Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold90
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: 1653315
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 63894 characters in sequence are not A, C, G, or T
File 4 of 10
Found at i:376482 original size:35 final size:36
Alignment explanation
Indices: 376443--376511 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
376433 TAATTGTAAT
* *
376443 GAATGTTTGCCTTGCTAT-TTTTTCATGAATGCAAA
1 GAATGTTTCCCTTGATATCTTTTTCATGAATGCAAA
*
376478 GAATGTTTCCCTTGATATCGTTTTTTATGAATGC
1 GAATGTTTCCCTTGATATC-TTTTTCATGAATGC
376512 TTGGGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 16 0.55
37 13 0.45
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (36 bp):
GAATGTTTCCCTTGATATCTTTTTCATGAATGCAAA
Found at i:376697 original size:47 final size:48
Alignment explanation
Indices: 376644--376742 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 48
376634 TTAAAGGGGA
* * *
376644 GAAATTGTTTTATAAAAGGGATATTTTGCTAAG-GGGGGTACTAAATT
1 GAAATTGTTTTATAAAAAGGATAATTTGCTAAGAGGGAGTACTAAATT
*
376691 GAAATTGTTTTATAAAAAGGATAATTTGTTAAGAGGGAGTACTAAATT
1 GAAATTGTTTTATAAAAAGGATAATTTGCTAAGAGGGAGTACTAAATT
376739 GAAA
1 GAAA
376743 AATGTCACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 30 0.64
48 17 0.36
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (48 bp):
GAAATTGTTTTATAAAAAGGATAATTTGCTAAGAGGGAGTACTAAATT
Found at i:377414 original size:20 final size:20
Alignment explanation
Indices: 377370--377421 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
377360 ACACCCAGAT
* *
377370 GTATCAATACATATTGCTTA
1 GTATCGATACATATTGATTA
377390 GTATCGATACATATTGAATTA
1 GTATCGATACATATTG-ATTA
377411 -TATCGATACAT
1 GTATCGATACAT
377422 GAAACTGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCGATACATATTGATTA
Found at i:378296 original size:17 final size:17
Alignment explanation
Indices: 378252--378297 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
378242 TGTCATTGTG
378252 TTTATTTTATTTATGTT
1 TTTATTTTATTTATGTT
* *
378269 TTTGTTATATTTAT-TT
1 TTTATTTTATTTATGTT
378285 TCTTATTTTATTT
1 T-TTATTTTATTT
378298 TGAGCTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATGTT
Found at i:379707 original size:40 final size:39
Alignment explanation
Indices: 379456--379709 Score: 142
Period size: 40 Copynumber: 6.5 Consensus size: 39
379446 TTTCGTGTTG
* * * *
379456 AAACCAAACCTTTATGTTCATTTTAGTAATTTTATGT-A
1 AAACCAATCCTTTAAGGTCATTTTAGTATTTTTATGTCA
* * * * * *
379494 AATAACAAGTCTTTTATA-ATCATGTTACTATTTTCATGTCA
1 AA-ACCAA-TCCTTTA-AGGTCATTTTAGTATTTTTATGTCA
* *
379535 AAACCGAAT-CTTT-A-GTCATTTTACTATTTTTATGTTA
1 AAACC-AATCCTTTAAGGTCATTTTAGTATTTTTATGTCA
* * * *
379572 AGATCAAACCTTTAATGTCATTTTAGTATTTTTTATGTCA
1 AAACCAATCCTTTAAGGTCATTTTAGTA-TTTTTATGTCA
* * ** ** * *
379612 AAACCAAGTCCCTT-AGGGCTATACTAGCGTTTTCACGTCA
1 AAACCAA-TCCTTTAAGGTC-ATTTTAGTATTTTTATGTCA
* **
379652 AAACTAATATTTTAAGGTCATTTTAGTATTTTTATGTCA
1 AAACCAATCCTTTAAGGTCATTTTAGTATTTTTATGTCA
*
379691 AAGCCAAGTCCTTTAAGGT
1 AAACCAA-TCCTTTAAGGT
379710 TGTTTTAGCG
Statistics
Matches: 156, Mismatches: 47, Indels: 24
0.69 0.21 0.11
Matches are distributed among these distances:
36 2 0.01
37 27 0.17
38 3 0.02
39 40 0.26
40 70 0.45
41 14 0.09
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.42
Consensus pattern (39 bp):
AAACCAATCCTTTAAGGTCATTTTAGTATTTTTATGTCA
Found at i:379744 original size:79 final size:77
Alignment explanation
Indices: 379563--379786 Score: 200
Period size: 79 Copynumber: 2.8 Consensus size: 77
379553 TTTTACTATT
* * *
379563 TTTATGTTAAGATCAAACCTTTAATGTCATTTTAGTATTTTTTATGTCAAAACCAAGTCCCTTAG
1 TTTATGTTAA-ATCAAACTTTTAAGGTCATTTTAGTA-TTTTTATGTCAAAACCAAGTCCCTTAA
*
379628 GGCTATACTAGCGT
64 GGCTATACTAGCGG
* * * * *
379642 TTTCACGTCAAAACTAATA-TTTTAAGGTCATTTTAGTATTTTTATGTCAAAGCCAAGTCCTTTA
1 TTT-ATGTTAAATC-AA-ACTTTTAAGGTCATTTTAGTATTTTTATGTCAAAACCAAGTCCCTTA
* * **
379706 AGGTTGTTTTAGCGCG
63 AGGCTATACTAGCG-G
* * * *
379722 TTTATGTTGAAATCAAACTTTTAAGGTCATATTATTATTTTTCTATATCAAAACCAAAT-CCTTA
1 TTTATGTT-AAATCAAACTTTTAAGGTCATTTTAGTA-TTTT-TATGTCAAAACCAAGTCCCTTA
379786 A
63 A
379787 AGTCGTGTGA
Statistics
Matches: 115, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
78 1 0.01
79 60 0.52
80 40 0.35
81 14 0.12
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (77 bp):
TTTATGTTAAATCAAACTTTTAAGGTCATTTTAGTATTTTTATGTCAAAACCAAGTCCCTTAAGG
CTATACTAGCGG
Found at i:381083 original size:15 final size:14
Alignment explanation
Indices: 381060--381129 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 14
381050 TGTACTCATT
381060 ATTAAAATAAAATTA
1 ATTAAAATAAAA-TA
*
381075 ATTATAATAAAATA
1 ATTAAAATAAAATA
** *
381089 ATTAATTTAATTATAA
1 ATTAAAATAA-AAT-A
381105 ATTAAAAT-AAATA
1 ATTAAAATAAAATA
*
381118 AAT-AAATAAAAT
1 ATTAAAATAAAAT
381130 TTATTTATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 11 0.26
15 14 0.33
16 7 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATTAAAATAAAATA
Found at i:382441 original size:17 final size:17
Alignment explanation
Indices: 382391--382444 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
382381 TTATACATTT
*
382391 TAATTATTATT-AATAA
1 TAATTTTTATTAAATAA
* *
382407 -AAATTTAATTATAA-AA
1 TAATTTTTATTA-AATAA
382423 TAATTTTTATTAAATAA
1 TAATTTTTATTAAATAA
382440 TAATT
1 TAATT
382445 ATATATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
17 18 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTTTATTAAATAA
Found at i:382837 original size:11 final size:11
Alignment explanation
Indices: 382781--382865 Score: 63
Period size: 11 Copynumber: 7.7 Consensus size: 11
382771 TACTAATTCA
382781 AATATAGAAAA-
1 AATATA-AAAAT
382792 AATA-AAAACAT
1 AATATAAAA-AT
*
382803 GATATAAAAAT
1 AATATAAAAAT
382814 AAT-TAAAACAT
1 AATATAAAA-AT
382825 AATATAAAAAT
1 AATATAAAAAT
* *
382836 AA-ATATGACAT
1 AATATA-AAAAT
382847 AAATATAAAAAT
1 -AATATAAAAAT
382859 -ATATAAA
1 AATATAAA
382866 TATATGTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
9 3 0.05
10 17 0.28
11 23 0.38
12 14 0.23
13 3 0.05
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:382858 original size:23 final size:22
Alignment explanation
Indices: 382781--382865 Score: 91
Period size: 22 Copynumber: 3.8 Consensus size: 22
382771 TACTAATTCA
*
382781 AATATAGAAA-AAATAAAAACAT
1 AATATAAAAATAAAT-AAAACAT
* *
382803 GATATAAAAATAATTAAAACAT
1 AATATAAAAATAAATAAAACAT
**
382825 AATATAAAAATAAATATGACAT
1 AATATAAAAATAAATAAAACAT
*
382847 AAATATAAAAATATATAAA
1 -AATATAAAAATAAATAAA
382866 TATATGTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
22 33 0.65
23 18 0.35
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
AATATAAAAATAAATAAAACAT
Found at i:383115 original size:17 final size:16
Alignment explanation
Indices: 383085--383128 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
383075 ATTTTATATT
383085 ATTAATAA-AAATTTA
1 ATTAATAATAAATTTA
*
383100 ATTATATAATAAATTTT
1 ATTA-ATAATAAATTTA
383117 ATTAAATAATAA
1 ATT-AATAATAA
383129 TTATGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 16 0.64
18 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAATAATAAATTTA
Found at i:383478 original size:23 final size:21
Alignment explanation
Indices: 383452--383511 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 21
383442 ATTACTTTAA
383452 ATATACAAAAAATAAAAAACAT
1 ATATA-AAAAAATAAAAAACAT
383474 GATAT-AAAAAATAATTAAAACAT
1 -ATATAAAAAAATAA--AAAACAT
383497 A-ATATAAAAAATAAA
1 ATATA-AAAAAATAAA
383512 TATGATACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 12 0.36
22 1 0.03
23 20 0.61
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (21 bp):
ATATAAAAAAATAAAAAACAT
Found at i:383514 original size:13 final size:12
Alignment explanation
Indices: 383451--383510 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
383441 TATTACTTTA
*
383451 AATATACAAAA-
1 AATATAAAAAAT
383462 AATA-AAAAACAT
1 AATATAAAAA-AT
*
383474 GATATAAAAAAT
1 AATATAAAAAAT
*
383486 AAT-TAAAACAT
1 AATATAAAAAAT
383497 AATATAAAAAAT
1 AATATAAAAAAT
383509 AA
1 AA
383511 ATATGATACG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
10 4 0.10
11 15 0.38
12 16 0.40
13 5 0.12
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:383674 original size:30 final size:30
Alignment explanation
Indices: 383618--383674 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
383608 ATATTAAAAT
*
383618 TTTCTTTTATTTCCCTTTTCATTTTCTTTC
1 TTTCTTTTATTTCCCTTTCCATTTTCTTTC
**
383648 TTTCTTTT-TTTTTCTTTCCATCTTTCT
1 TTTCTTTTATTTCCCTTTCCAT-TTTCT
383675 CTCTCTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTCTTTTATTTCCCTTTCCATTTTCTTTC
Found at i:383801 original size:12 final size:12
Alignment explanation
Indices: 383786--383818 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
383776 AAATTAATAC
383786 ATAATATGAAAA
1 ATAATATGAAAA
383798 ATAATATG-AAA
1 ATAATATGAAAA
383809 ATAATATGAA
1 ATAATATGAA
383819 TACATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (12 bp):
ATAATATGAAAA
Found at i:383959 original size:21 final size:21
Alignment explanation
Indices: 383924--383985 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
383914 TACGATATTT
**
383924 ATAAAAATATTTATAATATAAC
1 ATAAAAATACATAT-ATATAAC
*
383946 ATAAAAATA-ATATATATGAC
1 ATAAAAATACATATATATAAC
* *
383966 ACAAATATACATATATATAA
1 ATAAAAATACATATATATAA
383986 ATTTATATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 13 0.38
21 12 0.35
22 9 0.26
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAAAATACATATATATAAC
Found at i:384052 original size:22 final size:20
Alignment explanation
Indices: 384015--384064 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
384005 AATTATTAAT
*
384015 ATATAAAATTTTATATAAAA
1 ATATAATATTTTATATAAAA
384035 ATATAATATTTTAAATATAAAA
1 ATATAATATTTT--ATATAAAA
*
384057 AAATAATA
1 ATATAATA
384065 AAATATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 11 0.42
22 15 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATATTTTATATAAAA
Found at i:390395 original size:17 final size:17
Alignment explanation
Indices: 390373--390406 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
390363 TTAATGTTTC
390373 AAATAAAGGTACCAAAG
1 AAATAAAGGTACCAAAG
390390 AAATAAAGGTACCAAAG
1 AAATAAAGGTACCAAAG
390407 TTTTATTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (17 bp):
AAATAAAGGTACCAAAG
Found at i:399281 original size:18 final size:18
Alignment explanation
Indices: 399258--399365 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
399248 ATCTTCTTCT
399258 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
399276 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
399297 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
399318 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
399339 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
399360 CTCCTC
1 CTCCTC
399366 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 14 0.20
19 4 0.06
20 6 0.09
21 22 0.31
22 6 0.09
23 4 0.06
24 8 0.11
25 3 0.04
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:399313 original size:42 final size:42
Alignment explanation
Indices: 399261--399379 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
399251 TTCTTCTCTC
*
399261 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
399303 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
399345 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
399380 TTGAGGGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:399320 original size:12 final size:11
Alignment explanation
Indices: 399294--399369 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
399284 TCTATTATCT
*
399294 CTCCTGTCTCTC
1 CTCCTATCTC-C
399306 CTCCTATCATCC
1 CTCCTATC-TCC
399318 CTCCTATCT--
1 CTCCTATCTCC
*
399327 CTACTATCT--
1 CTCCTATCTCC
*
399336 CTCCTGTCTCTC
1 CTCCTATCTC-C
399348 CTCCTATCATCC
1 CTCCTATC-TCC
*
399360 CTCCTCTCTC
1 CTCCTATCTC
399370 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:401243 original size:13 final size:13
Alignment explanation
Indices: 401225--401250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
401215 CAAATTTTTG
401225 TGTATCGATACAT
1 TGTATCGATACAT
401238 TGTATCGATACAT
1 TGTATCGATACAT
401251 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:402005 original size:61 final size:61
Alignment explanation
Indices: 401910--402053 Score: 272
Period size: 61 Copynumber: 2.4 Consensus size: 61
401900 TTGTACATTT
401910 TCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTC
1 TCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTC
401971 TCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTC
1 TCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTC
402032 TCCCCCTTAATCAA-GTAATTCA
1 TCCCCCTTAAT-AAGGTAATTCA
402054 TATCAAAAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
61 80 0.98
62 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.06, T:0.38
Consensus pattern (61 bp):
TCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAATTC
Found at i:402050 original size:21 final size:21
Alignment explanation
Indices: 402009--402052 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
401999 CTCTCCTTTA
* *
402009 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
402030 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
402051 TC
1 TC
402053 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:403875 original size:13 final size:13
Alignment explanation
Indices: 403857--403882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
403847 ATAATCACCC
403857 TGTATCGATACAA
1 TGTATCGATACAA
403870 TGTATCGATACAA
1 TGTATCGATACAA
403883 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:405940 original size:15 final size:15
Alignment explanation
Indices: 405920--405950 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
405910 ATTTCGTTTG
*
405920 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
405935 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
405950 G
1 G
405951 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:407649 original size:21 final size:21
Alignment explanation
Indices: 407620--407664 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
407610 AAGTTTTCAT
*
407620 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
407640 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
407662 TTT
1 TTT
407665 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:409897 original size:13 final size:13
Alignment explanation
Indices: 409879--409904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
409869 CAATTTTTTG
409879 TGTATCGATACAT
1 TGTATCGATACAT
409892 TGTATCGATACAT
1 TGTATCGATACAT
409905 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:420307 original size:19 final size:19
Alignment explanation
Indices: 420283--420382 Score: 98
Period size: 19 Copynumber: 5.9 Consensus size: 19
420273 AATTCAACAA
*
420283 TTTGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
420302 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
420317 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
420334 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
420349 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
420366 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
420383 TTAGCTACTG
Statistics
Matches: 68, Mismatches: 1, Indels: 24
0.73 0.01 0.26
Matches are distributed among these distances:
13 22 0.32
15 4 0.06
17 4 0.06
19 38 0.56
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:420322 original size:13 final size:13
Alignment explanation
Indices: 420304--420360 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
420294 ACATAAGTTT
420304 TGTATCGATACAA
1 TGTATCGATACAA
420317 TGTATCGATACATAA
1 TGTATCGATAC--AA
420332 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
420349 TGTATCGATACA
1 TGTATCGATACA
420361 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:420328 original size:32 final size:32
Alignment explanation
Indices: 420285--420379 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
420275 TTCAACAATT
*
420285 TGTATCAATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
420317 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
*
420349 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
420380 TAATTAGCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:420440 original size:13 final size:13
Alignment explanation
Indices: 420422--420447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
420412 CATTTTTCTG
420422 TGTATCGATACAT
1 TGTATCGATACAT
420435 TGTATCGATACAT
1 TGTATCGATACAT
420448 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:420444 original size:33 final size:33
Alignment explanation
Indices: 420402--420468 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
420392 GCCAAGGAAA
***
420402 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
420435 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
420468 T
1 T
420469 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:422943 original size:17 final size:17
Alignment explanation
Indices: 422921--422955 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
422911 TCTTCACAAT
422921 CGAGGATACTCAAACCC
1 CGAGGATACTCAAACCC
* *
422938 CGAGGATATTCCAACCC
1 CGAGGATACTCAAACCC
422955 C
1 C
422956 ATTATTTCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.37, G:0.17, T:0.14
Consensus pattern (17 bp):
CGAGGATACTCAAACCC
Found at i:423051 original size:27 final size:28
Alignment explanation
Indices: 423019--423091 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
423009 TTTCATAATC
423019 GGGGATACTCCAACCCCGTTA-ATCATC-A
1 GGGGATACTCCAACCCCGTTATATC--CGA
* *
423047 -GGGATACTCCAATCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATATCCGA
423074 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
423092 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATATCCGA
Found at i:423167 original size:107 final size:107
Alignment explanation
Indices: 422941--423145 Score: 313
Period size: 107 Copynumber: 1.9 Consensus size: 107
422931 CAAACCCCGA
* * *
422941 GGATATTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTTCAAAAATATCA
1 GGATACTCCAATCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAATATCA
*
423006 ATTTTTCATAATCGGGGATACTCCAACCCCGTTAATCATCAG
66 ATTTCTCATAATCGGGGATACTCCAACCCCGTTAATCATCAG
* * * **
423048 GGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTG
1 GGATACTCCAATCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAATATCA
*
423112 ATTTCTCATAATTGGGGATACTCCAACCCCGTTA
66 ATTTCTCATAATCGGGGATACTCCAACCCCGTTA
423146 TTTTTGAGGG
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 42 0.48
107 46 0.52
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (107 bp):
GGATACTCCAATCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAATATCA
ATTTCTCATAATCGGGGATACTCCAACCCCGTTAATCATCAG
Found at i:435663 original size:11 final size:11
Alignment explanation
Indices: 435647--435712 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
435637 CCTTCTCTTC
435647 AAAAAAGAAAA
1 AAAAAAGAAAA
*
435658 AAAAAACAAAA
1 AAAAAAGAAAA
435669 AAACAAA-AAACA
1 AAA-AAAGAAA-A
435681 AAACAAAGAAAA
1 AAA-AAAGAAAA
** *
435693 AGGAGAGAAAA
1 AAAAAAGAAAA
*
435704 GAAAAAGAA
1 AAAAAAGAA
435713 CCTGCTTAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 28 0.64
12 13 0.30
13 3 0.07
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:435677 original size:20 final size:21
Alignment explanation
Indices: 435654--435692 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
435644 TTCAAAAAAG
435654 AAAAAAAAAACAAA-AAAACA
1 AAAAAAAAAACAAAGAAAACA
*
435674 AAAAACAAAACAAAGAAAA
1 AAAAAAAAAACAAAGAAAA
435693 AGGAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAGAAAACA
Found at i:435678 original size:15 final size:14
Alignment explanation
Indices: 435654--435693 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
435644 TTCAAAAAAG
435654 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
435668 AAAACAAAAAACAAA
1 AAAA-AAAAAACAAA
435683 ACAAAGAAAAA
1 A-AAA-AAAAA
435694 GGAGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:436759 original size:27 final size:27
Alignment explanation
Indices: 436729--436814 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
436719 TTGGTGGCAT
436729 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
436756 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
436784 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
436811 TTTC
1 TTTC
436815 AAAGCCCGCA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:437302 original size:55 final size:55
Alignment explanation
Indices: 436679--437301 Score: 922
Period size: 55 Copynumber: 11.3 Consensus size: 55
436669 TCCGCTTTTT
*
436679 AGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
436734 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
436789 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCGCACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* **
436844 AATCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-CCTCTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC-C
*
436899 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
**
436954 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-CCTCTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC-C
*
437009 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
437064 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
**
437119 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
437174 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* ** * *
437229 AGTCTTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
437284 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
437302 TACACTTTAT
Statistics
Matches: 520, Mismatches: 33, Indels: 30
0.89 0.06 0.05
Matches are distributed among these distances:
54 15 0.03
55 487 0.94
56 18 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:440012 original size:21 final size:21
Alignment explanation
Indices: 439979--440023 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
439969 TTGCAAGTTG
*
439979 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
440001 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
440021 AAA
1 AAA
440024 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:441839 original size:15 final size:15
Alignment explanation
Indices: 441819--441849 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
441809 TAAAAATGTC
*
441819 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
441834 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
441849 C
1 C
441850 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:443716 original size:8 final size:8
Alignment explanation
Indices: 443703--443727 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
443693 ATTTGATTAA
443703 ATTTTGTG
1 ATTTTGTG
443711 ATTTTGTG
1 ATTTTGTG
443719 ATTTTGTG
1 ATTTTGTG
443727 A
1 A
443728 ATGATGCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (8 bp):
ATTTTGTG
Found at i:443943 original size:13 final size:13
Alignment explanation
Indices: 443925--443950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
443915 ACATTTTTCT
443925 TTGTATCGATACA
1 TTGTATCGATACA
443938 TTGTATCGATACA
1 TTGTATCGATACA
443951 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:447921 original size:21 final size:21
Alignment explanation
Indices: 447897--447953 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
447887 ATTTTTTCCA
*
447897 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTATAG
* *
447918 AATGTATTGATACATTTATGG
1 AATGTATCGATACATTTATAG
447939 AATGTATCGATACAT
1 AATGTATCGATACAT
447954 ACATCCTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTATAG
Found at i:450936 original size:20 final size:20
Alignment explanation
Indices: 450870--450942 Score: 94
Period size: 19 Copynumber: 3.6 Consensus size: 20
450860 AAAAATTCCA
450870 AATGTATCGATACATTTGTAG
1 AATGTATCGATACA-TTGTAG
450891 AATGTATCGATACATTGT-G
1 AATGTATCGATACATTGTAG
* ** *
450910 GATGTATCGATACATCCTAC
1 AATGTATCGATACATTGTAG
450930 AATGTATCGATAC
1 AATGTATCGATAC
450943 TGGGTCCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.35
20 16 0.35
21 14 0.30
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGTAG
Found at i:451017 original size:32 final size:32
Alignment explanation
Indices: 450980--451042 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
450970 TTCAACAATT
* * *
450980 TGTATCGATACATAAGTTTTTTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
451012 TGTATCGATACATAAGTATTGTATCAATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
451043 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:451036 original size:19 final size:19
Alignment explanation
Indices: 450979--451045 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
450969 ATTCAACAAT
*
450979 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
*
450998 TTTTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
451012 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
*
451030 TTGTATCAATACATAA
1 TTGTATCGATACATAA
451046 TTAGCTACTG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
13 10 0.26
16 2 0.05
18 1 0.03
19 25 0.66
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:453609 original size:17 final size:17
Alignment explanation
Indices: 453583--453615 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
453573 TCACAATCGA
453583 GGATACTCCAACCCCGG
1 GGATACTCCAACCCCGG
*
453600 GGATATTCCAACCCCG
1 GGATACTCCAACCCCG
453616 TTATTTCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.39, G:0.21, T:0.15
Consensus pattern (17 bp):
GGATACTCCAACCCCGG
Found at i:453710 original size:27 final size:28
Alignment explanation
Indices: 453678--453750 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 28
453668 TTTCATAATC
453678 GGGGATACTCCAACCCCGTTA-ATCATC-A
1 GGGGATACTCCAACCCCGTTATATC--CGA
* *
453706 -GGGATACTCCAATCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATATCCGA
453733 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
453751 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATATCCGA
Found at i:453818 original size:106 final size:107
Alignment explanation
Indices: 453599--453825 Score: 330
Period size: 106 Copynumber: 2.1 Consensus size: 107
453589 TCCAACCCCG
* * * *
453599 GGGATATTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGACTTTATTTTCAAAAATATC
1 GGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAATATC
*
453664 GATTTTTCATAATCGGGGATACTCCAACCCCGTTAATCATCA
66 GATTTCTCATAATCGGGGATACTCCAACCCCGTTAATCATCA
* * *
453706 GGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATT
1 GGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAATATC
* * ** *
453770 GATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTTGA
66 GATTTCTCATAATCGGGGATACTCCAACCCCGTTAATCATCA
453812 GGGATACTCCAATC
1 GGGATACTCCAATC
453826 TCGATTTTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 60 0.56
107 47 0.44
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (107 bp):
GGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAATATC
GATTTCTCATAATCGGGGATACTCCAACCCCGTTAATCATCA
Found at i:460806 original size:12 final size:11
Alignment explanation
Indices: 460784--460901 Score: 63
Period size: 12 Copynumber: 10.9 Consensus size: 11
460774 AGAGAAAGAA
*
460784 GAGAGAGGAGG
1 GAGATAGGAGG
460795 GATGATAGGAGG
1 GA-GATAGGAGG
460807 AGAGATAGGA--
1 -GAGATAGGAGG
*
460817 GAGATAGTA--
1 GAGATAGGAGG
460826 GAGATAGGAGG
1 GAGATAGGAGG
460837 GATGATAGGAGG
1 GA-GATAGGAGG
*
460849 AGAGACAGGA--
1 -GAGATAGGAGG
**
460859 GAGATA--ATA
1 GAGATAGGAGG
*
460868 GAGAGAGGAGG
1 GAGATAGGAGG
460879 GATGATAGGAGG
1 GA-GATAGGAGG
*
460891 AGAGACAGGAG
1 -GAGATAGGAG
460902 AGATAATAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
7 1 0.01
9 26 0.31
11 7 0.08
12 45 0.53
13 6 0.07
ACGTcount: A:0.41, C:0.02, G:0.47, T:0.10
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:460820 original size:33 final size:30
Alignment explanation
Indices: 460774--460864 Score: 76
Period size: 33 Copynumber: 2.8 Consensus size: 30
460764 TAGCCCTCAA
* *
460774 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGAGAGAGGA--GA-GATAGGAGG
* *
460807 AGAGATAGGAGAGATAGTAGAGATAGGAGG
1 AGAGATAGGAGAGAGAGGAGAGATAGGAGG
460837 -GATGATAGGAGGAGAGACAGGAGAGATA
1 AGA-GATAGGA-GAGAG--AGGAGAGATA
460865 ATAGAGAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.04
30 16 0.33
31 6 0.12
33 24 0.50
ACGTcount: A:0.44, C:0.01, G:0.45, T:0.10
Consensus pattern (30 bp):
AGAGATAGGAGAGAGAGGAGAGATAGGAGG
Found at i:460829 original size:11 final size:9
Alignment explanation
Indices: 460804--460864 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
460794 GGATGATAGG
460804 AGGAGAGAT
1 AGGAGAGAT
460813 AGGAGAGAT
1 AGGAGAGAT
*
460822 AGTAGAGAT
1 AGGAGAGAT
*
460831 AGGAGGGAT
1 AGGAGAGAT
* *
460840 --GATAG-G
1 AGGAGAGAT
*
460846 AGGAGAGAC
1 AGGAGAGAT
460855 AGGAGAGAT
1 AGGAGAGAT
460864 A
1 A
460865 ATAGAGAGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:460835 original size:42 final size:42
Alignment explanation
Indices: 460783--460934 Score: 268
Period size: 42 Copynumber: 3.6 Consensus size: 42
460773 AAGAGAAAGA
* *
460783 AGAGAGAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
460825 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
460867 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
460909 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
460935 GAGAGAAGAA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.41, C:0.02, G:0.47, T:0.10
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:460876 original size:18 final size:18
Alignment explanation
Indices: 460849--460919 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
460839 TGATAGGAGG
460849 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAAT
* *
460867 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GATA--A-T
460891 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAAT
*
460909 AGAGAGAGGAG
1 AGAGACAGGAG
460920 GGATGACAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 19 0.45
19 1 0.02
20 2 0.05
21 8 0.19
22 2 0.05
23 1 0.02
24 9 0.21
ACGTcount: A:0.45, C:0.03, G:0.44, T:0.08
Consensus pattern (18 bp):
AGAGACAGGAGAGATAAT
Found at i:467978 original size:29 final size:33
Alignment explanation
Indices: 467945--468009 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 33
467935 TAAAAGTATC
*
467945 TTTAATTTTAT-ATTA-T-TATTATTA-ATTTA
1 TTTAATTTTATAATAATTCTATTATTACATTTA
*
467974 TTTAATTTTTTAATAATTCTATTATTACATTTA
1 TTTAATTTTATAATAATTCTATTATTACATTTA
468007 TTT
1 TTT
468010 CTATCAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.33
30 3 0.10
31 1 0.03
32 8 0.27
33 8 0.27
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTAATTTTATAATAATTCTATTATTACATTTA
Found at i:469796 original size:2 final size:2
Alignment explanation
Indices: 469752--469785 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
469742 TAGTAACTTG
*
469752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
469786 GGATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:470300 original size:12 final size:12
Alignment explanation
Indices: 470264--470303 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
470254 AATATATCTA
*
470264 TCCCATTCCCCC
1 TCCCCTTCCCCC
*
470276 ACCCCTTCCCCC
1 TCCCCTTCCCCC
*
470288 TCCCCTTCTCCC
1 TCCCCTTCCCCC
470300 TCCC
1 TCCC
470304 ATTTGTAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.70, G:0.00, T:0.25
Consensus pattern (12 bp):
TCCCCTTCCCCC
Found at i:472417 original size:41 final size:41
Alignment explanation
Indices: 472372--472499 Score: 175
Period size: 41 Copynumber: 3.1 Consensus size: 41
472362 TTAATTTAAC
* * *
472372 TTTTTACTATTCTATTAACAACTTTATATTCTTATGATAAT
1 TTTTTACTATTCAATTGATAACTTTATATTCTTATGATAAT
* * *
472413 TTTTTACTATTCGATTGATAATTTTATATTTTTATGATAAT
1 TTTTTACTATTCAATTGATAACTTTATATTCTTATGATAAT
* * *
472454 TTTTTACTATTCAATTGATTACTTTATATTCTTTTGATGAT
1 TTTTTACTATTCAATTGATAACTTTATATTCTTATGATAAT
472495 TTTTT
1 TTTTT
472500 TGTTAAATTG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (41 bp):
TTTTTACTATTCAATTGATAACTTTATATTCTTATGATAAT
Found at i:472423 original size:22 final size:21
Alignment explanation
Indices: 472394--472465 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
472384 TATTAACAAC
472394 TTTATATTCTTATGATAATTT
1 TTTATATTCTTATGATAATTT
*
472415 TTTACTATTC-GATTGATAA--T
1 TTTA-TATTCTTA-TGATAATTT
*
472435 TTTATATTTTTATGATAATTT
1 TTTATATTCTTATGATAATTT
472456 TTTACTATTC
1 TTTA-TATTC
472466 AATTGATTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 10 0.24
20 6 0.15
21 10 0.24
22 15 0.37
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTATATTCTTATGATAATTT
Found at i:472450 original size:19 final size:19
Alignment explanation
Indices: 472394--472456 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
472384 TATTAACAAC
*
472394 TTTATATTCTTATGATAAT
1 TTTATATTTTTATGATAAT
* **
472413 TTTTTACTATTCGATTGATAAT
1 TTTATA-T-TTTTA-TGATAAT
472435 TTTATATTTTTATGATAAT
1 TTTATATTTTTATGATAAT
472454 TTT
1 TTT
472457 TTACTATTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 15 0.44
20 4 0.12
21 3 0.09
22 12 0.35
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTATATTTTTATGATAAT
Found at i:472472 original size:22 final size:22
Alignment explanation
Indices: 472406--472472 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
472396 TATATTCTTA
*
472406 TGATAATTTTTTACTATTCGAT
1 TGATAATTTTTTACTATTCAAT
* **
472428 TGATAATTTTATA-T-TTTTA-
1 TGATAATTTTTTACTATTCAAT
472447 TGATAATTTTTTACTATTCAAT
1 TGATAATTTTTTACTATTCAAT
472469 TGAT
1 TGAT
472473 TACTTTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 12 0.33
20 4 0.11
21 4 0.11
22 16 0.44
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (22 bp):
TGATAATTTTTTACTATTCAAT
Found at i:475874 original size:13 final size:13
Alignment explanation
Indices: 475856--475880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
475846 ATATTGCACA
475856 GTATCGATACATT
1 GTATCGATACATT
475869 GTATCGATACAT
1 GTATCGATACAT
475881 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:475986 original size:19 final size:20
Alignment explanation
Indices: 475962--476010 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
475952 CTTAACTGTT
*
475962 TGTATCGATACA-CAC-AAGA
1 TGTATCGATACATC-CGAAAA
475981 TGTATCGATACATCCGAAAA
1 TGTATCGATACATCCGAAAA
476001 TGTATCGATA
1 TGTATCGATA
476011 TATTGGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCCGAAAA
Found at i:484120 original size:20 final size:20
Alignment explanation
Indices: 484095--484144 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
484085 ACCCTTAAAA
**
484095 GTATCGATACACCTTCAAAT
1 GTATCGATACACCACCAAAT
**
484115 GTATCGATACATGACCAAAT
1 GTATCGATACACCACCAAAT
484135 GTATCGATAC
1 GTATCGATAC
484145 TTGTTAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACACCACCAAAT
Found at i:484244 original size:13 final size:13
Alignment explanation
Indices: 484226--484251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
484216 TACACACAAG
484226 ATGTATCGATACA
1 ATGTATCGATACA
484239 ATGTATCGATACA
1 ATGTATCGATACA
484252 TCCTAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:484271 original size:33 final size:32
Alignment explanation
Indices: 484208--484271 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
484198 CTTAACTGTT
* *
484208 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCAATACAA
484240 TGTATCGATACATC-CTAAAATGTATCAATACA
1 TGTATCGATACA-CAC-AAAATGTATCAATACA
484272 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCAATACAA
Found at i:485777 original size:38 final size:38
Alignment explanation
Indices: 485733--485809 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
485723 TGATATAGAA
485733 TATTTTAGAATTCAATACTTTAGACTTTTTTCAAATAT
1 TATTTTAGAATTCAATACTTTAGACTTTTTTCAAATAT
485771 TATTTTAGAATTCAATACTTTAGACTTTTTTCAAATAT
1 TATTTTAGAATTCAATACTTTAGACTTTTTTCAAATAT
485809 T
1 T
485810 TTAGTGAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (38 bp):
TATTTTAGAATTCAATACTTTAGACTTTTTTCAAATAT
Found at i:488797 original size:13 final size:13
Alignment explanation
Indices: 488779--488803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
488769 CATTATGCTT
488779 TGTATCGATACAA
1 TGTATCGATACAA
488792 TGTATCGATACA
1 TGTATCGATACA
488804 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:488816 original size:19 final size:20
Alignment explanation
Indices: 488788--488844 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
488778 TTGTATCGAT
*
488788 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* * *
488807 TC-ATTGTATCAATATATGG
1 ACAATTGTATCGATACATGG
488826 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
488845 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:488907 original size:13 final size:13
Alignment explanation
Indices: 488889--488919 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
488879 CGATACATGG
*
488889 TACATTGTATCGA
1 TACATTGTATCAA
488902 TACATTGTATCAA
1 TACATTGTATCAA
488915 TACAT
1 TACAT
488920 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTGTATCAA
Found at i:488918 original size:33 final size:33
Alignment explanation
Indices: 488873--488940 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
488863 CTACCATTGT
* *
488873 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCAATACATGATGA-ATTGTATCGATACA
488906 TTGTATCAATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAATTGTATCGATACA
488939 TT
1 TT
488941 ACTTCTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (33 bp):
TTGTATCAATACATGATGAATTGTATCGATACA
Found at i:495079 original size:13 final size:13
Alignment explanation
Indices: 495063--495115 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
495053 ACAATATTCC
* *
495063 TTGTATCAATTCA
1 TTGTATCGATACA
495076 TTGTATCGATACA
1 TTGTATCGATACA
*
495089 TTGTATGGATACA
1 TTGTATCGATACA
495102 TTGTATCGATACA
1 TTGTATCGATACA
495115 T
1 T
495116 GGGTAACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:497650 original size:13 final size:13
Alignment explanation
Indices: 497632--497656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
497622 CATTATGCTT
497632 TGTATCGATACAA
1 TGTATCGATACAA
497645 TGTATCGATACA
1 TGTATCGATACA
497657 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:497653 original size:33 final size:32
Alignment explanation
Indices: 497611--497675 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
497601 ACACACCCAG
*
497611 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
497644 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
497676 TGGACAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:497687 original size:20 final size:20
Alignment explanation
Indices: 497641--497693 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
497631 TTGTATCGAT
*
497641 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
*
497660 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
*
497679 ACAATTGTATTGATA
1 ACAATTGTATCGATA
497694 TATGAAACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.04
19 16 0.57
20 11 0.39
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:497760 original size:13 final size:13
Alignment explanation
Indices: 497742--497794 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
497732 CGATACATGG
497742 TACATTGTATCGA
1 TACATTGTATCGA
497755 TACATTGTATCGA
1 TACATTGTATCGA
497768 TACA-TG-AT-G-
1 TACATTGTATCGA
497777 -A-ATTGTATCGA
1 TACATTGTATCGA
497788 TACATTG
1 TACATTG
497795 CTTTTAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:497768 original size:33 final size:33
Alignment explanation
Indices: 497726--497794 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
497716 CTACCACTAT
*
497726 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
497759 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
497792 TTG
1 TTG
497795 CTTTTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:500215 original size:25 final size:23
Alignment explanation
Indices: 500187--500233 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
500177 ATTTGAGTAT
500187 TTTCATAATTTATAATTATATTATC
1 TTTCAT-ATTTA-AATTATATTATC
* *
500212 TTTCATTTTTAAATTTTATTAT
1 TTTCATATTTAAATTATATTAT
500234 TATTTGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 4 0.20
25 6 0.30
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTCATATTTAAATTATATTATC
Found at i:500307 original size:50 final size:44
Alignment explanation
Indices: 500203--500291 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
500193 AATTTATAAT
*
500203 TATATTA-TCTTTCATTTTTAAATTTTATTATTATTTGGATTTAG
1 TATATTACT-TTTCATTTTTAAATTTTACTATTATTTGGATTTAG
*
500247 TATATTACTTTTCA-TTTTAAACTTTTGCTATTATTTGGATTTAG
1 TATATTACTTTTCATTTTTAAA-TTTTACTATTATTTGGATTTAG
500291 T
1 T
500292 TATGGATACT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 7 0.17
44 33 0.80
45 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.60
Consensus pattern (44 bp):
TATATTACTTTTCATTTTTAAATTTTACTATTATTTGGATTTAG
Found at i:505645 original size:238 final size:238
Alignment explanation
Indices: 505220--505683 Score: 802
Period size: 238 Copynumber: 1.9 Consensus size: 238
505210 TGATCCATGG
**
505220 TTTTGATAAAGGTTTTGATTGAAATTATGATTGTGGATGCATGATGGATATGTATGAATGCTCAT
1 TTTTGATAAAGGTTTTGATTGAAATTATGATAATGGATGCATGATGGATATGTATGAATGCTCAT
*
505285 GGCTTGAAAATTTTTCATTTTTCATTCAATTTTTTGCTTAATTAAGGCTACTTAAAAGTTCCTCT
66 GGCTTGAAAATTTTTCATTTTTCATTCAATTTTTTGCTTAATTAAGGCTACTTAAAAATTCCTCT
* *
505350 AAACCCATTAAAGCATGATCTGACTATTCTTGAAAGCATTTGAAGGAGGAACTTGATAGTAGGGT
131 AAACACATTAAAGCATGATCTGACTATTCTTGAAAGCATTTGAAGGAGGAACTTGATAGCAGGGT
* *
505415 ACTAACTATCGATCTTTCATCTGGTACTATTTTAGAATAAAGC
196 ACTAACTATCGATCTTGCATCTAGTACTATTTTAGAATAAAGC
*
505458 TTTTGATAAAGGTTTTGATTGAAATTATGATAATGGATGCATGATGGATATGTATGAATGTTCAT
1 TTTTGATAAAGGTTTTGATTGAAATTATGATAATGGATGCATGATGGATATGTATGAATGCTCAT
*
505523 GGCTTGAAAATTTTTCATTTTTCATTCAATTTTTTGCTTAATTAAGGCTACTTAAAAATTTCTCT
66 GGCTTGAAAATTTTTCATTTTTCATTCAATTTTTTGCTTAATTAAGGCTACTTAAAAATTCCTCT
* * * *
505588 AAACACATTAAAGCGTGATCTGATTGTTCTTGAAAGCATTTGAAGGAGGATCTTGATAGCAGGGT
131 AAACACATTAAAGCATGATCTGACTATTCTTGAAAGCATTTGAAGGAGGAACTTGATAGCAGGGT
*
505653 ACTGACTATCGATCTTGCATCTAGTACTATT
196 ACTAACTATCGATCTTGCATCTAGTACTATT
505684 AAAGAACTGG
Statistics
Matches: 212, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
238 212 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (238 bp):
TTTTGATAAAGGTTTTGATTGAAATTATGATAATGGATGCATGATGGATATGTATGAATGCTCAT
GGCTTGAAAATTTTTCATTTTTCATTCAATTTTTTGCTTAATTAAGGCTACTTAAAAATTCCTCT
AAACACATTAAAGCATGATCTGACTATTCTTGAAAGCATTTGAAGGAGGAACTTGATAGCAGGGT
ACTAACTATCGATCTTGCATCTAGTACTATTTTAGAATAAAGC
Found at i:507053 original size:13 final size:13
Alignment explanation
Indices: 507035--507059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507025 CTGCCAGTTT
507035 ATGTATCGATACA
1 ATGTATCGATACA
507048 ATGTATCGATAC
1 ATGTATCGATAC
507060 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:507072 original size:20 final size:20
Alignment explanation
Indices: 507047--507112 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
507037 GTATCGATAC
507047 AATGTATCGATACTAAGCAA
1 AATGTATCGATACTAAGCAA
507067 AATGTATCG--A-T-A-C--
1 AATGTATCGATACTAAGCAA
*
507080 AATGTATCGGTACTAAGCAA
1 AATGTATCGATACTAAGCAA
507100 AATGTATCGATAC
1 AATGTATCGATAC
507113 ATCTGGGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.24
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
20 21 0.55
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACTAAGCAA
Found at i:507077 original size:33 final size:33
Alignment explanation
Indices: 507035--507113 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
507025 CTGCCAGTTT
507035 ATGTATCGATACAATGTATCGATACTAAGCAAA
1 ATGTATCGATACAATGTATCGATACTAAGCAAA
*
507068 ATGTATCGATACAATGTATCGGTACTAAGCAAA
1 ATGTATCGATACAATGTATCGATACTAAGCAAA
507101 ATGTATCGATACA
1 ATGTATCGATACA
507114 TCTGGGTATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAATGTATCGATACTAAGCAAA
Found at i:515033 original size:49 final size:49
Alignment explanation
Indices: 514868--516957 Score: 1202
Period size: 49 Copynumber: 43.8 Consensus size: 49
514858 CGAAGAATGA
* *** * *
514868 CAATGTGCTGATTCATGGCCAGCGACATTAAACTTGAAGAAGAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
** * * * * *
514915 CAATGTGCTGAAACAAGGCCAGTGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GATGAAGGTGC
* * * * * * *
514967 CAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* ** * * *
515016 CAATGTGCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* *
515065 CAATGTGCTGATTTAAGG-CAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
515113 CAATATGCTGATTCACGGCCAACGATATTGGGT-TTAAAGATGAGAAAAAGGAT--
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGAT--G---AAGG-TGC
* * ** * ** * * * * * *
515166 AAAGGAACTAATATGTAGG-TAGCGATATTGGGCTCAAAGATGCGAAGAATGA
1 CAATGTGCTGAT-TCAAGGCCAGCGACATTGGTCTTAAAGAT--GAAG-GTGC
* * * * * **
515218 CAATGAGCTGATTCATGGCCAGCGACATTAGACTTGAAGAACAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
** * * * * * *
515265 CAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GATGAAGGTGC
* * * * * * *
515317 CAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* ** * * *
515366 CAATGTGCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* *
515415 CAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
515464 CAATATGCTGATTCACGGCCAACGATATTGGGT-TTAAAGATGAGAAAAAGGAT--
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGAT--G---AAGG-TGC
* * ** * ** * * * * * *
515517 AAAGGAACTAATATGTAGG-TAGCGATATTGGGCTCAAAGATGCGAAGAATGA
1 CAATGTGCTGAT-TCAAGGCCAGCGACATTGGTCTTAAAGAT--GAAG-GTGC
* * * * * **
515569 CAATGAGCTGATTCATGGCCAGCGACATTAGACTTGAAGAACAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
** * * * * * *
515616 CAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GATGAAGGTGC
* * * * * *
515668 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAAGTCC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
515717 CAATGTGCTGATGCAAGGCCAACGACATCGGT-TTAAAAGATGAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGATGAAGGTGC
* *
515766 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * * * * *
515815 TAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
515864 CAATATGCTGATTCAAGGCCAACGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
515903 CAATGTACTGATTCAAGGCTAGTGACATTGGTATTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * *
515952 CAATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* *
516001 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCATAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * * *
516050 CAATATGCTGA-TAAAGGCCAGCGATATCGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516098 CAATATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * *
516137 CAATGTACTGATTTAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516186 CAATGTGCTGATTCAAAGCCAAC-AGCATTGGTCTTAAAGATGAATGCGC
1 CAATGTGCTGATTCAAGGCCAGCGA-CATTGGTCTTAAAGATGAAGGTGC
* *
516235 TAATGTGCTGATTCAAGGCCAGCGACATTGGTCATAAAGAT-AATGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAA-GGTGC
* ** * * *
516284 CAATATATTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516333 CAATATGCTGATTCACGGCCAGCGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* ** * * *
516372 TAATGCACTGATTTAAGGCCAGTGACAATGGTCTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516421 CAATGTGCTGATTCAAAGCCAAC-AGCATTGGTCTTAAAGATGAATGCGC
1 CAATGTGCTGATTCAAGGCCAGCGA-CATTGGTCTTAAAGATGAAGGTGC
* * * *
516470 TAATGTGCTGATTCAAGGCCAGCGACATTGGTCATAAAGATAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * * ** *
516519 CAATATGCTGATTTAAGGCCAGCGATATCGAACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * * *
516568 CAATATGCTGATTCGAGGCCAGTGATATTGGGC-T-----T----GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
** *
516607 CAATGTGCTGATTCAAGGCCAATGACATTAGTCTTAAAAGAT-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGATGAAGGTGC
* * *
516656 CAATATGCTGATTCAAGGCCAGCGATATTGG-GTT-----T--A--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * *
516695 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTCAGAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516743 CAATATACTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516782 CAATGTGCTGATTCAAGGCTAGCAATATTGGTCTTAAAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* *
516830 CAATATGCTGATTCAAGGCCAGCGATATTCGG-C-T-----T--A--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGATGAAGGTGC
* * *
516869 CAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGA-CAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
* * * *
516917 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA-AAGA
516958 AGACGCCACC
Statistics
Matches: 1565, Mismatches: 352, Indels: 250
0.72 0.16 0.12
Matches are distributed among these distances:
38 2 0.00
39 210 0.13
40 7 0.00
41 3 0.00
42 1 0.00
43 4 0.00
45 3 0.00
46 4 0.00
47 87 0.06
48 189 0.12
49 808 0.52
50 39 0.02
51 6 0.00
52 140 0.09
53 46 0.03
54 14 0.01
55 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
Found at i:515855 original size:351 final size:351
Alignment explanation
Indices: 514761--515842 Score: 1920
Period size: 351 Copynumber: 3.1 Consensus size: 351
514751 GATAAAAGGA
* * *
514761 CCAATACGCTGATTC-CTGGCCAATGATATTGGTTTTAAAGATGAGAAAAAAGGATAAAGGAACT
1 CCAATATGCTGATTCAC-GGCCAACGATATTGGGTTTAAAGATGAG-AAAAAGGATAAAGGAACT
** * *
514825 AATATACAGGTAGCGATATTGGGCTCGAAGATGCGAAGAATGACAATGTGCTGATTCATGGCCAG
64 AATATGTAGGTAGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGAGCTGATTCATGGCCAG
* * * *
514890 CGACATTAAACTTGAAGAAGAATGCCAATGTGCTGAAACAAGGCCAGTGACATTGGGCTTAGGAA
129 CGACATTAGACTTGAAGAACAATGCCAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAA
514955 TGTTAAAGATGCCAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGCCAAT
194 TGTTAAAGATGCCAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGCCAAT
515020 GTGCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGCCAATGTGCTGATTTAAGG-C
259 GTGCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGCCAATGTGCTGATTTAAGGCC
515084 AGCGACATTGGTCTTAAAGATAAAGGTG
324 AGCGACATTGGTCTTAAAGATAAAGGTG
515112 CCAATATGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATAAAGGAACTAA
1 CCAATATGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATAAAGGAACTAA
515177 TATGTAGGTAGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGAGCTGATTCATGGCCAGCG
66 TATGTAGGTAGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGAGCTGATTCATGGCCAGCG
515242 ACATTAGACTTGAAGAACAATGCCAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATG
131 ACATTAGACTTGAAGAACAATGCCAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATG
515307 TTAAAGATGCCAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGCCAATGT
196 TTAAAGATGCCAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGCCAATGT
515372 GCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGCCAATGTGCTGATTTAAGGCCAG
261 GCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGCCAATGTGCTGATTTAAGGCCAG
515437 CGACATTGGTCTTAAAGATAAAGGTG
326 CGACATTGGTCTTAAAGATAAAGGTG
515463 CCAATATGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATAAAGGAACTAA
1 CCAATATGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATAAAGGAACTAA
515528 TATGTAGGTAGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGAGCTGATTCATGGCCAGCG
66 TATGTAGGTAGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGAGCTGATTCATGGCCAGCG
515593 ACATTAGACTTGAAGAACAATGCCAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATG
131 ACATTAGACTTGAAGAACAATGCCAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATG
* * *
515658 TTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAA-AGTCCCAATG
196 TTAAAGATGCCAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGA-TGCCAATG
* * * *
515722 TGCTGATGCAAGGCCAACGACATCGGT-TTAAAAGATGAAGGCGCCAATGTGTTGATTCAAGGCC
260 TGCTGATGCAAGGCCAATGACATCGGTCTT-AAAGATGATGGCGCCAATGTGCTGATTTAAGGCC
515786 AGCGACATTGGTCTTAAAGATAAAGGTG
324 AGCGACATTGGTCTTAAAGATAAAGGTG
* *
515814 CTAATATGCTGATTCAAGGCCAACGATAT
1 CCAATATGCTGATTCACGGCCAACGATAT
515843 CGGACTTAAA
Statistics
Matches: 707, Mismatches: 20, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
350 271 0.38
351 435 0.62
352 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (351 bp):
CCAATATGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATAAAGGAACTAA
TATGTAGGTAGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGAGCTGATTCATGGCCAGCG
ACATTAGACTTGAAGAACAATGCCAATGTGCTGAGACAAGGCCGGTGACATTGGGCTTAGGAATG
TTAAAGATGCCAATATGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGCCAATGT
GCTGATGCAAGGCCAATGACATCGGTCTTAAAGATGATGGCGCCAATGTGCTGATTTAAGGCCAG
CGACATTGGTCTTAAAGATAAAGGTG
Found at i:516010 original size:137 final size:137
Alignment explanation
Indices: 515764--516957 Score: 470
Period size: 137 Copynumber: 8.7 Consensus size: 137
515754 AGATGAAGGC
** * *
515764 GCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCTAATATGCTGATTC
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATTAAAGATAAAGGTGCCAATATGCTGATTC
* * *
515829 AAGGCCAACGATATCGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTG
66 AAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTG
515894 GGCTTGT
131 GGCTTGT
* * * *
515901 GCCAATGTACTGATTCAAGGCTAGTGACATTGGTATTAAAGATGAAGGTGCCAATGTGCTGATTC
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATTAAAGATAAAGGTGCCAATATGCTGATTC
* * * *
515966 AAGGCCAACGACATCGGTCTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTG
66 AAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTG
*
516031 GTCATAAAGATAAAGGT
131 GGC-T-----T----GT
* * * * * *
516048 GCCAATATGCTGA-TAAAGGCCAGCGATATCGG-ACTTAAAGATGAAGGTGCCAATATGCTGATT
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTA-TTAAAGATAAAGGTGCCAATATGCTGATT
* * * * * * * * **
516111 CAAGGCTAGCGATATTGGGCTT---G-T------GCCAATGTACTGATTTAAGGCCAGTGACATT
65 CAAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATT
*
516166 GGTCTTAAAGATGAAGGT
130 GGGC-T-----T----GT
* * * * * * * * *
516184 GCCAATGTGCTGATTCAAAGCCAAC-AGCATTGGTCTTAAAGATGAATGCGCTAATGTGCTGATT
1 GCCAATGTACTGATTCAAGGCCAGCGA-CATTGGTATTAAAGATAAAGGTGCCAATATGCTGATT
* * * * * * ** * * *
516248 CAAGGCCAGCGACATTGGTCATAAAGATAATGGTGCCAATATATTGATTCAAGGCCAGCGATATC
65 CAAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATT
*
516313 GGACTTAAAGATGAAGGT
130 GGGC-T-----T----GT
* * * * ** ** * *
516331 GCCAATATGCTGATTCACGGCCAGCGATATTGGGCTT-GTGCT-AA--TG-C---A--CTGATTT
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATTAAAGATAAAGGTGCCAATATGCTGATTC
** * * * * *
516386 AAGGCCAGTGACAAT-GGTCTTAAAGATGAAGGTGCCAATGTGCTGATTCAAAGCCAAC-AGCAT
66 AAGGCCAACGAC-ATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGA-CAT
*
516449 TGGTCTTAAAGATGAAT
129 TGGGC-T-----TG--T
* *
516466 GCGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCA-TAAAGATAAAGGTGTCAATATGCTGA
1 GC-C-AATGTACTGATTCAAGGCCAGCGACATTGGT-ATTAAAGATAAAGGTGCCAATATGCTGA
* * * * * * ** *
516530 TTTAAGGCCAGCGATATCGAACTTAAAGATAAAGGTGCCAATATGCTGATTCGAGGCCAGTGATA
63 TTCAAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACA
516595 TTGGGCTTGT
128 TTGGGCTTGT
* ** * *
516605 GCCAATGTGCTGATTCAAGGCCAATGACATTAGTCTTAAAAGAT-AAGGTGCCAATATGCTGATT
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATT-AAAGATAAAGGTGCCAATATGCTGATT
* * * * * * *
516669 CAAGGCCAGCGATATTGG-GTT-----T--A--TGCCAATGTGCTGATTCAAGGCCAGCGACATT
65 CAAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATT
**
516724 GGTCTCAGAGACAAGGT
130 -G-----G-G-C-TTGT
* * * * *
516741 GCCAATATACTGATTCAAGGCCAGCGATATTGG-------GCT-TA--TGCCAATGTGCTGATTC
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATTAAAGATAAAGGTGCCAATATGCTGATTC
* * * * * * * * * * *
516796 AAGGCTAGCAATATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTC
66 AAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTG
*
516860 GGCTTAT
131 GGCTTGT
* * *
516867 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGA-CAAGGTGCCAATATGCTGATTC
1 GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATTAAAGATAAAGGTGCCAATATGCTGATTC
* *
516931 AAGGCCAACGATATTGGACTTAGAAGA
66 AAGGCCAACGACATCGGACTTA-AAGA
516958 AGACGCCACC
Statistics
Matches: 838, Mismatches: 143, Indels: 153
0.74 0.13 0.13
Matches are distributed among these distances:
126 63 0.08
127 31 0.04
128 5 0.01
129 2 0.00
131 1 0.00
133 5 0.01
134 1 0.00
135 68 0.08
136 94 0.11
137 328 0.39
138 12 0.01
139 5 0.01
140 1 0.00
141 5 0.01
142 2 0.00
143 3 0.00
145 4 0.00
146 64 0.08
147 142 0.17
148 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (137 bp):
GCCAATGTACTGATTCAAGGCCAGCGACATTGGTATTAAAGATAAAGGTGCCAATATGCTGATTC
AAGGCCAACGACATCGGACTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTG
GGCTTGT
Found at i:516041 original size:186 final size:185
Alignment explanation
Indices: 515716--516076 Score: 508
Period size: 186 Copynumber: 1.9 Consensus size: 185
515706 GATGAAAGTC
* *
515716 CCAATGTGCTGATGCAAGGCCAACGACATCGGTTTAAAAGATGAAGGCGCCAATGTGTTGATTCA
1 CCAATGTACTGATGCAAGGCCAACGACATCGGTTTAAAAGATGAAGGCGCCAATGTGCTGATTCA
* * * * *
515781 AGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCTAATATGCTGATTCAAGGCCAACGATATCGG
66 AGGCCAACGACATCGGTCTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATCGG
* *
515846 ACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTGTG
131 ACATAAAGATAAAGGTGCCAATATGCTGA-TAAAGGCCAACGATATTGGGCTTGTG
* * ** * *
515902 CCAATGTACTGATTCAAGGCTAGTGACATTGGTATT-AAAGATGAAGGTGCCAATGTGCTGATTC
1 CCAATGTACTGATGCAAGGCCAACGACATCGGT-TTAAAAGATGAAGGCGCCAATGTGCTGATTC
* * * *
515966 AAGGCCAACGACATCGGTCTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATTG
65 AAGGCCAACGACATCGGTCTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATCG
* *
516031 GTCATAAAGATAAAGGTGCCAATATGCTGATAAAGGCCAGCGATAT
130 GACATAAAGATAAAGGTGCCAATATGCTGATAAAGGCCAACGATAT
516077 CGGACTTAAA
Statistics
Matches: 153, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
185 14 0.09
186 137 0.90
187 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (185 bp):
CCAATGTACTGATGCAAGGCCAACGACATCGGTTTAAAAGATGAAGGCGCCAATGTGCTGATTCA
AGGCCAACGACATCGGTCTTAAAGATAAAGGCGCCAATATGCTGATTCAAGGCCAACGACATCGG
ACATAAAGATAAAGGTGCCAATATGCTGATAAAGGCCAACGATATTGGGCTTGTG
Found at i:516216 original size:88 final size:87
Alignment explanation
Indices: 516046--516216 Score: 209
Period size: 88 Copynumber: 2.0 Consensus size: 87
516036 AAAGATAAAG
* *
516046 GTGCCAATATGCTGATAAAGGCCAGCGATATCGGACTTAAAGATGAAGGTGCCAATATGCTGATT
1 GTGCCAATATACTGATAAAGGCCAGCGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * *
516111 CAAGGCTAGCGATATTGGGCTT
66 CAAAGCCAACGACATTGGGCTT
* * * * * *
516133 GTGCCAATGTACTGATTTAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGAT
1 GTGCCAATATACTGA-TAAAGGCCAGCGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGAT
516198 TCAAAGCCAAC-AGCATTGG
65 TCAAAGCCAACGA-CATTGG
516217 TCTTAAAGAT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
87 14 0.20
88 56 0.80
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (87 bp):
GTGCCAATATACTGATAAAGGCCAGCGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGATT
CAAAGCCAACGACATTGGGCTT
Found at i:516409 original size:235 final size:235
Alignment explanation
Indices: 515665--516770 Score: 1580
Period size: 235 Copynumber: 4.8 Consensus size: 235
515655 ATGTTAAAGA
* * ** * * * * *
515665 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAAGTCCCAATGTGCTGATG
1 TGCCAATGTACTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
* * *
515730 CAAGGCCAACGACATCGGT-TTAAAAGATGAAGGCGCCAATGTGTTGATTCAAGGCCAGCGACAT
66 CAAGGCCAACGACATTGGTCTT-AAAGATGAATGCGCCAATGTGCTGATTCAAGGCCAGCGACAT
* * *
515794 TGGTCTTAAAGATAAAGGTGCTAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATAAA
130 TGGTCATAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATAAA
*
515859 GGTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTG
195 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTG
* *
515900 TGCCAATGTACTGATTCAAGGCTAGTGACATTGGTATTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATGTACTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
515965 CAAGGCCAACGACATCGGTCTTAAAGATGAAGGCGCCAATGTGCTGATTCAAGGCCAGCGACATT
66 CAAGGCCAACGACATTGGTCTTAAAGATGAATGCGCCAATGTGCTGATTCAAGGCCAGCGACATT
* *
516030 GGTCATAAAGATAAAGGTGCCAATATGCTGA-TAAAGGCCAGCGATATCGGACTTAAAGATGAAG
131 GGTCATAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATAAAG
*
516094 GTGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTG
196 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTG
*
516134 TGCCAATGTACTGATTTAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATGTACTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
516199 CAAAGCCAAC-AGCATTGGTCTTAAAGATGAATGCGCTAATGTGCTGATTCAAGGCCAGCGACAT
66 CAAGGCCAACGA-CATTGGTCTTAAAGATGAATGCGCCAATGTGCTGATTCAAGGCCAGCGACAT
* ** *
516263 TGGTCATAAAGATAATGGTGCCAATATATTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAA
130 TGGTCATAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATAAA
*
516328 GGTGCCAATATGCTGATTCACGGCCAGCGATATTGGGCTTG
195 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTG
* * * *
516369 TGCTAATGCACTGATTTAAGGCCAGTGACAATGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATGTACTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
516434 CAAAGCCAAC-AGCATTGGTCTTAAAGATGAATGCGCTAATGTGCTGATTCAAGGCCAGCGACAT
66 CAAGGCCAACGA-CATTGGTCTTAAAGATGAATGCGCCAATGTGCTGATTCAAGGCCAGCGACAT
* * *
516498 TGGTCATAAAGATAAAGGTGTCAATATGCTGATTTAAGGCCAGCGATATCGAACTTAAAGATAAA
130 TGGTCATAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATAAA
* *
516563 GGTGCCAATATGCTGATTCGAGGCCAGTGATATTGGGCTTG
195 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTG
* * * *
516604 TGCCAATGTGCTGATTCAAGGCCAATGACATTAGTCTTAAAAGAT-AAGGTGCCAATATGCTGAT
1 TGCCAATGTACTGATTCAAGGCCAGTGACATTGGTCTT-AAAGATGAAGGTGCCAATGTGCTGAT
* * *
516668 TCAAGGCCAGCGATATTGG-GTT-----T--AT--GCCAATGTGCTGATTCAAGGCCAGCGACAT
65 TCAAGGCCAACGACATTGGTCTTAAAGATGAATGCGCCAATGTGCTGATTCAAGGCCAGCGACAT
* * *
516723 TGGTC-TCAGAGA-CAAGGTGCCAATATACTGATTCAAGGCCAGCGATAT
130 TGGTCAT-AAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
516771 TGGGCTTATG
Statistics
Matches: 802, Mismatches: 63, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
224 33 0.04
225 38 0.05
227 2 0.00
229 1 0.00
233 1 0.00
234 219 0.27
235 499 0.62
236 9 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (235 bp):
TGCCAATGTACTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATGTGCTGATT
CAAGGCCAACGACATTGGTCTTAAAGATGAATGCGCCAATGTGCTGATTCAAGGCCAGCGACATT
GGTCATAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATAAAG
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTG
Found at i:516707 original size:39 final size:39
Alignment explanation
Indices: 516653--516899 Score: 183
Period size: 39 Copynumber: 5.9 Consensus size: 39
516643 AAAGATAAGG
516653 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTA
* * *
516692 TGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTCAGAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGT-T-------TA
* *
516738 GGTGCCAATATACTGATTCAAGGCCAGCGATATTGGGCTTA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTA
* * *
516779 TGCCAATGTGCTGATTCAAGGCTAGCAATATT-GGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGT-TT-------A
* *
516825 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTCGGCTTA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTA
* * *
516866 TGCCAATGTACTGATTCAAGGCCAGCGACATTGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGG
516900 TCTTAGAGAC
Statistics
Matches: 165, Mismatches: 21, Indels: 44
0.72 0.09 0.19
Matches are distributed among these distances:
38 5 0.03
39 91 0.55
41 2 0.01
46 2 0.01
48 61 0.37
49 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTA
Found at i:516763 original size:48 final size:48
Alignment explanation
Indices: 516692--516947 Score: 226
Period size: 48 Copynumber: 5.7 Consensus size: 48
516682 ATTGGGTTTA
* *
516692 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTCAGAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTCAGAGACAAGG
* * *
516740 TGCCAATATACTGATTCAAGGCCAGCGATATTGGGCT-------TA--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTCAGAGACAAGG
* * * * *
516779 TGCCAATGTGCTGATTCAAGGCTAGCAATATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTCAGAGACAAGG
*
516827 TGCCAATATGCTGATTCAAGGCCAGCGATA----T-TC-G-G-CTTA--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTCAGAGAC-AAGG
* * * *
516866 TGCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTCAGAGACAAGG
*
516914 TGCCAATATGCTGATTCAAGGCCAACGATATTGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGG
516948 ACTTAGAAGA
Statistics
Matches: 162, Mismatches: 26, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
39 59 0.36
40 1 0.01
41 3 0.02
43 2 0.01
44 2 0.01
45 1 0.01
46 3 0.02
47 1 0.01
48 90 0.56
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (48 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTCAGAGACAAGG
Found at i:516780 original size:87 final size:87
Alignment explanation
Indices: 516519--516952 Score: 616
Period size: 87 Copynumber: 5.0 Consensus size: 87
516509 ATAAAGGTGT
* * * * ** * *
516519 CAATATGCTGATTTAAGGCCAGCGATATCGAACTTAAAGATAAAGGTGCCAATATGCTGATTCGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAA
* *
516584 GGCCAGTGATATTGGGCTTGTGC
65 GGCCAGCGATATTGGGCTTATGC
** * *
516607 CAATGTGCTGATTCAAGGCCAATGACATTAGTCTTAAAAGATAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGACAAGGTGCCAATATGCTGATTCAA
*
516672 GGCCAGCGATATTGGGTTTATGC
65 GGCCAGCGATATTGGGCTTATGC
* * *
516695 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTCAGAGACAAGGTGCCAATATACTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAG
516760 GCCAGCGATATTGGGCTTATGC
66 GCCAGCGATATTGGGCTTATGC
* * *
516782 CAATGTGCTGATTCAAGGCTAGCAATATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAG
*
516847 GCCAGCGATATTCGGCTTATGC
66 GCCAGCGATATTGGGCTTATGC
* *
516869 CAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAG
* *
516934 GCCAACGATATTGGACTTA
66 GCCAGCGATATTGGGCTTA
516953 GAAGAAGACG
Statistics
Matches: 308, Mismatches: 37, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
87 204 0.66
88 99 0.32
89 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (87 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAG
GCCAGCGATATTGGGCTTATGC
Found at i:517091 original size:30 final size:30
Alignment explanation
Indices: 517015--517098 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
517005 CGTGCTTTTC
*
517015 AAGGTTGCCACTGACTTGTGGG-CTTTGAAA
1 AAGG-TGCCACTGACTTGTGGGTTTTTGAAA
* * **
517045 GAGGTGCTACCAACTTGTGGGTTTTTGAAA
1 AAGGTGCCACTGACTTGTGGGTTTTTGAAA
*
517075 AAGGTGCCACTGACTTGTAGGTTT
1 AAGGTGCCACTGACTTGTGGGTTT
517099 AAAAAGAGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 14 0.33
30 29 0.67
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (30 bp):
AAGGTGCCACTGACTTGTGGGTTTTTGAAA
Found at i:517134 original size:33 final size:33
Alignment explanation
Indices: 517097--517195 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
517087 ACTTGTAGGT
*
517097 TTAAAAAGAGAAAGATGCCATGGAGTTGTGGAC
1 TTAAAAAGAGAAAGATGCCACGGAGTTGTGGAC
517130 TT-AAAAG-G---G-TGCCACGGAGTTGTGGAC
1 TTAAAAAGAGAAAGATGCCACGGAGTTGTGGAC
* * *
517157 TTAAAAGGAAAAAGATGCCACAGAGTTGTGGAC
1 TTAAAAAGAGAAAGATGCCACGGAGTTGTGGAC
517190 TTAAAA
1 TTAAAA
517196 GGGTGCCACA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
27 19 0.34
28 5 0.09
31 1 0.02
32 6 0.11
33 25 0.45
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.21
Consensus pattern (33 bp):
TTAAAAAGAGAAAGATGCCACGGAGTTGTGGAC
Found at i:517148 original size:27 final size:27
Alignment explanation
Indices: 517119--517218 Score: 137
Period size: 27 Copynumber: 3.5 Consensus size: 27
517109 AGATGCCATG
*
517119 GAGTTGTGGACTTAAAAGGGTGCCACG
1 GAGTTGTGGACTTAAAAGGGTGCCACA
517146 GAGTTGTGGACTTAAAAGGAAAAAGATGCCACA
1 GAGTTGTGGACTTAAAAGG-----G-TGCCACA
517179 GAGTTGTGGACTTAAAAGGGTGCCACA
1 GAGTTGTGGACTTAAAAGGGTGCCACA
517206 GAGTTGTGGACTT
1 GAGTTGTGGACTT
517219 TGAAAAAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
27 39 0.59
28 1 0.02
32 1 0.02
33 25 0.38
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (27 bp):
GAGTTGTGGACTTAAAAGGGTGCCACA
Found at i:517161 original size:60 final size:60
Alignment explanation
Indices: 517097--517253 Score: 215
Period size: 60 Copynumber: 2.6 Consensus size: 60
517087 ACTTGTAGGT
* ** *
517097 TTAAAAAGAGAAAGATGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
1 TTAAAAAGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC
*
517157 TTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC
1 TTAAAAAGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC
* * * *
517217 TTTGAAAAAAAAAAAGGTGCCACAAAGTCGTGGACTT
1 -TT-AAAAAGAAAAAGATGCCACAGAGTTGTGGACTT
517254 TGGGAAGAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 55 0.65
61 2 0.02
62 28 0.33
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (60 bp):
TTAAAAAGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC
Found at i:517363 original size:125 final size:125
Alignment explanation
Indices: 517166--517449 Score: 328
Period size: 125 Copynumber: 2.3 Consensus size: 125
517156 CTTAAAAGGA
* * * *
517166 AAAAGATGCCAC-AGAGTTGTGGAC-TT-A-AAAGGGTGCCACAGAGTTGTGGACTTTGAAAAAA
1 AAAAGATGCCACTA-AGTAGTGGACTTTGAGAAAAGATGCCACAGAGTCGTGGACTTTG-AAAAA
* * * * ** *
517227 AAAAAGGTGCCACAAAGTCGTGGACTTTGGGAAGAGATGCCACTGAGTCGTGGACTTTG-AG
64 AAAAAGATGCCACAAAGTCATGGACATAGAAAAGAGATGCCACTAAGTCGTGGACTTTGAAG
* * *
517288 AAGAGATTGCCACTAAGTAGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTG-AAGA
1 AAAAGA-TGCCACTAAGTAGTGGACTTTG-AGAAAAGATGCCACAGAGTCGTGGACTTTGAAAAA
** *
517352 AAAAAGATGCCACTGAGTCATGGACATAGAAAAGAGATGCCACTAAGTTGTGGACTTTGAAG
64 AAAAAGATGCCACAAAGTCATGGACATAGAAAAGAGATGCCACTAAGTCGTGGACTTTGAAG
*
517414 AAAAGATGCCACTAAGTCGTGGACTTTGAGAAAAGA
1 AAAAGATGCCACTAAGTAGTGGACTTTGAGAAAAGA
517450 GATTTGAAGA
Statistics
Matches: 136, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
122 5 0.04
123 15 0.11
124 11 0.08
125 73 0.54
126 8 0.06
127 24 0.18
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.21
Consensus pattern (125 bp):
AAAAGATGCCACTAAGTAGTGGACTTTGAGAAAAGATGCCACAGAGTCGTGGACTTTGAAAAAAA
AAAGATGCCACAAAGTCATGGACATAGAAAAGAGATGCCACTAAGTCGTGGACTTTGAAG
Found at i:517416 original size:94 final size:91
Alignment explanation
Indices: 517165--517452 Score: 323
Period size: 94 Copynumber: 3.1 Consensus size: 91
517155 ACTTAAAAGG
* * * * *
517165 AAAAAGATGCCACAGAGTTGTGGACTTAAAAG-GGTGCCAC-AGAGTTGTGGACTTTGAAAAAAA
1 AAAAAGATGCCACTGAGTCGTGGACTGAAAAGAGATGCCACTA-AGTTGTGGACTTTG----AAG
* *
517228 AAAAGGTGCCACAAAGTCGTGGACTTTG-G-
61 AAAAGATGCCACTAAGTCGTGGACTTTGAGA
* * * *
517257 GAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTAAGTAGTGGACTTTGAAGAA
1 AAAAAGATGCCACTGAGTCGTGGAC--TGAAAAGAGA-TGCCACTAAGTTGTGGACTTTGAAGAA
*
517322 AAGATGCCACTGAGTCGTGGACTTTGAAGA
63 AAGATGCCACTAAGTCGTGGACTTTG-AGA
*
517352 AAAAAGATGCCACTGAGTCATGGACATAGAAAAGAGATGCCACTAAGTTGTGGACTTTGAAGAAA
1 AAAAAGATGCCACTGAGTCGTGGAC-T-GAAAAGAGATGCCACTAAGTTGTGGACTTTGAAGAAA
517417 AGATGCCACTAAGTCGTGGACTTTGAGA
64 AGATGCCACTAAGTCGTGGACTTTGAGA
*
517445 AAAGAGAT
1 AAAAAGAT
517453 TTGAAGAATT
Statistics
Matches: 167, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
92 48 0.29
93 10 0.06
94 58 0.35
95 31 0.19
96 19 0.11
97 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (91 bp):
AAAAAGATGCCACTGAGTCGTGGACTGAAAAGAGATGCCACTAAGTTGTGGACTTTGAAGAAAAG
ATGCCACTAAGTCGTGGACTTTGAGA
Found at i:517448 original size:30 final size:30
Alignment explanation
Indices: 517228--517449 Score: 257
Period size: 31 Copynumber: 7.2 Consensus size: 30
517218 TTGAAAAAAA
* * *
517228 AAAAGGTGCCACAAAGTCGTGGACTTTGGG
1 AAAAGATGCCACTAAGTCGTGGACTTTGAG
* *
517258 AAGAGATGCCACTGAGTCGTGGACTTTGAG
1 AAAAGATGCCACTAAGTCGTGGACTTTGAG
* *
517288 AAGAGATTGCCACTAAGTAGTGGACTTTGAAG
1 AAAAGA-TGCCACTAAGTCGTGGACTTTG-AG
*
517320 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTAAGTCGTGGACTTTG-AG
* * * *
517351 AAAAAAGATGCCACTGAGTCATGGACATAGA-
1 --AAAAGATGCCACTAAGTCGTGGACTTTGAG
*
517382 AAAGAGATGCCACTAAGTTGTGGACTTTGAAG
1 AAA-AGATGCCACTAAGTCGTGGACTTTG-AG
517414 AAAAGATGCCACTAAGTCGTGGACTTTGAG
1 AAAAGATGCCACTAAGTCGTGGACTTTGAG
517444 AAAAGA
1 AAAAGA
517450 GATTTGAAGA
Statistics
Matches: 166, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.02
30 59 0.36
31 68 0.41
32 11 0.07
33 25 0.15
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (30 bp):
AAAAGATGCCACTAAGTCGTGGACTTTGAG
Found at i:518745 original size:6 final size:6
Alignment explanation
Indices: 518726--518771 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
518716 TTTTTGTGTA
*
518726 TTTTT- TTTTAG TTTTTG TTTTTG TTTTTG TTTTT- TTTTTG TGTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T-TTTT
518772 TACTTTTGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 9 0.25
6 23 0.64
7 4 0.11
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:518771 original size:12 final size:11
Alignment explanation
Indices: 518714--518772 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
518704 GCCTTTGCAC
*
518714 TTTTTTTGTGT
1 TTTTTTTGTTT
*
518725 ATTTTTT-TTT
1 TTTTTTTGTTT
**
518735 AGTTTTTGTTT
1 TTTTTTTGTTT
518746 TTGTTTTTGTTT
1 TT-TTTTTGTTT
518758 TTTTTTTGTGTT
1 TTTTTTTGT-TT
518770 TTT
1 TTT
518773 ACTTTTGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.20
11 16 0.40
12 16 0.40
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:518778 original size:19 final size:19
Alignment explanation
Indices: 518716--518778 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
518706 CTTTGCACTT
* *
518716 TTTTTGTGTATTTTTTTTTAG
1 TTTTTGT-T-TTTGTTTTTAC
*
518737 TTTTTGTTTTTGTTTTT-G
1 TTTTTGTTTTTGTTTTTAC
*
518755 TTTTTTTTTTGTGTTTTTAC
1 TTTTTGTTTT-TGTTTTTAC
518775 TTTT
1 TTTT
518779 GACTTTTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.27
19 15 0.41
20 5 0.14
21 7 0.19
ACGTcount: A:0.05, C:0.02, G:0.13, T:0.81
Consensus pattern (19 bp):
TTTTTGTTTTTGTTTTTAC
Found at i:518779 original size:31 final size:31
Alignment explanation
Indices: 518712--518779 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
518702 TTGCCTTTGC
518712 ACTTTT-TTTGTGTATTTTTTTTTAGTTTTT
1 ACTTTTGTTTGTGTATTTTTTTTTAGTTTTT
** * *
518742 GTTTTTGTTTTTGT-TTTTTTTTTGTGTTTTT
1 ACTTTTGTTTGTGTATTTTTTTTT-AGTTTTT
518773 ACTTTTG
1 ACTTTTG
518780 ACTTTTTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.06, C:0.03, G:0.13, T:0.78
Consensus pattern (31 bp):
ACTTTTGTTTGTGTATTTTTTTTTAGTTTTT
Found at i:528124 original size:21 final size:22
Alignment explanation
Indices: 528098--528151 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
528088 TGGACATGTT
528098 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
528119 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
528141 AAAAATGCATG
1 AAAAATGCATG
528152 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:529111 original size:20 final size:20
Alignment explanation
Indices: 529064--529134 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
529054 AAAAAGACAT
*
529064 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
529083 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
529104 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
529124 AATGTATCGAT
1 AATGTATCGAT
529135 TCATCAGGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:530309 original size:57 final size:57
Alignment explanation
Indices: 529698--530796 Score: 1317
Period size: 57 Copynumber: 19.0 Consensus size: 57
529688 TTTAAAAAAT
* * * * *
529698 GTGCCACTAACTTGTGTAGGCTTTGAAAAAAGTTACCACTGACACATGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTG--GGCTTTGAAAAGAG-TGCCACTG--ACTTGTGGGCTTTG-AAAGG
** * * * *
529761 GTGTTACTAACTTGCGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGATTTGAAAGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGG
* * * *
529821 ATGCCATTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * * *
529877 GTGCCACTGACTCGTGGGCTTTGAAAAG-GTACCACTGACTCGTGGGC-TTGAAATG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* *
529932 GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTTCAAA-G
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC-TTTGAAAGG
*
529988 GTGCCACTAACTTGCGTGGGCTTT-AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGG
* * * * *
530049 GTGCCACTAACTTGTGGGCTTCG-AAAGGGTGCCACTGACTTGTGGGCTCTAAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
530105 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGG
* *
530163 GTGCCACTGATTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* *
530220 AGTGCCTCTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG
1 -GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
530278 GTGCCACTCACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGG
* *
530336 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGG
530393 GTGCCACTGACTTGCGTGGGCTTT-AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGG
* * * *
530454 GTGCCACTGACTTGTGGGTTTTGAAAA-AGTGCGACTGACTTGTGGGCTTCGTAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * * * * *
530510 GTGCCACTGACTTGTGGGCTTCG-AAAGGGGGCTACTCACTTGTGGGCTCTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
530566 GTGCCAATAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGCGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* *
530623 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTTATTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
* * *
530680 GTGCCACTGACTTGTGGGC-TTGAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGG
*
530737 GTGCCACTGACTTGCGTGGGCTTT-AAAAGGAGTGTCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAGG
530796 G
1 G
530797 ATGAACATTC
Statistics
Matches: 908, Mismatches: 93, Indels: 74
0.84 0.09 0.07
Matches are distributed among these distances:
54 4 0.00
55 49 0.05
56 210 0.23
57 242 0.27
58 187 0.21
59 66 0.07
60 60 0.07
61 54 0.06
62 16 0.02
63 17 0.02
65 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (57 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
Found at i:530794 original size:29 final size:29
Alignment explanation
Indices: 529698--530795 Score: 1288
Period size: 28 Copynumber: 38.0 Consensus size: 29
529688 TTTAAAAAAT
* **
529698 GTGCCACTAACTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGACTTGTG--GGCTTTGAAAGGA
* * *
529729 GTTACCACTGACACATGTGGGCTTTGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTGAAAGGA
** * *
529761 GTGTTACTAACTTGCGTGGGCTTTAAAAGG-
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
*
529791 GTGCCACTGACTTGCGTGGGATTTGAAA-GA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
* *
529821 ATGCCATTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
529850 -TGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
529877 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
529905 GTACCACTGACTCGTGGGC-TTGAAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
529932 GTGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
529960 GTGCCACTGACTCGTGGGCTTTTCAAA-G-
1 GTGCCACTGACTTGTGGGC-TTTGAAAGGA
* *
529988 GTGCCACTAACTTGCGTGGGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
530019 GTGCCACTGACTTGTGTGGGCTTTGAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
* *
530049 GTGCCACTAACTTGTGGGCTTCGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
530077 GTGCCACTGACTTGTGGGCTCTAAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530105 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
530134 GTGCCACTGATTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
530163 GTGCCACTGATTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
530192 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530221 GTGCCTCTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
530250 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
530278 GTGCCACTCACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
530307 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
530336 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530364 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530393 GTGCCACTGACTTGCGTGGGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
530424 GTGCCACTGACTTGTGTGGGCTTTGAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
* *
530454 GTGCCACTGACTTGTGGGTTTTGAAA-AA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
530482 GTGCGACTGACTTGTGGGCTTCGTAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530510 GTGCCACTGACTTGTGGGCTTCGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
530538 GGGCTACTCACTTGTGGGCTCTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
530566 GTGCCAATAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530595 GTGCCACTGACTTGTGCGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530623 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
530652 GTGCCACTTATTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530680 GTGCCACTGACTTGTGGGC-TTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
530708 GTGCCACTAATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
530737 GTGCCACTGACTTGCGTGGGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
*
530768 GTGTCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
530796 GATGAACATT
Statistics
Matches: 934, Mismatches: 100, Indels: 68
0.85 0.09 0.06
Matches are distributed among these distances:
27 34 0.04
28 396 0.42
29 306 0.33
30 62 0.07
31 107 0.11
32 21 0.02
33 2 0.00
34 6 0.01
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:532050 original size:20 final size:20
Alignment explanation
Indices: 532009--532048 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
531999 ATCTAGACCC
532009 TTCTATTTTTTGCTATTTTT
1 TTCTATTTTTTGCTATTTTT
*
532029 TTCTTTTTTTTG-T-TTTTT
1 TTCTATTTTTTGCTATTTTT
532047 TT
1 TT
532049 TTGGGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.82
Consensus pattern (20 bp):
TTCTATTTTTTGCTATTTTT
Found at i:545137 original size:22 final size:23
Alignment explanation
Indices: 545109--545164 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
545099 TGGACATGTT
545109 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
545131 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
545154 AAAAATGCATG
1 AAAAATGCATG
545165 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:546123 original size:20 final size:20
Alignment explanation
Indices: 546076--546146 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
546066 AAAAAGACAT
546076 AATGTATCGATACATT-ATA
1 AATGTATCGATACATTCATA
*
546095 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
546116 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
546136 AATGTATCGAT
1 AATGTATCGAT
546147 GCATCAGGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 40 0.93
21 3 0.07
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:619471 original size:26 final size:26
Alignment explanation
Indices: 619435--619489 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
619425 ATGAAGAAGC
619435 TTAACCTGAAAGAATAAAGTTGATTG
1 TTAACCTGAAAGAATAAAGTTGATTG
619461 TTAACCTGAAAGAATAAAGTTGATTG
1 TTAACCTGAAAGAATAAAGTTGATTG
619487 TTA
1 TTA
619490 TAAATAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (26 bp):
TTAACCTGAAAGAATAAAGTTGATTG
Found at i:620269 original size:27 final size:26
Alignment explanation
Indices: 620237--620288 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
620227 ACGTGAATTA
*
620237 TAATTTGTTACAATAAAATTTATTAAT
1 TAATTTGATACAAT-AAATTTATTAAT
* *
620264 TAATTTGATGCAATTAATTTATTAA
1 TAATTTGATACAATAAATTTATTAA
620289 CTTTTCCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (26 bp):
TAATTTGATACAATAAATTTATTAAT
Found at i:620697 original size:108 final size:105
Alignment explanation
Indices: 620567--620760 Score: 273
Period size: 107 Copynumber: 1.8 Consensus size: 105
620557 TTTAAATTTT
* ** * *
620567 ATGTGGACACTATTTTTTAATATTTAGTGCATTTAAATTTAAATAAATTAATAAAAATTACATAT
1 ATGTAGACACTATTTTAAAATATTTA-TGAATATAAATTTAAATAAATTAAT-AAAATTACATAT
620632 TTGAAAAAGGGAAAGTT-TATTAATTTTAAAGTCATTTAATATA
64 TT-AAAAA-GGAAAGTTCTATTAATTTTAAAGTCATTTAATATA
* *
620675 ATGTAGACTCTATTTTAAAATATTTATTAATATAAATTTAAATAAATTAATAAAATTACATATTT
1 ATGTAGACACTATTTTAAAATATTTATGAATATAAATTTAAATAAATTAATAAAATTACATATTT
*
620740 AAATAGGAAAGTTCTATTAAT
66 AAAAAGGAAAGTTCTATTAAT
620761 GTGAAATCTA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
104 8 0.10
105 11 0.14
106 14 0.18
107 22 0.29
108 22 0.29
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (105 bp):
ATGTAGACACTATTTTAAAATATTTATGAATATAAATTTAAATAAATTAATAAAATTACATATTT
AAAAAGGAAAGTTCTATTAATTTTAAAGTCATTTAATATA
Found at i:621382 original size:21 final size:22
Alignment explanation
Indices: 621356--621398 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
621346 GAATAGTAAT
*
621356 TTATC-AAAAGTAAATTATATC
1 TTATCAAAAAATAAATTATATC
621377 TTATCAAAAAATAAATTATATC
1 TTATCAAAAAATAAATTATATC
621399 ATGAGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TTATCAAAAAATAAATTATATC
Found at i:622615 original size:353 final size:353
Alignment explanation
Indices: 621969--622674 Score: 1387
Period size: 353 Copynumber: 2.0 Consensus size: 353
621959 GAAAAAGAAG
621969 ATTTTTTGGTATATTTTAGAGTATTATAATAGCTTATTTATATTACAGCCCTAGCTCCATCTAGC
1 ATTTTTTGGTATATTTTAGAGTATTATAATAGCTTATTTATATTACAGCCCTAGCTCCATCTAGC
622034 CTTAAGTCAACATAATCATAATCCCATGATTTATGAGATTTATTAGGAAAAATCAAATATTGATT
66 CTTAAGTCAACATAATCATAATCCCATGATTTATGAGATTTATTAGGAAAAATCAAATATTGATT
622099 CTAATCCCATAATTTATGGGAATCTTATCTTATATTCAAATTTTACAGTTTCTAAAATAGCACCT
131 CTAATCCCATAATTTATGGGAATCTTATCTTATATTCAAATTTTACAGTTTCTAAAATAGCACCT
*
622164 AGCTATACACATAGCTGTACACAATTTTACAGCTTCTAGAATAGCACCTAGCTGTACACATAGCT
196 AGCTATACACATAGCTGTACACAAATTTACAGCTTCTAGAATAGCACCTAGCTGTACACATAGCT
622229 ATTCACAGCACCTAGCACAGCTCCTCACACTCTCCCTTAAGCTGGTGAATAGATATTATCCATTC
261 ATTCACAGCACCTAGCACAGCTCCTCACACTCTCCCTTAAGCTGGTGAATAGATATTATCCATTC
622294 CCATCTTGGATACAATAGCCTGTAACAT
326 CCATCTTGGATACAATAGCCTGTAACAT
622322 ATTTTTTGGTATATTTTAGAGTATTATAATAGCTTATTTATATTACAGCCCTAGCTCCATCTAGC
1 ATTTTTTGGTATATTTTAGAGTATTATAATAGCTTATTTATATTACAGCCCTAGCTCCATCTAGC
622387 CTTAAGTCAACCATAATCATAATCCCATGATTTATGAGATTTATTAGGAAAAATCAAATATTGAT
66 CTTAAGTCAA-CATAATCATAATCCCATGATTTATGAGATTTATTAGGAAAAATCAAATATTGAT
622452 TCTAAT-CCATAATTTATGGGAATCTTATCTTATATTCAAATTTTACAGTTTCTAAAATAGCACC
130 TCTAATCCCATAATTTATGGGAATCTTATCTTATATTCAAATTTTACAGTTTCTAAAATAGCACC
622516 TAGCTATACACATAGCTGTACACAAATTTACAGCTTCTAGAATAGCACCTAGCTGTACACATAGC
195 TAGCTATACACATAGCTGTACACAAATTTACAGCTTCTAGAATAGCACCTAGCTGTACACATAGC
622581 TATTCACAGCACCTAGCACAGCTCCTCACACTCTCCCTTAAGCTGGTGAATAGATATTATCCATT
260 TATTCACAGCACCTAGCACAGCTCCTCACACTCTCCCTTAAGCTGGTGAATAGATATTATCCATT
622646 CCCATCTTGGATACAATAGCCTGTAACAT
325 CCCATCTTGGATACAATAGCCTGTAACAT
622675 TGGGCTACTT
Statistics
Matches: 351, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
353 291 0.83
354 60 0.17
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (353 bp):
ATTTTTTGGTATATTTTAGAGTATTATAATAGCTTATTTATATTACAGCCCTAGCTCCATCTAGC
CTTAAGTCAACATAATCATAATCCCATGATTTATGAGATTTATTAGGAAAAATCAAATATTGATT
CTAATCCCATAATTTATGGGAATCTTATCTTATATTCAAATTTTACAGTTTCTAAAATAGCACCT
AGCTATACACATAGCTGTACACAAATTTACAGCTTCTAGAATAGCACCTAGCTGTACACATAGCT
ATTCACAGCACCTAGCACAGCTCCTCACACTCTCCCTTAAGCTGGTGAATAGATATTATCCATTC
CCATCTTGGATACAATAGCCTGTAACAT
Found at i:627306 original size:44 final size:43
Alignment explanation
Indices: 627199--627358 Score: 171
Period size: 44 Copynumber: 3.7 Consensus size: 43
627189 ATGGTGACAG
*
627199 CAATAAAGGCTTAATAAAACAGATTCTGGAAAGAAAAAAAATTCCAA
1 CAATAAAGGCTGAATAAAACAGATTCT-G--A-AAAAAAAATTCCAA
* * * * *
627246 CAATGAAGGTTGAATAAAATAGATTCTGAAAAAATAAATTTCAG
1 CAATAAAGGCTGAATAAAACAGATTCTGAAAAAA-AAATTCCAA
* * *
627290 CAATAAAAGCTGAATAAAATAGATTTTG--AAAAAAATTCCAA
1 CAATAAAGGCTGAATAAAACAGATTCTGAAAAAAAAATTCCAA
*
627331 CAATGAAGGCTGAATAAAACAGATTCTG
1 CAATAAAGGCTGAATAAAACAGATTCTG
627359 GGAAGGTTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 31 0.32
42 4 0.04
43 5 0.05
44 32 0.33
46 1 0.01
47 23 0.24
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (43 bp):
CAATAAAGGCTGAATAAAACAGATTCTGAAAAAAAAATTCCAA
Found at i:627343 original size:41 final size:42
Alignment explanation
Indices: 627231--627358 Score: 168
Period size: 41 Copynumber: 3.0 Consensus size: 42
627221 ATTCTGGAAA
*
627231 GAAAAAAAATTCCAACAATGAAGGTTGAATAAAATAGATTCT
1 GAAAAAAAATTCCAACAATGAAGGCTGAATAAAATAGATTCT
* * * * *
627273 GAAAAAATAAATTTCAGCAATAAAAGCTGAATAAAATAGATTTT
1 G-AAAAA-AAATTCCAACAATGAAGGCTGAATAAAATAGATTCT
*
627317 G-AAAAAAATTCCAACAATGAAGGCTGAATAAAACAGATTCT
1 GAAAAAAAATTCCAACAATGAAGGCTGAATAAAATAGATTCT
627358 G
1 G
627359 GGAAGGTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 31 0.43
42 5 0.07
43 5 0.07
44 31 0.43
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.23
Consensus pattern (42 bp):
GAAAAAAAATTCCAACAATGAAGGCTGAATAAAATAGATTCT
Done.