Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:815941 original size:11 final size:11
Alignment explanation
Indices: 815909--815951 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
815899 GTTTATAATT
*
815909 AAACTATTTTT
1 AAACTATTTTA
815920 AAACTATTTTA
1 AAACTATTTTA
*
815931 AAACAATTTTA
1 AAACTATTTTA
*
815942 CAAAGTATTT
1 -AAACTATTT
815952 CGAGCCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (11 bp):
AAACTATTTTA
Found at i:816041 original size:21 final size:21
Alignment explanation
Indices: 816017--816076 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
816007 CAGATTGCCC
816017 AGGGGTACAGATTCCCCCCCA
1 AGGGGTACAGATTCCCCCCCA
816038 AGGGGTACAGATTCCCCCCCA
1 AGGGGTACAGATTCCCCCCCA
*
816059 AGGGGTACCGATTCCCCC
1 AGGGGTACAGATTCCCCC
816077 TGTCTAACGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.38, G:0.25, T:0.15
Consensus pattern (21 bp):
AGGGGTACAGATTCCCCCCCA
Found at i:816462 original size:34 final size:32
Alignment explanation
Indices: 816423--816492 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
816413 TTTTGTAAAG
*
816423 GGGAAAGGTTATAGGTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGGTTAGCCCG-G-AAAAACTA
* * *
816457 GGGAAATGTTTTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGGTTAGCCCGGAAAAACTA
816489 GGGA
1 GGGA
816493 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGGTTAGCCCGGAAAAACTA
Found at i:817425 original size:15 final size:14
Alignment explanation
Indices: 817405--817454 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
817395 GAGGATAGTG
817405 AAGGAAGATGAAGAA
1 AAGGAAGA-GAAGAA
817420 AAGGAAGAGAAGAA
1 AAGGAAGAGAAGAA
**
817434 AAACAAGAAGAAGAA
1 AAGGAAG-AGAAGAA
817449 GAAGGA
1 -AAGGA
817455 GGAGGTAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.38
15 15 0.52
16 3 0.10
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (14 bp):
AAGGAAGAGAAGAA
Found at i:818844 original size:16 final size:18
Alignment explanation
Indices: 818823--818859 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
818813 TTTGTTATTC
818823 TTTGTTGAAAT-TCAA-T
1 TTTGTTGAAATGTCAAGT
*
818839 TTTGTTTAAATGTCAAGT
1 TTTGTTGAAATGTCAAGT
818857 TTT
1 TTT
818860 TAAAGCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TTTGTTGAAATGTCAAGT
Found at i:819120 original size:21 final size:20
Alignment explanation
Indices: 819075--819131 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
819065 TATATTTTCC
819075 AACAATTGGTATC--TTTTT
1 AACAATTGGTATCATTTTTT
* *
819093 AATAATTGATATCATTTTGTT
1 AACAATTGGTATCATTTT-TT
819114 AACAATTGGTAT-ATTTTT
1 AACAATTGGTATCATTTTT
819132 CATTAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 1 0.03
20 8 0.25
21 12 0.38
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.51
Consensus pattern (20 bp):
AACAATTGGTATCATTTTTT
Found at i:819398 original size:20 final size:20
Alignment explanation
Indices: 819357--819400 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
819347 AATAGTAATT
**
819357 TACTGTATAAATAGTATTGA
1 TACTGTATAAATAGTACCGA
*
819377 TACTGTTTAAATAGTACCGA
1 TACTGTATAAATAGTACCGA
819397 TACT
1 TACT
819401 ATTTGAACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (20 bp):
TACTGTATAAATAGTACCGA
Found at i:819559 original size:21 final size:21
Alignment explanation
Indices: 819530--819569 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
819520 TTGAATTTTA
819530 TGAAAGGGTA-TCGATACCCAT
1 TGAAAGGGTACT-GATACCCAT
*
819551 TGAAGGGGTACTGATACCC
1 TGAAAGGGTACTGATACCC
819570 CCTGTATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (21 bp):
TGAAAGGGTACTGATACCCAT
Found at i:833605 original size:10 final size:10
Alignment explanation
Indices: 833590--833627 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
833580 CGTAACTGTC
833590 AGACGGGTCT
1 AGACGGGTCT
833600 AGACGGGTCT
1 AGACGGGTCT
*
833610 AGGCGGGTCT
1 AGACGGGTCT
*
833620 AGTCGGGT
1 AGACGGGT
833628 ACATCTCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.21
Consensus pattern (10 bp):
AGACGGGTCT
Found at i:835506 original size:112 final size:112
Alignment explanation
Indices: 835143--835605 Score: 766
Period size: 112 Copynumber: 4.1 Consensus size: 112
835133 TTGTCGGTTT
* *
835143 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
835208 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
835255 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGT-AAAAAAATGACAAAAC
*
835320 CGATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
835368 GTGTCGATACTTTATAAAAATATATCGATCTATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
835433 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
835480 GTGTCGATACTTTATAAAAGTGTATCGATCCATAATAATAAAAC-AGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* *
835544 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
835591 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
835606 TATAAGTATC
Statistics
Matches: 330, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
111 82 0.25
112 143 0.43
113 105 0.32
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:835792 original size:182 final size:182
Alignment explanation
Indices: 835479--835931 Score: 728
Period size: 182 Copynumber: 2.5 Consensus size: 182
835469 ATATGTTGAT
* * * *
835479 AGTGTCGATACTTTATAAAAGTGTATCGATCCATAATAATAAAACA-GTAAAAAAATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
** * *
835543 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
* *
835608 TAAGTATCAAAACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAA
131 TAAGTATCAAAACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
* *
835660 AGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
*
835725 CGGTCTCGAAATGACGAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
* *
835790 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
131 TAAGTATCAAAACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
* *
835842 AGTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
* *
835907 AGATCTCGAAATGACAAAACCGGTA
66 CGGTCTCGAAATGACAAAACCGGTA
835932 GTAAAAAAGT
Statistics
Matches: 249, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
181 42 0.17
182 207 0.83
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
TAAGTATCAAAACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
Found at i:836232 original size:23 final size:23
Alignment explanation
Indices: 836206--836253 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
836196 AAATAGGTTA
* *
836206 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
836229 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
836252 AT
1 AT
836254 TATATTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:838284 original size:15 final size:15
Alignment explanation
Indices: 838264--838301 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
838254 AGAACCTCTG
838264 AATCATTCAGCGCTT
1 AATCATTCAGCGCTT
838279 AATCATTCAGCGCTT
1 AATCATTCAGCGCTT
*
838294 AATTATTC
1 AATCATTC
838302 TGAAGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (15 bp):
AATCATTCAGCGCTT
Found at i:839522 original size:20 final size:20
Alignment explanation
Indices: 839499--839612 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
839489 ATTTTCTAAT
839499 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
839519 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
839540 TCGCAATTCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
839560 TCGCAATGCGAATACGAAAA
1 TCGCAATGCGAATACGTAAA
839580 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
839600 TCGCAACGCGAAT
1 TCGCAATGCGAAT
839613 CTGACTATCG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:839529 original size:81 final size:79
Alignment explanation
Indices: 839438--839624 Score: 198
Period size: 81 Copynumber: 2.3 Consensus size: 79
839428 GTTTCCAGAT
* ** * * * *
839438 TCGCAACGCGATTCTGACTATCGCATTGCGATTTCCCAAATCTGCGTTGCGATTTTC-TAATTCG
1 TCGCAACGCGATTCTGACTATCGCATT-CGATTACCCAAATC-GCAATGCGA-ATACGAAAATCG
839502 CAATGCGAATACGTAAA
63 CAATGCGAATACGTAAA
** **
839519 TCGCAACGCGAATT-TGGAAAATCGCAATTCGATTACGTAAATCGCAATGCGAATACGAAAATCG
1 TCGCAACGCG-ATTCT-GACTATCGC-ATTCGATTACCCAAATCGCAATGCGAATACGAAAATCG
839583 CAATGCGAATACGTAAA
63 CAATGCGAATACGTAAA
*
839600 TCGCAACGCGAATCTGACTATCGCA
1 TCGCAACGCGATTCTGACTATCGCA
839625 ACGAGATTCT
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
79 1 0.01
80 11 0.13
81 51 0.59
82 21 0.24
83 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (79 bp):
TCGCAACGCGATTCTGACTATCGCATTCGATTACCCAAATCGCAATGCGAATACGAAAATCGCAA
TGCGAATACGTAAA
Found at i:839622 original size:20 final size:20
Alignment explanation
Indices: 839599--839645 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
839589 GAATACGTAA
*
839599 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
839619 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
839639 ATCGCAA
1 ATCGCAA
839646 TACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:839623 original size:40 final size:40
Alignment explanation
Indices: 839499--839625 Score: 175
Period size: 40 Copynumber: 3.1 Consensus size: 40
839489 ATTTTCTAAT
*
839499 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAA
* * *
839540 TCGCAATTCGATTACGTAAATCGCAATGCGAATAC-GAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAAT-CTGAAAA
**
839580 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
839620 TCGCAA
1 TCGCAA
839626 CGAGATTCTG
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 44 0.59
41 30 0.40
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
Found at i:840517 original size:24 final size:24
Alignment explanation
Indices: 840485--840562 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
840475 GTATTCGAAA
840485 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
840509 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
840533 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
840557 TTTGAT
1 TTTGAT
840563 GATTTTTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:843018 original size:20 final size:19
Alignment explanation
Indices: 842993--843082 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 19
842983 CACCGCGGAA
842993 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
843013 ATCGCAACATG-GAAATGACT
1 ATCGCAAC--GCGAAATGACT
843033 ATCGCAACGCGAGAATCGACT
1 ATCGCAACGCGA-AAT-GACT
843054 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
843074 ATCGCAACG
1 ATCGCAACG
843083 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.02
19 2 0.03
20 38 0.59
21 20 0.31
22 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:843061 original size:41 final size:41
Alignment explanation
Indices: 842993--843091 Score: 148
Period size: 41 Copynumber: 2.4 Consensus size: 41
842983 CACCGCGGAA
*
842993 ATCGCAACGCGA-ATAT-GACTATCGCAACATGGAAATGACT
1 ATCGCAACGCGAGA-ATCGACTATCGCAACACGGAAATGACT
*
843033 ATCGCAACGCGAGAATCGACTATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAGAATCGACTATCGCAACACGGAAATGACT
*
843074 ATCGCAACGAGAGAATCG
1 ATCGCAACGCGAGAATCG
843092 CAATGCGAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 14 0.26
41 40 0.74
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.16
Consensus pattern (41 bp):
ATCGCAACGCGAGAATCGACTATCGCAACACGGAAATGACT
Found at i:843142 original size:34 final size:33
Alignment explanation
Indices: 843054--843149 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
843044 AGAATCGACT
* **
843054 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
843088 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
843121 ATCGCAATGCGAAAATGAAAATCGTAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
843150 CGAAATTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:843201 original size:33 final size:33
Alignment explanation
Indices: 843159--843228 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
843149 GCGAAATTAG
* **
843159 TTTCGCATTGCGATTCACTTGTTGCGATTTTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
*
843192 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
843225 TTTC
1 TTTC
843229 CGCGTTGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
Found at i:843366 original size:14 final size:14
Alignment explanation
Indices: 843347--843381 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
843337 TCAATTAAAT
843347 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
843361 AAATCATCTTTTAC
1 AAATCAACATTTAC
843375 AAATCAA
1 AAATCAA
843382 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:845371 original size:20 final size:20
Alignment explanation
Indices: 845348--845503 Score: 88
Period size: 20 Copynumber: 8.4 Consensus size: 20
845338 GAAACTTAAA
845348 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
845368 ATCGCAAAGCGAAACTGACT
1 ATCGCAACGCGAAAATGACT
*
845388 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* **
845402 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
845421 ATCGCAA--C-AACAA--A--
1 ATCGCAACGCGAA-AATGACT
845435 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** *
845455 ATCAAAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** **
845475 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
845495 ATCGCAACG
1 ATCGCAACG
845504 AGAGAATCGC
Statistics
Matches: 107, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
14 14 0.13
16 10 0.09
17 7 0.07
18 5 0.05
19 7 0.07
20 64 0.60
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:845438 original size:33 final size:34
Alignment explanation
Indices: 845368--845448 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
845358 GAAAATGACT
** * * *
845368 ATCGCAAAGCGAAACTGACTATCGCAACGAGAGA
1 ATCGCAAAGCGAAACTGAAAATCGCAACAACAAA
*
845402 ATCGCAATGCGAAA-TGAAAATCGCAACAACAAA
1 ATCGCAAAGCGAAACTGAAAATCGCAACAACAAA
*
845435 ATCGCAACGCGAAA
1 ATCGCAAAGCGAAA
845449 ATGACTATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (34 bp):
ATCGCAAAGCGAAACTGAAAATCGCAACAACAAA
Found at i:845567 original size:34 final size:37
Alignment explanation
Indices: 845528--845631 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 37
845518 CGATTTTCAT
845528 TTCGCATTGCGAT-TC-TTTCG-TTGCGATAGTCAAA
1 TTCGCATTGCGATATCATTTCGATTGCGATAGTCAAA
**
845562 TTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATA-TCA-TTTCG-ATTGCGATAGTCAAA
845602 TTCGCATTGCGATAGTCATTTTCGCATTGC
1 TTCGCATTGCGATA-TCA-TTTCG-ATTGC
845632 AATTTTGTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
34 13 0.21
36 2 0.03
38 5 0.08
40 42 0.68
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (37 bp):
TTCGCATTGCGATATCATTTCGATTGCGATAGTCAAA
Found at i:845573 original size:20 final size:20
Alignment explanation
Indices: 845548--845631 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
845538 GATTCTTTCG
**
845548 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
845568 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
845588 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
845608 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
845628 TTGC
1 TTGC
845632 AATTTTGTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:845615 original size:60 final size:53
Alignment explanation
Indices: 845510--845631 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 53
845500 AACGAGAGAA
* **
845510 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
**
845563 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCAAAT
845623 TCGCATTGC
1 TCGCATTGC
845632 AATTTTGTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
53 14 0.25
54 14 0.25
56 2 0.04
58 5 0.09
60 22 0.39
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (53 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
Found at i:847600 original size:20 final size:20
Alignment explanation
Indices: 847577--847631 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
847567 CTGAAACTTT
847577 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
847597 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
847617 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
847632 TTTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:847637 original size:20 final size:20
Alignment explanation
Indices: 847579--847648 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
847569 GAAACTTTAA
* **
847579 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
847599 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
847619 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
847639 ATCACAACGC
1 ATCGCAACGC
847649 AAGAATTGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:848080 original size:22 final size:22
Alignment explanation
Indices: 848025--848081 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
848015 ATGATTTTAC
*
848025 CGGAGATAGAGACTGATATCGT
1 CGGAGATAGGGACTGATATCGT
* * *
848047 CGGTGATGGGGACTGATTTCGT
1 CGGAGATAGGGACTGATATCGT
*
848069 CGGAGTTAGGGAC
1 CGGAGATAGGGAC
848082 GGATGTCGCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.39, T:0.25
Consensus pattern (22 bp):
CGGAGATAGGGACTGATATCGT
Found at i:848303 original size:20 final size:20
Alignment explanation
Indices: 848280--848351 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
848270 ATAGTCAGAT
848280 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* **
848300 TCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACGTAA
* *
848320 TTCGCGTTGCGATTTACGTAT
1 -TCGCATTGCGATTTACGTAA
848341 TCGCATTGCGA
1 TCGCATTGCGA
848352 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:859205 original size:512 final size:515
Alignment explanation
Indices: 858219--859247 Score: 1929
Period size: 512 Copynumber: 2.0 Consensus size: 515
858209 TTACTTTGGG
* *
858219 TCGCTCCGGTGGCCCTAATGTGACACATCGGATCAAATCGGGTCACCTGCATCGGTCTGTGAGTG
1 TCGCTCCGGTGGCCCTAA--TGACACATCGGATCAAATCGGGTCACCCGCATCGGTCTATGAGTG
*
858284 TTACCAGTATCTTGTGATCGTGGTTTACTAACAAAGTAATTTTATATAAACTCACAATTGATGAT
64 TTACCAGTATCTTGTGATCGTGGTTTACTAACAAAGTAATTTTACATAAACTCACAATTGATGAT
858349 AGAGACATCTCGTTATCAGTCTACTCTAATTTTATGTTTTTTACCCTAGTACTATATAATTGTAG
129 AGAGACATCTCGTTATCAGTCTACTCTAATTTTATGTTTTTTACCCTAGTACTATATAATTGTAG
*
858414 GAGCCGACAAAAATAGAGTAAAATATTAAAATCTTTCATAGAAAAACCTTGGTATTACTTTAATT
194 GAGCCGACAAAAATAGAGTAAAATATTAAAATCTTTCATAGAAAAACCTTGATATTACTTTAATT
858479 TGATTCTCCATTGTTCGAAACTCAATTTTTAAAGGTATATAATTATATTTATTATTTTTTAATTA
259 TGATTCTCCATTGTTCGAAACTCAATTTTTAAAGGTATATAATTATATTTATTATTTTTTAATTA
858544 GAATTATTTGATATTATATTTAATTTTAGTATTTCTTTAGTTAATCTAATAATTGTTAAGGTGAA
324 GAATTATTTGATATTATATTTAATTTTAGTATTTCTTTAGTTAATCTAATAATTGTTAAGGTGAA
858609 TGGTGATTACTAAATTTGATTTTTTATGTTCGTGAATTAATTTTATTATAAATACAGCTTGCCAT
389 TGGTGATTACTAAATTTGATTTTTTATGTTCGTGAATTAATTTTATTATAAATACAGCTTGCCAT
858674 GGGAAAAAATCCAACAATTATTGAGCTTTTTAAGAGAAAAAGTGGGAAAACTTCGAAAAATA
454 GGGAAAAAATCCAACAATTATTGAGCTTTTTAAGAGAAAAAGTGGGAAAACTTCGAAAAATA
*
858736 TCGCTCCGGTGGCCCT-A-GACACATCGGATCAGATCGGGTCACCCGCATCGGTCTATGAGTGTT
1 TCGCTCCGGTGGCCCTAATGACACATCGGATCAAATCGGGTCACCCGCATCGGTCTATGAGTGTT
*
858799 ACCAGTATCTTGTGATCGTGGTTTACTAACAAAGTAATTTTACATAAACTCATAATTGATGATAG
66 ACCAGTATCTTGTGATCGTGGTTTACTAACAAAGTAATTTTACATAAACTCACAATTGATGATAG
858864 AGACATCTCGTTATCAGTCTACTCTAATTTTATGTTTTTTACCCTAGTACTATATAATTGTAGGA
131 AGACATCTCGTTATCAGTCTACTCTAATTTTATGTTTTTTACCCTAGTACTATATAATTGTAGGA
*
858929 GCCGACAAAAATAGAGTAAAATATTAAACTCTTT-ATAGAAAAACCTTGATATTACTTTAATTTG
196 GCCGACAAAAATAGAGTAAAATATTAAAATCTTTCATAGAAAAACCTTGATATTACTTTAATTTG
*
858993 ATTTTCCATTGTTCGAAACTCAATTTTTAAAGGTATATAATTATATTTATTATTTTTTAATTAGA
261 ATTCTCCATTGTTCGAAACTCAATTTTTAAAGGTATATAATTATATTTATTATTTTTTAATTAGA
*
859058 ATTATTTGATATTATATTTAATTTTAGTATTTCTTTAGTTAATCTATTAATTGTTAAGGTGAATG
326 ATTATTTGATATTATATTTAATTTTAGTATTTCTTTAGTTAATCTAATAATTGTTAAGGTGAATG
*
859123 GTGATTATTAAATTTGATTTTTTATGTTCGTGAATTAATTTTATTATAAATACAGCTTGCCATGG
391 GTGATTACTAAATTTGATTTTTTATGTTCGTGAATTAATTTTATTATAAATACAGCTTGCCATGG
859188 GAAAAAATCCAACAATTATTGAGCTTTTTAAGAGAAAAAGTGGGAAAACTTCGAAAAATA
456 GAAAAAATCCAACAATTATTGAGCTTTTTAAGAGAAAAAGTGGGAAAACTTCGAAAAATA
859248 CAAGTACAAC
Statistics
Matches: 502, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
512 281 0.56
513 204 0.41
516 1 0.00
517 16 0.03
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (515 bp):
TCGCTCCGGTGGCCCTAATGACACATCGGATCAAATCGGGTCACCCGCATCGGTCTATGAGTGTT
ACCAGTATCTTGTGATCGTGGTTTACTAACAAAGTAATTTTACATAAACTCACAATTGATGATAG
AGACATCTCGTTATCAGTCTACTCTAATTTTATGTTTTTTACCCTAGTACTATATAATTGTAGGA
GCCGACAAAAATAGAGTAAAATATTAAAATCTTTCATAGAAAAACCTTGATATTACTTTAATTTG
ATTCTCCATTGTTCGAAACTCAATTTTTAAAGGTATATAATTATATTTATTATTTTTTAATTAGA
ATTATTTGATATTATATTTAATTTTAGTATTTCTTTAGTTAATCTAATAATTGTTAAGGTGAATG
GTGATTACTAAATTTGATTTTTTATGTTCGTGAATTAATTTTATTATAAATACAGCTTGCCATGG
GAAAAAATCCAACAATTATTGAGCTTTTTAAGAGAAAAAGTGGGAAAACTTCGAAAAATA
Found at i:871968 original size:30 final size:30
Alignment explanation
Indices: 871934--872020 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
871924 TTAAAAGTAT
*
871934 GTCCCTAATAACAAATATTGAAAAAATTGG
1 GTCCCTAATAACAAATATTGAAAAAATTAG
* *
871964 GTCCCTAATAACAAGTATTAAAAAAATTAG
1 GTCCCTAATAACAAATATTGAAAAAATTAG
* *
871994 G-CCTTTAATAACAAATGTTAGAAAAAA
1 GTCC-CTAATAACAAATATT-GAAAAAA
872021 AGAGGCAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.26
Consensus pattern (30 bp):
GTCCCTAATAACAAATATTGAAAAAATTAG
Found at i:872157 original size:174 final size:174
Alignment explanation
Indices: 871969--872341 Score: 737
Period size: 174 Copynumber: 2.1 Consensus size: 174
871959 ATTGGGTCCC
871969 TAATAACAAGTATTAAAAAAATTAGGCCTTTAATAACAAATGTTAGAAAAAAAGAGGCAAAAATT
1 TAATAACAAGTATTAAAAAAATTAGGCCTTTAATAACAAATGTTAGAAAAAAAGAGGCAAAAATT
872034 GAACTCTTATACAAATATTAGAAGAAAAAAATATATGAGTAGACTTCTAATAATAAATATTAGAA
66 GAACTCTTATACAAATATTAGAAGAAAAAAATATATGAGTAGACTTCTAATAATAAATATTAGAA
872099 AAACATGAGTCATAATAATAAACATTATGATAAAATTGAACCCT
131 AAACATGAGTCATAATAATAAACATTATGATAAAATTGAACCCT
872143 TAATAACAAGTATTAAAAAAATTAGGCCTTTAATAACAAATGTTAGAAAAAAAGAGGCAAAAATT
1 TAATAACAAGTATTAAAAAAATTAGGCCTTTAATAACAAATGTTAGAAAAAAAGAGGCAAAAATT
872208 GAACTCTTATACAAATATTAGAAGAAAAAAATATATGAGTAGACTTCTAATAATAAATATTAGAA
66 GAACTCTTATACAAATATTAGAAGAAAAAAATATATGAGTAGACTTCTAATAATAAATATTAGAA
872273 AAACATGAGTCATAATAATAAACATTATGATAAAATTGAACCCT
131 AAACATGAGTCATAATAATAAACATTATGATAAAATTGAACCCT
872317 TAATAACAAGTATTAAAAATAATTA
1 TAATAACAAGTATTAAAAA-AATTA
872342 TACCCTTAAC
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 193 0.97
175 5 0.03
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.27
Consensus pattern (174 bp):
TAATAACAAGTATTAAAAAAATTAGGCCTTTAATAACAAATGTTAGAAAAAAAGAGGCAAAAATT
GAACTCTTATACAAATATTAGAAGAAAAAAATATATGAGTAGACTTCTAATAATAAATATTAGAA
AAACATGAGTCATAATAATAAACATTATGATAAAATTGAACCCT
Found at i:874573 original size:57 final size:57
Alignment explanation
Indices: 874485--874600 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
874475 TGAGCTCGAG
874485 TGTTTTGGGATGTTTGGATCTGGACATTGAAGTGGTAAAATGAAACAAAAGTATCTT
1 TGTTTTGGGATGTTTGGATCTGGACATTGAAGTGGTAAAATGAAACAAAAGTATCTT
874542 TGTTTTGGGATGTTTGGATCTGGACATTGAAGTGGTAAAATGAAACAAAAGTATCTT
1 TGTTTTGGGATGTTTGGATCTGGACATTGAAGTGGTAAAATGAAACAAAAGTATCTT
874599 TG
1 TG
874601 GGGTCCCTGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (57 bp):
TGTTTTGGGATGTTTGGATCTGGACATTGAAGTGGTAAAATGAAACAAAAGTATCTT
Found at i:875756 original size:15 final size:16
Alignment explanation
Indices: 875736--875777 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
875726 TAAATTTTAA
*
875736 AAATAATATATATA-T
1 AAATAATATATACATT
*
875751 AAATAATAAATACATT
1 AAATAATATATACATT
875767 AAA-AATATATA
1 AAATAATATATA
875778 AGAGGTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATATATACATT
Found at i:884648 original size:35 final size:34
Alignment explanation
Indices: 884563--884649 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
884553 AATATAATTT
*
884563 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
884597 TAAATGATAA-ACAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
884635 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
884650 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:884682 original size:34 final size:33
Alignment explanation
Indices: 884644--884727 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 33
884634 GTAATAAACA
*
884644 AAATTAACCAAAATACATTAAAAAAAAGTCCAA-C
1 AAATTAA-CAAAATAAATTAAAAAAAA-TCCAACC
*
884678 AAATTTAACAAAATAAATTAAAATAAATCCAACC
1 AAA-TTAACAAAATAAATTAAAAAAAATCCAACC
**
884712 AAATTAATGAAATAAA
1 AAATTAACAAAATAAA
884728 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
33 16 0.36
34 24 0.55
35 4 0.09
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.21
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAAAAAAAATCCAACC
Found at i:884727 original size:33 final size:34
Alignment explanation
Indices: 884640--884716 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 34
884630 AATGGTAATA
* *
884640 AACAAAATTAACCAAAATACATTAAAAAAAAGTCC
1 AACAAATTTAA-CAAAATAAATTAAAAAAAAGTCC
*
884675 AACAAATTTAACAAAATAAATTAAAATAAA-TCC
1 AACAAATTTAACAAAATAAATTAAAAAAAAGTCC
884708 AACCAAATT
1 AA-CAAATT
884717 AATGAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 5 0.13
34 23 0.61
35 10 0.26
ACGTcount: A:0.62, C:0.16, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACAAAATAAATTAAAAAAAAGTCC
Found at i:886856 original size:31 final size:32
Alignment explanation
Indices: 886821--886880 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
886811 AATTAATTTT
886821 TAAATTA-ATAATAATACA-TTAAA-TAAATAAA
1 TAAATTATA-AATAATA-ATTTAAATTAAATAAA
886852 TAAATTATAAATAATAATTTAAATTAAAT
1 TAAATTATAAATAATAATTTAAATTAAAT
886881 TAAAATGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 1 0.04
31 19 0.73
32 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAATTATAAATAATAATTTAAATTAAATAAA
Found at i:887007 original size:17 final size:19
Alignment explanation
Indices: 886987--887028 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
886977 ATTAATTAAA
886987 TAAAATA-TTAAA-AAATT
1 TAAAATACTTAAATAAATT
887004 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAATT
*
887022 AAAAATA
1 TAAAATA
887029 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAATT
Found at i:887016 original size:24 final size:23
Alignment explanation
Indices: 886982--887052 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
886972 AAAAAATTAA
886982 TTAAATA--AAATATTAAAAAAT
1 TTAAATATTAAATATTAAAAAAT
887003 TTAAATACTTAAATAAATT-AAAAA-
1 TTAAATA-TTAAAT--ATTAAAAAAT
*
887027 TAAAATATTAAATA-TAATAAAAT
1 TTAAATATTAAATATTAA-AAAAT
887050 TTA
1 TTA
887053 CCTTAAACAG
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
20 1 0.03
21 9 0.22
22 4 0.10
23 8 0.20
24 10 0.25
25 5 0.12
26 3 0.08
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (23 bp):
TTAAATATTAAATATTAAAAAAT
Found at i:887517 original size:15 final size:13
Alignment explanation
Indices: 887474--887508 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
887464 AAAGACTGTT
887474 TATTTTATTGAAAA
1 TATTTT-TTGAAAA
887488 TATTTTTTGAAAA
1 TATTTTTTGAAAA
887501 TATTTTTT
1 TATTTTTT
887509 CGTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (13 bp):
TATTTTTTGAAAA
Found at i:887535 original size:20 final size:20
Alignment explanation
Indices: 887512--887557 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
887502 ATTTTTTCGT
* *
887512 AAAATAAATTATATTTTTAG
1 AAAATAAATTAAATTTTTAA
**
887532 AAAATATTTTAAATTTTTAA
1 AAAATAAATTAAATTTTTAA
887552 AAAATA
1 AAAATA
887558 TTGTTTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATAAATTAAATTTTTAA
Found at i:892351 original size:18 final size:18
Alignment explanation
Indices: 892328--892368 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
892318 ATGATTATCT
892328 GGAGCGGAACTTGCGGCA
1 GGAGCGGAACTTGCGGCA
892346 GGAGCGGAACTTGCGGCA
1 GGAGCGGAACTTGCGGCA
892364 GGAGC
1 GGAGC
892369 TGTTCGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.46, T:0.10
Consensus pattern (18 bp):
GGAGCGGAACTTGCGGCA
Found at i:893261 original size:16 final size:17
Alignment explanation
Indices: 893227--893261 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
893217 TTTCCTTCTA
893227 TGGTATCGATACCCCATT
1 TGGTATCGATA-CCCATT
893245 TGGTATCGATA-CCATT
1 TGGTATCGATACCCATT
893261 T
1 T
893262 TGACATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (17 bp):
TGGTATCGATACCCATT
Found at i:897130 original size:16 final size:17
Alignment explanation
Indices: 897097--897146 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
897087 GCCTGCAAAA
* * *
897097 AAATATGTAACAAAAAT
1 AAATATATAATAACAAT
*
897114 AAATA-ATAATAATAAT
1 AAATATATAATAACAAT
897130 -AATATATAATAACAAT
1 AAATATATAATAACAAT
897146 A
1 A
897147 TAATGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (17 bp):
AAATATATAATAACAAT
Found at i:897785 original size:13 final size:13
Alignment explanation
Indices: 897767--897807 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
897757 AATAGCACAT
897767 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
897780 GGGCTGCTAAGGGG
1 GGGCTGCTAA-GGG
897794 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
897807 G
1 G
897808 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:897796 original size:14 final size:14
Alignment explanation
Indices: 897767--897807 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
897757 AATAGCACAT
897767 GGGCTGCTAA-GGG
1 GGGCTGCTAAGGGG
897780 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
897794 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
897808 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (14 bp):
GGGCTGCTAAGGGG
Found at i:902287 original size:13 final size:13
Alignment explanation
Indices: 902269--902322 Score: 81
Period size: 13 Copynumber: 4.1 Consensus size: 13
902259 AATAGCACAT
902269 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
902282 GGGCTGCTAAGGGG
1 GGGCTGCTAA-GGG
902296 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
* *
902309 GGTCTGTTAAGGG
1 GGGCTGCTAAGGG
902322 G
1 G
902323 TAATTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 25 0.66
14 13 0.34
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.19
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:902298 original size:14 final size:14
Alignment explanation
Indices: 902269--902310 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
902259 AATAGCACAT
902269 GGGCTGCTAA-GGG
1 GGGCTGCTAAGGGG
902282 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
902296 GGGCTGCTAAGGGG
1 GGGCTGCTAAGGGG
902310 G
1 G
902311 TCTGTTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.14, C:0.14, G:0.57, T:0.14
Consensus pattern (14 bp):
GGGCTGCTAAGGGG
Found at i:902307 original size:27 final size:27
Alignment explanation
Indices: 902269--902322 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
902259 AATAGCACAT
902269 GGGCTGCTAAGGGGGGCTGCTAAGGGG
1 GGGCTGCTAAGGGGGGCTGCTAAGGGG
* *
902296 GGGCTGCTAAGGGGGTCTGTTAAGGGG
1 GGGCTGCTAAGGGGGGCTGCTAAGGGG
902323 TAATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.54, T:0.19
Consensus pattern (27 bp):
GGGCTGCTAAGGGGGGCTGCTAAGGGG
Found at i:904575 original size:125 final size:124
Alignment explanation
Indices: 904428--904698 Score: 440
Period size: 125 Copynumber: 2.2 Consensus size: 124
904418 TTAACATTAA
* *
904428 GTTTT-AAAAAATTGAAAGTTTAGGTACTAAAACAAACTAAAACTAATAGTTTAA-GTATTAAAT
1 GTTTTGAAAAAATTGAAAATTTAGGTACTAAAACAAACTAAAACTAATA-ATTAAGGTATTAAAT
*
904491 ACATGCATTAAGTTTTAAACGGTAAGTACTAAAATAAAACAAAAATTAAATGTTAAGCATG
65 ACATGCATTAAGTTTTAAACAGTAAGTACTAAAATAAAACAAAAATTAAATGTTAA-CATG
* **
904552 GTTTTGAAAAAATTAAAAATTTAGGTACTAAAACAGGCTAAAACTAATAATTAAGGTATTAAATA
1 GTTTTGAAAAAATTGAAAATTTAGGTACTAAAACAAACTAAAACTAATAATTAAGGTATTAAATA
*
904617 CATGCATTAAGTTTTTAACAGTAAGTACTAAAATAAAACAAAAATTAAATGTTAACATG
66 CATGCATTAAGTTTTAAACAGTAAGTACTAAAATAAAACAAAAATTAAATGTTAACATG
904676 GTTTTG-AAAAATTGAAAATTTAG
1 GTTTTGAAAAAATTGAAAATTTAG
904699 ATTCTAATTA
Statistics
Matches: 137, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
123 16 0.12
124 19 0.14
125 102 0.74
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (124 bp):
GTTTTGAAAAAATTGAAAATTTAGGTACTAAAACAAACTAAAACTAATAATTAAGGTATTAAATA
CATGCATTAAGTTTTAAACAGTAAGTACTAAAATAAAACAAAAATTAAATGTTAACATG
Found at i:924509 original size:19 final size:19
Alignment explanation
Indices: 924485--924522 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
924475 ATAATAGGTT
924485 TCCATTTTGTTATGAGTAA
1 TCCATTTTGTTATGAGTAA
924504 TCCATTTTGTTATGAGTAA
1 TCCATTTTGTTATGAGTAA
924523 GTTAGGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
TCCATTTTGTTATGAGTAA
Found at i:931462 original size:17 final size:18
Alignment explanation
Indices: 931440--931473 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
931430 TAGTATTGTC
931440 TATAAATAT-TTTTTTAA
1 TATAAATATATTTTTTAA
*
931457 TATAAATTTATTTTTTA
1 TATAAATATATTTTTTA
931474 TATTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATAAATATATTTTTTAA
Found at i:934829 original size:6 final size:6
Alignment explanation
Indices: 934818--934846 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
934808 ATAAATAGAG
934818 GGAAAA GGAAAA GGAAAA GGAAAA GGAAA
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAA
934847 GGCCGTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:939526 original size:31 final size:31
Alignment explanation
Indices: 939480--939566 Score: 122
Period size: 31 Copynumber: 2.8 Consensus size: 31
939470 ATTTGTCTTC
* *
939480 AAACTTTAGAAAAAATACTAATTTAACCCCT
1 AAACTTTAGATAAAATATTAATTTAACCCCT
* *
939511 AAA-TGTTAGATAAAATATTAAATTAACCCTT
1 AAACT-TTAGATAAAATATTAATTTAACCCCT
939542 AAACTTTAGATAAAATATTAATTTA
1 AAACTTTAGATAAAATATTAATTTA
939567 GTCCTCGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.02
31 47 0.96
32 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.34
Consensus pattern (31 bp):
AAACTTTAGATAAAATATTAATTTAACCCCT
Found at i:941613 original size:3 final size:3
Alignment explanation
Indices: 941605--941676 Score: 85
Period size: 3 Copynumber: 24.0 Consensus size: 3
941595 GATTGGGCCT
* *
941605 ATA ATA ATA TTTA TTA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
941650 ATT ATA ATA ATA ATA AT- ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA
941677 TTCAAATGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.07
3 53 0.87
4 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:942179 original size:113 final size:113
Alignment explanation
Indices: 942023--942788 Score: 982
Period size: 113 Copynumber: 6.7 Consensus size: 113
942013 ATACAAAAGC
* *
942023 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
942088 AAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAAT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
* * **
942136 TCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * * *
942201 CATTGCTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
* **
942249 TCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * *
942313 AATTGTTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 AAATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
**
942361 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
** * * * *
942425 AAATGTTGATGCTGATCTATCTCCTTCTGTGAT-AGAGTCATGCAAAGGGTTGAACAAGT
66 AAATGTTGAT-C----C-A--T-C--AAGTGATGA-ATTTAAGCAAAAGGTTGAACAAGT
* *
942484 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTAC-CTG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTG
* * *
942548 GCAATGTTGATCAATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
65 GAAATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
* *
942597 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * *
942662 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
* *
942710 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
942775 AAAAGCTGATCCAT
66 AAATGTTGATCCAT
942789 TGTGATGGAT
Statistics
Matches: 582, Mismatches: 55, Indels: 32
0.87 0.08 0.05
Matches are distributed among these distances:
112 124 0.21
113 357 0.61
114 1 0.00
115 1 0.00
116 1 0.00
117 1 0.00
118 2 0.00
121 1 0.00
122 1 0.00
123 80 0.14
124 13 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAGT
Found at i:942650 original size:348 final size:349
Alignment explanation
Indices: 942019--942765 Score: 1052
Period size: 348 Copynumber: 2.2 Consensus size: 349
942009 AGTCATACAA
* **
942019 AAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTTCT
1 AAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-T
* ** * * *
942084 CTGGAAAAGTTGAT-C----C-A--T-C--AAGTGAT-GAATTTAAGCAAAAGGTTGAACAAATT
65 CTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAG-AGTCATGCAAAAGGTTGAACAAATT
*
942137 CTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
129 CTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGC
* * * *
942202 ATTGCTGATCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
194 AATGCTGATCAACCAAGTGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
** ** * *
942267 CTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGAATTGTTGATCCACCGAG
259 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGCTGATCCACCAAG
942331 TGATGAATTTAAGCAAAAAGTTGAAC
324 TGATGAATTTAAGCAAAAAGTTGAAC
* *
942357 AAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTC
1 AAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTC
* *
942422 TGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAGGGTTGAACAAGTTCT
66 TGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAATTCT
* *
942487 TCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTACCTGGCAA
131 TCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAA
* * * *
942552 TGTTGATCAATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCT
196 TGCTGATCAACCAAGTGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
** *
942617 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTG
261 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGCTGATCCACCAAGTG
* * *
942682 ATGGATTTGAGCAAAAGGTTGAAC
326 ATGAATTTAAGCAAAAAGTTGAAC
*
942706 AAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAAC
1 AAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
942766 TTTCTCTGGA
Statistics
Matches: 357, Mismatches: 39, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
337 14 0.04
338 59 0.17
342 1 0.00
343 1 0.00
345 1 0.00
346 1 0.00
348 181 0.51
349 99 0.28
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (349 bp):
AAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTC
TGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAA
TGCTGATCAACCAAGTGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGCTGATCCACCAAGTG
ATGAATTTAAGCAAAAAGTTGAAC
Found at i:943972 original size:19 final size:17
Alignment explanation
Indices: 943948--943996 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
943938 AAAATAAAAG
943948 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTTTC--A
*
943967 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
943983 AATAAATTGAATTT
1 AATAAATTGAATTT
943997 AGAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:944364 original size:10 final size:10
Alignment explanation
Indices: 944349--944407 Score: 66
Period size: 10 Copynumber: 5.7 Consensus size: 10
944339 CTTGACCCTC
944349 CTTTTTTCTT
1 CTTTTTTCTT
*
944359 CTTTTTTTTT
1 CTTTTTTCTT
944369 CTTTTTCTCTT
1 CTTTTT-TCTT
*
944380 -TTTTTCCTT
1 CTTTTTTCTT
944389 CTTTTTTTCCTT
1 C-TTTTTT-CTT
944401 CTTTTTT
1 CTTTTTT
944408 TTTCCTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 3 0.07
10 20 0.49
11 14 0.34
12 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:944367 original size:12 final size:12
Alignment explanation
Indices: 944350--944409 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
944340 TTGACCCTCC
944350 TTTTTTCTTC-T
1 TTTTTTCTTCTT
944361 TTTTTT-TTC--
1 TTTTTTCTTCTT
944370 -TTTTTC-TCTT
1 TTTTTTCTTCTT
*
944380 TTTTTCCTTCTT
1 TTTTTTCTTCTT
*
944392 TTTTTCCTTCTT
1 TTTTTTCTTCTT
944404 TTTTTT
1 TTTTTT
944410 TCCTTCAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.17
10 3 0.07
11 11 0.26
12 21 0.50
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:947242 original size:17 final size:18
Alignment explanation
Indices: 947213--947246 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
947203 GATTATATCC
947213 TGAAAAGCCATCCATGAA
1 TGAAAAGCCATCCATGAA
947231 TGAAAA-CCATCCATGA
1 TGAAAAGCCATCCATGA
947247 CCTGCAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (18 bp):
TGAAAAGCCATCCATGAA
Found at i:951761 original size:15 final size:15
Alignment explanation
Indices: 951738--951769 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
951728 TGCAATGAAT
951738 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
951753 AATGCATGTATGCAA
1 AATGAATGTATGCAA
951768 AA
1 AA
951770 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:955058 original size:32 final size:33
Alignment explanation
Indices: 955022--955088 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
955012 CTCTGACAGA
*
955022 AAAAT-AAATAATGAAATAAAATACT-TGCAAAT
1 AAAATGAAATAAT-AAATAAAATACTATGAAAAT
* *
955054 AAAATGAAATAATATATATAATACTATGAAAAT
1 AAAATGAAATAATAAATAAAATACTATGAAAAT
955087 AA
1 AA
955089 TAAGTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (33 bp):
AAAATGAAATAATAAATAAAATACTATGAAAAT
Found at i:955110 original size:27 final size:26
Alignment explanation
Indices: 955061--955112 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
955051 AATAAAATGA
* *
955061 AATAATATATATAATACTATGAAAAT
1 AATAATATATATAAAAATATGAAAAT
*
955087 AATAAGTATATATAAAAATTTGAAAA
1 AATAA-TATATATAAAAATATGAAAA
955113 AAAGAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AATAATATATATAAAAATATGAAAAT
Found at i:955123 original size:27 final size:27
Alignment explanation
Indices: 955066--955138 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 27
955056 AATGAAATAA
* * * *
955066 TATATATAATACTATGAAAATAATAAG
1 TATATATAAAAATATGAAAAAAAGAAG
* *
955093 TATATATAAAAATTTGAAAAAAAGAAT
1 TATATATAAAAATATGAAAAAAAGAAG
* *
955120 TATAAATTAAATATATGAA
1 TATATA-TAAAAATATGAA
955139 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 26 0.72
28 10 0.28
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (27 bp):
TATATATAAAAATATGAAAAAAAGAAG
Found at i:957214 original size:18 final size:17
Alignment explanation
Indices: 957190--957249 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
957180 ATTGGGCCTG
957190 TAATAATATTTATTAATAA
1 TAATAATA-TTA-TAATAA
*
957209 -AATAATAATAATAATAA
1 TAATAAT-ATTATAATAA
957226 TAATAATAATTATAATAA
1 TAATAAT-ATTATAATAA
957244 TAATAA
1 TAATAA
957250 AAAAATATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 6 0.16
18 30 0.81
19 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATATTATAATAA
Found at i:957215 original size:3 final size:3
Alignment explanation
Indices: 957203--957249 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
957193 TAATATTTAT
*
957203 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
957250 AAAAATATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:957721 original size:24 final size:24
Alignment explanation
Indices: 957694--957740 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
957684 CCTACTAACA
957694 ATTTCCAAATAATAAAAAAGGCCC
1 ATTTCCAAATAATAAAAAAGGCCC
* * *
957718 ATTTCTAAATACTAGAAAAGGCC
1 ATTTCCAAATAATAAAAAAGGCC
957741 ATTAAGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (24 bp):
ATTTCCAAATAATAAAAAAGGCCC
Found at i:967916 original size:7 final size:7
Alignment explanation
Indices: 967906--967931 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
967896 GAAATTGAGA
967906 AAAAAAG
1 AAAAAAG
967913 AAAAAAG
1 AAAAAAG
967920 AAAAAAG
1 AAAAAAG
967927 AAAAA
1 AAAAA
967932 TTGGGTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:978319 original size:19 final size:19
Alignment explanation
Indices: 978276--978319 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
978266 TTGGGACACC
*
978276 ATAAAAACATGTGATTTTT
1 ATAAAAACATGTAATTTTT
* *
978295 GT-AAAACATTTAATTTTT
1 ATAAAAACATGTAATTTTT
978313 ATAAAAA
1 ATAAAAA
978320 TACCAAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (19 bp):
ATAAAAACATGTAATTTTT
Found at i:979536 original size:72 final size:72
Alignment explanation
Indices: 979459--979608 Score: 300
Period size: 72 Copynumber: 2.1 Consensus size: 72
979449 ATATATGGAC
979459 CAAATTGCATAAATTTGAAATTACTAAACTAAAAGAGAATAAATTAAACATGAAAAAGGGGCTAA
1 CAAATTGCATAAATTTGAAATTACTAAACTAAAAGAGAATAAATTAAACATGAAAAAGGGGCTAA
979524 ATTAAAA
66 ATTAAAA
979531 CAAATTGCATAAATTTGAAATTACTAAACTAAAAGAGAATAAATTAAACATGAAAAAGGGGCTAA
1 CAAATTGCATAAATTTGAAATTACTAAACTAAAAGAGAATAAATTAAACATGAAAAAGGGGCTAA
979596 ATTAAAA
66 ATTAAAA
979603 CAAATT
1 CAAATT
979609 AAAAATTAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (72 bp):
CAAATTGCATAAATTTGAAATTACTAAACTAAAAGAGAATAAATTAAACATGAAAAAGGGGCTAA
ATTAAAA
Found at i:979643 original size:17 final size:18
Alignment explanation
Indices: 979604--979646 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
979594 AAATTAAAAC
*
979604 AAATTAAAAATTAAAGTC
1 AAATTAAAAATTAAAGTA
* *
979622 TAATTCAAAA-TAAAGTA
1 AAATTAAAAATTAAAGTA
979639 AAATTAAA
1 AAATTAAA
979647 CAAATTAATG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATTAAAAATTAAAGTA
Found at i:990183 original size:17 final size:17
Alignment explanation
Indices: 990163--990198 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
990153 AAAAACCTAC
*
990163 AAAAAAAAAA-AATATT
1 AAAAAAAAAATAAAATT
990179 AAAAAAAAAATAAAATT
1 AAAAAAAAAATAAAATT
990196 AAA
1 AAA
990199 CTAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAAAAAATAAAATT
Found at i:991177 original size:519 final size:525
Alignment explanation
Indices: 990470--991515 Score: 1980
Period size: 519 Copynumber: 2.0 Consensus size: 525
990460 CTATAAGATA
990470 TTAGTAATAAAGAAAACAAGGAAATATTGTAAAATATGGTTGTAGAAAAGTTAGGTCGAGACAAA
1 TTAGTAATAAAGAAAACAAGGAAATATTGTAAAATATGGTTGTAGAAAAGTTAGGTCGAGACAAA
990535 ATAAATATGCAAAACTATCGAATTAAAATAAAGCAAAGACAAACATTGATTCAAATATATTCAAA
66 ATAAATATGCAAAACTATCGAATTAAAATAAAGCAAAGACAAACATTGATTCAAATATATTCAAA
* *
990600 ACAACCTCACATATTCAGACTTATCACAGAGCACTCATGCTAATCTTTTGTTATGCCAAGCAATT
131 ACAACCTCACATATTCAGACTTATCACAAAGCACTCATGCTAATATTTTGTTATGCCAAGCAATT
990665 ATTCTAAGTCCAG-ATGAATTGTTATGACATGCTTAGGCTGCCCGATAGGATTACTAAGTATTCT
196 ATTCTAAGTCCAGAATGAATTGTTATGACATGCTTAGGCTGCCCGATAGGATTACTAAGTATTCT
*
990729 TAGATGGTTGTTATAGTAAAA-TACTCAGCGTTAACTATAATCATTGGTTTGTCAGACTGTT-TT
261 TAGATGGTTGTTATAGTAAAACTACTCAGCGTTAACTACAATCATTGGTTTGTCAGACTGTTGTT
990792 GTAGCAAT-CTCTCAGTGGAAACTATAATCG-TGTCTATCCTACTCTAGCATCTATCCCTTTTAG
326 GTAGCAATACTCTCAGTGGAAACTATAATCGTTGTCTATCCTACTCTAGCATCTATCCCTTTTAG
990855 TCGATTGAAA-CCGCTCCTTATCTATAAGGTAGACAAGTTAGAACATCACCATCTCGGATCCATT
391 TCGATTGAAACCCGCTCCTTATCTATAAGGTAGACAAGTTAGAACATCACCATCTCGGATCCATT
990919 CCATTGTTCACGTAGATCTATCTTAATTCTCTCAAATCTAAGGATTAATATCTAGACAAATGGCA
456 CCATTGTTCACGTAGATCTATCTTAATTCTCTCAAATCTAAGGATTAATATCTAGACAAATGGCA
990984 ATCTC
521 ATCTC
990989 TTAGTAATAAAGCAAAACAA-GAAATATTGTAAAATATGGTTGTAGAAAAGTTAGGTCGAGACAA
1 TTAGTAATAAAG-AAAACAAGGAAATATTGTAAAATATGGTTGTAGAAAAGTTAGGTCGAGACAA
991053 AATAAATATGCAAAACTATCGAATTAAAATAAAGCAAAGACAAACATTGATTCAAATATATTCAA
65 AATAAATATGCAAAACTATCGAATTAAAATAAAGCAAAGACAAACATTGATTCAAATATATTCAA
*
991118 AACAACCTCACTTATTCAGACTTATCACAAAGCACTCATGCTAATATTTTGTTATGCCAAGCAAT
130 AACAACCTCACATATTCAGACTTATCACAAAGCACTCATGCTAATATTTTGTTATGCCAAGCAAT
*
991183 TATTCTAAGTCCAGAATGAATTGTTATGACATGCTTAGGTTGCCCGATAGGATTACTAAGTATTC
195 TATTCTAAGTCCAGAATGAATTGTTATGACATGCTTAGGCTGCCCGATAGGATTACTAAGTATTC
991248 TTAGATGGTTGTTATAGTAAAACTACTCAGCGTTAACTACAATCATTGGTTTGTCAGACTGTTGT
260 TTAGATGGTTGTTATAGTAAAACTACTCAGCGTTAACTACAATCATTGGTTTGTCAGACTGTTGT
991313 TGTAGCAATACCTCTCAGTGGAAACTATAATCGTTGTCTATCCTACTCTAGCATCTATCCCTTTT
325 TGTAGCAATA-CTCTCAGTGGAAACTATAATCGTTGTCTATCCTACTCTAGCATCTATCCCTTTT
991378 AGTCGATTGAAACCCGCTCCTTATCTATAAGGTAGACAAGTTAGAACATCACCATCTCGGATCCA
389 AGTCGATTGAAACCCGCTCCTTATCTATAAGGTAGACAAGTTAGAACATCACCATCTCGGATCCA
991443 TTCCATTGTTCACGTAGATCTATCTTAATTCTCTCAAATCTAAGGATTAATATCTAGACAAATGG
454 TTCCATTGTTCACGTAGATCTATCTTAATTCTCTCAAATCTAAGGATTAATATCTAGACAAATGG
991508 CAATCTC
519 CAATCTC
991515 T
1 T
991516 CGATGCTCTT
Statistics
Matches: 514, Mismatches: 5, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
519 197 0.38
520 78 0.15
521 39 0.08
522 10 0.02
524 22 0.04
525 43 0.08
526 125 0.24
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (525 bp):
TTAGTAATAAAGAAAACAAGGAAATATTGTAAAATATGGTTGTAGAAAAGTTAGGTCGAGACAAA
ATAAATATGCAAAACTATCGAATTAAAATAAAGCAAAGACAAACATTGATTCAAATATATTCAAA
ACAACCTCACATATTCAGACTTATCACAAAGCACTCATGCTAATATTTTGTTATGCCAAGCAATT
ATTCTAAGTCCAGAATGAATTGTTATGACATGCTTAGGCTGCCCGATAGGATTACTAAGTATTCT
TAGATGGTTGTTATAGTAAAACTACTCAGCGTTAACTACAATCATTGGTTTGTCAGACTGTTGTT
GTAGCAATACTCTCAGTGGAAACTATAATCGTTGTCTATCCTACTCTAGCATCTATCCCTTTTAG
TCGATTGAAACCCGCTCCTTATCTATAAGGTAGACAAGTTAGAACATCACCATCTCGGATCCATT
CCATTGTTCACGTAGATCTATCTTAATTCTCTCAAATCTAAGGATTAATATCTAGACAAATGGCA
ATCTC
Found at i:995845 original size:18 final size:18
Alignment explanation
Indices: 995818--995889 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
995808 AGGGTCTATA
* *
995818 TGGTCCTTCGACAGATAG
1 TGGTCTTTCGACACATAG
**
995836 TGGTCTTTCGGGACATAG
1 TGGTCTTTCGACACATAG
**
995854 TGGTCTTTTCGGGACATAG
1 TGGTC-TTTCGACACATAG
* *
995873 TGGTCCTTCGAGACATA
1 TGGTCTTTCGACACATA
995890 TGTGTTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 29 0.62
19 18 0.38
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (18 bp):
TGGTCTTTCGACACATAG
Found at i:995865 original size:19 final size:18
Alignment explanation
Indices: 995832--995889 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
995822 CCTTCGACAG
995832 ATAGTGGTCTTTCGGGAC
1 ATAGTGGTCTTTCGGGAC
995850 ATAGTGGTCTTTTCGGGAC
1 ATAGTGGTC-TTTCGGGAC
* *
995869 ATAGTGGTCCTTCGAGAC
1 ATAGTGGTCTTTCGGGAC
995887 ATA
1 ATA
995890 TGTGTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 19 0.51
19 18 0.49
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (18 bp):
ATAGTGGTCTTTCGGGAC
Found at i:1000431 original size:16 final size:17
Alignment explanation
Indices: 1000387--1000424 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1000377 ACTCGATTTG
*
1000387 TTTT-ATATGATTTATT
1 TTTTAATATTATTTATT
*
1000403 TTTTAATATTATTTGTT
1 TTTTAATATTATTTATT
1000420 TTTTA
1 TTTTA
1000425 TTTTATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTAATATTATTTATT
Found at i:1004070 original size:21 final size:21
Alignment explanation
Indices: 1004044--1004092 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1004034 TAATATGTAT
1004044 GATCATGACCAACCTATCCAA
1 GATCATGACCAACCTATCCAA
*
1004065 GATCATGACCAACTTATCCAA
1 GATCATGACCAACCTATCCAA
*
1004086 GAACATG
1 GATCATG
1004093 TAGTGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (21 bp):
GATCATGACCAACCTATCCAA
Found at i:1011675 original size:18 final size:19
Alignment explanation
Indices: 1011652--1011693 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1011642 TAGTTAAATA
*
1011652 TTGTATTTAGGAATAGC-T
1 TTGTATATAGGAATAGCAT
*
1011670 TTGTATATAGGAATTGCAT
1 TTGTATATAGGAATAGCAT
1011689 TTGTA
1 TTGTA
1011694 ATGTCATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (19 bp):
TTGTATATAGGAATAGCAT
Found at i:1012354 original size:42 final size:41
Alignment explanation
Indices: 1012307--1012421 Score: 187
Period size: 42 Copynumber: 2.8 Consensus size: 41
1012297 GATGAAAACA
* *
1012307 TTTTGTCACTAGTCTTAGTTGGTGATTTATGACGTTAATTG
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTG
1012348 TTTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTG
1 -TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTG
*
1012390 -GTTGTCACTAGTCTTAGTTGGTGATTTGTGAC
1 TTTTGTCACTAGTCTTAGTTGGTGATTTGTGAC
1012422 AACAATACTT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 31 0.44
42 39 0.56
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.47
Consensus pattern (41 bp):
TTTTGTCACTAGTCTTAGTTGGTGATTTGTGACGATAATTG
Found at i:1012814 original size:85 final size:85
Alignment explanation
Indices: 1012720--1012969 Score: 299
Period size: 85 Copynumber: 2.9 Consensus size: 85
1012710 TGAGAACCAA
* * *
1012720 AAACGCCGCAATATGCCAAGATCTATAGCGGCGTTTTTGGAACAAACGTCGAAAAAGGTCGATAT
1 AAACGCCGCAATAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAACGTCGAAAAAGATCGATAT
*
1012785 TTATAGCGGCGTTTTT-GAAC
65 CTATAGCGGCGTTTTTGGAAC
* * * *
1012805 AAACGCCGCAAAAGGTTGATATTTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAAGAT-GATA
1 AAACGCCGCAATAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAACGTCG-AAAAAGATCGATA
*
1012869 TCTATAGCGCCGTTTTTGGAAC
64 TCTATAGCGGCGTTTTTGGAAC
** * ** * *
1012891 AAACGCCATAATAGGTCAGATCTATAGCGGCGTTTTTTGAAACAAACACCGCAAAAGATC-AGAT
1 AAACGCCGCAATAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAACGTCGAAAAAGATCGATAT
1012955 CTATAGCGGCGTTTT
65 CTATAGCGGCGTTTT
1012970 GAATACAAAC
Statistics
Matches: 139, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
85 101 0.73
86 38 0.27
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (85 bp):
AAACGCCGCAATAGGTCAGATCTATAGCGGCGTTTTTGGAACAAACGTCGAAAAAGATCGATATC
TATAGCGGCGTTTTTGGAAC
Found at i:1012818 original size:42 final size:43
Alignment explanation
Indices: 1012740--1012969 Score: 270
Period size: 43 Copynumber: 5.4 Consensus size: 43
1012730 ATATGCCAAG
* *
1012740 ATCTATAGCGGCGTTTTTGGAACAAACGTCGAAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAT
* *
1012783 ATTTATAGCGGCGTTTTT-GAACAAACGCCGCAAAAGGTTGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAT
* * *
1012825 ATTTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAAGAT-GAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGC-AAAAGGTCGAT
* ** * *
1012868 ATCTATAGCGCCGTTTTTGGAACAAACGCCATAATAGGTC-AG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAT
* * * *
1012910 ATCTATAGCGGCGTTTTTTGAAACAAACACCGCAAAAGATC-AG
1 ATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGGTCGAT
1012953 ATCTATAGCGGCGTTTT
1 ATCTATAGCGGCGTTTT
1012970 GAATACAAAC
Statistics
Matches: 162, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
42 61 0.38
43 95 0.59
44 6 0.04
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (43 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCGAT
Found at i:1016637 original size:42 final size:40
Alignment explanation
Indices: 1016588--1016719 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 40
1016578 TATATCAGTT
1016588 TATAGCGGCATTTAAT-ATACAAACGCCACTAAAGTACGAGAA
1 TATAGCGGCATTT-ATCATA-AAA-GCCACTAAAGTACGAGAA
* * * * *
1016630 TTTAGCGGCGTTTGTGCTTAAAAGCCACTAAAGTACGAGTA
1 TATAGCGGCATTTAT-CATAAAAGCCACTAAAGTACGAGAA
* * * *
1016671 TATAGCGGCATTTGTACTTAAAATGTCACTAAAGTACGAGTA
1 TATAGCGGCATTTAT-CATAAAA-GCCACTAAAGTACGAGAA
1016713 TATAGCG
1 TATAGCG
1016720 ACGTTTGTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 38 0.49
42 38 0.49
43 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (40 bp):
TATAGCGGCATTTATCATAAAAGCCACTAAAGTACGAGAA
Found at i:1016659 original size:41 final size:42
Alignment explanation
Indices: 1016612--1016747 Score: 177
Period size: 42 Copynumber: 3.3 Consensus size: 42
1016602 ATATACAAAC
* * *
1016612 GCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTAAAA-
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
*
1016653 GCCACTAAAGTACGAGTATATAGCGGCATTTGTACTTAAAAT
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
* * * *
1016695 GTCACTAAAGTACGAGTATATAGCGACGTTTGTAC-AAGAAAC
1 GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTA-AAAT
1016737 GCCACTAAAGT
1 GCCACTAAAGT
1016748 TTAGTATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 38 0.46
42 45 0.54
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
GCCACTAAAGTACGAGTATATAGCGGCGTTTGTACTTAAAAT
Found at i:1018128 original size:18 final size:19
Alignment explanation
Indices: 1018105--1018153 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1018095 TTCGTATGAG
*
1018105 AAATTATATAA-ATTAACT
1 AAATTATATAACAATAACT
*
1018123 AAATTATCATAACAATAATT
1 AAATTAT-ATAACAATAACT
1018143 AATATTATATA
1 AA-ATTATATA
1018154 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
20 10 0.38
21 5 0.19
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTATATAACAATAACT
Found at i:1018868 original size:106 final size:103
Alignment explanation
Indices: 1018686--1018904 Score: 278
Period size: 106 Copynumber: 2.1 Consensus size: 103
1018676 GTGACAGAGT
* * *
1018686 TATTGTTAATAGTATCACATTTGGTCACTAAAAAAAACTTACTGTGGCAACATTGATGGTCAAAA
1 TATTGATAATAATATCACATTTGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAA
* * *
1018751 AATATACTTTTAGTATCAAATAAA-TTTATCACAATTTC
66 AATATACTTTTAGTATCAAA-AAAGATCATCACAATTTA
* * *
1018789 TATTGATAATAATATCAAACATTTGGTCACTAAAAACATACTTAGTGTGACAATATTGATGGTCA
1 TATTGATAATAATATC--ACATTTGGTCACTAAAAA-AAACTTACTGTGACAACATTGATGGTCA
* * * *
1018854 CAAAATATATTTTTAGTGTCAAAAAAGATCATCATAATTTA
63 AAAAATATACTTTTAGTATCAAAAAAGATCATCACAATTTA
1018895 TATTGATAAT
1 TATTGATAAT
1018905 TGTGTCGAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
103 14 0.14
105 21 0.21
106 64 0.65
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (103 bp):
TATTGATAATAATATCACATTTGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAA
AATATACTTTTAGTATCAAAAAAGATCATCACAATTTA
Found at i:1018922 original size:106 final size:105
Alignment explanation
Indices: 1018707--1018931 Score: 256
Period size: 106 Copynumber: 2.1 Consensus size: 105
1018697 GTATCACATT
*
1018707 TGGTCACTAAAAAAAACTTACTGTGGCAACATTGATGGTCAAAAAATATACTTTTAGTATCAAAT
1 TGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATCAAAT
* * * **
1018772 AAATTTATCACAATTTCTATTGATAATAATATCAAACATT
66 AAAATCATCACAATTTATATTGATAATAATATCAAACAGA
* * * * * *
1018812 TGGTCACTAAAAACATACTTAGTGTGACAATATTGATGGTCACAAAATATATTTTTAGTGTCAAA
1 TGGTCACTAAAAA-AAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATCAAA
* ** * * *
1018877 -AAAGATCATCATAATTTATATTGATAATTGTGTCGAATAGA
65 TAAA-ATCATCACAATTTATATTGATAATAATATCAAACAGA
1018918 TGGTCAC-AAAAAAA
1 TGGTCACTAAAAAAA
1018932 CGAACAATTG
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
104 1 0.01
105 21 0.21
106 77 0.78
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (105 bp):
TGGTCACTAAAAAAAACTTACTGTGACAACATTGATGGTCAAAAAATATACTTTTAGTATCAAAT
AAAATCATCACAATTTATATTGATAATAATATCAAACAGA
Found at i:1022945 original size:23 final size:25
Alignment explanation
Indices: 1022892--1022947 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
1022882 ATGTGAAATA
1022892 ATGAAAGTG-ATCACATGTGTGTAT
1 ATGAAAGTGAATCACATGTGTGTAT
1022916 ATG-AAGTGAAAT-ACATGT-T-TAT
1 ATGAAAGTG-AATCACATGTGTGTAT
1022938 ATGAAAGTGA
1 ATGAAAGTGA
1022948 TGAGAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 7 0.24
23 11 0.38
24 9 0.31
25 2 0.07
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.32
Consensus pattern (25 bp):
ATGAAAGTGAATCACATGTGTGTAT
Found at i:1023173 original size:22 final size:19
Alignment explanation
Indices: 1023145--1023240 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 19
1023135 GTTCTTAAGG
1023145 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGACA-AT
1023165 ACAGTGGTCCTTCGGGAC-AT
1 --AGTGGTCCTTCGGGACAAT
* *
1023185 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGACAAT
*
1023204 CAGTGGTCCTTCGGGA-TAT
1 -AGTGGTCCTTCGGGACAAT
*
1023223 AGTGGTCCTTCGAGACAA
1 AGTGGTCCTTCGGGACAA
1023241 ATATTCAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 28 0.44
19 5 0.08
20 15 0.23
22 16 0.25
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACAAT
Found at i:1023215 original size:38 final size:40
Alignment explanation
Indices: 1023145--1023234 Score: 139
Period size: 38 Copynumber: 2.3 Consensus size: 40
1023135 GTTCTTAAGG
*
1023145 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
* *
1023185 AGTGGTTCTTCGGAACA-AT-CAGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
1023223 AGTGGTCCTTCG
1 AGTGGTCCTTCG
1023235 AGACAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 29 0.63
39 2 0.04
40 15 0.33
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (40 bp):
AGTGGTCCTTCGGAACATATACAGTGGTCCTTCGGGACAT
Found at i:1039187 original size:2 final size:2
Alignment explanation
Indices: 1039174--1039227 Score: 99
Period size: 2 Copynumber: 26.5 Consensus size: 2
1039164 AGAACTTAGC
1039174 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1039217 TA TA TA TA TA T
1 TA TA TA TA TA T
1039228 GTGTGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1048447 original size:270 final size:258
Alignment explanation
Indices: 1047941--1048472 Score: 920
Period size: 270 Copynumber: 2.0 Consensus size: 258
1047931 TAGGGTTTTT
1047941 AAAACCCTGTTTGGACGGGTCGAATCCGGGTAGGGCTCCAGTTGAAGTTGGGCTTCGAGTTGGGC
1 AAAACCCTGTTTGGACGGGTCGAATCCGGGTAGGGCTCCAGTTGAAGTTGGGCTTCGAGTTGGGC
1048006 CGGGTCAAAAGTCTGGGTCGGATCTGTTGTTGTTGGGTTTGTTATAACTGGGTTTATGGGTGAGT
66 CGGGTCAAAAGTCTGGGTCGGATCTGTTGTTGTTGGGTTTGTTATAACTGGGTTTATGGGTGAGT
1048071 TTGCTTGTATTGGGTCCACTTGGTGATATGAGCCTGCAAAATATGTATTTATAATTAATAATAAT
131 TTGCTTGTATTGGGTCCACTTGGTGATATGAGCCTGCAAAATATGTATTTATAATTAATAATAAT
*
1048136 AATATAGTATTGTTTTAAACCCGGACAAAAACGGAGTGTACAAAAACATCGTAATGTTGTTAG
196 AATATAATATTGTTTTAAACCCGGACAAAAACGGAGTGTACAAAAACATCGTAATGTTGTTAG
*
1048199 AAAACCCTAGTTTGGACGGGTCGGATCCGGGTAGGGCTCCAGTTGAAGTTGGGCTTCGAGTTGGG
1 AAAACCCT-GTTTGGACGGGTCGAATCCGGGTAGGGCTCCAGTTGAAGTTGGGCTTCGAGTT--G
1048264 CTGGTACCGGGTCAAAAGTCTGGGTCGGATCTGTTGTTGTTTGGGTTTTAGTTATAACTGGGTTT
63 --GG--CCGGGTCAAAAGTCTGGGTCGGATCTGTTGTTG-TTGGG-TTT-GTTATAACTGGGTTT
* *
1048329 CTGGGTGAGTTTGCTTGTAATTGGGTCTACTTGGTGATATGAGCCTGCAAAATATGTATTTAATA
121 ATGGGTGAGTTTGCTTGT-ATTGGGTCCACTTGGTGATATGAGCCTGCAAAATATGTATTT-ATA
1048394 ATTAATAATAATAATATAATATTGTTTTAAACCCGGACAAAAACGGAGTGTACAAAAACATCGTA
184 ATTAATAATAATAATATAATATTGTTTTAAACCCGGACAAAAACGGAGTGTACAAAAACATCGTA
1048459 ATGTTGTTAG
249 ATGTTGTTAG
1048469 AAAA
1 AAAA
1048473 TTAGAGTTAG
Statistics
Matches: 258, Mismatches: 4, Indels: 12
0.94 0.01 0.04
Matches are distributed among these distances:
258 8 0.03
259 52 0.20
261 1 0.00
263 2 0.01
265 33 0.13
266 5 0.02
267 3 0.01
268 32 0.12
269 41 0.16
270 81 0.31
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (258 bp):
AAAACCCTGTTTGGACGGGTCGAATCCGGGTAGGGCTCCAGTTGAAGTTGGGCTTCGAGTTGGGC
CGGGTCAAAAGTCTGGGTCGGATCTGTTGTTGTTGGGTTTGTTATAACTGGGTTTATGGGTGAGT
TTGCTTGTATTGGGTCCACTTGGTGATATGAGCCTGCAAAATATGTATTTATAATTAATAATAAT
AATATAATATTGTTTTAAACCCGGACAAAAACGGAGTGTACAAAAACATCGTAATGTTGTTAG
Found at i:1048904 original size:20 final size:19
Alignment explanation
Indices: 1048879--1049004 Score: 103
Period size: 20 Copynumber: 6.3 Consensus size: 19
1048869 TTTTCCCAAT
1048879 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAAT-AGTAAA
* * *
1048899 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-T-AGTAAA
1048920 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAAT-AGTAAA
* * *
1048940 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-T-AGTAAA
*
1048961 TCGCAATGCG-ATACTAACTA
1 TCGCAATGCGAATAGTAA--A
1048981 TCGCAATGCGAATA-TAAA
1 TCGCAATGCGAATAGTAAA
1048999 TCGCAA
1 TCGCAA
1049005 CGAATACTTA
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
18 9 0.11
19 1 0.01
20 42 0.49
21 33 0.39
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
TCGCAATGCGAATAGTAAA
Found at i:1048922 original size:21 final size:21
Alignment explanation
Indices: 1048896--1048971 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1048886 GCGAATAAGT
1048896 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1048917 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1048937 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1048958 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1048972 TACTAACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1048924 original size:41 final size:41
Alignment explanation
Indices: 1048879--1048971 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1048869 TTTTCCCAAT
1048879 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1048920 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1048961 TCGCAATGCGA
1 TCGCAATGCGA
1048972 TACTAACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1048984 original size:41 final size:40
Alignment explanation
Indices: 1048879--1048993 Score: 160
Period size: 41 Copynumber: 2.8 Consensus size: 40
1048869 TTTTCCCAAT
*
1048879 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAACT-AATCGCAACGCGAATTGGGAAAA
*
1048920 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAACT-AATCGCAACGCGAATTGGGAAAA
*
1048961 TCGCAATGCGATACTAACT-ATCGCAATGCGAAT
1 TCGCAATGCGA-A-TAACTAATCGCAACGCGAAT
1048994 ATAAATCGCA
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
41 65 0.93
42 1 0.01
43 4 0.06
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (40 bp):
TCGCAATGCGAATAACTAATCGCAACGCGAATTGGGAAAA
Found at i:1049040 original size:20 final size:20
Alignment explanation
Indices: 1048961--1049069 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
1048951 ATTGGGAAAA
* *
1048961 TCGCAATGCGATACTAACTA
1 TCGCAACGCGATACTAACTT
* *
1048981 TCGCAATGCGAATA-TAA--A
1 TCGCAACGCG-ATACTAACTT
* *
1048999 TCGCAACG-AATACTTA-TT
1 TCGCAACGCGATACTAACTT
1049017 TCGCAACGCGATACTAACTT
1 TCGCAACGCGATACTAACTT
* *
1049037 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTAACTT
1049057 TCGCAACGCGATA
1 TCGCAACGCGATA
1049070 ATACATAATC
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
16 3 0.04
17 2 0.03
18 16 0.21
19 6 0.08
20 45 0.60
21 3 0.04
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTAACTT
Found at i:1049286 original size:22 final size:21
Alignment explanation
Indices: 1049258--1049306 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
1049248 CTCTCTCACC
1049258 CATCTCCGACGAAATCCGTCCT
1 CATCTCCGACGAAATCCGT-CT
1049280 CATCTCCGACGAAATCCGTCT
1 CATCTCCGACGAAATCCGTCT
1049301 -ATCTCC
1 CATCTCC
1049307 ATCTCTCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.22
21 2 0.07
22 19 0.70
ACGTcount: A:0.22, C:0.41, G:0.12, T:0.24
Consensus pattern (21 bp):
CATCTCCGACGAAATCCGTCT
Found at i:1049616 original size:20 final size:20
Alignment explanation
Indices: 1049562--1049620 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1049552 GCGATTATCT
**
1049562 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1049582 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1049602 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1049621 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1050957 original size:18 final size:18
Alignment explanation
Indices: 1050936--1050981 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1050926 CTACACTTCG
*
1050936 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
*
1050954 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
1050972 AGAGCCATCA
1 AGAGCCATCA
1050982 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:1051488 original size:20 final size:20
Alignment explanation
Indices: 1051463--1051508 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1051453 TAGTTTACTT
*
1051463 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1051483 TCGCAACGCGTAAATGGCTA
1 TCGCAACACGAAAATGACTA
1051503 TCGCAA
1 TCGCAA
1051509 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1051537 original size:14 final size:14
Alignment explanation
Indices: 1051518--1051575 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1051508 ATGCGAAATG
1051518 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1051532 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1051548 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1051564 AAAATCACAACG
1 AAAATCGCAACG
1051576 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1051560 original size:32 final size:33
Alignment explanation
Indices: 1051502--1051592 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1051492 GTAAATGGCT
1051502 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1051535 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1051567 ATCACAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1051593 TGCGATTGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1051614 original size:18 final size:18
Alignment explanation
Indices: 1051603--1051708 Score: 94
Period size: 19 Copynumber: 5.9 Consensus size: 18
1051593 TGCGATTGTG
1051603 TTTCGCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
1051621 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
1051637 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
1051654 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
* *
1051673 TTTCCGCGTTGCGCTAGTCA
1 TTT-CGCGTTGCGAT-TTCA
1051693 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
1051709 TAAGTTTCGT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
14 8 0.11
15 3 0.04
16 2 0.03
17 2 0.03
18 18 0.25
19 22 0.31
20 16 0.23
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:1051666 original size:19 final size:19
Alignment explanation
Indices: 1051603--1051725 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 19
1051593 TGCGATTGTG
1051603 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
1051621 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
1051637 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
1051654 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
* **
1051673 TTTCCGCGTTGCGCTAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
1051693 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
1051712 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
1051726 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 16 0.19
19 25 0.30
20 28 0.33
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1053585 original size:14 final size:14
Alignment explanation
Indices: 1053566--1053601 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1053556 GATTGTTAAT
1053566 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1053580 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1053594 TGATTTGT
1 TGATTTGT
1053602 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1053774 original size:19 final size:19
Alignment explanation
Indices: 1053718--1053766 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1053708 ATCGCAACGA
1053718 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1053737 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1053756 GAAAATCGCAA
1 GAAAATCGCAA
1053767 CAAGAAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1053827 original size:20 final size:20
Alignment explanation
Indices: 1053802--1053839 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1053792 TCGCATTGCG
*
1053802 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1053822 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1053840 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1054918 original size:24 final size:24
Alignment explanation
Indices: 1054891--1054944 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1054881 GTATTCGAAA
* *
1054891 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1054915 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1054939 TTTGAT
1 TTTGAT
1054945 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1057464 original size:33 final size:33
Alignment explanation
Indices: 1057422--1057548 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1057412 GGAAATTACT
1057422 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1057455 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
1057487 TTTCACAATGCGAAATGAAAATCGCAACGAGGGG
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1057521 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1057549 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.99
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1057532 original size:66 final size:66
Alignment explanation
Indices: 1057426--1057555 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
1057416 ATTACTATCG
*
1057426 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
1057491 A
66 A
* *
1057492 CAATGCGAAATGAAAATCGCAACGAGGGGATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1057556 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
A
Found at i:1057570 original size:19 final size:20
Alignment explanation
Indices: 1057548--1057590 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1057538 AAATCGCAAC
1057548 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1057567 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1057587 GCGA
1 GCGA
1057591 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1057575 original size:14 final size:14
Alignment explanation
Indices: 1057576--1057609 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1057566 TGCGATTTTC
1057576 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1057590 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1057604 ATTTTC
1 ATTTTC
1057610 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1057750 original size:14 final size:14
Alignment explanation
Indices: 1057731--1057767 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1057721 CATCAATTAA
1057731 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1057745 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1057759 ACAAATCAA
1 ACAAATCAA
1057768 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1059185 original size:21 final size:21
Alignment explanation
Indices: 1059119--1059185 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1059109 GTGAATCGGG
1059119 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
1059139 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
1059161 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
1059182 CTCT
1 CTCT
1059186 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:1061304 original size:14 final size:14
Alignment explanation
Indices: 1061285--1061321 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1061275 GGAAATGACT
*
1061285 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
1061299 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1061313 ATCGCAACG
1 ATCGCAACG
1061322 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Done.