Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006400.1 Hibiscus syriacus cultivar Beakdansim tig00015426_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1412076
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:374741 original size:22 final size:21
Alignment explanation
Indices: 374714--374798 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 21
374704 GTTCATAATG
374714 AGAAGAACTCATCCAATGAGGA
1 AGAAGAACTCATCCAATGA-GA
*
374736 AGAAGAAGTTCAT--AAT---A
1 AGAAGAA-CTCATCCAATGAGA
*
374753 AGAAGAACTCATCCAACGAGAA
1 AGAAGAACTCATCCAATGAG-A
*
374775 AGAAGAAGTTCAT--AATGAGA
1 AGAAGAA-CTCATCCAATGAGA
374795 AGAA
1 AGAA
374799 CTTGTTCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
16 4 0.08
17 8 0.16
18 2 0.04
20 5 0.10
21 8 0.16
22 15 0.30
23 8 0.16
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (21 bp):
AGAAGAACTCATCCAATGAGA
Found at i:374757 original size:39 final size:39
Alignment explanation
Indices: 374663--374800 Score: 189
Period size: 39 Copynumber: 3.7 Consensus size: 39
374653 CAATATTTAC
*
374663 AGAAG-AGTTCATAATGAGAAGAACTCGTCC--T-A-AA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCCAATGAGAA
*
374697 AG-AGAAAGTTCATAATGAGAAGAACTCATCCAATGAGGA
1 AGAAG-AAGTTCATAATGAGAAGAACTCATCCAATGAGAA
* *
374736 AGAAGAAGTTCATAATAAGAAGAACTCATCCAACGAGAA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCCAATGAGAA
374775 AGAAGAAGTTCATAATGAGAAGAACT
1 AGAAGAAGTTCATAATGAGAAGAACT
374801 TGTTCAATCC
Statistics
Matches: 91, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
33 2 0.02
34 2 0.02
35 24 0.26
37 1 0.01
38 1 0.01
39 59 0.65
40 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (39 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCCAATGAGAA
Found at i:374956 original size:3 final size:3
Alignment explanation
Indices: 374938--374983 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
374928 AAAATATATA
*
374938 TAT TA- TAT TA- TAT TAT TAT TA- TAT TAT TAA TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
374982 TA
1 TA
374984 ATGCTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 8 0.21
3 30 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:374956 original size:8 final size:8
Alignment explanation
Indices: 374938--374983 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
374928 AAAATATATA
374938 TATTATAT
1 TATTATAT
374946 TA-TATTAT
1 TATTA-TAT
374954 TATTATAT
1 TATTATAT
374962 TATTA-AT
1 TATTATAT
374969 ATATTATTAT
1 -TATTA-TAT
374979 TATTA
1 TATTA
374984 ATGCTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 4 0.12
8 20 0.61
9 7 0.21
10 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTATAT
Found at i:374957 original size:11 final size:11
Alignment explanation
Indices: 374936--374981 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
374926 TAAAAATATA
374936 TATATTA-TAT
1 TATATTATTAT
374946 TATATTATTAT
1 TATATTATTAT
*
374957 TATATTATTAA
1 TATATTATTAT
374968 TATATTATTAT
1 TATATTATTAT
374979 TAT
1 TAT
374982 TAATGCTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
10 7 0.21
11 26 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTATTAT
Found at i:378170 original size:40 final size:38
Alignment explanation
Indices: 378096--378170 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
378086 TAAAAGTTCG
**
378096 TTTATGTTCATTAATAAACGAACGAACATGAACAAGAT
1 TTTATGTTCATTAATAAACGAACGAACACAAACAAGAT
* *
378134 TTTATGTTCGTTTAATTAAATGAACGAACACAAACAA
1 TTTATGTTC-ATTAA-TAAACGAACGAACACAAACAA
378171 AAGGTTCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 9 0.29
39 4 0.13
40 18 0.58
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (38 bp):
TTTATGTTCATTAATAAACGAACGAACACAAACAAGAT
Found at i:379661 original size:109 final size:109
Alignment explanation
Indices: 379530--379738 Score: 328
Period size: 109 Copynumber: 1.9 Consensus size: 109
379520 CCGCCCCTGT
* *
379530 GCACAAGTTTATATTCATAAAAAATAATATAATTATTTTTAGGACTTTATTTATTTAAGTTAATC
1 GCACAAGTTTATATTCATAAAAAATAATATAATTAGTTTTAGGACTTTATTTATTTAAGTTAATA
379595 TTATAACAAATTCAAAATGAATTTGATTTGAATCAAGTACGTAC
66 TTATAACAAATTCAAAATGAATTTGATTTGAATCAAGTACGTAC
** * * **
379639 GCACAAGTTTATATTCATAAAAAATAATATTTTTAGTTTTATGATTTTATTTATTTAAGTTCGTA
1 GCACAAGTTTATATTCATAAAAAATAATATAATTAGTTTTAGGACTTTATTTATTTAAGTTAATA
* *
379704 TTATAACAAATTTAGAATGAATTTGATTTGAATCA
66 TTATAACAAATTCAAAATGAATTTGATTTGAATCA
379739 TTATTTCTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 90 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (109 bp):
GCACAAGTTTATATTCATAAAAAATAATATAATTAGTTTTAGGACTTTATTTATTTAAGTTAATA
TTATAACAAATTCAAAATGAATTTGATTTGAATCAAGTACGTAC
Found at i:381272 original size:36 final size:35
Alignment explanation
Indices: 381230--381417 Score: 199
Period size: 35 Copynumber: 5.4 Consensus size: 35
381220 ACAATATATT
*
381230 TATAGTTTTGAAAATATTTTTTAAACATATATAATA
1 TATAGTTTTGAAAACATTTTTTAAA-ATATATAATA
* *
381266 TATAGTTTTGAAAACA-TTTTGAAAACATATAATA
1 TATAGTTTTGAAAACATTTTTTAAAATATATAATA
* **
381300 TATCA-TTTTGAAAACGTTTTGGAAAATATATAATA
1 TAT-AGTTTTGAAAACATTTTTTAAAATATATAATA
* *
381335 TATAGTTTTGAAAATATTTTTTGAAAACATATACAATA
1 TATAGTTTTGAAAACATTTTTT--AAA-ATATATAATA
*
381373 TATAGTTTTGAAAACA--TTTT-GAATATAT-ATA
1 TATAGTTTTGAAAACATTTTTTAAAATATATAATA
*
381404 TATAATTTTGAAAA
1 TATAGTTTTGAAAA
381418 TGTTTTTAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
31 16 0.12
32 5 0.04
33 1 0.01
34 23 0.18
35 40 0.31
36 19 0.15
37 3 0.02
38 24 0.18
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (35 bp):
TATAGTTTTGAAAACATTTTTTAAAATATATAATA
Found at i:381397 original size:25 final size:25
Alignment explanation
Indices: 381340--381401 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
381330 TAATATATAG
* *
381340 TTTTGAAAATAT-TTTTTGAAAACA
1 TTTTGAATATATAGTTTTGAAAACA
* **
381364 TATACAATATATAGTTTTGAAAACA
1 TTTTGAATATATAGTTTTGAAAACA
381389 TTTTGAATATATA
1 TTTTGAATATATA
381402 TATATAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTTGAATATATAGTTTTGAAAACA
Found at i:381418 original size:69 final size:70
Alignment explanation
Indices: 381256--381424 Score: 224
Period size: 69 Copynumber: 2.4 Consensus size: 70
381246 TTTTTTAAAC
* *
381256 ATATATAATATATAGTTTTGAAAACA--TTTTGAAAACATATAATATATCATTTTGAAAACGTTT
1 ATATATAATATATAGTTTTGAAAATATTTTTTGAAAACATATAATATATCATTTTGAAAACATTT
381319 TGGAAA
66 TGG-AA
381325 ATATATAATATATAGTTTTGAAAATATTTTTTGAAAACATATACAATATAT-AGTTTTGAAAACA
1 ATATATAATATATAGTTTTGAAAATATTTTTTGAAAACATAT--AATATATCA-TTTTGAAAACA
381389 TTTT-G-A
63 TTTTGGAA
* *
381395 ATATAT-ATATATAATTTTGAAAATGTTTTT
1 ATATATAATATATAGTTTTGAAAATATTTTT
381425 AATTTAGAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
69 47 0.52
70 7 0.08
71 14 0.15
72 2 0.02
73 21 0.23
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (70 bp):
ATATATAATATATAGTTTTGAAAATATTTTTTGAAAACATATAATATATCATTTTGAAAACATTT
TGGAA
Found at i:381527 original size:15 final size:15
Alignment explanation
Indices: 381509--381544 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
381499 TTTTATAGTT
381509 TTTATTTACATTTTA
1 TTTATTTACATTTTA
* *
381524 TTTATTTCCTTTTTA
1 TTTATTTACATTTTA
381539 TTTATT
1 TTTATT
381545 CATTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTACATTTTA
Found at i:381555 original size:27 final size:26
Alignment explanation
Indices: 381507--381557 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
381497 ATTTTTATAG
*
381507 TTTTTATTTACATTTTATTTATTTCC
1 TTTTTATTTACATTTTAGTTATTTCC
381533 TTTTTATTTATTCATTTT-GTTATTT
1 TTTTTATTTA--CATTTTAGTTATTT
381558 TATTTTAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 6 0.27
28 6 0.27
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTTTATTTACATTTTAGTTATTTCC
Found at i:381563 original size:27 final size:26
Alignment explanation
Indices: 381507--381563 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
381497 ATTTTTATAG
* *
381507 TTTTTATTTACATTTTATTTATTTCC
1 TTTTTATTTACATTTTAGTTATTTCA
*
381533 TTTTTATTTATTCATTTT-GTTATTTTA
1 TTTTTATTTA--CATTTTAGTTATTTCA
381560 TTTT
1 TTTT
381564 AGGGCTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 10 0.38
27 10 0.38
28 6 0.23
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTTATTTACATTTTAGTTATTTCA
Found at i:388411 original size:36 final size:36
Alignment explanation
Indices: 388371--388601 Score: 220
Period size: 35 Copynumber: 6.2 Consensus size: 36
388361 AAAACATGTT
*
388371 TAATATATAGTTCTGAAAATA-TTTTTGAAACATATA
1 TAATATATAGTTTTGAAAATATTTTTTGAAA-ATATA
* *
388407 TAATATATAGTTTTGAAAACA--TTTTGAAAACATA
1 TAATATATAGTTTTGAAAATATTTTTTGAAAATATA
* * *
388441 TAATATATAATTTTGAAAA-AGTTTTGGAAAATATA
1 TAATATATAGTTTTGAAAATATTTTTTGAAAATATA
*
388476 TAATATATTGTTTTGAAAATATTTTTTGAAAACATATA
1 TAATATATAGTTTTGAAAATATTTTTTG-AAA-ATATA
* *
388514 TAATATATAGTTTTAAAAACATAGAAACCATTTTTGAAAATATATA
1 TAATATATAGTTTT-GAAA-AT----A--TTTTTTG-AAA-ATATA
388560 TAATATATGAG-TTTGAAAATATTTTTTGAAAATATA
1 TAATATAT-AGTTTTGAAAATATTTTTTGAAAATATA
388596 TAATAT
1 TAATAT
388602 TATTTTTATA
Statistics
Matches: 165, Mismatches: 16, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
33 1 0.01
34 22 0.13
35 36 0.22
36 36 0.22
37 6 0.04
38 24 0.15
39 3 0.02
40 3 0.02
44 3 0.02
45 3 0.02
46 26 0.16
47 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (36 bp):
TAATATATAGTTTTGAAAATATTTTTTGAAAATATA
Found at i:388478 original size:35 final size:36
Alignment explanation
Indices: 388362--388532 Score: 197
Period size: 36 Copynumber: 4.8 Consensus size: 36
388352 GTATTTAAAA
* * * *
388362 AAACATGTTTAATATATAGTTCTGAAAATATTTTTG
1 AAACATATATAATATATAGTTTTGAAAATATTTTGG
*
388398 AAACATATATAATATATAGTTTTGAAAACATTTT-G
1 AAACATATATAATATATAGTTTTGAAAATATTTTGG
* *
388433 AAA-ACATATAATATATAATTTTGAAAA-AGTTTTGG
1 AAACATATATAATATATAGTTTTGAAAATA-TTTTGG
* *
388468 AAA-ATATATAATATATTGTTTTGAAAATATTTTTTGA
1 AAACATATATAATATATAGTTTTGAAAATA--TTTTGG
*
388505 AAACATATATAATATATAGTTTTAAAAA
1 AAACATATATAATATATAGTTTTGAAAA
388533 CATAGAAACC
Statistics
Matches: 117, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.01
34 26 0.22
35 29 0.25
36 31 0.26
37 8 0.07
38 22 0.19
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (36 bp):
AAACATATATAATATATAGTTTTGAAAATATTTTGG
Found at i:390882 original size:3 final size:3
Alignment explanation
Indices: 390868--390902 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
390858 TTTTAAATTA
*
390868 ATT ATT -TT ATT ATT ATT ATT ATT ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
390903 TTAATACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:391571 original size:2 final size:2
Alignment explanation
Indices: 391528--391556 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
391518 CTTATATGTA
391528 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
391557 ATTCAATTAT
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:395037 original size:20 final size:20
Alignment explanation
Indices: 395014--395054 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
395004 CTGTTCACAT
* *
395014 AGTATCGGTACTATTTATAC
1 AGTATCGATACTATTCATAC
395034 AGTATCGATACTATTCATAC
1 AGTATCGATACTATTCATAC
395054 A
1 A
395055 TTACAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATTCATAC
Found at i:395400 original size:5 final size:5
Alignment explanation
Indices: 395390--395414 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
395380 ATCCTATTTT
395390 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
395415 TGAACGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:395478 original size:2 final size:2
Alignment explanation
Indices: 395471--395498 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
395461 AAATAAATAA
395471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
395499 TATTTTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:396996 original size:32 final size:32
Alignment explanation
Indices: 396960--397023 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
396950 TATTTATCAT
* *
396960 GAAAACTTAATATTA-TTATTTTTGAAATATTA
1 GAAAACTTAAT-TTATTTATTATTAAAATATTA
* *
396992 GAAAATTTTATTTATTTATTATTAAAATATTA
1 GAAAACTTAATTTATTTATTATTAAAATATTA
397024 TTTCTACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (32 bp):
GAAAACTTAATTTATTTATTATTAAAATATTA
Found at i:397379 original size:21 final size:22
Alignment explanation
Indices: 397355--397397 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
397345 TTGCATATAT
397355 TATTATAA-ATTAAAAATATTA
1 TATTATAATATTAAAAATATTA
**
397376 TATTATAATATTTGAAATATTA
1 TATTATAATATTAAAAATATTA
397398 ATAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTATAATATTAAAAATATTA
Found at i:397396 original size:22 final size:22
Alignment explanation
Indices: 397355--397417 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
397345 TTGCATATAT
**
397355 TATTATAA-ATTAAAAATATTA
1 TATTATAATATTTGAAATATTA
397376 TATTATAATATTTGAAATATTA
1 TATTATAATATTTGAAATATTA
397398 -A-TA-AATATAATTGAAATATT
1 TATTATAATAT--TTGAAATATT
397418 TTAATAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 5 0.14
20 2 0.05
21 19 0.51
22 11 0.30
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTATAATATTTGAAATATTA
Found at i:401333 original size:2 final size:2
Alignment explanation
Indices: 401326--401350 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
401316 CCTAACCCCC
401326 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 A
401351 GGGACATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:401836 original size:19 final size:19
Alignment explanation
Indices: 401792--401855 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
401782 GATGAGCACA
* *
401792 GAACCGGTAGAACCGGCTGA
1 GAACCGGTAAAACCGG-TGT
*
401812 GAACCGGTAAAACCGGGGT
1 GAACCGGTAAAACCGGTGT
*
401831 GAACCGGCAAAACCGGTGT
1 GAACCGGTAAAACCGGTGT
401850 GAACCG
1 GAACCG
401856 CCGATTCTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 24 0.62
20 15 0.38
ACGTcount: A:0.31, C:0.25, G:0.34, T:0.09
Consensus pattern (19 bp):
GAACCGGTAAAACCGGTGT
Found at i:409765 original size:44 final size:43
Alignment explanation
Indices: 409632--409766 Score: 114
Period size: 42 Copynumber: 3.1 Consensus size: 43
409622 GATCTTAATT
* *
409632 TTTTTTCAATCAT-AATTTTTATTTATATAATTGA-ACCCTTAA
1 TTTTTTCAAT-ATCAATTTTTATTTTTATAATCGAGACCCTTAA
* ** ** ** * *
409674 TTTTTTGAATCCCACCTTTTACCTTTATAATCTATG-CCCATAA
1 TTTTTTCAATATCAATTTTTATTTTTATAATCGA-GACCCTTAA
*
409717 TTTTTTCAATATCAATTTTTAGTTTTTATAATCGAGACCCTTAT
1 TTTTTTCAATATCAATTTTTA-TTTTTATAATCGAGACCCTTAA
409761 TTTTTT
1 TTTTTT
409767 AATTAAGTTC
Statistics
Matches: 67, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
42 23 0.34
43 23 0.34
44 21 0.31
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.52
Consensus pattern (43 bp):
TTTTTTCAATATCAATTTTTATTTTTATAATCGAGACCCTTAA
Found at i:410795 original size:16 final size:17
Alignment explanation
Indices: 410774--410805 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
410764 AAAATAAATC
410774 TTAAACT-AAACTCGAT
1 TTAAACTAAAACTCGAT
410790 TTAAACTAAAACTCGA
1 TTAAACTAAAACTCGA
410806 ACATGAGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (17 bp):
TTAAACTAAAACTCGAT
Found at i:411011 original size:26 final size:26
Alignment explanation
Indices: 410982--411033 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
410972 CATTAAGAAC
*
410982 TCAAGTCAAGTCCATTTAAATCGAGT
1 TCAAGTCAAGTCCATTCAAATCGAGT
* *
411008 TCAAGTCGAGTTCATTCAAATCGAGT
1 TCAAGTCAAGTCCATTCAAATCGAGT
411034 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (26 bp):
TCAAGTCAAGTCCATTCAAATCGAGT
Found at i:414924 original size:3 final size:3
Alignment explanation
Indices: 414916--414945 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
414906 AATTAACATA
414916 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
414946 TAATTAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:415451 original size:138 final size:138
Alignment explanation
Indices: 415196--415691 Score: 550
Period size: 138 Copynumber: 3.6 Consensus size: 138
415186 GATGATTTTG
* * * * * * * * * * *
415196 GAGACAACACGTTTCCAACGTGATGAGGGAGTCTGGTTATCTGATGATGATGATGCTCTTATGCG
1 GAGATAACACGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGTG
* * * ** *
415261 TTGAGGATATCTAGTCGGTGGATGACATCATTCCTACGTGATGAGGATGTCTAGTCGTCTTTAGG
66 TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCGTCTTTAGG
415326 GATAAA-T
131 GATAAATT
*
415333 GTAGATAACACGGTTCCTACATGATGAGGAAGTCTTGTTATCTGAGGATGACGCTGCTCCTACGT
1 G-AGATAACACGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGT
* *
415398 GTTGAGGAGATCTGGTCGGTGGACGACATTGTTTCTACGTGATGAAGACGTCTAG-CTGTCTTTA
65 GTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTC-GTCTTTA
415462 GGGATAAATT
129 GGGATAAATT
* * * * *
415472 GAGATAACATGGTTCCTACGTGATGAGGAAGGCTGGTTATCAGATGATGACGCTGCTCCTACGTG
1 GAGATAACACGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGTG
* ** * *
415537 TTGAGGAGATCTGGTCTGTACACGATATTGTTCCTACGTGATGAGGACGTAT-GTCCGTCTTTAG
66 TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGT-CGTCTTTAG
* *
415601 GGATGATTT
130 GGATAAATT
* * * * * * * * *
415610 AGAGACAACATGGTTCCTA-AGTGATGAGAAAATTTGGTTCTCTGAGGATGATGCCGCTCCTACA
1 -GAGATAACACGGTTCCTACA-TGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACG
415674 TGTTGAGGAGATCTGGTC
64 TGTTGAGGAGATCTGGTC
415692 ATAGTTGATG
Statistics
Matches: 305, Mismatches: 47, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
137 3 0.01
138 231 0.76
139 71 0.23
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (138 bp):
GAGATAACACGGTTCCTACATGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGTG
TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGTCGTCTTTAGG
GATAAATT
Found at i:416659 original size:7 final size:7
Alignment explanation
Indices: 416637--416738 Score: 66
Period size: 7 Copynumber: 14.3 Consensus size: 7
416627 TGAACACTCC
416637 TTTATTT
1 TTTATTT
*
416644 ATT-TTT
1 TTTATTT
416650 TTTATTTT
1 TTTA-TTT
416658 TTTATTTT
1 TTTA-TTT
416666 TTTATTTT
1 TTTA-TTT
416674 TTTATTT
1 TTTATTT
416681 TTCCT-TTT
1 TT--TATTT
**
416689 TTTCCTT
1 TTTATTT
416696 TTT-TTT
1 TTTATTT
*
416702 CTTATTT
1 TTTATTT
*
416709 TTCATTT
1 TTTATTT
*
416716 TTCATTT
1 TTTATTT
*
416723 TTCATTT
1 TTTATTT
*
416730 TTTCTTT
1 TTTATTT
416737 TT
1 TT
416739 CTTCTTCTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
6 10 0.12
7 41 0.51
8 28 0.35
9 1 0.01
ACGTcount: A:0.10, C:0.09, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTATTT
Found at i:416659 original size:8 final size:8
Alignment explanation
Indices: 416641--416682 Score: 75
Period size: 8 Copynumber: 5.1 Consensus size: 8
416631 CACTCCTTTA
416641 TTTATTTTT
1 TTTA-TTTT
416650 TTTATTTT
1 TTTATTTT
416658 TTTATTTT
1 TTTATTTT
416666 TTTATTTT
1 TTTATTTT
416674 TTTATTTT
1 TTTATTTT
416682 T
1 T
416683 CCTTTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 29 0.88
9 4 0.12
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:416690 original size:9 final size:9
Alignment explanation
Indices: 416678--416717 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
416668 TATTTTTTTA
416678 TTTTTCCTT
1 TTTTTCCTT
416687 TTTTTCCTT
1 TTTTTCCTT
*
416696 TTTTTTCTT
1 TTTTTCCTT
*
416705 ATTTTTCATT
1 -TTTTTCCTT
416715 TTT
1 TTT
416718 CATTTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:416702 original size:19 final size:19
Alignment explanation
Indices: 416645--416717 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 19
416635 CCTTTATTTA
416645 TTTTTT-TTATTTTT--TT
1 TTTTTTCTTATTTTTCATT
*
416661 ATTTTT-TTATTTTT--TT
1 TTTTTTCTTATTTTTCATT
* *
416677 ATTTTTCCTT-TTTTTCCTT
1 -TTTTTTCTTATTTTTCATT
416696 TTTTTTCTTATTTTTCATT
1 TTTTTTCTTATTTTTCATT
416715 TTT
1 TTT
416718 CATTTTTCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
16 15 0.32
17 9 0.19
18 10 0.21
19 13 0.28
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTCTTATTTTTCATT
Found at i:418851 original size:7 final size:7
Alignment explanation
Indices: 418841--418871 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
418831 TTGTATATGT
418841 TATAAGA
1 TATAAGA
418848 TATAAGA
1 TATAAGA
418855 TATAAGA
1 TATAAGA
*
418862 TATAGGA
1 TATAAGA
418869 TAT
1 TAT
418872 GAACATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (7 bp):
TATAAGA
Found at i:427747 original size:16 final size:16
Alignment explanation
Indices: 427726--427761 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
427716 GACACATAGT
427726 TCCTTGGTAGGCTATC
1 TCCTTGGTAGGCTATC
427742 TCCTTGGTAGGCTATC
1 TCCTTGGTAGGCTATC
427758 TCCT
1 TCCT
427762 CGCTCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.28, G:0.22, T:0.39
Consensus pattern (16 bp):
TCCTTGGTAGGCTATC
Found at i:429605 original size:12 final size:12
Alignment explanation
Indices: 429588--429612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
429578 CAAATAAGTG
429588 TCCTTGAAAATA
1 TCCTTGAAAATA
429600 TCCTTGAAAATA
1 TCCTTGAAAATA
429612 T
1 T
429613 TCAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCCTTGAAAATA
Found at i:431291 original size:3 final size:3
Alignment explanation
Indices: 431285--431342 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
431275 TAACATCATC
431285 ATA ATA ATA ATA 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 ATA ATA ATA ATA
431333 ATA ATA ATA A
1 ATA ATA ATA A
431343 ATTAGAACCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:431587 original size:2 final size:2
Alignment explanation
Indices: 431580--431604 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
431570 TTTTTAAAAG
431580 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 A
431605 CTTTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:439347 original size:21 final size:21
Alignment explanation
Indices: 439322--439365 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
439312 AATTTAAAAT
*
439322 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
439343 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
439364 GT
1 GT
439366 AATTTAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:441456 original size:13 final size:13
Alignment explanation
Indices: 441438--441474 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
441428 TTCACGGTAT
441438 AGAAGAAGAAAGA
1 AGAAGAAGAAAGA
441451 AGAAGAAGAAAGA
1 AGAAGAAGAAAGA
*
441464 AAAAGAAGAAA
1 AGAAGAAGAAA
441475 AGAGTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAGAAGAAAGA
Found at i:442292 original size:88 final size:88
Alignment explanation
Indices: 442143--442304 Score: 324
Period size: 88 Copynumber: 1.8 Consensus size: 88
442133 TACAATAATA
442143 TTTATTTCTTGGGGACCATAACCTCTTTATATAGTTGATTTAAGAATTAGTTATTGTTTGTACTT
1 TTTATTTCTTGGGGACCATAACCTCTTTATATAGTTGATTTAAGAATTAGTTATTGTTTGTACTT
442208 ATAACTTTGCCCATACGATACTT
66 ATAACTTTGCCCATACGATACTT
442231 TTTATTTCTTGGGGACCATAACCTCTTTATATAGTTGATTTAAGAATTAGTTATTGTTTGTACTT
1 TTTATTTCTTGGGGACCATAACCTCTTTATATAGTTGATTTAAGAATTAGTTATTGTTTGTACTT
442296 ATAACTTTG
66 ATAACTTTG
442305 ACACTCATTG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (88 bp):
TTTATTTCTTGGGGACCATAACCTCTTTATATAGTTGATTTAAGAATTAGTTATTGTTTGTACTT
ATAACTTTGCCCATACGATACTT
Found at i:446569 original size:21 final size:21
Alignment explanation
Indices: 446544--446593 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
446534 AAATGAGCAT
*
446544 ACATAATTGTCTCGAAGGACC
1 ACATAATTGTCCCGAAGGACC
* *
446565 ACATAGGTTTGTCCCGAATGACC
1 ACATA--ATTGTCCCGAAGGACC
446588 ACATAA
1 ACATAA
446594 AACCCTCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.22
23 18 0.78
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (21 bp):
ACATAATTGTCCCGAAGGACC
Found at i:457535 original size:18 final size:19
Alignment explanation
Indices: 457512--457550 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
457502 ATTGAAGAGG
457512 AAGATTTG-AAAAAGAGAA
1 AAGATTTGAAAAAAGAGAA
457530 AAGATTTGAAAAAAGAGAA
1 AAGATTTGAAAAAAGAGAA
457549 AA
1 AA
457551 ATATGATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (19 bp):
AAGATTTGAAAAAAGAGAA
Found at i:463279 original size:3 final size:3
Alignment explanation
Indices: 463273--463297 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
463263 TACGATTACA
463273 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
463298 ACTCCAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:465775 original size:8 final size:8
Alignment explanation
Indices: 465762--465790 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
465752 TGAATTAATC
465762 TATAATAT
1 TATAATAT
465770 TATAATAT
1 TATAATAT
465778 TATAATAT
1 TATAATAT
465786 TATAA
1 TATAA
465791 AAATTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TATAATAT
Found at i:475290 original size:36 final size:36
Alignment explanation
Indices: 475241--475636 Score: 360
Period size: 36 Copynumber: 11.4 Consensus size: 36
475231 AAGGATTGGG
* *
475241 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
475277 ATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
475313 GTTTCAAGGGAAATTGTCTTAAGAGAGACCAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * ** *
475349 GTTTCAAAAGAAACAT-TCTTAA-AG-TTC----TGT
1 GTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTT
* *
475379 GTTTCAAGAGAAACT-TCTCAAGGGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
475414 GTTTCAAGGGAACCTATCTCAAGAGAGATAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
475450 GTTTCAAGGGAACCTATCTCAAGAGAGATAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
475486 GTTTCAAGGGAAAC-GTTTTC-A-A-AG-----TTTAT
1 GTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-T
* *
475515 GTTTCAAGAGAAATTGTCTCAATG-GAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
*
475551 GTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
475587 GTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
475623 GTTTCAAGGGAAAC
1 GTTTCAAGGGAAAC
475637 AAAATTTGTT
Statistics
Matches: 298, Mismatches: 41, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 21 0.07
30 18 0.06
31 1 0.00
32 2 0.01
33 2 0.01
34 2 0.01
35 19 0.06
36 228 0.77
37 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:475435 original size:137 final size:137
Alignment explanation
Indices: 475241--476406 Score: 716
Period size: 137 Copynumber: 8.7 Consensus size: 137
475231 AAGGATTGGG
*
475241 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * * **
475306 AAAATTCGTTTCAAGGGAAATTGTCTTAAGAGAGACCAAATTTGTTTCAAAAGAAACATTCTT-A
66 AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACATT-TTCA
*
475370 AAGTTCTGT
130 AAGTT-TAT
* * *
475379 GTTTCAAGAGAAACT-TCTCAAGGGAGACAAAATTTGTTTCAAGGGAACCTATCTCAAGAGAGAT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * ** *
475443 AAAATTCGTTTCAAGGGAACCTATCTCAAGAGAGATAAAATTCGTTTCAAGGGAAACGTTTTCAA
66 AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACATTTTCAA
475508 AGTTTAT
131 AGTTTAT
* * *
475515 GTTTCAAGAGAAATTGTCTCAATGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* **
475580 AAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACA-----AA
66 AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACATTTTCAA
475640 A--TT-T
131 AGTTTAT
* * * * *
475644 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGGAAAC-GTTTTC-A-A-AG-
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGA
*** ** * * ** * *
475704 -TTTA-T-GTTTCAAGATAAACTATCTCAAG-GAAGACAAAATTCGTTTCAAGGGGAAC-TGTCT
65 CAAAATTCGTTTCAAGGGAAACTATCTCAAGAG-AGATAAAATTTGTTTCAAAAGAAACAT-TTT
475764 CAAGAG---A-
128 CAA-AGTTTAT
* ** * * * *
475771 G--ACAA-A-ATTC-GTTTTAAGGGAAACATTTTCAAAGTTTATGTTTCAAGGGAGACAAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACA-----AAA--TT-TGTTTCAA-GG-G---AAA-CT
* * * * *
475831 GTTTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAG
52 GTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAA
* * ***
475896 GGAAAC-TGTCTCAAGATAGACAAAATT
117 AGAAACAT-TTTC-A-A-AG--TTTA-T
* * * *
475923 CGTTTCAAGAGAAAC-GTTTTCAA---AG-----TTTATATTTCAAGAGAAACTGTCTCAAGAGA
1 -GTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT-TGTTTCAAGGGAAACTGTCTCAAGAGA
* * * * ** *
475979 GACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC-TGTC
63 GACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACAT-TT
***
476043 TCAAGAGAGACAAAATT
127 TC-A-A-AG--TTTA-T
* * * * *
476060 CGTTTCAAGGGAAAC-GTTCTCAA---AG-----TTTATGTTTCAAGAGAAACTATCTCAAGGGA
1 -GTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT-TGTTTCAAGGGAAACTGTCTCAAGAGA
* * * **
476116 GACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATTTT
63 GACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACATTTT
476181 CAAAGTTTAT
128 CAAAGTTTAT
* *
476191 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * * *** *
476256 AAAATTCATTTCTAGGG-AA--A---C---------AAAATTCGTTTCATGGGAAACATTCTCAA
66 AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACATTTTCAA
476306 AGTTTAT
131 AGTTTAT
*
476313 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
476378 AAAATTCGTTTCAAGGGAAACGT-TCTCAA
66 AAAATTCGTTTCAAGGGAAAC-TATCTCAA
476407 AGTTTATGTT
Statistics
Matches: 859, Mismatches: 99, Indels: 148
0.78 0.09 0.13
Matches are distributed among these distances:
121 1 0.00
122 166 0.19
123 5 0.01
124 1 0.00
125 3 0.00
126 2 0.00
127 7 0.01
128 4 0.00
129 51 0.06
130 27 0.03
131 5 0.01
132 5 0.01
133 2 0.00
134 2 0.00
135 4 0.00
136 25 0.03
137 442 0.51
138 21 0.02
139 2 0.00
141 2 0.00
142 2 0.00
143 60 0.07
144 2 0.00
145 3 0.00
150 1 0.00
153 1 0.00
155 4 0.00
156 1 0.00
157 3 0.00
158 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (137 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAAAGAAACATTTTCAA
AGTTTAT
Found at i:475518 original size:101 final size:101
Alignment explanation
Indices: 475413--475600 Score: 261
Period size: 101 Copynumber: 1.9 Consensus size: 101
475403 AGACAAAATT
* * * * *
475413 TGTTTCAAGGGAACCTATCTCAA-GAGAGATAAAATTCGTTTCAAGGGAACCTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTATCTCAATG-GAGACAAAATTCGTTTAAAGGGAAACTATCTCAAGAGAG
*
475477 ATAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTA
65 ACAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTA
* * * *
475514 TGTTTCAAGAGAAATTGTCTCAATGGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTATCTCAATGGAGACAAAATTCGTTTAAAGGGAAACTATCTCAAGAGAGA
*
475579 CAAAATTTGTTTCAAGGGAAAC
66 CAAAATTCGTTTCAAGGGAAAC
475601 TATCTCAAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
101 74 0.99
102 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTATCTCAATGGAGACAAAATTCGTTTAAAGGGAAACTATCTCAAGAGAGA
CAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTA
Found at i:475640 original size:21 final size:21
Alignment explanation
Indices: 475616--475657 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
475606 CAAGAGAGAT
475616 AAAATTTGTTTCAAGGGAAAC
1 AAAATTTGTTTCAAGGGAAAC
475637 AAAATTTGTTTCAAGGGAAAC
1 AAAATTTGTTTCAAGGGAAAC
475658 TGTCTCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAAATTTGTTTCAAGGGAAAC
Found at i:475657 original size:57 final size:57
Alignment explanation
Indices: 475569--475754 Score: 203
Period size: 57 Copynumber: 3.1 Consensus size: 57
475559 GGAAACTGTC
* * * *
475569 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTT
1 TCAAGGGAAACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTT
*
475626 TCAAGGGAAACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTT
1 TCAAGGGAAACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTT
* * **
475683 TAAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGATAAACTATCTCAAG-GAAGACAAAATTCGT
1 TCAAGGGAAA------CAAA-ATT-TGTTTCAAGGGAAACTATCTCAAGAG-AGACAAAATTCGT
475747 T
57 T
475748 TCAAGGG
1 TCAAGGG
475755 GAACTGTCTC
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
57 61 0.56
63 4 0.04
64 3 0.03
65 41 0.38
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (57 bp):
TCAAGGGAAACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTT
Found at i:475667 original size:194 final size:194
Alignment explanation
Indices: 475443--475794 Score: 571
Period size: 194 Copynumber: 1.8 Consensus size: 194
475433 CAAGAGAGAT
* * *
475443 AAAATTCGTTTCAAGGGAACCTATCTCAAGAGAGATAAAATTCGTTTCAAGGGAAACGTTTTCAA
1 AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGGGAAACGTTTTCAA
* * *
475508 AGTTTATGTTTCAAGAGAAATTGTCTCAATGG-AGACAAAATTTGTTTAAAGGGAAACTGTCTCA
66 AGTTTATGTTTCAAGAGAAACTATCTCAA-GGAAGACAAAATTCGTTTAAAGGGAAACTGTCTCA
*
475572 AGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAC
130 AGAGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAC
* *
475637 AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGGAAACGTTTTCAA
1 AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGGGAAACGTTTTCAA
* * *
475702 AGTTTATGTTTCAAGATAAACTATCTCAAGGAAGACAAAATTCGTTTCAAGGGGAACTGTCTCAA
66 AGTTTATGTTTCAAGAGAAACTATCTCAAGGAAGACAAAATTCGTTTAAAGGGAAACTGTCTCAA
*
475767 GAGAGACAAAATTCGTTTTAAGGGAAAC
131 GAGAGACAAAATTCGTTTCAAGGGAAAC
475795 ATTTTCAAAG
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
193 2 0.01
194 142 0.99
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (194 bp):
AAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGGGAAACGTTTTCAA
AGTTTATGTTTCAAGAGAAACTATCTCAAGGAAGACAAAATTCGTTTAAAGGGAAACTGTCTCAA
GAGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAC
Found at i:475765 original size:36 final size:36
Alignment explanation
Indices: 475709--476276 Score: 419
Period size: 36 Copynumber: 16.4 Consensus size: 36
475699 CAAAGTTTAT
** *
475709 GTTTCAAGATAAACTATCTCAAG-GAAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAATTC
*
475745 GTTTCAAGGGGAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
* * ***
475781 GTTTTAAGGGAAACAT-TTTC-A-A-AG--TTTA-T-
1 GTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTC
* * * *
475810 GTTTCAAGGGAGACAAAATTTGTTTCAAGGGAGACAAAATTT
1 GTTTCAA-GG-G---AAA-CTGTCTCAAGAGAGACAAAATTC
* *
475852 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
*
475888 GTTTCAAGGGAAACTGTCTCAAGATAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
* * ***
475924 GTTTCAAGAGAAAC-GTTTTC-A-A-AG--TTTA-T-
1 GTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTC
* * *
475953 ATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
475989 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
476025 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
***
476061 GTTTCAAGGGAAAC-GTTCTC-A-A-AG--TTTA-T-
1 GTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTC
* * * *
476090 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
*
476126 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
* ***
476162 GTTTCAAGGGAAACAT-TTTC-A-A-AG--TTTA-T-
1 GTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTC
* * * *
476191 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
*
476227 GTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
* *
476263 ATTTCTAGGGAAAC
1 GTTTCAAGGGAAAC
476277 AAAATTCGTT
Statistics
Matches: 424, Mismatches: 65, Indels: 86
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.00
29 55 0.13
30 10 0.02
31 6 0.01
32 6 0.01
33 8 0.02
34 11 0.03
35 13 0.03
36 294 0.69
37 6 0.01
38 2 0.00
40 2 0.00
41 3 0.01
42 7 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTC
Found at i:475801 original size:101 final size:105
Alignment explanation
Indices: 475626--475901 Score: 382
Period size: 101 Copynumber: 2.6 Consensus size: 105
475616 AAAATTTGTT
475626 TCAAGGGAA-ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGG
1 TCAA-GGAAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGG
* *
475690 AAACGTTTTCAAAGTTTATGTTTC-A-AGA-TAAA-CTATC
65 AAACATTTTCAAAGTTTATGTTTCAAGAGACAAAATCTATC
* * *
475727 TCAAGGAAGACAAAATTCGTTTCAAGGGGAACTGTCTCAAGAGAGACAAAATTCGTTTTAAGGGA
1 TCAAGGAAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGGA
* * *
475792 AACATTTTCAAAGTTTATGTTTCAAGGGAGACAAAATTTGTT
66 AACATTTTCAAAGTTTATGTTTCAA--GAGACAAAATCTATC
* * * *
475834 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
1 TCAAGGAAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGGA
475899 AAC
66 AAC
475902 TGTCTCAAGA
Statistics
Matches: 154, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
100 4 0.03
101 79 0.51
102 1 0.01
105 3 0.02
106 3 0.02
107 64 0.42
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (105 bp):
TCAAGGAAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGGGA
AACATTTTCAAAGTTTATGTTTCAAGAGACAAAATCTATC
Found at i:475833 original size:21 final size:21
Alignment explanation
Indices: 475809--475862 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
475799 TCAAAGTTTA
475809 TGTTTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAGACAAAATT
475830 TGTTTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAGACAAAATT
475851 TGTTTCAAGGGA
1 TGTTTCAAGGGA
475863 AACTATCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (21 bp):
TGTTTCAAGGGAGACAAAATT
Found at i:475983 original size:101 final size:101
Alignment explanation
Indices: 475853--476038 Score: 336
Period size: 101 Copynumber: 1.8 Consensus size: 101
475843 ACAAAATTTG
* *
475853 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGATAGACA
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
475918 AAATTCGTTTCAAGAGAAACGTTTTCAAAGTTTATA
66 AAATTCGTTTCAAGAGAAACGTTTTCAAAGTTTATA
*
475954 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
*
476019 AAATTCGTTTCAAGGGAAAC
66 AAATTCGTTTCAAGAGAAAC
476039 TGTCTCAAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (101 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
AAATTCGTTTCAAGAGAAACGTTTTCAAAGTTTATA
Found at i:476093 original size:101 final size:101
Alignment explanation
Indices: 475988--476277 Score: 481
Period size: 101 Copynumber: 2.9 Consensus size: 101
475978 AGACAAAATT
* * *
475988 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
476053 CAAAATTCGTTTCAAGGGAAACGTTCTCAAAGTTTA
66 CAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTA
*
476089 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* *
476154 CAAAATTTGTTTCAAGGGAAACATTTTCAAAGTTTA
66 CAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTA
* *
476190 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* *
476255 CAAAATTCATTTCTAGGGAAACA
66 CAAAATTCGTTTCAAGGGAAACA
476278 AAATTCGTTT
Statistics
Matches: 176, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 176 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
CAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTA
Found at i:476134 original size:21 final size:21
Alignment explanation
Indices: 476108--476172 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
476098 AGAAACTATC
476108 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
476129 TCAA-GG-G---AAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
*
476144 TCAAGAGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
476165 TCAAGGGA
1 TCAAGGGA
476173 AACATTTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 7 0.22
16 4 0.12
17 1 0.03
19 1 0.03
20 5 0.16
21 14 0.44
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:476146 original size:65 final size:65
Alignment explanation
Indices: 476025--476147 Score: 194
Period size: 65 Copynumber: 1.9 Consensus size: 65
476015 GACAAAATTC
* *
476025 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGTTTAT
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGTTTAT
* *
476090 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC-TGTCTCAA
1 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGT-TCTCAA
476148 GAGAGACAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 1 0.02
65 52 0.98
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (65 bp):
GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGTTTAT
Found at i:476280 original size:21 final size:21
Alignment explanation
Indices: 476254--476298 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
476244 CCCAAGAGAG
476254 ACAAAATTCATTTC-TAGGGAA
1 ACAAAATTCATTTCAT-GGGAA
*
476275 ACAAAATTCGTTTCATGGGAA
1 ACAAAATTCATTTCATGGGAA
476296 ACA
1 ACA
476299 TTCTCAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
ACAAAATTCATTTCATGGGAA
Found at i:476299 original size:122 final size:122
Alignment explanation
Indices: 476144--476398 Score: 438
Period size: 122 Copynumber: 2.1 Consensus size: 122
476134 GGAAACTGTC
* * * *
476144 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACATTTTCAAAGTTTATGTTTCAAGAGAAACTGTC
1 TCAAGGGAAACAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTGTC
476209 TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCATT
66 TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCATT
* *
476266 TCTAGGGAAACAAAATTCGTTTCATGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTGTC
1 TCAAGGGAAACAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTGTC
* *
476331 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCGTT
66 TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCATT
476388 TCAAGGGAAAC
1 TCAAGGGAAAC
476399 GTTCTCAAAG
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (122 bp):
TCAAGGGAAACAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTGTC
TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCATT
Found at i:476305 original size:223 final size:224
Alignment explanation
Indices: 476052--476490 Score: 727
Period size: 223 Copynumber: 2.0 Consensus size: 224
476042 CTCAAGAGAG
*
476052 ACAAAATTCGTTTCAAGGGAAACGTTCTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAG
1 ACAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAG
* * *
476117 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATTTTC
66 ACAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCGTTTCAAGGGAAACATTCTC
* **
476182 AAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAG-GGAAACTGTCC
131 AAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAATTTGTTTCAAGTAAAAACTGTCC
476246 CAAGAGAGACAAAATTCATTTCTAGGGAA
196 CAAGAGAGACAAAATTCATTTCTAGGGAA
* *
476275 ACAAAATTCGTTTCATGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAG
1 ACAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAG
*
476340 ACAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTCTC
66 ACAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCGTTTCAAGGGAAACATTCTC
* ** * *
476405 AAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTGAGTAAAAATTGTCT
131 AAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAATTTGTTTCAAGTAAAAACTGTCC
*
476470 CAAGTGAGACAAAATTCATTT
196 CAAGAGAGACAAAATTCATTT
476491 TTTGGAGAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
223 172 0.86
224 27 0.14
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (224 bp):
ACAAAATTCGTTTCAAGGGAAACATTCTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAG
ACAAAATTTGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATTCGTTTCAAGGGAAACATTCTC
AAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAATTTGTTTCAAGTAAAAACTGTCC
CAAGAGAGACAAAATTCATTTCTAGGGAA
Found at i:476362 original size:36 final size:36
Alignment explanation
Indices: 476312--476485 Score: 150
Period size: 36 Copynumber: 5.0 Consensus size: 36
476302 TCAAAGTTTA
476312 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * *
476348 TGTTTCAAGGGAAACTGTCCCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * *
476384 CGTTTCAAGGGAAAC-GTTCTCAA---AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATT
*
476412 ATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
** * * *
476449 TGTTTTGAGTAAAAATTGTCTCAAGTGAGACAAAATT
1 TGTTTCAAG-AGAAACTGTCTCAAGGGAGACAAAATT
476486 CATTTTTTGG
Statistics
Matches: 110, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.02
29 19 0.17
32 2 0.02
33 2 0.02
35 1 0.01
36 59 0.54
37 25 0.23
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:476471 original size:37 final size:36
Alignment explanation
Indices: 476430--476563 Score: 121
Period size: 37 Copynumber: 3.6 Consensus size: 36
476420 AGAGAAACTA
*
476430 TCTCAAGGGAGACAAAATTTGTTTTGAGTAAAAATTG
1 TCTCAAGTGAGACAAAATTTGTTTTGAG-AAAAATTG
*
476467 TCTCAAGTGAGACAAAATTCATTTTTTG-GAGAAAA-TG
1 TCTCAAGTGAGACAAAATT--TGTTTTGAGA-AAAATTG
** * * *
476504 ATCTCAAGTGAGATTAATTTTGTTTTAAGGAAAATTG
1 -TCTCAAGTGAGACAAAATTTGTTTTGAGAAAAATTG
*
476541 TCTCCAA-CGAGACAAAATTTGTT
1 TCT-CAAGTGAGACAAAATTTGTT
476564 CTCAGGAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
36 24 0.31
37 27 0.35
38 21 0.27
39 6 0.08
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (36 bp):
TCTCAAGTGAGACAAAATTTGTTTTGAGAAAAATTG
Found at i:476510 original size:38 final size:35
Alignment explanation
Indices: 476421--476563 Score: 105
Period size: 36 Copynumber: 3.9 Consensus size: 35
476411 TATGTTTCAA
* *
476421 GAGAAACT-ATCTCAAGGGAGACAAAATTTGTTTT
1 GAGAAAATGATCTCAAGTGAGACAAAATTTGTTTT
*
476455 GAGTAAAAATTG-TCTCAAGTGAGACAAAATTCATTTTTT
1 GAG--AAAA-TGATCTCAAGTGAGACAAAATT--TGTTTT
** *
476494 GGAGAAAATGATCTCAAGTGAGATTAATTTTGTTTT
1 -GAGAAAATGATCTCAAGTGAGACAAAATTTGTTTT
* *
476530 AAGGAAAATTG-TCTCCAA-CGAGACAAAATTTGTT
1 GA-GAAAA-TGATCT-CAAGTGAGACAAAATTTGTT
476564 CTCAGGAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
34 3 0.03
35 1 0.01
36 28 0.33
37 26 0.30
38 20 0.23
39 5 0.06
40 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (35 bp):
GAGAAAATGATCTCAAGTGAGACAAAATTTGTTTT
Found at i:476967 original size:38 final size:38
Alignment explanation
Indices: 476925--477013 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
476915 TAGTTTCTTA
* * *
476925 AAATCTTTTGTTTCGA-GTGAAACTATCTCAAGCGAGAT
1 AAATCTTATGTTTCAACG-GAAACTATCTCAAGCAAGAT
* * *
476963 AAATCTTCTATTTTAACGGAAACTATCTCAAGCAAGAT
1 AAATCTTATGTTTCAACGGAAACTATCTCAAGCAAGAT
477001 AAATCTTATGTTT
1 AAATCTTATGTTT
477014 TGAGAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 42 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (38 bp):
AAATCTTATGTTTCAACGGAAACTATCTCAAGCAAGAT
Found at i:478301 original size:6 final size:6
Alignment explanation
Indices: 478278--478334 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
478268 CTTATTGTCC
*
478278 TCTTTT TCTTTGT T-TTTT TC-TTT TCTTTT TC-TTT TCTTTT T-TTTC
1 TCTTTT TCTTT-T TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
478323 T-TTTT TCTTTT T
1 TCTTTT TCTTTT T
478335 TTCTCTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
5 20 0.45
6 22 0.50
7 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:478306 original size:11 final size:11
Alignment explanation
Indices: 478278--478342 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
478268 CTTATTGTCC
478278 TCTTTTTCTTT
1 TCTTTTTCTTT
*
478289 GTTTTTTTCTTT
1 -TCTTTTTCTTT
478301 TCTTTTTCTTT
1 TCTTTTTCTTT
478312 TC-TTTT-TTT
1 TCTTTTTCTTT
478321 TCTTTTTTCTTT
1 TC-TTTTTCTTT
*
478333 T-TTTCTCTTT
1 TCTTTTTCTTT
478343 GATTTCTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
9 5 0.11
10 12 0.26
11 16 0.34
12 14 0.30
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:478314 original size:16 final size:15
Alignment explanation
Indices: 478293--478342 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
478283 TTCTTTGTTT
478293 TTTTCTTTTCTTTTTC
1 TTTTCTTTT-TTTTTC
*
478309 TTTTCTTTTTTTTCTT
1 TTTTCTTTTTTTT-TC
*
478325 TTTTCTTTTTTTCTC
1 TTTTCTTTTTTTTTC
478340 TTT
1 TTT
478343 GATTTCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:478333 original size:5 final size:5
Alignment explanation
Indices: 478293--478326 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
478283 TTCTTTGTTT
478293 TTTTC TTTTC TTTTTC TTTTC TTTT- TTTTC TTTT
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT
478327 TTCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:478349 original size:35 final size:37
Alignment explanation
Indices: 478280--478361 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 37
478270 TATTGTCCTC
* * *
478280 TTTTTCTTTGTTTTTTTCTTTTCTTTTTCTTTTCTTT
1 TTTTTCTTTGTTTCTTTCTTTTCTCTTTCATTTCTTT
*
478317 TTTTTCTTT-TTTCTTT-TTTTCTCTTTGATTTCTTT
1 TTTTTCTTTGTTTCTTTCTTTTCTCTTTCATTTCTTT
* *
478352 CTTTGCTTTG
1 TTTTTCTTTG
478362 ATTTGATCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 23 0.61
36 6 0.16
37 9 0.24
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.79
Consensus pattern (37 bp):
TTTTTCTTTGTTTCTTTCTTTTCTCTTTCATTTCTTT
Found at i:479763 original size:37 final size:36
Alignment explanation
Indices: 479664--479783 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
479654 TGGCAACCAA
479664 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
479701 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
479736 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
479773 -GTTGAAAAATG
1 CTTTGAAAAATG
479784 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
35 32 0.41
36 18 0.23
37 28 0.36
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:480204 original size:16 final size:17
Alignment explanation
Indices: 480183--480217 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
480173 TACTATTCAC
*
480183 GTGAATAGT-GAATTTT
1 GTGAATAGTAAAATTTT
480199 GTGAATAGTAAAATTTT
1 GTGAATAGTAAAATTTT
480216 GT
1 GT
480218 CGGCGATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
GTGAATAGTAAAATTTT
Found at i:482209 original size:19 final size:19
Alignment explanation
Indices: 482185--482235 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
482175 ATTGTTTAAG
482185 GTGCATCGATGCACATGCA
1 GTGCATCGATGCACATGCA
482204 GTGCATCGATGCACATGCA
1 GTGCATCGATGCACATGCA
482223 GTGCATCGATGCA
1 GTGCATCGATGCA
482236 TGAATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.22
Consensus pattern (19 bp):
GTGCATCGATGCACATGCA
Found at i:482278 original size:64 final size:63
Alignment explanation
Indices: 482205--482364 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
482195 GCACATGCAG
* * *
482205 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTT
482268 A
63 A
* * *
482269 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTA
* *
482333 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGCAGTGCATCGATGCAT
482365 ACATTCATTG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTA
Found at i:482875 original size:17 final size:19
Alignment explanation
Indices: 482853--482888 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
482843 GATTTACATG
482853 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
482870 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
482889 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:483062 original size:31 final size:30
Alignment explanation
Indices: 483023--483115 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
483013 GTCGAGGGTT
483023 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTTT-GAGACATATGGACAG
**
483053 TATACCTATGTTCTAAG-GAACATATGGACAG
1 T-TACCTATGTTCTTTGAG-ACATATGGACAG
* * *
483084 TTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTACCTATGTTCTTTGAGACATATGGACAG
483114 TT
1 TT
483116 GTCGAGGTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
30 27 0.51
31 23 0.43
32 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (30 bp):
TTACCTATGTTCTTTGAGACATATGGACAG
Found at i:483135 original size:30 final size:30
Alignment explanation
Indices: 483044--483149 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
483034 TTTCGAGACA
* * * *
483044 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
483075 TATGGACAGTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
** *
483105 TATGGACAGTTGTCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
483135 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
483150 GGGTCTGTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
30 48 0.79
31 13 0.21
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:483993 original size:37 final size:36
Alignment explanation
Indices: 483894--484013 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
483884 TGGCAACCAA
483894 CTTTGAAAAATTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAGTTTGGTAAATGTTT
483931 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
483966 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
484003 -GTTGAAAAATG
1 CTTTGAAAAATG
484014 ATAACGGATA
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
35 32 0.41
36 18 0.23
37 28 0.36
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:487106 original size:15 final size:15
Alignment explanation
Indices: 487086--487115 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
487076 GATTAATATC
487086 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
487101 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
487116 ATAAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:493914 original size:43 final size:42
Alignment explanation
Indices: 493822--493925 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 42
493812 TTTGTTAACA
493822 AAAAACGCCGCAATAGGTAAGGATATATAGCAGCGTTTGTTC
1 AAAAACGCCGCAATAGGTAAGGATATATAGCAGCGTTTGTTC
* * * *
493864 AACAAACGCCGTAATAGTTAATGATATATAGC-GATGTTT-TTCC
1 AA-AAACGCCGCAATAGGTAAGGATATATAGCAG-CGTTTGTT-C
*
493907 TAAAAACGTCGCAATAGGT
1 -AAAAACGCCGCAATAGGT
493926 GTTGAGATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
42 5 0.10
43 44 0.86
44 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (42 bp):
AAAAACGCCGCAATAGGTAAGGATATATAGCAGCGTTTGTTC
Found at i:494033 original size:43 final size:43
Alignment explanation
Indices: 493910--494021 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
493900 TTTTTCCTAA
*
493910 AAACGTCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTATCAT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTATCAT
* * * * *
493953 AAATGCAGCAATAAGTGTTGAGATTTAGCGGCGTTTTTCTCGT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTATCAT
493996 AAACGCCGCAATAGGTGTTGAGATTT
1 AAACGCCGCAATAGGTGTTGAGATTT
494022 TGAAGTGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTATCAT
Found at i:494088 original size:44 final size:44
Alignment explanation
Indices: 494036--494227 Score: 242
Period size: 44 Copynumber: 4.4 Consensus size: 44
494026 GTGTTTTTTT
* * *
494036 ATACAAACGCCACTAAAGGTATGGTATGTAGCGGCGTTTTTAGG
1 ATACAAACGCCGCTAAAGGTATGGTATATAGCGGCATTTTTAGG
* * * *
494080 ATATAAACGCCGCTAAAGGTATGGTATATAGCGACGTTTTTAAG
1 ATACAAACGCCGCTAAAGGTATGGTATATAGCGGCATTTTTAGG
* *
494124 ATACAAACGTCGCTAAAGGTATGGTATATAACGGCATTTTTAGG
1 ATACAAACGCCGCTAAAGGTATGGTATATAGCGGCATTTTTAGG
* * * * *
494168 ATACAAAAGCCGCTAAATGTATGATATATTGCGGCATTTTT-TG
1 ATACAAACGCCGCTAAAGGTATGGTATATAGCGGCATTTTTAGG
*
494211 TTACAAACGCCGCTAAA
1 ATACAAACGCCGCTAAA
494228 TAACACAAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 16 0.12
44 112 0.88
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (44 bp):
ATACAAACGCCGCTAAAGGTATGGTATATAGCGGCATTTTTAGG
Found at i:494365 original size:22 final size:22
Alignment explanation
Indices: 494340--494384 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
494330 TTCATAATCT
*
494340 ATTATTTCCCTATTCGAAAGCA
1 ATTATTTCCCTATTCCAAAGCA
**
494362 ATTATTTTTCTATTCCAAAGCA
1 ATTATTTCCCTATTCCAAAGCA
494384 A
1 A
494385 AAAACACTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTATTTCCCTATTCCAAAGCA
Found at i:494926 original size:83 final size:81
Alignment explanation
Indices: 494821--495135 Score: 314
Period size: 83 Copynumber: 3.8 Consensus size: 81
494811 ATTAACAACA
* * * *
494821 TATTGCGGCGTTTGTAGGATAAATGCCGCTAAATTATTACTCTATTGTGGCGTTTGTTACACAAA
1 TATTGCGGCGTTTGTA-TATAAACGCCGCTAAATTATCACTCTATTGCGGCGTTTGTTA-ACAAA
*
494886 CGCCACTATCAACAACCC
64 CGCCACTATAAACAACCC
* * * * * *
494904 TATTGTGGCATTTGTTTTATAAACGCCGCTAAATTA-CTTCTCTATAGCGTCGTTTGTTGAACAA
1 TATTGCGGCGTTTG-TATATAAACGCCGCTAAATTATC-ACTCTATTGCGGCGTTTGTT-AACAA
* *
494968 ACACCA-TAATAAACAACCA
63 ACGCCACT-ATAAACAACCC
* * * *
494987 TATTGCGGCGTTTGTATAAAAACGCCGCTAAATTACCACTCTATTGCGGCATTTGTTGA-AAACG
1 TATTGCGGCGTTTGTATATAAACGCCGCTAAATTATCACTCTATTGCGGCGTTTGTTAACAAACG
*
495051 CCACTATAAACAACTC
66 CCACTATAAACAACCC
* * * * *
495067 TATTCCGACGTTTG-AGCTATAAATGCCGCTAAATTATCACTCTATTGCGACGTTTGTTTAAAAA
1 TATTGCGGCGTTTGTA--TATAAACGCCGCTAAATTATCACTCTATTGCGGCGTTTG-TTAACAA
495131 ACGCC
63 ACGCC
495136 GCTAAAGTAT
Statistics
Matches: 189, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
79 1 0.01
80 28 0.15
81 36 0.19
82 39 0.21
83 83 0.44
84 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (81 bp):
TATTGCGGCGTTTGTATATAAACGCCGCTAAATTATCACTCTATTGCGGCGTTTGTTAACAAACG
CCACTATAAACAACCC
Found at i:495032 original size:41 final size:40
Alignment explanation
Indices: 494821--495141 Score: 165
Period size: 41 Copynumber: 7.8 Consensus size: 40
494811 ATTAACAACA
* **
494821 TATTGCGGCGTTTG-TAGGATAAATGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTGTTA--A-AAACGCCGCTAAATTACAACTC
* * * *
494863 TATTGTGGCGTTTGTTACACAAACGCCACT--ATCAACAACCC
1 TATTGCGGCGTTTGTTA-A-AAACGCCGCTAAAT-TACAACTC
* * * **
494904 TATTGTGGCATTTGTTTTATAAACGCCGCTAAATTACTTCTC
1 TATTGCGGCGTTTG--TTAAAAACGCCGCTAAATTACAACTC
* * * * *
494946 TATAGCGTCGTTTGTTGAACAAACACC-AT-AATAAACAAC-C
1 TATTGCGGCGTTTGTT-AA-AAACGCCGCTAAAT-TACAACTC
*
494986 ATATTGCGGCGTTTGTATAAAAACGCCGCTAAATTACCACTC
1 -TATTGCGGCGTTTGT-TAAAAACGCCGCTAAATTACAACTC
* * *
495028 TATTGCGGCATTTGTTGAAAACGCCACTATAA--ACAACTC
1 TATTGCGGCGTTTGTTAAAAACGCCGCTA-AATTACAACTC
* * * * *
495067 TATTCCGACGTTTGAGCTATAAATGCCGCTAAATTATC-ACTC
1 TATTGCGGCGTTT--GTTAAAAACGCCGCTAAATTA-CAACTC
*
495109 TATTGCGACGTTTGTTTAAAAAACGCCGCTAAA
1 TATTGCGGCGTTTG-TT-AAAAACGCCGCTAAA
495142 GTATCATTTT
Statistics
Matches: 209, Mismatches: 48, Indels: 44
0.69 0.16 0.15
Matches are distributed among these distances:
39 16 0.08
40 29 0.14
41 79 0.38
42 77 0.37
43 8 0.04
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (40 bp):
TATTGCGGCGTTTGTTAAAAACGCCGCTAAATTACAACTC
Found at i:495099 original size:163 final size:165
Alignment explanation
Indices: 494814--495124 Score: 387
Period size: 163 Copynumber: 1.9 Consensus size: 165
494804 CGTCACGATT
* * ** * *
494814 AACAACATATTGCGGCGTTTGTAGGATAAATGCCGCTAAATTATTACTCTATTGTGGCGTTTGTT
1 AACAACATATTGCGGCGTTTGTAGGAAAAACGCCGCTAAATTACCACTCTATTGCGGCATTTGTT
* ** * *** *
494879 ACACAAACGCCACTATCAACAACCCTATTGTGGCATTTGTTTTATAAACGCCGCTAAATTA-CTT
66 ACACAAACGCCACTATAAACAACCCTATTCCGACATTTGAGCTATAAACGCCGCTAAATTATC-A
*
494943 CTCTATAGCGTCGTTTGTTGAACAAACACCATAATA
130 CTCTATAGCGACGTTTGTTGAACAAACACCATAATA
*
494979 AACAACCATATTGCGGCGTTTGTA-TAAAAACGCCGCTAAATTACCACTCTATTGCGGCATTTGT
1 AACAA-CATATTGCGGCGTTTGTAGGAAAAACGCCGCTAAATTACCACTCTATTGCGGCATTTGT
* * * *
495043 T-GA-AAACGCCACTATAAACAACTCTATTCCGACGTTTGAGCTATAAATGCCGCTAAATTATCA
65 TACACAAACGCCACTATAAACAACCCTATTCCGACATTTGAGCTATAAACGCCGCTAAATTATCA
*
495106 CTCTATTGCGACGTTTGTT
130 CTCTATAGCGACGTTTGTT
495125 TAAAAAACGC
Statistics
Matches: 123, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
163 64 0.52
164 2 0.02
165 39 0.32
166 18 0.15
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (165 bp):
AACAACATATTGCGGCGTTTGTAGGAAAAACGCCGCTAAATTACCACTCTATTGCGGCATTTGTT
ACACAAACGCCACTATAAACAACCCTATTCCGACATTTGAGCTATAAACGCCGCTAAATTATCAC
TCTATAGCGACGTTTGTTGAACAAACACCATAATA
Found at i:495137 original size:42 final size:41
Alignment explanation
Indices: 494987--495147 Score: 141
Period size: 42 Copynumber: 3.9 Consensus size: 41
494977 TAAACAACCA
* * *
494987 TATTGCGGCGTTTGTATAAAAACGCCGCTAAATTACCACTC
1 TATTGCGACGTTTGTTTAAAAACGCCGCTAAATTATCACTC
* * * *
495028 TATTGCGGCATTTG-TTGAAAACGCCACTATAA--A-CAACTC
1 TATTGCGACGTTTGTTTAAAAACGCCGCTA-AATTATC-ACTC
* ** * *
495067 TATTCCGACGTTTGAGCTATAAATGCCGCTAAATTATCACTC
1 TATTGCGACGTTTG-TTTAAAAACGCCGCTAAATTATCACTC
*
495109 TATTGCGACGTTTGTTTAAAAAACGCCGCTAAAGTATCA
1 TATTGCGACGTTTGTTT-AAAAACGCCGCTAAATTATCA
495148 TTTTGTGACA
Statistics
Matches: 94, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
38 1 0.01
39 16 0.17
40 14 0.15
41 26 0.28
42 36 0.38
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (41 bp):
TATTGCGACGTTTGTTTAAAAACGCCGCTAAATTATCACTC
Found at i:495655 original size:41 final size:41
Alignment explanation
Indices: 495610--495764 Score: 147
Period size: 42 Copynumber: 3.8 Consensus size: 41
495600 TAAACAACCA
*
495610 TATTGCGGCGTTTGTATAAAAACGCCGCTAAATTACCACTC
1 TATTGCGACGTTTGTATAAAAACGCCGCTAAATTACCACTC
* * * * *
495651 TATTGCGGCATTTGT-TGAAAACGCCACTATAA--ACAACTC
1 TATTGCGACGTTTGTATAAAAACGCCGCTA-AATTACCACTC
* * * *
495690 TATTCCGACGTTTG-AGCTATAAATGCCGCTAAATTATCACTC
1 TATTGCGACGTTTGTA--TAAAAACGCCGCTAAATTACCACTC
*
495732 TATTGCGACGTTTGTTTAAAAAACGCCGCTAAA
1 TATTGCGACGTTTGTAT-AAAAACGCCGCTAAA
495765 GTATCATTTT
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
39 17 0.19
40 14 0.16
41 27 0.30
42 31 0.35
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (41 bp):
TATTGCGACGTTTGTATAAAAACGCCGCTAAATTACCACTC
Found at i:496072 original size:623 final size:623
Alignment explanation
Indices: 494886--496132 Score: 2485
Period size: 623 Copynumber: 2.0 Consensus size: 623
494876 GTTACACAAA
494886 CGCCACTATCAACAACCCTATTGTGGCATTTGTTTTATAAACGCCGCTAAATTACTTCTCTATAG
1 CGCCACTATCAACAACCCTATTGTGGCATTTGTTTTATAAACGCCGCTAAATTACTTCTCTATAG
494951 CGTCGTTTGTTGAACAAACACCATAATAAACAACCATATTGCGGCGTTTGTATAAAAACGCCGCT
66 CGTCGTTTGTTGAACAAACACCATAATAAACAACCATATTGCGGCGTTTGTATAAAAACGCCGCT
495016 AAATTACCACTCTATTGCGGCATTTGTTGAAAACGCCACTATAAACAACTCTATTCCGACGTTTG
131 AAATTACCACTCTATTGCGGCATTTGTTGAAAACGCCACTATAAACAACTCTATTCCGACGTTTG
495081 AGCTATAAATGCCGCTAAATTATCACTCTATTGCGACGTTTGTTTAAAAAACGCCGCTAAAGTAT
196 AGCTATAAATGCCGCTAAATTATCACTCTATTGCGACGTTTGTTTAAAAAACGCCGCTAAAGTAT
495146 CATTTTGTGACATTTGTATTGTAAACGCCGCTACATGCTTAAATTTTGTGACGTTTGTCCTTAAA
261 CATTTTGTGACATTTGTATTGTAAACGCCGCTACATGCTTAAATTTTGTGACGTTTGTCCTTAAA
495211 ACGCCGCTAAAACGTTGCTGCAGAACACTTTTATTGTAGTGTAACCAGAAGCTCTGCGAATCCGA
326 ACGCCGCTAAAACGTTGCTGCAGAACACTTTTATTGTAGTGTAACCAGAAGCTCTGCGAATCCGA
*
495276 CCGTCCTCATCAGCCTTCACCACTTTTGAGGTATCAACATCTCCACTCCCAGTACTAAAAAACAA
391 CCGTCCTCATCAGCCTTCACCACTTTTGAGGTATCAACATCTCCACTACCAGTACTAAAAAACAA
495341 ATAAATACCTAATCAAGTAACTCGGAAAAATAATTGAAAATGAAAATAATCAACTTAGCACTCAA
456 ATAAATACCTAATCAAGTAACTCGGAAAAATAATTGAAAATGAAAATAATCAACTTAGCACTCAA
495406 ATAGTGCAGAAGGCTAGGAAGTACCAGTCAATAACATCCAAGATCTTTGGCTTCCCATCTGAAGT
521 ATAGTGCAGAAGGCTAGGAAGTACCAGTCAATAACATCCAAGATCTTTGGCTTCCCATCTGAAGT
495471 TAGTTGCAAGCCAGCAGCAGCCGGATCAACACCAGAAT
586 TAGTTGCAAGCCAGCAGCAGCCGGATCAACACCAGAAT
495509 CGCCACTATCAACAACCCTATTGTGGCATTTGTTTTATAAACGCCGCTAAATTACTTCTCTATAG
1 CGCCACTATCAACAACCCTATTGTGGCATTTGTTTTATAAACGCCGCTAAATTACTTCTCTATAG
495574 CGTCGTTTGTTGAACAAACACCATAATAAACAACCATATTGCGGCGTTTGTATAAAAACGCCGCT
66 CGTCGTTTGTTGAACAAACACCATAATAAACAACCATATTGCGGCGTTTGTATAAAAACGCCGCT
495639 AAATTACCACTCTATTGCGGCATTTGTTGAAAACGCCACTATAAACAACTCTATTCCGACGTTTG
131 AAATTACCACTCTATTGCGGCATTTGTTGAAAACGCCACTATAAACAACTCTATTCCGACGTTTG
495704 AGCTATAAATGCCGCTAAATTATCACTCTATTGCGACGTTTGTTTAAAAAACGCCGCTAAAGTAT
196 AGCTATAAATGCCGCTAAATTATCACTCTATTGCGACGTTTGTTTAAAAAACGCCGCTAAAGTAT
495769 CATTTTGTGACATTTGTATTGTAAACGCCGCTACATGCTTAAATTTTGTGACGTTTGTCCTTAAA
261 CATTTTGTGACATTTGTATTGTAAACGCCGCTACATGCTTAAATTTTGTGACGTTTGTCCTTAAA
495834 ACGCCGCTAAAACGTTGCTGCAGAACACTTTTATTGTAGTGTAACCAGAAGCTCTGCGAATCCGA
326 ACGCCGCTAAAACGTTGCTGCAGAACACTTTTATTGTAGTGTAACCAGAAGCTCTGCGAATCCGA
495899 CCGTCCTCATCAGCCTTCACCACTTTTGAGGTATCAACATCTCCACTACCAGTACTAAAAAACAA
391 CCGTCCTCATCAGCCTTCACCACTTTTGAGGTATCAACATCTCCACTACCAGTACTAAAAAACAA
495964 ATAAATACCTAATCAAGTAACTCGGAAAAATAATTGAAAATGAAAATAATCAACTTAGCACTCAA
456 ATAAATACCTAATCAAGTAACTCGGAAAAATAATTGAAAATGAAAATAATCAACTTAGCACTCAA
496029 ATAGTGCAGAAGGCTAGGAAGTACCAGTCAATAACATCCAAGATCTTTGGCTTCCCATCTGAAGT
521 ATAGTGCAGAAGGCTAGGAAGTACCAGTCAATAACATCCAAGATCTTTGGCTTCCCATCTGAAGT
496094 TAGTTGCAAGCCAGCAGCAGCCGGATCAACACCAGAAT
586 TAGTTGCAAGCCAGCAGCAGCCGGATCAACACCAGAAT
496132 C
1 C
496133 TGAAGAAAAA
Statistics
Matches: 623, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
623 623 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (623 bp):
CGCCACTATCAACAACCCTATTGTGGCATTTGTTTTATAAACGCCGCTAAATTACTTCTCTATAG
CGTCGTTTGTTGAACAAACACCATAATAAACAACCATATTGCGGCGTTTGTATAAAAACGCCGCT
AAATTACCACTCTATTGCGGCATTTGTTGAAAACGCCACTATAAACAACTCTATTCCGACGTTTG
AGCTATAAATGCCGCTAAATTATCACTCTATTGCGACGTTTGTTTAAAAAACGCCGCTAAAGTAT
CATTTTGTGACATTTGTATTGTAAACGCCGCTACATGCTTAAATTTTGTGACGTTTGTCCTTAAA
ACGCCGCTAAAACGTTGCTGCAGAACACTTTTATTGTAGTGTAACCAGAAGCTCTGCGAATCCGA
CCGTCCTCATCAGCCTTCACCACTTTTGAGGTATCAACATCTCCACTACCAGTACTAAAAAACAA
ATAAATACCTAATCAAGTAACTCGGAAAAATAATTGAAAATGAAAATAATCAACTTAGCACTCAA
ATAGTGCAGAAGGCTAGGAAGTACCAGTCAATAACATCCAAGATCTTTGGCTTCCCATCTGAAGT
TAGTTGCAAGCCAGCAGCAGCCGGATCAACACCAGAAT
Found at i:498161 original size:35 final size:32
Alignment explanation
Indices: 498054--498150 Score: 108
Period size: 35 Copynumber: 3.0 Consensus size: 32
498044 TTATTAAAAA
498054 TAAAAAAA-TAGAATTCAAATCTAACTTTAAT
1 TAAAAAAATTAGAATTCAAATCTAACTTTAAT
** *
498085 TAAAAAAATTAGAATTCAAAAAATAGAAAC-ATAAT
1 TAAAAAAATTAGAATTC---AAAT-CTAACTTTAAT
*
498120 GAAAAAAATTAGAATTCAAATCTAACTTTAA
1 TAAAAAAATTAGAATTCAAATCTAACTTTAA
498151 GTTATTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
31 11 0.21
32 15 0.28
35 24 0.45
36 3 0.06
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (32 bp):
TAAAAAAATTAGAATTCAAATCTAACTTTAAT
Found at i:498268 original size:22 final size:21
Alignment explanation
Indices: 498238--498278 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
498228 TTTTCATATT
* *
498238 ATATTATATTTTATATAAATAA
1 ATATGATA-TTTATAAAAATAA
498260 ATATGATATTTATAAAAAT
1 ATATGATATTTATAAAAAT
498279 TTAAAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATGATATTTATAAAAATAA
Found at i:498491 original size:6 final size:6
Alignment explanation
Indices: 498477--498525 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
498467 TCAAGGAAAT
*
498477 TAAAAA TAAAGA TAAAGA TAAAGA T--A-A TAAAGA TAAAGA TAAAGA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA
498522 TAAA
1 TAAA
498526 ATACAATGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 1 0.03
6 35 0.90
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.18
Consensus pattern (6 bp):
TAAAGA
Found at i:498507 original size:21 final size:21
Alignment explanation
Indices: 498481--498524 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
498471 GGAAATTAAA
498481 AATAAAGATAAAGATAAAGAT
1 AATAAAGATAAAGATAAAGAT
498502 AATAAAGATAAAGATAAAGAT
1 AATAAAGATAAAGATAAAGAT
498523 AA
1 AA
498525 AATACAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (21 bp):
AATAAAGATAAAGATAAAGAT
Found at i:498508 original size:15 final size:15
Alignment explanation
Indices: 498488--498518 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
498478 AAAAATAAAG
498488 ATAAAGATAAAGATA
1 ATAAAGATAAAGATA
498503 ATAAAGATAAAGATA
1 ATAAAGATAAAGATA
498518 A
1 A
498519 AGATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
ATAAAGATAAAGATA
Found at i:498578 original size:13 final size:13
Alignment explanation
Indices: 498560--498585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
498550 CATAGTTGAA
498560 CAGTCTTCATATG
1 CAGTCTTCATATG
498573 CAGTCTTCATATG
1 CAGTCTTCATATG
498586 TGCGTCTGTA
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:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:500790 original size:60 final size:60
Alignment explanation
Indices: 500679--500792 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
500669 AGCTAACAAC
* * *
500679 CATTTTAAATTAGTTCTTAAACTTTTGAACATTTCAATTTTATCCCTAAATTATGACATT
1 CATTCTAAATTAGTTCTTAAACTTTTGAACATCTCAATTTCATCCCTAAATTATGACATT
*
500739 CATTCTAAATTAG-TCTATAAACTTTTTGAACAATCT-AATTTCATTCC-AAATTAT
1 CATTCTAAATTAGTTCT-TAAAC-TTTTGAAC-ATCTCAATTTCATCCCTAAATTAT
500793 ACGTATATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
59 3 0.06
60 24 0.51
61 17 0.36
62 3 0.06
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (60 bp):
CATTCTAAATTAGTTCTTAAACTTTTGAACATCTCAATTTCATCCCTAAATTATGACATT
Found at i:502221 original size:15 final size:15
Alignment explanation
Indices: 502201--502231 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
502191 ACTGCACTTG
502201 TCACTATGCTTACCA
1 TCACTATGCTTACCA
502216 TCACTATGCTTACCA
1 TCACTATGCTTACCA
502231 T
1 T
502232 AACAGGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
TCACTATGCTTACCA
Found at i:509451 original size:249 final size:250
Alignment explanation
Indices: 509007--509630 Score: 959
Period size: 249 Copynumber: 2.5 Consensus size: 250
508997 AGGACTTCTG
* *
509007 TTCTCACACATGAATGAAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTCATC
1 TTCTCACACATGAATG-AATTAGTCCATGAATGCACAAGAATGTCAACTATGAAACTGATTGATC
*
509072 ATGTACAGATAGTCATGGC-AACTATAACATGCTCTGCTATATTTTGATGGTGTATGTTCCTTTT
65 ATGTACAGATAGTCATGGCAAACCATAACATG--CTGCTATATTTTGATGGTGTATGTTCCTTTT
* * *
509136 CTCACACATGAATGAATTAGTCCATGCATGCACAAGAATGTCAATTATGAAACTGAATGGTCATG
128 CTCACACATGAATGAATTAATCCATGCATGCACAAGAATGTCAACTATGAAACTGAATGATCATG
* * *
509201 TATATACAGTCATGGCAAACC-AACA-T-GCTGCTATATCTTGACGGTGTATGTTCTTT
193 TACAGACAGTCATGGC-AACCAAACATTCGCTGCTATATCTTGACGGTGTATGTTCCTT
* * * *
509257 TTCTCACACTTTGAATGAATTAGTCAATGTATGCACAAGAATGTCAACTATGAAACTGATTGTTC
1 TTCTCACAC-ATGAATGAATTAGTCCATGAATGCACAAGAATGTCAACTATGAAACTGATTGATC
*
509322 ATGTACAGATAGTCATGGCAAACCATAACGTGCTGCTATATTTTGATGGTGTATGTTCCTTTTCT
65 ATGTACAGATAGTCATGGCAAACCATAACATGCTGCTATATTTTGATGGTGTATGTTCCTTTTCT
* *
509387 CACACATGAATGGATTAATCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATCATGTA
130 CACACATGAATGAATTAATCCATGCATGCACAAGAATGTCAACTATGAAACTGAATGATCATGTA
* * *
509452 CAGACAGTCATGGCAACCATAACATTCTCTGCTATATTTTGATGGTGTATGTTCCTT
195 CAGACAGTCATGGCAACCA-AACATTCGCTGCTATATCTTGACGGTGTATGTTCCTT
509509 TTCTCACACATGAATGAATTAGTCCATGAATGCACAAGAATGTCAACTATGAAACTGATTGATCA
1 TTCTCACACATGAATGAATTAGTCCATGAATGCACAAGAATGTCAACTATGAAACTGATTGATCA
* *
509574 TATACAGATAAGTCATGGCAAACCATAACATGCTGCTGATATATTGATGGTGTATGT
66 TGTACAGAT-AGTCATGGCAAACCATAACATGCTGCT-ATATTTTGATGGTGTATGT
509631 ATGTTCTTTG
Statistics
Matches: 341, Mismatches: 25, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
248 4 0.01
249 105 0.31
250 76 0.22
251 77 0.23
252 61 0.18
253 18 0.05
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (250 bp):
TTCTCACACATGAATGAATTAGTCCATGAATGCACAAGAATGTCAACTATGAAACTGATTGATCA
TGTACAGATAGTCATGGCAAACCATAACATGCTGCTATATTTTGATGGTGTATGTTCCTTTTCTC
ACACATGAATGAATTAATCCATGCATGCACAAGAATGTCAACTATGAAACTGAATGATCATGTAC
AGACAGTCATGGCAACCAAACATTCGCTGCTATATCTTGACGGTGTATGTTCCTT
Found at i:509542 original size:126 final size:125
Alignment explanation
Indices: 509007--509630 Score: 932
Period size: 126 Copynumber: 5.0 Consensus size: 125
508997 AGGACTTCTG
*
509007 TTCTCACACATGAATGAAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTCATC
1 TTCTCACACATGAATG-AATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATC
* *
509072 ATGTACAGATAGTCATGGC-AACTATAACATGCTCTGCTATATTTTGATGGTGTATGTTCCTT
65 ATGTACAGACAGTCATGGCAAACCATAACATG--CTGCTATATTTTGATGGTGTATGTTCCTT
* * *
509134 TTCTCACACATGAATGAATTAGTCCATGCATGCACAAGAATGTCAATTATGAAACTGAATGGTCA
1 TTCTCACACATGAATGAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATCA
* * * * *
509199 TGTATATACAGTCATGGCAAACC--AACATGCTGCTATATCTTGACGGTGTATGTTCTTT
66 TGTACAGACAGTCATGGCAAACCATAACATGCTGCTATATTTTGATGGTGTATGTTCCTT
* * * *
509257 TTCTCACACTTTGAATGAATTAGTCAATGTATGCACAAGAATGTCAACTATGAAACTGATTGTTC
1 TTCTCACAC-ATGAATGAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATC
* *
509322 ATGTACAGATAGTCATGGCAAACCATAACGTGCTGCTATATTTTGATGGTGTATGTTCCTT
65 ATGTACAGACAGTCATGGCAAACCATAACATGCTGCTATATTTTGATGGTGTATGTTCCTT
* *
509383 TTCTCACACATGAATGGATTAATCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATCA
1 TTCTCACACATGAATGAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATCA
*
509448 TGTACAGACAGTCATGGC-AACCATAACATTCTCTGCTATATTTTGATGGTGTATGTTCCTT
66 TGTACAGACAGTCATGGCAAACCATAACA-T-GCTGCTATATTTTGATGGTGTATGTTCCTT
*
509509 TTCTCACACATGAATGAATTAGTCCATGAATGCACAAGAATGTCAACTATGAAACTGATTGATCA
1 TTCTCACACATGAATGAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATCA
* * *
509574 TATACAGATAAGTCATGGCAAACCATAACATGCTGCTGATATATTGATGGTGTATGT
66 TGTACAGA-CAGTCATGGCAAACCATAACATGCTGCT-ATATTTTGATGGTGTATGT
509631 ATGTTCTTTG
Statistics
Matches: 448, Mismatches: 40, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
123 35 0.08
124 79 0.18
125 74 0.17
126 203 0.45
127 47 0.10
128 10 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (125 bp):
TTCTCACACATGAATGAATTAGTCCATGCATGCACAAGAATGTCAACTATGAAACTGATTGATCA
TGTACAGACAGTCATGGCAAACCATAACATGCTGCTATATTTTGATGGTGTATGTTCCTT
Found at i:512757 original size:18 final size:18
Alignment explanation
Indices: 512734--512769 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
512724 TGGAGGTGGC
512734 CGCGGTGGAGGAAGAGGA
1 CGCGGTGGAGGAAGAGGA
512752 CGCGGTGGAGGAAGAGGA
1 CGCGGTGGAGGAAGAGGA
512770 GGGATGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.56, T:0.06
Consensus pattern (18 bp):
CGCGGTGGAGGAAGAGGA
Found at i:518038 original size:29 final size:29
Alignment explanation
Indices: 517979--518038 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
517969 ACATCACCCT
* * *
517979 AAACACGTCCATTGCATGGCCATATATGC
1 AAACACGTCCATTGCATGGCCAGAAAGGC
518008 AAACACGTCCATTGCATGGCCAGAAAGGC
1 AAACACGTCCATTGCATGGCCAGAAAGGC
518037 AA
1 AA
518039 CTCGCTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (29 bp):
AAACACGTCCATTGCATGGCCAGAAAGGC
Found at i:519553 original size:23 final size:23
Alignment explanation
Indices: 519537--519591 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
519527 CGTATAAATA
*
519537 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTACCACGTAGAATTG
*
519560 CACCGAAGTACCGCGTAGAATTG
1 CACCGAAGTACCACGTAGAATTG
519583 CACCGAAGT
1 CACCGAAGT
519592 TCCATATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
CACCGAAGTACCACGTAGAATTG
Found at i:531692 original size:24 final size:21
Alignment explanation
Indices: 531648--531694 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
531638 CTAATTGTAT
*
531648 TATCGATACCCTAGGGTTAAG
1 TATCGATACCCTAGAGTTAAG
531669 TATCGATACCCCTATGAGTATAAG
1 TATCGATA-CCCTA-GAGT-TAAG
531693 TA
1 TA
531695 CAAAAAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 5 0.23
23 3 0.14
24 6 0.27
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
TATCGATACCCTAGAGTTAAG
Found at i:535449 original size:15 final size:15
Alignment explanation
Indices: 535429--535458 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
535419 GACCCGTTCG
535429 GATTAGATTAGAACC
1 GATTAGATTAGAACC
535444 GATTAGATTAGAACC
1 GATTAGATTAGAACC
535459 TAATTACGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
GATTAGATTAGAACC
Found at i:535891 original size:21 final size:21
Alignment explanation
Indices: 535847--535889 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
535837 CGGTAAAAAA
*
535847 TTATCTAAAATATTATTATTT
1 TTATCTAAAATATTAATATTT
535868 TTATCTAAAATATTAA-ATTT
1 TTATCTAAAATATTAATATTT
535888 TT
1 TT
535890 TAATATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATCTAAAATATTAATATTT
Found at i:537283 original size:19 final size:20
Alignment explanation
Indices: 537247--537290 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
537237 TTATCCGGAA
*
537247 AAAAATTCGGTCTAGGGTTT
1 AAAAATCCGGTCTAGGGTTT
537267 AAAAATCCGGTCT-GGGTTT
1 AAAAATCCGGTCTAGGGTTT
537286 AAAAA
1 AAAAA
537291 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (20 bp):
AAAAATCCGGTCTAGGGTTT
Found at i:537338 original size:16 final size:17
Alignment explanation
Indices: 537317--537351 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
537307 TTTTACCAGA
537317 TTAAAAA-CCAGTTTTT
1 TTAAAAATCCAGTTTTT
537333 TTAAAAATCCAGTTTTT
1 TTAAAAATCCAGTTTTT
537350 TT
1 TT
537352 CAAACCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (17 bp):
TTAAAAATCCAGTTTTT
Found at i:539911 original size:2 final size:2
Alignment explanation
Indices: 539906--539945 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
539896 ATTTTTTTAA
*
539906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
539946 TAATTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:541308 original size:60 final size:59
Alignment explanation
Indices: 541230--541362 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 59
541220 GCATCATATG
* * * * * *
541230 TTCCTAAACTATGACCCTCATTTTAAATTAGTCCTTAAGTTTTCAAGCATTCTAATTTCA
1 TTCCAAAACTATGACCCTCATTTCAAATTAATCCTTAACTTTT-AAACATTCCAATTTCA
541290 TTCCAAAACTATGACCCTCATTTCAAATTAATCCTTAACTTTTAAACATTCCAATTTCA
1 TTCCAAAACTATGACCCTCATTTCAAATTAATCCTTAACTTTTAAACATTCCAATTTCA
* *
541349 TCCCCAAACTATGA
1 TTCCAAAACTATGA
541363 ATATCATTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 26 0.40
60 39 0.60
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
TTCCAAAACTATGACCCTCATTTCAAATTAATCCTTAACTTTTAAACATTCCAATTTCA
Found at i:542430 original size:71 final size:71
Alignment explanation
Indices: 542308--542460 Score: 243
Period size: 71 Copynumber: 2.2 Consensus size: 71
542298 GGATTTTTGG
* **
542308 TCCACCCGATCTGATTTGAGAACAATGACTCCTCCACCCGAAATACAACCCGACCCACATAATAT
1 TCCACCCGACCTGATCCGAGAACAATGACTCCTCCACCCGAAATACAACCCGACCCACATAATAT
542373 ATACCC
66 ATACCC
* * *
542379 TCCACCCGACCTGATCCGAGAACAATGACTCTTCCACCCGAAATCCGACCCGACCCACATAATAT
1 TCCACCCGACCTGATCCGAGAACAATGACTCCTCCACCCGAAATACAACCCGACCCACATAATAT
542444 ATACCC
66 ATACCC
*
542450 TTCACCCGACC
1 TCCACCCGACC
542461 CGACTCGACC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.31, C:0.40, G:0.10, T:0.18
Consensus pattern (71 bp):
TCCACCCGACCTGATCCGAGAACAATGACTCCTCCACCCGAAATACAACCCGACCCACATAATAT
ATACCC
Found at i:542913 original size:25 final size:25
Alignment explanation
Indices: 542865--542912 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
542855 ATTAATTATT
*
542865 TAATTTTACATTCTCTAAAATTTTA
1 TAATTTTACAGTCTCTAAAATTTTA
*
542890 TAATTTTACAGTC-CTAAATTTTT
1 TAATTTTACAGTCTCTAAAATTTT
542913 TTTATGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATTTTACAGTCTCTAAAATTTTA
Found at i:544647 original size:20 final size:20
Alignment explanation
Indices: 544622--544693 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
544612 ATTTTCAACT
* *
544622 ATCGCAATGCGAACTGAAAA
1 ATCGCAACGCGAAATGAAAA
* *
544642 ATCGCAACGCGAATTGGAAA
1 ATCGCAACGCGAAATGAAAA
*
544662 ATCGCAACGCAAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
544682 ATCGTAACGCGA
1 ATCGCAACGCGA
544694 TTTTCAACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:544711 original size:21 final size:21
Alignment explanation
Indices: 544682--544735 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
544672 AAAATGAAAA
*
544682 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
544703 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
544724 ATCGCAACGCGA
1 ATCGCAACGCGA
544736 AATGCAACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:547664 original size:27 final size:25
Alignment explanation
Indices: 547611--547664 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
547601 TAGATAAAAG
* *
547611 GAGTGTGTTGTGTAAGAGTTGAAAT
1 GAGTGTGTTGTGTAACAATTGAAAT
547636 GAGTGTGTTGTGTAAACAATTGAAGAT
1 GAGTGTGTTGTGT-AACAATTGAA-AT
547663 GA
1 GA
547665 TCTACATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
26 8 0.32
27 4 0.16
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33
Consensus pattern (25 bp):
GAGTGTGTTGTGTAACAATTGAAAT
Found at i:547840 original size:81 final size:80
Alignment explanation
Indices: 547693--547865 Score: 285
Period size: 81 Copynumber: 2.1 Consensus size: 80
547683 CATGTCTTGT
** *
547693 AGAGAATCTACATTATTCACGTCCTTTGTTTTTCATTGACATTTCACATCAACTCATATAAACTT
1 AGAGAATCTACATTATTCACGTCCTTTACTTTTCATTGACATTTCACATCAACTCAGATAAACTT
547758 AAAAATTTTAGAGAGTC
66 AAAAATTTT--AGAGTC
*
547775 AGAGAATTTACATTATTCACGTCCTTTACTTTTC-TTGACATTTCACATCAACTCAGATAAACTT
1 AGAGAATCTACATTATTCACGTCCTTTACTTTTCATTGACATTTCACATCAACTCAGATAAACTT
547839 AAAAATTTTAGAGTC
66 AAAAATTTTAGAGTC
547854 AGAGAATCTACA
1 AGAGAATCTACA
547866 CCATTCTACC
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
79 17 0.20
81 38 0.44
82 31 0.36
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (80 bp):
AGAGAATCTACATTATTCACGTCCTTTACTTTTCATTGACATTTCACATCAACTCAGATAAACTT
AAAAATTTTAGAGTC
Found at i:550828 original size:24 final size:23
Alignment explanation
Indices: 550800--550855 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
550790 GTATTTAGTA
*
550800 TTTAAAATATT-AATTTTTATTCGT
1 TTTAAAAT-TTAAACTTTTATT-GT
* *
550824 TTTAATATTTAAACTTTTATTTT
1 TTTAAAATTTAAACTTTTATTGT
550847 TTTAAAATT
1 TTTAAAATT
550856 ATACTTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTAAAATTTAAACTTTTATTGT
Found at i:558415 original size:2 final size:2
Alignment explanation
Indices: 558408--558443 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
558398 GTCTATAACA
558408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
558444 TATTTAGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:568562 original size:21 final size:22
Alignment explanation
Indices: 568491--568564 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
568481 ATAGGGATTT
568491 TTTTATATTATTAAAATATATT-
1 TTTTA-ATTATTAAAATATATTA
* *
568513 CTTTAATTATTAAAATATA-AA
1 TTTTAATTATTAAAATATATTA
***
568534 AACT-ATTA-TAAAATATATTA
1 TTTTAATTATTAAAATATATTA
568554 TTTTAATTATT
1 TTTTAATTATT
568565 TTAAGACATT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 9 0.23
20 6 0.15
21 19 0.49
22 5 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAATTATTAAAATATATTA
Found at i:568845 original size:2 final size:2
Alignment explanation
Indices: 568838--568877 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
568828 TTTCTAGTAA
568838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
568878 GAGAAAATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.