Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 189 of 207
Found at i:57344142 original size:106 final size:106
Alignment explanation
Indices: 57343957--57344169 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
57343947 TAGAGTTGAC
57343957 AATGAAGTGTTCACTGATTGATTTCTCATGCTTTGTTTCTCAAGTTCAAATATTTTCTTCTAATT
1 AATGAAGTGTTCACTGATTGATTTCTCATGCTTTGTTTCTCAAGTTCAAATATTTTCTTCTAATT
57344022 TCCTTTTAAGTCAAAATTTTCTTTAATAGATTGATGTCATT
66 TCCTTTTAAGTCAAAATTTTCTTTAATAGATTGATGTCATT
57344063 AATGAAGTGTTCACTGATTGATTTCTCATGCTTTGTTTCTCAAGTTCAAATATTTTCTTCTAATT
1 AATGAAGTGTTCACTGATTGATTTCTCATGCTTTGTTTCTCAAGTTCAAATATTTTCTTCTAATT
57344128 TCCTTTTAAGTCAAAATTTTCTTTAATAGATTGATGTCATT
66 TCCTTTTAAGTCAAAATTTTCTTTAATAGATTGATGTCATT
57344169 A
1 A
57344170 CCATGTTGTA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (106 bp):
AATGAAGTGTTCACTGATTGATTTCTCATGCTTTGTTTCTCAAGTTCAAATATTTTCTTCTAATT
TCCTTTTAAGTCAAAATTTTCTTTAATAGATTGATGTCATT
Found at i:57345876 original size:2 final size:2
Alignment explanation
Indices: 57345869--57345898 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
57345859 GATGTCCTTT
57345869 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57345899 TGTTAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:57352649 original size:9 final size:8
Alignment explanation
Indices: 57352622--57352652 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
57352612 TGTCCCATCG
57352622 CTGCTCAC
1 CTGCTCAC
57352630 CTGCTCAC
1 CTGCTCAC
57352638 CTGCTCCAC
1 CTGCT-CAC
57352647 CTGCTC
1 CTGCTC
57352653 TGCCGCTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.52, G:0.13, T:0.26
Consensus pattern (8 bp):
CTGCTCAC
Found at i:57352894 original size:16 final size:14
Alignment explanation
Indices: 57352867--57352912 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
57352857 ATTTTCGGTA
*
57352867 TATTTATTTTCTTT
1 TATTTTTTTTCTTT
57352881 TAGTTTTTTTTTCTCTT
1 TA--TTTTTTTTCT-TT
57352898 TATTTTTTTTCTTT
1 TATTTTTTTTCTTT
57352912 T
1 T
57352913 CGAATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.18
15 10 0.36
16 9 0.32
17 4 0.14
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (14 bp):
TATTTTTTTTCTTT
Found at i:57352904 original size:17 final size:16
Alignment explanation
Indices: 57352873--57352912 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
57352863 GGTATATTTA
57352873 TTTTCTTTTAGTTTTT
1 TTTTCTTTTAGTTTTT
57352889 TTTTCTCTTTA--TTTT
1 TTTTCT-TTTAGTTTTT
57352904 TTTTCTTTT
1 TTTTCTTTT
57352913 CGAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 6 0.26
17 4 0.17
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTAGTTTTT
Found at i:57352977 original size:1 final size:1
Alignment explanation
Indices: 57352971--57352995 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
57352961 CATAACATAT
57352971 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
57352996 CATACCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:57353611 original size:3 final size:3
Alignment explanation
Indices: 57353553--57353602 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
57353543 TTTGTTAACT
* *
57353553 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
57353598 GTA TT
1 TTA TT
57353603 GGTATTATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.03
3 38 0.97
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:57353683 original size:22 final size:23
Alignment explanation
Indices: 57353636--57353684 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
57353626 ATCTCTATTC
*
57353636 ATATATACTTATGTATTTTCAAAT
1 ATATATACTTATGTATTATC-AAT
57353660 ATATATATCTTAT-TATTATC-AT
1 ATATATA-CTTATGTATTATCAAT
57353682 ATA
1 ATA
57353685 AGTGCTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATACTTATGTATTATCAAT
Found at i:57353810 original size:36 final size:36
Alignment explanation
Indices: 57353731--57353810 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
57353721 AATTTGTTTA
* *
57353731 ATATATATACGTATACTCATATTTCTTTTTATATAT
1 ATATATATACATATACTCATATTTATTTTTATATAT
* *
57353767 ATCTATATACATATACAT-ATTTTTATTTTTATA-AGT
1 ATATATATACATATAC-TCATATTTATTTTTATATA-T
57353803 ATATATAT
1 ATATATAT
57353811 TTATATGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (36 bp):
ATATATATACATATACTCATATTTATTTTTATATAT
Found at i:57358697 original size:7 final size:8
Alignment explanation
Indices: 57358676--57358705 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
57358666 TCTCATGAAT
57358676 TCAAAAAA
1 TCAAAAAA
57358684 TCAAAAAA
1 TCAAAAAA
57358692 TCAAAAAAA
1 TC-AAAAAA
57358701 TCAAA
1 TCAAA
57358706 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (8 bp):
TCAAAAAA
Found at i:57359577 original size:24 final size:22
Alignment explanation
Indices: 57359542--57359592 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
57359532 ACTTTGATTC
*
57359542 AAAAAAAAAAAAAAGAAGAAGAT
1 AAAAAAAAAAAAAAGAAAAAG-T
* *
57359565 AAAAAAATGAAAAATGAAAAAGT
1 AAAAAAA-AAAAAAAGAAAAAGT
57359588 AAAAA
1 AAAAA
57359593 TGGAGAGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (22 bp):
AAAAAAAAAAAAAAGAAAAAGT
Found at i:57360971 original size:88 final size:88
Alignment explanation
Indices: 57360831--57361435 Score: 1097
Period size: 88 Copynumber: 6.9 Consensus size: 88
57360821 ATGAAGTTAA
57360831 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
57360896 ACAGCGAAGCAGATTGAAGACAC
66 ACAGCGAAGCAGATTGAAGACAC
*
57360919 AAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
57360984 ACAGCGAAGCAGA-TGAAGACAC
66 ACAGCGAAGCAGATTGAAGACAC
57361006 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
57361071 ACAGCGAAGCAGATTGAAGACAC
66 ACAGCGAAGCAGATTGAAGACAC
57361094 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
*
57361159 ACAGCGAAGCAGATCGAAGACAC
66 ACAGCGAAGCAGATTGAAGACAC
*
57361182 AAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
57361247 ACAGCGAAGCAGATTGAAGACAC
66 ACAGCGAAGCAGATTGAAGACAC
*
57361270 AAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
57361335 ACAGCGAAGCAGATTGAAGACAC
66 ACAGCGAAGCAGATTGAAGACAC
* * ** * *
57361358 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCTGCATTA
1 AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
*
57361422 ACAGCGGAGCAGAT
66 ACAGCGAAGCAGAT
57361436 CAAAGATAGT
Statistics
Matches: 503, Mismatches: 13, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
87 119 0.24
88 384 0.76
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
AAACCTTGCCTCTTTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTG
ACAGCGAAGCAGATTGAAGACAC
Found at i:57361506 original size:44 final size:44
Alignment explanation
Indices: 57361451--57361731 Score: 171
Period size: 44 Copynumber: 6.4 Consensus size: 44
57361441 ATAGTAATCC
* *
57361451 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGATCT
* * * ***
57361495 TATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-CAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGATCT
* * * * ** *
57361536 TATCTCTCTGAGGTTACAGTGTAGTAGACCGAAGAATTGCA-GATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TACAGGATCT
* * **
57361582 TATCCCCCTGAAGTTACAGTGGAGCAGATT-GAAGCCAGAGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG-GATCT
* * ** * ** *
57361626 TATCTCCCCG-AGATTACAGCGGAGCAGA-TCGAAGACACTATCC
1 TATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATACAGGATCT
** * *
57361669 TATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGATCT
* *
57361713 TATCTCTCTGAGGTTACAG
1 TATCTCCCTGAAGTTACAG
57361732 CAGAGTAGGT
Statistics
Matches: 179, Mismatches: 46, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
41 28 0.16
42 5 0.03
43 31 0.17
44 85 0.47
45 2 0.01
46 28 0.16
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAGGATCT
Found at i:57361687 original size:43 final size:44
Alignment explanation
Indices: 57361422--57361692 Score: 171
Period size: 44 Copynumber: 6.2 Consensus size: 44
57361412 TCCTGCATTA
* * *
57361422 ACAGCGGAGCAGATCAAAGATAGTA-ATCCTATCTCCCTGAAGTT
1 ACAGTGGAGCAGATCGAAGACAG-AGATCCTATCTCCCTGAAGTT
* * * * * * *
57361466 ACAGTGGAGCGGAT-TAAAATAAAGGATCTTATCTCTCTGAAGTT
1 ACAGTGGAGCAGATCGAAGACAGA-GATCCTATCTCCCTGAAGTT
* * * * * * *
57361510 ACAGTAGAGTAGATCGCA-TCAG-G-TCTTATCTCTCTGAGGTT
1 ACAGTGGAGCAGATCGAAGACAGAGATCCTATCTCCCTGAAGTT
* * * * *
57361551 ACAGTGTAGTAGACCGAAGA-ATTGCAGATCTTATCCCCCTGAAGTT
1 ACAGTGGAGCAGATCGAAGACA--G-AGATCCTATCTCCCTGAAGTT
* * * *
57361597 ACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCCG-AGATT
1 ACAGTGGAGCAGATCGAAGACAGAGATCCTATCTCCCTGAAG-TT
* **
57361641 ACAGCGGAGCAGATCGAAGACA-CTATCCTATCTCCCTGAAGTT
1 ACAGTGGAGCAGATCGAAGACAGAGATCCTATCTCCCTGAAGTT
57361684 ACAGTGGAG
1 ACAGTGGAG
57361693 TGGGTTAAAA
Statistics
Matches: 176, Mismatches: 39, Indels: 25
0.73 0.16 0.10
Matches are distributed among these distances:
41 32 0.18
42 2 0.01
43 30 0.17
44 78 0.44
45 3 0.02
46 30 0.17
47 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
ACAGTGGAGCAGATCGAAGACAGAGATCCTATCTCCCTGAAGTT
Found at i:57362116 original size:9 final size:8
Alignment explanation
Indices: 57362089--57362119 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
57362079 TGTCCCATCG
57362089 CTGCTCAC
1 CTGCTCAC
57362097 CTGCTCAC
1 CTGCTCAC
57362105 CTGCTCCAC
1 CTGCT-CAC
57362114 CTGCTC
1 CTGCTC
57362120 TGCCGCTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.52, G:0.13, T:0.26
Consensus pattern (8 bp):
CTGCTCAC
Found at i:57362361 original size:16 final size:14
Alignment explanation
Indices: 57362334--57362379 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
57362324 ATTTTCGGTA
*
57362334 TATTTATTTTCTTT
1 TATTTTTTTTCTTT
57362348 TAGTTTTTTTTTCTCTT
1 TA--TTTTTTTTCT-TT
57362365 TATTTTTTTTCTTT
1 TATTTTTTTTCTTT
57362379 T
1 T
57362380 CGAATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.18
15 10 0.36
16 9 0.32
17 4 0.14
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (14 bp):
TATTTTTTTTCTTT
Found at i:57362371 original size:17 final size:16
Alignment explanation
Indices: 57362340--57362379 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
57362330 GGTATATTTA
57362340 TTTTCTTTTAGTTTTT
1 TTTTCTTTTAGTTTTT
57362356 TTTTCTCTTTA--TTTT
1 TTTTCT-TTTAGTTTTT
57362371 TTTTCTTTT
1 TTTTCTTTT
57362380 CGAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 6 0.26
17 4 0.17
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTAGTTTTT
Found at i:57363077 original size:3 final size:3
Alignment explanation
Indices: 57363016--57363068 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
57363006 TTTGTTAACT
* *
57363016 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
57363061 TTA GTA TT
1 TTA TTA TT
57363069 GGTATTATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:57363149 original size:22 final size:23
Alignment explanation
Indices: 57363102--57363150 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
57363092 ATCTCTATTC
*
57363102 ATATATACTTATGTATTTTCAAAT
1 ATATATACTTATGTATTATC-AAT
57363126 ATATATATCTTAT-TATTATC-AT
1 ATATATA-CTTATGTATTATCAAT
57363148 ATA
1 ATA
57363151 AGTGCTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
24 13 0.57
25 5 0.22
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATACTTATGTATTATCAAT
Found at i:57363272 original size:34 final size:34
Alignment explanation
Indices: 57363197--57363274 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 34
57363187 AATTTGTTTA
* *
57363197 ATATATATACGTATACTCATATTTCTTTTTATAT
1 ATATATATACATATACTCATATTTATTTTTATAT
* *
57363231 ATCTATATACATATACAT-ATTTTTATTTTTATAAGT
1 ATATATATACATATAC-TCATATTTATTTTTAT-A-T
57363267 ATATATAT
1 ATATATAT
57363275 TTATATGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 26 0.72
35 2 0.06
36 8 0.22
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (34 bp):
ATATATATACATATACTCATATTTATTTTTATAT
Found at i:57368013 original size:34 final size:33
Alignment explanation
Indices: 57367970--57368078 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 33
57367960 AGAAAATATA
*
57367970 AAAATAAAATATTTGAAATATTTTAATATATTTT
1 AAAATAAAATATTT-AAATATTTTAATATAATTT
*
57368004 AAAATAAAATATTT---TATTTCAAAATATAATTT
1 AAAATAAAATATTTAAATATTT--TAATATAATTT
57368036 AAAATAAAATATTCTAAATATTTTAATATAATTT
1 AAAATAAAATATT-TAAATATTTTAATATAATTT
*
57368070 AATATAAAA
1 AAAATAAAA
57368079 ATAATTATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
30 5 0.08
32 22 0.34
33 1 0.02
34 32 0.49
36 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (33 bp):
AAAATAAAATATTTAAATATTTTAATATAATTT
Found at i:57368014 original size:17 final size:17
Alignment explanation
Indices: 57367994--57368047 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
57367984 GAAATATTTT
57367994 AATATATTTTAAAAT-A
1 AATATATTTTAAAATAA
**
57368010 AA-ATATTTT-ATTTCAA
1 AATATATTTTAAAAT-AA
*
57368026 AATATAATTTAAAATAA
1 AATATATTTTAAAATAA
57368043 AATAT
1 AATAT
57368048 TCTAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 2 0.07
15 7 0.24
16 5 0.17
17 13 0.45
18 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATATTTTAAAATAA
Found at i:57368017 original size:15 final size:15
Alignment explanation
Indices: 57367997--57368053 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
57367987 ATATTTTAAT
57367997 ATATTTTAAAATAAA
1 ATATTTTAAAATAAA
**
57368012 ATATTTT-ATTTCAAA
1 ATATTTTAAAAT-AAA
57368027 ATATAATTTAAAATAAA
1 ATAT--TTTAAAATAAA
*
57368044 ATATTCTAAA
1 ATATTTTAAA
57368054 TATTTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 2 0.06
15 19 0.58
17 10 0.30
18 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTTTAAAATAAA
Found at i:57368107 original size:21 final size:22
Alignment explanation
Indices: 57368081--57368150 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
57368071 ATATAAAAAT
57368081 AATTATATTA-AAAATTTATTA
1 AATTATATTATAAAATTTATTA
* **
57368102 AATTATA-TATTATTTTTATTA
1 AATTATATTATAAAATTTATTA
57368123 AATTATATTTAATAATAATTATATTA
1 AATTATA-TT-ATAA-AATT-TATTA
57368149 AA
1 AA
57368151 ATACGATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 22 0.59
23 1 0.03
24 3 0.08
25 2 0.05
26 7 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTATATTATAAAATTTATTA
Found at i:57372122 original size:30 final size:30
Alignment explanation
Indices: 57372086--57372156 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
57372076 AAATTTATCA
*
57372086 ATTCAGTTGTTAAGTGGCTACACTGAATCG
1 ATTCAGTTGTTAAGTGGCTACACTGAACCG
*
57372116 ATTCAGTTATTAAGTGGCTACACTGAACCG
1 ATTCAGTTGTTAAGTGGCTACACTGAACCG
*
57372146 ATTCTGTTGTT
1 ATTCAGTTGTT
57372157 TATTGAGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (30 bp):
ATTCAGTTGTTAAGTGGCTACACTGAACCG
Found at i:57374370 original size:29 final size:30
Alignment explanation
Indices: 57374311--57374368 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
57374301 TCCGAGCCTT
*
57374311 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
57374341 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
57374369 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:57374597 original size:13 final size:13
Alignment explanation
Indices: 57374579--57374610 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
57374569 TTTCCAGCAA
57374579 TTATGAATTTATT
1 TTATGAATTTATT
57374592 TTATGAATTTATT
1 TTATGAATTTATT
*
57374605 TGATGA
1 TTATGA
57374611 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:57374818 original size:50 final size:50
Alignment explanation
Indices: 57374705--57374946 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
57374695 ATTTGGGTAA
* * *
57374705 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
57374761 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
57374811 AGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
57374861 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
57374911 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
57374947 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 89 0.54
51 29 0.18
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:57374893 original size:100 final size:103
Alignment explanation
Indices: 57374705--57374954 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
57374695 ATTTGGGTAA
57374705 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
57374770 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * * *
57374811 AGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
57374873 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
57374911 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
57374955 GTTATTATCA
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 38 0.29
105 2 0.02
106 39 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:57380685 original size:25 final size:26
Alignment explanation
Indices: 57380654--57380703 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
57380644 AAGTAATTAC
57380654 AAATAATAA-AAATTACAAAAAAAAT
1 AAATAATAACAAATTACAAAAAAAAT
*
57380679 AAATAATAACGTAATTACAAAAAAA
1 AAATAATAAC-AAATTACAAAAAAA
57380704 GTGCACCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (26 bp):
AAATAATAACAAATTACAAAAAAAAT
Found at i:57385944 original size:6 final size:6
Alignment explanation
Indices: 57385933--57386152 Score: 426
Period size: 6 Copynumber: 37.0 Consensus size: 6
57385923 CTATTTTAAT
57385933 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
57385981 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
57386029 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATAC-
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
57386076 -ATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
57386123 TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA
57386153 CATTTATAAT
Statistics
Matches: 212, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.02
6 208 0.98
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:57390075 original size:6 final size:6
Alignment explanation
Indices: 57390058--57390105 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
57390048 TCCTGACAAG
*
57390058 GAGAAA GGGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GA-AAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
57390105 G
1 G
57390106 GATACAGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:57396550 original size:3 final size:3
Alignment explanation
Indices: 57396537--57396569 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
57396527 TGGCCTCCCA
*
57396537 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57396570 GTCGTATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:57409054 original size:5 final size:5
Alignment explanation
Indices: 57409037--57409065 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
57409027 TGTTTAAGTA
57409037 TATAT TATA- TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
57409066 AATAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:57409837 original size:24 final size:24
Alignment explanation
Indices: 57409810--57409856 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57409800 ATTGAAATGG
57409810 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
57409834 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
57409857 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:57411724 original size:28 final size:29
Alignment explanation
Indices: 57411656--57411728 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
57411646 GGGACTATAG
* * *
57411656 TGCTCACACAAGCTGATAGTTATCACGGT
1 TGCTCACACAAGCTGACAATTATCACAGT
* *
57411685 TGCTCACACAAGCTGACAATTATGA-ATT
1 TGCTCACACAAGCTGACAATTATCACAGT
57411713 TGCTCACACAAGCTGA
1 TGCTCACACAAGCTGA
57411729 AGTCGTATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 17 0.44
29 22 0.56
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (29 bp):
TGCTCACACAAGCTGACAATTATCACAGT
Found at i:57415424 original size:16 final size:16
Alignment explanation
Indices: 57415403--57415447 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
57415393 TCGTCTCATA
57415403 TTCATTTCTCATATTT
1 TTCATTTCTCATATTT
*
57415419 TTCATTTC-AATATTT
1 TTCATTTCTCATATTT
57415434 TCTCA--TCTCATATT
1 T-TCATTTCTCATATT
57415448 CATTTATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.08
15 12 0.48
16 11 0.44
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.58
Consensus pattern (16 bp):
TTCATTTCTCATATTT
Found at i:57415443 original size:43 final size:43
Alignment explanation
Indices: 57415389--57415474 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
57415379 TCATATTTCA
* * *
57415389 TTTCTCGTCTCATATTCATTTCTCATATTTTTCATTTCAATAT
1 TTTCTCATCTCATATTCATTTATCATATTTGTCATTTCAATAT
*
57415432 TTTCTCATCTCATATTCATTTATCATCTTTGTCATTTCAATAT
1 TTTCTCATCTCATATTCATTTATCATATTTGTCATTTCAATAT
57415475 CAATCACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.22, C:0.21, G:0.02, T:0.55
Consensus pattern (43 bp):
TTTCTCATCTCATATTCATTTATCATATTTGTCATTTCAATAT
Found at i:57427531 original size:16 final size:18
Alignment explanation
Indices: 57427500--57427537 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
57427490 TTTTAGAATT
*
57427500 TTTTTTAAAATTTAT-AA
1 TTTTTTAAAATATATAAA
57427517 TTTTTTAAAA-ATATAAA
1 TTTTTTAAAATATATAAA
57427534 TTTT
1 TTTT
57427538 GAAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTTAAAATATATAAA
Found at i:57427535 original size:17 final size:18
Alignment explanation
Indices: 57427499--57427537 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57427489 TTTTTAGAAT
* *
57427499 TTTTTTTAAAATTTATAA
1 TTTTTTAAAAATATATAA
57427517 TTTTTTAAAAATATA-AA
1 TTTTTTAAAAATATATAA
57427534 TTTT
1 TTTT
57427538 GAAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTTAAAAATATATAA
Found at i:57427558 original size:20 final size:20
Alignment explanation
Indices: 57427519--57427578 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 20
57427509 ATTTATAATT
57427519 TTTTAAAAATATAAATTTTGAAA
1 TTTTAAAAAT-T--ATTTTGAAA
57427542 TTTTTAAAAA-TATTTTG-AA
1 -TTTTAAAAATTATTTTGAAA
57427561 TTTTAAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
57427579 TTTTCTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
20 6 0.18
22 1 0.03
24 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAA
Found at i:57427564 original size:19 final size:20
Alignment explanation
Indices: 57427518--57427582 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 20
57427508 AATTTATAAT
57427518 TTTTTAAAAATATAAATTTTGAAA
1 TTTTTAAAAAT-T--ATTTTG-AA
57427542 TTTTTAAAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
57427561 -TTTTAAAAATTATTTTG-A
1 TTTTTAAAAATTATTTTGAA
57427579 TTTT
1 TTTT
57427583 CTTTTTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.26
19 12 0.31
20 6 0.15
22 1 0.03
24 10 0.26
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:57430879 original size:24 final size:23
Alignment explanation
Indices: 57430840--57430884 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
57430830 CCATTTACCC
57430840 ATATTAATTCGAAGTTTGTAATA
1 ATATTAATTCGAAGTTTGTAATA
*
57430863 ATATTATATTTGAAGTTTGTAA
1 ATATTA-ATTCGAAGTTTGTAA
57430885 ATTCATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (23 bp):
ATATTAATTCGAAGTTTGTAATA
Found at i:57434086 original size:11 final size:11
Alignment explanation
Indices: 57434070--57434101 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
57434060 TCGGTTTTAA
57434070 TTAAATAAATT
1 TTAAATAAATT
57434081 TTAAATAAATT
1 TTAAATAAATT
*
57434092 TTAAAAAAAT
1 TTAAATAAAT
57434102 AATTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAATAAATT
Found at i:57437534 original size:33 final size:33
Alignment explanation
Indices: 57437492--57437559 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
57437482 ATTTCATTTT
57437492 CGGAGACTTGATCCATAGAAATATCTTTGTTTC
1 CGGAGACTTGATCCATAGAAATATCTTTGTTTC
* * * *
57437525 CGGAGACTTGATCCGTTGCAATGTCTTTGTTTC
1 CGGAGACTTGATCCATAGAAATATCTTTGTTTC
57437558 CG
1 CG
57437560 TCCATGGCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (33 bp):
CGGAGACTTGATCCATAGAAATATCTTTGTTTC
Found at i:57438401 original size:18 final size:18
Alignment explanation
Indices: 57438374--57438465 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
57438364 TACGACCGTT
57438374 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
57438392 TACGGCACTATTCACATA
1 TACGGTACTATTCACGTA
*
57438410 TACAGTACTATT-ACGTA
1 TACGGTACTATTCACGTA
*
57438427 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
57438445 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
57438463 TAC
1 TAC
57438466 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 14 0.22
18 50 0.78
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:57438429 original size:35 final size:36
Alignment explanation
Indices: 57438378--57438465 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 36
57438368 ACCGTTTACG
57438378 GTACTATTCACGTATACGGCACTATTCACATATACA
1 GTACTATTCACGTATACGGCACTATTCACATATACA
* *
57438414 GTACTATT-ACGTATACGGCACTATTCACGTATACG
1 GTACTATTCACGTATACGGCACTATTCACATATACA
*
57438449 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
57438466 AGTAGTTGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
35 32 0.67
36 16 0.33
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (36 bp):
GTACTATTCACGTATACGGCACTATTCACATATACA
Found at i:57451178 original size:123 final size:124
Alignment explanation
Indices: 57450921--57451199 Score: 472
Period size: 123 Copynumber: 2.3 Consensus size: 124
57450911 TTATTTCGAG
*
57450921 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACTAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
**
57450985 GAAATCGTGCCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
65 GAAATCGAACCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
57451045 TTGACGTTTCTGAGCAAATAGTATTAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG-G
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
57451109 AAATCGAACCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGAACCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
* *
57451168 TTGACGTTTCTGAGCATATAATATAAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
57451200 GCCCTCGTGG
Statistics
Matches: 146, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
123 86 0.59
124 59 0.40
125 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGAACCATCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:57453266 original size:29 final size:29
Alignment explanation
Indices: 57453220--57453420 Score: 314
Period size: 29 Copynumber: 7.0 Consensus size: 29
57453210 CCTAAGACAC
*
57453220 GTTAGGGTTAGGATTTTTAATTAAATTAG
1 GTTAGGGTTAGGGTTTTTAATTAAATTAG
* *
57453249 GTTAGGGTTAAGGCTTTTAATTAAATTAG
1 GTTAGGGTTAGGGTTTTTAATTAAATTAG
*
57453278 GTTAGGATTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTAGGGTTTTTAATTAAATTAG
* * *
57453307 TTTAGGGTTAGGGCTTTTAATTAAATTAA
1 GTTAGGGTTAGGGTTTTTAATTAAATTAG
* *
57453336 ATTA-GGTTAGGGCTTTTAATTAAATTAG
1 GTTAGGGTTAGGGTTTTTAATTAAATTAG
57453364 GTTAGGGTTAGGGTTTTTAATTAAATTAG
1 GTTAGGGTTAGGGTTTTTAATTAAATTAG
57453393 GTTAGGGTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTAGGGTTTTTAATTAAATTA
57453421 CGATTTTTAT
Statistics
Matches: 157, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
28 26 0.17
29 131 0.83
ACGTcount: A:0.30, C:0.01, G:0.24, T:0.44
Consensus pattern (29 bp):
GTTAGGGTTAGGGTTTTTAATTAAATTAG
Found at i:57453375 original size:86 final size:87
Alignment explanation
Indices: 57453220--57453420 Score: 332
Period size: 86 Copynumber: 2.3 Consensus size: 87
57453210 CCTAAGACAC
* **
57453220 GTTAGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTAAGGCTTTTAATTAAATTAGGTTAGGA
1 GTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAAGGCTTTTAATTAAATTAGGTTAGGA
57453285 TTAGGGTTTTTAATTAAATTAG
66 TTAGGGTTTTTAATTAAATTAG
* * * *
57453307 TTTAGGGTTAGGGCTTTTAATTAAATTAAATTA-GGTTAGGGCTTTTAATTAAATTAGGTTAGGG
1 GTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAAGGCTTTTAATTAAATTAGGTTAGGA
57453371 TTAGGGTTTTTAATTAAATTAG
66 TTAGGGTTTTTAATTAAATTAG
57453393 GTTAGGGTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTAGGGTTTTTAATTAAATTA
57453421 CGATTTTTAT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 77 0.73
87 28 0.27
ACGTcount: A:0.30, C:0.01, G:0.24, T:0.44
Consensus pattern (87 bp):
GTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAAGGCTTTTAATTAAATTAGGTTAGGA
TTAGGGTTTTTAATTAAATTAG
Found at i:57455631 original size:25 final size:25
Alignment explanation
Indices: 57455581--57455636 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
57455571 CTTTTATAAC
*
57455581 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
57455606 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
57455629 AAATAATA
1 AAATAATA
57455637 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:57455761 original size:30 final size:30
Alignment explanation
Indices: 57455727--57455796 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
57455717 GCCATTGTTG
*
57455727 AAAATATTAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
*
57455757 AAAATATAAAAAAATTTAAATTTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
57455787 AAAA-ATAAAA
1 AAAATATAAAA
57455797 TTGAATGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 6 0.16
30 32 0.84
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:57455773 original size:20 final size:20
Alignment explanation
Indices: 57455727--57455773 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
57455717 GCCATTGTTG
* *
57455727 AAAATATTAAAAAATTTAAA
1 AAAATTTTAAAAAATATAAA
**
57455747 ATTATTTTAAAAAATATAAA
1 AAAATTTTAAAAAATATAAA
57455767 AAAATTT
1 AAAATTT
57455774 AAATTTATTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAAAAATATAAA
Found at i:57455851 original size:22 final size:21
Alignment explanation
Indices: 57455826--57455876 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
57455816 TAATATGGAT
*
57455826 TTGAGAGATTTTTGGAAGGAAA
1 TTGAGAGA-TTTTAGAAGGAAA
*
57455848 TTGAGAGGATTTTAGAAGGAAT
1 TTGAGA-GATTTTAGAAGGAAA
57455870 TTGAGAG
1 TTGAGAG
57455877 TTTGAGAGAA
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:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTAGAAGGAAA
Found at i:57455883 original size:30 final size:30
Alignment explanation
Indices: 57455848--57455906 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
57455838 TGGAAGGAAA
* *
57455848 TTGAGAGGATTTTAGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTAGAAGGAAATTGAGAGT
*
57455878 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTAGAAGGAAATTGAGAG
57455907 GATTTTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTAGAAGGAAATTGAGAGT
Found at i:57455883 original size:52 final size:52
Alignment explanation
Indices: 57455825--57455979 Score: 283
Period size: 52 Copynumber: 3.0 Consensus size: 52
57455815 TTAATATGGA
* *
57455825 TTTGAGAGATTTTTGGAAGGAAATTGAGAGGATTTTAGAAGGAATTTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAG
57455877 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAG
*
57455929 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGA
57455980 TAGGATTTGT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 100 1.00
ACGTcount: A:0.35, C:0.00, G:0.34, T:0.31
Consensus pattern (52 bp):
TTTGAGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAG
Found at i:57455903 original size:22 final size:22
Alignment explanation
Indices: 57455878--57455928 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
57455868 ATTTGAGAGT
57455878 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
57455900 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGAGAATTTTGGAAGGAAA
57455922 TTGAGAG
1 TTGAGAG
57455929 TTTGAGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:57455934 original size:30 final size:30
Alignment explanation
Indices: 57455900--57455958 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
57455890 TGGAAGGAAA
* *
57455900 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
57455930 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
57455959 GATTTTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:57455955 original size:22 final size:22
Alignment explanation
Indices: 57455930--57455979 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
57455920 ATTTGAGAGT
57455930 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
57455952 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
57455974 TTGAGA
1 TTGAGA
57455980 TAGGATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:57457199 original size:19 final size:19
Alignment explanation
Indices: 57457172--57457227 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
57457162 TTATTTTTTA
*
57457172 TTTTATATAATTTTAATAT
1 TTTTTTATAATTTTAATAT
*
57457191 TTTTTTATAATTACTAATAT
1 TTTTTTATAATT-TTAATAT
*
57457211 TTTTATT-TATTTTTAAT
1 TTTT-TTATAATTTTAAT
57457228 TTTGATTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 15 0.48
20 14 0.45
21 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTTATAATTTTAATAT
Found at i:57477277 original size:9 final size:9
Alignment explanation
Indices: 57477256--57477317 Score: 88
Period size: 9 Copynumber: 6.9 Consensus size: 9
57477246 TGGTTAAAAA
*
57477256 TTAACCGAC
1 TTAACCGAT
*
57477265 TTAACTGAT
1 TTAACCGAT
*
57477274 TTAACCGAC
1 TTAACCGAT
57477283 TTAACCGAT
1 TTAACCGAT
57477292 TTAACCGAT
1 TTAACCGAT
*
57477301 TTAACCGAC
1 TTAACCGAT
57477310 TTAACCGA
1 TTAACCGA
57477318 GAAATTGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (9 bp):
TTAACCGAT
Found at i:57477279 original size:18 final size:18
Alignment explanation
Indices: 57477256--57477317 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
57477246 TGGTTAAAAA
*
57477256 TTAACCGACTTAACTGAT
1 TTAACCGACTTAACCGAT
57477274 TTAACCGACTTAACCGAT
1 TTAACCGACTTAACCGAT
* *
57477292 TTAACCGATTTAACCGAC
1 TTAACCGACTTAACCGAT
57477310 TTAACCGA
1 TTAACCGA
57477318 GAAATTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (18 bp):
TTAACCGACTTAACCGAT
Found at i:57477286 original size:27 final size:27
Alignment explanation
Indices: 57477256--57477317 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
57477246 TGGTTAAAAA
*
57477256 TTAACCGACTTAACTGATTTAACCGAC
1 TTAACCGACTTAACCGATTTAACCGAC
*
57477283 TTAACCGATTTAACCGATTTAACCGAC
1 TTAACCGACTTAACCGATTTAACCGAC
57477310 TTAACCGA
1 TTAACCGA
57477318 GAAATTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (27 bp):
TTAACCGACTTAACCGATTTAACCGAC
Found at i:57483943 original size:110 final size:109
Alignment explanation
Indices: 57483652--57484047 Score: 614
Period size: 110 Copynumber: 3.6 Consensus size: 109
57483642 AGAAATCAAA
* * * * * *
57483652 ACCCAGCACATTAGGGCACG-CTCCTCGAATTTCTAAACGCAAAACATTGCCTTATTTTGAAATT
1 ACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATT
* * * * * *
57483716 TTTAAAAGGATATTTAGCCATTTGGTTGGATGAAAAAAATCGAT
66 TTTAAAAGGATATTAAGCAATTTGGTTGAACGAGAAAAATCGAC
* *
57483760 ACTCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
1 ACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATT
57483825 TTTAAAAGGATATTAAGCAATTTGGTTGAACGAGAAAAATCGAC
66 TTTAAAAGGATATTAAGCAATTTGGTTGAACGAGAAAAATCGAC
*
57483869 ACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGTCTTATTTTAAAAT
1 ACCCAGCACCTTAGGGCATGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTATTTTAAAAT
57483934 TTTTAAAAGGATATTAAGCAATTTGGTTGAACGAGAAAAATCGAC
65 TTTTAAAAGGATATTAAGCAATTTGGTTGAACGAGAAAAATCGAC
* *
57483979 ACCCAGCACCTTAGGGCATATTTTCTCGAATTTTTCAAACGCAAAACATTGCCTTATTTTAAAAT
1 ACCCAGCACCTTAGGGCATGTTTTCTCGAA-TTTCCAAACGCAAAACATTGCCTTATTTTAAAAT
57484044 TTTT
65 TTTT
57484048 CGTTTTTGAT
Statistics
Matches: 267, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
108 17 0.06
109 111 0.42
110 136 0.51
111 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (109 bp):
ACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAAATT
TTTAAAAGGATATTAAGCAATTTGGTTGAACGAGAAAAATCGAC
Found at i:57484691 original size:16 final size:16
Alignment explanation
Indices: 57484656--57484727 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 16
57484646 AAAAGATATA
* *
57484656 TATATATATATATAAG
1 TATATATATAAACAAG
*
57484672 TATATATATAAACAAT
1 TATATATATAAACAAG
*
57484688 TATATA-ATAAAAATAG
1 TATATATATAAACA-AG
57484704 TATA-ATA-AAAC-A-
1 TATATATATAAACAAG
*
57484716 TATATATCTAAA
1 TATATATATAAA
57484728 ACTTTCATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.09
13 3 0.07
14 3 0.07
15 10 0.22
16 25 0.56
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (16 bp):
TATATATATAAACAAG
Found at i:57484721 original size:14 final size:13
Alignment explanation
Indices: 57484657--57484721 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 13
57484647 AAAGATATAT
*
57484657 ATATATATATATAA
1 ATATATA-ATAAAA
*
57484671 GTATATATATAAACA
1 ATATATA-ATAAA-A
57484686 ATTATATAATAAAA
1 A-TATATAATAAAA
57484700 ATAGTATAATAAAA
1 ATA-TATAATAAAA
57484714 CATATATA
1 -ATATATA
57484722 TCTAAAACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
13 2 0.05
14 27 0.61
15 9 0.20
16 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (13 bp):
ATATATAATAAAA
Found at i:57484776 original size:3 final size:3
Alignment explanation
Indices: 57484756--57484822 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
57484746 AAATAAAAAC
* * * * *
57484756 ATA ACA ATA ATA ACA ATA ATA TTA ATA A-A TATA CTA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
57484801 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
57484823 AATTGCTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.96
4 1 0.02
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:57492303 original size:15 final size:17
Alignment explanation
Indices: 57492278--57492309 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57492268 TATTTCATTG
57492278 ATGATATATCT-CTTTT
1 ATGATATATCTACTTTT
57492294 ATGA-ATATCTACTTTT
1 ATGATATATCTACTTTT
57492310 CGATTGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
ATGATATATCTACTTTT
Found at i:57494180 original size:14 final size:14
Alignment explanation
Indices: 57494161--57494192 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
57494151 AGGTCATTTA
57494161 GCCCAACCAAACTG
1 GCCCAACCAAACTG
57494175 GCCCAACCAAACTG
1 GCCCAACCAAACTG
57494189 GCCC
1 GCCC
57494193 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:57496632 original size:18 final size:18
Alignment explanation
Indices: 57496609--57496651 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57496599 GTTCAAGGTG
57496609 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
57496627 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
57496645 TAATTAA
1 TAATTAA
57496652 AAAACCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:57500072 original size:24 final size:24
Alignment explanation
Indices: 57500024--57500068 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
57500014 AATACTCATA
**
57500024 TTTATATTATTAAAACGTTTATAT
1 TTTATATTATTAAAACACTTATAT
57500048 TTTATATTA-TAAAACACTTAT
1 TTTATATTATTAAAACACTTAT
57500069 TATTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTATATTATTAAAACACTTATAT
Found at i:57501033 original size:23 final size:23
Alignment explanation
Indices: 57500995--57501039 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
57500985 TCAATCGGTA
* * *
57500995 AATATTATTTTTATTTTATTTAG
1 AATATTAATTTGATTTGATTTAG
57501018 AATATTAATTTGATTTGATTTA
1 AATATTAATTTGATTTGATTTA
57501040 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
AATATTAATTTGATTTGATTTAG
Found at i:57502996 original size:49 final size:50
Alignment explanation
Indices: 57502943--57503037 Score: 133
Period size: 49 Copynumber: 1.9 Consensus size: 50
57502933 AGCTCTTGCG
57502943 AGCCAATT-ATCGGGAAGCTCAT-ATGAGCCATA-AAAGGGAAGCTCAAGAA
1 AGCC-ATTAATCGGGAAGCTCATGA-GAGCCATATAAAGGGAAGCTCAAGAA
* *
57502992 AGCCATTAATCGGGAAGCTCATGAGAGCCATATAACGGGATGCTCA
1 AGCCATTAATCGGGAAGCTCATGAGAGCCATATAAAGGGAAGCTCA
57503038 TAAGAGCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
48 3 0.07
49 26 0.63
50 12 0.29
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (50 bp):
AGCCATTAATCGGGAAGCTCATGAGAGCCATATAAAGGGAAGCTCAAGAA
Found at i:57503051 original size:25 final size:25
Alignment explanation
Indices: 57502942--57503061 Score: 95
Period size: 25 Copynumber: 4.8 Consensus size: 25
57502932 AAGCTCTTGC
* * *
57502942 GAGCCAATTATCGGGAAGCTCATAT
1 GAGCCAAATAACGGGAAGCTCATAA
57502967 GAGCCATAA-AA-GGGAAGCTCA-AGA
1 GAGCCA-AATAACGGGAAGCTCATA-A
* * *
57502991 AAGCC-ATTAATCGGGAAGCTCATGA
1 GAGCCAAATAA-CGGGAAGCTCATAA
* *
57503016 GAGCCATATAACGGGATGCTCATAA
1 GAGCCAAATAACGGGAAGCTCATAA
* *
57503041 GAGCTAAATAACGGGACGCTC
1 GAGCCAAATAACGGGAAGCTC
57503062 TTGCTAGCTG
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
22 1 0.01
23 3 0.04
24 14 0.19
25 52 0.70
26 4 0.05
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (25 bp):
GAGCCAAATAACGGGAAGCTCATAA
Found at i:57505296 original size:50 final size:46
Alignment explanation
Indices: 57505176--57505305 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 46
57505166 TCACATATCG
*
57505176 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCACTCATCTT
1 GTGCCGATGCCATGTCC-AGACATGGTCTTACACTGACACTCATCTT
* * * * *
57505223 GAGACGATGTCATGTCCCAGACATGGTCTTACACTGACTCTCCTCTGTCT
1 GTGCCGATGCCATGT-CCAGACATGGTCTTACACTGACACTCATC--T-T
57505273 GTGCCGATGCCATGTCTCAGACATGGTCTTACA
1 GTGCCGATGCCATGTC-CAGACATGGTCTTACA
57505306 GACATGGTCT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
47 36 0.52
48 2 0.03
49 2 0.03
50 29 0.42
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (46 bp):
GTGCCGATGCCATGTCCAGACATGGTCTTACACTGACACTCATCTT
Found at i:57505309 original size:14 final size:14
Alignment explanation
Indices: 57505290--57505319 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
57505280 TGCCATGTCT
57505290 CAGACATGGTCTTA
1 CAGACATGGTCTTA
57505304 CAGACATGGTCTTA
1 CAGACATGGTCTTA
57505318 CA
1 CA
57505320 CTAACACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (14 bp):
CAGACATGGTCTTA
Found at i:57505345 original size:64 final size:64
Alignment explanation
Indices: 57505240--57505369 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
57505230 TGTCATGTCC
* * * * *
57505240 CAGACATGGTCTTACACTGACTCTCCTCTGTCTGTGCCGATGCCATGTCTCAGACATGGTCTTA
1 CAGACATGGTCTTACACTAACACTCATCAGTCTGTGCCGATGCCATGTCCCAGACATGGTCTTA
*
57505304 CAGACATGGTCTTACACTAACACTCATCAGTCTGTGTCGATGCCATGTCCCAGACATGGTCTTA
1 CAGACATGGTCTTACACTAACACTCATCAGTCTGTGCCGATGCCATGTCCCAGACATGGTCTTA
57505368 CA
1 CA
57505370 CTAGCACACT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (64 bp):
CAGACATGGTCTTACACTAACACTCATCAGTCTGTGCCGATGCCATGTCCCAGACATGGTCTTA
Found at i:57505828 original size:42 final size:42
Alignment explanation
Indices: 57505779--57505875 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
57505769 CTTGGTAACG
** *
57505779 CACACTTAGTGCCCGTTATTTGACATCGCCATTTTTGTTT-T
1 CACACTTAGTGCCCGTTATTCAACATCGCCATTTTAGTTTCT
* *
57505820 GTACACTTAGTGCCCGTTATTCAACATCGTCATTTTAGTTTCT
1 -CACACTTAGTGCCCGTTATTCAACATCGCCATTTTAGTTTCT
57505863 CACACTTAGTGCC
1 CACACTTAGTGCC
57505876 ATTCGTATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (42 bp):
CACACTTAGTGCCCGTTATTCAACATCGCCATTTTAGTTTCT
Found at i:57508138 original size:38 final size:38
Alignment explanation
Indices: 57508088--57508163 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
57508078 AATTGGAAAT
*
57508088 TAATAATTTTAATACTTTTATATTTCAAAAAAATAATA
1 TAATAATTTTAATAATTTTATATTTCAAAAAAATAATA
*
57508126 TAATAATTTTAATAATTTTATATTTCAAAAAGATAATA
1 TAATAATTTTAATAATTTTATATTTCAAAAAAATAATA
57508164 AGTTTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (38 bp):
TAATAATTTTAATAATTTTATATTTCAAAAAAATAATA
Found at i:57509924 original size:28 final size:28
Alignment explanation
Indices: 57509869--57509924 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
57509859 CTATATTAAC
* *
57509869 TATTTAACTAATTAATAACATCATAAAA
1 TATTAAACTAATTAATAACATCAAAAAA
*
57509897 TATTAAACTAATTAATAACATTAAAAAA
1 TATTAAACTAATTAATAACATCAAAAAA
57509925 AGATCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (28 bp):
TATTAAACTAATTAATAACATCAAAAAA
Found at i:57512991 original size:23 final size:23
Alignment explanation
Indices: 57512965--57513009 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
57512955 TATTATAAAA
* *
57512965 TATTCAATAAATTTATTTATCTT
1 TATTCAAAAAAATTATTTATCTT
*
57512988 TATTTAAAAAAATTATTTATCT
1 TATTCAAAAAAATTATTTATCT
57513010 ATTTCCATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTCAAAAAAATTATTTATCTT
Found at i:57513259 original size:2 final size:2
Alignment explanation
Indices: 57513252--57513282 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57513242 TAGCTTCAAG
57513252 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
57513283 GTTTCCTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:57513650 original size:165 final size:164
Alignment explanation
Indices: 57513351--57513829 Score: 798
Period size: 160 Copynumber: 3.0 Consensus size: 164
57513341 TTTTATCTAC
* * *
57513351 TAATTCATTTGTTGTGTGTTTCCTGGATTTTGATTCTTTCGTTTTGTTCGTGGTTACTG-TT--T
1 TAATCCATTTGTT-TGTGTTTCCTGGATTTTGAATCTTTCGTTTTGTTCGTTGTTACTGTTTCCT
* * *
57513413 C--C-TTTTTTTATTTTTATAATTTGATGTTTTAGGATCTTATTTGCATTTGTATTTTAATTTCG
65 CTTCTTTTTTTTCTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTATTTTAATTTCG
57513475 AAGATCTATATGATGTTTATTTTTTGAATTGTGATT
130 AAGATCTATATGATGTTTATTTTTTGAATT-TGATT
*
57513511 TAATCCATTTGTTTGTGTTTCCTAGATTTTGAATCTTTCGTTTTGTTCGTTGTTACTGTTTCCTC
1 TAATCCATTTGTTTGTGTTTCCTGGATTTTGAATCTTTCGTTTTGTTCGTTGTTACTGTTTCCTC
57513576 TTCTTTTTTTTCTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTATTTTAATTTCGA
66 TTCTTTTTTTTCTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTATTTTAATTTCGA
57513641 AGATCTATATGATGTTTATTTTTT--A--TGATT
131 AGATCTATATGATGTTTATTTTTTGAATTTGATT
*
57513671 TAATCCATTTGTTTGTATTTCCTGGATTTTGAATCTTTCGTTTTGTTCGTTGTTACTGTTTCCTC
1 TAATCCATTTGTTTGTGTTTCCTGGATTTTGAATCTTTCGTTTTGTTCGTTGTTACTGTTTCCTC
57513736 TTCTTTTTTTTCTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTATTTTAATTTCGA
66 TTCTTTTTTTTCTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTATTTTAATTTCGA
57513801 AGATCTATATGATGTTTATTTTTTGAATT
131 AGATCTATATGATGTTTATTTTTTGAATT
57513830 ATGTAGTTCC
Statistics
Matches: 300, Mismatches: 9, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
159 42 0.14
160 171 0.57
162 3 0.01
163 1 0.00
164 1 0.00
165 82 0.27
ACGTcount: A:0.18, C:0.09, G:0.14, T:0.59
Consensus pattern (164 bp):
TAATCCATTTGTTTGTGTTTCCTGGATTTTGAATCTTTCGTTTTGTTCGTTGTTACTGTTTCCTC
TTCTTTTTTTTCTTTTTATAATTTGATGTTTTAGGATTTTATTTGCATTTTTATTTTAATTTCGA
AGATCTATATGATGTTTATTTTTTGAATTTGATT
Found at i:57514188 original size:13 final size:13
Alignment explanation
Indices: 57514149--57514187 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
57514139 CTATTTAGAG
57514149 TTTTTGTTTTTAATC
1 TTTTTGTTTTT--TC
57514164 TTTTTGTTTTTTC
1 TTTTTGTTTTTTC
57514177 TTTTT-TTTTTT
1 TTTTTGTTTTTT
57514188 TGCATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 7 0.29
15 11 0.46
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85
Consensus pattern (13 bp):
TTTTTGTTTTTTC
Found at i:57533649 original size:18 final size:18
Alignment explanation
Indices: 57533626--57533664 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
57533616 GAACTATTAC
* *
57533626 TATAATAATATTTTAACA
1 TATAATAATAATTAAACA
*
57533644 TATAATGATAATTAAACA
1 TATAATAATAATTAAACA
57533662 TAT
1 TAT
57533665 TAAAAAGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAATAATAATTAAACA
Found at i:57533832 original size:11 final size:11
Alignment explanation
Indices: 57533816--57533841 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57533806 GTTTATCATC
57533816 TTTTTTATGTT
1 TTTTTTATGTT
57533827 TTTTTTATGTT
1 TTTTTTATGTT
57533838 TTTT
1 TTTT
57533842 ATAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTATGTT
Found at i:57541567 original size:22 final size:25
Alignment explanation
Indices: 57541532--57541628 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 25
57541522 GTTCAACTTT
57541532 AAAATGTTATCATTTAA-TTATTTG
1 AAAATGTTATCATTTAAGTTATTTG
57541556 AAAAT-TT-TCATTTAAGTTATTGAGTTG
1 AAAATGTTATCATTTAAGTTA-T---TTG
*
57541583 TTAAATGTTATCATTTAA-TTATTTG
1 -AAAATGTTATCATTTAAGTTATTTG
57541608 AAAAT-TT-TCATTTAAGTTATT
1 AAAATGTTATCATTTAAGTTATT
57541629 GAGTTGTTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
22 16 0.26
23 12 0.19
24 10 0.16
25 3 0.05
27 3 0.05
28 5 0.08
29 5 0.08
30 8 0.13
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (25 bp):
AAAATGTTATCATTTAAGTTATTTG
Found at i:57541589 original size:52 final size:52
Alignment explanation
Indices: 57541533--57541640 Score: 216
Period size: 52 Copynumber: 2.1 Consensus size: 52
57541523 TTCAACTTTA
57541533 AAATGTTATCATTTAATTATTTGAAAATTTTCATTTAAGTTATTGAGTTGTT
1 AAATGTTATCATTTAATTATTTGAAAATTTTCATTTAAGTTATTGAGTTGTT
57541585 AAATGTTATCATTTAATTATTTGAAAATTTTCATTTAAGTTATTGAGTTGTT
1 AAATGTTATCATTTAATTATTTGAAAATTTTCATTTAAGTTATTGAGTTGTT
57541637 AAAT
1 AAAT
57541641 TCATTGATGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (52 bp):
AAATGTTATCATTTAATTATTTGAAAATTTTCATTTAAGTTATTGAGTTGTT
Found at i:57542254 original size:35 final size:35
Alignment explanation
Indices: 57542215--57542292 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
57542205 AAGTAAAGAT
57542215 ACAACACTGAAATAAAACCATTAAGTTCAAAAAAC
1 ACAACACTGAAATAAAACCATTAAGTTCAAAAAAC
**
57542250 ACAACACTGAAATAAAGTCATTAAGTTCAAAAAAC
1 ACAACACTGAAATAAAACCATTAAGTTCAAAAAAC
57542285 ACAACACT
1 ACAACACT
57542293 AACATAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (35 bp):
ACAACACTGAAATAAAACCATTAAGTTCAAAAAAC
Found at i:57546037 original size:106 final size:106
Alignment explanation
Indices: 57545787--57546201 Score: 386
Period size: 106 Copynumber: 3.9 Consensus size: 106
57545777 TGTTCCTGTT
* * * * * *
57545787 CATCGCCTAGGAAGGGGCACATCAGGTTCGCATACCCATTA-TTGCCTACTCGATGTGGACAACA
1 CATCGCCTAGGAA-GGGTACATCAAGTTTGCATACTCATTACTT-CTTACTCGATGTAGACAACA
* * **
57545851 TGACCAAA-GCATTATATTTCTTTATGTCATTGCTTACTTGTG
64 TGACCAAATGCATTATATTTCTTCATGTTATTGCTTACTCATG
* * * * *
57545893 CATCGCCTAGGAAGGTGTTCGTC-AGTTTTGTATACTCATTACTTCTTACTTGATGTAGATAACA
1 CATCGCCTAGGAAGG-GTACATCAAG-TTTGCATACTCATTACTTCTTACTCGATGTAGACAACA
*
57545957 TGA-CAAATGCATTATATTTCTTCATGTTGTTGCTTACTCATG
64 TGACCAAATGCATTATATTTCTTCATGTTATTGCTTACTCATG
* * * * *
57545999 CATCACCTAGCAAGGGTACATCAAGGTTTGCATGCTCATTA-TTGCTTACTCAATGTAGACAGCA
1 CATCGCCTAGGAAGGGTACATCAA-GTTTGCATACTCATTACTT-CTTACTCGATGTAGACAACA
* * *
57546063 TGACCAAGAT--TTTATATTTCTTCATGTTACTGCTTACTCTTG
64 TGACCAA-ATGCATTATATTTCTTCATGTTATTGCTTACTCATG
* * * *
57546105 GACCGCCTAGGAAGGGATACATTACA-TTTGCATACTCATTGCTGT-TTACTC-ATGCT-GACAA
1 CATCGCCTAGGAAGGG-TACATCA-AGTTTGCATACTCATTACT-TCTTACTCGATG-TAGACAA
*
57546166 CATGACC-AAGGCATTATATTTCTTCATGTTATTGCT
62 CATGACCAAATGCATTATATTTCTTCATGTTATTGCT
57546202 CGAGAGTAAG
Statistics
Matches: 252, Mismatches: 41, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
103 1 0.00
104 1 0.00
105 50 0.20
106 183 0.73
107 13 0.05
108 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (106 bp):
CATCGCCTAGGAAGGGTACATCAAGTTTGCATACTCATTACTTCTTACTCGATGTAGACAACATG
ACCAAATGCATTATATTTCTTCATGTTATTGCTTACTCATG
Found at i:57553421 original size:31 final size:31
Alignment explanation
Indices: 57553362--57553422 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
57553352 ATTAACGGCG
*
57553362 AGTGACTAAAATGATAAAAGTATGTAACAAT
1 AGTGACTAAAATGATAAAAGAATGTAACAAT
* * *
57553393 AGTGGCTAAAATGATAAGAGAATTTAACAA
1 AGTGACTAAAATGATAAAAGAATGTAACAA
57553423 CAATGCCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (31 bp):
AGTGACTAAAATGATAAAAGAATGTAACAAT
Found at i:57553433 original size:31 final size:31
Alignment explanation
Indices: 57553367--57553433 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
57553357 CGGCGAGTGA
* * * *
57553367 CTAAAATGATAAAAGTATGTAACAATAGTGG
1 CTAAAATGATAAAAGAATGTAACAACAATGC
* *
57553398 CTAAAATGATAAGAGAATTTAACAACAATGC
1 CTAAAATGATAAAAGAATGTAACAACAATGC
57553429 CTAAA
1 CTAAA
57553434 TTGCATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (31 bp):
CTAAAATGATAAAAGAATGTAACAACAATGC
Found at i:57558018 original size:82 final size:82
Alignment explanation
Indices: 57557812--57558707 Score: 1432
Period size: 82 Copynumber: 10.9 Consensus size: 82
57557802 TTCTTCTGTT
* * *
57557812 TGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
**
57557877 AGATCTGGTTTCTTTTGTC
66 AGATCT-G-TGGTTTTGTC
* * *
57557896 TGCTCTGCTACTACTTAGGGAGATAAGACTTGATGTGATCTGCTCCATTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
*
57557961 AGATTTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* * *
57557978 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGTTGCGATCTGCTCCACTATTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
**
57558043 AGATCTGGTTTCTTTTGTC
66 AGATCT-G-TGGTTTTGTC
* *
57558062 TGCTCCGCTACTACTTAGGGAGATAAGACTTGATGTGATCTGCTCCATTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558127 AGATCTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* * *
57558144 TGCTCCGTTACTGCTTAGGGAGATAAAACTTGATGTGATCTTCTCCACTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558209 AGATCTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* *
57558226 TGCTCCGCTACTACTTAGGGAGATAATACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558291 AGATCTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* *
57558308 TGCTCCGCTACTGCTTAGGGAGATAAAACTTGCTGTGATCTGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558373 AGATCTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* * *
57558390 TGCTTCGCTACTACTTAGAGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
*
57558455 AGATCTATGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* * * *
57558472 TGCTTCGCTACTGCTTAGGGAGATAAGATTTGCTGTGATCTGCTCCACTACTGCTTAGGGATATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558537 AGATCTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
*
57558554 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGGGATCTGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558619 AGATCTGTGGTTTTGTC
66 AGATCTGTGGTTTTGTC
* * * *
57558636 TGCTCTGCTACTGCTTAGGGAGATAAGACTTGACGCGATATGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
57558701 AGATCTG
66 AGATCTG
57558708 CTGGCTTCAA
Statistics
Matches: 752, Mismatches: 58, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
82 611 0.81
83 3 0.00
84 138 0.18
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (82 bp):
TGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGTGATCTGCTCCACTACTGCTTAGGGAGATA
AGATCTGTGGTTTTGTC
Found at i:57572684 original size:30 final size:31
Alignment explanation
Indices: 57572620--57572686 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
57572610 TGACATTAAG
* **
57572620 TTTTAGAGGTTTAATTAAAAAATTTCAACTA
1 TTTTAGAGGTTGAATTAAAAAATTTCAAAAA
* *
57572651 TTTTAGAGGTTGAA-TAAGAAATTTTAAAAA
1 TTTTAGAGGTTGAATTAAAAAATTTCAAAAA
57572681 TTTTAG
1 TTTTAG
57572687 GGGGCATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (31 bp):
TTTTAGAGGTTGAATTAAAAAATTTCAAAAA
Found at i:57574282 original size:3 final size:3
Alignment explanation
Indices: 57574274--57574306 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
57574264 AATTATTTTT
57574274 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57574307 AACACGTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57587742 original size:15 final size:14
Alignment explanation
Indices: 57587722--57587760 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
57587712 TTTAAATTTC
57587722 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
* *
57587736 AAAATTTAAGAGAAT
1 AAATTTTAA-AAAAT
57587751 AAATTTTAAA
1 AAATTTTAAA
57587761 TATACGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
AAATTTTAAAAAAT
Found at i:57588488 original size:23 final size:25
Alignment explanation
Indices: 57588432--57588488 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
57588422 AAATAATGTT
*
57588432 AAAATAATTATATAAAAAATATTAA
1 AAAATAATAATATAAAAAATATTAA
*
57588457 ATTAA-AATAATAT-AAAAATA-TAA
1 A-AAATAATAATATAAAAAATATTAA
57588480 AAAATAATA
1 AAAATAATA
57588489 TGGGGCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
22 2 0.07
23 8 0.30
24 7 0.26
25 8 0.30
26 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATAATAATATAAAAAATATTAA
Found at i:57589269 original size:16 final size:16
Alignment explanation
Indices: 57589217--57589272 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
57589207 TAAAATCAAT
57589217 CAAATTAATTTAATTA
1 CAAATTAATTTAATTA
* *
57589233 CAAA-T-ATTGAAAT-
1 CAAATTAATTTAATTA
*
57589246 C-GATTAATTTAATTA
1 CAAATTAATTTAATTA
57589261 CAAATTAATTTA
1 CAAATTAATTTA
57589273 TTTGTTTCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
12 1 0.03
13 2 0.07
14 12 0.40
15 2 0.07
16 13 0.43
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (16 bp):
CAAATTAATTTAATTA
Found at i:57589891 original size:26 final size:26
Alignment explanation
Indices: 57589862--57589920 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
57589852 AAGTGACGTA
*
57589862 GAAAAGTACCTTTT-AGAAGTATTTTG
1 GAAAAGTA-CTTTTCAGAAGTACTTTG
57589888 GAAAAGTACTTTTCAGAAGTACTTTG
1 GAAAAGTACTTTTCAGAAGTACTTTG
57589914 GAAAAGT
1 GAAAAGT
57589921 TTGATTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (26 bp):
GAAAAGTACTTTTCAGAAGTACTTTG
Found at i:57592460 original size:29 final size:29
Alignment explanation
Indices: 57592356--57592469 Score: 113
Period size: 29 Copynumber: 3.9 Consensus size: 29
57592346 AAAAATTTTG
* * *
57592356 CATTTTAACACCTGAACTTTTCTAAAATTA
1 CATTTTAACCCCTAAAATTTTC-AAAATTA
**
57592386 CATTTTAACCCCTAATTTTTTCAAAATTA
1 CATTTTAACCCCTAAAATTTTCAAAATTA
*
57592415 CATTTAAACCCCTAAAATTTT-ATAAATTA
1 CATTTTAACCCCTAAAATTTTCA-AAATTA
* * *
57592444 CATTTTGACCCCGAAAACTTCTCAAA
1 CATTTTAACCCCTAAAA-TTTTCAAA
57592470 CTAATATTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.01
29 45 0.64
30 23 0.33
31 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
CATTTTAACCCCTAAAATTTTCAAAATTA
Found at i:57592870 original size:10 final size:10
Alignment explanation
Indices: 57592855--57592906 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
57592845 AGGGTTTCCG
57592855 AAAGAAGAAA
1 AAAGAAGAAA
*
57592865 AAAGAAGAAG
1 AAAGAAGAAA
*
57592875 GAAGAAGAAGA
1 AAAGAAGAA-A
57592886 AAAGAA-AAA
1 AAAGAAGAAA
57592895 GAAAGAA-AAA
1 -AAAGAAGAAA
57592905 AA
1 AA
57592907 TTTATTATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 3 0.08
10 28 0.78
11 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:57593148 original size:10 final size:10
Alignment explanation
Indices: 57593129--57593239 Score: 97
Period size: 10 Copynumber: 10.9 Consensus size: 10
57593119 GAAGCAGGCC
57593129 GAAGAAAAAAA
1 GAAG-AAAAAA
57593140 GAAGGAAAAAAA
1 GAA-G-AAAAAA
57593152 GAA-AAGAAAA
1 GAAGAA-AAAA
57593162 -AAGAAAAAA
1 GAAGAAAAAA
*
57593171 GGAGAAAAAAA
1 GAAG-AAAAAA
57593182 GAAGAAAAAAGA
1 GAAG-AAAAA-A
57593194 GAAGAAAAAA
1 GAAGAAAAAA
57593204 GAAGAAAAAA
1 GAAGAAAAAA
*
57593214 G-A-AAAAAG
1 GAAGAAAAAA
*
57593222 GAGGAAAAAA
1 GAAGAAAAAA
57593232 GAA-AAAAA
1 GAAGAAAAA
57593240 GAGGTTCAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
8 6 0.07
9 14 0.16
10 27 0.31
11 23 0.27
12 16 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
GAAGAAAAAA
Found at i:57593149 original size:12 final size:11
Alignment explanation
Indices: 57593129--57593213 Score: 106
Period size: 11 Copynumber: 7.9 Consensus size: 11
57593119 GAAGCAGGCC
57593129 GAAGAAAAAAA
1 GAAGAAAAAAA
57593140 GAAGGAAAAAAA
1 GAA-GAAAAAAA
*
57593152 GAA-AAGAAAA
1 GAAGAAAAAAA
57593162 -AAG-AAAAAA
1 GAAGAAAAAAA
*
57593171 GGAGAAAAAAA
1 GAAGAAAAAAA
57593182 GAAGAAAAAAGA
1 GAAGAAAAAA-A
57593194 GAAG-AAAAAA
1 GAAGAAAAAAA
57593204 GAAGAAAAAA
1 GAAGAAAAAA
57593214 GAAAAAAGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
9 7 0.11
10 13 0.20
11 28 0.44
12 16 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAGAAAAAAA
Found at i:57593190 original size:40 final size:40
Alignment explanation
Indices: 57593130--57593236 Score: 144
Period size: 40 Copynumber: 2.6 Consensus size: 40
57593120 AAGCAGGCCG
57593130 AAGAAAAAAAGAAGGAAAAAAAGAAAAGAAAAAAGAA-AAAA
1 AAGAAAAAAAGAA-G-AAAAAAGAAAAGAAAAAAGAAGAAAA
* *
57593171 GGAGAAAAAAAGAAGAAAAAAGAGAAGAAAAAAGAAGAAAA
1 -AAGAAAAAAAGAAGAAAAAAGAAAAGAAAAAAGAAGAAAA
* *
57593212 AAGAAAAAAGGAGGAAAAAAGAAAA
1 AAGAAAAAAAGAAGAAAAAAGAAAA
57593237 AAAGAGGTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 41 0.71
41 5 0.09
42 12 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (40 bp):
AAGAAAAAAAGAAGAAAAAAGAAAAGAAAAAAGAAGAAAA
Found at i:57593214 original size:50 final size:52
Alignment explanation
Indices: 57593129--57593239 Score: 167
Period size: 50 Copynumber: 2.2 Consensus size: 52
57593119 GAAGCAGGCC
57593129 GAAGAAAAAAAGAAGGAAAAAAAGAAAAGAAAAAAGAAAAAAGGAGAAAAAAA
1 GAAGAAAAAAAGAAGGAAAAAAAG-AAAGAAAAAAGAAAAAAGGAGAAAAAAA
*
57593182 GAAGAAAAAAGAGAA-G-AAAAAAG-AAGAAAAAAGAAAAAAGGAGGAAAAAA
1 GAAGAAAAAA-AGAAGGAAAAAAAGAAAGAAAAAAGAAAAAAGGAGAAAAAAA
57593232 GAA-AAAAA
1 GAAGAAAAA
57593240 GAGGTTCAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
49 5 0.09
50 29 0.52
52 7 0.12
53 11 0.20
54 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (52 bp):
GAAGAAAAAAAGAAGGAAAAAAAGAAAGAAAAAAGAAAAAAGGAGAAAAAAA
Found at i:57593228 original size:18 final size:17
Alignment explanation
Indices: 57593157--57593243 Score: 81
Period size: 18 Copynumber: 5.1 Consensus size: 17
57593147 AAAAAGAAAA
57593157 GAAAAAAGAAAAAAGGAG
1 GAAAAAAGAAAAAA-GAG
*
57593175 AAAAAAAGAAGAAAA-A-
1 GAAAAAAGAA-AAAAGAG
* * *
57593191 -AGAGAAGAAAAAAGAA
1 GAAAAAAGAAAAAAGAG
57593207 GAAAAAAGAAAAAAGGAG
1 GAAAAAAGAAAAAA-GAG
57593225 GAAAAAAGAAAAAAAGAG
1 GAAAAAAG-AAAAAAGAG
57593243 G
1 G
57593244 TTCAATTCGT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.07
15 8 0.14
17 12 0.21
18 23 0.40
19 10 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAAAAGAG
Found at i:57593400 original size:5 final size:5
Alignment explanation
Indices: 57593390--57593432 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
57593380 CATTTATATT
*
57593390 TTTAA TTTAA TTTAA TTTTAA TTTTAA TTTTAA TTTAT TTTAA
1 TTTAA TTTAA TTTAA -TTTAA -TTTAA -TTTAA TTTAA TTTAA
57593433 ATACTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTTAA
Found at i:57593407 original size:23 final size:24
Alignment explanation
Indices: 57593381--57593431 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
57593371 GTATTTTGGC
*
57593381 ATTTATATTTTTAA-TTTAATTTA
1 ATTTATAATTTTAATTTTAATTTA
57593404 ATTT-TAATTTTAATTTTAATTTA
1 ATTTATAATTTTAATTTTAATTTA
*
57593427 TTTTA
1 ATTTA
57593432 AATACTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTATAATTTTAATTTTAATTTA
Found at i:57593409 original size:6 final size:6
Alignment explanation
Indices: 57593389--57593425 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
57593379 GCATTTATAT
57593389 TTTTAA -TTTAA -TTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
57593426 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:57593417 original size:22 final size:22
Alignment explanation
Indices: 57593390--57593432 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
57593380 CATTTATATT
57593390 TTTAA-TTTAATTTAATTTTAAT
1 TTTAATTTTAATTT-ATTTTAAT
57593412 TTTAATTTTAATTTATTTTAA
1 TTTAATTTTAATTTATTTTAA
57593433 ATACTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTAATTTTAATTTATTTTAAT
Found at i:57593617 original size:19 final size:20
Alignment explanation
Indices: 57593595--57593637 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57593585 TATATTTTGC
57593595 AAAA-TTTT-TCGTGTCTTCA
1 AAAATTTTTCTCGTGT-TTCA
57593614 AAAATTTTTCTCGTGTTTCA
1 AAAATTTTTCTCGTGTTTCA
57593634 AAAA
1 AAAA
57593638 AAATATTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 12 0.55
21 6 0.27
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (20 bp):
AAAATTTTTCTCGTGTTTCA
Found at i:57593910 original size:18 final size:18
Alignment explanation
Indices: 57593884--57594405 Score: 230
Period size: 17 Copynumber: 28.7 Consensus size: 18
57593874 AAAAAATTAT
57593884 TTTTC-AAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
57593901 TTTTCAAAAAATTCTCGTG
1 TTTTC-AAAAATTTTCGTG
*
57593920 -TTTCAAAAAATCTTCGTG
1 TTTTC-AAAAATTTTCGTG
*
57593938 TTTTC-AAGA-TTTCG-G
1 TTTTCAAAAATTTTCGTG
* *
57593953 TGTTTCCAAAATTTTCATG
1 T-TTTCAAAAATTTTCGTG
57593972 TTTTCAAAAAAAAATTTCTCGTG
1 TTTTC----AAAAATTT-TCGTG
57593995 TTTT-AAAAATTTTTGCGT-
1 TTTTCAAAAA-TTTT-CGTG
* **
57594013 TTTTAAAAACAAATTCGTG
1 TTTTCAAAA-ATTTTCGTG
**
57594032 TTTTCAAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTG
* * *
57594050 TTTACAAAAATTCTGGTG
1 TTTTCAAAAATTTTCGTG
* * *
57594068 -GTTCAATAA-TTCCTGTG
1 TTTTCAAAAATTTTC-GTG
*
57594085 TTTT-AAAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
* *
57594102 TTTTCAAAAAAAATCTTCGTA
1 TTTTC---AAAAATTTTCGTG
**
57594123 TTTTCAAAAAAAAATT--TG
1 TTTTC--AAAAATTTTCGTG
**
57594141 -TTTCAAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTG
57594158 TTTTCAAAAA-TTTCAGTG
1 TTTTCAAAAATTTTC-GTG
*
57594176 -TTTCAAAGA-TTTCGTG
1 TTTTCAAAAATTTTCGTG
*
57594192 TTTTCAAAAA-TTCCGGTG
1 TTTTCAAAAATTTTC-GTG
57594210 ATTTTACAAAAA-TTTCGTG
1 -TTTT-CAAAAATTTTCGTG
*
57594229 TTTTCTAAAAAAATTTCCGTG
1 TTTTC---AAAAATTTTCGTG
*
57594250 -TTTCAAAAATTTTCATG
1 TTTTCAAAAATTTTCGTG
**
57594267 TTTTCAAAAAATTCCCGTG
1 TTTTC-AAAAATTTTCGTG
* * *
57594286 -CTTCACAAATGTTCGTG
1 TTTTCAAAAATTTTCGTG
* *
57594303 TTTT--AAATTTTTTGTG
1 TTTTCAAAAATTTTCGTG
*
57594319 TTTTCAAAAAAAATTCTCGTG
1 TTTTC---AAAAATTTTCGTG
* *
57594340 -TTTCAAAAAATGTCGTG
1 TTTTCAAAAATTTTCGTG
* *
57594357 TTTTAAAAAAGAATTTCGTG
1 TTTT-CAAAA-ATTTTCGTG
* *
57594377 -TTTCTAAAGTTTTCGTG
1 TTTTCAAAAATTTTCGTG
57594394 -TTTCAAAAATTT
1 TTTTCAAAAATTT
57594406 CGTTTTTTTT
Statistics
Matches: 388, Mismatches: 70, Indels: 94
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.02
16 24 0.06
17 111 0.29
18 99 0.26
19 61 0.16
20 40 0.10
21 30 0.08
22 7 0.02
23 8 0.02
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:57593985 original size:22 final size:22
Alignment explanation
Indices: 57593960--57594003 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57593950 CGGTGTTTCC
57593960 AAAATTT-TCATGTTTTCAAAAA
1 AAAATTTCTCATGTTTT-AAAAA
*
57593982 AAAATTTCTCGTGTTTTAAAAA
1 AAAATTTCTCATGTTTTAAAAA
57594004 TTTTTGCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (22 bp):
AAAATTTCTCATGTTTTAAAAA
Found at i:57594003 original size:23 final size:22
Alignment explanation
Indices: 57593960--57594003 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
57593950 CGGTGTTTCC
*
57593960 AAAATTTTCATGTTTTCAAAAA
1 AAAATTTTCATGTTTTAAAAAA
*
57593982 AAAATTTCTCGTGTTTTAAAAA
1 AAAATTT-TCATGTTTTAAAAA
57594004 TTTTTGCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (22 bp):
AAAATTTTCATGTTTTAAAAAA
Found at i:57594133 original size:130 final size:131
Alignment explanation
Indices: 57593895--57594132 Score: 297
Period size: 130 Copynumber: 1.8 Consensus size: 131
57593885 TTTCAAAATT
* * * * *
57593895 TTCGTGTTTTCAAAAAATTCTCGTGTTTCAAAAAATCTTCGTGTTTTCAAGATTTCGGTGTTTCC
1 TTCGTGTTTTCAAAAAATCCTCGTGTTTCAAAAAATCTTCGTGTGTTCAAAATTCCGGTGTTTCA
* * *
57593960 AAAATTTTCATGTTTTCAAAAAAAAATTTCTCGTGTTTTAAAAATTTTTGCGTTTTTAAAAACAA
66 AAAATTTCCATGTTTTCAAAAAAAAATCTCTCGTATTTTAAAAATTTTTGCGTTTTTAAAAACAA
57594025 A
131 A
* * *
57594026 TTCGTGTTTTC-AAAAATCCTCGTGTTTACAAAAATTC-TGGTG-GTTCAATAATTCCTGTGTTT
1 TTCGTGTTTTCAAAAAATCCTCGTGTTT-CAAAAAATCTTCGTGTGTTCAA-AATTCCGGTGTTT
* *
57594088 TAAAAATTTCCGTGTTTTC-AAAAAAAATCT-TCGTATTTTCAAAAA
64 CAAAAATTTCCATGTTTTCAAAAAAAAATCTCTCGTATTTT-AAAAA
57594133 AAAATTTGTT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
128 8 0.09
129 20 0.22
130 44 0.48
131 19 0.21
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (131 bp):
TTCGTGTTTTCAAAAAATCCTCGTGTTTCAAAAAATCTTCGTGTGTTCAAAATTCCGGTGTTTCA
AAAATTTCCATGTTTTCAAAAAAAAATCTCTCGTATTTTAAAAATTTTTGCGTTTTTAAAAACAA
A
Found at i:57594137 original size:22 final size:21
Alignment explanation
Indices: 57594089--57594135 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
57594079 CCTGTGTTTT
*
57594089 AAAAATTTCCGTGTTTTCAAA
1 AAAAATTTCCGTATTTTCAAA
57594110 AAAAATCTT-CGTATTTTCAAA
1 AAAAAT-TTCCGTATTTTCAAA
57594131 AAAAA
1 AAAAA
57594136 ATTTGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (21 bp):
AAAAATTTCCGTATTTTCAAA
Found at i:57594301 original size:74 final size:73
Alignment explanation
Indices: 57594163--57594306 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 73
57594153 TCGTGTTTTC
* * * *
57594163 AAAAATTTCAGTGTTTCAAAGATTTCGTGTTTTCAAAAATTCCGGTGATTTTACAAAAATTTCGT
1 AAAAATTTCAGTGTTTCAAAAATTTCATGTTTTCAAAAATTCCCGTGA-CTTACAAAAATTTCGT
57594228 GTTTTCTAA
65 GTTTTCTAA
* *
57594237 AAAAATTTCCGTGTTTCAAAAATTTTCATGTTTTCAAAAAATTCCCGTG-CTT-CACAAATGTTC
1 AAAAATTTCAGTGTTTCAAAAA-TTTCATGTTTTC-AAAAATTCCCGTGACTTACAAAAAT-TTC
57594300 GTGTTTT
63 GTGTTTT
57594307 AAATTTTTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
73 6 0.10
74 32 0.52
75 11 0.18
76 12 0.20
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (73 bp):
AAAAATTTCAGTGTTTCAAAAATTTCATGTTTTCAAAAATTCCCGTGACTTACAAAAATTTCGTG
TTTTCTAA
Found at i:57594340 original size:37 final size:38
Alignment explanation
Indices: 57594297--57594402 Score: 121
Period size: 37 Copynumber: 2.9 Consensus size: 38
57594287 TTCACAAATG
* *
57594297 TTCGTGTTT-TAAATTTTTTGTGTTTTCAAAAAA-AAT
1 TTCGTGTTTCTAAAATTTTCGTGTTTTCAAAAAAGAAT
* * *
57594333 TCTCGTGTTTCAAAAAATGTCGTGTTTT-AAAAAAGAAT
1 T-TCGTGTTTCTAAAATTTTCGTGTTTTCAAAAAAGAAT
*
57594371 TTCGTGTTTCTAAAGTTTTCGTG-TTTCAAAAA
1 TTCGTGTTTCTAAAATTTTCGTGTTTTCAAAAA
57594403 TTTCGTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
36 4 0.07
37 37 0.65
38 16 0.28
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.45
Consensus pattern (38 bp):
TTCGTGTTTCTAAAATTTTCGTGTTTTCAAAAAAGAAT
Found at i:57606286 original size:71 final size:73
Alignment explanation
Indices: 57606115--57606711 Score: 418
Period size: 78 Copynumber: 7.8 Consensus size: 73
57606105 CTGTTTTTTT
* * ** *
57606115 AAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGG-GTCATGCCGAGGTATTTCGTTTACA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTA-A
* **
57606179 TTTCTGTTCTTTT
65 -AT-T-TT-TTAA
* * * *
57606192 TAAATTAACTCATATTGCGAGAGGTGAGTTGAGCTTCGGACACATGCCGTGGTATTTCTTTTAAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
*
57606257 -TTTTT-G
66 TTTTTTAA
57606263 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
*
57606328 TTTCTGTTCTTCA
66 --T-T-TT-TTAA
* * *
57606341 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCGTTTAAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
57606406 TTTCTGTTTTTCAAAA
66 ----T-TTTTT---AA
* * *
57606422 AAAATCAACTCATAATGAGAGAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-GACACATGCCGAGGTATTTCTTTTAA
57606487 ATTTCGTATTTTCAAA
65 A--T--T-TTTT--AA
* * ** * * *
57606503 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT-TGAGTCATGTCGAGGTA-TT-TTTCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
**
57606565 TGCTGTTTTTC
66 T--T-TTTTAA
* * * * *
57606576 AAAATTAACTCATAATGCGAGAGATGAGATGAGCCTCGGGTCACATGCCGAGGTA--TCTTTTCA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTT-A
*
57606639 ATTTCTGTTTTCCAAA
64 A-AT-T-TTTT---AA
* * * * * * *
57606655 AAAATCAACTCATAATGCTAAATGTGAGTTGAGCCTCGGGCCACACGCCGAGCTATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCGAGGTATT
57606712 CTCGATTTCA
Statistics
Matches: 429, Mismatches: 65, Indels: 48
0.79 0.12 0.09
Matches are distributed among these distances:
71 61 0.14
72 2 0.00
73 33 0.08
74 2 0.00
75 22 0.05
76 11 0.03
77 44 0.10
78 85 0.20
79 60 0.14
80 5 0.01
81 74 0.17
82 30 0.07
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCTTTTAAA
TTTTTTAA
Found at i:57606385 original size:149 final size:150
Alignment explanation
Indices: 57606109--57606711 Score: 600
Period size: 149 Copynumber: 3.9 Consensus size: 150
57606099 CAATTTCTGT
* *
57606109 TTTTTTAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGT--CATGCCGAGGTATTTC
1 TTTTTAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCGAGGTATTTC
* * *** * * * *
57606172 GTTTACATTTCTGTTCTT-TTTAAATTAACTCATATTGCGAGAGGTGAGTTGAGCTTCGGACACA
65 TTTTAAATTTCTGTTCTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGTCACA
*
57606236 TGCCGTGGTATTTCTTTTAAA
130 TGCCGAGGTATTTCTTTTAAA
* * *
57606257 TTTTTGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTCT
1 TTTTTAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCT
57606322 TTTAAATTTCTGTTCTTC-AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGTCACAT
66 TTTAAATTTCTGTTCTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGTCACAT
*
57606386 GCCGAGGTATTTCGTTTAAA
131 GCCGAGGTATTTCTTTTAAA
*
57606406 TTTCTGTTTTTCAAAAAAAATCAACTCATAATGAGAGAGGTGAGTTGAGCCTCGAGTCACATGCC
1 ------TTTTT----AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG-GTCACATGCC
*
57606471 GAGGTATTTCTTTTAAATTTC-GTATTTTCAAAAAAATCAACTCATATTGC-AAGAGGTGAGTTG
55 GAGGTATTTCTTTTAAATTTCTGT-TCTTC-AAAAAATCAACTCATATTGCGAA-AGGTGAGTTG
* * ***
57606534 AGCCTTGAGT--CATGTCGAGGTATTT-TTCAATTGCTG
117 AGCCTCG-GTCACATGCCGAGGTATTTCTT---TT-AAA
* * * *
57606570 TTTTTCAAAATTAACTCATAATGCGAGAGATGAGATGAGCCTCGGGTCACATGCCGAGGTA--TC
1 TTTTTAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCGAGGTATTTC
* * * * *
57606633 TTTTCAATTTCTGTT-TTCCAAAAAAATCAACTCATAATGCTAAATGTGAGTTGAGCCTCGGGCC
65 TTTTAAATTTCTGTTCTT-C-AAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTC-GGTC
* *
57606697 ACACGCCGAGCTATT
127 ACATGCCGAGGTATT
57606712 CTCGATTTCA
Statistics
Matches: 387, Mismatches: 38, Indels: 54
0.81 0.08 0.11
Matches are distributed among these distances:
147 2 0.01
148 40 0.10
149 90 0.23
151 2 0.01
152 49 0.13
153 5 0.01
154 60 0.16
155 6 0.02
158 5 0.01
159 38 0.10
160 35 0.09
161 16 0.04
162 35 0.09
163 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (150 bp):
TTTTTAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCT
TTTAAATTTCTGTTCTTCAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGTCACAT
GCCGAGGTATTTCTTTTAAA
Done.