Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 16
Found at i:1079245 original size:27 final size:26
Alignment explanation
Indices: 1079214--1079289 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
1079204 ATACTTAAAT
1079214 ACTTTATATTATATACTTATACTTT-AG
1 ACTTTATATT-TATACTTATA-TTTAAG
* * *
1079241 CCTTTATAATTATACTTTATATTTAAT
1 ACTTTATATTTATAC-TTATATTTAAG
1079268 ACTTTATATTTAATACTTATAT
1 ACTTTATATTT-ATACTTATAT
1079290 ACTTTAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 8 0.20
27 29 0.71
28 4 0.10
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (26 bp):
ACTTTATATTTATACTTATATTTAAG
Found at i:1079422 original size:22 final size:21
Alignment explanation
Indices: 1079397--1079439 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1079387 CTCTTTGTAA
1079397 TTATACTTTATATATATAATAT
1 TTATACTTTATAT-TATAATAT
*
1079419 TTATACTTTATATTATTATAT
1 TTATACTTTATATTATAATAT
1079440 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATACTTTATATTATAATAT
Found at i:1079424 original size:133 final size:136
Alignment explanation
Indices: 1079266--1079596 Score: 348
Period size: 133 Copynumber: 2.5 Consensus size: 136
1079256 TTTATATTTA
*
1079266 ATACTTTATAT-T-TAATACTTATATACTTTAAATTATTATATTCATATATATATATATATATAT
1 ATACTTTATATATATAATA-TT-TATACTTTATATTATTATATT-ATATATATATATATATATAT
* ** * * *
1079329 AC-ACACACACTT-TATATTTA-GTAC-TTAT-ATAT-TTTATA-TTATATGCTTATATACTTTA
63 ACTA-A-A-ACTTATATATATACACACTTTATAACATACTTATACTTATATACTTATATACTTTA
1079387 CTCTTTGTAATT
125 CTCTTTGTAATT
* *
1079399 ATACTTTATATATATAATATTTATACTTTATATTATTATA-TATGTATATATA-CT-T-TATACT
1 ATACTTTATATATATAATATTTATACTTTATATTATTATATTATATATATATATATATATATACT
* *
1079460 AAAACTTATATATATACACACTTTATACACATACTTATACTTTATATACTTATATACTTTAGTTT
66 AAAACTTATATATATACACACTTTATA-ACATACTTATAC-TTATATACTTATATACTTTACTCT
1079525 TTGTAATT
129 TTGTAATT
* * *
1079533 ATACTTTATATATAT-ATATATATACTTTATATTATTATATATGTATATATACTTTATATATATA
1 ATACTTTATATATATAATATTTATACTTTATATTATTATAT-TATATATATA-TATATATATATA
1079597 TATACTTTAT
Statistics
Matches: 165, Mismatches: 16, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
126 4 0.02
127 8 0.05
128 8 0.05
129 6 0.04
130 1 0.01
131 13 0.08
132 6 0.04
133 52 0.32
134 47 0.28
135 13 0.08
136 1 0.01
137 1 0.01
138 1 0.01
139 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (136 bp):
ATACTTTATATATATAATATTTATACTTTATATTATTATATTATATATATATATATATATATACT
AAAACTTATATATATACACACTTTATAACATACTTATACTTATATACTTATATACTTTACTCTTT
GTAATT
Found at i:1079434 original size:27 final size:27
Alignment explanation
Indices: 1079398--1079600 Score: 91
Period size: 27 Copynumber: 7.9 Consensus size: 27
1079388 TCTTTGTAAT
1079398 TATACTTTATA-TA-TATA-ATAT-T-
1 TATACTTTATATTATTATATATATATA
*
1079420 TATACTTTATATTATTATATATGTATA
1 TATACTTTATATTATTATATATATATA
* **
1079447 TATACTTTATACTAAAACTTATATATATA
1 TATACTTTATATTATTA--TATATATATA
* * * * *
1079476 CACACTTTATA-CA-CATACTTATACTTTA
1 TATACTTTATATTATTATA--TATA-TATA
* *
1079504 TATACTTATATACTTTAGTT-TTTGTA-AT-
1 TATACTT-TATA--TTA-TTATATATATATA
1079532 TATAC-TT-TA-TA-TA--TATATATA
1 TATACTTTATATTATTATATATATATA
*
1079553 TATACTTTATATTATTATATATGTATA
1 TATACTTTATATTATTATATATATATA
1079580 TATACTTTATA-TA-TATATATA
1 TATACTTTATATTATTATATATA
1079601 CTTTATATTT
Statistics
Matches: 136, Mismatches: 20, Indels: 47
0.67 0.10 0.23
Matches are distributed among these distances:
19 3 0.02
20 3 0.02
21 5 0.04
22 15 0.11
23 4 0.03
24 6 0.04
25 16 0.12
26 4 0.03
27 38 0.28
28 14 0.10
29 23 0.17
31 3 0.02
32 1 0.01
33 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.51
Consensus pattern (27 bp):
TATACTTTATATTATTATATATATATA
Found at i:1079470 original size:29 final size:29
Alignment explanation
Indices: 1079437--1079517 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
1079427 TATATTATTA
1079437 TATATGTATATATACTTTATACTA-AAACT
1 TATAT-TATATATACTTTATACTACAAACT
* * *
1079466 TATATATATACACACTTTATAC-ACATACT
1 TATAT-TATATATACTTTATACTACAAACT
1079495 TATACTT-TATATACTTATATACT
1 TATA-TTATATATACTT-TATACT
1079518 TTAGTTTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 8 0.19
29 33 0.79
30 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (29 bp):
TATATTATATATACTTTATACTACAAACT
Found at i:1079546 original size:2 final size:2
Alignment explanation
Indices: 1079539--1079600 Score: 65
Period size: 2 Copynumber: 31.0 Consensus size: 2
1079529 AATTATACTT
* *
1079539 TA TA TA TA TA TA TA TA TA CTT TA TA T- TA T- TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
1079580 TA TA CTT TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA
1079601 CTTTATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
1 2 0.04
2 46 0.92
3 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1079674 original size:27 final size:27
Alignment explanation
Indices: 1079541--1079675 Score: 105
Period size: 27 Copynumber: 4.9 Consensus size: 27
1079531 TTATACTTTA
* *
1079541 TATATATATATATATACTTTATATTAT
1 TATATATTTATATATACTTTATATAAT
*
1079568 TATATATGTATATATACTTTATAT-AT
1 TATATATTTATATATACTTTATATAAT
* *
1079594 ATATATACTTTATATTTGAC-CTATATAAAT
1 -TATATA-TTTATATAT-ACTTTATAT-AAT
* * * *
1079624 TATATAATTTATACACAATATATATAAT
1 TATAT-ATTTATATATACTTTATATAAT
*
1079652 T-TATAGTTTATATATAGTTTATAT
1 TATATA-TTTATATATACTTTATAT
1079676 TAATAAAATA
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.03
27 46 0.53
28 17 0.20
29 18 0.21
30 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (27 bp):
TATATATTTATATATACTTTATATAAT
Found at i:1079712 original size:20 final size:20
Alignment explanation
Indices: 1079624--1079716 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
1079614 CTATATAAAT
1079624 TATATAATTTATACACA-ATA
1 TATATAATTTATACA-ATATA
* *
1079644 TATATAATTTAT--AGTTTA
1 TATATAATTTATACAATATA
* * *
1079662 TATATAGTTTATATTAATAAAA
1 TATATAATTTATA-CAAT-ATA
* *
1079684 TAGATAATTTATACAATGTA
1 TATATAATTTATACAATATA
1079704 TATATAATTTATA
1 TATATAATTTATA
1079717 ATTATACATA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
18 14 0.25
20 25 0.45
21 5 0.09
22 12 0.21
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATAATTTATACAATATA
Found at i:1079727 original size:17 final size:18
Alignment explanation
Indices: 1079687--1079735 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1079677 AATAAAATAG
*
1079687 ATAATTTATACAATGTATAT
1 ATAATTTAT--AATGTATAC
1079707 ATAATTTATAAT-TATAC
1 ATAATTTATAATGTATAC
*
1079724 ATAATATATAAT
1 ATAATTTATAAT
1079736 ATAAGTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 15 0.56
18 3 0.11
20 9 0.33
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
ATAATTTATAATGTATAC
Found at i:1079794 original size:20 final size:21
Alignment explanation
Indices: 1079764--1079816 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1079754 AATATAATTC
1079764 ATATAAATTTACATT-TAAACT
1 ATAT-AATTTACATTATAAACT
*
1079785 ATATAATTTATATTAATAAACT
1 ATATAATTTACATT-ATAAACT
*
1079807 ATATAGTTTA
1 ATATAATTTA
1079817 TATATGGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.32
21 4 0.14
22 15 0.54
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATAATTTACATTATAAACT
Found at i:1079870 original size:2 final size:2
Alignment explanation
Indices: 1079863--1079932 Score: 70
Period size: 2 Copynumber: 34.0 Consensus size: 2
1079853 TTATACATTG
* * * *
1079863 TA TA TA TA GTC TA TA CA TA -A TA TA TA TA TA GTT TT TA TA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
1079907 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
1079933 CACACGCATA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
1 1 0.02
2 53 0.91
3 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1079870 original size:20 final size:20
Alignment explanation
Indices: 1079847--1079912 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1079837 ATATAAACTC
1079847 TATAGTTTATACATTGTATA
1 TATAGTTTATACATTGTATA
* *
1079867 TATAGTCTATACATAATATATA
1 TATAGTTTATACAT--TGTATA
* * *
1079889 TATAGTTTTTATATAGTATA
1 TATAGTTTATACATTGTATA
1079909 TATA
1 TATA
1079913 TATATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 21 0.57
22 16 0.43
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (20 bp):
TATAGTTTATACATTGTATA
Found at i:1080103 original size:2 final size:2
Alignment explanation
Indices: 1080096--1081157 Score: 155
Period size: 2 Copynumber: 535.0 Consensus size: 2
1080086 ATTATACTTT
*
1080096 TA TA TA TA TA -A TA TA CT- TA TA T- TT TA TA T- TA T- 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
* * * *
1080134 TG TA TA TA TA CTT TA TA CTA -A AA CTT 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
* * * * *
1080176 TA TA TA T- TA TA CTT TG TA GTT TA TA TA TT TA -A TA TT 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
* * *
1080218 CTT TA TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TA T- TA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
1080258 TA TA CA TA TA TA TA CTT TA TT TT TA -A TA CT- TA TA TA T- TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
1080299 TA T- TA TA TA CT- TA TA TA CA T- TA TA T- TA TA TGC T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* * * * *
1080338 CTT TA -A TG TG TA TA -A T- TA TA CTT TT TA TA TA TA TA -A TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
1080378 CT- TA TA CTT TA TA T- TA T- TA TA TG TA TA TA TA CTT TA TA CTA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* *
1080419 -A AA CTT 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
* * * * * *
1080461 TA TA TA TA TA TT TA TA CTT TG TA GTT TA TA TA TA CT- TT TA CTT
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA -TA
* * * * *
1080504 TA TA AA TA CA TA CT- TA TA CTT TA TA TG TA TA TA TA CTT TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
1080546 TA CT- TA CA TA -A TT TA GTC TT TA TA -A T- TA TA CTT TA TA TA
1 TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
*
1080585 TA TA TA TA TA -A TA TA CT- TA TA CTT TA TA T- 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
* * * * *
1080626 -A TT TA T- TG TT TA TA TA TA TA CT- TA -A GTA CTT TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA -TA TA TA TA TA
* * * * * * *
1080665 AA CTA TA TA AA CTA TA TA -A TT TA TA CA TA GTG TA AA TA -A TT
1 TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
1080706 TA TA -A T- TA TA CA TA -A TA TA TA AA TA TA -A GT- TG 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
* * * *
1080744 TT TA AA TA TA -A T- TCA TA TA TA -A TT TA TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
1080785 -A TT TA TA T- TA -A TA AA CTA TA TA GTT TA TA TA TA GT- TCA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA T-A TA
* * * * *
1080824 TA GT- TCA TA TA TA AA CTC TA TA GTT TA TA TA TGG TA TA TA GTT
1 TA -TA T-A TA TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA -TA
* *
1080867 TA TA CA TA -A TA TA TA T- TT TA TA TA TA GTA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
1080906 AA TA TA AA CTA TA TA GTT TA TA TA TA -A TA TA TA CTT TA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
1080948 TA CA CTA TA TA -A TT TA TA -A TA TA GTT TA TA CA T- TA TA TC TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
1080989 TA GTT TA TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
1081030 TA GT- TT TA -A TA TA TA -A CA TA TA TA CTT TA TA TG TA CA CTA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
1081070 TA TA GTT TA TA TA TA GTT TA TA -A TA -A TA TA AA TA TA AA CTA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
1081111 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
1081153 T- TA TA
1 TA TA TA
1081158 ATTGTTTCAA
Statistics
Matches: 749, Mismatches: 174, Indels: 274
0.63 0.15 0.23
Matches are distributed among these distances:
1 73 0.10
2 612 0.82
3 64 0.09
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1080134 original size:25 final size:25
Alignment explanation
Indices: 1080082--1080133 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1080072 CTTTAGTCTT
1080082 TATAATTATACTTTTATATATATAA
1 TATAATTATACTTTTATATATATAA
* *
1080107 TATACTTATA-TTTTATAT-TATTA
1 TATAATTATACTTTTATATATATAA
1080130 TATA
1 TATA
1080134 TGTATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.32
24 8 0.32
25 9 0.36
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TATAATTATACTTTTATATATATAA
Found at i:1080201 original size:59 final size:60
Alignment explanation
Indices: 1080130--1080262 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 60
1080120 TATATTATTA
1080130 TATATGTA-TATATACTTT-ATA-CTA-AAACTTTATATATATATATATATATATATTATACTT
1 TATA-GTATTATATACTTTAATATCTATAAACTTTATAT-TAT-TATATATATATA-TATACTT
* * * *
1080190 TGTAGT-TTATATA-TTTAATATTTATATACTTTATATTATTATATATGTATATATACTT
1 TATAGTATTATATACTTTAATATCTATAAACTTTATATTATTATATATATATATATACTT
*
1080248 TATATTATTATATAC
1 TATAGTATTATATAC
1080263 ATATATATAC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
58 14 0.23
59 29 0.48
60 8 0.13
61 10 0.16
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (60 bp):
TATAGTATTATATACTTTAATATCTATAAACTTTATATTATTATATATATATATATACTT
Found at i:1080212 original size:7 final size:8
Alignment explanation
Indices: 1079949--1080476 Score: 162
Period size: 8 Copynumber: 65.2 Consensus size: 8
1079939 CATACATACT
1079949 TATACTTTA
1 TATA-TTTA
* *
1079958 TATGTATA
1 TATATTTA
1079966 TATACTTTA
1 TATA-TTTA
1079975 TATACTTT-
1 TATA-TTTA
1079983 T-TATTTA
1 TATATTTA
*
1079990 -ATACTTA
1 TATATTTA
*
1079997 TAGACTTTA
1 TATA-TTTA
1080006 TATTATTATA
1 TA-TATT-TA
* *
1080016 TACATATA
1 TATATTTA
*
1080024 TATAGTT-
1 TATATTTA
1080031 TATATTTA
1 TATATTTA
*
1080039 -ATACTTA
1 TATATTTA
1080046 TATATTT-
1 TATATTTA
1080053 TATA-TTA
1 TATATTTA
**
1080060 TATGCTTA
1 TATATTTA
1080068 TATACTTTA
1 TATA-TTTA
* *
1080077 -GTCTTTA
1 TATATTTA
1080084 TA-A-TTA
1 TATATTTA
1080090 TACT-TTTA
1 TA-TATTTA
*
1080098 TATATATAA
1 TATAT-TTA
*
1080107 TATACTTA
1 TATATTTA
1080115 TAT-TTTA
1 TATATTTA
1080122 TAT-TATTA
1 TATAT-TTA
1080130 TATATGTATA
1 TATAT-T-TA
1080140 TATACTTTA
1 TATA-TTTA
1080149 TACTAAAACTTTA
1 TA-T---A-TTTA
*
1080162 TATATATA
1 TATATTTA
*
1080170 TATATATA
1 TATATTTA
1080178 TATA-TTA
1 TATATTTA
* *
1080185 TA-CTTTG
1 TATATTTA
*
1080192 TA-GTTTA
1 TATATTTA
1080199 TATATTTA
1 TATATTTA
1080207 -ATATTTA
1 TATATTTA
1080214 TATACTTTA
1 TATA-TTTA
1080223 TAT-TATTA
1 TATAT-TTA
1080231 TATATGTATA
1 TATAT-T-TA
1080241 TATACTTTA
1 TATA-TTTA
1080250 TATTATTATA
1 TA-TATT-TA
* *
1080260 TACATATA
1 TATATTTA
1080268 TATACTTTA
1 TATA-TTTA
1080277 T-T-TTTA
1 TATATTTA
*
1080283 -ATACTTA
1 TATATTTA
1080290 TATATTT-
1 TATATTTA
1080297 TATA-TTA
1 TATATTTA
*
1080304 TATACTTA
1 TATATTTA
**
1080312 TATACAT-
1 TATATTTA
1080319 TATA-TTA
1 TATATTTA
**
1080326 TATGCTTA
1 TATATTTA
1080334 TATACTTTA
1 TATA-TTTA
* *
1080343 -ATGTGTA
1 TATATTTA
1080350 TA-A-TTA
1 TATATTTA
*
1080356 TACTTTTTA
1 TA-TATTTA
*
1080365 TATATATAA
1 TATAT-TTA
*
1080374 TATACTTA
1 TATATTTA
*
1080382 TA-CTTTA
1 TATATTTA
1080389 TAT-TATTA
1 TATAT-TTA
* *
1080397 TATGTATA
1 TATATTTA
1080405 TATACTTTA
1 TATA-TTTA
1080414 TACTAAAACTTTA
1 TA-T---A-TTTA
*
1080427 TATATATA
1 TATATTTA
*
1080435 TATATATA
1 TATATTTA
*
1080443 TATATATA
1 TATATTTA
*
1080451 TATATATA
1 TATATTTA
*
1080459 TATATATA
1 TATATTTA
1080467 TATATTTA
1 TATATTTA
1080475 TA
1 TA
1080477 CTTTGTAGTT
Statistics
Matches: 398, Mismatches: 63, Indels: 117
0.69 0.11 0.20
Matches are distributed among these distances:
6 22 0.06
7 86 0.22
8 162 0.41
9 81 0.20
10 27 0.07
11 2 0.01
12 2 0.01
13 16 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (8 bp):
TATATTTA
Found at i:1080214 original size:116 final size:115
Alignment explanation
Indices: 1080002--1080316 Score: 280
Period size: 116 Copynumber: 2.6 Consensus size: 115
1079992 ACTTATAGAC
* * * * *
1080002 TTTATATTATTATATACATATATATAGTTTATATTTAATACTTATATATTTTATATTATATGCTT
1 TTTATATTATTATATACATATATATACTTTATATCTAAAACTTATATATTATATATTATAT-CAT
*
1080067 ATATACTTTAGTCTTTATAATTATACTTTTATATATATAATATACTTATAT
65 ATATACTTTAGTCTTTATAATTATAATTTTATATATATAATATACTTATAT
**
1080118 TTTATATTATTATATATGTATATATACTTTATA-CTAAAACTT-TATATATATATATATATAT-A
1 TTTATATTATTATATACATATATATACTTTATATCTAAAACTTATATAT-TATATAT-TATATCA
* *
1080180 TATTATACTTT-GTAGTTTATATATT-TAATATTTATATACTTTATATTATTATATATGTATATA
64 TA-TATACTTTAGT-CTTTATA-ATTAT-A-ATTT-TATA---TATA-TA--ATATA-CT-TATA
1080243 T
115 T
* * * *
1080244 ACTTTATATTATTATATACATATATATACTTTATTTTTAATACTTATATATTTTATATTATATAC
1 --TTTATATTATTATATACATATATATACTTTATATCTAAAACTTATATATTATATATTATAT-C
*
1080309 TTATATAC
63 ATATATAC
1080317 ATTATATTAT
Statistics
Matches: 160, Mismatches: 17, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
114 9 0.06
115 28 0.17
116 39 0.24
117 3 0.02
118 4 0.03
121 4 0.03
122 2 0.01
124 5 0.03
125 1 0.01
126 5 0.03
128 35 0.22
129 18 0.11
130 7 0.04
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (115 bp):
TTTATATTATTATATACATATATATACTTTATATCTAAAACTTATATATTATATATTATATCATA
TATACTTTAGTCTTTATAATTATAATTTTATATATATAATATACTTATAT
Found at i:1080252 original size:76 final size:75
Alignment explanation
Indices: 1080019--1080315 Score: 197
Period size: 76 Copynumber: 3.9 Consensus size: 75
1080009 TATTATATAC
* **
1080019 ATATATATAGTTTATA-TTTAATACTTATATATTTT-ATA-TTATATGCTTATATACTT-TAGTC
1 ATATATATA--TTATACTTT-ATACTT-TATATTTTAATATTTATATACTT-TATA-TTATAAAC
*
1080080 TTTATA-ATTATACTTTT
60 TATATATA-TATAC-TTT
* * * *
1080097 ATATATATAATATAC-TTATATTTTATATTATTATATATGTATATATACTTTATACTA-AAACTT
1 ATATATATATTATACTTTATACTTTATATT-TTA-ATAT-T-TATATACTTTATATTATAAACTA
*
1080160 TATATATATA-TAT
62 TATATATATACTTT
* * * *
1080173 ATATATATATTATACTTTGTAGTTTATATATTTAATATTTATATACTTTATATTATTATA-TATG
1 ATATATATATTATACTTTATACTTTATAT-TTTAATATTTATATACTTTATATTA-TAAACTATA
1080237 TATATATACTTT
64 TATATATACTTT
* * *
1080249 ATAT-TAT-TATATACATATATATACTTTAT-TTTTAATACTTATATATTTTATATTATATACT-
1 ATATATATAT-TATAC-T-T-TATACTTTATATTTTAATATTTATATACTTTATATTATAAACTA
1080310 TATATA
62 TATATA
1080316 CATTATATTA
Statistics
Matches: 180, Mismatches: 20, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
74 22 0.12
75 35 0.19
76 59 0.33
77 19 0.11
78 31 0.17
79 6 0.03
80 8 0.04
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.55
Consensus pattern (75 bp):
ATATATATATTATACTTTATACTTTATATTTTAATATTTATATACTTTATATTATAAACTATATA
TATATACTTT
Found at i:1080398 original size:26 final size:24
Alignment explanation
Indices: 1079948--1080661 Score: 197
Period size: 22 Copynumber: 29.5 Consensus size: 24
1079938 GCATACATAC
* *
1079948 TTATACTTTATATGTATATATACTT
1 TTATACTTTATATATATATATA-TA
* *
1079973 TATATACTTTTTATTTA-ATACT-TA
1 T-TATACTTTATATATATATA-TATA
* *
1079997 -TAGACTTTATATTATTATATACATA
1 TTATACTTTATA-TA-TATATATATA
* *
1080022 TATATAGTTTATATTTA-ATACT-TA
1 T-TATACTTTATATATATATA-TATA
* *
1080046 -TATATTTTATAT-TATATGCT-TA
1 TTATACTTTATATATATAT-ATATA
* *
1080068 -TATACTTTA-GTCT-T-TATA-A
1 TTATACTTTATATATATATATATA
1080087 TTATACTTT-TATATATATAATATA
1 TTATACTTTATATATATAT-ATATA
* *
1080111 CTTATATTTTATATTATTATATATGTA
1 -TTATACTTTATA-TA-TATATATATA
*
1080138 TATATACTTTATACTA-A-A-A-CT-
1 T-TATACTTTATA-TATATATATATA
*
1080159 TTATA-TATATATATATATATATA
1 TTATACTTTATATATATATATATA
*
1080182 TTATACTTTGTAGT-T-TATATAT-
1 TTATACTTTATA-TATATATATATA
*
1080204 TTAATA-TTTATATACTTTATAT-TA
1 TT-ATACTTTATATA-TATATATATA
*
1080228 TTATA-TATGTATATATACTTTATATTA
1 TTATACT-T-TATATATA-TATATA-TA
** * *
1080255 TTATA-TACATATATATACTTTATTT
1 TTATACTTTATATATATA-TATA-TA
*
1080280 TTAATAC-TTATATAT-TTTATAT-
1 TT-ATACTTTATATATATATATATA
*
1080302 TATATAC-TTATATACAT-TATAT-
1 T-TATACTTTATATATATATATATA
* * * *
1080324 TATATGCTTATATACTTTAATGTGTATAA
1 T-TATACTT-TATA-TAT-ATATATAT-A
*
1080353 TTATACTTTTTATATATATAATATA
1 TTATACTTTATATATATAT-ATATA
*
1080378 CTTATACTTTATAT-TATTATATGTA
1 -TTATACTTTATATATA-TATATATA
* *
1080403 TATATACTTTATACTA-AAACTTTATA
1 T-TATACTTTATA-TATATA-TATATA
*
1080429 -TATA-TATATATATATATATATA
1 TTATACTTTATATATATATATATA
*
1080451 -TATA-TATATATATATATATAT-
1 TTATACTTTATATATATATATATA
*
1080472 TTATACTTTGTAGT-T-TATATATA
1 TTATACTTTATA-TATATATATATA
* * *
1080495 CTTTTACTTTATA-A-ATACATA-C
1 -TTATACTTTATATATATATATATA
* *
1080517 TTATACTTTATATGTATATATACTT
1 TTATACTTTATATATATATATA-TA
* * * *
1080542 TATATACTTACATAATTTAGTCTTTATAA
1 T-TATACTT-TAT-ATATA-TATATAT-A
1080571 TTATACTTTATATATATATATATA
1 TTATACTTTATATATATATATATA
* *
1080595 ATATAC-TTATACTTTATATTATATA
1 TTATACTTTATA-TATATA-TATATA
* * *
1080620 TATATAATTTATTGTTTATATATATA
1 T-TATACTTTA-TATATATATATATA
1080646 CTTAAGTACTTTATAT
1 -TT-A-TACTTTATAT
1080662 TTAAACTATA
Statistics
Matches: 521, Mismatches: 83, Indels: 168
0.67 0.11 0.22
Matches are distributed among these distances:
18 2 0.00
19 8 0.02
20 16 0.03
21 19 0.04
22 106 0.20
23 58 0.11
24 59 0.11
25 81 0.16
26 77 0.15
27 59 0.11
28 30 0.06
29 6 0.01
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (24 bp):
TTATACTTTATATATATATATATA
Found at i:1080507 original size:17 final size:18
Alignment explanation
Indices: 1080473--1080512 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1080463 TATATATATT
*
1080473 TATACTTTGTAGTTTATA
1 TATACTTTGTACTTTATA
1080491 TATACTTT-TACTTTATA
1 TATACTTTGTACTTTATA
*
1080508 AATAC
1 TATAC
1080513 ATACTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (18 bp):
TATACTTTGTACTTTATA
Found at i:1080771 original size:9 final size:10
Alignment explanation
Indices: 1080706--1080792 Score: 54
Period size: 11 Copynumber: 8.3 Consensus size: 10
1080696 GTAAATAATT
1080706 TATAATTATA
1 TATAATTATA
*
1080716 CATAATATATAAA
1 TATAAT-TAT--A
*
1080729 TATAAGTTGTA
1 TATAA-TTATA
* *
1080740 TATATTTAAA
1 TATAATTATA
1080750 TATAATTCATA
1 TATAATT-ATA
1080761 TATAATTTATA
1 TATAA-TTATA
1080772 TATAA--ACTA
1 TATAATTA-TA
1080781 TATAATT-TA
1 TATAATTATA
1080790 TAT
1 TAT
1080793 TAATAAACTA
Statistics
Matches: 60, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
8 1 0.02
9 12 0.20
10 14 0.23
11 23 0.38
12 2 0.03
13 7 0.12
14 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (10 bp):
TATAATTATA
Found at i:1080894 original size:75 final size:76
Alignment explanation
Indices: 1080759--1080973 Score: 211
Period size: 75 Copynumber: 2.8 Consensus size: 76
1080749 ATATAATTCA
* * * * *
1080759 TATATAATTTATATATAAACTATATAATTTATATTAATAAACTATATAGTTTATATATAGTT-CA
1 TATATAGTTTATATAT-AA-TATATACTTTATA--CATACACTATATAATTTATATATAGTTACA
* *
1080823 ATAGTTCATATATAAAC
62 ATA-AT-AAATATAAAC
* ** * * *
1080840 TCTATAGTTTATATATGGTATATAGTTTATACATA-A-TATATATTTTATATATAGTATATAATA
1 TATATAGTTTATATATAATATATACTTTATACATACACTATATAATTTATATATAGT-TACAATA
1080903 ATAAATATAAAC
65 ATAAATATAAAC
*
1080915 TATATAGTTTATATATAATATATACTTTATATATACACTATATAATTTATAATATAGTT
1 TATATAGTTTATATATAATATATACTTTATACATACACTATATAATTTAT-ATATAGTT
1080974 TATACATTAT
Statistics
Matches: 113, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
75 57 0.50
76 4 0.04
77 19 0.17
78 7 0.06
79 12 0.11
81 14 0.12
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (76 bp):
TATATAGTTTATATATAATATATACTTTATACATACACTATATAATTTATATATAGTTACAATAA
TAAATATAAAC
Found at i:1080911 original size:57 final size:54
Alignment explanation
Indices: 1080858--1081014 Score: 162
Period size: 57 Copynumber: 2.9 Consensus size: 54
1080848 TTATATATGG
* *
1080858 TATATAGTTTATACATAATATATATTTTATATATAGTATATAATAATAAATATAAAC
1 TATATAGTTTATACATAATATATACTTTATATATAGTATATAATAAT-AATAT--AT
* *
1080915 TATATAGTTTATATATAATATATACTTTATATATA-CACTAT-ATAAT--T-TAT
1 TATATAGTTTATACATAATATATACTTTATATATAGTA-TATAATAATAATATAT
* * *
1080965 AATATAGTTTATACATTATATCTATAGTTTATATATAGTATATAATAATA
1 TATATAGTTTATACA-TA-ATATATACTTTATATATAGTATATAATAATA
1081015 TAAATATAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
50 14 0.16
51 2 0.02
52 20 0.24
53 7 0.08
56 6 0.07
57 36 0.42
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (54 bp):
TATATAGTTTATACATAATATATACTTTATATATAGTATATAATAATAATATAT
Found at i:1083949 original size:132 final size:132
Alignment explanation
Indices: 1083702--1084071 Score: 500
Period size: 132 Copynumber: 2.8 Consensus size: 132
1083692 ATAATTCTAA
* * * *
1083702 GAGAGAAAAA-GATAATATCTAATTATTTTCGATCGAGAATAAACGACCTCTCATGCCTTAAAGA
1 GAGAGAAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * *
1083766 AGTCATTTATTACTCCAATTGAAATGAAGAGATTTCACTATTTCATCTTAAAATTCAATATTAAT
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCATCTTAAAAGTCAATATTAAT
1083831 TC
131 TC
* *
1083833 GAGTGAAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
1 GAGAGAAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
*
1083898 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCA-TGATTCCATCTTAAAAGTCAATATTGA
66 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACT-ATTCCATCTTAAAAGTCAATATTAA
1083962 TTC
130 TTC
* * * *
1083965 GAGAG-AAAACGGTAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCACGCCTTAAAAC
1 GAGAGAAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * *
1084029 AAT-GTTTCATTACTCCAA-CTGAAATGAAAAGATA-CTACTATTC
66 AGTCATTT-ATTACTCCAATC-GAAATGAAGAGATATC-ACTATTC
1084072 TCAATATCGA
Statistics
Matches: 213, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
130 5 0.02
131 94 0.44
132 114 0.54
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (132 bp):
GAGAGAAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCATCTTAAAAGTCAATATTAAT
TC
Found at i:1086074 original size:3 final size:3
Alignment explanation
Indices: 1086066--1086117 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
1086056 CTGCAAAATA
*
1086066 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1086114 AAT A
1 AAT A
1086118 GTGGGATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1086741 original size:132 final size:130
Alignment explanation
Indices: 1086305--1086747 Score: 456
Period size: 135 Copynumber: 3.4 Consensus size: 130
1086295 GTTTGAAAAG
* * *
1086305 AGATCT-GAAAATTTTGATTCATTCCGCTGTTTTTCAAGGAAGATTGAATCGAGGCAGACTTGTT
1 AGATCTAG-AAATGTTGATTCATTCCACTGTTTTTCAGGGAAGATTGAATCGAGGCAGACTTGTT
* * **
1086369 CCA------CAGGGAAGATCAAATCTGGAAAAAAGAGGGATCTGTTCTG-ATGCTGAGGGAAAAT
65 CCAGTTCCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGAACTGTTCTGCTTATTGAGGGAAAAT
1086427 C
130 C
* * * * * * *
1086428 AAATATAGAAATGTTGATTCGTTCCACTGTTTTTCCA-GAAAGATTGGATCGAGGTAGAATTGTT
1 AGATCTAGAAATGTTGATTCATTCCACTGTTTTT-CAGGGAAGATTGAATCGAGGCAGACTTGTT
** * * * * *
1086492 CCATTGTTCCTTGGGGAAGATCAAATATGGAAAAAATAGAGATA-TGTTCCTCTGCTTCTTGTGG
65 CCA--GTTCCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGA-ACTG-T--TCTGCTTATTGAGG
1086556 GAAAATC
124 GAAAATC
* * * *
1086563 AGATCTGGAAATGTTGATTCATTCAATTGTTTTTTAGGGAAGATTGAATCGAGGCAGACTTGTTC
1 AGATCTAGAAATGTTGATTCATTCCACTGTTTTTCAGGGAAGATTGAATCGAGGCAGACTTGTTC
* *
1086628 CACCGTTCCTCAGGGAATATCAAATCTGGAAAAAAGAGGGAACTGTGCTGCTTATTGAGGGAAAA
66 CA--GTTCCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGAACTGTTCTGCTTATTGAGGGAAAA
1086693 TC
129 TC
* * *
1086695 AGATCTATAAATGTTGATTCATTCTACTGTTCTTCAGGGAAGATTGAATCGAG
1 AGATCTAGAAATGTTGATTCATTCCACTGTTTTTCAGGGAAGATTGAATCGAG
1086748 TTCGATTTTC
Statistics
Matches: 256, Mismatches: 47, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
123 53 0.21
124 3 0.01
131 28 0.11
132 66 0.26
134 7 0.03
135 99 0.39
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (130 bp):
AGATCTAGAAATGTTGATTCATTCCACTGTTTTTCAGGGAAGATTGAATCGAGGCAGACTTGTTC
CAGTTCCTCAGGGAAGATCAAATCTGGAAAAAAGAGGGAACTGTTCTGCTTATTGAGGGAAAATC
Found at i:1087921 original size:13 final size:15
Alignment explanation
Indices: 1087897--1087928 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1087887 TTGAACCCCC
1087897 TTTTATTTTTTC-TA
1 TTTTATTTTTTCTTA
1087911 TTTTA-TTTTTCTTA
1 TTTTATTTTTTCTTA
1087925 TTTT
1 TTTT
1087929 CCCTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTATTTTTTCTTA
Found at i:1087953 original size:6 final size:6
Alignment explanation
Indices: 1087942--1088037 Score: 51
Period size: 6 Copynumber: 16.2 Consensus size: 6
1087932 TTTTTTCCCC
** **
1087942 TCTTTT TC-TTT T-TTTT TCAGTT TC--TT TCTTTT TCTTTTT TCAGTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT TCTTTT
* *
1087987 TC--TT TCTTTT TCTTTTT TCTTTT CATTTTTT TCTTTT CACTTTT TCTTTT
1 TCTTTT TCTTTT TC-TTTT TCTTTT --TCTTTT TCTTTT -TCTTTT TCTTTT
1088037 T
1 T
1088038 TTTCTTCAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
4 8 0.11
5 8 0.11
6 33 0.46
7 17 0.24
8 5 0.07
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:1087979 original size:23 final size:23
Alignment explanation
Indices: 1087953--1088023 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1087943 CTTTTTCTTT
1087953 TTTTTTCAGTTTCTTTCTTTTTC
1 TTTTTTCAGTTTCTTTCTTTTTC
1087976 TTTTTTCAGTTTCTTTCTTTTTC
1 TTTTTTCAGTTTCTTTCTTTTTC
* *
1087999 TTTTTTC-TTTTCATT-TTTTTC
1 TTTTTTCAGTTTCTTTCTTTTTC
1088020 TTTT
1 TTTT
1088024 CACTTTTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.22
22 6 0.13
23 30 0.65
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.77
Consensus pattern (23 bp):
TTTTTTCAGTTTCTTTCTTTTTC
Found at i:1088010 original size:22 final size:22
Alignment explanation
Indices: 1087942--1088043 Score: 109
Period size: 23 Copynumber: 4.6 Consensus size: 22
1087932 TTTTTTCCCC
1087942 TCTTTTTCTTT-TTTTTTCAGTT
1 TCTTTTT-TTTCTTTTTTCAGTT
1087964 TCTTTCTTTTTCTTTTTTCAGTT
1 TCTTT-TTTTTCTTTTTTCAGTT
*
1087987 TCTTTCTTTTTCTTTTTTC-TTT
1 TCTTT-TTTTTCTTTTTTCAGTT
* ** **
1088009 TCATTTTTTTCTTTTCACTTTT
1 TCTTTTTTTTCTTTTTTCAGTT
1088031 TCTTTTTTTTCTT
1 TCTTTTTTTTCTT
1088044 CAGGCGAAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
21 11 0.15
22 29 0.40
23 32 0.44
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (22 bp):
TCTTTTTTTTCTTTTTTCAGTT
Found at i:1088019 original size:27 final size:27
Alignment explanation
Indices: 1087945--1088036 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
1087935 TTTCCCCTCT
1087945 TTTTC-TTTTT-TTTTCAGTTTCTTTC
1 TTTTCTTTTTTCTTTTCAGTTTCTTTC
*
1087970 --TT-TTTCTT-TTTTCAGTTTCTTTC
1 TTTTCTTTTTTCTTTTCAGTTTCTTTC
*
1087993 TTTTTCTTTTTTCTTTTCA-TTTTTTTC
1 -TTTTCTTTTTTCTTTTCAGTTTCTTTC
*
1088020 TTTTCACTTTTTCTTTT
1 TTTTC-TTTTTTCTTTT
1088037 TTTTCTTCAG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
23 21 0.38
26 7 0.12
27 22 0.39
28 6 0.11
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTCTTTTTTCTTTTCAGTTTCTTTC
Found at i:1088037 original size:14 final size:14
Alignment explanation
Indices: 1087969--1088037 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
1087959 CAGTTTCTTT
1087969 CTTTTTCTTTTTTCA
1 CTTTTTC-TTTTTCA
*
1087984 GTTTCTTTCTTTTTC-
1 -CTT-TTTCTTTTTCA
*
1087999 TTTTTTC-TTTTCA
1 CTTTTTCTTTTTCA
*
1088012 -TTTTTTTCTTTTCA
1 CTTTTTCT-TTTTCA
1088026 CTTTTTCTTTTT
1 CTTTTTCTTTTT
1088038 TTTCTTCAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 10 0.22
13 4 0.09
14 13 0.29
15 6 0.13
16 8 0.18
17 4 0.09
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.77
Consensus pattern (14 bp):
CTTTTTCTTTTTCA
Found at i:1094909 original size:29 final size:30
Alignment explanation
Indices: 1094856--1094916 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
1094846 TTTTGGTCCT
**
1094856 TAAACTTTTCAAAGTTTATATTTTAGCCAC
1 TAAACTTTTCAAAACTTATATTTTAGCCAC
*
1094886 TAAACTTTT-AAAACTTATATTTTAGTCAC
1 TAAACTTTTCAAAACTTATATTTTAGCCAC
1094915 TA
1 TA
1094917 GACAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATATTTTAGCCAC
Found at i:1100324 original size:20 final size:20
Alignment explanation
Indices: 1100296--1100335 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1100286 ATCACAGAAT
*
1100296 GTAATGAGGGTATCGATACC
1 GTAAGGAGGGTATCGATACC
1100316 GTAAGGAGGGTATCGATACC
1 GTAAGGAGGGTATCGATACC
1100336 CTCTAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.23
Consensus pattern (20 bp):
GTAAGGAGGGTATCGATACC
Found at i:1101792 original size:19 final size:19
Alignment explanation
Indices: 1101762--1101805 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
1101752 TGAGATTAGT
1101762 CTTTTATTATTATTATTTA
1 CTTTTATTATTATTATTTA
1101781 -TTTTATTTATTATTATTTA
1 CTTTTA-TTATTATTATTTA
1101800 CTTTTA
1 CTTTTA
1101806 CTCGGGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTATTATTATTATTTA
Found at i:1101796 original size:10 final size:10
Alignment explanation
Indices: 1101768--1101799 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1101758 TAGTCTTTTA
1101768 TTATTATTAT
1 TTATTATTAT
1101778 TTATT-TTAT
1 TTATTATTAT
1101787 TTATTATTAT
1 TTATTATTAT
1101797 TTA
1 TTA
1101800 CTTTTACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTATTAT
Found at i:1114179 original size:22 final size:22
Alignment explanation
Indices: 1114154--1114202 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1114144 CATATTTAAG
1114154 ATGTAGCT-TACATAGTGTGCAT
1 ATGTAG-TGTACATAGTGTGCAT
* * *
1114176 ATGTTGTGTACATTGTGTTCAT
1 ATGTAGTGTACATAGTGTGCAT
1114198 ATGTA
1 ATGTA
1114203 TATGCGTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (22 bp):
ATGTAGTGTACATAGTGTGCAT
Found at i:1115391 original size:19 final size:19
Alignment explanation
Indices: 1115362--1115411 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1115352 AATATATATT
* *
1115362 TTTTTTTTTTTTTTTTACTA
1 TTTTTATTTTTGTTTT-CTA
* *
1115382 TTTTTCTTTTTGTTTTCTT
1 TTTTTATTTTTGTTTTCTA
1115401 TTTTTATTTTT
1 TTTTTATTTTT
1115412 CTCCTAACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.86
Consensus pattern (19 bp):
TTTTTATTTTTGTTTTCTA
Found at i:1115391 original size:25 final size:25
Alignment explanation
Indices: 1115358--1115413 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1115348 TATTAATATA
**
1115358 TATTTTT-TTTTT-TTTT-TTTTAC
1 TATTTTTCTTTTTGTTTTCTTTTTT
1115380 TATTTTTCTTTTTGTTTTCTTTTTT
1 TATTTTTCTTTTTGTTTTCTTTTTT
1115405 TATTTTTCT
1 TATTTTTCT
1115414 CCTAACGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.24
23 5 0.17
24 4 0.14
25 13 0.45
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (25 bp):
TATTTTTCTTTTTGTTTTCTTTTTT
Found at i:1115596 original size:3 final size:3
Alignment explanation
Indices: 1115588--1115621 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
1115578 TGTTTGTTTT
1115588 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
1115622 GCTTTTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1122899 original size:201 final size:200
Alignment explanation
Indices: 1122547--1122948 Score: 795
Period size: 201 Copynumber: 2.0 Consensus size: 200
1122537 CTTGATACAG
1122547 TTTTTGAGTAAGTCATTTTAGGACTTGACATAAAGAGAATTGAGCGGTAAAAGGCAAGAGTGAAC
1 TTTTTGAGTAAGTCATTTTAGGACTTGACATAAAGAGAATTGAGCGGTAAAAGGCAAGAGTGAAC
1122612 ACCAAGGGTAAAAGCCATCTCGAGTTAAACACGAGTGTTGAGCGACATTCAAGTTTTCTTTGGAG
66 ACCAAGGGTAAAAGCCATCTCGAGTTAAACACGAGTGTTGAGCGACATTCAAGTTTTCTTTGGAG
1122677 TGTATCGGTGAGATTTTTTTTTTATGTTAGTAACATTTATTTTGATTTTTATTAATATTTTTCTT
131 TGTATCGGTGAGATTTTTTTTTTATGTTAGTAACATTTATTTTGATTTTTATTAATATTTTTCTT
1122742 TTCAT
196 TTCAT
1122747 TTTTTGAGTAAAGTCATTTTAGGACTTGACATAAAGAGAATTGAGCGGTAAAAGGCAAGAGTGAA
1 TTTTTGAGT-AAGTCATTTTAGGACTTGACATAAAGAGAATTGAGCGGTAAAAGGCAAGAGTGAA
1122812 CACCAAGGGTAAAAGCCATCTCGAGTTAAACACGAGTGTTGAGCGACATTCAAGTTTTCTTTGGA
65 CACCAAGGGTAAAAGCCATCTCGAGTTAAACACGAGTGTTGAGCGACATTCAAGTTTTCTTTGGA
1122877 GTGTATCGGTGAGATTTTTTTTTTATGTTAGTAACATTTATTTTGATTTTTATTAATATTTTTCT
130 GTGTATCGGTGAGATTTTTTTTTTATGTTAGTAACATTTATTTTGATTTTTATTAATATTTTTCT
1122942 TTTCAT
195 TTTCAT
1122948 T
1 T
1122949 ATGTCTCGAA
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
200 9 0.04
201 192 0.96
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (200 bp):
TTTTTGAGTAAGTCATTTTAGGACTTGACATAAAGAGAATTGAGCGGTAAAAGGCAAGAGTGAAC
ACCAAGGGTAAAAGCCATCTCGAGTTAAACACGAGTGTTGAGCGACATTCAAGTTTTCTTTGGAG
TGTATCGGTGAGATTTTTTTTTTATGTTAGTAACATTTATTTTGATTTTTATTAATATTTTTCTT
TTCAT
Found at i:1124956 original size:10 final size:10
Alignment explanation
Indices: 1124931--1124966 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1124921 GGATATGAGT
1124931 TTTTCGATGCG
1 TTTTCGATG-G
*
1124942 TTTTCGGTGG
1 TTTTCGATGG
1124952 TTTTCGATGG
1 TTTTCGATGG
1124962 TTTTC
1 TTTTC
1124967 TTCTTCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.06, C:0.14, G:0.28, T:0.53
Consensus pattern (10 bp):
TTTTCGATGG
Found at i:1125428 original size:184 final size:181
Alignment explanation
Indices: 1125103--1125468 Score: 592
Period size: 184 Copynumber: 2.0 Consensus size: 181
1125093 GTTCAGCCTC
*
1125103 CGTTTGAGGTGTTTGATGATGGTATTTCAGAATGAAAGTGCCTTTGGTGGCCAATTCCTTGGTTG
1 CGTTTGAGGTGTTTGATGATGGTATTTCAGAATGAAAGTACCTTTGGTGGCCAATTCCTTGGTTG
*
1125168 CGCCAAATTTTGCTTATATGCAGAGGAATGTGGACATTTATGGAATAAGGCTTTGATGGGTTCTC
66 CGCCAAATTTTGCTTATATGCAGAGGAATGTAGACATTTATGGAATAAGGCTTTGATGGGTTCTC
*
1125233 GTGTTCAGGTCAG-TTAGAGGGTACTAATCTTTACATTTTTTCATTTACTT
131 ATGTTCAGGTCAGTTTAGAGGGTACTAATCTTTACATTTTTTCATTTACTT
*
1125283 CGTTTGAGG-GTTTGATGATGGTATTTCAGAATGAAAGCTATCTTTGGTGGGCCAATTCCTTGTG
1 CGTTTGAGGTGTTTGATGATGGTATTTCAGAATGAAAG-TACCTTTGGT-GGCCAATTCC-T-TG
* *
1125347 GTTGCGCCGAATTTTGCTTATATGCAGAGGAATGTAGACAATTTGTGGAATAAGGCTTTGATGGG
62 GTTGCGCCAAATTTTGCTTATATGCAGAGGAATGTAGAC-ATTTATGGAATAAGGCTTTGATGGG
** *
1125412 TTCTCATGTTCAGGTCAGTTTAGAGGGTACTAATCTTTATGTTTTTTCGTTTACTT
126 TTCTCATGTTCAGGTCAGTTTAGAGGGTACTAATCTTTACATTTTTTCATTTACTT
1125468 C
1 C
1125469 TTAATCTTCC
Statistics
Matches: 171, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
179 28 0.16
180 17 0.10
181 10 0.06
182 1 0.01
183 39 0.23
184 41 0.24
185 35 0.20
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (181 bp):
CGTTTGAGGTGTTTGATGATGGTATTTCAGAATGAAAGTACCTTTGGTGGCCAATTCCTTGGTTG
CGCCAAATTTTGCTTATATGCAGAGGAATGTAGACATTTATGGAATAAGGCTTTGATGGGTTCTC
ATGTTCAGGTCAGTTTAGAGGGTACTAATCTTTACATTTTTTCATTTACTT
Found at i:1126823 original size:15 final size:15
Alignment explanation
Indices: 1126790--1126892 Score: 88
Period size: 15 Copynumber: 6.7 Consensus size: 15
1126780 TAATAAGGTT
1126790 ATTTATT-TAAAAT-
1 ATTTATTATAAAATA
1126803 ATTTATTATAAAATA
1 ATTTATTATAAAATA
*
1126818 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
*
1126833 AATTATTATAAAATATAGA
1 ATTTATTAT-AAA-AT--A
*
1126852 TTGATTTATTTTAAAATA
1 ---ATTTATTATAAAATA
1126870 ATTTATT-T-AAATA
1 ATTTATTATAAAATA
1126883 ATTTATTATA
1 ATTTATTATA
1126893 TGGATTGATT
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
13 19 0.26
14 8 0.11
15 28 0.38
16 3 0.04
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 3 0.04
22 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:1126887 original size:65 final size:68
Alignment explanation
Indices: 1126790--1126941 Score: 183
Period size: 67 Copynumber: 2.3 Consensus size: 68
1126780 TAATAAGGTT
1126790 ATTTATTTAAAAT-ATTTATTATAAAATAATTTATT-T-TAAAATAAATTATTATAAAATATAGA
1 ATTTATTTAAAATAATTTATTATAAAATAATTTATTATATAAAATAAATTATTATAAAATATAGA
1126852 TTG
66 TTG
** * * * * *
1126855 ATTTATTTTAAAATAATTTATT-T-AAATAATTTATTATATGGATTGATTTATTTTAAAATATGG
1 ATTTA-TTTAAAATAATTTATTATAAAATAATTTATTATATAAAATAAATTATTATAAAATATAG
1126918 ATTG
65 ATTG
1126922 A-TTATTT-AAATAATTTATTA
1 ATTTATTTAAAATAATTTATTA
1126942 GTATGGATTG
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
64 12 0.16
65 20 0.27
66 13 0.17
67 30 0.40
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (68 bp):
ATTTATTTAAAATAATTTATTATAAAATAATTTATTATATAAAATAAATTATTATAAAATATAGA
TTG
Found at i:1126957 original size:18 final size:18
Alignment explanation
Indices: 1126883--1126981 Score: 52
Period size: 22 Copynumber: 5.4 Consensus size: 18
1126873 TATTTAAATA
1126883 ATTTATT-ATATGGATTG
1 ATTTATTAATATGGATTG
1126900 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1126922 A-TTATTTAA-AT--A---
1 ATTTA-TTAATATGGATTG
*
1126934 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1126952 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1126974 ATTTATTA
1 ATTTATTA
1126982 TTGTATTTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 31
0.66 0.02 0.32
Matches are distributed among these distances:
12 4 0.06
13 5 0.08
15 2 0.03
17 7 0.11
18 8 0.12
19 2 0.03
20 7 0.11
21 3 0.05
22 26 0.41
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1126961 original size:52 final size:52
Alignment explanation
Indices: 1126850--1127088 Score: 229
Period size: 52 Copynumber: 4.6 Consensus size: 52
1126840 ATAAAATATA
1126850 GATTGATTTATTTTAAAATA---A-T--TTATTTAAATAATTTATTA-TATG
1 GATTGATTTATTTTAAAATATGGATTGATTATTTAAATAATTTATTAGTATG
1126895 GATTGATTTATTTTAAAATATGGATTGATTATTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAAATATGGATTGATTATTTAAATAATTTATTAGTATG
* *
1126947 GATTGATTTATTTTAAAATATGGATTGATT-TATT--AT--TGTATTTGTATG
1 GATTGATTTATTTTAAAATATGGATTGATTAT-TTAAATAATTTATTAGTATG
*
1126995 GATTGATTTATTTTAAATAATTTATAGTATGGATTGATTTTTTTTAAATAATTTATTAGTATG
1 GATTGATTTA-TTT---TAA---A-A-TATGGATTGA--TTATTTAAATAATTTATTAGTATG
1127058 G---GATTTATTTTAAAATATGGGATTGATTATT
1 GATTGATTTATTTTAAAATAT-GGATTGATTATT
1127089 ATTGTAGTTG
Statistics
Matches: 164, Mismatches: 5, Indels: 45
0.77 0.02 0.21
Matches are distributed among these distances:
45 20 0.12
48 21 0.13
49 4 0.02
50 6 0.04
51 23 0.14
52 47 0.29
53 1 0.01
55 1 0.01
56 4 0.02
57 10 0.06
59 7 0.04
60 7 0.04
61 2 0.01
63 11 0.07
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (52 bp):
GATTGATTTATTTTAAAATATGGATTGATTATTTAAATAATTTATTAGTATG
Found at i:1126980 original size:22 final size:22
Alignment explanation
Indices: 1126835--1126928 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 22
1126825 TTAAAATAAA
* *
1126835 TTATTATAAAATATAGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
1126857 TTATTTTAAAATAATTTATTTAA
1 TTATTTTAAAAT-ATGGATTGAT
* * **
1126880 ATAATTTATTATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
1126902 TTATTTTAAAATATGGATTGA-
1 TTATTTTAAAATATGGATTGAT
1126923 TTATTT
1 TTATTT
1126929 AAATAATTTA
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
21 6 0.11
22 34 0.63
23 14 0.26
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:1127025 original size:31 final size:32
Alignment explanation
Indices: 1126985--1127071 Score: 128
Period size: 31 Copynumber: 2.8 Consensus size: 32
1126975 TTTATTATTG
*
1126985 TATTTGTATGGATTGATTTATTTTAAATAATT
1 TATTAGTATGGATTGATTTATTTTAAATAATT
*
1127017 TA-TAGTATGGATTGATTTTTTTTAAATAATT
1 TATTAGTATGGATTGATTTATTTTAAATAATT
1127048 TATTAGTATGG---GATTTATTTTAAA
1 TATTAGTATGGATTGATTTATTTTAAA
1127072 ATATGGGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
29 12 0.24
31 29 0.57
32 10 0.20
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (32 bp):
TATTAGTATGGATTGATTTATTTTAAATAATT
Found at i:1127088 original size:108 final size:110
Alignment explanation
Indices: 1126913--1127150 Score: 366
Period size: 108 Copynumber: 2.2 Consensus size: 110
1126903 TATTTTAAAA
1126913 TATGGATTGA--TTATTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTTATTTAAATAATTTATTAGTATGG--TGATTTATTTTAAAATATGGATTGAT
* *
1126976 TTATTATTGTATTTGTATGGATTGATTTATTTTAAATAATTTA-TAG
64 TTATTATTGTAGTTGTATGCATTGATTTATTTTAAATAATTTATTAG
*
1127022 TATGGATTGATTTTTTTTAAATAATTTATTAGTATGG-GATTTATTTTAAAATATGGGATTGA-T
1 TATGGATTGATTTTATTTAAATAATTTATTAGTATGGTGATTTATTTTAAAATAT-GGATTGATT
1127085 TATTATTGTAGTTGTATGCATTGATTTATTTTAAATAATTTATTAG
65 TATTATTGTAGTTGTATGCATTGATTTATTTTAAATAATTTATTAG
1127131 TA-GGATTGA--TTATTTAAATA
1 TATGGATTGATTTTATTTAAATA
1127151 TGGATTGATT
Statistics
Matches: 121, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
106 10 0.08
108 65 0.54
109 22 0.18
111 24 0.20
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (110 bp):
TATGGATTGATTTTATTTAAATAATTTATTAGTATGGTGATTTATTTTAAAATATGGATTGATTT
ATTATTGTAGTTGTATGCATTGATTTATTTTAAATAATTTATTAG
Found at i:1127157 original size:19 final size:21
Alignment explanation
Indices: 1127133--1127171 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1127123 TTTATTAGTA
1127133 GGATTGA-TTA-TTTAAATAT
1 GGATTGATTTATTTTAAATAT
1127152 GGATTGATTTATTTTAAATA
1 GGATTGATTTATTTTAAATA
1127172 ATTTATTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (21 bp):
GGATTGATTTATTTTAAATAT
Found at i:1127157 original size:184 final size:180
Alignment explanation
Indices: 1126913--1127350 Score: 586
Period size: 184 Copynumber: 2.4 Consensus size: 180
1126903 TATTTTAAAA
*
1126913 TATGGATTGA-TTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTA-TTTAAAATATGGATTGAT
* * *
1126976 TTATT-AT-TGTATTTGTATGGATTGATTTATTTTAAATAATTTATAGTATGGATTGATTTTTTT
64 TTATTAATATGTATTAGTATGGATTAATTTA-TTT---TAA---A-A-TATGGATTGATTTATTT
*
1127039 TAAATAATTTATTAGTATGG-GATTTATTTTAAAATATGGGATTGA-TTATTATTGTAGTTG
120 TAAATAATTTATTAGTATGGTAATTTATTTTAAAATAT-GGATTGATTTATTATTGTAGTTG
*
1127099 TATGCATTGATTTATTTTAAATAATTTATTAGTA-GGATTGATTATTT-AAATATGGATTGATTT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTAAAATATGGATTGATTT
*
1127162 ATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
66 A--TT-AAT-ATGTATTAGTATGGATTAATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
1127227 TTTATTAGTATGGATTAATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
127 TTTATTAGTATGG--TAATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
*
1127283 TATGAATTGATTTATTTTTAATAATTTATTAGTATGGATTGATTATTTAAAATATGGATTGATTT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTAAAATATGGATTGATTT
1127348 ATT
66 ATT
1127351 TTAAATAATT
Statistics
Matches: 230, Mismatches: 8, Indels: 30
0.86 0.03 0.11
Matches are distributed among these distances:
181 36 0.16
182 1 0.00
183 8 0.03
184 82 0.36
185 16 0.07
186 34 0.15
187 10 0.04
188 21 0.09
189 3 0.01
190 19 0.08
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (180 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTAAAATATGGATTGATTT
ATTAATATGTATTAGTATGGATTAATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA
TTAGTATGGTAATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:1127185 original size:108 final size:107
Alignment explanation
Indices: 1126958--1127272 Score: 331
Period size: 108 Copynumber: 2.9 Consensus size: 107
1126948 ATTGATTTAT
1126958 TTTAAAATATGGATTGATTTATTATTGTATTTGTATGGATTGATTTATTTTAAATAATTTA-TAG
1 TTTAAAATATGGATTGA-TTATTATTGTA-TTGTATGGATTGATTTATTTTAAATAATTTATTAG
* * * ** *
1127022 TATGGATTGATTTTTTTTAAATA---ATTTATTAGTATGGGATTTAT
64 TATGGATTGA-TTTATTTAAATATGGATTGATT--TATTGGAAATAA
*
1127066 TTTAAAATATGGGATTGATTATTATTGTAGTTGTATGCATTGATTTATTTTAAATAATTTATTAG
1 TTTAAAATAT-GGATTGATTATTATTGTA-TTGTATGGATTGATTTATTTTAAATAATTTATTAG
**
1127131 TA-GGATTGA-TTATTTAAATATGGATTGATTTATTTTAAATAA
64 TATGGATTGATTTATTTAAATATGGATTGATTTATTGGAAATAA
* * * * ***
1127173 TTTATTAGTATGGATT-AAT-TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGT
1 TTTA-AAATATGGATTGATTATTATTGTATTGTATGGATTGATTTATTTTAAATAATTTATTAGT
*
1127236 ATGGATTAATTTATTTTAAAATATGGATTGATTTATT
65 ATGGATTGATTTA-TTT-AAATATGGATTGATTTATT
1127273 ATTGTAGTTG
Statistics
Matches: 178, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
104 33 0.19
105 13 0.07
106 15 0.08
107 18 0.10
108 81 0.46
109 18 0.10
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (107 bp):
TTTAAAATATGGATTGATTATTATTGTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTA
TGGATTGATTTATTTAAATATGGATTGATTTATTGGAAATAA
Found at i:1127187 original size:32 final size:32
Alignment explanation
Indices: 1127149--1127255 Score: 126
Period size: 32 Copynumber: 3.7 Consensus size: 32
1127139 ATTATTTAAA
*
1127149 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTAATTTATTTTAAATAATTTATTAG
1127181 TATGGATTAATTTA-TTT---TAA---A--A-
1 TATGGATTAATTTATTTTAAATAATTTATTAG
*
1127203 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTAATTTATTTTAAATAATTTATTAG
1127235 TATGGATTAATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
1127256 ATATGGATTG
Statistics
Matches: 62, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
22 13 0.21
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 33 0.53
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (32 bp):
TATGGATTAATTTATTTTAAATAATTTATTAG
Found at i:1127193 original size:18 final size:18
Alignment explanation
Indices: 1127170--1127250 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
1127160 TTATTTTAAA
1127170 TAATTTATTAGTATGGAT
1 TAATTTATTAGTATGGAT
*
1127188 TAATTTATTTTAAAATATGGAT
1 TAATTTA--TT--AGTATGGAT
* * *
1127210 TGATTTATT--T-T-AAA
1 TAATTTATTAGTATGGAT
1127224 TAATTTATTAGTATGGAT
1 TAATTTATTAGTATGGAT
1127242 TAATTTATT
1 TAATTTATT
1127251 TTAAAATATG
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
14 9 0.19
15 1 0.02
16 2 0.04
17 1 0.02
18 17 0.35
20 4 0.08
22 14 0.29
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TAATTTATTAGTATGGAT
Found at i:1127197 original size:22 final size:22
Alignment explanation
Indices: 1127181--1127223 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1127171 AATTTATTAG
1127181 TATGGATTAATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
*
1127203 TATGGATTGATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
1127224 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:1127228 original size:54 final size:54
Alignment explanation
Indices: 1127099--1127272 Score: 302
Period size: 54 Copynumber: 3.3 Consensus size: 54
1127089 ATTGTAGTTG
* *
1127099 TATGCATTGATTTATTTTAAATAATTTATTAGTA-GGATTGA-TTA-TTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAA
1127149 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAA
1127203 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAA
1127257 TATGGATTGATTTATT
1 TATGGATTGATTTATT
1127273 ATTGTAGTTG
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
50 33 0.28
51 6 0.05
52 3 0.03
53 3 0.03
54 73 0.62
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAA
Found at i:1127308 original size:80 final size:78
Alignment explanation
Indices: 1127203--1127350 Score: 251
Period size: 80 Copynumber: 1.9 Consensus size: 78
1127193 TATTTTAAAA
*
1127203 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTAA-TTA-TTTAAAATATGGATTGAT
1127268 TTATTATTGTAGTTG
64 TTATTATTGTAGTTG
* *
1127283 TATGAATTGATTTATTTTTAATAATTTATTAGTATGGATTGATTATTTAAAATATGGATTGATTT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTATTTAAAATATGGATTGATTT
1127348 ATT
66 ATT
1127351 TTAAATAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 23 0.35
79 3 0.05
80 39 0.60
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (78 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTATTTAAAATATGGATTGATTT
ATTATTGTAGTTG
Found at i:1127340 original size:20 final size:21
Alignment explanation
Indices: 1127315--1127357 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1127305 AATTTATTAG
1127315 TATGGATTGA-TTATTTAAAA
1 TATGGATTGATTTATTTAAAA
*
1127335 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAAA
1127356 TA
1 TA
1127358 ATTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
TATGGATTGATTTATTTAAAA
Found at i:1127416 original size:30 final size:30
Alignment explanation
Indices: 1127380--1127436 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1127370 AGTTGTATGG
* * *
1127380 ATTATTTAAATTTTAGTATTGTAAAACAAA
1 ATTATTTAAATCTCAGTATTGCAAAACAAA
1127410 ATTATTTAAATCTCAGTATTGCAAAAC
1 ATTATTTAAATCTCAGTATTGCAAAAC
1127437 TCTTTAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (30 bp):
ATTATTTAAATCTCAGTATTGCAAAACAAA
Found at i:1128094 original size:38 final size:38
Alignment explanation
Indices: 1127974--1128094 Score: 93
Period size: 39 Copynumber: 3.1 Consensus size: 38
1127964 GTGAATTATT
1127974 TGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGG
1 TGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGG
* * ** * * * ** * *
1128012 TGGCTTGAGGATTTTCCT-GATTCTTTTGTTGAGTA-TTGTT
1 TGGCTCGA-AAGCTTCATAGAGT-GTTAATT-AATACTTG-G
1128052 TGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGG
1 TGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGG
1128090 TGGCT
1 TGGCT
1128095 TGAGGATTTT
Statistics
Matches: 55, Mismatches: 22, Indels: 12
0.62 0.25 0.13
Matches are distributed among these distances:
38 18 0.33
39 24 0.44
40 13 0.24
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.40
Consensus pattern (38 bp):
TGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGG
Found at i:1128101 original size:78 final size:78
Alignment explanation
Indices: 1127972--1128123 Score: 304
Period size: 78 Copynumber: 1.9 Consensus size: 78
1127962 AGGTGAATTA
1127972 TTTGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGGTGGCTTGAGGATTTTCCTGATTCTT
1 TTTGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGGTGGCTTGAGGATTTTCCTGATTCTT
1128037 TTGTTGAGTATTG
66 TTGTTGAGTATTG
1128050 TTTGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGGTGGCTTGAGGATTTTCCTGATTCTT
1 TTTGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGGTGGCTTGAGGATTTTCCTGATTCTT
1128115 TTGTTGAGT
66 TTGTTGAGT
1128124 TCAATGCTCA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.43
Consensus pattern (78 bp):
TTTGGCTCGAAAGCTTCATAGAGTGTTAATTAATACTTGGTGGCTTGAGGATTTTCCTGATTCTT
TTGTTGAGTATTG
Found at i:1129046 original size:3 final size:3
Alignment explanation
Indices: 1129038--1129068 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1129028 ATATTTTTAT
1129038 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1129069 TTTTTCGACC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1129369 original size:38 final size:38
Alignment explanation
Indices: 1129318--1129410 Score: 177
Period size: 38 Copynumber: 2.4 Consensus size: 38
1129308 TTAAACAAGT
1129318 TCTTCTCATTATAAACTTCTTCTTCCTCGTTGGATGAG
1 TCTTCTCATTATAAACTTCTTCTTCCTCGTTGGATGAG
1129356 TCTTCTCATTATAAACTTCTTCTTCCTCGTTGGATGAG
1 TCTTCTCATTATAAACTTCTTCTTCCTCGTTGGATGAG
*
1129394 TCTTCTCATTATGAACT
1 TCTTCTCATTATAAACT
1129411 CTCCATTGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (38 bp):
TCTTCTCATTATAAACTTCTTCTTCCTCGTTGGATGAG
Found at i:1129587 original size:105 final size:105
Alignment explanation
Indices: 1129394--1129621 Score: 334
Period size: 105 Copynumber: 2.2 Consensus size: 105
1129384 GTTGGATGAG
* *
1129394 TCTTCTCATTATGAACTCTCCATTGAAAGTGTTGATCCACCTCCTTCTGTGATGGACTTGAAAGG
1 TCTTCTCATTATGAACTCT-CATTGAAAGTATTGATCCACCTCCTTCTGTGATGAACTTGAAAGG
*
1129459 ACAAGTTCTTCTCATTATGAACTTTTTCCTTTAGGACGAGT
65 ACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGT
* * * * *
1129500 TCTTCTCATTATGAACTCT-TTTGGAAA-TATTGGTTCACCTCCTTCTGTGGTGAATTTGAAAGG
1 TCTTCTCATTATGAACTCTCATT-GAAAGTATTGATCCACCTCCTTCTGTGATGAACTTGAAAGG
*
1129563 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACTAGT
65 -ACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGT
1129605 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1129622 ATCCATTAGA
Statistics
Matches: 111, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
104 32 0.29
105 60 0.54
106 19 0.17
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (105 bp):
TCTTCTCATTATGAACTCTCATTGAAAGTATTGATCCACCTCCTTCTGTGATGAACTTGAAAGGA
CAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGT
Found at i:1129622 original size:20 final size:20
Alignment explanation
Indices: 1129562--1129622 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
1129552 AATTTGAAAG
*
1129562 GAACAAGTTCTTCTCATTAT
1 GAACTAGTTCTTCTCATTAT
*
1129582 GAACT--TTC-TC-CTTTA-
1 GAACTAGTTCTTCTCATTAT
*
1129597 GGACTAGTTCTTCTCATTAT
1 GAACTAGTTCTTCTCATTAT
1129617 GAACTA
1 GAACTA
1129623 TCCATTAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 5 0.16
18 5 0.16
19 4 0.13
20 9 0.29
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (20 bp):
GAACTAGTTCTTCTCATTAT
Found at i:1129801 original size:136 final size:134
Alignment explanation
Indices: 1129562--1129906 Score: 484
Period size: 136 Copynumber: 2.6 Consensus size: 134
1129552 AATTTGAAAG
*
1129562 GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CCT-TTAGGACT-AGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTA-GA-TGAGTTCTTCTCATTATGAACT
* * * *
1129622 ATCCATTAGAAATATCAATCCCTCAAGCGAGGCGTCAATGATTCGAAATGTCGTGAATCGAGTGA
64 CTCCATTGGAAATATCAATCCCTCAAGCAAGGCGTCAATGATTCGAAATGTCATGAATCGAGTGA
1129687 TACATC
129 TACATC
1129693 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-T-AGATGAGTTCTTCTCATTATGAACT
* * * * *
1129758 CTCAATTGGAAATATTAATCCCTCAAGTAAGGCTTCACTGATTCGAAATGTCATGAATCGAGTGA
64 CTCCATTGGAAATATCAATCCCTCAAGCAAGGCGTCAATGATTCGAAATGTCATGAATCGAGTGA
**
1129823 TAGGTC
129 TACATC
*
1129829 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTTGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC--TTAGATGAGTTCTTCTCATTATGAACT
1129894 CTCCATTGGAAAT
64 CTCCATTGGAAAT
1129907 GTTGAAAACA
Statistics
Matches: 191, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
131 23 0.12
132 1 0.01
133 4 0.02
134 3 0.02
135 2 0.01
136 155 0.81
137 2 0.01
138 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (134 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTAGATGAGTTCTTCTCATTATGAACTCT
CCATTGGAAATATCAATCCCTCAAGCAAGGCGTCAATGATTCGAAATGTCATGAATCGAGTGATA
CATC
Found at i:1129987 original size:42 final size:42
Alignment explanation
Indices: 1129936--1130018 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1129926 GAGGTCTTAT
* * *
1129936 CATCTTGCTCGAAACACTTACAT-ATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAACACTTAC-TGATAACCCAAAGGATTTAAG
*
1129978 CATCATGCTCGAAAGACTTACTGATAACCCAAAGGATTTAA
1 CATCATGCTCGAAACACTTACTGATAACCCAAAGGATTTAA
1130019 AAATCAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (42 bp):
CATCATGCTCGAAACACTTACTGATAACCCAAAGGATTTAAG
Found at i:1130203 original size:39 final size:39
Alignment explanation
Indices: 1130139--1131162 Score: 1645
Period size: 39 Copynumber: 26.3 Consensus size: 39
1130129 TTAGATTCTT
* * *
1130139 ATAAAATCTTTTATTTCGAGAGAAACTATCTCAAGTGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
1130178 ATAAAATCTTCTGTTACGAGGGAAACCATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1130217 ACAAAATATTCTATTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1130256 ATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* * *
1130295 ATAAAATCTTTTGTATCGAGGCAAACTATCTAAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1130334 ATAAAATCTTTTGTTTTGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* * **
1130373 ATAAAATATTTTGTTTCGAGGGAAACTAACTCAAGAAAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1130412 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1130451 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1130490 ATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1130529 ACAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1130568 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1130607 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1130646 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1130685 ATAAAATCTTTTGTTTCGAGGAAAACTATCTCAAGCAAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1130724 ACAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1130763 AAAAAATATTTTGTTTCGAGGGAAATTATATCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1130802 ATAAAATCTTTTGTTTCAAGGGAAACTGTCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* *
1130841 ATAAAATCTTTTGTTTCAAGGGAAACTGTCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1130880 ATAAAATCTTTTGTTTCGAGGGAAACTGTCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1130919 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAT
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
* * * *
1130958 AAAAAATATTTTGTTTCGAGGGACACTATCTCAAGAGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1130997 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1131036 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCAAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1131075 ATAAAATCTTCTT-TTTCGAGTGAAACTATCTCAAGCGAG
1 ATAAAATCTT-TTGTTTCGAGGGAAACTATCTCAAGCGAG
*
1131114 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
1131153 ATAAAATCTT
1 ATAAAATCTT
1131163 ATTTAAAAAC
Statistics
Matches: 910, Mismatches: 73, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
38 1 0.00
39 907 1.00
40 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (39 bp):
ATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAG
Found at i:1131641 original size:44 final size:44
Alignment explanation
Indices: 1131588--1131676 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
1131578 CTCAAGCAAT
1131588 CTTGGTTCTCTTCTTGATCTGTTCATCTTCATTCTTCTCTCACA
1 CTTGGTTCTCTTCTTGATCTGTTCATCTTCATTCTTCTCTCACA
*
1131632 CTTGGTTCTCTTCTTGATCTGTTCGTCTTCATTCTTCTCTCACA
1 CTTGGTTCTCTTCTTGATCTGTTCATCTTCATTCTTCTCTCACA
1131676 C
1 C
1131677 CAAGGTGTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.10, C:0.30, G:0.10, T:0.49
Consensus pattern (44 bp):
CTTGGTTCTCTTCTTGATCTGTTCATCTTCATTCTTCTCTCACA
Found at i:1132705 original size:40 final size:40
Alignment explanation
Indices: 1132661--1132738 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
1132651 TCTTCGAGTA
*
1132661 AAGTGATTCTGGAATAATTGTTCTTGATCAATCTCATATG
1 AAGTGATTCTGGAATAATTGTGCTTGATCAATCTCATATG
1132701 AAGTGATTCTGGAATAATTGTGCTTGATCAATCTCATA
1 AAGTGATTCTGGAATAATTGTGCTTGATCAATCTCATA
1132739 GTTTGAAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (40 bp):
AAGTGATTCTGGAATAATTGTGCTTGATCAATCTCATATG
Found at i:1133042 original size:14 final size:14
Alignment explanation
Indices: 1133023--1133050 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1133013 ACATATATGG
1133023 ATAAATGAAACAAA
1 ATAAATGAAACAAA
1133037 ATAAATGAAACAAA
1 ATAAATGAAACAAA
1133051 GTCGTTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAATGAAACAAA
Found at i:1135008 original size:63 final size:63
Alignment explanation
Indices: 1134926--1135089 Score: 213
Period size: 63 Copynumber: 2.6 Consensus size: 63
1134916 GATCATACAT
* * * * * *
1134926 AATGTGAATATGCAAATGCAGATGCAAAAGTGATGATCCTTTGAAATGCAATACATCATGTAA
1 AATGCGAAAATGCAAATGCAGATGCAAAAATGATGATCCTCTGAAATGCAATACACCATGCAA
* * *
1134989 AATGCGAAAATGCAAATGCAGATGTAAAATTGATGATCCTCTGAAATGCAATGCACCATGCAA
1 AATGCGAAAATGCAAATGCAGATGCAAAAATGATGATCCTCTGAAATGCAATACACCATGCAA
* *
1135052 AATGCGAAGATGCAAATGCA-ACTGCAAAAATGTTGATC
1 AATGCGAAAATGCAAATGCAGA-TGCAAAAATGATGATC
1135090 GCAACGATGG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 1 0.01
63 87 0.99
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (63 bp):
AATGCGAAAATGCAAATGCAGATGCAAAAATGATGATCCTCTGAAATGCAATACACCATGCAA
Found at i:1138374 original size:2 final size:2
Alignment explanation
Indices: 1138367--1138406 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1138357 GGGCATAGTA
1138367 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
1138407 TAAAAAAAAC
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:1139482 original size:2 final size:2
Alignment explanation
Indices: 1139475--1139503 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1139465 TTTAGTCTTT
1139475 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 T
1139504 TTAGCACCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1151261 original size:8 final size:8
Alignment explanation
Indices: 1151225--1151312 Score: 61
Period size: 8 Copynumber: 10.1 Consensus size: 8
1151215 TGCTTGAAGA
1151225 AAAAAATG
1 AAAAAATG
*
1151233 AACAAAT-
1 AAAAAATG
1151240 AAAAAGATG
1 AAAAA-ATG
1151249 AAAAAAATG
1 -AAAAAATG
*
1151258 AAAAAATAAA
1 AAAAAAT--G
1151268 AAAAAGATG
1 AAAAA-ATG
*
1151277 AAAAAAATA
1 -AAAAAATG
*
1151286 AAAAAATAA
1 AAAAAAT-G
1151295 AAAAAATG
1 AAAAAATG
1151303 AGAAAAATG
1 A-AAAAATG
1151312 A
1 A
1151313 GAGGTTGAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
7 4 0.06
8 23 0.35
9 21 0.32
10 15 0.23
11 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.10, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:1151271 original size:19 final size:20
Alignment explanation
Indices: 1151249--1151291 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1151239 TAAAAAGATG
1151249 AAAAAAATG-AAAAAATAAA
1 AAAAAAATGAAAAAAATAAA
*
1151268 AAAAAGATGAAAAAAATAAA
1 AAAAAAATGAAAAAAATAAA
1151288 AAAA
1 AAAA
1151292 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAAAATGAAAAAAATAAA
Found at i:1151271 original size:28 final size:28
Alignment explanation
Indices: 1151223--1151309 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
1151213 TATGCTTGAA
*
1151223 GAAAAAAATGAACAAAT---AAAAAGAT
1 GAAAAAAATGAAAAAATAAAAAAAAGAT
1151248 GAAAAAAATGAAAAAATAAAAAAAAGAT
1 GAAAAAAATGAAAAAATAAAAAAAAGAT
*
1151276 GAAAAAAATAAAAAAATAAAAAAAATGA-
1 GAAAAAAATGAAAAAATAAAAAAAA-GAT
1151304 GAAAAA
1 GAAAAA
1151310 TGAGAGGTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
25 16 0.29
28 38 0.68
29 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.10, T:0.10
Consensus pattern (28 bp):
GAAAAAAATGAAAAAATAAAAAAAAGAT
Found at i:1151300 original size:45 final size:44
Alignment explanation
Indices: 1151224--1151310 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 44
1151214 ATGCTTGAAG
* * *
1151224 AAAAAAATGAACAAATAAAAAGATGAAAAAAATGA-AAAAATAA
1 AAAAAAATGAAAAAATAAAAAAATAAAAAAAATGAGAAAAATAA
1151267 AAAAAAGATGAAAAAAATAAAAAAATAAAAAAAATGAGAAAAAT
1 AAAAAA-ATG-AAAAAATAAAAAAATAAAAAAAATGAGAAAAAT
1151311 GAGAGGTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 6 0.16
44 3 0.08
45 23 0.61
46 6 0.16
ACGTcount: A:0.78, C:0.01, G:0.09, T:0.11
Consensus pattern (44 bp):
AAAAAAATGAAAAAATAAAAAAATAAAAAAAATGAGAAAAATAA
Found at i:1151314 original size:9 final size:9
Alignment explanation
Indices: 1151223--1151312 Score: 89
Period size: 9 Copynumber: 10.2 Consensus size: 9
1151213 TATGCTTGAA
1151223 GAAAAAAAT
1 GAAAAAAAT
*
1151232 G-AACAAAT
1 GAAAAAAAT
*
1151240 -AAAAAGAT
1 GAAAAAAAT
1151248 GAAAAAAAT
1 GAAAAAAAT
1151257 G-AAAAAAT
1 GAAAAAAAT
*
1151265 AAAAAAAAGAT
1 -GAAAAAA-AT
1151276 GAAAAAAAT
1 GAAAAAAAT
1151285 -AAAAAAAT
1 GAAAAAAAT
*
1151293 AAAAAAAAT
1 GAAAAAAAT
*
1151302 GAGAAAAAT
1 GAAAAAAAT
1151311 GA
1 GA
1151313 GAGGTTGAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
8 26 0.39
9 28 0.42
10 11 0.16
11 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.11, T:0.11
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:1152562 original size:117 final size:112
Alignment explanation
Indices: 1152325--1152618 Score: 375
Period size: 117 Copynumber: 2.6 Consensus size: 112
1152315 ACATTTTCAA
*
1152325 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAGG-AG-A-AAGTTCATAATGAGAAGAACTTGTT
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1152387 ---CCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
65 CAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
*
1152432 GAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA--AGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
1152497 TCAACCTTGGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTG
64 TCAACC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
** * *
1152549 AAGAGTTCATAATGAGAAGATTTCATCCAACAAGAGAGAAGAAGTTCATAATGAGAAAAAACTTG
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGGA-AGAAGAAGTTCATAATGAG-AAGAACTTG
1152614 TTCAA
63 TTCAA
1152619 TCCAACGCTT
Statistics
Matches: 162, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
106 2 0.01
107 26 0.16
108 3 0.02
109 2 0.01
110 1 0.01
111 25 0.15
114 2 0.01
115 1 0.01
116 3 0.02
117 84 0.52
118 13 0.08
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (112 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
Found at i:1156959 original size:3 final size:3
Alignment explanation
Indices: 1156918--1156951 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1156908 ATATTTGTGT
1156918 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1156952 TTAATAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1163779 original size:7 final size:7
Alignment explanation
Indices: 1163767--1163845 Score: 59
Period size: 7 Copynumber: 11.3 Consensus size: 7
1163757 CATAATCGAA
1163767 TTTAGGG
1 TTTAGGG
1163774 TTTAGGG
1 TTTAGGG
* *
1163781 ATTAGAG
1 TTTAGGG
* *
1163788 TTTAAGA
1 TTTAGGG
1163795 TTTAGGG
1 TTTAGGG
* *
1163802 TTTAAGA
1 TTTAGGG
**
1163809 TTTATAG
1 TTTAGGG
*
1163816 TTTATGG
1 TTTAGGG
*
1163823 TTTAGGT
1 TTTAGGG
*
1163830 TTTAAGG
1 TTTAGGG
1163837 TTTAGGG
1 TTTAGGG
1163844 TT
1 TT
1163846 AATTACAAAT
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 53 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:1163798 original size:21 final size:21
Alignment explanation
Indices: 1163773--1163845 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
1163763 CGAATTTAGG
*
1163773 GTTTAGGGATTAGAG-TTTAA
1 GTTTAGGGTTTAGAGATTTAA
1163793 GATTTAGGGTTTA-AGATTTATA
1 G-TTTAGGGTTTAGAGATTTA-A
* *
1163815 GTTTATGGTTTAG-GTTTTAA
1 GTTTAGGGTTTAGAGATTTAA
1163835 GGTTTAGGGTT
1 -GTTTAGGGTT
1163846 AATTACAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 4 0.09
21 38 0.86
22 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.47
Consensus pattern (21 bp):
GTTTAGGGTTTAGAGATTTAA
Found at i:1163817 original size:28 final size:28
Alignment explanation
Indices: 1163766--1163841 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
1163756 ACATAATCGA
*
1163766 ATTTAGGGTTTAGGGA-TTAGAGTTTAAG
1 ATTTAGGGTTTA-AGATTTAGAGTTTAAG
* *
1163794 ATTTAGGGTTTAAGATTTATAGTTTATG
1 ATTTAGGGTTTAAGATTTAGAGTTTAAG
* * *
1163822 GTTTAGGTTTTAAGGTTTAG
1 ATTTAGGGTTTAAGATTTAG
1163842 GGTTAATTAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 2 0.05
28 38 0.95
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (28 bp):
ATTTAGGGTTTAAGATTTAGAGTTTAAG
Found at i:1163968 original size:11 final size:11
Alignment explanation
Indices: 1163952--1164014 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1163942 GTATTATAGA
1163952 ATTTTTAATAT
1 ATTTTTAATAT
1163963 ATTTTTAA-A-
1 ATTTTTAATAT
1163972 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
1163983 ATCAATAATGT
1 ATTTTTAATAT
1163994 ATTTTTAATAT
1 ATTTTTAATAT
1164005 ATTTTTAATA
1 ATTTTTAATA
1164015 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:1164902 original size:19 final size:19
Alignment explanation
Indices: 1164878--1164919 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1164868 CATTACTTCA
1164878 TTTCATTGAGATTTATCAT
1 TTTCATTGAGATTTATCAT
*
1164897 TTTCATTGAGATTTATCTT
1 TTTCATTGAGATTTATCAT
1164916 TTTC
1 TTTC
1164920 CAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTCATTGAGATTTATCAT
Found at i:1167040 original size:20 final size:20
Alignment explanation
Indices: 1167015--1167060 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1167005 TCATCCTAAC
1167015 AGGGAAGATCTCCAAATAAT
1 AGGGAAGATCTCCAAATAAT
1167035 AGGGAAGATCTCCAAATAAT
1 AGGGAAGATCTCCAAATAAT
*
1167055 GGGGAA
1 AGGGAA
1167061 ACCAACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.17
Consensus pattern (20 bp):
AGGGAAGATCTCCAAATAAT
Found at i:1169104 original size:19 final size:19
Alignment explanation
Indices: 1169082--1169120 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1169072 TTTTTAAATT
*
1169082 TAATTAAAATAATATTTTA
1 TAATTAAAATAATATATTA
1169101 TAATTAAAATAATATATTA
1 TAATTAAAATAATATATTA
1169120 T
1 T
1169121 TTCTATTTTC
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATTAAAATAATATATTA
Found at i:1169682 original size:26 final size:26
Alignment explanation
Indices: 1169637--1169687 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1169627 ATTTAGGAGG
* **
1169637 ATAAAAATATATTTTTAATAAATAAC
1 ATAAAAAAATATTTAAAATAAATAAC
*
1169663 ATAAAAAAATATTTAAAATATATAA
1 ATAAAAAAATATTTAAAATAAATAA
1169688 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAAAAAAATATTTAAAATAAATAAC
Found at i:1170171 original size:44 final size:44
Alignment explanation
Indices: 1170094--1170219 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 44
1170084 TTTTTAACTA
* * *
1170094 ATTTTTGGTAAAAAAAATAATATTTTAGATAGCGTATAATATTAAT
1 ATTTTCGGT-AAAAAAATAAT-GTTTAGGTAGCGTATAATATTAAT
** *
1170140 ATTTTCGGTAAAAAAATAATGTTTAGGTAGCGCCTAATATTACT
1 ATTTTCGGTAAAAAAATAATGTTTAGGTAGCGTATAATATTAAT
* *
1170184 A-TTCCGGTAGAACAAATAATGTTTTAGGTAGCGTAT
1 ATTTTCGGTA-AAAAAATAATG-TTTAGGTAGCGTAT
1170220 TACCGAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 7 0.10
44 30 0.44
45 23 0.34
46 8 0.12
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (44 bp):
ATTTTCGGTAAAAAAATAATGTTTAGGTAGCGTATAATATTAAT
Found at i:1171026 original size:16 final size:17
Alignment explanation
Indices: 1170995--1171027 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1170985 TCAGACGGTT
*
1170995 GATGACAGAGATCGAAG
1 GATGACAGAAATCGAAG
1171012 GATGA-AGAAATCGAAG
1 GATGACAGAAATCGAAG
1171028 AATCCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.33, T:0.12
Consensus pattern (17 bp):
GATGACAGAAATCGAAG
Found at i:1174438 original size:3 final size:3
Alignment explanation
Indices: 1174410--1174502 Score: 100
Period size: 3 Copynumber: 31.0 Consensus size: 3
1174400 TATCTCATTT
* *
1174410 TTA TTT TTA TT- TTGA TTA TT- TTA TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1174454 ATA TTA TTA TTA TTA ATA GTA TTA TTA ATA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
1174500 TTA
1 TTA
1174503 AATAAAACTT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
2 4 0.05
3 66 0.88
4 5 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1175847 original size:2 final size:2
Alignment explanation
Indices: 1175836--1175872 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1175826 ATATCATGCT
1175836 TA TA -A 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
1175873 CTTCATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1176023 original size:138 final size:140
Alignment explanation
Indices: 1175879--1176151 Score: 403
Period size: 142 Copynumber: 2.0 Consensus size: 140
1175869 TATACTTCAT
*
1175879 TTTTATTTAAATTATTTTTA-GAAAAATCAT-ATTATTATTAATATTTA-T-TTTTTTATTATT-
1 TTTTATTTAAATTATTTTTAGGAAAAATCATCA-TATT-TTAATATTTATTATTTTTTAATATTA
* * *
1175939 AAGAAAGGGGTTGTCTTAAAGCAACTAGATGTATTTTTCTCATATTTTTAAATAAATAAAATACT
64 AAGAAAGAGGTTGTCTTAAAGCAACTAGATGTACTTTTCTCATATTTTTAAATAAAT-AAATACC
1176004 ATATTTAATTTAG
128 ATATTTAATTTAG
*
1176017 TTTTATTTAAATTATTTTTAGGAAAAATTATCATATTTTAATATTTATTTATTTTTTAATATTAA
1 TTTTATTTAAATTATTTTTAGGAAAAATCATCATATTTTAATATTTA-TTATTTTTTAATATTAA
* * *
1176082 AGAAATAGGTTGTCTTAAAGCAACTAGATGTCCTTTTCTGATATTTTTAAATAAATAAATACCAT
65 AGAAAGAGGTTGTCTTAAAGCAACTAGATGTACTTTTCTCATATTTTTAAATAAATAAATACCAT
1176147 ATTTA
130 ATTTA
1176152 TAATTTATAA
Statistics
Matches: 121, Mismatches: 8, Indels: 9
0.88 0.06 0.07
Matches are distributed among these distances:
138 30 0.25
139 13 0.11
140 2 0.02
141 24 0.20
142 52 0.43
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (140 bp):
TTTTATTTAAATTATTTTTAGGAAAAATCATCATATTTTAATATTTATTATTTTTTAATATTAAA
GAAAGAGGTTGTCTTAAAGCAACTAGATGTACTTTTCTCATATTTTTAAATAAATAAATACCATA
TTTAATTTAG
Found at i:1181426 original size:11 final size:11
Alignment explanation
Indices: 1181404--1181435 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1181394 CATCAGAGAA
1181404 AAAAAAGAAAGG
1 AAAAAAG-AAGG
1181416 AAAAAAGAAGG
1 AAAAAAGAAGG
1181427 AAAAAAGAA
1 AAAAAAGAA
1181436 AAGAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGG
Found at i:1181429 original size:16 final size:14
Alignment explanation
Indices: 1181401--1181498 Score: 73
Period size: 14 Copynumber: 7.3 Consensus size: 14
1181391 ATCCATCAGA
1181401 GAAAAAAAAGAAAG
1 GAAAAAAAAGAAAG
1181415 G--AAAAAAG-AAG
1 GAAAAAAAAGAAAG
*
1181426 GAAAAAAGA-AAAG
1 GAAAAAAAAGAAAG
*
1181439 AAAAATAAAGAGAAAG
1 GAAAA-AAA-AGAAAG
*
1181455 AAAAAAAAAGAAA-
1 GAAAAAAAAGAAAG
* *
1181468 -AAAAAAAAAAAAA
1 GAAAAAAAAGAAAG
* *
1181481 GAAAGAAAAGAAAA
1 GAAAAAAAAGAAAG
1181495 GAAA
1 GAAA
1181499 TTGAATCAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.06
12 18 0.26
13 12 0.17
14 23 0.33
15 4 0.06
16 9 0.13
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (14 bp):
GAAAAAAAAGAAAG
Found at i:1181437 original size:5 final size:5
Alignment explanation
Indices: 1181400--1181498 Score: 81
Period size: 5 Copynumber: 21.0 Consensus size: 5
1181390 CATCCATCAG
* *
1181400 AGAAA A-AAA AGAAA GGAAA A-AAGA AG-GA A-AAA AGAAA AGAAA A-ATAA
1 AGAAA AGAAA AGAAA AGAAA AGAA-A AGAAA AGAAA AGAAA AGAAA AGA-AA
*
1181447 AGAGAA AGAAA AAAAA AGAAA A-AAA A-AAA A-AAA AG-AA AGAAA AGAAA
1 AGA-AA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
1181494 AGAAA
1 AGAAA
1181499 TTGAATCAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
4 27 0.35
5 45 0.58
6 6 0.08
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (5 bp):
AGAAA
Found at i:1181452 original size:17 final size:17
Alignment explanation
Indices: 1181398--1181496 Score: 84
Period size: 16 Copynumber: 6.2 Consensus size: 17
1181388 CTCATCCATC
*
1181398 AGAGAAAA-AAAAGAAA
1 AGAGAAAAGAAAAAAAA
* * **
1181414 GGAAAAAAGAAGGAAAA
1 AGAGAAAAGAAAAAAAA
*
1181431 A-AGAAAAGAAAAATAA
1 AGAGAAAAGAAAAAAAA
1181447 AGAG-AAAGAAAAAAAA
1 AGAGAAAAGAAAAAAAA
1181463 AGA-AAAA-AAAAAAAA
1 AGAGAAAAGAAAAAAAA
* *
1181478 AAAG-AAAGAAAAGAAA
1 AGAGAAAAGAAAAAAAA
1181494 AGA
1 AGA
1181497 AATTGAATCA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
15 13 0.20
16 44 0.69
17 7 0.11
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (17 bp):
AGAGAAAAGAAAAAAAA
Found at i:1181465 original size:31 final size:31
Alignment explanation
Indices: 1181400--1181498 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
1181390 CATCCATCAG
** *
1181400 AGAAAAAAAAGAAAGGAAA-AAAGAAGGAAAAA
1 AGAAAAAAAA-AAAAAAAAGAAAGAA-AAAAAA
* * *
1181432 AGAAAAGAAAAATAAAGAGAAAGAAAAAAAA
1 AGAAAAAAAAAAAAAAAAGAAAGAAAAAAAA
*
1181463 AGAAAAAAAAAAAAAAAAGAAAGAAAAGAAA
1 AGAAAAAAAAAAAAAAAAGAAAGAAAAAAAA
1181494 AGAAA
1 AGAAA
1181499 TTGAATCAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
31 41 0.73
32 15 0.27
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (31 bp):
AGAAAAAAAAAAAAAAAAGAAAGAAAAAAAA
Found at i:1183078 original size:39 final size:39
Alignment explanation
Indices: 1183024--1183192 Score: 250
Period size: 39 Copynumber: 4.3 Consensus size: 39
1183014 GAGTATCTTG
1183024 AAGTCTCACATCAGTATAAAGAAACGTTGGGGCATTTTA
1 AAGTCTCACATCAGTATAAAGAAACGTTGGGGCATTTTA
* *
1183063 AAGTCTCACATCAGTATGAAGAAACGTTGGGGCATTTTG
1 AAGTCTCACATCAGTATAAAGAAACGTTGGGGCATTTTA
* ** * *
1183102 AAGTCTCACATCAGTATGAAGAATTGTTTGGGCATTTTG
1 AAGTCTCACATCAGTATAAAGAAACGTTGGGGCATTTTA
*
1183141 AAGTCTCACATCAGTATAAAGAAACATTGGGGCATTTTGA
1 AAGTCTCACATCAGTATAAAGAAACGTTGGGGCATTTT-A
1183181 AAG-CTCACATCA
1 AAGTCTCACATCA
1183193 ACAAGAAGTA
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 115 0.97
40 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (39 bp):
AAGTCTCACATCAGTATAAAGAAACGTTGGGGCATTTTA
Found at i:1183646 original size:54 final size:54
Alignment explanation
Indices: 1183565--1183779 Score: 324
Period size: 54 Copynumber: 4.0 Consensus size: 54
1183555 TGATTGAGAA
* * *
1183565 ATCTG-GCAGAAGCCACATGAAAGAATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGTGCACAAGCCACAGGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
* *
1183618 ATCTGTGCACAAGCCATATGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
1 ATCTGTGCACAAGCCACAGGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
1183672 ATCTGTGCACAAGCCACAGGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
1 ATCTGTGCACAAGCCACAGGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
* * * * * *
1183726 ATCTGTGCAGAAACCATAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGTGCACAAGCCACAGGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
1183780 CAGTGATTAT
Statistics
Matches: 150, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
53 5 0.03
54 145 0.97
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (54 bp):
ATCTGTGCACAAGCCACAGGAAAGAATGAATGTGTTATCAAATGTTTTACGAAC
Found at i:1184879 original size:42 final size:42
Alignment explanation
Indices: 1184824--1184918 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
1184814 AGTCTTTCGA
* * ** *
1184824 GCATGATTTTTAAAACCTTCGGGTCATCTGTAAGACCTTTAGT
1 GCATGA-TGTTAAAACCTTCAGGTCATCCATAAGACCTTCAGT
*
1184867 GCATGATGTTAAAGCCTTCAGGTCATCCATAAGACCTTCAGT
1 GCATGATGTTAAAACCTTCAGGTCATCCATAAGACCTTCAGT
*
1184909 GCAGGATGTT
1 GCATGATGTT
1184919 TTCAAATGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 39 0.87
43 6 0.13
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
GCATGATGTTAAAACCTTCAGGTCATCCATAAGACCTTCAGT
Found at i:1185031 original size:42 final size:42
Alignment explanation
Indices: 1184966--1185050 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1184956 TCTTGTTCTG
* * *
1184966 TAAATCCTTCGGGTCATCTATAAGACCTTCAGTGTAAGATGT
1 TAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAAGATGT
* *
1185008 TAAAGCCTTCGGGTTATCCATAAGACCTTCAGTGCAGGATGT
1 TAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAAGATGT
1185050 T
1 T
1185051 TTAAAATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
TAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAAGATGT
Found at i:1185077 original size:132 final size:132
Alignment explanation
Indices: 1184834--1185346 Score: 807
Period size: 132 Copynumber: 3.9 Consensus size: 132
1184824 GCATGATTTT
* * *
1184834 TAAAACCTTCGGGTCATCTGTAAGACCTTTAGTGCATGATGTTAAAGCCTTCAGGTCATCCATAA
1 TAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
* *
1184899 GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGAGGGTTTCTTGTTC
66 GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCGAGGGTTTCTTGATC
1184964 TG
131 TG
* * * *
1184966 TAAATCCTTCGGGTCATCTATAAGACCTTCAGTGTAAGATGTTAAAGCCTTCGGGTTATCCATAA
1 TAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
* *
1185031 GACCTTCAGTGCAGGATGTTTTAAAATGAGATTTTAGAAACCAAGCCTTCAAGGGTTTCTTGATC
66 GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCGAGGGTTTCTTGATC
1185096 TG
131 TG
* *
1185098 TAAATCCTTAGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
1 TAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
* * * * * *
1185163 GACATTCAATGCA--ATGTTTTCAAATAAGATTTTATAAACTAAGCCTTCGGGGGTTTCTTGATC
66 GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCGAGGGTTTCTTGATC
1185226 TG
131 TG
* *
1185228 TAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATTTTAAAGCCCTCGGGTCATCCATAA
1 TAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
*
1185293 GACCTTCAGTGTAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTC-AGGG
66 GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCGAGGG
1185347 ATTTACTAAT
Statistics
Matches: 345, Mismatches: 34, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
130 117 0.34
131 3 0.01
132 225 0.65
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (132 bp):
TAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCGAGGGTTTCTTGATC
TG
Found at i:1185311 original size:262 final size:263
Alignment explanation
Indices: 1184834--1185343 Score: 833
Period size: 262 Copynumber: 1.9 Consensus size: 263
1184824 GCATGATTTT
* * *
1184834 TAAAACCTTCGGGTCATCTGTAAGACCTTTAGTGCATGATGTTAAAGCCTTCAGGTCATCCATAA
1 TAAAACCTTAGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCAGGTCATCCATAA
* * * *
1184899 GACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTTCGAGGGTTTCTTGTTC
66 GACATTCAATGCA-GATGTTTTCAAATAAGATTTTAGAAACTAAGCCTTCGAGGGTTTCTTGATC
* * * *
1184964 TGTAAATCCTTCGGGTCATCTATAAGACCTTCAGTGTAAGATGTTAAAGCCTTCGGGTTATCCAT
130 TGTAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCAAGATGTTAAAGCCCTCGGGTCATCCAT
1185029 AAGACCTTCAGTGCAGGATGTTTTAAAATGAGATTTTAGAAACCAAGCCTTCAAGGGTTTCTTGA
195 AAGACCTTCAGTGCAGGATGTTTTAAAATGAGATTTTAGAAACCAAGCCTTCAAGGGTTTCTTGA
1185094 TCTG
260 TCTG
* *
1185098 TAAATCCTTAGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCGGGTCATCCATAA
1 TAAAACCTTAGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCAGGTCATCCATAA
* *
1185163 GACATTCAATGCA-ATGTTTTCAAATAAGATTTTATAAACTAAGCCTTCGGGGGTTTCTTGATCT
66 GACATTCAATGCAGATGTTTTCAAATAAGATTTTAGAAACTAAGCCTTCGAGGGTTTCTTGATCT
* *
1185227 GTAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCAAGATTTTAAAGCCCTCGGGTCATCCATA
131 GTAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCAAGATGTTAAAGCCCTCGGGTCATCCATA
* *
1185292 AGACCTTCAGTGTAGGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTCA
196 AGACCTTCAGTGCAGGATGTTTTAAAATGAGATTTTAGAAACCAAGCCTTCA
1185344 GGGATTTACT
Statistics
Matches: 227, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
262 156 0.69
264 71 0.31
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (263 bp):
TAAAACCTTAGGGTCATCTGTAAGACCTTCAGTGCAAGATGTTAAAGCCTTCAGGTCATCCATAA
GACATTCAATGCAGATGTTTTCAAATAAGATTTTAGAAACTAAGCCTTCGAGGGTTTCTTGATCT
GTAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCAAGATGTTAAAGCCCTCGGGTCATCCATA
AGACCTTCAGTGCAGGATGTTTTAAAATGAGATTTTAGAAACCAAGCCTTCAAGGGTTTCTTGAT
CTG
Found at i:1185701 original size:14 final size:14
Alignment explanation
Indices: 1185682--1185752 Score: 63
Period size: 15 Copynumber: 4.8 Consensus size: 14
1185672 CCCGTTTTGT
1185682 TTTTATT-TTGATTA
1 TTTTATTATT-ATTA
1185696 TTTTATTATTATTA
1 TTTTATTATTATTA
* *
1185710 TTATAAATATTATTA
1 TT-TTATTATTATTA
*
1185725 TTAATATTATATATTA
1 TT-TTATTAT-TATTA
1185741 TTATTATTATTA
1 TT-TTATTATTA
1185753 AATAAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
14 13 0.27
15 21 0.44
16 14 0.29
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:1185706 original size:3 final size:3
Alignment explanation
Indices: 1185692--1185752 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
1185682 TTTTATTTTG
* * *
1185692 ATT ATT -TT ATT ATT ATT ATT ATA AAT ATT ATT ATT AAT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
1185737 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
1185753 AATAAAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1185763 original size:28 final size:25
Alignment explanation
Indices: 1185692--1185768 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
1185682 TTTTATTTTG
* * *
1185692 ATTATT-TTATTATTATTAT-TATA
1 ATTATTATTATTAATAATATATATT
* *
1185715 AATATTATTATTAATATTATATATT
1 ATTATTATTATTAATAATATATATT
*
1185740 ATTATTATTATTAAATAAAATATA-T
1 ATTATTATTATT-AATAATATATATT
1185765 ATTA
1 ATTA
1185769 CAGGCCCAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.11
24 12 0.27
25 19 0.42
26 9 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTATTATTATTAATAATATATATT
Found at i:1190159 original size:19 final size:19
Alignment explanation
Indices: 1190121--1190160 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1190111 AACAGAATGT
* *
1190121 CCAGGGGGTATAGATTCCC
1 CCAGGGGGTACAGATGCCC
*
1190140 CCAGGGGGTACCGATGCCC
1 CCAGGGGGTACAGATGCCC
1190159 CC
1 CC
1190161 CTGTCTAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.35, G:0.33, T:0.15
Consensus pattern (19 bp):
CCAGGGGGTACAGATGCCC
Found at i:1196640 original size:21 final size:23
Alignment explanation
Indices: 1196615--1196664 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
1196605 ATAAATACTG
* *
1196615 AAAATTTAAAGG-CTAAAA-AAT
1 AAAATATAAAGGTCTAAAATAAA
1196636 AAAATATAAAGGTCTAAAATAAA
1 AAAATATAAAGGTCTAAAATAAA
1196659 AAAATA
1 AAAATA
1196665 AAGTGCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.44
22 6 0.24
23 8 0.32
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (23 bp):
AAAATATAAAGGTCTAAAATAAA
Found at i:1198467 original size:14 final size:15
Alignment explanation
Indices: 1198431--1198464 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1198421 ATATATATAG
*
1198431 TTTTGAAAATGATTT
1 TTTTTAAAATGATTT
1198446 TTTTTAAAATGATTT
1 TTTTTAAAATGATTT
1198461 TTTT
1 TTTT
1198465 AAATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATGATTT
Found at i:1199595 original size:43 final size:44
Alignment explanation
Indices: 1199497--1199596 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 44
1199487 AAAAAATGTC
* * *
1199497 TCTTTTAATACTACTGATACAAATCTCAAAGACACTAACAATCCT
1 TCTTTAAATTCTACTGACACAAATCTCAAAGACAC-AACAATCCT
* * *
1199542 TCTTTGAATTCTACTGACACTAATCTCAAAGACA-AACAATTCT
1 TCTTTAAATTCTACTGACACAAATCTCAAAGACACAACAATCCT
1199585 TCTTTAAATTCT
1 TCTTTAAATTCT
1199597 GAATTAGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 19 0.39
45 30 0.61
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (44 bp):
TCTTTAAATTCTACTGACACAAATCTCAAAGACACAACAATCCT
Found at i:1203702 original size:36 final size:37
Alignment explanation
Indices: 1203610--1203755 Score: 190
Period size: 38 Copynumber: 3.9 Consensus size: 37
1203600 TATAGTTTTT
1203610 ATATATATATATATAATAGTTTTTGAAAACATTTTTGAAA
1 ATATATATATATAT-ATAG-TTTTGAAAACA-TTTTGAAA
* *
1203650 A-ACATATATATTATATAGTTTTGAAAACATTTTGAAT
1 ATATATATATA-TATATAGTTTTGAAAACATTTTGAAA
*
1203687 ATATATATATAATATATAGTTTTTAAAACATTTTGAAA
1 ATATATATAT-ATATATAGTTTTGAAAACATTTTGAAA
*
1203725 ATATATATAT-TATATAGTTTT-TAAACATTTT
1 ATATATATATATATATAGTTTTGAAAACATTTT
1203756 TTTATTTTTT
Statistics
Matches: 97, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
35 9 0.09
36 11 0.11
37 8 0.08
38 52 0.54
39 13 0.13
40 4 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
ATATATATATATATATAGTTTTGAAAACATTTTGAAA
Found at i:1204711 original size:4 final size:4
Alignment explanation
Indices: 1204704--1204764 Score: 53
Period size: 4 Copynumber: 16.0 Consensus size: 4
1204694 TTTATTTAGC
1204704 ATTT ATTT ATTT A-TT A-TT A-TT ATTT -TTT -TTCCT A-TT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT--T ATTT ATTT ATTT
1204748 ATTT ATTT ATCTT ATTT
1 ATTT ATTT AT-TT ATTT
1204765 CCTTTTGATT
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
3 16 0.31
4 29 0.57
5 6 0.12
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1220134 original size:39 final size:39
Alignment explanation
Indices: 1220085--1220174 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
1220075 TGCTCACAAC
* * *
1220085 AAGTTCTTACCTCAGGCACCTCGA-CTTTGTGCTCAGGGT
1 AAGTCCTTACCGCAGGC-CCTCGATCTTTGTGCTAAGGGT
* * **
1220124 AAGTCTTTACCGCAGGCTCTTTATCTTTGTGCTAAGGGT
1 AAGTCCTTACCGCAGGCCCTCGATCTTTGTGCTAAGGGT
1220163 AAGTCCTTACCG
1 AAGTCCTTACCG
1220175 TATGCTCCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 3 0.07
39 39 0.93
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (39 bp):
AAGTCCTTACCGCAGGCCCTCGATCTTTGTGCTAAGGGT
Found at i:1220191 original size:39 final size:39
Alignment explanation
Indices: 1220109--1220210 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 39
1220099 GGCACCTCGA
* * * *
1220109 CTTTGTGCTCAGGGTAAGTCTTTACCGCAGGCTCTTTAT
1 CTTTGTGCTAAGGGTAAGTCCTTACCGCAGGCTCTCTAG
* *
1220148 CTTTGTGCTAAGGGTAAGTCCTTACCGTATGCTCCTCT-G
1 CTTTGTGCTAAGGGTAAGTCCTTACCGCAGGCT-CTCTAG
*
1220187 CTTTGTGC-ACAAGGTAAGTCCTTA
1 CTTTGTGCTA-AGGGTAAGTCCTTA
1220211 TGCTATGTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 1 0.02
39 50 0.93
40 3 0.06
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.36
Consensus pattern (39 bp):
CTTTGTGCTAAGGGTAAGTCCTTACCGCAGGCTCTCTAG
Found at i:1234376 original size:3 final size:3
Alignment explanation
Indices: 1234363--1234400 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1234353 TTAAATAAGG
1234363 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1234401 CATAATTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1234881 original size:39 final size:39
Alignment explanation
Indices: 1234820--1234987 Score: 210
Period size: 39 Copynumber: 4.3 Consensus size: 39
1234810 TCTATGACTT
*
1234820 GTAAGTCCTTACCGTAGGCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* *
1234859 GTAAGACCTTACCGCAGTCTCCTCGGCTTTGTGCTCAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * * *
1234898 GTATGTCTTTACCGCAGGCTCCTCGGCTTTGTACTTAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
* * ** * * *
1234937 GTAAGCCCTTACCGCAGGTTCCTCTTCTCTGTACACAGG
1 GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
1234976 GTAAGTCCTTAC
1 GTAAGTCCTTAC
1234988 GCTATGTATA
Statistics
Matches: 110, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.15, C:0.29, G:0.24, T:0.31
Consensus pattern (39 bp):
GTAAGTCCTTACCGCAGGCTCCTCGGCTTTGTGCTCAGG
Found at i:1236160 original size:21 final size:21
Alignment explanation
Indices: 1236136--1236175 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1236126 CGTTAGCAGA
*
1236136 ATAAACTGTCATCTCAGCAAC
1 ATAAACTGCCATCTCAGCAAC
* *
1236157 ATAAAGTGCCATGTCAGCA
1 ATAAACTGCCATCTCAGCA
1236176 CTATAACAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (21 bp):
ATAAACTGCCATCTCAGCAAC
Done.