Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 12 of 276
Found at i:3497595 original size:16 final size:17
Alignment explanation
Indices: 3497567--3497614 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
3497557 AAAGTGATTG
3497567 AAAAAAGTACAAAAAAA-
1 AAAAAA-TACAAAAAAAT
*
3497584 AGAAAATACAAAAAAAT
1 AAAAAATACAAAAAAAT
3497601 AAAAAATA-AAAAAA
1 AAAAAATACAAAAAA
3497615 TTATTATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.08
Consensus pattern (17 bp):
AAAAAATACAAAAAAAT
Found at i:3511360 original size:15 final size:15
Alignment explanation
Indices: 3511335--3511370 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3511325 AAATTAACAA
3511335 TAATATTAATATAAAT
1 TAAT-TTAATATAAAT
*
3511351 TAATTTAATATAATT
1 TAATTTAATATAAAT
3511366 TAATT
1 TAATT
3511371 ATAGAACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTTAATATAAAT
Found at i:3511525 original size:8 final size:9
Alignment explanation
Indices: 3511498--3511527 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3511488 AAAGCTGTAA
3511498 AAAATTAAT
1 AAAATTAAT
3511507 AAAATTAAT
1 AAAATTAAT
3511516 AAAA-TAAT
1 AAAATTAAT
3511524 AAAA
1 AAAA
3511528 ATAGAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATTAAT
Found at i:3511571 original size:20 final size:19
Alignment explanation
Indices: 3511539--3511576 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3511529 TAGAAATTAC
3511539 AAAAAAATATAAAAATATG
1 AAAAAAATATAAAAATATG
*
3511558 AAAAAATATTTAAAAATAT
1 AAAAAA-ATATAAAAATAT
3511577 AGAACCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAAAATATAAAAATATG
Found at i:3516598 original size:40 final size:40
Alignment explanation
Indices: 3516512--3516600 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
3516502 TACTCTCACA
*
3516512 AGAA-GGTATCGTGAAAGGGTACTCATGGGAAGGTACTAT
1 AGAAGGGTACCGTGAAAGGGTACTCATGGGAAGGTACTAT
* * * * *
3516551 TGGAGGGTACCGTGGAAGGGTACTCGTGGGAGGGTA-TCAT
1 AGAAGGGTACCGTGAAAGGGTACTCATGGGAAGGTACT-AT
3516591 AGAAGGGTAC
1 AGAAGGGTAC
3516601 TTGCAAAAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.08
40 37 0.93
ACGTcount: A:0.28, C:0.11, G:0.39, T:0.21
Consensus pattern (40 bp):
AGAAGGGTACCGTGAAAGGGTACTCATGGGAAGGTACTAT
Found at i:3516656 original size:14 final size:14
Alignment explanation
Indices: 3516567--3516658 Score: 50
Period size: 14 Copynumber: 6.6 Consensus size: 14
3516557 GTACCGTGGA
**
3516567 AGGGTACTCGTGGG
1 AGGGTACTCGTAAG
*
3516581 AGGGTA-TCAT-AG
1 AGGGTACTCGTAAG
* * *
3516593 AAGGGTACTTGCAAA
1 -AGGGTACTCGTAAG
3516608 AGGGTACTCTCGTAAG
1 AGGGTA--CTCGTAAG
3516624 AGGGTAGCAT-G-AA-
1 AGGGTA-C-TCGTAAG
3516637 AGGGTACTCGTAAG
1 AGGGTACTCGTAAG
3516651 AGGGTACT
1 AGGGTACT
3516659 GTGTATTGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
11 1 0.02
12 3 0.05
13 17 0.29
14 23 0.39
15 3 0.05
16 12 0.20
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (14 bp):
AGGGTACTCGTAAG
Found at i:3517978 original size:56 final size:55
Alignment explanation
Indices: 3517882--3517988 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 55
3517872 CTTCTTTCGT
* *
3517882 GTCCACAACTCGTCTTTTCCCGCATCCACAACTCACCATCCCCTTGTCCGCCTGAC
1 GTCCACAACTCGCCTTTTCCCACATCCACAACTCACCAT-CCCTTGTCCGCCTGAC
* * ***
3517938 GTCCACAACTCGCCTTTTCCCACGTCCACGACTTGTCATCCCTTGTCCGCC
1 GTCCACAACTCGCCTTTTCCCACATCCACAACTCACCATCCCTTGTCCGCC
3517989 GGATGGCTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
55 12 0.27
56 32 0.73
ACGTcount: A:0.16, C:0.46, G:0.12, T:0.26
Consensus pattern (55 bp):
GTCCACAACTCGCCTTTTCCCACATCCACAACTCACCATCCCTTGTCCGCCTGAC
Found at i:3524355 original size:7 final size:8
Alignment explanation
Indices: 3524312--3524358 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
3524302 TTTAATATGA
3524312 TAAAATAAT
1 TAAAAT-AT
*
3524321 TTAAATA-
1 TAAAATAT
3524328 TAATAATAT
1 TAA-AATAT
3524337 TAAAATAT
1 TAAAATAT
3524345 TAAAA-AT
1 TAAAATAT
3524352 TAAAATA
1 TAAAATA
3524359 AATATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 9 0.27
8 16 0.48
9 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATAT
Found at i:3547611 original size:3 final size:3
Alignment explanation
Indices: 3547603--3547636 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
3547593 CTACTTCTTA
3547603 ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
3547637 TTAATACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3547625 original size:16 final size:16
Alignment explanation
Indices: 3547604--3547637 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3547594 TACTTCTTAA
3547604 TTATTATTATTATTAT
1 TTATTATTATTATTAT
3547620 TTATTATTATTATTAT
1 TTATTATTATTATTAT
3547636 TT
1 TT
3547638 TAATACTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:3551850 original size:3 final size:3
Alignment explanation
Indices: 3551842--3551886 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3551832 TTCATAAACA
3551842 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3551887 TAGAATAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3553342 original size:3 final size:3
Alignment explanation
Indices: 3553334--3553364 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3553324 ATTCAAGCTC
3553334 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3553365 TGCACGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3557588 original size:7 final size:7
Alignment explanation
Indices: 3557576--3557602 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3557566 ATTTGGGACT
3557576 ACAAAAA
1 ACAAAAA
3557583 ACAAAAA
1 ACAAAAA
3557590 ACAAAAA
1 ACAAAAA
3557597 ACAAAA
1 ACAAAA
3557603 CAAAAGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:3558706 original size:43 final size:43
Alignment explanation
Indices: 3558579--3558739 Score: 216
Period size: 43 Copynumber: 3.8 Consensus size: 43
3558569 GCGCCGCAAA
** ** * *
3558579 AAACGCCGCTAAAGGTCATGGTCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCGAC
* * *
3558622 AAACGTCACTAAAGACCATTACC-TTAGCGGCGCTTTTCCGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCGAC
*
3558664 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTATCCGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCGAC
*
3558707 AAACGCCGCTAAAGACCATGACCTTTAACGGCG
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCG
3558740 TTTGTAGCGG
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 37 0.36
43 66 0.64
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCGAC
Found at i:3562290 original size:43 final size:43
Alignment explanation
Indices: 3562243--3562325 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
3562233 CGCTTGCCAA
* * *
3562243 ACAAACGCCGCTAAAGACCCTGATCTTTAGCGGCATTTTTCCC
1 ACAAACGCCGCAAAAGACCCTGACCTTTAGCGACATTTTTCCC
*
3562286 ACAAACGCCGCAAAAGACCCTTACCTTTAGCGACATTTTT
1 ACAAACGCCGCAAAAGACCCTGACCTTTAGCGACATTTTT
3562326 TTAAAACGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.25
Consensus pattern (43 bp):
ACAAACGCCGCAAAAGACCCTGACCTTTAGCGACATTTTTCCC
Found at i:3562826 original size:66 final size:66
Alignment explanation
Indices: 3562666--3562828 Score: 202
Period size: 66 Copynumber: 2.5 Consensus size: 66
3562656 CGCTGCTCTA
* * * * *
3562666 CTTCCCTCGCTGCAGCCTCTGCTTTAAGCTGCAGCTGGAGTTCTTCATACTTTCATTGAACCTCA
1 CTTCTCTCGCTGCTGCCTCTGCTTTAAGTTGCAGCTAGAGTTCTTCATACTTTCATTGAACATCA
3562731 G
66 G
* * ** *
3562732 CTTCTCTCGCTGCTGCATATGCTTTAAGTTTTAGCTAGAGTTCTTCATATCTTT-TTTGAACATC
1 CTTCTCTCGCTGCTGCCTCTGCTTTAAGTTGCAGCTAGAGTTCTTCATA-CTTTCATTGAACATC
3562796 AG
65 AG
* *
3562798 CTTCTCTCGATGCTGCCTCCGCTTTAAGTTG
1 CTTCTCTCGCTGCTGCCTCTGCTTTAAGTTG
3562829 TGTAATTTGC
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
66 77 0.95
67 4 0.05
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (66 bp):
CTTCTCTCGCTGCTGCCTCTGCTTTAAGTTGCAGCTAGAGTTCTTCATACTTTCATTGAACATCA
G
Found at i:3568159 original size:9 final size:9
Alignment explanation
Indices: 3568142--3568429 Score: 103
Period size: 9 Copynumber: 33.7 Consensus size: 9
3568132 AATTTATGTA
*
3568142 TTATATAAG
1 TTATGTAAG
3568151 TTATGTAAG
1 TTATGTAAG
*
3568160 TTACGT-A-
1 TTATGTAAG
3568167 TTATGTAAG
1 TTATGTAAG
*
3568176 CTATGTAAG
1 TTATGTAAG
**
3568185 -T-TGTATT
1 TTATGTAAG
*
3568192 TTATGTTAG
1 TTATGTAAG
* *
3568201 CTAT-TTA-
1 TTATGTAAG
3568208 TTATGTAAG
1 TTATGTAAG
*
3568217 TTGTGT-A-
1 TTATGTAAG
3568224 TTATGTAAG
1 TTATGTAAG
*
3568233 CTATGT-A-
1 TTATGTAAG
*
3568240 TTATGTTAG
1 TTATGTAAG
**
3568249 TTATGTCTG
1 TTATGTAAG
3568258 TTATGT-A-
1 TTATGTAAG
*
3568265 TTATGTATG
1 TTATGTAAG
*
3568274 TCATGTAAG
1 TTATGTAAG
*
3568283 TTGTGT-AG
1 TTATGTAAG
*
3568291 -AATGTAAG
1 TTATGTAAG
*
3568299 CTATGTAAG
1 TTATGTAAG
*
3568308 TTATGTGAG
1 TTATGTAAG
*
3568317 TTATATATAAG
1 -T-TATGTAAG
* *
3568328 TTATCTTAATAA
1 TTAT-GT-A-AG
*
3568340 TTATATAAG
1 TTATGTAAG
*
3568349 CTATGT-A-
1 TTATGTAAG
*
3568356 TTATGTTAG
1 TTATGTAAG
**
3568365 TTATGCCAG
1 TTATGTAAG
3568374 TTATGT-A-
1 TTATGTAAG
*
3568381 TTATGTATG
1 TTATGTAAG
*
3568390 TTTTGTAAG
1 TTATGTAAG
*
3568399 TTGTGT-AG
1 TTATGTAAG
*
3568407 -AATGTAAG
1 TTATGTAAG
*
3568415 CTATGTAAG
1 TTATGTAAG
3568424 TTATGT
1 TTATGT
3568430 TAGAAATTTT
Statistics
Matches: 205, Mismatches: 49, Indels: 50
0.67 0.16 0.16
Matches are distributed among these distances:
7 45 0.22
8 24 0.12
9 119 0.58
10 4 0.02
11 8 0.04
12 5 0.02
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3568214 original size:32 final size:32
Alignment explanation
Indices: 3568177--3568324 Score: 111
Period size: 32 Copynumber: 4.5 Consensus size: 32
3568167 TTATGTAAGC
* * *
3568177 TATGTAAGTTGTATTTTATGTTAGCTATTTAT
1 TATGTAAGTTGTATATTATGTAAGCTATGTAT
*
3568209 TATGTAAGTTGTGTATTATGTAAGCTATGTAT
1 TATGTAAGTTGTATATTATGTAAGCTATGTAT
* * * *
3568241 TATGTTAGTTATGTCTGTTATGT-A-TTATGTAT
1 TATGTAAG-T-TGTATATTATGTAAGCTATGTAT
* **
3568273 GTCATGTAAGTTGTGTAGAATGTAAGCTATGTAAGT
1 -T-ATGTAAGTTGTATATTATGTAAGCTATGT-A-T
* *
3568309 TATGTGAGTTATATAT
1 TATGTAAGTTGTATAT
3568325 AAGTTATCTT
Statistics
Matches: 90, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
32 50 0.56
33 5 0.06
34 32 0.36
35 2 0.02
36 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.49
Consensus pattern (32 bp):
TATGTAAGTTGTATATTATGTAAGCTATGTAT
Found at i:3568252 original size:25 final size:25
Alignment explanation
Indices: 3568135--3568313 Score: 116
Period size: 25 Copynumber: 7.2 Consensus size: 25
3568125 GCCTGGAAAT
* *
3568135 TTATGTATTATATAAGTTATGTAAG
1 TTATGTATTATGTTAGTTATGTAAG
* * *
3568160 TTACGTATTATGTAAGCTATGTAAG
1 TTATGTATTATGTTAGTTATGTAAG
* * * * *
3568185 TTGTATTTTATGTTAGCTAT-TTA-
1 TTATGTATTATGTTAGTTATGTAAG
*
3568208 TTATGTAAGT-TGTGTA-TTATGTAAG
1 TTATGT-ATTATGT-TAGTTATGTAAG
* **
3568233 CTATGTATTATGTTAGTTATGTCTG
1 TTATGTATTATGTTAGTTATGTAAG
*
3568258 TTATGTATTATG-TATGTCATGTAAG
1 TTATGTATTATGTTA-GTTATGTAAG
* ** * *
3568283 TTGTGTAGAATGTAAGCTATGTAAG
1 TTATGTATTATGTTAGTTATGTAAG
3568308 TTATGT
1 TTATGT
3568314 GAGTTATATA
Statistics
Matches: 116, Mismatches: 30, Indels: 16
0.72 0.19 0.10
Matches are distributed among these distances:
23 10 0.09
24 13 0.11
25 92 0.79
26 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (25 bp):
TTATGTATTATGTTAGTTATGTAAG
Found at i:3568254 original size:16 final size:16
Alignment explanation
Indices: 3568151--3568245 Score: 78
Period size: 16 Copynumber: 6.4 Consensus size: 16
3568141 ATTATATAAG
* *
3568151 TTATGTAAGTTACGTA
1 TTATGTAAGCTATGTA
3568167 TTATGTAAGCTATGTA
1 TTATGTAAGCTATGTA
*
3568183 --A-GT-TG-TAT-T-
1 TTATGTAAGCTATGTA
* *
3568192 TTATGTTAGCTATTTA
1 TTATGTAAGCTATGTA
* *
3568208 TTATGTAAGTTGTGTA
1 TTATGTAAGCTATGTA
3568224 TTATGTAAGCTATGTA
1 TTATGTAAGCTATGTA
3568240 TTATGT
1 TTATGT
3568246 TAGTTATGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
10 1 0.02
11 4 0.06
12 3 0.05
13 3 0.05
14 4 0.06
15 1 0.02
16 46 0.74
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.49
Consensus pattern (16 bp):
TTATGTAAGCTATGTA
Found at i:3568400 original size:25 final size:25
Alignment explanation
Indices: 3568340--3568429 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 25
3568330 ATCTTAATAA
* *
3568340 TTATATAAGCTATGTATTATGT-TAG
1 TTATGTAAGTTATGTATTATGTAT-G
**
3568365 TTATGCCAGTTATGTATTATGTATG
1 TTATGTAAGTTATGTATTATGTATG
* * ** *
3568390 TTTTGTAAGTTGTGTAGAATGTAAG
1 TTATGTAAGTTATGTATTATGTATG
*
3568415 CTATGTAAGTTATGT
1 TTATGTAAGTTATGT
3568430 TAGAAATTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTATG
Found at i:3568466 original size:20 final size:20
Alignment explanation
Indices: 3568438--3568548 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
3568428 GTTAGAAATT
*
3568438 TTATATTAATATTATATAAG
1 TTATCTTAATATTATATAAG
3568458 TTATCTTAATAATTATATAAG
1 TTATCTTAAT-ATTATATAAG
* *
3568479 TTAT-GT-A-ATTAGA-AA-
1 TTATCTTAATATTATATAAG
* * *
3568494 TTTTCATAATACTATATAAG
1 TTATCTTAATATTATATAAG
*
3568514 TAATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
3568534 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
3568549 GTAATTAGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
15 3 0.04
16 3 0.04
17 6 0.08
18 4 0.06
19 3 0.04
20 39 0.54
21 14 0.19
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:3568544 original size:56 final size:58
Alignment explanation
Indices: 3568429--3568537 Score: 170
Period size: 56 Copynumber: 1.9 Consensus size: 58
3568419 GTAAGTTATG
* * *
3568429 TTAGAAATTTTATATTAATATTATATAAGTTATCTTAATAATTATATAAGTTATGTAA
1 TTAGAAATTTTACATTAATACTATATAAGTAATCTTAATAATTATATAAGTTATGTAA
3568487 TTAGAAATTTT-CA-TAATACTATATAAGTAATCTTAAT-ATTATATAAGTTAT
1 TTAGAAATTTTACATTAATACTATATAAGTAATCTTAATAATTATATAAGTTAT
3568538 CTTAATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
55 14 0.29
56 22 0.46
57 1 0.02
58 11 0.23
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (58 bp):
TTAGAAATTTTACATTAATACTATATAAGTAATCTTAATAATTATATAAGTTATGTAA
Found at i:3568561 original size:66 final size:65
Alignment explanation
Indices: 3568479--3568669 Score: 199
Period size: 66 Copynumber: 2.9 Consensus size: 65
3568469 ATTATATAAG
*
3568479 TTATGTAATTAGAAATT-T-TCATAATACTATATAA-GTAATCTTAATATTATATAAGTTATCTT
1 TTATGTAATTAGAAATTATGT-ATAAT--TAGA-AATGTAATCTTAATATTATATAAGTTATCTT
3568541 AATT
62 AATT
* ** * *
3568545 TTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAT
1 TTATGTAATTAGAAATT-ATGTATAATTAGAAATGTAATCTTAATATTATATAAGTTATCTTAAT
3568610 T
65 T
* ** * * *
3568611 TTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATCTTAATATTATAAAAGTTAT
1 TTATGTAATTAGAAATT-ATGTATAATTAGAAATGTAATCTTAATATTATATAAGTTAT
3568670 GAAGTGTCCT
Statistics
Matches: 114, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
65 2 0.02
66 108 0.95
68 3 0.03
69 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.47
Consensus pattern (65 bp):
TTATGTAATTAGAAATTATGTATAATTAGAAATGTAATCTTAATATTATATAAGTTATCTTAATT
Found at i:3571447 original size:15 final size:15
Alignment explanation
Indices: 3571420--3571484 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
3571410 ACCCTTGACA
3571420 CCCTAAA-CACTAAAT
1 CCCTAAATC-CTAAAT
* *
3571435 CCCTAACTCCT-AAC
1 CCCTAAATCCTAAAT
*
3571449 CCCTAAATCCCAAA-
1 CCCTAAATCCTAAAT
*
3571463 CCCCAAATCCCTAAAT
1 CCCTAAAT-CCTAAAT
3571479 CCCTAA
1 CCCTAA
3571485 CACCTAACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
14 18 0.46
15 15 0.38
16 6 0.15
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.18
Consensus pattern (15 bp):
CCCTAAATCCTAAAT
Found at i:3571454 original size:22 final size:22
Alignment explanation
Indices: 3571429--3571499 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
3571419 ACCCTAAACA
*
3571429 CTAAATCCCTAACTCCTAACCC
1 CTAAATCCCTAACACCTAACCC
* * * *
3571451 CTAAATCCCAAACCCCAAATCC
1 CTAAATCCCTAACACCTAACCC
3571473 CTAAATCCCTAACACCTAACCC
1 CTAAATCCCTAACACCTAACCC
*
3571495 TTAAA
1 CTAAA
3571500 CCAATAAACC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (22 bp):
CTAAATCCCTAACACCTAACCC
Found at i:3572068 original size:41 final size:41
Alignment explanation
Indices: 3572004--3572159 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
3571994 AAATGTTTTT
* *
3572004 GCGGCGTTTCTTCAAAAGCGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* *
3572045 GCGGTGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
*
3572086 GCGGCGCTTCGTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
*
3572127 GTGGCGCTTCTTCAAAAACGCCAG-TAAAGGCCC
1 GCGGCGCTTCTTCAAAAACGCC-GCTAAAGGCCC
3572160 CCAAAACTCA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
41 104 0.99
42 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
Found at i:3572243 original size:39 final size:38
Alignment explanation
Indices: 3572195--3572269 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
3572185 GGGCTTAGGC
3572195 TTTTTGCGGCGCTTTCCAAAAAACGCCGCTAATGCTTA
1 TTTTTGCGGCGCTTTCCAAAAAACGCCGCTAATGCTTA
* * * *
3572233 TTTTTAGCGGCGTTTTCCAACAATCGCTGCTAATGCT
1 TTTTT-GCGGCGCTTTCCAAAAAACGCCGCTAATGCT
3572270 CAACCTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (38 bp):
TTTTTGCGGCGCTTTCCAAAAAACGCCGCTAATGCTTA
Found at i:3572660 original size:22 final size:22
Alignment explanation
Indices: 3572635--3572676 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3572625 TATATTCATC
3572635 TCACAAAAGAATTTGAAAATGA
1 TCACAAAAGAATTTGAAAATGA
* **
3572657 TCACCAAAGTTTTTGAAAAT
1 TCACAAAAGAATTTGAAAAT
3572677 AAATTATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (22 bp):
TCACAAAAGAATTTGAAAATGA
Found at i:3573579 original size:23 final size:22
Alignment explanation
Indices: 3573539--3573581 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3573529 TATAAGCATA
* *
3573539 TTGTTTAGCCAATGGAGTTGGT
1 TTGTTTACCCAATCGAGTTGGT
3573561 TTGTTTGACCCAATCGAGTTG
1 TTGTTT-ACCCAATCGAGTTG
3573582 TATTTGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.40
Consensus pattern (22 bp):
TTGTTTACCCAATCGAGTTGGT
Found at i:3577335 original size:20 final size:19
Alignment explanation
Indices: 3577289--3577335 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
3577279 TTTAAAGAAG
3577289 TTTGAATTTTTATAAATAT
1 TTTGAATTTTTATAAATAT
*
3577308 TTTAAATTTTTA-AAATTTAT
1 TTTGAATTTTTATAAA--TAT
3577328 TTTGAATT
1 TTTGAATT
3577336 ATTTTGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 11 0.46
20 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTGAATTTTTATAAATAT
Found at i:3581159 original size:18 final size:18
Alignment explanation
Indices: 3581128--3581178 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3581118 TAAATGATAT
*
3581128 TTTTATTAAATAATAATG
1 TTTTATTAAATAATAATA
* *
3581146 TTTTAATAAGTAATAATA
1 TTTTATTAAATAATAATA
*
3581164 TTTTATTAATTAATA
1 TTTTATTAAATAATA
3581179 TTATAACACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTTATTAAATAATAATA
Found at i:3586566 original size:38 final size:38
Alignment explanation
Indices: 3586507--3586611 Score: 156
Period size: 38 Copynumber: 2.8 Consensus size: 38
3586497 AATTGGTACG
* **
3586507 TAAAGTGCATCTTGACGCACAAAGCGCATACTGGCACA
1 TAAAGTACATCTTGAAACACAAAGCGCATACTGGCACA
*
3586545 TGAAGTACATCTTGAAACACAAAGCGCATACTGGCACA
1 TAAAGTACATCTTGAAACACAAAGCGCATACTGGCACA
* *
3586583 TAAATTACATCTTGAAACACAAAGTGCAT
1 TAAAGTACATCTTGAAACACAAAGCGCAT
3586612 CTTAACACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (38 bp):
TAAAGTACATCTTGAAACACAAAGCGCATACTGGCACA
Found at i:3586614 original size:19 final size:19
Alignment explanation
Indices: 3586547--3586631 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 19
3586537 CTGGCACATG
*
3586547 AAGTACATCTTGAAACACA
1 AAGTGCATCTTGAAACACA
* ** *
3586566 AAGCGCATAC-TGGCACATA
1 AAGTGCAT-CTTGAAACACA
* *
3586585 AATTACATCTTGAAACACA
1 AAGTGCATCTTGAAACACA
3586604 AAGTGCATCTT--AACACA
1 AAGTGCATCTTGAAACACA
3586621 AAGTGCATCTT
1 AAGTGCATCTT
3586632 AGCGCATGAA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
17 17 0.33
18 1 0.02
19 32 0.63
20 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (19 bp):
AAGTGCATCTTGAAACACA
Found at i:3586620 original size:17 final size:17
Alignment explanation
Indices: 3586598--3586632 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3586588 TACATCTTGA
3586598 AACACAAAGTGCATCTT
1 AACACAAAGTGCATCTT
3586615 AACACAAAGTGCATCTT
1 AACACAAAGTGCATCTT
3586632 A
1 A
3586633 GCGCATGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (17 bp):
AACACAAAGTGCATCTT
Found at i:3586701 original size:58 final size:57
Alignment explanation
Indices: 3586616--3586763 Score: 170
Period size: 58 Copynumber: 2.6 Consensus size: 57
3586606 GTGCATCTTA
* * * * * * *
3586616 ACACAAAGTGCATCTTAGCGCATGAAGCGCATATCTGGCACATGAACTGTATCTTAAC
1 ACACAAAGTGCATCTTGGAGCA-GAAGCGCATATATGGCAAACGAACTGCATCCTAAC
* *
3586674 ACACAAAGTGCATCTTGGAGCACGAAGCGCATATATGGCAAACGAAGTGCATCCTAGC
1 ACACAAAGTGCATCTTGGAGCA-GAAGCGCATATATGGCAAACGAACTGCATCCTAAC
* * *
3586732 ACACGAGGTGCATCTTGGAGCATAAGCGCATA
1 ACACAAAGTGCATCTTGGAGCAGAAGCGCATA
3586764 ATCCCATACA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 9 0.12
58 68 0.88
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (57 bp):
ACACAAAGTGCATCTTGGAGCAGAAGCGCATATATGGCAAACGAACTGCATCCTAAC
Found at i:3588158 original size:11 final size:11
Alignment explanation
Indices: 3588114--3588173 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
3588104 CTAAAAAATT
3588114 AAATTAAATTAA
1 AAATT-AATTAA
*
3588126 AAATCAA-TAA
1 AAATTAATTAA
**
3588136 AAATATTTTTAA
1 AAAT-TAATTAA
3588148 AAATTAATTAA
1 AAATTAATTAA
3588159 AAATTAA--AA
1 AAATTAATTAA
3588168 AAATTA
1 AAATTA
3588174 TAAACTAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 8 0.20
10 7 0.17
11 14 0.35
12 11 0.28
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATTAATTAA
Found at i:3589217 original size:17 final size:17
Alignment explanation
Indices: 3589177--3589227 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
3589167 TGGTGAAGGT
* *
3589177 ATGAAGAGAAGATTAAAA
1 ATGAAAAGAA-ATAAAAA
*
3589195 AGGAAAAGAAATAAAAA
1 ATGAAAAGAAATAAAAA
3589212 ATGAAAAGAAA-AAAAA
1 ATGAAAAGAAATAAAAA
3589228 TTAACGAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 5 0.17
17 16 0.55
18 8 0.28
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (17 bp):
ATGAAAAGAAATAAAAA
Found at i:3589335 original size:21 final size:22
Alignment explanation
Indices: 3589301--3589349 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3589291 AGTTTATAAT
3589301 TTTTTATTTAATTT-TAAAAATA
1 TTTTTATTTAATTTAT-AAAATA
* *
3589323 TTTTTA-TTGATTTATAATATA
1 TTTTTATTTAATTTATAAAATA
3589344 TTTTTA
1 TTTTTA
3589350 GATTATGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTTATTTAATTTATAAAATA
Found at i:3590726 original size:30 final size:31
Alignment explanation
Indices: 3590672--3590739 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
3590662 TAGCTTAAAT
* *
3590672 TTTTAT-AATTTTAAAAGGATTAAATCAAAA
1 TTTTATCATTTTTAAAAGGACTAAATCAAAA
* *
3590702 TTTTATCATTTTTAAAAGG-CTAAATTATAA
1 TTTTATCATTTTTAAAAGGACTAAATCAAAA
3590732 -TTTATCAT
1 TTTTATCAT
3590740 ATACTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.24
30 14 0.42
31 11 0.33
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (31 bp):
TTTTATCATTTTTAAAAGGACTAAATCAAAA
Found at i:3591134 original size:17 final size:17
Alignment explanation
Indices: 3591107--3591146 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
3591097 TGACTTTTTG
3591107 AGAGAAGAGATGAAAGAA
1 AGAG-AGAGATGAAAGAA
3591125 AGAGAGAGATGAAAGAA
1 AGAGAGAGATGAAAGAA
3591142 AGAGA
1 AGAGA
3591147 TGGTCTCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.05
Consensus pattern (17 bp):
AGAGAGAGATGAAAGAA
Found at i:3592437 original size:216 final size:215
Alignment explanation
Indices: 3592058--3592495 Score: 858
Period size: 216 Copynumber: 2.0 Consensus size: 215
3592048 AACATTTTAA
3592058 TTGTTTAATTTAATTTTTAGGCCTTAGGAATATTACATGTTAAATTCGGCCCAAACAGCCCATTT
1 TTGTTTAATTTAATTTTTAGGCCTTAGGAATATTACATGTTAAATTCGGCCCAAACAGCCCATTT
3592123 GAGTGCATGGCCGAATTTTCCCTTTATTTTTATTAATTAGGTTTAATTTTTTAAGTTTACTACTG
66 GAGTGCATGGCCGAATTTTCCCTTTATTTTTATTAATTAGGTTTAATTTTTTAAGTTTACTACTG
3592188 AGATTAGGATTAGTTTGAGGCCTATATAAGTGATGACCGGCCACCCCTTGTACACACACTTAGAA
131 AGATTAGGATTAGTTTGAGGCCTATATAAGTGATGACCGGCCACCCCTTGTACACACACTTAGAA
3592253 TTTTTATCAAAGTTTCAGAT
196 TTTTTATCAAAGTTTCAGAT
3592273 TTGTTGTAATTTAATTTTTAGGCCTTAGGAATATTACATGTTAAATTCGGCCCAAACAGCCCATT
1 TTGTT-TAATTTAATTTTTAGGCCTTAGGAATATTACATGTTAAATTCGGCCCAAACAGCCCATT
3592338 TGAGTGCATGGCCGAATTTTCCCTTTATTTTTATTAATTAGGTTTAATTTTTTAAGTTTACTACT
65 TGAGTGCATGGCCGAATTTTCCCTTTATTTTTATTAATTAGGTTTAATTTTTTAAGTTTACTACT
*
3592403 GAGATTAGGATTAGTTTGAGGCCTATATAAGTGATGGCCGGCCACCCCTTGTACACACACTTAGA
130 GAGATTAGGATTAGTTTGAGGCCTATATAAGTGATGACCGGCCACCCCTTGTACACACACTTAGA
3592468 ATTTTTATCAAAGTTTCAGAT
195 ATTTTTATCAAAGTTTCAGAT
3592489 TTGTTTA
1 TTGTTTA
3592496 GAGCAGAATT
Statistics
Matches: 221, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
215 7 0.03
216 214 0.97
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (215 bp):
TTGTTTAATTTAATTTTTAGGCCTTAGGAATATTACATGTTAAATTCGGCCCAAACAGCCCATTT
GAGTGCATGGCCGAATTTTCCCTTTATTTTTATTAATTAGGTTTAATTTTTTAAGTTTACTACTG
AGATTAGGATTAGTTTGAGGCCTATATAAGTGATGACCGGCCACCCCTTGTACACACACTTAGAA
TTTTTATCAAAGTTTCAGAT
Found at i:3593682 original size:20 final size:20
Alignment explanation
Indices: 3593654--3593708 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
3593644 AAAAACTACC
**
3593654 AAAATAATTCAAAATAAATTT
1 AAAA-AATTCAAAATAAATAG
* *
3593675 CAAAAATTCAAAATATATAG
1 AAAAAATTCAAAATAAATAG
3593695 AAAAAATTCAAAAT
1 AAAAAATTCAAAAT
3593709 TTATATTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAAATTCAAAATAAATAG
Found at i:3593713 original size:20 final size:20
Alignment explanation
Indices: 3593676--3593713 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3593666 AATAAATTTC
3593676 AAAAATTCAAAATATATAGA
1 AAAAATTCAAAATATATAGA
*
3593696 AAAAATTCAAAATTTATA
1 AAAAATTCAAAATATATA
3593714 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATTCAAAATATATAGA
Found at i:3598940 original size:16 final size:16
Alignment explanation
Indices: 3598919--3598951 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3598909 TTAAATATTT
3598919 TTATTAGAAAA-ATAAA
1 TTATTA-AAAATATAAA
3598935 TTATTAAAAATATAAA
1 TTATTAAAAATATAAA
3598951 T
1 T
3598952 AAGGAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTATTAAAAATATAAA
Found at i:3602648 original size:101 final size:100
Alignment explanation
Indices: 3602533--3602752 Score: 266
Period size: 101 Copynumber: 2.2 Consensus size: 100
3602523 GCACGGATTG
* * *
3602533 TGTGTAGGCCACTATGTAAAAGTGAAAGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTATT
1 TGTGTAGGCTACTATGT-AAAG-GAAAGT-ATCGATCACGTGTGTAGTACTATGTGCAGGCTACT
*
3602597 ACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGTACTA
63 ACGTGTACCGG-ATGATAATGGTCACATGTGTAGTACTA
** * *
3602634 TGTGTAGGCTACTATGCGTACCGGATAGTTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGGCTACTAT--GTAAAGGAAAGTATCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
** *
3602699 CGTGTATTGGATGGTAATGGTCACATGTGTAGTACTA
64 CGTGTACCGGATGATAATGGTCACATGTGTAGTACTA
3602736 TGTGTAGGCTACTATGT
1 TGTGTAGGCTACTATGT
3602753 GAACTGAACA
Statistics
Matches: 103, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
100 7 0.07
101 59 0.57
102 35 0.34
103 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (100 bp):
TGTGTAGGCTACTATGTAAAGGAAAGTATCGATCACGTGTGTAGTACTATGTGCAGGCTACTACG
TGTACCGGATGATAATGGTCACATGTGTAGTACTA
Found at i:3602687 original size:51 final size:51
Alignment explanation
Indices: 3602563--3602749 Score: 209
Period size: 51 Copynumber: 3.7 Consensus size: 51
3602553 AGTGAAAGTG
* * *
3602563 ATGGTCACGTGTGTAGTACTATGTGCAGGCTATTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
3602612 ATAGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * ** *
3602663 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
*
3602715 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
3602750 TGTGAACTGA
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.34
51 71 0.63
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.33
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:3602811 original size:45 final size:45
Alignment explanation
Indices: 3602760--3602848 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
3602750 TGTGAACTGA
* *
3602760 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
3602805 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
3602849 AGTATCTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:3608411 original size:101 final size:100
Alignment explanation
Indices: 3608296--3608515 Score: 241
Period size: 101 Copynumber: 2.2 Consensus size: 100
3608286 GCACGGATTG
* *
3608296 TGTGTAGGCC-ACTATGTAAAAGTGAAAGTGAT-GGTCACGTGTGTAGTACTATGTGTAGGCTAC
1 TGTGTA-GCCTACTATGT-AAAG-GAAA-TGATCGATCACGTGTGTAGTACTATGTGCAGGCTAC
*
3608359 TACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGTACTA
62 TACGTGTACCGG-ATGATAATGGTCACATGTGTAGTACTA
** * **
3608397 TGTGTAGCCTACTATGCGTACCGGATATTTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGCCTACTAT--GTAAAGGAAATGATCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
* *
3608462 CGTGTATCGGATGGTAATGGTCACATGTGTAGTACTA
64 CGTGTACCGGATGATAATGGTCACATGTGTAGTACTA
* *
3608499 TGTGCAGGCTACTATGT
1 TGTGTAGCCTACTATGT
3608516 GAACCGAACA
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
100 11 0.11
101 55 0.54
102 33 0.33
103 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (100 bp):
TGTGTAGCCTACTATGTAAAGGAAATGATCGATCACGTGTGTAGTACTATGTGCAGGCTACTACG
TGTACCGGATGATAATGGTCACATGTGTAGTACTA
Found at i:3608460 original size:51 final size:50
Alignment explanation
Indices: 3608326--3608521 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 50
3608316 AGTGAAAGTG
* * *
3608326 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ATG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATATA
* * * * * *
3608375 ATAGGTCGCATGTGTAGTACTATGTGTAGCCTACTATGCGTACCGGATATT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATATA
* * * * *
3608426 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-ATA
* *
3608478 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
3608522 AACATCATTG
Statistics
Matches: 120, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 2 0.02
50 39 0.32
51 77 0.64
52 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATATA
Found at i:3608516 original size:26 final size:26
Alignment explanation
Indices: 3608436--3608516 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
3608426 TTCGATCACG
3608436 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
3608462 CGTGTA-T-CGGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
3608487 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
3608513 TGTG
1 TGTG
3608517 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:3608574 original size:45 final size:45
Alignment explanation
Indices: 3608523--3608609 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
3608513 TGTGAACCGA
* *
3608523 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACTGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
*
3608568 ACATCATTGATTAATAAGGTGGTTGTTATGTGCTGAATCCAC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
3608610 CGAGTATCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
Found at i:3611984 original size:24 final size:24
Alignment explanation
Indices: 3611957--3612008 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3611947 TTAGTAAGTC
*
3611957 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3611981 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3612005 AAAT
1 AAAT
3612009 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3612736 original size:20 final size:20
Alignment explanation
Indices: 3612702--3612743 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3612692 AACTATTTAA
** *
3612702 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
3612722 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
3612742 AT
1 AT
3612744 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:3620447 original size:16 final size:16
Alignment explanation
Indices: 3620408--3620447 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
3620398 ATAAAACACC
3620408 GACATAAA-CCTGCTA
1 GACATAAAGCCTGCTA
* *
3620423 GGCACAAAGCCTGCTA
1 GACATAAAGCCTGCTA
3620439 GACATAAAG
1 GACATAAAG
3620448 TCTGAAGTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (16 bp):
GACATAAAGCCTGCTA
Found at i:3620474 original size:41 final size:41
Alignment explanation
Indices: 3620429--3620538 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 41
3620419 GCTAGGCACA
**
3620429 AAGCCTGCTAGACATAAAGTCTGAAGTAATTCACCGGCATC
1 AAGCCTGCTAGACATAAAGTCTGAAACAATTCACCGGCATC
* * *
3620470 AAGCCTGCTAGACATTAAGTCTGAAACATTTCATCGGCATC
1 AAGCCTGCTAGACATAAAGTCTGAAACAATTCACCGGCATC
* * * *
3620511 AAGCTTCCTAGACGTAAAGTTTGAAACA
1 AAGCCTGCTAGACATAAAGTCTGAAACA
3620539 TCTTATTTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (41 bp):
AAGCCTGCTAGACATAAAGTCTGAAACAATTCACCGGCATC
Found at i:3621208 original size:16 final size:17
Alignment explanation
Indices: 3621187--3621221 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3621177 ATCTAATAAT
3621187 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
3621203 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
3621220 TT
1 TT
3621222 CAACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:3633666 original size:20 final size:19
Alignment explanation
Indices: 3633643--3633696 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
3633633 TATTTACTGT
3633643 AAAATAAATTTAAAAAATGG
1 AAAAT-AATTTAAAAAATGG
** *
3633663 AAAATTTTTTAAAAAATGT
1 AAAATAATTTAAAAAATGG
3633682 AAAAT--TTTAAAAAAT
1 AAAATAATTTAAAAAAT
3633697 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.32
19 16 0.52
20 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AAAATAATTTAAAAAATGG
Found at i:3633675 original size:19 final size:18
Alignment explanation
Indices: 3633651--3633712 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
3633641 GTAAAATAAA
3633651 TTTAAAAAATGGAAAATTT
1 TTTAAAAAAT-GAAAATTT
3633670 TTTAAAAAATGTAAAA--T
1 TTTAAAAAATG-AAAATTT
*
3633687 TTTAAAAAAT--ATATTT
1 TTTAAAAAATGAAAATTT
3633703 TTTAAAAAAT
1 TTTAAAAAAT
3633713 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
14 2 0.05
16 11 0.28
17 11 0.28
18 1 0.03
19 14 0.36
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
TTTAAAAAATGAAAATTT
Found at i:3634366 original size:13 final size:14
Alignment explanation
Indices: 3634340--3634371 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3634330 CTTTAACACA
3634340 AAAAATAATAAATT
1 AAAAATAATAAATT
3634354 AAAAATAAT-AATT
1 AAAAATAATAAATT
3634367 AAAAA
1 AAAAA
3634372 ATGACATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATAATAAATT
Found at i:3634372 original size:14 final size:15
Alignment explanation
Indices: 3634339--3634373 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
3634329 GCTTTAACAC
3634339 AAAAAATAATAAATT
1 AAAAAATAATAAATT
3634354 -AAAAATAAT-AATT
1 AAAAAATAATAAATT
3634367 AAAAAAT
1 AAAAAAT
3634374 GACATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAATAATAAATT
Found at i:3634618 original size:2 final size:2
Alignment explanation
Indices: 3634613--3634641 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3634603 AACACTATTG
3634613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3634642 AAATAAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3641322 original size:18 final size:19
Alignment explanation
Indices: 3641299--3641337 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3641289 GTGCGAGAGC
*
3641299 AAATGAATAAG-AAAAGAA
1 AAATGAAAAAGAAAAAGAA
3641317 AAATGAAAAAGAAAAAGAA
1 AAATGAAAAAGAAAAAGAA
3641336 AA
1 AA
3641338 GAGTTCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAATGAAAAAGAAAAAGAA
Found at i:3641374 original size:26 final size:27
Alignment explanation
Indices: 3641322--3641389 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
3641312 AAGAAAAATG
3641322 AAAA-AGA-AAAAGAAAAGAGTTCAGAAA
1 AAAAGAGAGAAAAG-AAAGAGTT-AGAAA
*
3641349 AAAAGAGAGGAAAGAAAGAGTT-GAAA
1 AAAAGAGAGAAAAGAAAGAGTTAGAAA
* *
3641375 ACAAGTGAGAAAAGA
1 AAAAGAGAGAAAAGA
3641390 GAAAACGAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 16 0.46
27 4 0.11
28 11 0.31
29 4 0.11
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (27 bp):
AAAAGAGAGAAAAGAAAGAGTTAGAAA
Found at i:3657736 original size:21 final size:21
Alignment explanation
Indices: 3657697--3657736 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3657687 AAATGACGTA
* * *
3657697 GTTTTGCCTTTTAACTTAATG
1 GTTTTGACTTTGAAATTAATG
3657718 GTTTTGACTTTGAAATTAA
1 GTTTTGACTTTGAAATTAA
3657737 GAAAAGGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (21 bp):
GTTTTGACTTTGAAATTAATG
Found at i:3660477 original size:30 final size:29
Alignment explanation
Indices: 3660430--3660490 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
3660420 ATTTTGGCCA
*
3660430 TCACACAGGCCTATCCACACGGTCGTGTG
1 TCACACAGGCCTATCCACACGGTCGCGTG
* *
3660459 TCACACACGGCTTATCCACATGGTCGCGTG
1 TCACACA-GGCCTATCCACACGGTCGCGTG
3660489 TC
1 TC
3660491 TTAATGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (29 bp):
TCACACAGGCCTATCCACACGGTCGCGTG
Found at i:3663655 original size:47 final size:47
Alignment explanation
Indices: 3663586--3663677 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
3663576 TATCACGTTT
*
3663586 AAGACACATTAAACATGCTTAAGACACATCTAAAAGGTGTAATAACA
1 AAGACACATTAAACATGCTTAAGACACATCTAAAAGATGTAATAACA
* * *
3663633 AAGACACATTAAACCTGCTTAAGACACATTTAAAATATGTAATAA
1 AAGACACATTAAACATGCTTAAGACACATCTAAAAGATGTAATAA
3663678 ACTAGGACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (47 bp):
AAGACACATTAAACATGCTTAAGACACATCTAAAAGATGTAATAACA
Found at i:3668605 original size:38 final size:38
Alignment explanation
Indices: 3668529--3668665 Score: 102
Period size: 38 Copynumber: 3.7 Consensus size: 38
3668519 AATATTGTCG
* **
3668529 GATTCACCGACTAGTGCT-GG-ACACATATATTTGGCA
1 GATTCACCGACCAGTGCTGGGCACACATATATCCGGCA
* * *
3668565 GATTCACTGACCAGTGCTGGGCACACCTATATCCGTCA
1 GATTCACCGACCAGTGCTGGGCACACATATATCCGGCA
** * * * *
3668603 GATAAACCGACCAATGCTGGGCAAACATACTATTC-TCA
1 GATTCACCGACCAGTGCTGGGCACACATA-TATCCGGCA
* *
3668641 -ATTTTACCGACCAGTGCAGGGCACA
1 GA-TTCACCGACCAGTGCTGGGCACA
3668666 TATACTTATC
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
36 16 0.20
37 3 0.04
38 56 0.71
39 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (38 bp):
GATTCACCGACCAGTGCTGGGCACACATATATCCGGCA
Found at i:3668671 original size:38 final size:36
Alignment explanation
Indices: 3668608--3668692 Score: 89
Period size: 38 Copynumber: 2.3 Consensus size: 36
3668598 CGTCAGATAA
* * * *
3668608 ACCGACCAATGCTGGGCAAACATACTATTCTCAATTTT
1 ACCGACCAGTGCAGGGCAAACATAC--TTATCAATTCT
* * *
3668646 ACCGACCAGTGCAGGGCACATATACTTATCGATTCT
1 ACCGACCAGTGCAGGGCAAACATACTTATCAATTCT
3668682 ACCGACCAGTG
1 ACCGACCAGTG
3668693 TTGGGCGCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 19 0.47
38 21 0.52
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (36 bp):
ACCGACCAGTGCAGGGCAAACATACTTATCAATTCT
Found at i:3671681 original size:10 final size:9
Alignment explanation
Indices: 3671668--3671740 Score: 59
Period size: 8 Copynumber: 8.4 Consensus size: 9
3671658 TATGTTTTAA
3671668 ATATATTA-
1 ATATATTAT
3671676 ATATATTAT
1 ATATATTAT
*
3671685 -TTTATTAT
1 ATATATTAT
3671693 ATA-A-TAT
1 ATATATTAT
3671700 ATTATATTAT
1 A-TATATTAT
*
3671710 AT-TATAAT
1 ATATATTAT
3671718 AATTATATTAT
1 -A-TATATTAT
3671729 AT-TATTAT
1 ATATATTAT
3671737 ATAT
1 ATAT
3671741 TAAATAAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
7 4 0.08
8 31 0.60
9 6 0.12
10 6 0.12
11 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATATTAT
Found at i:3671727 original size:5 final size:5
Alignment explanation
Indices: 3671669--3671742 Score: 70
Period size: 5 Copynumber: 15.4 Consensus size: 5
3671659 ATGTTTTAAA
*
3671669 TATAT TA-A- TATAT TAT-T T-TAT TATAT AATATAT TATAT TATAT TATAA
1 TATAT TATAT TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT
3671717 TA-AT TATAT TATAT TAT-T ATATAT TA
1 TATAT TATAT TATAT TATAT -TATAT TA
3671743 AATAAACTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
3 3 0.05
4 10 0.17
5 39 0.67
6 1 0.02
7 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:3672367 original size:23 final size:24
Alignment explanation
Indices: 3672332--3672376 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3672322 AATATGACAA
3672332 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
3672355 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
3672377 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:3673017 original size:21 final size:23
Alignment explanation
Indices: 3672975--3673017 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3672965 TATTATTCCG
*
3672975 GGTGTGTTTAGGTTGGATATTCT
1 GGTGTGTTTAGGGTGGATATTCT
3672998 GGTGTGTTT-GGGTGGA-ATTC
1 GGTGTGTTTAGGGTGGATATTC
3673018 GCGTATCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.44
Consensus pattern (23 bp):
GGTGTGTTTAGGGTGGATATTCT
Found at i:3677197 original size:16 final size:16
Alignment explanation
Indices: 3677178--3677211 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3677168 GCAATTAAAA
*
3677178 TCATAAATTCATTCAT
1 TCATAAATTCAATCAT
*
3677194 TCATATATTCAATCAT
1 TCATAAATTCAATCAT
3677210 TC
1 TC
3677212 TAATCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
TCATAAATTCAATCAT
Found at i:3688148 original size:14 final size:15
Alignment explanation
Indices: 3688131--3688164 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3688121 AAAAGACTAT
*
3688131 AAATAAAA-TTATAA
1 AAATAAAATTTACAA
3688145 AAATAAAATTTACAA
1 AAATAAAATTTACAA
3688160 AAATA
1 AAATA
3688165 TGATAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAAATTTACAA
Found at i:3688820 original size:20 final size:20
Alignment explanation
Indices: 3688797--3688856 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 20
3688787 ATAAATTTTC
3688797 AAAAATCAAAATAATATATT
1 AAAAATCAAAATAATATATT
* * *
3688817 AAAAGTGAAAATTAT-TA-T
1 AAAAATCAAAATAATATATT
* *
3688835 AAAAATTAAAAAAATAT-TT
1 AAAAATCAAAATAATATATT
3688854 AAA
1 AAA
3688857 TTTCAAGTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 12 0.39
19 7 0.23
20 12 0.39
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAAATCAAAATAATATATT
Found at i:3688949 original size:24 final size:24
Alignment explanation
Indices: 3688900--3688951 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3688890 TTTAAATACC
* *
3688900 TTTTAAGAATTTTATAAATATATA
1 TTTTAAGAATTTTATAAAAAAATA
3688924 TTTT-AGAATTTTATAAAAAAATTA
1 TTTTAAGAATTTTATAAAAAAA-TA
3688948 TTTT
1 TTTT
3688952 TAAACTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTTAAGAATTTTATAAAAAAATA
Found at i:3688992 original size:28 final size:31
Alignment explanation
Indices: 3688943--3688999 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 31
3688933 TTTATAAAAA
*
3688943 AATTATTTTTAAACTCTCTTTTTAAAATTAC
1 AATTATTTTTAAACTATCTTTTTAAAATTAC
*
3688974 AATT-TTTTTAAA-TAT-TTTTTACAATT
1 AATTATTTTTAAACTATCTTTTTAAAATT
3689000 TTTTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
29 2 0.08
30 8 0.33
31 4 0.17
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (31 bp):
AATTATTTTTAAACTATCTTTTTAAAATTAC
Found at i:3696224 original size:153 final size:153
Alignment explanation
Indices: 3695946--3696252 Score: 569
Period size: 153 Copynumber: 2.0 Consensus size: 153
3695936 TCAAATCCTA
3695946 ATAGAATTTATCTTCCTTATTTATATTTATTCCCCTCATCTTCTTCATCTTTTCCTATGAAAATA
1 ATAGAATTTATCTTCCTTATTTATATTTATTCCCCTCATCTTCTTCATCTTTTCCTATGAAAATA
*
3696011 TTTTTTCTCAATTGTTGATAATTATTTTATTCTCGAATCAAAATCTGTTCTCGATTTCAACACGT
66 TTTTTTCTCAATTGTTGATAATTATTTTATTCTCGAATCAAAATCTATTCTCGATTTCAACACGT
3696076 TTCTCTATCAGTTGATTTTCGTC
131 TTCTCTATCAGTTGATTTTCGTC
*
3696099 ATAGAATTTATCTTCCTTATTTATATTTATTCCCCTCATCTTTTTCATCTTTTCCTATGAAAATA
1 ATAGAATTTATCTTCCTTATTTATATTTATTCCCCTCATCTTCTTCATCTTTTCCTATGAAAATA
*
3696164 TTTTTTCTCAATTGTTGATAATTATTTTATTCTCGAATCAAAATCTATTCTCGATTTCAACTCGT
66 TTTTTTCTCAATTGTTGATAATTATTTTATTCTCGAATCAAAATCTATTCTCGATTTCAACACGT
* *
3696229 TTCTCTATCGGTTGATTTTTGTC
131 TTCTCTATCAGTTGATTTTCGTC
3696252 A
1 A
3696253 ATGACATCCC
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 149 1.00
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (153 bp):
ATAGAATTTATCTTCCTTATTTATATTTATTCCCCTCATCTTCTTCATCTTTTCCTATGAAAATA
TTTTTTCTCAATTGTTGATAATTATTTTATTCTCGAATCAAAATCTATTCTCGATTTCAACACGT
TTCTCTATCAGTTGATTTTCGTC
Found at i:3718923 original size:27 final size:27
Alignment explanation
Indices: 3718892--3719069 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3718882 TAAATTGTAC
3718892 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3718919 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3718945 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3718973 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3719001 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3719028 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3719055 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3719070 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3719006 original size:82 final size:81
Alignment explanation
Indices: 3718893--3719048 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3718883 AAATTGTACA
* *
3718893 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3718957 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3718974 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3719039 TGCGAGTTGA
65 TGCGAATTGA
3719049 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3719060 original size:82 final size:81
Alignment explanation
Indices: 3718889--3719069 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3718879 GATTAAATTG
* *
3718889 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3718954 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3718970 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3719034 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3719052 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3719070 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3720993 original size:62 final size:63
Alignment explanation
Indices: 3720921--3721054 Score: 171
Period size: 62 Copynumber: 2.1 Consensus size: 63
3720911 ACACAGATGC
* * *
3720921 GTGTCTAGGCTGTGTAACTCACTATTTTGGATTTAGGGTC-CACAAGCTAGGGACATGGGCAT
1 GTGTCCAGGCTATGTAACTCACTATTTTGGATTTAGGGTCACACAAGCCAGGGACATGGGCAT
* * * * * *
3720983 TTGTCCAGGCTATGTTATTCACTGTTTTGGATTTAGGGTCACACAGGCCATGGACATGGGCAT
1 GTGTCCAGGCTATGTAACTCACTATTTTGGATTTAGGGTCACACAAGCCAGGGACATGGGCAT
*
3721046 GTGTTCAGG
1 GTGTCCAGG
3721055 TCGTGTGAGG
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
62 34 0.57
63 26 0.43
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (63 bp):
GTGTCCAGGCTATGTAACTCACTATTTTGGATTTAGGGTCACACAAGCCAGGGACATGGGCAT
Found at i:3724468 original size:19 final size:21
Alignment explanation
Indices: 3724446--3724490 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3724436 TTTGAACCCC
3724446 AAACC-TCAA-ATCAAACCAT
1 AAACCTTCAATATCAAACCAT
* *
3724465 AAACCTTGAATCTCAAACCAT
1 AAACCTTCAATATCAAACCAT
3724486 AAACC
1 AAACC
3724491 CTAAAACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 3 0.14
21 14 0.64
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (21 bp):
AAACCTTCAATATCAAACCAT
Found at i:3736302 original size:34 final size:34
Alignment explanation
Indices: 3736259--3736328 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
3736249 GTCTAAATTC
3736259 TTCTCAAAATCGTTAATAATTTCATACATTTTGT
1 TTCTCAAAATCGTTAATAATTTCATACATTTTGT
**
3736293 TTCTCAAAATCGTTAATAATTTTTTACATTTTGT
1 TTCTCAAAATCGTTAATAATTTCATACATTTTGT
3736327 TT
1 TT
3736329 ACTTTCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (34 bp):
TTCTCAAAATCGTTAATAATTTCATACATTTTGT
Found at i:3737280 original size:18 final size:17
Alignment explanation
Indices: 3737238--3737284 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3737228 TGTCGTTCGT
3737238 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
3737255 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
3737274 TTTC-AAACATT
1 TTTCAAAACATT
3737285 TTTTATTGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:3755517 original size:33 final size:33
Alignment explanation
Indices: 3755479--3755708 Score: 130
Period size: 33 Copynumber: 6.6 Consensus size: 33
3755469 ATGATACGTT
3755479 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * * *
3755512 GGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGG
1 GGAATCAGCACTTAGCAACCAC---CA-A--TGA-AT-CGG
* *
3755553 TGGGATCAACACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * * *
3755587 GGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGG
1 GGAATCAGCACTTAGCAACCAC---CA-A--TGA-AT-CGG
* * *
3755628 TGGGATCAACACTTAGCAACCACCAATGAATCAG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
*
3755662 GGAATCAGCACTTAGCAACC-CC-TTG-A---G
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
3755689 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
3755709 CCCTTTATAT
Statistics
Matches: 156, Mismatches: 23, Indels: 42
0.71 0.10 0.19
Matches are distributed among these distances:
27 21 0.13
30 1 0.01
31 2 0.01
32 2 0.01
33 55 0.35
34 5 0.03
35 4 0.03
36 8 0.05
37 2 0.01
38 2 0.01
39 8 0.05
40 4 0.03
41 6 0.04
42 36 0.23
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:3755577 original size:75 final size:75
Alignment explanation
Indices: 3755430--3755685 Score: 404
Period size: 75 Copynumber: 3.4 Consensus size: 75
3755420 GTTATCCGTT
* * * * * * *
3755430 ATCGGTGGATTCAACACTTAGTAACCCCTTTCACATTCAATGATACGTTGGAATCAGCACTTAGC
1 ATCGG-GGAATCATCACTTAGAAACCCCTTTCACATTTAA-GATACGGTGGGATCAACACTTAGC
3755495 AACCACCAATGA
64 AACCACCAATGA
3755507 ATCGGGGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAA
1 ATCGGGGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAA
3755572 CCACCAATGA
66 CCACCAATGA
3755582 ATCGGGGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAA
1 ATCGGGGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAA
3755647 CCACCAATGA
66 CCACCAATGA
* * *
3755657 ATCAGGGAATCAGCACTTAGCAACCCCTT
1 ATCGGGGAATCATCACTTAGAAACCCCTT
3755686 GAGGGAATCA
Statistics
Matches: 169, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
75 134 0.79
76 30 0.18
77 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (75 bp):
ATCGGGGAATCATCACTTAGAAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAA
CCACCAATGA
Found at i:3755814 original size:51 final size:51
Alignment explanation
Indices: 3755728--3755928 Score: 221
Period size: 51 Copynumber: 4.0 Consensus size: 51
3755718 TTTAAAGATA
* * *
3755728 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
3755779 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * * * *
3755830 CCGGTACGCATAATAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
** * *
3755880 TTGGTACACGTAGTAGCCTACACATAGTACTACACACATGACCATCACT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
3755929 TTCACTTTTA
Statistics
Matches: 123, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
49 4 0.03
50 38 0.31
51 78 0.63
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:3757899 original size:24 final size:24
Alignment explanation
Indices: 3757867--3757913 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3757857 CTAAATTTAT
*
3757867 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
3757891 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
3757914 ATTTCTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:3762912 original size:25 final size:25
Alignment explanation
Indices: 3762884--3762932 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3762874 TATAGTCTAT
* *
3762884 CTATAGTAGTCTCAGTATATACTAC
1 CTATAGCAGTCTCAGGATATACTAC
*
3762909 CTATAGCAGTTTCAGGATATACTA
1 CTATAGCAGTCTCAGGATATACTA
3762933 TCAATGATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (25 bp):
CTATAGCAGTCTCAGGATATACTAC
Found at i:3765433 original size:5 final size:5
Alignment explanation
Indices: 3765423--3765449 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3765413 TTTTGAAAAG
3765423 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
3765450 ATAATCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:3766745 original size:194 final size:194
Alignment explanation
Indices: 3766411--3766786 Score: 549
Period size: 194 Copynumber: 1.9 Consensus size: 194
3766401 TTTGAGACGC
* ** *
3766411 TATTGCAAATCATTTTGATCGAGCCTAGGGAGAAGAGGTCATCGGACTCATCAAGCAAACATGGA
1 TATTACAAATCACATTGATCGAGCCTAGGGAGAAGAGGTCATCGGACTCATCAAGCAAACATAGA
* * * *
3766476 GCTCAACACCATGCGTTCTATACAGCTTTTTGTAAGTTGAATTTTAGCTAAATAATTCTCGGACT
66 GCTCAACACCATGCGTTCCATAAAGCTTTTTGCAAGCTGAATTTTAGCTAAATAATTCTCGGACT
* *
3766541 GAACTTTTAATATGTTTAGCTTAATTAATTCAGTTTTTTTAATTGTT-TTTAGGTTTCGAGATGT
131 GAACTTTTAATATGTTTAGCTTAATTAATTAAGTTGTTTTAATT-TTCTTTAGGTTTCGAGATGT
* * * ** *
3766605 TATTACAAATCACATTGATCGAGCTTGGGGAGAGGAGGTGGTTGGACTCATCAAGCAAACATAGA
1 TATTACAAATCACATTGATCGAGCCTAGGGAGAAGAGGTCATCGGACTCATCAAGCAAACATAGA
* *
3766670 GCTCAACACCATG-GATTCCATAAAGCTTTTTGCAAGCTGAATTTTAGCTAAATAATTGTTGGAC
66 GCTCAACACCATGCG-TTCCATAAAGCTTTTTGCAAGCTGAATTTTAGCTAAATAATTCTCGGAC
*
3766734 TGAACTTTTAATATGTTTAGTTTAATTAATTAAGTTGTTTTAATTTTCTTTAG
130 TGAACTTTTAATATGTTTAGCTTAATTAATTAAGTTGTTTTAATTTTCTTTAG
3766787 TTGCTTAAAT
Statistics
Matches: 161, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
193 3 0.02
194 158 0.98
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (194 bp):
TATTACAAATCACATTGATCGAGCCTAGGGAGAAGAGGTCATCGGACTCATCAAGCAAACATAGA
GCTCAACACCATGCGTTCCATAAAGCTTTTTGCAAGCTGAATTTTAGCTAAATAATTCTCGGACT
GAACTTTTAATATGTTTAGCTTAATTAATTAAGTTGTTTTAATTTTCTTTAGGTTTCGAGATGT
Found at i:3766802 original size:49 final size:47
Alignment explanation
Indices: 3766749--3766844 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 47
3766739 TTTTAATATG
3766749 TTTAGTTTAATTAATTAAGTTGTTTT-AATTTTCTTTAGTTGCTTAAATA
1 TTTAGTTTAATTAATTAAGTTGTTTTGAA--TT-TTTAGTTGCTTAAATA
3766798 TTTAGTTTAATTAATTAAGTTGTTTTGAATTTTTAGTTGCTTAAATA
1 TTTAGTTTAATTAATTAAGTTGTTTTGAATTTTTAGTTGCTTAAATA
3766845 ATTCCGGCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
47 16 0.35
48 2 0.04
49 26 0.57
50 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.56
Consensus pattern (47 bp):
TTTAGTTTAATTAATTAAGTTGTTTTGAATTTTTAGTTGCTTAAATA
Found at i:3771464 original size:27 final size:27
Alignment explanation
Indices: 3771431--3771910 Score: 852
Period size: 27 Copynumber: 17.6 Consensus size: 27
3771421 TAAATTGTGC
*
3771431 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771458 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771485 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771512 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771539 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771566 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
3771593 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
3771621 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771648 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771675 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
3771703 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
3771731 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
3771759 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
3771787 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
3771814 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
3771841 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
3771869 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
3771896 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3771911 GACTTAATAT
Statistics
Matches: 444, Mismatches: 6, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
27 281 0.63
28 163 0.37
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:3771671 original size:82 final size:82
Alignment explanation
Indices: 3771431--3771910 Score: 874
Period size: 82 Copynumber: 5.9 Consensus size: 82
3771421 TAAATTGTGC
*
3771431 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
3771495 GTGCGAGTTGACTATGT
66 GTGCGAGTTGACTATGT
3771512 AGCACTAAGTGTGCGAG-TTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
3771576 GTGCGAGTTGACTATGT
66 GTGCGAGTTGACTATGT
*
3771593 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
3771658 GTGCGAGTTGACTATGT
66 GTGCGAGTTGACTATGT
3771675 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAG
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAG-TTGACTATGTAGCACTAAG
3771740 TGTGCGAGTTTGACTATGT
65 TGTGCGAG-TTGACTATGT
3771759 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
3771824 GTGCGAGTTGACTATGT
66 GTGCGAGTTGACTATGT
* * * *
3771841 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGT
1 AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
3771906 GTGCG
66 GTGCG
3771911 GACTTAATAT
Statistics
Matches: 389, Mismatches: 6, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
81 97 0.25
82 183 0.47
83 54 0.14
84 55 0.14
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (82 bp):
AGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGT
GTGCGAGTTGACTATGT
Found at i:3780090 original size:27 final size:27
Alignment explanation
Indices: 3780059--3780236 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
3780049 TAAATTGTAC
3780059 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
3780086 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3780112 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
3780140 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
3780168 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
3780195 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
3780222 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
3780237 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:3780173 original size:82 final size:81
Alignment explanation
Indices: 3780060--3780215 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
3780050 AAATTGTACA
* *
3780060 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
3780124 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
3780141 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
3780206 TGCGAGTTGA
65 TGCGAATTGA
3780216 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:3780227 original size:82 final size:81
Alignment explanation
Indices: 3780056--3780236 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
3780046 GATTAAATTG
* *
3780056 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
3780121 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
3780137 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
3780201 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
3780219 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
3780237 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3781875 original size:13 final size:14
Alignment explanation
Indices: 3781854--3781895 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3781844 GAGAGACTGT
3781854 AGAAAAAGAAAAA-
1 AGAAAAAGAAAAAG
3781867 AGAACAAGAGAAAAAG
1 AGAA-AA-AGAAAAAG
*
3781883 AGAAAAATAAAAA
1 AGAAAAAGAAAAA
3781896 TAAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 9 0.36
16 4 0.16
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AGAAAAAGAAAAAG
Found at i:3785151 original size:194 final size:194
Alignment explanation
Indices: 3784813--3785201 Score: 688
Period size: 194 Copynumber: 2.0 Consensus size: 194
3784803 TCGTGCTAAG
* *
3784813 AAGTTTCGAGACGCTATTGCAAATCACATTGATCGAGCTTGGGGAGAGGAAGTGGTTGGACTCAT
1 AAGTTTCGAAACGCTATTGCAAATCACATTGATCGAGCTTGGGGAGAGGAAGTGGTCGGACTCAT
* *
3784878 CAAGCAAACATGGAGTTCAACACCATGCGCTCCATACAGCTTTTTGCAAGCTGAATTTTAGCTAA
66 CAAGCAAACATGAAGCTCAACACCATGCGCTCCATACAGCTTTTTGCAAGCTGAATTTTAGCTAA
*
3784943 ATAATTGCTGGACTGAACTTTTAATATGTTTAGTTTAATTAATTCAGTTGTTTTAATTTTCTTT
131 AAAATTGCTGGACTGAACTTTTAATATGTTTAGTTTAATTAATTCAGTTGTTTTAATTTTCTTT
*
3785007 AAGTTTCGAAACGCTATTGCAAATCACATTGATCGAGCTTGGGGAGAGGAGGTGGTCGGACTCAT
1 AAGTTTCGAAACGCTATTGCAAATCACATTGATCGAGCTTGGGGAGAGGAAGTGGTCGGACTCAT
* * *
3785072 CAAGCAAACATGAAGCTCAACACCATGTGTTTCATACAGCTTTTTGCAAGCTGAATTTTAGCTAA
66 CAAGCAAACATGAAGCTCAACACCATGCGCTCCATACAGCTTTTTGCAAGCTGAATTTTAGCTAA
*
3785137 AAAATTGTTGGACTGAACTTTTAATATGTTTAGTTTAATTAATTCAGTTGTTTTAATTTTCTTT
131 AAAATTGCTGGACTGAACTTTTAATATGTTTAGTTTAATTAATTCAGTTGTTTTAATTTTCTTT
3785201 A
1 A
3785202 GTTGCTTAAA
Statistics
Matches: 185, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
194 185 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (194 bp):
AAGTTTCGAAACGCTATTGCAAATCACATTGATCGAGCTTGGGGAGAGGAAGTGGTCGGACTCAT
CAAGCAAACATGAAGCTCAACACCATGCGCTCCATACAGCTTTTTGCAAGCTGAATTTTAGCTAA
AAAATTGCTGGACTGAACTTTTAATATGTTTAGTTTAATTAATTCAGTTGTTTTAATTTTCTTT
Found at i:3785235 original size:49 final size:47
Alignment explanation
Indices: 3785165--3785260 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 47
3785155 TTTTAATATG
*
3785165 TTTAGTTTAATTAATTCAGTTGTTTT-AATTTTCTTTAGTTGCTTAAATA
1 TTTAGTTTAATTAATTAAGTTGTTTTGAA--TT-TTTAGTTGCTTAAATA
3785214 TTTAGTTTAATTAATTAAGTTGTTTTGAATTTTTAGTTGCTTAAATA
1 TTTAGTTTAATTAATTAAGTTGTTTTGAATTTTTAGTTGCTTAAATA
3785261 ATTTTTTCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
47 16 0.36
48 2 0.04
49 25 0.56
50 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.56
Consensus pattern (47 bp):
TTTAGTTTAATTAATTAAGTTGTTTTGAATTTTTAGTTGCTTAAATA
Found at i:3787135 original size:21 final size:20
Alignment explanation
Indices: 3787095--3787133 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3787085 GATACTTGAT
*
3787095 AAAAGGTAACGATATTTTTG
1 AAAAGGTAACAATATTTTTG
*
3787115 AAAAGGTATCAATATTTTT
1 AAAAGGTAACAATATTTTT
3787134 TGTGGTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
AAAAGGTAACAATATTTTTG
Found at i:3791511 original size:30 final size:29
Alignment explanation
Indices: 3791466--3791544 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
3791456 TAATAAAAGG
3791466 AAATA-TTTTTTTATTTTTATAATTTATT
1 AAATATTTTTTTTATTTTTATAATTTATT
* * * *
3791494 CAATATTTTTTTGTATTTTTTTCATTTTTT
1 AAATATTTTTTT-TATTTTTATAATTTATT
* *
3791524 AAACATTTTTTTTAGTTTTAT
1 AAATATTTTTTTTATTTTTAT
3791545 CCAAAAGATG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.10
29 13 0.32
30 24 0.59
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (29 bp):
AAATATTTTTTTTATTTTTATAATTTATT
Found at i:3798881 original size:3 final size:3
Alignment explanation
Indices: 3798873--3798927 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
3798863 TAATCTGATA
3798873 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3798921 AAT AAT A
1 AAT AAT A
3798928 TTCTAATGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3803306 original size:150 final size:150
Alignment explanation
Indices: 3803147--3803426 Score: 551
Period size: 150 Copynumber: 1.9 Consensus size: 150
3803137 AGGGAGTAAA
3803147 AATTTTGGGGGAAAATAAAAGGTTTTAAGGGTTTTGGGGAGTAAAATTTTGGGAAAAAGTAAATG
1 AATTTTGGGGGAAAATAAAAGGTTTTAAGGGTTTTGGGGAGTAAAATTTTGGGAAAAAGTAAATG
*
3803212 GGAGAGTAAAATTTTGGTAGGAAATAGATTTTGGGTAGATTGGGGGGTTGGGAGGGGAGGGGAGG
66 AGAGAGTAAAATTTTGGTAGGAAATAGATTTTGGGTAGATTGGGGGGTTGGGAGGGGAGGGGAGG
3803277 AAAAGTTTTGGGGGAAAGTG
131 AAAAGTTTTGGGGGAAAGTG
3803297 AATTTTGGGGGAAAATAAAAGGTTTTAAGGGTTTTGGGGAGTAAAATTTTGGGAAAAAGTAAATG
1 AATTTTGGGGGAAAATAAAAGGTTTTAAGGGTTTTGGGGAGTAAAATTTTGGGAAAAAGTAAATG
3803362 AGAGAGTAAAATTTTGGTAGGAAATAGATTTTGGGTAGATTGGGGGGTTGGGAGGGGAGGGGAGG
66 AGAGAGTAAAATTTTGGTAGGAAATAGATTTTGGGTAGATTGGGGGGTTGGGAGGGGAGGGGAGG
3803427 GGAGTAAAAG
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 129 1.00
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.28
Consensus pattern (150 bp):
AATTTTGGGGGAAAATAAAAGGTTTTAAGGGTTTTGGGGAGTAAAATTTTGGGAAAAAGTAAATG
AGAGAGTAAAATTTTGGTAGGAAATAGATTTTGGGTAGATTGGGGGGTTGGGAGGGGAGGGGAGG
AAAAGTTTTGGGGGAAAGTG
Found at i:3803544 original size:9 final size:9
Alignment explanation
Indices: 3803530--3803566 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3803520 TATAGTTTGA
3803530 TATTCGAAT
1 TATTCGAAT
3803539 TATTCGAAT
1 TATTCGAAT
* *
3803548 TATTTGAGT
1 TATTCGAAT
3803557 TATTCGAAT
1 TATTCGAAT
3803566 T
1 T
3803567 CGAAAAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3803637 original size:9 final size:9
Alignment explanation
Indices: 3803620--3803650 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3803610 TCGAATTGAT
3803620 TCGAATAAC
1 TCGAATAAC
*
3803629 TCGATTAAC
1 TCGAATAAC
3803638 TCGAATAAC
1 TCGAATAAC
3803647 TCGA
1 TCGA
3803651 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3805971 original size:30 final size:30
Alignment explanation
Indices: 3805909--3805971 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3805899 ACTTAATTTA
*
3805909 TTGTTAATTTTATTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* *
3805939 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
3805969 TTG
1 TTG
3805972 CTTATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:3808866 original size:13 final size:13
Alignment explanation
Indices: 3808848--3808872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3808838 GCTCAGAGAC
3808848 TAAATTGAATAAT
1 TAAATTGAATAAT
3808861 TAAATTGAATAA
1 TAAATTGAATAA
3808873 AAGTAAAACT
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TAAATTGAATAAT
Found at i:3809405 original size:27 final size:25
Alignment explanation
Indices: 3809375--3809444 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
3809365 CGTTTCGACC
3809375 CACAGCTCGTGTGAGCATGCCCATTTT
1 CACAGCTCGTGTGAGCATGCCCA--TT
* * * **
3809402 CACAACTTGTGTGAGCATTCTGATT
1 CACAGCTCGTGTGAGCATGCCCATT
3809427 CACAGCTCGTGTGAGCAT
1 CACAGCTCGTGTGAGCAT
3809445 ATATATATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 18 0.50
27 18 0.50
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCATGCCCATT
Found at i:3822738 original size:44 final size:44
Alignment explanation
Indices: 3822688--3822774 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
3822678 GGATTATATG
3822688 CTTGTGTATTATAGGGAGAACCTTACTCCTATTAGATACATAGA
1 CTTGTGTATTATAGGGAGAACCTTACTCCTATTAGATACATAGA
*
3822732 CTTGTGTATTATAGGGAGAACCTTACTCCTATTGGATACATAG
1 CTTGTGTATTATAGGGAGAACCTTACTCCTATTAGATACATAG
3822775 GCTCATACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (44 bp):
CTTGTGTATTATAGGGAGAACCTTACTCCTATTAGATACATAGA
Found at i:3830554 original size:32 final size:32
Alignment explanation
Indices: 3830511--3830723 Score: 160
Period size: 32 Copynumber: 6.7 Consensus size: 32
3830501 TAATGTGATT
*
3830511 GGCACAAAGCCATCAGTAGTAGTGATATGACC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * * * *
3830543 GGCATACAGCCATCAGTAACGGTAACATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
*
3830575 GGCACAAAGCCATCAGTAGCAGTGATATGATC
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* * * * *
3830607 AGCACACAA-CCATTAGTAACAGTGAAATGATC
1 GGCACA-AAGCCATCAGTAGCAGTGATATGACC
* * * * **
3830639 GGCACATAGCCATCGGTAACAGTAATATGATT
1 GGCACAAAGCCATCAGTAGCAGTGATATGACC
* *** *
3830671 GGCACAAAGCCACCAGTAATGGT-ACTATGATC
1 GGCACAAAGCCATCAGTAGCAGTGA-TATGACC
*
3830703 GGTACAAAGCCATCAGTAGCA
1 GGCACAAAGCCATCAGTAGCA
3830724 TCGCAGCAAA
Statistics
Matches: 142, Mismatches: 36, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
31 2 0.01
32 138 0.97
33 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAGCAGTGATATGACC
Found at i:3830589 original size:64 final size:64
Alignment explanation
Indices: 3830506--3830723 Score: 251
Period size: 64 Copynumber: 3.4 Consensus size: 64
3830496 TACAGTAATG
* * * *
3830506 TGATTGGCACAAAGCCATCAGTAGTAGTGATATGACCGGCATACAGCCATCAGTAACGGTAACA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACA
* * * *
3830570 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCAGCACACAACCATTAGTAACAGTGAA-A
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGT-AACA
* * * * * * * *
3830634 TGATCGGCACATAGCCATCGGTAACAGTAATATGATTGGCACAAAGCCACCAGTAATGGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAAC-A
*
3830698 TGATCGGTACAAAGCCATCAGTAGCA
1 TGATCGGCACAAAGCCATCAGTAGCA
3830724 TCGCAGCAAA
Statistics
Matches: 127, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
62 1 0.01
64 124 0.98
65 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (64 bp):
TGATCGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACACAGCCATCAGTAACGGTAACA
Found at i:3830752 original size:26 final size:26
Alignment explanation
Indices: 3830723--3830776 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
3830713 CATCAGTAGC
*
3830723 ATCGCAGCAAAGTTGCCAGCAACAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
* *
3830749 ATCGCAGCAAAGCTGCCAGTAATAGT
1 ATCGCAGCAAAGCTGCCAGCAACAGT
3830775 AT
1 AT
3830777 ATGTGGGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGCAACAGT
Found at i:3830794 original size:27 final size:27
Alignment explanation
Indices: 3830764--3830827 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
3830754 AGCAAAGCTG
*
3830764 CCAGTAATAGT-ATATGTGGGCA-AGCCA
1 CCAGTAACAGTGAT-TGT-GGCAGAGCCA
3830791 CCAGTAACAGTGATTGTGGCAGAGCCA
1 CCAGTAACAGTGATTGTGGCAGAGCCA
3830818 CCAGT-ACAGT
1 CCAGTAACAGT
3830828 ACTTCCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 9 0.26
27 23 0.68
28 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAGAGCCA
Found at i:3831146 original size:17 final size:17
Alignment explanation
Indices: 3831124--3831163 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3831114 CCAATATTGA
3831124 AGAATCCACTTTAAGTC
1 AGAATCCACTTTAAGTC
3831141 AGAATCCACTTTAAGTC
1 AGAATCCACTTTAAGTC
3831158 AGAATC
1 AGAATC
3831164 AATATTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (17 bp):
AGAATCCACTTTAAGTC
Found at i:3831171 original size:17 final size:16
Alignment explanation
Indices: 3831133--3831180 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3831123 AAGAATCCAC
*
3831133 TTTAAGTCAGAATCCAC
1 TTTAAGTCAGAAT-CAA
3831150 TTTAAGTCAGAATCAA
1 TTTAAGTCAGAATCAA
*
3831166 TATTAA-TCACAATCA
1 T-TTAAGTCAGAATCA
3831181 TAAATCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (16 bp):
TTTAAGTCAGAATCAA
Found at i:3832631 original size:16 final size:16
Alignment explanation
Indices: 3832610--3832641 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3832600 GTTTTGTTGC
*
3832610 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
3832626 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
3832642 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:3832945 original size:51 final size:50
Alignment explanation
Indices: 3832869--3833009 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 50
3832859 CCGGTTCACA
* * *
3832869 TAGTAGCCTGCATATAGTACTACACATGTGACCATCACTAT-TTGATACATG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCTAG-TACACG
*
3832920 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-TTCTAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTTCTAGTACACG
* * *
3832970 TAATAGCCTGCACATAGTACTACCCACGTGACCATCACTT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
3833010 TCACTTTCAC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
49 4 0.05
50 37 0.47
51 34 0.43
52 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCTAGTACACG
Done.