Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 113 of 290
Found at i:38396486 original size:22 final size:21
Alignment explanation
Indices: 38396473--38396520 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
38396463 ACCTTAAACT
38396473 TAAACCCTAAAAACCCTAACC
1 TAAACCCTAAAAACCCTAACC
* *
38396494 TAAATCCTAAAAAACTCTAACCC
1 TAAACCCT-AAAAACCCTAA-CC
38396517 TAAA
1 TAAA
38396521 TCAATTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 10 0.43
23 6 0.26
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCCTAAAAACCCTAACC
Found at i:38399686 original size:15 final size:15
Alignment explanation
Indices: 38399668--38399699 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
38399658 TAAGATTTTT
38399668 TTAAACCTTATTAAA
1 TTAAACCTTATTAAA
38399683 TTAAACCTTATTAAA
1 TTAAACCTTATTAAA
38399698 TT
1 TT
38399700 CTATCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAACCTTATTAAA
Found at i:38404313 original size:12 final size:12
Alignment explanation
Indices: 38404282--38404306 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38404272 TTGTGTGTTC
38404282 TTTATTTTATTT
1 TTTATTTTATTT
38404294 TTTATTTTATTT
1 TTTATTTTATTT
38404306 T
1 T
38404307 ATTTTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:38412198 original size:22 final size:21
Alignment explanation
Indices: 38412144--38412198 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
38412134 ATTTTTCTCA
* *
38412144 TAAAAGTTATAAAAAGTATGT
1 TAAAAATTATAAAAAGTATAT
*
38412165 TAAAAA-TA-AAAAATTAGTAT
1 TAAAAATTATAAAAAGTA-TAT
38412185 TAAAAATTATAAAA
1 TAAAAATTATAAAA
38412199 TAAGATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.25
20 10 0.36
21 7 0.25
22 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
TAAAAATTATAAAAAGTATAT
Found at i:38414168 original size:26 final size:22
Alignment explanation
Indices: 38414105--38414150 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
38414095 CTAGGAGTCA
38414105 TTAATTTGATCAATTAAGCTTG
1 TTAATTTGATCAATTAAGCTTG
38414127 TTAATTTGATCAATTAAGCTTG
1 TTAATTTGATCAATTAAGCTTG
38414149 TT
1 TT
38414151 TTAAATGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (22 bp):
TTAATTTGATCAATTAAGCTTG
Found at i:38415282 original size:24 final size:22
Alignment explanation
Indices: 38415233--38415274 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
38415223 TATTTAAACT
38415233 TATTTTTTTCATAAATGGTACC
1 TATTTTTTTCATAAATGGTACC
38415255 TATTTTTTTC-TCAAATGGTA
1 TATTTTTTTCAT-AAATGGTA
38415275 GCTCTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (22 bp):
TATTTTTTTCATAAATGGTACC
Found at i:38416968 original size:47 final size:49
Alignment explanation
Indices: 38416915--38417034 Score: 131
Period size: 47 Copynumber: 2.5 Consensus size: 49
38416905 GAATTGACGG
*
38416915 TTAAGGATACCATGTAAGACCATGTCAAGACATGGCATCGACA-T-TGA
1 TTAAGGATACCATGTAAGACCATGTCAAGACATGGCATCGACACTAAGA
** ** * *
38416962 TTAAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGA
1 TTAAGGA-TACCATGTAAGACCATGTCAAGACATGGCATCGACACTAAGA
*
38417011 -CAAGGATACCATGTAAGACCATGT
1 TTAAGGATACCATGTAAGACCATGT
38417035 TTGGAACATG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
47 36 0.61
48 21 0.36
49 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (49 bp):
TTAAGGATACCATGTAAGACCATGTCAAGACATGGCATCGACACTAAGA
Found at i:38417065 original size:47 final size:47
Alignment explanation
Indices: 38417006--38417128 Score: 219
Period size: 47 Copynumber: 2.6 Consensus size: 47
38416996 GCATTGGCAC
*
38417006 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGTATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
38417053 TAAGACAAGGATACCATGTAAGACCATATTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
38417100 TAAGACAAGGATATCATGTAAGACCATGT
1 TAAGACAAGGATACCATGTAAGACCATGT
38417129 CAAGGCATGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:38417170 original size:54 final size:54
Alignment explanation
Indices: 38417106--38417323 Score: 235
Period size: 54 Copynumber: 4.0 Consensus size: 54
38417096 TTGGTAAGAC
* *
38417106 AAGGATATCATGTAAGACCATGTCAAGGCATGGCATTGATAAGTTCTATAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
* * * *
38417160 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTATTATAAGGCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGG-A
* * * * * *
38417216 AAGG-TCCCATGTAAGACCAT-TCTAAGGCATGACATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGTC-AAGACATGGCATTGATAAGTTCTATAAGGA
* * * * *
38417268 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTCAAAAAGGA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
38417322 AA
1 AA
38417324 AGGTTCCCGA
Statistics
Matches: 138, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
52 4 0.03
53 38 0.28
54 53 0.38
55 38 0.28
56 5 0.04
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGA
Found at i:38422127 original size:14 final size:14
Alignment explanation
Indices: 38422108--38422138 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38422098 TGCCAACATC
*
38422108 ATAAATATATATAT
1 ATAAATATAAATAT
38422122 ATAAATATAAATAT
1 ATAAATATAAATAT
38422136 ATA
1 ATA
38422139 TTATTATCTT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAATATAAATAT
Found at i:38423604 original size:40 final size:38
Alignment explanation
Indices: 38423513--38423608 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 38
38423503 CCAACTCTGA
* *
38423513 CCAACCCAACACACCATGTGAGGATAAAATCGACCCAC
1 CCAACCCTACACACCATATGAGGATAAAATCGACCCAC
* * * * * *
38423551 CCATCTCTGCACACCGTATATGGGGATACAATCGACCCAT
1 CCAACCCTACACACC--ATATGAGGATAAAATCGACCCAC
38423591 CCAACCCTACACACCATA
1 CCAACCCTACACACCATA
38423609 AAGTACCGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
38 14 0.31
40 31 0.69
ACGTcount: A:0.34, C:0.38, G:0.12, T:0.16
Consensus pattern (38 bp):
CCAACCCTACACACCATATGAGGATAAAATCGACCCAC
Found at i:38433602 original size:26 final size:26
Alignment explanation
Indices: 38433573--38433682 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
38433563 TGGTACAAAT
*
38433573 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTCCA
38433599 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
38433625 TGATAAT-GGATTAGGTAAATGTTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
* *
38433651 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
38433677 TGATAA
1 TGATAA
38433683 AAATTTCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
25 2 0.03
26 76 0.95
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:38435341 original size:27 final size:27
Alignment explanation
Indices: 38435300--38435412 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
38435290 GAAGAAGCGT
*
38435300 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
38435327 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
38435354 TTTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
38435382 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
38435408 TCTGG
1 TCTGG
38435413 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 54 0.74
28 14 0.19
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:38435405 original size:54 final size:54
Alignment explanation
Indices: 38435302--38435408 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
38435292 AGAAGCGTTC
*
38435302 TGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTTT
1 TGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTTT
* * * *
38435356 TGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 TGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
38435409 CTGGCAGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (54 bp):
TGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTTT
Found at i:38443511 original size:21 final size:21
Alignment explanation
Indices: 38443486--38443539 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
38443476 CACTGTTATT
38443486 CCTGTTTTTCCTGTTTTGGAA
1 CCTGTTTTTCCTGTTTTGGAA
38443507 CCTGTTTTTCCTGTTTTGGAA
1 CCTGTTTTTCCTGTTTTGGAA
38443528 CCTGTTTTTCCT
1 CCTGTTTTTCCT
38443540 ATCTCCACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.07, C:0.22, G:0.17, T:0.54
Consensus pattern (21 bp):
CCTGTTTTTCCTGTTTTGGAA
Found at i:38443512 original size:12 final size:12
Alignment explanation
Indices: 38443495--38443535 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
38443485 TCCTGTTTTT
38443495 CCTGTTTTGGAA
1 CCTGTTTTGGAA
*
38443507 CCTGTTTT---T
1 CCTGTTTTGGAA
38443516 CCTGTTTTGGAA
1 CCTGTTTTGGAA
38443528 CCTGTTTT
1 CCTGTTTT
38443536 TCCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.33
12 16 0.67
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.51
Consensus pattern (12 bp):
CCTGTTTTGGAA
Found at i:38450506 original size:18 final size:18
Alignment explanation
Indices: 38450483--38450530 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
38450473 ATGAAAAAGG
38450483 TTATTTATATTAATATTT
1 TTATTTATATTAATATTT
*
38450501 TTATTT-TTTATAATATTT
1 TTATTTATAT-TAATATTT
*
38450519 TTA-ATATATTAA
1 TTATTTATATTAA
38450531 ATCATTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTATATTAATATTT
Found at i:38453633 original size:16 final size:16
Alignment explanation
Indices: 38453609--38453654 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
38453599 ATTTCTTATT
38453609 TAAAT-TATTTTTTTA
1 TAAATATATTTTTTTA
38453624 TAAATATATTTTTTTA
1 TAAATATATTTTTTTA
38453640 TATAATTATATTTTT
1 TA-AA-TATATTTTT
38453655 CATCCACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.18
16 12 0.43
17 2 0.07
18 9 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TAAATATATTTTTTTA
Found at i:38453643 original size:18 final size:18
Alignment explanation
Indices: 38453604--38453654 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
38453594 ATATCATTTC
*
38453604 TTATTTAAAT-TA-TTTT
1 TTATATAAATATATTTTT
38453620 TT-TATAAATATATTTTT
1 TTATATAAATATATTTTT
*
38453637 TTATATAATTATATTTTT
1 TTATATAAATATATTTTT
38453655 CATCCACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.20
16 4 0.13
17 6 0.20
18 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATAAATATATTTTT
Found at i:38462225 original size:23 final size:23
Alignment explanation
Indices: 38462164--38462229 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
38462154 CCTAATCAGT
*
38462164 ATACGACACATAAAGTGACT-AA
1 ATACGACACATAAAGTGCCTGAA
** *
38462186 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
38462208 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
38462230 TCGGTAAAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 14 0.40
22 4 0.11
23 17 0.49
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:38462626 original size:15 final size:14
Alignment explanation
Indices: 38462602--38462658 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
38462592 GATATATATT
38462602 ATATAATTCAATCA
1 ATATAATTCAATCA
38462616 ATATGAATTCAATCA
1 ATAT-AATTCAATCA
* *
38462631 AAATAATTTCAGTCA
1 ATATAA-TTCAATCA
38462646 ATATAAATTCAAT
1 ATAT-AATTCAAT
38462659 AAATTCGTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.17
15 28 0.78
16 2 0.06
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (14 bp):
ATATAATTCAATCA
Found at i:38463086 original size:19 final size:19
Alignment explanation
Indices: 38463048--38463100 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
38463038 AATAACATTG
*
38463048 TATTATTACTTAT-T-TAT
1 TATTATTACATATGTATAT
*
38463065 TATT-TGTACATGTGTATAT
1 TATTAT-TACATATGTATAT
38463084 TATTATTACATATGTAT
1 TATTATTACATATGTAT
38463101 CCATAGATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 9 0.31
18 1 0.03
19 17 0.59
20 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.57
Consensus pattern (19 bp):
TATTATTACATATGTATAT
Found at i:38463195 original size:17 final size:20
Alignment explanation
Indices: 38463174--38463214 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
38463164 ATTATTTAAC
38463174 TAATAAATATCTTTT-ATAAA
1 TAATAAATATCTTTTAAT-AA
38463194 TAATAAATATCTTTTAATAA
1 TAATAAATATCTTTTAATAA
38463214 T
1 T
38463215 TAAATACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATAAATATCTTTTAATAA
Found at i:38464551 original size:13 final size:13
Alignment explanation
Indices: 38464533--38464557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38464523 TCATACTCAC
38464533 AAAATTCCCCAAT
1 AAAATTCCCCAAT
38464546 AAAATTCCCCAA
1 AAAATTCCCCAA
38464558 CTGCTGTGCA
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:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATTCCCCAAT
Found at i:38466058 original size:12 final size:12
Alignment explanation
Indices: 38466036--38466082 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
38466026 TGTTAAGTTT
38466036 TTTAGATTTTGTG
1 TTTAGATTTTG-G
38466049 TTTA-ATTTTGG
1 TTTAGATTTTGG
* **
38466060 TTTTGATTTTCT
1 TTTAGATTTTGG
38466072 TTTAGATTTTG
1 TTTAGATTTTG
38466083 TTAAGTTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 4 0.14
12 20 0.71
13 4 0.14
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.66
Consensus pattern (12 bp):
TTTAGATTTTGG
Found at i:38466080 original size:24 final size:25
Alignment explanation
Indices: 38466035--38466082 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
38466025 TTGTTAAGTT
*
38466035 TTTTAGATTTTGTGTTTAATTTTGG
1 TTTTAGATTTTCTGTTTAATTTTGG
38466060 TTTT-GATTTTCT-TTTAGATTTTG
1 TTTTAGATTTTCTGTTTA-ATTTTG
38466083 TTAAGTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.67
Consensus pattern (25 bp):
TTTTAGATTTTCTGTTTAATTTTGG
Found at i:38467263 original size:13 final size:13
Alignment explanation
Indices: 38467245--38467292 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
38467235 AGTTTGGCAA
38467245 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
38467258 TGCTTTTGAGAAA
1 TGCTTTTGAGAAG
* * *
38467271 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
38467284 TGCTTTTGA
1 TGCTTTTGA
38467293 AAAATTTAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:38468541 original size:12 final size:12
Alignment explanation
Indices: 38468524--38468550 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38468514 GAAAATAGGG
38468524 TTTTAGCGACGT
1 TTTTAGCGACGT
38468536 TTTTAGCGACGT
1 TTTTAGCGACGT
38468548 TTT
1 TTT
38468551 ATCAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (12 bp):
TTTTAGCGACGT
Found at i:38468681 original size:41 final size:41
Alignment explanation
Indices: 38468605--38469571 Score: 1837
Period size: 41 Copynumber: 23.6 Consensus size: 41
38468595 CGTTTTAAGA
* * **
38468605 AAAACGCCGCTAAAAA-CAGAGCAATAGCGGCGCTTTTCTT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
*
38468645 AAAACGCCGCTAAAAACCAGAGCATTAGCTGTGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
* * *
38468686 AAAACACCGCTAAAAACCAGAGCACTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468727 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468768 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468809 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468850 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468891 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468932 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38468973 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469014 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469055 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469096 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469137 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469178 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469219 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469260 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469301 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469342 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469383 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
*
38469424 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469465 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
*
38469506 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
38469547 AAAACGCCGCTAAAAACCAGAGCAT
1 AAAACGCCGCTAAAAACCAGAGCAT
38469572 GTCATATAAC
Statistics
Matches: 911, Mismatches: 15, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
40 16 0.02
41 895 0.98
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCTGCGCTTTTGGT
Found at i:38472454 original size:40 final size:40
Alignment explanation
Indices: 38472278--38472500 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
38472268 TCCTCGTTCA
* * * * *
38472278 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
38472317 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
38472357 AATGCCTTCGGGACTTGACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
38472397 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
38472437 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
38472477 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38472501 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:38472500 original size:120 final size:119
Alignment explanation
Indices: 38472278--38472500 Score: 265
Period size: 120 Copynumber: 1.9 Consensus size: 119
38472268 TCCTCGTTCA
* * * *
38472278 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
38472343 TAACAACTCGCACGAATGCCTTCGGGACTTGACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTGACCCGGATTTAATAACTCGCACG
* * * * *
38472397 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
*
38472461 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTT-AGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTGA-CCCGGA
38472501 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
119 38 0.44
120 43 0.49
121 6 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTGACCCGGATTTAATAACTCGCACG
Found at i:38480290 original size:40 final size:40
Alignment explanation
Indices: 38480192--38480454 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
38480182 TCCTCGTTCA
* * * * *
38480192 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
38480231 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38480271 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
38480311 AATGCCTTCGGGACTTAACCCGGATATAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
38480351 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
38480391 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
38480431 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38480455 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:38481670 original size:100 final size:102
Alignment explanation
Indices: 38481520--38481722 Score: 392
Period size: 101 Copynumber: 2.0 Consensus size: 102
38481510 AATCCCCCCC
38481520 TTTCTCTTCTTTAGCTCACGGCAATGGGGGGACAAACACTACACACACA-TTTTTTTTTCTTTTG
1 TTTCTCTTCTTTAGCTCACGGCAATGGGGGGACAAACACTACACACACATTTTTTTTTTCTTTTG
38481584 TTTTCCATTTCTTTATTACCCATACTCCTTATTTTAT
66 TTTTCCATTTCTTTATTACCCATACTCCTTATTTTAT
38481621 TTTCTCTTCTTTAGCTCACGGCAAT-GGGGGACAAACACTACACACACATTTTTTTTTTCTTTTG
1 TTTCTCTTCTTTAGCTCACGGCAATGGGGGGACAAACACTACACACACATTTTTTTTTTCTTTTG
38481685 TTTTCCATTTCTTTATTACCCATACTCCTTATTTTAT
66 TTTTCCATTTCTTTATTACCCATACTCCTTATTTTAT
38481722 T
1 T
38481723 CTTCCACTAA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
100 23 0.23
101 78 0.77
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.46
Consensus pattern (102 bp):
TTTCTCTTCTTTAGCTCACGGCAATGGGGGGACAAACACTACACACACATTTTTTTTTTCTTTTG
TTTTCCATTTCTTTATTACCCATACTCCTTATTTTAT
Found at i:38483716 original size:16 final size:16
Alignment explanation
Indices: 38483695--38483728 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38483685 TAATAAAAAG
38483695 ATATAGTGCCTTCCTC
1 ATATAGTGCCTTCCTC
38483711 ATATAGTGCCTTCCTC
1 ATATAGTGCCTTCCTC
38483727 AT
1 AT
38483729 CAATGGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (16 bp):
ATATAGTGCCTTCCTC
Found at i:38485584 original size:13 final size:14
Alignment explanation
Indices: 38485568--38485596 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38485558 TTCTAAATAT
38485568 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
38485581 TTATAATTGTTTAA
1 TTATAATTGTTTAA
38485595 TT
1 TT
38485597 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:38486038 original size:21 final size:21
Alignment explanation
Indices: 38486011--38486065 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
38486001 ACTTAGAGCG
38486011 GAGGCAGCAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
* *
38486032 GCGGCAGCAGTGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
*
38486053 GAGGTAGCAGCGA
1 GAGGCAGCAGCGA
38486066 TGGTAGCAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.51, T:0.04
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:38486505 original size:42 final size:42
Alignment explanation
Indices: 38486450--38486529 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
38486440 GTTTTTCTGG
* *
38486450 CAAACAGCCCTAAAAGCCATTACTTTTAGCAACGCTTTCCAA
1 CAAACAGCCCTAAAAACCATGACTTTTAGCAACGCTTTCCAA
* *
38486492 CAAAC-GCCGCTAAAAACCATGACTTTTAGTAGCGCTTT
1 CAAACAGCC-CTAAAAACCATGACTTTTAGCAACGCTTT
38486530 TTTTACAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.09
42 30 0.91
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (42 bp):
CAAACAGCCCTAAAAACCATGACTTTTAGCAACGCTTTCCAA
Found at i:38488975 original size:21 final size:21
Alignment explanation
Indices: 38488928--38488975 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
38488918 ATAATAAATT
* *
38488928 TTGCTTTTAGACATATTACTC
1 TTGCTTCTAAACATATTACTC
** *
38488949 CCGCTTCTAAACATATTATTC
1 TTGCTTCTAAACATATTACTC
38488970 TTGCTT
1 TTGCTT
38488976 AAAAAAATCG
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (21 bp):
TTGCTTCTAAACATATTACTC
Found at i:38489540 original size:16 final size:17
Alignment explanation
Indices: 38489519--38489552 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38489509 AAGTTTTATT
*
38489519 TATTTATTATAT-TTAA
1 TATTTAATATATATTAA
38489535 TATTTAATATATATTAA
1 TATTTAATATATATTAA
38489552 T
1 T
38489553 TAATATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTAATATATATTAA
Found at i:38496691 original size:24 final size:25
Alignment explanation
Indices: 38496613--38496718 Score: 90
Period size: 25 Copynumber: 4.2 Consensus size: 25
38496603 GTAACTCCGA
* **
38496613 AGAGCCATTTATCAGGAAGCTCCGG
1 AGAGCCATATATCAGGAAGCTCAAG
* *
38496638 ATAGCCATATATCAGGAAGTTCAAG
1 AGAGCCATATATCAGGAAGCTCAAG
* * *
38496663 TGAGCCA-ATATCGGGAAGCTCTAG
1 AGAGCCATATATCAGGAAGCTCAAG
* *
38496687 AGAGCCAT-TAATTAGGAAGCTCACAA
1 AGAGCCATAT-ATCAGGAAGCTCA-AG
38496713 AGAGCC
1 AGAGCC
38496719 TTTAATCGAG
Statistics
Matches: 63, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
24 21 0.33
25 35 0.56
26 7 0.11
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (25 bp):
AGAGCCATATATCAGGAAGCTCAAG
Found at i:38502392 original size:20 final size:20
Alignment explanation
Indices: 38502363--38502412 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
38502353 AGCACATGTA
* *
38502363 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
38502383 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
38502403 TTCATTAAAA
1 TTCA-TAAAA
38502413 ATCACTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:38506769 original size:21 final size:20
Alignment explanation
Indices: 38506745--38506783 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
38506735 TACATGGTCA
* *
38506745 CTAATCAAATTACACTTTTTT
1 CTAATAAAAATACA-TTTTTT
38506766 CTAATAAAAATACATTTT
1 CTAATAAAAATACATTTT
38506784 AATTTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (20 bp):
CTAATAAAAATACATTTTTT
Found at i:38524723 original size:25 final size:25
Alignment explanation
Indices: 38524689--38524739 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
38524679 GAAAAGAAAA
*
38524689 AGAAAACTTAGGTTCGGCCATTCTC
1 AGAAAACTTAGGTTCGACCATTCTC
*
38524714 AGAAAACTTAGGTTTGACCATTCTC
1 AGAAAACTTAGGTTCGACCATTCTC
38524739 A
1 A
38524740 AGCTTGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (25 bp):
AGAAAACTTAGGTTCGACCATTCTC
Found at i:38525572 original size:46 final size:45
Alignment explanation
Indices: 38525494--38525671 Score: 230
Period size: 45 Copynumber: 3.9 Consensus size: 45
38525484 TTATGCTATA
* *
38525494 TGTTTTCGTGTAAGAACATATCTGGGGCGTTGGCATCGATATATG
1 TGTTTTCGTGTAAGACCACATCTGGGGCGTTGGCATCGATATATG
* *
38525539 TGTGTTCGTGTAAGACCCACATTTGGGGCGTTGGCATCGATATATG
1 TGTTTTCGTGTAAGA-CCACATCTGGGGCGTTGGCATCGATATATG
* ** *
38525585 TGTTTTCGTGTAAGACCACGTCTGGGATGTTGGTATCGATATATG
1 TGTTTTCGTGTAAGACCACATCTGGGGCGTTGGCATCGATATATG
** * * *
38525630 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGATAT
1 TGTTTTCGTGTAAGACCACATCTGGGGCGTTGGCATCGATAT
38525672 GTGGTTACGA
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
45 76 0.65
46 41 0.35
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (45 bp):
TGTTTTCGTGTAAGACCACATCTGGGGCGTTGGCATCGATATATG
Found at i:38525686 original size:43 final size:44
Alignment explanation
Indices: 38525494--38525702 Score: 186
Period size: 45 Copynumber: 4.7 Consensus size: 44
38525484 TTATGCTATA
* * * * *
38525494 TGTTTTCGTGTAAGAACATATCTGGGGCGTTGGCATCGATATATG
1 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGA-ATATG
* ** * * * *
38525539 TGTGTTCGTGTAAGACCCACATTTGGGGCGTTGGCATCGATATATG
1 TGTTTTCGTGTAAGA-CCATGTCTGGGACATTGACATCGA-ATATG
* ** **
38525585 TGTTTTCGTGTAAGACCACGTCTGGGATGTTGGTATCGATATATG
1 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGA-ATATG
38525630 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCG-ATATG
1 TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGAATATG
* * * *
38525673 TGGTTACGAGTAAGACCATGTTTGGGACAT
1 TGTTTTCGTGTAAGACCATGTCTGGGACAT
38525703 CGTCATTGTA
Statistics
Matches: 144, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
43 31 0.22
45 72 0.50
46 41 0.28
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCGAATATG
Found at i:38525740 original size:41 final size:42
Alignment explanation
Indices: 38525580--38525783 Score: 124
Period size: 43 Copynumber: 4.7 Consensus size: 42
38525570 TGGCATCGAT
* * ** * **
38525580 ATATGTGTTTTCGTGTAAGACCACGTCTGGGATGTTGGTATCG
1 ATATGTG-ATTCGTGTAAGACCATGTCTGGGACATCGACATCG
* *
38525623 ATATATGTGTTTTCGTGTAAGACCATGTCTGGGACATTGACATCG
1 --ATATGTG-ATTCGTGTAAGACCATGTCTGGGACATCGACATCG
* * * * *
38525668 ATATGTGGTTACGAGTAAGACCATGTTTGGGACATCGTCATTG
1 ATATGTGATT-CGTGTAAGACCATGTCTGGGACATCGACATCG
* * * * *
38525711 -TATTTGATTCGTGTAAGACCCTATCTGGGACAGT-GGCATTG
1 ATATGTGATTCGTGTAAGACCATGTCTGGGACA-TCGACATCG
* * * *
38525752 ATATGAGATAGCATGTAAGACCACGTCTGGGA
1 ATATGTGAT-TCGTGTAAGACCATGTCTGGGA
38525784 TGTTGGAATT
Statistics
Matches: 130, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
41 25 0.19
42 16 0.12
43 51 0.39
45 38 0.29
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
ATATGTGATTCGTGTAAGACCATGTCTGGGACATCGACATCG
Found at i:38527376 original size:39 final size:39
Alignment explanation
Indices: 38527348--38527499 Score: 164
Period size: 39 Copynumber: 4.2 Consensus size: 39
38527338 GGACTTTAAC
* * **
38527348 CCGGACATATTTCCAGCATGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
*
38527387 CCGGTTATAATTCCAGCACATAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
38527426 CCGGATATAATTCCAGCAC--A-----C---CC-TAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
*
38527454 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
*
38527493 CTGGATA
1 CCGGATA
38527500 AACATCACTG
Statistics
Matches: 95, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
28 24 0.25
29 2 0.02
30 1 0.01
32 1 0.01
35 1 0.01
37 1 0.01
38 2 0.02
39 63 0.66
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
Found at i:38542587 original size:21 final size:21
Alignment explanation
Indices: 38542561--38542629 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
38542551 TTCGGGTGGA
38542561 TCAGCTCTTTTGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
38542582 TCAGCTCTTTTGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
* *
38542603 TAAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
*
38542624 TTAGCT
1 TCAGCT
38542630 TTCAAGCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (21 bp):
TCAGCTCTTTTGAGCTTCTGT
Found at i:38542590 original size:72 final size:71
Alignment explanation
Indices: 38542465--38542598 Score: 169
Period size: 72 Copynumber: 1.9 Consensus size: 71
38542455 GCGTTTTACT
* * *
38542465 TTCTACTTGGCGTGATTGGGTGGATTAGCTCTCACGAGCTTTTATTCAACTCTTATGAGCTTTTA
1 TTCTACTTGGCGAGATTGGGTGGATCAGCTCTCACGAGCTTCTATTCAACTCTTATGAGCTTTTA
38542530 GTCAGC
66 GTCAGC
* *** * * *
38542536 TTCTATTTGGCGAGATTCGGGTGGATCAGCTCTTTTGAGCTTCTGTTCAGCTCTTTTGAGCTT
1 TTCTACTTGGCGAGATT-GGGTGGATCAGCTCTCACGAGCTTCTATTCAACTCTTATGAGCTT
38542599 CTGTTAAGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
71 15 0.29
72 37 0.71
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (71 bp):
TTCTACTTGGCGAGATTGGGTGGATCAGCTCTCACGAGCTTCTATTCAACTCTTATGAGCTTTTA
GTCAGC
Found at i:38543671 original size:20 final size:20
Alignment explanation
Indices: 38543634--38543672 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38543624 CCTATAGTTC
* **
38543634 AAAATTTTTAAATTTTTCCT
1 AAAATTTTCAAAAGTTTCCT
38543654 AAAATTTTCAAAAGTTTCC
1 AAAATTTTCAAAAGTTTCC
38543673 GATTTAGTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAATTTTCAAAAGTTTCCT
Found at i:38545132 original size:48 final size:48
Alignment explanation
Indices: 38545072--38545200 Score: 186
Period size: 48 Copynumber: 2.6 Consensus size: 48
38545062 TATGTGTGCT
* ** *
38545072 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGGTATACAAGCC
1 AGTGTAAAACATGTCTGGGACATGCATCAACCTCGAGATATACAAGCC
*
38545120 AGTGTAAAACATGTCTGGGACATGCATCAACCTCGAGATATACAAGCT
1 AGTGTAAAACATGTCTGGGACATGCATCAACCTCGAGATATACAAGCC
*
38545168 AGTGTAAGACCATGTCTGGGACATGGCATCAAC
1 AGTGTAA-AACATGTCTGGGACAT-GCATCAAC
38545201 TTGTTGTGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
48 50 0.68
49 15 0.21
50 8 0.11
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (48 bp):
AGTGTAAAACATGTCTGGGACATGCATCAACCTCGAGATATACAAGCC
Found at i:38545314 original size:49 final size:49
Alignment explanation
Indices: 38545072--38545386 Score: 285
Period size: 49 Copynumber: 6.5 Consensus size: 49
38545062 TATGTGTGCT
* * ** *
38545072 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGGTAT-ACAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGA-AAGTC
* * * *
38545120 AGTGTAAAACATGTCTGGGACAT-GCATCAACCTCGAGATAT-ACAAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGA-AAGTC
* * * *
38545167 TAGTGTAAGACCATGTCTGGGACATGGCATCA-ACTTG-T-TGTG--TGTC
1 -AGTGTAAGACC-TGTCTGGGACATGGCATCAGCCTCGATATATGAAAGTC
* * * * *
38545213 AGTGTAAGACCTGTCTGGGACATGGCCTC-GACAC-CAATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAG-C-CTCGATATATGAAAGTC
*
38545262 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTTGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGAAAGTC
* * *
38545311 AGTGTAAGACCTGTTTGGGACACGGCATTAGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGAAAGTC
38545360 AGTGTAAGACCATGTCTGGGACATGGC
1 AGTGTAAGACC-TGTCTGGGACATGGC
38545387 GTCGGCATCT
Statistics
Matches: 221, Mismatches: 31, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
44 17 0.08
45 12 0.05
46 3 0.01
47 5 0.02
48 52 0.24
49 112 0.51
50 20 0.09
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGATATATGAAAGTC
Found at i:38548721 original size:15 final size:15
Alignment explanation
Indices: 38548701--38548732 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38548691 TATTTCACTA
38548701 TTATGTCTTCTATAT
1 TTATGTCTTCTATAT
*
38548716 TTATGTCTTTTATAT
1 TTATGTCTTCTATAT
38548731 TT
1 TT
38548733 TACATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (15 bp):
TTATGTCTTCTATAT
Found at i:38552049 original size:49 final size:49
Alignment explanation
Indices: 38551989--38552117 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 49
38551979 ATTAAAGTCG
* * *
38551989 ATGCCGTGTCCCAGACATGACTTACACTGACTTTCATATATTGAG-GCCA
1 ATGCCATGTCCCAGACATGTCTTACACTGACTCTCATATATTG-GTGCCA
* * * * *
38552038 ATGCCATGTCCCAGACATGTCTTACATTGGCTCTCATCTATTGGTGTCG
1 ATGCCATGTCCCAGACATGTCTTACACTGACTCTCATATATTGGTGCCA
* *
38552087 ATGCCATGTCCCAGAGAGGTCTTACACTGAC
1 ATGCCATGTCCCAGACATGTCTTACACTGAC
38552118 ACACAACAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 66 0.99
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGTCTTACACTGACTCTCATATATTGGTGCCA
Found at i:38556542 original size:85 final size:85
Alignment explanation
Indices: 38556293--38556727 Score: 816
Period size: 85 Copynumber: 5.1 Consensus size: 85
38556283 GGCCGGCCAT
*
38556293 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
*
38556358 GCAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
38556378 GAGCATGGGTGGACAAGATGTTATGGCTAAAAAACATGTCATAAACATGTTGGGGTAGTGCATTA
1 GAGCATGGGTGGACAAGATGTTATGGCT-AAAAACATGTCATAAACATGTTGGGGTAGTGCATTA
38556443 TGTAAGGATTAATAAAATAAA
65 TGTAAGGATTAATAAAATAAA
38556464 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
*
38556529 GTAAGGATTAATAAAATGAA
66 GTAAGGATTAATAAAATAAA
38556549 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
*
38556614 GTAAGGATTAATAAAATGAA
66 GTAAGGATTAATAAAATAAA
38556634 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38556699 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
38556719 GGGCATGGG
1 GAGCATGGG
38556728 CAATAAAATA
Statistics
Matches: 344, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
85 261 0.76
86 83 0.24
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:38563444 original size:85 final size:85
Alignment explanation
Indices: 38563301--38563734 Score: 814
Period size: 85 Copynumber: 5.1 Consensus size: 85
38563291 GGCCGGCCAT
*
38563301 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38563366 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
38563386 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38563451 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
38563471 GACCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
*
38563536 GTAAGGATTAATAAAATGAA
66 GTAAGGATTAATAAAATAAA
38563556 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
*
38563621 GTAAGGATTAATAAAATGAA
66 GTAAGGATTAATAAAATAAA
38563641 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
38563706 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
38563726 GGGCATGGG
1 GAGCATGGG
38563735 CAATAAAATA
Statistics
Matches: 343, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 343 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.27
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:38569821 original size:44 final size:44
Alignment explanation
Indices: 38569758--38569920 Score: 166
Period size: 44 Copynumber: 3.6 Consensus size: 44
38569748 TGGTGTCGAT
*
38569758 GCCATGTCGTAGACAGGTCTTACACTGACACACAACAAGCTGAC
1 GCCATGTCCTAGACAGGTCTTACACTGACACACAACAAGCTGAC
* * * * * * *
38569802 GCCATGTCCTAGATAGGTCTTACACT-AGCTCTCATCTATTGGTTGCGAT
1 GCCATGTCCTAGACAGGTCTTACACTGA-CACACAAC-A--AGCT--GAC
* *
38569851 GCCATGTCGTAGACAGGTCTTACATTGACACACAACAAGCTGAC
1 GCCATGTCCTAGACAGGTCTTACACTGACACACAACAAGCTGAC
*
38569895 GCCATGTCCTAGATAGGTCTTACACT
1 GCCATGTCCTAGACAGGTCTTACACT
38569921 AGCTTGTATA
Statistics
Matches: 92, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
43 1 0.01
44 54 0.59
45 1 0.01
46 2 0.02
47 2 0.02
48 1 0.01
49 30 0.33
50 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (44 bp):
GCCATGTCCTAGACAGGTCTTACACTGACACACAACAAGCTGAC
Found at i:38569855 original size:93 final size:93
Alignment explanation
Indices: 38569611--38569924 Score: 477
Period size: 93 Copynumber: 3.3 Consensus size: 93
38569601 CGAGGCCGAT
38569611 GCCATGTCCCAGATAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCATGTCGTAGACAG
1 GCCATGTCCCAGATAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCATGTCGTAGACAG
* * * * *
38569676 GTCTTACACTGACTTTCATATATCGAGGCCGAT
66 GTCTTACACTGAC--ACACA-A-C-AAGCTGAC
**
38569709 GCCATGTCCCAGATAGGTCTTACACTATATCTCATCTATTGGTGTCGATGCCATGTCGTAGACAG
1 GCCATGTCCCAGATAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCATGTCGTAGACAG
38569774 GTCTTACACTGACACACAACAAGCTGAC
66 GTCTTACACTGACACACAACAAGCTGAC
*
38569802 GCCATGTCCTAGATAGGTCTTACACTAGCTCTCATCTATTGGT-TGCGATGCCATGTCGTAGACA
1 GCCATGTCCCAGATAGGTCTTACACTAGCTCTCATCTATTGGTGT-CGATGCCATGTCGTAGACA
*
38569866 GGTCTTACATTGACACACAACAAGCTGAC
65 GGTCTTACACTGACACACAACAAGCTGAC
*
38569895 GCCATGTCCTAGATAGGTCTTACACTAGCT
1 GCCATGTCCCAGATAGGTCTTACACTAGCT
38569925 TGTATATCCC
Statistics
Matches: 204, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
92 1 0.00
93 122 0.60
94 1 0.00
95 1 0.00
96 3 0.01
98 76 0.37
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (93 bp):
GCCATGTCCCAGATAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCATGTCGTAGACAG
GTCTTACACTGACACACAACAAGCTGAC
Found at i:38569869 original size:49 final size:49
Alignment explanation
Indices: 38569566--38569874 Score: 262
Period size: 49 Copynumber: 6.4 Consensus size: 49
38569556 GTTGATGCTG
* * * * *
38569566 TGTCCCAGACAGGTCTTACACT-GACTTTCATATATCGAG-GCCGATGCCA
1 TGTCCTAGACAGGTCTTACACTAG-CTCTCATCTATTG-GTGTCGATGCCA
* *
38569615 TGTCCCAGATAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCA
1 TGTCCTAGACAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCA
* * * * *
38569664 TGTCGTAGACAGGTCTTACACT-GACTTTCATATATCGAG-GCCGATGCCA
1 TGTCCTAGACAGGTCTTACACTAG-CTCTCATCTATTG-GTGTCGATGCCA
* * **
38569713 TGTCCCAGATAGGTCTTACACTATATCTCATCTATTGGTGTCGATGCCA
1 TGTCCTAGACAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCA
* * * * * * *
38569762 TGTCGTAGACAGGTCTTACACT-GACACACAAC-A--AG-CT-GACGCCA
1 TGTCCTAGACAGGTCTTACACTAG-CTCTCATCTATTGGTGTCGATGCCA
*
38569806 TGTCCTAGATAGGTCTTACACTAGCTCTCATCTATTGGT-TGCGATGCCA
1 TGTCCTAGACAGGTCTTACACTAGCTCTCATCTATTGGTGT-CGATGCCA
*
38569855 TGTCGTAGACAGGTCTTACA
1 TGTCCTAGACAGGTCTTACA
38569875 TTGACACACA
Statistics
Matches: 205, Mismatches: 41, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
44 31 0.15
45 3 0.01
46 1 0.00
47 2 0.01
48 4 0.02
49 162 0.79
50 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (49 bp):
TGTCCTAGACAGGTCTTACACTAGCTCTCATCTATTGGTGTCGATGCCA
Found at i:38583255 original size:12 final size:12
Alignment explanation
Indices: 38583238--38583300 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
38583228 TTTTAATAAG
38583238 ATTTAATATTAA
1 ATTTAATATTAA
38583250 ATTTAATA-TAA
1 ATTTAATATTAA
*
38583261 TATTT-ATCAAGATAA
1 -ATTTAAT--A-TTAA
38583276 ATATT-ATATTAA
1 AT-TTAATATTAA
38583288 ATTTAATATTAA
1 ATTTAATATTAA
38583300 A
1 A
38583301 GTTTTTAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
11 7 0.16
12 25 0.58
13 2 0.05
14 2 0.05
15 7 0.16
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:38583275 original size:59 final size:58
Alignment explanation
Indices: 38583165--38583295 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 58
38583155 TCCAAAAATA
* * * **
38583165 ATATTATTTTAAT-AGTTTAATATTAAATTTAATTTAATGTTTTTCTTGATAAACATT
1 ATATTATTTTAATAAGTTTAATATTAAATTTAATATAATATTTATCAAGATAAACATT
* *
38583222 CTATTATTTTAATAAGATTTAATATTAAATTTAATATAATATTTATCAAGATAAATATT
1 ATATTATTTTAATAAG-TTTAATATTAAATTTAATATAATATTTATCAAGATAAACATT
*
38583281 ATATTAAATTTAATA
1 ATATT-ATTTTAATA
38583296 TTAAAGTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 12 0.19
58 2 0.03
59 40 0.65
60 8 0.13
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTATTTTAATAAGTTTAATATTAAATTTAATATAATATTTATCAAGATAAACATT
Found at i:38585012 original size:41 final size:41
Alignment explanation
Indices: 38584966--38585049 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
38584956 TGTTGATTAG
*
38584966 TCCTTAGAGAATTGATCGTTTACTATTTTGACCAGGAAAGA
1 TCCTTAGAGAATTGATCATTTACTATTTTGACCAGGAAAGA
38585007 TCCTTAGAGAATTGATCATTTACTATTTTGACCAGGAAAGA
1 TCCTTAGAGAATTGATCATTTACTATTTTGACCAGGAAAGA
38585048 TC
1 TC
38585050 GTACGGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (41 bp):
TCCTTAGAGAATTGATCATTTACTATTTTGACCAGGAAAGA
Found at i:38587524 original size:226 final size:226
Alignment explanation
Indices: 38587130--38587584 Score: 910
Period size: 226 Copynumber: 2.0 Consensus size: 226
38587120 TACACATGTG
38587130 ACCTCACAATAGATCATTCGTATCGTTTCTATTCTGAAGGCTCAACCAGGAAATTCCTCACTTTC
1 ACCTCACAATAGATCATTCGTATCGTTTCTATTCTGAAGGCTCAACCAGGAAATTCCTCACTTTC
38587195 CAACATGTTACAAATTTATTCATAGTCCTTTTTCGATTTGCAATTTACAACAAAGAGTCATTCTA
66 CAACATGTTACAAATTTATTCATAGTCCTTTTTCGATTTGCAATTTACAACAAAGAGTCATTCTA
38587260 TAGGCAGCCACATTTCATATGACAACAAAATATAATAAAATAAAAAGAATCGATAAATTATTTAC
131 TAGGCAGCCACATTTCATATGACAACAAAATATAATAAAATAAAAAGAATCGATAAATTATTTAC
38587325 GTACAAACTTGTTGAAATCTCATCAGGTACA
196 GTACAAACTTGTTGAAATCTCATCAGGTACA
38587356 ACCTCACAATAGATCATTCGTATCGTTTCTATTCTGAAGGCTCAACCAGGAAATTCCTCACTTTC
1 ACCTCACAATAGATCATTCGTATCGTTTCTATTCTGAAGGCTCAACCAGGAAATTCCTCACTTTC
38587421 CAACATGTTACAAATTTATTCATAGTCCTTTTTCGATTTGCAATTTACAACAAAGAGTCATTCTA
66 CAACATGTTACAAATTTATTCATAGTCCTTTTTCGATTTGCAATTTACAACAAAGAGTCATTCTA
38587486 TAGGCAGCCACATTTCATATGACAACAAAATATAATAAAATAAAAAGAATCGATAAATTATTTAC
131 TAGGCAGCCACATTTCATATGACAACAAAATATAATAAAATAAAAAGAATCGATAAATTATTTAC
38587551 GTACAAACTTGTTGAAATCTCATCAGGTACA
196 GTACAAACTTGTTGAAATCTCATCAGGTACA
38587582 ACC
1 ACC
38587585 GTGTAGCAAT
Statistics
Matches: 229, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 229 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (226 bp):
ACCTCACAATAGATCATTCGTATCGTTTCTATTCTGAAGGCTCAACCAGGAAATTCCTCACTTTC
CAACATGTTACAAATTTATTCATAGTCCTTTTTCGATTTGCAATTTACAACAAAGAGTCATTCTA
TAGGCAGCCACATTTCATATGACAACAAAATATAATAAAATAAAAAGAATCGATAAATTATTTAC
GTACAAACTTGTTGAAATCTCATCAGGTACA
Found at i:38591347 original size:18 final size:18
Alignment explanation
Indices: 38591314--38591371 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
38591304 AAGGTTTTCT
38591314 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
38591329 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
* *
38591347 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
38591365 TATTGAT
1 TATTGAT
38591372 CGTGACCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
18 26 0.68
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:38592320 original size:28 final size:28
Alignment explanation
Indices: 38592280--38592345 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
38592270 CCATCGCAAA
* * * *
38592280 AACAGTATCAGGTGGGTCTTAGCCCAAT
1 AACAGAATCAGGTAGGCCTAAGCCCAAT
*
38592308 AACAGAATTAGGTAGGCCTAAGCCCAAT
1 AACAGAATCAGGTAGGCCTAAGCCCAAT
38592336 -ACAGAATCAG
1 AACAGAATCAG
38592346 TATCAGATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (28 bp):
AACAGAATCAGGTAGGCCTAAGCCCAAT
Found at i:38595016 original size:28 final size:27
Alignment explanation
Indices: 38594984--38595036 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
38594974 AATAGTATCG
* *
38594984 GGTGGGCCTTAGCCTAATAACAGAATTA
1 GGTGGGCCTAAGCCCAAT-ACAGAATTA
38595012 GGTGGGCCTAAGCCCAATACAGAAT
1 GGTGGGCCTAAGCCCAATACAGAAT
38595037 CAGTATCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTGGGCCTAAGCCCAATACAGAATTA
Found at i:38599070 original size:50 final size:50
Alignment explanation
Indices: 38598996--38599091 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
38598986 ATTTTGATTG
*
38598996 GGGGCAAAAAAAGTTTTTTGGCATCGCGATACCGAACATTTGGTATCGCT
1 GGGGCAAAAAAAGTTTTTAGGCATCGCGATACCGAACATTTGGTATCGCT
*
38599046 GGGGCCAAAAAAGTTTTTAGGCATCGCGATACCGAACATTTGGTAT
1 GGGGCAAAAAAAGTTTTTAGGCATCGCGATACCGAACATTTGGTAT
38599092 GTAAAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (50 bp):
GGGGCAAAAAAAGTTTTTAGGCATCGCGATACCGAACATTTGGTATCGCT
Found at i:38604552 original size:34 final size:33
Alignment explanation
Indices: 38604514--38604577 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
38604504 TAGCGGTAAC
*
38604514 AGTCTGGGCCTGAGCCCATTTCAGTATCAGTGGT
1 AGTCTGGACCTGAGCCCATTTCAGTA-CAGTGGT
* *
38604548 AGTCTGGACCTTAGCCTATTTCAGTACAGT
1 AGTCTGGACCTGAGCCCATTTCAGTACAGT
38604578 ATGCAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.31
Consensus pattern (33 bp):
AGTCTGGACCTGAGCCCATTTCAGTACAGTGGT
Found at i:38607339 original size:68 final size:67
Alignment explanation
Indices: 38607267--38607416 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
38607257 CATCATGTGT
* * * *
38607267 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
38607329 ATGTAG
62 ATGTAG
** * *
38607335 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
38607400 AG
66 AG
38607402 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
38607417 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:38607372 original size:64 final size:64
Alignment explanation
Indices: 38607291--38607474 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
38607281 AGACATTATG
* *
38607291 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
38607355 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
38607420 AA
63 AA
* * * *
38607422 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
38607475 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:38614597 original size:23 final size:23
Alignment explanation
Indices: 38614565--38614652 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
38614555 AACATGTAAT
* *
38614565 ATTCTGTTAAGCCTTTATGGCAC
1 ATTCTATTAAGCCTTTGTGGCAC
*
38614588 ATTCTATTAAGCCTTTGCGGC-C
1 ATTCTATTAAGCCTTTGTGGCAC
* * *
38614610 TATTTTATAAAGCCTTTGTGGCAT
1 -ATTCTATTAAGCCTTTGTGGCAC
*
38614634 ATTCTGTTAAGCCTTTGTG
1 ATTCTATTAAGCCTTTGTG
38614653 ATGCATTCTG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.02
23 52 0.98
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (23 bp):
ATTCTATTAAGCCTTTGTGGCAC
Found at i:38621842 original size:22 final size:22
Alignment explanation
Indices: 38621817--38621878 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
38621807 CCACGTTCAG
*
38621817 GCTATGGCTCAACACAGGGGCT
1 GCTACGGCTCAACACAGGGGCT
* * *
38621839 GCTACGGCTAAACATAAGGGCT
1 GCTACGGCTCAACACAGGGGCT
* *
38621861 GTTACGACTCAACACAGG
1 GCTACGGCTCAACACAGG
38621879 ATGTGTGTCA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (22 bp):
GCTACGGCTCAACACAGGGGCT
Found at i:38624453 original size:14 final size:15
Alignment explanation
Indices: 38624427--38624460 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
38624417 TAACTAATCT
38624427 AATAAATTAAAATAA
1 AATAAATTAAAATAA
38624442 AATAAA-TAAAATAA
1 AATAAATTAAAATAA
38624456 AATAA
1 AATAA
38624461 TATCTTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAATTAAAATAA
Found at i:38624459 original size:5 final size:5
Alignment explanation
Indices: 38624427--38624460 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
38624417 TAACTAATCT
*
38624427 AATAA ATTAA AATAA AAT-A AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA
38624461 TATCTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:38625057 original size:4 final size:4
Alignment explanation
Indices: 38625048--38625083 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
38625038 TCAAACAGTC
*
38625048 TTTA TTTA TTTA TTTA TTTA TTTA TTAA TATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
38625084 TTTGAAGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:38641024 original size:29 final size:27
Alignment explanation
Indices: 38640991--38641069 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 27
38640981 GGTTGGTTTT
38640991 CAGCACTAAGTGTGCGGGTTTAAATTGTA
1 CAGCACTAAGTGTGCGGGTTTAAA--GTA
*
38641020 CAGCACTAAGTGTGCGAGTTTAAAGTA
1 CAGCACTAAGTGTGCGGGTTTAAAGTA
38641047 CATGGCACTAAGTGTGCGCGGTT
1 CA--GCACTAAGTGTGCG-GGTT
38641070 GATTATTAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
27 5 0.11
29 37 0.82
30 3 0.07
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
CAGCACTAAGTGTGCGGGTTTAAAGTA
Found at i:38641337 original size:173 final size:174
Alignment explanation
Indices: 38641022--38641348 Score: 566
Period size: 173 Copynumber: 1.9 Consensus size: 174
38641012 AAATTGTACA
* *
38641022 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* * *
38641087 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
38641152 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
38641196 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
38641261 TGTGC-AACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
38641325 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
38641349 ACCTTGAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 80 0.56
174 64 0.44
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTATATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:38644413 original size:19 final size:19
Alignment explanation
Indices: 38644389--38644425 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
38644379 TGGATCAATC
38644389 GGCTTTCTTCTAGTAATTT
1 GGCTTTCTTCTAGTAATTT
38644408 GGCTTTCTTCTAGTAATT
1 GGCTTTCTTCTAGTAATT
38644426 CCTTGCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (19 bp):
GGCTTTCTTCTAGTAATTT
Found at i:38665110 original size:16 final size:18
Alignment explanation
Indices: 38665076--38665113 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38665066 ATCCTTATTT
*
38665076 AAATAAAATATAATGGTA
1 AAATAAAATATAATAGTA
38665094 AAATAAAATA-AA-AGTA
1 AAATAAAATATAATAGTA
38665110 AAAT
1 AAAT
38665114 CCAAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATAAAATATAATAGTA
Found at i:38669947 original size:11 final size:11
Alignment explanation
Indices: 38669928--38669960 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
38669918 ATTAAACCAT
*
38669928 TATTA-TTAAC
1 TATTATTTAAA
38669938 TATTATTTAAA
1 TATTATTTAAA
38669949 TATTATTTAAA
1 TATTATTTAAA
38669960 T
1 T
38669961 TGGATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTATTTAAA
Found at i:38670151 original size:13 final size:13
Alignment explanation
Indices: 38670135--38670160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38670125 AAAATTCCAT
38670135 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
38670148 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
38670161 GAAAGTTGCA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:38675997 original size:34 final size:34
Alignment explanation
Indices: 38675927--38675997 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 34
38675917 TGCTGGGTTG
* * **
38675927 TATGGCTGAGTGTTGTGCAAATGACGTGTTACTC
1 TATGGCTAAGTGTGGTGCAAATGACGAATTACTC
* * *
38675961 TATGGCTAAGTGTGGTTCAAATGATGAATTATTC
1 TATGGCTAAGTGTGGTGCAAATGACGAATTACTC
38675995 TAT
1 TAT
38675998 AGTTGAATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (34 bp):
TATGGCTAAGTGTGGTGCAAATGACGAATTACTC
Found at i:38677231 original size:72 final size:71
Alignment explanation
Indices: 38677155--38677297 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 71
38677145 TCGTAAATTG
*
38677155 ATCGTTTTAATAAAATGTTTGATTTAAAACAACGATTTTTGGTATACAAAGTTTAGAAAACAGGT
1 ATCGTTTTAATAAAATGTTTGATGTAAAACAACGATTTTTGGTATACAAAGTTTAGAAAACAGGT
38677220 TCAGCA
66 TCAGCA
* * * *
38677226 NATCGTTTTAATGAGATGTTTGATGTAAAACAACGATTTTTGGTCTACAAAGTTTAGAAAACGGG
1 -ATCGTTTTAATAAAATGTTTGATGTAAAACAACGATTTTTGGTATACAAAGTTTAGAAAACAGG
38677291 TTCAGCA
65 TTCAGCA
38677298 GTCGGTTACG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.34
Consensus pattern (71 bp):
ATCGTTTTAATAAAATGTTTGATGTAAAACAACGATTTTTGGTATACAAAGTTTAGAAAACAGGT
TCAGCA
Found at i:38677970 original size:13 final size:13
Alignment explanation
Indices: 38677952--38677977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38677942 AAATAAAGTG
38677952 ATAAAAATAAAAA
1 ATAAAAATAAAAA
38677965 ATAAAAATAAAAA
1 ATAAAAATAAAAA
38677978 TGCAAGACGC
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:38680648 original size:42 final size:42
Alignment explanation
Indices: 38680558--38680650 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
38680548 TACCGTATCA
*
38680558 ATGCCATATCCTGGACATGGTCTTACATGAAATATCATATCG
1 ATGCCATATCCTGGACATGGTCTTACATGAAATATCAAATCG
* * * *
38680600 ACGCCATGTCCTTGACATGGTCTTATATGAAATCA-CACAAT-G
1 ATGCCATATCCTGGACATGGTCTTACATGAAAT-ATCA-AATCG
38680642 ATGCCATAT
1 ATGCCATAT
38680651 ACCAGATATG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCTGGACATGGTCTTACATGAAATATCAAATCG
Found at i:38681754 original size:13 final size:13
Alignment explanation
Indices: 38681738--38681763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38681728 GCCCAAATGT
38681738 CAAAATTTTCAAA
1 CAAAATTTTCAAA
38681751 CAAAATTTTCAAA
1 CAAAATTTTCAAA
38681764 AAATCATTTC
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAAATTTTCAAA
Found at i:38683226 original size:44 final size:44
Alignment explanation
Indices: 38683150--38683269 Score: 116
Period size: 44 Copynumber: 2.7 Consensus size: 44
38683140 TCATTCCAAC
* * * * *
38683150 CCACTGCAATTTTCAGGAATATAAGAATTGTAA-TTTCAGTCTACT
1 CCACTGCAA-CTTCAGGGAGATCAGACTTGTAACTTT-AGTCTACT
* * * *
38683195 CCATTGTAACTTCAGGGAGATCAGACTTGTAACTTTTGTCTGCT
1 CCACTGCAACTTCAGGGAGATCAGACTTGTAACTTTAGTCTACT
* *
38683239 CCACTGCAACTTTAGGGAGATGAGACTTGTA
1 CCACTGCAACTTCAGGGAGATCAGACTTGTA
38683270 TCTTCAATTT
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
44 51 0.84
45 10 0.16
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATCAGACTTGTAACTTTAGTCTACT
Found at i:38683355 original size:51 final size:52
Alignment explanation
Indices: 38683300--38683412 Score: 176
Period size: 51 Copynumber: 2.2 Consensus size: 52
38683290 AACTTTAGAG
38683300 AGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTCA-GGA
1 AGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTCAGGGA
* * * *
38683351 AGATAAGATTTGTAACTTGTAGCTTTAATCTTTTCCATTGCAACTTTAGGGA
1 AGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTCAGGGA
38683403 A-ATAAGATTT
1 AGATAAGATTT
38683413 TCTATCTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (52 bp):
AGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTCAGGGA
Found at i:38683438 original size:45 final size:45
Alignment explanation
Indices: 38683189--38684093 Score: 314
Period size: 44 Copynumber: 19.8 Consensus size: 45
38683179 GTAATTTCAG
* * * * * * **
38683189 TCTACTCCATTGTAACTTCAGGGAGATCAGA-CTTGTAACTTTTG
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * * * *
38683233 TCTGCTCCACTGCAACTTTAGGGAGATGAGA-CTTGTATCTTCAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * *
38683277 TTTACT-CAGCTACAACTTTAGAGAGATAAGATTTGTAACTTGTAGCTTTAA
1 TCTACTCCA-CTGCAACTTTAGGGAGATAAGA--T-T---TTGTAGCTTTAA
** * * *
38683328 TCTGTTCCACTGCAAATTCAGGAAGATAAGATTTGTAACTTGTAGCTTTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGA--T-T---TTGTAGCTTTAA
** * * * *
38683379 TCTTTTCCATTGCAACTTTAGGGAAATAAGATTTTCTATCTTTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
** * * * *
38683424 TCTACTATACTGCAACTTCAGAGAGATGAGA-TTTGTAGCTTCAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * * *
38683468 CCTGCTCCACCGTAACTTTAGGGAGATAAGATATGCAACTTGTAGCTTTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGAT-T-----TTGTAGCTTTAA
* * ** *
38683519 TCTACTCCACTGCAACTTCAGGGAAATAAGATTCGGTA-TTTTCAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTT-AA
*
38683564 TCTACTCCATTGCAACTTTAGGGAGATAAGA--TT-T-G---T-A
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * ** * * * * * * *
38683601 TCTATTCCATTATAAATTCAGGGAGGTAA-AATTGGTAACTTTGA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
** * *
38683645 TCTTTTCCATTGCAACTTTAGGGAGATAAGATTTGTGGCTTTAAGCTTTAG
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTT-T-G---T-AGCTTTAA
* * * * * *
38683696 TCTATTCCACTACAACTTCA-GGAGATAAGGTTTGCTATGGTAGATCTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAA-GATT--T-T-GTAGCTTTAA
* * * * * *
38683745 TCTAAC-CTACTGCAACTTTAGAGG-TATAGGA-CTTGTCGCTTCAA
1 TCT-ACTCCACTGCAACTTTAG-GGAGATAAGATTTTGTAGCTTTAA
* * ** * * *
38683789 TCTACTCCATTGTAACTCCAAGGAGATAAGA-TTAGTAGCTTCAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * * * * *
38683833 TCTGCTCCACTGTAACTTCAGGGAGATAACA-TTAGTAGCTTCAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * * *
38683877 TCTATTCCACTGTAACTTCAGGGAGATAAGACTTGCTATGGTAGATTTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGA-TT--T-T-GTAGCTTTAA
* * * * * * * * *
38683927 TCTGAC-CTATTACAACTTCAGAGG-TATAGGA-CTTATCG-TTTCAA
1 TCT-ACTCCACTGCAACTTTAG-GGAGATAAGATTTTGTAGCTTT-AA
* **
38683971 TCTGCTCCACTTAAACTTTAGGGAGATAAGA-TTTGTAGCTTTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
* * *
38684015 TCTACTCTACTGCAACTTTAGAGAGATAAGA-TTTGCTATCTTTAA
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTG-TAGCTTTAA
**
38684060 TCTACTCCACTATAACTTTAGGGAGATAAGATTT
1 TCTACTCCACTGCAACTTTAGGGAGATAAGATTT
38684094 GCCATAATGA
Statistics
Matches: 644, Mismatches: 162, Indels: 108
0.70 0.18 0.12
Matches are distributed among these distances:
36 1 0.00
37 24 0.04
38 1 0.00
39 2 0.00
42 1 0.00
43 13 0.02
44 275 0.43
45 108 0.17
46 6 0.01
47 1 0.00
48 2 0.00
49 21 0.03
50 42 0.07
51 141 0.22
52 2 0.00
53 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (45 bp):
TCTACTCCACTGCAACTTTAGGGAGATAAGATTTTGTAGCTTTAA
Found at i:38683551 original size:95 final size:96
Alignment explanation
Indices: 38683418--38683595 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
38683408 GATTTTCTAT
* * * * * *
38683418 CTTTAATCTACTATACTGCAACTTCAGAGAGATGAGATT-TGTAGCTTCAACCTGCTCCACCGTA
1 CTTTAATCTACTACACTGCAACTTCAGAGAAATAAGATTCGGTAGCTTCAACCTACTCCACCGCA
38683482 ACTTTAGGGAGATAAGATATGCAACTTGTAG
66 ACTTTAGGGAGATAAGATATGCAACTTGTAG
* * ** * **
38683513 CTTTAATCTACTCCACTGCAACTTCAGGGAAATAAGATTCGGTATTTTCAATCTACTCCATTGCA
1 CTTTAATCTACTACACTGCAACTTCAGAGAAATAAGATTCGGTAGCTTCAACCTACTCCACCGCA
38683578 ACTTTAGGGAGATAAGAT
66 ACTTTAGGGAGATAAGAT
38683596 TTGTATCTAT
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
95 34 0.49
96 35 0.51
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (96 bp):
CTTTAATCTACTACACTGCAACTTCAGAGAAATAAGATTCGGTAGCTTCAACCTACTCCACCGCA
ACTTTAGGGAGATAAGATATGCAACTTGTAG
Found at i:38683970 original size:94 final size:93
Alignment explanation
Indices: 38683709--38684144 Score: 284
Period size: 94 Copynumber: 4.8 Consensus size: 93
38683699 ATTCCACTAC
* * * *
38683709 AACTTCA-GGAGATAAGGTTTGCTATGGTAGATCTAATCTAACCTACTGCAACTTTAGAGGTATA
1 AACTTCAGGGAGATAA-GATTGCTATGGTAGATTTAATCTGACCTACTGCAACTTCAGAGGTATA
* *
38683773 GGACTTGTCGCTTCAATCTACTCCATTGT
65 GGACTTATCGCTTCAATCTACTCCACTGT
* * * * * * *
38683802 AACTCCAAGGAGATAAGA-T--TA--GTAGCTTCAATCTG-CTCCACTGTAACTTCAG-GGAGAT
1 AACTTCAGGGAGATAAGATTGCTATGGTAGATTTAATCTGAC-CTACTGCAACTTCAGAGG-TAT
* *
38683860 A--ACATTAGTAGCTTCAATCTATTCCACTGT
64 AGGAC-TTA-TCGCTTCAATCTACTCCACTGT
* *
38683890 AACTTCAGGGAGATAAGACTTGCTATGGTAGATTTAATCTGACCTATTACAACTTCAGAGGTATA
1 AACTTCAGGGAGATAAGA-TTGCTATGGTAGATTTAATCTGACCTACTGCAACTTCAGAGGTATA
* *
38683955 GGACTTATCGTTTCAATCTGCTCCACT-T
65 GGACTTATCGCTTCAATCTACTCCACTGT
* * *
38683983 AAACTTTAGGGAGATAAGA-T--T-T-GTAGCTTTAATCT-ACTCTACTGCAACTTTAGAGAG-A
1 -AACTTCAGGGAGATAAGATTGCTATGGTAGATTTAATCTGAC-CTACTGCAACTTCAGAG-GTA
* * * ** * *
38684041 TAAGATTTGCTATCTTTAATCTACTCCACTAT
63 TAGGACTT-ATCGCTTCAATCTACTCCACTGT
* * ** * *
38684073 AACTTTAGGGAGATAAGATTTGCCATAAT-GATTTCAATC-CATCTACTGCAACTTCA-AGGGTA
1 AACTTCAGGGAGATAAGA-TTGCTATGGTAGATTT-AATCTGACCTACTGCAACTTCAGA-GGTA
*
38684135 TAGGATTTAT
63 TAGGACTTAT
38684145 GGTTTCTCTG
Statistics
Matches: 266, Mismatches: 47, Indels: 60
0.71 0.13 0.16
Matches are distributed among these distances:
86 2 0.01
87 7 0.03
88 93 0.35
89 35 0.13
90 5 0.02
91 1 0.00
92 4 0.02
93 11 0.04
94 94 0.35
95 12 0.05
96 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (93 bp):
AACTTCAGGGAGATAAGATTGCTATGGTAGATTTAATCTGACCTACTGCAACTTCAGAGGTATAG
GACTTATCGCTTCAATCTACTCCACTGT
Found at i:38684002 original size:182 final size:183
Alignment explanation
Indices: 38683696--38684095 Score: 509
Period size: 182 Copynumber: 2.2 Consensus size: 183
38683686 TAAGCTTTAG
* * *
38683696 TCTATTCCACTACAACTTCA-GGAGATAAGGTTTGCTATGGTAGATCTAATCTAACCTACTGCAA
1 TCTATTCCACTATAACTTCAGGGAGATAAGATTTGCTATGGTAGATCTAATCTAACCTACTACAA
* * *
38683760 CTTTAGAGGTATAGGACTTGTCGCTTCAATCTACTCCATTGTAACTCCAAGGAGATAAGATTAGT
66 CTTCAGAGGTATAGGACTTATCGCTTCAATCTACTCCATTGAAACTCCAAGGAGATAAGATTAGT
* * *
38683825 AGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAACATTAG-TAGCTTCAA
131 AGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAACATTAGCTAGCTTCAA
* * * * *
38683877 TCTATTCCACTGTAACTTCAGGGAGATAAGACTTGCTATGGTAGATTTAATCTGACCTATTACAA
1 TCTATTCCACTATAACTTCAGGGAGATAAGATTTGCTATGGTAGATCTAATCTAACCTACTACAA
* * ** * *
38683942 CTTCAGAGGTATAGGACTTATCGTTTCAATCTGCTCCACTT-AAACTTTAGGGAGATAAGATTTG
66 CTTCAGAGGTATAGGACTTATCGCTTCAATCTACTCCA-TTGAAACTCCAAGGAGATAAGATTAG
* * * * * * *
38684006 TAGCTTTAATCTACTCTACTGCAACTTTAGAGAGATAAGATTTGCTATCTTTAA
130 TAGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAACATTAGCTAGCTTCAA
* *
38684060 TCTACTCCACTATAACTTTAGGGAGATAAGATTTGC
1 TCTATTCCACTATAACTTCAGGGAGATAAGATTTGC
38684096 CATAATGATT
Statistics
Matches: 185, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
181 18 0.10
182 126 0.68
183 41 0.22
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (183 bp):
TCTATTCCACTATAACTTCAGGGAGATAAGATTTGCTATGGTAGATCTAATCTAACCTACTACAA
CTTCAGAGGTATAGGACTTATCGCTTCAATCTACTCCATTGAAACTCCAAGGAGATAAGATTAGT
AGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAACATTAGCTAGCTTCAA
Found at i:38684094 original size:45 final size:44
Alignment explanation
Indices: 38683960--38684095 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 44
38683950 GTATAGGACT
*
38683960 TATCGTTTCAATCTGCTCCACTTAAACTTTAGGGAGATAAGATTTG-
1 TATC-TTT-AATCTACTCCACTT-AACTTTAGGGAGATAAGATTTGC
* * * *
38684006 TAGCTTTAATCTACTCTACTGCAACTTTAGAGAGATAAGATTTGC
1 TATCTTTAATCTACTCCACT-TAACTTTAGGGAGATAAGATTTGC
38684051 TATCTTTAATCTACTCCACTATAACTTTAGGGAGATAAGATTTGC
1 TATCTTTAATCTACTCCACT-TAACTTTAGGGAGATAAGATTTGC
38684096 CATAATGATT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
44 32 0.41
45 43 0.55
46 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (44 bp):
TATCTTTAATCTACTCCACTTAACTTTAGGGAGATAAGATTTGC
Found at i:38684127 original size:182 final size:182
Alignment explanation
Indices: 38683696--38684150 Score: 470
Period size: 182 Copynumber: 2.5 Consensus size: 182
38683686 TAAGCTTTAG
* * ** * ** * *
38683696 TCTATTCCACTACAACTTCA-GGAGATAAGGTTTGCTATGGTAGATCTAATCTAACCTACTGCAA
1 TCTACTCCACTATAACTTCAGGGAGATAAGACTTGCCATAATAGATTTAATCTCACCTACTGCAA
* * * *
38683760 CTTTAGAGGTATAGGACTTGTCGCTTCAATCTACTCCATTGTAACTCCAAGGAGATAAGATTAGT
66 CTTCAGAGGTATAGGACTTATCGTTTCAATCTACTCCATTGAAACTCCAAGGAGATAAGATTAGT
* * *
38683825 AGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAACATTAGTAGCTTCAA
131 AGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAACATTAGTAGCTTCAA
* * * ** * * *
38683877 TCTATTCCACTGTAACTTCAGGGAGATAAGACTTGCTATGGTAGATTTAATCTGACCTATTACAA
1 TCTACTCCACTATAACTTCAGGGAGATAAGACTTGCCATAATAGATTTAATCTCACCTACTGCAA
* ** * *
38683942 CTTCAGAGGTATAGGACTTATCGTTTCAATCTGCTCCACTT-AAACTTTAGGGAGATAAGATTTG
66 CTTCAGAGGTATAGGACTTATCGTTTCAATCTACTCCA-TTGAAACTCCAAGGAGATAAGATTAG
* * * * * * *
38684006 TAGCTTTAATCTACTCTACTGCAACTTTAGAGAGATAAGATTTGCTATCTTTAA
130 TAGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAACATTAG-TAGCTTCAA
* * *
38684060 TCTACTCCACTATAACTTTAGGGAGATAAGATTTGCCATAAT-GATTTCAATC-CATCTACTGCA
1 TCTACTCCACTATAACTTCAGGGAGATAAGACTTGCCATAATAGATTT-AATCTCACCTACTGCA
* *
38684123 ACTTCA-AGGGTATAGGATTTATGGTTTC
65 ACTTCAGA-GGTATAGGACTTATCGTTTC
38684151 TCTGATCTTG
Statistics
Matches: 229, Mismatches: 40, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
181 19 0.08
182 162 0.71
183 48 0.21
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (182 bp):
TCTACTCCACTATAACTTCAGGGAGATAAGACTTGCCATAATAGATTTAATCTCACCTACTGCAA
CTTCAGAGGTATAGGACTTATCGTTTCAATCTACTCCATTGAAACTCCAAGGAGATAAGATTAGT
AGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAACATTAGTAGCTTCAA
Found at i:38687169 original size:12 final size:13
Alignment explanation
Indices: 38687147--38687175 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38687137 TAATTAAATG
38687147 AATTAAAAAGCCA
1 AATTAAAAAGCCA
38687160 AATT-AAAAGCCA
1 AATTAAAAAGCCA
38687172 AATT
1 AATT
38687176 TTGTCCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTAAAAAGCCA
Found at i:38688082 original size:42 final size:42
Alignment explanation
Indices: 38688010--38688130 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 42
38688000 ACATTAGGGT
* *
38688010 TACTAAGATTATGTGTAATACCATATCTGGGATATGGCATCGA
1 TACT-AGATTACGTGTAAGACCATATCTGGGATATGGCATCGA
* *
38688053 TA-TGAGACTT-CGTGTAAGACCATAGCTGGGCTATTGGCATCGA
1 TACT-AGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGA
* *
38688096 TACTAGATTACATGTAAGACTATATCTGGGATATG
1 TACTAGATTACGTGTAAGACCATATCTGGGATATG
38688131 ACATTGGTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
42 27 0.42
43 37 0.57
44 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (42 bp):
TACTAGATTACGTGTAAGACCATATCTGGGATATGGCATCGA
Found at i:38701825 original size:13 final size:13
Alignment explanation
Indices: 38701807--38701832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38701797 AAATAAAGTG
38701807 ATAAAAATAAAAA
1 ATAAAAATAAAAA
38701820 ATAAAAATAAAAA
1 ATAAAAATAAAAA
38701833 TGCAAGATGC
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:38702024 original size:4 final size:4
Alignment explanation
Indices: 38701992--38702045 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
38701982 ATCTTGTTTG
* * * * *
38701992 TAAA TATA TAAA -AAA TAAG CAAG TAAA TAAA TAAA TAGA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
38702039 TAAA TAA
1 TAAA TAA
38702046 TAGTTATAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:38706181 original size:29 final size:29
Alignment explanation
Indices: 38706139--38706227 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
38706129 AAAGCATGAC
* *
38706139 TATGTATGTGATTTGGGCCTAATGGGCGA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
*
38706168 TATGAATGTGATTTGAGCCTAATGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
* **
38706197 TATGAATGAGA-TTGGGCCTTGTGGGCCA
1 TATGAATGTGATTTGGGCCTAATGGGCCA
38706225 TAT
1 TAT
38706228 ACATATATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 17 0.32
29 36 0.68
ACGTcount: A:0.24, C:0.12, G:0.31, T:0.33
Consensus pattern (29 bp):
TATGAATGTGATTTGGGCCTAATGGGCCA
Found at i:38713287 original size:140 final size:140
Alignment explanation
Indices: 38712346--38713212 Score: 1734
Period size: 140 Copynumber: 6.2 Consensus size: 140
38712336 TTTGTGCGCT
38712346 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
38712411 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
66 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
38712476 GATGTAAGCC
131 GATGTAAGCC
38712486 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
38712551 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
66 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
38712616 GATGTAAGCC
131 GATGTAAGCC
38712626 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
38712691 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
66 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
38712756 GATGTAAGCC
131 GATGTAAGCC
38712766 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
38712831 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
66 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
38712896 GATGTAAGCC
131 GATGTAAGCC
38712906 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
38712971 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
66 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
38713036 GATGTAAGCC
131 GATGTAAGCC
38713046 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
38713111 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
66 GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
38713176 GATGTAAGCC
131 GATGTAAGCC
38713186 AGTGTAAGACATGTCTGGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
38713213 CGGCTATGAG
Statistics
Matches: 727, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 727 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATTAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
GATATGGCAATGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGGGGCATGCGTCGGCCTCGA
GATGTAAGCC
Found at i:38723728 original size:94 final size:94
Alignment explanation
Indices: 38723567--38724470 Score: 1767
Period size: 94 Copynumber: 9.6 Consensus size: 94
38723557 TCATTTGTGC
38723567 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38723632 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38723661 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38723726 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38723755 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38723820 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38723849 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38723914 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38723943 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38724008 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38724037 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38724102 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38724131 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38724196 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38724225 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38724290 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
38724319 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
38724384 TAGGACATGGCAACGACATTGAGACGAGA
66 TAGGACATGGCAACGACATTGAGACGAGA
*
38724413 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGTA-AGCCAGTGTAAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCCAGTGTAAGA
38724471 GATGTCTGAG
Statistics
Matches: 807, Mismatches: 1, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
94 805 1.00
95 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGAACATGTC
TAGGACATGGCAACGACATTGAGACGAGA
Found at i:38724665 original size:96 final size:97
Alignment explanation
Indices: 38723570--38724684 Score: 413
Period size: 94 Copynumber: 11.8 Consensus size: 97
38723560 TTTGTGCGCT
* * * * *
38723570 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGTC
* * * * *** *
38723632 TAGGACATGGCAACGACATTGA-GACGAGAG-C
65 TAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38723663 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38723725 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38723757 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38723819 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38723851 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38723913 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38723945 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38724007 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38724039 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38724101 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38724133 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38724195 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38724227 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38724289 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* * * * *
38724321 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTATGAGAGCCAGTGTAAGAACATGT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGA-TGTGAGAGCCAGTGTAAGACCATGT
* * * * *** *
38724383 CTAGGACATGGCAACGACATTGA-GACGAGAG-C
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
* *
38724415 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-GAGATGT-A-AGCCAGTGTAAGA-GAT
1 -AGTGTAAGACCATGTCTGGGACATGGCATC-G--ACTTAGATGTGAGAGCCAGTGTAAGACCAT
** *
38724474 GTCTGAGG-CAT-GCATCGG-CT--A-TGAGATGTGTC
62 GTCT-AGGACATGGCATCGGCCTCGATTTTGAT-AGTC
* * * * **
38724506 CGTGTCAGACCATGTTTGGGACATGGCATTGGGTTGAAGATGTGAGAGCCAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTT--AGATGTGAGAGCCAGTGTAAGACCATGT
*
38724571 CTGGGACATGGCATCGGCCTCGATTTTGATAGTC
64 CTAGGACATGGCATCGGCCTCGATTTTGATAGTC
*
38724605 AGTGTAAGACCATGTCTGGGACATGGCATCGACTT-GATG-GATGAGCTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGATGTGA-GAGCCAGTGTAAGACCATGTC
38724668 TAGGACATGGCATCGGC
65 TAGGACATGGCATCGGC
38724685 ATTACACCCT
Statistics
Matches: 967, Mismatches: 33, Indels: 40
0.93 0.03 0.04
Matches are distributed among these distances:
89 3 0.00
90 8 0.01
91 16 0.02
92 15 0.02
93 10 0.01
94 811 0.84
95 13 0.01
96 49 0.05
97 5 0.01
99 33 0.03
100 4 0.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTAGATGTGAGAGCCAGTGTAAGACCATGTCT
AGGACATGGCATCGGCCTCGATTTTGATAGTC
Found at i:38729852 original size:20 final size:20
Alignment explanation
Indices: 38729807--38729853 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
38729797 TTACTTTGCT
*
38729807 TTTCTTTTTAGGATATTTTAA
1 TTTC-TTTTAAGATATTTTAA
*
38729828 GTTCTTTTAAGATATTTCT-A
1 TTTCTTTTAAGATATTT-TAA
38729848 TTTCTT
1 TTTCTT
38729854 GCATAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTCTTTTAAGATATTTTAA
Found at i:38731373 original size:40 final size:40
Alignment explanation
Indices: 38731344--38731489 Score: 118
Period size: 40 Copynumber: 3.6 Consensus size: 40
38731334 GCTCCTCGTT
*
38731344 CAAATGCCTTCGGGACATAGCCCGGATATAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAACAACTCGCA
* * * ** *
38731384 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATATAACAACTCGCA
* * * * *
38731424 CAAAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATATA-ACAAC-TCGCA
* *
38731465 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
38731490 CAGCATTCAA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
39 3 0.04
40 71 0.84
41 11 0.13
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATATAACAACTCGCA
Found at i:38739206 original size:40 final size:40
Alignment explanation
Indices: 38739153--38739384 Score: 374
Period size: 40 Copynumber: 5.8 Consensus size: 40
38739143 CAGCCGCAAA
* * * *
38739153 CATATTTGCCTTCGGGTCTTAACCCGGACATATGAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
38739193 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCCCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
38739233 CATAATTGCCTTCGGGTCATAGCCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
*
38739273 CATAATTGCCTTCGGGTCTTAGCCCGGATATGTCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
* *
38739313 CATAATTGCCTTCGGGTCATAACCCGGATATATCAACTCG
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
38739353 CATAATTGCCTTCGGGTCTTAGCCCGGATATA
1 CATAATTGCCTTCGGGTCTTAGCCCGGATATA
38739385 ATCCAATGTT
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 176 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
CATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCG
Found at i:38742549 original size:21 final size:22
Alignment explanation
Indices: 38742523--38742566 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
38742513 CCCATTTCAT
38742523 TGGAGATG-TTTCTTTGATTCC
1 TGGAGATGTTTTCTTTGATTCC
38742544 TGGAGATGTTTTCTTTGATTCC
1 TGGAGATGTTTTCTTTGATTCC
38742566 T
1 T
38742567 TTTGCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (22 bp):
TGGAGATGTTTTCTTTGATTCC
Found at i:38752062 original size:36 final size:36
Alignment explanation
Indices: 38752019--38752090 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
38752009 CCAAATACGC
38752019 CACCTACCTCCACTACACCTATCCCATCACATTCAA
1 CACCTACCTCCACTACACCTATCCCATCACATTCAA
* *
38752055 CACCTACCTCCACTACACCTTTTCCATCACATTCAA
1 CACCTACCTCCACTACACCTATCCCATCACATTCAA
38752091 TGTCTCACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.25
Consensus pattern (36 bp):
CACCTACCTCCACTACACCTATCCCATCACATTCAA
Found at i:38755139 original size:21 final size:21
Alignment explanation
Indices: 38755110--38755158 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
38755100 ATCTTGATAA
38755110 TAATCATAGTAATTTATATATT
1 TAAT-ATAGTAATTTATATATT
38755132 TAATATAGTAATTTATATATT
1 TAATATAGTAATTTATATATT
38755153 TAATAT
1 TAATAT
38755159 TTATTTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
TAATATAGTAATTTATATATT
Found at i:38755636 original size:28 final size:28
Alignment explanation
Indices: 38755604--38755676 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 28
38755594 ATATTTAATG
*
38755604 TAATTATATATGCTTTAATTAATGATAA
1 TAATTATACATGCTTTAATTAATGATAA
* *
38755632 TAATTACACATGCGTCCTTTGATTAATGATAA
1 TAATTATACAT--G--CTTTAATTAATGATAA
38755664 TAATTATACATGC
1 TAATTATACATGC
38755677 GTCCTTACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 10 0.27
30 2 0.05
32 25 0.68
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (28 bp):
TAATTATACATGCTTTAATTAATGATAA
Found at i:38755662 original size:32 final size:32
Alignment explanation
Indices: 38755616--38755682 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
38755606 ATTATATATG
38755616 CTTTAATTAATGATAATAATTACACATGCGTC
1 CTTTAATTAATGATAATAATTACACATGCGTC
* *
38755648 CTTTGATTAATGATAATAATTATACATGCGTC
1 CTTTAATTAATGATAATAATTACACATGCGTC
38755680 CTT
1 CTT
38755683 ACTTCCTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (32 bp):
CTTTAATTAATGATAATAATTACACATGCGTC
Found at i:38755760 original size:5 final size:5
Alignment explanation
Indices: 38755750--38755782 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
38755740 CTAAATACAA
38755750 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
38755783 GATACATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:38760211 original size:18 final size:19
Alignment explanation
Indices: 38760188--38760225 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
38760178 GGAAGCAAGC
*
38760188 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
38760206 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
38760225 A
1 A
38760226 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:38769212 original size:35 final size:35
Alignment explanation
Indices: 38769171--38769330 Score: 203
Period size: 35 Copynumber: 4.6 Consensus size: 35
38769161 AAATGTGACT
* * * *
38769171 TTAAAAAGGTTGGGATAAACTCGTTTAAGTCAACC
1 TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
* *
38769206 TTAAAAAAGTTGGGATACACCCGTCTAAGGCAACC
1 TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
* * * **
38769241 TTAAAAAGGTTGAGATAGATCCGTCTAAGGAAATT
1 TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
38769276 TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
1 TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
**
38769311 TTAAAAATATTGGGATAGAC
1 TTAAAAAGGTTGGGATAGAC
38769331 ATGTCTAATG
Statistics
Matches: 106, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 106 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (35 bp):
TTAAAAAGGTTGGGATAGACCCGTCTAAGGCAACC
Found at i:38771578 original size:9 final size:9
Alignment explanation
Indices: 38771563--38771596 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
38771553 ATATCCATTA
38771563 CTTCTTTTT
1 CTTCTTTTT
*
38771572 TTTCTTTTT
1 CTTCTTTTT
*
38771581 CTTCTTCTT
1 CTTCTTTTT
38771590 CTTCTTT
1 CTTCTTT
38771597 AGCTGTGCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
CTTCTTTTT
Found at i:38772632 original size:140 final size:140
Alignment explanation
Indices: 38772380--38772642 Score: 393
Period size: 140 Copynumber: 1.9 Consensus size: 140
38772370 AAAAGTCGGC
* * *
38772380 ATAGTGTTAGACAAGGGCGACTCTTATTTAAGTGTTGCCTTAGGCATGCATATCCCAACCATTAT
1 ATAGTGTTAGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGACATGCATATCCCAACCATTAT
* * *
38772445 ACAAAAAGTTGGCCAAAGCGTATGTCTGCAAGTTTATCCCAACACTTAGGAAAATGTCAGCCCAA
66 ACAAAAAGTTGGCCAAAGCATATATCTGCAAGTCTATCCCAACACTTAGGAAAATGTCAGCCCAA
38772510 AAGTACCGGT
131 AAGTACCGGT
* * * * *
38772520 ATAGTGTTGGACAAAGCCGACTGTTATTTAAGTTTTGCCTTAGACATGCATATCGCAACCCTTAT
1 ATAGTGTTAGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGACATGCATATCCCAACCATTAT
* *
38772585 ACAAAGAGTTGGCCAAAGCATATAT-TGGCAAGTCTATCCCAACACTTAGGAAACTGTC
66 ACAAAAAGTTGGCCAAAGCATATATCT-GCAAGTCTATCCCAACACTTAGGAAAATGTC
38772643 GACCCAGAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
139 1 0.01
140 108 0.99
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (140 bp):
ATAGTGTTAGACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGACATGCATATCCCAACCATTAT
ACAAAAAGTTGGCCAAAGCATATATCTGCAAGTCTATCCCAACACTTAGGAAAATGTCAGCCCAA
AAGTACCGGT
Found at i:38773301 original size:17 final size:17
Alignment explanation
Indices: 38773279--38773313 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38773269 TGGCATCAAA
38773279 TATTCATCAAAATACAC
1 TATTCATCAAAATACAC
* *
38773296 TATTCATGAGAATACAC
1 TATTCATCAAAATACAC
38773313 T
1 T
38773314 TCGAAGTAGC
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:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (17 bp):
TATTCATCAAAATACAC
Found at i:38777630 original size:19 final size:19
Alignment explanation
Indices: 38777606--38777644 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38777596 GAGACTGTGC
38777606 GGGAACCCCTGGATCGTGT
1 GGGAACCCCTGGATCGTGT
38777625 GGGAACCCCTGGATCGTGT
1 GGGAACCCCTGGATCGTGT
38777644 G
1 G
38777645 AAGGGGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (19 bp):
GGGAACCCCTGGATCGTGT
Found at i:38781705 original size:26 final size:24
Alignment explanation
Indices: 38781663--38781710 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
38781653 AAAACTATTA
38781663 AAAAATAGAAAAAATAAATTTAGT
1 AAAAATAGAAAAAATAAATTTAGT
*
38781687 AAAAATATAAAAATTATAAATTTA
1 AAAAATAGAAAAA--ATAAATTTA
38781711 AAAAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
26 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAATAGAAAAAATAAATTTAGT
Found at i:38781897 original size:36 final size:36
Alignment explanation
Indices: 38781850--38781921 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
38781840 ACATTTAGTA
38781850 GAGTTTGAACATAAGATTATTATCTCTTGGAATGTC
1 GAGTTTGAACATAAGATTATTATCTCTTGGAATGTC
*
38781886 GAGTTTGAACATAAGATTATTATTTCTTGGAATGTC
1 GAGTTTGAACATAAGATTATTATCTCTTGGAATGTC
38781922 ACATTCCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (36 bp):
GAGTTTGAACATAAGATTATTATCTCTTGGAATGTC
Found at i:38784588 original size:13 final size:13
Alignment explanation
Indices: 38784570--38784595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38784560 GGTTTTATTC
38784570 AAAATGAAAATGA
1 AAAATGAAAATGA
38784583 AAAATGAAAATGA
1 AAAATGAAAATGA
38784596 CCTGAAAATA
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Done.