Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 10 of 335
Found at i:3406752 original size:75 final size:73
Alignment explanation
Indices: 3406664--3406835 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
3406654 GGTTTTCCTC
** * * **
3406664 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
3406728 TCAGTATGG
65 TCAGTATGG
*
3406737 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
3406802 CTCAGTATGG
64 CTCAGTATGG
3406812 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
3406836 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:3408262 original size:14 final size:14
Alignment explanation
Indices: 3408243--3408273 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3408233 CCTGCGGGAT
3408243 TTAACCCGGATATA
1 TTAACCCGGATATA
*
3408257 TTAACCCGGTTATA
1 TTAACCCGGATATA
3408271 TTA
1 TTA
3408274 CCAGCACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (14 bp):
TTAACCCGGATATA
Found at i:3408283 original size:52 final size:54
Alignment explanation
Indices: 3408205--3408309 Score: 178
Period size: 52 Copynumber: 2.0 Consensus size: 54
3408195 GTTACAGGAT
3408205 TTAACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTTAA-CCCGGATATA
1 TTAACCCGGATATAATACCAGCACGAAGCCTGCGGGATTTTAAGCCCGGATATA
* *
3408257 TTAACCCGGTTATATTACCAGCACGAAGCCTGCGGGATTTTAAGCCCGGATAT
1 TTAACCCGGATATAATACCAGCACGAAGCCTGCGGGATTTTAAGCCCGGATAT
3408310 CATATTTCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 35 0.71
53 5 0.10
54 9 0.18
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (54 bp):
TTAACCCGGATATAATACCAGCACGAAGCCTGCGGGATTTTAAGCCCGGATATA
Found at i:3411367 original size:16 final size:16
Alignment explanation
Indices: 3411299--3411367 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
3411289 CACATTTTTT
3411299 ATTTTTTATTT-TCAAA
1 ATTTTTTATTTAT-AAA
* *
3411315 ATTTTTTATTTTTAATTT
1 ATTTTTTATTTATAA--A
*
3411333 ATCTTTTTAATTA-ATAA
1 AT-TTTTTATTTATA-AA
3411350 ATTTTTTATTTATAAA
1 ATTTTTTATTTATAAA
3411366 AT
1 AT
3411368 CAAATAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
16 26 0.62
17 4 0.10
18 3 0.07
19 9 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTATTTATAAA
Found at i:3411401 original size:16 final size:16
Alignment explanation
Indices: 3411371--3411411 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3411361 ATAAAATCAA
*
3411371 ATAATTATT-GTAAAT
1 ATAATTTTTAGTAAAT
*
3411386 ATTATTTTTAGTAAAT
1 ATAATTTTTAGTAAAT
3411402 ATAATTTTTA
1 ATAATTTTTA
3411412 TACGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
ATAATTTTTAGTAAAT
Found at i:3413485 original size:2 final size:2
Alignment explanation
Indices: 3413480--3413508 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3413470 TAATGAACAA
3413480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3413509 AAGAACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3414004 original size:17 final size:17
Alignment explanation
Indices: 3413982--3414016 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3413972 TTTACATGTC
3413982 ATTTAATGATTAAATTA
1 ATTTAATGATTAAATTA
3413999 ATTTAATGATTAAATTA
1 ATTTAATGATTAAATTA
3414016 A
1 A
3414017 CGGTTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTTAATGATTAAATTA
Found at i:3416416 original size:44 final size:45
Alignment explanation
Indices: 3416326--3416454 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
3416316 GACAGAACGA
*
3416326 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
3416372 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
3416416 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3416455 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:3420582 original size:72 final size:72
Alignment explanation
Indices: 3420460--3420603 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
3420450 TGATTTGAAT
* * * * *
3420460 GATTTACTATTTTGTTGTCTGTAATACTTCGTAACCCTGTTCTGATGACGGATACGGGTTAG-GG
1 GATTGACTATTTTGTTGTCTGTAATACTCCGTAACCCTGTTCAGACGACGGATACGAGTTAGAGG
3420524 TGTTACA
66 TGTTACA
*
3420531 GATTGACTATTTTGTTGTCTTGTAATACTCCGTAACCTTGTTCCAG-CGACGGATACGAGTTAGA
1 GATTGACTATTTTGTTGTC-TGTAATACTCCGTAACCCTGTT-CAGACGACGGATACGAGTTAGA
*
3420595 TGTGTTACA
64 GGTGTTACA
3420604 TATAAATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
71 18 0.29
72 35 0.56
73 10 0.16
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (72 bp):
GATTGACTATTTTGTTGTCTGTAATACTCCGTAACCCTGTTCAGACGACGGATACGAGTTAGAGG
TGTTACA
Found at i:3439343 original size:24 final size:24
Alignment explanation
Indices: 3439291--3439350 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
3439281 GAGCCTCCCC
3439291 TCACCACTCACCACTCACCGCTCA
1 TCACCACTCACCACTCACCGCTCA
* *
3439315 CCACC-CTCCACCACTCCATCGC-CA
1 TCACCACT-CACCACT-CACCGCTCA
3439339 TCACCA-TCACCA
1 TCACCACTCACCA
3439351 TCCACTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 7 0.23
24 18 0.60
25 5 0.17
ACGTcount: A:0.25, C:0.57, G:0.03, T:0.15
Consensus pattern (24 bp):
TCACCACTCACCACTCACCGCTCA
Found at i:3454132 original size:20 final size:19
Alignment explanation
Indices: 3454107--3454148 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3454097 CTTTAATTCA
3454107 TTTTAATTCTTTTTTTTAAT
1 TTTTAATT-TTTTTTTTAAT
3454127 TTTTAATTTTTTTTTTAAT
1 TTTTAATTTTTTTTTTAAT
3454146 TTT
1 TTT
3454149 ATACATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTAATTTTTTTTTTAAT
Found at i:3461884 original size:27 final size:27
Alignment explanation
Indices: 3461825--3461884 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
3461815 GAATTTTTTT
* **
3461825 AAAAAAAAATATTATATGTTAATATAG
1 AAAAAAAAATATTAGATCCTAATATAG
3461852 ACAAAAAAAAT-TTAGATCCTAATATAAG
1 A-AAAAAAAATATTAGATCCTAATAT-AG
3461880 AAAAA
1 AAAAA
3461885 TTGCTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.27
Consensus pattern (27 bp):
AAAAAAAAATATTAGATCCTAATATAG
Found at i:3462660 original size:2 final size:2
Alignment explanation
Indices: 3462653--3462684 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3462643 TGGGCTGTTT
3462653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3462685 GTTTGAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3467416 original size:10 final size:10
Alignment explanation
Indices: 3467401--3467426 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3467391 ATCCACTTTC
3467401 TTTTTTTGTT
1 TTTTTTTGTT
3467411 TTTTTTTGTT
1 TTTTTTTGTT
3467421 TTTTTT
1 TTTTTT
3467427 GTGTGTGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:3467951 original size:2 final size:2
Alignment explanation
Indices: 3467946--3467972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3467936 TTTGTTTTGG
3467946 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3467973 GCTGAGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3473084 original size:16 final size:16
Alignment explanation
Indices: 3473065--3473119 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
3473055 AATAAAAACG
3473065 ATCTAAAACTAAAATA
1 ATCTAAAACTAAAATA
*
3473081 ATCT-AAACTCAAATTA
1 ATCTAAAACT-AAAATA
* *
3473097 AT-TTAAACAAAAATA
1 ATCTAAAACTAAAATA
*
3473112 ATCCAAAA
1 ATCTAAAA
3473120 AATTTAAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (16 bp):
ATCTAAAACTAAAATA
Found at i:3480440 original size:39 final size:38
Alignment explanation
Indices: 3480397--3480506 Score: 170
Period size: 39 Copynumber: 2.9 Consensus size: 38
3480387 TGAAGTATAT
3480397 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCACAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC-CAC
* * *
3480436 AAGTGCTAAACGGAATCCTGAAGGCTAACTGAAG-CAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCCAC
3480473 -AGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
3480507 TCATCAGAGC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
36 30 0.47
37 3 0.05
39 31 0.48
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (38 bp):
AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCCAC
Found at i:3480495 original size:36 final size:37
Alignment explanation
Indices: 3480397--3480506 Score: 168
Period size: 36 Copynumber: 2.9 Consensus size: 37
3480387 TGAAGTATAT
3480397 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCACAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAG--CAC
* * *
3480436 AAGTGCTAAACGGAATCCTGAAGGCTAACTGAAGCAC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCAC
3480473 -AGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
1 AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGC
3480507 TCATCAGAGC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 31 0.48
37 3 0.05
39 31 0.48
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (37 bp):
AAGTGCTAAATGGAAGCCCGAAGGCTAACTGAAGCAC
Found at i:3484057 original size:46 final size:46
Alignment explanation
Indices: 3483990--3484164 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
3483980 TGTAACCCGC
3483990 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
3484036 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGT-TACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCCT--TCT-CAT
* * * * ** * *
3484086 -C-TCA-CGAACTCGGACTCAGCTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
*
3484129 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
3484165 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 4 0.04
46 62 0.57
47 25 0.23
48 6 0.06
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCAT
Found at i:3484113 original size:93 final size:93
Alignment explanation
Indices: 3483998--3484168 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
3483988 GCCCATAAGT
** * *
3483998 GAACTCGGACTCAACTCAACGAGCTCGGGCCTTCTCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3484063 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* *
3484091 GAACTCGGACTCAGCTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3484156 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3484169 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:3489639 original size:59 final size:59
Alignment explanation
Indices: 3489562--3489673 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
3489552 TTTTTATCAC
*
3489562 CTAATTATGAAAAGTTACAAAAT-AGTCACCCAAATATTAATAAATTTATTTTTAGGTCA
1 CTAATTATAAAAAGTTACAAAATGA-TCACCCAAATATTAATAAATTTATTTTTAGGTCA
* ** * *
3489621 CTAATTATAAAAAGTTACAAGATGATCACTTAACTATTAGTAAATTTATTTTT
1 CTAATTATAAAAAGTTACAAAATGATCACCCAAATATTAATAAATTTATTTTT
3489674 TCATCCCTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (59 bp):
CTAATTATAAAAAGTTACAAAATGATCACCCAAATATTAATAAATTTATTTTTAGGTCA
Found at i:3493461 original size:23 final size:24
Alignment explanation
Indices: 3493435--3493486 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3493425 CTGGTTTTAG
* *
3493435 ATATGTGATGACGTTATCTT-AAA
1 ATATGTCATGAAGTTATCTTGAAA
*
3493458 ATATG-CATGAATTTATCTTGAAA
1 ATATGTCATGAAGTTATCTTGAAA
3493481 ATATGT
1 ATATGT
3493487 TGAATTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (24 bp):
ATATGTCATGAAGTTATCTTGAAA
Found at i:3500135 original size:25 final size:24
Alignment explanation
Indices: 3500079--3500281 Score: 227
Period size: 25 Copynumber: 8.4 Consensus size: 24
3500069 CACTAATGAA
*
3500079 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACTGACGTGCTAATAT
3500101 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
* *
3500126 CAGGGAGCACTGACATGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
3500151 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
** *
3500176 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
*
3500198 CAGAGAGCACTGGCGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAAT-AT
*
3500223 CAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACTGACGTGCTAATA-T
*
3500248 CAGAGAGCTCT-AGCGTGCTAATAAT
1 CAGAGAGCACTGA-CGTGCTAAT-AT
3500273 CAGAGAGCA
1 CAGAGAGCA
3500282 TGCTGAGGTC
Statistics
Matches: 157, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
22 35 0.22
23 2 0.01
24 4 0.03
25 115 0.73
26 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTAATAT
Found at i:3500200 original size:72 final size:73
Alignment explanation
Indices: 3500071--3500281 Score: 227
Period size: 72 Copynumber: 2.9 Consensus size: 73
3500061 TTATTATGCA
* ** *
3500071 CTAATGAA-CAGAGAGCACTGAAGTGCT-ATA-CAGAGAGCACTGACGTGCTAAATATCAGGGAG
1 CTAAT-AATCAGAGAGCACTGACGTGCTAATATCAGAGAGCACAAACGTGCT-AATATCAGAGAG
3500133 CACTGACATG
64 CACTGACATG
*
3500143 CTAA-ATATCAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCT-A-ATCAGAGAG
1 CTAATA-ATCAGAGAGCACTGACGTGCT-AATATCAGAGAGCACAAACGTGCTAATATCAGAGAG
* *
3500205 CACTGGCGTG
64 CACTGACATG
* * * *
3500215 CTAATAATCAGAGAGCACTGGCGTGCTAATATTCAGAGAGCTCTAGCGTGCTAATAATCAGAGAG
1 CTAATAATCAGAGAGCACTGACGTGCTAATA-TCAGAGAGCACAAACGTGCTAAT-ATCAGAGAG
3500280 CA
64 CA
3500282 TGCTGAGGTC
Statistics
Matches: 117, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
70 1 0.01
71 5 0.04
72 78 0.67
73 3 0.03
74 3 0.03
75 27 0.23
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (73 bp):
CTAATAATCAGAGAGCACTGACGTGCTAATATCAGAGAGCACAAACGTGCTAATATCAGAGAGCA
CTGACATG
Found at i:3500251 original size:97 final size:97
Alignment explanation
Indices: 3500071--3500281 Score: 256
Period size: 97 Copynumber: 2.2 Consensus size: 97
3500061 TTATTATGCA
* *
3500071 CTAATGAA-CAGAGAGCACTGAAGTGCTATACAGAGAGCACTGACGTGCTAAATATCAGGGAGCA
1 CTAAT-AATCAGAGAGCACTAAAGTGCTATACAGAGAGCACTGACGTGCTAAATATCAGAGAGCA
3500135 CTGACATGCTAAATATCAGAGAGCACT-GACGTG
65 CTGACATGCTAAATATCAGAGAGCACTAG-CGTG
*
3500168 CTAA-ATATCAGAGAGCAC-AAATGTGCTA-ATCAGAGAGCACTGGCGTGCT-AATAATCAGAGA
1 CTAATA-ATCAGAGAGCACTAAA-GTGCTATA-CAGAGAGCACTGACGTGCTAAAT-ATCAGAGA
* * *
3500229 GCACTGGCGTGCT-AATATTCAGAGAGCTCTAGCGTG
62 GCACTGACATGCTAAATA-TCAGAGAGCACTAGCGTG
3500265 CTAATAATCAGAGAGCA
1 CTAATAATCAGAGAGCA
3500282 TGCTGAGGTC
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
95 1 0.01
96 11 0.11
97 86 0.86
98 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (97 bp):
CTAATAATCAGAGAGCACTAAAGTGCTATACAGAGAGCACTGACGTGCTAAATATCAGAGAGCAC
TGACATGCTAAATATCAGAGAGCACTAGCGTG
Found at i:3500886 original size:70 final size:70
Alignment explanation
Indices: 3500768--3500921 Score: 247
Period size: 70 Copynumber: 2.2 Consensus size: 70
3500758 AAACAAATTT
* *
3500768 CATTAGAGTCGAGAGATATCACACTATCACATATTTTAATGACATGTGTTTTTAGACTTCATATA
1 CATTTGAGTCGAGAGATATCACACTATCACATATTTTAATGACATGTGTTTTTAGACTTCACATA
3500833 TACTA
66 TACTA
* * *
3500838 CGTTTGAGTCGATAGATATCACACTATCATATATTTTAATGACATGTGTTTTTAGACTTCACATA
1 CATTTGAGTCGAGAGATATCACACTATCACATATTTTAATGACATGTGTTTTTAGACTTCACATA
3500903 TACTA
66 TACTA
3500908 CATTTG-GTCCGAGA
1 CATTTGAGT-CGAGA
3500922 ACCGACTAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
69 2 0.03
70 74 0.97
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (70 bp):
CATTTGAGTCGAGAGATATCACACTATCACATATTTTAATGACATGTGTTTTTAGACTTCACATA
TACTA
Found at i:3507334 original size:12 final size:12
Alignment explanation
Indices: 3507317--3507348 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3507307 AGTTAGAAAA
3507317 AAGAAATTATTG
1 AAGAAATTATTG
3507329 AAGAAATTATTG
1 AAGAAATTATTG
3507341 AAGAAATT
1 AAGAAATT
3507349 GGGTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (12 bp):
AAGAAATTATTG
Found at i:3510515 original size:37 final size:38
Alignment explanation
Indices: 3510449--3510526 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
3510439 ATAAGAGTTG
* **
3510449 AAAATAGATATTATGTAAAAATCTGAAAT-AAATAAAT
1 AAAATAGAAATTATGTAAAAAAATGAAATAAAATAAAT
*
3510486 AAAATAGAAATT-TGTAAAAAAATGAAAATAAAATGAAT
1 AAAATAGAAATTATGTAAAAAAATG-AAATAAAATAAAT
3510524 AAA
1 AAA
3510527 TAAATACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 10 0.29
37 15 0.43
38 10 0.29
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (38 bp):
AAAATAGAAATTATGTAAAAAAATGAAATAAAATAAAT
Found at i:3510562 original size:3 final size:3
Alignment explanation
Indices: 3510549--3510583 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3510539 GGGAAAAAAC
3510549 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3510584 TAAATTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3510625 original size:20 final size:19
Alignment explanation
Indices: 3510600--3510641 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3510590 GATTAGTTTG
*
3510600 GTAATAGGACAGTAATAATA
1 GTAATAAGACAGTAATAA-A
*
3510620 GTAATAATACAGTAATAAA
1 GTAATAAGACAGTAATAAA
3510639 GTA
1 GTA
3510642 GAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (19 bp):
GTAATAAGACAGTAATAAA
Found at i:3510648 original size:20 final size:20
Alignment explanation
Indices: 3510608--3510648 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3510598 TGGTAATAGG
*
3510608 ACAGTAATAATAGTAATAAT
1 ACAGTAATAATAGTAAAAAT
3510628 ACAGTAATAA-AGTAGAAAAT
1 ACAGTAATAATAGTA-AAAAT
3510648 A
1 A
3510649 ATAATGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (20 bp):
ACAGTAATAATAGTAAAAAT
Found at i:3510767 original size:20 final size:20
Alignment explanation
Indices: 3510744--3510781 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3510734 TAACACTATA
3510744 TTAATAAAAATAATAATAGG
1 TTAATAAAAATAATAATAGG
* *
3510764 TTAATAATAATAGTAATA
1 TTAATAAAAATAATAATA
3510782 AAAAGGTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
TTAATAAAAATAATAATAGG
Found at i:3510774 original size:26 final size:24
Alignment explanation
Indices: 3510745--3510811 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
3510735 AACACTATAT
*
3510745 TAATAAAAATAATAATAGGTTAATAA
1 TAATAAAAATAATAA-AGGTGAA-AA
**
3510771 TAATAGTAATAA-AAAGGTGAAAA
1 TAATAAAAATAATAAAGGTGAAAA
3510794 TAATAATAAAATAATAAA
1 TAAT-A-AAAATAATAAA
3510812 ACACAATTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 6 0.18
24 7 0.21
25 7 0.21
26 13 0.39
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (24 bp):
TAATAAAAATAATAAAGGTGAAAA
Found at i:3510876 original size:21 final size:21
Alignment explanation
Indices: 3510852--3510921 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
3510842 TAAAGAAAAC
*
3510852 AGTAATAGTA-TATAGAATAAT
1 AGTAATAGTAGTA-AAAATAAT
*
3510873 AGTAAAAGTAGTAAAAATAAT
1 AGTAATAGTAGTAAAAATAAT
* * * *
3510894 AATAATAATAATAATAATAAT
1 AGTAATAGTAGTAAAAATAAT
*
3510915 AATAATA
1 AGTAATA
3510922 ATAATAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 39 0.95
22 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
AGTAATAGTAGTAAAAATAAT
Found at i:3510894 original size:3 final size:3
Alignment explanation
Indices: 3510888--3510931 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3510878 AAGTAGTAAA
3510888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3510932 CACTCTCCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3512862 original size:13 final size:13
Alignment explanation
Indices: 3512846--3512879 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3512836 TAAATTATAA
*
3512846 ATTATTATTAACT
1 ATTATTATTAAAT
3512859 ATTATTATTAAAT
1 ATTATTATTAAAT
*
3512872 AATATTAT
1 ATTATTAT
3512880 ATATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATTATTAAAT
Found at i:3512931 original size:17 final size:17
Alignment explanation
Indices: 3512909--3512943 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3512899 AAATGAAGAA
*
3512909 AAAGAATAAAAAGAAAC
1 AAAGAAGAAAAAGAAAC
*
3512926 AAAGAAGAATAAGAAAC
1 AAAGAAGAAAAAGAAAC
3512943 A
1 A
3512944 GAGAGCATTC
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:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAC
Found at i:3514568 original size:39 final size:39
Alignment explanation
Indices: 3514461--3514595 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
3514451 GACCTCGAGT
* * * *
3514461 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAT-TATTACTTCGGCTAG-TC
** ** * *
3514502 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC
*
3514540 CGATGAGACACTGGGTGTCAATTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAATTATTACTTCG-GCTAGTC
*
3514579 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
3514596 CCATATTGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 18 0.24
39 36 0.49
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC
Found at i:3520644 original size:13 final size:13
Alignment explanation
Indices: 3520628--3520661 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3520618 TAAATTATAA
*
3520628 ATTATTATTAACT
1 ATTATTATTAAAT
3520641 ATTATTATTAAAT
1 ATTATTATTAAAT
*
3520654 AATATTAT
1 ATTATTAT
3520662 ATATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATTATTAAAT
Found at i:3520713 original size:17 final size:17
Alignment explanation
Indices: 3520691--3520725 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3520681 AAATGAAGAA
*
3520691 AAAGAATAAAAAGAAAC
1 AAAGAAGAAAAAGAAAC
*
3520708 AAAGAAGAATAAGAAAC
1 AAAGAAGAAAAAGAAAC
3520725 A
1 A
3520726 GAGAGCATTC
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:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAC
Found at i:3522351 original size:39 final size:39
Alignment explanation
Indices: 3522244--3522378 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
3522234 GACCTCGAGT
* * * *
3522244 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAT-TATTACTTCGGCTAG-TC
** ** * *
3522285 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC
*
3522323 CGATGAGACACTGGGTGTCAATTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAATTATTACTTCG-GCTAGTC
*
3522362 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
3522379 CCATATTGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 18 0.24
39 36 0.49
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC
Found at i:3523447 original size:17 final size:15
Alignment explanation
Indices: 3523429--3523480 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
3523419 CAGGCAAGTG
3523429 GGGTGATGGAGTTAGT
1 GGGTG-TGGAGTTAGT
*
3523445 GGG-GTGG-TTTAGT
1 GGGTGTGGAGTTAGT
3523458 GGGTGTTGGAGTTAGT
1 GGGTG-TGGAGTTAGT
3523474 GGG-GTGG
1 GGGTGTGG
3523481 TTTAATGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 8 0.26
14 7 0.23
15 5 0.16
16 11 0.35
ACGTcount: A:0.12, C:0.00, G:0.56, T:0.33
Consensus pattern (15 bp):
GGGTGTGGAGTTAGT
Found at i:3523458 original size:13 final size:13
Alignment explanation
Indices: 3523440--3523507 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 13
3523430 GGTGATGGAG
3523440 TTAGTGGGGTGGT
1 TTAGTGGGGTGGT
*
3523453 TTAGTGGGTGTTGGAG
1 TTAGTGGG-G-TGG-T
3523469 TTAGTGGGGTGGT
1 TTAGTGGGGTGGT
*
3523482 TTAATGGGGTGGT
1 TTAGTGGGGTGGT
* *
3523495 ATAATGGGGTGGT
1 TTAGTGGGGTGGT
3523508 ATTTGGGTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
13 32 0.67
14 4 0.08
15 4 0.08
16 8 0.17
ACGTcount: A:0.13, C:0.00, G:0.50, T:0.37
Consensus pattern (13 bp):
TTAGTGGGGTGGT
Found at i:3523468 original size:29 final size:29
Alignment explanation
Indices: 3523429--3523489 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
3523419 CAGGCAAGTG
*
3523429 GGGTGATGGAGTTAGTGGGGTGGTTTAGT
1 GGGTGATGGAGTTAGTGGGGTGGTTTAAT
*
3523458 GGGTGTTGGAGTTAGTGGGGTGGTTTAAT
1 GGGTGATGGAGTTAGTGGGGTGGTTTAAT
3523487 GGG
1 GGG
3523490 GTGGTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.00, G:0.52, T:0.34
Consensus pattern (29 bp):
GGGTGATGGAGTTAGTGGGGTGGTTTAAT
Found at i:3523847 original size:44 final size:44
Alignment explanation
Indices: 3523794--3524208 Score: 161
Period size: 44 Copynumber: 9.4 Consensus size: 44
3523784 TCCAGCCTAT
* * *
3523794 TTCC-CTACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCTG
1 TTCCACTACTGCTTAGGGAGATAAGGCTCACCGTTTTCAATCTG
* * * *** *
3523837 TTCCAGTACTGTTTAGGGAGATAA--CATATATAATTTTCAACCTG
1 TTCCACTACTGCTTAGGGAGATAAGGC-T-CACCGTTTTCAATCTG
* * * *
3523881 TTTCC-CTACTTCTTAGGGGGATAAGGCTCACCGTCTTCGATCTG
1 -TTCCACTACTGCTTAGGGAGATAAGGCTCACCGTTTTCAATCTG
* * * *** * *
3523925 CTCTACTACTGCTTAGGGAGATAA-GATCTATAATTTTC-AGCTTA
1 TTCCACTACTGCTTAGGGAGATAAGGCTC-ACCGTTTTCAATC-TG
* * *
3523969 TTCC-CTGCTACTTAGGGGGATAAGGCTCACCGTTTTCAATCTG
1 TTCCACTACTGCTTAGGGAGATAAGGCTCACCGTTTTCAATCTG
* * * * * * **
3524012 CTCCATTACTGCTTAGGGAGATAAGATCTGTA--ATTTTTAGCCTG
1 TTCCACTACTGCTTAGGGAGATAAG-GCT-CACCGTTTTCAATCTG
* * * * *
3524056 TTTCC-CTACTGCTTAGGGGGATAAGGCTTACCGTCTTCAACCTA
1 -TTCCACTACTGCTTAGGGAGATAAGGCTCACCGTTTTCAATCTG
* * * ** * * **
3524100 CTCCACTACTACTTAGGGAGAT-AGGGTGGTCTGTCATCTTTAGCCTG
1 TTCCACTACTGCTTAGGGAGATAAGGCT-CACCGT--T-TTCAATCTG
* ** * *
3524147 TTTCTTTACTGCTTAGGG-GATAAGGCTCACCGTCTTCGATCTG
1 TTCCACTACTGCTTAGGGAGATAAGGCTCACCGTTTTCAATCTG
*
3524190 ATCCACTACTGCTTAGGGA
1 TTCCACTACTGCTTAGGGA
3524209 TAAGTTGGTG
Statistics
Matches: 256, Mismatches: 92, Indels: 47
0.65 0.23 0.12
Matches are distributed among these distances:
42 3 0.01
43 66 0.26
44 146 0.57
45 10 0.04
46 8 0.03
47 23 0.09
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (44 bp):
TTCCACTACTGCTTAGGGAGATAAGGCTCACCGTTTTCAATCTG
Found at i:3523853 original size:88 final size:88
Alignment explanation
Indices: 3523744--3524208 Score: 569
Period size: 88 Copynumber: 5.3 Consensus size: 88
3523734 TTTTGTTTCA
* * * * *
3523744 ATCTGCTTCACTACTGCTTAGGGAGATAAGATTTGTAACTTCCAGCCTATTTCCCTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
3523809 GGGGATAAGGCTCACCGTCTTCG
66 GGGGATAAGGCTCACCGTCTTCG
* * * * * * * *
3523832 ATCTGTTCCAGTACTGTTTAGGGAGATAACATATATAATTTTCAACCTGTTTCCCTACTTCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
3523897 GGGGATAAGGCTCACCGTCTTCG
66 GGGGATAAGGCTCACCGTCTTCG
* * * *
3523920 ATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAATTTTCAG-CT-TATTCCCTGCTACTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGT-TTCCCTACTGCTTA
* *
3523983 GGGGGATAAGGCTCACCGTTTTCA
65 GGGGGATAAGGCTCACCGTCTTCG
* *
3524007 ATCTGCTCCATTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTTCCCTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
* *
3524072 GGGGATAAGGCTTACCGTCTTCA
66 GGGGATAAGGCTCACCGTCTTCG
* * * * * * **
3524095 ACCTACTCCACTACTACTTAGGGAGATAGGGTGGTCTGTCATCTTT-AGCCTGTTTCTTTACTGC
1 ATCTGCTCCACTACTGCTTAGGGAGATA---AGATCTGTAAT-TTTCAGCCTGTTTCCCTACTGC
3524159 TTA-GGGGATAAGGCTCACCGTCTTCG
62 TTAGGGGGATAAGGCTCACCGTCTTCG
*
3524185 ATCTGATCCACTACTGCTTAGGGA
1 ATCTGCTCCACTACTGCTTAGGGA
3524209 TAAGTTGGTG
Statistics
Matches: 324, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
86 1 0.00
87 77 0.24
88 174 0.54
89 1 0.00
90 41 0.13
91 27 0.08
92 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (88 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
GGGGATAAGGCTCACCGTCTTCG
Found at i:3524048 original size:175 final size:176
Alignment explanation
Indices: 3523740--3524208 Score: 541
Period size: 175 Copynumber: 2.7 Consensus size: 176
3523730 GAATTTTTGT
* * *
3523740 TTCAATCTGCT-TCACTACTGCTTAGGGAGATAAGATTTGTAACTTCCAGCCTATTTCCCTACTG
1 TTCAATCTGCTCT-ACTACTGCTTAGGGAGATAAGATCTATAACTTCCAGCCTATTTCCCTACTA
* * *
3523804 CTTAGGGGGATAAGGCTCACCGTCTTCGATCTGTTCCAGTACTGTTTAGGGAGATAACATATATA
65 CTTAGGGGGATAAGGCTCACCGTCTTCAATCTGCTCCAGTACTGCTTAGGGAGATAACATATATA
*
3523869 ATTTTCAACCTGTTTCCCTACTTCTTAGGGGGATAAGGCTCACCGTC
130 ATTTTCAACCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCGTC
* * * * *
3523916 TTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAATTTTCAGCTTA-TTCCCTGCTAC
1 TTCAATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAACTTCCAGCCTATTTCCCTACTAC
* * * * *
3523980 TTAGGGGGATAAGGCTCACCGTTTTCAATCTGCTCCATTACTGCTTAGGGAGATAAGATCTGTAA
66 TTAGGGGGATAAGGCTCACCGTCTTCAATCTGCTCCAGTACTGCTTAGGGAGATAACATATATAA
* * *
3524045 TTTTTAGCCTGTTTCCCTACTGCTTAGGGGGATAAGGCTTACCGTC
131 TTTTCAACCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCGTC
* * * * * * * * * * **
3524091 TTCAACCTACTCCACTACTACTTAGGGAGATAGGGTGGTCTGTCATCTT-TAGCCTGTTTCTTTA
1 TTCAATCTGCTCTACTACTGCTTAGGGAGATA---AGATCTAT-AACTTCCAGCCTATTTCCCTA
* * * *
3524155 CTGCTTA-GGGGATAAGGCTCACCGTCTTCGATCTGATCCACTACTGCTTAGGGA
62 CTACTTAGGGGGATAAGGCTCACCGTCTTCAATCTGCTCCAGTACTGCTTAGGGA
3524209 TAAGTTGGTG
Statistics
Matches: 246, Mismatches: 41, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
175 135 0.55
176 45 0.18
177 1 0.00
178 52 0.21
179 13 0.05
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (176 bp):
TTCAATCTGCTCTACTACTGCTTAGGGAGATAAGATCTATAACTTCCAGCCTATTTCCCTACTAC
TTAGGGGGATAAGGCTCACCGTCTTCAATCTGCTCCAGTACTGCTTAGGGAGATAACATATATAA
TTTTCAACCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCGTC
Found at i:3524272 original size:263 final size:260
Alignment explanation
Indices: 3523740--3524339 Score: 582
Period size: 263 Copynumber: 2.3 Consensus size: 260
3523730 GAATTTTTGT
* * * *
3523740 TTCAATCTGCTTCACTACTGCTTAGGGAGATAAGATTTGTAACTTCCAGCCTATTTCCCTACTGC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTATTTCCCTACTGC
* * ** * **
3523805 TTAGGGGGATAAGGCTCACCGTCTTCGATCTGTTCCAGTACTGTTTAGGGAGATAACATATATAA
66 TTAGGGGGATAAGGCTCACCGTCTTCAACCTACTCCACTACTACTTAGGGAGATAACATATATAA
* * *
3523870 TTTTCAACCTGTTTCCCTACTTCTTAGGGGGATAAGGCTCACCGTCTTCGATCTGCTCTACTACT
131 TTTTCAACCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCTGATCCACTACT
* * *
3523935 GCTTAGGGAGATAAGATCTATAATTTTCAGCTTATTCCCTGCTACTTAGGGGGATAAGGCTCACC
196 GCTTAGGGAGATAAGATCTATAAATTT-AGCTTATTCCCTGCTAC-TA-GGAGATAAGACTCACC
*
3524000 GTT
258 GTC
* * *
3524003 TTCAATCTGCTCCATTACTGCTTAGGGAGATAAGATCTGTAATTTTTAGCCTGTTTCCCTACTGC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTATTTCCCTACTGC
* *** * *
3524068 TTAGGGGGATAAGGCTTACCGTCTTCAACCTACTCCACTACTACTTAGGGAGATAGGGTGGTCTG
66 TTAGGGGGATAAGGCTCACCGTCTTCAACCTACTCCACTACTACTTAGGGAGATA---ACATATA
* * **
3524133 TCATCTTT-AGCCTGTTTCTTTACTGCTTA-GGGGATAAGGCTCACCGTCTTCGATCTGATCCAC
128 TAAT-TTTCAACCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCTGATCCAC
*
3524196 TACTGCTTA-GG-GATAAGTTGGTGGCT-TAAATTT-GCTCTATTACCACTGC-A-TA-GAGATA
192 TACTGCTTAGGGAGATAA---GAT--CTATAAATTTAGCT-TATT-CC-CTGCTACTAGGAGATA
* * *
3524254 AGATTCGCTGTC
249 AGACTCACCGTC
* * *** * *
3524266 TTCAATCTACTCCACTATTGCTTACATAGATAAGACCTGTAATTTTCA----A--ACCCTACTGC
1 TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTATTTCCCTACTGC
3524325 TTAGGGGGATAAGGC
66 TTAGGGGGATAAGGC
3524340 AAGTGAATTC
Statistics
Matches: 280, Mismatches: 45, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
257 24 0.09
263 162 0.58
264 2 0.01
265 46 0.16
266 28 0.10
267 12 0.04
268 6 0.02
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (260 bp):
TTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTATTTCCCTACTGC
TTAGGGGGATAAGGCTCACCGTCTTCAACCTACTCCACTACTACTTAGGGAGATAACATATATAA
TTTTCAACCTGTTTCCCTACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCTGATCCACTACT
GCTTAGGGAGATAAGATCTATAAATTTAGCTTATTCCCTGCTACTAGGAGATAAGACTCACCGTC
Found at i:3526162 original size:20 final size:20
Alignment explanation
Indices: 3526133--3526187 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
3526123 TTCCACAATT
3526133 TTTTTGTTGTTTTTGTTTTTA
1 TTTTT-TTGTTTTTGTTTTTA
*
3526154 TTTTTTTGTTCTTT-TTTTTC
1 TTTTTTTGTT-TTTGTTTTTA
* *
3526174 TTTCTTTCTTTTTG
1 TTTTTTTGTTTTTG
3526188 GCTGTCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.10
20 18 0.62
21 8 0.28
ACGTcount: A:0.02, C:0.07, G:0.09, T:0.82
Consensus pattern (20 bp):
TTTTTTTGTTTTTGTTTTTA
Found at i:3529074 original size:26 final size:25
Alignment explanation
Indices: 3529043--3529113 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
3529033 AGATATTATT
3529043 TAAAAATCTGAAATAAATAAATAAAA
1 TAAAAAT-TGAAATAAATAAATAAAA
3529069 TAAAAATTTGTAAA-AAA-AAATGAAAA
1 TAAAAA-TTG-AAATAAATAAAT-AAAA
3529095 T-AAAA-TG-AATAAATAAATA
1 TAAAAATTGAAATAAATAAATA
3529114 CAAAAAGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
21 2 0.05
22 4 0.10
23 6 0.15
25 8 0.20
26 16 0.40
27 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (25 bp):
TAAAAATTGAAATAAATAAATAAAA
Found at i:3529350 original size:26 final size:26
Alignment explanation
Indices: 3529307--3529378 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
3529297 TAACACTATA
* *
3529307 TTAATAAAAATAAAAATAATAATAGG
1 TTAATAATAATAATAATAATAATAGG
*
3529333 TTAATAATAATAGTAATAA-AA-AGG
1 TTAATAATAATAATAATAATAATAGG
*
3529357 TGAA-AATAATAATAA-AATAATA
1 TTAATAATAATAATAATAATAATA
3529379 AAAATATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 2 0.05
23 12 0.31
24 7 0.18
25 2 0.05
26 16 0.41
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (26 bp):
TTAATAATAATAATAATAATAATAGG
Found at i:3529382 original size:20 final size:20
Alignment explanation
Indices: 3529315--3529384 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
3529305 TATTAATAAA
***
3529315 AATAAAAATAATAATAGGTT
1 AATAAAAATAATAATAAAAT
* *
3529335 AATAATAATAGTAATAAAA-
1 AATAAAAATAATAATAAAAT
* *
3529354 AGGTGAAAATAATAATAAAAT
1 A-ATAAAAATAATAATAAAAT
3529375 AATAAAAATA
1 AATAAAAATA
3529385 TTATTTCGTT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
AATAAAAATAATAATAAAAT
Found at i:3530702 original size:40 final size:40
Alignment explanation
Indices: 3530658--3530738 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
3530648 AGAAAAAGAA
3530658 AGAAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
1 AGAAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
*
3530698 AGAAAAAAAGGGGGAGCGGTTTCTACGTTAAAAGCTAAAC
1 AGAAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
3530738 A
1 A
3530739 TCTTTTCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.17
Consensus pattern (40 bp):
AGAAAAAAAGGAGGAGCGGTTTCTACGTTAAAAGCTAAAC
Found at i:3541515 original size:28 final size:28
Alignment explanation
Indices: 3541475--3541539 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
3541465 TTTAATTAAG
*
3541475 AATTTTTTATACCTGATATATTTTTTAC
1 AATTTTTTATACCTGATATAATTTTTAC
*
3541503 AATTTTTTATACCTGTTATAATTTTTAC
1 AATTTTTTATACCTGATATAATTTTTAC
3541531 AATTTTTTA
1 AATTTTTTA
3541540 AAATTCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.58
Consensus pattern (28 bp):
AATTTTTTATACCTGATATAATTTTTAC
Found at i:3555550 original size:7 final size:7
Alignment explanation
Indices: 3555533--3555561 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3555523 TGAATGGGAA
3555533 AAAAAAG
1 AAAAAAG
3555540 -AAAAAG
1 AAAAAAG
3555546 AAAAAAG
1 AAAAAAG
3555553 AAAAAAG
1 AAAAAAG
3555560 AA
1 AA
3555562 TTGGTGGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:3555551 original size:13 final size:13
Alignment explanation
Indices: 3555533--3555557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3555523 TGAATGGGAA
3555533 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
3555546 AAAAAAGAAAAA
1 AAAAAAGAAAAA
3555558 AGAATTGGTG
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:3559255 original size:45 final size:45
Alignment explanation
Indices: 3559178--3559306 Score: 141
Period size: 46 Copynumber: 2.8 Consensus size: 45
3559168 TTGTTCAACA
* * * * *
3559178 GATGTCATAGCGTCTCTCATCTACGGTCTTATTTATTTTTGACAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGACAT
* *
3559223 GATGCCATAGTGTCTTTCAACTATGGTTTTATTTATTTTTTGTCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTTA-TTTTTGACAT
* * * * *
3559269 GTTGCCATGGTATCTTTCAACCATGGTCTTGTTTATTT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTT
3559307 CATATCACGT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
45 32 0.46
46 38 0.54
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (45 bp):
GATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTTGACAT
Found at i:3559285 original size:46 final size:46
Alignment explanation
Indices: 3559202--3559483 Score: 210
Period size: 46 Copynumber: 6.2 Consensus size: 46
3559192 TCTCATCTAC
* * * * *
3559202 GGTCTTATTTATTT-TTGA-CATGATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTTATTTCAT-ATCATGTTGCCATGGTATCTTTCAACCAT
* ** *
3559247 GGTTTTATTTATTTTTTGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTTATTTCATATCATGTTGCCATGGTATCTTTCAACCAT
* * * *
3559293 GGTCTTGTTTATTTCATATCACGTTGTCATGCTATCTTTCAACCAT
1 GGTCTTATTTATTTCATATCATGTTGCCATGGTATCTTTCAACCAT
*** * * * * *
3559339 GGTCTTACACATTTCATATTAGGTTGTCATGGTATCTTTTAACTAT
1 GGTCTTATTTATTTCATATCATGTTGCCATGGTATCTTTCAACCAT
* *** * * * * *
3559385 GGTTTTACAAATTTTATATTAGGTTGCTATGATATCTTTCAACCAT
1 GGTCTTATTTATTTCATATCATGTTGCCATGGTATCTTTCAACCAT
*** * *
3559431 GGTCTTACGCATTTCATATCA-GATTGCCATAGTATCTTTCAATCAT
1 GGTCTTATTTATTTCATATCATG-TTGCCATGGTATCTTTCAACCAT
3559477 GGTCTTA
1 GGTCTTA
3559484 CACATTTTAT
Statistics
Matches: 194, Mismatches: 40, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
45 14 0.07
46 180 0.93
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (46 bp):
GGTCTTATTTATTTCATATCATGTTGCCATGGTATCTTTCAACCAT
Found at i:3559484 original size:46 final size:45
Alignment explanation
Indices: 3559269--3559495 Score: 238
Period size: 46 Copynumber: 4.9 Consensus size: 45
3559259 TTTTTGTCAT
**** *
3559269 GTTGCCATGGTATCTTTCAACCATGGTCTTGTTTATTTCATATCAC
1 GTTGCCAT-GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* *
3559315 GTTGTCATGCTATCTTTCAACCATGGTCTTACACATTTCATATTAG
1 GTTGCCATG-TATCTTTCAACCATGGTCTTACACATTTCATATCAG
* * * * * * *
3559361 GTTGTCATGGTATCTTTTAACTATGGTTTTACAAATTTTATATTAG
1 GTTGCCAT-GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
* *
3559407 GTTGCTATGATATCTTTCAACCATGGTCTTACGCATTTCATATCAG
1 GTTGCCATG-TATCTTTCAACCATGGTCTTACACATTTCATATCAG
* * *
3559453 ATTGCCATAGTATCTTTCAATCATGGTCTTACACATTTTATAT
1 GTTGCCAT-GTATCTTTCAACCATGGTCTTACACATTTCATAT
3559496 TAGAGAGCAC
Statistics
Matches: 151, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
45 2 0.01
46 147 0.97
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.44
Consensus pattern (45 bp):
GTTGCCATGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
Found at i:3559496 original size:92 final size:91
Alignment explanation
Indices: 3559270--3559498 Score: 271
Period size: 92 Copynumber: 2.5 Consensus size: 91
3559260 TTTTGTCATG
**** * * * *
3559270 TTGCCATGGTATCTTTCAACCATGGTCTTGTTTATTTCATATCACGTTGTCATGCTATCTTTCAA
1 TTGCCATGGTATCTTTCAA-CATGGTCTTACAAATTTTATATTAGGTTGTCATGATATCTTTCAA
* *
3559335 CCATGGTCTTACACATTTCATATTAGG
65 CCATGGTCTTACACATTTCATATCAGA
* * *
3559362 TTGTCATGGTATCTTTTAACTATGGTTTTACAAATTTTATATTAGGTTG-CTATGATATCTTTCA
1 TTGCCATGGTATCTTTCAAC-ATGGTCTTACAAATTTTATATTAGGTTGTC-ATGATATCTTTCA
*
3559426 ACCATGGTCTTACGCATTTCATATCAGA
64 ACCATGGTCTTACACATTTCATATCAGA
* *
3559454 TTGCCATAGTATCTTTCAATCATGGTCTTACACATTTTATATTAG
1 TTGCCATGGTATCTTTCAA-CATGGTCTTACAAATTTTATATTAG
3559499 AGAGCACACT
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
91 2 0.02
92 112 0.97
93 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (91 bp):
TTGCCATGGTATCTTTCAACATGGTCTTACAAATTTTATATTAGGTTGTCATGATATCTTTCAAC
CATGGTCTTACACATTTCATATCAGA
Found at i:3561425 original size:20 final size:20
Alignment explanation
Indices: 3561362--3561434 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 20
3561352 TAATTAACAA
*
3561362 TAAAATAATA-ATGAAATAA-
1 TAAAATAATATAT-AACTAAT
* *
3561381 TAAAATAATAAAATAACTCAT
1 TAAAATAAT-ATATAACTAAT
*
3561402 TAAAATAATATATATCTAAT
1 TAAAATAATATATAACTAAT
3561422 T-AAATAAT-TATAA
1 TAAAATAATATATAA
3561435 AATATCATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.09
19 16 0.36
20 14 0.31
21 11 0.24
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (20 bp):
TAAAATAATATATAACTAAT
Found at i:3562083 original size:35 final size:35
Alignment explanation
Indices: 3562037--3562106 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3562027 CCACAACAAG
3562037 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
1 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
3562072 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
1 GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
3562107 AACTCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (35 bp):
GTTTGATATCAAAAGACCTAATATCCCACTTTCCT
Found at i:3562802 original size:31 final size:31
Alignment explanation
Indices: 3562767--3562830 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
3562757 GAAAATCCTA
*
3562767 AAGCTCAAG-CTTCAATATGAGAATAATTGTC
1 AAGCTCAAGTC-TCAATATGAGAACAATTGTC
*
3562798 AAGCTTAAGTCTCAATATGAGAACAATTGTC
1 AAGCTCAAGTCTCAATATGAGAACAATTGTC
3562829 AA
1 AA
3562831 TTTTTGAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (31 bp):
AAGCTCAAGTCTCAATATGAGAACAATTGTC
Found at i:3565424 original size:24 final size:24
Alignment explanation
Indices: 3565380--3565439 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
3565370 GATGTGAATT
3565380 TAATGAAAATAATTTACTAAATAAA-
1 TAAT-AAAATAATTTACTAAA-AAAG
*
3565405 TAATAAAATATATTT-TTAAAAAAG
1 TAATAAAATA-ATTTACTAAAAAAG
*
3565429 TACTAAAATAA
1 TAATAAAATAA
3565440 AATAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 4 0.13
24 19 0.61
25 8 0.26
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (24 bp):
TAATAAAATAATTTACTAAAAAAG
Found at i:3568425 original size:30 final size:30
Alignment explanation
Indices: 3568391--3568497 Score: 92
Period size: 30 Copynumber: 3.6 Consensus size: 30
3568381 CAGAGATAAT
3568391 GGAGCTGGAGCTGGTGGAAATGATGCTTTC
1 GGAGCTGGAGCTGGTGGAAATGATGCTTTC
* **** *
3568421 GGAGCTGGAGCTGGAGCCGCTGCA-GCTAGT-
1 GGAGCTGGAGCTGGTGGAAATG-ATGCT-TTC
*** *
3568451 GGTTTTGGAGCTGGTGGAAATAATGCTTTC
1 GGAGCTGGAGCTGGTGGAAATGATGCTTTC
3568481 GGAGCTGGAGCTGGTGG
1 GGAGCTGGAGCTGGTGG
3568498 TTTTGGAGAT
Statistics
Matches: 54, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
29 2 0.04
30 50 0.93
31 2 0.04
ACGTcount: A:0.18, C:0.15, G:0.42, T:0.25
Consensus pattern (30 bp):
GGAGCTGGAGCTGGTGGAAATGATGCTTTC
Found at i:3568515 original size:9 final size:9
Alignment explanation
Indices: 3568501--3568526 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3568491 CTGGTGGTTT
3568501 TGGAGATGG
1 TGGAGATGG
3568510 TGGAGATGG
1 TGGAGATGG
3568519 TGGAGATG
1 TGGAGATG
3568527 ATGGTTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (9 bp):
TGGAGATGG
Found at i:3573181 original size:27 final size:25
Alignment explanation
Indices: 3573151--3573212 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
3573141 AAATATTTTA
* *
3573151 AAATAATAATAAATTTATATTTATATT
1 AAATAAAAAT-AA-TTATATTGATATT
*
3573178 AAATAAAAATCATTATATTGATATT
1 AAATAAAAATAATTATATTGATATT
3573203 AAATATAAAA
1 AAATA-AAAA
3573213 GAGTCCCCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.55
26 5 0.16
27 9 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATAAAAATAATTATATTGATATT
Found at i:3573391 original size:18 final size:18
Alignment explanation
Indices: 3573368--3573405 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3573358 TTAAAATTAT
3573368 TTTTTTACATTT-TTATAA
1 TTTTTTA-ATTTCTTATAA
*
3573386 TTTTTTATTTTCTTATAA
1 TTTTTTAATTTCTTATAA
3573404 TT
1 TT
3573406 AAGATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTAATTTCTTATAA
Found at i:3593483 original size:40 final size:40
Alignment explanation
Indices: 3593427--3593512 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
3593417 ATAGTCAGAG
*
3593427 AAAGATTCTCATAGCAGATTATTCTAAAACAGGATAAAGA
1 AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
3593467 AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
1 AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
3593507 AAAGAT
1 AAAGAT
3593513 ATTATGTAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (40 bp):
AAAGATTCTCACAGCAGATTATTCTAAAACAGGATAAAGA
Found at i:3601088 original size:17 final size:18
Alignment explanation
Indices: 3601058--3601093 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3601048 ATATAAGATA
*
3601058 TTTATATTTATATTTATT
1 TTTATATATATATTTATT
3601076 TTTATATAT-TATTTATT
1 TTTATATATATATTTATT
3601093 T
1 T
3601094 GTATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATATATATATTTATT
Found at i:3605133 original size:12 final size:12
Alignment explanation
Indices: 3605116--3605199 Score: 61
Period size: 12 Copynumber: 7.2 Consensus size: 12
3605106 TATATTTGAT
3605116 TTTAATATTTAA
1 TTTAATATTTAA
3605128 TTTAATATTTAAA
1 TTTAATATTT-AA
**
3605141 TTTTTTATCTTAA
1 TTTAATAT-TTAA
*
3605154 TTTAATACTT-A
1 TTTAATATTTAA
* *
3605165 ---AA-CTTGAA
1 TTTAATATTTAA
3605173 TTTAATATTTAA
1 TTTAATATTTAA
3605185 TTTAATATTTGAA
1 TTTAATATTT-AA
3605198 TT
1 TT
3605200 AAACAATATC
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.02
8 3 0.06
11 3 0.06
12 26 0.48
13 19 0.35
14 2 0.04
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (12 bp):
TTTAATATTTAA
Found at i:3605138 original size:19 final size:19
Alignment explanation
Indices: 3605096--3605194 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 19
3605086 TAAAGAGATC
* *
3605096 ATTTAATATCTATATTTGAT
1 ATTTAATATTTA-ATTTAAT
3605116 -TTTAATATTTAATTTAAT
1 ATTTAATATTTAATTTAAT
* *
3605134 ATTTAAATTTTTTATCTT-A-
1 ATTT-AATATTTAAT-TTAAT
* * *
3605153 ATTTAATACTTAAACTTGA-
1 ATTTAATA-TTTAATTTAAT
3605172 ATTTAATATTTAATTTAAT
1 ATTTAATATTTAATTTAAT
3605191 ATTT
1 ATTT
3605195 GAATTAAACA
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
18 18 0.29
19 33 0.53
20 9 0.15
21 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTAATATTTAATTTAAT
Found at i:3605143 original size:26 final size:26
Alignment explanation
Indices: 3605114--3605199 Score: 84
Period size: 26 Copynumber: 3.1 Consensus size: 26
3605104 TCTATATTTG
3605114 ATTTTAATATTTAATTTAATATTTAA
1 ATTTTAATATTTAATTTAATATTTAA
* *
3605140 ATTTT-TTATCTTAATTTAATACTTAA
1 ATTTTAATAT-TTAATTTAATATTTAA
*
3605166 ACTTGAATTTAATATTTAATTTAATATTTGA
1 A--T---TTTAATATTTAATTTAATATTTAA
3605197 ATT
1 ATT
3605200 AAACAATATC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
25 3 0.06
26 22 0.46
28 1 0.02
29 1 0.02
31 18 0.38
32 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (26 bp):
ATTTTAATATTTAATTTAATATTTAA
Found at i:3605201 original size:12 final size:13
Alignment explanation
Indices: 3605107--3605199 Score: 66
Period size: 13 Copynumber: 6.8 Consensus size: 13
3605097 TTTAATATCT
*
3605107 ATATTTGATTTTA
1 ATATTTGAATTTA
3605120 ATATTT-AATTTA
1 ATATTTGAATTTA
* *
3605132 ATATTTAAATTTT
1 ATATTTGAATTTA
*
3605145 TTATCTT-AATTTA
1 ATAT-TTGAATTTA
3605158 ATACTTAAACTTGAATTTA
1 ATA--T----TTGAATTTA
3605177 ATATTT-AATTTA
1 ATATTTGAATTTA
3605189 ATATTTGAATT
1 ATATTTGAATT
3605200 AAACAATATC
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
12 23 0.35
13 27 0.41
14 2 0.03
15 1 0.02
17 1 0.02
18 3 0.05
19 9 0.14
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (13 bp):
ATATTTGAATTTA
Found at i:3607021 original size:214 final size:215
Alignment explanation
Indices: 3606646--3607080 Score: 712
Period size: 213 Copynumber: 2.0 Consensus size: 215
3606636 AATTGTTAGG
*
3606646 ATTTTGTTGAATTCTAAATCTCATTGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
*
3606711 GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGGATTCTACAATATTTATA
* * *
3606776 GCTGGACAAACTTAAAAAGAGAAGAGG-AAAAAAAAAGAGCAATCAGTCTATGGTTGTTGTTACC
131 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAAAGAGCAATCAATCTATGGTTGTTGTTACC
3606840 GCATGACGATGTATCTAACC
196 GCATGACGATGTATCTAACC
3606860 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
* * *
3606925 GGTATA-ATCTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGGATTCTACAATATTTATA
66 GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGGATTCTACAATATTTATA
* *
3606989 TCGGGACAAACTTAAAAAGAAAAGAGGGAAAAAAAAAAAAAAGAGCAATCAATTTATGGTTGTTG
131 GCGGGACAAACTTAAAAAGAAAAGA-GG----AAAAAAAAAAGAGCAATCAATCTATGGTTGTTG
*
3607054 TTACTGCATGACGATGTATCTAACC
191 TTACCGCATGACGATGTATCTAACC
3607079 AT
1 AT
3607081 ATAACGAACA
Statistics
Matches: 204, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
213 76 0.37
214 72 0.35
219 56 0.27
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (215 bp):
ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
GGTATATAGCTTCTTCCATAGCACTTGAAGATGTTCGATTCTTCTTGGATTCTACAATATTTATA
GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAAAGAGCAATCAATCTATGGTTGTTGTTACC
GCATGACGATGTATCTAACC
Found at i:3622089 original size:22 final size:21
Alignment explanation
Indices: 3622064--3622106 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
3622054 TAAATAAAAT
3622064 TTTAAAATAATTTAATAATTAA
1 TTTAAAATAATTTAA-AATTAA
* **
3622086 TTTATAATTTTTTAAAATTAA
1 TTTAAAATAATTTAAAATTAA
3622107 GTTATTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAAATAATTTAAAATTAA
Found at i:3622131 original size:16 final size:14
Alignment explanation
Indices: 3622097--3622150 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
3622087 TTATAATTTT
*
3622097 TTAAAATTAAGTTA
1 TTAAAATTAAATTA
3622111 TTAAAATGTAAATTAA
1 TTAAAAT-TAAATT-A
3622127 TTAAAA--AAATTA
1 TTAAAATTAAATTA
*
3622139 AT-AAATTAAATT
1 TTAAAATTAAATT
3622151 GCAGATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 3 0.09
12 2 0.06
13 10 0.29
14 7 0.21
15 5 0.15
16 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (14 bp):
TTAAAATTAAATTA
Found at i:3627218 original size:8 final size:9
Alignment explanation
Indices: 3627195--3627221 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3627185 TTTTGCTACT
3627195 TATTTTTAA
1 TATTTTTAA
3627204 TATTTTTAA
1 TATTTTTAA
3627213 TATTTTTAA
1 TATTTTTAA
3627222 AGTGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:3628327 original size:42 final size:42
Alignment explanation
Indices: 3628234--3628327 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
3628224 GAGGCATTCA
* *
3628234 ACATGAAGAGCCTGTTAAGATAAAATGCTCAAATCTTAACAG
1 ACATGAAGAGCCTGTTAAGATAAAATACTCAAATCTAAACAG
* *
3628276 ACATAAAGAGTCTGTTAAGATAAAATACTCAAATGC-AAACAG
1 ACATGAAGAGCCTGTTAAGATAAAATACTCAAAT-CTAAACAG
* *
3628318 GCCTGAAGAG
1 ACATGAAGAG
3628328 GTAATTTTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (42 bp):
ACATGAAGAGCCTGTTAAGATAAAATACTCAAATCTAAACAG
Found at i:3630337 original size:1 final size:1
Alignment explanation
Indices: 3630297--3630321 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3630287 TAAAGACCCC
3630297 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3630322 GTGCGTGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3630993 original size:2 final size:2
Alignment explanation
Indices: 3630986--3631014 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3630976 TCTTATTAAT
3630986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3631015 GTTAGATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3633414 original size:23 final size:23
Alignment explanation
Indices: 3633382--3633482 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 23
3633372 TTAACAAGCC
*
3633382 AATAACTTAAATAAAATATTTTA
1 AATAATTTAAATAAAATATTTTA
* *
3633405 AATAATTTAATTATGAAATTTTTTA
1 AATAATTTAA--ATAAAATATTTTA
*
3633430 AATAATTT-AAT-AAATTTTTTA
1 AATAATTTAAATAAAATATTTTA
* *
3633451 AATGA-TTAAA-AATAA-ATTTATT
1 AATAATTTAAATAA-AATATTT-TA
3633473 AATAATTTAA
1 AATAATTTAA
3633483 TGATATTAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
20 2 0.03
21 20 0.31
22 9 0.14
23 13 0.20
24 1 0.02
25 19 0.30
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (23 bp):
AATAATTTAAATAAAATATTTTA
Found at i:3633429 original size:25 final size:23
Alignment explanation
Indices: 3633382--3633483 Score: 95
Period size: 23 Copynumber: 4.5 Consensus size: 23
3633372 TTAACAAGCC
* *
3633382 AATAACTTAA-ATAAAATATTTTA
1 AATAATTTAATAT-AAATTTTTTA
3633405 AATAATTTAATTATGAAATTTTTTA
1 AATAATTTAA-TAT-AAATTTTTTA
3633430 AATAATTT-A-ATAAATTTTTTA
1 AATAATTTAATATAAATTTTTTA
* * * *
3633451 AATGATTAAAAATAAATTTATT-
1 AATAATTTAATATAAATTTTTTA
3633473 AATAATTTAAT
1 AATAATTTAAT
3633484 GATATTAGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
21 16 0.24
22 11 0.17
23 19 0.29
24 1 0.02
25 19 0.29
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (23 bp):
AATAATTTAATATAAATTTTTTA
Found at i:3635265 original size:17 final size:17
Alignment explanation
Indices: 3635209--3635265 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
3635199 GAAGCAGAAA
3635209 TGTTAGTTTATAATTTT
1 TGTTAGTTTATAATTTT
* * *
3635226 TGTGGAGTAATT-TGATTTC
1 TGT-TAGT--TTATAATTTT
3635245 TGTTAGTTTATAATTTT
1 TGTTAGTTTATAATTTT
3635262 TGTT
1 TGTT
3635266 TTCTCCATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.07
17 12 0.40
18 6 0.20
19 8 0.27
20 2 0.07
ACGTcount: A:0.21, C:0.02, G:0.18, T:0.60
Consensus pattern (17 bp):
TGTTAGTTTATAATTTT
Found at i:3640069 original size:34 final size:34
Alignment explanation
Indices: 3640026--3640093 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3640016 TTCCTAACTT
3640026 GAGAAAGCCCAATGATGATGCATCAGTCAACATG
1 GAGAAAGCCCAATGATGATGCATCAGTCAACATG
3640060 GAGAAAGCCCAATGATGATGCATCAGTCAACATG
1 GAGAAAGCCCAATGATGATGCATCAGTCAACATG
3640094 AAACGCGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.18
Consensus pattern (34 bp):
GAGAAAGCCCAATGATGATGCATCAGTCAACATG
Found at i:3644559 original size:10 final size:10
Alignment explanation
Indices: 3644544--3644682 Score: 62
Period size: 10 Copynumber: 14.2 Consensus size: 10
3644534 TGACATGTGG
3644544 TAAAAAATTA
1 TAAAAAATTA
3644554 TAAAAAA-TA
1 TAAAAAATTA
* *
3644563 T-TAAATTTAAA
1 TAAAAAATT--A
3644574 TAAAAATATT-
1 TAAAAA-ATTA
* *
3644584 T-GAAATTTA
1 TAAAAAATTA
*
3644593 TTAAAAATTA
1 TAAAAAATTA
*
3644603 GAAAAAATT-
1 TAAAAAATTA
*
3644612 TATAAAATATA
1 TAAAAAAT-TA
*
3644623 TAGAAAATTA
1 TAAAAAATTA
3644633 TAAAAAATGTA
1 TAAAAAAT-TA
*
3644644 -AATAAA-TA
1 TAAAAAATTA
*
3644652 T--AAAATTCT
1 TAAAAAATT-A
3644661 TAAAAAATTA
1 TAAAAAATTA
*
3644671 TAAAAATTTA
1 TAAAAAATTA
3644681 TA
1 TA
3644683 GTACCAAAAG
Statistics
Matches: 95, Mismatches: 19, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
7 3 0.03
8 8 0.08
9 15 0.16
10 47 0.49
11 17 0.18
12 3 0.03
13 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:3644610 original size:21 final size:22
Alignment explanation
Indices: 3644586--3644629 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
3644576 AAAATATTTG
3644586 AAATTTATTAAAA-AT-TAGAAA
1 AAATTTA-TAAAATATATAGAAA
3644607 AAATTTATAAAATATATAGAAA
1 AAATTTATAAAATATATAGAAA
3644629 A
1 A
3644630 TTATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAATTTATAAAATATATAGAAA
Found at i:3644656 original size:27 final size:28
Alignment explanation
Indices: 3644616--3644668 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
3644606 AAAATTTATA
*
3644616 AAATATATAGAAAATT-ATAAAAAATGT
1 AAATAAATAGAAAATTCATAAAAAATGT
* *
3644643 AAATAAATATAAAATTCTTAAAAAAT
1 AAATAAATAGAAAATTCATAAAAAAT
3644669 TATAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (28 bp):
AAATAAATAGAAAATTCATAAAAAATGT
Found at i:3644918 original size:21 final size:20
Alignment explanation
Indices: 3644894--3644946 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3644884 ATCTACAATC
*
3644894 TTTTACAATTTTTATAATTTT
1 TTTTAAAATTTTTAT-ATTTT
* *
3644915 TTTTATAATTTTTATGTTTT
1 TTTTAAAATTTTTATATTTT
3644935 TTATTAAAATTT
1 TT-TTAAAATTT
3644947 AATCATTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTAAAATTTTTATATTTT
Found at i:3644919 original size:12 final size:12
Alignment explanation
Indices: 3644902--3644927 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3644892 TCTTTTACAA
3644902 TTTTTATAATTT
1 TTTTTATAATTT
3644914 TTTTTATAATTT
1 TTTTTATAATTT
3644926 TT
1 TT
3644928 ATGTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:3654636 original size:6 final size:6
Alignment explanation
Indices: 3654625--3654658 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3654615 AAAAAAGATA
3654625 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCA
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCA
3654659 GCAACTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.35, T:0.15
Consensus pattern (6 bp):
GGCAAT
Found at i:3654672 original size:6 final size:6
Alignment explanation
Indices: 3654663--3654693 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3654653 ATGGCAGCAA
3654663 CTGAAG CTGAAG CTGAAG CTGAAG CTGAAG C
1 CTGAAG CTGAAG CTGAAG CTGAAG CTGAAG C
3654694 AGAGCAGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAAG
Found at i:3656852 original size:31 final size:31
Alignment explanation
Indices: 3656814--3656875 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3656804 CTACGCCTAG
3656814 ATTAGTATCAAAGAACGTTTGGTCGATTAAT
1 ATTAGTATCAAAGAACGTTTGGTCGATTAAT
3656845 ATTAGTATCAAAGAACGTTTGGTCGATTAAT
1 ATTAGTATCAAAGAACGTTTGGTCGATTAAT
3656876 CCTTAACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (31 bp):
ATTAGTATCAAAGAACGTTTGGTCGATTAAT
Found at i:3687111 original size:19 final size:19
Alignment explanation
Indices: 3687087--3687126 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3687077 ATTTAGAATT
3687087 TGAAATT-TAAAATTACATA
1 TGAAATTATAAAA-TACATA
3687106 TGAAATTAATAAAATACATA
1 TGAAATT-ATAAAATACATA
3687126 T
1 T
3687127 AAAGAGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
TGAAATTATAAAATACATA
Found at i:3698124 original size:25 final size:25
Alignment explanation
Indices: 3698086--3698139 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3698076 AAAGCAGGAG
* *
3698086 AGAAAGAAACGAAACAGGGAAAGAA
1 AGAAAGAAACGAAAAAGAGAAAGAA
*
3698111 AGAAAGGAAA-GAAAAAGAGAAGGAA
1 AGAAA-GAAACGAAAAAGAGAAAGAA
3698136 AGAA
1 AGAA
3698140 GGAGAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.67, C:0.04, G:0.30, T:0.00
Consensus pattern (25 bp):
AGAAAGAAACGAAAAAGAGAAAGAA
Found at i:3698133 original size:16 final size:15
Alignment explanation
Indices: 3698109--3698139 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
3698099 ACAGGGAAAG
3698109 AAAGAAAGGAAAGAA
1 AAAGAAAGGAAAGAA
3698124 AAAGAGAAGGAAAGAA
1 AAAGA-AAGGAAAGAA
3698140 GGAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAAAGAA
Found at i:3707233 original size:107 final size:108
Alignment explanation
Indices: 3707110--3707325 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 108
3707100 TAAACAAAAA
3707110 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
3707175 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
* *
3707217 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
3707282 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
3707325 A
1 A
3707326 CGTGTTTTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 93 0.88
108 13 0.12
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
Found at i:3713790 original size:41 final size:41
Alignment explanation
Indices: 3713689--3713882 Score: 241
Period size: 41 Copynumber: 4.8 Consensus size: 41
3713679 AAATAGGGCT
* * *
3713689 TTAGCGGCGTTTTACCA-AAAACGTCGCTAAAAA-CAGAGCA
1 TTAGCGGCGCTTT-CGATAAAACGCCGCTAAAAACCAGAGCA
* * * * *
3713729 ATAGCTGCGTTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
* *
3713770 TTAGTGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGAA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
*
3713811 TTAGCGGCGCTTTCGAT-AAACGCCACTAAAAACCAGAGCA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
**
3713851 TTAGCGGCGCTTTCGGCAAAACGCCGCTAAAA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
3713883 GTCATATAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
40 62 0.47
41 70 0.53
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
Found at i:3713841 original size:81 final size:81
Alignment explanation
Indices: 3713689--3713882 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 81
3713679 AAATAGGGCT
* * * * * * *
3713689 TTAGCGGCGTTTTACCA-AAAACGTCGCTAAAAACAGAGCAATAGCTGCGTTTTTGGTAAAACGC
1 TTAGCGGCGCTTT-CGACAAAACGCCGCTAAAAACAGAGCAATAGCGGCGCTTTCGATAAAACGC
*
3713753 CGCTAAAAACCAGAGCA
65 CACTAAAAACCAGAGCA
* *
3713770 TTAGTGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAG-AATTAGCGGCGCTTTCGAT-AAACG
1 TTAGCGGCGCTTTCGACAAAACGCCGCTAAAAA-CAGAGCAA-TAGCGGCGCTTTCGATAAAACG
3713833 CCACTAAAAACCAGAGCA
64 CCACTAAAAACCAGAGCA
*
3713851 TTAGCGGCGCTTTCGGCAAAACGCCGCTAAAA
1 TTAGCGGCGCTTTCGACAAAACGCCGCTAAAA
3713883 GTCATATAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
80 2 0.02
81 79 0.81
82 17 0.17
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (81 bp):
TTAGCGGCGCTTTCGACAAAACGCCGCTAAAAACAGAGCAATAGCGGCGCTTTCGATAAAACGCC
ACTAAAAACCAGAGCA
Found at i:3720464 original size:11 final size:11
Alignment explanation
Indices: 3720448--3720478 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3720438 TGCTTGGATG
3720448 TTGGTTTTGGT
1 TTGGTTTTGGT
3720459 TTGGTTTTGGT
1 TTGGTTTTGGT
3720470 TTGGTTTTG
1 TTGGTTTTG
3720479 TTCTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (11 bp):
TTGGTTTTGGT
Found at i:3724900 original size:107 final size:108
Alignment explanation
Indices: 3724777--3724992 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 108
3724767 TAAACAAAAA
3724777 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
3724842 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
* *
3724884 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
3724949 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
3724992 A
1 A
3724993 CGTGTTTTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 93 0.88
108 13 0.12
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
Found at i:3731460 original size:41 final size:41
Alignment explanation
Indices: 3731359--3731552 Score: 241
Period size: 41 Copynumber: 4.8 Consensus size: 41
3731349 AAATAGGGCT
* * *
3731359 TTAGCGGCGTTTTACCA-AAAACGTCGCTAAAAA-CAGAGCA
1 TTAGCGGCGCTTT-CGATAAAACGCCGCTAAAAACCAGAGCA
* * * * *
3731399 ATAGCTGCGTTTTTGGTAAAACGCCGCTAAAAACCAGAGCA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
* *
3731440 TTAGTGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGAA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
*
3731481 TTAGCGGCGCTTTCGAT-AAACGCCACTAAAAACCAGAGCA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
**
3731521 TTAGCGGCGCTTTCGGCAAAACGCCGCTAAAA
1 TTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
3731553 GTCATATAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
40 62 0.47
41 70 0.53
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAGCA
Found at i:3731511 original size:81 final size:81
Alignment explanation
Indices: 3731359--3731552 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 81
3731349 AAATAGGGCT
* * * * * * *
3731359 TTAGCGGCGTTTTACCA-AAAACGTCGCTAAAAACAGAGCAATAGCTGCGTTTTTGGTAAAACGC
1 TTAGCGGCGCTTT-CGACAAAACGCCGCTAAAAACAGAGCAATAGCGGCGCTTTCGATAAAACGC
*
3731423 CGCTAAAAACCAGAGCA
65 CACTAAAAACCAGAGCA
* *
3731440 TTAGTGGCGCTTTCGATAAAACGCCGCTAAAAACCAGAG-AATTAGCGGCGCTTTCGAT-AAACG
1 TTAGCGGCGCTTTCGACAAAACGCCGCTAAAAA-CAGAGCAA-TAGCGGCGCTTTCGATAAAACG
3731503 CCACTAAAAACCAGAGCA
64 CCACTAAAAACCAGAGCA
*
3731521 TTAGCGGCGCTTTCGGCAAAACGCCGCTAAAA
1 TTAGCGGCGCTTTCGACAAAACGCCGCTAAAA
3731553 GTCATATAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
80 2 0.02
81 79 0.81
82 17 0.17
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (81 bp):
TTAGCGGCGCTTTCGACAAAACGCCGCTAAAAACAGAGCAATAGCGGCGCTTTCGATAAAACGCC
ACTAAAAACCAGAGCA
Found at i:3738135 original size:11 final size:11
Alignment explanation
Indices: 3738119--3738149 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3738109 TGCTTGGATG
3738119 TTGGTTTTGGT
1 TTGGTTTTGGT
3738130 TTGGTTTTGGT
1 TTGGTTTTGGT
3738141 TTGGTTTTG
1 TTGGTTTTG
3738150 TTCTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (11 bp):
TTGGTTTTGGT
Found at i:3749669 original size:24 final size:24
Alignment explanation
Indices: 3749637--3749685 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3749627 TAACGGTTCA
3749637 GTTTAGTGTAAAGACTTCTAACTC
1 GTTTAGTGTAAAGACTTCTAACTC
3749661 GTTTAGTGTAAAGACTTCTAACTC
1 GTTTAGTGTAAAGACTTCTAACTC
3749685 G
1 G
3749686 AAGAGTGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (24 bp):
GTTTAGTGTAAAGACTTCTAACTC
Found at i:3749692 original size:24 final size:24
Alignment explanation
Indices: 3749641--3749692 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3749631 GGTTCAGTTT
***
3749641 AGTGTAAAGACTTCTAACTCGTTT
1 AGTGTAAAGACTTCTAACTCGAAG
3749665 AGTGTAAAGACTTCTAACTCGAAG
1 AGTGTAAAGACTTCTAACTCGAAG
3749689 AGTG
1 AGTG
3749693 ATCCTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (24 bp):
AGTGTAAAGACTTCTAACTCGAAG
Found at i:3754041 original size:13 final size:13
Alignment explanation
Indices: 3754023--3754051 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3754013 AATACCCAGA
3754023 AAGCGTACAAAGG
1 AAGCGTACAAAGG
3754036 AAGCGTACAAAGG
1 AAGCGTACAAAGG
3754049 AAG
1 AAG
3754052 AACCAGGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.14, G:0.31, T:0.07
Consensus pattern (13 bp):
AAGCGTACAAAGG
Found at i:3759699 original size:56 final size:57
Alignment explanation
Indices: 3759613--3759726 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
3759603 AAGTAATGCA
*
3759613 TTCAAAACTACTATCTTTAATTGGTATAA-TTTTTATGAAAAGTAGCAAGTTTCGCT
1 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
3759669 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
1 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
3759726 T
1 T
3759727 CTAATGTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 28 0.50
57 28 0.50
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (57 bp):
TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
Found at i:3760625 original size:4 final size:4
Alignment explanation
Indices: 3760616--3760653 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
3760606 CTTTCTAGTT
3760616 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
3760654 ACTTAATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3762445 original size:9 final size:9
Alignment explanation
Indices: 3762428--3762459 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
3762418 GCATCATCTT
3762428 CATCTTCCTC
1 CATC-TCCTC
3762438 CATCTCCTC
1 CATCTCCTC
3762447 CATCTCCTC
1 CATCTCCTC
3762456 CATC
1 CATC
3762460 ACATAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.34
Consensus pattern (9 bp):
CATCTCCTC
Found at i:3765295 original size:17 final size:17
Alignment explanation
Indices: 3765273--3765306 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3765263 ATTTAAGGGG
3765273 TTGAAGTGTAATTATAA
1 TTGAAGTGTAATTATAA
3765290 TTGAAGTGTAATTATAA
1 TTGAAGTGTAATTATAA
3765307 AAAAATTGAA
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:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TTGAAGTGTAATTATAA
Found at i:3767731 original size:46 final size:46
Alignment explanation
Indices: 3767679--3767860 Score: 213
Period size: 46 Copynumber: 4.0 Consensus size: 46
3767669 AGTGTGCTCT
* *
3767679 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
3767725 CTGATATGAAATGTGTAAGACCATGGTTAAAAGATACCATGGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
3767771 GTAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
3767817 ATGACA-GAAAAAGAGTAAAACCATAGTTGAAAGACACTATGGCA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
3767861 TCATGACAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
45 1 0.01
46 117 0.99
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3767850 original size:92 final size:92
Alignment explanation
Indices: 3767684--3767860 Score: 239
Period size: 92 Copynumber: 1.9 Consensus size: 92
3767674 GCTCTCTGAT
** * * * * *
3767684 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAGTAAAACCAT
* *
3767749 GGTTAAAAGATACCATGGCAGCGTAAC
66 AGTTAAAAGACACCATGGCAGCGTAAC
3767776 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAAAGAGTAAAACCA
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAAAGAGTAAAACCA
* *
3767840 TAGTTGAAAGACACTATGGCA
65 TAGTTAAAAGACACCATGGCA
3767861 TCATGACAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
91 1 0.01
92 72 0.99
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (92 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAGTAAAACCAT
AGTTAAAAGACACCATGGCAGCGTAAC
Found at i:3770160 original size:2 final size:2
Alignment explanation
Indices: 3770153--3770177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3770143 CCTTTTATTT
3770153 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3770178 CAACAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3778088 original size:19 final size:21
Alignment explanation
Indices: 3778047--3778093 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3778037 TCTTATATAT
*
3778047 AAATAAAAGTCATAAATTT-A
1 AAATAAAAATCATAAATTTAA
*
3778067 AAATAAAAAT-ATATATTTAA
1 AAATAAAAATCATAAATTTAA
3778087 AAATAAA
1 AAATAAA
3778094 TAATGAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAAAAATCATAAATTTAA
Found at i:3781484 original size:7 final size:7
Alignment explanation
Indices: 3781472--3781510 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
3781462 ATTCCAATTT
3781472 TTTTTTA
1 TTTTTTA
3781479 TTTTTTA
1 TTTTTTA
3781486 TTTTTTA
1 TTTTTTA
3781493 TTTTTTA
1 TTTTTTA
3781500 TTTTTTA
1 TTTTTTA
3781507 TTTT
1 TTTT
3781511 ATAAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:3783413 original size:18 final size:17
Alignment explanation
Indices: 3783378--3783410 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3783368 CTTTTTATTC
3783378 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
3783395 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
3783411 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:3793332 original size:25 final size:25
Alignment explanation
Indices: 3793304--3793362 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3793294 ATGGCTCTTA
* *
3793304 TGAGCTTGCCGATATACAGCTCGAT
1 TGAGCTTCCCGATATACAACTCGAT
* *
3793329 TGAGCTTCCCGTTATACAACTCGAA
1 TGAGCTTCCCGATATACAACTCGAT
*
3793354 AGAGCTTCC
1 TGAGCTTCC
3793363 TGTTTACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (25 bp):
TGAGCTTCCCGATATACAACTCGAT
Found at i:3794005 original size:2 final size:2
Alignment explanation
Indices: 3793998--3794050 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3793988 ATACATTTCG
3793998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3794040 AT AT AT AT AT A
1 AT AT AT AT AT A
3794051 GTCTTATAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3801726 original size:1 final size:1
Alignment explanation
Indices: 3801720--3801744 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3801710 ATCTATCACC
3801720 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3801745 CAGTCTTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.