Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007841.1 Hibiscus syriacus cultivar Beakdansim tig00110195_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: 1873963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:1101715 original size:2 final size:2
Alignment explanation
Indices: 1101708--1101735 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1101698 GGTACGACCA
1101708 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1101736 GTATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1107425 original size:2 final size:2
Alignment explanation
Indices: 1107386--1107414 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1107376 ATGAAACTAA
1107386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1107415 ATTTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1113116 original size:32 final size:32
Alignment explanation
Indices: 1113075--1113139 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1113065 TTGACGTGAT
1113075 AATTTTTTAAGTTTTTTCAATGATGATATGAC
1 AATTTTTTAAGTTTTTTCAATGATGATATGAC
* *
1113107 AATTTTTTAAGTTTTTTTAATGATGATGTGAC
1 AATTTTTTAAGTTTTTTCAATGATGATATGAC
1113139 A
1 A
1113140 TTATCTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.51
Consensus pattern (32 bp):
AATTTTTTAAGTTTTTTCAATGATGATATGAC
Found at i:1113159 original size:21 final size:22
Alignment explanation
Indices: 1113126--1113170 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1113116 AGTTTTTTTA
** *
1113126 ATGATGATGTGACATTATC-TT
1 ATGATGACATGACAATATCATT
1113147 ATGATGACATGACAATATCATT
1 ATGATGACATGACAATATCATT
1113169 AT
1 AT
1113171 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATGACATGACAATATCATT
Found at i:1116778 original size:16 final size:15
Alignment explanation
Indices: 1116749--1116784 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1116739 TAAAGATCTT
1116749 AATT-TATTTTTATA
1 AATTATATTTTTATA
1116763 AATTATATTGTTTATA
1 AATTATATT-TTTATA
1116779 AATTAT
1 AATTAT
1116785 GAATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.20
15 4 0.20
16 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
AATTATATTTTTATA
Found at i:1127733 original size:30 final size:32
Alignment explanation
Indices: 1127682--1127743 Score: 110
Period size: 30 Copynumber: 2.0 Consensus size: 32
1127672 TATTATTAAA
1127682 ATATTAAGATTATATTTTTATAACAATTTGAC
1 ATATTAAGATTATATTTTTATAACAATTTGAC
1127714 ATATTAAGATTA-A-TTTTATAACAATTTGAC
1 ATATTAAGATTATATTTTTATAACAATTTGAC
1127744 GTTTTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 17 0.57
31 1 0.03
32 12 0.40
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (32 bp):
ATATTAAGATTATATTTTTATAACAATTTGAC
Found at i:1131851 original size:26 final size:26
Alignment explanation
Indices: 1131822--1131879 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
1131812 TTTTTTAACT
1131822 ATTATACGTTATA-AAATAATTTCTCA
1 ATTATACGTTA-AGAAATAATTTCTCA
*
1131848 ATTATATGTTAAGAAATAATTTCTCA
1 ATTATACGTTAAGAAATAATTTCTCA
1131874 ATTATA
1 ATTATA
1131880 GAACGTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (26 bp):
ATTATACGTTAAGAAATAATTTCTCA
Found at i:1138373 original size:9 final size:9
Alignment explanation
Indices: 1138359--1138400 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1138349 CATCAGTTCC
1138359 ACCACCTAA
1 ACCACCTAA
1138368 ACCACC-AA
1 ACCACCTAA
* *
1138376 CCCCGCCTAA
1 -ACCACCTAA
1138386 ACCACCTAA
1 ACCACCTAA
1138395 ACCACC
1 ACCACC
1138401 AACTCCGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.38, C:0.52, G:0.02, T:0.07
Consensus pattern (9 bp):
ACCACCTAA
Found at i:1138412 original size:30 final size:27
Alignment explanation
Indices: 1138359--1138424 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 27
1138349 CATCAGTTCC
*
1138359 ACCACCTAAACCACCAACCCCGCCTAA
1 ACCACCTAAACCACCAACCCCGCCCAA
1138386 ACCACCTAAACCACCAACTCCGCCGCCCAA
1 ACCACCTAAACCACCAA--CC-CCGCCCAA
*
1138416 ACCGCCTAA
1 ACCACCTAA
1138425 TCCGCCTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 17 0.50
29 2 0.06
30 15 0.44
ACGTcount: A:0.35, C:0.52, G:0.06, T:0.08
Consensus pattern (27 bp):
ACCACCTAAACCACCAACCCCGCCCAA
Found at i:1139804 original size:2 final size:2
Alignment explanation
Indices: 1139797--1139826 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1139787 GAGTTTTGAA
1139797 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
1139827 GGGCATGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1140442 original size:9 final size:9
Alignment explanation
Indices: 1140420--1140461 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
1140410 AAAGAAAACT
*
1140420 TAAAAATAA
1 TAAAATTAA
*
1140429 AAAAATTAA
1 TAAAATTAA
1140438 TAAAATTAA
1 TAAAATTAA
1140447 TAAAATTAA
1 TAAAATTAA
1140456 TAAAAT
1 TAAAAT
1140462 GCCCAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAAATTAA
Found at i:1145175 original size:21 final size:21
Alignment explanation
Indices: 1145149--1145193 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1145139 TCACATGGTG
*
1145149 TAATCTAACTAATTAATGATA
1 TAATCTAACTAATTAATAATA
* *
1145170 TAATCTGATTAATTAATAATA
1 TAATCTAACTAATTAATAATA
1145191 TAA
1 TAA
1145194 CTTTTATGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (21 bp):
TAATCTAACTAATTAATAATA
Found at i:1146349 original size:23 final size:23
Alignment explanation
Indices: 1146316--1146362 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1146306 TGATAGGGGA
*
1146316 GTTTGGTACTAGGCCCATATGTC
1 GTTTGGCACTAGGCCCATATGTC
*
1146339 GTTTGGCACTAGGCCTATATGTC
1 GTTTGGCACTAGGCCCATATGTC
1146362 G
1 G
1146363 AACCACATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (23 bp):
GTTTGGCACTAGGCCCATATGTC
Found at i:1149330 original size:6 final size:6
Alignment explanation
Indices: 1149319--1149348 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1149309 CGGTGGAGCT
1149319 TCCTTC TCCTTC TCCTTC TCCTTC -CCTTC T
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC T
1149349 TCCACGTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCCTTC
Found at i:1154316 original size:2 final size:2
Alignment explanation
Indices: 1154309--1154333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1154299 AATTAAAAGC
1154309 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
1154334 GATAAAAACG
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:1156033 original size:2 final size:2
Alignment explanation
Indices: 1156026--1156121 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
1156016 ACCTTAAATC
1156026 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
1156068 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
1156110 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1156122 ATAAAAAGAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1166215 original size:18 final size:21
Alignment explanation
Indices: 1166188--1166234 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1166178 TATCGAAAAT
*
1166188 ATAAAAA-AATAATATTTTAG
1 ATAAAAATAATAATATTTAAG
1166208 ATAAAAATAATAATATTTAAG
1 ATAAAAATAATAATATTTAAG
1166229 ATAAAA
1 ATAAAA
1166235 TTTTATCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (21 bp):
ATAAAAATAATAATATTTAAG
Found at i:1168144 original size:23 final size:23
Alignment explanation
Indices: 1168118--1168163 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1168108 AGAGTTATAT
1168118 TATACATCGAGTGTTTAAAGTTC
1 TATACATCGAGTGTTTAAAGTTC
1168141 TATACATCGAGTGTTTAAAGTTC
1 TATACATCGAGTGTTTAAAGTTC
1168164 ACACAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (23 bp):
TATACATCGAGTGTTTAAAGTTC
Found at i:1170390 original size:32 final size:32
Alignment explanation
Indices: 1170349--1170431 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
1170339 TAAGATTAAT
*
1170349 TGATGATGTGAT-ATATATCACGTCATTTAAAG
1 TGATGATGTG-TCATATATCACATCATTTAAAG
* * *
1170381 TGATGATGTGTCATGTGTCACATCATTTTAAG
1 TGATGATGTGTCATATATCACATCATTTAAAG
1170413 TGATGATGTGTCATTATAT
1 TGATGATGTGTCA-TATAT
1170432 ATGTCACATC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 39 0.91
33 3 0.07
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (32 bp):
TGATGATGTGTCATATATCACATCATTTAAAG
Found at i:1170437 original size:37 final size:34
Alignment explanation
Indices: 1170349--1170443 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 34
1170339 TAAGATTAAT
* *
1170349 TGATGATGTG--ATATATATCACGTCATTTAAAG
1 TGATGATGTGTCATATATGTCACATCATTTAAAG
* *
1170381 TGATGATGTGTC--ATGTGTCACATCATTTTAAG
1 TGATGATGTGTCATATATGTCACATCATTTAAAG
1170413 TGATGATGTGTCATTATATATGTCACATCAT
1 TGATGATGTGTC---ATATATGTCACATCAT
1170444 CAATCAATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
32 38 0.75
37 13 0.25
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (34 bp):
TGATGATGTGTCATATATGTCACATCATTTAAAG
Found at i:1171961 original size:29 final size:29
Alignment explanation
Indices: 1171927--1172014 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
1171917 AATATGTTGC
1171927 GACTCTAGTTGATATCGAGTTTCAGCCAT
1 GACTCTAGTTGATATCGAGTTTCAGCCAT
*
1171956 GACTCTAGTTTATATCGAGTTTCAGCCAT
1 GACTCTAGTTGATATCGAGTTTCAGCCAT
*
1171985 GACTCTAGTTTG-TATCGAGTTTCATCCAT
1 GACTCTAG-TTGATATCGAGTTTCAGCCAT
1172014 G
1 G
1172015 GCTGAAGTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 53 0.96
30 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (29 bp):
GACTCTAGTTGATATCGAGTTTCAGCCAT
Found at i:1181150 original size:3 final size:3
Alignment explanation
Indices: 1181144--1181173 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1181134 AAAAAAGGAA
*
1181144 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1181174 GGGTCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1182487 original size:31 final size:32
Alignment explanation
Indices: 1182399--1182495 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
1182389 TTAGTGATCG
* *
1182399 TTTTATAATAATTTATTAAAATTTAATGATTA
1 TTTTATAATAATTTAATAAAATTTAATTATTA
* *
1182431 TTTTATAACAGA-TAAATAAAATTTAATTATTA
1 TTTTATAATA-ATTTAATAAAATTTAATTATTA
* *
1182463 TTTTATAGTAATTTAAT-AAATTTAATTACTA
1 TTTTATAATAATTTAATAAAATTTAATTATTA
1182494 TT
1 TT
1182496 ATAATATCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 16 0.29
32 38 0.69
33 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (32 bp):
TTTTATAATAATTTAATAAAATTTAATTATTA
Found at i:1182930 original size:11 final size:11
Alignment explanation
Indices: 1182899--1182974 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
1182889 TTAATTTTGT
1182899 AAATTA-AAAA
1 AAATTACAAAA
*
1182909 AAA-T-CAGAA
1 AAATTACAAAA
1182918 AAATTACAAAA
1 AAATTACAAAA
1182929 AAA-T-CAAAA
1 AAATTACAAAA
1182938 AAATTACAAAA
1 AAATTACAAAA
1182949 AAA-T-CAAAA
1 AAATTACAAAA
1182958 AAATTACAAAA
1 AAATTACAAAA
1182969 AAATTA
1 AAATTA
1182975 GTATGATTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
9 23 0.40
10 8 0.14
11 26 0.46
ACGTcount: A:0.74, C:0.08, G:0.01, T:0.17
Consensus pattern (11 bp):
AAATTACAAAA
Found at i:1182930 original size:20 final size:20
Alignment explanation
Indices: 1182899--1182972 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
1182889 TTAATTTTGT
*
1182899 AAATTA-AAAAAAATCAGAA
1 AAATTACAAAAAAATCAAAA
1182918 AAATTACAAAAAAATCAAAA
1 AAATTACAAAAAAATCAAAA
1182938 AAATTACAAAAAAATCAAAA
1 AAATTACAAAAAAATCAAAA
1182958 AAATTACAAAAAAAT
1 AAATTACAAAAAAAT
1182973 TAGTATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 6 0.11
20 47 0.89
ACGTcount: A:0.74, C:0.08, G:0.01, T:0.16
Consensus pattern (20 bp):
AAATTACAAAAAAATCAAAA
Found at i:1185761 original size:2 final size:2
Alignment explanation
Indices: 1185754--1185778 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1185744 TTTTATGTTA
1185754 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1185779 TTGTTGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1195244 original size:20 final size:20
Alignment explanation
Indices: 1195219--1195265 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1195209 GGTCAAATTT
1195219 TATTATTAGTCCTTATATTA
1 TATTATTAGTCCTTATATTA
*
1195239 TATTATTAGTTCTTATATTA
1 TATTATTAGTCCTTATATTA
1195259 TACTTAT
1 TA-TTAT
1195266 GTTATGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (20 bp):
TATTATTAGTCCTTATATTA
Found at i:1217748 original size:35 final size:34
Alignment explanation
Indices: 1217679--1217790 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
1217669 AAAACAATCC
*
1217679 TCAATTTCATTCT-AACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
1217713 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
1217748 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
1217783 TCAATTTC
1 TCAATTTC
1217791 TGTCTTTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
34 14 0.20
35 50 0.71
36 6 0.09
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1218890 original size:35 final size:34
Alignment explanation
Indices: 1218842--1218953 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
1218832 ATTCCTCCTT
* *
1218842 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
* *
1218877 TAATTGAATTATTTTGGAATTTAGGGTTTATAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
1218912 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
1218947 AAATTGA
1 AAATTGA
1218954 GGAATGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 65 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:1233742 original size:21 final size:22
Alignment explanation
Indices: 1233717--1233759 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1233707 TGTTTTCTAT
*
1233717 TTTCACCC-CTAAAATCTTATA
1 TTTCACCCTCTAAAATATTATA
*
1233738 TTTCACCCTTTAAAATATTATA
1 TTTCACCCTCTAAAATATTATA
1233760 AACTTGGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTCACCCTCTAAAATATTATA
Found at i:1238700 original size:31 final size:31
Alignment explanation
Indices: 1238654--1238737 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
1238644 AAATCAAATA
*
1238654 TTATAA-AATAAAATTTTAAAATTATTTTAT
1 TTATAATATTAAAATTTTAAAATTATTTTAT
* *
1238684 TTATAATATTAAAATTTTTAATTTATTTTAT
1 TTATAATATTAAAATTTTAAAATTATTTTAT
1238715 TTATAATATTAAAA-TTTAAAATT
1 TTATAATATTAAAATTTTAAAATT
1238738 TAAATTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 13 0.27
31 35 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTATAATATTAAAATTTTAAAATTATTTTAT
Found at i:1248548 original size:6 final size:6
Alignment explanation
Indices: 1248537--1248572 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1248527 TGGTCATATT
1248537 ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA
1 ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA
1248573 GATCATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
ATAGAA
Found at i:1256616 original size:11 final size:11
Alignment explanation
Indices: 1256594--1256632 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1256584 TCAAGTCATC
*
1256594 AAAAAAATATT
1 AAAAAAAAATT
*
1256605 AATAAAAAATT
1 AAAAAAAAATT
1256616 AAAAAAAAAATT
1 -AAAAAAAAATT
1256628 AAAAA
1 AAAAA
1256633 TTACTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAAAAATT
Found at i:1256623 original size:12 final size:12
Alignment explanation
Indices: 1256594--1256632 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1256584 TCAAGTCATC
*
1256594 AAAAAAATATT-
1 AAAAAAAAATTA
*
1256605 AATAAAAAATTA
1 AAAAAAAAATTA
1256617 AAAAAAAAATTA
1 AAAAAAAAATTA
1256629 AAAA
1 AAAA
1256633 TTACTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:1257234 original size:11 final size:11
Alignment explanation
Indices: 1257218--1257242 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1257208 TGCCATTACC
1257218 AATAAACAAAA
1 AATAAACAAAA
1257229 AATAAACAAAA
1 AATAAACAAAA
1257240 AAT
1 AAT
1257243 TAATCGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (11 bp):
AATAAACAAAA
Found at i:1260436 original size:2 final size:2
Alignment explanation
Indices: 1260429--1260473 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1260419 AGTCAATGCA
1260429 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
1260471 AT A
1 AT A
1260474 CACACACAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1260680 original size:17 final size:17
Alignment explanation
Indices: 1260658--1260692 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1260648 TCATTTTTCA
1260658 GATACCCATTACTGCTT
1 GATACCCATTACTGCTT
1260675 GATACCCATTACTGCTT
1 GATACCCATTACTGCTT
1260692 G
1 G
1260693 TACAAAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (17 bp):
GATACCCATTACTGCTT
Found at i:1265337 original size:28 final size:29
Alignment explanation
Indices: 1265292--1265346 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
1265282 AAGCATGTAT
*
1265292 AAAATTTAAACCAATAATTAA-AGATATTA
1 AAAAATTAAACCAATAA-TAAGAGATATTA
*
1265321 AAAAATTAAA-CATTAATAAGAGATAT
1 AAAAATTAAACCAATAATAAGAGATAT
1265347 GTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 11 0.48
29 9 0.39
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAAATTAAACCAATAATAAGAGATATTA
Found at i:1273970 original size:12 final size:12
Alignment explanation
Indices: 1273953--1273977 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1273943 ATTCTTTTTG
1273953 TTTAAATTTATT
1 TTTAAATTTATT
1273965 TTTAAATTTATT
1 TTTAAATTTATT
1273977 T
1 T
1273978 ATTTATTTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:1274000 original size:20 final size:19
Alignment explanation
Indices: 1273953--1274001 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1273943 ATTCTTTTTG
* *
1273953 TTTAAATTTATTTTTAAAT
1 TTTATATTTATTTTAAAAT
*
1273972 TTATTTATTTATTTTAAAACT
1 TT-TATATTTATTTTAAAA-T
1273993 TTTATATTT
1 TTTATATTT
1274002 TGAACGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATTTATTTTAAAAT
Found at i:1274918 original size:24 final size:23
Alignment explanation
Indices: 1274865--1274919 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1274855 GGTGTTCGCG
* *
1274865 TTCGTTTAATGTTCGCGAACATG
1 TTCGTTTAATGTTCGCAAACATA
*
1274888 TTCGTTTATATGTTCGCAAACGTA
1 TTCGTTTA-ATGTTCGCAAACATA
*
1274912 TTTGTTTA
1 TTCGTTTA
1274920 GGATTCGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (23 bp):
TTCGTTTAATGTTCGCAAACATA
Found at i:1288936 original size:20 final size:20
Alignment explanation
Indices: 1288913--1288978 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1288903 ATCTCCAGCA
1288913 TCGCAAATCAGTTTCTGGAT
1 TCGCAAATCAGTTTCTGGAT
** *
1288933 TCGCAACGC-GATTCT-GACT
1 TCGCAAATCAGTTTCTGGA-T
1288952 ATCGCAAATCAGTTTCTGGAT
1 -TCGCAAATCAGTTTCTGGAT
1288973 TCGCAA
1 TCGCAA
1288979 CGCGATTCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.06
19 6 0.17
20 20 0.56
21 6 0.17
22 2 0.06
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (20 bp):
TCGCAAATCAGTTTCTGGAT
Found at i:1288938 original size:40 final size:40
Alignment explanation
Indices: 1288892--1288998 Score: 164
Period size: 40 Copynumber: 2.7 Consensus size: 40
1288882 CGATCGCCAT
1288892 TTCGCAACGCGATCTCCAG-C-ATCGCAAATCAGTTTCTGGA
1 TTCGCAACGCGAT-T-CAGACTATCGCAAATCAGTTTCTGGA
*
1288932 TTCGCAACGCGATTCTGACTATCGCAAATCAGTTTCTGGA
1 TTCGCAACGCGATTCAGACTATCGCAAATCAGTTTCTGGA
*
1288972 TTCGCAACGCGATTCTGACTATCGCAA
1 TTCGCAACGCGATTCAGACTATCGCAA
1288999 TGCGATTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 60 0.94
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (40 bp):
TTCGCAACGCGATTCAGACTATCGCAAATCAGTTTCTGGA
Found at i:1288996 original size:20 final size:20
Alignment explanation
Indices: 1288933--1289005 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1288923 GTTTCTGGAT
1288933 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
1288953 TCGCAAATCAGTTTCTGGA-T-
1 TCGCAACGC-GATTCT-GACTA
1288973 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
1288993 TCGCAATGCGATT
1 TCGCAACGCGATT
1289006 TTTCGGATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.05
19 6 0.14
20 26 0.62
21 6 0.14
22 2 0.05
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1289026 original size:41 final size:40
Alignment explanation
Indices: 1288912--1288998 Score: 174
Period size: 40 Copynumber: 2.2 Consensus size: 40
1288902 GATCTCCAGC
1288912 ATCGCAAATCAGTTTCTGGATTCGCAACGCGATTCTGACT
1 ATCGCAAATCAGTTTCTGGATTCGCAACGCGATTCTGACT
1288952 ATCGCAAATCAGTTTCTGGATTCGCAACGCGATTCTGACT
1 ATCGCAAATCAGTTTCTGGATTCGCAACGCGATTCTGACT
1288992 ATCGCAA
1 ATCGCAA
1288999 TGCGATTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
ATCGCAAATCAGTTTCTGGATTCGCAACGCGATTCTGACT
Found at i:1290662 original size:14 final size:14
Alignment explanation
Indices: 1290643--1290672 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1290633 GCATTTGACT
1290643 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
1290657 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1290671 AT
1 AT
1290673 GACTATCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1290682 original size:20 final size:20
Alignment explanation
Indices: 1290657--1290745 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
1290647 CAACGAGAAA
1290657 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1290677 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*** *
1290697 ATCGCAATAAGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1290717 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
1290737 ATCGCAACG
1 ATCGCAACG
1290746 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1290832 original size:14 final size:14
Alignment explanation
Indices: 1290813--1290865 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1290803 TATTTTCGCA
1290813 TTGCGATTATCTCG
1 TTGCGATTATCTCG
*
1290827 TTGCGATTTCATTTCG
1 TTGCGA-TT-ATCTCG
*
1290843 CATTGCGATTCTCTCG
1 --TTGCGATTATCTCG
1290859 TTGCGAT
1 TTGCGAT
1290866 AGTCATTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 13 0.41
15 2 0.06
16 9 0.28
17 2 0.06
18 6 0.19
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (14 bp):
TTGCGATTATCTCG
Found at i:1290847 original size:32 final size:32
Alignment explanation
Indices: 1290792--1290874 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 32
1290782 AACTAATTCA
*
1290792 CGTTGCGATTTTATTTTCGCATTGCGATTATCT
1 CGTTGCGATTTCA-TTTCGCATTGCGATTATCT
*
1290825 CGTTGCGATTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTCATTTCGCATTGCGATTATCT
*
1290857 CGTTGCGATAGTCATTTC
1 CGTTGCGAT-TTCATTTC
1290875 CGCGTTACGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 27 0.59
33 19 0.41
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (32 bp):
CGTTGCGATTTCATTTCGCATTGCGATTATCT
Found at i:1292444 original size:21 final size:21
Alignment explanation
Indices: 1292420--1292493 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
1292410 GTGAGAGGGA
1292420 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGTGG
* * **
1292441 CCTCTTGAACGGTGGGAG-GG
1 CCTCTTCAACGATGACAGTGG
1292461 ACCTCTTCAACGATGACAGTGG
1 -CCTCTTCAACGATGACAGTGG
*
1292483 CCTCTTGAACG
1 CCTCTTCAACG
1292494 GTGGGAGGGG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:1292473 original size:42 final size:42
Alignment explanation
Indices: 1292400--1292544 Score: 184
Period size: 42 Copynumber: 3.5 Consensus size: 42
1292390 GTGAATCGGG
* * *
1292400 CTCTGGAATGGTGAGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1292442 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
* ** * *
1292484 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
* *
1292526 CTCTTGAACGATTGGAGGG
1 CTCTTGAACGGTGGGAGGG
1292545 GACTCTTGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
41 3 0.03
42 85 0.92
43 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
Found at i:1292508 original size:21 final size:21
Alignment explanation
Indices: 1292442--1292553 Score: 84
Period size: 21 Copynumber: 5.3 Consensus size: 21
1292432 TGACAGTGGC
1292442 CTCTTGAACGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1292462 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1292484 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
1292505 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGA
* *
1292526 CTCTTGAACGATTGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1292547 CTCTTGA
1 CTCTTGA
1292554 GGGATGACAG
Statistics
Matches: 66, Mismatches: 22, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
20 3 0.05
21 59 0.89
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1292545 original size:42 final size:42
Alignment explanation
Indices: 1292430--1292563 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
1292420 CCTCTTCAAC
* **
1292430 GATGACAGTGGCCTCTTGAACGGTGGGA-GGGACCTCTTCAAC
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGA-CTCTTGAGG
1292472 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
* * * *
1292514 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1292556 GATGACAG
1 GATGACAG
1292564 GTGAGTCGGG
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 79 0.95
43 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
Found at i:1292941 original size:20 final size:20
Alignment explanation
Indices: 1292916--1292984 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1292906 GAAACTTAAA
*
1292916 ATCGCAACGCCAAAAAGACT
1 ATCGCAACGCGAAAAAGACT
* *
1292936 ATCGCAACGCGAAAAGGGCT
1 ATCGCAACGCGAAAAAGACT
***
1292956 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAAAGACT
1292976 ATCGCAACG
1 ATCGCAACG
1292985 AGACAATCGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAAAGACT
Found at i:1293018 original size:33 final size:34
Alignment explanation
Indices: 1292956--1293049 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
1292946 GAAAAGGGCT
** ** *
1292956 ATCGCAACGCGAATTTGACTATCGCAACGAGACA
1 ATCGCAACGCGAAAATGAAAATCGCAACGAGAAA
*
1292990 ATCGCAATGCG-AAATGAAAATCGCAACGAGAAA
1 ATCGCAACGCGAAAATGAAAATCGCAACGAGAAA
1293023 ATCGCAACGCGAAAATGAAAATCGCAA
1 ATCGCAACGCGAAAATGAAAATCGCAA
1293050 TGCGAAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAAAATCGCAACGAGAAA
Found at i:1293042 original size:20 final size:19
Alignment explanation
Indices: 1292989--1293057 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
1292979 GCAACGAGAC
1292989 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1293008 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
*
1293022 AATCGCAACGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
1293042 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1293058 TAGTTTCGCG
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 13 0.30
20 14 0.33
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1293056 original size:14 final size:14
Alignment explanation
Indices: 1292976--1293038 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 14
1292966 GAATTTGACT
*
1292976 ATCGCAACGAGACA
1 ATCGCAACGAGAAA
1292990 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1293009 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
1293023 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1293037 AT
1 AT
1293039 GAAAATCGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 26 0.62
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1293083 original size:19 final size:19
Alignment explanation
Indices: 1293061--1293097 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1293051 GCGAAATTAG
*
1293061 TTTCGCGTTGCGATTCTCA
1 TTTCGCATTGCGATTCTCA
1293080 TTTCGCATTGCGATTCTC
1 TTTCGCATTGCGATTCTC
1293098 TCGTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.27, G:0.19, T:0.43
Consensus pattern (19 bp):
TTTCGCATTGCGATTCTCA
Found at i:1293124 original size:20 final size:20
Alignment explanation
Indices: 1293099--1293166 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1293089 GCGATTCTCT
1293099 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
1293119 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGTCATTTTCG
*
1293139 CGTTGCGATAGTCAGTTT-G
1 CGTTGCGATAGTCATTTTCG
*
1293158 CATTGCGAT
1 CGTTGCGAT
1293167 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 8 0.19
20 34 0.81
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1293326 original size:22 final size:22
Alignment explanation
Indices: 1293301--1293358 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
1293291 TAGACCAAAA
1293301 CTAATCAGCATTCAAACGATTT
1 CTAATCAGCATTCAAACGATTT
*
1293323 CTAATCAACATTCAAACGATTT
1 CTAATCAGCATTCAAACGATTT
1293345 CTAATCAGCATTCA
1 CTAATCAGCATTCA
1293359 GACAAATTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (22 bp):
CTAATCAGCATTCAAACGATTT
Found at i:1293372 original size:22 final size:22
Alignment explanation
Indices: 1293325--1293439 Score: 106
Period size: 22 Copynumber: 5.3 Consensus size: 22
1293315 AACGATTTCT
* * * *
1293325 AATCAACATTCAAACGATTTCT
1 AATCAACATTCAGACCAATTCC
* *
1293347 AATCAGCATTCAGACAAATTCC
1 AATCAACATTCAGACCAATTCC
*
1293369 AATCAACATTCAGACCAAGTCC
1 AATCAACATTCAGACCAATTCC
* * *
1293391 ATTCAACACTCAGACCAAGTCC
1 AATCAACATTCAGACCAATTCC
* * *
1293413 AGTCAGCATTCATACCAA-TCC
1 AATCAACATTCAGACCAATTCC
1293434 AATCAA
1 AATCAA
1293440 TAGTAAAGCC
Statistics
Matches: 77, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
21 7 0.09
22 70 0.91
ACGTcount: A:0.40, C:0.30, G:0.08, T:0.23
Consensus pattern (22 bp):
AATCAACATTCAGACCAATTCC
Found at i:1293690 original size:21 final size:21
Alignment explanation
Indices: 1293665--1293712 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1293655 TAGAAAGGCT
1293665 ACCTCACCAAATAAAGTAGAC
1 ACCTCACCAAATAAAGTAGAC
**
1293686 ACCTCACCACGTAAAGTAGAC
1 ACCTCACCAAATAAAGTAGAC
1293707 ACCTCA
1 ACCTCA
1293713 ACACGCCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.33, G:0.10, T:0.15
Consensus pattern (21 bp):
ACCTCACCAAATAAAGTAGAC
Found at i:1293717 original size:21 final size:21
Alignment explanation
Indices: 1293676--1293717 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1293666 CCTCACCAAA
*
1293676 TAAAGTAGACACCTCACCACG
1 TAAAGTAGACACCTCAACACG
1293697 TAAAGTAGACACCTCAACACG
1 TAAAGTAGACACCTCAACACG
1293718 CCATGCACCA
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:0.40, C:0.31, G:0.14, T:0.14
Consensus pattern (21 bp):
TAAAGTAGACACCTCAACACG
Found at i:1293969 original size:18 final size:18
Alignment explanation
Indices: 1293946--1293993 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1293936 CGGGTCGATC
1293946 AGGTGATTGCTCTGGGTG
1 AGGTGATTGCTCTGGGTG
1293964 AGGTGA-TGACTCTGGGTG
1 AGGTGATTG-CTCTGGGTG
*
1293982 AGGTGATGGCTC
1 AGGTGATTGCTC
1293994 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 24 0.89
19 1 0.04
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (18 bp):
AGGTGATTGCTCTGGGTG
Found at i:1295368 original size:14 final size:14
Alignment explanation
Indices: 1295349--1295433 Score: 64
Period size: 14 Copynumber: 5.5 Consensus size: 14
1295339 GAAAATGCCT
1295349 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
1295363 ATCGCAATACGAATTAAA
1 ATCGC-A-ACG-A-GAGA
1295381 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1295395 ATCGCAATGCGA-ATTGAA
1 ATCGCAA--CGAGA--G-A
1295413 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1295427 ATCGCAA
1 ATCGCAA
1295434 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
14 22 0.39
15 4 0.07
16 12 0.21
17 4 0.07
18 15 0.26
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1295417 original size:18 final size:17
Alignment explanation
Indices: 1295362--1295419 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
1295352 GCAACGAGAG
*
1295362 AATCGCAATACGAATTAA
1 AATCGCAAT-CGAATTGA
1295380 AATCGCAA-CG-A--GA
1 AATCGCAATCGAATTGA
1295393 GAATCGCAATGCGAATTGA
1 -AATCGCAAT-CGAATTGA
1295412 AATCGCAA
1 AATCGCAA
1295420 CGAGAGAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
13 1 0.03
14 8 0.24
15 1 0.03
16 4 0.12
17 1 0.03
18 16 0.48
19 2 0.06
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (17 bp):
AATCGCAATCGAATTGA
Found at i:1295435 original size:32 final size:32
Alignment explanation
Indices: 1295349--1295438 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
1295339 GAAAATGCCT
*
1295349 ATCGCAACGAGAGAATCGCAATACGAATTAAA
1 ATCGCAACGAGAGAATCGCAATGCGAATTAAA
*
1295381 ATCGCAACGAGAGAATCGCAATGCGAATTGAA
1 ATCGCAACGAGAGAATCGCAATGCGAATTAAA
1295413 ATCGCAACGAGAGAATCGCAATGCGA
1 ATCGCAACGAGAGAATCGCAATGCGA
1295439 TTTTGTTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (32 bp):
ATCGCAACGAGAGAATCGCAATGCGAATTAAA
Found at i:1295466 original size:14 final size:14
Alignment explanation
Indices: 1295444--1295473 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1295434 TGCGATTTTG
1295444 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
1295458 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
1295472 TT
1 TT
1295474 CAATTCGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.23, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:1295481 original size:32 final size:33
Alignment explanation
Indices: 1295445--1295523 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
1295435 GCGATTTTGT
* *
1295445 TTCGCGTTGCGATTTTCTCGTTGCGAT-TTCAA
1 TTCGCGTTGCGATTCTCTCGTTGCGATATCCAA
*
1295477 TTCGCATTGCGATTCTCTCGTTGCGATAGTCCAA
1 TTCGCGTTGCGATTCTCTCGTTGCGATA-TCCAA
1295511 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1295524 ATTCATTTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 25 0.61
34 16 0.39
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.39
Consensus pattern (33 bp):
TTCGCGTTGCGATTCTCTCGTTGCGATATCCAA
Found at i:1295520 original size:20 final size:19
Alignment explanation
Indices: 1295495--1295582 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 19
1295485 GCGATTCTCT
*
1295495 CGTTGCGATAGTCCAATTCG
1 CGTTGCGATA-TCCATTTCG
*
1295515 CGTTGCGATATTCATTTCCG
1 CGTTGCGATATCCATTT-CG
*
1295535 CGTTGCGATAGT-CATTTTCT
1 CGTTGCGATA-TCCA-TTTCG
1295555 CGTTGCGAT-TCTCATTTCG
1 CGTTGCGATATC-CATTTCG
1295574 CGTTGCGAT
1 CGTTGCGAT
1295583 TCTCGGCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
18 1 0.02
19 18 0.31
20 36 0.61
21 4 0.07
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.39
Consensus pattern (19 bp):
CGTTGCGATATCCATTTCG
Found at i:1295559 original size:40 final size:39
Alignment explanation
Indices: 1295495--1295582 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 39
1295485 GCGATTCTCT
1295495 CGTTGCGATAGTCCAATTCGCGTTGCGATAT-TCATTTCCG
1 CGTTGCGATAGTCCAATTCGCGTTGCGAT-TCTCATTT-CG
* *
1295535 CGTTGCGATAGT-CATTTTCTCGTTGCGATTCTCATTTCG
1 CGTTGCGATAGTCCA-ATTCGCGTTGCGATTCTCATTTCG
1295574 CGTTGCGAT
1 CGTTGCGAT
1295583 TCTCGGCTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
39 14 0.32
40 30 0.68
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.39
Consensus pattern (39 bp):
CGTTGCGATAGTCCAATTCGCGTTGCGATTCTCATTTCG
Found at i:1295938 original size:22 final size:22
Alignment explanation
Indices: 1295911--1295968 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1295901 GATGGAGATA
1295911 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
**
1295933 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1295955 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1295969 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1296173 original size:20 final size:20
Alignment explanation
Indices: 1296148--1296221 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1296138 CGCTTTGAAA
*
1296148 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1296168 ATCGCGTTGCGATTTTGT-AGT
1 ATCGCGTTGCGA--TAGTCAGT
*
1296189 ATCGCGTTGCGATAGTCTGT
1 ATCGCGTTGCGATAGTCAGT
1296209 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
1296222 TTTCCAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.06
20 27 0.57
21 15 0.32
22 2 0.04
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1296191 original size:21 final size:21
Alignment explanation
Indices: 1296148--1296244 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
1296138 CGCTTTGAAA
***
1296148 ATCGCGTTGCGAAAGTC-AGT
1 ATCGCGTTGCGATTTTCTAGT
*
1296168 ATCGCGTTGCGATTTTGTAGT
1 ATCGCGTTGCGATTTTCTAGT
**
1296189 ATCGCGTTGCGATAGTCT-GT
1 ATCGCGTTGCGATTTTCTAGT
* *
1296209 ATCGCGTTGCGATTTTCCA-A
1 ATCGCGTTGCGATTTTCTAGT
1296229 ATTCGCGTTGCGATTT
1 A-TCGCGTTGCGATTT
1296245 ACGTATTCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
20 31 0.49
21 32 0.51
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCTAGT
Found at i:1296235 original size:41 final size:41
Alignment explanation
Indices: 1296148--1296242 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
1296138 CGCTTTGAAA
* ** *
1296148 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAGT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCAAAT
*
1296189 ATCGCGTTGCGATAGTCTGTATCGCGTTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAAT
1296231 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1296243 TTACGTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCAAAT
Found at i:1296254 original size:20 final size:19
Alignment explanation
Indices: 1296169--1296261 Score: 71
Period size: 20 Copynumber: 4.6 Consensus size: 19
1296159 AAAGTCAGTA
*
1296169 TCGCGTTGCGATTTTGTAGT
1 TCGCGTTGCGATTTCGTA-T
*
1296189 ATCGCGTTGCGATAGTCTGTA-
1 -TCGCGTTGCGAT-TTC-GTAT
**
1296210 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGA-TTT-CGTAT
1296231 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTT-CGTAT
*
1296251 TCGCATTGCGA
1 TCGCGTTGCGA
1296262 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
20 29 0.50
21 25 0.43
22 1 0.02
23 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (19 bp):
TCGCGTTGCGATTTCGTAT
Found at i:1296303 original size:21 final size:21
Alignment explanation
Indices: 1296254--1296303 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1296244 TACGTATTCG
** *
1296254 CATTGCGAATTGGGAAAATCG
1 CATTGCGAATCCGGAAAATCA
**
1296275 CAACGCGAATCCGGAAAATCA
1 CATTGCGAATCCGGAAAATCA
1296296 CATTGCGA
1 CATTGCGA
1296304 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (21 bp):
CATTGCGAATCCGGAAAATCA
Found at i:1296847 original size:60 final size:59
Alignment explanation
Indices: 1296782--1296894 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
1296772 CAGATGGTTC
* * * * *
1296782 TCGATTATAATATGTTATTTTATTAAATTTATTGATTATTAAAAGTTATAAAATAATATA
1 TCGATTATAAGATGTTATTTTATT-AAGTCATTGACTATTAAAAGTTACAAAATAATATA
* * *
1296842 TCGATTATAAGATGTTGTTTTGTTGAGTCATTGACTATTAAAAGTTACAAAAT
1 TCGATTATAAGATGTTATTTTATTAAGTCATTGACTATTAAAAGTTACAAAAT
1296895 GATCATCCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 24 0.53
60 21 0.47
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (59 bp):
TCGATTATAAGATGTTATTTTATTAAGTCATTGACTATTAAAAGTTACAAAATAATATA
Found at i:1301115 original size:44 final size:42
Alignment explanation
Indices: 1301057--1301142 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 42
1301047 AGGTGTGTTA
* *
1301057 TAAGCTTTGTATGTTTTGTAAGTTGGGTTATGTTGTCTATGTGT
1 TAAGCTCTGTATGTTTTGTAAATTGGGTTATG-T-TCTATGTGT
1301101 TAAGCTCTGTATGTTTTGTAAATTGGGTTATGTTCTATGTGT
1 TAAGCTCTGTATGTTTTGTAAATTGGGTTATGTTCTATGTGT
1301143 AACTTTGCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 9 0.22
43 1 0.03
44 30 0.75
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (42 bp):
TAAGCTCTGTATGTTTTGTAAATTGGGTTATGTTCTATGTGT
Found at i:1315689 original size:20 final size:20
Alignment explanation
Indices: 1315664--1315702 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1315654 ATGAAAGTTT
1315664 ATTGTAGATTGTTTATTAGA
1 ATTGTAGATTGTTTATTAGA
*
1315684 ATTGTAGGTTGTTTATTAG
1 ATTGTAGATTGTTTATTAG
1315703 GTTCTTTTTA
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:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (20 bp):
ATTGTAGATTGTTTATTAGA
Found at i:1322940 original size:72 final size:72
Alignment explanation
Indices: 1322822--1323043 Score: 313
Period size: 72 Copynumber: 3.1 Consensus size: 72
1322812 CAATTTCCTG
** *
1322822 AGGGATGGAACCTTCAAGTTGGTTATCATAAAGGTAC-AAATATTGCAAATTGGTTAATTGACCC
1 AGGGATGGAACCTTCAAGTTGGTTATCAGCAAGGTTCAAAAT-TTGCAAATTGGTTAATTGACCC
1322886 AAAGCAGA
65 AAAGCAGA
*
1322894 AGGGATGGAACCTTCAAGTTGGTTATAAGCAAGGTTCAAAATTTGCAAATTGGTTAATTGACCCA
1 AGGGATGGAACCTTCAAGTTGGTTATCAGCAAGGTTCAAAATTTGCAAATTGGTTAATTGACCCA
1322959 AAGCAGA
66 AAGCAGA
* * * ** * *
1322966 AGGGATGGATCCATT-AATTTGGTTACCAGCAAGACTCAAAGTTCGCAAATTGGTTAATTGACCC
1 AGGGATGGAACC-TTCAAGTTGGTTATCAGCAAGGTTCAAAATTTGCAAATTGGTTAATTGACCC
1323030 AAAGCAGA
65 AAAGCAGA
1323038 AGGGAT
1 AGGGAT
1323044 AGGACCATGA
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
72 130 0.96
73 6 0.04
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (72 bp):
AGGGATGGAACCTTCAAGTTGGTTATCAGCAAGGTTCAAAATTTGCAAATTGGTTAATTGACCCA
AAGCAGA
Found at i:1324659 original size:82 final size:81
Alignment explanation
Indices: 1324489--1324810 Score: 211
Period size: 82 Copynumber: 4.0 Consensus size: 81
1324479 CATAAATTAA
* * * * * * * *
1324489 ATACAAATTATTGATACTATTCAAAAGTGTCAAGTTTTCCATAAATAGGAAGAA-CTATGAATTA
1 ATACAAATCATTGAAACTATTCAAAAGTATCAA-ATTTCTATAAATCGAAAGAATC-ATAAATTA
* *
1324553 GTTTGATGACTAATT-ATAT
64 -ATTGATGA-TTATTCATAT
* * *
1324572 TTACAAGTCATTGAAACTATTCCAAAGTATCAAATTTCTATAAATCGAAAGAATCATAAATTAAT
1 ATACAAATCATTGAAACTATTCAAAAGTATCAAATTTCTATAAATCGAAAGAATCATAAATTAAT
1324637 ATGATGATTATTCATAT
66 -TGATGATTATTCATAT
* * * * * ** **
1324654 ATACAAATTATT-AAGACTATTAAAAAATGT-TAATTT-T-T---TC--ATTAAT--TAAAAGAA
1 ATACAAATCATTGAA-ACTATTCAAAAGTATCAAATTTCTATAAATCGAAAGAATCATAAATTAA
1324708 CCTTGATGATTATTCATAT
65 --TTGATGATTATTCATAT
* * ** * *
1324727 ATACAAATCATTGATACTATTCAAAAGTATCAAATTTTTACGAATTGAGAGAATCATAAATTAAT
1 ATACAAATCATTGAAACTATTCAAAAGTATCAAATTTCTATAAATCGAAAGAATCATAAATTAAT
*
1324792 GTGATGATTATTTATAT
66 -TGATGATTATTCATAT
1324809 AT
1 AT
1324811 GAGTCTTTAA
Statistics
Matches: 182, Mismatches: 39, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
72 6 0.03
73 39 0.21
74 11 0.06
75 1 0.01
76 2 0.01
79 2 0.01
80 1 0.01
81 16 0.09
82 70 0.38
83 34 0.19
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (81 bp):
ATACAAATCATTGAAACTATTCAAAAGTATCAAATTTCTATAAATCGAAAGAATCATAAATTAAT
TGATGATTATTCATAT
Found at i:1330635 original size:111 final size:110
Alignment explanation
Indices: 1330495--1330698 Score: 374
Period size: 111 Copynumber: 1.8 Consensus size: 110
1330485 AGTTTAATAT
1330495 AAATTTTATAAATTCATATATTTTATATTTTTATTTATTTATTTTCATAATAATTTCATCATTAT
1 AAATTTTATAAATTCATATATTTTATATTTTTATTTATTTATTTTCATAATAATTTCATCATTAT
*
1330560 AAAAAATAATCTT-ATGTAATAAATTTACAATTTACGAGTCAAAAC
66 AAAAAATAAT-TTCATGGAATAAATTTACAATTTACGAGTCAAAAC
1330605 AAATTATTATAAATTCATATATTTTATATTTTTATTTATTTATTTTCATAATAATTTCATCATTA
1 AAATT-TTATAAATTCATATATTTTATATTTTTATTTATTTATTTTCATAATAATTTCATCATTA
1330670 TAAAAAATAATTTCATGGAATAAATTTAC
65 TAAAAAATAATTTCATGGAATAAATTTAC
1330699 TGTAATAAGA
Statistics
Matches: 91, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
110 7 0.08
111 84 0.92
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (110 bp):
AAATTTTATAAATTCATATATTTTATATTTTTATTTATTTATTTTCATAATAATTTCATCATTAT
AAAAAATAATTTCATGGAATAAATTTACAATTTACGAGTCAAAAC
Found at i:1337631 original size:2 final size:2
Alignment explanation
Indices: 1337624--1337658 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1337614 ATCAGTTTAA
1337624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1337659 GGTTGATCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1340440 original size:30 final size:30
Alignment explanation
Indices: 1340392--1340455 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1340382 TAAATAATTA
* * * * *
1340392 TTTTTTGGAGAATTAATTATTTGTCAATGT
1 TTTTTTAGAAAATCAATTAATTGTCAATAT
*
1340422 TTTTTTAGAAAATCAATTAATTGTTAATAT
1 TTTTTTAGAAAATCAATTAATTGTCAATAT
1340452 TTTT
1 TTTT
1340456 ATTGACATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (30 bp):
TTTTTTAGAAAATCAATTAATTGTCAATAT
Found at i:1345955 original size:28 final size:28
Alignment explanation
Indices: 1345921--1345983 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
1345911 TATTTGGAAG
1345921 GAATTTCATGGTTTTTTATTTAGTATCT
1 GAATTTCATGGTTTTTTATTTAGTATCT
1345949 GAATTTCATGGTTTTTTATTTAGTATCT
1 GAATTTCATGGTTTTTTATTTAGTATCT
1345977 GAATTTC
1 GAATTTC
1345984 TAAAGTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.56
Consensus pattern (28 bp):
GAATTTCATGGTTTTTTATTTAGTATCT
Found at i:1345991 original size:29 final size:28
Alignment explanation
Indices: 1345921--1345991 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1345911 TATTTGGAAG
**
1345921 GAATTTCATGGTTTTTTATTTAGTATCT
1 GAATTTCAAAGTTTTTTATTTAGTATCT
**
1345949 GAATTTCATGGTTTTTTATTTAGTATCT
1 GAATTTCAAAGTTTTTTATTTAGTATCT
1345977 GAATTTCTAAAGTTT
1 GAATTTC-AAAGTTT
1345992 ATTCTCTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (28 bp):
GAATTTCAAAGTTTTTTATTTAGTATCT
Found at i:1347076 original size:60 final size:60
Alignment explanation
Indices: 1346983--1347102 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
1346973 TAAACAGCTT
* * * *
1346983 GATATCGTTTAAGCAATATCTCGAGTTCGAGTCCTTGTATGCATAATATCTTTGTTGGGA
1 GATATAGTTTAAGCAAGATCTCGAGTTCGAGTCCTTGTATGCAGAAAATCTTTGTTGGGA
1347043 GATATAGTTTAAGCAAGATCTCGAGTTCGAGTCCTTGTATGCAGAAAATCTTTGTTGGGA
1 GATATAGTTTAAGCAAGATCTCGAGTTCGAGTCCTTGTATGCAGAAAATCTTTGTTGGGA
1347103 AACTCGCCCG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (60 bp):
GATATAGTTTAAGCAAGATCTCGAGTTCGAGTCCTTGTATGCAGAAAATCTTTGTTGGGA
Found at i:1349774 original size:37 final size:40
Alignment explanation
Indices: 1349694--1349775 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 40
1349684 TGCTTAATAC
* * *
1349694 TTTAACCAAATAAAAAACATATTTCAAGATATCTATATTA
1 TTTATCCAAATAAAAAACATAATTCAAGAAATCTATATTA
*
1349734 TTTATCCAAAT-AAAAACATAATT-AA-AAATGTATATTA
1 TTTATCCAAATAAAAAACATAATTCAAGAAATCTATATTA
1349771 TTTAT
1 TTTAT
1349776 TAAACCACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 15 0.39
38 2 0.05
39 11 0.29
40 10 0.26
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (40 bp):
TTTATCCAAATAAAAAACATAATTCAAGAAATCTATATTA
Found at i:1350569 original size:16 final size:16
Alignment explanation
Indices: 1350548--1350581 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1350538 GTGAGCACAT
1350548 TTAATA-AAATAAATAA
1 TTAATATAAA-AAATAA
1350564 TTAATATAAAAAATAA
1 TTAATATAAAAAATAA
1350580 TT
1 TT
1350582 TTAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAATATAAAAAATAA
Found at i:1351407 original size:21 final size:23
Alignment explanation
Indices: 1351382--1351428 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1351372 ATATTTATAT
*
1351382 TTTTTATGT-TTTAAAGTTAA-A
1 TTTTTATGTATTTAAACTTAATA
*
1351403 TTTTTATTTATTTAAACTTAATA
1 TTTTTATGTATTTAAACTTAATA
1351426 TTT
1 TTT
1351429 GTTGTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTTATGTATTTAAACTTAATA
Found at i:1359793 original size:15 final size:15
Alignment explanation
Indices: 1359756--1359827 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
1359746 TTTCGGATCG
*
1359756 AATTATTTTAAATTT
1 AATTTTTTTAAATTT
* * *
1359771 TATCTTTTTGAATTT
1 AATTTTTTTAAATTT
* *
1359786 AATTTTTTTTATTTT
1 AATTTTTTTAAATTT
* *
1359801 AAATTCTTTTAAACTT
1 -AATTTTTTTAAATTT
*
1359817 GATTTTTTTAA
1 AATTTTTTTAA
1359828 TAGTCTGAGG
Statistics
Matches: 42, Mismatches: 14, Indels: 2
0.72 0.24 0.03
Matches are distributed among these distances:
15 31 0.74
16 11 0.26
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (15 bp):
AATTTTTTTAAATTT
Found at i:1370671 original size:19 final size:19
Alignment explanation
Indices: 1370647--1370689 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1370637 AGTTTGAATT
1370647 TAATTTTAG-TTAAAATATA
1 TAATTTT-GTTTAAAATATA
*
1370666 TAA-TTTGTTTAAAATTTA
1 TAATTTTGTTTAAAATATA
1370684 TAATTT
1 TAATTT
1370690 ATTTGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TAATTTTGTTTAAAATATA
Found at i:1371042 original size:20 final size:21
Alignment explanation
Indices: 1370970--1371046 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 21
1370960 TTATCTCTCT
* *
1370970 ATATATTATTTTCTTCAATTAA
1 ATATATTATTTTATT-AAATAA
* *
1370992 AT-TTTTATTTTTATTGAATAA
1 ATATATTA-TTTTATTAAATAA
*
1371013 A-AGTAATATTTT-TTAAATAA
1 ATA-TATTATTTTATTAAATAA
1371033 ATATATTATTTTAT
1 ATATATTATTTTAT
1371047 ATCAGGTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
20 16 0.38
21 15 0.36
22 11 0.26
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
ATATATTATTTTATTAAATAA
Found at i:1376759 original size:26 final size:25
Alignment explanation
Indices: 1376730--1376780 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1376720 TGTTTGTGTG
1376730 TTCTAGTGATATATTGCTTTGAGAAC
1 TTCTAGTGATATATTGC-TTGAGAAC
* *
1376756 TTCTAGTGATGTGTTGCTTGAGAAC
1 TTCTAGTGATATATTGCTTGAGAAC
1376781 CAGTATCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (25 bp):
TTCTAGTGATATATTGCTTGAGAAC
Found at i:1378617 original size:3 final size:3
Alignment explanation
Indices: 1378609--1378639 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1378599 TAATCACTTT
1378609 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1378640 AACTACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1379945 original size:28 final size:28
Alignment explanation
Indices: 1379907--1379964 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1379897 CCGAACCCGA
1379907 CCCGACCCGAATATCACACTTAAAAAAC
1 CCCGACCCGAATATCACACTTAAAAAAC
*
1379935 CCCGACCCGAATATCACATTTAAAAAAC
1 CCCGACCCGAATATCACACTTAAAAAAC
1379963 CC
1 CC
1379965 AACTCGAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.36, G:0.07, T:0.16
Consensus pattern (28 bp):
CCCGACCCGAATATCACACTTAAAAAAC
Found at i:1379972 original size:27 final size:28
Alignment explanation
Indices: 1379911--1379972 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1379901 ACCCGACCCG
*
1379911 ACCCGAATATCACACTTAAAAAACCCCG
1 ACCCGAATATCACACTTAAAAAACCCCA
*
1379939 ACCCGAATATCACATTTAAAAAA-CCCA
1 ACCCGAATATCACACTTAAAAAACCCCA
*
1379966 ACTCGAA
1 ACCCGAA
1379973 CCGAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.45, C:0.32, G:0.06, T:0.16
Consensus pattern (28 bp):
ACCCGAATATCACACTTAAAAAACCCCA
Found at i:1393061 original size:12 final size:12
Alignment explanation
Indices: 1393036--1393069 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1393026 GAAAGTTTCA
*
1393036 AGAGAGACAAAG
1 AGAGAGAGAAAG
*
1393048 AGATAGAGAAAG
1 AGAGAGAGAAAG
1393060 AGAGAGAGAA
1 AGAGAGAGAA
1393070 GAGTTTAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.35, T:0.03
Consensus pattern (12 bp):
AGAGAGAGAAAG
Found at i:1399786 original size:100 final size:100
Alignment explanation
Indices: 1399514--1399788 Score: 354
Period size: 102 Copynumber: 2.7 Consensus size: 100
1399504 AAAAAAAAAA
* * *
1399514 AAAAGACATTTTATACATAATGAAAAAGAACGGGGCTAAGAGAATCCATGCATATCTTTTAAGGT
1 AAAATACATTTTATATATAATGAAAAAGAACGGGGATAAGAGAATCCATGCATATCTTTTAAGGT
* * * *
1399579 CGACTAGAAGTTGTATTAGTGTCTAGATGGAATGC
66 CGAGTAGAAGTTGTACTAGTATCTAGACGGAATGC
* * * * *
1399614 AAAATACATTTAATACATAAAATGAAAAAGAATGGGGATAAGAGAATCCATGCATATATTTTACG
1 AAAATACATTT--TATATATAATGAAAAAGAACGGGGATAAGAGAATCCATGCATATCTTTTAAG
1399679 GTCGAGTAGAAGTTGTACTAGTATCTAGACGGAATGC
64 GTCGAGTAGAAGTTGTACTAGTATCTAGACGGAATGC
* * * * *
1399716 AAAA-ACCATTTTATATATGATGAAAAAGGACGGAGTTAAGAGGATCCATGCATATCTTTTAAGG
1 AAAATA-CATTTTATATATAATGAAAAAGAACGGGGATAAGAGAATCCATGCATATCTTTTAAGG
*
1399780 TTGAGTAGA
65 TCGAGTAGA
1399789 CGTTATGGAA
Statistics
Matches: 149, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
100 61 0.41
101 1 0.01
102 87 0.58
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (100 bp):
AAAATACATTTTATATATAATGAAAAAGAACGGGGATAAGAGAATCCATGCATATCTTTTAAGGT
CGAGTAGAAGTTGTACTAGTATCTAGACGGAATGC
Found at i:1412590 original size:2 final size:2
Alignment explanation
Indices: 1412583--1412634 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1412573 TATAAAATTC
1412583 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
1412625 AT AT AT AT AT
1 AT AT AT AT AT
1412635 TAAAAAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1415330 original size:18 final size:18
Alignment explanation
Indices: 1415304--1415340 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1415294 TGACTTACCT
1415304 TATCATTAAAATGAAATA
1 TATCATTAAAATGAAATA
*
1415322 TATCGTTAAAATGAAATA
1 TATCATTAAAATGAAATA
1415340 T
1 T
1415341 TAATCTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (18 bp):
TATCATTAAAATGAAATA
Found at i:1417846 original size:26 final size:27
Alignment explanation
Indices: 1417816--1417866 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1417806 TATTTTCCCC
1417816 CTCC-TTAAAATTTTATAAGTTCGTAT
1 CTCCTTTAAAATTTTATAAGTTCGTAT
1417842 CTCCTTTAAAATTTTATAAGTTCGT
1 CTCCTTTAAAATTTTATAAGTTCGT
1417867 CCCCTCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (27 bp):
CTCCTTTAAAATTTTATAAGTTCGTAT
Found at i:1420575 original size:2 final size:2
Alignment explanation
Indices: 1420568--1420606 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1420558 GGATTTTCTT
1420568 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
1420607 GTATTGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1420910 original size:18 final size:18
Alignment explanation
Indices: 1420870--1420913 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1420860 TCTTTTAGCT
1420870 AAAGTAATAATACTATTA
1 AAAGTAATAATACTATTA
* *
1420888 CAAGTATTAA-ACTATTTA
1 AAAGTAATAATACTA-TTA
1420906 AAAGTAAT
1 AAAGTAAT
1420914 TACAGTGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (18 bp):
AAAGTAATAATACTATTA
Found at i:1423071 original size:21 final size:21
Alignment explanation
Indices: 1423017--1423073 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1423007 GGCTATGCAA
*
1423017 ATCAGTTGAATTCTTCACGGT
1 ATCAGTTGAATTCTTCACAGT
*
1423038 ATC-GATTGGATTCTTCACAGT
1 ATCAG-TTGAATTCTTCACAGT
1423059 ATCAGTTGAATTCTT
1 ATCAGTTGAATTCTT
1423074 ATCTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (21 bp):
ATCAGTTGAATTCTTCACAGT
Found at i:1424915 original size:22 final size:21
Alignment explanation
Indices: 1424887--1424927 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1424877 GATACCTTAT
*
1424887 ATATATATATTTAAAATAAAAA
1 ATATATA-AATTAAAATAAAAA
1424909 ATATATAAATTAAAATAAA
1 ATATATAAATTAAAATAAA
1424928 TGTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATATAAATTAAAATAAAAA
Found at i:1432310 original size:63 final size:63
Alignment explanation
Indices: 1432211--1432388 Score: 241
Period size: 63 Copynumber: 2.8 Consensus size: 63
1432201 TACCTTCTCT
* * * *
1432211 TCATCTTTTCTTACTTGAACTTCTTCGTTTCGCAATGGATTCAGCTCCTCC-TCCTTATCCACG
1 TCATCTTTTCTTACTTGAATTTCTTCGTTTTGCAATGGATTCAGCGCCTCCAT-CATATCCACG
* * *
1432274 TCATCTTTACTTACTTGAATTTCTTCGTTTTGCAATGGATTCAACGCCTCCATCATATCCACT
1 TCATCTTTTCTTACTTGAATTTCTTCGTTTTGCAATGGATTCAGCGCCTCCATCATATCCACG
* * * *
1432337 TCATCTTTTCTTACTTTATTTTTTTCGTTTTGCAATGGATTCAGCGCTTCCA
1 TCATCTTTTCTTACTTGAATTTCTTCGTTTTGCAATGGATTCAGCGCCTCCA
1432389 CCTGATTCAC
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 100 0.99
64 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (63 bp):
TCATCTTTTCTTACTTGAATTTCTTCGTTTTGCAATGGATTCAGCGCCTCCATCATATCCACG
Found at i:1450438 original size:33 final size:33
Alignment explanation
Indices: 1450396--1450458 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
1450386 TGCTATAATC
1450396 AATGTTCTAGTTACACTTTCCAGCATTTCACTG
1 AATGTTCTAGTTACACTTTCCAGCATTTCACTG
1450429 AATGTTCTAGTTACACTTTCCAGCATTTCA
1 AATGTTCTAGTTACACTTTCCAGCATTTCA
1450459 ATGTTCTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (33 bp):
AATGTTCTAGTTACACTTTCCAGCATTTCACTG
Found at i:1452450 original size:2 final size:2
Alignment explanation
Indices: 1452443--1452468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1452433 TGTGAAATCA
1452443 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
1452469 TATTTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1464330 original size:14 final size:14
Alignment explanation
Indices: 1464311--1464354 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
1464301 TTCATCAAAC
1464311 AGAGAGAGAGAGAA
1 AGAGAGAGAGAGAA
1464325 AGAGAGAGAGAGGAA
1 AGAGAGAGAGA-GAA
*
1464340 AGGGAAGAGAGAGAA
1 AGAG-AGAGAGAGAA
1464355 TAAACTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.41
15 9 0.33
16 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGAGAA
Found at i:1464959 original size:14 final size:13
Alignment explanation
Indices: 1464937--1464980 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1464927 AATGTCTATA
1464937 TTAATTATAATTC
1 TTAATTATAATTC
*
1464950 TTATATTATAAATC
1 TTA-ATTATAATTC
*
1464964 TTAATTATAATTA
1 TTAATTATAATTC
1464977 TTAA
1 TTAA
1464981 ATTAATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAATTATAATTC
Found at i:1464972 original size:13 final size:13
Alignment explanation
Indices: 1464937--1464973 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1464927 AATGTCTATA
*
1464937 TTAATTATAATTC
1 TTAATTATAAATC
1464950 TTATATTATAAATC
1 TTA-ATTATAAATC
1464964 TTAATTATAA
1 TTAATTATAA
1464974 TTATTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATTATAAATC
Found at i:1465211 original size:2 final size:2
Alignment explanation
Indices: 1465204--1465238 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1465194 ATAGTATACT
1465204 TA TA TA TA 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 TA TA TA TA T
1465239 TCACATGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1465365 original size:19 final size:19
Alignment explanation
Indices: 1465316--1465353 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1465306 TAAAAAGAAC
1465316 AATT-GTTTTTTTAGGGAA
1 AATTGGTTTTTTTAGGGAA
1465334 AATTGGTTTTTTTAGGGAA
1 AATTGGTTTTTTTAGGGAA
1465353 A
1 A
1465354 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (19 bp):
AATTGGTTTTTTTAGGGAA
Found at i:1465747 original size:2 final size:2
Alignment explanation
Indices: 1465740--1465766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1465730 TCATACATAC
1465740 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
1465767 CTTAAACTTT
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:1465872 original size:22 final size:22
Alignment explanation
Indices: 1465840--1465893 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
1465830 TATATATACT
*
1465840 TATATAC--ATACATATTATAAG
1 TATATACATATACATA-CATAAG
*
1465861 TATA-ACATATACTTACATAAG
1 TATATACATATACATACATAAG
1465882 TATATACATATA
1 TATATACATATA
1465894 ATGAATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 13 0.46
22 13 0.46
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (22 bp):
TATATACATATACATACATAAG
Found at i:1467966 original size:26 final size:25
Alignment explanation
Indices: 1467915--1467966 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1467905 TATAATTAAG
* * *
1467915 TCAATATTTAACTTTAATCAAGTTA
1 TCAATAGTTAACTTTAATAAAATTA
1467940 TCAATAGTTAACTCTTAATAAAATTA
1 TCAATAGTTAACT-TTAATAAAATTA
1467966 T
1 T
1467967 TAACATAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (25 bp):
TCAATAGTTAACTTTAATAAAATTA
Found at i:1472762 original size:28 final size:28
Alignment explanation
Indices: 1472730--1472799 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 28
1472720 TTCTACAATG
1472730 TTATAAGTAA-TG-ATAAACTTTGATAAAT
1 TTATAA-TAATTGAATAAAC-TTGATAAAT
*
1472758 TTATAATAATTGAATAAGCTTGATAAACATT
1 TTATAATAATTGAATAAACTTGAT-AA-A-T
1472789 TTATAATAATT
1 TTATAATAATT
1472800 CGATAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 13 0.36
29 7 0.19
30 1 0.03
31 12 0.33
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (28 bp):
TTATAATAATTGAATAAACTTGATAAAT
Found at i:1472993 original size:31 final size:31
Alignment explanation
Indices: 1472940--1473027 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
1472930 TTAAATAATA
1472940 ATAAACTTTGAT-AA-A-TTTATAATAATT-G
1 ATAAAC-TTGATAAACATTTTATAATAATTCG
*
1472968 AATAAGCTTGATAAACATTTTATAATAATTCG
1 -ATAAACTTGATAAACATTTTATAATAATTCG
* *
1473000 ATAAATTTGATAATCATTTTATAA-AATT
1 ATAAACTTGATAAACATTTTATAATAATT
1473028 TTAATATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
28 5 0.10
29 7 0.14
30 5 0.10
31 33 0.65
32 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (31 bp):
ATAAACTTGATAAACATTTTATAATAATTCG
Done.