Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 6 of 100
Found at i:912858 original size:26 final size:26
Alignment explanation
Indices: 912829--912885 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
912819 AAAATAAATT
912829 GAAACAAAAACAT-AGATATCACCATC
1 GAAA-AAAAACATCAGATATCACCATC
* * *
912855 GAAAAATAACTTCGGATATCACCATC
1 GAAAAAAAACATCAGATATCACCATC
912881 GAAAA
1 GAAAA
912886 GATACGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.18
Consensus pattern (26 bp):
GAAAAAAAACATCAGATATCACCATC
Found at i:912964 original size:57 final size:56
Alignment explanation
Indices: 912903--913050 Score: 152
Period size: 57 Copynumber: 2.6 Consensus size: 56
912893 ATAACTTTAA
* *
912903 ATATCGCCACCGAAAAAAATATGGATATCACTACCAAGAAGATACAAATGACTTCGG
1 ATATCGCCACCGAAAAAAAT-TGGATATCACCACCAAGAAAATACAAATGACTTCGG
* * * * ** * *
912960 ATATCACCATCGAAAAAAACTCGAATATCACCATTAAGAAAATGCAAATGATTTCGG
1 ATATCGCCACCGAAAAAAA-TTGGATATCACCACCAAGAAAATACAAATGACTTCGG
* * *
913017 ATATTGGCACCGAAGAAAAATTAGATATCACCAC
1 ATATCGCCACCGAA-AAAAATTGGATATCACCAC
913051 TAAAAATATG
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
57 65 0.92
58 6 0.08
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (56 bp):
ATATCGCCACCGAAAAAAATTGGATATCACCACCAAGAAAATACAAATGACTTCGG
Found at i:913045 original size:114 final size:114
Alignment explanation
Indices: 912843--913116 Score: 257
Period size: 114 Copynumber: 2.4 Consensus size: 114
912833 CAAAAACATA
** * * * * * **
912843 GATATCACCATCGAAAAATAACTTCGGATATCACCATCGAAAAGATACGAATAACTTT-AAATAT
1 GATATCACCATCGAAAAA-AAC-TCAAATATCACCATCAAAAAAATGCAAATGA-TTTCGGATAT
* * * * *
912907 CGCCACCGAAAAAAATATGGATATCACTACCAAGAAGATACAAATGACT-TCG
63 TGGCACCGAAAAAAATATAGATATCACCACCAAAAAGATACAAATGACTAT-G
* * *
912959 GATATCACCATCGAAAAAAACTCGAATATCACCATTAAGAAAATGCAAATGATTTCGGATATTGG
1 GATATCACCATCGAAAAAAACTCAAATATCACCATCAAAAAAATGCAAATGATTTCGGATATTGG
* * ***
913024 CACCGAAGAAAAAT-TAGATATCACCACTAAAAATATGTGAATGACTATG
66 CACCGAA-AAAAATATAGATATCACCACCAAAAAGATACAAATGACTATG
* * *
913073 GATATCGCCATTGAAAAAAGCTCAAATATCACCATCAAAAAAAT
1 GATATCACCATCGAAAAAAACTCAAATATCACCATCAAAAAAAT
913117 ACAATTCTAG
Statistics
Matches: 129, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
113 3 0.02
114 98 0.76
115 10 0.08
116 18 0.14
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (114 bp):
GATATCACCATCGAAAAAAACTCAAATATCACCATCAAAAAAATGCAAATGATTTCGGATATTGG
CACCGAAAAAAATATAGATATCACCACCAAAAAGATACAAATGACTATG
Found at i:913269 original size:24 final size:24
Alignment explanation
Indices: 913208--913272 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
913198 GATGCAAATG
* *
913208 ATTTTGGATATCACCACCGAAAAC
1 ATTTTGGATATCATCACCGAAAAA
*
913232 ATTTTGAATATCATCACC-AAAGAA
1 ATTTTGGATATCATCACCGAAA-AA
*
913256 ATTTCGGATATCATCAC
1 ATTTTGGATATCATCAC
913273 TGAAGGAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (24 bp):
ATTTTGGATATCATCACCGAAAAA
Found at i:913436 original size:98 final size:97
Alignment explanation
Indices: 913263--913442 Score: 263
Period size: 98 Copynumber: 1.8 Consensus size: 97
913253 GAAATTTCGG
*
913263 ATATCATCACTGAAGGAAACTCAAATATCACCATCGAAAAAATATAATTTCAGCTTTAACACTCA
1 ATATCATCACTGAAGGAAACTCAAATATCACCACCGAAAAAATATAATTTCAGCTTTAACACTCA
* *
913328 GATATCACCATCGAGAAGATATATGATTTTAA
66 GACATCACCATAGAGAAGATATATGATTTTAA
* * * *
913360 ATATCATCA-TCGAAGGAAACTCAAATATCATCACCTAGAAATATGTAATTTCAGCTTTAACACT
1 ATATCATCACT-GAAGGAAACTCAAATATCACCACCGA-AAAAATATAATTTCAGCTTTAACACT
*
913424 CAGACATTACCATAGAGAA
64 CAGACATCACCATAGAGAA
913443 AATGCAAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
96 1 0.01
97 32 0.44
98 40 0.55
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (97 bp):
ATATCATCACTGAAGGAAACTCAAATATCACCACCGAAAAAATATAATTTCAGCTTTAACACTCA
GACATCACCATAGAGAAGATATATGATTTTAA
Found at i:914801 original size:13 final size:13
Alignment explanation
Indices: 914768--914801 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
914758 ACCCTAAAGC
*
914768 TTTTTTTTTTTTA
1 TTTTTTTGTTTTA
*
914781 ATTTTTTGTTTTA
1 TTTTTTTGTTTTA
914794 TTTTTTTG
1 TTTTTTTG
914802 ACGATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTA
Found at i:916649 original size:23 final size:23
Alignment explanation
Indices: 916604--916650 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
916594 TCAAAAGTTG
* *
916604 ATTCTGGATAAGTTAGGGTAATA
1 ATTCTAGATAAGATAGGGTAATA
916627 ATTCTAGATAAGATATGGG-AATA
1 ATTCTAGATAAGATA-GGGTAATA
916650 A
1 A
916651 GGTCGACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTCTAGATAAGATAGGGTAATA
Found at i:919811 original size:2 final size:2
Alignment explanation
Indices: 919804--919828 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
919794 CCTTTAGGAT
919804 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
919829 TTGTTCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:921102 original size:9 final size:10
Alignment explanation
Indices: 921054--921114 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 10
921044 AAGTTTATGC
*
921054 AAAAATAAAA
1 AAAAATAATA
921064 TAAAAATAATA
1 -AAAAATAATA
*
921075 GAAAAATCATA
1 -AAAAATAATA
921086 AATTAAATAATA
1 AA--AAATAATA
*
921098 AAAATATATTA
1 AAAA-ATAATA
921109 AAAAAT
1 AAAAAT
921115 TGAGCAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
10 6 0.14
11 27 0.64
12 9 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (10 bp):
AAAAATAATA
Found at i:926587 original size:23 final size:24
Alignment explanation
Indices: 926556--926604 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
926546 TTAATTTAGT
* * *
926556 TTAATTTTTTTATTCGA-TTCAGA
1 TTAAGTTTTATATTAGATTTCAGA
926579 TTAAGTTTTATATTAGATTTCAGA
1 TTAAGTTTTATATTAGATTTCAGA
926603 TT
1 TT
926605 GAGAAGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (24 bp):
TTAAGTTTTATATTAGATTTCAGA
Found at i:927017 original size:2 final size:2
Alignment explanation
Indices: 927010--927037 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
927000 AACTTGTTCA
927010 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
927038 CAAACGCTTA
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:927798 original size:2 final size:2
Alignment explanation
Indices: 927793--927823 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
927783 ATATTTCTTC
927793 AT AT AT AT AT A- 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
927824 TGGTAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:935803 original size:2 final size:2
Alignment explanation
Indices: 935796--935820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
935786 GTACGTTTAT
935796 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
935821 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:941255 original size:21 final size:19
Alignment explanation
Indices: 941203--941273 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 19
941193 GATCTGAATT
* * *
941203 ATAATATATAAT-TTTTAT
1 ATAAAATATAATATTATAC
941221 ATAAAATATAATATTAATAC
1 ATAAAATATAATATT-ATAC
* *
941241 ATAAAATTTTAATATTTTAC
1 ATAAAA-TATAATATTATAC
*
941261 ATAATATA-AATAT
1 ATAAAATATAATAT
941274 ATAAATTATC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 16 0.37
19 3 0.07
20 16 0.37
21 8 0.19
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATATAATATTATAC
Found at i:957448 original size:50 final size:50
Alignment explanation
Indices: 957393--957512 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
957383 TAAATTTATT
* * * * *
957393 AATTAA-AGTAATATTTAATCTTAA-TGTAAGAGTATAATCGATCGAATTTA
1 AATTAATA-TAATATTAAAT-TTAAGTATAAGAATATAATCGATCAAATTCA
*
957443 AATTAATATAGTATTAAATTTAAGTATAAGAATATAATCGATCAAATTCA
1 AATTAATATAATATTAAATTTAAGTATAAGAATATAATCGATCAAATTCA
*
957493 AATTAATATAGTATTAAATT
1 AATTAATATAATATTAAATT
957513 CGAGCTCGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
49 4 0.06
50 57 0.92
51 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.38
Consensus pattern (50 bp):
AATTAATATAATATTAAATTTAAGTATAAGAATATAATCGATCAAATTCA
Found at i:958047 original size:29 final size:30
Alignment explanation
Indices: 958010--958068 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
958000 GTTAAAAAGA
958010 TTAATAATTCAACTAACACATTAAATATTT
1 TTAATAATTCAACTAACACATTAAATATTT
* * * *
958040 TTAA-AATTTAATTACCACATTTAATATTT
1 TTAATAATTCAACTAACACATTAAATATTT
958069 CATCATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (30 bp):
TTAATAATTCAACTAACACATTAAATATTT
Found at i:968786 original size:18 final size:20
Alignment explanation
Indices: 968752--968789 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
968742 CAATTCTCTT
968752 AATATTCTAATAATTTAAAA
1 AATATTCTAATAATTTAAAA
968772 AATATTC-AA-AATTTAAAA
1 AATATTCTAATAATTTAAAA
968790 TTTAACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATTCTAATAATTTAAAA
Found at i:969147 original size:21 final size:20
Alignment explanation
Indices: 969106--969152 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
969096 TGGAATTAGC
*
969106 ATAATAAAAATATTATTAAA
1 ATAATAAAAATATCATTAAA
969126 ATAAGTAAAAAT-TCATTAAAA
1 ATAA-TAAAAATATCATT-AAA
969147 ATAATA
1 ATAATA
969153 TAACTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAATAAAAATATCATTAAA
Found at i:970171 original size:24 final size:24
Alignment explanation
Indices: 970138--970190 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
970128 AAGTCTTGTC
* * *
970138 ATATTTGTATTTTATTTTTATATT
1 ATATTCGTATTATATTATTATATT
*
970162 GTATTCGTATTATATTATTATATT
1 ATATTCGTATTATATTATTATATT
970186 ATATT
1 ATATT
970191 TTAAATTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTCGTATTATATTATTATATT
Found at i:974558 original size:21 final size:21
Alignment explanation
Indices: 974513--974562 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
974503 ACTTTAAAAT
974513 TTTAATAAAAATTATAAATAAA
1 TTTAAT-AAAATTATAAATAAA
974535 TTTAATAAAA-TA-AAATATATA
1 TTTAATAAAATTATAAATA-A-A
974556 TTTAATA
1 TTTAATA
974563 TTTTCATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 12 0.46
22 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAATAAAATTATAAATAAA
Found at i:974941 original size:30 final size:30
Alignment explanation
Indices: 974882--974948 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
974872 CATACAATAT
* *
974882 TTCAATAAAATTAAAAATGTAATGAAAAAA
1 TTCAATAAAATTAAAAATATAATAAAAAAA
*
974912 TTCAATAAAATT-AAATTATAATAACAAAAA
1 TTCAATAAAATTAAAAATATAATAA-AAAAA
*
974942 TTTAATA
1 TTCAATA
974949 TTAAACATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (30 bp):
TTCAATAAAATTAAAAATATAATAAAAAAA
Found at i:975208 original size:35 final size:35
Alignment explanation
Indices: 975164--975231 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
975154 TCACGATTTT
975164 TAATGTTAAAA-ATTAAAAAG-AAAATTTATAAAAAA
1 TAATGTTAAAATA-TAAAAAGAAAAATTT-TAAAAAA
*
975199 TAATTTTAAAATATAAAAAGTAAAAATTTTAAA
1 TAATGTTAAAATATAAAAAG-AAAAATTTTAAA
975232 TGTTAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 17 0.59
36 5 0.17
37 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (35 bp):
TAATGTTAAAATATAAAAAGAAAAATTTTAAAAAA
Found at i:975246 original size:23 final size:23
Alignment explanation
Indices: 975193--975247 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
975183 GAAAATTTAT
*
975193 AAAAAATAATTTTAAAATATAAA
1 AAAAAAAAATTTTAAAATATAAA
** *
975216 AAGTAAAAATTTT-AAATGTTAAA
1 AAAAAAAAATTTTAAAAT-ATAAA
975239 AAAAAAAAA
1 AAAAAAAAA
975248 AGATATCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAAAAAAATTTTAAAATATAAA
Found at i:976112 original size:7 final size:7
Alignment explanation
Indices: 976095--976138 Score: 58
Period size: 6 Copynumber: 6.6 Consensus size: 7
976085 ACATATATAT
976095 AAATT-A
1 AAATTAA
976101 AAATTAA
1 AAATTAA
976108 AAATTAA
1 AAATTAA
976115 AAA-TAA
1 AAATTAA
976121 AAA-TAA
1 AAATTAA
976127 AAATTAA
1 AAATTAA
976134 TAAAT
1 -AAAT
976139 GTATATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 17 0.49
7 14 0.40
8 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATTAA
Found at i:976113 original size:13 final size:13
Alignment explanation
Indices: 976095--976138 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
976085 ACATATATAT
976095 AAATTAAAATTAA
1 AAATTAAAATTAA
*
976108 AAATTAAAAATAA
1 AAATTAAAATTAA
*
976121 AAATAAAAATTAA
1 AAATTAAAATTAA
976134 TAAAT
1 -AAAT
976139 GTATATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATTAAAATTAA
Found at i:976127 original size:19 final size:20
Alignment explanation
Indices: 976093--976138 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
976083 TTACATATAT
*
976093 ATAAATTAAAATTAAAAATTA
1 ATAAA-TAAAAATAAAAATTA
976114 A-AAATAAAAATAAAAATTA
1 ATAAATAAAAATAAAAATTA
976133 ATAAAT
1 ATAAAT
976139 GTATATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.65
20 7 0.30
21 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAATAAAAATAAAAATTA
Found at i:976217 original size:25 final size:23
Alignment explanation
Indices: 976185--976230 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
976175 TAATTTATAT
*
976185 ATAATTTACATATATATATAAATAA
1 ATAATTT--ATATAAATATAAATAA
976210 ATAATTTATATAAATATAAAT
1 ATAATTTATATAAATATAAAT
976231 TTGGATCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
25 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATTTATATAAATATAAATAA
Found at i:976361 original size:12 final size:14
Alignment explanation
Indices: 976335--976366 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
976325 AATAAATTTT
976335 AATTTTTTATCTAA
1 AATTTTTTATCTAA
976349 AATTTTTT-T-TAA
1 AATTTTTTATCTAA
976361 AATTTT
1 AATTTT
976367 GAAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTTTTATCTAA
Found at i:977465 original size:84 final size:84
Alignment explanation
Indices: 977319--977489 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 84
977309 AATTTAAAAT
977319 ATTGAATTCTTAAATCTTACGTATATATAAGATATTTTATTTAAATTTTTTAATGATATAAAATT
1 ATTGAATTCTTAAATCTTACGTATATATAAGATATTTTATTTAAATTTTTTAATGATATAAAATT
977384 TTTTATTTATATATGAATC
66 TTTTATTTATATATGAATC
* *
977403 ATTGGATTCTTAAATCTTATGTATATATAAGATATTTTATTTAAATTTTTTAATGATATAAAATT
1 ATTGAATTCTTAAATCTTACGTATATATAAGATATTTTATTTAAATTTTTTAATGATATAAAATT
977468 TTTTATTTATATATGAATC
66 TTTTATTTATATATGAATC
977487 ATT
1 ATT
977490 TCAATGATCT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.52
Consensus pattern (84 bp):
ATTGAATTCTTAAATCTTACGTATATATAAGATATTTTATTTAAATTTTTTAATGATATAAAATT
TTTTATTTATATATGAATC
Found at i:984909 original size:6 final size:6
Alignment explanation
Indices: 984898--984925 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
984888 GCTGCCTCCT
984898 CTGGGG CTGGGG CTGGGG CTGGGG CTGG
1 CTGGGG CTGGGG CTGGGG CTGGGG CTGG
984926 AGTCGGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.64, T:0.18
Consensus pattern (6 bp):
CTGGGG
Found at i:990623 original size:30 final size:31
Alignment explanation
Indices: 990587--990647 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
990577 ACATTACAAG
*
990587 TGTAAATTAAC-GTAATTTT-GTTGAATTATT
1 TGTAAATTAACAG-AATTTTCGTTAAATTATT
990617 TGTAAATTAACAGAATTTTCGTTAAATTATT
1 TGTAAATTAACAGAATTTTCGTTAAATTATT
990648 CTTAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (31 bp):
TGTAAATTAACAGAATTTTCGTTAAATTATT
Found at i:991368 original size:6 final size:6
Alignment explanation
Indices: 991352--991384 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
991342 ACAATGCCAA
991352 AAAAAC AAAAAAC AAAAAC AAAAAC -AAAAC AAA
1 AAAAAC -AAAAAC AAAAAC AAAAAC AAAAAC AAA
991385 CCAACAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:991374 original size:12 final size:12
Alignment explanation
Indices: 991352--991384 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
991342 ACAATGCCAA
991352 AAAAACAAAAAAC
1 AAAAAC-AAAAAC
991365 AAAAACAAAAAC
1 AAAAACAAAAAC
991377 -AAAACAAA
1 AAAAACAAA
991385 CCAACAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 6 0.30
13 6 0.30
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAC
Found at i:993841 original size:6 final size:6
Alignment explanation
Indices: 993830--993870 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
993820 AAAGAATTTA
* *
993830 AGAGAG AGAGAG AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
993871 ATGCAAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.39, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:995687 original size:22 final size:22
Alignment explanation
Indices: 995661--995703 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
995651 TGTATATTTA
995661 TATTTGAAT-CTCTAGAATTAAG
1 TATTTGAATCCT-TAGAATTAAG
*
995683 TATTTGTATCCTTAGAATTAA
1 TATTTGAATCCTTAGAATTAA
995704 AGACAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (22 bp):
TATTTGAATCCTTAGAATTAAG
Found at i:996779 original size:85 final size:85
Alignment explanation
Indices: 996647--996818 Score: 299
Period size: 85 Copynumber: 2.0 Consensus size: 85
996637 AAACAAAAAA
* * *
996647 CCCATCTAGGTAAAGAAGAAATCAAGAAAGAGAAAAAGAAAGAATTAAATAGAGATGAAGTTCTC
1 CCCATCTAGGTAAAGAAGAAATCAAGAAAGAGAAAAAAAAAGAATTAAATAGAGAAGAAATTCTC
996712 ACGGAATATAAAAAGCAGCT
66 ACGGAATATAAAAAGCAGCT
996732 CCCATCTAGGTAAAGAAGAAATCAAGAAAGAGAAAAAAAAAGAATTAAATAGAGAAGAAATTCTC
1 CCCATCTAGGTAAAGAAGAAATCAAGAAAGAGAAAAAAAAAGAATTAAATAGAGAAGAAATTCTC
**
996797 ACGGAATATGCAAAGCAGCT
66 ACGGAATATAAAAAGCAGCT
996817 CC
1 CC
996819 ATGGCGAGAC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (85 bp):
CCCATCTAGGTAAAGAAGAAATCAAGAAAGAGAAAAAAAAAGAATTAAATAGAGAAGAAATTCTC
ACGGAATATAAAAAGCAGCT
Found at i:1000697 original size:18 final size:18
Alignment explanation
Indices: 1000674--1000708 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1000664 TTATAAAAAT
*
1000674 TTAATAAATATATATAAA
1 TTAATAAAAATATATAAA
1000692 TTAATAAAAATATATAA
1 TTAATAAAAATATATAA
1000709 TTCGATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAATAAAAATATATAAA
Found at i:1000748 original size:12 final size:12
Alignment explanation
Indices: 1000740--1000799 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 12
1000730 ATTTTTAATT
1000740 TTTAATTTAAAA
1 TTTAATTTAAAA
1000752 TTTAATTT-AAA
1 TTTAATTTAAAA
* *
1000763 TCTAATTTATATA
1 TTTAATTTA-AAA
*
1000776 TTTAATATATAAA
1 TTTAATTTA-AAA
*
1000789 TTTAATCTAAA
1 TTTAATTTAAA
1000800 TTACAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 10 0.25
12 10 0.25
13 20 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAATTTAAAA
Found at i:1000780 original size:31 final size:30
Alignment explanation
Indices: 1000735--1000798 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
1000725 TTTATATTTT
* *
1000735 TAATTTTTAATTTAAAAT-TTAATTTAAATC
1 TAATTTATAATTTAAAATATAAATTT-AATC
*
1000765 TAATTTATATATTTAATATATAAATTTAATC
1 TAATTTATA-ATTTAAAATATAAATTTAATC
1000796 TAA
1 TAA
1000799 ATTACAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 8 0.28
31 15 0.52
32 6 0.21
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATTTATAATTTAAAATATAAATTTAATC
Found at i:1001370 original size:23 final size:23
Alignment explanation
Indices: 1001344--1001387 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1001334 TCCAAAATGG
*
1001344 ATAAGA-ATAAAAATATTAAAATA
1 ATAAGAGA-AAAAACATTAAAATA
*
1001367 ATAATAGAAAAAACATTAAAA
1 ATAAGAGAAAAAACATTAAAA
1001388 ATTCATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (23 bp):
ATAAGAGAAAAAACATTAAAATA
Found at i:1001475 original size:13 final size:13
Alignment explanation
Indices: 1001457--1001481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1001447 ATCCCATTAA
1001457 TTTGTTTTTTATT
1 TTTGTTTTTTATT
1001470 TTTGTTTTTTAT
1 TTTGTTTTTTAT
1001482 CATAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTGTTTTTTATT
Found at i:1001953 original size:27 final size:27
Alignment explanation
Indices: 1001930--1002012 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 27
1001920 AGTCAATGTT
1001930 GGAGGAGAACTTGCGGGTGCCAATGAC
1 GGAGGAGAACTTGCGGGTGCCAATGAC
* *
1001957 GGAGGAGAACTTGCGGGTGTCAAAGAC
1 GGAGGAGAACTTGCGGGTGCCAATGAC
* * *
1001984 GGAGGAGAACTTGCCGGTGTCAACGAC
1 GGAGGAGAACTTGCGGGTGCCAATGAC
1002011 GG
1 GG
1002013 TGGTGTAGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.18, G:0.41, T:0.14
Consensus pattern (27 bp):
GGAGGAGAACTTGCGGGTGCCAATGAC
Found at i:1005684 original size:12 final size:12
Alignment explanation
Indices: 1005667--1005691 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1005657 CCCTACATCT
1005667 TCTTCAGATTCA
1 TCTTCAGATTCA
1005679 TCTTCAGATTCA
1 TCTTCAGATTCA
1005691 T
1 T
1005692 TTTTCTCCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTTCAGATTCA
Found at i:1005793 original size:15 final size:15
Alignment explanation
Indices: 1005753--1005800 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1005743 TAATGCCATT
* *
1005753 TTCAGTTTCCTCCTC
1 TTCATTTTCTTCCTC
*
1005768 TTCATTCTCTTCCTC
1 TTCATTTTCTTCCTC
* *
1005783 TTCCTTTTCTTCTTC
1 TTCATTTTCTTCCTC
1005798 TTC
1 TTC
1005801 TTCTTCAGAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.04, C:0.38, G:0.02, T:0.56
Consensus pattern (15 bp):
TTCATTTTCTTCCTC
Found at i:1010205 original size:17 final size:19
Alignment explanation
Indices: 1010185--1010219 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1010175 TTTTTTAGAT
1010185 TAAAATA-TAT-TTTATAA
1 TAAAATATTATATTTATAA
1010202 TAAAATATTATATTTATA
1 TAAAATATTATATTTATA
1010220 TTATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATATTATATTTATAA
Found at i:1010537 original size:22 final size:24
Alignment explanation
Indices: 1010512--1010558 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1010502 TATATATAAT
*
1010512 TATTT-TTT-ATTTTTTAGTTATA
1 TATTTATTTAATTTTATAGTTATA
*
1010534 TATTTATTTAATTTTATATTTATA
1 TATTTATTTAATTTTATAGTTATA
1010558 T
1 T
1010559 TAAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 3 0.14
24 13 0.62
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TATTTATTTAATTTTATAGTTATA
Found at i:1010567 original size:17 final size:17
Alignment explanation
Indices: 1010532--1010581 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1010522 TTTTTAGTTA
**
1010532 TATATTTAT-TTAATTT
1 TATATTTATATTAAAAT
1010548 TATATTTATATTAAAAT
1 TATATTTATATTAAAAT
*
1010565 TATATTTTATAATAAAA
1 TATA-TTTATATTAAAA
1010582 ATTTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 9 0.31
17 9 0.31
18 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTATATTAAAAT
Found at i:1010582 original size:19 final size:17
Alignment explanation
Indices: 1010547--1010593 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
1010537 TTATTTAATT
*
1010547 TTATATTTATATTAAAA
1 TTATATTTATATAAAAA
1010564 TTATATTTTATAATAAAAA
1 TTATA-TTTAT-ATAAAAA
1010583 TT-T-TTTATATA
1 TTATATTTATATA
1010594 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.11
16 5 0.19
17 5 0.19
18 6 0.22
19 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATTTATATAAAAA
Found at i:1010597 original size:25 final size:24
Alignment explanation
Indices: 1010565--1010614 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1010555 ATATTAAAAT
*
1010565 TATATTTTATAATAAA-AATTTTTTA
1 TATATTTTA-AA-AAATAATATTTTA
1010590 TATATTTTAAAAAATAATATTTTA
1 TATATTTTAAAAAATAATATTTTA
1010614 T
1 T
1010615 TAATTTCAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 11 0.48
25 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATTTTAAAAAATAATATTTTA
Found at i:1012424 original size:371 final size:372
Alignment explanation
Indices: 1011734--1012707 Score: 1563
Period size: 371 Copynumber: 2.6 Consensus size: 372
1011724 ACTTCAGCTT
*
1011734 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACTCGGGCATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGGCATTCACCCT
* * *
1011799 TCCGACGTCTTGGATCAGCCTGACCGCCACGGTTCACACCATTGTGAGGTATTATCCTCTCTGGC
66 TCCGACGTCTCGGATCAGCCTGACCGCCACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGGC
* *
1011864 CCCCCTTGGCCTCACGGTTTTATCCTTCAAAAGACGTCTCACAAGGCGGAGATGGTGTGAACCCT
131 CCCCCTTGGCCTCACGGTTTTATCCTTCAAAAGACGACTCACAAGGCGGAGGTGGTGTGAACCCT
* *
1011929 TTTATACCCTAGTGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCTTCCTTAGGTCCGTG
196 TTTATACCCCAATGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCTTCCTTAGGTCCGTG
*
1011994 ACATTCTCCCGCACCCAACCTCGTGACGCCCTCATCACGGAGGCTAGCCACCCTGCCTACCTCCC
261 ACATTCTCCCGCACCCAACCTCGTGACGCCCTCATCACGGAGGCTAGCCACCATGCCTACCTCCC
* *
1012059 TCGAGGTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGCTCTGATAC
326 TCGAGGTGCTTGGCGTGGATCAAACGGTTTAGGACTGGCTCTGATAC
*
1012106 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCTGGGACCCGGGCATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGGCATTCACCCT
* * * * * *
1012171 TCCGACATCCCGAATCAGCCTGACCACCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTAGC
66 TCCGACGTCTCGGATCAGCCTGACCGCCACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGGC
* * * *
1012236 CCCTC-TGACCTCACGGTTTTATCCTTCAAAAGGCGCCTCACAAGGCGGAGGTGGTGTGAACCCT
131 CCCCCTTGGCCTCACGGTTTTATCCTTCAAAAGACGACTCACAAGGCGGAGGTGGTGTGAACCCT
*
1012300 TTTATACCCCAATGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCTTCTTTAGGTCCGTG
196 TTTATACCCCAATGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCTTCCTTAGGTCCGTG
* * *
1012365 ACATTCTCCCGCACCTAACCTCGTGACGCCCTCGTCACGGAGGCTAGTCACCATGCCTACCTCCC
261 ACATTCTCCCGCACCCAACCTCGTGACGCCCTCATCACGGAGGCTAGCCACCATGCCTACCTCCC
* *
1012430 TCGAGGTGCTTGGCGTGGATCAAACGGTTTAGGATTGGCTCTGATAT
326 TCGAGGTGCTTGGCGTGGATCAAACGGTTTAGGACTGGCTCTGATAC
* *
1012477 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGACTCCGGGACCCGAGCATTCACCCT
1 CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGGCATTCACCCT
* * *
1012542 TCCGGCGTCTCGGATCAGCCTAACCGTCACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGGC
66 TCCGACGTCTCGGATCAGCCTGACCGCCACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGGC
* * * * ** * *
1012607 CCCCCTTGGCCTTACAGTTTTATCTTTCAAAAGATGACTCACAAGATGAAGGTAGTGTGAACCCT
131 CCCCCTTGGCCTCACGGTTTTATCCTTCAAAAGACGACTCACAAGGCGGAGGTGGTGTGAACCCT
*
1012672 TTTATACTCCAATGACCCTCCTATTATGTTCGATGT
196 TTTATACCCCAATGACCCTCCTATTATGTTCGATGT
1012708 AAGATTCATG
Statistics
Matches: 549, Mismatches: 52, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
371 343 0.62
372 206 0.38
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (372 bp):
CACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGGGACCCGGGCATTCACCCT
TCCGACGTCTCGGATCAGCCTGACCGCCACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGGC
CCCCCTTGGCCTCACGGTTTTATCCTTCAAAAGACGACTCACAAGGCGGAGGTGGTGTGAACCCT
TTTATACCCCAATGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCTTCCTTAGGTCCGTG
ACATTCTCCCGCACCCAACCTCGTGACGCCCTCATCACGGAGGCTAGCCACCATGCCTACCTCCC
TCGAGGTGCTTGGCGTGGATCAAACGGTTTAGGACTGGCTCTGATAC
Found at i:1013045 original size:18 final size:18
Alignment explanation
Indices: 1013024--1013083 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1013014 ATTATACCAC
1013024 ATAATATTTATATAAAAT
1 ATAATATTTATATAAAAT
* *
1013042 ATAATATAAATATATAAATT
1 ATAATAT--TTATATAAAAT
*
1013062 ATTAATATTT-TATAAAAC
1 A-TAATATTTATATAAAAT
1013080 ATAA
1 ATAA
1013084 ATACCTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.09
18 14 0.41
19 1 0.03
20 10 0.29
21 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATATTTATATAAAAT
Found at i:1013075 original size:20 final size:19
Alignment explanation
Indices: 1013024--1013075 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1013014 ATTATACCAC
1013024 ATAATA-TTTATATAAAAT
1 ATAATATTTTATATAAAAT
** *
1013042 ATAATATAAATATATAAATT
1 ATAATAT-TTTATATAAAAT
1013062 ATTAATATTTTATA
1 A-TAATATTTTATA
1013076 AAACATAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATATTTTATATAAAAT
Found at i:1013105 original size:2 final size:2
Alignment explanation
Indices: 1013098--1013122 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1013088 CTAAATTATC
1013098 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
1013123 AAAAAAAAAC
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:1015925 original size:22 final size:22
Alignment explanation
Indices: 1015883--1015939 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
1015873 TAATTTTAAT
*
1015883 TTTTTATATATTATTTTAATAACA
1 TTTTTATATA-TATTTAAATAA-A
1015907 TTTTTA-ATATATTTAAATAAA
1 TTTTTATATATATTTAAATAAA
*
1015928 TTTATATATATA
1 TTTTTATATATA
1015940 ATAATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.20
22 15 0.50
23 3 0.10
24 6 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTATATATATTTAAATAAA
Found at i:1022824 original size:22 final size:22
Alignment explanation
Indices: 1022798--1022863 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
1022788 CATTGGTGTT
1022798 TGCTTGATTTGGTCGTTTCCAG
1 TGCTTGATTTGGTCGTTTCCAG
*
1022820 TGCTTGACATTGGT-G-TT----
1 TGCTTGA-TTTGGTCGTTTCCAG
1022837 TGCTTGATTTGGTCGTTTCCAG
1 TGCTTGATTTGGTCGTTTCCAG
1022859 TGCTT
1 TGCTT
1022864 ACAGATTCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 5 0.14
17 8 0.23
18 2 0.06
21 2 0.06
22 13 0.37
23 5 0.14
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (22 bp):
TGCTTGATTTGGTCGTTTCCAG
Found at i:1022831 original size:39 final size:39
Alignment explanation
Indices: 1022785--1022863 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1022775 AGTTGGTTGA
1022785 TGACATTGGTGTTTGCTTGATTTGGTCGTTTCCAGTGCT
1 TGACATTGGTGTTTGCTTGATTTGGTCGTTTCCAGTGCT
1022824 TGACATTGGTGTTTGCTTGATTTGGTCGTTTCCAGTGCT
1 TGACATTGGTGTTTGCTTGATTTGGTCGTTTCCAGTGCT
1022863 T
1 T
1022864 ACAGATTCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.47
Consensus pattern (39 bp):
TGACATTGGTGTTTGCTTGATTTGGTCGTTTCCAGTGCT
Found at i:1023059 original size:11 final size:11
Alignment explanation
Indices: 1023045--1023087 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
1023035 TAATTTTTAA
1023045 TTTATATTATT
1 TTTATATTATT
1023056 TTTATATTTTATT
1 TTTATA--TTATT
*
1023069 TTTATATTATA
1 TTTATATTATT
1023080 TTTATATT
1 TTTATATT
1023088 GTATCATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 18 0.62
13 11 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATATTATT
Found at i:1023064 original size:24 final size:25
Alignment explanation
Indices: 1023018--1023108 Score: 75
Period size: 24 Copynumber: 3.7 Consensus size: 25
1023008 TTATTAAAAT
*
1023018 TATTTATAATTATTAATTA-ATTTTTA
1 TATTTAT-ATTATT-TTTATATTTTTA
1023044 -ATTTATATTATTTTTATA-TTTTA
1 TATTTATATTATTTTTATATTTTTA
* * *
1023067 TTTTTATATTATATTTATA-TTGTA
1 TATTTATATTATTTTTATATTTTTA
1023091 TCA-TTATATTATATTTTA
1 T-ATTTATATTAT-TTTTA
1023109 AATTATCAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
23 8 0.15
24 37 0.67
25 10 0.18
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (25 bp):
TATTTATATTATTTTTATATTTTTA
Found at i:1023812 original size:34 final size:33
Alignment explanation
Indices: 1023740--1023813 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
1023730 TATATCTAAA
* * *
1023740 AAATTAAATAATTTATCGATTTACGTATTTGAT
1 AAATTATATAATTTATCGATTTACATATTCGAT
*
1023773 AAATTATATAATTTATTTC-ATTTTCATATTCGAT
1 AAATTATATAATTTA--TCGATTTACATATTCGAT
1023807 AAATTAT
1 AAATTAT
1023814 TTAAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 14 0.40
34 19 0.54
35 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (33 bp):
AAATTATATAATTTATCGATTTACATATTCGAT
Found at i:1024333 original size:27 final size:27
Alignment explanation
Indices: 1024301--1024365 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
1024291 AGATTTACGC
* *
1024301 TTTATTTAAATGTTTGATGAAAATCTT
1 TTTATTTAAATATTCGATGAAAATCTT
* * *
1024328 TTTATTTAACTATTCGATGAAATTTTT
1 TTTATTTAAATATTCGATGAAAATCTT
1024355 TTTATTATAAA
1 TTTATT-TAAA
1024366 CAATTTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.54
Consensus pattern (27 bp):
TTTATTTAAATATTCGATGAAAATCTT
Found at i:1024466 original size:26 final size:26
Alignment explanation
Indices: 1024416--1024464 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
1024406 TGTTCGGTTT
1024416 AAAAAATATTTTTTATTTTCATTTTA
1 AAAAAATATTTTTTATTTTCATTTTA
1024442 AAAAAATA-TTTTTATTTT-ATTTT
1 AAAAAATATTTTTTATTTTCATTTT
1024465 TTGGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 8 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
AAAAAATATTTTTTATTTTCATTTTA
Found at i:1024519 original size:26 final size:26
Alignment explanation
Indices: 1024474--1024525 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
1024464 TTTGGTTTTT
1024474 TAAAAATTTATTTAGTAAATG-AAAA
1 TAAAAATTTATTTAGTAAATGCAAAA
*
1024499 TAAAAATTATTTTCTAG-AAATGCAAAA
1 TAAAAATT-TATT-TAGTAAATGCAAAA
1024526 ATAAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 8 0.35
26 8 0.35
27 7 0.30
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (26 bp):
TAAAAATTTATTTAGTAAATGCAAAA
Found at i:1025278 original size:22 final size:21
Alignment explanation
Indices: 1025253--1025303 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
1025243 TTCGAAATTA
*
1025253 TAATATTTGATTTGATTTTTAT
1 TAATATTTGATTCGATTTTT-T
* *
1025275 TAATTTTTTTATTCGATTTTTT
1 TAA-TATTTGATTCGATTTTTT
1025297 TAATATT
1 TAATATT
1025304 AAATATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 7 0.29
23 14 0.58
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (21 bp):
TAATATTTGATTCGATTTTTT
Found at i:1025449 original size:21 final size:21
Alignment explanation
Indices: 1025420--1025468 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1025410 TTATTATATA
*
1025420 TAAAATTTTATTTAAATAAAT
1 TAAAATTTTATTAAAATAAAT
*
1025441 TAAATTTTTATTAAAATAACAT
1 TAAAATTTTATTAAAATAA-AT
1025463 ATAAAA
1 -TAAAA
1025469 AAATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATTTTATTAAAATAAAT
Found at i:1025478 original size:23 final size:24
Alignment explanation
Indices: 1025452--1025503 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
1025442 AAATTTTTAT
1025452 TAAAAT-AACATATAAAAAAA-TAA
1 TAAAATCAA-ATATAAAAAAATTAA
*
1025475 T-AAATCAAATTTAAAAAAATTAA
1 TAAAATCAAATATAAAAAAATTAA
1025498 TAAAAT
1 TAAAAT
1025504 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 14 0.56
23 7 0.28
24 4 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
TAAAATCAAATATAAAAAAATTAA
Found at i:1025503 original size:19 final size:20
Alignment explanation
Indices: 1025467--1025508 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1025457 TAACATATAA
*
1025467 AAAAATAATAAATCAAATTT
1 AAAAATAATAAATAAAATTT
*
1025487 AAAAA-AATTAATAAAATTT
1 AAAAATAATAAATAAAATTT
1025506 AAA
1 AAA
1025509 TTTAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATAATAAATAAAATTT
Found at i:1025530 original size:19 final size:19
Alignment explanation
Indices: 1025506--1025637 Score: 52
Period size: 16 Copynumber: 7.3 Consensus size: 19
1025496 AATAAAATTT
1025506 AAATTTAAATTAAATTTTA
1 AAATTTAAATTAAATTTTA
*
1025525 AAATTT-CA-T-AATTTT-
1 AAATTTAAATTAAATTTTA
1025540 AAA--TAAATTAAATTTT-
1 AAATTTAAATTAAATTTTA
** * **
1025556 TTA-TTAAAATAACATATAAA
1 AAATTTAAATTAA-AT-TTTA
* * *
1025576 AAATAATAAATCAAATTTAAA
1 AAAT-TTAAATTAAATTT-TA
* *
1025597 AAAATT-AA-TAAAATTT-
1 AAATTTAAATTAAATTTTA
1025613 AAATTTAAATTAAATTTTA
1 AAATTTAAATTAAATTTTA
1025632 AAATTT
1 AAATTT
1025638 CATAATTTTA
Statistics
Matches: 80, Mismatches: 20, Indels: 26
0.63 0.16 0.21
Matches are distributed among these distances:
13 1 0.01
14 1 0.01
15 4 0.05
16 18 0.22
17 10 0.12
18 15 0.19
19 15 0.19
20 3 0.04
21 7 0.09
22 6 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTAAATTAAATTTTA
Found at i:1025544 original size:107 final size:107
Alignment explanation
Indices: 1025430--1025647 Score: 420
Period size: 107 Copynumber: 2.0 Consensus size: 107
1025420 TAAAATTTTA
1025430 TTTAAATAAATTAAA-TTTTTATTAAAATAACATATAAAAAAATAATAAATCAAATTTAAAAAAA
1 TTTAAATAAATTAAATTTTTTATTAAAATAACATAT-AAAAAATAATAAATCAAATTTAAAAAAA
1025494 TTAATAAAATTTAAATTTAAATTAAATTTTAAAATTTCATAAT
65 TTAATAAAATTTAAATTTAAATTAAATTTTAAAATTTCATAAT
1025537 TTTAAATAAATTAAATTTTTTATTAAAATAACATATAAAAAATAATAAATCAAATTTAAAAAAAT
1 TTTAAATAAATTAAATTTTTTATTAAAATAACATATAAAAAATAATAAATCAAATTTAAAAAAAT
1025602 TAATAAAATTTAAATTTAAATTAAATTTTAAAATTTCATAAT
66 TAATAAAATTTAAATTTAAATTAAATTTTAAAATTTCATAAT
1025644 TTTA
1 TTTA
1025648 TATATTATTT
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 90 0.82
108 20 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (107 bp):
TTTAAATAAATTAAATTTTTTATTAAAATAACATATAAAAAATAATAAATCAAATTTAAAAAAAT
TAATAAAATTTAAATTTAAATTAAATTTTAAAATTTCATAAT
Found at i:1025637 original size:25 final size:25
Alignment explanation
Indices: 1025573--1025621 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1025563 AATAACATAT
*
1025573 AAAAAA-TAAT-AAA-TCAAATTTA
1 AAAAAATTAATAAAATTTAAATTTA
1025595 AAAAAATTAATAAAATTTAAATTTA
1 AAAAAATTAATAAAATTTAAATTTA
1025620 AA
1 AA
1025622 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 4 0.17
24 3 0.13
25 10 0.43
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAATTAATAAAATTTAAATTTA
Found at i:1026218 original size:6 final size:6
Alignment explanation
Indices: 1026204--1026284 Score: 71
Period size: 6 Copynumber: 13.7 Consensus size: 6
1026194 ATATGTTAAA
* *
1026204 AAATTT AAATAT AAA-TT AAATTT AAAATTT -AACTT AAATTT -AA-TT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT
* *
1026249 AAATTTT AATTTTT AAATTT AAATTT AAATTA AAAT
1 AAA-TTT AA-ATTT AAATTT AAATTT AAATTT AAAT
1026285 AATATTAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.03
5 12 0.20
6 32 0.52
7 15 0.25
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:1026224 original size:11 final size:10
Alignment explanation
Indices: 1026208--1026302 Score: 52
Period size: 11 Copynumber: 9.0 Consensus size: 10
1026198 GTTAAAAAAT
1026208 TTAAATATAAA
1 TTAAAT-TAAA
1026219 TTAAATTTAAAA
1 TTAAA-TT-AAA
*
1026231 TTTAACTTAAA
1 -TTAAATTAAA
*
1026242 TTTAATTAAA
1 TTAAATTAAA
* *
1026252 TTTTAATT--T
1 -TTAAATTAAA
1026261 TTAAATTTAAA
1 TTAAA-TTAAA
1026272 TTTAAATTAAA
1 -TTAAATTAAA
*
1026283 ATAATATTAAA
1 TTAA-ATTAAA
1026294 TT-AATTAAA
1 TTAAATTAAA
1026303 CTATATTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.06
9 8 0.12
10 12 0.18
11 28 0.42
12 11 0.16
13 4 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (10 bp):
TTAAATTAAA
Found at i:1026225 original size:5 final size:5
Alignment explanation
Indices: 1026208--1026302 Score: 52
Period size: 5 Copynumber: 18.0 Consensus size: 5
1026198 GTTAAAAAAT
* * *
1026208 TTAAA TATAAA TTAAA TTTAAAA TTTAAC TTAAA TTTAA TTAAA TTTTAA
1 TTAAA T-TAAA TTAAA -TT-AAA -TTAAA TTAAA TTAAA TTAAA -TTAAA
* *
1026258 TT--T TTAAA TTTAAA TTTAAA TTAAA ATAATA TTAAA TT-AA TTAAA
1 TTAAA TTAAA -TTAAA -TTAAA TTAAA TTAA-A TTAAA TTAAA TTAAA
1026303 CTATATTATT
Statistics
Matches: 72, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
3 2 0.03
4 4 0.06
5 32 0.44
6 28 0.39
7 6 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (5 bp):
TTAAA
Found at i:1026266 original size:14 final size:14
Alignment explanation
Indices: 1026219--1026274 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
1026209 TAAATATAAA
*
1026219 TTAAATTTAAA-AT
1 TTAAATTTAAATTT
*
1026232 TT-AACTTAAATTT
1 TTAAATTTAAATTT
*
1026245 AATTAAATTTTAATTT
1 --TTAAATTTAAATTT
1026261 TTAAATTTAAATTT
1 TTAAATTTAAATTT
1026275 AAATTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 13 0.38
15 2 0.06
16 9 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATTTAAATTT
Found at i:1026716 original size:119 final size:120
Alignment explanation
Indices: 1026551--1026785 Score: 436
Period size: 119 Copynumber: 2.0 Consensus size: 120
1026541 AATTTTATCT
*
1026551 AAATTAAACTTAAATAATTTTGTAAATATTAATATATCATTTATATTTTTAATTGAGAGCTTTTA
1 AAATTAAACTTAAATAATTTTATAAATATTAATATATCATTTATATTTTTAATTGAGAGCTTTTA
*
1026616 ATCTCTACGGTAATTCATCTATTTTCATAGCAAGGTTTAGGGCACAATTTGAAGC
66 ATCTCTAAGGTAATTCATCTATTTTCATAGCAAGGTTTAGGGCACAATTTGAAGC
1026671 AAATTAAACTTAAATAA-TTTATAAATATTAATATATCATTTATATTTTTAATTGAGAGCTTTTA
1 AAATTAAACTTAAATAATTTTATAAATATTAATATATCATTTATATTTTTAATTGAGAGCTTTTA
*
1026735 ATCTCTAAGGTAGTTCATCTATTTTCATAGCAAGGTTTAGGGCACAATTTG
66 ATCTCTAAGGTAATTCATCTATTTTCATAGCAAGGTTTAGGGCACAATTTG
1026786 GAGCCCCTGA
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
119 95 0.85
120 17 0.15
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.42
Consensus pattern (120 bp):
AAATTAAACTTAAATAATTTTATAAATATTAATATATCATTTATATTTTTAATTGAGAGCTTTTA
ATCTCTAAGGTAATTCATCTATTTTCATAGCAAGGTTTAGGGCACAATTTGAAGC
Found at i:1027357 original size:31 final size:33
Alignment explanation
Indices: 1027322--1027396 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 33
1027312 ATATTTTTAT
* *
1027322 ATTTTTATATTAACAT-TAAT-TATAATATAT-A
1 ATTTTTATATTAAAATATAATATA-AATACATAA
1027353 ATTTTTATA-TAAAATATAATATAAATACATAA
1 ATTTTTATATTAAAATATAATATAAATACATAA
*
1027385 ATTTTAATATTA
1 ATTTTTATATTA
1027397 CATATTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 5 0.14
31 19 0.51
32 11 0.30
33 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTTTATATTAAAATATAATATAAATACATAA
Found at i:1028790 original size:33 final size:35
Alignment explanation
Indices: 1028725--1028792 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
1028715 AATATAAATA
*
1028725 AAAAATATAAAAGTAATATAATTTAAAATTTTATT
1 AAAAATATAAAAATAATATAATTTAAAATTTTATT
* * *
1028760 AAAAAT-TAAAAAT-ATATATTTTATAGTTTTATT
1 AAAAATATAAAAATAATATAATTTAAAATTTTATT
1028793 TTAATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 17 0.59
34 6 0.21
35 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (35 bp):
AAAAATATAAAAATAATATAATTTAAAATTTTATT
Found at i:1029143 original size:33 final size:30
Alignment explanation
Indices: 1029081--1029149 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
1029071 CGTTTACATG
*
1029081 AATTTTTTTTTTACACATAAAAAAATTATT
1 AATTTTTTTTTGACACATAAAAAAATTATT
* * *
1029111 AAATTTTTTTTAATGACACATAAGATATTTATT
1 -AATTTTTTTT--TGACACATAAAAAAATTATT
1029144 AATTTT
1 AATTTT
1029150 AAATTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.31
32 6 0.19
33 16 0.50
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (30 bp):
AATTTTTTTTTGACACATAAAAAAATTATT
Found at i:1030348 original size:62 final size:63
Alignment explanation
Indices: 1030273--1030392 Score: 149
Period size: 62 Copynumber: 1.9 Consensus size: 63
1030263 ATTGAAGGCG
* * * *
1030273 TTTTTGGTCAAAAACA-CATTTAATAATCCCTTTTAATTTT-TA-TGAGGTGATTATTCAAAATA
1 TTTTTGCTCAAAAACATC-TTGAATAATCCCCTCTAATTTTATATTG-GG-GATTATTCAAAATA
1030335 T
63 T
1030336 TTTTTGCT-AAAAACATCTTGAATAATCCCCTCTAATTTTATATTGGGGATTATTCAA
1 TTTTTGCTCAAAAACATCTTGAATAATCCCCTCTAATTTTATATTGGGGATTATTCAA
1030393 GGCTTTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
62 36 0.72
63 12 0.24
64 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (63 bp):
TTTTTGCTCAAAAACATCTTGAATAATCCCCTCTAATTTTATATTGGGGATTATTCAAAATAT
Found at i:1030401 original size:62 final size:63
Alignment explanation
Indices: 1030259--1030426 Score: 143
Period size: 62 Copynumber: 2.7 Consensus size: 63
1030249 TATTTAATAA
* * * * * *
1030259 GATTATTGAAGGC-GTTTTTGGTCAAAAACACATTTAATAATCCCTTTTAATTTTTATGAGGT
1 GATTATTCAAGGCTTTTTTTGCTCAAAAACACATTGAATAATCCCCTCTAATTTTTATGAGGT
**
1030321 GATTATTCAA-AATATTTTTTGCT-AAAAACATC-TTGAATAATCCCCTCTAATTTTATATTG-G
1 GATTATTCAAGGCT-TTTTTTGCTCAAAAACA-CATTGAATAATCCCCTCTAATTTT-TA-TGAG
1030382 G-
62 GT
* * *
1030383 GATTATTCAAGGCTTTTTTT-CCCAGAATACGCATTGAATAATCC
1 GATTATTCAAGGCTTTTTTTGCTCA-AAAACACATTGAATAATCC
1030427 ACTCATAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
61 1 0.01
62 53 0.63
63 28 0.33
64 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (63 bp):
GATTATTCAAGGCTTTTTTTGCTCAAAAACACATTGAATAATCCCCTCTAATTTTTATGAGGT
Found at i:1030883 original size:62 final size:63
Alignment explanation
Indices: 1030817--1030946 Score: 144
Period size: 62 Copynumber: 2.1 Consensus size: 63
1030807 TTGAAGGCCT
* * *
1030817 TTTTTTGTC-AAAAATGA-CTTTAATAATCCCCTTCAATTTT-TATAAGGTGATTATTCAA-GT-
1 TTTTTTGGCTAAAAAT-ACCTTGAATAATCCCCTTCAATTTTGTAT-AGGGGATTATTCAATGTG
* * *
1030877 TGTTTTTGGCTAAAAATACCTTGAATAATCTCTTTCAATTTTGTATTGGGGATTATTCAATGTG
1 T-TTTTTGGCTAAAAATACCTTGAATAATCCCCTTCAATTTTGTATAGGGGATTATTCAATGTG
1030941 TTTTTT
1 TTTTTT
1030947 TTCTCATAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
60 1 0.02
61 8 0.14
62 38 0.66
63 10 0.17
64 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (63 bp):
TTTTTTGGCTAAAAATACCTTGAATAATCCCCTTCAATTTTGTATAGGGGATTATTCAATGTG
Found at i:1031205 original size:63 final size:62
Alignment explanation
Indices: 1031130--1031449 Score: 188
Period size: 63 Copynumber: 5.1 Consensus size: 62
1031120 GTTAAATGTG
* * * * *
1031130 TTTTTGACAAAAAACGTTTTTAATAATCTCCTCCAATTTTTTACAAGGGATTATTGAAAGTA
1 TTTTTGTCAAAAAATGTTTTCAATAATCTCCTCAAATTTTTTAGAAGGGATTATTGAAAGTA
* * * * * * * *
1031192 TTTTTGTCTAAAAAATATTTTCAATAATCCCCTTAAATATTTTTGGAGGGGATTATTCAATGCA
1 TTTTTGTC-AAAAAATGTTTTCAATAATCTCCTCAAAT-TTTTTAGAAGGGATTATTGAAAGTA
* * * * * ** *
1031256 TTTTTTGTC-AAAAATGCTTTGAGTAATCTCCTCTAACTTTTTAGAAGACATTATTGAAGGTA
1 -TTTTTGTCAAAAAATGTTTTCAATAATCTCCTCAAATTTTTTAGAAGGGATTATTGAAAGTA
** * * *
1031318 TTTTTGGTCAAAAATAT-TTTT-AAT-AT-TCCTCTTTCATTTTTATTGAATGGATTATTGAAGG
1 TTTTT-GTCAAAAA-ATGTTTTCAATAATCTCCTC--AAATTTTT-TAGAAGGGATTATTGAAAG
1031379 TA
61 TA
* * ** *
1031381 TTTTTTTGTC-AAAAATGTATT-AAGTAATC-CTTTTTAATTTTTTAGAAAGGATTATTGAAAGT
1 --TTTTTGTCAAAAAATGTTTTCAA-TAATCTC-CTCAAATTTTTTAGAAGGGATTATTGAAAGT
*
1031443 G
62 A
1031444 TTTTTG
1 TTTTTG
1031450 GCTAAACATA
Statistics
Matches: 198, Mismatches: 44, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
60 5 0.03
61 13 0.07
62 38 0.19
63 93 0.47
64 32 0.16
65 16 0.08
66 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (62 bp):
TTTTTGTCAAAAAATGTTTTCAATAATCTCCTCAAATTTTTTAGAAGGGATTATTGAAAGTA
Found at i:1031321 original size:62 final size:62
Alignment explanation
Indices: 1031255--1031397 Score: 148
Period size: 62 Copynumber: 2.3 Consensus size: 62
1031245 TATTCAATGC
*
1031255 ATTTTTTGTCAAAAATGCTTTGAGTAATCTCCTCTAAC-TTTTTA-GAA-GACATTATTGAAGGT
1 ATTTTTTGTCAAAAATGCTTTGAAT-AT-TCCTCTAACATTTTTATGAATG-CATTATTGAAGGT
* ** * ** *
1031317 ATTTTTGGTCAAAAATATTTTTAATATTCCTCTTTCATTTTTATTGAATGGATTATTGAAGGT
1 ATTTTTTGTCAAAAATGCTTTGAATATTCCTCTAACATTTTTA-TGAATGCATTATTGAAGGT
1031380 ATTTTTTTGTCAAAAATG
1 A-TTTTTTGTCAAAAATG
1031398 TATTAAGTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
60 7 0.11
61 8 0.12
62 20 0.30
63 16 0.24
64 15 0.23
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (62 bp):
ATTTTTTGTCAAAAATGCTTTGAATATTCCTCTAACATTTTTATGAATGCATTATTGAAGGT
Found at i:1031386 original size:126 final size:126
Alignment explanation
Indices: 1031149--1031499 Score: 349
Period size: 126 Copynumber: 2.8 Consensus size: 126
1031139 AAAAACGTTT
* * *
1031149 TTAA-TAATCTCCTCCAATTTTTTACAAGGGATTATTGAAAGTATTTTT-GTCTAAAAAATATTT
1 TTAAGTAATCTCCTCTAATTTTTTAGAAGAGATTATTGAAAGTATTTTTGGTCT-AAAAATATTT
* * * ** * *
1031212 TCAATAATCCCCTTAAATATTTT-TGGAGGGGATTATTCAATGCATTTTTTGTCAAAAATGCT-
65 TTAATATTCCACTTTCAT-TTTTATTGAGGGGATTATTCAAGGCATTTTTTGTCAAAAATG-TA
* * * *
1031274 TTGAGTAATCTCCTCTAACTTTTTAGAAGACATTATTGAAGGTATTTTTGGTC-AAAAATATTTT
1 TTAAGTAATCTCCTCTAATTTTTTAGAAGAGATTATTGAAAGTATTTTTGGTCTAAAAATATTTT
* ** * *
1031338 TAATATTCCTCTTTCATTTTTATTGAATGGATTATTGAAGGTATTTTTTTGTCAAAAATGTA
66 TAATATTCCACTTTCATTTTTATTGAGGGGATTATTCAAGGCA-TTTTTTGTCAAAAATGTA
* * * * **
1031400 TTAAGTAATC-CTTTTTAATTTTTTAGAA-AGGATTATTGAAAGTGTTTTTGG-CTAAACATACC
1 TTAAGTAATCTC-CTCTAATTTTTTAGAAGA-GATTATTGAAAGTATTTTTGGTCTAAAAATATT
* *
1031462 TTTAATATTTCACTCTCATTTTTATTGAGGGGATTATT
64 TTTAATATTCCACTTTCATTTTTATTGAGGGGATTATT
1031500 TAACGTAGTT
Statistics
Matches: 185, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
124 4 0.02
125 45 0.24
126 133 0.72
127 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (126 bp):
TTAAGTAATCTCCTCTAATTTTTTAGAAGAGATTATTGAAAGTATTTTTGGTCTAAAAATATTTT
TAATATTCCACTTTCATTTTTATTGAGGGGATTATTCAAGGCATTTTTTGTCAAAAATGTA
Found at i:1033042 original size:25 final size:25
Alignment explanation
Indices: 1032992--1033042 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1032982 TATATTAATA
* *
1032992 TAAAAATTTAAAATATATTTTTTAT
1 TAAAAATTTAAAATATATTATGTAT
* *
1033017 TAAAATTTTAAATTATATTATGTAT
1 TAAAAATTTAAAATATATTATGTAT
1033042 T
1 T
1033043 TTTTCACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TAAAAATTTAAAATATATTATGTAT
Found at i:1042953 original size:16 final size:16
Alignment explanation
Indices: 1042932--1042992 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
1042922 ATTTTTAAAT
* *
1042932 ATAAATGTAAGATTAA
1 ATAAATATAAAATTAA
* *
1042948 ATAAATATAAAAATAT
1 ATAAATATAAAATTAA
1042964 ATAAATATAAAATTAA
1 ATAAATATAAAATTAA
1042980 ATAAATAATAAAA
1 ATAAAT-ATAAAA
1042993 AAATATAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
16 32 0.84
17 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAAATATAAAATTAA
Found at i:1042963 original size:8 final size:8
Alignment explanation
Indices: 1042950--1043001 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
1042940 AAGATTAAAT
1042950 AAATATAA
1 AAATATAA
*
1042958 AAATATAT
1 AAATATAA
1042966 AAATATAA
1 AAATATAA
*
1042974 AATTAAATAA
1 AA--ATATAA
*
1042984 ATAATAAAA
1 A-AATATAA
1042993 AAATATAA
1 AAATATAA
1043001 A
1 A
1043002 TAGAAGGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 23 0.66
9 5 0.14
10 6 0.17
11 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AAATATAA
Found at i:1042968 original size:32 final size:33
Alignment explanation
Indices: 1042928--1043003 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 33
1042918 TATTATTTTT
* *
1042928 AAATATAAATGTAAGATTAAATAAAT-ATAAAA
1 AAATATAAATATAAAATTAAATAAATAATAAAA
*
1042960 ATATATAAATATAAAATTAAATAAATAATAAAA
1 AAATATAAATATAAAATTAAATAAATAATAAAA
1042993 AAATATAAATA
1 AAATATAAATA
1043004 GAAGGTTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 23 0.59
33 16 0.41
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (33 bp):
AAATATAAATATAAAATTAAATAAATAATAAAA
Found at i:1050590 original size:11 final size:11
Alignment explanation
Indices: 1050574--1050599 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1050564 TTTTAAATTG
1050574 TATTATTTTTA
1 TATTATTTTTA
1050585 TATTATTTTTA
1 TATTATTTTTA
1050596 TATT
1 TATT
1050600 GTATTATCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:1055825 original size:19 final size:19
Alignment explanation
Indices: 1055785--1055832 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1055775 ACATTTAGAC
**
1055785 ATAATATGAATAAACATGA
1 ATAATATGAATAAACACAA
*
1055804 ATAATATGAATATACACAA
1 ATAATATGAATAAACACAA
1055823 ATAGATATGA
1 ATA-ATATGA
1055833 TTAATACGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.27
Consensus pattern (19 bp):
ATAATATGAATAAACACAA
Found at i:1055876 original size:29 final size:29
Alignment explanation
Indices: 1055800--1055877 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
1055790 ATGAATAAAC
*
1055800 ATGAATAATATGAATATACACAAATAGAT
1 ATGAATAATATGAATATATACAAATAGAT
* * * *
1055829 ATGATTAATACGGATATATACGAATAGAT
1 ATGAATAATATGAATATATACAAATAGAT
*
1055858 ATGACTAATATGAATATATA
1 ATGAATAATATGAATATATA
1055878 TAAAAATATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (29 bp):
ATGAATAATATGAATATATACAAATAGAT
Found at i:1056477 original size:34 final size:36
Alignment explanation
Indices: 1056427--1056495 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
1056417 AATAAATACG
1056427 AAATATATTTTTTAAAAC-ATATATAATTTTTTTCA
1 AAATATATTTTTTAAAACAATATATAATTTTTTTCA
1056462 AAATAT-TTTTTTAAAACATATATATAATTTTTTT
1 AAATATATTTTTTAAAACA-ATATATAATTTTTTT
1056496 TATATTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 11 0.34
35 6 0.19
36 15 0.47
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (36 bp):
AAATATATTTTTTAAAACAATATATAATTTTTTTCA
Found at i:1057308 original size:14 final size:14
Alignment explanation
Indices: 1057289--1057318 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1057279 TTTGTGAATT
1057289 GGGGAAGGAAAAGA
1 GGGGAAGGAAAAGA
1057303 GGGGAAGGAAAAGA
1 GGGGAAGGAAAAGA
1057317 GG
1 GG
1057319 TCTAGCCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (14 bp):
GGGGAAGGAAAAGA
Found at i:1068756 original size:20 final size:20
Alignment explanation
Indices: 1068731--1068769 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1068721 CTTAATTAAA
1068731 TACCTATGATCAAACAATTT
1 TACCTATGATCAAACAATTT
*
1068751 TACCTATGATCAACCAATT
1 TACCTATGATCAAACAATT
1068770 AATGAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.33
Consensus pattern (20 bp):
TACCTATGATCAAACAATTT
Found at i:1069901 original size:29 final size:29
Alignment explanation
Indices: 1069838--1069905 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1069828 ACGAATAAAT
* * *
1069838 ATGAATA-ATATGAATAGACACGACTAAT
1 ATGAATATATACGAATAGACACAACTAAC
* * *
1069866 ATAAATATATACGAATAGATACAATTAAC
1 ATGAATATATACGAATAGACACAACTAAC
1069895 ATGAATATATA
1 ATGAATATATA
1069906 TAAAAATACA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (29 bp):
ATGAATATATACGAATAGACACAACTAAC
Found at i:1070847 original size:3 final size:3
Alignment explanation
Indices: 1070839--1070865 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1070829 GGGGGCAGCC
1070839 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1070866 TTATGGCAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1075524 original size:17 final size:17
Alignment explanation
Indices: 1075485--1075517 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1075475 TGGATTCCAA
1075485 GGGAAAGTGTGATATCC
1 GGGAAAGTGTGATATCC
*
1075502 GGGAAAGTGTGTTATC
1 GGGAAAGTGTGATATC
1075518 GAGGAAAAGT
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:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (17 bp):
GGGAAAGTGTGATATCC
Found at i:1077807 original size:77 final size:77
Alignment explanation
Indices: 1077680--1077829 Score: 230
Period size: 77 Copynumber: 1.9 Consensus size: 77
1077670 ATTCTGTGAT
* * *
1077680 TCCCAAATTCTTCCCTAAAGTTTCAACTTTTTAGAAATCAAGGGTTCTTTACAAATTAAGGTTTT
1 TCCCAAATTCTTCCCTAAAGGTTCAACCTTTTAGAAATCAAGGATTCTTTACAAATTAAGGTTTT
1077745 GATTTTTCGCAA
66 GATTTTTCGCAA
* * *
1077757 TCCCAAATTCTTCACC-AAAGGTTCAACCTTTTGGAAATCAAGGATTCTTTACAAGTTAGGGTTT
1 TCCCAAATTCTTC-CCTAAAGGTTCAACCTTTTAGAAATCAAGGATTCTTTACAAATTAAGGTTT
1077821 TGATTTTTC
65 TGATTTTTC
1077830 CCAAAATTAG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
77 64 0.97
78 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (77 bp):
TCCCAAATTCTTCCCTAAAGGTTCAACCTTTTAGAAATCAAGGATTCTTTACAAATTAAGGTTTT
GATTTTTCGCAA
Found at i:1087850 original size:1 final size:1
Alignment explanation
Indices: 1087844--1087868 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1087834 TACAAAACTG
1087844 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1087869 GAAGCCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1092903 original size:22 final size:24
Alignment explanation
Indices: 1092859--1092915 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
1092849 ATCTGTACTC
*
1092859 AATTTATAAAATATTATTTATTTT
1 AATTTATAAAATATTATTAATTTT
*
1092883 AATTTA-AAAATTTTA-TAATTTT
1 AATTTATAAAATATTATTAATTTT
*
1092905 ATTTTATAAAA
1 AATTTATAAAA
1092916 AGATTTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.38
23 12 0.41
24 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTTATAAAATATTATTAATTTT
Found at i:1095663 original size:12 final size:12
Alignment explanation
Indices: 1095646--1095687 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1095636 ATTTTTATAT
1095646 TAATATAAATTA
1 TAATATAAATTA
*
1095658 TAATAT-AATTT
1 TAATATAAATTA
*
1095669 TTATATAAATTA
1 TAATATAAATTA
1095681 TTAATAT
1 -TAATAT
1095688 TTTACGAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATATAAATTA
Found at i:1095683 original size:36 final size:36
Alignment explanation
Indices: 1095604--1095687 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 36
1095594 ATACAATCTA
1095604 AAATT-TTAATA-AAATTAAAATATATATTTTATAT
1 AAATTATTAATATAAATTAAAATATATATTTTATAT
*** *
1095638 TTTTATATTAATATAAATTATAATATA-ATTTTTATAT
1 AAAT-TATTAATATAAATTAAAATATATA-TTTTATAT
1095675 AAATTATTAATAT
1 AAATTATTAATAT
1095688 TTTACGAGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
34 1 0.03
35 1 0.03
36 16 0.41
37 21 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AAATTATTAATATAAATTAAAATATATATTTTATAT
Found at i:1097633 original size:7 final size:7
Alignment explanation
Indices: 1097623--1097648 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1097613 AATATTTAAT
1097623 AATTTTA
1 AATTTTA
1097630 AATTTTA
1 AATTTTA
1097637 AATTTTA
1 AATTTTA
1097644 AATTT
1 AATTT
1097649 AAGAGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:1102278 original size:23 final size:23
Alignment explanation
Indices: 1102252--1102295 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1102242 TAATTAAGTT
*
1102252 TATTTAAAATAAATAGATAAATC
1 TATTCAAAATAAATAGATAAATC
* *
1102275 TATTCATAATAAATAGTTAAA
1 TATTCAAAATAAATAGATAAA
1102296 AATATATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (23 bp):
TATTCAAAATAAATAGATAAATC
Found at i:1106010 original size:23 final size:23
Alignment explanation
Indices: 1105984--1106054 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
1105974 AAATAAAGAA
1105984 AGATAATTAAATTTATTCAAAAT
1 AGATAATTAAATTTATTCAAAAT
* *
1106007 AGATAGA-TAAGTCTATTCAAAAT
1 AGATA-ATTAAATTTATTCAAAAT
* * *
1106030 AAATAATTTTAA-TTGTTCAAAAT
1 AGATAA-TTAAATTTATTCAAAAT
1106053 AG
1 AG
1106055 GCAGTTTGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
22 1 0.03
23 33 0.89
24 3 0.08
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (23 bp):
AGATAATTAAATTTATTCAAAAT
Found at i:1114402 original size:113 final size:113
Alignment explanation
Indices: 1114195--1114423 Score: 386
Period size: 113 Copynumber: 2.0 Consensus size: 113
1114185 GTGACCTTAG
*
1114195 ATCAGTACTTGTGTCAGCTTTCAGAATCAGAATACGTCATAAGGTGGCTGTACATGGTTGGTGTC
1 ATCAGTACTTGTGTCAGCTTTCAGAATCAGAATACGTCATAAGGTGGCTATACATGGTTGGTGTC
* *
1114260 CATTTTAAAATTGAAAACTTCATGTCACGGGTCTTTGGATTCATACAA
66 AATTTTAAAATTGAAAACTTCATGCCACGGGTCTTTGGATTCATACAA
****
1114308 ATCAGTACTTGTGTGTTTTTTCAGAATCAGAATACGTCATAAGGTGGCTATACATGGTTGGTGTC
1 ATCAGTACTTGTGTCAGCTTTCAGAATCAGAATACGTCATAAGGTGGCTATACATGGTTGGTGTC
*
1114373 AATTTTAAAATTGAAAACTTTATGCCACGGGTCTTTGGATTCATACAA
66 AATTTTAAAATTGAAAACTTCATGCCACGGGTCTTTGGATTCATACAA
1114421 ATC
1 ATC
1114424 TGATATATTT
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (113 bp):
ATCAGTACTTGTGTCAGCTTTCAGAATCAGAATACGTCATAAGGTGGCTATACATGGTTGGTGTC
AATTTTAAAATTGAAAACTTCATGCCACGGGTCTTTGGATTCATACAA
Found at i:1120353 original size:14 final size:14
Alignment explanation
Indices: 1120334--1120360 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1120324 CAGCTTACTT
1120334 TTTATTTTATTTTC
1 TTTATTTTATTTTC
1120348 TTTATTTTATTTT
1 TTTATTTTATTTT
1120361 TTAATTAAAC
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:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTC
Found at i:1120391 original size:7 final size:8
Alignment explanation
Indices: 1120379--1120414 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
1120369 ACAAAATTAC
1120379 AAAAATG-
1 AAAAATGA
1120386 AAAAATGA
1 AAAAATGA
1120394 AAAAATGA
1 AAAAATGA
1120402 AAAAATGA
1 AAAAATGA
1120410 AAAAA
1 AAAAA
1120415 AAAAACAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:1121294 original size:10 final size:11
Alignment explanation
Indices: 1121276--1121303 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1121266 CGATTCAGGT
1121276 AATTTTTTTAA
1 AATTTTTTTAA
1121287 AATTTTTTTAA
1 AATTTTTTTAA
1121298 AATTTT
1 AATTTT
1121304 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
AATTTTTTTAA
Found at i:1121432 original size:14 final size:14
Alignment explanation
Indices: 1121413--1121453 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1121403 AATAAACTTT
1121413 AATAATAATAAATA
1 AATAATAATAAATA
1121427 AATAATAATAAAATA
1 AATAATAAT-AAATA
*
1121442 AAAAATAA-AAAT
1 AATAATAATAAAT
1121454 GAACTTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 12 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAATAAATA
Found at i:1122358 original size:10 final size:10
Alignment explanation
Indices: 1122343--1122380 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1122333 AAAATTATCT
1122343 TTTTAATAAA
1 TTTTAATAAA
1122353 TTTTAATAAA
1 TTTTAATAAA
1122363 TTTT-A-AAA
1 TTTTAATAAA
*
1122371 TTTTATTAAA
1 TTTTAATAAA
1122381 ACGATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 17 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:1122637 original size:18 final size:20
Alignment explanation
Indices: 1122614--1122651 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1122604 TTTTAATAAG
1122614 AAAAAAGCAA-AAA-AAAAA
1 AAAAAAGCAACAAACAAAAA
*
1122632 AAAAAATCAACAAACAAAAA
1 AAAAAAGCAACAAACAAAAA
1122652 GGAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (20 bp):
AAAAAAGCAACAAACAAAAA
Found at i:1125725 original size:6 final size:6
Alignment explanation
Indices: 1125709--1125808 Score: 87
Period size: 6 Copynumber: 16.3 Consensus size: 6
1125699 TTATTTAAAG
* **
1125709 AAAATA AAAAAA TAAAATA AAAATA AAAATA AGGATA AAAATAA AAAATA
1 AAAATA AAAATA -AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA
* * * *
1125759 AAAATA AAAAT- AAAAT- AAGATA AGAAATA CTAAATA ATAATA ATAATA
1 AAAATA AAAATA AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA
1125807 AA
1 AA
1125809 TGAATAAATA
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
5 9 0.12
6 48 0.62
7 20 0.26
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:1125747 original size:31 final size:31
Alignment explanation
Indices: 1125712--1125771 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
1125702 TTTAAAGAAA
1125712 ATAAAAA-AATAAAATAAAAATAAAAATAAGG
1 ATAAAAATAA-AAAATAAAAATAAAAATAAGG
1125743 ATAAAAATAAAAAATAAAAATAAAAATAA
1 ATAAAAATAAAAAATAAAAATAAAAATAA
1125772 AATAAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (31 bp):
ATAAAAATAAAAAATAAAAATAAAAATAAGG
Found at i:1125761 original size:36 final size:35
Alignment explanation
Indices: 1125709--1125834 Score: 121
Period size: 36 Copynumber: 3.3 Consensus size: 35
1125699 TTATTTAAAG
1125709 AAAATAAAAAAATAAAATAAAAATAAAAATAAGGATA
1 AAAAT-AAAAAATAAAATAAAAATAAAAATAA-GATA
1125746 AAAATAAAAAATAAAAATAAAAAT-AAAATAAGATA
1 AAAATAAAAAAT-AAAATAAAAATAAAAATAAGATA
1125781 AGAAATACTAAATAATAATAATAATAAATGAATAAATAA-ATA
1 A-AAATA--AAA-AATAA-AATAA-AAAT-AA-AAATAAGATA
*
1125823 AATAAGAAAAAA
1 AA-AATAAAAAA
1125835 AATCTTTGGA
Statistics
Matches: 77, Mismatches: 1, Indels: 20
0.79 0.01 0.20
Matches are distributed among these distances:
35 5 0.06
36 19 0.25
37 16 0.21
38 5 0.06
39 10 0.13
40 7 0.09
41 1 0.01
42 8 0.10
43 6 0.08
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (35 bp):
AAAATAAAAAATAAAATAAAAATAAAAATAAGATA
Found at i:1126649 original size:24 final size:24
Alignment explanation
Indices: 1126622--1126713 Score: 113
Period size: 22 Copynumber: 4.0 Consensus size: 24
1126612 TGATAACAAT
1126622 AATAATAATAGATAAATATAAAAA
1 AATAATAATAGATAAATATAAAAA
* *
1126646 AATATTAATAGAT-AA-ATAAATA
1 AATAATAATAGATAAATATAAAAA
1126668 AATAATAATAGATAAATAT-AAAA
1 AATAATAATAGATAAATATAAAAA
*
1126691 AAT-ATATTA-ATAAATAATAAAAA
1 AATAATAATAGATAAAT-ATAAAAA
1126714 TGTATATATA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
21 6 0.10
22 25 0.42
23 14 0.24
24 14 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (24 bp):
AATAATAATAGATAAATATAAAAA
Found at i:1126673 original size:46 final size:47
Alignment explanation
Indices: 1126622--1126788 Score: 173
Period size: 46 Copynumber: 3.5 Consensus size: 47
1126612 TGATAACAAT
1126622 AATAATAATAGATAAATATAAAAAAATATTAATAGATAAATAAA-TA
1 AATAATAATAGATAAATATAAAAAAATATTAATAGATAAATAAAGTA
* *
1126668 AATAATAATAGATAAATATAAAAAATATATTAATAAATAATAAAAATGTA
1 AATAATAATAGATAAATATAAAAAA-ATATTAATAGATAA-ATAAA-GTA
* **
1126718 TATATATTAATAGAT-AA-AT-AAAAAAGGTTAATAGATAAATAATAGTA
1 -A-ATAATAATAGATAAATATAAAAAAATATTAATAGATAAATAA-AGTA
* *
1126765 AATATATAA-AAATAAAAATAAAAA
1 AATA-ATAATAGATAAATATAAAAA
1126789 TAAACAAATG
Statistics
Matches: 101, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
45 6 0.06
46 31 0.31
47 21 0.21
48 20 0.20
49 5 0.05
50 4 0.04
51 3 0.03
52 11 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (47 bp):
AATAATAATAGATAAATATAAAAAAATATTAATAGATAAATAAAGTA
Found at i:1126729 original size:74 final size:74
Alignment explanation
Indices: 1126647--1126789 Score: 191
Period size: 74 Copynumber: 1.9 Consensus size: 74
1126637 ATATAAAAAA
* **
1126647 ATATTAATAGATAAATAAATAAATAATAATAGATAAAT-ATA-AAAAATATATTAATAAATAATA
1 ATATTAATAGATAAATAAA-AAAGAATAATAGATAAATAATAGAAAAATATAAAAATAAA-AATA
1126710 AAAATGTATAT
64 AAAATGTATAT
** *
1126721 ATATTAATAGATAAATAAAAAAGGTTAATAGATAAATAATAGTAAATATATAAAAATAAAAATAA
1 ATATTAATAGATAAATAAAAAAGAATAATAGATAAATAATAG-AAAAATATAAAAATAAAAATAA
1126786 AAAT
65 AAAT
1126790 AAACAAATGG
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
73 15 0.25
74 22 0.37
75 9 0.15
76 14 0.23
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (74 bp):
ATATTAATAGATAAATAAAAAAGAATAATAGATAAATAATAGAAAAATATAAAAATAAAAATAAA
AATGTATAT
Found at i:1144494 original size:12 final size:12
Alignment explanation
Indices: 1144469--1144556 Score: 58
Period size: 12 Copynumber: 7.0 Consensus size: 12
1144459 AATTTTAATT
1144469 AAAA-AAAATCAA
1 AAAATAAAAT-AA
1144481 AAAATAAAAT-A
1 AAAATAAAATAA
1144492 AAAATAAAA-ATA
1 AAAATAAAATA-A
*
1144504 AAGATAAAA-ATA
1 AAAATAAAATA-A
1144516 AAAATAAAATAA
1 AAAATAAAATAA
*
1144528 GAAATACTAAATAA
1 AAAATA--AAATAA
1144542 TAATAATAATAATAA
1 -AA-AATAA-AATAA
1144557 TAATAATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
11 10 0.16
12 30 0.48
13 6 0.10
14 7 0.11
15 6 0.10
16 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:1144545 original size:3 final size:3
Alignment explanation
Indices: 1144483--1144563 Score: 60
Period size: 3 Copynumber: 27.0 Consensus size: 3
1144473 AAAATCAAAA
* * * *
1144483 AAT AA- AAT AAA AAT AAA AAT AA- AGAT AAA AAT AAA AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* *
1144526 AAGA AAT ACT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AA-T AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
1144564 TAAAGAAATA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
2 5 0.08
3 50 0.83
4 5 0.08
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (3 bp):
AAT
Found at i:1144563 original size:6 final size:6
Alignment explanation
Indices: 1144480--1144559 Score: 83
Period size: 6 Copynumber: 13.3 Consensus size: 6
1144470 AAAAAAATCA
*
1144480 AAAAAT -AAAAT AAAAAT AAAAAT AAAGAT AAAAAT AAAAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * *
1144526 AAGAAAT ACTAAAT AATAAT AATAAT AATAAT AA
1 AA-AAAT A-AAAAT AAAAAT AAAAAT AAAAAT AA
1144560 TAATTAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
5 10 0.15
6 45 0.69
7 10 0.15
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (6 bp):
AAAAAT
Done.