Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008785.1 Hibiscus syriacus cultivar Beakdansim tig00111917_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: 1341157
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1142222 original size:31 final size:31
Alignment explanation
Indices: 1142036--1142209 Score: 321
Period size: 31 Copynumber: 5.6 Consensus size: 31
1142026 AGGGTCGAGG
*
1142036 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1142067 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1142098 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1142129 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1142160 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1142191 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
1142210 AATCTATAGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 140 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1146682 original size:31 final size:31
Alignment explanation
Indices: 1146618--1146772 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
1146608 AGGGTCGAGG
1146618 GTTTACCTATGTTCTTCGGGACATAT-GACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1146648 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1146679 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1146710 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1146741 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1146772 G
1 G
1146773 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
30 26 0.22
31 93 0.77
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1153299 original size:26 final size:26
Alignment explanation
Indices: 1153260--1153319 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1153250 TTCGCTTATT
*
1153260 TCGCTCAAATGTTTAAGGTGCAAGAA
1 TCGCTCAAAGGTTTAAGGTGCAAGAA
**
1153286 TCGCTCAAAGGTTTCGGGTGCAAGAA
1 TCGCTCAAAGGTTTAAGGTGCAAGAA
*
1153312 TCACTCAA
1 TCGCTCAA
1153320 GCATAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (26 bp):
TCGCTCAAAGGTTTAAGGTGCAAGAA
Found at i:1153699 original size:32 final size:32
Alignment explanation
Indices: 1153639--1153701 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1153629 GAATCTGTAT
**
1153639 TGCACTATTTTCCTACACGGTTTGAACCAAAC
1 TGCACTATTTTCCTACACGGTTCAAACCAAAC
* *
1153671 TGCACTATTTTTCTACACTGTTCAAACCAAA
1 TGCACTATTTTCCTACACGGTTCAAACCAAA
1153702 TCTATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (32 bp):
TGCACTATTTTCCTACACGGTTCAAACCAAAC
Found at i:1154655 original size:15 final size:15
Alignment explanation
Indices: 1154632--1154663 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1154622 TTTCCCTTAG
1154632 TATCAATACTAGCCT
1 TATCAATACTAGCCT
*
1154647 TATCGATACTAGCCT
1 TATCAATACTAGCCT
1154662 TA
1 TA
1154664 CAGTATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (15 bp):
TATCAATACTAGCCT
Found at i:1156058 original size:14 final size:14
Alignment explanation
Indices: 1156039--1156069 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1156029 TCCTCTGCCC
1156039 CTATAAAAAGGTTA
1 CTATAAAAAGGTTA
1156053 CTATAAAAAGGTTA
1 CTATAAAAAGGTTA
1156067 CTA
1 CTA
1156070 AGTCAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (14 bp):
CTATAAAAAGGTTA
Found at i:1158323 original size:19 final size:20
Alignment explanation
Indices: 1158295--1158344 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1158285 TCTTTTCCTT
*
1158295 AGTATCGATAC-ATATCATC
1 AGTATTGATACTATATCATC
* *
1158314 AGTATTGATACTCTCTCATC
1 AGTATTGATACTATATCATC
1158334 AGTATTGATAC
1 AGTATTGATAC
1158345 CTTACCCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
AGTATTGATACTATATCATC
Found at i:1171568 original size:20 final size:20
Alignment explanation
Indices: 1171543--1171596 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1171533 CATTCTGATA
1171543 AGGGGTTTTGAAACCAGGCT
1 AGGGGTTTTGAAACCAGGCT
*
1171563 AGGGGTTTCGAAACCAGGCT
1 AGGGGTTTTGAAACCAGGCT
1171583 AGGGGTTTTGAAAC
1 AGGGGTTTTGAAAC
1171597 ATGTATTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (20 bp):
AGGGGTTTTGAAACCAGGCT
Found at i:1202428 original size:14 final size:14
Alignment explanation
Indices: 1202409--1202435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1202399 AACTTTTTGG
1202409 GTCAAAGTCAACGA
1 GTCAAAGTCAACGA
1202423 GTCAAAGTCAACG
1 GTCAAAGTCAACG
1202436 GGATGACTCA
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:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (14 bp):
GTCAAAGTCAACGA
Found at i:1204103 original size:7 final size:7
Alignment explanation
Indices: 1204093--1204124 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1204083 AGACAGGGAT
*
1204093 AATTTAT
1 AATTTAA
1204100 AATTTAA
1 AATTTAA
1204107 AATTTAA
1 AATTTAA
1204114 AATTTAA
1 AATTTAA
1204121 AATT
1 AATT
1204125 ATCATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AATTTAA
Found at i:1205388 original size:27 final size:26
Alignment explanation
Indices: 1205340--1205396 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1205330 TTTGTACTTT
* *
1205340 TTTATAATATTATTTAATATATCAAA
1 TTTATAATAATATTTAATATATAAAA
1205366 TTTATCAATAATATATTAA-ATATAAAA
1 TTTAT-AATAATAT-TTAATATATAAAA
1205393 TTTA
1 TTTA
1205397 GGTGGAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 18 0.67
28 4 0.15
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTATAATAATATTTAATATATAAAA
Found at i:1208636 original size:6 final size:6
Alignment explanation
Indices: 1208627--1208658 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1208617 ATAACTCTGT
1208627 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CT
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CT
1208659 GGTCCTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCA
Found at i:1211840 original size:14 final size:14
Alignment explanation
Indices: 1211821--1211863 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1211811 GTCTACGTCC
1211821 AATATATATAA-AAT
1 AATATA-ATAATAAT
1211835 AATATAATAATAAT
1 AATATAATAATAAT
* *
1211849 AATACAATAAAAAT
1 AATATAATAATAAT
1211863 A
1 A
1211864 GTAATGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AATATAATAATAAT
Found at i:1211883 original size:2 final size:2
Alignment explanation
Indices: 1211876--1211906 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1211866 AATGTCATGA
1211876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1211907 AACATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1212914 original size:32 final size:32
Alignment explanation
Indices: 1212873--1212936 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1212863 AGGGAGGGAA
*
1212873 AGAACGTTAGGACGTTAGAGGAGAGAGAGAGT
1 AGAACGTTAGGACGTTAGAGAAGAGAGAGAGT
1212905 AGAACGTTAGGACGTTAGAGAAGAGAGAGAGT
1 AGAACGTTAGGACGTTAGAGAAGAGAGAGAGT
1212937 TTGTTAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.16
Consensus pattern (32 bp):
AGAACGTTAGGACGTTAGAGAAGAGAGAGAGT
Found at i:1214430 original size:23 final size:23
Alignment explanation
Indices: 1214404--1214456 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1214394 CACCACAACT
*
1214404 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
1214427 CGTAGAATTACACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
1214450 CGTAGAA
1 CGTAGAA
1214457 TTGCACCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:1214471 original size:23 final size:23
Alignment explanation
Indices: 1214412--1214464 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1214402 CTCGTATAAA
1214412 TACACCGAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
1214435 TACACCGAAGTGCCGCGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
1214458 TGCACCG
1 TACACCG
1214465 TATTGCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:1222072 original size:62 final size:64
Alignment explanation
Indices: 1222002--1222137 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
1221992 ACACCACACC
* * *
1222002 ATGCATCGATGCA-TAAAT-CCTATTCGATGTTTATA-TTT-AAGGGGTGCATCGATGCACTCCT
1 ATGCATCGATGCACT-AATGCC-ATTCGATGTTTATATTTTAAAAGAGTGCATCGATGCACTCCA
1222063 T
64 T
* * * *
1222064 ATGCATCGATGCACTGATGGCATTCGATGTTTGTATTTTAAAAGAGTGCATCGATGCACTTCAT
1 ATGCATCGATGCACTAATGCCATTCGATGTTTATATTTTAAAAGAGTGCATCGATGCACTCCAT
*
1222128 GTGCATCGAT
1 ATGCATCGAT
1222138 ACACCTTGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
62 28 0.45
63 5 0.08
64 29 0.47
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTAATGCCATTCGATGTTTATATTTTAAAAGAGTGCATCGATGCACTCCAT
Found at i:1227546 original size:14 final size:15
Alignment explanation
Indices: 1227529--1227557 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1227519 ATCTTTTAAA
1227529 AACATT-TTTAAAAG
1 AACATTATTTAAAAG
1227543 AACATTATTTAAAAG
1 AACATTATTTAAAAG
1227558 CTAAACTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
AACATTATTTAAAAG
Found at i:1228094 original size:2 final size:2
Alignment explanation
Indices: 1228087--1228126 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1228077 TGAATATTTC
1228087 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
1228127 TCATAGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1228241 original size:15 final size:15
Alignment explanation
Indices: 1228179--1228261 Score: 59
Period size: 15 Copynumber: 5.6 Consensus size: 15
1228169 TTAAAACACT
* *
1228179 AAAATTAATGTATTA
1 AAAATTAAAGTAATA
1228194 AAAATGTAAAGTAA-A
1 AAAAT-TAAAGTAATA
1228209 AAAATTAGAA--AATA
1 AAAATTA-AAGTAATA
1228223 GAAAATTAAAGTAAT-
1 -AAAATTAAAGTAATA
*
1228238 GAAATTAAA-TAAATA
1 AAAATTAAAGT-AATA
*
1228253 AAAAGTAAA
1 AAAATTAAA
1228262 TGGCATAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
13 3 0.05
14 16 0.29
15 27 0.49
16 9 0.16
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (15 bp):
AAAATTAAAGTAATA
Found at i:1228242 original size:29 final size:29
Alignment explanation
Indices: 1228192--1228261 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1228182 ATTAATGTAT
*
1228192 TAAAAATGTAAAGTAAAAAAATTAGA-AAA
1 TAAAAAT-TAAAGTAAAAAAATTAAATAAA
**
1228221 TAGAAAATTAAAGTAATGAAATTAAATAAA
1 TA-AAAATTAAAGTAAAAAAATTAAATAAA
*
1228251 TAAAAAGTAAA
1 TAAAAATTAAA
1228262 TGGCATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (29 bp):
TAAAAATTAAAGTAAAAAAATTAAATAAA
Found at i:1228945 original size:19 final size:19
Alignment explanation
Indices: 1228923--1228961 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1228913 TTATTGATAC
1228923 ACGTGGAGGGGCTGCTGAA
1 ACGTGGAGGGGCTGCTGAA
*
1228942 ACGTGGAGGGGTTGCTGAA
1 ACGTGGAGGGGCTGCTGAA
1228961 A
1 A
1228962 TCTGCTGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.46, T:0.18
Consensus pattern (19 bp):
ACGTGGAGGGGCTGCTGAA
Found at i:1229783 original size:136 final size:137
Alignment explanation
Indices: 1229407--1230130 Score: 1042
Period size: 136 Copynumber: 5.3 Consensus size: 137
1229397 AAACTGGTGT
* * * * * *
1229407 ATGACACTGTTCCTTCGTGATGAGGACAGT-TGGTCATGTTTAGAGATAAATTGAGATAACATGG
1 ATGACATTGTTCCTTCGTGATGAGGACA-TCTGGCCATCTTTAAAGAT-ATTTGAGATAACATAG
* * ** * * * * * *
1229471 TTCCTTTGTGATAAGGAATTTTGGCTATCAAAGAATGACACGACTCTTTCGTGATGAGGAGTTCA
64 TTCCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCT
1229536 GATTGGTAG
129 GATTGGTAG
* *
1229545 ATGACATTGTTCCTTCGTGATGAGGATATCTGGACATCTTTAAAGATATTTGAGATAACATAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATAGTT
* * * * * *
1229610 CCTTCGTGATAAGAACGTCTGGTTATTTAAGGCTGACACGACTCCTTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCTGA
1229675 TTGGTAG
131 TTGGTAG
*
1229682 ATGACATTGTTCCTTCATGATGAGGACAT-TGGCCATCTTTAAAGATATTTGAGATAACATAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATAGTT
* *
1229746 CATTCGTGATGAGGACGTCTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCTGA
66 CCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCTGA
1229811 TTGGTAG
131 TTGGTAG
* * * *
1229818 ATGACATTGTTCCTTCGTGAAGAGGACATCTGACCATCTTT-AAGACATCTGAGATAACATAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATAGTT
* *
1229882 CCTTCTTGATGAGGACGTTTGGTTATCTAAGGATGACACTACTCCTTCGTGATGAAGAGTTCTGA
66 CCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCTGA
1229947 TTGGTAG
131 TTGGTAG
* * *
1229954 ATGACATTGTTCATTCGTGATGAGGACATCTGGCCATCTTT-AAGACATCTGAGATAACATAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATAGTT
* *
1230018 CCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACATGACTCCTTCTTGATGAAGAGTTCTGA
66 CCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCTGA
1230083 TTGGTAG
131 TTGGTAG
**
1230090 ATGACATTGTTCCTTCGTGATGAGGACATCTGATCATCTTT
1 ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTT
1230131 GAGATAACAC
Statistics
Matches: 537, Mismatches: 47, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
136 383 0.71
137 114 0.21
138 40 0.07
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACATAGTT
CCTTCGTGATGAGGACGTTTGGTTATCTAAGGATGACACGACTCCTTCGTGATGAAGAGTTCTGA
TTGGTAG
Found at i:1230314 original size:14 final size:14
Alignment explanation
Indices: 1230295--1230325 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1230285 ATAAAGACCC
1230295 TCTCTCATTGGCCA
1 TCTCTCATTGGCCA
1230309 TCTCTCATTGGCCA
1 TCTCTCATTGGCCA
1230323 TCT
1 TCT
1230326 TGTGACTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.35, G:0.13, T:0.39
Consensus pattern (14 bp):
TCTCTCATTGGCCA
Found at i:1240809 original size:17 final size:17
Alignment explanation
Indices: 1240787--1240819 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1240777 CTATGTCCAT
1240787 ACGGAGGTGAAAACCAC
1 ACGGAGGTGAAAACCAC
1240804 ACGGAGGTGAAAACCA
1 ACGGAGGTGAAAACCA
1240820 TACGAGGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.30, T:0.06
Consensus pattern (17 bp):
ACGGAGGTGAAAACCAC
Found at i:1241279 original size:13 final size:13
Alignment explanation
Indices: 1241261--1241290 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1241251 CGAATACCTA
1241261 AAAATCATCTTTT
1 AAAATCATCTTTT
*
1241274 AAAATCATTTTTT
1 AAAATCATCTTTT
1241287 AAAA
1 AAAA
1241291 GAATATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATCATCTTTT
Found at i:1241942 original size:15 final size:14
Alignment explanation
Indices: 1241910--1241988 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 14
1241900 TTAAAAGACT
1241910 AAAATTAAAGTATTAA
1 AAAATTAAAGTA--AA
1241926 AAAATTTAAAGTAAA
1 AAAA-TTAAAGTAAA
**
1241941 AATAATTAAAAAAAA
1 AA-AATTAAAGTAAA
*
1241956 GAAAATTAAAGTAAT
1 -AAAATTAAAGTAAA
*
1241971 GAAATTAAA-TAAA
1 AAAATTAAAGTAAA
1241984 TAAAA
1 -AAAA
1241989 AGTAAATGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
13 3 0.06
14 11 0.22
15 21 0.41
16 8 0.16
17 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
AAAATTAAAGTAAA
Found at i:1241970 original size:24 final size:24
Alignment explanation
Indices: 1241910--1241970 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
1241900 TTAAAAGACT
***
1241910 AAAATTAAAGT-ATTAAAAAATTT
1 AAAATTAAAGTAATTAAAAAAAAG
* * *
1241933 AAAGTAAAAATAATTAAAAAAAAG
1 AAAATTAAAGTAATTAAAAAAAAG
1241957 AAAATTAAAGTAAT
1 AAAATTAAAGTAAT
1241971 GAAATTAAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (24 bp):
AAAATTAAAGTAATTAAAAAAAAG
Found at i:1242030 original size:26 final size:26
Alignment explanation
Indices: 1241980--1242028 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1241970 TGAAATTAAA
*
1241980 TAAATAAAAAGTAAATGACATAAATT
1 TAAATAAAAAGTAAAGGACATAAATT
*
1242006 TAAATATAAAGTAAAGGAC-TAAA
1 TAAATAAAAAGTAAAGGACATAAA
1242029 ATAAAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.24
Consensus pattern (26 bp):
TAAATAAAAAGTAAAGGACATAAATT
Found at i:1244897 original size:2 final size:2
Alignment explanation
Indices: 1244886--1244920 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1244876 GAATGATCAA
1244886 AT AT -T 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
1244921 TTTAACAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1245010 original size:36 final size:36
Alignment explanation
Indices: 1244939--1245011 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1244929 GTTGAAAAAT
*
1244939 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
1244975 ATTTATATATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATT-AAAATCATAAA
1245011 A
1 A
1245012 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:1258128 original size:14 final size:15
Alignment explanation
Indices: 1258100--1258129 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1258090 TTGGATTTAA
1258100 TTGTTTGATTTTGGT
1 TTGTTTGATTTTGGT
1258115 TTGTTTGA-TTTGGT
1 TTGTTTGATTTTGGT
1258129 T
1 T
1258130 GAATGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.07, C:0.00, G:0.27, T:0.67
Consensus pattern (15 bp):
TTGTTTGATTTTGGT
Found at i:1258460 original size:14 final size:14
Alignment explanation
Indices: 1258428--1258465 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
1258418 AGCGGGAGTA
*
1258428 ATTTTTCAAAATTG
1 ATTTTTCAAAAATG
1258442 A--TTTCAAAAATG
1 ATTTTTCAAAAATG
1258454 ATTTTTCAAAAA
1 ATTTTTCAAAAA
1258466 GAAAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.52
14 10 0.48
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (14 bp):
ATTTTTCAAAAATG
Found at i:1258609 original size:17 final size:18
Alignment explanation
Indices: 1258567--1258612 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1258557 TTAATGAATT
* *
1258567 TTAAAATTTTATATTCGA
1 TTAAAATTATATATTCAA
1258585 TTCAAAATTATATATTCAA
1 TT-AAAATTATATATTCAA
1258604 TT-AAATTAT
1 TTAAAATTAT
1258613 TCGAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 16 0.64
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAAAATTATATATTCAA
Found at i:1262873 original size:26 final size:24
Alignment explanation
Indices: 1262844--1262894 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1262834 TCAATTTTTC
1262844 AAATAAAAGTCGTAATTGTTTTTTAA
1 AAATAAAA-T-GTAATTGTTTTTTAA
* *
1262870 AAATAATATTTAATTGTTTTTTAA
1 AAATAAAATGTAATTGTTTTTTAA
1262894 A
1 A
1262895 TGGTTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 1 0.04
26 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (24 bp):
AAATAAAATGTAATTGTTTTTTAA
Found at i:1264461 original size:43 final size:43
Alignment explanation
Indices: 1264403--1264653 Score: 289
Period size: 43 Copynumber: 5.9 Consensus size: 43
1264393 CAAACACCGT
1264403 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGACGC
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGACGC
* * * * * * *
1264446 AATAGTTTTTAAGATTTAGCAGC-ATTTTCCCACAAACGTCGC
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGACGC
1264488 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAAC-AC-C
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGACGC
* * * *
1264529 ACGATAGGTGTTTAGGTTTAGCAGCGTTTTTCTCAC-AA-GCCGC
1 A--ATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGACGC
* *
1264572 AATAGGTGTTGAGATTTAGTGGCGTTTTTCTCACAAA-TACCGC
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGA-CGC
* * *
1264615 AATAGGTGTTGAGATTTAGCGGCATTTTCCCCACAAACG
1 AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACG
1264654 TCGTTAAAGG
Statistics
Matches: 171, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
41 31 0.18
42 41 0.24
43 99 0.58
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (43 bp):
AATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGACGC
Found at i:1264620 original size:84 final size:85
Alignment explanation
Indices: 1264392--1264653 Score: 343
Period size: 84 Copynumber: 3.1 Consensus size: 85
1264382 ATGATATTGA
* * *
1264392 ACAAACACCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACGA-CGCAATA-GTTTT
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAAC-ACCGCAATAGGTGTT
1264455 TAAGATTTAGCAGCATTTTCCC
65 T-AGATTTAGCAGCATTTTCCC
* * *
1264477 ACAAACGTCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACCACGATAGGTGTTT
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACCGCAATAGGTGTTT
* * *
1264542 AGGTTTAGCAGCGTTTTTCTC
66 AGATTTAGCAGC-ATTTTCCC
* * *
1264563 AC-AA-GCCGCAATAGGTGTTGAGATTTAGTGGCGTTTTTCTCACAAATACCGCAATAGGTGTTG
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACCGCAATAGGTGTTT
*
1264626 AGATTTAGCGGCATTTTCCCC
66 AGATTTAGCAGCATTTT-CCC
1264647 ACAAACG
1 ACAAACG
1264654 TCGTTAAAGG
Statistics
Matches: 152, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
83 4 0.03
84 68 0.45
85 66 0.43
86 14 0.09
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (85 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACCGCAATAGGTGTTT
AGATTTAGCAGCATTTTCCC
Found at i:1265135 original size:21 final size:21
Alignment explanation
Indices: 1265111--1265158 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1265101 GTGCTACCAC
**
1265111 TGCTTCTCTCTCTACTTCTGT
1 TGCTTCTCTCTCTACTTCCCT
* *
1265132 TGCTGCTCTCTCTGCTTCCCT
1 TGCTTCTCTCTCTACTTCCCT
1265153 TGCTTC
1 TGCTTC
1265159 ATTTTCGACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.38, G:0.12, T:0.48
Consensus pattern (21 bp):
TGCTTCTCTCTCTACTTCCCT
Found at i:1268071 original size:18 final size:17
Alignment explanation
Indices: 1268048--1268084 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
1268038 TATCAAAATG
1268048 AAATAAGACAACAATACA
1 AAATAAGACAACAA-ACA
1268066 AAATAAGACAACAAACA
1 AAATAAGACAACAAACA
1268083 AA
1 AA
1268085 CTAAACTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.08
Consensus pattern (17 bp):
AAATAAGACAACAAACA
Found at i:1268452 original size:39 final size:39
Alignment explanation
Indices: 1268393--1268479 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1268383 ACATCATTAG
*
1268393 CAATTGATTTTATTTATTATTAAGTTCAATATAGTACCT
1 CAATAGATTTTATTTATTATTAAGTTCAATATAGTACCT
1268432 CAATAGATTTTATTTATTATTAAGTTCAATATAGTACCT
1 CAATAGATTTTATTTATTATTAAGTTCAATATAGTACCT
1268471 CAATAGATT
1 CAATAGATT
1268480 CTTCTTGTGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (39 bp):
CAATAGATTTTATTTATTATTAAGTTCAATATAGTACCT
Found at i:1271548 original size:22 final size:23
Alignment explanation
Indices: 1271518--1271565 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1271508 TCACGTTTTC
1271518 AAAAGCTATTA-TTTTCCTATTCG
1 AAAAGCTATTATTTTTCC-ATTCG
1271541 AAAA-CTATTATTTTTCCATTCG
1 AAAAGCTATTATTTTTCCATTCG
1271563 AAA
1 AAA
1271566 GCAGAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (23 bp):
AAAAGCTATTATTTTTCCATTCG
Found at i:1273455 original size:18 final size:18
Alignment explanation
Indices: 1273412--1273448 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1273402 ATAGCTTGAG
1273412 ATATCTAAACAAAATAAA
1 ATATCTAAACAAAATAAA
* *
1273430 ATACCTAAAGAAAATAAA
1 ATATCTAAACAAAATAAA
1273448 A
1 A
1273449 CTTCTAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.11, G:0.03, T:0.19
Consensus pattern (18 bp):
ATATCTAAACAAAATAAA
Found at i:1276508 original size:82 final size:82
Alignment explanation
Indices: 1276397--1277241 Score: 1212
Period size: 82 Copynumber: 10.3 Consensus size: 82
1276387 ATTGTTCTAA
* * *
1276397 ATAAAATATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1276462 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* *
1276479 ATAAAAGATTAATGGCGTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1276544 GGTTAAATACCCTTTGAG
66 GGTTAAATA-CCTTTGAG
* * * * *
1276562 -TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGGAATGTGTTAATTATGTCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1276626 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
*
1276643 ATAAAAGATTAATGGACTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
1276708 GGTTAAATACCTTTTAG
66 GGTTAAATACCTTTGAG
** * * *
1276725 ATAAAAGATGGATGGTCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTATATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1276790 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* ** * * * *
1276807 ATAAAATATTAATGGTGTAGCTATGCATTTGACAAAAAGGTGTCAAGTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
1276872 GGTTAAATACCTTAGAG
66 GGTTAAATACCTTTGAG
* *
1276889 -TAAAATATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
1276953 TGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* * * * * *
1276970 ATAGAAGATTAATGACCTAGATGTGCATTTGACAAAAAAGTGTCAATTATGTCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
** *
1277035 GGTTAAATATTTTTTAG
66 GGTTAAATACCTTTGAG
* * * * *
1277052 ATAAAAAATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1277117 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* * ** * *
1277134 ATAAAAGATTAATGCCCTAGTTGTGAATGGGA-AAAAATGTGTCAATTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1277198 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
*
1277215 -TAAAAGATTAATGGCTTAGTTGTGCAT
1 ATAAAAGATTAATGGCCTAGTTGTGCAT
1277242 AGTTGGCATG
Statistics
Matches: 681, Mismatches: 79, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
80 24 0.04
81 127 0.19
82 522 0.77
83 8 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (82 bp):
ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
GGTTAAATACCTTTGAG
Found at i:1276997 original size:245 final size:246
Alignment explanation
Indices: 1276397--1277241 Score: 1266
Period size: 245 Copynumber: 3.4 Consensus size: 246
1276387 ATTGTTCTAA
* * *
1276397 ATAAAATATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
1276462 GGTTAAATACCTTTGAGATAAAAGATTAATGGCGTAGTTGTGCATTTGACAGAAAGGTGTCAATT
66 GGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATT
* *
1276527 ATGTCAGTTAGATGAAAGGTTAAATACCCTTTGAG-TAAAAGATTAATGGCCTAGCTGTGCATTT
131 ATGTCAGTTAGATGAAAGGTTAAATA-CCTTTGAGATAAAAAATTAATGGTCTAGCTGTGCATTT
* * *
1276591 GACAGGAATGTGTTAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAG
195 GACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
*
1276643 ATAAAAGATTAATGGACTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* ** * *
1276708 GGTTAAATACCTTTTAGATAAAAGATGGATGGTCTAGTTGTGCATTTGACAGAAATGTGTCAATT
66 GGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATT
* * * * *
1276773 ATGCCAGTTATATGAAAGGTTAAATACCTTTGAGATAAAATATTAATGGTGTAGCTATGCATTTG
131 ATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAAAATTAATGGTCTAGCTGTGCATTTG
* * * *
1276838 ACAAAAAGGTGTCAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTAGAG
196 ACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
* *
1276889 -TAAAATATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* * * * *
1276953 TGTTAAATACCTTTGAGATAGAAGATTAATGACCTAGATGTGCATTTGACAAAAAAGTGTCAATT
66 GGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATT
** *
1277018 ATGTCAGTTAGATGAAAGGTTAAATATTTTTTAGATAAAAAATTAATGGTCTAGCTGTGCATTTG
131 ATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAAAATTAATGGTCTAGCTGTGCATTTG
*
1277083 ACAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAAATACCTTTGAG
196 ACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
* * ** * *
1277134 ATAAAAGATTAATGCCCTAGTTGTGAATGGGA-AAAAATGTGTCAATTATGCCAGTTAGATGAAA
1 ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
1277198 GGTTAAATACCTTTGAG-TAAAAGATTAATGGCTTAGTTGTGCAT
66 GGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGTTGTGCAT
1277242 AGTTGGCATG
Statistics
Matches: 535, Mismatches: 62, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
244 23 0.04
245 272 0.51
246 240 0.45
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (246 bp):
ATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
GGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAAGTGTCAATT
ATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAAAATTAATGGTCTAGCTGTGCATTTG
ACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
Found at i:1277304 original size:46 final size:46
Alignment explanation
Indices: 1277237--1277352 Score: 178
Period size: 46 Copynumber: 2.5 Consensus size: 46
1277227 GGCTTAGTTG
* *
1277237 TGCATAGTTGGCATGAAAGGATGTCATAAATGAAAATGTATAACAA
1 TGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACAA
* * *
1277283 TGCATAATTTGCATGAGAGGATGCCATAAATGAAAATGTATGACAA
1 TGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACAA
*
1277329 TGCATAATTGGCATGAAATGATGC
1 TGCATAATTGGCATGAAAGGATGC
1277353 AACAAATAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (46 bp):
TGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACAA
Found at i:1282594 original size:17 final size:17
Alignment explanation
Indices: 1282567--1282613 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
1282557 GATGCACCTT
* *
1282567 TGCACCAATGCATACCA
1 TGCACCGATGCACACCA
*
1282584 TGCATCGATGCACACCA
1 TGCACCGATGCACACCA
1282601 TGCACCGATGCAC
1 TGCACCGATGCAC
1282614 TGAGGATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.36, G:0.17, T:0.17
Consensus pattern (17 bp):
TGCACCGATGCACACCA
Found at i:1282714 original size:64 final size:64
Alignment explanation
Indices: 1282583--1282723 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 64
1282573 AATGCATACC
* * *
1282583 ATGCATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAAGAACATCAAATTCATTTG
1 ATGCATCGATGCACCACCATGCACCAATGCACTGAGGATTTTATAAGAACATCAAATGCACTTG
* * *
1282646 ATGCATCGATGCACCAGCCATGCATCAATGCACTCG-GGCTATTT-TAA-AACATCGAATGCACT
1 ATGCATCGATGCACCA-CCATGCACCAATGCACT-GAGGAT-TTTATAAGAACATCAAATGCACT
1282708 TG
63 TG
1282710 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1282724 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
63 13 0.19
64 30 0.44
65 21 0.31
66 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACCACCATGCACCAATGCACTGAGGATTTTATAAGAACATCAAATGCACTTG
Found at i:1282723 original size:17 final size:19
Alignment explanation
Indices: 1282695--1282743 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1282685 TATTTTAAAA
1282695 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1282713 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1282732 CACCGATGCACT
1 CATCGATGCACT
1282744 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1282741 original size:64 final size:62
Alignment explanation
Indices: 1282583--1282743 Score: 150
Period size: 64 Copynumber: 2.5 Consensus size: 62
1282573 AATGCATACC
* *
1282583 ATGCATCGATGCACACCA-TGCACCGATGCACTGAGGATTTTATAAGAACATCAAATTCATTTG
1 ATGCATCGATG--CACCAGTGCACCGATGCACTGAGGATTTTATAAGAACATCAAATGCACTTG
* * * *
1282646 ATGCATCGATGCACCAGCCATGCATCAATGCACTCG-GGCTATTT-TAA-AACATCGAATGCACT
1 ATGCATCGATGCACCAG---TGCACCGATGCACT-GAGGAT-TTTATAAGAACATCAAATGCACT
1282708 TG
61 TG
1282710 ATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 ATGCATCGATGCAC-C--AGTGCACCGATGCACT
1282744 AAGGTTCCAA
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
61 5 0.06
63 11 0.14
64 40 0.49
65 19 0.23
66 4 0.05
67 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (62 bp):
ATGCATCGATGCACCAGTGCACCGATGCACTGAGGATTTTATAAGAACATCAAATGCACTTG
Found at i:1290179 original size:21 final size:21
Alignment explanation
Indices: 1290150--1290193 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1290140 ACTCCGGGAG
* *
1290150 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
1290171 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
1290192 CT
1 CT
1290194 CCTCCTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:1292175 original size:19 final size:19
Alignment explanation
Indices: 1292129--1292166 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1292119 AAAGGGGAAG
1292129 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
1292148 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
1292167 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:1292618 original size:17 final size:17
Alignment explanation
Indices: 1292596--1292628 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1292586 CGAATGTATT
*
1292596 CCATGCATCGATGCACA
1 CCATGCACCGATGCACA
1292613 CCATGCACCGATGCAC
1 CCATGCACCGATGCAC
1292629 TGAGGATTTT
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:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCACCGATGCACA
Found at i:1293629 original size:17 final size:18
Alignment explanation
Indices: 1293594--1293639 Score: 85
Period size: 17 Copynumber: 2.6 Consensus size: 18
1293584 GATGTAATTA
1293594 GTATCGATACTGAAGGGG
1 GTATCGATACTGAAGGGG
1293612 GTATCGATACTG-AGGGG
1 GTATCGATACTGAAGGGG
1293629 GTATCGATACT
1 GTATCGATACT
1293640 TTGGAGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.26
Consensus pattern (18 bp):
GTATCGATACTGAAGGGG
Found at i:1294914 original size:55 final size:54
Alignment explanation
Indices: 1294826--1295016 Score: 267
Period size: 55 Copynumber: 3.5 Consensus size: 54
1294816 AATATATATA
* * *
1294826 CACTTAGTATGAAATTTCCT-AGTTTTGCACATAAAGTACCCATATGAAAATTCATC
1 CACTTAGTATG-AATTTCTTAAG-TTTACACATAAAGTGCCCATA-GAAAATTCATC
* *
1294882 CACTTAGTATGAATTTCTTAAGTCTACACATAAAGTGCCCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA-GAAAATTCATC
*
1294937 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAGA-AAATTCATC
*
1294992 CACTTCGTATGAATTTCTTAAGTTT
1 CACTTAGTATGAATTTCTTAAGTTT
1295017 TTGCACACTT
Statistics
Matches: 123, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
55 110 0.89
56 13 0.11
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (54 bp):
CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAGAAAATTCATC
Found at i:1295404 original size:22 final size:19
Alignment explanation
Indices: 1295372--1295423 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 19
1295362 TACCCCCACC
1295372 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACT-CT-TA-T
*
1295394 ATGGTACCGATACTCTTAT
1 ATGGTATCGATACTCTTAT
1295413 ATGGTATCGAT
1 ATGGTATCGAT
1295424 GCCATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 2 0.07
21 2 0.07
22 13 0.46
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
ATGGTATCGATACTCTTAT
Found at i:1296447 original size:82 final size:82
Alignment explanation
Indices: 1296311--1297131 Score: 1285
Period size: 82 Copynumber: 10.1 Consensus size: 82
1296301 ACACTAGCTA
* * *
1296311 TGCATTTGATAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAAATAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
* **
1296376 TATTAATGGCCTAGTAA
66 GATTAATGGCCTAGTTG
1296393 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
1296458 GATTAATGGCCTAGTTG
66 GATTAATGGCCTAGTTG
*
1296475 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATACCTTTGAGATAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
*
1296540 GAGTAATGGCCTAGTTG
66 GATTAATGGCCTAGTTG
*
1296557 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG-TAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
1296621 GATTAATGGCCTAGTTG
66 GATTAATGGCCTAGTTG
*
1296638 TGCA-TTGAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAA
1 TGCATTTG-ACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAA
* * *
1296702 AGATTAATGGTCTAGCTA
65 AGATTAATGGCCTAGTTG
* *
1296720 TGCATTTGACAGAAATATGCCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
** *
1296785 GATTAATGATCTAGCTG
66 GATTAATGGCCTAGTTG
*
1296802 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAG-TAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
*
1296866 TATTAATGGCCTAGTTG
66 GATTAATGGCCTAGTTG
*
1296883 TGCATTTGA-AGAAAGGTGTTC-ATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAA
1 TGCATTTGACAGAAATGTG-TCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAA
* * *
1296946 ATATTAATGGTCTAGCTG
65 AGATTAATGGCCTAGTTG
* * *
1296964 TGCATTTGACATAAAGGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
*
1297029 GATTAATGGCCTAGATG
66 GATTAATGGCCTAGTTG
** *
1297046 TGCATGGGACAGAAATGTGTCAATTATGCCAGCTAGATGAAAGGTTAAATACCTTTGAG-TAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
* *
1297110 GATTAATGGCTTAGCTG
66 GATTAATGGCCTAGTTG
1297127 TGCAT
1 TGCAT
1297132 AGTTGGCATT
Statistics
Matches: 689, Mismatches: 43, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
80 47 0.07
81 161 0.23
82 478 0.69
83 3 0.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (82 bp):
TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGATAAAA
GATTAATGGCCTAGTTG
Found at i:1296746 original size:245 final size:245
Alignment explanation
Indices: 1296311--1297131 Score: 1324
Period size: 245 Copynumber: 3.4 Consensus size: 245
1296301 ACACTAGCTA
* * *
1296311 TGCATTTGATAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAAATAAAA
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTG-AGTAAAA
* ** *
1296376 TATTAATGGCCTAGTAATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAA
65 GATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAA
* *
1296441 ATACCTTTGAGATAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCA
130 ATACCTTTGAGATAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCA
* * *
1296506 GTTAGATGAAAGGCTAAATACCTTTGAGATAAAAGAGTAATGGCCTAGTTG
195 GTTAGATGAAAGGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGATG
*
1296557 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1296622 ATTAATGGCCTAGTTGTGCA-TTGAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAA
66 ATTAATGGCCTAGTTGTGCATTTG-ACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAA
* * *
1296686 ATACCTTTGAGATAAAAGATTAATGGTCTAGCTATGCATTTGACAGAAATATGCCAATTATGCCA
130 ATACCTTTGAGATAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCA
** *
1296751 GTTAGATGAAAGGTTAAATACCTTTGAGATAAAAGATTAATGATCTAGCTG
195 GTTAGATGAAAGGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGATG
* *
1296802 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAT
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1296867 ATTAATGGCCTAGTTGTGCATTTGA-AGAAAGGTGTTC-ATTATGCCAGTTAGATGAAAGGTTAA
66 ATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTG-TCAATTATGCCAGTTAGATGAAAGGTTAA
* * * *
1296930 ATACCTTTGAGATAAAATATTAATGGTCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGTCA
130 ATACCTTTGAGATAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCA
1296995 GTTAGATGAAAGGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGATG
195 GTTAGATGAAAGGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGATG
** *
1297046 TGCATGGGACAGAAATGTGTCAATTATGCCAGCTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* *
1297111 ATTAATGGCTTAGCTGTGCAT
66 ATTAATGGCCTAGTTGTGCAT
1297132 AGTTGGCATT
Statistics
Matches: 534, Mismatches: 38, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
244 223 0.42
245 254 0.48
246 57 0.11
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (245 bp):
TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
ATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
TACCTTTGAGATAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAG
TTAGATGAAAGGTTAAATACCTTTGAGATAAAAGATTAATGGCCTAGATG
Found at i:1297202 original size:46 final size:46
Alignment explanation
Indices: 1297127--1297255 Score: 177
Period size: 46 Copynumber: 2.8 Consensus size: 46
1297117 GGCTTAGCTG
* * * *
1297127 TGCATAGTTGGCATTAAAAGATGTTATAAATGAAAATGTAAAACAA
1 TGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGTAAAACAA
* *
1297173 TGCATAATTAGCATGAAAGGATGTCATAAATGAAAATGTATAACAA
1 TGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGTAAAACAA
* * *
1297219 TGCATAATTGGCATGAAAGGATGCCACAAATAAAAAT
1 TGCATAATTGGCATGAAAGGATGTCATAAATGAAAAT
1297256 ACTTAATGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (46 bp):
TGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGTAAAACAA
Found at i:1301004 original size:16 final size:16
Alignment explanation
Indices: 1300967--1300997 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1300957 GATTAGAGGA
*
1300967 TATTTTTATATATTTG
1 TATTTTTATATAGTTG
1300983 TATTTTTATATAGTT
1 TATTTTTATATAGTT
1300998 TAGTTTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTTTATATAGTTG
Found at i:1301710 original size:3 final size:3
Alignment explanation
Indices: 1301702--1301767 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1301692 ATGGAATTTA
1301702 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1301750 GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT
1301768 TTCGAATTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1303816 original size:14 final size:14
Alignment explanation
Indices: 1303797--1303825 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1303787 TAATCTTCGT
1303797 TCTTTTAATTTATC
1 TCTTTTAATTTATC
1303811 TCTTTTAATTTATC
1 TCTTTTAATTTATC
1303825 T
1 T
1303826 TTACCATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (14 bp):
TCTTTTAATTTATC
Found at i:1303862 original size:22 final size:21
Alignment explanation
Indices: 1303840--1303882 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1303830 CATATCAAAT
1303840 TTAAATTAGT-TAATTAATAAA
1 TTAAATT-GTATAATTAATAAA
1303861 TTAAATTGTAATAATTAATAAA
1 TTAAATTGT-ATAATTAATAAA
1303883 AATGTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 7 0.35
22 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (21 bp):
TTAAATTGTATAATTAATAAA
Found at i:1304548 original size:22 final size:22
Alignment explanation
Indices: 1304520--1304573 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1304510 AACCCACCCC
* *
1304520 CTTCTTCTTCTCCATATTATTT
1 CTTCTTCTTCTCCAGATTACTT
* * *
1304542 CTTCTTCTTTTCCGGGTTACTT
1 CTTCTTCTTCTCCAGATTACTT
1304564 CTTCTTCTTC
1 CTTCTTCTTC
1304574 ATCATCTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.07, C:0.30, G:0.06, T:0.57
Consensus pattern (22 bp):
CTTCTTCTTCTCCAGATTACTT
Found at i:1307846 original size:20 final size:20
Alignment explanation
Indices: 1307816--1307875 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
1307806 AGTCGTTGAG
*
1307816 GCCTGATGGTATCGATATTAT
1 GCCT-ATGGTATCGATACTAT
1307837 GCCTATGGTATCGATACTAT
1 GCCTATGGTATCGATACTAT
1307857 GCCTATGGTATCGATACTA
1 GCCTATGGTATCGATACTA
1307876 CTATACAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
GCCTATGGTATCGATACTAT
Found at i:1310899 original size:22 final size:22
Alignment explanation
Indices: 1310874--1310964 Score: 66
Period size: 22 Copynumber: 4.4 Consensus size: 22
1310864 ATTACGGGTC
1310874 TTATTAATAAAATTAATGATAT
1 TTATTAATAAAATTAATGATAT
* * * *
1310896 TTATTAATGATATTTATAAT-T
1 TTATTAATAAAATTAATGATAT
*** *
1310917 TTA-TAA-ATTGTTAAT-A-AA
1 TTATTAATAAAATTAATGATAT
*
1310935 TTGTTAATAAAATTAATGATAT
1 TTATTAATAAAATTAATGATAT
1310957 TTATTAAT
1 TTATTAAT
1310965 TTCATAAAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
18 3 0.06
19 8 0.16
20 9 0.18
21 5 0.10
22 24 0.49
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TTATTAATAAAATTAATGATAT
Found at i:1310903 original size:13 final size:13
Alignment explanation
Indices: 1310885--1310912 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1310875 TATTAATAAA
1310885 ATTAATGATATTT
1 ATTAATGATATTT
1310898 ATTAATGATATTT
1 ATTAATGATATTT
1310911 AT
1 AT
1310913 AATTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTAATGATATTT
Found at i:1310935 original size:11 final size:11
Alignment explanation
Indices: 1310919--1310945 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1310909 TTATAATTTT
1310919 ATAAATTGTTA
1 ATAAATTGTTA
1310930 ATAAATTGTTA
1 ATAAATTGTTA
1310941 ATAAA
1 ATAAA
1310946 ATTAATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (11 bp):
ATAAATTGTTA
Found at i:1311118 original size:43 final size:43
Alignment explanation
Indices: 1311063--1311152 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1311053 AATTTAATAA
* * *
1311063 TATTATTATTTTAATAAGTAATTAATATCATTAATAATATTTT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATAATTT
*
1311106 TATTATTATTTTAATAAATAATTAATATAATTTATAATAATTT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATAATTT
1311149 TATT
1 TATT
1311153 TTAATTAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (43 bp):
TATTATTATTTTAATAAATAATTAATATAATTAATAATAATTT
Found at i:1311289 original size:22 final size:20
Alignment explanation
Indices: 1311239--1311302 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
1311229 ATAAATAATA
*
1311239 TTAAATAAATTATTATAATATT
1 TTAAAT-AATTATTATTAT-TT
1311261 TTAAATATATTATTATTATTT
1 TTAAATA-ATTATTATTATTT
* * *
1311282 TGTTAATAAATAATATTATTT
1 T-TAAATAATTATTATTATTT
1311303 ATTGCATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAAATAATTATTATTATTT
Found at i:1325965 original size:73 final size:73
Alignment explanation
Indices: 1325824--1325970 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 73
1325814 GGGGTATAAC
* * * *
1325824 ACTGCCTATAAGGGATATAAATGCTTGGATGATTATGGCATGGTGATTATTTTGAGGCATGCTAT
1 ACTGCCCATAAGGGATATAAATGCTTGGATGATTATGGCAGGGTAATTATTTCGAGGCATGCTAT
*
1325889 TTTTTATG
66 TTTTGATG
* * *
1325897 ACTGCCCATAAGGGATATAAATGCTTGGATGATTCTGGCAGGGTAATTATTTCGAGGCATGTTGT
1 ACTGCCCATAAGGGATATAAATGCTTGGATGATTATGGCAGGGTAATTATTTCGAGGCATGCTAT
1325962 TTTTGATG
66 TTTTGATG
1325970 A
1 A
1325971 AAGGGTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (73 bp):
ACTGCCCATAAGGGATATAAATGCTTGGATGATTATGGCAGGGTAATTATTTCGAGGCATGCTAT
TTTTGATG
Found at i:1327973 original size:23 final size:23
Alignment explanation
Indices: 1327955--1328015 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1327945 CTCGTATAAA
1327955 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
**
1327978 TGCACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1328001 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1328016 TATAAGATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1328355 original size:24 final size:25
Alignment explanation
Indices: 1328317--1328363 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1328307 ATGCACATAG
*
1328317 TATGAATTCATATCATGCTTCAAAA
1 TATGAATTCATATCATGCATCAAAA
*
1328342 TATGAATTGA-ATCATGCATCAA
1 TATGAATTCATATCATGCATCAA
1328364 TGTATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (25 bp):
TATGAATTCATATCATGCATCAAAA
Found at i:1333612 original size:23 final size:23
Alignment explanation
Indices: 1333586--1333669 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
1333576 CTCGTATAAA
*
1333586 TGCACCAAAGTGCCCCGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
1333609 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
* *
1333632 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
1333655 TGCACCATAGTGCCA
1 TGCACCAAAGTGCCA
1333670 TATAAGATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:1337605 original size:7 final size:7
Alignment explanation
Indices: 1337595--1338101 Score: 797
Period size: 7 Copynumber: 74.7 Consensus size: 7
1337585 TAAAGATTAA
1337595 AATTTAT
1 AATTTAT
1337602 AATTTAT
1 AATTTAT
1337609 AATTTAT
1 AATTTAT
1337616 AATTTAT
1 AATTTAT
1337623 AATTTAT
1 AATTTAT
1337630 AATTTAT
1 AATTTAT
1337637 AATTTAT
1 AATTTAT
1337644 AATTTAT
1 AATTTAT
1337651 AATTTAT
1 AATTTAT
1337658 AATTTAT
1 AATTTAT
1337665 AATTTAT
1 AATTTAT
1337672 AATTTAT
1 AATTTAT
1337679 AATTTAT
1 AATTTAT
1337686 AATTTAT
1 AATTTAT
1337693 AATTTAT
1 AATTTAT
1337700 AATTTAT
1 AATTTAT
1337707 AATTTAT
1 AATTTAT
1337714 AATTTAT
1 AATTTAT
1337721 AATTTAT
1 AATTTAT
1337728 AATTTAT
1 AATTTAT
1337735 AATTTAT
1 AATTTAT
1337742 AATTTAT
1 AATTTAT
1337749 AATTTAT
1 AATTTAT
1337756 AA-TTAT
1 AATTTAT
1337762 AATTTAT
1 AATTTAT
1337769 AA-TTAT
1 AATTTAT
1337775 AATTTAT
1 AATTTAT
1337782 AATTTAT
1 AATTTAT
1337789 AATTTAT
1 AATTTAT
1337796 AATTTAT
1 AATTTAT
1337803 AATTTAT
1 AATTTAT
1337810 AA-TTAT
1 AATTTAT
1337816 AATTTAT
1 AATTTAT
1337823 AATTT-T
1 AATTTAT
1337829 AA-TT-T
1 AATTTAT
1337834 AA-TTAT
1 AATTTAT
1337840 AA-TTAT
1 AATTTAT
1337846 -ATTTAT
1 AATTTAT
1337852 -ATTTAT
1 AATTTAT
1337858 AATTTAT
1 AATTTAT
1337865 AATTTAT
1 AATTTAT
1337872 AATTTAT
1 AATTTAT
1337879 AATTTAT
1 AATTTAT
1337886 -ATTTAT
1 AATTTAT
1337892 AA-TT-T
1 AATTTAT
1337897 AATTTAT
1 AATTTAT
1337904 AA-TTAT
1 AATTTAT
1337910 -ATTTA-
1 AATTTAT
1337915 AATTTAT
1 AATTTAT
1337922 AATTTAT
1 AATTTAT
1337929 AATTTTAT
1 AA-TTTAT
1337937 AA-TTAT
1 AATTTAT
1337943 AATTTAT
1 AATTTAT
1337950 AATTTAT
1 AATTTAT
1337957 AAATAATTAT
1 -AAT--TTAT
1337967 AA-TT-T
1 AATTTAT
1337972 -ATTTAT
1 AATTTAT
1337978 AATTTAT
1 AATTTAT
1337985 AATTTAT
1 AATTTAT
1337992 -ATTT-T
1 AATTTAT
1337997 AATTTAT
1 AATTTAT
1338004 AATTTAT
1 AATTTAT
1338011 AATTTAT
1 AATTTAT
1338018 AATTTAT
1 AATTTAT
1338025 AATTTAT
1 AATTTAT
1338032 AATTTAT
1 AATTTAT
1338039 AATTTAT
1 AATTTAT
1338046 AATTTAT
1 AATTTAT
1338053 AATTTAT
1 AATTTAT
1338060 AATTTATT
1 AATTTA-T
*
1338068 ATAATTAT
1 A-ATTTAT
1338076 AATTTAT
1 AATTTAT
1338083 AATTTAT
1 AATTTAT
1338090 AATTTAT
1 AATTTAT
1338097 AATTT
1 AATTT
1338102 TTAAATATAA
Statistics
Matches: 474, Mismatches: 2, Indels: 48
0.90 0.00 0.09
Matches are distributed among these distances:
4 1 0.00
5 16 0.03
6 77 0.16
7 356 0.75
8 14 0.03
9 6 0.01
10 4 0.01
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTAT
Done.