -GTAAATGTTTTTGAA--GGGATTTTTCTC-AGTTTTAAT
* * * * * **
3517768 TTTTAAAATTCATCAAATATTATTG-TTTGATCCATATTAAATTAGTTTTGAAAAATTAATTTGT
1 TTTTAAAATTCAT-AAATATTATTGATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCAT
* * * *
3517832 TTTCATGAGTTTTGAATTTTTTCTTTGAAATTTTCCTATTTTTGCAAA-ACCG-AGTTTTCTATT
65 TTTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTG-AAATA-CGAAGTTTTCTATT
*
3517895 CCATAAATGTTTT
128 -CGTAAATGTTTT
3517908 CAGGAGATTT
Statistics
Matches: 261, Mismatches: 28, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
163 5 0.02
164 12 0.05
165 106 0.41
166 81 0.31
167 52 0.20
168 5 0.02
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (164 bp):
TTTTAAAATTCATAAATATTATTGATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCATT
TTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTGAAATACGAAGTTTTCTATTCGT
AAATGTTTTTGAAGGGATTTTTCTCAGTTTTAAT
Found at i:3517839 original size:165 final size:162
Alignment explanation
Indices: 3517436--3517957 Score: 486
Period size: 166 Copynumber: 3.1 Consensus size: 162
3517426 GGGTTTAAAA
* * * *
3517436 TTTTAAAATTCATTAAATATTATTATTTAACTCATATTAAATCGGTTTTCAAAAATTCATTCATT
1 TTTTAAAATTCATCAAATATTATTGTTTATC-CATATTAAATCAGTTTTCAAAAATTCATTCATT
** * * * *
3517501 TTCACAAATTTTTAAATTTTTTCCTTGAAACTCTCTTT-T-TTTTT-AAATATGAAATTTCCTAC
65 TTCATGAGTTTTTAAA-TTTTTCCTTGAAA-T-T-TTTCTATTTTTGAAATACGAAGTTTTCTA-
* *
3517563 TTCGTAAATGTTTTTGAA-TGGATTTTTCTCAGTTTTAAT
125 TTCGTAAAT-TTTTT-AAGGGGATTTTTCTCATTTTTAAT
** *
3517602 TTTTAAAATTCAT-AAA-ATTATATGATTTAAGTTTAAATTAAATCAGTTTTCAAAAATTCATTC
1 TTTTAAAATTCATCAAATATTAT-TG-TTT-A-TCCATATTAAATCAGTTTTCAAAAATTCATTC
*
3517665 ATCTTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTGAAATACGAAGTTTTCTATT
62 ATTTTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTGAAATACGAAGTTTTCTATT
3517730 CTGT-AATTTTTTAAGGGGGATTTTTCTCAATTTTTAAT
127 C-GTAAATTTTTTAA-GGGGATTTTTCTC-ATTTTTAAT
* * * **
3517768 TTTTAAAATTCATCAAATATTATTGTTTGATCCATATTAAATTAGTTTTGAAAAATTAATTTGTT
1 TTTTAAAATTCATCAAATATTATTGTTT-ATCCATATTAAATCAGTTTTCAAAAATTCATTCATT
* * * *
3517833 TTCATGAGTTTTGAATTTTTTCTTTGAAATTTTCCTATTTTTGCAAA-ACCG-AGTTTTCTATTC
65 TTCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTG-AAATA-CGAAGTTTTCTATT-
* * * * * **
3517896 CATAAATGTTTTCAGGAGATTTTTTCTTGATTTAAAAT
127 CGTAAATTTTTTAAGGGGA-TTTTTC-TCATTTTTAAT
* *
3517934 TTTAAAAATTCATCTAATATTATT
1 TTTTAAAATTCATCAAATATTATT
3517958 ATTAAACTTC
Statistics
Matches: 299, Mismatches: 38, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
163 5 0.02
164 12 0.04
165 109 0.36
166 119 0.40
167 49 0.16
168 5 0.02
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (162 bp):
TTTTAAAATTCATCAAATATTATTGTTTATCCATATTAAATCAGTTTTCAAAAATTCATTCATTT
TCATGAGTTTTTAAATTTTTCCTTGAAATTTTTCTATTTTTGAAATACGAAGTTTTCTATTCGTA
AATTTTTTAAGGGGATTTTTCTCATTTTTAAT
Found at i:3519784 original size:3 final size:3
Alignment explanation
Indices: 3519776--3519821 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3519766 AAGACATTCT
3519776 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3519822 GATTTCCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3522681 original size:5 final size:6
Alignment explanation
Indices: 3522642--3522726 Score: 50
Period size: 6 Copynumber: 13.7 Consensus size: 6
3522632 AATATGCCCA
* * *
3522642 TTTTCT TTTGTCT TTTTCT TGATTT-T TTAT-T TTTTCT TTTTCT TTTCCC
1 TTTTCT TTT-TCT TTTTCT T--TTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* *
3522691 TTTTCT ATTTTGT TTCTTC- ATTTCAT TTTTCT TTTT
1 TTTTCT -TTTTCT TT-TTCT TTTTC-T TTTTCT TTTT
3522727 TTCCACAAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
5 9 0.15
6 30 0.49
7 19 0.31
8 3 0.05
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTTCT
Found at i:3524068 original size:33 final size:32
Alignment explanation
Indices: 3524004--3524068 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3523994 GCCAGTTTCA
*
3524004 TGTATCGATACAATGAACATGCATCGATACAT
1 TGTATCGATACAAAGAACATGCATCGATACAT
*
3524036 TGTATCGATACAAAGCATA-ATGTATCGATACAT
1 TGTATCGATACAAAG-A-ACATGCATCGATACAT
3524069 CTAGGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGCATCGATACAT
Found at i:3524627 original size:26 final size:26
Alignment explanation
Indices: 3524583--3524634 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3524573 GATATCAAAG
* *
3524583 TTTTCGTTTTTCTCACCCTTTAAAAA
1 TTTTCGTTTTGCTCACCCTATAAAAA
* *
3524609 TTTTTGTTTTGCTCCCCCTATAAAAA
1 TTTTCGTTTTGCTCACCCTATAAAAA
3524635 AAATTTTCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTCGTTTTGCTCACCCTATAAAAA
Found at i:3524676 original size:24 final size:22
Alignment explanation
Indices: 3524620--3524695 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
3524610 TTTTGTTTTG
* *
3524620 CTCCCCCTATAAAAAAAATT-T
1 CTCCCCCTATATAAAAGATTAT
*
3524641 -T-CCCCTAGATAAAAACGATTAT
1 CTCCCCCTATAT-AAAA-GATTAT
* *
3524663 CTCTCCCTATATAAAAGATTTT
1 CTCCCCCTATATAAAAGATTAT
3524685 CTCCCCCTATA
1 CTCCCCCTATA
3524696 AGAGAATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.16
20 5 0.12
21 3 0.07
22 16 0.37
23 5 0.12
24 7 0.16
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.32
Consensus pattern (22 bp):
CTCCCCCTATATAAAAGATTAT
Found at i:3529384 original size:13 final size:13
Alignment explanation
Indices: 3529366--3529390 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3529356 TTTCATCATG
3529366 TATCGATACATTA
1 TATCGATACATTA
3529379 TATCGATACATT
1 TATCGATACATT
3529391 GTACCATGTA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:3535594 original size:24 final size:22
Alignment explanation
Indices: 3535550--3535599 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
3535540 AATGGAGAAG
**
3535550 AAAATAACGAACAAATTTACAC
1 AAAATAACGAACAAAAATACAC
*
3535572 AAAATAACGCACACAAAAATACAT
1 AAAATAACG-A-ACAAAAATACAC
3535596 AAAA
1 AAAA
3535600 AGGATGGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 1 0.04
24 13 0.57
ACGTcount: A:0.64, C:0.18, G:0.04, T:0.14
Consensus pattern (22 bp):
AAAATAACGAACAAAAATACAC
Found at i:3538360 original size:20 final size:19
Alignment explanation
Indices: 3538317--3538377 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
3538307 AGGGTGGTTT
**
3538317 TGTATTGATACATTTTAGGCA
1 TGTATTGATACA-TTTA-TTA
3538338 TGTATTGATACATTTACTTA
1 TGTATTGATACATTTA-TTA
*
3538358 TGTATCGATACATTTATTA
1 TGTATTGATACATTTATTA
3538377 T
1 T
3538378 TTTTATCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.11
20 20 0.56
21 12 0.33
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.48
Consensus pattern (19 bp):
TGTATTGATACATTTATTA
Found at i:3539180 original size:43 final size:43
Alignment explanation
Indices: 3539095--3539192 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
3539085 TCTTCGAGGT
* *
3539095 CAAAGGAAAAA-GGAGAATGAAATAGGTCCTCCTCCTTAAAGA
1 CAAAGGAAAAAGGGAAAAAGAAATAGGTCCTCCTCCTTAAAGA
* * *
3539137 CAAAGGAAAAAGGGAAAAAGGAA-AGTGTCCTGCTCCTTGAAGA
1 CAAAGGAAAAAGGGAAAAAGAAATAG-GTCCTCCTCCTTAAAGA
*
3539180 CAAAGGGAAAAGG
1 CAAAGGAAAAAGG
3539193 AGTATGTCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 13 0.27
43 35 0.73
ACGTcount: A:0.46, C:0.14, G:0.27, T:0.13
Consensus pattern (43 bp):
CAAAGGAAAAAGGGAAAAAGAAATAGGTCCTCCTCCTTAAAGA
Found at i:3539303 original size:42 final size:41
Alignment explanation
Indices: 3539257--3539538 Score: 152
Period size: 42 Copynumber: 6.7 Consensus size: 41
3539247 TCTTTAAGAC
* *
3539257 AAAGGGAAAAAGAATGCATCCTGCT-TTTCGAAGACAAAGGAA
1 AAAGGGAAAAA-AATACATCCTACTCTTT-GAAGACAAAGGAA
* * * *
3539299 AAAGGAGAATAAACTACGTCCTACTCTTTGAGGACAAAGGAA
1 AAAGG-GAAAAAAATACATCCTACTCTTTGAAGACAAAGGAA
* * * * *
3539341 AAAAGGAAATGAAGTACGTCCTGCTCTTTGAAGACAAAGGGAA
1 AAAGGGAAA-AAAATACATCCTACTCTTTGAAGACAAA-GGAA
* *
3539384 AAGAAGGAAATAAAATGCATCCTACT-TTTCG-AGAACAAAGGAGA
1 AA-AGGGAAA-AAAATACATCCTACTCTTT-GAAG-ACAAAGGA-A
* * * *
3539428 AAA--GAAAATAAAGTACCTCCTGCTCTTTGAGGATAAAGGAGA
1 AAAGGGAAAA-AAA-TACATCCTACTCTTTGAAGACAAAGGA-A
* *
3539470 AAA-GGAAATAAAGTGCATCCTACTCTTTG-AGAACAAAAGG-A
1 AAAGGGAAA-AAAATACATCCTACTCTTTGAAG-AC-AAAGGAA
** *
3539511 AAA--GAAGGAAATGCATCCTACTCTTTGA
1 AAAGGGAAAAAAATACATCCTACTCTTTGA
3539539 GGACTAAAAG
Statistics
Matches: 192, Mismatches: 31, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
39 18 0.09
40 4 0.02
41 15 0.08
42 89 0.46
43 38 0.20
44 28 0.15
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAGGGAAAAAAATACATCCTACTCTTTGAAGACAAAGGAA
Found at i:3539442 original size:86 final size:84
Alignment explanation
Indices: 3539275--3539516 Score: 294
Period size: 86 Copynumber: 2.9 Consensus size: 84
3539265 AAAGAATGCA
* * * *
3539275 TCCTGCT-TTTCGAAGACAAAGG-AAAAAGGAGAATAAACTACGTCCTACTCTTTGAGGACAAAG
1 TCCTGCTCTTT-GAAGACAAAGGAAAAAAGGA-AATAAAATGCATCCTACTCTTTGAGAACAAAG
* * * *
3539338 GAAAAAAGGAAATGAAGTACG
64 GAGAAAAGAAAATAAAGTACC
3539359 TCCTGCTCTTTGAAGACAAAGGGAAAAGAAGGAAATAAAATGCATCCTACT-TTTCGAGAACAAA
1 TCCTGCTCTTTGAAGACAAA-GGAAAA-AAGGAAATAAAATGCATCCTACTCTTT-GAGAACAAA
3539423 GGAGAAAAGAAAATAAAGTACC
63 GGAGAAAAGAAAATAAAGTACC
* * * * *
3539445 TCCTGCTCTTTGAGGATAAAGGAGAAAAGGAAATAAAGTGCATCCTACTCTTTGAGAACAAAAG-
1 TCCTGCTCTTTGAAGACAAAGGAAAAAAGGAAATAAAATGCATCCTACTCTTTGAGAACAAAGGA
3539509 GAAAAGAA
66 GAAAAGAA
3539517 GGAAATGCAT
Statistics
Matches: 139, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
83 8 0.06
84 48 0.35
85 16 0.12
86 62 0.45
87 5 0.04
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.19
Consensus pattern (84 bp):
TCCTGCTCTTTGAAGACAAAGGAAAAAAGGAAATAAAATGCATCCTACTCTTTGAGAACAAAGGA
GAAAAGAAAATAAAGTACC
Found at i:3539496 original size:128 final size:129
Alignment explanation
Indices: 3539261--3539522 Score: 354
Period size: 128 Copynumber: 2.0 Consensus size: 129
3539251 TAAGACAAAG
* * *
3539261 GGAAA-AAGAATGCATCCTGCTTTTCGAAGACAAAGGAAAAAGGAGAATAAACTACGTCCTACTC
1 GGAAATAAGAATGCATCCTACTTTTCGAAGACAAAGGAAAAAGGAAAATAAACTACCTCCTACTC
* * * *
3539325 TTTGAGGACAAAGGAAAAAAGGAAATGAAGTACGTCCTGCTCTTTGA-AGACAAAGGGAAAAGAA
66 TTTGAGGACAAAGGAAAAAAGGAAATAAAGTACATCCTACTCTTTGAGA-ACAAAAGGAAAAGAA
* *
3539389 GGAAATAA-AATGCATCCTACTTTTCG-AGAACAAAGGAGAAAA-GAAAATAAAGTACCTCCTGC
1 GGAAATAAGAATGCATCCTACTTTTCGAAG-ACAAAGGA-AAAAGGAAAATAAACTACCTCCTAC
* * *
3539451 TCTTTGAGGATAAAGGAGAAAAGGAAATAAAGTGCATCCTACTCTTTGAGAACAAAAGGAAAAGA
64 TCTTTGAGGACAAAGGAAAAAAGGAAATAAAGTACATCCTACTCTTTGAGAACAAAAGGAAAAGA
3539516 A
129 A
3539517 GGAAAT
1 GGAAAT
3539523 GCATCCTACT
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
127 2 0.02
128 109 0.92
129 7 0.06
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (129 bp):
GGAAATAAGAATGCATCCTACTTTTCGAAGACAAAGGAAAAAGGAAAATAAACTACCTCCTACTC
TTTGAGGACAAAGGAAAAAAGGAAATAAAGTACATCCTACTCTTTGAGAACAAAAGGAAAAGAA
Found at i:3539630 original size:42 final size:42
Alignment explanation
Indices: 3539548--3539630 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
3539538 AGGACTAAAA
* * *
3539548 GGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAATAGAAAC
1 GGTGCCACCAACTTGTGTGGGCTTAAAAAGCAAAATAGAAAC
3539590 GGTGCCACCAA-TTGTGTGGGCTTAAAGAAAGCAAAA-AGAAA
1 GGTGCCACCAACTTGTGTGGGCTT-AA-AAAGCAAAATAGAAA
3539631 GCGTCCTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 12 0.33
42 16 0.44
43 8 0.22
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (42 bp):
GGTGCCACCAACTTGTGTGGGCTTAAAAAGCAAAATAGAAAC
Found at i:3539783 original size:61 final size:61
Alignment explanation
Indices: 3539590--3540088 Score: 538
Period size: 62 Copynumber: 8.0 Consensus size: 61
3539580 AAATAGAAAC
* * * *
3539590 GGTGCCACCAA-TTGTGTGGGCTTAAAGAAAGCAAAAAGAAAGCGTCCTGCTTTTTG-AGAACTA
1 GGTGCCACCAACTCGTGTGGGCTT-TA-AAAG-AAAAAG---GCGTCCTACTCTTTGAAG-ACTA
3539653 AAA
59 AAA
* * * * * *
3539656 TGTGCCACCAACTCGTGTGGGCTTTAAAAAAGAAAAGGTGT-CTAACTCTTTGAGGATTGAAA
1 GGTGCCACCAACTCGTGTGGGCTTTAAAAGA-AAAAGGCGTCCT-ACTCTTTGAAGACTAAAA
* * *
3539718 GGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAAGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTGAAGACTAAAA
* * * * **
3539779 GGTGCCACCAACTCATGTGGGCTTCAAAAAAAAAAGGCATCCTGTTCTTT-AAGGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTGAA-GACTAAAA
* * * * *
3539840 GGTGCCACTAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAGGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTGAAGACTAAAA
* ** * *
3539901 GGTGCCACCAACTAGTGTGCACTTTAAAAAGAAAAAGGCGTCCTACTATTTGAGGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGGCGTCCTACTCTTTGAAGACTAAAA
* * *
3539963 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTTTTTGAAGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGGCGTCCTACTCTTTGAAGACTAAAA
* * *
3540025 GGTGTCACCAACTCGTGTGGGCTCTAAAAAGAAAAAGGCGTCCTACTATTTGAAGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCT-TTAAAAGAAAAAGGCGTCCTACTCTTTGAAGACTAAAA
3540087 GG
1 GG
3540089 ATAAAAAGGG
Statistics
Matches: 374, Mismatches: 50, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
60 2 0.01
61 149 0.40
62 190 0.51
63 2 0.01
64 1 0.00
65 8 0.02
66 11 0.03
67 11 0.03
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (61 bp):
GGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCGTCCTACTCTTTGAAGACTAAAA
Found at i:3539861 original size:122 final size:123
Alignment explanation
Indices: 3539649--3540088 Score: 566
Period size: 122 Copynumber: 3.6 Consensus size: 123
3539639 CTTTTTGAGA
* * * *
3539649 ACTAAAATGTGCCACCAACTCGTGTGGGCTTTAAAAA-AGAAAAGGTGT-CTAACTCTTTGAGGA
1 ACTAAAAGGTGCCACCAACTCATGTGGGCTTCAAAAAGA-AAAAGGCGTCCT-ACTCTTTGAGGA
* *
3539712 TTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAAG
64 CTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAAG
* ** *
3539772 ACTAAAAGGTGCCACCAACTCATGTGGGCTTCAAAAA-AAAAAGGCATCCTGTTCTTTAAGGACT
1 ACTAAAAGGTGCCACCAACTCATGTGGGCTTCAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACT
* *
3539836 AAAAGGTGCCACTAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAGG
66 AAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAAG
** * *
3539894 ACTAAAAGGTGCCACCAACT-AGTGTGCACTTTAAAAAGAAAAAGGCGTCCTACTATTTGAGGAC
1 ACTAAAAGGTGCCACCAACTCA-TGTGGGCTTCAAAAAGAAAAAGGCGTCCTACTCTTTGAGGAC
* ** * * *
3539958 TAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGTGTCCTACTTTTTGAAG
65 TAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGGCATCTTGCTCTTTGAAG
* * * *
3540018 ACTAAAAGGTGTCACCAACTCGTGTGGGC-TCTAAAAAGAAAAAGGCGTCCTACTATTTGAAGAC
1 ACTAAAAGGTGCCACCAACTCATGTGGGCTTC-AAAAAGAAAAAGGCGTCCTACTCTTTGAGGAC
3540082 TAAAAGG
65 TAAAAGG
3540089 ATAAAAAGGG
Statistics
Matches: 277, Mismatches: 34, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
121 1 0.00
122 104 0.38
123 87 0.31
124 85 0.31
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (123 bp):
ACTAAAAGGTGCCACCAACTCATGTGGGCTTCAAAAAGAAAAAGGCGTCCTACTCTTTGAGGACT
AAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGAAAAAGGCATCTTGCTCTTTGAAG
Found at i:3540177 original size:32 final size:31
Alignment explanation
Indices: 3540091--3540187 Score: 126
Period size: 32 Copynumber: 3.2 Consensus size: 31
3540081 CTAAAAGGAT
* *
3540091 AAAAAG-GGTGCCACAGAGTCGTGGACTTTG
1 AAAAAGAGATGCCACTGAGTCGTGGACTTTG
* *
3540121 -AAAAGAGATGTCACTAAGTCGTGGACTTTG
1 AAAAAGAGATGCCACTGAGTCGTGGACTTTG
*
3540151 AAGAAAGAGATGCCACTGAGTTGTGGACTTTG
1 AA-AAAGAGATGCCACTGAGTCGTGGACTTTG
3540183 AAAAA
1 AAAAA
3540188 AGTTGCTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.09
30 20 0.35
31 4 0.07
32 28 0.49
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (31 bp):
AAAAAGAGATGCCACTGAGTCGTGGACTTTG
Found at i:3541462 original size:23 final size:22
Alignment explanation
Indices: 3541404--3541463 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
3541394 CATATCCTTG
* *
3541404 CTTTTTAATTTTTTTCGTTTCT
1 CTTTTTTATTTTTTGCGTTTCT
* *
3541426 CTTTTTCTTTTTTTTTGCTTTTACT
1 C-TTTT-TTATTTTTTGCGTTT-CT
3541451 CTTTTTTATTTTT
1 CTTTTTTATTTTT
3541464 ATTTCTCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 11 0.37
24 15 0.50
25 3 0.10
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (22 bp):
CTTTTTTATTTTTTGCGTTTCT
Found at i:3541462 original size:25 final size:23
Alignment explanation
Indices: 3541405--3541468 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
3541395 ATATCCTTGC
*
3541405 TTTTTAATTTTTTTCGTTTCTCT
1 TTTTTATTTTTTTTCGTTTCTCT
*
3541428 TTTTCT-TTTTTTTTGCTTTTACTCT
1 TTTT-TATTTTTTTT-CGTTT-CTCT
3541453 TTTTTATTTTTATTTC
1 TTTTTATTTTT-TTTC
3541469 TCTTGTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 11 0.32
24 6 0.18
25 14 0.41
26 3 0.09
ACGTcount: A:0.08, C:0.12, G:0.03, T:0.77
Consensus pattern (23 bp):
TTTTTATTTTTTTTCGTTTCTCT
Found at i:3545619 original size:20 final size:20
Alignment explanation
Indices: 3545594--3545646 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
3545584 TTTGCCTGCA
3545594 TGTATCGATACATTTCATAG
1 TGTATCGATACATTTCATAG
3545614 TGTATCGATACATTTCATAG
1 TGTATCGATACATTTCATAG
3545634 TGTATCGATACAT
1 TGTATCGATACAT
3545647 CTCGGCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTCATAG
Found at i:3545692 original size:52 final size:51
Alignment explanation
Indices: 3545614--3545781 Score: 248
Period size: 52 Copynumber: 3.2 Consensus size: 51
3545604 CATTTCATAG
*
3545614 TGTATCGATACATTTCATAGTGTATCGATACATCTCGGCAAATTTGCTTGCA
1 TGTATCGATACATTTCATAGTGTATCGATACATCT-GGCAAATTTGCCTGCA
*
3545666 TGTATCGATACATTTTATAGTGTATCGATACATCTGAGCAAATTTGCCTGCA
1 TGTATCGATACATTTCATAGTGTATCGATACATCTG-GCAAATTTGCCTGCA
***
3545718 TGTATCGATACA-AAGATCAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
1 TGTATCGATACATTTCAT-AGTGTATCGATACATCT-GGCAAATTTGCCTGCA
3545770 TGTATCGATACA
1 TGTATCGATACA
3545782 AAGATCAGTG
Statistics
Matches: 108, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
51 3 0.03
52 104 0.96
53 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGTATCGATACATTTCATAGTGTATCGATACATCTGGCAAATTTGCCTGCA
Found at i:3545782 original size:52 final size:52
Alignment explanation
Indices: 3545632--3545801 Score: 270
Period size: 52 Copynumber: 3.3 Consensus size: 52
3545622 TACATTTCAT
* * ***
3545632 AGTGTATCGATACATCTCGGCAAATTTGCTTGCATGTATCGATACATTTTAT-
1 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAGATC
*
3545684 AGTGTATCGATACATCTGAGCAAATTTGCCTGCATGTATCGATACAAAGATC
1 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAGATC
3545736 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAGATC
1 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAGATC
3545788 AGTGTATCGATACA
1 AGTGTATCGATACA
3545802 ATGTATCGAT
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 108 0.98
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (52 bp):
AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAGATC
Found at i:3545808 original size:13 final size:13
Alignment explanation
Indices: 3545790--3545814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3545780 CAAAGATCAG
3545790 TGTATCGATACAA
1 TGTATCGATACAA
3545803 TGTATCGATACA
1 TGTATCGATACA
3545815 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3545894 original size:13 final size:13
Alignment explanation
Indices: 3545876--3545900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3545866 ACAAAACTTA
3545876 TGTATCGATACAT
1 TGTATCGATACAT
3545889 TGTATCGATACA
1 TGTATCGATACA
3545901 AATCGTTGAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3552010 original size:20 final size:21
Alignment explanation
Indices: 3551966--3552037 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
3551956 AATTCTACAT
* *
3551966 TGTATCGATACAAGCAGT-AAA
1 TGTATCGATACATG-ATTGAAA
3551987 TGTATCGATACAT-ATGTG-AA
1 TGTATCGATACATGAT-TGAAA
*
3552007 TGTATCGATACATGCTTGAAA
1 TGTATCGATACATGATTGAAA
3552028 TGTATCGATA
1 TGTATCGATA
3552038 TAAAACCACT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.41
21 25 0.57
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATGATTGAAA
Found at i:3559585 original size:15 final size:15
Alignment explanation
Indices: 3559533--3559586 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3559523 AAAATTAATT
3559533 ATTTAAATTTAAAATA
1 ATTTAAATTT-AAATA
* * *
3559549 ATTCAAAACTTAAATG
1 ATT-TAAATTTAAATA
*
3559565 ATTTAAATTTGAATA
1 ATTTAAATTTAAATA
3559580 ATTTAAA
1 ATTTAAA
3559587 ATATATTTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 15 0.50
16 10 0.33
17 5 0.17
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
ATTTAAATTTAAATA
Found at i:3560047 original size:18 final size:17
Alignment explanation
Indices: 3560023--3560061 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 17
3560013 TGTTTTACAA
3560023 TTATATAATATATATTAATT
1 TTATAT-AT-TATA-TAATT
3560043 TTATATATTATATAATT
1 TTATATATTATATAATT
3560060 TT
1 TT
3560062 TATCACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 2 0.11
20 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATATTATATAATT
Found at i:3563716 original size:29 final size:29
Alignment explanation
Indices: 3563661--3563719 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
3563651 ATAATAAAAA
* *
3563661 ATTATTTTAATTTTTATATTATTAAATTT
1 ATTATTTTAAGTTTCATATTATTAAATTT
* *
3563690 ATTATTTT-AGTTTCATATTTTTAAAATT
1 ATTATTTTAAGTTTCATATTATTAAATTT
3563718 AT
1 AT
3563720 AATAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (29 bp):
ATTATTTTAAGTTTCATATTATTAAATTT
Found at i:3563881 original size:20 final size:20
Alignment explanation
Indices: 3563856--3563894 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3563846 TTACATCATA
3563856 TAATATATT-AATATTTTTAT
1 TAATAT-TTAAATATTTTTAT
3563876 TAATATTTAAATATTTTTA
1 TAATATTTAAATATTTTTA
3563895 ACACTGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATATTTAAATATTTTTAT
Found at i:3563943 original size:15 final size:15
Alignment explanation
Indices: 3563923--3563974 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3563913 TTATTATAAT
3563923 TTAAAAATATAAATA
1 TTAAAAATATAAATA
3563938 TT-AAAATACTAAAT-
1 TTAAAAATA-TAAATA
* * *
3563952 TTAATAACATAAAAA
1 TTAAAAATATAAATA
3563967 TTAAAAAT
1 TTAAAAAT
3563975 TCCTTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATATAAATA
Found at i:3564893 original size:3 final size:3
Alignment explanation
Indices: 3564885--3564920 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3564875 TATGAAATTT
3564885 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3564921 CTTGGACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3566661 original size:5 final size:5
Alignment explanation
Indices: 3566646--3566704 Score: 84
Period size: 5 Copynumber: 11.6 Consensus size: 5
3566636 TACTTTATCT
*
3566646 TATTA TAATTA TATTA TATTA TACTA GT-TTA TATTA TATTA TATTA TATTA
1 TATTA T-ATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA
3566697 TATTA TAT
1 TATTA TAT
3566705 CCTAGGAAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
4 1 0.02
5 42 0.86
6 6 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
TATTA
Done.