Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 130 of 150
Found at i:39168121 original size:20 final size:20
Alignment explanation
Indices: 39168098--39168141 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
39168088 AATAATCTTT
*
39168098 AAAAATTC-AAAATTTTATA
1 AAAAATTCTAAAAATTTATA
39168117 AAAAATTCTAAAAATTTATA
1 AAAAATTCTAAAAATTTATA
39168137 AAAAA
1 AAAAA
39168142 AATATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCTAAAAATTTATA
Found at i:39169532 original size:20 final size:20
Alignment explanation
Indices: 39169507--39169548 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
39169497 ATTTTGAATA
*
39169507 AAGAATATCCTTGGTTATTT
1 AAGAATATCCTCGGTTATTT
39169527 AAGAATATCCTCGGTTATTT
1 AAGAATATCCTCGGTTATTT
39169547 AA
1 AA
39169549 TATCATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (20 bp):
AAGAATATCCTCGGTTATTT
Found at i:39171949 original size:44 final size:44
Alignment explanation
Indices: 39171862--39172835 Score: 818
Period size: 44 Copynumber: 22.0 Consensus size: 44
39171852 ATAAGACTTG
* * *
39171862 TATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGC
1 TATCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGC
* * *
39171907 TATCTTTGATCTACTTCACACCAATACATGAAGACAATATCTGC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * *** *
39171951 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGG
1 TATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGC
39171996 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * ****
39172040 T-TTTTTCGATCTACTTCACCACCAGTGTGGGAAGACAAGATCTG-
1 TATCTTT-GATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGC
* * *
39172084 TATCTTTGATTTACTTCACGCTAGTACATGAAGATAAGATCTGC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * * ***
39172128 TTTCTTCGATTTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGC
* *
39172173 TATCTTTGATCTACTTCATGCCAGTACATGAAGACAATATCTGC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * *** * *
39172217 TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGG
1 TATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGC
39172262 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * *** *
39172306 TTTTTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGG
1 TATCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGC
* * *
39172351 TATCTTTGATCTACTTCAAGCCAGTACATGAAGATAAGATCTAC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * *
39172395 TTTCTTCGATCTACTTCACTCCAATACATGAAGACAAGATCT--
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * *
39172437 TTTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTG-
1 TAT-CTT-TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * *
39172482 TCATATTCGATCTACTTCATGCCAATACATGAAGATAAGATCTGC
1 T-ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * * *
39172527 TATATTTAATCAACTTCGCTGCCAGTACAGGAAGACAAGATCTGC
1 TATCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGC
* ** * ***
39172572 TTTCTTCAATCTACTTTGC-CACCAGTATGGGAAGACAAGATCTGC
1 TATCTTTGATCTAC-TT-CACGCCAGTACATGAAGACAAGATCTGC
* * *
39172617 TTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * *
39172661 TTTCTTTGATCTACTTCACGCCAATACATGAAGGCAAGATCTG-
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * * *
39172704 T-TGGTTCTGATCCACTTCATGTCTA-TACATGAAGACAAGATCTG-
1 TAT-CTT-TGATCTACTTCACG-CCAGTACATGAAGACAAGATCTGC
* ** * *
39172748 TCATCTTCGATCTACTTCATACCAATA-ATGAAGATAAGATCTGC
1 T-ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
* * ** * *
39172792 TATATTTGATCAACTTCGTTGCCAGTACAGGAAGATAAGATCTG
1 TATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTG
39172836 TTTCATTTTC
Statistics
Matches: 750, Mismatches: 153, Indels: 52
0.79 0.16 0.05
Matches are distributed among these distances:
42 4 0.01
43 58 0.08
44 411 0.55
45 271 0.36
46 5 0.01
47 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC
Found at i:39171987 original size:89 final size:89
Alignment explanation
Indices: 39171892--39172839 Score: 1021
Period size: 89 Copynumber: 10.7 Consensus size: 89
39171882 GCCAATACAA
* * *
39171892 GAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAATACATGAAGACAATATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
39171957 CGATCTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* *
39171981 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
39172046 CGATCTACTTCACCACCAGTGTGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
39172070 GAAGACAAGATCTG-TATCTTTGATTTACTTCACGCTAGTACATGAAGATAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
*
39172134 CGATTTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* *
39172158 GAAGACAAGATCTGCTATCTTTGATCTACTTCATGCCAGTACATGAAGACAATATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
39172223 CGATCTACTTCGCCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* * *
39172247 GAAGATAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
39172312 TGATCTACTTCACCACCAGTATGG
66 CGATCTACTTCGCCACCAGTATGG
* * * *
39172336 GAAGACAAGATCTGGTATCTTTGATCTACTTCAAGCCAGTACATGAAGATAAGATCTACTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * * ***
39172401 CGATCTACTTC-ACTCCAATACAT
66 CGATCTACTTCGCCACCAGTATGG
* * * * * *
39172424 GAAGACAAGATCT--TTTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTG-TCAT
1 GAAGACAAGATCTGCTAT-CTT-TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TT
* ***
39172486 ATTCGATCTACTTCATGCCA--A-TACAT
63 CTTCGATCTACTTC--GCCACCAGTATGG
* * * * * *
39172512 GAAGATAAGATCTGCTATATTTAATCAACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTTTCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCAC-GCCAGTACATGAAGACAAGATCTGCTTTCT
* *
39172577 TCAATCTACTTTGCCACCAGTATGG
65 TCGATCTACTTCGCCACCAGTATGG
* * *
39172602 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * * * ***
39172667 TGATCTACTTC-ACGCCAATACAT
66 CGATCTACTTCGCCACCAGTATGG
* * * * * *
39172690 GAAGGCAAGATCTG-T-TGGTTCTGATCCACTTCATGTCTA-TACATGAAGACAAGATCTG-TCA
1 GAAGACAAGATCTGCTAT-CTT-TGATCTACTTCACG-CCAGTACATGAAGACAAGATCTGCT-T
** *
39172751 TCTTCGATCTACTTC-ATACCAATAAT--
62 TCTTCGATCTACTTCGCCACCAGT-ATGG
* * * ** * *
39172777 GAAGATAAGATCTGCTATATTTGATCAACTTCGTTGCCAGTACAGGAAGATAAGATCTG-TTTC
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTC
39172840 ATTTTCAACC
Statistics
Matches: 732, Mismatches: 104, Indels: 48
0.83 0.12 0.05
Matches are distributed among these distances:
86 3 0.00
87 37 0.05
88 264 0.36
89 395 0.54
90 32 0.04
91 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (89 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCGCCACCAGTATGG
Found at i:39172339 original size:266 final size:266
Alignment explanation
Indices: 39171864--39172835 Score: 1164
Period size: 266 Copynumber: 3.7 Consensus size: 266
39171854 AAGACTTGTA
* * * **
39171864 TCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCTAT-CTT-TGATCTACTTCACA
1 TCTTCGATCTACTTCAC-ACCAATACATGAAGACAAGATCTG-TATGCTTCTGATCCACTTCATG
* * * *
39171927 CCAATACATGAAGACAATATCTG-CTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGA
64 CCAGTACATGAAGACAAGATCTGTC-ATCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGA
* * * *
39171991 TCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTACTT
128 TCTGCTATATTTGATCAACTTCACGCCAGTACAGGAAGACAAGATCTGCTTTTTTCGATCTACTT
* * *
39172056 CACCACCAGTGTGGGAAGACAAGATCTGTATCTTTGATTTACTTCACGCTAGTACATGAAGATAA
193 CACCACCAGTATGGGAAGACAAGATCTGTATCTTTGATCTACTTCACGCCAGTACATGAAGATAA
39172121 GATCTGCTT
258 GATCTGCTT
* * * *** *
39172130 TCTTCGATTTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAT-CTT-TGATCTACTTCATG
1 TCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTG-TATGCTTCTGATCCACTTCATG
* *
39172193 CCAGTACATGAAGACAATATCTG-CTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGA
64 CCAGTACATGAAGACAAGATCTGTC-ATCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGA
* * * * *
39172257 TCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTTGATCTACTT
128 TCTGCTATATTTGATCAACTTCACGCCAGTACAGGAAGACAAGATCTGCTTTTTTCGATCTACTT
*
39172322 CACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCAAGCCAGTACATGAAGATA
193 CACCACCAGTATGGGAAGACAAGATCT-GTATCTTTGATCTACTTCACGCCAGTACATGAAGATA
*
39172387 AGATCTACTT
257 AGATCTGCTT
* * * *
39172397 TCTTCGATCTACTTCACTCCAATACATGAAGACAAGATCT-TTTGGTTCTGATCCACTTCATGTC
1 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGTATGCTTCTGATCCACTTCATGCC
* ***
39172461 AGTACATGAAGACAAGATCTGTCATATTCGATCTACTTCATGCCA--A-TACATGAAGATAAGAT
66 AGTACATGAAGACAAGATCTGTCATCTTCGATCTACTTC--GCCACCAGTATGGGAAGATAAGAT
* * * *
39172523 CTGCTATATTTAATCAACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTTTCTTCAATCTACTT
129 CTGCTATATTTGATCAACTTCAC-GCCAGTACAGGAAGACAAGATCTGCTTTTTTCGATCTACTT
** * * * *
39172588 TGCCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACA
193 CACCACCAGTATGGGAAGACAAGATCTG-TATCTTTGATCTACTTCACGCCAGTACATGAAGATA
39172653 AGATCTGCTT
257 AGATCTGCTT
* * * *
39172663 TCTTTGATCTACTTCACGCCAATACATGAAGGCAAGATCTGT-TGGTTCTGATCCACTTCATGTC
1 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGTATGCTTCTGATCCACTTCATG-C
* ** *
39172727 TA-TACATGAAGACAAGATCTGTCATCTTCGATCTACTTC-ATACCAATAAT--GAAGATAAGAT
65 CAGTACATGAAGACAAGATCTGTCATCTTCGATCTACTTCGCCACCAGT-ATGGGAAGATAAGAT
** *
39172788 CTGCTATATTTGATCAACTTCGTTGCCAGTACAGGAAGATAAGATCTG
129 CTGCTATATTTGATCAACTTC-ACGCCAGTACAGGAAGACAAGATCTG
39172836 TTTCATTTTC
Statistics
Matches: 626, Mismatches: 64, Indels: 33
0.87 0.09 0.05
Matches are distributed among these distances:
263 1 0.00
264 2 0.00
265 89 0.14
266 468 0.75
267 62 0.10
268 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (266 bp):
TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGTATGCTTCTGATCCACTTCATGCC
AGTACATGAAGACAAGATCTGTCATCTTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCT
GCTATATTTGATCAACTTCACGCCAGTACAGGAAGACAAGATCTGCTTTTTTCGATCTACTTCAC
CACCAGTATGGGAAGACAAGATCTGTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAGAT
CTGCTT
Found at i:39172477 original size:310 final size:309
Alignment explanation
Indices: 39171869--39172839 Score: 838
Period size: 310 Copynumber: 3.1 Consensus size: 309
39171859 TTGTATCTTC
* * * * ** * * *
39171869 GATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACACCAATA
1 GATCTACTTCA-TGCCAGTACATGAAGATAAGATCTGCTTTCTTCAATCAACTTCGCCACCAGTA
* * * * * ** * *
39171933 CATGAAGACAATATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTA
65 CAGGAAGACAAGATCTGCTATCTTCAATCTACTTTGCCACCAGTACAGGAAGACAAGATCTGCTT
* * * * *
39171998 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTTTTCGATCTACTTCACCA-
130 TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCTTT-GATCTACTTCA--AG
* **** * ** * * * *
39172061 CCAGTGTGGGAAGACAAGATCTGTAT-CTT-TGATTTACTTCACGCTAGTACATGAAGATAAGAT
192 CCAATACATGAAGACAAGATCTCT-TGCTTCTGATCCACTTCATGCCAATACATGAAGACAAGAT
* ** ** * *
39172124 CTG-CTTTCTTCGATTTACTTCGCCACCAGT-ATGGGAAGACAAGATCTGCTATCTTT
256 CTGTC-ATCTTCGATCCACTTC-ATACCAATAAT--GAAGACAAGATCTGCTATATTT
* * * * *
39172180 GATCTACTTCATGCCAGTACATGAAGACAATATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 GATCTACTTCATGCCAGTACATGAAGATAAGATCTGCTTTCTTCAATCAACTTCGCCACCAGTAC
* * * ** * *
39172245 GGGAAGATAAGATCTGGTATCTTTGATCTAC-TT-CACGCCAGTACATGAAGACAAGATCTGCTT
66 AGGAAGACAAGATCTGCTATCTTCAATCTACTTTGC-CACCAGTACAGGAAGACAAGATCTGCTT
* * * ** *
39172308 TTTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCAAGCC
130 TCTTCGATCTACTTCA-CACCAATACAGGAAGACAAGATCTGCTATCTTTGATCTACTTCAAGCC
* * * *
39172373 AGTACATGAAGATAAGATCTACTTTCTTC-GATCTACTTCACT-CCAATACATGAAGACAAGATC
194 AATACATGAAGACAAGATCT-CTTGCTTCTGATCCACTTCA-TGCCAATACATGAAGACAAGATC
* * ** * *
39172436 T-T-TTGGTTCTGATCCACTTCATGTCAGTACATGAAGACAAGATCTG-TCATATTC
257 TGTCAT-CTTC-GATCCACTTCATACCAATA-ATGAAGACAAGATCTGCT-ATATTT
* * * * **
39172490 GATCTACTTCATGCCAATACATGAAGATAAGATCTGCTATATTTAATCAACTTCGCTGCCAGTAC
1 GATCTACTTCATGCCAGTACATGAAGATAAGATCTGCTTTCTTCAATCAACTTCGCCACCAGTAC
* **
39172555 AGGAAGACAAGATCTGCTTTCTTCAATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTTT
66 AGGAAGACAAGATCTGCTATCTTCAATCTACTTTGCCACCAGTACAGGAAGACAAGATCTGCTTT
* * * *
39172620 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACGCCAA
131 CTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCTTTGATCTACTTCAAGCCAA
* * * * *
39172685 TACATGAAGGCAAGATCTGTTGGTTCTGATCCACTTCATGTCTATACATGAAGACAAGATCTGTC
196 TACATGAAGACAAGATCTCTTGCTTCTGATCCACTTCATGCCAATACATGAAGACAAGATCTGTC
* *
39172750 ATCTTCGATCTACTTCATACCAATAATGAAGATAAGATCTGCTATATTT
261 ATCTTCGATCCACTTCATACCAATAATGAAGACAAGATCTGCTATATTT
* * *
39172799 GATCAACTTCGTTGCCAGTACAGGAAGATAAGATCTG-TTTC
1 GATCTACTTC-ATGCCAGTACATGAAGATAAGATCTGCTTTC
39172840 ATTTTCAACC
Statistics
Matches: 534, Mismatches: 103, Indels: 48
0.78 0.15 0.07
Matches are distributed among these distances:
309 42 0.08
310 324 0.61
311 160 0.30
312 8 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (309 bp):
GATCTACTTCATGCCAGTACATGAAGATAAGATCTGCTTTCTTCAATCAACTTCGCCACCAGTAC
AGGAAGACAAGATCTGCTATCTTCAATCTACTTTGCCACCAGTACAGGAAGACAAGATCTGCTTT
CTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCTTTGATCTACTTCAAGCCAA
TACATGAAGACAAGATCTCTTGCTTCTGATCCACTTCATGCCAATACATGAAGACAAGATCTGTC
ATCTTCGATCCACTTCATACCAATAATGAAGACAAGATCTGCTATATTT
Found at i:39189385 original size:116 final size:116
Alignment explanation
Indices: 39189181--39189409 Score: 386
Period size: 116 Copynumber: 2.0 Consensus size: 116
39189171 GCAGGCTGGG
* *
39189181 GTTAATCCTTTGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGTTTATTTTTCAGGTTT
1 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGGTTATTTTTCAGGTTT
* *
39189246 AATTAAATTTTGTTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTATGAT
66 AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTATGAT
* * * *
39189297 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTATTTTAGATTGTATGGTTATTTTTCATGTTT
1 GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGGTTATTTTTCAGGTTT
39189362 AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTAT
66 AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTAT
39189410 CTAGCTTATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (116 bp):
GTTAATCCTATGGCAGGTATCCTTTTGATTAATTACTTCAGATTGCATGGTTATTTTTCAGGTTT
AATTAAATTTAGGTTCTTTTGAATGATGGGTTTTTGCTTCGTTGGTATGAT
Found at i:39198815 original size:5 final size:5
Alignment explanation
Indices: 39198805--39198848 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
39198795 TCTGTTACAC
39198805 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATG
1 AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATGT AATG
39198849 AGACAAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (5 bp):
AATGT
Found at i:39202427 original size:11 final size:12
Alignment explanation
Indices: 39202406--39202430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39202396 GTTTTATGAG
39202406 AAAGAAAAAAAA
1 AAAGAAAAAAAA
39202418 AAAGAAAAAAAA
1 AAAGAAAAAAAA
39202430 A
1 A
39202431 GAAGCAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:39208918 original size:20 final size:22
Alignment explanation
Indices: 39208893--39208932 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39208883 TAAGATGAGC
39208893 AACAAAT-AAA-ATACATAATA
1 AACAAATCAAAGATACATAATA
39208913 AACAAATCAAAGATACATAA
1 AACAAATCAAAGATACATAA
39208933 AATAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.68, C:0.12, G:0.03, T:0.17
Consensus pattern (22 bp):
AACAAATCAAAGATACATAATA
Found at i:39209120 original size:3 final size:3
Alignment explanation
Indices: 39209112--39209160 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
39209102 CAAGACATAG
* *
39209112 ATA ATA ATA ATA TTA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39209160 A
1 A
39209161 AACTAAATAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39212365 original size:18 final size:17
Alignment explanation
Indices: 39212339--39212392 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
39212329 TCAATAATAA
39212339 AAAATAAAATTATAAAAAC
1 AAAA-AAAATTA-AAAAAC
* *
39212358 CAAAAAAATGTAAAATTAC
1 AAAAAAAAT-TAAAA-AAC
39212377 AAAAAAAATTAAAAAA
1 AAAAAAAATTAAAAAA
39212393 TTATGGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 13 0.45
19 15 0.52
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAAAAAATTAAAAAAC
Found at i:39212390 original size:8 final size:8
Alignment explanation
Indices: 39212379--39212509 Score: 50
Period size: 9 Copynumber: 14.9 Consensus size: 8
39212369 AAAATTACAA
39212379 AAAAAATT
1 AAAAAATT
39212387 AAAAAATT
1 AAAAAATT
**
39212395 ATGGAAATAT
1 A-AAAAAT-T
39212405 AAAAAATTT
1 AAAAAA-TT
*
39212414 AGAAAATT
1 AAAAAATT
39212422 ATAAAAATTT
1 A-AAAAA-TT
**
39212432 ATAAATTTAT
1 A-AAAAAT-T
*
39212442 AAAAAAAT
1 AAAAAATT
39212450 AGAAAAA-T
1 A-AAAAATT
39212458 AAAAAATT
1 AAAAAATT
*
39212466 ATAGAAAACT
1 A-A-AAAATT
*
39212476 ATTAAAATCAT
1 A-AAAAAT--T
39212487 AAAAAATT
1 AAAAAATT
39212495 -AAAAATT
1 AAAAAATT
39212502 ATAAAAAT
1 A-AAAAAT
39212510 CATAGAAAAG
Statistics
Matches: 94, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
7 12 0.13
8 19 0.20
9 37 0.39
10 24 0.26
11 2 0.02
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (8 bp):
AAAAAATT
Found at i:39212407 original size:18 final size:18
Alignment explanation
Indices: 39212382--39212533 Score: 88
Period size: 18 Copynumber: 8.6 Consensus size: 18
39212372 ATTACAAAAA
*
39212382 AAAT-TAAAAAATTATGG
1 AAATATAAAAAATTATAG
39212399 AAATATAAAAAATT-TAG
1 AAATATAAAAAATTATAG
*
39212416 AAAATTATAAAAATTTATA-
1 -AAA-TATAAAAAATTATAG
*
39212435 AATTTATAAAAAA--ATAG
1 AA-ATATAAAAAATTATAG
*
39212452 AAAAATAAAAAATTATAG
1 AAATATAAAAAATTATAG
* *
39212470 AAA-ACTATTAAAATCATA-
1 AAATA-TA-AAAAATTATAG
* * *
39212488 AAAAATTAAAAATTATAA
1 AAATATAAAAAATTATAG
*
39212506 AAATCATAGAAAAGTTATA-
1 AAAT-ATA-AAAAATTATAG
39212525 AAA-ATAAAA
1 AAATATAAAA
39212534 TTTTATAAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 29
0.71 0.09 0.19
Matches are distributed among these distances:
16 14 0.13
17 20 0.19
18 38 0.36
19 24 0.22
20 11 0.10
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATATAAAAAATTATAG
Found at i:39212508 original size:26 final size:26
Alignment explanation
Indices: 39212379--39212527 Score: 104
Period size: 27 Copynumber: 5.5 Consensus size: 26
39212369 AAAATTACAA
* **
39212379 AAAAAATTAAAAAATTATGGAAATAT
1 AAAAAATTAGAAAATTATAAAAATAT
*
39212405 AAAAAATTTAGAAAATTATAAAAATTT
1 AAAAAA-TTAGAAAATTATAAAAATAT
* * * **
39212432 ATAAATTTATAAAAAAATAGAAAA-AT
1 AAAAAATTAGAAAATTATA-AAAATAT
* *
39212458 AAAAAATTATAGAAAACTATTAAAATCAT
1 AAAAAA-T-TAGAAAATTATAAAAAT-AT
39212487 AAAAAATTA-AAAATTATAAAAATCAT
1 AAAAAATTAGAAAATTATAAAAAT-AT
* *
39212513 AGAAAAGTTATAAAA
1 A-AAAAATTAGAAAA
39212528 ATAAAATTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
26 37 0.39
27 38 0.40
28 13 0.14
29 8 0.08
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (26 bp):
AAAAAATTAGAAAATTATAAAAATAT
Found at i:39213154 original size:18 final size:18
Alignment explanation
Indices: 39213131--39213225 Score: 88
Period size: 18 Copynumber: 5.1 Consensus size: 18
39213121 ATTCTATATT
*
39213131 TTTTTAGAATTTTTAATA
1 TTTTTATAATTTTTAATA
*
39213149 TTTTTATAAGTGTTT-ATA
1 TTTTTATAA-TTTTTAATA
39213167 TTTTTATATTATTTTT-AT-
1 TTTTTATA--ATTTTTAATA
39213185 TTTTTATAATTTTCTATATA
1 TTTTTATAATTTT-TA-ATA
39213205 TTTTTTATAATTTTCTAATA
1 -TTTTTATAATTTT-TAATA
39213225 T
1 T
39213226 ATTCTAAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
16 5 0.08
17 1 0.02
18 27 0.41
19 13 0.20
20 4 0.06
21 16 0.24
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTATAATTTTTAATA
Found at i:39213168 original size:38 final size:38
Alignment explanation
Indices: 39213122--39213225 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
39213112 TTAGATTTCA
*
39213122 TTCTATATTTTTTTAGAATTTTTAATATTTTTATAAGTG
1 TTCTATATTTTTTTATAATTTTTAATATTTTTATAA-TG
* * *
39213161 TT-TATATTTTTATATTATTTTT-AT-TTTTTATAATT
1 TTCTATATTTTTTTATAATTTTTAATATTTTTATAATG
39213196 TTCTATATATTTTTTATAATTTTCTAATAT
1 TTCTATAT-TTTTTTATAATTTT-TAATAT
39213226 ATTCTAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
35 3 0.06
36 14 0.26
37 14 0.26
38 18 0.33
39 4 0.07
40 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (38 bp):
TTCTATATTTTTTTATAATTTTTAATATTTTTATAATG
Found at i:39213261 original size:17 final size:18
Alignment explanation
Indices: 39213227--39213272 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
39213217 TTCTAATATA
*
39213227 TTCTAA-AAATTT-TAAT
1 TTCTAATAATTTTATAAT
39213243 TT-TAATAATTTTATAAT
1 TTCTAATAATTTTATAAT
*
39213260 TTCTAATAGTTTT
1 TTCTAATAATTTT
39213273 TTTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.12
16 7 0.28
17 6 0.24
18 9 0.36
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (18 bp):
TTCTAATAATTTTATAAT
Found at i:39216667 original size:18 final size:17
Alignment explanation
Indices: 39216634--39216672 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39216624 TTTTATAAAT
39216634 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
39216652 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
39216669 TGTG
1 TGTG
39216673 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:39216917 original size:23 final size:23
Alignment explanation
Indices: 39216891--39217011 Score: 136
Period size: 23 Copynumber: 5.3 Consensus size: 23
39216881 GTGTTATTGA
* * *
39216891 TCAGTGGCAACTTCGGCTATATT
1 TCAGTGGTAGCTTCGGCTACATT
* * *
39216914 TCAGTGGTAGCTACTGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
39216937 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* *
39216960 TCAGTGGTAGCTAT-GGCTACGTA
1 TCAGTGGTAGCT-TCGGCTACATT
* *
39216983 TCAGTGGTAGCTCCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
39217006 TCAGTG
1 TCAGTG
39217012 TGGCACTTAT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
23 82 0.99
24 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:39216961 original size:46 final size:46
Alignment explanation
Indices: 39216890--39217011 Score: 174
Period size: 46 Copynumber: 2.7 Consensus size: 46
39216880 AGTGTTATTG
* * *
39216890 ATCAGTGGCAACTTCGGCTATATTTCAGTGGTAGCTACT-GCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTA-TGGCTACAT
*
39216936 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGGCTACAT
* *
39216982 ATCAGTGGTAGCTCCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
39217012 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGGCTACAT
Found at i:39218039 original size:2 final size:2
Alignment explanation
Indices: 39218032--39218056 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39218022 TGTATTATTC
39218032 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39218057 TCATNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39220171 original size:4 final size:4
Alignment explanation
Indices: 39220162--39220191 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
39220152 CTAATATCCC
39220162 ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
39220192 GATAACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:39222421 original size:28 final size:28
Alignment explanation
Indices: 39222362--39222423 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
39222352 TTTAATTTTT
* * * *
39222362 TTAAAATTCTTAACAATAATTCTATTTT
1 TTAAAATTCTTAAAAATAATTATAATTA
39222390 TTAAAA-TCTTAAAAATAATTATAAATTA
1 TTAAAATTCTTAAAAATAATTAT-AATTA
39222418 TTAAAA
1 TTAAAA
39222424 ATAATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (28 bp):
TTAAAATTCTTAAAAATAATTATAATTA
Found at i:39224725 original size:2 final size:2
Alignment explanation
Indices: 39224718--39224742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39224708 TTTTTCTCAG
39224718 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
39224743 ATCTTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:39226169 original size:11 final size:11
Alignment explanation
Indices: 39226153--39226177 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39226143 ATTGATAAAA
39226153 ATAAGGATGAC
1 ATAAGGATGAC
39226164 ATAAGGATGAC
1 ATAAGGATGAC
39226175 ATA
1 ATA
39226178 GAATGGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (11 bp):
ATAAGGATGAC
Found at i:39244293 original size:30 final size:30
Alignment explanation
Indices: 39244257--39244317 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
39244247 TAAAAGAGGT
39244257 TAGTTTCATGGTTTCATTGCTGTTTTCGCA
1 TAGTTTCATGGTTTCATTGCTGTTTTCGCA
39244287 TAGTTTCATGGTTTCATTGCTGTTTTCGCA
1 TAGTTTCATGGTTTCATTGCTGTTTTCGCA
39244317 T
1 T
39244318 CCTTACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.20, T:0.51
Consensus pattern (30 bp):
TAGTTTCATGGTTTCATTGCTGTTTTCGCA
Found at i:39245818 original size:18 final size:17
Alignment explanation
Indices: 39245779--39245822 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
39245769 CATTGTGTAA
39245779 TTTGATTTTC--TTTCT
1 TTTGATTTTCTTTTTCT
39245794 TTT--TTTTCTTTTTACT
1 TTTGATTTTCTTTTT-CT
39245810 TTTGATTTTCTTT
1 TTTGATTTTCTTT
39245823 GTGACCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.21
15 6 0.25
16 5 0.21
18 8 0.33
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTGATTTTCTTTTTCT
Found at i:39249708 original size:30 final size:31
Alignment explanation
Indices: 39249640--39249699 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
39249630 GACTTAAATA
* *
39249640 AAAACTTTTGAATAGTTCAATGGCTTGAATG
1 AAAACTTTCGAATAGTTCAATGGATTGAATG
39249671 AAAACTTTCGAATAGTTCAAT-GATTGAAT
1 AAAACTTTCGAATAGTTCAATGGATTGAAT
39249700 TGTAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (31 bp):
AAAACTTTCGAATAGTTCAATGGATTGAATG
Found at i:39250643 original size:22 final size:20
Alignment explanation
Indices: 39250624--39250661 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39250614 GATAAAATTG
*
39250624 TTATTCTCAAAAAATAAAAT
1 TTATACTCAAAAAATAAAAT
*
39250644 TTATACTTAAAAAATAAA
1 TTATACTCAAAAAATAAA
39250662 TTCTCACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TTATACTCAAAAAATAAAAT
Found at i:39255824 original size:23 final size:23
Alignment explanation
Indices: 39255798--39255841 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
39255788 ATGATATCTG
39255798 TCAACATCATCAACTATCCACTA
1 TCAACATCATCAACTATCCACTA
*
39255821 TCAACATCATCCACTATCCAC
1 TCAACATCATCAACTATCCAC
39255842 ATTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.25
Consensus pattern (23 bp):
TCAACATCATCAACTATCCACTA
Found at i:39255834 original size:16 final size:16
Alignment explanation
Indices: 39255813--39255843 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39255803 ATCATCAACT
39255813 ATCCACTATCAACATC
1 ATCCACTATCAACATC
*
39255829 ATCCACTATCCACAT
1 ATCCACTATCAACAT
39255844 TTAATTAAAC
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:0.35, C:0.39, G:0.00, T:0.26
Consensus pattern (16 bp):
ATCCACTATCAACATC
Found at i:39262971 original size:22 final size:22
Alignment explanation
Indices: 39262946--39262987 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39262936 TGCAAATAGA
* *
39262946 AATAATCATTTAAATGGTTTCC
1 AATAATAATATAAATGGTTTCC
39262968 AATAATAATATAAATGGTTT
1 AATAATAATATAAATGGTTT
39262988 TAATGAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
AATAATAATATAAATGGTTTCC
Found at i:39267549 original size:34 final size:34
Alignment explanation
Indices: 39267511--39267575 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
39267501 ATAGATTTTA
* *
39267511 AAATTGAATTAATTAACTAGATGCAAATTAACCG
1 AAATTAAATTAATTAACTAGATGAAAATTAACCG
*
39267545 AAATTAAATTAATTAACTAGATTAAAATTAA
1 AAATTAAATTAATTAACTAGATGAAAATTAA
39267576 TCAGCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (34 bp):
AAATTAAATTAATTAACTAGATGAAAATTAACCG
Found at i:39270218 original size:2 final size:2
Alignment explanation
Indices: 39270211--39270238 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39270201 GTCATCCAAG
39270211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39270239 GCTTACCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39272345 original size:5 final size:5
Alignment explanation
Indices: 39272300--39272333 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
39272290 TGAAAAATAT
39272300 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
39272334 ATATTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:39276337 original size:21 final size:21
Alignment explanation
Indices: 39276313--39276365 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
39276303 CATTGTTTCT
*
39276313 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* * *
39276334 AATCTCACTGTTACAGTAACT
1 AATCTCACCGCTACAGTAACC
39276355 AATCTCACCGC
1 AATCTCACCGC
39276366 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:39282582 original size:3 final size:3
Alignment explanation
Indices: 39282567--39282616 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
39282557 TATGTATATA
* * * *
39282567 ATT ATT ATA ATT ATT AACT ATA ATA ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39282613 ATT A
1 ATT A
39282617 AATAAAGTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:39282589 original size:22 final size:22
Alignment explanation
Indices: 39282563--39282604 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39282553 ATTATATGTA
*
39282563 TATAATTATTATAATTATTAAC
1 TATAATAATTATAATTATTAAC
*
39282585 TATAATAATTATTATTATTA
1 TATAATAATTATAATTATTA
39282605 TTATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATAATTATAATTATTAAC
Found at i:39284189 original size:39 final size:38
Alignment explanation
Indices: 39284127--39284230 Score: 103
Period size: 33 Copynumber: 2.9 Consensus size: 38
39284117 TTACTGATCA
* * *
39284127 GGCAC-TTATGTGCCGACTACTGTTACTGTTACCGATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTA-CGATTC
39284165 GGCACTTTGTGTGTCGAATACTGTTAC----A-GATTC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTACGATTC
* * *
39284198 AGCACTTTGTGTGTTGAATATTGTTACTGTTAC
1 GGCACTTTGTGTGTCGAATACTGTTACTGTTAC
39284231 TGTTACTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
33 29 0.54
35 1 0.02
37 1 0.02
38 5 0.09
39 18 0.33
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (38 bp):
GGCACTTTGTGTGTCGAATACTGTTACTGTTACGATTC
Found at i:39284197 original size:33 final size:33
Alignment explanation
Indices: 39284150--39284224 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
39284140 CGACTACTGT
* *
39284150 TACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
39284183 TACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
39284216 TATTGTTAC
1 TACTGTTAC
39284225 TGTTACTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (33 bp):
TACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:39284230 original size:6 final size:6
Alignment explanation
Indices: 39284219--39284265 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
39284209 TGTTGAATAT
*
39284219 TGTTAC TGTTAC TGTTAC TGTTAC TGCTA- TCGTTAC TGATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC T-GTTAC TG-TTAC TGTT
39284266 TATTGGTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 1 0.03
6 28 0.78
7 7 0.19
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TGTTAC
Found at i:39286517 original size:64 final size:63
Alignment explanation
Indices: 39286447--39286617 Score: 173
Period size: 64 Copynumber: 2.6 Consensus size: 63
39286437 GCTAGAACAG
* * * * * *
39286447 TAAACACAAAAGAGATAATCTATTGAGACAATAAACATAGAATAGAGATAGT-TCGTTGGGACAA
1 TAAACACAAAAGAGATAGTCTATTG-GACAGTAAACACAGAACAGAGATAGTCT-GTTAGGAAAA
* * ** *
39286511 TAAACACAGAATAGATAGTCCGCTTGGACAGTAAATACAGAACAGAGATAGTCTGTTAGGAAAA
1 TAAACACAAAAGAGATAGT-CTATTGGACAGTAAACACAGAACAGAGATAGTCTGTTAGGAAAA
*
39286575 TAAACACAGAATAGAGATAGTCTGTTGGGACAGTAAACACAGA
1 TAAACACA-AA-AGAGATAGTCTATT-GGACAGTAAACACAGA
39286618 TAAAGTCCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
64 54 0.63
65 9 0.10
66 23 0.27
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (63 bp):
TAAACACAAAAGAGATAGTCTATTGGACAGTAAACACAGAACAGAGATAGTCTGTTAGGAAAA
Found at i:39286584 original size:33 final size:31
Alignment explanation
Indices: 39286424--39286617 Score: 160
Period size: 33 Copynumber: 6.0 Consensus size: 31
39286414 TATGACATTC
* * * *
39286424 AAAGAGATAGTCCGCTAGAACAGTAAACACA-
1 AAAGAGATAGTCTG-TTGGACAATAAACACAG
* * *
39286455 AAAGAGATAATCTATTGAGACAATAAACATAG
1 AAAGAGATAGTCTGTTG-GACAATAAACACAG
39286487 AATAGAGATAGT-TCGTTGGGACAATAAACACAG
1 AA-AGAGATAGTCT-GTT-GGACAATAAACACAG
* * * *
39286520 -AATAGATAGTCCGCTTGGACAGTAAATACAG
1 AAAGAGATAGTCTG-TTGGACAATAAACACAG
*
39286551 AACAGAGATAGTCTGTTAGGAAAATAAACACAG
1 AA-AGAGATAGTCTGTT-GGACAATAAACACAG
*
39286584 AATAGAGATAGTCTGTTGGGACAGTAAACACAG
1 AA-AGAGATAGTCTGTT-GGACAATAAACACAG
39286617 A
1 A
39286618 TAAAGTCCAC
Statistics
Matches: 130, Mismatches: 23, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
30 2 0.02
31 43 0.33
32 9 0.07
33 75 0.58
34 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (31 bp):
AAAGAGATAGTCTGTTGGACAATAAACACAG
Found at i:39286592 original size:97 final size:95
Alignment explanation
Indices: 39286428--39286642 Score: 260
Period size: 97 Copynumber: 2.3 Consensus size: 95
39286418 ACATTCAAAG
* *
39286428 AGATAGTCCGCTAGAACAGTAAACACAAAAGAGATAATCTATTGAGACAATAAACATAGAATAGA
1 AGATAGTCCGCTAGAACAGTAAACACAAAAGAGATAATCTATTGAGAAAATAAACACAGAATAGA
39286493 GATAGT-TCGTTGGGACAATAAACACAGAAT
66 GATAGTCT-GTTGGGACAATAAACACAGAAT
* * * * *
39286523 AGATAGTCCGCTTGGACAGTAAATACAGAACAGAGATAGTCTGTT-AGGAAAATAAACACAGAAT
1 AGATAGTCCGCTAGAACAGTAAACACA-AA-AGAGATAATCTATTGA-GAAAATAAACACAGAAT
*
39286587 AGAGATAGTCTGTTGGGACAGTAAACACAG-AT
63 AGAGATAGTCTGTTGGGACAATAAACACAGAAT
* * *
39286619 A-A-AGTCCACCAGGACAGTAAACAC
1 AGATAGTCCGCTAGAACAGTAAACAC
39286643 GGGGTAAGTC
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
94 18 0.17
95 25 0.24
96 6 0.06
97 54 0.52
98 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (95 bp):
AGATAGTCCGCTAGAACAGTAAACACAAAAGAGATAATCTATTGAGAAAATAAACACAGAATAGA
GATAGTCTGTTGGGACAATAAACACAGAAT
Found at i:39302842 original size:25 final size:24
Alignment explanation
Indices: 39302814--39302871 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
39302804 TCAAGCTGAA
*
39302814 TATCGGTAAGCTCATACGAGTTGAG
1 TATCGGTAAGCTCATAAGAGTTG-G
* *
39302839 TATCGATAATCTCATAAGAGTTGG
1 TATCGGTAAGCTCATAAGAGTTGG
*
39302863 AATCGGTAA
1 TATCGGTAA
39302872 ACCTAATGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (24 bp):
TATCGGTAAGCTCATAAGAGTTGG
Found at i:39303991 original size:11 final size:11
Alignment explanation
Indices: 39303975--39303999 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39303965 ACATGCTTTA
39303975 AATATTAAAAT
1 AATATTAAAAT
39303986 AATATTAAAAT
1 AATATTAAAAT
39303997 AAT
1 AAT
39304000 TTTTTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:39305980 original size:23 final size:24
Alignment explanation
Indices: 39305929--39305975 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
39305919 TTCGAACCAT
*
39305929 GTAACGGGAAGCTCATGTGAGCTAA
1 GTAACGGGAAGCTCATGAGAGC-AA
39305954 GTAACGGGAAGCTCATGAGAGC
1 GTAACGGGAAGCTCATGAGAGC
39305976 CGTAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.34, T:0.17
Consensus pattern (24 bp):
GTAACGGGAAGCTCATGAGAGCAA
Found at i:39306013 original size:50 final size:50
Alignment explanation
Indices: 39305958--39306075 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 50
39305948 AGCTAAGTAA
*
39305958 CGGGAAGCTCATGAGAGCCGTAAAT-T-A-GATAGC-TAAGGAGAGCTATTAAT
1 CGGGAAGCTCATGAGAGCC--AAATATCAGGA-AGCTTAA-GAGAGCCATTAAT
*
39306008 GGGGAAGCTCAT-ACGAGCCAAATATCAGGAAGCTTAAGAGAGCCATTAAT
1 CGGGAAGCTCATGA-GAGCCAAATATCAGGAAGCTTAAGAGAGCCATTAAT
*
39306058 CAGGAAGCTCATGAGAGC
1 CGGGAAGCTCATGAGAGC
39306076 TGTGGTGCGT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
48 4 0.07
49 2 0.03
50 46 0.79
51 6 0.10
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (50 bp):
CGGGAAGCTCATGAGAGCCAAATATCAGGAAGCTTAAGAGAGCCATTAAT
Found at i:39306050 original size:25 final size:25
Alignment explanation
Indices: 39306022--39306075 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
39306012 AAGCTCATAC
*
39306022 GAGCCAA-ATATCAGGAAGCTTAAGA
1 GAGCCAATA-ATCAGGAAGCTCAAGA
* *
39306047 GAGCCATTAATCAGGAAGCTCATGA
1 GAGCCAATAATCAGGAAGCTCAAGA
39306072 GAGC
1 GAGC
39306076 TGTGGTGCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
GAGCCAATAATCAGGAAGCTCAAGA
Found at i:39309069 original size:20 final size:19
Alignment explanation
Indices: 39309037--39309075 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
39309027 GTTAGGTTTT
39309037 TTAACAAAAAAAAATATTAA
1 TTAACAAAAAAAAA-ATTAA
39309057 TTAA-AAAATAAAAAATTAA
1 TTAACAAAA-AAAAAATTAA
39309076 AACAACATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
TTAACAAAAAAAAAATTAA
Found at i:39309478 original size:20 final size:19
Alignment explanation
Indices: 39309432--39309483 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
39309422 AAAAAAATTC
* *
39309432 AAAAAAATATAAAATTTTGA
1 AAAAAAATAT-AAATTATAA
39309452 AAAAAAATATAAATTATAA
1 AAAAAAATATAAATTATAA
39309471 AAATAAAAT-TAAA
1 AAA-AAAATATAAA
39309484 AAATGTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAAAATATAAATTATAA
Found at i:39309479 original size:14 final size:14
Alignment explanation
Indices: 39309453--39309487 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
39309443 AAATTTTGAA
39309453 AAAAAATATAAATT
1 AAAAAATATAAATT
39309467 ATAAAAATA-AAATT
1 A-AAAAATATAAATT
39309481 AAAAAAT
1 AAAAAAT
39309488 GTGATAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 7 0.35
15 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAATATAAATT
Found at i:39314848 original size:17 final size:17
Alignment explanation
Indices: 39314781--39314848 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
39314771 TATGTGAATG
*
39314781 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
39314797 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
39314816 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
39314835 TAAAATTATTAATT
1 TAAAATTATTAATT
39314849 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:39314904 original size:117 final size:116
Alignment explanation
Indices: 39314667--39314911 Score: 411
Period size: 117 Copynumber: 2.1 Consensus size: 116
39314657 TAAGTTTGTG
* *
39314667 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATCAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** *
39314732 CTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
66 CTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
39314783 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
*
39314847 TTGTTAGTACCAGGAAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 CTGTTAGTACCA-G-AAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
39314900 AAATTATTAATT
1 AAATTATTAATT
39314912 TCATTTAGGG
Statistics
Matches: 121, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
115 39 0.32
116 35 0.29
117 47 0.39
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
CTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:39314944 original size:23 final size:23
Alignment explanation
Indices: 39314916--39315532 Score: 660
Period size: 23 Copynumber: 27.8 Consensus size: 23
39314906 TTAATTTCAT
39314916 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39314939 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAATTTAATTAGG
* * **
39314960 TTAGAGTTTTTAA-GTAA-CGGG
1 TTAGGGTTTTTAATTTAATTAGG
*
39314981 TTAGGGTTTTTAAGTTT-A--GGG
1 TTAGGGTTTTTAA-TTTAATTAGG
* *
39315002 TTTAAGGTTTTTAATTAAATTAGG
1 -TTAGGGTTTTTAATTTAATTAGG
*
39315026 TTAGGGTTTTTAAGTTAA--AGG
1 TTAGGGTTTTTAATTTAATTAGG
39315047 TTAGGG-TTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
39315069 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
*
39315092 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315115 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAATTTAATTAGG
*
39315136 TTAGGG-TTTTAATTTAATTAGA
1 TTAGGGTTTTTAATTTAATTAGG
*
39315158 TTAGGGTTTTTAATTTAACTAGG
1 TTAGGGTTTTTAATTTAATTAGG
39315181 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
*
39315204 TTAGGGTTTTTAAGTT-A--AGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315224 ATTAGGGTTTTTAAGTTAA--GGG
1 -TTAGGGTTTTTAATTTAATTAGG
39315246 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
39315269 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315292 TTAAGGTTTTTTATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315315 TTAGGGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAATTTAATTAGG
*
39315336 TTAAGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315359 TTAGGGTTTTTTAAGTTAA-GA-G
1 TTAGGG-TTTTTAATTTAATTAGG
39315381 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315404 TTAGGGTTTTTTAAGTTAA-GA-G
1 TTAGGG-TTTTTAATTTAATTAGG
39315426 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAATTTAATTAGG
* * *
39315449 TTAGAGTTTTTAAGTTAA--GGG
1 TTAGGGTTTTTAATTTAATTAGG
* * *
39315470 TTAGGGTTTTTAAGTTAAGT-GT
1 TTAGGGTTTTTAATTTAATTAGG
* *
39315492 TTAAGGTTTTTAA-TTAATTTAGT
1 TTAGGGTTTTTAATTTAA-TTAGG
*
39315515 TTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAATTTAA
39315533 GGGTATTAAT
Statistics
Matches: 511, Mismatches: 53, Indels: 59
0.82 0.09 0.09
Matches are distributed among these distances:
20 26 0.05
21 147 0.29
22 64 0.13
23 246 0.48
24 28 0.05
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAATTTAATTAGG
Found at i:39315130 original size:89 final size:89
Alignment explanation
Indices: 39314916--39315532 Score: 655
Period size: 89 Copynumber: 6.9 Consensus size: 89
39314906 TTAATTTCAT
* * * * **
39314916 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGAGTTTTTAA-GTAA-CG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAG-GGTTTTAATTTAATTA
*
39314979 GGTTAGGGTTTTTAAGTTT-A--GGG
65 GGTTAGGGTTTTTAA-TTTAATTAGG
*
39315002 TTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTAATTTAATTA
1 -TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTAATTTAATTA
39315067 GGTTAGGGTTTTTAATTTAATTAGG
65 GGTTAGGGTTTTTAATTTAATTAGG
*
39315092 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTAATTTAATTAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTAATTTAATTAG
* *
39315157 ATTAGGGTTTTTAATTTAACTAGG
66 GTTAGGGTTTTTAATTTAATTAGG
* *
39315181 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-AAGGATTAGGGTTTTTAAGTTAA--
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGG-TTAGGG-TTTTAATTTAATT
*
39315243 GGGTTAGGGTTTTTAATTTAATTAGG
64 AGGTTAGGGTTTTTAATTTAATTAGG
* * * * *
39315269 TTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTTATTTAATTAGGTTAGGGTTTTTAAGTTAA-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAA--AGGTTAGGG-TTTTAATTTAAT
* *
39315333 -GGGTTAAGGTTTTTAATTTAATTAGG
63 TAGGTTAGGGTTTTTAATTTAATTAGG
* *
39315359 TTAGGG-TTTT--TTAAGTTAAGAGTTAGGGTTTTTAATTTAATTAGGTTAGGG-TTT--TTTAA
1 TTAGGGTTTTTAATTAAATT-AG-GTTAGGGTTTTTAAGTTAA--AGGTTAGGGTTTTAATTTAA
39315418 GTTAAGAGTTAGGGTTTTTAATTTAATTAGG
62 -TT-AG-GTTAGGGTTTTTAATTTAATTAGG
* * *
39315449 TTAGAGTTTTTAAGTT-AA--GGGTTAGGGTTTTTAAGTT-AAGTGTTTAAGGTTTTTAA-TTAA
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTAAAG-G-TT-AGGGTTTTAATTTAA
* *
39315509 TTTAGTTTAGGGTTTTTAAGTTAA
62 -TTAGGTTAGGGTTTTTAATTTAA
39315533 GGGTATTAAT
Statistics
Matches: 466, Mismatches: 37, Indels: 52
0.84 0.07 0.09
Matches are distributed among these distances:
85 4 0.01
86 9 0.02
87 60 0.13
88 83 0.18
89 199 0.43
90 95 0.20
91 13 0.03
93 1 0.00
94 2 0.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (89 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTAATTTAATTAG
GTTAGGGTTTTTAATTTAATTAGG
Found at i:39315280 original size:200 final size:201
Alignment explanation
Indices: 39315025--39315536 Score: 770
Period size: 200 Copynumber: 2.6 Consensus size: 201
39315015 ATTAAATTAG
39315025 GTTAGGGTTTTTAAGTTAAAGGTTAGGG-TTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATT
1 GTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATT
*
39315089 AGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTT-AGGGTTTTAATTTAA
66 AGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAAGGGTTTTAATTTAA
* *
39315153 TTAGATTAGGG-TTTTTAATTTAACTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGG-TTTTTA
131 TTAGATTAGGGTTTTTTAAGTTAA-GA-GTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTTA
39315216 AGTTAAG-
194 AGTTAAGA
*
39315223 GATTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAT
1 G-TTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAAT
* * *
39315288 TAGGTTAAGGTTTTTTATTTAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTTTTAATTTA
65 TAGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAAGGGTTTTAATTTA
*
39315353 ATTAGGTTAGGGTTTTTTAAGTTAAGAGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTTAA
130 ATTAGATTAGGGTTTTTTAAGTTAAGAGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTTAA
39315418 GTTAAGA
195 GTTAAGA
* * * * *
39315425 GTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAAGTTAA--GGGTTAGGGTTTTTAAGTTAA
1 GTTAGGGTTTTTAAGTTAA--AGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAA
* * * *
39315488 GT-GTTTAAGGTTTTTAATTAATTTAGTTTAGGGTTTTTAAGTTAAGGGT
64 TTAGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGT
39315537 ATTAATTGTT
Statistics
Matches: 286, Mismatches: 20, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
198 1 0.00
199 26 0.09
200 154 0.54
201 75 0.26
202 12 0.04
203 18 0.06
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (201 bp):
GTTAGGGTTTTTAAGTTAAAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATT
AGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAAGGGTTAAGGGTTTTAATTTAA
TTAGATTAGGGTTTTTTAAGTTAAGAGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTTAAG
TTAAGA
Found at i:39315613 original size:25 final size:24
Alignment explanation
Indices: 39315576--39315631 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 24
39315566 ATCAAAATAT
39315576 TCAAA-AAATTCTATTTTATTACA
1 TCAAATAAATTCTATTTTATTACA
39315599 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAA-TTCTATTTTATTACA
39315624 TCAAATAA
1 TCAAATAA
39315632 TATCAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 5 0.16
24 3 0.10
25 23 0.74
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
TCAAATAAATTCTATTTTATTACA
Found at i:39316964 original size:20 final size:20
Alignment explanation
Indices: 39316927--39316964 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39316917 TTTATTTTTA
*
39316927 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
39316947 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
39316965 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:39324330 original size:24 final size:24
Alignment explanation
Indices: 39324303--39324358 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
39324293 GTACAAGATC
39324303 AAAATTTACTAATTATATTTAATA
1 AAAATTTACTAATTATATTTAATA
39324327 AAAATTTACTAATTATATTTAATA
1 AAAATTTACTAATTATATTTAATA
39324351 AAAATTTA
1 AAAATTTA
39324359 TGTATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATTTACTAATTATATTTAATA
Found at i:39326037 original size:298 final size:290
Alignment explanation
Indices: 39325513--39326057 Score: 661
Period size: 298 Copynumber: 1.8 Consensus size: 290
39325503 TTTTTTTACG
* * * *
39325513 TTTTCAAATCAATCTTTTAATTTGTTTTTGTTGTTTTTTCTCGAAAAAGGAGTATATTAGGTTTA
1 TTTTAAAAACAATCTTTTAATTTCTTTTCGTTGTTTTTTCTCGAAAAAGGAGTATATTAGGTTTA
* *
39325578 GATTTAACGTTTTAGGTAATGATTGAGTATTTACTAGCGTCTGGACTCTGTAAAGTCTTCTAATT
66 GATTTAACGTTTTAGGTAATGATTGAGTATTTACTAGCGTCTGGACCCTGGAAAGTCTTCTAATT
* ** * * *
39325643 TTATTTTATTGTTTCTGCTAAGCGCTGGATCCAAAAAGTAATAAAAGCACTTCTTTTTCTACGTT
131 TAATTACATCGTTTCTGCTAAGCACTGGATCCAAAAAGTAATAAAAGCA--TCTTATTCTACGTT
*
39325708 TAAGAGCTTATTGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTTCATCTTATATGA
194 TAAGAACTTATTGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTTCATCTTATATGA
39325773 TGAGAGGAAAACCGAATTTGTTTAAGATTTTT
259 TGAGAGGAAAACCGAATTTGTTTAAGATTTTT
*
39325805 TTTTAAAAACAATCTTTTTAATTTCTTTTCGTT-TTTTTTCTCGTAAAAGG-GATATATTAGGTT
1 TTTTAAAAACAATC-TTTTAATTTCTTTTCGTTGTTTTTTCTCGAAAAAGGAG-TATATTAGGTT
* * * * *
39325868 TAAGGTTTAACATTTTTTAGGTAATGGTTTGAGTATTTTCTAGCGTCTCTGGACCCTGGGAAGTC
64 T-AGATTTAAC--GTTTTAGGTAAT-GATTGAGTATTTACTAGCG--TCTGGACCCTGGAAAGTC
* * *
39325933 -TC--ATATTAATTACATCGTTTCTGCTAATCATTTGATCCAAACTCAAAAGTAATAAAAGCA-C
123 TTCTAAT-TTAATTACATCGTTTCTGCTAAGCACTGGATCC--A---AAAAGTAATAAAAGCATC
* * * * *
39325994 TTATTCTGCGTTTAGGAATTTCTTGATCGATGTATGTTCAAATTTATTGCAGGCATTAGCGTCT
182 TTATTCTACGTTTAAGAACTTATTGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCT
39326058 CCAACTCAGA
Statistics
Matches: 212, Mismatches: 27, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
291 1 0.00
292 40 0.19
293 24 0.11
295 13 0.06
296 42 0.20
297 2 0.01
298 74 0.35
301 16 0.08
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (290 bp):
TTTTAAAAACAATCTTTTAATTTCTTTTCGTTGTTTTTTCTCGAAAAAGGAGTATATTAGGTTTA
GATTTAACGTTTTAGGTAATGATTGAGTATTTACTAGCGTCTGGACCCTGGAAAGTCTTCTAATT
TAATTACATCGTTTCTGCTAAGCACTGGATCCAAAAAGTAATAAAAGCATCTTATTCTACGTTTA
AGAACTTATTGATCGATGTATGTTCAAATTGATTGCAGGCATTAGCGTCTTCATCTTATATGATG
AGAGGAAAACCGAATTTGTTTAAGATTTTT
Found at i:39335960 original size:45 final size:45
Alignment explanation
Indices: 39335902--39335989 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
39335892 ATAATATTCA
* *
39335902 ATTATTTTTATATGTGAAATATTTCA-ATTAATTATTTCAAATATC
1 ATTATATTTATATGTGAAATATTTCAGA-TAATTATTTAAAATATC
39335947 ATTATATTTATATGTGAAATATTTCAGATAATTATTTAAAATA
1 ATTATATTTATATGTGAAATATTTCAGATAATTATTTAAAATA
39335990 CACGTATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (45 bp):
ATTATATTTATATGTGAAATATTTCAGATAATTATTTAAAATATC
Found at i:39343692 original size:23 final size:23
Alignment explanation
Indices: 39343648--39343692 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39343638 TTAATTAATT
* * *
39343648 AAAATAAATATATAGAATATCTC
1 AAAATAAATATAGAAAAAATCTC
*
39343671 AAAATATATATAGAAAAAATCT
1 AAAATAAATATAGAAAAAATCT
39343693 AGACATGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAATAAATATAGAAAAAATCTC
Found at i:39347067 original size:20 final size:22
Alignment explanation
Indices: 39347044--39347086 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
39347034 ACAATATAAT
*
39347044 TATTTTTAT-TATG-TTTTAAA
1 TATTTTTATATAGGTTTTTAAA
39347064 TATTTTTATATAGGTTTTTAAA
1 TATTTTTATATAGGTTTTTAAA
39347086 T
1 T
39347087 TTAAACCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TATTTTTATATAGGTTTTTAAA
Found at i:39347409 original size:32 final size:32
Alignment explanation
Indices: 39347347--39347410 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
39347337 TTAAAATATG
* * *
39347347 TTTGTTAAAAATTTTTAAATTCTTATTTTTTT
1 TTTGTGAAAAATTTTAAAATTCTTAATTTTTT
*
39347379 TTTGTGAATAATTTTAAAATT-TTCAATTTTTT
1 TTTGTGAAAAATTTTAAAATTCTT-AATTTTTT
39347411 AAACACATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (32 bp):
TTTGTGAAAAATTTTAAAATTCTTAATTTTTT
Found at i:39350259 original size:5 final size:5
Alignment explanation
Indices: 39350249--39350289 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
39350239 CCCAAGTATT
39350249 CAACC CAACC CAATTACC CAACC CAACC CAACC CAACC CAA
1 CAACC CAACC C-A--ACC CAACC CAACC CAACC CAACC CAA
39350290 TCATAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 27 0.82
6 1 0.03
7 1 0.03
8 4 0.12
ACGTcount: A:0.41, C:0.54, G:0.00, T:0.05
Consensus pattern (5 bp):
CAACC
Found at i:39350260 original size:18 final size:18
Alignment explanation
Indices: 39350237--39350279 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39350227 ACCCAATCTA
**
39350237 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
39350255 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
39350273 AACCCAA
1 AACCCAA
39350280 CCCAACCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:39350414 original size:9 final size:9
Alignment explanation
Indices: 39350397--39350463 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
39350387 GTAGTGATTC
*
39350397 AATTTGGTT
1 AATTCGGTT
39350406 AATTCGGTT
1 AATTCGGTT
*
39350415 AATTCGGGT
1 AATTCGGTT
*
39350424 AATTCGGAT
1 AATTCGGTT
*
39350433 AATTCGGGT
1 AATTCGGTT
39350442 AATTCGGTT
1 AATTCGGTT
39350451 AATTCGGTT
1 AATTCGGTT
39350460 AATT
1 AATT
39350464 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39351158 original size:26 final size:26
Alignment explanation
Indices: 39351079--39351158 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
39351069 GCACACCGCA
* *
39351079 GCTCTTA-TGAACATCCCGTTATATG
1 GCTCTTAGTGAACTTCCCATTATATG
* * * *
39351104 GCTCTTAGAGAGCTTTCCGATTA-AAG
1 GCTCTTAGTGAAC-TTCCCATTATATG
*
39351130 GCTCTTTGTGAACTTCCCATTATATG
1 GCTCTTAGTGAACTTCCCATTATATG
39351156 GCT
1 GCT
39351159 ATCCGGTGTT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
25 15 0.37
26 20 0.49
27 6 0.15
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (26 bp):
GCTCTTAGTGAACTTCCCATTATATG
Found at i:39351210 original size:24 final size:24
Alignment explanation
Indices: 39351174--39351219 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
39351164 GTGTTTCCCA
39351174 TTAATTGTACTTTGGAGCTACCTG
1 TTAATTGTACTTTGGAGCTACCTG
39351198 TTAATTGCT-CTTTGGAGCTACC
1 TTAATTG-TACTTTGGAGCTACC
39351220 CATTATAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (24 bp):
TTAATTGTACTTTGGAGCTACCTG
Found at i:39351534 original size:15 final size:16
Alignment explanation
Indices: 39351507--39351537 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39351497 CGGGTTACAA
39351507 AAATTCATTCAAATTT
1 AAATTCATTCAAATTT
39351523 AAATTC-TTCAAATTT
1 AAATTCATTCAAATTT
39351538 TTAACATGCT
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:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTCATTCAAATTT
Found at i:39353228 original size:16 final size:16
Alignment explanation
Indices: 39353207--39353238 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39353197 GTTTTGTTGC
*
39353207 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39353223 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39353239 CTTTCAATCG
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:39353492 original size:26 final size:26
Alignment explanation
Indices: 39353462--39353542 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
39353452 GATACTAGTT
39353462 CACATAGTAGCATGCACATAGTACTA
1 CACATAGTAGCATGCACATAGTACTA
* *
39353488 CACAT-GTGACCAT-CAC-TA-TCCGATA
1 CACATAGT-AGCATGCACATAGTAC--TA
* *
39353513 CACGTAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCATGCACATAGTACTA
39353539 CACA
1 CACA
39353543 CGTGATCGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 14 0.34
26 19 0.46
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (26 bp):
CACATAGTAGCATGCACATAGTACTA
Found at i:39353529 original size:51 final size:51
Alignment explanation
Indices: 39353466--39353656 Score: 237
Period size: 51 Copynumber: 3.8 Consensus size: 51
39353456 CTAGTTCACA
* * *
39353466 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * *
39353517 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* * **
39353568 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TTTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
39353618 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
39353657 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.34
51 71 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:39353633 original size:101 final size:102
Alignment explanation
Indices: 39353464--39353648 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
39353454 TACTAGTTCA
*
39353464 CATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
39353529 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* ** *
39353566 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TTTGGTACACGTAGTAGCCTGC
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
39353629 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
39353649 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 39 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:39358444 original size:36 final size:36
Alignment explanation
Indices: 39358404--39358474 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
39358394 AGAAGATATA
* *
39358404 ATTATGGAATCTTAGAGTTCTAATTGTATATAGCTG
1 ATTATGGAAGCTTAGAGTTCTAATTGTATACAGCTG
*
39358440 ATTATGTAAGCTTAGAGTTCTAATTGTATACAGCT
1 ATTATGGAAGCTTAGAGTTCTAATTGTATACAGCT
39358475 TTTAATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (36 bp):
ATTATGGAAGCTTAGAGTTCTAATTGTATACAGCTG
Found at i:39358774 original size:48 final size:48
Alignment explanation
Indices: 39358702--39358794 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
39358692 GGGAATTCTG
** * *
39358702 TTGAATCCTTTATCGTTGCGAGTTAAGTTGACTTAGGCGTTTTTACTA
1 TTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCGTTTTTACTA
* *
39358750 TTGAATCCTTTATCACTGCAAGTTAGGCTGACTTATGCGTTTTTA
1 TTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
39358795 AGCAAAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (48 bp):
TTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCGTTTTTACTA
Found at i:39363582 original size:36 final size:36
Alignment explanation
Indices: 39363542--39363612 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
39363532 AGAAGATATA
*
39363542 ATTATGGAATCTTAGAGTTCTAATTGTATATAGCTG
1 ATTATGGAAGCTTAGAGTTCTAATTGTATATAGCTG
*
39363578 ATTATGTAAGCTTAGAGTTCTAATTGTATATAGCT
1 ATTATGGAAGCTTAGAGTTCTAATTGTATATAGCT
39363613 TTTAATGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (36 bp):
ATTATGGAAGCTTAGAGTTCTAATTGTATATAGCTG
Found at i:39363912 original size:48 final size:48
Alignment explanation
Indices: 39363837--39363932 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
39363827 TAAGGGAATT
** * *
39363837 CTGTTGAATCCTTTATCGTTGCGAGTTAAGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCATTTTTA
*
39363885 CTGTTGAATCCTTTATCACTGCAAGTTAGGCTGACTTAGGCATTTTTA
1 CTGTTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCATTTTTA
39363933 AGCAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCACTGCAAGTTAAGCTGACTTAGGCATTTTTA
Found at i:39373465 original size:2 final size:2
Alignment explanation
Indices: 39373458--39373485 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39373448 AAATAAAATG
39373458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39373486 GACTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39376732 original size:3 final size:3
Alignment explanation
Indices: 39376726--39376776 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
39376716 GAGAGAAAGG
*
39376726 AGA AGA AG- AGA A-A GAGA AAA AGA AGA AG- AGA AGA AGA AGA AGAA
1 AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A
39376770 AGA AGA A
1 AGA AGA A
39376777 AAAAAGGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 5 0.12
3 32 0.78
4 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39376740 original size:23 final size:20
Alignment explanation
Indices: 39376726--39376775 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39376716 GAGAGAAAGG
39376726 AGAAGAAGAGAAAGAGAAAA
1 AGAAGAAGAGAAAGAGAAAA
*
39376746 AGAAGAAGAG-AAGAAGAAGA
1 AGAAGAAGAGAAAG-AGAAAA
39376766 AGAAAGAAGA
1 AG-AAGAAGA
39376776 AAAAAAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.11
20 17 0.63
21 7 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAGAAAGAGAAAA
Found at i:39376742 original size:14 final size:14
Alignment explanation
Indices: 39376725--39376776 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
39376715 AGAGAGAAAG
39376725 GAGAAGAAG-AGAAA
1 GAGAAGAAGAAG-AA
*
39376739 GAGAAAAAGAAGAA
1 GAGAAGAAGAAGAA
39376753 GAGAAGAAGAAGAA
1 GAGAAGAAGAAGAA
39376767 GA-AAGAAGAA
1 GAGAAGAAGAA
39376777 AAAAAGGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 8 0.23
14 25 0.71
15 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAGAAGAAGAAGAA
Found at i:39376965 original size:22 final size:21
Alignment explanation
Indices: 39376939--39377272 Score: 159
Period size: 22 Copynumber: 15.0 Consensus size: 21
39376929 TAGATTAGAA
*
39376939 TTTTGTATGAATATTTTAACTT
1 TTTTGTATGAATATTATAA-TT
39376961 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
39376982 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
* *
39377000 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTATAATT
*
39377021 ATTT-TAT--A-ATTA-AATT
1 TTTTGTATGAATATTATAATT
** *
39377037 TGTATT-TATAGTTTTGGATTAGTAAAT
1 T-T-TTGTAT-G-AAT--ATTA-TAATT
*
39377064 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
39377083 TTTTGTATGAATATTATAATTTT
1 TTTTGTATGAATATTATAA--TT
*
39377106 TTTTGTATGAATATTGTAATATTATAG
1 TTTTGTATGAATA-T-T-ATA--AT-T
**
39377133 TTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTATAA-TT
* *
39377155 TTTTGTACGAATATTGTAATTTT
1 TTTTGTATGAATATTATAA--TT
39377178 GTAACTTTGTATGAATATTATAATTT
1 -T---TTTGTATGAATATTATAA-TT
*
39377204 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATA-T-T-ATA--AT-T
*
39377231 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTATAA-TT
*
39377253 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
39377273 ATTGTAATTT
Statistics
Matches: 250, Mismatches: 24, Indels: 77
0.71 0.07 0.22
Matches are distributed among these distances:
16 4 0.02
17 4 0.02
18 9 0.04
19 32 0.13
20 16 0.06
21 12 0.05
22 71 0.28
23 19 0.08
24 7 0.03
25 14 0.06
26 14 0.06
27 47 0.19
28 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:39376989 original size:20 final size:20
Alignment explanation
Indices: 39376939--39377108 Score: 100
Period size: 19 Copynumber: 8.3 Consensus size: 20
39376929 TAGATTAGAA
* *
39376939 TTTTGTATGAATATTTTAACT
1 TTTTTTATGAATATTATAA-T
39376960 TTTTTGTATGAATATTATAAT
1 TTTTT-TATGAATATTATAAT
*
39376981 TTTTTTATGAATATTGTAA-
1 TTTTTTATGAATATTATAAT
* * *
39377000 TGTTGTATGAATATTGTAAT
1 TTTTTTATGAATATTATAAT
*
39377020 TATTTTAT--A-ATTA-AAT
1 TTTTTTATGAATATTATAAT
**
39377036 TTGTATTTATAGTTTTGGATTAGTAAAT
1 TT-T-TTTAT-G-AAT--ATTA-T-AAT
* *
39377064 TTTTGTATGAATATTGTAA-
1 TTTTTTATGAATATTATAAT
*
39377083 TTTTGTATGAATATTATAAT
1 TTTTTTATGAATATTATAAT
39377103 TTTTTT
1 TTTTTT
39377109 TGTATGAATA
Statistics
Matches: 118, Mismatches: 16, Indels: 31
0.72 0.10 0.19
Matches are distributed among these distances:
16 4 0.03
17 4 0.03
18 6 0.05
19 35 0.30
20 26 0.22
21 11 0.09
22 16 0.14
24 1 0.01
25 5 0.04
26 4 0.03
27 1 0.01
28 5 0.04
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTTTTATGAATATTATAAT
Found at i:39377144 original size:27 final size:25
Alignment explanation
Indices: 39377073--39377299 Score: 233
Period size: 27 Copynumber: 9.1 Consensus size: 25
39377063 TTTTTGTATG
*
39377073 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
39377100 AAT-TTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
39377123 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
* *
39377149 CA-ATTT-TTTTGTACGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
* * *
39377172 AATTTTGTAACTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
39377199 -A-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
39377221 AATATTATAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
39377248 -A-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
39377270 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
39377297 AAT
1 AAT
39377300 GTGGGGATAT
Statistics
Matches: 170, Mismatches: 11, Indels: 38
0.78 0.05 0.17
Matches are distributed among these distances:
22 47 0.28
23 22 0.13
24 13 0.08
25 13 0.08
26 5 0.03
27 70 0.41
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:39377187 original size:49 final size:49
Alignment explanation
Indices: 39377073--39377352 Score: 370
Period size: 49 Copynumber: 5.7 Consensus size: 49
39377063 TTTTTGTATG
*
39377073 AATATTGTAATTTTGTATGAATATTATAATTTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAA-TTTTTTTGTATGAATATTGT
* * * *
39377123 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTACGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* * *
39377172 AATTTTGTAACTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
*
39377221 AATATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* ** *
39377270 AATATTGTAATTTTGTATGAATATTGTAA--TGTGGGGAT--ATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* *
39377315 AATATTGTAATTTTTTGTATGAATATTATAATTATTTT
1 AATATTGTAA--TTTTGTATGAATATTGTAATTTTTTT
39377353 ATAATTTATT
Statistics
Matches: 200, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
45 17 0.09
47 23 0.12
49 135 0.68
50 25 0.12
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
Found at i:39377226 original size:8 final size:8
Alignment explanation
Indices: 39377213--39377325 Score: 50
Period size: 8 Copynumber: 13.4 Consensus size: 8
39377203 TTTTTGTATG
39377213 AATATTGT
1 AATATTGT
*
39377221 AATATTAT
1 AATATTGT
*
39377229 AATTTTGTAT
1 AATATTG--T
39377239 GAATATTGT
1 -AATATTGT
* *
39377248 AATTTTTT
1 AATATTGT
**
39377256 TGTA-TG-
1 AATATTGT
39377262 AATATTGT
1 AATATTGT
39377270 AATATTGT
1 AATATTGT
*
39377278 AATTTTGTAT
1 AATATTG--T
39377288 GAATATTGT
1 -AATATTGT
* * *
39377297 AATGTGGGG
1 AATAT-TGT
39377306 ATATATTGT
1 A-ATATTGT
39377315 AATATTGT
1 AATATTGT
39377323 AAT
1 AAT
39377326 TTTTTGTATG
Statistics
Matches: 75, Mismatches: 20, Indels: 20
0.65 0.17 0.17
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 47 0.63
9 6 0.08
10 5 0.07
11 12 0.16
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (8 bp):
AATATTGT
Found at i:39377429 original size:60 final size:60
Alignment explanation
Indices: 39377343--39377461 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
39377333 ATGAATATTA
* * * * *
39377343 TAATTATTTTATAATTTATTTGTTAGTAATTT-GAGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTTATTTATTAGTAATTTAG-GATTAAGCTATAAATTGTTGTGTTTG
*
39377403 TAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGTTT
1 TAATTATTTTAAAATTT-ATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTTT
39377462 AGTTTAGTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
59 9 0.18
60 41 0.80
61 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (60 bp):
TAATTATTTTAAAATTTATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGTTTG
Found at i:39377540 original size:38 final size:38
Alignment explanation
Indices: 39377495--39377576 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
39377485 CATATAAAGT
39377495 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
39377533 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
39377571 TTATAA
1 TTATAA
39377577 CTGGCTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:39377654 original size:15 final size:15
Alignment explanation
Indices: 39377613--39377654 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
39377603 GTTAACTCAT
*
39377613 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
39377628 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
39377644 TTAAATTTTAT
1 TTAAATTTTAT
39377655 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:39381151 original size:11 final size:11
Alignment explanation
Indices: 39381135--39381164 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39381125 TGTTGAAACT
39381135 GGAAACTTGTA
1 GGAAACTTGTA
39381146 GGAAACTTGTA
1 GGAAACTTGTA
*
39381157 GAAAACTT
1 GGAAACTT
39381165 TTGATATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (11 bp):
GGAAACTTGTA
Found at i:39381584 original size:22 final size:21
Alignment explanation
Indices: 39381549--39381593 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
39381539 TACCTAATTT
*
39381549 TTTTCTTCTTTTCCTTCATTC
1 TTTTCTTCTCTTCCTTCATTC
*
39381570 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCATTC
39381592 TT
1 TT
39381594 ATTTCTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCATTC
Found at i:39381708 original size:27 final size:27
Alignment explanation
Indices: 39381678--39381749 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
39381668 CTTTCAGAAT
*
39381678 GGCACCAACATTGGCGCCTCCCAGGTA
1 GGCACCACCATTGGCGCCTCCCAGGTA
*
39381705 GGCACCACCATTGGTGCCTCCCAGGTA
1 GGCACCACCATTGGCGCCTCCCAGGTA
39381732 GGCACCACCATTGGCGCC
1 GGCACCACCATTGGCGCC
39381750 AATACTATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.19, C:0.39, G:0.26, T:0.15
Consensus pattern (27 bp):
GGCACCACCATTGGCGCCTCCCAGGTA
Found at i:39389213 original size:22 final size:21
Alignment explanation
Indices: 39389178--39389311 Score: 77
Period size: 19 Copynumber: 6.7 Consensus size: 21
39389168 AAAGGGTATC
* *
39389178 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
39389199 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
39389222 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
39389241 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
39389260 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
39389279 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
39389298 TGCATATCATATCT
1 TACAAATCATATCT
39389312 AAGATTGCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
17 2 0.02
19 60 0.64
21 7 0.07
22 15 0.16
23 10 0.11
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:39389221 original size:23 final size:22
Alignment explanation
Indices: 39389178--39389235 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39389168 AAAGGGTATC
* *
39389178 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39389199 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39389222 TGCATATCATATCT
1 TACAAATCATATCT
39389236 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39389238 original size:19 final size:19
Alignment explanation
Indices: 39389214--39389324 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
39389204 AATCATATCT
39389214 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
39389233 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
39389252 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
39389271 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
39389290 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39389309 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
39389325 CCTGAAGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39389261 original size:38 final size:38
Alignment explanation
Indices: 39389214--39389317 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
39389204 AATCATATCT
39389214 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
39389252 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
39389290 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
39389318 GCATATCCCT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:39389769 original size:44 final size:44
Alignment explanation
Indices: 39389720--39389933 Score: 110
Period size: 44 Copynumber: 4.9 Consensus size: 44
39389710 ACTGTAACCA
* *
39389720 CAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCT
1 CAGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCT
* * * * ** * *
39389764 TAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTG-T
1 CAGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCT
* * ** *** * * *
39389807 CCAGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTA-TAACCA
1 -CAGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACT--GCT
* * *
39389852 CAGGGAGGTAAAATCCGCCATCTTCGATTTGCTCCACTACTGCT
1 CAGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCT
* * * * ** *
39389896 TAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
1 CAGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACT
39389934 GGTGTCCAGG
Statistics
Matches: 118, Mismatches: 46, Indels: 12
0.67 0.26 0.07
Matches are distributed among these distances:
42 1 0.01
43 18 0.15
44 82 0.69
45 16 0.14
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
CAGGGAGGTAAAATCCGCCATCTTCAATCTACTCCACTACTGCT
Found at i:39389872 original size:132 final size:132
Alignment explanation
Indices: 39389650--39390016 Score: 605
Period size: 132 Copynumber: 2.8 Consensus size: 132
39389640 TAGGACTTAC
* * *
39389650 AATCTTCAACCTATTCCACT-GCTGACTAGGG-AGATATG-ATTACTGGCTTCAATGTACTCCAC
1 AATCTTCAATCTATTCCACTAG-TGTCCAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCAC
39389712 TGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
63 TGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
39389777 TCTGA
128 TCTGA
* *
39389782 AATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTAGTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
39389847 AACCACAGGGAGGTAAAATCCGCCATCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
39389912 GA
131 GA
* *
39389914 AATCTTCAATCTATTCCACTGGTGTCCAGGGAAGTAGAATTACTGGTTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTAGTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
39389979 AACCACAGGGAGGTAAAATCGGCCATCTTCGATCTGCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
39390017 TTGCTGTCAA
Statistics
Matches: 220, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
131 1 0.00
132 217 0.99
133 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTAGTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
GA
Found at i:39394050 original size:24 final size:24
Alignment explanation
Indices: 39394022--39394067 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39394012 ATCATTTTTT
* *
39394022 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
39394046 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
39394068 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:39397026 original size:22 final size:21
Alignment explanation
Indices: 39396990--39397124 Score: 79
Period size: 19 Copynumber: 6.7 Consensus size: 21
39396980 TAAAGGGTAT
* *
39396990 TTACAAATTAAATCTCTAAGA
1 TTACAAATCATATCTCTAAGA
39397011 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATC-TCTAAGA
* *
39397034 TTACATATCATA--TCTAAAA
1 TTACAAATCATATCTCTAAGA
* *
39397053 TTATATATCATA--TCTAAGA
1 TTACAAATCATATCTCTAAGA
* *
39397072 TTGCATATCATAT-T-TAAGA
1 TTACAAATCATATCTCTAAGA
* * *
39397091 TTATATAT--TATATCTAAGA
1 TTACAAATCATATCTCTAAGA
* *
39397110 TTGCATATCATATCT
1 TTACAAATCATATCT
39397125 AAGATTGCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
17 3 0.03
18 1 0.01
19 55 0.59
20 1 0.01
21 8 0.09
22 15 0.16
23 11 0.12
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40
Consensus pattern (21 bp):
TTACAAATCATATCTCTAAGA
Found at i:39397034 original size:23 final size:22
Alignment explanation
Indices: 39396990--39397048 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
39396980 TAAAGGGTAT
* *
39396990 TTACAAATTAAATC-TCTAAGA
1 TTACAAATCATATCTTCTAAGA
39397011 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATCTTCTAAGA
*
39397034 TTACATATCATATCT
1 TTACAAATCATATCT
39397049 AAAATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
23 11 0.33
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.37
Consensus pattern (22 bp):
TTACAAATCATATCTTCTAAGA
Found at i:39397055 original size:19 final size:19
Alignment explanation
Indices: 39397004--39397137 Score: 151
Period size: 19 Copynumber: 6.8 Consensus size: 19
39396994 AAATTAAATC
*
39397004 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
39397024 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
* *
39397046 TCTAAAATTATATATCATA
1 TCTAAGATTACATATCATA
*
39397065 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
* * *
39397084 TTTAAGATTATATATTATA
1 TCTAAGATTACATATCATA
*
39397103 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
39397122 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
39397138 CCTGAAGATT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
19 79 0.81
22 7 0.07
23 11 0.11
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:39397104 original size:57 final size:57
Alignment explanation
Indices: 39397029--39397137 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
39397019 TCATATCTTC
*
39397029 TAAGATTACATATCATATCTAAAATTATATATCATATCTAAGATTGCATATCATATT
1 TAAGATTACATATCATATCTAAAATTACATATCATATCTAAGATTGCATATCATATT
* * * *
39397086 TAAGATTATATATTATATCTAAGATTGCATATCATATCTAAGATTGCATATC
1 TAAGATTACATATCATATCTAAAATTACATATCATATCTAAGATTGCATATC
39397138 CCTGAAGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (57 bp):
TAAGATTACATATCATATCTAAAATTACATATCATATCTAAGATTGCATATCATATT
Found at i:39397128 original size:38 final size:38
Alignment explanation
Indices: 39397027--39397130 Score: 172
Period size: 38 Copynumber: 2.7 Consensus size: 38
39397017 AATCATATCT
* *
39397027 TCTAAGATTACATATCATATCTAAAATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
* *
39397065 TCTAAGATTGCATATCATATTTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
39397103 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
39397131 GCATATCCCT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 61 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:39400773 original size:28 final size:28
Alignment explanation
Indices: 39400715--39400769 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
39400705 ACCAAAAATT
**
39400715 TATTTTAAAAATAAAAACATTTTAAAAA
1 TATTTTAAAAATAAAAACATTAAAAAAA
*
39400743 TATTTTAAAATTAAAAA-ATTAAAAAAA
1 TATTTTAAAAATAAAAACATTAAAAAAA
39400770 ATATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TATTTTAAAAATAAAAACATTAAAAAAA
Found at i:39401202 original size:24 final size:24
Alignment explanation
Indices: 39401187--39401238 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39401177 AATCAAAGTC
39401187 AAATATATTATACTAAAAAATGCT
1 AAATATATTATACTAAAAAATGCT
* * *
39401211 AAATATATTATACTTATAAATACT
1 AAATATATTATACTAAAAAATGCT
39401235 AAAT
1 AAAT
39401239 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAAAAAATGCT
Found at i:39403975 original size:21 final size:21
Alignment explanation
Indices: 39403941--39403983 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39403931 TATATCAAAA
*
39403941 TAATATTATTTTAATAG-ATT
1 TAATATTATCTTAATAGTATT
39403961 TAATATTTATCTTAATAGTATT
1 TAATA-TTATCTTAATAGTATT
39403983 T
1 T
39403984 TATTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
TAATATTATCTTAATAGTATT
Found at i:39404019 original size:31 final size:29
Alignment explanation
Indices: 39403984--39404041 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
39403974 AATAGTATTT
*
39403984 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
39404015 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
39404042 GTAGATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:39404126 original size:59 final size:62
Alignment explanation
Indices: 39404011--39404127 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
39404001 AGTGATTATC
* * * *
39404011 TTAATATTAAATTAAATTTAATGTTTATCTTGTAGATGAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTAAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAAGAT
* *
39404073 TTAATATTAAGTTTAATCTAATATTTATC-T-TA-ATAAATATTATATTAATTTAATA
1 TTAATATTAAATTAAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATA
39404128 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 21 0.43
60 2 0.04
61 1 0.02
62 25 0.51
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (62 bp):
TTAATATTAAATTAAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAAGAT
Found at i:39407374 original size:37 final size:37
Alignment explanation
Indices: 39407333--39407408 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
39407323 CTAATGCATA
39407333 GACTGAATATGTACATATTCATTAAACACACTTAGCC
1 GACTGAATATGTACATATTCATTAAACACACTTAGCC
39407370 GACTGAATATGTACATATTCATTAAACACACTTAGCC
1 GACTGAATATGTACATATTCATTAAACACACTTAGCC
39407407 GA
1 GA
39407409 AGGTATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (37 bp):
GACTGAATATGTACATATTCATTAAACACACTTAGCC
Found at i:39407622 original size:42 final size:42
Alignment explanation
Indices: 39407482--39407624 Score: 152
Period size: 41 Copynumber: 3.5 Consensus size: 42
39407472 TTTAAACAGA
* * * *
39407482 TTCACTGGCACTTAGCCTGCTAGACTTAAAGCCTG--ATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAAATT-AT
* * *
39407523 TACACCGGCACTTAGCCTGCTAGACATATAGTCTGAAA-TGT
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAAATTAT
*
39407564 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
1 TTCACCGGCACTT-AGCCTGCTAGACATAAAGTCTGAAATTAT
39407606 TTCACCGGCA-TTAAGCCTG
1 TTCACCGGCACTT-AGCCTG
39407625 ATAGGCACTG
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.02
41 62 0.71
42 22 0.25
43 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (42 bp):
TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAAATTAT
Found at i:39407801 original size:2 final size:2
Alignment explanation
Indices: 39407794--39407824 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39407784 ACATCCGAAC
39407794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39407825 ACTTAATACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39415069 original size:167 final size:167
Alignment explanation
Indices: 39414788--39415123 Score: 636
Period size: 167 Copynumber: 2.0 Consensus size: 167
39414778 TGCATAAATC
*
39414788 GAAAGCATGTATGTATATTTTTACAAATGCATAGACCGAATATGTACATATTCATTAAACACACT
1 GAAAACATGTATGTATATTTTTACAAATGCATAGACCGAATATGTACATATTCATTAAACACACT
39414853 TAGCCGAAGGTATATATGCTCATCAATTAAAGATAACCAAAATCATATAACTGTACACTTAATCA
66 TAGCCGAAGGTATATATGCTCATCAATTAAAGATAACCAAAATCATATAACTGTACACTTAATCA
39414918 CATTCTTTAAACAGATTCACTGGCACTTAGCCTGCTA
131 CATTCTTTAAACAGATTCACTGGCACTTAGCCTGCTA
* * *
39414955 GAAAACATGTATTTATATTTTTACTAATGCATAGACTGAATATGTACATATTCATTAAACACACT
1 GAAAACATGTATGTATATTTTTACAAATGCATAGACCGAATATGTACATATTCATTAAACACACT
39415020 TAGCCGAAGGTATATATGCTCATCAATTAAAGATAACCAAAATCATATAACTGTACACTTAATCA
66 TAGCCGAAGGTATATATGCTCATCAATTAAAGATAACCAAAATCATATAACTGTACACTTAATCA
39415085 CATTCTTTAAACAGATTCACTGGCACTTAGCCTGCTA
131 CATTCTTTAAACAGATTCACTGGCACTTAGCCTGCTA
39415122 GA
1 GA
39415124 CTTAAAGCCT
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (167 bp):
GAAAACATGTATGTATATTTTTACAAATGCATAGACCGAATATGTACATATTCATTAAACACACT
TAGCCGAAGGTATATATGCTCATCAATTAAAGATAACCAAAATCATATAACTGTACACTTAATCA
CATTCTTTAAACAGATTCACTGGCACTTAGCCTGCTA
Found at i:39415240 original size:42 final size:42
Alignment explanation
Indices: 39415100--39415242 Score: 152
Period size: 41 Copynumber: 3.5 Consensus size: 42
39415090 TTTAAACAGA
* * * *
39415100 TTCACTGGCACTTAGCCTGCTAGACTTAAAGCCTG--ATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAAATT-AT
* * *
39415141 TACACCGGCACTTAGCCTGCTAGACATATAGTCTGAAA-TGT
1 TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAAATTAT
*
39415182 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAAATTAT
1 TTCACCGGCACTT-AGCCTGCTAGACATAAAGTCTGAAATTAT
39415224 TTCACCGGCA-TTAAGCCTG
1 TTCACCGGCACTT-AGCCTG
39415243 ATAGGCACTG
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.02
41 62 0.71
42 22 0.25
43 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (42 bp):
TTCACCGGCACTTAGCCTGCTAGACATAAAGTCTGAAATTAT
Found at i:39415419 original size:2 final size:2
Alignment explanation
Indices: 39415412--39415442 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39415402 ACATCCGAAC
39415412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39415443 ACTTAATACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39415991 original size:22 final size:22
Alignment explanation
Indices: 39415963--39416115 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
39415953 TTTATTGTTC
*
39415963 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
39415985 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
39416007 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
39416029 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
39416051 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
39416073 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
39416095 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
39416116 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:39417641 original size:28 final size:30
Alignment explanation
Indices: 39417581--39417641 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
39417571 CTGGGCATTT
* *
39417581 CCACACGAGCTGGGCACACACCCGTGTGAG
1 CCACACGAGCTGGGCACACACCCCTATGAG
* *
39417611 CCACACGGGCT-GGC-CACACCCCTATGTG
1 CCACACGAGCTGGGCACACACCCCTATGAG
39417639 CCA
1 CCA
39417642 GCCCATTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 14 0.52
29 3 0.11
30 10 0.37
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.11
Consensus pattern (30 bp):
CCACACGAGCTGGGCACACACCCCTATGAG
Done.