Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006270.1 Hibiscus syriacus cultivar Beakdansim tig00014949_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: 949592
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 3 of 5
Found at i:555540 original size:21 final size:21
Alignment explanation
Indices: 555514--555630 Score: 180
Period size: 21 Copynumber: 5.6 Consensus size: 21
555504 GTTTCCAGAT
* *
555514 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
555535 TCGCAATGCAAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
555556 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
555577 TCCCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
555598 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
555619 TCTCAATGCGAA
1 TCGCAATGCGAA
555631 TATGTAAATC
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:555669 original size:21 final size:21
Alignment explanation
Indices: 555639--555824 Score: 175
Period size: 21 Copynumber: 8.9 Consensus size: 21
555629 AATATGTAAA
* **
555639 TCGCAATGCGATAGTTGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
555660 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
555681 TCACGTTGCGATAGTTCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
555702 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
555722 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
555743 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
555764 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
555785 TCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
555808 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
555825 AATCGCAACG
Statistics
Matches: 140, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
19 7 0.05
20 17 0.12
21 104 0.74
22 1 0.01
23 11 0.08
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:555794 original size:62 final size:61
Alignment explanation
Indices: 555684--555824 Score: 178
Period size: 62 Copynumber: 2.3 Consensus size: 61
555674 TCGAAGTTCA
* * *
555684 CGTTGCGATAGTTCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTA-CATATT
1 CGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCATTGCGATTTATCAAATT
* *
555744 CGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT-TCGCGTTGCGATTTATTCCAAAT
1 CG--TTGCGATAGTCCAAGTTCGCATTGCGATAGT-CAACTATCGCATTGCGATTTA-T-CAAAT
555808 T
61 T
555809 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
555825 AATCGCAACG
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
60 2 0.03
62 44 0.63
63 17 0.24
65 7 0.10
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (61 bp):
CGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACTATCGCATTGCGATTTATCAAATT
Found at i:555830 original size:104 final size:103
Alignment explanation
Indices: 555639--555831 Score: 255
Period size: 104 Copynumber: 1.9 Consensus size: 103
555629 AATATGTAAA
** * *
555639 TCGCAATGCGATAGTTGAAGTTCGCATTGCGATAGTCGAAGTTCACGTTGCGATAGTTCAAGTTC
1 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCACGTTGCGATAGTTCAAATTC
* **
555704 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
66 G-ATTGCGATAGTCCAAAATCGCATTGCGATTTACATAT
* *
555743 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTA-TTCCAAA
1 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCACGTTGCGA--TAGTT-CAAA
555807 TTCG-TTGCGATAGTCCAAAATCGCA
63 TTCGATTGCGATAGTCCAAAATCGCA
555832 ACGATTGGTG
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
104 66 0.86
105 2 0.03
106 9 0.12
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (103 bp):
TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCACGTTGCGATAGTTCAAATTC
GATTGCGATAGTCCAAAATCGCATTGCGATTTACATAT
Found at i:555925 original size:6 final size:6
Alignment explanation
Indices: 555914--555956 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
555904 GACACGTATT
555914 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA-G ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
555957 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:556429 original size:6 final size:6
Alignment explanation
Indices: 556418--556458 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
556408 AGGGTCTCGC
* * *
556418 GGGTCG GGGTCG GGGTCG GGGTCG TGGTCG TGGTCG TGGTC
1 GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTCG GGGTC
556459 ATGGTAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.17, G:0.59, T:0.24
Consensus pattern (6 bp):
GGGTCG
Found at i:556463 original size:6 final size:6
Alignment explanation
Indices: 556419--556463 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
556409 GGGTCTCGCG
* * * *
556419 GGTCGG GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTCAT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
556464 AATACATGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.02, C:0.16, G:0.56, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:556605 original size:21 final size:21
Alignment explanation
Indices: 556553--556717 Score: 115
Period size: 21 Copynumber: 7.9 Consensus size: 21
556543 CGTTGCGATT
*
556553 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
*
556572 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
556595 TTGGACTATCGCAATGC-AAA
1 TTGGACTATCGCAATGCGAAC
* *
556615 TATGTA-AATCGCAATGCGATA-
1 T-TGGACTATCGCAATGCGA-AC
* * * *
556636 GTCGACTATTGCAATGCAAAC
1 TTGGACTATCGCAATGCGAAC
* *
556657 TTGGACTATCGCAACGCAAAC
1 TTGGACTATCGCAATGCGAAC
* **
556678 TTCGACTATCGCAATGAAAAC
1 TTGGACTATCGCAATGCGAAC
* *
556699 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
556718 TTTACATATT
Statistics
Matches: 115, Mismatches: 22, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
19 6 0.05
20 16 0.14
21 82 0.71
22 1 0.01
23 10 0.09
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:556643 original size:41 final size:41
Alignment explanation
Indices: 556578--556693 Score: 119
Period size: 41 Copynumber: 2.8 Consensus size: 41
556568 GAATTTGGAA
* *
556578 TAAATCGCAATGCGAACTTGGACTATCGCAATGCAAATATG
1 TAAATCGCAATGCGAACGTCGACTATCGCAATGCAAATATG
*
556619 TAAATCGCAATGCGATA-GTCGACTATTGCAATGCAAACT-TG
1 TAAATCGCAATGCGA-ACGTCGACTATCGCAATGCAAA-TATG
* * * * *
556660 GACTATCGCAACGCAAACTTCGACTATCGCAATG
1 TA-AATCGCAATGCGAACGTCGACTATCGCAATG
556694 AAAACTTCGA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 36 0.58
42 26 0.42
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (41 bp):
TAAATCGCAATGCGAACGTCGACTATCGCAATGCAAATATG
Found at i:556753 original size:21 final size:19
Alignment explanation
Indices: 556699--556760 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 19
556689 CAATGAAAAC
556699 TTCGACTATCGCATTGCGA
1 TTCGACTATCGCATTGCGA
*
556718 TT-TACATATTCGCATTGCGA
1 TTCGAC-TA-TCGCATTGCGA
556738 TAGTCGACTATCGCATTGCGA
1 T--TCGACTATCGCATTGCGA
556759 TT
1 TT
556761 TTGGAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 2 0.06
19 5 0.14
20 12 0.33
21 12 0.33
22 3 0.08
23 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (19 bp):
TTCGACTATCGCATTGCGA
Found at i:556765 original size:104 final size:103
Alignment explanation
Indices: 556545--556765 Score: 234
Period size: 104 Copynumber: 2.1 Consensus size: 103
556535 CCACCAGTCG
* * ** *
556545 TTGCGATTTTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTGGACTATCGCAAT
1 TTGCGATTTTGGACTATCGCAACGAACTTCGAAT-AATCGCAATGAAAACTTCGACTATCGCAAT
*
556610 GCAAATATGTAAATCGCAATGCGATAGTCGACTATTGCA
65 GCAAATATGTAAATCGCAATGCGATAGTCGACTATCGCA
* * ** * *
556649 ATGCAAACTTGGACTATCGCAACGCAAACTTCGACT-ATCGCAATGAAAACTTCGACTATCGCAT
1 TTGCGATTTTGGACTATCGCAACG--AACTTCGAATAATCGCAATGAAAACTTCGACTATCGCAA
* *
556713 TGC-GAT-T-TACATATTCGCATTGCGATAGTCGACTATCGCA
64 TGCAAATATGTA-A-A-TCGCAATGCGATAGTCGACTATCGCA
556753 TTGCGATTTTGGA
1 TTGCGATTTTGGA
556766 ATAAATTCTT
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
101 2 0.02
102 2 0.02
103 3 0.03
104 80 0.85
106 7 0.07
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (103 bp):
TTGCGATTTTGGACTATCGCAACGAACTTCGAATAATCGCAATGAAAACTTCGACTATCGCAATG
CAAATATGTAAATCGCAATGCGATAGTCGACTATCGCA
Found at i:556929 original size:21 final size:21
Alignment explanation
Indices: 556905--557033 Score: 147
Period size: 21 Copynumber: 6.2 Consensus size: 21
556895 TTTGGAATAA
556905 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
* *
556926 ATCGCAATGCGAA-TATGTA-A
1 ATCGCAATGCGAACT-TGGACT
* *
556946 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTGGACT
556967 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
* * *
556988 ATCACAACGCGAACTTTGACT
1 ATCGCAATGCGAACTTGGACT
*
557009 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTGGACT
557030 ATCG
1 ATCG
557034 TATTGCGATT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.18
21 74 0.82
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGGACT
Found at i:556967 original size:41 final size:41
Alignment explanation
Indices: 556902--557021 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 41
556892 CAATTTGGAA
* *
556902 TAAATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
1 TAAATCGCAATGCGAACGTCGACTATCGCAATGCGAATATG
556943 TAAATCGCAATGCGATA-GTCGACTATCGCAATGCGAACT-TG
1 TAAATCGCAATGCGA-ACGTCGACTATCGCAATGCGAA-TATG
* * * * * *
556984 GACTATCACAACGCGAACTTTGACTATCGCAATGCGAA
1 TA-AATCGCAATGCGAACGTCGACTATCGCAATGCGAA
557022 CTTCGACTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
41 37 0.55
42 30 0.45
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
TAAATCGCAATGCGAACGTCGACTATCGCAATGCGAATATG
Found at i:557060 original size:20 final size:20
Alignment explanation
Indices: 557035--557103 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
557025 CGACTATCGT
557035 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
*
557055 ATTGCGATAGT-CGACTA-TCGC
1 ATTGCGAT-TTAC-A-TATTCGC
*
557076 ATTGTGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
557096 ATTGCGAT
1 ATTGCGAT
557104 AGTCCAAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTGCGATTTACATATTCGC
Found at i:557069 original size:41 final size:41
Alignment explanation
Indices: 557024--557165 Score: 155
Period size: 41 Copynumber: 3.4 Consensus size: 41
557014 AATGCGAACT
*
557024 TCGACTATCGTATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
*
557065 TCGACTATCGCATTGTGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
* * * * *
557106 TCCAAGT-TCGCATTGCGATAGTCCA-AGTTCGCATTACGATAG
1 T-CGACTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAG
*
557148 TCGAAGT-TCGCATTGCGA
1 TCG-ACTATCGCATTGCGA
557166 ATCTGGAAAC
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
41 53 0.60
42 35 0.40
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (41 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
Found at i:557077 original size:21 final size:21
Alignment explanation
Indices: 556946--557165 Score: 77
Period size: 21 Copynumber: 10.6 Consensus size: 21
556936 GAATATGTAA
*
556946 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* * *
556967 ATCGCAATGCGA-ACTTGGACT
1 ATCGCATTGCGATA-GTCGACT
* ** * *
556988 ATCACAACGCGA-ACTTTGACT
1 ATCGCATTGCGATA-GTCGACT
* *
557009 ATCGCAATGCGA-ACTTCGACT
1 ATCGCATTGCGATA-GTCGACT
* *
557030 ATCGTATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
557049 ATTCGCATTGCGATAGTCGACT
1 A-TCGCATTGCGATAGTCGACT
* *
557071 ATCGCATTGTGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
557090 ATTCGCATTGCGATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
* *
557113 -TCGCATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGT-CGACT
* *
557134 -TCGCATTACGATAGTCGAAGT
1 ATCGCATTGCGATAGTCG-ACT
557155 -TCGCATTGCGA
1 ATCGCATTGCGA
557166 ATCTGGAAAC
Statistics
Matches: 164, Mismatches: 21, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.02
19 6 0.04
20 24 0.15
21 122 0.74
22 4 0.02
23 3 0.02
24 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:559574 original size:13 final size:13
Alignment explanation
Indices: 559558--559583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
559548 CTAGTTTTGT
559558 TGTTTTTATATTA
1 TGTTTTTATATTA
559571 TGTTTTTATATTA
1 TGTTTTTATATTA
559584 AGGATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
TGTTTTTATATTA
Found at i:561913 original size:23 final size:23
Alignment explanation
Indices: 561876--561938 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
561866 AAACATAATT
561876 CAGGTCAAGTATCATATCAGAATC
1 CAGGTC-AGTATCATATCAGAATC
*
561900 CATGTCAGTATCATATCAGAATC
1 CAGGTCAGTATCATATCAGAATC
*
561923 CGGGTCAGGTATCATA
1 CAGGTCA-GTATCATA
561939 ACAAAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (23 bp):
CAGGTCAGTATCATATCAGAATC
Found at i:562386 original size:23 final size:23
Alignment explanation
Indices: 562313--562408 Score: 120
Period size: 24 Copynumber: 4.0 Consensus size: 23
562303 TTATCCATAG
*
562313 ATCAGAATTCAGGTCAAGTATCAT
1 ATCAGAATCCAGGTC-AGTATCAT
*
562337 ATCAGAATCAAGGTCATGTATCAT
1 ATCAGAATCCAGGTCA-GTATCAT
* *
562361 ATCAGAATCCATGTCAGCATCAT
1 ATCAGAATCCAGGTCAGTATCAT
*
562384 ATCAAAATCCAGGTCAGGTATCAT
1 ATCAGAATCCAGGTCA-GTATCAT
562408 A
1 A
562409 ACAAAATTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 21 0.34
24 41 0.66
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAGAATCCAGGTCAGTATCAT
Found at i:562386 original size:47 final size:48
Alignment explanation
Indices: 562313--562408 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 48
562303 TTATCCATAG
* * * *
562313 ATCAGAATTCAGGTCAAGTATCATATCAGAATCAAGGTCATGTATCAT
1 ATCAGAATCCAGGTCAAGCATCATATCAAAATCAAGGTCAGGTATCAT
* *
562361 ATCAGAATCCATGTC-AGCATCATATCAAAATCCAGGTCAGGTATCAT
1 ATCAGAATCCAGGTCAAGCATCATATCAAAATCAAGGTCAGGTATCAT
562408 A
1 A
562409 ACAAAATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 29 0.69
48 13 0.31
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (48 bp):
ATCAGAATCCAGGTCAAGCATCATATCAAAATCAAGGTCAGGTATCAT
Found at i:562764 original size:470 final size:470
Alignment explanation
Indices: 561877--562786 Score: 1649
Period size: 470 Copynumber: 1.9 Consensus size: 470
561867 AACATAATTC
* * *
561877 AGGTCAAGTATCATATCAGAATCCATGTCAGTATCATATCAGAATCCGGGTCAGGTATCATAACA
1 AGGTCAAGTATCATATCAGAATCCATGTCAGCATCATATCAAAATCCAGGTCAGGTATCATAACA
561942 AAATTCAAATCGAAAATCAGTTAAAATATTCATGTGATTAGGGAACACACCAGACTTTACAGATA
66 AAATTCAAATCGAAAATCAGTTAAAATATTCATGTGATTAGGGAACACACCAGACTTTACAGATA
562007 TTACTCAGAGGTACTGGATAATCTTAACAGACATAGAAACACGGATCTTCAGTATACTGATAAAA
131 TTACTCAGAGGTACTGGATAATCTTAACAGACATAGAAACACGGATCTTCAGTATACTGATAAAA
* *
562072 TGTCAGAATTTTGAATCACTATAGGAAGAGTTCAATAACTAATGGAATCATCAATTATTTAGAAT
196 TGTCAGAATTTAGAATCACTATAGGAAGAGTTCAATAACTAATGGAATCATCAATTATTCAGAAT
* *
562137 ATGACTTCAGTTGATAAGGAAGAAATGAAGGTTCAGGTCATTTACAGTCTATGTCGATTGATTTC
261 ATGACTTCAGCTGATAAGGAAGAAATAAAGGTTCAGGTCATTTACAGTCTATGTCGATTGATTTC
* *
562202 ATTATCAAACAACTCCAGATGAATATCTCCCAGAATTAATGCTTGTCGATTTGTAAATTCATTGT
326 ATTATCAAACAAATCCAGATGAATATCTCCCAGAATTAATGCTTGTCGATTGGTAAATTCATTGT
*
562267 CCTTCTAGGGAATTTACTTTTTAATACCAAAAATTCTTATCCATAGATCAGAATTCAGGTCAAGT
391 CCTTCCAGGGAATTTACTTTTTAATACCAAAAATTCTTATCCATAGATCAGAATTCAGGTCAAGT
562332 ATCATATCAGAATCA
456 ATCATATCAGAATCA
*
562347 AGGTCATGTATCATATCAGAATCCATGTCAGCATCATATCAAAATCCAGGTCAGGTATCATAACA
1 AGGTCAAGTATCATATCAGAATCCATGTCAGCATCATATCAAAATCCAGGTCAGGTATCATAACA
*
562412 AAATTCAAATCGGAAATCAGTTAAAATATTCATGTGATTAGGGAACACACCAGACTTTACAGATA
66 AAATTCAAATCGAAAATCAGTTAAAATATTCATGTGATTAGGGAACACACCAGACTTTACAGATA
* * *
562477 TTATTCAGAGGTACTGGATAATCTTAACAGGCATAGAAACACGGATCTTTAGTATACTGATAAAA
131 TTACTCAGAGGTACTGGATAATCTTAACAGACATAGAAACACGGATCTTCAGTATACTGATAAAA
562542 TGTCAGAATTTAGAATCACTATAGGAAGAGTTCAATAACTAATGGAATCATCAATTATTCAGAAT
196 TGTCAGAATTTAGAATCACTATAGGAAGAGTTCAATAACTAATGGAATCATCAATTATTCAGAAT
*
562607 ATGACTTGAGCTGATAAGGAAGAAATAAAGGTTCAGGTCATTTACAGTCTATGTCGATTGATTTC
261 ATGACTTCAGCTGATAAGGAAGAAATAAAGGTTCAGGTCATTTACAGTCTATGTCGATTGATTTC
* *
562672 ATTGTCAAACAAATCCAGATGAATATCTCCCTGAATTAATGCTTGTCGATTGGTAAATTCATTGT
326 ATTATCAAACAAATCCAGATGAATATCTCCCAGAATTAATGCTTGTCGATTGGTAAATTCATTGT
*
562737 CCTTCCAGGGTATTTACTTTTTAATACCAAAAATTCTTATCCATAGATCA
391 CCTTCCAGGGAATTTACTTTTTAATACCAAAAATTCTTATCCATAGATCA
562787 TTTTTGGAAT
Statistics
Matches: 421, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
470 421 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (470 bp):
AGGTCAAGTATCATATCAGAATCCATGTCAGCATCATATCAAAATCCAGGTCAGGTATCATAACA
AAATTCAAATCGAAAATCAGTTAAAATATTCATGTGATTAGGGAACACACCAGACTTTACAGATA
TTACTCAGAGGTACTGGATAATCTTAACAGACATAGAAACACGGATCTTCAGTATACTGATAAAA
TGTCAGAATTTAGAATCACTATAGGAAGAGTTCAATAACTAATGGAATCATCAATTATTCAGAAT
ATGACTTCAGCTGATAAGGAAGAAATAAAGGTTCAGGTCATTTACAGTCTATGTCGATTGATTTC
ATTATCAAACAAATCCAGATGAATATCTCCCAGAATTAATGCTTGTCGATTGGTAAATTCATTGT
CCTTCCAGGGAATTTACTTTTTAATACCAAAAATTCTTATCCATAGATCAGAATTCAGGTCAAGT
ATCATATCAGAATCA
Found at i:564714 original size:19 final size:19
Alignment explanation
Indices: 564680--564728 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
564670 TAAAAGTTTT
564680 GGTCAACGGTGGTCAACGCC
1 GGTCAACGG-GGTCAACGCC
564700 GGTCAACGGGGTCAACGCC
1 GGTCAACGGGGTCAACGCC
*
564719 GCTCAACGGG
1 GGTCAACGGG
564729 TCGGGTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.20, C:0.31, G:0.37, T:0.12
Consensus pattern (19 bp):
GGTCAACGGGGTCAACGCC
Found at i:564724 original size:10 final size:10
Alignment explanation
Indices: 564680--564726 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
564670 TAAAAGTTTT
**
564680 GGTCAACGGT
1 GGTCAACGCC
564690 GGTCAACGCC
1 GGTCAACGCC
*
564700 GGTCAACG-G
1 GGTCAACGCC
564709 GGTCAACGCC
1 GGTCAACGCC
*
564719 GCTCAACG
1 GGTCAACG
564727 GGTCGGGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.21, C:0.32, G:0.34, T:0.13
Consensus pattern (10 bp):
GGTCAACGCC
Found at i:569342 original size:224 final size:226
Alignment explanation
Indices: 568943--569394 Score: 728
Period size: 224 Copynumber: 2.0 Consensus size: 226
568933 AACCCAAATC
*
568943 CCACGTGCCTTGTATTATTTTCAAACCACAACTCACTTCATTTTTTTTCCCAATCGAAACCTAGC
1 CCACGTGCCTTGTATTATTTTCAAAACACAACTCACTTCA-TTTTTTTCCCAATCGAAACCTAGC
* * *
569008 CTCATATTCTATATTTTTTCTTTCTTCCATAAGCTGCACACTATTCTCACCATTGAACATAGCCA
65 CTCATATTCTATATTTTTTCTTTCTTCCACAAACTGCACACTATTCTCACCATTGAACATAACCA
* * * *
569073 TCGTCCAAACCCATCACCTCTTCTCGACTCTTACACAAGCATCATGGTTTACACAAAACTTTTGA
130 TCGTCCAAACCCATCACCTCTTCTCGACTCCTACACAACCATCATGGTTCACACAAAACGTTTGA
*
569138 ACCGAGCTACCCTGTGCCCATCAGTCTCACCA
195 ACCGAGCTACCCTCTGCCCATCAGTCTCACCA
* *
569170 CCACGTGCCTTGTATTATTTTCAAAACGCAACTCACTTCA-TTTTTT-CCAATCGAAACCTAGTC
1 CCACGTGCCTTGTATTATTTTCAAAACACAACTCACTTCATTTTTTTCCCAATCGAAACCTAGCC
* * * *
569233 TCATATTTTATATTTTTTCTTTCTTTCACAAACTGCACATTATTCTGACCATTGAACATAACCAT
66 TCATATTCTATATTTTTTCTTTCTTCCACAAACTGCACACTATTCTCACCATTGAACATAACCAT
569298 CGTCCAAACCCATCACCTCTTCTCGACTCCTACACAACCATCATGGTTCACACAAAACGTTTGAA
131 CGTCCAAACCCATCACCTCTTCTCGACTCCTACACAACCATCATGGTTCACACAAAACGTTTGAA
* *
569363 TCGAGCTACCCTCTGCCCATCGGTCTCACCA
196 CCGAGCTACCCTCTGCCCATCAGTCTCACCA
569394 C
1 C
569395 ATCGTGACCG
Statistics
Matches: 208, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
224 164 0.79
225 6 0.03
227 38 0.18
ACGTcount: A:0.27, C:0.32, G:0.09, T:0.33
Consensus pattern (226 bp):
CCACGTGCCTTGTATTATTTTCAAAACACAACTCACTTCATTTTTTTCCCAATCGAAACCTAGCC
TCATATTCTATATTTTTTCTTTCTTCCACAAACTGCACACTATTCTCACCATTGAACATAACCAT
CGTCCAAACCCATCACCTCTTCTCGACTCCTACACAACCATCATGGTTCACACAAAACGTTTGAA
CCGAGCTACCCTCTGCCCATCAGTCTCACCA
Found at i:572652 original size:14 final size:14
Alignment explanation
Indices: 572633--572679 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
572623 AGGGTATGTT
572633 TGTTTGGAATAAAA
1 TGTTTGGAATAAAA
*
572647 TGTTTGGAGTAAAA
1 TGTTTGGAATAAAA
*
572661 TGTTTAGAGA-AAAA
1 TGTTTGGA-ATAAAA
572675 TGTTT
1 TGTTT
572680 TACAGAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (14 bp):
TGTTTGGAATAAAA
Found at i:575163 original size:11 final size:11
Alignment explanation
Indices: 575147--575180 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
575137 GCATAAAACC
575147 AAATATAAATA
1 AAATATAAATA
575158 AAATATAAATA
1 AAATATAAATA
*
575169 AAA-AAAAATA
1 AAATATAAATA
575179 AA
1 AA
575181 GAAGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATATAAATA
Found at i:575243 original size:19 final size:18
Alignment explanation
Indices: 575153--575243 Score: 52
Period size: 18 Copynumber: 5.3 Consensus size: 18
575143 AACCAAATAT
*
575153 AAATAAAATATAAATA-A
1 AAATAAAATAAAAATAGA
*
575170 AAA-AAAATAAAGA-AGA
1 AAATAAAATAAAAATAGA
* *
575186 TAATAACAATAACAAT---
1 AAATAA-AATAAAAATAGA
*
575202 ACA-AAAATAAAAATAGA
1 AAATAAAATAAAAATAGA
* *
575219 AGATAAAATAAAATATATA
1 AAATAAAATAAAA-ATAGA
575238 AAATAA
1 AAATAA
575244 TAAATATATC
Statistics
Matches: 54, Mismatches: 11, Indels: 16
0.67 0.14 0.20
Matches are distributed among these distances:
14 8 0.15
15 3 0.06
16 12 0.22
17 7 0.13
18 15 0.28
19 9 0.17
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (18 bp):
AAATAAAATAAAAATAGA
Found at i:575250 original size:16 final size:16
Alignment explanation
Indices: 575221--575294 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
575211 AAAATAGAAG
575221 ATAAAAT-A-AAATAT
1 ATAAAATAATAAATAT
575235 ATAAAATAATAAATAT
1 ATAAAATAATAAATAT
*
575251 ATCTAACAT-AT-AATA-
1 A--TAAAATAATAAATAT
*
575266 ATAGTAATAA-AAATAT
1 ATA-AAATAATAAATAT
575282 ATAAAAATAATAA
1 AT-AAAATAATAA
575295 TGATAGATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
13 2 0.04
14 9 0.20
15 7 0.15
16 18 0.39
17 5 0.11
18 5 0.11
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (16 bp):
ATAAAATAATAAATAT
Found at i:575974 original size:37 final size:37
Alignment explanation
Indices: 575919--576019 Score: 141
Period size: 37 Copynumber: 2.7 Consensus size: 37
575909 CTTGTGGATT
* **
575919 CTATCTTTAGGAGTTTGAATCCTAGTATGA-CTCTATC
1 CTATTTTTAGGAGTTTGAATCCTAGTAAAATC-CTATC
*
575956 CTATTTTTAGGAGTTTGAATCCTAATAAAATCCTATC
1 CTATTTTTAGGAGTTTGAATCCTAGTAAAATCCTATC
*
575993 ATATTTTTAGGAGTTTGAATCCTAGTA
1 CTATTTTTAGGAGTTTGAATCCTAGTA
576020 GGACAAAAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 56 0.98
38 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTGAATCCTAGTAAAATCCTATC
Found at i:576923 original size:106 final size:106
Alignment explanation
Indices: 576738--577165 Score: 691
Period size: 106 Copynumber: 4.0 Consensus size: 106
576728 TGTATTATTC
*
576738 CGAGTCCAATATCC-TCTG-TCGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGA
1 CGAGTCCAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGA
*
576801 CAACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
576844 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
576909 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
576950 CGAGTCCAATAT-CTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* *
577014 ACCAGTCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
577055 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGTTCTGAAACTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* *
577120 ACCATCCGTCACTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
577161 CGAGT
1 CGAGT
577166 GGCACGATAT
Statistics
Matches: 301, Mismatches: 18, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
105 100 0.33
106 198 0.66
107 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:577137 original size:211 final size:212
Alignment explanation
Indices: 576738--577165 Score: 698
Period size: 211 Copynumber: 2.0 Consensus size: 212
576728 TGTATTATTC
*
576738 CGAGTCCAATATCCTCTGTCGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCTGTCGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
* * *
576803 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGA
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGA
* * *
576868 AGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAG
131 AGTTGAAATTGGCTCTGAAACTGAGAAATTATTTGTTGACAACCAGCCGTCACTTCGTTGTGAAG
576933 TTGAACTTGTGTTGTCT
196 TTGAACTTGTGTTGTCT
* * *
576950 CGAGTCCAATATCTTC-G-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAC
1 CGAGTCCAATATCCTCTGTC-GTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGAC
* *
577013 AACCAGTCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTG
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTG
* * *
577078 AAGTTGAAATTGGTTCTGAAACTGAGAAATTGTTTGTTGACAACCATCCGTCACTTCGTTGTGAA
130 AAGTTGAAATTGGCTCTGAAACTGAGAAATTATTTGTTGACAACCAGCCGTCACTTCGTTGTGAA
577143 GTTGAACTTGTGTTGTCT
195 GTTGAACTTGTGTTGTCT
577161 CGAGT
1 CGAGT
577166 GGCACGATAT
Statistics
Matches: 200, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
210 1 0.00
211 184 0.92
212 15 0.08
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (212 bp):
CGAGTCCAATATCCTCTGTCGTAAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGA
AGTTGAAATTGGCTCTGAAACTGAGAAATTATTTGTTGACAACCAGCCGTCACTTCGTTGTGAAG
TTGAACTTGTGTTGTCT
Found at i:579076 original size:15 final size:17
Alignment explanation
Indices: 579058--579108 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
579048 TTTTTTTTAT
579058 TTTTGCTCTT-TTTC-C
1 TTTTGCTCTTGTTTCTC
*
579073 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
579090 TTTTTCT-TTGTTTTTC
1 TTTTGCTCTTGTTTCTC
579106 TTT
1 TTT
579109 GCTTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 9 0.30
16 15 0.50
17 6 0.20
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:579115 original size:22 final size:25
Alignment explanation
Indices: 579059--579117 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 25
579049 TTTTTTTATT
*
579059 TTTGCTCTTTTTCCTTTTGTTCTTG
1 TTTGCTCTTTTTCCTTTTGTTCTTC
*
579084 TTT-CTCTTTTT-C-TTTGTTTTTC
1 TTTGCTCTTTTTCCTTTTGTTCTTC
*
579106 TTTGCTTTTTTT
1 TTTGCTCTTTTT
579118 TGCTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 11 0.37
23 8 0.27
24 8 0.27
25 3 0.10
ACGTcount: A:0.00, C:0.17, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTGCTCTTTTTCCTTTTGTTCTTC
Found at i:579126 original size:10 final size:11
Alignment explanation
Indices: 579089--579125 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
579079 TCTTGTTTCT
579089 CTTTTTCTTTG
1 CTTTTTCTTTG
579100 -TTTTTCTTTG
1 CTTTTTCTTTG
579110 CTTTTT-TTTG
1 CTTTTTCTTTG
579120 CTTTTT
1 CTTTTT
579126 TAATATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (11 bp):
CTTTTTCTTTG
Found at i:581369 original size:21 final size:21
Alignment explanation
Indices: 581343--581416 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
581333 ATTATTACTA
581343 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
581364 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* *
581385 TCGCATTGAGATTTTTCCAA-T
1 TCGCAATGCGA-TTTTCCAATT
581406 TCGCAATGCGA
1 TCGCAATGCGA
581417 ATAAGTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 40 0.83
22 8 0.17
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:581375 original size:41 final size:41
Alignment explanation
Indices: 581314--581539 Score: 142
Period size: 41 Copynumber: 5.5 Consensus size: 41
581304 CGCAAATCAG
* *
581314 TTTCCAGATTCGCAACGCGATTATTACTATCGCAATGCGAT
1 TTTCCAAATTCGCAATGCGATTATTACTATCGCAATGCGAT
* * * * *
581355 TTTCCAATTTCGCAATGCGATT-TTCCAATTTCGCATTGAGATT
1 TTTCCAAATTCGCAATGCGATTATT--ACTATCGCAATGCGA-T
* * * *
581398 TTTCC-AATTCGCAATGCGAATAAGTA-AATCGCAATGCGAA
1 TTTCCAAATTCGCAATGCG-ATTATTACTATCGCAATGCGAT
** * *
581438 TTTGGAAAATCGCAATGCGA-TACTGACTATCGCAATGCGAT
1 TTTCCAAATTCGCAATGCGATTA-TTACTATCGCAATGCGAT
** * * **
581479 AATACAAAATCGCAATGCGA-T-TTACGTATTCGCGTTGCGAT
1 TTTCCAAATTCGCAATGCGATTATTAC-TA-TCGCAATGCGAT
581520 TTT-CATAATTCGCAATGCGA
1 TTTCCA-AATTCGCAATGCGA
581540 ATACGTAAAT
Statistics
Matches: 141, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
39 4 0.03
40 11 0.08
41 93 0.66
42 24 0.17
43 8 0.06
44 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (41 bp):
TTTCCAAATTCGCAATGCGATTATTACTATCGCAATGCGAT
Found at i:581579 original size:61 final size:61
Alignment explanation
Indices: 581403--581613 Score: 182
Period size: 61 Copynumber: 3.4 Consensus size: 61
581393 AGATTTTTCC
* ** *
581403 AATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGCAATGCGA-TACTGACT
1 AATTCGCAATGCGAATACGTAAATCGCAATGCG-ATTAAGTAAATCGCAATGCGATTA-TGA-T
* * * ** * *
581466 -A-TCGCAATGCGATAATAC-AAAATCGCAATGCGATTTACGT-ATTCGCGTTGCGATTTTCAT
1 AATTCGCAATGCG--AATACGTAAATCGCAATGCGA-TTAAGTAAATCGCAATGCGATTATGAT
* * *
581526 AATTCGCAATGCGAATACGTAAATCGTAACGCGATTAAGTAAATCGCAATGCGAATTAGGA-
1 AATTCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAATGCG-ATTATGAT
*
581587 AAATCGCAATGCGAATACGTAAATCGC
1 AATTCGCAATGCGAATACGTAAATCGC
581614 GTTGCGATAG
Statistics
Matches: 117, Mismatches: 22, Indels: 20
0.74 0.14 0.13
Matches are distributed among these distances:
60 11 0.09
61 70 0.60
62 32 0.27
63 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (61 bp):
AATTCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAATGCGATTATGAT
Found at i:581620 original size:20 final size:20
Alignment explanation
Indices: 581406--581613 Score: 136
Period size: 20 Copynumber: 10.2 Consensus size: 20
581396 TTTTTCCAAT
*
581406 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
** *
581426 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
581447 TCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGAATACGT-A-AA
*
581467 TCGCAATGCGATAATAC-AAAA
1 TCGCAATGCG--AATACGTAAA
* *
581488 TCGCAATGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
** * * * *
581508 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
581529 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
581549 TCGTAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
581569 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
581590 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
581610 TCGC
1 TCGC
581614 GTTGCGATAG
Statistics
Matches: 145, Mismatches: 33, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.02
20 82 0.57
21 55 0.38
22 1 0.01
23 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:581638 original size:21 final size:21
Alignment explanation
Indices: 581613--581683 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
581603 ACGTAAATCG
581613 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
581634 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
581652 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
581675 CGTTGCGAT
1 CGTTGCGAT
581684 TTTCCATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.23
21 18 0.46
22 4 0.10
23 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:581641 original size:41 final size:41
Alignment explanation
Indices: 581607--581713 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 41
581597 GCGAATACGT
* *
581607 AAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCC
1 AAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATATACC
** * *
581648 ATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCC
1 AAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATATACC
** *
581689 ATTTCGCGTTGCAATAGTCTACAGT
1 AAATCGCGTTGCGATAGTCTACAGT
581714 AAATTAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
AAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATATACC
Found at i:581659 original size:20 final size:20
Alignment explanation
Indices: 581634--581700 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
581624 TCTACAGTGT
581634 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
581654 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
581674 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
581695 CGTTGC
1 CGTTGC
581701 AATAGTCTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 11 0.31
22 4 0.11
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:582508 original size:41 final size:41
Alignment explanation
Indices: 582428--582547 Score: 190
Period size: 41 Copynumber: 3.0 Consensus size: 41
582418 TTTTTAATTT
582428 ACTGTAGACTATCGCAA--CGAAATTGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAA-TGGAAAATCGCAACGAC
* *
582468 ACTGTACACTATCCCAACGCGAAATGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
*
582509 ACTGTAGACTATCGCAACGCGAAAAGGAAAATCGCAACG
1 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACG
582548 CGCGAAATGG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 15 0.21
41 53 0.73
42 5 0.07
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (41 bp):
ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
Found at i:582554 original size:22 final size:22
Alignment explanation
Indices: 582519--582571 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
582509 ACTGTAGACT
582519 ATCGCAA--CGCGAAAAGGAAA
1 ATCGCAACGCGCGAAAAGGAAA
*
582539 ATCGCAACGCGCGAAATGGAAA
1 ATCGCAACGCGCGAAAAGGAAA
582561 ATCGCAACGCG
1 ATCGCAACGCG
582572 ATTTTGAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.23
22 23 0.77
ACGTcount: A:0.42, C:0.25, G:0.26, T:0.08
Consensus pattern (22 bp):
ATCGCAACGCGCGAAAAGGAAA
Found at i:583864 original size:30 final size:30
Alignment explanation
Indices: 583829--583891 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
583819 AAAAGGTAGT
* * * *
583829 AAAAATTAATATAATAAAGAAGGTGAAATA
1 AAAAATAAATACAATAAAGAAGATAAAATA
* *
583859 AAAAATAAATGCAATAAAGTAGATAAAATA
1 AAAAATAAATACAATAAAGAAGATAAAATA
583889 AAA
1 AAA
583892 CAGATAAAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.21
Consensus pattern (30 bp):
AAAAATAAATACAATAAAGAAGATAAAATA
Found at i:584038 original size:19 final size:18
Alignment explanation
Indices: 584000--584038 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
583990 TAACAATACA
*
584000 AAAATAAAAATAGAAGAT
1 AAAATAAAAATAGAAAAT
*
584018 AAAATAAAATATATAAAAT
1 AAAATAAAA-ATAGAAAAT
584037 AA
1 AA
584039 TAAGTATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAATAAAAATAGAAAAT
Found at i:584115 original size:2 final size:2
Alignment explanation
Indices: 584110--584146 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
584100 AAAAATTAAA
584110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
584147 GAATATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:584781 original size:37 final size:37
Alignment explanation
Indices: 584731--584829 Score: 137
Period size: 37 Copynumber: 2.7 Consensus size: 37
584721 GGATCCTATC
584731 TTTAGGAGTTTGAATCCTAGTAGGACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAGGACTCTATCATATT
* * ** * *
584768 TTTAGGAGTTTGAATCATAATAAAATTCTATCTTATT
1 TTTAGGAGTTTGAATCCTAGTAGGACTCTATCATATT
584805 TTTAGGAGTTTGAAT-CTAGTAGGAC
1 TTTAGGAGTTTGAATCCTAGTAGGAC
584830 GAAAAGGTGT
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 5 0.10
37 46 0.90
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGGACTCTATCATATT
Found at i:586304 original size:55 final size:54
Alignment explanation
Indices: 586226--586653 Score: 610
Period size: 55 Copynumber: 7.8 Consensus size: 54
586216 ATGTACTATA
* *
586226 TGTGC-AAACTAAAAAATTCATAATAAGTTTATGAATTTCCGTATAGGCACTATG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCACTGTG
*
586280 TGTGCAAAACTAATAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCACTGTG
* *
586335 TGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGACACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG-CACTGTG
*
586390 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGACACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGG-CACTGTG
*
586445 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGAGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG-GCACTGTG
* *
586500 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGTATTTCCTTATGGGCTA-TGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGC-ACTGTG
* * * * * *
586555 TGTGC-AAACTAAGAAACTCATAATAAGTTTATAAATTTTCGTATAGACAATTTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGCACTGTG
* *
586609 TGTGCAAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
586654 TGGTAGTGGG
Statistics
Matches: 342, Mismatches: 25, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
53 1 0.00
54 51 0.15
55 287 0.84
56 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (54 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGCACTGTG
Found at i:587410 original size:17 final size:17
Alignment explanation
Indices: 587388--587434 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
587378 GTCATTATGC
587388 ACTCAAGTAGTTCTGCT
1 ACTCAAGTAGTTCTGCT
587405 ACTCAAGTAGTTCTGCT
1 ACTCAAGTAGTTCTGCT
587422 ACTCAAGTAGTTC
1 ACTCAAGTAGTTC
587435 CTAATGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (17 bp):
ACTCAAGTAGTTCTGCT
Found at i:595079 original size:21 final size:20
Alignment explanation
Indices: 595042--595081 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
595032 ATCAACATTT
*
595042 TTTGCATCTGCATTTGCATC
1 TTTGCATCTGCACTTGCATC
*
595062 TTTGCATTTTGCACTTGCAT
1 TTTGCA-TCTGCACTTGCAT
595082 TCCATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATCTGCACTTGCATC
Found at i:595710 original size:109 final size:108
Alignment explanation
Indices: 595518--595714 Score: 263
Period size: 109 Copynumber: 1.8 Consensus size: 108
595508 GACATTTGAA
* * * * *
595518 GAATGATGGGGCATTCGATGCTAGTCAAGAAGAGATCTTTTCATCTATCATGAAGTTTTCCTACA
1 GAATGATGGAGCATTCGATGCTAATCAAGAAAAGATCTTTGCATCTATCAGGAAGTTTTCCTACA
*
595583 CATGCATTAAGAGTATTGTTTTGAACTCATTTTTGTTATGTTT
66 CATGCATTAAGAGCATTGTTTTGAACTCATTTTTGTTATGTTT
*
595626 GAATGATGGAGCATTCTGATGCTAATCAAGAAAAGATCTTTGCATCT-TCCAGGAAGTTTTCTTA
1 GAATGATGGAGCATTC-GATGCTAATCAAGAAAAGATCTTTGCATCTAT-CAGGAAGTTTTCCTA
* * *
595690 TGA-TTGTATTAAGAGCATTGTTTTG
64 -CACATGCATTAAGAGCATTGTTTTG
595715 TTTGAACTCG
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
108 16 0.21
109 59 0.78
110 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (108 bp):
GAATGATGGAGCATTCGATGCTAATCAAGAAAAGATCTTTGCATCTATCAGGAAGTTTTCCTACA
CATGCATTAAGAGCATTGTTTTGAACTCATTTTTGTTATGTTT
Found at i:596652 original size:18 final size:17
Alignment explanation
Indices: 596595--596677 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
596585 CAAAGCAAAG
**
596595 AAAAAAGAGCAAAA-CA
1 AAAAAAGAAAAAAAGCA
*
596611 AAAAAAGAGAAATGAAGC-
1 AAAAAAGA-AAA-AAAGCA
596629 AAAAAAGAAAAAAAGCA
1 AAAAAAGAAAAAAAGCA
* *
596646 AAGAAAA-AAAAGAAGAA
1 AA-AAAAGAAAAAAAGCA
596663 AAAGAAAGAAAAAAA
1 AAA-AAAGAAAAAAA
596678 AATGATCAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
16 13 0.25
17 19 0.36
18 20 0.38
19 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAAAGCA
Found at i:596657 original size:9 final size:9
Alignment explanation
Indices: 596629--596678 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
596619 GAAATGAAGC
596629 AAAAAAG-A
1 AAAAAAGAA
*
596637 AAAAAAGCA
1 AAAAAAGAA
*
596646 AAGAAA-AA
1 AAAAAAGAA
*
596654 AAAGAAGAA
1 AAAAAAGAA
596663 AAAGAAAGAA
1 AAA-AAAGAA
596673 AAAAAA
1 AAAAAA
596679 ATGATCAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
8 12 0.35
9 14 0.41
10 8 0.24
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:596657 original size:22 final size:22
Alignment explanation
Indices: 596629--596678 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
596619 GAAATGAAGC
596629 AAAAAAGAA-AAAAAGCAAAGAA
1 AAAAAAGAAGAAAAAG-AAAGAA
596651 AAAAAAGAAGAAAAAGAAAGAA
1 AAAAAAGAAGAAAAAGAAAGAA
596673 AAAAAA
1 AAAAAA
596679 ATGATCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAAAAGAAAGAA
Found at i:596665 original size:13 final size:12
Alignment explanation
Indices: 596631--596679 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
596621 AATGAAGCAA
596631 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
596644 CAAAGAAAAAAAAG
1 -AAA-AAAAAAAAG
*
596658 AAGAAAAAGAAAG
1 AA-AAAAAAAAAG
596671 AAAAAAAAA
1 AAAAAAAAA
596680 TGATCAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 6 0.19
13 12 0.39
14 12 0.39
15 1 0.03
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:597299 original size:25 final size:25
Alignment explanation
Indices: 597271--597320 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
597261 GGGCATTTTG
597271 GTCCTTTAAGGGGAAATAAATTTAA
1 GTCCTTTAAGGGGAAATAAATTTAA
597296 GTCCTTTAAGGGGAAATAAATTTAA
1 GTCCTTTAAGGGGAAATAAATTTAA
597321 AATTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (25 bp):
GTCCTTTAAGGGGAAATAAATTTAA
Found at i:597831 original size:81 final size:81
Alignment explanation
Indices: 597696--598044 Score: 476
Period size: 81 Copynumber: 4.4 Consensus size: 81
597686 CTATTCTAAA
* *
597696 ATAAAAGACTAAATGCCTAACTGCT-CATTTGGTAGAAAA-GTGTCAATAATGCAAGTTAGATGA
1 ATAAAAGACTAAATGCCTAACTG-TGCATTTGGCA-AAAAGGTGCCAATAATGCAAGTTAGATGA
*
597759 AAGGTTAAATGCCTTTAG
64 AAGGTTAAATGCCTTTGG
* *
597777 ATAAAAGAATAAATGCCTAACTGTGCATTTGGCAAAAAGGTACCAATAATGCAAGTTAGATGAAA
1 ATAAAAGACTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
* *
597842 GGATAAATGTCTTTGG
66 GGTTAAATGCCTTTGG
* * *
597858 AT-AAAGACTAAATGCCTAACTGTGTA-TTGGCAGAATGGTGCCAATAATGCAAGTTAGATG-AA
1 ATAAAAGACTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
597920 GGTTAAATGCCTTTGG
66 GGTTAAATGCCTTTGG
* * * * *
597936 ATAAAAGACTAAATGCCCAACTGTGCACTTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
1 ATAAAAGACTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
*
598001 GGTTAAACGCCTTTGG
66 GGTTAAATGCCTTTGG
* *
598017 -TAAAAGACTAAATGCATAACGGTGCATT
1 ATAAAAGACTAAATGCCTAACTGTGCATT
598045 ACCGACATGA
Statistics
Matches: 239, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
78 18 0.08
79 53 0.22
80 82 0.34
81 86 0.36
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (81 bp):
ATAAAAGACTAAATGCCTAACTGTGCATTTGGCAAAAAGGTGCCAATAATGCAAGTTAGATGAAA
GGTTAAATGCCTTTGG
Found at i:598176 original size:44 final size:45
Alignment explanation
Indices: 598026--598182 Score: 237
Period size: 45 Copynumber: 3.5 Consensus size: 45
598016 GTAAAAGACT
* * *
598026 AAATGCATAACGGTGCATTACCGACATGAAAGGATGCCATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATG
598071 AAATGCATAA-AGGTGCATTATCGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACA-GTGCATTATCGGCATGAAAGGATGCCATAAATG
* * *
598116 AAATGCATAACGGTGCATTATCGGCTTGAAATGATG-CATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATG
598160 AAATGCATAACAGTGCATTATCG
1 AAATGCATAACAGTGCATTATCG
598183 ATATGAAAAG
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
44 30 0.29
45 73 0.71
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (45 bp):
AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATG
Found at i:598189 original size:89 final size:90
Alignment explanation
Indices: 598026--598190 Score: 253
Period size: 89 Copynumber: 1.8 Consensus size: 90
598016 GTAAAAGACT
598026 AAATGCATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAATGCATAAAGGTGCATTA
1 AAATGCATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAATGCATAAAGGTGCATTA
*
598091 TCGGCATGAAAGGATGCCATAAATG
66 TCGACATGAAAGGATGCCATAAATG
* * * *
598116 AAATGCATAACGGTGCATTATCGGCTTGAAATGATG-CATAAATGAAATGCATAACA-GTGCATT
1 AAATGCATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAATGCATAA-AGGTGCATT
*
598179 ATCGATATGAAA
65 ATCGACATGAAA
598191 AGATTCATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
89 35 0.51
90 33 0.49
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (90 bp):
AAATGCATAACGGTGCATTACCGACATGAAAGGATGCCATAAATGAAATGCATAAAGGTGCATTA
TCGACATGAAAGGATGCCATAAATG
Found at i:601416 original size:81 final size:81
Alignment explanation
Indices: 601163--601400 Score: 327
Period size: 81 Copynumber: 3.0 Consensus size: 81
601153 AAGATAATGC
* * * **
601163 CTAACTATGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTATATGAAATGTT-AATG-AATTGG
1 CTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTTTGG
*
601226 ATAAAAGACTAAATGT
66 ATAAAAGACTAAAAGT
* * * *
601242 CTAACTGTCCATTTGGCATAAAGGTGTCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTCTGG
1 CTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTTTGG
601307 ATAAAAGACTAAAAGT
66 ATAAAAGACTAAAAGT
* * *
601323 CTAACTGTGCATTTGGAAGAAAGATGCCAATAATGAAAGTTAGATGAAAGGTTAAATGCCTTTGG
1 CTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTTTGG
* *
601388 AAAAAATACTAAA
66 ATAAAAGACTAAA
601401 CGCATAAGGG
Statistics
Matches: 138, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
79 47 0.34
80 4 0.03
81 87 0.63
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (81 bp):
CTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAGGTTAAATGCCTTTGG
ATAAAAGACTAAAAGT
Found at i:601472 original size:44 final size:44
Alignment explanation
Indices: 601409--601756 Score: 459
Period size: 44 Copynumber: 7.8 Consensus size: 44
601399 AACGCATAAG
601409 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAAC
* * *
601453 GGTGCATTATCGGCATGAAAGGATTCTATAAATGAAATGTGTAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATG-CTAAC
* * *
601498 GGTGCATTATCAGCATGAAATGATGCCATAAATGAAATGCTAAT
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAAC
* * * * *
601542 GATGCATTATCGACATGAAAGGGGTACCATAAATGAAATACATAAC
1 GGTGCATTATCGGCATGAAA-GGATGCCATAAATGAAATGC-TAAC
* *
601588 GATGCATTATCGACATGAAAGG-TGCCATAAATG-AATGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGC-TAAC
* * *
601631 GGTGCATTATTGACATGAAAGGATGTCATAAATGAAATGCATAAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGC-TAAC
*
601676 GGTGCATTATCGGCATGAAAGAATGCCATAAATGAAATGC-ATAC
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTA-AC
*
601720 AGTGCATTATCGGCATGAAAGGATGCCATAAATGAAA
1 GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAA
601757 ATAATGAATA
Statistics
Matches: 270, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
43 30 0.11
44 114 0.42
45 103 0.38
46 23 0.09
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.24
Consensus pattern (44 bp):
GGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAAC
Found at i:601517 original size:89 final size:89
Alignment explanation
Indices: 601402--601756 Score: 475
Period size: 89 Copynumber: 4.0 Consensus size: 89
601392 AATACTAAAC
* *
601402 GCATAAGGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAACGGTGCATTATCGGC
1 GCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAACGGTGCATTATCGAC
*
601467 ATGAAAGGATTCTATAAATGAAAT
66 ATGAAAGGATTCCATAAATGAAAT
** * * * *
601491 GTGTAACGGTGCATTATCAGCATGAAATGATGCCATAAATGAAATGCTAATGATGCATTATCGAC
1 GCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAACGGTGCATTATCGAC
* *
601556 ATGAAAGGGGTACCATAAATGAAAT
66 ATGAAA-GGATTCCATAAATGAAAT
* * * *
601581 ACATAACGATGCATTATCGACATGAAAGG-TGCCATAAATG-AATGCATAACGGTGCATTATTGA
1 GCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGC-TAACGGTGCATTATCGA
601644 CATGAAAGGATGT-CATAAATGAAAT
65 CATGAAAGGAT-TCCATAAATGAAAT
* * *
601669 GCATAACGGTGCATTATCGGCATGAAAGAATGCCATAAATGAAATGC-ATACAGTGCATTATCGG
1 GCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTA-ACGGTGCATTATCGA
*
601733 CATGAAAGGATGCCATAAATGAAA
65 CATGAAAGGATTCCATAAATGAAA
601757 ATAATGAATA
Statistics
Matches: 228, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
88 46 0.20
89 140 0.61
90 42 0.18
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (89 bp):
GCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAATGCTAACGGTGCATTATCGAC
ATGAAAGGATTCCATAAATGAAAT
Found at i:604828 original size:36 final size:36
Alignment explanation
Indices: 604796--604924 Score: 119
Period size: 36 Copynumber: 3.7 Consensus size: 36
604786 ATTTGAGATT
*
604796 GTTTTTCTTGAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
* * **
604832 GTTTCTCTTGAAAC--A---TGAAC-C-TTTGAGATT
1 GTTTCTCTTGAAACAAATTTTG-TCTCGCTTGAGACA
* *
604862 GTTTCTCTCGAAACAAAGTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
*
604898 GTTTCTCTTGAAACAAAGTTTTATCTC
1 GTTTCTCTTGAAACAAA-TTTTGTCTC
604925 TCTTAAAACA
Statistics
Matches: 71, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
30 19 0.27
31 3 0.04
32 2 0.03
34 2 0.03
35 3 0.04
36 35 0.49
37 7 0.10
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA
Found at i:604857 original size:66 final size:66
Alignment explanation
Indices: 604787--604912 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 66
604777 ATTGATAACA
* * *
604787 TTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATGAAC
1 TTTGAGATTGTTTCTCTCGAAACAAAGTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATGAAC
604852 C
66 C
604853 TTTGAGATTGTTTCTCTCGAAACAAAGTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 TTTGAGATTGTTTCTCTCGAAACAAAGTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
604913 AAGTTTTATC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (66 bp):
TTTGAGATTGTTTCTCTCGAAACAAAGTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATGAAC
C
Found at i:604984 original size:88 final size:88
Alignment explanation
Indices: 604835--605002 Score: 264
Period size: 88 Copynumber: 1.9 Consensus size: 88
604825 TGAGACAGTT
* * ** * *
604835 TCTCTTGAAACATGAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTGTCTCGCTTGAGACAGT
1 TCTCTTAAAACATAAACAATTGAGATTGTTTCCCTCGAAACAAAGTTTGTCTCGCTTGAGACAAT
604900 TTCTCTTGAAACAAAGTTTTATC
66 TTCTCTTGAAACAAAGTTTTATC
* *
604923 TCTCTTAAAACATAAACAATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAAT
1 TCTCTTAAAACATAAACAATTGAGATTGTTTCCCTCGAAACAAAGTTTGTCTCGCTTGAGACAAT
604988 TTCTCTTGAAACAAA
66 TTCTCTTGAAACAAA
605003 TTATCCCTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 72 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (88 bp):
TCTCTTAAAACATAAACAATTGAGATTGTTTCCCTCGAAACAAAGTTTGTCTCGCTTGAGACAAT
TTCTCTTGAAACAAAGTTTTATC
Found at i:605279 original size:137 final size:137
Alignment explanation
Indices: 604999--605335 Score: 464
Period size: 137 Copynumber: 2.5 Consensus size: 137
604989 TCTCTTGAAA
*
604999 CAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCATCGACCAGA
1 CAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCATCGACCAAA
** * *
605064 TCTCCTCATCATGTAGGAGCACCATCATCCTTAGATAATCAGACTTCCTCATCACATAGAAACCT
66 TCTCCTCATCACCTAGGAGCACCATCATCCTAAGATAATCAGACTTCCTCATAACATAGAAACCT
605129 GTTATCT
131 GTTATCT
* * * *
605136 CCAATTATCCCTAAAGACGGCTAGATC-TCCTTATCTCGTAGGAACAATGTCGTCCACCGACCAA
1 CAAATTATCCCTAAAGACGGCTAGA-CGTCCTCATCACGTAGGAACAATGTCGTCCATCGACCAA
*** * *
605200 ATCTCCTCATCACCTAGGAGCAGTGTCATCCTAAGATAATC-GACTTCCTCATAACGTAGAAATC
65 ATCTCCTCATCACCTAGGAGCACCATCATCCTAAGATAATCAGACTTCCTCATAACATAGAAACC
605264 -GTTTATCT
130 TG-TTATCT
** * *
605272 CTAAATTATCCCTAAAGACAACTAGACGTCCTCATCACATAAGAACAATGTCGTCCATCGACCA
1 C-AAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCATCGACCA
605336 GAACTATCAC
Statistics
Matches: 174, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
135 1 0.01
136 28 0.16
137 144 0.83
138 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (137 bp):
CAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCGTCCATCGACCAAA
TCTCCTCATCACCTAGGAGCACCATCATCCTAAGATAATCAGACTTCCTCATAACATAGAAACCT
GTTATCT
Found at i:607799 original size:16 final size:17
Alignment explanation
Indices: 607770--607801 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
607760 TAACACATAC
607770 CAATTTTATCTTAAAAA
1 CAATTTTATCTTAAAAA
607787 CAATTTT-TCTTAAAA
1 CAATTTTATCTTAAAA
607802 TTGTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
CAATTTTATCTTAAAAA
Found at i:609317 original size:31 final size:32
Alignment explanation
Indices: 609282--609370 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 32
609272 CTAATGGAGC
* *
609282 ACTTTGGGGCCTTAAAGCCTATCCAA-GGAAT
1 ACTTTGGGGCCTCAAAGCCTACCCAATGGAAT
* *
609313 ACTTTGGGGCCTCAGAGCCTACCCAATGGAGT
1 ACTTTGGGGCCTCAAAGCCTACCCAATGGAAT
*
609345 ACCTTT-GGGCCT-AAGAGCATACCCAA
1 A-CTTTGGGGCCTCAA-AGCCTACCCAA
609371 GGGAGTATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
31 24 0.49
32 21 0.43
33 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (32 bp):
ACTTTGGGGCCTCAAAGCCTACCCAATGGAAT
Found at i:609362 original size:32 final size:32
Alignment explanation
Indices: 609264--609399 Score: 118
Period size: 32 Copynumber: 4.3 Consensus size: 32
609254 TTGGGAGTAG
* * *
609264 GAGCCAACCTAATGGAGCACTTTGGGGCCTTAA
1 GAGCCTACCCAATGGAGTACTTTGGGGCC-TAA
* * *
609297 -AGCCTATCCAA-GGAATACTTTGGGGCCTCA
1 GAGCCTACCCAATGGAGTACTTTGGGGCCTAA
609327 GAGCCTACCCAATGGAGTACCTTT-GGGCCTAA
1 GAGCCTACCCAATGGAGTA-CTTTGGGGCCTAA
* * *
609359 GAGCATACCCAAGGGAGTA-TCTCGGGGCCTAA
1 GAGCCTACCCAATGGAGTACT-TTGGGGCCTAA
* *
609391 AAACCTACC
1 GAGCCTACC
609400 TAAGAGTCAC
Statistics
Matches: 83, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
30 3 0.04
31 25 0.30
32 51 0.61
33 4 0.05
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (32 bp):
GAGCCTACCCAATGGAGTACTTTGGGGCCTAA
Found at i:611733 original size:18 final size:18
Alignment explanation
Indices: 611702--611740 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
611692 TCAAAAGTTA
*
611702 AAGTTTACGACTCGACTC
1 AAGTTAACGACTCGACTC
*
611720 AAGTTAACGGCTCGACTC
1 AAGTTAACGACTCGACTC
611738 AAG
1 AAG
611741 CCGCTGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (18 bp):
AAGTTAACGACTCGACTC
Found at i:614904 original size:27 final size:26
Alignment explanation
Indices: 614846--614907 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
614836 TAAATGACCT
614846 CTAAAAAGTTGCATTATGTCTACAAA
1 CTAAAAAGTTGCATTATGTCTACAAA
*
614872 CTAAAAAGTTGCATTAT-TGCTGCAAA
1 CTAAAAAGTTGCATTATGT-CTACAAA
*
614898 CTGAAAAGTT
1 CTAAAAAGTT
614908 ACTGAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (26 bp):
CTAAAAAGTTGCATTATGTCTACAAA
Found at i:619079 original size:25 final size:23
Alignment explanation
Indices: 619046--619091 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
619036 ATTTTTAAAC
*
619046 TAAGTTAATAATAAAATATATTTAA
1 TAAGGTAAT-ATAAAA-ATATTTAA
619071 TAAGGTAATATAAAAATATTT
1 TAAGGTAATATAAAAATATTT
619092 CTCAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
TAAGGTAATATAAAAATATTTAA
Found at i:620419 original size:3 final size:3
Alignment explanation
Indices: 620401--620510 Score: 188
Period size: 3 Copynumber: 37.0 Consensus size: 3
620391 ATTTGGGCTT
*
620401 ATA AT- ATA ATTA ATA ATA ATT A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
620445 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
620493 ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
620511 TGGTGGAACG
Statistics
Matches: 102, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
2 3 0.03
3 96 0.94
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:623318 original size:20 final size:21
Alignment explanation
Indices: 623272--623318 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
623262 TGTTTTTCAT
*
623272 TTACCTACTATGTCGATGCTA
1 TTACCTACTATATCGATGCTA
* * *
623293 TAACCTACTTTAT-GATGCTG
1 TTACCTACTATATCGATGCTA
623313 TTACCT
1 TTACCT
623319 TTTTGCAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (21 bp):
TTACCTACTATATCGATGCTA
Found at i:624943 original size:39 final size:39
Alignment explanation
Indices: 624804--624948 Score: 122
Period size: 39 Copynumber: 3.8 Consensus size: 39
624794 TTGAACAAGG
*
624804 TAACATTTTAAGCTG-AACCGAAAATGTTATC-TTCTCCA
1 TAACATTTTAAGTTGCAACCGAAAATGTTA-CATTCTCCA
* * * * *
624842 TAATATTTTCAGTTGCAGCCAAAAATGTTATAAATTCAT--A
1 TAACATTTTAAGTTGCAACCGAAAATG-T-TACATTC-TCCA
*
624882 TAAC-TTTTAGGTTG-AACCGAAAATGTTACATTCTCCA
1 TAACATTTTAAGTTGCAACCGAAAATGTTACATTCTCCA
** *
624919 TAACATTTTTTGTTGCAACCGAAAAAGTTA
1 TAACATTTTAAGTTGCAACCGAAAATGTTA
624949 TAAATTTGTA
Statistics
Matches: 83, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
35 1 0.01
36 6 0.07
37 6 0.07
38 29 0.35
39 30 0.36
40 5 0.06
41 5 0.06
42 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (39 bp):
TAACATTTTAAGTTGCAACCGAAAATGTTACATTCTCCA
Found at i:624949 original size:77 final size:78
Alignment explanation
Indices: 624817--624976 Score: 218
Period size: 77 Copynumber: 2.1 Consensus size: 78
624807 CATTTTAAGC
* *
624817 TGAACCGAAAATGTTATCTTCTCCATAATATTTTCAGTTGCAGCCAAAAATGTTATAAATTCATA
1 TGAACCGAAAATGTTATCTTCTCCATAACATTTTCAGTTGCAACCAAAAATGTTATAAATTCATA
624882 TAAC-TTTTAGGT
66 TAACTTTTTAGGT
** **
624894 TGAACCGAAAATGTTA-CATTCTCCATAACATTTTTTGTTGCAACCGAAAAA-GTTATAAATTTG
1 TGAACCGAAAATGTTATC-TTCTCCATAACATTTTCAGTTGCAACC-AAAAATGTTATAAATTCA
*
624957 TATAACTTTTTAGTT
64 TATAACTTTTTAGGT
624972 TGAAC
1 TGAAC
624977 ATAGGTTGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
76 1 0.01
77 55 0.75
78 17 0.23
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (78 bp):
TGAACCGAAAATGTTATCTTCTCCATAACATTTTCAGTTGCAACCAAAAATGTTATAAATTCATA
TAACTTTTTAGGT
Found at i:624967 original size:39 final size:39
Alignment explanation
Indices: 624853--624967 Score: 94
Period size: 39 Copynumber: 3.0 Consensus size: 39
624843 AATATTTTCA
* * *
624853 GTTGCAGCC-AAAAATGTTATAAATTCATATAACTTTTAG
1 GTTGCAACCGAAAAA-GTTATAAATTTATATAACTTTTTG
* * ** *
624892 GTTG-AACCGAAAATG-T-TACATTCTCCATAACATTTTTT
1 GTTGCAACCGAAAAAGTTATAAATT-TATATAAC-TTTTTG
*
624930 GTTGCAACCGAAAAAGTTATAAATTTGTATAACTTTTT
1 GTTGCAACCGAAAAAGTTATAAATTTATATAACTTTTT
624968 AGTTTGAACA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
36 5 0.09
37 6 0.10
38 12 0.21
39 23 0.40
40 7 0.12
41 5 0.09
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (39 bp):
GTTGCAACCGAAAAAGTTATAAATTTATATAACTTTTTG
Found at i:626492 original size:22 final size:22
Alignment explanation
Indices: 626464--626509 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
626454 TTTAGAATTA
*
626464 AATTTAAATTACTGTCTTAATG
1 AATTTAAATCACTGTCTTAATG
626486 AATTTAAATCACTGTCTTAATG
1 AATTTAAATCACTGTCTTAATG
626508 AA
1 AA
626510 CTAGTCTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (22 bp):
AATTTAAATCACTGTCTTAATG
Found at i:627800 original size:16 final size:16
Alignment explanation
Indices: 627779--627811 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
627769 TGTTGCTCGA
627779 CTCGTTACTCATTAAG
1 CTCGTTACTCATTAAG
*
627795 CTCGTTACTCCTTAAG
1 CTCGTTACTCATTAAG
627811 C
1 C
627812 CCGATGCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.36
Consensus pattern (16 bp):
CTCGTTACTCATTAAG
Found at i:629055 original size:3 final size:3
Alignment explanation
Indices: 629047--629098 Score: 77
Period size: 3 Copynumber: 16.7 Consensus size: 3
629037 ATATATATGT
*
629047 TAA TAA TAA TAA TAAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
629094 TAA TA
1 TAA TA
629099 TATATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:630120 original size:3 final size:3
Alignment explanation
Indices: 630112--630178 Score: 64
Period size: 3 Copynumber: 21.0 Consensus size: 3
630102 ATGAATAAGA
* *
630112 AAT AAT AAT AAAT AAT AGT AAT AAAT AAT AAT AAAT AAC AAT AAT AAAT
1 AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT -AAT
630161 AAT AAT AAAT AA- AAT AAT
1 AAT AAT -AAT AAT AAT AAT
630179 TTAAAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 2 0.04
3 37 0.69
4 15 0.28
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:630124 original size:10 final size:10
Alignment explanation
Indices: 630097--630177 Score: 83
Period size: 10 Copynumber: 7.5 Consensus size: 10
630087 TGGACAGAAA
630097 AATAAATGAAT
1 AATAAAT-AAT
*
630108 AAGAAATAAT
1 AATAAATAAT
630118 AATAAATAATAGT
1 AATAAAT-A-A-T
630131 AATAAATAAT
1 AATAAATAAT
630141 AATAAATAACAAT
1 AATAAAT---AAT
630154 AATAAATAAT
1 AATAAATAAT
630164 AATAAATAA-
1 AATAAATAAT
630173 AATAA
1 AATAA
630178 TTTAAAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
9 5 0.08
10 29 0.47
11 8 0.13
12 2 0.03
13 18 0.29
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (10 bp):
AATAAATAAT
Found at i:630141 original size:23 final size:23
Alignment explanation
Indices: 630105--630178 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
630095 AAAATAAATG
* *
630105 AATAAGAAATAATAATAAATAAT
1 AATAATAAATAATAATAAATAAC
*
630128 AGTAATAAATAATAATAAATAAC
1 AATAATAAATAATAATAAATAAC
630151 AATAATAAATAATAATAAATAA-
1 AATAATAAATAATAATAAATAAC
630173 AATAAT
1 AATAAT
630179 TTAAAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 6 0.13
23 41 0.87
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (23 bp):
AATAATAAATAATAATAAATAAC
Found at i:630231 original size:41 final size:38
Alignment explanation
Indices: 630186--630281 Score: 95
Period size: 41 Copynumber: 2.4 Consensus size: 38
630176 AATTTAAAAA
* *
630186 AAAAACTATATAATATAATTTTTTAAAAACATTTCTTTTTT
1 AAAAACTATATAATATAA-ATTTTAAAAA-ATGT-TTTTTT
*
630227 AAAAACTACATATTATATATAAATTTTCAAAAATGTTTTTTT
1 AAAAACT--ATA-TA-ATATAAATTTTAAAAAATGTTTTTTT
630269 -AAAACTATATAAT
1 AAAAACTATATAAT
630282 TTTCAAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
37 2 0.04
38 2 0.04
39 3 0.06
41 13 0.27
42 6 0.12
43 6 0.12
44 10 0.21
45 6 0.12
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (38 bp):
AAAAACTATATAATATAAATTTTAAAAAATGTTTTTTT
Found at i:630285 original size:31 final size:32
Alignment explanation
Indices: 630242--630323 Score: 130
Period size: 31 Copynumber: 2.5 Consensus size: 32
630232 CTACATATTA
630242 TATATAAATTTTCAAAAATGTTTTTTT-AAAAC
1 TATAT-AATTTTCAAAAATGTTTTTTTAAAAAC
630274 TATATAATTTTCAAAAATGTTTTTTTAAAAAAAC
1 TATATAATTTTCAAAAATGTTTTTTT--AAAAAC
630308 TATATAATTTTCAAAA
1 TATATAATTTTCAAAA
630324 GAGTTTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
31 21 0.45
32 5 0.11
34 21 0.45
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (32 bp):
TATATAATTTTCAAAAATGTTTTTTTAAAAAC
Found at i:630331 original size:31 final size:31
Alignment explanation
Indices: 630242--630335 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 31
630232 CTACATATTA
***
630242 TATATAAATTTTCAAAAATGTTTTTTTAAAAC
1 TATAT-AATTTTCAAAAATGTTTTAAAAAAAC
630274 TATATAATTTTCAAAAATGTTTTTTTAAAAAAAC
1 TATATAATTTTCAAAAATG---TTTTAAAAAAAC
630308 TATATAATTTTCAAAAGA-GTTTTAAAAA
1 TATATAATTTTCAAAA-ATGTTTTAAAAA
630336 TTATATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
31 23 0.42
32 5 0.09
34 26 0.47
35 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTAAAAAAAC
Found at i:630446 original size:35 final size:36
Alignment explanation
Indices: 630308--630537 Score: 211
Period size: 36 Copynumber: 6.1 Consensus size: 36
630298 TTAAAAAAAC
* *
630308 TATATAATTTTCAAAA-GAGTTTTAAAAATTATATAT
1 TATATAGTTTTCAAAATGA-TTTTAAAAACTATATAT
630344 TATTTATAAGTTTTCAAAACT-ATTTTCAAAAACTATATAT
1 TA--TAT-AGTTTTCAAAA-TGATTTT-AAAAACTATATAT
* *
630384 TATATAAGTTTTCAAAAAATGATTTT-AAAATTCATATCT
1 TATAT-AGTTTTC--AAAATGATTTTAAAAACT-ATATAT
630423 TATATA-TTTTCTAAAAT-ATTTTAAAAACTATATAT
1 TATATAGTTTTC-AAAATGATTTTAAAAACTATATAT
* *
630458 TATATAGTTTTCAAAAGTG-TCTTAAAAACTATATAC
1 TATATAGTTTTCAAAA-TGATTTTAAAAACTATATAT
* *
630494 TATATACATTTTCAAAATGTTTTTAAAAAACCTATATAT
1 TATATA-GTTTTCAAAATGATTTT-AAAAA-CTATATAT
630533 TATAT
1 TATAT
630538 GTATTTTCAA
Statistics
Matches: 164, Mismatches: 12, Indels: 33
0.78 0.06 0.16
Matches are distributed among these distances:
35 20 0.12
36 41 0.25
37 17 0.10
38 25 0.15
39 37 0.23
40 24 0.15
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATAGTTTTCAAAATGATTTTAAAAACTATATAT
Found at i:630518 original size:73 final size:72
Alignment explanation
Indices: 630272--630537 Score: 233
Period size: 72 Copynumber: 3.6 Consensus size: 72
630262 TTTTTTTAAA
* * * *
630272 ACTATATAATTTTCAAAAATGTTTTTTTAAAA--A-A-ACTATATAATTTTCAAAAGAGTTTTAA
1 ACTATATAATTTTCAAAAATG-TTTTTAAAAACTATATATTATATAGTTTTCAAAAGTG-TTTAA
630333 AAATTATAT
64 AAATTATAT
* * * * *
630342 ATTATTTATAAGTTTTCAAAACTATTTTCAAAAACTATATATTATATAAGTTTTCAAAAAATGAT
1 ACTA--TATAA-TTTTCAAAAATGTTTTTAAAAACTATATATTATAT-AGTTTTC-AAAAGTG-T
*
630407 TTTAAAATTCATAT
60 TTAAAAATT-ATAT
* *
630421 -CT-TATATATTTTCTAAAAT-ATTTTAAAAACTATATATTATATAGTTTTCAAAAGTGTCTTAA
1 ACTATATA-ATTTTCAAAAATGTTTTTAAAAACTATATATTATATAGTTTTCAAAAGTGT-TTAA
*
630483 AAACTATAT
64 AAATTATAT
630492 ACTATATACATTTTC-AAAATGTTTTTAAAAAACCTATATATTATAT
1 ACTATATA-ATTTTCAAAAATGTTTTT-AAAAA-CTATATATTATAT
630538 GTATTTTCAA
Statistics
Matches: 158, Mismatches: 21, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
70 3 0.02
71 5 0.03
72 33 0.21
73 31 0.20
74 27 0.17
75 27 0.17
76 7 0.04
77 6 0.04
78 15 0.09
79 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (72 bp):
ACTATATAATTTTCAAAAATGTTTTTAAAAACTATATATTATATAGTTTTCAAAAGTGTTTAAAA
ATTATAT
Found at i:631360 original size:84 final size:82
Alignment explanation
Indices: 631123--631943 Score: 625
Period size: 84 Copynumber: 10.0 Consensus size: 82
631113 GCTATGCTAT
* *
631123 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-GCAGATAGCCCTTATA
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTA
* * * * **
631186 GCCTTGAGCTATACCAC
66 GACTTAAGTTATGCTGC
* * * * * * * * * * *
631203 AAATAATGTATCGTT-TAGTTGAGTGTAATCAAACTCAAAGGTCTTTGTTGGCAGATACCCCTTC
1 AAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-GCAGATAACCCTTC
* *
631267 TAGCCTTGAGTTATGCTGC
64 TAGACTTAAGTTATGCTGC
* * * * *
631286 AAATGATATGCCTTAGAGCTGAACGTAGTCGAACTCGAAAGTCTTTTGGTGACAAATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTG-CAGATAACCCTTC
* * *
631351 TAGCCTTGAGTTATGCTGT
64 TAGACTTAAGTTATGCTGC
* * * * ** *
631370 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAGATAGCCCTTCT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCT
* *
631433 CGACTTAAGCTATGCTGC
65 AGACTTAAGTTATGCTGC
* *
631451 AAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGATAGATAACCCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAGATAACCCTTCT
* * *
631516 AGCCTTGAGTTATGCTGT
65 AGACTTAAGTTATGCTGC
* * * * ** *
631534 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGT--AGATAGCCCTTCT
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCT
*
631597 CGACTTAAGTTATGCTGC
65 AGACTTAAGTTATGCTGC
*
631615 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGTCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TG-CAGATAACCCTTC
*
631680 TCGACTTAAGTTATGCTGC
64 TAGACTTAAGTTATGCTGC
* * *
631699 AAATGATATGCCTTGGAGCTGAGC---GT----CTCGAAGGTCTTTTGGTTACAGATAACGCTT-
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG-TGCAGATAACCCTTC
*** * * **
631756 TTTCCTTGAGTTATACTAT
64 TAGACTTAAGTTATGCTGC
* * * * * * * * *
631775 AAATGATGTTACCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-ACAGATAGCCCTTTT
1 AAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCT
* * *
631838 CGACTTAAGCTATGCTAC
65 AGACTTAAGTTATGCTGC
* * * * * * *
631856 AAATAATATGACTGGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGCAGATAACTCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-GCAGATAACCCTTC
* *
631921 TA-ACATTGAGTTATGCTAC
64 TAGAC-TTAAGTTATGCTGC
631940 AAAT
1 AAAT
631944 ATTTTCTTTT
Statistics
Matches: 582, Mismatches: 128, Indels: 58
0.76 0.17 0.08
Matches are distributed among these distances:
76 19 0.03
77 32 0.05
78 7 0.01
80 132 0.23
81 99 0.17
82 6 0.01
83 96 0.16
84 167 0.29
85 24 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (82 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTA
GACTTAAGTTATGCTGC
Found at i:631422 original size:248 final size:247
Alignment explanation
Indices: 631088--631901 Score: 679
Period size: 248 Copynumber: 3.3 Consensus size: 247
631078 ATAATTTTAT
* * * * *
631088 TGACAAATAGCCCTTCTTGCTTTGGGCTATGCTATAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAAATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * *
631153 GAACTCGAAGGTCTTTGGCAGATAGCCCTTATAGCCTTGAGCTATACCACAAATAATGTATCGTT
66 GAACTCGAAGGTCTTTGGCAGATAGCCCTTATAGACTTAAGCTATACCACAAATAATGT-GCCTT
* * * * * *
631218 -TAGTTGAGTGTAATCAAACTCAAAGGTCTTTGTTGGCAGATACCCCTTCTAGCCTTGAGTTATG
130 GGAGCTGAGCGTAATCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* *
631282 CTGCAAATGATATGCCTTAG-AGCTGAACGTAGTCGAACTCGAAAGTCTTTTGG
195 CTGCAAATGATATGCCCTAGAAGCTGAACGTAATCGAACTCGAAAGTC-TTTGG
* * * * *
631335 TGACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAAATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGT
** * * * ** *
631400 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
65 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTATAGACTTAAGCTATACCACAAATAATGTGCCTT
* * *
631465 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATG
130 GGAGCTGAGCGTAATCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * ** ***
631530 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
195 CTGCAAATGATATGCCCTAGAAGCTGAACGTAATCGAACTCGAAAGTCTTTGG
* * * * *
631583 T---AGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAAATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * * * * ** * *
631645 GAACTCGAAGGTATTTGGTTGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
66 GAACTCGAAGGTCTTT-G--G-CAGATAGCCCTTATAGACTTAAGCTATACCACAAATAATGTGC
* * * **
631710 CTTGGAGCTGAGCG---T----CTCGAAGGTCTTTTGGTTACAGATAACGCTT-TTTCCTTGAGT
127 CTTGGAGCTGAGCGTAATCAAACTCAAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGT
* ** * ** * ** **
631767 TATACTATAAATGATGTTACCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TT--
191 TATGCTGCAAATGATATGCCCTAGAAGCTGAACGTAATCGAACTCGAAAGTCTTTGG
* * * * * * ** * * * *
631821 TGACAGATAGCCCTTTTCGACTTAAGCTATGCTACAAATAATATGACTGGGAGCTGAGCGTAGTC
1 TGACAAATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
631886 GAACTTGAAGGTCTTT
66 GAACTCGAAGGTCTTT
631902 TGTTGGCAGA
Statistics
Matches: 480, Mismatches: 76, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
238 1 0.00
240 2 0.00
241 134 0.28
242 17 0.04
244 29 0.06
245 37 0.08
247 43 0.09
248 196 0.41
249 21 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (247 bp):
TGACAAATAGCCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGGCAGATAGCCCTTATAGACTTAAGCTATACCACAAATAATGTGCCTTG
GAGCTGAGCGTAATCAAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
TGCAAATGATATGCCCTAGAAGCTGAACGTAATCGAACTCGAAAGTCTTTGG
Found at i:631455 original size:165 final size:164
Alignment explanation
Indices: 631123--631710 Score: 761
Period size: 164 Copynumber: 3.6 Consensus size: 164
631113 GCTATGCTAT
* *
631123 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G-CAGATAGCCCTTAT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
* * *** * ** * ** * * ***
631185 AGCCTTGAGCTATACCACAAATAATGTATCGT-TTAGTTGAGTGTAATCAAACTCAAAGGTCTTT
66 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T
* * * *
631249 GTTGGCAGATACCCCTTCTAGCCTTGAGTTATGCTGC
129 -TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
* * * * *
631286 AAATGATATGCCTTAGAGCTGAACGTAGTCGAACTCGAAAGTCTTTTGGTGACAAATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTC
631351 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
65 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
*
631416 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
130 TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
* *
631451 AAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGATAGATAACCCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
631516 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
66 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
*
631581 GGTAGATAGCCCTTCTCGACTTAAGTTATGCTGC
131 GGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
* *
631615 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGTCAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTC
* * * * *
631680 TCGACTTAAGTTATGCTGCAAATGATATGCC
65 TAGCCTTGAGTTATGCTGTAAATGATGTGCC
631711 TTGGAGCTGA
Statistics
Matches: 373, Mismatches: 46, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
163 39 0.10
164 166 0.45
165 110 0.29
166 2 0.01
167 34 0.09
168 22 0.06
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (164 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
GGCAGATAGCCCTTCTCGACTTAAGTTATGCTGC
Found at i:631800 original size:241 final size:241
Alignment explanation
Indices: 631235--631943 Score: 723
Period size: 241 Copynumber: 2.9 Consensus size: 241
631225 GTGTAATCAA
* * * * * ** *
631235 ACTCAAAGGTCTTTGTTGGCAGATACCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATG-CCT
1 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGACCT
* ** * ** * * * * *
631299 -TAGAGCTGAACGTAGTCGAACTCGAAAGTCTTTTGGTGACAAATAACCCTTCTAGCCTTGAGTT
66 CGA-AGCTGAGTGTAATCGAACTCGAGGGTC--TT--TGACAGATAGCCCTTCTCGACTTAAGTT
* * * * ** *
631363 ATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG--GCAGATAG
126 ATGCTGCAAATGATGTG-CCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGATAA
* *
631426 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
190 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGC--AGT
* * * *
631480 CAAACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
1 ---ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGA
* **
631545 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGTTAT
63 CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAAGTTAT
* *
631610 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGTCAGATAAC
128 GCTGCAAATGATGTGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTG-CAGATAAC
631675 CCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGC-GT
191 CCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCAGT
* * ** *
631725 -CTCGAAGGTCTTTTGGTTACAGATAACGCTT-TTTCCTTGAGTTATACTATAAATGATGTTACC
1 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGACC
* *
631788 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTTTCGACTTAAGCTATGC
65 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAAGTTATGC
* * * * * * *
631853 TACAAATAATATGACTGGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGCAGATAACTC
130 TGCAAATGATGTGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTT-GCAGATAACCC
* * *
631918 TTCT-AACATTGAGTTATGCTACAAAT
193 TTCTCGAC-TTAAGTTATGCTGCAAAT
631944 ATTTTCTTTT
Statistics
Matches: 394, Mismatches: 57, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
240 2 0.01
241 167 0.42
242 21 0.05
244 29 0.07
245 40 0.10
247 3 0.01
248 107 0.27
249 24 0.06
250 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (241 bp):
ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGACCT
CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCGACTTAAGTTATGCT
GCAAATGATGTGCCTCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTC
TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCAGT
Found at i:636112 original size:2 final size:2
Alignment explanation
Indices: 636105--636142 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
636095 TTGATAGAGA
636105 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
636143 ATAAAGAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:636128 original size:17 final size:17
Alignment explanation
Indices: 636106--636139 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
636096 TGATAGAGAA
636106 TATATATATATATATAT
1 TATATATATATATATAT
636123 TATATATATATATATAT
1 TATATATATATATATAT
636140 ATAATAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:636196 original size:18 final size:17
Alignment explanation
Indices: 636172--636215 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
636162 CTAGAAAGGG
636172 AAAAAATAAAGATAAATA
1 AAAAAATAAA-ATAAATA
* *
636190 AATAAATTAAATTAAATA
1 AA-AAAATAAAATAAATA
636208 AAAAAATA
1 AAAAAATA
636216 TATAATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
19 7 0.32
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAAAATAAAATAAATA
Found at i:636261 original size:33 final size:34
Alignment explanation
Indices: 636208--636271 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
636198 AAATTAAATA
*
636208 AAAAAATATATAATGATAATAGTAATAATAAAGG
1 AAAAAATATATAATGATAATAATAATAATAAAGG
*
636242 AAAAAATATAT-ATGTTAATAATAATAATAA
1 AAAAAATATATAATGATAATAATAATAATAA
636272 TAATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (34 bp):
AAAAAATATATAATGATAATAATAATAATAAAGG
Found at i:636265 original size:3 final size:3
Alignment explanation
Indices: 636257--636282 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
636247 ATATATATGT
636257 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
636283 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:636283 original size:33 final size:32
Alignment explanation
Indices: 636204--636287 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 32
636194 AATTAAATTA
*
636204 AATAAAAAAATATATAATGATAATAGTAATAAT
1 AATAAAAAAATATAT-ATGATAATAATAATAAT
*
636237 AA-AGGAAAAAATATATATGTTAATAATAATAAT
1 AATA--AAAAAATATATATGATAATAATAATAAT
*
636270 AATAATAATAATATATAT
1 AATAA-AAAAATATATAT
636288 ATATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
32 2 0.05
33 30 0.68
34 12 0.27
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (32 bp):
AATAAAAAAATATATATGATAATAATAATAAT
Found at i:636287 original size:2 final size:2
Alignment explanation
Indices: 636280--636306 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
636270 AATAATAATA
636280 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
636307 AACTAGTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:637342 original size:3 final size:3
Alignment explanation
Indices: 637334--637377 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
637324 ATGAATAAGA
*
637334 AAT AAT AAT AAAT AAT AAT AAAT AAC AAT AAT AAAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AA
637378 ATAAATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:637346 original size:10 final size:11
Alignment explanation
Indices: 637319--637386 Score: 79
Period size: 10 Copynumber: 6.3 Consensus size: 11
637309 TGGACAGAAA
*
637319 AATAAATGAAT
1 AATAAATAAAT
*
637330 AAGAAAT-AAT
1 AATAAATAAAT
637340 AATAAAT-AAT
1 AATAAATAAAT
637350 AATAAATAACAAT
1 AATAAAT-A-AAT
637363 AATAAAT-AAT
1 AATAAATAAAT
637373 AATAAATAAAT
1 AATAAATAAAT
637384 AAT
1 AAT
637387 TATTTTTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
10 29 0.57
11 12 0.24
13 10 0.20
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:637363 original size:23 final size:23
Alignment explanation
Indices: 637337--637381 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
637327 AATAAGAAAT
637337 AATAATAAATAATAATAAATAAC
1 AATAATAAATAATAATAAATAAC
637360 AATAATAAATAATAATAAATAA
1 AATAATAAATAATAATAAATAA
637382 ATAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
AATAATAAATAATAATAAATAAC
Found at i:637485 original size:44 final size:40
Alignment explanation
Indices: 637389--637494 Score: 124
Period size: 44 Copynumber: 2.5 Consensus size: 40
637379 TAAATAATTA
* * *
637389 TTTTTTAAAAAAACTATATAATATAATTTTTTAAAAACGT
1 TTTTTTTAAAAAACTATATAATATAAATTTCTAAAAACGT
*
637429 TTCTTTTT-AAAAACTGCATATTATATATAAATTTCTAAAAATGT
1 TT-TTTTTAAAAAACT--ATA-TA-ATATAAATTTCTAAAAACGT
637473 TTTTTTTAAAAAACTATATAAT
1 TTTTTTTAAAAAACTATATAAT
637495 TTCCAAAAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
40 11 0.20
41 6 0.11
42 6 0.11
43 7 0.12
44 26 0.46
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (40 bp):
TTTTTTTAAAAAACTATATAATATAAATTTCTAAAAACGT
Found at i:637631 original size:35 final size:36
Alignment explanation
Indices: 637506--637650 Score: 147
Period size: 35 Copynumber: 3.9 Consensus size: 36
637496 TCCAAAAGAG
637506 TTTTAAAAATTATATATTATATATAAGTTTTCAAAAATA
1 TTTTAAAAATTATATA-T-TATAT-AGTTTTCAAAAATA
*
637545 TTTTCAAAAA--A-ACTTTTATA-AGTTTTCAAAAAATGA
1 TTTT-AAAAATTATA-TATTATATAGTTTTC-AAAAAT-A
* * *
637581 TTTTAAAAATCATATATTATATATTTTTCTAAAATA
1 TTTTAAAAATTATATATTATATAGTTTTCAAAAATA
637617 TTTT-AAAATTATATATTATATAGTTTTCAGAAAA
1 TTTTAAAAATTATATATTATATAGTTTTCA-AAAA
637651 AAAAGGTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
34 7 0.08
35 33 0.37
36 18 0.20
37 14 0.16
38 9 0.10
39 4 0.04
40 5 0.06
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTAAAAATTATATATTATATAGTTTTCAAAAATA
Found at i:638122 original size:16 final size:16
Alignment explanation
Indices: 638101--638131 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
638091 AAATTTGTGA
638101 AGGAATTAGAATCTGT
1 AGGAATTAGAATCTGT
*
638117 AGGAATTGGAATCTG
1 AGGAATTAGAATCTG
638132 AATCTGAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
AGGAATTAGAATCTGT
Found at i:638540 original size:31 final size:31
Alignment explanation
Indices: 638497--638572 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
638487 CCCGAGACCC
638497 GACCCGACCCGACCAAAATAAAGTTTCACAT
1 GACCCGACCCGACCAAAATAAAGTTTCACAT
* *
638528 GACCCGAACCGACCAAAATAAATTTTCACAT
1 GACCCGACCCGACCAAAATAAAGTTTCACAT
638559 GACCCGACCCGACC
1 GACCCGACCCGACC
638573 CGAATATATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.37, C:0.36, G:0.13, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGACCAAAATAAAGTTTCACAT
Found at i:647185 original size:23 final size:24
Alignment explanation
Indices: 647159--647208 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
647149 AATCTATGTC
*
647159 CTTGTGAC-ACGCTTTTCTCTACT
1 CTTGCGACAACGCTTTTCTCTACT
* * *
647182 CTTGCGGCAAGGTTTTTCTCTACT
1 CTTGCGACAACGCTTTTCTCTACT
647206 CTT
1 CTT
647209 ATGGCATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.44
Consensus pattern (24 bp):
CTTGCGACAACGCTTTTCTCTACT
Found at i:647556 original size:29 final size:30
Alignment explanation
Indices: 647519--647579 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
647509 TCTTGAAATT
* * * *
647519 TTCAAGGACTAAATTG-AATTTTGATTAAA
1 TTCAAGGACCAAAGTGAAAATTTAATTAAA
*
647548 TTCAGGGACCAAAGTGAAAATTTAATTAAA
1 TTCAAGGACCAAAGTGAAAATTTAATTAAA
647578 TT
1 TT
647580 TAGATCCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (30 bp):
TTCAAGGACCAAAGTGAAAATTTAATTAAA
Found at i:648921 original size:38 final size:39
Alignment explanation
Indices: 648789--648930 Score: 130
Period size: 39 Copynumber: 3.7 Consensus size: 39
648779 CTTACACTTT
* ** *
648789 CTGCAAGCTCCT-TGGCTTTGTGTTCAGTGTAAGTCCTTA
1 CTGCAGGCTCCTCT-GCTTTGTGCACAGTATAAGTCCTTA
** *
648828 CTGCAGGCTCCTC-GACTTTGTGCTTAGTGTAAGTCCTTA
1 CTGCAGGCTCCTCTG-CTTTGTGCACAGTATAAGTCCTTA
* * * *
648867 CTACA-GCTCATATGCTTTGTGCACAG-ATAAGACCTTA
1 CTGCAGGCTCCTCTGCTTTGTGCACAGTATAAGTCCTTA
*
648904 GTGCAGGCTCCTCTGCTTTGTGCACAG
1 CTGCAGGCTCCTCTGCTTTGTGCACAG
648931 GGTAGTCCTT
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
37 12 0.14
38 35 0.41
39 38 0.45
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (39 bp):
CTGCAGGCTCCTCTGCTTTGTGCACAGTATAAGTCCTTA
Found at i:648941 original size:38 final size:39
Alignment explanation
Indices: 648789--648941 Score: 136
Period size: 38 Copynumber: 4.0 Consensus size: 39
648779 CTTACACTTT
* ** *
648789 CTGCAAGCTCCT-TGGCTTTGTGTTCAGTGTAAGTCCTTA
1 CTGCAGGCTCCTCT-GCTTTGTGCACAGGGTAAGTCCTTA
** *
648828 CTGCAGGCTCCTC-GACTTTGTGCTTAGTGTAAGTCCTTA
1 CTGCAGGCTCCTCTG-CTTTGTGCACAGGGTAAGTCCTTA
* * * * *
648867 CTACA-GCTCATATGCTTTGTGCACA-GATAAGACCTTA
1 CTGCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
*
648904 GTGCAGGCTCCTCTGCTTTGTGCACAGGGT-AGTCCTTA
1 CTGCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
648942 TTGGGTGTAC
Statistics
Matches: 92, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
37 12 0.13
38 40 0.43
39 40 0.43
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (39 bp):
CTGCAGGCTCCTCTGCTTTGTGCACAGGGTAAGTCCTTA
Found at i:657903 original size:13 final size:13
Alignment explanation
Indices: 657885--657919 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
657875 TGCGTCATAA
*
657885 ATTTATGACTCAC
1 ATTTATGACACAC
657898 ATTTATGACACAC
1 ATTTATGACACAC
*
657911 ATTAATGAC
1 ATTTATGAC
657920 GCTCATTGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:659573 original size:2 final size:2
Alignment explanation
Indices: 659568--659593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
659558 CACACATTTA
659568 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
659594 TAATAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:667320 original size:55 final size:55
Alignment explanation
Indices: 667252--667646 Score: 596
Period size: 55 Copynumber: 7.2 Consensus size: 55
667242 AAGTTAAAAT
*
667252 ATTCATACTAAGTGTATGAATTTCCGTATGGCCACTATGTGTGCAAAATTAAGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
* *
667307 ATTAATTCTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
* *
667362 ATTCATACTAAGTGTATGAATTTCCGTATGGCCACTATTTGTGCAAAATTAAGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
* *
667417 ATTAATTCTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
* ** *
667472 A-TCATACCAAGTGTATGAATTTCCGTATAAGCACTATGTGTGAAAAATTAAGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
* *
667526 ATTCATACTAAGTGTATGAATTTTCGTATGGACACTATGTGTGCAAAATTAAGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
* * * * *
667581 ATTCATACTATGTGTGTGAATTTCCGTGTGGGCACTATGTGTG-AAGAAGTATGAA
1 ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAA-AATTAAGAA
*
667636 ATTCAAACTAA
1 ATTCATACTAA
667647 TAAGTTTGTG
Statistics
Matches: 306, Mismatches: 32, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
54 50 0.16
55 256 0.84
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (55 bp):
ATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
Found at i:667531 original size:164 final size:165
Alignment explanation
Indices: 667256--667623 Score: 594
Period size: 164 Copynumber: 2.2 Consensus size: 165
667246 TAAAATATTC
* * *
667256 ATACTAAGTGTATGAATTTCCGTATGGCCACTATGTGTGCAAAATTAAGAAATTAATTCTAAGTG
1 ATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAAATTAATACCAAGTG
** *
667321 TATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATGAATTTC
66 TATGAATTTCCGTATAAGCACTATGTGTGAAAAATTAAGAAATTCATACTAAGTGTATGAATTTC
* *
667386 CGTATGGCCACTATTTGTGCAAAATTAAGAAATTA
131 CGTATGGACACTATGTGTGCAAAATTAAGAAATTA
* *
667421 ATTCTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAAA-TCATACCAAGTG
1 ATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAAATTAATACCAAGTG
*
667485 TATGAATTTCCGTATAAGCACTATGTGTGAAAAATTAAGAAATTCATACTAAGTGTATGAATTTT
66 TATGAATTTCCGTATAAGCACTATGTGTGAAAAATTAAGAAATTCATACTAAGTGTATGAATTTC
*
667550 CGTATGGACACTATGTGTGCAAAATTAAGAAATTC
131 CGTATGGACACTATGTGTGCAAAATTAAGAAATTA
* * *
667585 ATACTATGTGTGTGAATTTCCGTGTGGGCACTATGTGTG
1 ATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTG
667624 AAGAAGTATG
Statistics
Matches: 187, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
164 137 0.73
165 50 0.27
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (165 bp):
ATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAAATTAATACCAAGTG
TATGAATTTCCGTATAAGCACTATGTGTGAAAAATTAAGAAATTCATACTAAGTGTATGAATTTC
CGTATGGACACTATGTGTGCAAAATTAAGAAATTA
Found at i:667535 original size:28 final size:28
Alignment explanation
Indices: 667504--667596 Score: 73
Period size: 28 Copynumber: 3.4 Consensus size: 28
667494 CCGTATAAGC
667504 ACTATGTGTGAAAAATTAAGAAATTCAT
1 ACTATGTGTGAAAAATTAAGAAATTCAT
* * * ** * ** *
667532 ACTAAGTGT-ATGAATTTTCG-TATGGAC
1 ACTATGTGTGA-AAAATTAAGAAATTCAT
*
667559 ACTATGTGTGCAAAATTAAGAAATTCAT
1 ACTATGTGTGAAAAATTAAGAAATTCAT
667587 ACTATGTGTG
1 ACTATGTGTG
667597 TGAATTTCCG
Statistics
Matches: 43, Mismatches: 19, Indels: 6
0.63 0.28 0.09
Matches are distributed among these distances:
27 17 0.40
28 26 0.60
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (28 bp):
ACTATGTGTGAAAAATTAAGAAATTCAT
Found at i:667713 original size:113 final size:110
Alignment explanation
Indices: 667252--667722 Score: 414
Period size: 110 Copynumber: 4.3 Consensus size: 110
667242 AAGTTAAAAT
* * * * * * **
667252 ATTCATACTAAGTGTATGAATTTCCGTAT-GGCCACTATGTGTGCAAAATTAAGAAATTAATTCT
1 ATTCATAATAAGTGTGTGAATTTCCGTATAAG-CACTATGTGTGAAAAAGTAAGAAATTCATAAT
* * ** *
667316 AAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
65 AAGTGTATGAATTTTCGTATGGACACTACATGTACAAAATTAAGAA
* * * * * * * **
667362 ATTCATACTAAGTGTATGAATTTCCGTAT-GGCCACTATTTGTGCAAAATTAAGAAATTAATTCT
1 ATTCATAATAAGTGTGTGAATTTCCGTATAAG-CACTATGTGTGAAAAAGTAAGAAATTCATAAT
* * ** *
667426 AAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAATTAAGAA
65 AAGTGTATGAATTTTCGTATGGACACTACATGTACAAAATTAAGAA
** * * *
667472 A-TCATACCAAGTGTATGAATTTCCGTATAAGCACTATGTGTGAAAAATTAAGAAATTCATACTA
1 ATTCATAATAAGTGTGTGAATTTCCGTATAAGCACTATGTGTGAAAAAGTAAGAAATTCATAATA
** *
667536 AGTGTATGAATTTTCGTATGGACACTATGTGTGCAAAATTAAGAA
66 AGTGTATGAATTTTCGTATGGACACTACATGTACAAAATTAAGAA
* * * ** * *
667581 ATTCATACTATGTGTGTGAATTTCCGTGTGGGCACTATGTGTGAAGAAGTATGAAATTCAAACTA
1 ATTCATAATAAGTGTGTGAATTTCCGTATAAGCACTATGTGTGAAAAAGTAAGAAATTC--A-TA
* * *
667646 ATAAGTTTGTGAATTTTCGTATGGGA-ACTACATGTACAAGCA-TAAGAA
63 ATAAGTGTATGAATTTTCGTAT-GGACACTACATGTACAA-AATTAAGAA
*
667694 ATTCATAATAAGTAG-GTGAATTTTCGTAT
1 ATTCATAATAAGT-GTGTGAATTTCCGTAT
667723 TTGTAGTGGG
Statistics
Matches: 324, Mismatches: 29, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
109 99 0.31
110 159 0.49
112 1 0.00
113 60 0.19
114 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (110 bp):
ATTCATAATAAGTGTGTGAATTTCCGTATAAGCACTATGTGTGAAAAAGTAAGAAATTCATAATA
AGTGTATGAATTTTCGTATGGACACTACATGTACAAAATTAAGAA
Found at i:671712 original size:245 final size:245
Alignment explanation
Indices: 671269--671758 Score: 916
Period size: 245 Copynumber: 2.0 Consensus size: 245
671259 TTTAACCCTT
671269 TCAGGAGGTTCAACCAAAGTCCATACTTGATTAACTAACACAGAACCCATCGGAACCTCATGGCT
1 TCAGGAGGTTCAACCAAAGTCCATACTTGATTAACTAACACAGAACCCATCGGAACCTCATGGCT
671334 TCAAGCCATTTCTTAGAGTTTCAGCTCGACACCACTTCCTGAAAAGTTCTACGCTCATCTTGATC
66 TCAAGCCATTTCTTAGAGTTTCAGCTCGACACCACTTCCTGAAAAGTTCTACGCTCATCTTGATC
671399 ATAAAAGAATGTCTTCAAGTGTGGGTAAAGAGAAATCATATCTCTCAGGTAAATGATGTTCTTTT
131 ATAAAAGAATGTCTTCAAGTGTGGGTAAAGAGAAATCATATCTCTCAGGTAAATGATGTTCTTTT
671464 ATGGACATTCACGGTGGTTGTGTTTCTATATTTG-TGATTGCTCCTCAAC
196 ATGGACATTCACGGTGGTTGTGTTTCTATATTTGTTGATTGCTCCTCAAC
671513 TCAGGAGGTTCAACCAAAGTCCATACTTGATTAACTAACACAGAACCCATCTCGG-ACCTCATGG
1 TCAGGAGGTTCAACCAAAGTCCATACTTGATTAACTAACACAGAACCCA--TCGGAACCTCATGG
671577 CTTCAAGCCATTTCTTAGAGTTTCAGCTCGACACCACTTCCTGAAAAGTTCTACGCTCATCTTGA
64 CTTCAAGCCATTTCTTAGAGTTTCAGCTCGACACCACTTCCTGAAAAGTTCTACGCTCATCTTGA
671642 TCCATAAAAGAATGTCTTCAAGTGT-GGTAAAGAGAAATCCATATCTCTCAGGTAAATGATGTTC
129 T-CATAAAAGAATGTCTTCAAGTGTGGGTAAAGAGAAAT-CATATCTCTCAGGTAAATGATGTTC
671706 -TTTATGGACATTCACGGTGGTTGTGTTTCTATATTTGTTGATTGCTCCTCAAC
192 TTTTATGGACATTCACGGTGGTTGTGTTTCTATATTTGTTGATTGCTCCTCAAC
671759 AACTTGTAGA
Statistics
Matches: 241, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
244 49 0.20
245 125 0.52
246 67 0.28
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (245 bp):
TCAGGAGGTTCAACCAAAGTCCATACTTGATTAACTAACACAGAACCCATCGGAACCTCATGGCT
TCAAGCCATTTCTTAGAGTTTCAGCTCGACACCACTTCCTGAAAAGTTCTACGCTCATCTTGATC
ATAAAAGAATGTCTTCAAGTGTGGGTAAAGAGAAATCATATCTCTCAGGTAAATGATGTTCTTTT
ATGGACATTCACGGTGGTTGTGTTTCTATATTTGTTGATTGCTCCTCAAC
Found at i:674199 original size:23 final size:23
Alignment explanation
Indices: 674173--674221 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
674163 ATAAAGAACC
*
674173 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
674196 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
674219 AAA
1 AAA
674222 CTAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:679298 original size:24 final size:24
Alignment explanation
Indices: 679268--679315 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
679258 GACATCCTTT
*
679268 TTGTTCACTAAGTATTTTATAGCC
1 TTGTTCACTAAGTATTTTACAGCC
679292 TTGTTCACTAAGTATTTTACAGCC
1 TTGTTCACTAAGTATTTTACAGCC
679316 GAATGATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (24 bp):
TTGTTCACTAAGTATTTTACAGCC
Found at i:683766 original size:11 final size:11
Alignment explanation
Indices: 683750--683774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
683740 AGAATGGTAA
683750 AAACAGTAAAT
1 AAACAGTAAAT
683761 AAACAGTAAAT
1 AAACAGTAAAT
683772 AAA
1 AAA
683775 ATAAAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAACAGTAAAT
Done.