Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 116 of 136
Found at i:39373227 original size:22 final size:19
Alignment explanation
Indices: 39373196--39373242 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
39373186 AAAGATGATA
39373196 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
39373219 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
39373238 ATTAT
1 ATTAT
39373243 CAGTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:39373238 original size:16 final size:15
Alignment explanation
Indices: 39373198--39373239 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
39373188 AGATGATAAT
39373198 TATTAATATATAATTA
1 TATTAAT-TATAATTA
39373214 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
39373230 TATTAATTAT
1 TATTAATTAT
39373240 TATCAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:39380697 original size:27 final size:27
Alignment explanation
Indices: 39380662--39380759 Score: 169
Period size: 27 Copynumber: 3.6 Consensus size: 27
39380652 CATTAAACAT
*
39380662 ACAGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAAGGGCATA
*
39380689 ATAGTCATTTTATAACATAAGGGCATA
1 ACAGTCATTTTATAACATAAGGGCATA
39380716 ACAGTCATTTTATAACATAAGGGCATA
1 ACAGTCATTTTATAACATAAGGGCATA
*
39380743 ACCGTCATTTTATAACA
1 ACAGTCATTTTATAACA
39380760 GTTTGGGGGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAAGGGCATA
Found at i:39388235 original size:27 final size:27
Alignment explanation
Indices: 39388195--39388323 Score: 190
Period size: 27 Copynumber: 4.8 Consensus size: 27
39388185 ATAACATTAA
* *
39388195 GCATAA-ATTCATTTTCTAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
*
39388221 GCATGATAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
39388248 GCATAATAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
*
39388275 GCATAACAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
*
39388302 GCATAACCA-TCATTTTATAACA
1 GCATAA-TAGTCATTTTATAACA
39388324 GTTTGGGGGT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
26 5 0.05
27 89 0.93
28 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (27 bp):
GCATAATAGTCATTTTATAACATAGGG
Found at i:39399922 original size:50 final size:50
Alignment explanation
Indices: 39399807--39400100 Score: 417
Period size: 50 Copynumber: 5.9 Consensus size: 50
39399797 GATCATAACA
* ** * **
39399807 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* ** *
39399858 TGCCCATACCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
39399908 TGCCAACGCCATGTCCGAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
39399958 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
39400008 TGACAACGCCATGTACCAGACAAGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
39400058 TGCCAACGACATGTCCCAGACATGGTTTTACATTGGACCTCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC
39400101 TACCTAAATG
Statistics
Matches: 217, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
50 184 0.85
51 33 0.15
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:39401506 original size:33 final size:33
Alignment explanation
Indices: 39401422--39401526 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 33
39401412 AGACAAAAAC
39401422 AATATTC-AGCAAACACAATGAATGGGGAGAAG-
1 AATATTCGA-CAAACACAATGAATGGGGAGAAGT
* * * *
39401454 AGGT-TTCGGCAAACGCAATGAATGGAGAGAAGT
1 A-ATATTCGACAAACACAATGAATGGGGAGAAGT
* *
39401487 CATATTCGACAAACTCAATGAATGGGGAGAAGT
1 AATATTCGACAAACACAATGAATGGGGAGAAGT
39401520 AATATTC
1 AATATTC
39401527 AGGAAAGGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
32 26 0.44
33 33 0.56
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (33 bp):
AATATTCGACAAACACAATGAATGGGGAGAAGT
Found at i:39404845 original size:12 final size:13
Alignment explanation
Indices: 39404828--39404856 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39404818 AGATGAGCAA
39404828 AATTTGGC-TTTT
1 AATTTGGCTTTTT
39404840 AATTTGGCTTTTT
1 AATTTGGCTTTTT
39404853 AATT
1 AATT
39404857 CATTTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (13 bp):
AATTTGGCTTTTT
Found at i:39406113 original size:17 final size:17
Alignment explanation
Indices: 39406080--39406114 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39406070 CTACAGGGGT
* *
39406080 CACACAGCCGTGTGACA
1 CACACAGCCGAGAGACA
39406097 CACACAGCCGAGAGACA
1 CACACAGCCGAGAGACA
39406114 C
1 C
39406115 GCCCGTGTCT
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:0.34, C:0.37, G:0.23, T:0.06
Consensus pattern (17 bp):
CACACAGCCGAGAGACA
Found at i:39407524 original size:25 final size:25
Alignment explanation
Indices: 39407444--39407562 Score: 91
Period size: 25 Copynumber: 4.8 Consensus size: 25
39407434 ATGTATGCTT
* * *
39407444 ATACGAGCTGTA-AATGGTAAGCTC
1 ATACGAGCTGAATAACGATAAGCTC
* * * *
39407468 TTCCGAGATGAATAACGATAAACTC
1 ATACGAGCTGAATAACGATAAGCTC
* * *
39407493 CTCCGAGCTGAATAACGGTAAGCTC
1 ATACGAGCTGAATAACGATAAGCTC
*
39407518 ATACGAGCT-AAGTATCGATAAGCTC
1 ATACGAGCTGAA-TAACGATAAGCTC
* *
39407543 ATATGAGCTGAA-ATCGATAA
1 ATACGAGCTGAATAACGATAA
39407563 CACTAATGAC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
24 18 0.24
25 56 0.74
26 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (25 bp):
ATACGAGCTGAATAACGATAAGCTC
Found at i:39408622 original size:151 final size:151
Alignment explanation
Indices: 39408405--39408706 Score: 532
Period size: 151 Copynumber: 2.0 Consensus size: 151
39408395 GAAATCGCGC
* *
39408405 CCTCGTGGACGCGATTTTGCTACAGTAGCAAGTTTGGGCTGAGGCTATAAATTAGGCAGAAAATG
1 CCTCGTGGACACGATTTTGCTACAGTAGCAAGTTTGGACTGAGGCTATAAATTAGGCAGAAAATG
*
39408470 TTCTTAGAATGCATAAGTCATAGCAGAAAAAATTTAGAGAGGCTAAGAAAGTTAGAATTTCAAAA
66 TTCTTAGAATGCATAAGTCATAGCAGAAAAAATTTAGAGAGCCTAAGAAAGTTAGAATTTCAAAA
39408535 TGAGTGAACGTATTAGTGCTG
131 TGAGTGAACGTATTAGTGCTG
*
39408556 CCTCGTGGACACGATTTTGCTACAGTAGCAAGTTTGGACTGAGGCTATAAATTAGGCAGAACATG
1 CCTCGTGGACACGATTTTGCTACAGTAGCAAGTTTGGACTGAGGCTATAAATTAGGCAGAAAATG
* * * *
39408621 TTGTTAGAATTCATAAGTCATAGCAGAAACAATTTAGAGAGCCTAAGAAAGTTAGAGTTTCAAAA
66 TTCTTAGAATGCATAAGTCATAGCAGAAAAAATTTAGAGAGCCTAAGAAAGTTAGAATTTCAAAA
39408686 TGAGTGAACGTATTAGTGCTG
131 TGAGTGAACGTATTAGTGCTG
39408707 TTATTTACTA
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
151 143 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (151 bp):
CCTCGTGGACACGATTTTGCTACAGTAGCAAGTTTGGACTGAGGCTATAAATTAGGCAGAAAATG
TTCTTAGAATGCATAAGTCATAGCAGAAAAAATTTAGAGAGCCTAAGAAAGTTAGAATTTCAAAA
TGAGTGAACGTATTAGTGCTG
Found at i:39410281 original size:7 final size:7
Alignment explanation
Indices: 39410271--39410295 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39410261 TTATATACAT
39410271 AATACTA
1 AATACTA
39410278 AATACTA
1 AATACTA
39410285 AATACTA
1 AATACTA
39410292 AATA
1 AATA
39410296 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:39411277 original size:15 final size:16
Alignment explanation
Indices: 39411252--39411282 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39411242 ATAATTATCT
39411252 AAAAATACATAAATAA
1 AAAAATACATAAATAA
39411268 AAAAAT-CATAAATAA
1 AAAAATACATAAATAA
39411283 TAATTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATACATAAATAA
Found at i:39411417 original size:29 final size:29
Alignment explanation
Indices: 39411375--39411439 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
39411365 GCCATTGATG
*
39411375 AAAATATAAAAAAAA-TTAAAATTATTTTA
1 AAAAAATAAAAAAAATTTAAAATTA-TTTA
* *
39411404 AAAAAATATAAAAAATTTGAAATTATTTA
1 AAAAAATAAAAAAAATTTAAAATTATTTA
39411433 AAAAAAT
1 AAAAAAT
39411440 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAATAAAAAAAATTTAAAATTATTTA
Found at i:39411421 original size:20 final size:20
Alignment explanation
Indices: 39411383--39411421 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39411373 TGAAAATATA
*
39411383 AAAAAAATTAAAATTATTTT
1 AAAAAAATTAAAATAATTTT
39411403 AAAAAAATATAAAA-AATTT
1 AAAAAAAT-TAAAATAATTT
39411422 GAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATTAAAATAATTTT
Found at i:39411427 original size:30 final size:30
Alignment explanation
Indices: 39411375--39411439 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
39411365 GCCATTGATG
39411375 AAAATATAAAAAAAATTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTA-TTTAAA
* *
39411406 AAAATAT-AAAAAATTTGAAATTATTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTAAA
39411435 AAAAT
1 AAAAT
39411440 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.34
30 14 0.44
31 7 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATATAAAAAAAATTAAAATTATTTAAA
Found at i:39411498 original size:22 final size:21
Alignment explanation
Indices: 39411473--39411523 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
39411463 TAATATGGAT
* *
39411473 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGAAAGGAAA
39411495 TTGAGAGGATTTTGAAAGGAAA
1 TTGAGA-GATTTTGAAAGGAAA
39411517 TTGAGAG
1 TTGAGAG
39411524 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGAAAGGAAA
Found at i:39411547 original size:52 final size:52
Alignment explanation
Indices: 39411476--39411574 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
39411466 TATGGATTTG
* *
39411476 AGAGATTTTTGGAATGAAATTGAGAGGATTTTGAAAGGAAATTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGAAAGGAAATTGAGAGTTTA
*
39411528 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGAAAGGAAATTGAGA
39411575 TAGGATTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.29
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGAAAGGAAATTGAGAGTTTA
Found at i:39411558 original size:22 final size:22
Alignment explanation
Indices: 39411528--39411574 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39411518 TGAGAGTTTA
39411528 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
*
39411550 AGAGGATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
39411572 AGA
1 AGA
39411575 TAGGATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:39414962 original size:46 final size:46
Alignment explanation
Indices: 39414779--39414962 Score: 208
Period size: 46 Copynumber: 4.0 Consensus size: 46
39414769 TTTTGCCCAA
* *
39414779 GTTCTGAGTTCCTGCATGTGTTGCAGACTCGAGAATATAGGAATA-
1 GTTCTGAGCTCCTGCATATGTTGCAGACTCGAGAATATAGGAATAT
* * * * * * *
39414824 GTTTTCGAACTCTTGCATATGCTGCAGATTCAAGAATATAGGAATAG
1 GTTCT-GAGCTCCTGCATATGTTGCAGACTCGAGAATATAGGAATAT
* * * *
39414871 GTTCTGAGCTCTTGCATATATTGCAGACTCGAGAATACATGAATAT
1 GTTCTGAGCTCCTGCATATGTTGCAGACTCGAGAATATAGGAATAT
* * *
39414917 GTCCTGAGCCCCTGCATATGTTGCGGACTCGAGAATATAGGAATAT
1 GTTCTGAGCTCCTGCATATGTTGCAGACTCGAGAATATAGGAATAT
39414963 TAAACCCTAG
Statistics
Matches: 113, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
45 4 0.04
46 105 0.93
47 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (46 bp):
GTTCTGAGCTCCTGCATATGTTGCAGACTCGAGAATATAGGAATAT
Found at i:39418520 original size:30 final size:29
Alignment explanation
Indices: 39418486--39418565 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
39418476 GAGAATGTAA
39418486 TGCTCACACAAGCTGACAGTATTTCAAT-G-T
1 TGCTCACACAAGCTGACA-T-TTT-AATGGAT
*
39418516 TGCTCAGACAAGCTGACATTTTAATGGAAT
1 TGCTCACACAAGCTGACATTTTAATGG-AT
*
39418546 TGCTCACACAAGTTGACATT
1 TGCTCACACAAGCTGACATT
39418566 GTATCGAGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.07
28 4 0.09
29 1 0.02
30 36 0.82
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (29 bp):
TGCTCACACAAGCTGACATTTTAATGGAT
Found at i:39426445 original size:58 final size:58
Alignment explanation
Indices: 39426364--39426498 Score: 238
Period size: 58 Copynumber: 2.3 Consensus size: 58
39426354 TAAAATTTAA
39426364 AAGTTATTTTTAAAAAGTTTATTAAACCGGATTTGAAAGAACAATTTAATTTTGGTTC
1 AAGTTATTTTTAAAAAGTTTATTAAACCGGATTTGAAAGAACAATTTAATTTTGGTTC
39426422 AAGTTATTTTTAAAAA-TTATATTAAACCGGATTTGAAAGAACAATTTAATTTTGGTTC
1 AAGTTATTTTTAAAAAGTT-TATTAAACCGGATTTGAAAGAACAATTTAATTTTGGTTC
39426480 AAGTTA-TTTTAAAACAGTT
1 AAGTTATTTTTAAAA-AGTT
39426499 GTAAAAATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
57 10 0.14
58 62 0.84
59 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (58 bp):
AAGTTATTTTTAAAAAGTTTATTAAACCGGATTTGAAAGAACAATTTAATTTTGGTTC
Found at i:39430070 original size:48 final size:46
Alignment explanation
Indices: 39429984--39430089 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 46
39429974 TTTGCATGTA
* * * * *
39429984 TATATATTCTTTCTTTCTATCTGTTTGTGTATATATATATTTTCTTT
1 TATATATTCTTCCTTTCTATCTATATGTGTATACATATACTTT-TTT
* *
39430031 TCATATATTCTTCCTTTCTATCTATATGTGTGTGCATATACTTTTTT
1 T-ATATATTCTTCCTTTCTATCTATATGTGTATACATATACTTTTTT
39430078 TATATAATTCTT
1 TATAT-ATTCTT
39430090 TCTATCTTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 4 0.08
47 11 0.22
48 35 0.70
ACGTcount: A:0.21, C:0.13, G:0.07, T:0.59
Consensus pattern (46 bp):
TATATATTCTTCCTTTCTATCTATATGTGTATACATATACTTTTTT
Found at i:39434820 original size:41 final size:41
Alignment explanation
Indices: 39434763--39434844 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
39434753 TTCTTAAGTT
39434763 TGCAATGGAGGAGCAAATACAAAAGTTTGGATAGTTGTCCC
1 TGCAATGGAGGAGCAAATACAAAAGTTTGGATAGTTGTCCC
39434804 TGCAATGGAGGAGCAAATACAAAAGTTTGGATAGTTGTCCC
1 TGCAATGGAGGAGCAAATACAAAAGTTTGGATAGTTGTCCC
39434845 AGTTGTGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (41 bp):
TGCAATGGAGGAGCAAATACAAAAGTTTGGATAGTTGTCCC
Found at i:39435813 original size:15 final size:15
Alignment explanation
Indices: 39435804--39435836 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39435794 CAAATGCTAT
39435804 AATAATAAATACAAC
1 AATAATAAATACAAC
*
39435819 AATAATAAATACATC
1 AATAATAAATACAAC
39435834 AAT
1 AAT
39435837 GGCATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:39435862 original size:13 final size:12
Alignment explanation
Indices: 39435844--39435882 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
39435834 AATGGCATAA
39435844 AAATAATATAAAC
1 AAATAA-ATAAAC
39435857 AAATAAATAAAC
1 AAATAAATAAAC
39435869 GAAATAAA-AAAC
1 -AAATAAATAAAC
39435881 AA
1 AA
39435883 TAATCCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:39436191 original size:12 final size:12
Alignment explanation
Indices: 39436176--39436209 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39436166 AATCACAGTG
*
39436176 ATAATATTAACA
1 ATAATAATAACA
39436188 ATAATAATAACA
1 ATAATAATAACA
*
39436200 ATACTAATAA
1 ATAATAATAA
39436210 TTATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:39436824 original size:4 final size:4
Alignment explanation
Indices: 39436817--39436880 Score: 60
Period size: 4 Copynumber: 15.8 Consensus size: 4
39436807 ATTTAGGCAA
* * *
39436817 AAAT AAAT AAAT AAAT AAAT AGAGA- AAAT AAAA AAAT AAAAT ATAT ATAT
1 AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT -AAAT AAAT AAAT
39436867 AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAA
39436881 AGAACGATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 4 0.08
4 40 0.78
5 6 0.12
6 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:39437671 original size:132 final size:132
Alignment explanation
Indices: 39437431--39437678 Score: 403
Period size: 132 Copynumber: 1.9 Consensus size: 132
39437421 CTGCAACTTC
*
39437431 AGGGAGATAAGACTTACAATCTTCAACCTATCCCACTGCTGTCCAGGGAGATATGATTACTGGCT
1 AGGGAGATAAGACTGACAATCTTCAACCTATCCCACTGCTGTCCAGGGAGATATGATTACTGGCT
39437496 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC
39437561 TT
131 TT
* * *
39437563 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCCAGGGA-AGTA-GAATTACTG
1 AGGGAGATAAGA-CTGACAATCTTCAACCTATCCCACTGCTGTCCAGGGAGA-TATG-ATTACTG
*
39437625 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATC
63 GCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATC
39437679 GGCTCCCCTG
Statistics
Matches: 108, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
131 2 0.02
132 103 0.95
133 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (132 bp):
AGGGAGATAAGACTGACAATCTTCAACCTATCCCACTGCTGTCCAGGGAGATATGATTACTGGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC
TT
Found at i:39437780 original size:89 final size:89
Alignment explanation
Indices: 39437670--39437895 Score: 346
Period size: 88 Copynumber: 2.6 Consensus size: 89
39437660 AAATCCGCCA
* * * * *
39437670 TCTTCGATCGGCTCCCCTGTCGGCGCAGGAAGGCAATATCTGCTATTTTTTAACCTACTCTGCTG
1 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTTAACCTACTCCGCTG
*
39437735 CAACCCAGGGAGGAAAGGCTGGTG
66 CAACCCAAGGAGGAAAGGCTGGTG
* *
39437759 TCTTCGATCTGTTTTGCTGTCGGCGCAGGAAGGCAAGATCTGCTA-TTTTTAACCTACTCCGCTG
1 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTTAACCTACTCCGCTG
*
39437823 CAACCCAAGGAGGCAAGGCTGGTG
66 CAACCCAAGGAGGAAAGGCTGGTG
* *
39437847 TCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTTCTATTTT
1 TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTT
39437896 CATTGATCTG
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
88 81 0.66
89 42 0.34
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (89 bp):
TCTTCGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTTAACCTACTCCGCTG
CAACCCAAGGAGGAAAGGCTGGTG
Found at i:39446250 original size:12 final size:13
Alignment explanation
Indices: 39446233--39446261 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39446223 GCGCGTGAAT
39446233 ATAAAAATAA-AA
1 ATAAAAATAATAA
39446245 ATAAAAATAATAA
1 ATAAAAATAATAA
39446258 ATAA
1 ATAA
39446262 TAACTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAAAATAATAA
Found at i:39446891 original size:4 final size:4
Alignment explanation
Indices: 39446884--39446949 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
39446874 ATTTAGGCAA
* *
39446884 AAAT AAAT AAAT AAAT AAAT AAAT AGAGA- AAAT AAAA AAAT -AAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT AAAT
* *
39446932 ATAT AAAT GAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
39446950 AGAACGATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 6 0.12
4 42 0.82
5 2 0.04
6 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:39446925 original size:29 final size:30
Alignment explanation
Indices: 39446882--39446950 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
39446872 TTATTTAGGC
*
39446882 AAAAATAAATAAATAA-ATA-A-ATAAATAG
1 AAAAATAAAAAAATAATATATATATAAAT-G
39446910 AGAAAATAAAAAAATAATATATATATAAATG
1 A-AAAATAAAAAAATAATATATATATAAATG
39446941 AAAAATAAAA
1 AAAAATAAAA
39446951 GAACGATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 14 0.39
30 12 0.33
31 3 0.08
32 6 0.17
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (30 bp):
AAAAATAAAAAAATAATATATATATAAATG
Found at i:39449125 original size:19 final size:19
Alignment explanation
Indices: 39449101--39449154 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
39449091 AATCTTCAAG
* *
39449101 GATATGCAATCTTTGATAT
1 GATATGCAATCTTAGATAA
39449120 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
39449139 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
39449155 AGATAAGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:39449180 original size:22 final size:22
Alignment explanation
Indices: 39449115--39449177 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 22
39449105 TGCAATCTTT
*
39449115 GATATGATATGCAATCTT---A
1 GATAAGATATGCAATCTTAGAA
39449134 GATAAGATATGCAATCTTAGAA
1 GATAAGATATGCAATCTTAGAA
* *
39449156 GATAAGACTTTGTAATCTTAGA
1 GATAAGA-TATGCAATCTTAGA
39449178 GATTTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.46
22 8 0.22
23 12 0.32
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
GATAAGATATGCAATCTTAGAA
Found at i:39454008 original size:32 final size:32
Alignment explanation
Indices: 39453967--39454033 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
39453957 TAAAACAAGA
39453967 TTTGGGCCAAACCTATTTATGTAGAGTAGTGT
1 TTTGGGCCAAACCTATTTATGTAGAGTAGTGT
39453999 TTTGGGCCAAACCTATTTATGTAGAGTAGTGT
1 TTTGGGCCAAACCTATTTATGTAGAGTAGTGT
39454031 TTT
1 TTT
39454034 TTTGGGTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (32 bp):
TTTGGGCCAAACCTATTTATGTAGAGTAGTGT
Found at i:39455067 original size:15 final size:16
Alignment explanation
Indices: 39455047--39455076 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39455037 TTCTCCTATT
39455047 TCTCTTT-TTCTTTAC
1 TCTCTTTATTCTTTAC
39455062 TCTCTTTATTCTTTA
1 TCTCTTTATTCTTTA
39455077 TTTTTATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTCTTTATTCTTTAC
Found at i:39459670 original size:24 final size:24
Alignment explanation
Indices: 39459642--39459693 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
39459632 TTTCAAGAAG
* *
39459642 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
39459666 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
39459690 ATTT
1 ATTT
39459694 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:39476081 original size:11 final size:11
Alignment explanation
Indices: 39476041--39476107 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
39476031 ACTTAATCAC
39476041 TTTAATATTAAA
1 TTTAATATT-AA
*
39476053 TTTAAT-CTAA
1 TTTAATATTAA
39476063 TATT-ATATTAA
1 T-TTAATATTAA
*
39476074 TTTAATATAAAA
1 TTTAATAT-TAA
39476086 TATT-ATATTAA
1 T-TTAATATTAA
39476097 TTTAATATTAA
1 TTTAATATTAA
39476108 ATATTATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
10 9 0.20
11 21 0.47
12 13 0.29
13 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTAATATTAA
Found at i:39476091 original size:23 final size:22
Alignment explanation
Indices: 39476045--39476114 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 22
39476035 AATCACTTTA
*
39476045 ATATTAAATTTAATCT-AATATT
1 ATATT-AATTTAATATAAATATT
39476067 ATATTAATTTAATATAAAATATT
1 ATATTAATTTAATAT-AAATATT
39476090 ATATTAATTTAATATTAAATATT
1 ATATTAATTTAATA-TAAATATT
39476113 AT
1 AT
39476115 TAAAATAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 9 0.20
22 5 0.11
23 29 0.66
24 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATTTAATATAAATATT
Found at i:39476112 original size:7 final size:6
Alignment explanation
Indices: 39476042--39476113 Score: 57
Period size: 5 Copynumber: 12.5 Consensus size: 6
39476032 CTTAATCACT
* *
39476042 TTAATA TTAA-A TTTAAT- CTAATA TT-ATA TTAAT- TTAATA TAAAATA
1 TTAATA TTAATA -TTAATA TTAATA TTAATA TTAATA TTAATA T-TAATA
39476088 TT-ATA TTAAT- TTAATA TTAAATA TTA
1 TTAATA TTAATA TTAATA TT-AATA TTA
39476114 TTAAAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
5 25 0.47
6 17 0.32
7 11 0.21
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:39483068 original size:48 final size:47
Alignment explanation
Indices: 39482994--39483207 Score: 288
Period size: 48 Copynumber: 4.5 Consensus size: 47
39482984 NNNNNNNNNA
*
39482994 ATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCG
1 ATTTTGAGTATATTGATGCTGTCCA-TTTTAATGTATAATGCTGTCCG
* * **
39483042 ATTTTAAGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAA
1 ATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCG
*
39483089 ATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCG
1 ATTTTGAGTATATTGATGCTGTCCA-TTTTAATGTATAATGCTGTCCG
* * * *
39483137 ATTTTAAGTATATTGATGCTGTCTAATTTGATGTATAATGCTGTCC-
1 ATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCG
*
39483183 ATTTTGAGCATATT-ATCGCTGTCCA
1 ATTTTGAGTATATTGAT-GCTGTCCA
39483208 ATTTGCTGAA
Statistics
Matches: 146, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
45 2 0.01
46 19 0.13
47 61 0.42
48 64 0.44
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (47 bp):
ATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCG
Found at i:39483156 original size:95 final size:94
Alignment explanation
Indices: 39482993--39483207 Score: 342
Period size: 95 Copynumber: 2.3 Consensus size: 94
39482983 NNNNNNNNNN
39482993 AATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTATATTGA
1 AATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTATATTGA
*
39483058 TGCTGCCCATTTTAATGTATAATGCTGTC
66 TGCTGCCCAATTTAATGTATAATGCTGTC
39483087 AAATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTATATTG
1 -AATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTATATTG
* * *
39483152 ATGCTGTCTAATTTGATGTATAATGCTGTC
65 ATGCTGCCCAATTTAATGTATAATGCTGTC
* **
39483182 CATTTTGAGCATATT-ATCGCTGTCCA
1 AATTTTGAGTGTATTGAT-GCTGTCCA
39483208 ATTTGCTGAA
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
93 2 0.02
94 20 0.18
95 90 0.80
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (94 bp):
AATTTTGAGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTATATTGA
TGCTGCCCAATTTAATGTATAATGCTGTC
Found at i:39483172 original size:25 final size:25
Alignment explanation
Indices: 39483004--39483211 Score: 117
Period size: 25 Copynumber: 8.8 Consensus size: 25
39482994 ATTTTGAGTG
*
39483004 TATTGATGCTGTCCATTTTTAATGTA
1 TATTGATGCTGTCCA-ATTTAATGTA
*
39483030 TA---ATGCTGTCCGATTTTAA-GTA
1 TATTGATGCTGTCC-AATTTAATGTA
* *
39483052 TATTGATGCTGCCCATTTTAATGTA
1 TATTGATGCTGTCCAATTTAATGTA
* * *
39483077 TA---ATGCTGTCAAATTTTGA-GTG
1 TATTGATGCTGTCCAA-TTTAATGTA
*
39483099 TATTGATGCTGTCCATTTTTAATGTA
1 TATTGATGCTGTCCA-ATTTAATGTA
*
39483125 TA---ATGCTGTCCGATTTTAA-GTA
1 TATTGATGCTGTCC-AATTTAATGTA
* *
39483147 TATTGATGCTGTCTAATTTGATGTA
1 TATTGATGCTGTCCAATTTAATGTA
* * *
39483172 TA---ATGCTGTCCATTTTGA-GCA
1 TATTGATGCTGTCCAATTTAATGTA
39483193 TATT-ATCGCTGTCCAATTT
1 TATTGAT-GCTGTCCAATTT
39483212 GCTGAATAAT
Statistics
Matches: 146, Mismatches: 17, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
21 4 0.03
22 36 0.25
23 36 0.25
24 25 0.17
25 39 0.27
26 6 0.04
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (25 bp):
TATTGATGCTGTCCAATTTAATGTA
Found at i:39483227 original size:23 final size:22
Alignment explanation
Indices: 39483154--39483228 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
39483144 GTATATTGAT
* *
39483154 GCTGTCTAATTTGATGTATAAT-
1 GCTGTCCAATTTG-TGAATAATC
* * *
39483176 GCTGTCCATTTTGAGCATATTATC
1 GCTGTCCAATTTGTG-A-ATAATC
39483200 GCTGTCCAATTTGCTGAATAATC
1 GCTGTCCAATTTG-TGAATAATC
39483223 GCTGTC
1 GCTGTC
39483229 TAAAACAGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
21 1 0.02
22 11 0.27
23 15 0.37
24 13 0.32
25 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (22 bp):
GCTGTCCAATTTGTGAATAATC
Found at i:39483227 original size:47 final size:47
Alignment explanation
Indices: 39483004--39483228 Score: 211
Period size: 47 Copynumber: 4.7 Consensus size: 47
39482994 ATTTTGAGTG
* * * *
39483004 TATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTA
1 TATTGATGCTGTCCA-ATTTGATGAATAATGCTGTCCGATTTTAAGCA
* * * * ** * **
39483052 TATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTG
1 TATTGATGCTGTCCAATTTGATGAATAATGCTGTCCGATTTTAAGCA
* * * *
39483099 TATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTAAGTA
1 TATTGATGCTGTCCA-ATTTGATGAATAATGCTGTCCGATTTTAAGCA
* * *
39483147 TATTGATGCTGTCTAATTTGATGTATAATGCTGTCC-ATTTTGAGCA
1 TATTGATGCTGTCCAATTTGATGAATAATGCTGTCCGATTTTAAGCA
*
39483193 TATT-ATCGCTGTCCAATTTGCTGAATAATCGCTGTC
1 TATTGAT-GCTGTCCAATTTGATGAATAAT-GCTGTC
39483229 TAAAACAGGG
Statistics
Matches: 156, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
45 2 0.01
46 31 0.20
47 67 0.43
48 56 0.36
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (47 bp):
TATTGATGCTGTCCAATTTGATGAATAATGCTGTCCGATTTTAAGCA
Found at i:39490643 original size:48 final size:47
Alignment explanation
Indices: 39490559--39490908 Score: 470
Period size: 48 Copynumber: 7.4 Consensus size: 47
39490549 NNNNNNNNNN
*
39490559 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTG
1 AGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCAAATTTTG
* ** *
39490606 AGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTA
1 AGTATATTGATGCTGTCCA-TTTTAATGTATAATGCTGTCAAATTTTG
*
39490654 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTG
1 AGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCAAATTTTG
* ** *
39490701 AGTGTATTGATGCTGTCCATTTTTAATGTATAATGCTGTCCGATTTTA
1 AGTATATTGATGCTGTCCA-TTTTAATGTATAATGCTGTCAAATTTTG
*
39490749 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTG
1 AGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCAAATTTTG
* * * *
39490796 AGTGTATTGATGCTGTCCATTTTTAATGTATAATGATGTCCAATTTTA
1 AGTATATTGATGCTGTCCA-TTTTAATGTATAATGCTGTCAAATTTTG
* * * *
39490844 AGTATATTGATGCTGTCTAATTTGATGTATAATGCTGTC-CATTTTG
1 AGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCAAATTTTG
*
39490890 AGCATATT-ATCGCTGTCCA
1 AGTATATTGAT-GCTGTCCA
39490909 AAATAGGGTT
Statistics
Matches: 265, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
45 2 0.01
46 19 0.07
47 118 0.45
48 126 0.48
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (47 bp):
AGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCAAATTTTG
Found at i:39490722 original size:95 final size:95
Alignment explanation
Indices: 39490559--39490908 Score: 596
Period size: 95 Copynumber: 3.7 Consensus size: 95
39490549 NNNNNNNNNN
39490559 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
1 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
39490624 ATTTTTAATGTATAATGCTGTCCGATTTTA
66 ATTTTTAATGTATAATGCTGTCCGATTTTA
39490654 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
1 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
39490719 ATTTTTAATGTATAATGCTGTCCGATTTTA
66 ATTTTTAATGTATAATGCTGTCCGATTTTA
39490749 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
1 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
* *
39490814 ATTTTTAATGTATAATGATGTCCAATTTTA
66 ATTTTTAATGTATAATGCTGTCCGATTTTA
* * * * * **
39490844 AGTATATTGATGCTGTCTAATTTGATGTATAATGCTGTC-CATTTTGAGCATATT-ATCGCTGTC
1 AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGAT-GCTGTC
39490907 CA
65 CA
39490909 AAATAGGGTT
Statistics
Matches: 245, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 2 0.01
94 20 0.08
95 223 0.91
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (95 bp):
AGTATATTGATGCTGCCCATTTTAATGTATAATGCTGTCAAATTTTGAGTGTATTGATGCTGTCC
ATTTTTAATGTATAATGCTGTCCGATTTTA
Found at i:39494210 original size:26 final size:26
Alignment explanation
Indices: 39494180--39494237 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 26
39494170 CTCATTTGTG
39494180 AGTCATC-TGGAGACAATCTCTCTGAA
1 AGTCATCTTGG-GACAATCTCTCTGAA
39494206 AGTCATCTTGGGACAATCTCTCTGAA
1 AGTCATCTTGGGACAATCTCTCTGAA
39494232 AGTCAT
1 AGTCAT
39494238 GCATGACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (26 bp):
AGTCATCTTGGGACAATCTCTCTGAA
Found at i:39502090 original size:148 final size:148
Alignment explanation
Indices: 39501817--39502117 Score: 503
Period size: 148 Copynumber: 2.0 Consensus size: 148
39501807 TCCAGTGTGA
* * *
39501817 GTATCGATACTTTTACCTAGAATGCTAAAATTTCACAAGTTAAAACTTTTTTCAAGCTCAAAACA
1 GTATTGATACTTTTACCCAGAATGCTAAAATTTCACAAGTTAAAACGTTTTTCAAGCTCAAAACA
* * * *
39501882 TATTCCTACTCAACATACAAATAATATCTATTTTAACCAAGCATACTATCATCTTTTAACCATGC
66 TATTCCTACTCAACATACAAATAATACCAAATTAAACCAAGCATACTATCATCTTTTAACCATGC
39501947 TACATGCCATATTAACAC
131 TACATGCCATATTAACAC
*
39501965 GTATTGATACTTTTACCCAGAATGCTAAAATTTCACAAGTTAAAACGTTTTTCATGCTCAAAACA
1 GTATTGATACTTTTACCCAGAATGCTAAAATTTCACAAGTTAAAACGTTTTTCAAGCTCAAAACA
* *
39502030 TATTCCTACTCAACATACAAATAATGCCAAATTAAACCAAGCATACTATCATCTTTTAACCATTC
66 TATTCCTACTCAACATACAAATAATACCAAATTAAACCAAGCATACTATCATCTTTTAACCATGC
*
39502095 TACATGCCTTATTAACAC
131 TACATGCCATATTAACAC
39502113 GTATT
1 GTATT
39502118 TATTAAGCAA
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 142 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.34
Consensus pattern (148 bp):
GTATTGATACTTTTACCCAGAATGCTAAAATTTCACAAGTTAAAACGTTTTTCAAGCTCAAAACA
TATTCCTACTCAACATACAAATAATACCAAATTAAACCAAGCATACTATCATCTTTTAACCATGC
TACATGCCATATTAACAC
Found at i:39526374 original size:19 final size:20
Alignment explanation
Indices: 39526332--39526374 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
39526322 TAGTCTAAAA
* *
39526332 AAATTAATGATTTAATAGTT
1 AAATTAATGATATAATAATT
39526352 -AATTAATG-TATAATAATT
1 AAATTAATGATATAATAATT
39526370 AAATT
1 AAATT
39526375 GTAAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
AAATTAATGATATAATAATT
Found at i:39527557 original size:20 final size:20
Alignment explanation
Indices: 39527516--39527631 Score: 87
Period size: 20 Copynumber: 5.8 Consensus size: 20
39527506 TACTTTCATA
* *
39527516 CTCTTTTTAGCATTAAGGTG
1 CTCTTGTTAGCATTACGGTG
* *
39527536 CTCCTGTTAGCATTACGATG
1 CTCTTGTTAGCATTACGGTG
*
39527556 CTCTTGATAGCACATT-C-GTG
1 CTCTTGTTAG--CATTACGGTG
*
39527576 CTCTTGTTAGCACTACGGTG
1 CTCTTGTTAGCATTACGGTG
* *
39527596 CTCTTGATT-GCA-CATCTGTG
1 CTCTTG-TTAGCATTA-CGGTG
*
39527616 CTCTTATTAGCATTAC
1 CTCTTGTTAGCATTAC
39527632 AATATTCTTG
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 60 0.80
21 4 0.05
22 4 0.05
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CTCTTGTTAGCATTACGGTG
Found at i:39527567 original size:40 final size:39
Alignment explanation
Indices: 39527533--39527663 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
39527523 TAGCATTAAG
*
39527533 GTGCTCCTGTTAGCATTACGATGCTCTTGATAGCACATTC
1 GTGCTCCTGTTAGCACTACGATGCTCTTGATAG-ACATTC
* * *
39527573 GTGCTCTTGTTAGCACTACGGTGCTCTTGATTGCACA-TC
1 GTGCTCCTGTTAGCACTACGATGCTCTTGATAG-ACATTC
* * * * ** *
39527612 TGTGCTCTTATTAGCATTACAATATTCTTGATAGCATATTC
1 -GTGCTCCTGTTAGCACTACGATGCTCTTGATAG-ACATTC
*
39527653 ATGCTCCTGTT
1 GTGCTCCTGTT
39527664 TGCATTATGA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 2 0.03
40 70 0.95
41 2 0.03
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (39 bp):
GTGCTCCTGTTAGCACTACGATGCTCTTGATAGACATTC
Found at i:39528558 original size:13 final size:13
Alignment explanation
Indices: 39528540--39528566 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39528530 AAGGAGAAGA
39528540 GAAGCCCAATTCG
1 GAAGCCCAATTCG
39528553 GAAGCCCAATTCG
1 GAAGCCCAATTCG
39528566 G
1 G
39528567 CAAGGATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (13 bp):
GAAGCCCAATTCG
Found at i:39540323 original size:14 final size:15
Alignment explanation
Indices: 39540304--39540333 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39540294 CCTCATAAAT
39540304 AAAAAT-TAAAACCA
1 AAAAATCTAAAACCA
39540318 AAAAATCTAAAACCA
1 AAAAATCTAAAACCA
39540333 A
1 A
39540334 TAATGAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATCTAAAACCA
Found at i:39541654 original size:22 final size:23
Alignment explanation
Indices: 39541607--39541657 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
39541597 TATCCTTCAA
* *
39541607 ATTTATTATGTATTATTTTATAT
1 ATTTATTATGTATAATTTAATAT
39541630 ATTT-TTATGTA-AATTTAATATT
1 ATTTATTATGTATAATTTAATA-T
39541652 ATTTAT
1 ATTTAT
39541658 AAACAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 7 0.29
22 12 0.50
23 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTTATTATGTATAATTTAATAT
Found at i:39546591 original size:18 final size:15
Alignment explanation
Indices: 39546554--39546610 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
39546544 CAGATTCAAT
39546554 CAAAAAAAAGAAGAA
1 CAAAAAAAAGAAGAA
39546569 CAAAAAAAAGAAGAA
1 CAAAAAAAAGAAGAA
*
39546584 C-AAAAAAAGAACAA
1 CAAAAAAAAGAAGAA
*
39546598 AAAACAAAAAGAA
1 CAAA-AAAAAGAA
39546611 ACAAAAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 12 0.32
15 18 0.47
16 8 0.21
ACGTcount: A:0.81, C:0.09, G:0.11, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAGAAGAA
Found at i:39546595 original size:26 final size:29
Alignment explanation
Indices: 39546558--39546617 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 29
39546548 TTCAATCAAA
*
39546558 AAAAAGAAGAACAAAAAA-AAGAAG-AAC
1 AAAAAGAAGAACAAAAAACAAAAAGAAAC
39546585 AAAAA-AAGAACAAAAAACAAAAAGAAAC
1 AAAAAGAAGAACAAAAAACAAAAAGAAAC
39546613 AAAAA
1 AAAAA
39546618 CTTCTACCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 12 0.40
27 10 0.33
28 8 0.27
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (29 bp):
AAAAAGAAGAACAAAAAACAAAAAGAAAC
Found at i:39547767 original size:3 final size:3
Alignment explanation
Indices: 39547759--39547785 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39547749 GGCCAAACAG
39547759 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
39547786 CGAACCGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39549249 original size:7 final size:7
Alignment explanation
Indices: 39549219--39549277 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
39549209 TAAATTCGTA
*
39549219 AACCCCA
1 AACCCCT
*
39549226 AATCCCT
1 AACCCCT
* *
39549233 AACTCTT
1 AACCCCT
39549240 AACCCCT
1 AACCCCT
**
39549247 AACATCT
1 AACCCCT
39549254 AACCCCT
1 AACCCCT
39549261 AAACCCCT
1 -AACCCCT
39549269 AACCCCT
1 AACCCCT
39549276 AA
1 AA
39549278 ACCTTAAATC
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
7 33 0.82
8 7 0.17
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCCCT
Found at i:39549335 original size:15 final size:15
Alignment explanation
Indices: 39549300--39549337 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
39549290 AACCCTTAAT
39549300 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
39549314 T-AATCCATAATCCC
1 TAAATCCATAATCCC
39549328 TAAATCCATA
1 TAAATCCATA
39549338 TATACTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:39549791 original size:24 final size:24
Alignment explanation
Indices: 39549759--39549808 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
39549749 TCTTAAAAAA
*
39549759 CGCCGCTAAAATCTC-GAGCATTAG
1 CGCCGCTAAAA-CCCAGAGCATTAG
39549783 CGCCGCTAAAACCCAGAGCATTAG
1 CGCCGCTAAAACCCAGAGCATTAG
39549807 CG
1 CG
39549809 GTGCTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (24 bp):
CGCCGCTAAAACCCAGAGCATTAG
Found at i:39549803 original size:65 final size:65
Alignment explanation
Indices: 39549721--39549849 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
39549711 ACAAAAACGA
* *
39549721 CGCTAAAACCCCGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAATCTC-GAGCATTAGCG
1 CGCTAAAACCCAGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAA-CCCAGAGCATTAGCG
39549785 C
65 C
* * *
39549786 CGCTAAAACCCAGAGCATTAGCGGTGCTTTTTAGAAAACGCCGCTAAAACCCAGAGCATTAGCG
1 CGCTAAAACCCAGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAACCCAGAGCATTAGCG
39549850 GCGATTCTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 2 0.03
65 56 0.97
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.19
Consensus pattern (65 bp):
CGCTAAAACCCAGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAAAACCCAGAGCATTAGCGC
Found at i:39549828 original size:41 final size:41
Alignment explanation
Indices: 39549783--39550119 Score: 408
Period size: 41 Copynumber: 8.2 Consensus size: 41
39549773 CGAGCATTAG
* *
39549783 CGCCGCTAAAACCCAGAGCATTAGCGGTGCTTTTTAGAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
* * *
39549824 CGCCGCTAAAACCCAGAGCATTAGCGGCGATTCTTAGAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
* * *
39549865 CGCCGCTAAAACCTAGAGCATTAGCAGCGCTTTTTAGAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
* *
39549906 CACCGCTAAAACCCAGAGCATTAGCGGCGCTATTTAAAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
* * * *
39549947 TGCCGCTAAAACCCCGAGCATTAGCGACGC-TTTCACAAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTA-AAAAA
* * * * *
39549988 CGCCGCTAAAACCCATAGCTTTAGCGACTCTTCTTAAAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
* * *
39550029 TGCCGCT-AAACCCCGAGCATTAGCGGCGCTTTCTAAAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
* * * *
39550069 CGTCGCTAAAACCCTGAGCATTAGCGGCGCTTTCTCAAAAA
1 CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
*
39550110 CGCCACTAAA
1 CGCCGCTAAA
39550120 GCCACTGAAG
Statistics
Matches: 254, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
40 34 0.13
41 217 0.85
42 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (41 bp):
CGCCGCTAAAACCCAGAGCATTAGCGGCGCTTTTTAAAAAA
Found at i:39565365 original size:13 final size:11
Alignment explanation
Indices: 39565331--39565357 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
39565321 ATACAACTAT
39565331 ATAAATATTTA
1 ATAAATATTTA
39565342 ATAAATATTTA
1 ATAAATATTTA
39565353 ATAAA
1 ATAAA
39565358 AATATTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAATATTTA
Found at i:39566451 original size:12 final size:11
Alignment explanation
Indices: 39566430--39566469 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
39566420 AAGCATAAAC
39566430 AAATAAAATGA
1 AAATAAAATGA
39566441 AAATGAAAATGAA
1 AAAT-AAAATG-A
39566454 AAACTAAAATGA
1 AAA-TAAAATGA
39566466 AAAT
1 AAAT
39566470 TTTCTAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 10 0.38
14 1 0.04
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (11 bp):
AAATAAAATGA
Found at i:39566462 original size:13 final size:12
Alignment explanation
Indices: 39566430--39566468 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
39566420 AAGCATAAAC
39566430 AAATAAAATG-A
1 AAATAAAATGAA
39566441 AAATGAAAATGAA
1 AAAT-AAAATGAA
39566454 AAACTAAAATGAA
1 AAA-TAAAATGAA
39566467 AA
1 AA
39566469 TTTTCTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.16
12 6 0.24
13 14 0.56
14 1 0.04
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (12 bp):
AAATAAAATGAA
Found at i:39569922 original size:22 final size:21
Alignment explanation
Indices: 39569888--39569932 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
39569878 AAATAACATG
* *
39569888 AAAATAATTTAATTGATGCACA
1 AAAATAATATAATAGA-GCACA
*
39569910 AAAATCATATAATAGAGCACA
1 AAAATAATATAATAGAGCACA
39569931 AA
1 AA
39569933 TTTGCATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (21 bp):
AAAATAATATAATAGAGCACA
Found at i:39571286 original size:15 final size:16
Alignment explanation
Indices: 39571261--39571290 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39571251 ATATTGCCTT
39571261 ACCCCCTTTTAAAAAG
1 ACCCCCTTTTAAAAAG
39571277 ACCCCC-TTTAAAAA
1 ACCCCCTTTTAAAAA
39571291 AAAGCAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.23
Consensus pattern (16 bp):
ACCCCCTTTTAAAAAG
Found at i:39571291 original size:16 final size:16
Alignment explanation
Indices: 39571261--39571291 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39571251 ATATTGCCTT
*
39571261 ACCCCCTTTTAAAAAG
1 ACCCCCTTTAAAAAAG
39571277 ACCCCCTTTAAAAAA
1 ACCCCCTTTAAAAAA
39571292 AAGCAATGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.32, G:0.03, T:0.23
Consensus pattern (16 bp):
ACCCCCTTTAAAAAAG
Found at i:39574345 original size:129 final size:129
Alignment explanation
Indices: 39574177--39574640 Score: 618
Period size: 129 Copynumber: 3.6 Consensus size: 129
39574167 CCATCATTTT
* * * * * * * **
39574177 GATCCGCTCCACTGTAACTTCA-AGGAGATAGGATTTGTGGTTCTAATCCACTCCACAACAACTT
1 GATCTGCTCTACTGCAACTTCAGA-GAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTT
* * * * * * *
39574241 TAGGGAGATAGTATTGGTTTCTTCTATCTTCTCCACTACAACTTTAGAGAGATAAGACTAGATGC
65 CAGGGAGATAGGATTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
39574306 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCT---C--CAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTC
39574366 AGGGAGATAGGATTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
66 AGGGAGATAGGATTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
*
39574430 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTC
* * * * *
39574495 GGGGAGATAGGATTGGTTTCATCTGTCTGCTCCACTGCAACATCAGGGAGATAAGACTGGATAC
66 AGGGAGATAGGATTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
* * * *
39574559 GATCTGCTCTACTACAACTTTAGAGAGATAA-AGTCTATGGTTTTAATCCGCTTCACTGCAACTT
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGA-TCTGTGGTTTTAATCCGCTCCACTGCAACTT
*
39574623 CAGGGAGATAGGACTGGT
65 CAGGGAGATAGGATTGGT
39574641 ATGGGATCTT
Statistics
Matches: 301, Mismatches: 27, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
124 115 0.38
126 1 0.00
127 1 0.00
128 1 0.00
129 182 0.60
130 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (129 bp):
GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTC
AGGGAGATAGGATTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
Found at i:39574502 original size:44 final size:43
Alignment explanation
Indices: 39574138--39574632 Score: 182
Period size: 44 Copynumber: 11.6 Consensus size: 43
39574128 AATGTGATCT
* * * * ** *
39574138 GCTCTACTGCAACTTCAGAGAGATGAGATCCATCATTTTGATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-CTTGGTTTTAATCC
* * * * *
39574182 GCTCCACTGTAACTTCAAGGAGATAGGATTTGTGGTTCTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-TGGTTTTAATCC
* ** * * * *
39574226 ACTCCACAACAACTTTAGGGAGAT-AG-TATTGGTTTCTTCTATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGG-TT-TT-AATCC
* * * * * * *** *
39574270 TCTCCACTACAACTTTAGAGAGATAAGA-C-TAGATGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
* *
39574311 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-TGGTTTTAATCC
* * *
39574355 GCT---C--CAACTTCAGGGAGATAGGA--TTGGTTTCTTCTATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGG-TT-TT-AATCC
* * * * *** *
39574394 TCTCCACTACAACATCAGGGAGATAAGA-C-TGGATACGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
* * *
39574435 GCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-TGGTTTTAATCC
* * *
39574479 GCTCCACTGCAACTTCGGGGAGATAGGA--TTGG-TTTCATCTGTC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATC---C
* * *** *
39574522 TGCTCCACTGCAACATCAGGGAGATAAGA-C-TGGATACGATCT
1 -GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
* * * *
39574564 GCTCTACTACAACTTTAGAGAGATAA-AGTCTATGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TCT-TGGTTTTAATCC
*
39574608 GCTTCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
39574633 GGACTGGTAT
Statistics
Matches: 328, Mismatches: 92, Indels: 62
0.68 0.19 0.13
Matches are distributed among these distances:
36 3 0.01
37 3 0.01
38 2 0.01
39 22 0.07
40 7 0.02
41 82 0.25
42 9 0.03
43 5 0.02
44 189 0.58
45 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTTGGTTTTAATCC
Found at i:39574564 original size:253 final size:256
Alignment explanation
Indices: 39574177--39574640 Score: 641
Period size: 253 Copynumber: 1.8 Consensus size: 256
39574167 CCATCATTTT
* * *
39574177 GATCCGCTCCACTGTAACTTCAAGGAGATAGGATTTGTGGTTCTAATCCACTCCACAACAACTTT
1 GATCCGCTCCACTGTAACTTCAAGGAGATAAGATCTGTGGTTCTAATCCACTCCACAACAACTTC
* * * * * *
39574242 AGGGAGATAGTATTGGTTTCTTCTATCTTCTCCACTACAACTTTAGAGAGATAAGACTAGATGCG
66 AGGGAGATAGGATTGGTTTCATCTATCTGCTCCACTACAACATCAGAGAGATAAGACTAGATACG
* *
39574307 ATCTGCTCTACTGCAACTTCAGAGAGAT-AAGATCTGTGGTTTTAATCCGC-T-C-CAACTTCAG
131 ATCTGCTCTACTACAACTTCAGAGAGATAAAG-TCTATGGTTTTAATCCGCTTACGCAACTTCAG
*
39574368 GGAGATAGGATTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
195 GGAGATAGGACTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
* * * * **
39574430 GATCTGCTCTACTGTAACTTC-AGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTT
1 GATCCGCTCCACTGTAACTTCAAG-GAGATAAGATCTGTGGTTCTAATCCACTCCACAACAACTT
* * * * *
39574494 CGGGGAGATAGGATTGGTTTCATCTGTCTGCTCCACTGCAACATCAGGGAGATAAGACTGGATAC
65 CAGGGAGATAGGATTGGTTTCATCTATCTGCTCCACTACAACATCAGAGAGATAAGACTAGATAC
*
39574559 GATCTGCTCTACTACAACTTTAGAGAGATAAAGTCTATGGTTTTAATCCGCTTCACTGCAACTTC
130 GATCTGCTCTACTACAACTTCAGAGAGATAAAGTCTATGGTTTTAATCCGCTT-AC-GCAACTTC
39574624 AGGGAGATAGGACTGGT
193 AGGGAGATAGGACTGGT
39574641 ATGGGATCTT
Statistics
Matches: 180, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
252 2 0.01
253 150 0.83
254 4 0.02
256 1 0.01
258 23 0.13
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (256 bp):
GATCCGCTCCACTGTAACTTCAAGGAGATAAGATCTGTGGTTCTAATCCACTCCACAACAACTTC
AGGGAGATAGGATTGGTTTCATCTATCTGCTCCACTACAACATCAGAGAGATAAGACTAGATACG
ATCTGCTCTACTACAACTTCAGAGAGATAAAGTCTATGGTTTTAATCCGCTTACGCAACTTCAGG
GAGATAGGACTGGTTTCTTCTATCTTCTCCACTACAACATCAGGGAGATAAGACTGGATAC
Found at i:39574742 original size:88 final size:88
Alignment explanation
Indices: 39574646--39575341 Score: 926
Period size: 88 Copynumber: 7.9 Consensus size: 88
39574636 CTGGTATGGG
* * * * *
39574646 ATCTTCGATCTACTTCGCTACCAATACGGGAAGACAAGATCTGTTATCTTTAACCAACTCCACTA
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
*
39574711 CTGCTCAGGGAGACAAGGCTAAT
66 CTGCTCAGGGAGACAAGGCTGAT
* * * *
39574734 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATTTTCAACCTACTCTACTG
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
* * *
39574799 TTGCTCAGGGAGATAAGGCTGAG
66 CTGCTCAGGGAGACAAGGCTGAT
* * * *
39574822 GTCTTCGATCAACTTCGCTGCTAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTG
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
*
39574887 CTGCTCAGGGAGACAAGGCTGGT
66 CTGCTCAGGGAGACAAGGCTGAT
*
39574910 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
* * * *
39574975 CTGCTGAGAGAGATAAGGCTGAG
66 CTGCTCAGGGAGACAAGGCTGAT
* ** * *
39574998 GTCTTTAATCTACTTCGCTGCCAATACAGGAAGATAATATCT-CTTATTTTTAACCTACTCCACT
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGC-TATTTTTAACCTACTCCACT
* *
39575062 GCTGCTCAGGGAGACAAGGCTGGT
65 ACTGCTCAGGGAGACAAGGCTGAT
* * * * *
39575086 ACCTTCGATCTACTTCGATGCTAATACAGGAAGACAAGATCTGCTCTTTTTTTAACCTACTCCGC
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG--CTATTTTTAACCTACTCCAC
* * *
39575151 TGCTGCACAGGGAGACAAGGCTGGT
64 TACTGCTCAGGGAGACAAGGCTGAT
* * *
39575176 ATCTTCGATCTACTTTGCTACCAATACAAGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
* * * *
39575241 TTGCTTAGGGAGATAAGGCTGAG
66 CTGCTCAGGGAGACAAGGCTGAT
* * *
39575264 GTCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
39575329 CTGCTCAGGGAGA
66 CTGCTCAGGGAGA
39575342 TAGGATTTAT
Statistics
Matches: 527, Mismatches: 77, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
87 1 0.00
88 447 0.85
90 78 0.15
91 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (88 bp):
ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
CTGCTCAGGGAGACAAGGCTGAT
Found at i:39574903 original size:44 final size:44
Alignment explanation
Indices: 39574848--39575169 Score: 134
Period size: 44 Copynumber: 7.3 Consensus size: 44
39574838 GCTGCTAATA
39574848 CAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTGCTGCT
1 CAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTGCTGCT
* * * * ** * * * ***
39574892 CAGGGAGACAAG-GCTGGTATCTTCGATCTACTTCGCTGCCAAT
1 CAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTGCTGCT
* *
39574935 ACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGCT
1 -CAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTGCTGCT
* * * *** * * * * ***
39574980 GA-GAGAGATAAG-GCTGAGGTCTTTAATCTACTTCGCTGCCAAT
1 CAGGA-AGACAAGATCTGCTATTTTTAACCTACTCCACTGCTGCT
* *
39575023 ACAGGAAGATAATATCT-CTTATTTTTAACCTACTCCACTGCTGCT
1 -CAGGAAGACAAGATCTGC-TATTTTTAACCTACTCCACTGCTGCT
* * * ** ** * * **
39575068 CAGGGAGACAAG-GCTGGTACCTTCGATCTACTTCGA-TGCTAAT
1 CAGGAAGACAAGATCTGCTATTTTTAACCTAC-TCCACTGCTGCT
* * *
39575111 ACAGGAAGACAAGATCTGCTCTTTTTTTAACCTACTCCGCTGCTGCA
1 -CAGGAAGACAAGATCTG--CTATTTTTAACCTACTCCACTGCTGCT
*
39575158 CAGGGAGACAAG
1 CAGGAAGACAAG
39575170 GCTGGTATCT
Statistics
Matches: 184, Mismatches: 80, Indels: 26
0.63 0.28 0.09
Matches are distributed among these distances:
43 56 0.30
44 59 0.32
45 44 0.24
46 13 0.07
47 12 0.07
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
CAGGAAGACAAGATCTGCTATTTTTAACCTACTCCACTGCTGCT
Found at i:39575116 original size:264 final size:263
Alignment explanation
Indices: 39574646--39575341 Score: 1038
Period size: 264 Copynumber: 2.6 Consensus size: 263
39574636 CTGGTATGGG
* * *
39574646 ATCTTCGATCTACTTCGCTACCAATACGGGAAGACAAGATCTGTTATCTTTAACCAACTCCACTA
1 ATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTAT-TTTAACCTACTCCACTA
* * **
39574711 CTGCTCAGGGAGACAAGGCTAATATCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCT
65 CTGCTCAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCT
* * * *
39574776 GCTATTTTCAACCTACTCTACTGTTGCTCAGGGAGATAAGGCTGAGGTCTTCGATCAACTTCGCT
130 GCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCT-AGGTCTTCGATCAACTTCGAT
*
39574841 GCTAATACAGGAAGACAAGATCTG-CTATTTTTAACCTACTCCACTGCTGCTCAGGGAGACAAGG
194 GCTAATACAGGAAGACAAGATCTGCCTATTTTTAACCTACTCCACTGCTGCACAGGGAGACAAGG
39574905 CTGGT
259 CTGGT
*
39574910 ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 ATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTATTTT-AACCTACTCCACTA
* * ** *
39574975 CTGCTGAGAGAGATAAGGCTGAGGTCTTTAATCTACTTCGCTGCCAATACAGGAAGATAATATCT
65 CTGCTCAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCT
* *
39575040 -CTTATTTTTAACCTACTCCACTGCTGCTCAGGGAGACAAGGCT-GGTACCTTCGATCTACTTCG
130 GC-TATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTAGGT--CTTCGATCAACTTCG
* *
39575103 ATGCTAATACAGGAAGACAAGATCTGCTCTTTTTTTAACCTACTCCGCTGCTGCACAGGGAGACA
192 ATGCTAATACAGGAAGACAAGATCTGC-CTATTTTTAACCTACTCCACTGCTGCACAGGGAGACA
39575168 AGGCTGGT
256 AGGCTGGT
* *
39575176 ATCTTCGATCTACTTTGCTACCAATACAAGAAGACAAGATCTGCTATTTTTAACCTACTCCACTA
1 ATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA-TTTTAACCTACTCCACTA
* * * *
39575241 TTGCTTAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCT
65 CTGCTCAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCT
*
39575306 GCTATTTTCAACCTACTCCACTACTGCTCAGGGAGA
130 GCTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
39575342 TAGGATTTAT
Statistics
Matches: 389, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
262 3 0.01
263 4 0.01
264 189 0.49
266 188 0.48
267 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (263 bp):
ATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTATTTTAACCTACTCCACTAC
TGCTCAGGGAGATAAGGCTGAGGTCTTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTG
CTATTTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTAGGTCTTCGATCAACTTCGATGC
TAATACAGGAAGACAAGATCTGCCTATTTTTAACCTACTCCACTGCTGCACAGGGAGACAAGGCT
GGT
Found at i:39578538 original size:14 final size:14
Alignment explanation
Indices: 39578519--39578545 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39578509 CTTAATTAAA
39578519 CTATAATCCCTAAT
1 CTATAATCCCTAAT
39578533 CTATAATCCCTAA
1 CTATAATCCCTAA
39578546 ATCCATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (14 bp):
CTATAATCCCTAAT
Found at i:39578806 original size:22 final size:21
Alignment explanation
Indices: 39578758--39578806 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
39578748 AACCTTAAAT
*
39578758 CCCTAACTCTTAACCACTAAC
1 CCCTAACTCTAAACCACTAAC
** *
39578779 ATCTAACTCATAAACCCCTAAC
1 CCCTAACTC-TAAACCACTAAC
39578801 CCCTAA
1 CCCTAA
39578807 ACCGTAAATC
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.37, C:0.41, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCTAACTCTAAACCACTAAC
Found at i:39578935 original size:318 final size:318
Alignment explanation
Indices: 39578343--39579022 Score: 1025
Period size: 318 Copynumber: 2.1 Consensus size: 318
39578333 TAAATTATAC
*
39578343 ATCTTTTACAATTACATAAAAACATATTTAAAATATAAAT--AAAAATTAATCTAAACCAAAAAC
1 ATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCAAAAAC
* * * *
39578406 CCTAACCTGACCCCTGAAAGCCTAAATCCTAAATCCCTAACTCTTAAGCACTAACGTCTAACCCT
66 CCTAACCCGACCCCTGAAAGCCTAAATCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCA
* * *
39578471 TAAACCCCTAACCCCTAAACCTTAAATCCCGACCAACCCTTAATTAAACTATAATCCCTAATCTA
131 TAAACCCCTAACCCCTAAACCGTAAATCCCGACCAACCCTTAATTAAACCATAATCCCTAATCCA
** * * *
39578536 TAATCCCTAAATCCATATATATAGTACTCCCTAAACCTTTAAATATGAACTCCTAAACCAGCCTT
196 TAATCCCTAAATAAATACATATAGTACTACCTAAACCTTAAAATATGAACTCCTAAACCAGCCTT
* *
39578601 AAATATTAAATTATCATATACCGTAAACTAATTAAAAACCCTCAACAATTTTATTATT
261 AAATATTAAATTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
* *
39578659 ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
1 ATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCAAAAAC
*
39578724 CCTAACCCGACCCCTGAAA-CCTTAAA-CCTTAAATCCCTAACTCTTAACCACTAACATCTAACT
66 CCTAACCCGACCCCTGAAAGCC-TAAATCC-TAAATCCCTAACTCTTAACCACTAACATCTAACC
*
39578787 CATAAACCCCTAACCCCTAAACCGTAAATCCCGGCCAACCCTTAATTAAACCATAATCCCTAATC
129 CATAAACCCCTAACCCCTAAACCGTAAATCCCGACCAACCCTTAATTAAACCATAATCCCTAATC
** * *
39578852 CATAATCCCTAGCTAAATCCATATA-TACTACCTAAACCTTAAAATATGAACTCCTAAACCGGCC
194 CATAATCCCTAAATAAATACATATAGTACTACCTAAACCTTAAAATATGAACTCCTAAACCAGCC
*
39578916 TTAAATCTTAAATTTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
259 TTAAATATTAAA-TTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
*
39578977 ATCTCTTTTACAATTACAT-ATATA-ATA-ATAAAATATAAATAAAAAA
1 A--TCTTTTACAATTACATAATA-ACATATTTAAAATATAAATAAAAAA
39579023 TAAATAAAAA
Statistics
Matches: 330, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
316 38 0.12
317 51 0.15
318 219 0.66
319 6 0.02
320 16 0.05
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (318 bp):
ATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCAAAAAC
CCTAACCCGACCCCTGAAAGCCTAAATCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCA
TAAACCCCTAACCCCTAAACCGTAAATCCCGACCAACCCTTAATTAAACCATAATCCCTAATCCA
TAATCCCTAAATAAATACATATAGTACTACCTAAACCTTAAAATATGAACTCCTAAACCAGCCTT
AAATATTAAATTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
Found at i:39579014 original size:13 final size:12
Alignment explanation
Indices: 39578996--39579035 Score: 55
Period size: 11 Copynumber: 3.2 Consensus size: 12
39578986 ACAATTACAT
39578996 ATATAATAATAAA
1 ATATAATAA-AAA
39579009 ATATAAATAAAAA
1 ATAT-AATAAAAA
39579022 ATA-AATAAAAA
1 ATATAATAAAAA
39579033 ATA
1 ATA
39579036 ATCTAAAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.42
13 10 0.38
14 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
ATATAATAAAAA
Found at i:39579019 original size:11 final size:11
Alignment explanation
Indices: 39579003--39579036 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
39578993 CATATATAAT
*
39579003 AATAAAATATA
1 AATAAAAAATA
39579014 AATAAAAAATA
1 AATAAAAAATA
39579025 AATAAAAAATA
1 AATAAAAAATA
39579036 A
1 A
39579037 TCTAAAGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:39580877 original size:43 final size:43
Alignment explanation
Indices: 39580804--39581078 Score: 374
Period size: 43 Copynumber: 6.4 Consensus size: 43
39580794 TTTTCCAAAA
*
39580804 TTAGCGGCGTTTGT-GGTAAAGCGCCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCT
* *
39580846 TTAGCGGCGTTTGTGGGTAAAGCGCTGCTAAATGTCATGTTCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCT
* * *
39580889 TTAGCGACATTTGTGGGGTAAAGCGCCGCTAAAGGTCATGTACT
1 TTAGCGGCGTTTGT-GGGTAAAGCGCCGCTAAAGGTCATGTTCT
* * * *
39580933 TTCGCGGCGTTTGTGGGTGAAGCGTCGCTAAAGGTCACGTTCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCT
* * *
39580976 TTAACGGCGTTTATGGGTGAAGCGCCGCTAAAGGTCATGTT-T
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCT
* *
39581018 GTTAGCGGCGTTTGTGGGTGAAGCACCGCTAAAGGTCATGTTCT
1 -TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCT
*
39581062 TTAGCGGCGTTTTTGGG
1 TTAGCGGCGTTTGTGGG
39581079 CCCGAGTTAC
Statistics
Matches: 205, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
42 15 0.07
43 152 0.74
44 38 0.19
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCATGTTCT
Found at i:39580918 original size:87 final size:86
Alignment explanation
Indices: 39580818--39581067 Score: 342
Period size: 87 Copynumber: 2.9 Consensus size: 86
39580808 CGGCGTTTGT
* * *
39580818 GGTAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGTAAAGCGCTGCTAAATGTCA
1 GGTAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTGAAGCGCTGCTAAAGGTCA
*
39580883 TGTTCTTTAGCGACATTTGTGG
66 TGTTCTTTAGCGACATTTAT-G
* *
39580905 GGTAAAGCGCCGCTAAAGGTCATGTACTTTCGCGGCGTTTGTGGGTGAAGCG-TCGCTAAAGGTC
1 GGTAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTGAAGCGCT-GCTAAAGGTC
* * * *
39580969 ACGTTCTTTAACGGCGTTTATG
65 ATGTTCTTTAGCGACATTTATG
* * *
39580991 GGTGAAGCGCCGCTAAAGGTCATGTT-TGTTAGCGGCGTTTGTGGGTGAAGCACCGCTAAAGGTC
1 GGTAAAGCGCCGCTAAAGGTCATGTTCT-TTAGCGGCGTTTGTGGGTGAAGCGCTGCTAAAGGTC
39581055 ATGTTCTTTAGCG
65 ATGTTCTTTAGCG
39581068 GCGTTTTTGG
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
85 1 0.01
86 69 0.48
87 73 0.51
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (86 bp):
GGTAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGTGAAGCGCTGCTAAAGGTCA
TGTTCTTTAGCGACATTTATG
Found at i:39584596 original size:16 final size:16
Alignment explanation
Indices: 39584575--39584606 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39584565 GTTTTGTTGT
*
39584575 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39584591 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39584607 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:39584892 original size:51 final size:50
Alignment explanation
Indices: 39584834--39585024 Score: 185
Period size: 51 Copynumber: 3.8 Consensus size: 50
39584824 CCGGTTCATA
*
39584834 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACAAG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCATCACTAT-CGATACAAG
* ** * *
39584885 TAGTAGCCTCCACATAGTACTACACA--C-ATGATCGAAGCTATTCGGTACGCA-
1 TAGTAGCCTGCACATAGTACTACACATGCGACCATC--A-CTA-TCGATAC-AAG
* * * *
39584936 TAGTAGCCTGCACATTGTACTACACATGCGACCTATCATTAT-GATATACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCGATACAAG
*
39584986 TAGTAGCCTGCACATAGTACTACACAAGCGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACATGCGACCATCACT
39585025 TTCACTTTCA
Statistics
Matches: 112, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
48 4 0.04
49 5 0.04
50 35 0.31
51 58 0.52
52 4 0.04
53 2 0.02
54 1 0.01
55 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCGATACAAG
Found at i:39585040 original size:101 final size:100
Alignment explanation
Indices: 39584827--39585011 Score: 228
Period size: 102 Copynumber: 1.8 Consensus size: 100
39584817 AATGATGCCG
* *
39584827 GTTCATATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACAAGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTAT-CGATACAAGTAGTAGC
** *
39584892 CTCCACATAGTACTACACACATGATCGAAGCTATTCG
65 CTCCACATAGTACTACACACACCATC-AAGCTATTCC
* * * * * *
39584929 GTACGCATAGTAGCCTGCACATTGTACTACACATGCGACCTATCATTAT-GATATACGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCGATACAAGTAGTAGC
*
39584993 CTGCACATAGTACTACACA
65 CTCCACATAGTACTACACA
39585012 AGCGACCATC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 31 0.42
102 35 0.48
103 7 0.10
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (100 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCGATACAAGTAGTAGCC
TCCACATAGTACTACACACACCATCAAGCTATTCC
Found at i:39592206 original size:9 final size:9
Alignment explanation
Indices: 39592192--39592218 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39592182 CTTAACAACT
39592192 TTCAATTTA
1 TTCAATTTA
39592201 TTCAATTTA
1 TTCAATTTA
39592210 TTCAATTTA
1 TTCAATTTA
39592219 GTCCTTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (9 bp):
TTCAATTTA
Found at i:39598560 original size:20 final size:20
Alignment explanation
Indices: 39598518--39598574 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
39598508 ATTCATATAT
* **
39598518 ATTTA-TTTTTATTTGCTTT
1 ATTTATTTTTTATTTTCTGG
39598537 ATTTATTTTTTATTTTCTGG
1 ATTTATTTTTTATTTTCTGG
39598557 ATTTATATCTTTTATTTT
1 ATTTAT-T-TTTTATTTT
39598575 ATTTTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 17 0.53
21 1 0.03
22 9 0.28
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (20 bp):
ATTTATTTTTTATTTTCTGG
Found at i:39598593 original size:47 final size:48
Alignment explanation
Indices: 39598494--39598594 Score: 109
Period size: 49 Copynumber: 2.1 Consensus size: 48
39598484 TTATTTTTTA
* * *
39598494 TTTTTATTTTTTGTATTCATATATATTTATTTTTATTTGCTTTATTTAT
1 TTTTTATTTTCTGGATTCATATATATTTATTTTTATTT-CTTTATGTAT
* *
39598543 TTTTTATTTTCTGGATTTATATCT-TTTA-TTTTATTT-TATTATGTACT
1 TTTTTATTTTCTGGATTCATATATATTTATTTTTATTTCT-TTATGTA-T
39598590 TTTTT
1 TTTTT
39598595 GTTATATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
45 1 0.02
46 6 0.13
47 14 0.31
48 4 0.09
49 20 0.44
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (48 bp):
TTTTTATTTTCTGGATTCATATATATTTATTTTTATTTCTTTATGTAT
Found at i:39608385 original size:22 final size:22
Alignment explanation
Indices: 39608325--39608382 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
39608315 AATCTTCAAG
39608325 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
39608344 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
39608366 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
39608383 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:39609519 original size:24 final size:24
Alignment explanation
Indices: 39609492--39609537 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
39609482 GGAAAGGTGA
**
39609492 TTTTCTTTGTTTTCTTCTTTTCCT
1 TTTTCTTTAATTTCTTCTTTTCCT
* *
39609516 TTTTTTTTAATTTCTTTTTTTC
1 TTTTCTTTAATTTCTTCTTTTC
39609538 TCTTGGTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTTCTTTAATTTCTTCTTTTCCT
Found at i:39610372 original size:3 final size:3
Alignment explanation
Indices: 39610364--39610397 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
39610354 TAATTTTAAT
39610364 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39610398 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39610402 original size:3 final size:3
Alignment explanation
Indices: 39610396--39610423 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39610386 AATAATAATA
39610396 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39610424 CTTGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:39614891 original size:12 final size:12
Alignment explanation
Indices: 39614851--39614898 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
39614841 TTAGATCCTT
39614851 TCAAAA-AAAAA
1 TCAAAATAAAAA
*
39614862 TCAAAATCAAAA
1 TCAAAATAAAAA
*
39614874 TCAAAATCAAAA
1 TCAAAATAAAAA
*
39614886 TAAAAAATAAAAA
1 T-CAAAATAAAAA
39614899 ATGAGAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 6 0.19
12 17 0.53
13 9 0.28
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (12 bp):
TCAAAATAAAAA
Found at i:39614891 original size:18 final size:18
Alignment explanation
Indices: 39614851--39614898 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
39614841 TTAGATCCTT
39614851 TCAAAA-AAAAATCAAAA
1 TCAAAATAAAAATCAAAA
*
39614868 TCAAAATCAAAATCAAAA
1 TCAAAATAAAAATCAAAA
*
39614886 TAAAAAATAAAAA
1 T-CAAAATAAAAA
39614899 ATGAGAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
TCAAAATAAAAATCAAAA
Found at i:39614894 original size:7 final size:7
Alignment explanation
Indices: 39614882--39614945 Score: 65
Period size: 7 Copynumber: 8.6 Consensus size: 7
39614872 AATCAAAATC
*
39614882 AAAATAA
1 AAAAGAA
*
39614889 AAAATAA
1 AAAAGAA
39614896 AAAATGAGA
1 AAAA-GA-A
39614905 GAAAAAGAA
1 -AAA-AGAA
*
39614914 AGAAGAA
1 AAAAGAA
39614921 AAAAGAA
1 AAAAGAA
39614928 AAAAGAA
1 AAAAGAA
39614935 AAAAGAA
1 AAAAGAA
39614942 AAAA
1 AAAA
39614946 TCTAGATGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
7 39 0.78
8 3 0.06
9 2 0.04
10 5 0.10
11 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAAAGAA
Found at i:39614898 original size:6 final size:6
Alignment explanation
Indices: 39614858--39614890 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
39614848 CTTTCAAAAA
39614858 AAAATC AAAATC AAAATC AAAATC AAAAT- AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
39614891 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:39617441 original size:44 final size:45
Alignment explanation
Indices: 39617343--39617441 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 45
39617333 GAAGAATTTC
* ** **
39617343 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAAATAAA
* * * *
39617388 A-ATCCTATCTCCCTAAGATTACAGTGGAGCGGGTT-AAAATAAA
1 AGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAAATAAA
39617431 AGATCTTATCT
1 AGATCTTATCT
39617442 ATTTGAAGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 5 0.12
44 37 0.86
45 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (45 bp):
AGATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAAATAAA
Found at i:39617461 original size:175 final size:175
Alignment explanation
Indices: 39617170--39617541 Score: 611
Period size: 175 Copynumber: 2.1 Consensus size: 175
39617160 AAGATGGTGA
* * * * * *
39617170 ATCTTATCTCTCTGAGATTATAGTGGAGCAGAATGAAGCCAGTAATCCTATTTCTCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGAATGAAGCCAGTAATCCTATCTCCCTAAGATTAC
*
39617235 AGTGGAGCGGATTAAAATAAAGGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAGCGGATTAAAATAAAAGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
*
39617300 TCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAGAATTTCAG
131 TCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTTCAG
* *
39617345 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGAATGAAGCCAGTAATCCTATCTCCCTAAGATTAC
*
39617410 AGTGGAGCGGGTTAAAATAAAAGATCTTATCTATT-TGAAGTTACAGTAGAGTAGATCGCATCAG
66 AGTGGAGCGGATTAAAATAAAAGATCTTATCT-TTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
39617474 GTCTTATCTCCCTGAGATTACAGTGAAATAGACCGAAGAATTTTAG
130 GTCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTTCAG
39617520 ATCTTATCTCCCTGAGATTACA
1 ATCTTATCTCCCTGAGATTACA
39617542 TGGAGCGGGT
Statistics
Matches: 183, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
175 181 0.99
176 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGAATGAAGCCAGTAATCCTATCTCCCTAAGATTAC
AGTGGAGCGGATTAAAATAAAAGATCTTATCTTTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGAGATTACAGTGAAATAAACCGAAGAATTTCAG
Found at i:39617566 original size:130 final size:131
Alignment explanation
Indices: 39617393--39617678 Score: 466
Period size: 130 Copynumber: 2.2 Consensus size: 131
39617383 CTAGTAATCC
* * *
39617393 TATCTCCCTAAGATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTATTTGAAGTTACAGTA
1 TATCTCCCTGAGATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTATCTGAAGTTACAGAA
* ***
39617458 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAGACCGAAGAATTTTAGATC
66 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAGACCGAAAAATCACAGATC
39617523 T
131 T
* *
39617524 TATCTCCCTGAGATTACA-TGGAGCGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAA
1 TATCTCCCTGAGATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTATCTGAAGTTACAGAA
*
39617588 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATCACAGATC
66 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAGACCGAAAAATCACAGATC
39617653 T
131 T
*
39617654 TATCTCCCTGAGATTACAGCGGAGC
1 TATCTCCCTGAGATTACAGTGGAGC
39617679 AGATTGAAGA
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
130 121 0.85
131 22 0.15
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (131 bp):
TATCTCCCTGAGATTACAGTGGAGCGGGTTAAAATAAAAGATCTTATCTATCTGAAGTTACAGAA
GAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGAAATAGACCGAAAAATCACAGATC
T
Found at i:39617672 original size:46 final size:45
Alignment explanation
Indices: 39617300--39617672 Score: 149
Period size: 46 Copynumber: 8.5 Consensus size: 45
39617290 TCGCATCAGG
* * *
39617300 TCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAA-AAATACAGA
* ** ** ** *
39617346 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTG-AAGCTAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATA-CAGA
* * * * *
39617390 TCCTATCTCCCTAAGATTACAGTGG---AG-CGGGTTAAAATAAAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGAC-CG-AAAAAT-ACAGA
*** * * * * *
39617434 TCTTATCTATTTGA-AGTTACAGTAGAGTAGATCG---CAT-CAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGACCGAAAAATACAGA
* * **
39617475 TCTTATCTCCCTGAGATTACAGTGAAATAGACCGAAGAATTTTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAA-AAATACAGA
* * *
39617521 TCTTATCTCCCTGAGATTACA-TGG---AG-CGGGTTAAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGAC-CG-AAAAATACA-GA
* ** * * * *
39617564 TCTTATCTCTCTGA-AGTTACAGAAGAGTAGATCG---CAT-CAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGACCGAAAAATACAGA
39617605 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATCACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAAT-ACAGA
39617651 TCTTATCTCCCTGAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
39617673 CGGAGCAGAT
Statistics
Matches: 234, Mismatches: 61, Indels: 64
0.65 0.17 0.18
Matches are distributed among these distances:
41 59 0.25
42 11 0.05
43 30 0.13
44 47 0.20
45 5 0.02
46 76 0.32
47 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATACAGA
Found at i:39617788 original size:305 final size:306
Alignment explanation
Indices: 39617225--39617836 Score: 1012
Period size: 305 Copynumber: 2.0 Consensus size: 306
39617215 TCCTATTTCT
* *
39617225 CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTTTCTGAAGTTACAGTAGAGTAGA
1 CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGA
* **
39617290 TCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAGAATTTCAGATCTTATCTC
66 TCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAAAATCACAGATCTTATCTC
* *
39617355 CCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGGAGCGG
131 CCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGGAACGA
* *
39617420 GTTAAAATAAAAGATCTTATCTATTTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCC
196 ATTAAAATAAAAGATCTTATCTATCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCC
* * *
39617485 CTGAGATTACAGTGAAATAGACCGAAGAATTTTAGATCTTATCTCC
261 CTGAGATTAAAGTGAAATAGACCGAAGAATTTCAGACCTTATCTCC
*
39617531 CTGAGATTACA-TGGAGCGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGA
1 CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGA
*
39617595 TCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATCACAGATCTTATCTC
66 TCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAAAATCACAGATCTTATCTC
* * *
39617660 CCTGAGATTACAGCGGAGCAGATTGAAGAC-AGTAATCCTATTTCCTTGAGATTACAGTGGAACG
131 CCTGAGATTACAGCGGAGCAGATTGAAG-CTAGTAATCCTATCTCCCTAAGATTACAGTGGAACG
* * *
39617724 AATTAAAATAAATGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATCAGGTCTTATCTC
195 AATTAAAATAAAAGATCTTATCTATCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTC
*
39617789 CCTGAGATTAAAGTGGAATAGACCGAAGAATTTCAGACCTTATCTCC
260 CCTGAGATTAAAGTGAAATAGACCGAAGAATTTCAGACCTTATCTCC
39617836 C
1 C
39617837 AGATAATGTA
Statistics
Matches: 284, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
305 272 0.96
306 12 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (306 bp):
CTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGA
TCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAAAATCACAGATCTTATCTC
CCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGGAACGA
ATTAAAATAAAAGATCTTATCTATCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCC
CTGAGATTAAAGTGAAATAGACCGAAGAATTTCAGACCTTATCTCC
Found at i:39617855 original size:175 final size:174
Alignment explanation
Indices: 39617532--39617858 Score: 492
Period size: 175 Copynumber: 1.9 Consensus size: 174
39617522 CTTATCTCCC
* **
39617532 TGAGATTACATGGAGCGGGTTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGATC
1 TGAGATTACATGGAACGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGATC
* *
39617597 GCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATCACAGATCTTATCTCCC
66 GCATCAGGTCTTATCTCCCTGAGATTAAAGTGGAATAGACCGAAAAATCACAGACCTTATCTCCC
* *
39617662 TGAGATTACAGCGGAGCAGATTGAAGACAGTAATCCTATTTCCT
131 AGAGAATACAGCGGAGCAGATTGAAGACAGTAATCCTATTTCCT
* * *
39617706 TGAGATTACAGTGGAACGAATTAAAATAAATGATCTTATCTCTCTGAAGTTATAGTAGAGTAGAT
1 TGAGATTACA-TGGAACGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGAT
* **
39617771 CGCATCAGGTCTTATCTCCCTGAGATTAAAGTGGAATAGACCGAAGAATTTCAGACCTTATCTCC
65 CGCATCAGGTCTTATCTCCCTGAGATTAAAGTGGAATAGACCGAAAAATCACAGACCTTATCTCC
* ** *
39617836 CAGATAATGTAGTGGAGCAGATT
130 CAGAGAATACAGCGGAGCAGATT
39617859 AAAGCCACAA
Statistics
Matches: 135, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
174 10 0.07
175 125 0.93
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (174 bp):
TGAGATTACATGGAACGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGAAGAGTAGATC
GCATCAGGTCTTATCTCCCTGAGATTAAAGTGGAATAGACCGAAAAATCACAGACCTTATCTCCC
AGAGAATACAGCGGAGCAGATTGAAGACAGTAATCCTATTTCCT
Found at i:39617929 original size:50 final size:49
Alignment explanation
Indices: 39617854--39618328 Score: 273
Period size: 50 Copynumber: 9.5 Consensus size: 49
39617844 GTAGTGGAGC
*
39617854 AGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAATTAGAA
1 AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGACATTGC-ATTAGAA
* * * * ** * *
39617904 AGATTAAAGCTACAACAGCGAATCTT-ACTCCCTAAGCGA-TGCAGTGGAA
1 AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGA-C-ATTGCATTAGAA
* * * * *
39617953 TAGATTAAAGCCACATCTGTGAATCTTGCTTCCCCGACATTGCGGTTAAAA
1 -AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGACATTGC-ATTAGAA
* * * * * * * * *
39618004 AGATTAAATCTATAACGGGGAATCTT-ACTCCCCAGGCAGTGCAGTGGAA
1 AGATTAAAGCCACAACGGTGAATCTTGATTCCCC-GACATTGCATTAGAA
* * * *
39618053 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAA
1 -AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGACATTGCA-TTAGAA
* * * * * ***
39618104 AGATTAAAGCTACAACAGCGAATCTT-ACTCCCCAGGCGA-TGCAGCGGAA
1 AGATTAAAGCCACAACGGTGAATCTTGATTCCCC-GAC-ATTGCATTAGAA
* * * *
39618153 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAA
1 -AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGACATTGCA-TTAGAA
* * * * **
39618204 AGATTAAAGCTACAACAGTGAATCTT-ACTCCCCAGGCGA-TGCA-GCGCAA
1 AGATTAAAGCCACAACGGTGAATCTTGATTCCCC-GAC-ATTGCATTAG-AA
* * * * *
39618253 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGTATTAAAA
1 -AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGACATTGCATTAGAA
* * *
39618303 AGATTAAAGCAACAATGGCGAATCTT
1 AGATTAAAGCCACAACGGTGAATCTT
39618329 ACTTTCCAAA
Statistics
Matches: 304, Mismatches: 98, Indels: 47
0.68 0.22 0.10
Matches are distributed among these distances:
49 56 0.18
50 217 0.71
51 31 0.10
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (49 bp):
AGATTAAAGCCACAACGGTGAATCTTGATTCCCCGACATTGCATTAGAA
Found at i:39618027 original size:100 final size:100
Alignment explanation
Indices: 39617853--39618331 Score: 728
Period size: 100 Copynumber: 4.8 Consensus size: 100
39617843 TGTAGTGGAG
* * * * *
39617853 CAGATTAAAGCCACAACGGTGAATCTTGTTTCCCCGACATTGCAATTAGAAAGATTAAAGCTACA
1 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * *
39617918 ACAGCGAATCTTACTCCCTAAGCGATGCAGTGGAA
66 ACAGCGAATCTTACTCCCCAGGCGATGCAGCGGAA
* * * * * *
39617953 TAGATTAAAGCCACATCTGTGAATCTTGCTTCCCCGACATTGCGGTTAAAAAGATTAAATCTATA
1 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * *
39618018 ACGGGGAATCTTACTCCCCAGGC-AGTGCAGTGGAA
66 ACAGCGAATCTTACTCCCCAGGCGA-TGCAGCGGAA
39618053 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
39618118 ACAGCGAATCTTACTCCCCAGGCGATGCAGCGGAA
66 ACAGCGAATCTTACTCCCCAGGCGATGCAGCGGAA
39618153 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* *
39618218 ACAGTGAATCTTACTCCCCAGGCGATGCAGCGCAA
66 ACAGCGAATCTTACTCCCCAGGCGATGCAGCGGAA
* *
39618253 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGTA-TTAAAAAGATTAAAGCAACA
1 CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
**
39618317 ATGGCGAATCTTACT
66 ACAGCGAATCTTACT
39618332 TTCCAAAGGT
Statistics
Matches: 348, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
99 32 0.09
100 315 0.91
101 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (100 bp):
CAGATTAAAGCCACATCGGTGAATCATGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
ACAGCGAATCTTACTCCCCAGGCGATGCAGCGGAA
Found at i:39619073 original size:26 final size:25
Alignment explanation
Indices: 39619021--39619081 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
39619011 GGAAAGGTGA
* *
39619021 TTTTCTTTGTTTTCTTCTTTTCCTT
1 TTTTTTTTGTTTTCTTCTCTTCCTT
* **
39619046 TTTTTATTTGTTTTTTTCTCTTGGTT
1 TTTTT-TTTGTTTTCTTCTCTTCCTT
*
39619072 TTCTTTTTGT
1 TTTTTTTTGT
39619082 GTATCAAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (25 bp):
TTTTTTTTGTTTTCTTCTCTTCCTT
Found at i:39621912 original size:27 final size:27
Alignment explanation
Indices: 39621872--39621973 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 27
39621862 GTGTACCCTA
*
39621872 AAAGGAATGCCTTTGTGGCATATTTTG
1 AAAGGAATGCCTTTGTGGCATATTCTG
* * ** *
39621899 AAAGGAATGTCTTTGTAGTGTACTCTG
1 AAAGGAATGCCTTTGTGGCATATTCTG
*
39621926 AAAGGAATGCCTTTGTGGCATATCCTG
1 AAAGGAATGCCTTTGTGGCATATTCTG
* * * *
39621953 AATGGATTGCTTTTATGGCAT
1 AAAGGAATGCCTTTGTGGCAT
39621974 GTCCTGTATG
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (27 bp):
AAAGGAATGCCTTTGTGGCATATTCTG
Found at i:39622235 original size:26 final size:26
Alignment explanation
Indices: 39622199--39622249 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39622189 TTTCACTGCA
*
39622199 TAGGTGTTCGCCTATGAATTGTGATG
1 TAGGTGTTCGCCTATAAATTGTGATG
39622225 TAGGTGTTCGCCTATAAATTGTGAT
1 TAGGTGTTCGCCTATAAATTGTGAT
39622250 TGTGTACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (26 bp):
TAGGTGTTCGCCTATAAATTGTGATG
Found at i:39625399 original size:58 final size:58
Alignment explanation
Indices: 39625309--39625425 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 58
39625299 AGTGATTCTT
* *
39625309 TCTTGGTTAATATGACCAAGTCTCAAATGTTAAAAGTACGCGTTATTAGACTGAGAAG
1 TCTTGGTTAACATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGACTGAGAAG
* * *
39625367 TCTTGGTTAACATGACCAAGTCTGAAATGTTAAAGGTACGCCTTATTAGAGTGAGAAG
1 TCTTGGTTAACATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGACTGAGAAG
39625425 T
1 T
39625426 TTTAAGTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (58 bp):
TCTTGGTTAACATGACCAAGTCTCAAATGTTAAAAGTACGCCTTATTAGACTGAGAAG
Found at i:39627185 original size:22 final size:23
Alignment explanation
Indices: 39627147--39627204 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
39627137 CATTCCAAAT
*
39627147 CATCCATTA-AACATTCAACTAAA
1 CATCCATTATAA-GTTCAACTAAA
* *
39627170 CAT-CATTATAAGTTCACCTATA
1 CATCCATTATAAGTTCAACTAAA
39627192 CATGCCATTATAA
1 CAT-CCATTATAA
39627205 CCTTGGCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 16 0.55
23 5 0.17
24 8 0.28
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.31
Consensus pattern (23 bp):
CATCCATTATAAGTTCAACTAAA
Found at i:39631530 original size:16 final size:17
Alignment explanation
Indices: 39631504--39631535 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39631494 TTTAAATAGA
39631504 TAAATTAATTTTCTAAT
1 TAAATTAATTTTCTAAT
39631521 TAAA-TAATTTTCTAA
1 TAAATTAATTTTCTAA
39631536 ACCAAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAATTTTCTAAT
Found at i:39644506 original size:5 final size:5
Alignment explanation
Indices: 39644496--39644541 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
39644486 GCATACCCAT
* *
39644496 CAATC CAATC CAATC CAATC CAATC CAATG CAATG CAATC CAATC C
1 CAATC CAATC CAATC CAATC CAATC CAATC CAATC CAATC CAATC C
39644542 TCACGGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.39, C:0.37, G:0.04, T:0.20
Consensus pattern (5 bp):
CAATC
Found at i:39652150 original size:19 final size:19
Alignment explanation
Indices: 39652126--39652164 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39652116 CCATTATAGA
*
39652126 GAGGTGGCAAGGTGATGGT
1 GAGGTGGCAAGGTGACGGT
*
39652145 GAGGTGGTAAGGTGACGGT
1 GAGGTGGCAAGGTGACGGT
39652164 G
1 G
39652165 GTGCAAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.54, T:0.21
Consensus pattern (19 bp):
GAGGTGGCAAGGTGACGGT
Found at i:39657957 original size:19 final size:20
Alignment explanation
Indices: 39657935--39657977 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
39657925 GCCCACGTTC
*
39657935 AGGCT-TATGGCTCAATACA
1 AGGCTATATGGCTCAACACA
*
39657954 AGGCTACTATGGTTCAACACA
1 AGGCTA-TATGGCTCAACACA
39657975 AGG
1 AGG
39657978 TTACGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
21 15 0.75
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (20 bp):
AGGCTATATGGCTCAACACA
Found at i:39660368 original size:14 final size:14
Alignment explanation
Indices: 39660349--39660375 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39660339 GCTACCATTT
39660349 TACTATTATGTTGC
1 TACTATTATGTTGC
39660363 TACTATTATGTTG
1 TACTATTATGTTG
39660376 TTATTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (14 bp):
TACTATTATGTTGC
Found at i:39660443 original size:30 final size:30
Alignment explanation
Indices: 39660409--39660471 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
39660399 ACTTATTTTA
* *
39660409 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
*
39660439 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
39660469 TTG
1 TTG
39660472 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:39660774 original size:16 final size:15
Alignment explanation
Indices: 39660753--39660782 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39660743 TTTTAGTTGA
39660753 GTCCGGCCCGAGCCCG
1 GTCCGGCCCG-GCCCG
39660769 GTCCGGCCCGGCCC
1 GTCCGGCCCGGCCC
39660783 ATGAGCACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.03, C:0.53, G:0.37, T:0.07
Consensus pattern (15 bp):
GTCCGGCCCGGCCCG
Found at i:39661445 original size:15 final size:13
Alignment explanation
Indices: 39661425--39661459 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
39661415 TTATCTAAAG
39661425 GTTAATTAGGTTAA
1 GTTAATTA-GTTAA
39661439 TGTTAATTAGTTAA
1 -GTTAATTAGTTAA
39661453 GTTAATT
1 GTTAATT
39661460 TAAGTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 5 0.25
15 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (13 bp):
GTTAATTAGTTAA
Found at i:39663622 original size:130 final size:130
Alignment explanation
Indices: 39663379--39663625 Score: 352
Period size: 130 Copynumber: 1.9 Consensus size: 130
39663369 ACACTGCCGT
** ** * *
39663379 GTGTTCAACAAATTTAGGTTGTTTTTTAGTTCACACGGTTTGGCGACACGACTGTGTGACACTTA
1 GTGTTCAACAAATTTAGGTTGTTTTTTAGTTCACACGGCCTGGCGACACGACCATATGACACTGA
** * **
39663444 GTTACATGGCATGCAATTGTTGTACGATTTGGGGTCACAACTTTGTGATGGCACTGTGAACGGTC
66 GTTACATGGCATGCAATTGTTCCACGATTTGGGGACACAACTGGGTGATGGCACTGTGAACGGTC
*
39663509 GTGTTCAACAAATTTAGGTTGTTTTTTAGTTCACACGGCCTGGCGACACGGCCATATGACACTCG
1 GTGTTCAACAAATTTAGGTTGTTTTTTAGTTCACACGGCCTGGCGACACGACCATATGACACT-G
* *
39663574 A-TTACATGGCATGCAATTGTTCCACGATTTGTGGACACGACTGGGTGATGGC
65 AGTTACATGGCATGCAATTGTTCCACGATTTGGGGACACAACTGGGTGATGGC
39663626 GCCACACAGC
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 101 0.99
131 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (130 bp):
GTGTTCAACAAATTTAGGTTGTTTTTTAGTTCACACGGCCTGGCGACACGACCATATGACACTGA
GTTACATGGCATGCAATTGTTCCACGATTTGGGGACACAACTGGGTGATGGCACTGTGAACGGTC
Found at i:39667882 original size:18 final size:17
Alignment explanation
Indices: 39667841--39667890 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
39667831 ATAAATCTAA
*
39667841 AAAATCTTTAAAATAAAT
1 AAAAT-TTTAAAAAAAAT
39667859 ATAAATTTTAAAAAAAATT
1 A-AAATTTTAAAAAAAA-T
*
39667878 AAAATATTAAAAA
1 AAAATTTTAAAAA
39667891 TCATGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTTTAAAAAAAAT
Found at i:39673387 original size:39 final size:39
Alignment explanation
Indices: 39673333--39673412 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
39673323 TAGGGATCCT
*
39673333 AAGGATTAAAAATATAAATAATAGAACATGTAAAACGTG
1 AAGGATTAAAAATATAAATAATAGAACATGTAAAACATG
* *
39673372 AAGGATTAAGAATATAAATAATAGAGCATGTAAAACATG
1 AAGGATTAAAAATATAAATAATAGAACATGTAAAACATG
39673411 AA
1 AA
39673413 ATCTATCTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (39 bp):
AAGGATTAAAAATATAAATAATAGAACATGTAAAACATG
Done.