Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 18
Found at i:813073 original size:9 final size:9
Alignment explanation
Indices: 813059--813098 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
813049 GTGAACTATA
813059 TATATAAAC
1 TATATAAAC
813068 TATAT--A-
1 TATATAAAC
*
813074 TGTATAAAC
1 TATATAAAC
813083 TATATAAAC
1 TATATAAAC
813092 TATATAA
1 TATATAA
813099 TTATATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
6 4 0.15
7 1 0.04
8 1 0.04
9 20 0.77
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (9 bp):
TATATAAAC
Found at i:813103 original size:15 final size:14
Alignment explanation
Indices: 813052--813088 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
813042 TGTTTATGTG
813052 AACTATATA-TATA
1 AACTATATAGTATA
813065 AACTATATATGTATA
1 AACTATATA-GTATA
813080 AACTATATA
1 AACTATATA
813089 AACTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
15 13 0.59
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (14 bp):
AACTATATAGTATA
Found at i:813128 original size:2 final size:2
Alignment explanation
Indices: 813115--813193 Score: 94
Period size: 2 Copynumber: 41.0 Consensus size: 2
813105 GTTAATTTTA
* *
813115 AT AT AT AGT AT AT AT AT -T GT AT A- AT A- AT AT AT AG A- AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
813154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
813194 TAAAAAACAC
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
1 4 0.06
2 62 0.91
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:813463 original size:42 final size:42
Alignment explanation
Indices: 813399--813503 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
813389 ATAGTTAATT
*
813399 TATGTAACTTATAGTATGTGTATACATGCAATGTAAACTATA
1 TATGTAACTTATAGTATATGTATACATGCAATGTAAACTATA
* *
813441 TATGTAACATATAGTATATGTATACATGTAATGTAAACTATA
1 TATGTAACTTATAGTATATGTATACATGCAATGTAAACTATA
*
813483 TA--TAACTTATAGTACATGTAT
1 TATGTAACTTATAGTATATGTAT
813504 GTATGTATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 17 0.29
42 41 0.71
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (42 bp):
TATGTAACTTATAGTATATGTATACATGCAATGTAAACTATA
Found at i:813947 original size:21 final size:21
Alignment explanation
Indices: 813895--813947 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
813885 TAGTGTACTA
* *
813895 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
813916 TATTGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
813937 TATAGTTTATA
1 TATAGTTTATA
813948 TTAATGTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:814408 original size:161 final size:161
Alignment explanation
Indices: 814106--814426 Score: 626
Period size: 161 Copynumber: 2.0 Consensus size: 161
814096 ATAAATATCA
814106 TTTCTCCCGCCTCTTCCCACCAAACCCTCCCTCCTTTAGTTTTGGTCTCTATTCTTCCCCGCTCA
1 TTTCTCCCGCCTCTTCCCACCAAACCCTCCCTCCTTTAGTTTTGGTCTCTATTCTTCCCCGCTCA
814171 TCATCCCAAAATTATGTTTCCCTCGTTTTGCCTCTTCTTCCCCACTCAGCATCCAAAAGTTGCCG
66 TCATCCCAAAATTATGTTTCCCTCGTTTTGCCTCTTCTTCCCCACTCAGCATCCAAAAGTTGCCG
814236 AACACGGTCAGTAAGGGATCTGAGTTGCAGT
131 AACACGGTCAGTAAGGGATCTGAGTTGCAGT
814267 TTTCTCCCGCCTCTTCCCACCAAACCCTCCCTCCTTTAGTTTTGGTCTCTATTCTTCCCCGCTCA
1 TTTCTCCCGCCTCTTCCCACCAAACCCTCCCTCCTTTAGTTTTGGTCTCTATTCTTCCCCGCTCA
814332 TCAT-CCAAAATTATGTTTCCCTCGTTTTGCCTCTTCTTCCCCACTCAGCATCCAAAAGTTGCCG
66 TCATCCCAAAATTATGTTTCCCTCGTTTTGCCTCTTCTTCCCCACTCAGCATCCAAAAGTTGCCG
814396 AACACGGGTCAGTAAGGGATCTGAGTTGCAG
131 AACAC-GGTCAGTAAGGGATCTGAGTTGCAG
814427 GCTCAGTTGA
Statistics
Matches: 159, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
160 65 0.41
161 94 0.59
ACGTcount: A:0.18, C:0.35, G:0.14, T:0.33
Consensus pattern (161 bp):
TTTCTCCCGCCTCTTCCCACCAAACCCTCCCTCCTTTAGTTTTGGTCTCTATTCTTCCCCGCTCA
TCATCCCAAAATTATGTTTCCCTCGTTTTGCCTCTTCTTCCCCACTCAGCATCCAAAAGTTGCCG
AACACGGTCAGTAAGGGATCTGAGTTGCAGT
Found at i:815707 original size:33 final size:33
Alignment explanation
Indices: 815667--815735 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
815657 TTAATATTTT
815667 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
1 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
815700 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
1 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
815733 ATA
1 ATA
815736 GTTCATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (33 bp):
ATATTTATTATGTTTATTTAATAAAAGTTTCAA
Found at i:815835 original size:20 final size:20
Alignment explanation
Indices: 815812--815856 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
815802 ATTCTATTTT
**
815812 ATATTGTTTGCTTCTGTTTG
1 ATATTGTTTGCTTCTACTTG
*
815832 ATATTGTTTGTTTCTACTTG
1 ATATTGTTTGCTTCTACTTG
815852 ATATT
1 ATATT
815857 TGTAAGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.60
Consensus pattern (20 bp):
ATATTGTTTGCTTCTACTTG
Found at i:815999 original size:23 final size:23
Alignment explanation
Indices: 815949--816002 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
815939 CTTAATGCAG
* *
815949 GATGCTTGTTGAATTGATGCAAT
1 GATGCTTGATGAATTGATACAAT
* * *
815972 AATGCTTGATGAATTGGTACATT
1 GATGCTTGATGAATTGATACAAT
815995 GATGCTTG
1 GATGCTTG
816003 CCGGTTGCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (23 bp):
GATGCTTGATGAATTGATACAAT
Found at i:816583 original size:15 final size:15
Alignment explanation
Indices: 816519--816584 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 15
816509 AATATTCAGC
816519 TATTATCAATTTAAT
1 TATTATCAATTTAAT
*
816534 TATTAATCATGTTTAA-
1 TATT-ATCA-ATTTAAT
*
816550 TATTAAC-A-TTAAGT
1 TATTATCAATTTAA-T
816564 TATTATCAATTTAAT
1 TATTATCAATTTAAT
816579 TATTAT
1 TATTAT
816585 TTTATTGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 4 0.10
14 6 0.15
15 14 0.34
16 12 0.29
17 5 0.12
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (15 bp):
TATTATCAATTTAAT
Found at i:816698 original size:23 final size:24
Alignment explanation
Indices: 816672--816721 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
816662 TTATTTTTTC
816672 TTTATATAAATTAAAATATA-TAA
1 TTTATATAAATTAAAATATATTAA
*
816695 TTTATATAAATTAAATTATATTAA
1 TTTATATAAATTAAAATATATTAA
816719 TTT
1 TTT
816722 TCCTTTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAATTAAAATATATTAA
Found at i:816761 original size:25 final size:22
Alignment explanation
Indices: 816732--816794 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 22
816722 TCCTTTTGCA
816732 TTATTAATAATGTTTTATCTAATT
1 TTATTAATAAT-TTTTAT-TAATT
816756 TATATTTAATTAA-TTTTATTAATT
1 T-TA-TTAA-TAATTTTTATTAATT
816780 TTATTAAATAATTTT
1 TTATT-AATAATTTT
816795 ATATAATAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 7 0.21
25 8 0.24
26 4 0.12
27 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTAATAATTTTTATTAATT
Found at i:816999 original size:16 final size:16
Alignment explanation
Indices: 816978--817048 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
816968 CGGATCATTT
*
816978 ACAGGTCAGGTTAAAA
1 ACAGGTCAAGTTAAAA
816994 ACAGGTCAAGTTAAAA
1 ACAGGTCAAGTTAAAA
*
817010 ACAGGTCAAGTTGAAA
1 ACAGGTCAAGTTAAAA
* * *
817026 ACAAGTCAGGTTGAAA
1 ACAGGTCAAGTTAAAA
817042 ACAGGTC
1 ACAGGTC
817049 GGGTAATACC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (16 bp):
ACAGGTCAAGTTAAAA
Found at i:819541 original size:48 final size:48
Alignment explanation
Indices: 819478--819595 Score: 202
Period size: 48 Copynumber: 2.5 Consensus size: 48
819468 TGATTTTTTA
819478 TCCAATTTTTT-TCAAACCGGTTTTTAATCCTGTAAAAAATCCGATCG
1 TCCAATTTTTTCTCAAACCGGTTTTTAATCCTGTAAAAAATCCGATCG
* *
819525 TCCAATTTTTTCTCAAACCGATTTTTAATCCTGTAAAAAATCTGATCG
1 TCCAATTTTTTCTCAAACCGGTTTTTAATCCTGTAAAAAATCCGATCG
*
819573 TACAATTTTTTCTCAAACCGGTT
1 TCCAATTTTTTCTCAAACCGGTT
819596 ATACTATCCG
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 11 0.17
48 55 0.83
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (48 bp):
TCCAATTTTTTCTCAAACCGGTTTTTAATCCTGTAAAAAATCCGATCG
Found at i:819641 original size:20 final size:20
Alignment explanation
Indices: 819601--819642 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
819591 CGGTTATACT
* * *
819601 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTAAAAAAAACCG
819621 ATCCGGTTTAAAAAAAACCG
1 ATCCGGTTTAAAAAAAACCG
819641 AT
1 AT
819643 TTTTCTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (20 bp):
ATCCGGTTTAAAAAAAACCG
Found at i:825206 original size:43 final size:44
Alignment explanation
Indices: 825124--825208 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 44
825114 TCTATTTGAC
*
825124 TGAAAACGGTTAAGGGATAAAAAAAATCAATCTATAAATTTTAG
1 TGAAAACGGATAAGGGATAAAAAAAATCAATCTATAAATTTTAG
* * * *
825168 TGAAAAC-GATAAGTGAT-AAAAAATTCAATTTATAAAATTTA
1 TGAAAACGGATAAGGGATAAAAAAAATCAATCTATAAATTTTA
825209 ATGAGTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 21 0.58
43 8 0.22
44 7 0.19
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (44 bp):
TGAAAACGGATAAGGGATAAAAAAAATCAATCTATAAATTTTAG
Found at i:827712 original size:14 final size:14
Alignment explanation
Indices: 827693--827722 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
827683 ACCACTGTCT
827693 AAGAGCTTGTTTTA
1 AAGAGCTTGTTTTA
827707 AAGAGCTTGTTTTA
1 AAGAGCTTGTTTTA
827721 AA
1 AA
827723 TCATACAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
AAGAGCTTGTTTTA
Found at i:835684 original size:18 final size:19
Alignment explanation
Indices: 835663--835704 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
835653 ATTAATTAAT
*
835663 TAAAGTTAATTAT-ATATA
1 TAAAGTTAATTATAAAATA
*
835681 TAAATTTAATTATAAAATA
1 TAAAGTTAATTATAAAATA
835700 TAAAG
1 TAAAG
835705 ATATGTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAAGTTAATTATAAAATA
Found at i:836968 original size:19 final size:18
Alignment explanation
Indices: 836930--836969 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
836920 ATTTTTTATA
* *
836930 TTTTTTTAAAAATAATAT
1 TTTTTTTAAAAACAAAAT
836948 TTTTGTTTAAAAACAAAAT
1 TTTT-TTTAAAAACAAAAT
836967 TTT
1 TTT
836970 CAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTTTTAAAAACAAAAT
Found at i:842125 original size:15 final size:15
Alignment explanation
Indices: 842105--842143 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
842095 CTACATGGAG
842105 CGATGAAGAAAGTTC
1 CGATGAAGAAAGTTC
842120 CGATGAAGAAAGTTC
1 CGATGAAGAAAGTTC
842135 CGATGAAGA
1 CGATGAAGA
842144 GGAACAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.18
Consensus pattern (15 bp):
CGATGAAGAAAGTTC
Found at i:848436 original size:19 final size:19
Alignment explanation
Indices: 848414--848452 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
848404 TGTGTTTTAA
848414 GTGTTTTAAAATGATAAAT
1 GTGTTTTAAAATGATAAAT
848433 GTGTTTTAAAATGATAAAT
1 GTGTTTTAAAATGATAAAT
848452 G
1 G
848453 GGAGAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (19 bp):
GTGTTTTAAAATGATAAAT
Found at i:850903 original size:18 final size:18
Alignment explanation
Indices: 850880--850914 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
850870 TATCCTGAAG
850880 GACCACTATGTCCCGAAT
1 GACCACTATGTCCCGAAT
850898 GACCACTATGTCCCGAA
1 GACCACTATGTCCCGAA
850915 GAACCACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
GACCACTATGTCCCGAAT
Found at i:850920 original size:18 final size:17
Alignment explanation
Indices: 850880--850921 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
850870 TATCCTGAAG
850880 GACCACTATGTCCCGAA
1 GACCACTATGTCCCGAA
850897 TGACCACTATGTCCCGAA
1 -GACCACTATGTCCCGAA
850915 GAACCAC
1 G-ACCAC
850922 GTAAAACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (17 bp):
GACCACTATGTCCCGAA
Found at i:851105 original size:15 final size:14
Alignment explanation
Indices: 851084--851118 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
851074 CATTGAGTCT
851084 CATATCTCATTATCA
1 CATATCTCA-TATCA
*
851099 TATATCTCATATCA
1 CATATCTCATATCA
851113 CATATC
1 CATATC
851119 ACATGGCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (14 bp):
CATATCTCATATCA
Found at i:862216 original size:35 final size:35
Alignment explanation
Indices: 862165--862273 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
862155 AAAACAACCC
* * *
862165 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAAATTCATTCTAAACCCCAAATTCCAAAATAAT
*
862200 TCAAATTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAAATTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
862235 TC-AATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAAATT-CATTCTAAACCCCAAATTCCAAAATAAT
862270 TCAA
1 TCAA
862274 TTTAAGGTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 4 0.06
35 58 0.92
36 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAAATTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:863421 original size:18 final size:19
Alignment explanation
Indices: 863398--863435 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
863388 CCCAGTAATC
863398 TTATTCTC-TGGTAATCTT
1 TTATTCTCATGGTAATCTT
863416 TTATTCTCGATGGTAATCTT
1 TTATTCTC-ATGGTAATCTT
863436 ACATTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (19 bp):
TTATTCTCATGGTAATCTT
Found at i:867376 original size:2 final size:2
Alignment explanation
Indices: 867371--867414 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
867361 TTTTTGTCCC
867371 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
867412 AT A
1 AT A
867415 GAGAATTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:868871 original size:17 final size:15
Alignment explanation
Indices: 868835--868865 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
868825 AAATTCTAAA
868835 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
868850 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
868865 T
1 T
868866 TTATTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:870618 original size:57 final size:57
Alignment explanation
Indices: 870548--870672 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
870538 GGAGAACATA
* *
870548 TATGCATTATGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTTTTATATGGCT
1 TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
*
870605 TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCTAGCTTCTTATATGGCT
1 TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
870662 TATGCATTCTG
1 TATGCATTCTG
870673 AGAAGTCATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (57 bp):
TATGCATTCTGCATCTCTACACTTATTTTTCTTGTCTATCCAGCTTCTTATATGGCT
Found at i:872492 original size:204 final size:204
Alignment explanation
Indices: 872142--872547 Score: 713
Period size: 204 Copynumber: 2.0 Consensus size: 204
872132 GGAAACCATT
* *
872142 CTGAAGTTCGGATCCCTGAGTCGTTTCGGACATAGCGTTGAACGAGAGATTTCTGTTCTACGCCG
1 CTGAAGTTCGGATCCCTGAGTCATTTCGGACATAGCGTTGAACGAGAGATTTCCGTTCTACGCCG
* *
872207 AAACGGGATCGAAGAACAAAGAGAGAGAGAGAGAGCGAGAAGGCAAAAACAACAACGCTTGGGAG
66 AAACAGGATCGAAGAACAAAGAGAGAGAGAGAGAGAGAGAAGGCAAAAACAACAACGCTTGGGAG
* *
872272 AAGATATCGCAAAGGCAAACGGGAAAAGAAGAGTATTTTAGCCCTTAACACACGGAAATAAAAGA
131 AAGATATCGCAAAGGCAAACGGGAAAAGAAGAGTATTTTAACCCTTAACACACGGAAATAAAAAA
872337 ATACCTATA
196 ATACCTATA
*
872346 CTGAAGTTCGGATCCCTGAGTCATTTCGGATATAGCGTTGAACGAGAGATTTCCGTTCTACGCCG
1 CTGAAGTTCGGATCCCTGAGTCATTTCGGACATAGCGTTGAACGAGAGATTTCCGTTCTACGCCG
*
872411 AAACAGGATCGAAGAACAAAGAGAGAGAGAGAGAGAGCGAAGGCAAAAACAACAACGCTTGGGAG
66 AAACAGGATCGAAGAACAAAGAGAGAGAGAGAGAGAGAGAAGGCAAAAACAACAACGCTTGGGAG
* * *
872476 AAGATATCGTAAAGGCAAACGGGAAAAGAAGAGTATTTTAACCCTTAGCACACGGGAATAAAAAA
131 AAGATATCGCAAAGGCAAACGGGAAAAGAAGAGTATTTTAACCCTTAACACACGGAAATAAAAAA
872541 ATACCTA
196 ATACCTA
872548 ACGAGTGTGG
Statistics
Matches: 191, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
204 191 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (204 bp):
CTGAAGTTCGGATCCCTGAGTCATTTCGGACATAGCGTTGAACGAGAGATTTCCGTTCTACGCCG
AAACAGGATCGAAGAACAAAGAGAGAGAGAGAGAGAGAGAAGGCAAAAACAACAACGCTTGGGAG
AAGATATCGCAAAGGCAAACGGGAAAAGAAGAGTATTTTAACCCTTAACACACGGAAATAAAAAA
ATACCTATA
Found at i:872958 original size:20 final size:20
Alignment explanation
Indices: 872933--872970 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
872923 TTTGATTCAC
872933 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
872953 GGAATGTAATATTACCAG
1 GGAATGTAAGATTACCAG
872971 AGAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:873764 original size:13 final size:13
Alignment explanation
Indices: 873746--873770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
873736 TAACCTGGTA
873746 AACGAAGATGTAT
1 AACGAAGATGTAT
873759 AACGAAGATGTA
1 AACGAAGATGTA
873771 ATGAGGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.20
Consensus pattern (13 bp):
AACGAAGATGTAT
Found at i:875200 original size:11 final size:11
Alignment explanation
Indices: 875184--875246 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
875174 AAAATTACAT
875184 TATTAAAAATA
1 TATTAAAAATA
875195 TATTAAAAATA
1 TATTAAAAATA
* ***
875206 CATTATTGATA
1 TATTAAAAATA
875217 -ATTATAAAAT-
1 TATTA-AAAATA
875227 T-TTAAAAATA
1 TATTAAAAATA
875237 TATTAAAAAT
1 TATTAAAAAT
875247 TCTTTATCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:875291 original size:17 final size:16
Alignment explanation
Indices: 875273--875312 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
875263 AATATTTAAT
*
875273 ATATTTCTAATAA-TA
1 ATATTTTTAATAACTA
875288 ATATTTTTAATAACTA
1 ATATTTTTAATAACTA
875304 AT-TTTTTAA
1 ATATTTTTAA
875313 ATTATTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTAATAACTA
Found at i:875461 original size:7 final size:7
Alignment explanation
Indices: 875446--875479 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
875436 ATTTGTAATG
875446 AACCCTA
1 AACCCTA
*
875453 AACCTTA
1 AACCCTA
875460 AACCCTA
1 AACCCTA
875467 AACCCTA
1 AACCCTA
875474 AACCCT
1 AACCCT
875480 TAATCCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:876533 original size:23 final size:25
Alignment explanation
Indices: 876481--876533 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
876471 TATATATTTG
**
876481 AAAATCGAGATGGATTTGTAAAATT
1 AAAATCGAGATGGATTTGTAAAACA
*
876506 GAAATCGAGA-GG-TTTGTAAAACA
1 AAAATCGAGATGGATTTGTAAAACA
876529 AAAAT
1 AAAAT
876534 TGTATGCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 13 0.54
24 2 0.08
25 9 0.38
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAATCGAGATGGATTTGTAAAACA
Found at i:879282 original size:203 final size:203
Alignment explanation
Indices: 879057--879459 Score: 806
Period size: 203 Copynumber: 2.0 Consensus size: 203
879047 CAAGGTGCCG
879057 AAAAAACGAAAAATGTACCTTTACAATCTCTTAGAGTTGAGTTTGAAATGTTGAAAATGAGAAAT
1 AAAAAACGAAAAATGTACCTTTACAATCTCTTAGAGTTGAGTTTGAAATGTTGAAAATGAGAAAT
879122 ACGGAAAACATCAATGATTACATTAGTCATGTAAAAGTGATAGTGAATGAAATGAAGAGAAATGG
66 ACGGAAAACATCAATGATTACATTAGTCATGTAAAAGTGATAGTGAATGAAATGAAGAGAAATGG
879187 TGAATCACTCAACGAGGTTAGAGTGATGGAAAAATTTTTGCGATCATTAACAATAAAATTTGATT
131 TGAATCACTCAACGAGGTTAGAGTGATGGAAAAATTTTTGCGATCATTAACAATAAAATTTGATT
879252 ACGTGCGA
196 ACGTGCGA
879260 AAAAAACGAAAAATGTACCTTTACAATCTCTTAGAGTTGAGTTTGAAATGTTGAAAATGAGAAAT
1 AAAAAACGAAAAATGTACCTTTACAATCTCTTAGAGTTGAGTTTGAAATGTTGAAAATGAGAAAT
879325 ACGGAAAACATCAATGATTACATTAGTCATGTAAAAGTGATAGTGAATGAAATGAAGAGAAATGG
66 ACGGAAAACATCAATGATTACATTAGTCATGTAAAAGTGATAGTGAATGAAATGAAGAGAAATGG
879390 TGAATCACTCAACGAGGTTAGAGTGATGGAAAAATTTTTGCGATCATTAACAATAAAATTTGATT
131 TGAATCACTCAACGAGGTTAGAGTGATGGAAAAATTTTTGCGATCATTAACAATAAAATTTGATT
879455 ACGTG
196 ACGTG
879460 GTCTTGGAAA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 200 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (203 bp):
AAAAAACGAAAAATGTACCTTTACAATCTCTTAGAGTTGAGTTTGAAATGTTGAAAATGAGAAAT
ACGGAAAACATCAATGATTACATTAGTCATGTAAAAGTGATAGTGAATGAAATGAAGAGAAATGG
TGAATCACTCAACGAGGTTAGAGTGATGGAAAAATTTTTGCGATCATTAACAATAAAATTTGATT
ACGTGCGA
Found at i:884334 original size:26 final size:27
Alignment explanation
Indices: 884282--884334 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
884272 TATTTTAAAA
* * *
884282 AACCCAAACATTTTGAAAAACTTTAAT
1 AACCCAAAAACTTTGAAAAACTCTAAT
884309 AACCCAAAAACTTTG-AAAACTCTAAT
1 AACCCAAAAACTTTGAAAAACTCTAAT
884335 TTCAACCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (27 bp):
AACCCAAAAACTTTGAAAAACTCTAAT
Found at i:884658 original size:10 final size:9
Alignment explanation
Indices: 884642--884678 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
884632 AGAAATTAGG
884642 ATTTTTTTA
1 ATTTTTTTA
884651 ATTTTTTTAA
1 ATTTTTTT-A
884661 ATTTTTTTA
1 ATTTTTTTA
884670 ACTTTTTTT
1 A-TTTTTTT
884679 TTCAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 10 0.38
10 16 0.62
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:885018 original size:57 final size:59
Alignment explanation
Indices: 884885--885019 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 59
884875 TAAAGTAAAT
*
884885 AAATGGTCCCCCAACTATAGAGCACTACTTTGTTGAGTCCTCTGACGATTAAAAGTTACA
1 AAATGGT-CCCTAACTATAGAGCACTACTTTGTTGAGTCCTCTGACGATTAAAAGTTACA
* * * * *
884945 AAATGATCCATCAACTATA-A-CATTGCTTTGTTGAGT-CTCTGACTATTAAAAGTTACA
1 AAATGGTCCCT-AACTATAGAGCACTACTTTGTTGAGTCCTCTGACGATTAAAAGTTACA
885002 AAATGGTCACCTAACTAT
1 AAATGGTC-CCTAACTAT
885020 TCATATGTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
57 33 0.51
58 16 0.25
59 3 0.05
60 13 0.20
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (59 bp):
AAATGGTCCCTAACTATAGAGCACTACTTTGTTGAGTCCTCTGACGATTAAAAGTTACA
Found at i:889042 original size:19 final size:19
Alignment explanation
Indices: 888995--889044 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
888985 AAAATATATT
888995 ATTAATAAAATATATATAAA
1 ATTAA-AAAATATATATAAA
* * *
889015 AATATAAAATATATATGAA
1 ATTAAAAAATATATATAAA
*
889034 TTTAAAAAATA
1 ATTAAAAAATA
889045 AAAAAAGGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATTAAAAAATATATATAAA
Found at i:889642 original size:18 final size:16
Alignment explanation
Indices: 889608--889662 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 16
889598 ACAAATTAAC
*
889608 AAAAAAAGAAAATAAT
1 AAAAAAAGAAAAAAAT
889624 AAAAGAAAGTAAAAAAAT
1 AAAA-AAAG-AAAAAAAT
889642 AAAAAATCAGGAAAAAAAT
1 AAAAAA--A-GAAAAAAAT
889661 AA
1 AA
889663 CGCAACTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 11 0.33
19 11 0.33
20 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAT
Found at i:894890 original size:18 final size:20
Alignment explanation
Indices: 894869--894919 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
894859 AAAACAAATC
894869 ATAAAAATAAAATT-G-AAA
1 ATAAAAATAAAATTGGAAAA
*
894887 ATAAAAATAAATTTGGAAAA
1 ATAAAAATAAAATTGGAAAA
894907 ATGAAAAATAAAA
1 AT-AAAAATAAAA
894920 ATTAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
20 5 0.18
21 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
ATAAAAATAAAATTGGAAAA
Found at i:895367 original size:13 final size:12
Alignment explanation
Indices: 895336--895366 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
895326 TCAAAGAAGA
895336 TTAAAAAGAAAG
1 TTAAAAAGAAAG
895348 TTAAAAAGAAAG
1 TTAAAAAGAAAG
895360 TTAAAAA
1 TTAAAAA
895367 AATCAATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (12 bp):
TTAAAAAGAAAG
Found at i:903542 original size:2 final size:2
Alignment explanation
Indices: 903535--903561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
903525 ATTAACCTTG
903535 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
903562 TATTTTTTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:904772 original size:108 final size:114
Alignment explanation
Indices: 904564--904776 Score: 285
Period size: 108 Copynumber: 1.9 Consensus size: 114
904554 CATTACAAAC
904564 GTAACTACTCTAAACTGACACCTCTAAAAAAATTCCATACGAAATTAACATTTTATTTGTGTCTC
1 GTAACTACTCTAAACTGACACCTCTAAAAAAATTCCATACG--A--AACATTTTATTTGTGTCTC
* * * *
904629 ATTCATATGGAAACAATTATCTTATTAGTACATATGTATACACACATTCAGAT
62 ATTCATATGGAAAAAAATATATTATTAATACATATGTATACACACATTCAGAT
* * *
904682 GTAACTATTCTAAACTGACAGCTCT-AAAAAATTCCATACG-AA-ATTTTA-TT-TGTCTCCTTC
1 GTAACTACTCTAAACTGACACCTCTAAAAAAATTCCATACGAAACATTTTATTTGTGTCTCATTC
904742 ATAT-GAAAAAAATATATTATTAATACATATGTATA
66 ATATGGAAAAAAATATATTATTAATACATATGTATA
904777 TATCATGAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
108 27 0.31
109 13 0.15
110 2 0.02
111 6 0.07
112 2 0.02
117 15 0.17
118 23 0.26
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (114 bp):
GTAACTACTCTAAACTGACACCTCTAAAAAAATTCCATACGAAACATTTTATTTGTGTCTCATTC
ATATGGAAAAAAATATATTATTAATACATATGTATACACACATTCAGAT
Found at i:905915 original size:33 final size:33
Alignment explanation
Indices: 905870--905935 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
905860 ATTCTCAGAC
905870 TTAGGGGCTGTTTGTTTACTTCATAATGATTAA
1 TTAGGGGCTGTTTGTTTACTTCATAATGATTAA
*
905903 TTAGGGGTTGTTTGTTTACTTCATAATGATTAA
1 TTAGGGGCTGTTTGTTTACTTCATAATGATTAA
905936 GTGTTGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (33 bp):
TTAGGGGCTGTTTGTTTACTTCATAATGATTAA
Found at i:906041 original size:27 final size:27
Alignment explanation
Indices: 906003--906069 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
905993 TTTATTGGCT
906003 CTGAATCATTCAAAATGTACTTCTGTG
1 CTGAATCATTCAAAATGTACTTCTGTG
*
906030 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAAAATGTACTTCTGTG
906057 CTGAATCATTCAA
1 CTGAATCATTCAA
906070 CATTATTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAAAATGTACTTCTGTG
Found at i:906198 original size:31 final size:31
Alignment explanation
Indices: 906160--906222 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
906150 CAACGCTGAA
906160 TGGTTTCATTAAGAGGTAAACAAACATCCCC
1 TGGTTTCATTAAGAGGTAAACAAACATCCCC
906191 TGGTTTCATTAAGAGGTAAACAAACATCCCC
1 TGGTTTCATTAAGAGGTAAACAAACATCCCC
906222 T
1 T
906223 TAGTTTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (31 bp):
TGGTTTCATTAAGAGGTAAACAAACATCCCC
Found at i:906760 original size:31 final size:30
Alignment explanation
Indices: 906715--906805 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 30
906705 AGAGAGACAT
* *
906715 TGATCAAATTAATATTTTATCTAAAGTTTA
1 TGATCAAAATAATATTATATCTAAAGTTTA
* **
906745 GTGATTAAAATAATATGCTATCTAAAGTTTA
1 -TGATCAAAATAATATTATATCTAAAGTTTA
* * *
906776 TGGTCAACATAATATTATATATAAAGTTTA
1 TGATCAAAATAATATTATATCTAAAGTTTA
906806 AGGGTCAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 24 0.48
31 26 0.52
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (30 bp):
TGATCAAAATAATATTATATCTAAAGTTTA
Found at i:907307 original size:20 final size:20
Alignment explanation
Indices: 907254--907307 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
907244 TTTAATGGAT
* *
907254 TTAAAAATAATTTGATTCAA
1 TTAAATATAATTTGACTCAA
*
907274 TTAAATTTAAATTTGACTC-A
1 TTAAATAT-AATTTGACTCAA
907294 TTAAATATATATTT
1 TTAAATATA-ATTT
907308 AAATTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
21 9 0.32
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (20 bp):
TTAAATATAATTTGACTCAA
Found at i:914014 original size:16 final size:16
Alignment explanation
Indices: 913993--914029 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
913983 AGTTTAATTT
913993 GTTTTATTTCATTTTA
1 GTTTTATTTCATTTTA
914009 GTTTTATTTCATTTTA
1 GTTTTATTTCATTTTA
914025 GTTTT
1 GTTTT
914030 GACAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.70
Consensus pattern (16 bp):
GTTTTATTTCATTTTA
Found at i:914093 original size:25 final size:26
Alignment explanation
Indices: 914039--914096 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
914029 TGACAAATTT
**
914039 ATTGTATTAATAATAATTATTTATGTA
1 ATTGTATTAATAAT-ATTATTTATCAA
914066 ATTGTATTAAATAAT-TTATTT-TCAA
1 ATTGTATT-AATAATATTATTTATCAA
914091 ATTGTA
1 ATTGTA
914097 GCGAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.29
26 6 0.21
27 8 0.29
28 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (26 bp):
ATTGTATTAATAATATTATTTATCAA
Found at i:916099 original size:19 final size:19
Alignment explanation
Indices: 916075--916126 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
916065 GAATGCAATC
916075 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
916094 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
916113 AGTGCATCGATGCA
1 AGTGCATCGATGCA
916127 CCTACTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:918890 original size:20 final size:20
Alignment explanation
Indices: 918867--918930 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
918857 TACTGAAACT
*
918867 GATATTGCTGAGGCAGTACC
1 GATACTGCTGAGGCAGTACC
*
918887 GATACTGCTGAGACAGTACC
1 GATACTGCTGAGGCAGTACC
918907 GATACTGCTGAGGCAGTACC
1 GATACTGCTGAGGCAGTACC
918927 GATA
1 GATA
918931 TTGTCAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (20 bp):
GATACTGCTGAGGCAGTACC
Found at i:923123 original size:2 final size:2
Alignment explanation
Indices: 923116--923143 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
923106 CTAGTAATAA
923116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
923144 TAATACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:927370 original size:26 final size:24
Alignment explanation
Indices: 927341--927412 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
927331 AAAATCCAAC
927341 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
*
927367 AAA-TGAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
927389 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
927413 AAAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 8 0.22
26 10 0.27
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:927927 original size:18 final size:18
Alignment explanation
Indices: 927904--927940 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
927894 GAAAGGCGGT
*
927904 GATATCATATATGGCTGC
1 GATATCATAAATGGCTGC
*
927922 GATATCATAAATGGTTGC
1 GATATCATAAATGGCTGC
927940 G
1 G
927941 GTGGCTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (18 bp):
GATATCATAAATGGCTGC
Found at i:929640 original size:17 final size:18
Alignment explanation
Indices: 929620--929660 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
929610 AAATTATATT
929620 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
929637 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
929655 ATTAAA
1 AGTAAA
929661 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:929716 original size:10 final size:10
Alignment explanation
Indices: 929701--929725 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
929691 CTTAAGTAGA
929701 GAGAGTATTT
1 GAGAGTATTT
929711 GAGAGTATTT
1 GAGAGTATTT
929721 GAGAG
1 GAGAG
929726 AATATGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (10 bp):
GAGAGTATTT
Found at i:952513 original size:27 final size:27
Alignment explanation
Indices: 952447--952516 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
952437 AAAAATATTT
*
952447 TTTTAATTTTTATTAATGGAAGAAATAA
1 TTTTAATTTTTATTAAT-GAAAAAATAA
* *
952475 TTCATAACTTTTATTAAT-AAAAAATAA
1 TT-TTAATTTTTATTAATGAAAAAATAA
952502 TCTTTAATTTTTATT
1 T-TTTAATTTTTATT
952517 TGTTAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 19 0.54
28 3 0.09
29 13 0.37
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTTAATTTTTATTAATGAAAAAATAA
Found at i:952615 original size:15 final size:17
Alignment explanation
Indices: 952591--952628 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
952581 TATTTATTTG
952591 ATTA-AAAAAATTA-AA
1 ATTATAAAAAATTATAA
952606 A-TATAAAAAATTATAA
1 ATTATAAAAAATTATAA
952622 ATTATAA
1 ATTATAA
952629 TTAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 10 0.50
16 3 0.15
17 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATTATAAAAAATTATAA
Found at i:952629 original size:69 final size:69
Alignment explanation
Indices: 952550--952700 Score: 259
Period size: 69 Copynumber: 2.2 Consensus size: 69
952540 ATATAGCTAT
*
952550 TAAATTATAATTAATAAATAAAA-TCAATATTTATTTATTTGATTAAAAAAATTAAAATATAAAA
1 TAAATTATAATTAATAAATAAAAGTCAATAATTATTTATTTGATT-AAAAAATTAAAATATAAAA
952614 AATTA
65 AATTA
*
952619 TAAATTATAATTAATAAATAAAAGTCAATAATTATTTATTTGATTAAAAATTTAAAATATAAAAA
1 TAAATTATAATTAATAAATAAAAGTCAATAATTATTTATTTGATTAAAAAATTAAAATATAAAAA
*
952684 ATTG
66 ATTA
952688 TAAATTATAATTA
1 TAAATTATAATTA
952701 TTTATTAGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 58 0.74
70 20 0.26
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (69 bp):
TAAATTATAATTAATAAATAAAAGTCAATAATTATTTATTTGATTAAAAAATTAAAATATAAAAA
ATTA
Found at i:952683 original size:16 final size:17
Alignment explanation
Indices: 952664--952697 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
952654 TTATTTGATT
952664 AAAAATT-TAAAATATA
1 AAAAATTGTAAAATATA
*
952680 AAAAATTGTAAATTATA
1 AAAAATTGTAAAATATA
952697 A
1 A
952698 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAAAATTGTAAAATATA
Found at i:956870 original size:10 final size:10
Alignment explanation
Indices: 956855--956884 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
956845 TCAACGACTT
956855 TATACATATA
1 TATACATATA
956865 TATACATATA
1 TATACATATA
956875 TATACATATA
1 TATACATATA
956885 CACAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
TATACATATA
Found at i:963695 original size:213 final size:215
Alignment explanation
Indices: 963326--963752 Score: 831
Period size: 213 Copynumber: 2.0 Consensus size: 215
963316 GAGACCAACT
963326 GGCTTATGGAAATCGTTGCTGTTCTTCTTCGTCAGTTTGAGAATCTAATTTCGGAATACAACCAT
1 GGCTTATGGAAATCGTTGCTGTTCTTCTTCGTCAGTTTGAGAATCTAATTTCGGAATACAACCAT
963391 TGTGAGGACTATATCGATGAAGACCAGAATACAACACCAAACGGAGAATCGGCTATATCCGATTC
66 TGTGAGGAC-ATATCGATGAAGACCAGAATACAACACCAAACGGAGAATCGGCTATATCCGATTC
963456 TCTTGTTGAAGCATTGCATGCTTTGAAGAATCATCTTCATGTTCTTATGAAGAATCTTAATCGAA
130 TCTTGTTGAAGCATTGCATGCTTTGAAGAATCATCTTCATGTTCTTATGAAGAATCTTAATCGAA
963521 AAGACTTC-TGGACTTGTGTG
195 AAGACTTCTTGGACTTGTGTG
963541 GGCTTATGGAAATCGTTGCTGTTCTTCTTCGTCAGTTTGAGAATCTAATTTCGGAATACAACCAT
1 GGCTTATGGAAATCGTTGCTGTTCTTCTTCGTCAGTTTGAGAATCTAATTTCGGAATACAACCAT
963606 TGTGAGGAC-TATCGATGAAGACCAGAATACAACACCAAACGGAGAATCGGCTATATCCGATTCT
66 TGTGAGGACATATCGATGAAGACCAGAATACAACACCAAACGGAGAATCGGCTATATCCGATTCT
963670 CTTGTTGAAGCATTGCATGCTTTGAAGAATCATCTTCATGTTCTTATGAAGAATCTTAATCGAAA
131 CTTGTTGAAGCATTGCATGCTTTGAAGAATCATCTTCATGTTCTTATGAAGAATCTTAATCGAAA
963735 AGACTTCTTGGACTTGTG
196 AGACTTCTTGGACTTGTG
963753 GCGAAGTGTG
Statistics
Matches: 211, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
213 127 0.60
214 10 0.05
215 74 0.35
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (215 bp):
GGCTTATGGAAATCGTTGCTGTTCTTCTTCGTCAGTTTGAGAATCTAATTTCGGAATACAACCAT
TGTGAGGACATATCGATGAAGACCAGAATACAACACCAAACGGAGAATCGGCTATATCCGATTCT
CTTGTTGAAGCATTGCATGCTTTGAAGAATCATCTTCATGTTCTTATGAAGAATCTTAATCGAAA
AGACTTCTTGGACTTGTGTG
Found at i:970030 original size:13 final size:13
Alignment explanation
Indices: 970012--970036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
970002 AGTTTGTAAT
970012 TAAAATTGAGAAA
1 TAAAATTGAGAAA
970025 TAAAATTGAGAA
1 TAAAATTGAGAA
970037 GACGTAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
TAAAATTGAGAAA
Found at i:972323 original size:181 final size:182
Alignment explanation
Indices: 972019--972381 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 182
972009 ACATATACAA
972019 ACTAAAAATAGGGCCAATAACGATTGTAAGCTAACAATGATAACATATTGAAAGGTGTAGAACCA
1 ACTAAAAATAGGGCCAATAACGATTGTAAGCTAACAATGATAACATATTGAAAGGTGTAGAACCA
972084 TAGGTTTATGATAGACTTCAGCCCTGTAAGAGAATATACTTATTTTGGACTGGTTGTATTTTTCT
66 TAGGTTTATGATAGACTTCAGCCCTGTAAGAGAATATACTTATTTTGGACTGGTTGTATTTTTCT
972149 GTGTTCTTTTAATTAGGTAATGTCATTCTAATTAG-TATTAGTCACCTTAAG
131 GTGTTCTTTTAATTAGGTAATGTCATTCTAATTAGTTATTAGTCACCTTAAG
972200 ACTAAAAATAGGGCCAATAACGATTGTAAGCTAACAATGATAACATATTGAAAGGTGTAGAACCA
1 ACTAAAAATAGGGCCAATAACGATTGTAAGCTAACAATGATAACATATTGAAAGGTGTAGAACCA
972265 TAGGTTTATGATAGACTTCAGCCCTGTAAGAGAATATACTTATTTTGGACTGGTTGTATTTTTCT
66 TAGGTTTATGATAGACTTCAGCCCTGTAAGAGAATATACTTATTTTGGACTGGTTGTATTTTTCT
972330 GTGTTCTTTTAATTAGGTAATGTCATTCTAATTAGTTATTAGTCACCTTAAG
131 GTGTTCTTTTAATTAGGTAATGTCATTCTAATTAGTTATTAGTCACCTTAAG
972382 GTATGTTATG
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 165 0.91
182 16 0.09
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (182 bp):
ACTAAAAATAGGGCCAATAACGATTGTAAGCTAACAATGATAACATATTGAAAGGTGTAGAACCA
TAGGTTTATGATAGACTTCAGCCCTGTAAGAGAATATACTTATTTTGGACTGGTTGTATTTTTCT
GTGTTCTTTTAATTAGGTAATGTCATTCTAATTAGTTATTAGTCACCTTAAG
Found at i:973674 original size:106 final size:106
Alignment explanation
Indices: 973489--973700 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
973479 GTGATCTACT
973489 ATTAAGTTCCACTCACTGGAAGCAGTGAACTTTGAAGACTTCTCAATCTGAAGGACCAAACACAT
1 ATTAAGTTCCACTCACTGGAAGCAGTGAACTTTGAAGACTTCTCAATCTGAAGGACCAAACACAT
973554 ACTTACAAGAGATTTGAAGTTCAACCTTGGTTAACACTTTC
66 ACTTACAAGAGATTTGAAGTTCAACCTTGGTTAACACTTTC
973595 ATTAAGTTCCACTCACTGGAAGCAGTGAACTTTGAAGACTTCTCAATCTGAAGGACCAAACACAT
1 ATTAAGTTCCACTCACTGGAAGCAGTGAACTTTGAAGACTTCTCAATCTGAAGGACCAAACACAT
973660 ACTTACAAGAGATTTGAAGTTCAACCTTGGTTAACACTTTC
66 ACTTACAAGAGATTTGAAGTTCAACCTTGGTTAACACTTTC
973701 CAACTGGAGG
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (106 bp):
ATTAAGTTCCACTCACTGGAAGCAGTGAACTTTGAAGACTTCTCAATCTGAAGGACCAAACACAT
ACTTACAAGAGATTTGAAGTTCAACCTTGGTTAACACTTTC
Found at i:975821 original size:21 final size:21
Alignment explanation
Indices: 975775--975821 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
975765 ATTTCCATTT
* * *
975775 AATTCTTACTTTAATTATTAA
1 AATTTTTAATTTAATCATTAA
975796 AATTTTTAATTTAATCATTAA
1 AATTTTTAATTTAATCATTAA
975817 AATTT
1 AATTT
975822 AAAAATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTTAATTTAATCATTAA
Found at i:977182 original size:22 final size:22
Alignment explanation
Indices: 977148--977193 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
977138 GTACATATTA
*
977148 TTCTGCCTTTATGACAAGTTTT
1 TTCTGCCTCTATGACAAGTTTT
* *
977170 TTCTGTCTCTATGACATGTTTT
1 TTCTGCCTCTATGACAAGTTTT
977192 TT
1 TT
977194 GTTGTTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.13, T:0.54
Consensus pattern (22 bp):
TTCTGCCTCTATGACAAGTTTT
Found at i:986305 original size:18 final size:19
Alignment explanation
Indices: 986279--986315 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
986269 ACATTAAAGA
*
986279 TTCATAAAATTCAGAAATT
1 TTCATAAAATTCAAAAATT
986298 TTCA-AAAATTCAAAAATT
1 TTCATAAAATTCAAAAATT
986316 CATAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (19 bp):
TTCATAAAATTCAAAAATT
Found at i:988854 original size:99 final size:99
Alignment explanation
Indices: 988678--988875 Score: 344
Period size: 99 Copynumber: 2.0 Consensus size: 99
988668 GGATTTTAGG
*
988678 TGGGTAACTAATTAACAGTTGATTACATTTTTAATTCAATCCTATTTGGATATCTGCAGTTTCAA
1 TGGGTAACTAATTAACAGTTGATTACATTTGTAATTCAATCCTATTTGGATATCTGCAGTTTCAA
* * *
988743 ACTGGGTGATCACAGATTTGTATTCTATCTGCTT
66 ACTGAGTAATCACAGATTTGTATTCTATCAGCTT
988777 TGGGTAACTAATTAACAGTTGATTACATTTGTAATTCAATCCTATTTGGATATCTGCAGTTTCAA
1 TGGGTAACTAATTAACAGTTGATTACATTTGTAATTCAATCCTATTTGGATATCTGCAGTTTCAA
988842 ACCT-AGTAATCACAGATTTGTATTCTATCAGCTT
66 A-CTGAGTAATCACAGATTTGTATTCTATCAGCTT
988876 CTTATTTTGG
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
99 92 0.98
100 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (99 bp):
TGGGTAACTAATTAACAGTTGATTACATTTGTAATTCAATCCTATTTGGATATCTGCAGTTTCAA
ACTGAGTAATCACAGATTTGTATTCTATCAGCTT
Found at i:992487 original size:2 final size:2
Alignment explanation
Indices: 992480--992507 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
992470 ATTTTAGGGC
992480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
992508 CCGAGCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:993668 original size:30 final size:30
Alignment explanation
Indices: 993593--993668 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
993583 AAACATTATA
* *
993593 ACAATTAAATGATCATTAAAACTAAGCATT
1 ACAATTAACTGATCATTAAAACTAAACATT
* * *
993623 ATAATCAACAT-ATCATTAAAATTAAACATT
1 ACAATTAAC-TGATCATTAAAACTAAACATT
*
993653 ACAATTAGCTGATCAT
1 ACAATTAACTGATCAT
993669 GAACACCTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 1 0.03
30 34 0.94
31 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
ACAATTAACTGATCATTAAAACTAAACATT
Found at i:996078 original size:369 final size:369
Alignment explanation
Indices: 995592--996702 Score: 2195
Period size: 369 Copynumber: 3.0 Consensus size: 369
995582 GGGCTTTCTA
995592 GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
1 GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
*
995657 TTTATGTTGCTAGAGGGAATTCATGCTGAAAGGGACATTACTTGTTGGAACACTATAATTGCTGG
66 TTTATGTTGCTAGAGGGAATTCATGCTGAAAAGGACATTACTTGTTGGAACACTATAATTGCTGG
995722 TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
131 TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
995787 ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
196 ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
995852 ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
261 ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
995917 ATGCATTAATCACTATGTATGGAAGATGCGGTCACACTAAGAGT
326 ATGCATTAATCACTATGTATGGAAGATGCGGTCACACTAAGAGT
995961 GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
1 GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
996026 TTTATGTTGCTAGAGGGAATTCATGCTGAAAAGGACATTACTTGTTGGAACACTATAATTGCTGG
66 TTTATGTTGCTAGAGGGAATTCATGCTGAAAAGGACATTACTTGTTGGAACACTATAATTGCTGG
996091 TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
131 TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
996156 ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
196 ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
996221 ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
261 ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
*
996286 ATGCATTAATCACTATGTATGGAAGATGCAGTCACACTAAGAGT
326 ATGCATTAATCACTATGTATGGAAGATGCGGTCACACTAAGAGT
996330 GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
1 GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
996395 TTTATGTTGCTAGAGGGAATTCATGCTGAAAAGGACATTACTTGTTGGAACACTATAATTGCTGG
66 TTTATGTTGCTAGAGGGAATTCATGCTGAAAAGGACATTACTTGTTGGAACACTATAATTGCTGG
996460 TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
131 TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
996525 ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
196 ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
996590 ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
261 ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
*
996655 ATGCATTAATCACTATGTATGGAAGATGCGGACACACTAAGAGT
326 ATGCATTAATCACTATGTATGGAAGATGCGGTCACACTAAGAGT
996699 GCAA
1 GCAA
996703 AATCTGTGTT
Statistics
Matches: 738, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
369 738 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (369 bp):
GCAATATTCTTATAGTTAATTCCCTCATGCACATGTATGTTAATTTTGGGGACGTACCTGCTGCT
TTTATGTTGCTAGAGGGAATTCATGCTGAAAAGGACATTACTTGTTGGAACACTATAATTGCTGG
TTGTAAAAGGAATGGCCATTTTCGAGAAGCTTTAGCAACATTCAATTGGATGAGGCAGGAAATAA
ATGTTATGCGGGACGCAATCACACTTGTGATGTTATATCAGCTTGTAGAAATCTTGCGTTGATTT
ATGAAGGAAAATCCCTGCAGGCCTTGCTGTTAAAGCTTTTGTGGGATCGGAAACTTGTGTGCAGA
ATGCATTAATCACTATGTATGGAAGATGCGGTCACACTAAGAGT
Found at i:1000036 original size:2 final size:2
Alignment explanation
Indices: 1000029--1000058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1000019 CCTTCACATG
1000029 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1000059 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1000063 original size:2 final size:2
Alignment explanation
Indices: 1000058--1000086 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1000048 ACACACACAC
1000058 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1000087 AGAAAACAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1002624 original size:15 final size:16
Alignment explanation
Indices: 1002596--1002628 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1002586 GATCTAATTT
1002596 AAATTAATAAAAAATA
1 AAATTAATAAAAAATA
*
1002612 AAATTAA-AGAAAATA
1 AAATTAATAAAAAATA
1002627 AA
1 AA
1002629 TAAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATTAATAAAAAATA
Found at i:1006646 original size:2 final size:2
Alignment explanation
Indices: 1006639--1006667 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1006629 ATTTTAGGGC
1006639 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1006668 TACCGAGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1006977 original size:14 final size:14
Alignment explanation
Indices: 1006958--1006987 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1006948 CTATCGATTA
1006958 ATAATTAATAAATT
1 ATAATTAATAAATT
*
1006972 ATAATTAATTAATT
1 ATAATTAATAAATT
1006986 AT
1 AT
1006988 TATTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTAATAAATT
Found at i:1008906 original size:22 final size:22
Alignment explanation
Indices: 1008881--1008923 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1008871 TTGATAAAAA
*
1008881 TTTATCTAAAATATTATTATTT
1 TTTATCGAAAATATTATTATTT
*
1008903 TTTATCGAAAATGTTATTATT
1 TTTATCGAAAATATTATTATT
1008924 GGACACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTATCGAAAATATTATTATTT
Found at i:1009050 original size:21 final size:21
Alignment explanation
Indices: 1009026--1009069 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1009016 GAAAATATTA
*
1009026 AAAAACATTAATGTTTTAAGT
1 AAAAACAATAATGTTTTAAGT
* *
1009047 AAAAATAATAATGTTTTACGT
1 AAAAACAATAATGTTTTAAGT
1009068 AA
1 AA
1009070 TATTTTACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATGTTTTAAGT
Found at i:1014766 original size:35 final size:35
Alignment explanation
Indices: 1014727--1014836 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
1014717 CAATTTTGAA
*
1014727 AAAATGGTTTTCAAAATTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1014762 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
** * *
1014797 AAAAATAATTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1014833 AAAA
1 AAAA
1014837 ATGATAATGG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
35 38 0.56
36 8 0.12
37 22 0.32
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:1015269 original size:16 final size:16
Alignment explanation
Indices: 1015248--1015281 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1015238 TTACTATTCA
*
1015248 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1015264 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1015280 CG
1 CG
1015282 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1019379 original size:21 final size:21
Alignment explanation
Indices: 1019355--1019415 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1019345 AACTTTGAAA
1019355 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1019376 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1019390 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1019411 AAATG
1 AAATG
1019416 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1019446 original size:37 final size:37
Alignment explanation
Indices: 1019347--1019465 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1019337 TGGTAACCAA
1019347 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1019384 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1019419 CTTTGAAAAATAGTTTTTCAAAGTTTGGTATATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1019456 -GTTGAAAAAT
1 CTTTGAAAAAT
1019466 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1022383 original size:16 final size:17
Alignment explanation
Indices: 1022346--1022388 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1022336 AAGTTAAATT
**
1022346 ATTTTAAATTTAGATTGT
1 ATTTT-AATTTAGATTAA
1022364 A-TTTAATTTAGATTAA
1 ATTTTAATTTAGATTAA
1022380 ATTTTAATT
1 ATTTTAATT
1022389 CGTGTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 10 0.45
18 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (17 bp):
ATTTTAATTTAGATTAA
Found at i:1025238 original size:15 final size:16
Alignment explanation
Indices: 1025218--1025251 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1025208 ATTTTAGTTG
1025218 AACCGAAA-TAACCCA
1 AACCGAAAGTAACCCA
1025233 AACCGAAAGTAACCCA
1 AACCGAAAGTAACCCA
1025249 AAC
1 AAC
1025252 TGAATGCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.53, C:0.32, G:0.09, T:0.06
Consensus pattern (16 bp):
AACCGAAAGTAACCCA
Found at i:1026051 original size:31 final size:32
Alignment explanation
Indices: 1025991--1026138 Score: 210
Period size: 31 Copynumber: 4.7 Consensus size: 32
1025981 AGGTTGTTCA
*
1025991 ATCTGATATTGACCCGACCTGAAAATCAATCG
1 ATCTGATATTGACCCGACCCGAAAATCAATCG
* *
1026023 ATCTGATATTGATCCGACACG-AAATCAATCG
1 ATCTGATATTGACCCGACCCGAAAATCAATCG
* *
1026054 ATATGATATTGACCCGACCCG-AAATCAATCA
1 ATCTGATATTGACCCGACCCGAAAATCAATCG
* * *
1026085 ATCTGGTATTGACACGACCCGAAAATCAACCG
1 ATCTGATATTGACCCGACCCGAAAATCAATCG
1026117 ATCTGATATTGACCCGACCCGA
1 ATCTGATATTGACCCGACCCGA
1026139 TACCCAACCC
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 55 0.54
32 46 0.46
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (32 bp):
ATCTGATATTGACCCGACCCGAAAATCAATCG
Found at i:1026064 original size:63 final size:63
Alignment explanation
Indices: 1025994--1026138 Score: 204
Period size: 63 Copynumber: 2.3 Consensus size: 63
1025984 TTGTTCAATC
* * *
1025994 TGATATTGACCCGACCTGAAAATCAATCGATCTGATATTGATC-CGACACG-AAATCAATCGATA
1 TGATATTGACCCGACCCG-AAATCAATCAATCTGATATTGA-CACGACACGAAAATCAACCGATA
* * *
1026057 TGATATTGACCCGACCCGAAATCAATCAATCTGGTATTGACACGACCCGAAAATCAACCGATC
1 TGATATTGACCCGACCCGAAATCAATCAATCTGATATTGACACGACACGAAAATCAACCGATA
1026120 TGATATTGACCCGACCCGA
1 TGATATTGACCCGACCCGA
1026139 TACCCAACCC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
61 1 0.01
62 26 0.35
63 47 0.64
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (63 bp):
TGATATTGACCCGACCCGAAATCAATCAATCTGATATTGACACGACACGAAAATCAACCGATA
Found at i:1027243 original size:18 final size:19
Alignment explanation
Indices: 1027207--1027243 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1027197 TATGTACAGT
1027207 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
1027227 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
1027244 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:1038273 original size:33 final size:34
Alignment explanation
Indices: 1038233--1038301 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1038223 AGATAAAAAT
*
1038233 AAATATCAAT-AAAAATATGAAGAAAATATTTAA
1 AAATATCAATAAAAAATACGAAGAAAATATTTAA
1038266 AAATATCAATAAAAAATACGAAGAAAATATTTAA
1 AAATATCAATAAAAAATACGAAGAAAATATTTAA
1038300 AA
1 AA
1038302 TTATATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.29
34 24 0.71
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (34 bp):
AAATATCAATAAAAAATACGAAGAAAATATTTAA
Found at i:1039527 original size:24 final size:23
Alignment explanation
Indices: 1039494--1039541 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1039484 AGTCATAGGG
*
1039494 AACATGCCACAAAAGCATTAAAAA
1 AACATACCACAAAAGCA-TAAAAA
*
1039518 AACATACCACAAGAGCATAAAAA
1 AACATACCACAAAAGCATAAAAA
1039541 A
1 A
1039542 TGTGTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.60, C:0.21, G:0.08, T:0.10
Consensus pattern (23 bp):
AACATACCACAAAAGCATAAAAA
Found at i:1040486 original size:110 final size:110
Alignment explanation
Indices: 1040347--1040566 Score: 386
Period size: 110 Copynumber: 2.0 Consensus size: 110
1040337 ACAATTAGAA
*
1040347 TTATGTTAGTTACTAGTAAGATATGTGGTAGTTCTGTTATACGACAGTCTAATTTAAGACTAAAG
1 TTATATTAGTTACTAGTAAGATATGTGGTAGTTCTGTTATACGACAGTCTAATTTAAGACTAAAG
**
1040412 AAAGGTGCAACAGAAAATGTTAAACTCTTTTTAACATTTCCAGTT
66 AAAGGCACAACAGAAAATGTTAAACTCTTTTTAACATTTCCAGTT
* * *
1040457 TTATATTAGTTATTAGTAAGATATGTGGTAGTTCTGTTATACGGCAGTCTAATTTAAGACTAAGG
1 TTATATTAGTTACTAGTAAGATATGTGGTAGTTCTGTTATACGACAGTCTAATTTAAGACTAAAG
1040522 AAAGGCACAACAGAAAATGTTAAACTCTTTTTAACATTTCCAGTT
66 AAAGGCACAACAGAAAATGTTAAACTCTTTTTAACATTTCCAGTT
1040567 GAGTGAAACC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 104 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (110 bp):
TTATATTAGTTACTAGTAAGATATGTGGTAGTTCTGTTATACGACAGTCTAATTTAAGACTAAAG
AAAGGCACAACAGAAAATGTTAAACTCTTTTTAACATTTCCAGTT
Found at i:1041211 original size:6 final size:6
Alignment explanation
Indices: 1041200--1041228 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1041190 AACTCCATAG
1041200 ATGCAC ATGCAC ATGCAC ATGCAC ATGCA
1 ATGCAC ATGCAC ATGCAC ATGCAC ATGCA
1041229 TTGTCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGCAC
Found at i:1068105 original size:20 final size:20
Alignment explanation
Indices: 1068080--1068130 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
1068070 ATCATATTCC
1068080 CTGATAATCTTTTATTTTCA
1 CTGATAATCTTTTATTTTCA
1068100 CTGATAATCTTTTATTTTCA
1 CTGATAATCTTTTATTTTCA
1068120 CT-AGTAATCTT
1 CTGA-TAATCTT
1068131 ATACTCCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (20 bp):
CTGATAATCTTTTATTTTCA
Found at i:1068159 original size:23 final size:23
Alignment explanation
Indices: 1068129--1068174 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1068119 ACTAGTAATC
1068129 TTATACTCCGTAAACCAAATACA
1 TTATACTCCGTAAACCAAATACA
1068152 TTATACTCCGTAAACCAAATACA
1 TTATACTCCGTAAACCAAATACA
1068175 CCCTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.26
Consensus pattern (23 bp):
TTATACTCCGTAAACCAAATACA
Found at i:1070437 original size:23 final size:24
Alignment explanation
Indices: 1070394--1070438 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1070384 ATAAAAATTT
*
1070394 AAAAGATAAAATAAATTTTTAATA
1 AAAAGATAAAATAAATATTTAATA
*
1070418 AAAATATAAAAT-AATATTTAA
1 AAAAGATAAAATAAATATTTAA
1070439 AGATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAGATAAAATAAATATTTAATA
Found at i:1072312 original size:36 final size:36
Alignment explanation
Indices: 1072272--1072344 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1072262 GTAAATTATT
1072272 GTATAGAATTGAATTGAAAAGAAGAAGGAATAGAAG
1 GTATAGAATTGAATTGAAAAGAAGAAGGAATAGAAG
1072308 GTATAGAATTGAATTGAAAAGAAGAAGGAATAGAAG
1 GTATAGAATTGAATTGAAAAGAAGAAGGAATAGAAG
1072344 G
1 G
1072345 GCAAAGAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.52, C:0.00, G:0.29, T:0.19
Consensus pattern (36 bp):
GTATAGAATTGAATTGAAAAGAAGAAGGAATAGAAG
Found at i:1073064 original size:65 final size:63
Alignment explanation
Indices: 1072947--1073108 Score: 161
Period size: 65 Copynumber: 2.5 Consensus size: 63
1072937 TTGTTGAAGG
* * * *
1072947 TGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATGCATCGAAT-GCCATTAA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAC-CATTTAAAATAAATACATCGAATAG-CATTAA
* * *
1073011 TGCATCGATGCATAAGGAGTGGCATCGATGCACCTTCTTAAAATACAA-ACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGT-GCATCGATGCACCAT-TTAAAATA-AATACATCGAATAGCATTA
1073075 A
63 A
*
1073076 TGCA-CTGATGCAT-GGGTAGTGCATCGATGCACC
1 TGCATC-GATGCATAAGG-AGTGCATCGATGCACC
1073109 CGTCAAGGGA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
64 36 0.43
65 45 0.54
66 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACCATTTAAAATAAATACATCGAATAGCATTAA
Found at i:1073675 original size:22 final size:22
Alignment explanation
Indices: 1073647--1073742 Score: 146
Period size: 22 Copynumber: 4.5 Consensus size: 22
1073637 GGATATATTA
1073647 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
1073669 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
1073691 GTCTTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
1073713 GTCCTTCAGGAC--AT--AGTG
1 GTCCTTCGGGACGTATCCAGTG
1073731 GTCCTTCGGGAC
1 GTCCTTCGGGAC
1073743 AAATACTGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.21
20 2 0.03
22 53 0.76
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:1073732 original size:18 final size:18
Alignment explanation
Indices: 1073709--1073743 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1073699 GGACGTATCC
1073709 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
1073727 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
1073744 AATACTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:1080158 original size:12 final size:12
Alignment explanation
Indices: 1080141--1080176 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1080131 TATCATGTTT
*
1080141 TCATATAACATG
1 TCATATCACATG
*
1080153 TCATATCACATA
1 TCATATCACATG
1080165 TCATATCACATG
1 TCATATCACATG
1080177 AACATATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1086849 original size:12 final size:12
Alignment explanation
Indices: 1086832--1086867 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1086822 TATCATGTTT
*
1086832 TCATATAACATG
1 TCATATCACATG
*
1086844 TCATATCACATA
1 TCATATCACATG
1086856 TCATATCACATG
1 TCATATCACATG
1086868 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1087243 original size:64 final size:63
Alignment explanation
Indices: 1087170--1087326 Score: 190
Period size: 64 Copynumber: 2.5 Consensus size: 63
1087160 TAATGAAGGT
* * **
1087170 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGCATTCGATG-TTTCATTATTAATGGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATT-TTAA-AAG
* * ** *
1087234 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATTTTAAAAG
*
1087297 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTAATGCATCGAT
1087327 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 2 0.02
64 73 0.90
65 6 0.07
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATTTTAAAAG
Found at i:1089225 original size:18 final size:18
Alignment explanation
Indices: 1089202--1089237 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1089192 GGGACGTATC
1089202 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
*
1089220 TAGTGGTCCTTTGGGACA
1 TAGTGGTCCTTCGGGACA
1089238 AATACTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:1090862 original size:22 final size:22
Alignment explanation
Indices: 1090813--1090891 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
1090803 TTCTGGGCAA
*
1090813 GGGGAATCGGTACCCATTCAA-
1 GGGGAATCGATACCCATTCAAT
*
1090834 -GGGAATCGGTACCCATTCAAT
1 GGGGAATCGATACCCATTCAAT
1090855 GGGGAATCGATACCCATTCAAT
1 GGGGAATCGATACCCATTCAAT
1090877 GGGGAATCGATACCC
1 GGGGAATCGATACCC
1090892 CCCTCAAACG
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
20 20 0.36
22 35 0.64
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGGAATCGATACCCATTCAAT
Found at i:1090971 original size:23 final size:22
Alignment explanation
Indices: 1090927--1090971 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1090917 AATCTCATAG
*
1090927 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
1090949 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
1090972 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:1091429 original size:19 final size:20
Alignment explanation
Indices: 1091394--1091438 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
1091384 ATAAGTCGAG
*
1091394 AGATGTAGGGAAATAGACAT
1 AGATGTAGGGAAATAGAAAT
1091414 AGATGTAGGG-AATAGAAAT
1 AGATGTAGGGAAATAGAAAT
1091433 AGATGT
1 AGATGT
1091439 TTATAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.22
Consensus pattern (20 bp):
AGATGTAGGGAAATAGAAAT
Found at i:1092378 original size:23 final size:23
Alignment explanation
Indices: 1092316--1092378 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
1092306 GACATTATTA
* *
1092316 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
* * *
1092339 CGGAAC-TCCGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
1092361 TGGCACTTCAGTGCAATT
1 TGGCACTTCAGTGCAATT
1092379 ATAGCTGTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTCTACG
Found at i:1093262 original size:2 final size:2
Alignment explanation
Indices: 1093255--1093309 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1093245 ACTCTAAAAT
1093255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1093297 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1093310 GCACCATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1095095 original size:20 final size:20
Alignment explanation
Indices: 1095059--1095096 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1095049 TTATGTAAAT
*
1095059 TTTTTATAATCAAATAATTA
1 TTTTTATAATAAAATAATTA
1095079 TTTTTATAA-AAATATAAT
1 TTTTTATAATAAA-ATAAT
1095097 AAAAAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTTATAATAAAATAATTA
Found at i:1096439 original size:19 final size:19
Alignment explanation
Indices: 1096415--1096455 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1096405 TAGGTCTCCA
*
1096415 GGAGTACACGGCGATCTAT
1 GGAGTACACGGCGACCTAT
**
1096434 GGAGTACTTGGCGACCTAT
1 GGAGTACACGGCGACCTAT
1096453 GGA
1 GGA
1096456 ACTGTAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (19 bp):
GGAGTACACGGCGACCTAT
Found at i:1103675 original size:33 final size:34
Alignment explanation
Indices: 1103629--1103694 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
1103619 CACATGTTCA
1103629 AAGTTAGGCCACCAACCAAGATGAAATTTCCAAT
1 AAGTTAGGCCACCAACCAAGATGAAATTTCCAAT
1103663 AAGTT-GGCCACCAACCAAGATGAAATTTCCAA
1 AAGTTAGGCCACCAACCAAGATGAAATTTCCAA
1103695 CTTGTCAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (34 bp):
AAGTTAGGCCACCAACCAAGATGAAATTTCCAAT
Found at i:1110900 original size:30 final size:30
Alignment explanation
Indices: 1110829--1110888 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1110819 ACAATTTAAG
1110829 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
1110859 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
1110889 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:1111094 original size:21 final size:21
Alignment explanation
Indices: 1111068--1111143 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
1111058 ATGCAATTAG
1111068 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
1111089 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
1111110 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
1111130 TGCATCCATGCATC
1 TGCATCGATGCATC
1111144 AAGTCTGCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:1112473 original size:21 final size:19
Alignment explanation
Indices: 1112431--1112479 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1112421 AACGATTTTC
*
1112431 TTTTGAAAACAAAAATAGAT
1 TTTTGAAAACAAAAATA-AA
* *
1112451 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAAT-AAA
1112471 TTTTGAAAA
1 TTTTGAAAA
1112480 AGATTTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (19 bp):
TTTTGAAAACAAAAATAAA
Found at i:1113651 original size:21 final size:21
Alignment explanation
Indices: 1113625--1113664 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1113615 CAACAATTGG
1113625 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1113646 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1113665 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1113845 original size:30 final size:30
Alignment explanation
Indices: 1113774--1113833 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1113764 ACAATTTAAG
1113774 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
1113804 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
1113834 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Done.