Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009067.1 Hibiscus syriacus cultivar Beakdansim tig00112491_pilon, whole genome shotgun sequence
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: 2329927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1316692 original size:15 final size:15
Alignment explanation
Indices: 1316672--1316701 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1316662 GGAGCTCTTA
1316672 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
*
1316687 ATTTTAATCATTGAT
1 ATTTTAATAATTGAT
1316702 TAATAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Found at i:1316891 original size:2 final size:2
Alignment explanation
Indices: 1316870--1316921 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
1316860 CTTTCATTAT
* *
1316870 TA TA TT TA T- TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1316911 TA TA TA TA TA T
1 TA TA TA TA TA T
1316922 TTTGGTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1317827 original size:18 final size:19
Alignment explanation
Indices: 1317797--1317834 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1317787 AGAGCCAAAC
1317797 TGATTAGAAAATATAAATA
1 TGATTAGAAAATATAAATA
*
1317816 TGATTA-AAAATATATATA
1 TGATTAGAAAATATAAATA
1317834 T
1 T
1317835 CTCTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TGATTAGAAAATATAAATA
Found at i:1328363 original size:20 final size:21
Alignment explanation
Indices: 1328324--1328363 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1328314 TATTTCCGCA
*
1328324 TCCTTCTCTCTGCAAAGAACC
1 TCCTTATCTCTGCAAAGAACC
*
1328345 TCCTTATCTC-GCAATGAAC
1 TCCTTATCTCTGCAAAGAAC
1328364 ACCTTCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.35, G:0.10, T:0.30
Consensus pattern (21 bp):
TCCTTATCTCTGCAAAGAACC
Found at i:1334079 original size:2 final size:2
Alignment explanation
Indices: 1334072--1334119 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
1334062 ATAGGAGGAC
* * * *
1334072 AT AT AT AT AT AT AT AT AT -T AC AG AT AC AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1334113 AT AT AT A
1 AT AT AT A
1334120 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1337653 original size:2 final size:2
Alignment explanation
Indices: 1337646--1337673 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1337636 TGTAGGAAAC
1337646 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
1337674 TATCTTTTGT
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:1340201 original size:4 final size:4
Alignment explanation
Indices: 1340192--1340219 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1340182 TATGTGCATA
1340192 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
1340220 AATATATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1351257 original size:22 final size:22
Alignment explanation
Indices: 1351231--1351274 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1351221 TCTCTATGGG
1351231 TATGTTCCTCCTACTATGACAT
1 TATGTTCCTCCTACTATGACAT
1351253 TATGTTCCTCCTACTATGACAT
1 TATGTTCCTCCTACTATGACAT
1351275 GGTCAACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGTTCCTCCTACTATGACAT
Found at i:1351978 original size:24 final size:24
Alignment explanation
Indices: 1351950--1351996 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1351940 ATTGAGAAAA
*
1351950 GAGTTAGGGATTTCGAATTTACAG
1 GAGTTAGGGATTTCGAAATTACAG
*
1351974 GAGTTAGGGATTTTGAAATTACA
1 GAGTTAGGGATTTCGAAATTACA
1351997 TGATGCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (24 bp):
GAGTTAGGGATTTCGAAATTACAG
Found at i:1363732 original size:4 final size:4
Alignment explanation
Indices: 1363725--1366581 Score: 5357
Period size: 4 Copynumber: 724.2 Consensus size: 4
1363715 CCCGAGTATA
1363725 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1363773 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1363821 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1363869 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1363917 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
1363965 ACAT ACAT ACAT ACAT ATAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364013 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364059 ACAT ACAT ACAT A-A- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364105 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364151 ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364198 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364246 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364294 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364341 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364388 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364436 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364483 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364529 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364575 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364623 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364671 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364719 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364767 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364814 ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364860 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364908 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1364956 ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365002 ACAT ACAT ACAT AC-T -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365048 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365094 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1365142 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATACT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T ACAT ACAT
1365191 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365239 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365286 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365332 ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365376 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365424 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365472 ACAT ACAT ACAT ACAT ACA- ACAAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT
1365519 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365567 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365614 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T AC-T ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1365660 ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365708 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365756 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365804 ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1365851 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACCT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365899 ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365946 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1365994 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366042 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366089 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366137 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366185 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366233 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366280 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366328 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366375 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366423 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT --AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366469 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366517 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1366565 ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT A
1366582 AACAAACTTG
Statistics
Matches: 2800, Mismatches: 10, Indels: 86
0.97 0.00 0.03
Matches are distributed among these distances:
2 24 0.01
3 51 0.02
4 2720 0.97
5 5 0.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1367198 original size:17 final size:17
Alignment explanation
Indices: 1367172--1367204 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1367162 AGCAATCGAG
1367172 GGTCCATAAGAAACAAT
1 GGTCCATAAGAAACAAT
*
1367189 GGTCCGTAAGAAACAA
1 GGTCCATAAGAAACAA
1367205 AGGAAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (17 bp):
GGTCCATAAGAAACAAT
Found at i:1374938 original size:20 final size:20
Alignment explanation
Indices: 1374893--1374938 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1374883 AACCAACAAA
* *
1374893 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
1374913 -TCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATCTCCAAT
1374932 ATCGCAA
1 ATCGCAA
1374939 ATCCGCGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:1375712 original size:41 final size:41
Alignment explanation
Indices: 1375632--1375855 Score: 330
Period size: 41 Copynumber: 5.5 Consensus size: 41
1375622 TTTTTAATTT
*
1375632 ACTGTAGACTATCGCAA--CGAATTTGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAACGAC
1375672 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
* *
1375713 ACTGTAGACTATCGCAACGCGAGATGGAAAATCGCACCGAC
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
* * * *
1375754 ACTGTACACTAT--TAACGCGCAATGAAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
*
1375793 ACTGTAGACTATCGCAACGCGAAATGGAAAATCACAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
*
1375834 ATTGTAGACTATCGCAACGCGA
1 ACTGTAGACTATCGCAACGCGA
1375856 TTTTCAACTA
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 33 0.20
40 17 0.10
41 111 0.67
42 4 0.02
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
Found at i:1375748 original size:20 final size:20
Alignment explanation
Indices: 1375682--1375748 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1375672 ACTGTAGACT
*
1375682 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAGATGGAAA
* **
1375702 ATCGCAACGAC-ACTG-TAGACT
1 ATCGCAACG-CGA--GATGGAAA
1375723 ATCGCAACGCGAGATGGAAA
1 ATCGCAACGCGAGATGGAAA
1375743 ATCGCA
1 ATCGCA
1375749 CCGACACTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 1 0.03
20 20 0.57
21 14 0.40
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAGATGGAAA
Found at i:1375799 original size:80 final size:81
Alignment explanation
Indices: 1375632--1375855 Score: 319
Period size: 80 Copynumber: 2.8 Consensus size: 81
1375622 TTTTTAATTT
*
1375632 ACTGTAGACTATCGCAA--CGAATTTGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAA
1 ACTGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAACGACACTGTAGACTATC-CAACGCGAA
*
1375695 ATGGAAAATCGCAACGAC
64 ATGAAAAATCGCAACGAC
* * * * *
1375713 ACTGTAGACTATCGCAACGCGAGATGGAAAATCGCACCGACACTGTACACTAT-TAACGCGCAAT
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCCAACGCGAAAT
1375777 GAAAAATCGCAACGAC
66 GAAAAATCGCAACGAC
* *
1375793 ACTGTAGACTATCGCAACGCGAAATGGAAAATCACAACGACATTGTAGACTATCGCAACGCGA
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATC-CAACGCGA
1375856 TTTTCAACTA
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
80 72 0.58
81 17 0.14
82 33 0.26
83 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (81 bp):
ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCCAACGCGAAAT
GAAAAATCGCAACGAC
Found at i:1382968 original size:21 final size:21
Alignment explanation
Indices: 1382942--1382984 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1382932 ATGATAATTA
1382942 TCGTCTATCACGTTAATTAAT
1 TCGTCTATCACGTTAATTAAT
*
1382963 TCGTCTATCATGTTAATTAAT
1 TCGTCTATCACGTTAATTAAT
1382984 T
1 T
1382985 TCTAATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (21 bp):
TCGTCTATCACGTTAATTAAT
Found at i:1388824 original size:42 final size:41
Alignment explanation
Indices: 1388743--1388828 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 41
1388733 CCCAGCCTTC
* *
1388743 CAGTTCATATGTCATCTCCTCAAGGGTATATGCCAAGCCCAT
1 CAGTTCATATGTCATCTCCGCAAGGGTACATGCCAAGCCC-T
* * * *
1388785 CAGTTTATATGTCATCTCCGCAAGGTTACATTCCTAGCCCT
1 CAGTTCATATGTCATCTCCGCAAGGGTACATGCCAAGCCCT
1388826 CAG
1 CAG
1388829 GGTTACATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 4 0.11
42 34 0.89
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.30
Consensus pattern (41 bp):
CAGTTCATATGTCATCTCCGCAAGGGTACATGCCAAGCCCT
Found at i:1388874 original size:21 final size:21
Alignment explanation
Indices: 1388802--1388874 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1388792 TATGTCATCT
*
1388802 CCGCAAGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
1388823 CCTCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
* *
1388844 CTGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
*
1388865 CCGAAGGGTT
1 CCGCAGGGTT
1388875 TTATGACACC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.93
22 2 0.05
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.25
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:1389548 original size:14 final size:14
Alignment explanation
Indices: 1389529--1389573 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
1389519 TTTTATTGAT
*
1389529 AACATATACATTGA
1 AACATATACATTAA
1389543 AACATATACATTAA
1 AACATATACATTAA
1389557 AACATATACATTAA
1 AACATATACATTAA
1389571 AAC
1 AAC
1389574 CAACTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1389721 original size:23 final size:23
Alignment explanation
Indices: 1389661--1389723 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
1389651 TCACTTCACA
* *
1389661 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATTCATAACAT
1389684 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
1389707 TTTATCCAATTTATTCA
1 TTTATCCAATTTATTCA
1389724 AGCTTCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATCCAATTTATTCATAACAT
Found at i:1393982 original size:21 final size:21
Alignment explanation
Indices: 1393956--1393997 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1393946 CCAGAATGGG
*
1393956 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1393977 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1393998 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1394228 original size:29 final size:31
Alignment explanation
Indices: 1394196--1394255 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1394186 AAATTTTGAA
*
1394196 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1394225 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1394256 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1396033 original size:2 final size:2
Alignment explanation
Indices: 1396026--1396070 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1396016 CATACAATGT
1396026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1396068 TA T
1 TA T
1396071 TAACATACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1398493 original size:22 final size:22
Alignment explanation
Indices: 1398468--1398527 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1398458 ATAAAATGAT
1398468 TAATTATATTTATTTATTATAA
1 TAATTATATTTATTTATTATAA
1398490 TAATTA-ATATTATTTATTATAA
1 TAATTATAT-TTATTTATTATAA
* *
1398512 AAATTATTATTAATTT
1 TAATTA-TATTTATTT
1398528 TAAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 24 0.73
23 5 0.15
24 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATTATATTTATTTATTATAA
Found at i:1398519 original size:19 final size:20
Alignment explanation
Indices: 1398477--1398537 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
1398467 TTAATTATAT
*
1398477 TTATTTATTATAATAATTAATA
1 TTATTTATTATAA-AA-TATTA
1398499 TTATTTATTATAAAA-ATTA
1 TTATTTATTATAAAATATTA
* *
1398518 TTATTAATTTTAAAATATTA
1 TTATTTATTATAAAATATTA
1398538 AAATAATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.46
20 4 0.11
21 2 0.06
22 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTTATTATAAAATATTA
Found at i:1398881 original size:11 final size:11
Alignment explanation
Indices: 1398861--1398896 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1398851 ATATTGATAT
*
1398861 ATAATATATTA
1 ATAATTTATTA
1398872 ATAATTTATTA
1 ATAATTTATTA
1398883 ATAATTTA-TA
1 ATAATTTATTA
1398893 ATAA
1 ATAA
1398897 CAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATTTATTA
Found at i:1399043 original size:61 final size:60
Alignment explanation
Indices: 1398934--1399051 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 60
1398924 AAAAAAACCA
* *
1398934 GCGTGACATCTGACTCAATATAACCTACGTAAAGCGCATCCCCTGGGATGCGCCTTTCAC
1 GCGTGACATCTGACTCAATATAACCCACGTAAAGCGCATCCCCGGGGATGCGCCTTTCAC
* * *
1398994 GCGTGGCATCTGACTCAGCATA-AACCCAGGTAAAGCGCGTCCCCGGGGATGCGCCTTT
1 GCGTGACATCTGACTCA--ATATAACCCACGTAAAGCGCATCCCCGGGGATGCGCCTTT
1399052 GTGCCACCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
60 16 0.31
61 32 0.63
62 3 0.06
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (60 bp):
GCGTGACATCTGACTCAATATAACCCACGTAAAGCGCATCCCCGGGGATGCGCCTTTCAC
Found at i:1400561 original size:2 final size:2
Alignment explanation
Indices: 1400556--1400580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1400546 CTTTTTTGGA
1400556 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 A
1400581 ATGAATCGCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1400994 original size:2 final size:2
Alignment explanation
Indices: 1400989--1401013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1400979 TTTTTAGACA
1400989 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 A
1401014 ATTATTTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1403849 original size:2 final size:2
Alignment explanation
Indices: 1403842--1403868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1403832 TCACGATGTA
1403842 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1403869 GTTAATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1403951 original size:2 final size:2
Alignment explanation
Indices: 1403939--1403986 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
1403929 TAATACAATA
1403939 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1403982 AT AT A
1 AT AT A
1403987 CACACACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1409109 original size:3 final size:3
Alignment explanation
Indices: 1409101--1409128 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1409091 TAATTTTTTC
1409101 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1409129 AATTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1414288 original size:28 final size:26
Alignment explanation
Indices: 1414253--1414318 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 26
1414243 TTTTTCATTA
*
1414253 CATTTTTATTTTTTTATGTTTGCATTTG
1 CATTTTTATTTTTTTA--TTTACATTTG
* *
1414281 CATTTTTATATTTTTATTTACATTTT
1 CATTTTTATTTTTTTATTTACATTTG
1414307 CATTTTATATTT
1 CATTTT-TATTT
1414319 GCATCTTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 14 0.42
27 4 0.12
28 15 0.45
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.68
Consensus pattern (26 bp):
CATTTTTATTTTTTTATTTACATTTG
Found at i:1414328 original size:47 final size:46
Alignment explanation
Indices: 1414222--1414331 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 46
1414212 CCTTTACTGC
*
1414222 ATTTGCATTTTGCATTCGTATTTTTTCATTACATTTTTATTTTTTTAT
1 ATTTGCATTTTGCATTCGTATTTTTTCATTACATTTTCA--TTTTTAT
* **
1414270 GTTTGCA-TTTGCATTTTTATATTTTT-ATTTACATTTTCA-TTTTAT
1 ATTTGCATTTTGCATTCGTAT-TTTTTCA-TTACATTTTCATTTTTAT
1414315 ATTTGCATCTTTGCATT
1 ATTTGCAT-TTTGCATT
1414332 GCACAGTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
45 12 0.23
47 20 0.38
48 21 0.40
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (46 bp):
ATTTGCATTTTGCATTCGTATTTTTTCATTACATTTTCATTTTTAT
Found at i:1419357 original size:54 final size:53
Alignment explanation
Indices: 1419275--1419436 Score: 225
Period size: 54 Copynumber: 3.0 Consensus size: 53
1419265 CTGACCAGAA
* *
1419275 ATCTGGGCAGAAGCCACATGAAAGGATGAATGTATTGTCAAATATTTTACGAAC
1 ATCTGGGCAGAAACCACATGAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
* * * *
1419329 ATCTGGGCAGAAACCACAGGAAATGATGAATGTGTTGTTAAATGTTTTATGAAC
1 ATCTGGGCAGAAACCACATGAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
**
1419383 ATCTTTGCAGAAACCACATGAAAGAATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAACCACATGAAAG-ATGAATGTATTGTCAAATGTTTTACGAAC
1419437 CAGTTATGGT
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 93 0.99
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (53 bp):
ATCTGGGCAGAAACCACATGAAAGATGAATGTATTGTCAAATGTTTTACGAAC
Found at i:1419822 original size:22 final size:22
Alignment explanation
Indices: 1419797--1419919 Score: 131
Period size: 22 Copynumber: 5.6 Consensus size: 22
1419787 ACATATACAT
* *
1419797 TCTTTAAAGATGATAGATTATC
1 TCTTCAAAGATGATAGATTCTC
* * *
1419819 TCTTCAAATATGATATATTCTT
1 TCTTCAAAGATGATAGATTCTC
* * *
1419841 TCTTCAAAGATAATAAATTCTT
1 TCTTCAAAGATGATAGATTCTC
*
1419863 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
* *
1419885 TCATCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
1419907 AT-TTCAAAGATGA
1 -TCTTCAAAGATGA
1419920 AAAATTAATT
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
22 85 0.99
23 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1419913 original size:66 final size:66
Alignment explanation
Indices: 1419796--1419925 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
1419786 TACATATACA
* * * *
1419796 TTCTTTAAAGATGATAGATTATCTCTTCAAATATGATATATTCTTTCTTCAAAGAT-AATAAATT
1 TTCTTCAAAGATGATAGATTATCTCATCAAAGATGATAGATTCTTTCTTCAAAGATGAA-AAATT
1419860 CT
65 CT
*
1419862 TTCTTCAAAGATGATAGATTTTCTCATCAAAGATGATAGA-T-TTTCATTTCAAAGATGAAAAAT
1 TTCTTCAAAGATGATAGATTATCTCATCAAAGATGATAGATTCTTTC--TTCAAAGATGAAAAAT
1419925 T
64 T
1419926 AATTGGATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
64 4 0.07
65 1 0.02
66 49 0.88
67 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.41
Consensus pattern (66 bp):
TTCTTCAAAGATGATAGATTATCTCATCAAAGATGATAGATTCTTTCTTCAAAGATGAAAAATTC
T
Found at i:1420727 original size:22 final size:22
Alignment explanation
Indices: 1420699--1420761 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 22
1420689 GGGTCATTTG
1420699 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGCAAGATGA
* * * *
1420721 TAAGACCT-TAGGGC--CATCCA
1 TAAGACCTACAGTGCAAGAT-GA
1420741 TAAGACCTACAGTGCAAGATG
1 TAAGACCTACAGTGCAAGATG
1420762 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 8 0.28
22 8 0.28
23 2 0.07
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (22 bp):
TAAGACCTACAGTGCAAGATGA
Found at i:1420823 original size:116 final size:116
Alignment explanation
Indices: 1420574--1420979 Score: 566
Period size: 116 Copynumber: 3.5 Consensus size: 116
1420564 CTATTTCCAA
* * * * *
1420574 CATCTGTAAGACCTACAATGCATGATGTTTTTAA-AGCCTCCGGGTCATCCATAAGACCTACAGT
1 CATCTGTAAGACCTACAGTGCAAGATG---ATAAGA-CCTCAGGGCCATCCATAAGACCTACAGT
*
1420638 GCATA-ATGTTTTCAAAAAGCCTTTAGGAGCTTTTTGATATTTAAAGCCTCTGGGT
62 GCA-AGATGTTTTCAAAAAGCCTTTAGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* *
1420693 CATTTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCATAAGACCTACAGTGCAA
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAA
** *
1420758 GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCCTCCGGGC
66 GATGTTTTCAAAAAGCCTTTAGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * *
1420809 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCACAGGGCCATCCATAAGACCTATA-TGCAG
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAA
* * *
1420873 GATGTTTTCAAAAAGTCTTTAGTAGCTTTTTGATATTTAAAGCCTTCGGGT
66 GATGTTTTCAAAAAGCCTTTAGGAGCTTTTTGATATTTAAAGCCTCCGGGT
* * *
1420924 CATCTGTAAGACATACAATGCAAGATGATAAGACCTCAGGGCCATTCATAAGACCT
1 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCT
1420980 CTAGGCATAA
Statistics
Matches: 259, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
115 102 0.39
116 132 0.51
117 1 0.00
119 24 0.09
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (116 bp):
CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAA
GATGTTTTCAAAAAGCCTTTAGGAGCTTTTTGATATTTAAAGCCTCCGGGT
Found at i:1421115 original size:3 final size:3
Alignment explanation
Indices: 1421109--1421152 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1421099 TATTTTTTTC
*
1421109 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT A-A ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1421153 CATGCCAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1421131 original size:17 final size:17
Alignment explanation
Indices: 1421109--1421152 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1421099 TATTTTTTTC
*
1421109 ATTATTATTATTATATT
1 ATTATTATTATTATATA
1421126 ATTATTATTATTAT-TAA
1 ATTATTATTATTATAT-A
1421143 ATTATTATTA
1 ATTATTATTA
1421153 CATGCCAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTATTATTATATA
Found at i:1421134 original size:20 final size:20
Alignment explanation
Indices: 1421109--1421152 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1421099 TATTTTTTTC
*
1421109 ATTATTATTATTATATTATT
1 ATTATTATTATTAAATTATT
1421129 ATTATTATTATTAAATTATT
1 ATTATTATTATTAAATTATT
1421149 ATTA
1 ATTA
1421153 CATGCCAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATTATTATTAAATTATT
Found at i:1423064 original size:23 final size:24
Alignment explanation
Indices: 1423012--1423065 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1423002 CTTATTATTG
* *
1423012 TACTTTAAAAATAAATAAATATCT
1 TACTTTATAAATAAATAAATATCA
* *
1423036 TA-TTTATAAATATATATATAT-A
1 TACTTTATAAATAAATAAATATCA
1423058 TACTTTAT
1 TACTTTAT
1423066 TTTTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 2 0.08
23 21 0.84
24 2 0.08
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TACTTTATAAATAAATAAATATCA
Found at i:1425009 original size:45 final size:45
Alignment explanation
Indices: 1424957--1425042 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
1424947 TTTTTCTGGA
* ** * *
1424957 TTTTTAACA-TATTTGATTGGTTCTGCTCTTTTTCCTTTATCCCCT
1 TTTTTAACAGT-TTTGATAGGTTCCACTCCTTTGCCTTTATCCCCT
1425002 TTTTTAACAGTTTTGATAGGTTCCACTCCTTTGCCTTTATC
1 TTTTTAACAGTTTTGATAGGTTCCACTCCTTTGCCTTTATC
1425043 TGAGGAGCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
45 34 0.97
46 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.10, T:0.52
Consensus pattern (45 bp):
TTTTTAACAGTTTTGATAGGTTCCACTCCTTTGCCTTTATCCCCT
Found at i:1426924 original size:14 final size:14
Alignment explanation
Indices: 1426905--1426945 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1426895 TTTCTGTCTA
1426905 TATGCAGAGATTAT
1 TATGCAGAGATTAT
1426919 TATGCAGAGATTTAT
1 TATGCAGAGA-TTAT
*
1426934 TA-GCAGGGATTA
1 TATGCAGAGATTA
1426946 CTTCCCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (14 bp):
TATGCAGAGATTAT
Found at i:1435607 original size:123 final size:123
Alignment explanation
Indices: 1435377--1435622 Score: 370
Period size: 123 Copynumber: 2.0 Consensus size: 123
1435367 ACGCATCTAG
* * * *
1435377 AAAAATTATATCATACTCCAGTTCTTCCCCAATATTCTAGCCCAAATCCTTTCTTCAGCTGAATC
1 AAAAATTATAGCATACTCCAGTTCTTCCCCAATATCCTAGCCCAAATCCTTTCCTCAGCGGAATC
*
1435442 AATAGTTAAATCCTTTTTCTATACTACTCTTCAAGGTGAAGCTATCAAATATACCATGT
66 AATAGTTAAATCATTTTTCTATACTACTCTTCAAGGTGAAGCTATCAAA-ATACCATGT
*
1435501 AAAAA-TATAGCATACTCCAGTTCTTCTCCAATATCCTAGCCCAAATCCTTTCCTCAGCCGGAA-
1 AAAAATTATAGCATACTCCAGTTCTTCCCCAATATCCTAGCCCAAATCCTTTCCTCAG-CGGAAT
* * * *
1435564 CAATAGTTAAATCATTTTTCTATATTACTCTTCGAGGTGAAGCTCTCGAAATACCATGT
65 CAATAGTTAAATCATTTTTCTATACTACTCTTCAAGGTGAAGCTATCAAAATACCATGT
1435623 CCACTAGTCT
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
122 9 0.08
123 93 0.84
124 9 0.08
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.34
Consensus pattern (123 bp):
AAAAATTATAGCATACTCCAGTTCTTCCCCAATATCCTAGCCCAAATCCTTTCCTCAGCGGAATC
AATAGTTAAATCATTTTTCTATACTACTCTTCAAGGTGAAGCTATCAAAATACCATGT
Found at i:1439978 original size:13 final size:14
Alignment explanation
Indices: 1439953--1439982 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1439943 AAACAATAAC
1439953 AAAATTAACAGGAA
1 AAAATTAACAGGAA
1439967 AAAATTAA-AGGAA
1 AAAATTAACAGGAA
1439980 AAA
1 AAA
1439983 GAAAATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAATTAACAGGAA
Found at i:1440917 original size:13 final size:14
Alignment explanation
Indices: 1440892--1440921 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1440882 AAACAATAAC
1440892 AAAATTAACAGGAA
1 AAAATTAACAGGAA
1440906 AAAATTAA-AGGAA
1 AAAATTAACAGGAA
1440919 AAA
1 AAA
1440922 GAAAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAATTAACAGGAA
Found at i:1441986 original size:941 final size:941
Alignment explanation
Indices: 1439613--1442253 Score: 4574
Period size: 940 Copynumber: 2.8 Consensus size: 941
1439603 AAAATTAACA
* * *
1439613 GAAAAGAGTGAGAAAACAAATCAAAACTTGTTGTGCATAACATAATTCTTCCTTTCTGTTAGGCG
1 GAAAAGAGAGAGAAAACAAATCAAAACTTGTTGTGCTTAACACAATTCTTCCTTTCTGTTAGGCG
*
1439678 ATCCAGAAAATATAAAAGAATTAATGTAAAATATACGTTAACTCAAGTCTCAATATGTAGTTC-T
66 ATCCAGAAAATATAAAAGAATTAATGTAAAATATACGCTAACTCAAGTCTCAATATGTAGTTCAT
1439742 TTGTCTTCCTTTTTCTGTTTCTGAACACCAAAATTTTCTTAACCCGGATAGAAAACAGAAGAAAA
131 TT-TCTTCCTTTTTCTGTTTCTGAACACCAAAATTTTCTTAACCCGGATAGAAAACAGAAGAAAA
1439807 AGATATGTATAAAAACCAGTGGTGCTTCACAAGGCTCTT-CTGTTTTTGCTAGTTTATGATCGAT
195 AGATATGTATAAAAACCAGTGGTGCTTCACAAGGCTCTTCCT-TTTTTGCTAGTTTATGATCGAT
** *
1439871 AATATTTTTTTTTTAAATGAAGTAAAATCCCAAAGTATCATTTTCCTGTTTCTAACCAACAAAAT
259 AATA-TTTTTTTAAAAATGAAGTAAAATCCCAAAGTATCATTTTCCTGTTTCTTACCAACAAAAT
*
1439936 CTTCTGAAAACAATAACAAAATTAACAGGAAAAAATTAAAGGAAAAAGAAAATGAAGATATCGAT
323 CTTCTGAAAACAATAACAAAATTAACAGGAAAAAATTAAAGGAAAAAGAAAATAAAGATATCGAT
* *
1440001 CAAAACCTATTGTGCTTGAGGTGACTCTTCCTTTTTACTTGTCATTTTCTGAT-AAAAAATAATG
388 CAAAACCTATTGTGCTTGAGGTGGCTCTTCCTTTTTACCTGTCATTTTCTGATAAAAAAATAATG
1440065 TAAAATATCCATTAAATCACATTGTAGTTTTTAAAACATATTCTGTTTCTGAACACCAAATTCTC
453 TAAAATATCCATTAAATCACATTGTAGTTTTTAAAACATATTCTGTTTCTGAACACCAAATTCTC
*
1440130 CTAAAACCGAATTAGGATAAAAGAGAAAATCAAACCAGCTGTGTTTTAGACAGATCTTCCTTTTT
518 CTAAAACCGAATTAGGATAAAAGAGAAAATCAAACCAGCTGTGTTTTAGACGGATCTTCCTTTTT
* * *
1440195 GCAAGCTATTTTCTGAAAATAAAAGAAAAACAAAGTAAAATCTCCATTAAAAATACAAAATTTTG
583 GCAAGCTATTTTCTGAAAAGAAAAGAAAAACGAAGTAAAATCTCCATTAAAAATACAAAATGTTG
*
1440260 CTACATTTTCTGCTTCTTGAGAATGAACATCAAAGGCTTGTGTAAACCATCTTGAAATTCAACCG
648 CTACATTTTCTGCTTCTTGAGAATGAACATCAAAGCCTTGTGTAAACCATCTTGAAATTCAACCG
*
1440325 AAAATGAAGAAAAATCAGTAAAATCATGTTGTGATTAATCCTTTTTGGTAGCCATAATAATCCTT
713 AAAATGAAGAAAAATCAGTAAAATCATGTTGTGATTCATCCTTTTTGGTAGCCATAATAATCCTT
* *
1440390 GATCTTTCGGAAATCAAAAAATTCACATCCCAAACGGATCACAAAATCAACAAACAGCACCAACC
778 GATCTTTCGGAAATAAAAAAAATCACATCCCAAACGGATCACAAAATCAACAAACAGCACCAACC
*
1440455 TTTCACTCATCAATCTCGGTAATGCCGCTCATTCACAACATTTAAACAAGCAAACACTTAGATTC
843 TTTCACTCATCAATCTCGGTAATGCCGCTCATTCACAACACTTAAACAAGCAAACACTTAGATTC
*
1440520 AAACCAAAATAACCCTTTGAAACTAACATAGTGT
908 AAACCAAAATAACCCTTTGAAACGAACATAGTGT
*
1440554 GAAAAGAGAGAGAAAA-AAATCAAAACTTGTTGTGCTTAACACAATTTTTCCTTTCTGTTAGGCG
1 GAAAAGAGAGAGAAAACAAATCAAAACTTGTTGTGCTTAACACAATTCTTCCTTTCTGTTAGGCG
* *
1440618 ATGCAGAAAATATAAGAGAATTAATGTAAAATATACGCTAACTCAAGTCTCAATATGTAGTTCAT
66 ATCCAGAAAATATAAAAGAATTAATGTAAAATATACGCTAACTCAAGTCTCAATATGTAGTTCAT
* *
1440683 TTTCTTCCTTTTTCTGTTTCTAAACACCAAAATTTTCTTAACCCGGGTAGAAAACAGAAGAAAAA
131 TTTCTTCCTTTTTCTGTTTCTGAACACCAAAATTTTCTTAACCCGGATAGAAAACAGAAGAAAAA
* *
1440748 GATATGTATAAAAACCAGTGGTGTTTCACAAGGCTCTTCCTTTTTTGATAGTTTATGATCGATAA
196 GATATGTATAAAAACCAGTGGTGCTTCACAAGGCTCTTCCTTTTTTGCTAGTTTATGATCGATAA
* *
1440813 TATTTTTTTAAAAATGAAGTAAAAACCCAAAGTATCATTTTCCTGTTTCTTGCCAACAAAATCTT
261 TATTTTTTTAAAAATGAAGTAAAATCCCAAAGTATCATTTTCCTGTTTCTTACCAACAAAATCTT
1440878 CTGAAAACAATAACAAAATTAACAGGAAAAAATTAAAGGAAAAAGAAAATAAAGATATCGATCAA
326 CTGAAAACAATAACAAAATTAACAGGAAAAAATTAAAGGAAAAAGAAAATAAAGATATCGATCAA
* *
1440943 AACCTATTGTGCTCGAGGTGGCTATTCCTTTTTACCTGTCATTTTCTGATAAAAAAATAATGTAA
391 AACCTATTGTGCTTGAGGTGGCTCTTCCTTTTTACCTGTCATTTTCTGATAAAAAAATAATGTAA
*
1441008 AATATCCATTAAATCACATTGTAGTTTTTAAAACATATTTTGTTTCTGAACACCAAATTCTCCTA
456 AATATCCATTAAATCACATTGTAGTTTTTAAAACATATTCTGTTTCTGAACACCAAATTCTCCTA
* * * *
1441073 AAATCGAATTAGGATAAAAGTGAAAATCAAACCAACTGTGTTTTAGACGGGTCTTCCTTTTTGCA
521 AAACCGAATTAGGATAAAAGAGAAAATCAAACCAGCTGTGTTTTAGACGGATCTTCCTTTTTGCA
* *
1441138 AGCTATTTTCTGAAAAGAAAAGAAAAACGAAGTAAAACCTCCAATAAAAATACAAAATGTTGCTA
586 AGCTATTTTCTGAAAAGAAAAGAAAAACGAAGTAAAATCTCCATTAAAAATACAAAATGTTGCTA
* * *
1441203 CATTTTCTGCTTCTTGAGAATAAACATCAAAGCCTTATGTAAACCATCTTGAAATTCAACCAAAA
651 CATTTTCTGCTTCTTGAGAATGAACATCAAAGCCTTGTGTAAACCATCTTGAAATTCAACCGAAA
* * *
1441268 ACGAAGAAATATCAGTAAAATCCTGTTGTGATTCATCCTTTTTGGTAGCCATAATAATCCTTGAT
716 ATGAAGAAAAATCAGTAAAATCATGTTGTGATTCATCCTTTTTGGTAGCCATAATAATCCTTGAT
* *
1441333 CTTTCGGAAATAAAAAAAATCACGTCCCAAACGGATCACAAAATCAACAAACAGCACCGACCTTT
781 CTTTCGGAAATAAAAAAAATCACATCCCAAACGGATCACAAAATCAACAAACAGCACCAACCTTT
*
1441398 CACTCATCAATCTCGGTAATGCCTCTCATTCACAACACTTAAACAAGCAAACACTTAGATTCAAA
846 CACTCATCAATCTCGGTAATGCCGCTCATTCACAACACTTAAACAAGCAAACACTTAGATTCAAA
*
1441463 CCGAAATAACCCTTTGAAACGAACATAGTGT
911 CCAAAATAACCCTTTGAAACGAACATAGTGT
* * *
1441494 GAGAAGAGAGAGAAAACAAATCAAAACTTGTTGTGCTTAACACAATTCTTACTTTCTGTTAGGTG
1 GAAAAGAGAGAGAAAACAAATCAAAACTTGTTGTGCTTAACACAATTCTTCCTTTCTGTTAGGCG
1441559 ATCCAGAAAATATAAAAGAATTAATGTAAAATATACGCTAACTCAAGTCTCAATATGTAGTTCAT
66 ATCCAGAAAATATAAAAGAATTAATGTAAAATATACGCTAACTCAAGTCTCAATATGTAGTTCAT
*
1441624 ATTCTTCCTTTTTCTGTTTCTGAACACCAAAATTTTCTTAACCCGGATAGAAAACAGAAGAAAAA
131 TTTCTTCCTTTTTCTGTTTCTGAACACCAAAATTTTCTTAACCCGGATAGAAAACAGAAGAAAAA
* * * *
1441689 GATATGTATAAAAATCAGTGGTGCTTCACAAGGCTCTTCCTTTTTTGCTAGTTTTTTATTGATAA
196 GATATGTATAAAAACCAGTGGTGCTTCACAAGGCTCTTCCTTTTTTGCTAGTTTATGATCGATAA
* *
1441754 TA-TATTTTAAAATATGAAGTAAAATCCCAAAGTATCATTTTCCTGTTTATTACCAACAAAATCT
261 TATTTTTTTAAAA-ATGAAGTAAAATCCCAAAGTATCATTTTCCTGTTTCTTACCAACAAAATCT
*
1441818 TCTGAAAACAATAACAAAATTAACATGAAAAAATTAAAGGAAAAAGAAAATAAAGATATCGATCA
325 TCTGAAAACAATAACAAAATTAACAGGAAAAAATTAAAGGAAAAAGAAAATAAAGATATCGATCA
1441883 AAACCTATTGTGCTTGAGGTGGCTCTTCCTTTTTACCCT-TCATTTTCTGATAAAAAAATAATGT
390 AAACCTATTGTGCTTGAGGTGGCTCTTCCTTTTTA-CCTGTCATTTTCTGATAAAAAAATAATGT
*
1441947 AAAATATCCATTAAATCACATTGTAGTTTTTAAAACATATTCTGTTTCTGAACACCAAATTATCC
454 AAAATATCCATTAAATCACATTGTAGTTTTTAAAACATATTCTGTTTCTGAACACCAAATTCTCC
* * *
1442012 TAAAACCAAATTAGGATAAAAGAGAAAATCAAACCAGCTGTGTTTTAGACGGATATTCCTTATTG
519 TAAAACCGAATTAGGATAAAAGAGAAAATCAAACCAGCTGTGTTTTAGACGGATCTTCCTTTTTG
* *
1442077 GAAGCTATTTTCTGAAAAGAAAAGAAAAACGAAGTAAAATCTTCATTAAAAATACAAAATGTTGC
584 CAAGCTATTTTCTGAAAAGAAAAGAAAAACGAAGTAAAATCTCCATTAAAAATACAAAATGTTGC
*
1442142 TACATTTTCTGCTTCTTGAGAATGAACATCAAAGCCTTGTGTAAAACATCTTGAAATTCAACCGA
649 TACATTTTCTGCTTCTTGAGAATGAACATCAAAGCCTTGTGTAAACCATCTTGAAATTCAACCGA
* * *
1442207 AAATGAAGAAAGATCAGTAAAAACATGTTGTGATTCATCATTTTTGG
714 AAATGAAGAAAAATCAGTAAAATCATGTTGTGATTCATCCTTTTTGG
1442254 CCGGGGAAAA
Statistics
Matches: 1602, Mismatches: 92, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
939 168 0.10
940 725 0.45
941 706 0.44
942 3 0.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (941 bp):
GAAAAGAGAGAGAAAACAAATCAAAACTTGTTGTGCTTAACACAATTCTTCCTTTCTGTTAGGCG
ATCCAGAAAATATAAAAGAATTAATGTAAAATATACGCTAACTCAAGTCTCAATATGTAGTTCAT
TTTCTTCCTTTTTCTGTTTCTGAACACCAAAATTTTCTTAACCCGGATAGAAAACAGAAGAAAAA
GATATGTATAAAAACCAGTGGTGCTTCACAAGGCTCTTCCTTTTTTGCTAGTTTATGATCGATAA
TATTTTTTTAAAAATGAAGTAAAATCCCAAAGTATCATTTTCCTGTTTCTTACCAACAAAATCTT
CTGAAAACAATAACAAAATTAACAGGAAAAAATTAAAGGAAAAAGAAAATAAAGATATCGATCAA
AACCTATTGTGCTTGAGGTGGCTCTTCCTTTTTACCTGTCATTTTCTGATAAAAAAATAATGTAA
AATATCCATTAAATCACATTGTAGTTTTTAAAACATATTCTGTTTCTGAACACCAAATTCTCCTA
AAACCGAATTAGGATAAAAGAGAAAATCAAACCAGCTGTGTTTTAGACGGATCTTCCTTTTTGCA
AGCTATTTTCTGAAAAGAAAAGAAAAACGAAGTAAAATCTCCATTAAAAATACAAAATGTTGCTA
CATTTTCTGCTTCTTGAGAATGAACATCAAAGCCTTGTGTAAACCATCTTGAAATTCAACCGAAA
ATGAAGAAAAATCAGTAAAATCATGTTGTGATTCATCCTTTTTGGTAGCCATAATAATCCTTGAT
CTTTCGGAAATAAAAAAAATCACATCCCAAACGGATCACAAAATCAACAAACAGCACCAACCTTT
CACTCATCAATCTCGGTAATGCCGCTCATTCACAACACTTAAACAAGCAAACACTTAGATTCAAA
CCAAAATAACCCTTTGAAACGAACATAGTGT
Found at i:1443468 original size:182 final size:182
Alignment explanation
Indices: 1443161--1443795 Score: 1002
Period size: 182 Copynumber: 3.5 Consensus size: 182
1443151 TTTTTACTAT
* * * *
1443161 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTATTATGGATGGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* *
1443226 ATTTTTATAAAATATCGACACTTTATTGGCCCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* * *
1443291 CTATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTAC
** * *
1443343 CGGTTTTGTCATTTCGAGACCGATTTTAAAATATTTTTACATGTTATATTGTTATAGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
1443408 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
*
1443473 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTGAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTAC
*
1443525 CGGTTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
1443590 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTTCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* * *
1443655 CGATACTTATAATAAAGTATCGACACTATCAACATATCCAGTAGCGATTTAC
131 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTAC
* ** * * *
1443707 CTGTTTTGTCATTTATATACCGGTTTTGTCAT-TTGTTTACCTGTTATATTGTTATGGATCGATA
1 CGGTTTTGTCATTTCGAGACCGATTTTATCATATT-TTTACCTGTTATATTGTTATGGATCGATA
1443771 CATTTTTATAAAGTATCGACACTTT
65 CATTTTTATAAAGTATCGACACTTT
1443796 CAATATATCT
Statistics
Matches: 420, Mismatches: 32, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
181 2 0.00
182 418 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.42
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTAC
Found at i:1443747 original size:20 final size:20
Alignment explanation
Indices: 1443701--1443747 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1443691 TCCAGTAGCG
*
1443701 ATTTACCTGTTTTGTCATTT
1 ATTTACCGGTTTTGTCATTT
*
1443721 ATATACCGGTTTTGTCATTT
1 ATTTACCGGTTTTGTCATTT
*
1443741 GTTTACC
1 ATTTACC
1443748 TGTTATATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (20 bp):
ATTTACCGGTTTTGTCATTT
Found at i:1444036 original size:112 final size:112
Alignment explanation
Indices: 1443666--1444128 Score: 730
Period size: 112 Copynumber: 4.1 Consensus size: 112
1443656 GATACTTATA
* * * *
1443666 ATAAAGTATCGACACTATCAACATATCCAGTAGCGATTTACCTGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1443731 TTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
** *
1443778 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTTTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1443843 TTTGTCATTTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * *
1443891 ATAAAGTATCGACACTTTCAATATATCTAGTAGCGCTTTACATGTTTTATCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1443956 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * *
1444003 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACGGGT
1 ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1444068 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
1444114 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1444129 AAACCGACAA
Statistics
Matches: 326, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
111 53 0.16
112 167 0.51
113 106 0.33
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:1444057 original size:225 final size:223
Alignment explanation
Indices: 1443666--1444128 Score: 746
Period size: 225 Copynumber: 2.1 Consensus size: 223
1443656 GATACTTATA
* * *
1443666 ATAAAGTATCGACACTATCAACATATCCAGTAGCGATTTACCTGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTATCAACATATCCAGTAGCGATTTACATGTTTTATCATTTATAGACCGGT
* *
1443731 TTTGTCATTTGTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTGTTTACCTGTTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTTT
* * *
1443796 CAATATATCTGGTAGCGCTTTACCTTTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACC
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCA--TTTTTTACC
*
1443861 TGTTATATTATTATGGATCGATACATTTTT
194 TGTTATATTATTATGGATCAATACATTTTT
* * * *
1443891 ATAAAGTATCGACACTTTCAATATATCTAGTAGCGCTTTACATGTTTTATCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCAGTAGCGATTTACATGTTTTATCATTTATAGACCGGT
* *
1443956 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATATATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTGTTTACCTGTTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTTT
*
1444021 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACGGGTTTTGTCATTTTTTACCTG
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTACCTG
* *
1444086 TTATATTGTTATGGATCAATATATTTTT
196 TTATATTATTATGGATCAATACATTTTT
1444114 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1444129 AAACCGACAA
Statistics
Matches: 220, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
223 51 0.23
225 169 0.77
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (223 bp):
ATAAAGTATCGACACTATCAACATATCCAGTAGCGATTTACATGTTTTATCATTTATAGACCGGT
TTTGTCATTTGTTTACCTGTTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTACCTG
TTATATTATTATGGATCAATACATTTTT
Found at i:1445968 original size:2 final size:2
Alignment explanation
Indices: 1445961--1446002 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1445951 ACTAAAAATA
1445961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1446003 TAAATATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1448323 original size:14 final size:14
Alignment explanation
Indices: 1448304--1448330 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1448294 ACCACACACA
1448304 TATATATATGTATG
1 TATATATATGTATG
1448318 TATATATATGTAT
1 TATATATATGTAT
1448331 TCAGTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:1449692 original size:18 final size:18
Alignment explanation
Indices: 1449669--1449711 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1449659 ATTGGCATCA
1449669 CAATTCCTGAACCAATGT
1 CAATTCCTGAACCAATGT
1449687 CAATTCCTGAACCAATGT
1 CAATTCCTGAACCAATGT
1449705 CAATTCC
1 CAATTCC
1449712 ACTACTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (18 bp):
CAATTCCTGAACCAATGT
Found at i:1449956 original size:13 final size:14
Alignment explanation
Indices: 1449938--1449966 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1449928 TTTCCCAATT
1449938 TTCTATTTTT-TCC
1 TTCTATTTTTGTCC
1449951 TTCTATTTTTGTCC
1 TTCTATTTTTGTCC
1449965 TT
1 TT
1449967 TGTTCTGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.07, C:0.21, G:0.03, T:0.69
Consensus pattern (14 bp):
TTCTATTTTTGTCC
Found at i:1450133 original size:20 final size:20
Alignment explanation
Indices: 1450108--1450157 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1450098 TCAGTTTTTA
* *
1450108 AAATCGTAACGTAAATCTGT
1 AAATCGCAACGCAAATCTGT
*
1450128 AAATCGCAACGCGAATCTGT
1 AAATCGCAACGCAAATCTGT
*
1450148 AATTCGCAAC
1 AAATCGCAAC
1450158 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
AAATCGCAACGCAAATCTGT
Found at i:1454389 original size:13 final size:14
Alignment explanation
Indices: 1454364--1454396 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1454354 AAATTGATGT
1454364 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
1454378 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
1454391 ATTTGT
1 ATTTGT
1454397 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:1454459 original size:63 final size:64
Alignment explanation
Indices: 1454375--1454525 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 64
1454365 TTTGTAAAAG
*
1454375 TTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTGTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTGTACTTGTTTAA
* * * *** *
1454437 TTGATTTGTAAAAGTTAATTTGTTTAATTGATGTGTAAATAATCCTTATTTTTTTACTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTGTACTTGTTTAA
1454502 TTGATTTGTAAAAGTTGATTTGTT
1 TTGATTTGTAAAAGTTGATTTGTT
1454526 GTTTTAAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
62 9 0.12
63 32 0.42
65 36 0.47
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (64 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTGTACTTGTTTAA
Found at i:1457465 original size:16 final size:16
Alignment explanation
Indices: 1457444--1457477 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1457434 AAATCATTGA
*
1457444 AAAATTATATAGAAAT
1 AAAATTATATAAAAAT
*
1457460 AAAATTATGTAAAAAT
1 AAAATTATATAAAAAT
1457476 AA
1 AA
1457478 TTAGAGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:1457661 original size:20 final size:20
Alignment explanation
Indices: 1457636--1457714 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
1457626 AACTAAAACC
1457636 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1457656 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* **
1457676 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* * *
1457696 CGTTGCGAATTTGAAATTC
1 TGTTGCGAAATTAAAATTC
1457715 AATGTTACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 8 0.17
20 33 0.70
21 6 0.13
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1458408 original size:15 final size:15
Alignment explanation
Indices: 1458390--1458420 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1458380 AAATTCTAAA
1458390 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1458405 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1458420 T
1 T
1458421 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1459529 original size:28 final size:30
Alignment explanation
Indices: 1459475--1459530 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
1459465 TTGTGATCGT
*
1459475 TTATTTATTTTTGAAGGTATTTATGTTCAC
1 TTATTTATTTTTGAAGGTAGTTATGTTCAC
1459505 TTATTT-TTTTT-AAGGT-GTTAGTGTTC
1 TTATTTATTTTTGAAGGTAGTTA-TGTTC
1459531 GTTCGTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.12
28 10 0.42
29 5 0.21
30 6 0.25
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (30 bp):
TTATTTATTTTTGAAGGTAGTTATGTTCAC
Found at i:1459678 original size:22 final size:22
Alignment explanation
Indices: 1459653--1459695 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1459643 ACCTCTAAAT
*
1459653 TTCATCATGTGTTCAATTTAAG
1 TTCATCACGTGTTCAATTTAAG
1459675 TTCATCACGTGTTCAATTTAA
1 TTCATCACGTGTTCAATTTAA
1459696 TTCCTACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (22 bp):
TTCATCACGTGTTCAATTTAAG
Found at i:1466243 original size:182 final size:182
Alignment explanation
Indices: 1465925--1466376 Score: 690
Period size: 182 Copynumber: 2.5 Consensus size: 182
1465915 TTTACTACTG
1465925 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACAT
1 GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACAT
* * * * *
1465990 TTTTATAAAGCATCGACATTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCA
*
1466055 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTAC-C
131 ATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACAC
* * *
1466106 GATTTTCTCATTTCGAGACCGATTTTGTCACATTTTTACCTGTTATATTGTTATGGATCGATACA
1 G-TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACA
* *
1466171 TTTTTATAAAGTATCGACACTTTATTAGTGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTC
65 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
* *
1466236 AATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGTTTTACAT
130 AATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACAC
** * * * * * *
1466289 GTTTTGTCATTTATATACTGATTTTGTCATTTTTTTTGCTTGTTATATTGTTATAGATTGATACA
1 GTTTTGTCATTTCGAGACCGATTTTGTCA-TATTTTTACTTGTTATATTGTTATGGATCGATACA
1466354 TTTTTATAAAGTATCGACACTTT
65 TTTTTATAAAGTATCGACACTTT
1466377 CAATATATTC
Statistics
Matches: 244, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
181 1 0.00
182 190 0.78
183 53 0.22
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
GTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACAT
TTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCA
ATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACAC
Found at i:1466487 original size:112 final size:112
Alignment explanation
Indices: 1466246--1466637 Score: 613
Period size: 112 Copynumber: 3.5 Consensus size: 112
1466236 AATACTTATA
* * * * *
1466246 ATAAAGTATCGACACTATCAACATATCCGGTAGCGTTTTACATGTTTTGTCATTTATATACTGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACATGTTTTGTCATTTATAGACCGAT
* * * *
1466311 TTTGTCATTTTTTTTGCTTGTTATATTGTTATAGATTGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
1466359 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACATGTTTTGTCATTTATAGACCGAT
*
1466424 TTTATCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1466471 ATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACATGTTTTGTCATTTATAGACCGAT
*
1466536 TTTGTCATTTTTTTACCTGTTATATTGGTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
1466583 ATAAAGTATTGACACTTTCAATATATCCGATAGCGTTTTACATGTTTTGTCATTT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACATGTTTTGTCATTT
1466638 TTTTTACTTA
Statistics
Matches: 259, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
112 195 0.75
113 64 0.25
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGATAGCGTTTTACATGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:1466654 original size:93 final size:93
Alignment explanation
Indices: 1466534--1466730 Score: 306
Period size: 93 Copynumber: 2.1 Consensus size: 93
1466524 TTATAGACCG
* * *
1466534 GTTTTGTCA-TTTTTTTACCTGTTATATTGGTATGGATCGATACATTTTTATAAAGTATTGACAC
1 GTTTTGTCATTTTTTTTACCTATTATATTGGTATCGATCGATACATTTTTATAAAGTATCGACAC
1466598 TTTCAATATATCCGATAGCGTTTTACAT
66 TTTCAATATATCCGATAGCGTTTTACAT
* * * *
1466626 GTTTTGTCATTTTTTTTACTTATTATATTGTTATCGATTGATATATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTATTATATTGGTATCGATCGATACATTTTTATAAAGTATCGACAC
* *
1466691 TTTTAATATATCCGATAGCGTTTTACCT
66 TTTCAATATATCCGATAGCGTTTTACAT
1466719 GTTTTGTCATTT
1 GTTTTGTCATTT
1466731 ATAGACCGAT
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 9 0.09
93 86 0.91
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (93 bp):
GTTTTGTCATTTTTTTTACCTATTATATTGGTATCGATCGATACATTTTTATAAAGTATCGACAC
TTTCAATATATCCGATAGCGTTTTACAT
Found at i:1466686 original size:205 final size:204
Alignment explanation
Indices: 1466423--1466802 Score: 634
Period size: 205 Copynumber: 1.9 Consensus size: 204
1466413 TATAGACCGA
* *
1466423 TTTTATCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTTATCATTTTTTTACCTATTATATTGTTATCGATCGATACATTTTTATAAAGTATCGACACTT
*
1466488 TCAATATATCCGATAGCGTTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACC
66 TCAATATATCCGATAGCGTTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACC
* *
1466553 TGTTATATTGGTATGGATCGATACATTTTTATAAAGTATTGACACTTTCAATATATCCGATAGCG
131 TGTTATATTGGTATGGATCAATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCG
1466618 TTTTACATG
196 TTTTACATG
* * * *
1466627 TTTTGTCATTTTTTTTACTTATTATATTGTTATCGATTGATATATTTTTATAAAGTATCGACACT
1 TTTTATCA-TTTTTTTACCTATTATATTGTTATCGATCGATACATTTTTATAAAGTATCGACACT
*
1466692 TTTAATATATCCGATAGCGTTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTAC
65 TTCAATATATCCGATAGCGTTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTAC
* * *
1466757 TTGTTATATTGTTATGGATCAATATATTTTTATAAAGTATCGACAC
130 CTGTTATATTGGTATGGATCAATACATTTTTATAAAGTATCGACAC
1466803 AAACCGACAA
Statistics
Matches: 162, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
204 7 0.04
205 155 0.96
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (204 bp):
TTTTATCATTTTTTTACCTATTATATTGTTATCGATCGATACATTTTTATAAAGTATCGACACTT
TCAATATATCCGATAGCGTTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACC
TGTTATATTGGTATGGATCAATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCG
TTTTACATG
Found at i:1470254 original size:2 final size:2
Alignment explanation
Indices: 1470247--1470291 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1470237 TTTCACATTT
1470247 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1470289 TA T
1 TA T
1470292 TTCAGGGTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1481723 original size:12 final size:11
Alignment explanation
Indices: 1481700--1481738 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1481690 TTTAGGATGC
*
1481700 GAAAAAATAGA
1 GAAAAAAGAGA
1481711 GAAAAAGAGAGA
1 GAAAAA-AGAGA
1481723 GAGAAAAAGAGA
1 GA-AAAAAGAGA
1481735 GAAA
1 GAAA
1481739 GAAATGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 8 0.32
12 13 0.52
13 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (11 bp):
GAAAAAAGAGA
Found at i:1481727 original size:14 final size:14
Alignment explanation
Indices: 1481708--1481742 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1481698 GCGAAAAAAT
1481708 AGAGAAAAAGAGAG
1 AGAGAAAAAGAGAG
1481722 AGAGAAAAAGAGAG
1 AGAGAAAAAGAGAG
*
1481736 AAAGAAA
1 AGAGAAA
1481743 TGGATGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAGAGAG
Found at i:1482064 original size:14 final size:14
Alignment explanation
Indices: 1482047--1482074 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1482037 TCACTCTCTT
1482047 TCTCTCTCAGTGTC
1 TCTCTCTCAGTGTC
1482061 TCTCTCTCAGTGTC
1 TCTCTCTCAGTGTC
1482075 GCACGCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.36, G:0.14, T:0.43
Consensus pattern (14 bp):
TCTCTCTCAGTGTC
Found at i:1484313 original size:12 final size:11
Alignment explanation
Indices: 1484290--1484328 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1484280 TTTAGGATGC
*
1484290 GAAAAAATAGA
1 GAAAAAAGAGA
1484301 GAAAAAGAGAGA
1 GAAAAA-AGAGA
1484313 GAGAAAAAGAGA
1 GA-AAAAAGAGA
1484325 GAAA
1 GAAA
1484329 GAAATGGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 8 0.32
12 13 0.52
13 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (11 bp):
GAAAAAAGAGA
Found at i:1484317 original size:14 final size:14
Alignment explanation
Indices: 1484298--1484332 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1484288 GCGAAAAAAT
1484298 AGAGAAAAAGAGAG
1 AGAGAAAAAGAGAG
1484312 AGAGAAAAAGAGAG
1 AGAGAAAAAGAGAG
*
1484326 AAAGAAA
1 AGAGAAA
1484333 TGGGAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAGAGAG
Found at i:1486467 original size:26 final size:26
Alignment explanation
Indices: 1486431--1486486 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
1486421 TTGTATGACA
*
1486431 CATGCACGTCCCAACACATAGGTCGC
1 CATGCACGTCCCAACACATAGATCGC
*
1486457 CATGCACGTCCCAACACATAGATCGT
1 CATGCACGTCCCAACACATAGATCGC
1486483 CATG
1 CATG
1486487 TCCTCCGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.18
Consensus pattern (26 bp):
CATGCACGTCCCAACACATAGATCGC
Found at i:1486530 original size:29 final size:29
Alignment explanation
Indices: 1486488--1486559 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1486478 ATCGTCATGT
1486488 CCTCCGGGCGACCTTGTAGGTCGCCATAC
1 CCTCCGGGCGACCTTGTAGGTCGCCATAC
*
1486517 CCTCCGGGCGACCTTGTAGGTCGCCATGC
1 CCTCCGGGCGACCTTGTAGGTCGCCATAC
* *
1486546 ACTCTGGGCGACCT
1 CCTCCGGGCGACCT
1486560 ACACTCGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (29 bp):
CCTCCGGGCGACCTTGTAGGTCGCCATAC
Found at i:1488125 original size:6 final size:6
Alignment explanation
Indices: 1488114--1488152 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1488104 GGTGCCTTAA
*
1488114 TGGAGG TGGAGG TAGAGG TGGAGG TGGAGG TGGAGG TGG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGG
1488153 TACTTTTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.00, G:0.64, T:0.18
Consensus pattern (6 bp):
TGGAGG
Found at i:1489535 original size:22 final size:22
Alignment explanation
Indices: 1489494--1489561 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
1489484 CTCGTATAAA
1489494 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1489517 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1489539 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1489561 T
1 T
1489562 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1489891 original size:29 final size:29
Alignment explanation
Indices: 1489855--1489927 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
1489845 TTTTCTGCAT
**
1489855 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1489884 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
*
1489913 ATTTCATGTAATGTA
1 A-TTCATGTCATGTA
1489928 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1490374 original size:69 final size:69
Alignment explanation
Indices: 1490230--1490382 Score: 213
Period size: 70 Copynumber: 2.2 Consensus size: 69
1490220 TTTTTCTCAT
* * *
1490230 GGGGGAATCGGTT--CCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
1490293 ATGA
66 ATGA
* * *
1490297 GGGGGTATCGGTTCCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC
1 GGGGGTATCGGTTCCCCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATAC
*
1490361 GTTGA
65 GATGA
1490366 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1490383 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 12 0.16
69 31 0.41
70 33 0.43
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
ATGA
Found at i:1496482 original size:22 final size:22
Alignment explanation
Indices: 1496441--1496508 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
1496431 CTCGTATAAA
1496441 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1496464 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1496486 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1496508 T
1 T
1496509 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1502665 original size:22 final size:22
Alignment explanation
Indices: 1502624--1502691 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
1502614 CTCGTATAAA
*
1502624 TGCACTGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1502647 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1502669 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1502691 T
1 T
1502692 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 33 0.75
23 11 0.25
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1503018 original size:29 final size:29
Alignment explanation
Indices: 1502985--1503057 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
1502975 TTTTCTGCAT
**
1502985 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1503014 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1503043 ATTTCATGTCATGTA
1 A-TTCATGTCATGTA
1503058 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1503500 original size:67 final size:67
Alignment explanation
Indices: 1503359--1503508 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
1503349 TTTTTCTCAT
* * *
1503359 GGGGGAATCGGTT-CCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
1503423 GA
66 GA
* * * *
1503425 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
1503489 TGA
65 TGA
1503492 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1503509 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 12 0.16
67 30 0.40
68 33 0.44
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:1503520 original size:67 final size:67
Alignment explanation
Indices: 1503359--1503530 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
1503349 TTTTTCTCAT
* * *
1503359 GGGGGAATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
1503423 GA
66 GA
* * * *
1503425 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
1503489 TGA
65 TGA
* *
1503492 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
1503531 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
65 6 0.06
66 12 0.13
67 42 0.45
68 33 0.35
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:1505345 original size:31 final size:30
Alignment explanation
Indices: 1505276--1505368 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
1505266 GAACCTCGAC
* *
1505276 AACTGTCCATAGGTCCCAAAGAACCTAGGT
1 AACTGTCCATATGTCCCAAAGAACATAGGT
* **
1505306 AACTGTCCATATGTTCCTTAGAACATAGGT
1 AACTGTCCATATGTCCCAAAGAACATAGGT
* *
1505336 ATACTGTCCATATATCTCGAAAG-ACATAGGT
1 A-ACTGTCCATATGTC-CCAAAGAACATAGGT
1505367 AA
1 AA
1505369 AATCCTCGAC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
30 27 0.53
31 21 0.41
32 3 0.06
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (30 bp):
AACTGTCCATATGTCCCAAAGAACATAGGT
Found at i:1505535 original size:17 final size:19
Alignment explanation
Indices: 1505501--1505538 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
1505491 ACCATATATC
1505501 TTATATCATATCACATGTA
1 TTATATCATATCACATGTA
1505520 TTATAT-ATAT-ACATGTA
1 TTATATCATATCACATGTA
1505537 TT
1 TT
1505539 CATGTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (19 bp):
TTATATCATATCACATGTA
Found at i:1506135 original size:64 final size:64
Alignment explanation
Indices: 1506027--1506186 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
1506017 CAATGAATGT
* * ** *
1506027 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAA-AAGC
* * *
1506091 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAATC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAAAGC
* *
1506155 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTGTGCATCGATGCA
1506187 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 5 0.06
64 71 0.86
65 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAAGC
Found at i:1509134 original size:31 final size:31
Alignment explanation
Indices: 1509047--1509139 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 31
1509037 GAACCTCGGC
* *
1509047 AACTGTCCATAGGTC-CCAAAGAACCTAGGT
1 AACTGTCCATATGTCTCCAAAGAACATAGGT
* **
1509077 AACTGTCCACATGT-TCCTTAGAACATAGGT
1 AACTGTCCATATGTCTCCAAAGAACATAGGT
*
1509107 ATACTGTCCATATGTCTCGAAAG-ACATAGGT
1 A-ACTGTCCATATGTCTCCAAAGAACATAGGT
1509138 AA
1 AA
1509140 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 26 0.51
31 21 0.41
32 4 0.08
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCTCCAAAGAACATAGGT
Found at i:1509306 original size:17 final size:19
Alignment explanation
Indices: 1509274--1509309 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1509264 CATATATCTC
1509274 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
1509293 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
1509310 CGTGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:1509906 original size:64 final size:64
Alignment explanation
Indices: 1509798--1509957 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 64
1509788 CAATGAATGT
* * * ** *
1509798 ATGCATCGATGCACTACTTGTGCATTGGTGCATAAAATGCATTCGATGTTTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAA-AAGC
* * *
1509862 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAATC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAAAGC
* *
1509926 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTGTGCATCGATGCA
1509958 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 5 0.06
64 70 0.85
65 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAAGC
Found at i:1512875 original size:24 final size:24
Alignment explanation
Indices: 1512813--1512861 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1512803 TTTATTAAAC
*
1512813 TTAAAAA-TATT-AT-ATTATATT
1 TTAAAAATTATTAATAAATATATT
1512834 TTAAAAATTATTAATAAATATATT
1 TTAAAAATTATTAATAAATATATT
1512858 TTAA
1 TTAA
1512862 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 4 0.17
23 2 0.08
24 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAAATTATTAATAAATATATT
Found at i:1513256 original size:23 final size:24
Alignment explanation
Indices: 1513146--1513256 Score: 67
Period size: 23 Copynumber: 4.9 Consensus size: 24
1513136 AAACTATCAT
* *
1513146 ATATTATTATAATA-TAACTAACT
1 ATATTATTATAATATTAAATAACA
* * *
1513169 ATATTATTGTAATAATAAA-AATA
1 ATATTATTATAATATTAAATAACA
*
1513192 ATATTATTAT-AT-TTTAATAA-A
1 ATATTATTATAATATTAAATAACA
* *
1513213 TGTATT-TTA-AATATTGTAATAA-A
1 -ATATTATTATAATATT-AAATAACA
*
1513236 ATATTATTTTAATATTAAATA
1 ATATTATTATAATATTAAATA
1513257 TATTAAATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
21 9 0.13
22 14 0.20
23 37 0.54
24 9 0.13
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.47
Consensus pattern (24 bp):
ATATTATTATAATATTAAATAACA
Found at i:1517200 original size:22 final size:21
Alignment explanation
Indices: 1517152--1517200 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
1517142 TTAGTTAAGG
1517152 AAAATCAAAATAGATGGAATT
1 AAAATCAAAATAGATGGAATT
*
1517173 ACAAATC-AAATTGATAGGATATT
1 A-AAATCAAAATAGAT-GGA-ATT
1517196 AAAAT
1 AAAAT
1517201 ATTGAGGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 12 0.50
23 4 0.17
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (21 bp):
AAAATCAAAATAGATGGAATT
Found at i:1520067 original size:23 final size:23
Alignment explanation
Indices: 1520037--1520090 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1520027 GAAAACAGAC
1520037 TGTAGAAAGAAAACAGACTGTAT
1 TGTAGAAAGAAAACAGACTGTAT
*
1520060 TGTAGAAAGAAAATAGACTGTAT
1 TGTAGAAAGAAAACAGACTGTAT
1520083 TGTAGAAA
1 TGTAGAAA
1520091 ATTGACTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (23 bp):
TGTAGAAAGAAAACAGACTGTAT
Found at i:1524056 original size:18 final size:18
Alignment explanation
Indices: 1524033--1524084 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
1524023 GATACCATGT
*
1524033 AGAAAATAGACTGTAGAA
1 AGAAAACAGACTGTAGAA
1524051 AGAAAACAGACTGTAGAA
1 AGAAAACAGACTGTAGAA
1524069 AGAAAACAGACTGTAG
1 AGAAAACAGACTGTAG
1524085 GAAACAGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.54, C:0.10, G:0.23, T:0.13
Consensus pattern (18 bp):
AGAAAACAGACTGTAGAA
Found at i:1531630 original size:47 final size:48
Alignment explanation
Indices: 1531561--1531654 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 48
1531551 TAATGTGAAA
1531561 ATTAGTTTAGATTAGGATAAACTCTATCCTAAGTTTAAA-TAAGAGTG
1 ATTAGTTTAGATTAGGATAAACTCTATCCTAAGTTTAAATTAAGAGTG
1531608 ATTAGTTTAGATTAGGATAAACTCTATCCTAAGTTTAAATTAAGAGT
1 ATTAGTTTAGATTAGGATAAACTCTATCCTAAGTTTAAATTAAGAGT
1531655 TGTACAGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 39 0.85
48 7 0.15
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (48 bp):
ATTAGTTTAGATTAGGATAAACTCTATCCTAAGTTTAAATTAAGAGTG
Found at i:1544204 original size:2 final size:2
Alignment explanation
Indices: 1544197--1544223 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1544187 AACAGCGGTG
1544197 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1544224 CACTTTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1548677 original size:61 final size:60
Alignment explanation
Indices: 1548582--1548698 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 60
1548572 GAGGAAGCAC
* * *
1548582 AAAGGCGCATCCCCGGGGAAGCGCTTTACCTGGGTTTATGCTGAGTCGGATGCCACGTGTG
1 AAAGGCGCATCCCCGGGGAAGCGCTTTACATGGG-TTATGCTGAATCAGATGCCACGTGTG
* ** *
1548643 AAAGGCGCGTCCCCGGGGATTCGCTTTATATGGGTTATGCTGAATCAGATGCCACG
1 AAAGGCGCATCCCCGGGGAAGCGCTTTACATGGGTTATGCTGAATCAGATGCCACG
1548699 ATGGTATTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 20 0.41
61 29 0.59
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (60 bp):
AAAGGCGCATCCCCGGGGAAGCGCTTTACATGGGTTATGCTGAATCAGATGCCACGTGTG
Found at i:1549269 original size:22 final size:20
Alignment explanation
Indices: 1549221--1549278 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1549211 TTATTATAAT
* *
1549221 ATTTTAAAATTAATAATTAA
1 ATTTTATAATAAATAATTAA
*
1549241 ATTTTATAATAAATAATATTA
1 ATTTTATAATAAATAAT-TAA
*
1549262 ATTATTATATTAAATAA
1 ATT-TTATAATAAATAA
1549279 ATATCATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 15 0.47
21 5 0.16
22 12 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTATAATAAATAATTAA
Found at i:1552679 original size:138 final size:138
Alignment explanation
Indices: 1552430--1552777 Score: 590
Period size: 138 Copynumber: 2.5 Consensus size: 138
1552420 TCGGGGGGGT
*
1552430 GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTG-TCCTATTATGTCACTCATATCCCCCGG
1 GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCT-CTATTATGTCACTCATGTCCCCCGG
* *
1552494 GGAACTATTCATATTAGTACCTATTATTTCTGAGGGGACTTGACAAAGTGGTGAAAGTGCGTTCC
65 GGAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGACAAAGTGGTGAAAGCGCGTTCC
*
1552559 CAGAGGTGC
130 CAGAGGAGC
1552568 GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGTCCCCCGGG
1 GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGTCCCCCGGG
* *
1552633 GAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTCCC
66 GAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGACAAAGTGGTGAAAGCGCGTTCCC
* *
1552698 GGGGGAGC
131 AGAGGAGC
* *
1552706 GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCCCAGG
1 GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGTCCCCCGGG
1552771 GAACTAT
66 GAACTAT
1552778 ATATGGATGG
Statistics
Matches: 199, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
138 198 0.99
139 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (138 bp):
GCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGTCCCCCGGG
GAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGACAAAGTGGTGAAAGCGCGTTCCC
AGAGGAGC
Found at i:1552938 original size:23 final size:23
Alignment explanation
Indices: 1552912--1553014 Score: 87
Period size: 23 Copynumber: 4.7 Consensus size: 23
1552902 ATGTGAAGTT
1552912 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
*
1552935 TGAATAAATTGAAT-AAATGTTAA
1 TGAATAAATTGGATAAAATGTT-A
*
1552958 GTG-ATCAATTGG-T----TGTT-
1 -TGAATAAATTGGATAAAATGTTA
*
1552975 TGAATATATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
1552998 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
1553015 TGTGAAGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
16 2 0.03
17 7 0.11
18 1 0.02
19 4 0.06
22 12 0.19
23 35 0.56
24 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.18, T:0.37
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:1552977 original size:63 final size:63
Alignment explanation
Indices: 1552909--1553033 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
1552899 GTTATGTGAA
*
1552909 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTTAAGTGATCAA-TTGGTT
1 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGAT-AAGTTGGTT
* *
1552972 GTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGT
1 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGT
1553034 CGTGACATTG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 2 0.03
63 56 0.97
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTGGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:1553008 original size:40 final size:41
Alignment explanation
Indices: 1552930--1553008 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
1552920 TTGGATAAAA
*
1552930 TGTTATGAATAAATTGAATAAATGTTAAGTGATCAATTGGT
1 TGTTATGAATAAATTGAATAAATGTTAAGTGATAAATTGGT
* * *
1552971 TGTT-TGAATATATTGGATAAAATGTTATG-GATAAATTG
1 TGTTATGAATAAATTGAAT-AAATGTTAAGTGATAAATTG
1553009 AATAAATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 20 0.61
41 13 0.39
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (41 bp):
TGTTATGAATAAATTGAATAAATGTTAAGTGATAAATTGGT
Found at i:1553265 original size:34 final size:34
Alignment explanation
Indices: 1553226--1553298 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
1553216 TTAAGTTGAA
1553226 TTTAATGTTAAATTTTG-AATACCATAATTTGTAT
1 TTTAATGTTAAATTTTGAAAT-CCATAATTTGTAT
* *
1553260 TTTAATTTTAAATTTTGAAATCTATAATTTGTAT
1 TTTAATGTTAAATTTTGAAATCCATAATTTGTAT
*
1553294 ATTAA
1 TTTAA
1553299 AAATATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 32 0.91
35 3 0.09
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTTGAAATCCATAATTTGTAT
Found at i:1553843 original size:21 final size:20
Alignment explanation
Indices: 1553826--1553875 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
1553816 TGAGCTAGAC
*
1553826 ATGTAACCTGGCGGGCTAGGA
1 ATGTAACCT-GAGGGCTAGGA
1553847 ATGTAACCCTGAGGGCTAGGA
1 ATGTAA-CCTGAGGGCTAGGA
1553868 ATGTAACC
1 ATGTAACC
1553876 CTGCGGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.07
21 22 0.81
22 3 0.11
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (20 bp):
ATGTAACCTGAGGGCTAGGA
Found at i:1553876 original size:21 final size:21
Alignment explanation
Indices: 1553838--1553878 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1553828 GTAACCTGGC
1553838 GGGCTAGGAATGTAACCCTGA
1 GGGCTAGGAATGTAACCCTGA
1553859 GGGCTAGGAATGTAACCCTG
1 GGGCTAGGAATGTAACCCTG
1553879 CGGAGATGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.34, T:0.20
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCCTGA
Found at i:1555635 original size:20 final size:20
Alignment explanation
Indices: 1555610--1555647 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1555600 ATAACTGCAG
1555610 ACAAAAAA-AATATAATTAGT
1 ACAAAAAATAAT-TAATTAGT
1555630 ACAAAAAATAATTAATTA
1 ACAAAAAATAATTAATTA
1555648 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAGT
Found at i:1555662 original size:10 final size:10
Alignment explanation
Indices: 1555647--1555673 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1555637 ATAATTAATT
1555647 AATAAATTTA
1 AATAAATTTA
1555657 AATAAATTTA
1 AATAAATTTA
1555667 AATAAAT
1 AATAAAT
1555674 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AATAAATTTA
Found at i:1557390 original size:16 final size:17
Alignment explanation
Indices: 1557353--1557394 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1557343 ACATTATTTA
1557353 AAAACTTATTTTTTATT
1 AAAACTTATTTTTTATT
1557370 AAAACTTATTTTTTATT
1 AAAACTTATTTTTTATT
*
1557387 AAACCTTA
1 AAAACTTA
1557395 ACTCCCACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAACTTATTTTTTATT
Found at i:1557741 original size:52 final size:51
Alignment explanation
Indices: 1557625--1557810 Score: 241
Period size: 51 Copynumber: 3.6 Consensus size: 51
1557615 CACCCTTAGC
* * * * **
1557625 AGTAAAGCGCGCCCCTTGCACCGCGCTATACGATAATTTGGC-GCCACGTGG
1 AGTATAGCGCGCCCC-TGCACCGCGCTATACGGTGATCTGGCATACACGTGG
1557676 AGTATAGCGCGCCCCATGCACCGCGCTATACGGTGATCTGGCATACACGTGG
1 AGTATAGCGCGCCCC-TGCACCGCGCTATACGGTGATCTGGCATACACGTGG
* *
1557728 AGTATAACGCGCCCCCTACACCGCGCTATACGGTGATCTGGCATACACGTGG
1 AGTATAGCGCG-CCCCTGCACCGCGCTATACGGTGATCTGGCATACACGTGG
*
1557780 -GTATAGCGCGACCCCTGCAGCGCGCTATACG
1 AGTATAGCGCG-CCCCTGCACCGCGCTATACG
1557811 CCACGTAGGG
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
51 64 0.53
52 52 0.43
53 4 0.03
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.19
Consensus pattern (51 bp):
AGTATAGCGCGCCCCTGCACCGCGCTATACGGTGATCTGGCATACACGTGG
Found at i:1561663 original size:3 final size:3
Alignment explanation
Indices: 1561652--1561688 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1561642 TCATCATCAC
* *
1561652 CGT CAT CGT CGT CGT CGT CGT CAT CGT CGT CGT CGT C
1 CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT C
1561689 TTGCGCAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.35, G:0.27, T:0.32
Consensus pattern (3 bp):
CGT
Found at i:1563768 original size:110 final size:111
Alignment explanation
Indices: 1563574--1563794 Score: 390
Period size: 110 Copynumber: 2.0 Consensus size: 111
1563564 ATTGCAAAAA
* * *
1563574 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCACGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1563639 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
1563685 TTAATTCTTAATCTAATAATCACGCATTAAATAAAT-AACTAAATATTAGTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCACGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1563749 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1563795 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCACGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:1563932 original size:12 final size:10
Alignment explanation
Indices: 1563918--1563958 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1563908 ACCTTAAAAA
*
1563918 GAGAGTATTT
1 GAGAGAATTT
1563928 GAGAGAAATTT
1 GAGAG-AATTT
1563939 -AGAGAATTT
1 GAGAGAATTT
1563948 GAGAGAATTT
1 GAGAGAATTT
1563958 G
1 G
1563959 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1564184 original size:51 final size:51
Alignment explanation
Indices: 1564080--1564206 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 51
1564070 GATATCCAGA
* * ** * *
1564080 TATAGCGCGCTGCAGGGGCCGCATTATACCCACGTGTATGTCAGATCACCG
1 TATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGTATGCCAAATCACCG
* * *
1564131 TATAGCGTGGTGCAGGGGGCGCGCTATACCCCACGTG-GTGCCAAATCATCG
1 TATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTGTATGCCAAATCACCG
* *
1564182 TATAACGCGGTGCATGGGGCGCGCT
1 TATAGCGCGGTGCAGGGGGCGCGCT
1564207 TTACTGCTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
51 55 0.87
52 8 0.13
ACGTcount: A:0.20, C:0.28, G:0.32, T:0.20
Consensus pattern (51 bp):
TATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGTATGCCAAATCACCG
Found at i:1564280 original size:30 final size:29
Alignment explanation
Indices: 1564218--1564280 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
1564208 TACTGCTAAG
*
1564218 GGTGTTAGATCGAAAAATATAATATGACC
1 GGTGTTAGATCGAAAAATATAATATCACC
*
1564247 GGTGTTAGATCGAAAAATATACTATTCACC
1 GGTGTTAGATCGAAAAATATAATA-TCACC
1564277 GGTG
1 GGTG
1564281 ATATATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAAAAATATAATATCACC
Found at i:1564291 original size:29 final size:29
Alignment explanation
Indices: 1564218--1564293 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
1564208 TACTGCTAAG
* *
1564218 GGTGTTAGATCGAAAAATATAATATGACC
1 GGTGATAGATCGAAAAATATAATATCACC
* *
1564247 GGTGTTAGATCGAAAAATATACTATTCACC
1 GGTGATAGATCGAAAAATATAATA-TCACC
* *
1564277 GGTGATATATCAAAAAA
1 GGTGATAGATCGAAAAA
1564294 ATCGCCGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (29 bp):
GGTGATAGATCGAAAAATATAATATCACC
Found at i:1565346 original size:35 final size:35
Alignment explanation
Indices: 1565305--1565373 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1565295 AATATTAAAA
* *
1565305 ATTATAATGATTTAT-TTAAAATTAATTA-TAATTTT
1 ATTATAAT--TTTATATTAAAAATAATAATTAATTTT
1565340 ATTATAATTTTATATTAAAAATAATAATTAATTT
1 ATTATAATTTTATATTAAAAATAATAATTAATTT
1565374 AAGTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 11 0.37
35 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (35 bp):
ATTATAATTTTATATTAAAAATAATAATTAATTTT
Found at i:1566463 original size:41 final size:36
Alignment explanation
Indices: 1566382--1566479 Score: 124
Period size: 39 Copynumber: 2.6 Consensus size: 36
1566372 ATTTATTTAT
* *
1566382 TATATATTATATAGTTTGCAAATGATTTTTGAAATA
1 TATATATTATATAATTTGAAAATGATTTTTGAAATA
*
1566418 TATATACTATATATAATTTTGAAAATGATTTTTTGAAAATG
1 TATATA-T-TATATAA-TTTGAAAATGA-TTTTTG-AAATA
1566459 TATATATTATATAATTTGAAA
1 TATATATTATATAATTTGAAA
1566480 TCATTTTGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
36 6 0.11
37 1 0.02
38 13 0.24
39 17 0.31
40 7 0.13
41 10 0.19
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (36 bp):
TATATATTATATAATTTGAAAATGATTTTTGAAATA
Done.