Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:2204232 original size:29 final size:29
Alignment explanation
Indices: 2204199--2204257 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2204189 GTGATATCGA
*
2204199 TTTTAATGTTAATTATCGATTTTCAATTC
1 TTTTAATGTTAATTATCGACTTTCAATTC
* * *
2204228 TTTTAATGTTAGTTGTCGACTTTCGATTC
1 TTTTAATGTTAATTATCGACTTTCAATTC
2204257 T
1 T
2204258 CTTCTCTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (29 bp):
TTTTAATGTTAATTATCGACTTTCAATTC
Found at i:2211322 original size:18 final size:19
Alignment explanation
Indices: 2211291--2211326 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2211281 TTTAAAAATT
2211291 AAAATAATATATTTTAGTA
1 AAAATAATATATTTTAGTA
*
2211310 AAAATATTA-ATTTTAGT
1 AAAATAATATATTTTAGT
2211327 TCCATATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
AAAATAATATATTTTAGTA
Found at i:2211719 original size:148 final size:147
Alignment explanation
Indices: 2211544--2211839 Score: 583
Period size: 148 Copynumber: 2.0 Consensus size: 147
2211534 CAATATAAAC
2211544 AACTTTTATATGTACAATTGAATTAAAATTAAAATCTTATATAAATTTGACCCAAAAAATATACT
1 AACTTTTATATGTACAATTGAATTAAAATTAAAATCTTATATAAATTTGACCCAAAAAATATACT
2211609 GAATTACAAATTAAAGATCATATACCGAATTACAAATTTGACCAAAAATACGTCACCGGGCTGCG
66 GAATTACAAATTAAAGATCATATACCGAATTACAAATTTGACCAAAAATACGTCACC-GGCTGCG
2211674 GAAAAACACCGTATGTCA
130 GAAAAACACCGTATGTCA
2211692 AACTTTTATATGTACAATTGAATTAAAATTAAAATCTTATATAAATTTGACCCAAAAAATATACT
1 AACTTTTATATGTACAATTGAATTAAAATTAAAATCTTATATAAATTTGACCCAAAAAATATACT
2211757 GAATTACAAATTAAAGATCATATACCGAATTACAAATTTGACCAAAAATACGTCACCGGCTGCGG
66 GAATTACAAATTAAAGATCATATACCGAATTACAAATTTGACCAAAAATACGTCACCGGCTGCGG
2211822 AAAAACACCGTATGTCA
131 AAAAACACCGTATGTCA
2211839 A
1 A
2211840 TAAAGATCCA
Statistics
Matches: 148, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 26 0.18
148 122 0.82
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (147 bp):
AACTTTTATATGTACAATTGAATTAAAATTAAAATCTTATATAAATTTGACCCAAAAAATATACT
GAATTACAAATTAAAGATCATATACCGAATTACAAATTTGACCAAAAATACGTCACCGGCTGCGG
AAAAACACCGTATGTCA
Found at i:2215014 original size:4 final size:4
Alignment explanation
Indices: 2215005--2215039 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2214995 GGTCCTTTTT
2215005 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2215040 TACAAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2221140 original size:16 final size:16
Alignment explanation
Indices: 2221121--2221154 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2221111 TGAAATCTAA
*
2221121 ATTTTTTTTATTAATT
1 ATTTATTTTATTAATT
*
2221137 ATTTATTTTATTGATT
1 ATTTATTTTATTAATT
2221153 AT
1 AT
2221155 ATTAACTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTTATTTTATTAATT
Found at i:2221283 original size:2 final size:2
Alignment explanation
Indices: 2221276--2221317 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2221266 AAGCTTTTTA
2221276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2221318 TATGAGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2226114 original size:36 final size:34
Alignment explanation
Indices: 2226066--2226174 Score: 103
Period size: 36 Copynumber: 3.1 Consensus size: 34
2226056 AAACCCCTCG
*
2226066 CAATGTAATTTTTCGATTACAACCGAAAATACTA
1 CAATATAATTTTTCGATTACAACCGAAAATACTA
* *** *
2226100 CAAGTATAACTTTTTCGATATA-AACCCTAAACCCCTCG
1 CAA-TATAA-TTTTTCGAT-TACAA-CCGAAAATACT-A
*
2226138 CAATGTAATTTTTCGATTACAACCGAAAATACTA
1 CAATATAATTTTTCGATTACAACCGAAAATACTA
2226172 CAA
1 CAA
2226175 ATTTATATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
34 6 0.11
35 13 0.23
36 22 0.39
37 13 0.23
38 3 0.05
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.30
Consensus pattern (34 bp):
CAATATAATTTTTCGATTACAACCGAAAATACTA
Found at i:2226118 original size:72 final size:72
Alignment explanation
Indices: 2226031--2226174 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
2226021 TTATAAATTT
2226031 GTATAACTTTTTCGATATAAACCCTAAACCCCTCGCAATGTAATTTTTCGATTACAACCGAAAAT
1 GTATAACTTTTTCGATATAAACCCTAAACCCCTCGCAATGTAATTTTTCGATTACAACCGAAAAT
2226096 ACTACAA
66 ACTACAA
2226103 GTATAACTTTTTCGATATAAACCCTAAACCCCTCGCAATGTAATTTTTCGATTACAACCGAAAAT
1 GTATAACTTTTTCGATATAAACCCTAAACCCCTCGCAATGTAATTTTTCGATTACAACCGAAAAT
2226168 ACTACAA
66 ACTACAA
2226175 ATTTATATAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.31
Consensus pattern (72 bp):
GTATAACTTTTTCGATATAAACCCTAAACCCCTCGCAATGTAATTTTTCGATTACAACCGAAAAT
ACTACAA
Found at i:2231628 original size:29 final size:29
Alignment explanation
Indices: 2231596--2231654 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2231586 TCACCTTTTA
* * *
2231596 AATTAAAATTCAAGTCAAATTTATTTAAC
1 AATTAAAATTCAAATCAAATTAACTTAAC
*
2231625 AATTAAACTTCAAATCAAATTAACTTAAC
1 AATTAAAATTCAAATCAAATTAACTTAAC
2231654 A
1 A
2231655 CAATTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.34
Consensus pattern (29 bp):
AATTAAAATTCAAATCAAATTAACTTAAC
Found at i:2234987 original size:32 final size:34
Alignment explanation
Indices: 2234932--2234996 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 34
2234922 TTTATAAATA
*
2234932 TTTTTTTTATCAAAGTAGATATTTGAAGTATTTG
1 TTTTTTTTATCAAAGTAGATATTTAAAGTATTTG
* * *
2234966 TTTTTTTT-TCATA-TAGGTATTTAAATTATTT
1 TTTTTTTTATCAAAGTAGATATTTAAAGTATTT
2234997 TGAATCAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 15 0.56
33 4 0.15
34 8 0.30
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (34 bp):
TTTTTTTTATCAAAGTAGATATTTAAAGTATTTG
Found at i:2235429 original size:29 final size:29
Alignment explanation
Indices: 2235397--2235455 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2235387 TCACCTTTTA
* * *
2235397 AATTAAAATTCAAGTCAAATTTATTTAAC
1 AATTAAAATTCAAATCAAATTAACTTAAC
*
2235426 AATTAAACTTCAAATCAAATTAACTTAAC
1 AATTAAAATTCAAATCAAATTAACTTAAC
2235455 A
1 A
2235456 CAATTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.34
Consensus pattern (29 bp):
AATTAAAATTCAAATCAAATTAACTTAAC
Found at i:2238804 original size:32 final size:34
Alignment explanation
Indices: 2238749--2238813 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 34
2238739 TTTATAAATA
*
2238749 TTTTTTTTATCAAAGTAGATATTTGAAGTATTTG
1 TTTTTTTTATCAAAGTAGATATTTAAAGTATTTG
* * *
2238783 TTTTTTTT-TCATA-TAGGTATTTAAATTATTT
1 TTTTTTTTATCAAAGTAGATATTTAAAGTATTT
2238814 TGAATCAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 15 0.56
33 4 0.15
34 8 0.30
ACGTcount: A:0.28, C:0.03, G:0.11, T:0.58
Consensus pattern (34 bp):
TTTTTTTTATCAAAGTAGATATTTAAAGTATTTG
Found at i:2239281 original size:29 final size:30
Alignment explanation
Indices: 2239223--2239299 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
2239213 CTCACCCTTT
* * * *
2239223 TAAATTAAAATTCAAGTCAAATTTATTTAA
1 TAAATTAAATTTCAAATCAAATTAACTTAA
2239253 -AAATTAAATTTCAAATCAAATTAACTTAA
1 TAAATTAAATTTCAAATCAAATTAACTTAA
* *
2239282 TACATTTAAATTTAAAAT
1 TA-AATTAAATTTCAAAT
2239300 GAATATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 25 0.64
30 1 0.03
31 13 0.33
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (30 bp):
TAAATTAAATTTCAAATCAAATTAACTTAA
Found at i:2239427 original size:17 final size:17
Alignment explanation
Indices: 2239405--2239438 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2239395 ACGAATTGAA
*
2239405 TGGATTTGACTCGAGTT
1 TGGATTTAACTCGAGTT
*
2239422 TGGATTTAACTTGAGTT
1 TGGATTTAACTCGAGTT
2239439 CGTAATGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (17 bp):
TGGATTTAACTCGAGTT
Found at i:2240482 original size:9 final size:9
Alignment explanation
Indices: 2240468--2240493 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2240458 AAATAGTACA
2240468 ATAAATAAT
1 ATAAATAAT
2240477 ATAAATAAT
1 ATAAATAAT
2240486 ATAAATAA
1 ATAAATAA
2240494 AAATTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAAATAAT
Found at i:2241378 original size:7 final size:7
Alignment explanation
Indices: 2241366--2241400 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
2241356 GAATTAACAA
2241366 AAATATT
1 AAATATT
2241373 AAATATT
1 AAATATT
2241380 AAATATT
1 AAATATT
2241387 ATATATATT
1 A-A-ATATT
2241396 AAATA
1 AAATA
2241401 CATATGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.69
8 2 0.08
9 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATATT
Found at i:2241396 original size:16 final size:14
Alignment explanation
Indices: 2241366--2241400 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2241356 GAATTAACAA
2241366 AAATATTAAATATT
1 AAATATTAAATATT
2241380 AAATATTATATATATT
1 AAATATTA-A-ATATT
2241396 AAATA
1 AAATA
2241401 CATATGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 1 0.05
16 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATTAAATATT
Found at i:2253177 original size:2 final size:2
Alignment explanation
Indices: 2253172--2253233 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
2253162 CCCCCCCCCC
* * * *
2253172 CT CT CT CT CT CT CT CT CT CT CC CT CT TT CT CT CC CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2253214 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
2253234 ATCTATATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2253242 original size:2 final size:2
Alignment explanation
Indices: 2253237--2253263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2253227 TCTCTCTATC
2253237 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
2253264 CGTGCTCAGT
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:2253621 original size:38 final size:39
Alignment explanation
Indices: 2253566--2253642 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
2253556 TTTAGTTGAT
2253566 TCTTTTTAAAAGCTGAGGGTTTAATTGA-TTTTTTATAA
1 TCTTTTTAAAAGCTGAGGGTTTAATTGATTTTTTTATAA
** *
2253604 TCTTTTTAAAATTTGAGGGTTTCATTGATTTTTTTATAA
1 TCTTTTTAAAAGCTGAGGGTTTAATTGATTTTTTTATAA
2253643 AGTTTGATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.53
Consensus pattern (39 bp):
TCTTTTTAAAAGCTGAGGGTTTAATTGATTTTTTTATAA
Found at i:2253714 original size:16 final size:15
Alignment explanation
Indices: 2253686--2253719 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2253676 AATTATTTAA
*
2253686 ATTTAAATTTAAAAT
1 ATTTAAATATAAAAT
2253701 ATTTAAAATATAAAAT
1 ATTT-AAATATAAAAT
2253717 ATT
1 ATT
2253720 ATTAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTAAATATAAAAT
Found at i:2253724 original size:27 final size:28
Alignment explanation
Indices: 2253694--2253762 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 28
2253684 AAATTTAAAT
2253694 TTAAAATATTTAAAATATAAAAT-A-TTA
1 TTAAAATATTTAAAATA-AAAATAATTTA
* *
2253721 TTAAAGTATTCAAAATAAAAATAATTTTTA
1 TTAAAATATTTAAAATAAAAATAA--TTTA
2253751 TTAAAATATTTA
1 TTAAAATATTTA
2253763 TTTTTTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.15
27 16 0.47
30 13 0.38
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
TTAAAATATTTAAAATAAAAATAATTTA
Found at i:2253805 original size:25 final size:25
Alignment explanation
Indices: 2253759--2253819 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
2253749 TATTAAAATA
* * *
2253759 TTTATTTTTTAATATTCTAAT-ATT
1 TTTATATTTTAAAATTCAAATAATT
2253783 TTTATATTTTAAAATTCAAAATAATT
1 TTTATATTTTAAAATTC-AAATAATT
*
2253809 TCT-TATTTTAA
1 TTTATATTTTAA
2253820 TTTTTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 15 0.48
25 11 0.35
26 5 0.16
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTATATTTTAAAATTCAAATAATT
Found at i:2254011 original size:27 final size:29
Alignment explanation
Indices: 2253980--2254045 Score: 109
Period size: 28 Copynumber: 2.3 Consensus size: 29
2253970 CCATTGGTCG
2253980 AAGGATTACAATAA-TTTTTTCTCAGTTT
1 AAGGATTACAATAATTTTTTTCTCAGTTT
2254008 -AGGATTACAATAATTTTTTTCTCAGTTT
1 AAGGATTACAATAATTTTTTTCTCAGTTT
2254036 AAAGGATTAC
1 -AAGGATTAC
2254046 CATTAACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 13 0.37
28 14 0.40
30 8 0.23
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (29 bp):
AAGGATTACAATAATTTTTTTCTCAGTTT
Found at i:2266623 original size:2 final size:2
Alignment explanation
Indices: 2266612--2266680 Score: 115
Period size: 2 Copynumber: 35.0 Consensus size: 2
2266602 AACCTTCAAC
2266612 TA TA -A 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
2266653 TA TA TCA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
2266681 AATTGAAATC
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 60 0.94
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2266697 original size:32 final size:32
Alignment explanation
Indices: 2266632--2266716 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
2266622 ATATATATAT
* * *
2266632 ATATATATATATATATATATATATATCATATA
1 ATATATATATATATATAAATATAAATCAAATA
2266664 ATATATATATATATATAAAT-TGAAATCAAATA
1 ATATATATATATATATAAATAT-AAATCAAATA
2266696 ATATCATA-ATAT-TATAAATAT
1 ATAT-ATATATATATATAAATAT
2266717 TTAAAATTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.17
32 36 0.77
33 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (32 bp):
ATATATATATATATATAAATATAAATCAAATA
Found at i:2269587 original size:24 final size:22
Alignment explanation
Indices: 2269550--2269594 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
2269540 TTTGTATGAC
*
2269550 ACATTTTTCTTGCTTTTGTGGT
1 ACATTTTTCTTGCTCTTGTGGT
2269572 ACATTTCTTCTATGCTCTTGTGG
1 ACATTT-TTCT-TGCTCTTGTGG
2269595 CATGTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 4 0.20
24 10 0.50
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (22 bp):
ACATTTTTCTTGCTCTTGTGGT
Found at i:2271547 original size:16 final size:15
Alignment explanation
Indices: 2271526--2271558 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2271516 TTATTACCCT
2271526 ATAATAATAATTAAAA
1 ATAATAATAA-TAAAA
2271542 ATAATAATAATAAAA
1 ATAATAATAATAAAA
2271557 AT
1 AT
2271559 TTATATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAATAATAATAAAA
Found at i:2271921 original size:28 final size:28
Alignment explanation
Indices: 2271881--2271936 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2271871 AAAATATAAT
*
2271881 ATACTTTAAATACATATTTTAACCAAAA
1 ATACTTTAAATACATATTTCAACCAAAA
*
2271909 ATACTTTAAATACATATTTCGACCAAAA
1 ATACTTTAAATACATATTTCAACCAAAA
2271937 TGATAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (28 bp):
ATACTTTAAATACATATTTCAACCAAAA
Found at i:2273813 original size:63 final size:63
Alignment explanation
Indices: 2273714--2273849 Score: 186
Period size: 63 Copynumber: 2.2 Consensus size: 63
2273704 TTTTATTGAG
* * *
2273714 TTTAACGAGCAATCAGTCGAGTTGAGTATCAAAATTTTTTAATGAGCACGAGTCGAGCACAAT
1 TTTAACGAGCAATCAGTCGAGTTGAGCATCAAAATTTTTTAACGAGCACGAGTCGAACACAAT
* * *
2273777 TTTAACGAGTAA-CGAGTCGAGTTGAGCAGT-AAAATTTTTTAGCGAGCATGAGTCGAACACAAT
1 TTTAACGAGCAATC-AGTCGAGTTGAGCA-TCAAAATTTTTTAACGAGCACGAGTCGAACACAAT
2273840 TTTAACGAGC
1 TTTAACGAGC
2273850 TTAACGAACA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
62 1 0.02
63 62 0.97
64 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (63 bp):
TTTAACGAGCAATCAGTCGAGTTGAGCATCAAAATTTTTTAACGAGCACGAGTCGAACACAAT
Found at i:2276915 original size:8 final size:8
Alignment explanation
Indices: 2276902--2276926 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2276892 AAGGGTAAAA
2276902 TGGTCATT
1 TGGTCATT
2276910 TGGTCATT
1 TGGTCATT
2276918 TGGTCATT
1 TGGTCATT
2276926 T
1 T
2276927 AAGGAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (8 bp):
TGGTCATT
Found at i:2278642 original size:103 final size:103
Alignment explanation
Indices: 2278417--2278634 Score: 375
Period size: 103 Copynumber: 2.1 Consensus size: 103
2278407 GTCGAGGGTC
*
2278417 TATGTGATCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTCGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTCGTGAGACACATAC
* *
2278482 TTGATCCTTGGTATATTTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
* *
2278520 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTCGTGAGACACATAC
2278585 TTGATTCC-TAGTATATGTATATGATTCTTAAGGAATGA
66 TTGA-TCCTTAGTATATGTATATGATTCTTAAGGAATGA
2278623 TATGTGGTCCTT
1 TATGTGGTCCTT
2278635 ATGGACATTA
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 105 0.97
104 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTCGTGAGACACATAC
TTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:2278717 original size:23 final size:23
Alignment explanation
Indices: 2278641--2278718 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
2278631 CCTTATGGAC
*
2278641 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2278665 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2278688 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2278711 ATTATATG
1 ATTATATG
2278719 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2287650 original size:31 final size:31
Alignment explanation
Indices: 2287612--2287670 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2287602 CATCCAATCT
2287612 AACAGAGGGTAAGAGAAGAATACCGTAGTCC
1 AACAGAGGGTAAGAGAAGAATACCGTAGTCC
**
2287643 AACAGAGGGTGCGAGAAGAATACCGTAG
1 AACAGAGGGTAAGAGAAGAATACCGTAG
2287671 CTTGTTGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.32, T:0.12
Consensus pattern (31 bp):
AACAGAGGGTAAGAGAAGAATACCGTAGTCC
Found at i:2300118 original size:53 final size:53
Alignment explanation
Indices: 2300056--2300161 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
2300046 GCACTCCTGG
2300056 TTTCCCAAATTTAGCAATGATATTGCAGTTTGCAATAAAGCTTTCAATAATGA
1 TTTCCCAAATTTAGCAATGATATTGCAGTTTGCAATAAAGCTTTCAATAATGA
2300109 TTTCCCAAATTTAGCAATGATATTGCAGTTTGCAATAAAGCTTTCAATAATGA
1 TTTCCCAAATTTAGCAATGATATTGCAGTTTGCAATAAAGCTTTCAATAATGA
2300162 ACAATCACTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (53 bp):
TTTCCCAAATTTAGCAATGATATTGCAGTTTGCAATAAAGCTTTCAATAATGA
Found at i:2300549 original size:22 final size:21
Alignment explanation
Indices: 2300519--2300561 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
2300509 ATATAATGTT
2300519 AAAAAAATGATCGAATTATTC
1 AAAAAAATGATCGAATTATTC
2300540 AAAACAAATGATCGAATTATTC
1 AAAA-AAATGATCGAATTATTC
2300562 TGCAGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAAAATGATCGAATTATTC
Found at i:2303144 original size:37 final size:37
Alignment explanation
Indices: 2303095--2303169 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 37
2303085 ATTAATATGG
2303095 ATGGATTTACATTGAACG-TGCACATCAAAACATATT
1 ATGGATTTACATTGAACGTTGCACATCAAAACATATT
2303131 ATGGATTTTACATTGAACGTTGCACATCAAAACATATT
1 ATGGA-TTTACATTGAACGTTGCACATCAAAACATATT
2303169 A
1 A
2303170 ATGCAATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 5 0.14
37 13 0.35
38 19 0.51
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (37 bp):
ATGGATTTACATTGAACGTTGCACATCAAAACATATT
Found at i:2303180 original size:37 final size:36
Alignment explanation
Indices: 2303102--2303180 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 36
2303092 TGGATGGATT
* *
2303102 TACATTGAACGTGCACATCAAAACATATTATGGATTT
1 TACATTGAACGTGCACATCAAAACATATTATGCA-TA
2303139 TACATTGAACGTTGCACATCAAAACATATTAATGCA-A
1 TACATTGAACG-TGCACATCAAAACATATT-ATGCATA
2303176 TACAT
1 TACAT
2303181 CGAAACACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 16 0.42
38 18 0.47
39 4 0.11
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (36 bp):
TACATTGAACGTGCACATCAAAACATATTATGCATA
Found at i:2304025 original size:20 final size:20
Alignment explanation
Indices: 2303989--2304048 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2303979 AATATTATAT
*
2303989 TTAAAATTAAAT-CAAAATAA
1 TTAAAA-TAAATATAAAATAA
2304009 TTAAAATAAATATAAAAT--
1 TTAAAATAAATATAAAATAA
*
2304027 TT-TAATAATATATAAAATAA
1 TTAAAATAA-ATATAAAATAA
2304047 TT
1 TT
2304049 TATATGATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 5 0.15
20 13 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAATAAATATAAAATAA
Found at i:2304050 original size:20 final size:19
Alignment explanation
Indices: 2304002--2304050 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2303992 AAATTAAATC
*
2304002 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
2304022 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
2304040 AAAATAATTTA
1 AAAATAATTTA
2304051 TATGATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:2304116 original size:22 final size:22
Alignment explanation
Indices: 2304088--2304162 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 22
2304078 ATAATATTAA
2304088 AAAATTAATATTTAATTTATTT
1 AAAATTAATATTTAATTTATTT
*
2304110 AAAATTAATATCTATAATATAATATTA
1 AAAATTAATAT-T-TAAT-T--TATTT
*
2304137 AAAATTAATATTTCATTTATTT
1 AAAATTAATATTTAATTTATTT
2304159 AAAA
1 AAAA
2304163 AATTGATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 19 0.42
23 1 0.02
24 5 0.11
25 4 0.09
26 1 0.02
27 15 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATTAATATTTAATTTATTT
Found at i:2304140 original size:27 final size:26
Alignment explanation
Indices: 2304059--2304147 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 26
2304049 TATATGATAC
2304059 AAAATTAAATATCTTTAATATAATATTAA
1 AAAATT-AATATC-TTAATATAATATT-A
*
2304088 AAAATTAATAT-TTAAT-T--TATTT
1 AAAATTAATATCTTAATATAATATTA
2304110 AAAATTAATATCTATAATATAATATTA
1 AAAATTAATATCT-TAATATAATATTA
2304137 AAAATTAATAT
1 AAAATTAATAT
2304148 TTCATTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
22 11 0.21
23 5 0.09
24 4 0.08
25 2 0.04
26 5 0.09
27 15 0.28
28 5 0.09
29 6 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATTAATATCTTAATATAATATTA
Found at i:2304159 original size:49 final size:51
Alignment explanation
Indices: 2304059--2304162 Score: 176
Period size: 49 Copynumber: 2.1 Consensus size: 51
2304049 TATATGATAC
*
2304059 AAAATTAAATATCTTTAATATAATATTAAAAAATTAATATTTAATTTATTT
1 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT
*
2304110 AAAATT-AATATCTATAATATAATATT-AAAAATTAATATTTCATTTATTT
1 AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT
2304159 AAAA
1 AAAA
2304163 AATTGATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 26 0.51
50 19 0.37
51 6 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (51 bp):
AAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT
Found at i:2304171 original size:24 final size:23
Alignment explanation
Indices: 2304082--2304172 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 23
2304072 TTTAATATAA
*
2304082 TATTAAAAAATTAATATTTAATT
1 TATTTAAAAATTAATATTTAATT
2304105 TATTT-AAAATTAATATCTATAATAT
1 TATTTAAAAATTAATAT-T-TAAT-T
* *
2304130 AATATTAAAAATTAATATTTCATT
1 TAT-TTAAAAATTAATATTTAATT
*
2304154 TATTTAAAAAATTGATATT
1 TATTT-AAAAATTAATATT
2304173 AAAATCAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 11 0.19
23 7 0.12
24 19 0.33
25 6 0.11
26 3 0.05
27 11 0.19
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (23 bp):
TATTTAAAAATTAATATTTAATT
Found at i:2306329 original size:3 final size:3
Alignment explanation
Indices: 2306321--2306352 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2306311 TAAAAAATAT
2306321 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2306353 CTATGACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2307444 original size:19 final size:19
Alignment explanation
Indices: 2307420--2307458 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2307410 TAAACAATAT
2307420 TACGATGTGACTATTACAC
1 TACGATGTGACTATTACAC
* *
2307439 TACGATGTGATTGTTACAC
1 TACGATGTGACTATTACAC
2307458 T
1 T
2307459 GTATTATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (19 bp):
TACGATGTGACTATTACAC
Found at i:2310804 original size:12 final size:13
Alignment explanation
Indices: 2310778--2310810 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2310768 GTTTTTAATA
2310778 AAAATAAATACTT
1 AAAATAAATACTT
2310791 AAAATAAA-ACTT
1 AAAATAAATACTT
2310803 AAATATAA
1 AAA-ATAA
2310811 TTTAGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATAAATACTT
Found at i:2313842 original size:147 final size:146
Alignment explanation
Indices: 2313554--2313835 Score: 406
Period size: 147 Copynumber: 1.9 Consensus size: 146
2313544 AACGAGACGT
* * * * *
2313554 TTTATGAAGTGATAAGGGCTGGTGAGCGAACCAAACTCTTTGGCATGCTACTTCGCTACACAATT
1 TTTATGAAGTGATAAGGACTGGTGAGCGAACCAAACTCTCTGACAGGCTACTTCGCTACACAATC
* * *
2313619 TTGATTATGTCGATAAACAACATTTTACTAAAGAGGGGATCTGACTATACGTGACCACCGACAAA
66 ATGATTATATCGATAAACAACATTTTACTAAAGAGGAGATCTGACTATACGTGACCACCGACAAA
*
2313684 TCAATCAAAATATTTC
131 TCAACCAAAATATTTC
*
2313700 TTTATGAAGTGATAAAGGACTGGTGAGCGAACTAAACTCTCTGACAGGCTACTTCGCTACACAAT
1 TTTATGAAGTGAT-AAGGACTGGTGAGCGAACCAAACTCTCTGACAGGCTACTTCGCTACACAAT
** * * *
2313765 CATGATTATATCGATAAACATTATTTTAC-CAA-AGGAGATCTGACTATACGTGATCACCTACAA
65 CATGATTATATCGATAAACAACATTTTACTAAAGAGGAGATCTGACTATACGTGACCACCGACAA
2313828 ATCAACCA
130 ATCAACCA
2313836 GAAAATAAAT
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
145 35 0.29
146 15 0.12
147 70 0.58
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (146 bp):
TTTATGAAGTGATAAGGACTGGTGAGCGAACCAAACTCTCTGACAGGCTACTTCGCTACACAATC
ATGATTATATCGATAAACAACATTTTACTAAAGAGGAGATCTGACTATACGTGACCACCGACAAA
TCAACCAAAATATTTC
Found at i:2323707 original size:13 final size:13
Alignment explanation
Indices: 2323689--2323715 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2323679 TCATAACCCG
2323689 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2323702 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2323715 A
1 A
2323716 TCCGTTGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.44, G:0.15, T:0.22
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:2324854 original size:18 final size:18
Alignment explanation
Indices: 2324828--2324862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2324818 TCGAAAGGAC
*
2324828 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2324846 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2324863 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2328596 original size:13 final size:13
Alignment explanation
Indices: 2328578--2328611 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2328568 ACCCGACCCG
2328578 ACCCGACCCGTTT
1 ACCCGACCCGTTT
2328591 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
2328604 ATCCGACC
1 ACCCGACC
2328612 AGTTGACCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.47, G:0.15, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:2328625 original size:7 final size:7
Alignment explanation
Indices: 2328608--2328657 Score: 73
Period size: 7 Copynumber: 6.7 Consensus size: 7
2328598 CCGTTTATCC
2328608 GACCAGTT
1 GACC-GTT
2328616 GACCGTT
1 GACCGTT
2328623 GACCTGTT
1 GACC-GTT
2328631 GACCGTT
1 GACCGTT
2328638 GACCTGTT
1 GACC-GTT
2328646 GACCGTT
1 GACCGTT
2328653 GACCG
1 GACCG
2328658 GCGTTGACCA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
7 22 0.55
8 18 0.45
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
GACCGTT
Found at i:2328631 original size:15 final size:15
Alignment explanation
Indices: 2328608--2328656 Score: 89
Period size: 15 Copynumber: 3.3 Consensus size: 15
2328598 CCGTTTATCC
*
2328608 GACCAGTTGACCGTT
1 GACCTGTTGACCGTT
2328623 GACCTGTTGACCGTT
1 GACCTGTTGACCGTT
2328638 GACCTGTTGACCGTT
1 GACCTGTTGACCGTT
2328653 GACC
1 GACC
2328657 GGCGTTGACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (15 bp):
GACCTGTTGACCGTT
Found at i:2329793 original size:18 final size:18
Alignment explanation
Indices: 2329767--2329801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2329757 TCGAAAGGAC
*
2329767 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2329785 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2329802 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2348083 original size:26 final size:28
Alignment explanation
Indices: 2348054--2348107 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2348044 CAAATTTTTC
2348054 GTTGGT-CT-CCTCTTTTTCTAATCTCT
1 GTTGGTGCTCCCTCTTTTTCTAATCTCT
* *
2348080 GTTGGTGGTCCCTTTTTTTCTAATCTCT
1 GTTGGTGCTCCCTCTTTTTCTAATCTCT
2348108 TTTTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.07, C:0.24, G:0.15, T:0.54
Consensus pattern (28 bp):
GTTGGTGCTCCCTCTTTTTCTAATCTCT
Found at i:2348581 original size:53 final size:53
Alignment explanation
Indices: 2348487--2348740 Score: 348
Period size: 53 Copynumber: 4.8 Consensus size: 53
2348477 TGATAGGTAT
* * **** *
2348487 GCTCCCTCTTG-TTCAGGGATTAAGAAACTTGAACAATCTTCTAAAAATGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGT-AG-AACTCGAACAATCTTCTGCTTACGGGTTC
* * *
2348541 GCTCCCTATTGCTTCAGGGAGTAGAACTCGAACACTCTTCTGTTTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
* *
2348594 GCTCCCTCTTGCTTCAGGGAGTAGAACTAGAATAATCTTCTGCTTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
* *
2348647 GCTCCCTCTTGCTTCAGGGAGTATAACTCGAACAATCTTCTGCTTACGAGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
*
2348700 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCT
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
2348741 AGTGTGATTC
Statistics
Matches: 179, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
53 158 0.88
54 12 0.07
55 9 0.05
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (53 bp):
GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
Found at i:2349262 original size:80 final size:80
Alignment explanation
Indices: 2349129--2349378 Score: 410
Period size: 80 Copynumber: 3.1 Consensus size: 80
2349119 TATTGATGGC
* *
2349129 ACTTACTAACGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
2349194 TATCATGCTCGAAAG
66 TATCATGCTCGAAAG
* * *
2349209 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAATGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
*
2349274 CATCATGCTCGAAAG
66 TATCATGCTCGAAAG
* * * *
2349289 ACTTATTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTATAAATTACCCTAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
2349354 TATCATGCTCGAAAG
66 TATCATGCTCGAAAG
2349369 ACTTACTGAT
1 ACTTACTGAT
2349379 TGCCCTAAGG
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 156 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (80 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
TATCATGCTCGAAAG
Found at i:2349401 original size:42 final size:42
Alignment explanation
Indices: 2349339--2349425 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
2349329 TTATAAATTA
** *
2349339 CCCTAAGGATTTAATTATCATGCTCGAAAGACTTACTGATTG
1 CCCTAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGG
*
2349381 CCCTAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGG
1 CCCTAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGG
2349423 CCC
1 CCC
2349426 GAATGACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (42 bp):
CCCTAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGG
Found at i:2359523 original size:26 final size:28
Alignment explanation
Indices: 2359494--2359547 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2359484 CAAATTTTTC
2359494 GTTGGT-CT-CCTCTTTTTCTAATCTCT
1 GTTGGTGCTCCCTCTTTTTCTAATCTCT
* *
2359520 GTTGGTGGTCCCTTTTTTTCTAATCTCT
1 GTTGGTGCTCCCTCTTTTTCTAATCTCT
2359548 TTTTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.07, C:0.24, G:0.15, T:0.54
Consensus pattern (28 bp):
GTTGGTGCTCCCTCTTTTTCTAATCTCT
Found at i:2360289 original size:30 final size:31
Alignment explanation
Indices: 2360250--2360327 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
2360240 CTTGAACTTA
* * *
2360250 AGATAAAATATTAATTTGAC-CTTAAATTTT
1 AGATAAAATATCAATTTGACTCTGAAAGTTT
* *
2360280 AGTTAAAATATCATTTTGACTCTGAAAGTTT
1 AGATAAAATATCAATTTGACTCTGAAAGTTT
*
2360311 GGATAAAATATCAATTT
1 AGATAAAATATCAATTT
2360328 AGTCATTGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (31 bp):
AGATAAAATATCAATTTGACTCTGAAAGTTT
Found at i:2361143 original size:31 final size:31
Alignment explanation
Indices: 2361108--2361181 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
2361098 AATGATTAAA
2361108 TTAAAATTTAAGAATTAAATTAATAT-TATAT
1 TTAAAATTTAAGAATTAAATTAATATAT-TAT
* * *
2361139 TTAAAACTCAAGGATTAAATTAATATATTAT
1 TTAAAATTTAAGAATTAAATTAATATATTAT
* *
2361170 CTAAATTTTAAG
1 TTAAAATTTAAG
2361182 GGTCAAATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (31 bp):
TTAAAATTTAAGAATTAAATTAATATATTAT
Found at i:2361279 original size:11 final size:11
Alignment explanation
Indices: 2361263--2361295 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2361253 TTATTATTTT
2361263 TAGTGATTAAA
1 TAGTGATTAAA
2361274 TAGTGATTAAA
1 TAGTGATTAAA
*
2361285 TAGTGAATAAA
1 TAGTGATTAAA
2361296 AATGAAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (11 bp):
TAGTGATTAAA
Found at i:2369810 original size:23 final size:21
Alignment explanation
Indices: 2369786--2369827 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2369776 GAAAATATTA
*
2369786 AAAAAATTGATATTTTAGGTAT
1 AAAAAA-TAATATTTTAGGTAT
*
2369808 AAATAATAATATTTTAGGTA
1 AAAAAATAATATTTTAGGTA
2369828 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
AAAAAATAATATTTTAGGTAT
Found at i:2379467 original size:2 final size:2
Alignment explanation
Indices: 2379460--2379489 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2379450 AAGATTATGA
2379460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2379490 TCACTATAAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2410263 original size:33 final size:33
Alignment explanation
Indices: 2410224--2410289 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2410214 CCGATAAAAT
2410224 TATATTTAAATTATACGAGAATTGAAATTTTTA
1 TATATTTAAATTATACGAGAATTGAAATTTTTA
2410257 TATATTTAAATTATACGAGAATTGAAATTTTTA
1 TATATTTAAATTATACGAGAATTGAAATTTTTA
2410290 AAGGATGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (33 bp):
TATATTTAAATTATACGAGAATTGAAATTTTTA
Found at i:2415076 original size:17 final size:17
Alignment explanation
Indices: 2415054--2415088 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2415044 GTTTAAAAAG
*
2415054 AAATTATCTGATTGAAT
1 AAATTAGCTGATTGAAT
2415071 AAATTAGCTGATTGAAT
1 AAATTAGCTGATTGAAT
2415088 A
1 A
2415089 TTGATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (17 bp):
AAATTAGCTGATTGAAT
Found at i:2417760 original size:26 final size:27
Alignment explanation
Indices: 2417710--2417765 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2417700 TATATGAAAG
2417710 AGAAAATTGATTAATTTTTAAAAATAAA
1 AGAAAATT-ATTAATTTTTAAAAATAAA
* *
2417738 AGAAAATT-TTATTTTTTTAAAATAAA
1 AGAAAATTATTAATTTTTAAAAATAAA
2417764 AG
1 AG
2417766 TCTATTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 18 0.69
28 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (27 bp):
AGAAAATTATTAATTTTTAAAAATAAA
Found at i:2417829 original size:16 final size:15
Alignment explanation
Indices: 2417780--2417830 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2417770 TTTAACTTTT
2417780 AAATAAA-AATATTTA
1 AAATAAACAATA-TTA
* *
2417795 AAATATAACTATATAA
1 AAATA-AACAATATTA
2417811 AAATAAACAATTATTA
1 AAATAAACAA-TATTA
2417827 AAAT
1 AAAT
2417831 TATTAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 9 0.31
16 17 0.59
17 3 0.10
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAAACAATATTA
Found at i:2417873 original size:19 final size:18
Alignment explanation
Indices: 2417859--2417902 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2417849 CTATTAAACT
2417859 TTTAAATAGAAATTAAAAA
1 TTTAAA-AGAAATTAAAAA
*
2417878 TTTAAAAGATATTAAAAA
1 TTTAAAAGAAATTAAAAA
*
2417896 TATAAAA
1 TTTAAAA
2417903 TTATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
TTTAAAAGAAATTAAAAA
Found at i:2417893 original size:18 final size:18
Alignment explanation
Indices: 2417831--2417902 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
2417821 TTATTAAAAT
* *
2417831 TATTAAAAATAAAAAATA
1 TATTAAAAATATAAAAGA
** *
2417849 CTATTAAACTTTTAAATAGA
1 -TATTAAAAATATAAA-AGA
* *
2417869 AATTAAAAATTTAAAAGA
1 TATTAAAAATATAAAAGA
2417887 TATTAAAAATATAAAA
1 TATTAAAAATATAAAA
2417903 TTATAAATTA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
18 17 0.40
19 23 0.55
20 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
TATTAAAAATATAAAAGA
Found at i:2424304 original size:2 final size:2
Alignment explanation
Indices: 2424268--2424292 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2424258 TGTTATGTGC
2424268 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2424293 CGCCCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2429043 original size:23 final size:22
Alignment explanation
Indices: 2428977--2429035 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
2428967 AACGACATAA
2428977 AAAACGTGTCATAAAAGCAGAG
1 AAAACGTGTCATAAAAGCAGAG
** *
2428999 AAAAGCGTACCATAAAGGCAGAGG
1 AAAA-CGTGTCATAAAAGCAGA-G
2429023 AAAACGTGTCATA
1 AAAACGTGTCATA
2429036 CATGCAGACT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 4 0.13
23 21 0.70
24 5 0.17
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.14
Consensus pattern (22 bp):
AAAACGTGTCATAAAAGCAGAG
Found at i:2432700 original size:9 final size:9
Alignment explanation
Indices: 2432686--2432720 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2432676 GTCTTTTATA
2432686 TTTATTTTT
1 TTTATTTTT
2432695 TTTATTTTT
1 TTTATTTTT
*
2432704 TTTATTTAT
1 TTTATTTTT
2432713 TTTATTTT
1 TTTATTTT
2432721 ATTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTATTTTT
Found at i:2432709 original size:18 final size:18
Alignment explanation
Indices: 2432686--2432739 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
2432676 GTCTTTTATA
*
2432686 TTTATTTTTTTTATTTTT
1 TTTATTTATTTTATTTTT
2432704 TTTATTTATTTTATTTTAT
1 TTTATTTATTTTATTTT-T
*
2432723 TATTATTAATTGTTATT
1 T-TTATTTATT-TTATT
2432740 ATTAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 16 0.52
19 2 0.06
20 8 0.26
21 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTATTTATTTTATTTTT
Found at i:2432709 original size:22 final size:23
Alignment explanation
Indices: 2432679--2432723 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2432669 TGTCCGGGTC
2432679 TTTTATATTTATTTT-TTTTATT
1 TTTTATATTTATTTTATTTTATT
*
2432701 TTTTTTATTTATTTTATTTTATT
1 TTTTATATTTATTTTATTTTATT
2432724 ATTATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTATATTTATTTTATTTTATT
Found at i:2432726 original size:13 final size:13
Alignment explanation
Indices: 2432681--2432752 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 13
2432671 TCCGGGTCTT
*
2432681 TTATATTTATTTTTT
1 TTAT-TTTA-TTTTA
2432696 TTATTTT-TTTTA
1 TTATTTTATTTTA
2432708 TTTATTTTATTTTA
1 -TTATTTTATTTTA
2432722 TTATTATTAATTGTTA
1 TTATT-TT-ATT-TTA
2432738 TTATTAATTATTTTA
1 TTATT--TTATTTTA
2432753 CATATTACAT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
12 4 0.08
13 12 0.24
14 10 0.20
15 10 0.20
16 11 0.22
17 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:2432885 original size:26 final size:25
Alignment explanation
Indices: 2432832--2432977 Score: 274
Period size: 25 Copynumber: 5.8 Consensus size: 25
2432822 ACCCACCAGA
2432832 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
2432857 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
2432883 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
2432909 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
2432934 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
2432959 TTAGGGTTTCAAACCCTAA
1 TTAGGGTTTCAAACCCTAA
2432978 TCCCCAACTG
Statistics
Matches: 120, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
25 69 0.57
26 51 0.43
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAGT
Found at i:2432893 original size:51 final size:51
Alignment explanation
Indices: 2432832--2432977 Score: 276
Period size: 51 Copynumber: 2.9 Consensus size: 51
2432822 ACCCACCAGA
2432832 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAAATCAGT
2432883 TTAGGGTTTCAAACCCTAAAATCAGTTTAGGGTTTCAAACCCT-AAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGTTTAGGGTTTCAAACCCTAAAATCAGT
2432934 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAA
1 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAA
2432978 TCCCCAACTG
Statistics
Matches: 93, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
50 25 0.27
51 43 0.46
52 25 0.27
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (51 bp):
TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAAATCAGT
Found at i:2436756 original size:21 final size:21
Alignment explanation
Indices: 2436730--2436780 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2436720 AGAAAACGGA
2436730 AGCTCTTCTAACGTCTGCGCG
1 AGCTCTTCTAACGTCTGCGCG
2436751 AGCTCTTCTAACGTCTGCGCG
1 AGCTCTTCTAACGTCTGCGCG
2436772 AGCTCTTCT
1 AGCTCTTCT
2436781 TGGTGCAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.33, G:0.22, T:0.31
Consensus pattern (21 bp):
AGCTCTTCTAACGTCTGCGCG
Found at i:2436906 original size:15 final size:15
Alignment explanation
Indices: 2436886--2436921 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
2436876 TAATAAGGTT
2436886 ATTTATTTTTAAATA
1 ATTTATTTTTAAATA
2436901 ATTTA-TTTTAAATA
1 ATTTATTTTTAAATA
2436915 ATTTATT
1 ATTTATT
2436922 AGTATGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATTTTTAAATA
Found at i:2436940 original size:22 final size:22
Alignment explanation
Indices: 2436924--2436966 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2436914 AATTTATTAG
2436924 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2436946 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2436967 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2436942 original size:32 final size:31
Alignment explanation
Indices: 2436901--2436998 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
2436891 TTTTTAAATA
2436901 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
2436933 ATTTA-TTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
2436955 ATTTATTTTAAATAATTTATTACTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
2436987 ATTTATTTTAAA
1 ATTTATTTTAAA
2436999 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.25
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 26 0.46
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTATATGGATTG
Found at i:2436963 original size:54 final size:54
Alignment explanation
Indices: 2436901--2437244 Score: 249
Period size: 54 Copynumber: 6.4 Consensus size: 54
2436891 TTTTTAAATA
2436901 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
2436955 ATTTATTTTAAATAATTTATTACTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
2437009 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * *
2437053 A-TTACTATGAATTGATTTATTTTAAAATATGGATTGATTTGTTTTAAATAATTTATTAGTATGG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTT-ATTT---TAA---A--A-TATGG
2437117 ATTG
51 ATTG
* * * * *** *
2437121 ATTTATTTT-AA-AA--CA-TAG-ATTGATTTA-TTATTGTAGTTGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
2437169 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
2437223 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
2437245 TTGTAGTTGT
Statistics
Matches: 222, Mismatches: 33, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
43 3 0.01
44 4 0.02
46 1 0.00
47 5 0.02
48 39 0.18
49 4 0.02
50 7 0.03
51 2 0.01
52 3 0.01
53 5 0.02
54 108 0.49
55 10 0.05
56 2 0.01
57 2 0.01
58 8 0.04
59 2 0.01
61 1 0.00
62 1 0.00
64 2 0.01
65 2 0.01
66 1 0.00
67 1 0.00
68 6 0.03
69 3 0.01
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2436992 original size:18 final size:18
Alignment explanation
Indices: 2436969--2437016 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
2436959 ATTTTAAATA
*
2436969 ATTTATTACTATGGATTG
1 ATTTATTAATATGGATTG
2436987 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
2437009 ATTTATTA
1 ATTTATTA
2437017 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:2437047 original size:134 final size:134
Alignment explanation
Indices: 2436901--2437244 Score: 625
Period size: 134 Copynumber: 2.6 Consensus size: 134
2436891 TTTTTAAATA
2436901 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* * *
2436966 ATAATTTATTACTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
66 ATAATTTATTACTATGGATTGATTTATTTTAAAACATAGATTGATTTATTATTGTAGTTGTATAG
2437031 ATTG
131 ATTG
* * *
2437035 ATTTATTTTAAATAATTTATTACTATGAATTGATTTATTTTAAAATATGGATTGATTTGTTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
2437100 ATAATTTATTAGTATGGATTGATTTATTTTAAAACATAGATTGATTTATTATTGTAGTTGTATAG
66 ATAATTTATTACTATGGATTGATTTATTTTAAAACATAGATTGATTTATTATTGTAGTTGTATAG
2437165 ATTG
131 ATTG
2437169 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
2437234 ATAATTTATTA
66 ATAATTTATTA
2437245 TTGTAGTTGT
Statistics
Matches: 200, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 200 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (134 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTACTATGGATTGATTTATTTTAAAACATAGATTGATTTATTATTGTAGTTGTATAG
ATTG
Found at i:2437072 original size:32 final size:31
Alignment explanation
Indices: 2437026--2437132 Score: 115
Period size: 32 Copynumber: 3.7 Consensus size: 31
2437016 ATTGTAGTTG
2437026 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
*
2437057 CTATGAATTGATTTA-TTT---TAA---A--A
1 -TATGGATTGATTTATTTTAAATAATTTATTA
*
2437080 TATGGATTGATTTGTTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
2437111 GTATGGATTGATTTATTTTAAA
1 -TATGGATTGATTTATTTTAAA
2437133 ACATAGATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
22 12 0.20
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 33 0.54
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (31 bp):
TATGGATTGATTTATTTTAAATAATTTATTA
Found at i:2437083 original size:22 final size:22
Alignment explanation
Indices: 2437058--2437100 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2437048 AATTTATTAC
2437058 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
* *
2437080 TATGGATTGATTTGTTTTAAA
1 TATGAATTGATTTATTTTAAA
2437101 TAATTTATTA
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:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2437217 original size:22 final size:22
Alignment explanation
Indices: 2437192--2437234 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2437182 AATTTATTAG
2437192 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2437214 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2437235 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2437316 original size:31 final size:31
Alignment explanation
Indices: 2437259--2437317 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2437249 AGTTGTATGG
* **
2437259 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
2437290 ATTATTTAAATTTCAATATTACAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
2437318 CTTTTTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:2440394 original size:2 final size:2
Alignment explanation
Indices: 2440387--2440424 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2440377 TTTGCACTTG
2440387 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2440425 GCTTTTCCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2443958 original size:4 final size:4
Alignment explanation
Indices: 2443949--2443973 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2443939 CTATGCCTTC
2443949 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2443974 TCTCAGGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2451746 original size:5 final size:5
Alignment explanation
Indices: 2451736--2451838 Score: 188
Period size: 5 Copynumber: 20.2 Consensus size: 5
2451726 ATGTCATACC
2451736 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
2451786 TATAA TATAA TATAA TATAA TATAAA TATATA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TAT-AA TATA-A TATAA TATAA TATAA TATAA
2451838 T
1 T
2451839 TGAATCACAC
Statistics
Matches: 96, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
5 86 0.90
6 10 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:2455715 original size:3 final size:3
Alignment explanation
Indices: 2455707--2455735 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2455697 ATGTCTATAC
2455707 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2455736 CCCTTTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2456779 original size:27 final size:27
Alignment explanation
Indices: 2456745--2456805 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
2456735 ATATTATAAT
2456745 TTAAAATACTCCAAAAAGGAATAAAAA
1 TTAAAATACTCCAAAAAGGAATAAAAA
2456772 TTAAAATACTCCAAAAAGGAATAAAAA
1 TTAAAATACTCCAAAAAGGAATAAAAA
2456799 TTAAAAT
1 TTAAAAT
2456806 GATCGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (27 bp):
TTAAAATACTCCAAAAAGGAATAAAAA
Found at i:2468642 original size:33 final size:33
Alignment explanation
Indices: 2468600--2468665 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2468590 CAAGGCACTA
2468600 TCTGTCCTGTAAGATGAAACCCATTAGAACAAC
1 TCTGTCCTGTAAGATGAAACCCATTAGAACAAC
2468633 TCTGTCCTGTAAGATGAAACCCATTAGAACAAC
1 TCTGTCCTGTAAGATGAAACCCATTAGAACAAC
2468666 CATCAGCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (33 bp):
TCTGTCCTGTAAGATGAAACCCATTAGAACAAC
Found at i:2475477 original size:3 final size:3
Alignment explanation
Indices: 2475471--2475515 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
2475461 TCAATTCTTC
2475471 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
2475516 GTCTTCAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2477044 original size:16 final size:17
Alignment explanation
Indices: 2477023--2477059 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2477013 CCATGACTCC
*
2477023 AAGCCAA-CTTAACCTA
1 AAGCCAACCCTAACCTA
2477039 AAGCCAACCCTAACCTA
1 AAGCCAACCCTAACCTA
2477056 AAGC
1 AAGC
2477060 AGTCCCCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.43, C:0.35, G:0.08, T:0.14
Consensus pattern (17 bp):
AAGCCAACCCTAACCTA
Found at i:2484719 original size:21 final size:21
Alignment explanation
Indices: 2484670--2484719 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2484660 GTTTGTTTGT
*
2484670 TAAAATGATAAACGAACACAAA
1 TAAAAT-ATAAAAGAACACAAA
2484692 T-AAATATAAAAGAACA-AATA
1 TAAAATATAAAAGAACACAA-A
2484712 TAAAATAT
1 TAAAATAT
2484720 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 12 0.48
21 10 0.40
22 1 0.04
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.20
Consensus pattern (21 bp):
TAAAATATAAAAGAACACAAA
Found at i:2492412 original size:12 final size:12
Alignment explanation
Indices: 2492395--2492419 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2492385 AAACCAAATG
2492395 TTTGGTCACACA
1 TTTGGTCACACA
2492407 TTTGGTCACACA
1 TTTGGTCACACA
2492419 T
1 T
2492420 CATACCGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTGGTCACACA
Found at i:2494463 original size:52 final size:52
Alignment explanation
Indices: 2494406--2494510 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
2494396 TTGGTTAGCC
2494406 TTTGACCTAGTTTCATTAATTTTAATGAAGAAATTTGATAAATCAACAAGCT
1 TTTGACCTAGTTTCATTAATTTTAATGAAGAAATTTGATAAATCAACAAGCT
2494458 TTTGACCTAGTTTCATTAATTTTAATGAAGAAATTTGATAAATCAACAAGCT
1 TTTGACCTAGTTTCATTAATTTTAATGAAGAAATTTGATAAATCAACAAGCT
2494510 T
1 T
2494511 ATCTTAGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (52 bp):
TTTGACCTAGTTTCATTAATTTTAATGAAGAAATTTGATAAATCAACAAGCT
Found at i:2503564 original size:40 final size:42
Alignment explanation
Indices: 2503510--2503590 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 42
2503500 TCAGGCCGGG
*
2503510 TATATATATATTTAAATTAAATATATAAATATTATATATATT
1 TATATATATATTTAAATTAAATATATAAATAATATATATATT
* * *
2503552 TATAT-TA-ATTTAATTTAAATTTATTAATAATATATATAT
1 TATATATATATTTAAATTAAATATATAAATAATATATATAT
2503591 ATAATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 28 0.80
41 2 0.06
42 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (42 bp):
TATATATATATTTAAATTAAATATATAAATAATATATATATT
Found at i:2506337 original size:2 final size:2
Alignment explanation
Indices: 2506287--2506319 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2506277 AAATTTATTA
*
2506287 AT AT AT AT GT 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 A
2506320 GTTTCAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2528002 original size:10 final size:11
Alignment explanation
Indices: 2527978--2528003 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2527968 AGATTATTCG
2527978 AAAATCTGATA
1 AAAATCTGATA
2527989 AAAATCTGATA
1 AAAATCTGATA
2528000 AAAA
1 AAAA
2528004 ATCTTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAATCTGATA
Found at i:2528005 original size:12 final size:12
Alignment explanation
Indices: 2527978--2528012 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2527968 AGATTATTCG
2527978 AAAATCTGAT-A
1 AAAATCTGATAA
2527989 AAAATCTGATAA
1 AAAATCTGATAA
*
2528001 AAAATCTTATAA
1 AAAATCTGATAA
2528013 TCTATACGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (12 bp):
AAAATCTGATAA
Found at i:2530758 original size:2 final size:2
Alignment explanation
Indices: 2530751--2530775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2530741 CTTATTTTCA
2530751 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2530776 ACATGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2532849 original size:2 final size:2
Alignment explanation
Indices: 2532842--2532867 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2532832 ATTTAGTTTC
2532842 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2532868 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2534971 original size:9 final size:9
Alignment explanation
Indices: 2534959--2534993 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2534949 AAATTTAAAT
2534959 TTTTATATA
1 TTTTATATA
*
2534968 TTTTAGATA
1 TTTTATATA
*
2534977 TTTTTTATA
1 TTTTATATA
2534986 TTTTATAT
1 TTTTATAT
2534994 TAAAAATGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTATATA
Found at i:2547733 original size:9 final size:9
Alignment explanation
Indices: 2547719--2547759 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
2547709 AAATTATTTT
2547719 ATATTTATA
1 ATATTTATA
2547728 ATATTTATA
1 ATATTTATA
2547737 ATA-TTA-A
1 ATATTTATA
*
2547744 TTATTTATA
1 ATATTTATA
2547753 AT-TTTAT
1 ATATTTAT
2547760 GAGGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
7 3 0.11
8 11 0.39
9 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTTATA
Found at i:2552076 original size:26 final size:26
Alignment explanation
Indices: 2552037--2552086 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2552027 AATATATGAT
2552037 CACTCACCGATAAAAAACTAACAAAA
1 CACTCACCGATAAAAAACTAACAAAA
* * *
2552063 CACTCACCGTTAAAAGATTAACAA
1 CACTCACCGATAAAAAACTAACAA
2552087 CACTATCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.06, T:0.16
Consensus pattern (26 bp):
CACTCACCGATAAAAAACTAACAAAA
Found at i:2562196 original size:27 final size:31
Alignment explanation
Indices: 2562139--2562196 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 31
2562129 TAAATTTGCG
*
2562139 ATATAATATTGTATGTTTTGAATACATATATA
1 ATATAATATTGTATGTTTTG-ATACAAATATA
2562171 ATAT-ATATTGTAT-TTTTG-TA-AAATAT
1 ATATAATATTGTATGTTTTGATACAAATAT
2562197 GTATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 5 0.20
28 2 0.08
30 5 0.20
31 9 0.36
32 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.50
Consensus pattern (31 bp):
ATATAATATTGTATGTTTTGATACAAATATA
Found at i:2564922 original size:199 final size:201
Alignment explanation
Indices: 2564568--2564961 Score: 621
Period size: 199 Copynumber: 2.0 Consensus size: 201
2564558 TATTATTAGC
* * * *
2564568 TTCTTAATCATTCTCATTGTTATGTTCATCAATCACTACATCGTTGGGATTAAAAACCAGCATAT
1 TTCTTAATCATTCTCATTGCTATGTTCATCAATCACTACATAGTTGGGATTAAAAACCAACACAT
* * *
2564633 AGTTCCTTTTTTCAACCTTCTCTTCATCCCAATTCCAACTTGCATCTTCATTAAACTCCACATTT
66 AGTTCCATTTTTCAACCTTCTCTTCATCCCAAATCCAACTTGCATCTTCATTAAACTCCACATCT
* * *
2564698 CTACTGATCGTGATCTTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTTGCTTGAGAATCATA
131 CTACTGATCATGATATTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
2564763 TCTAGT
196 TCTAGT
* *
2564769 TTCTTCATCATTCTCATTGCTATGTTCATCACTCACTACATAGTTGGGATTAAAAA-CAACACAT
1 TTCTTAATCATTCTCATTGCTATGTTCATCAATCACTACATAGTTGGGATTAAAAACCAACACAT
* * *
2564833 AGTT-CATTTTTCAACCTTCTCTTTATCCCAAATCCAGCTTGCATCTTCATTAAACTGCACATCT
66 AGTTCCATTTTTCAACCTTCTCTTCATCCCAAATCCAACTTGCATCTTCATTAAACTCCACATCT
* *
2564897 CTATTGATCATGATATTCTCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
131 CTACTGATCATGATATTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
2564962 GCCAATGAAG
Statistics
Matches: 176, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
199 114 0.65
200 10 0.06
201 52 0.30
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (201 bp):
TTCTTAATCATTCTCATTGCTATGTTCATCAATCACTACATAGTTGGGATTAAAAACCAACACAT
AGTTCCATTTTTCAACCTTCTCTTCATCCCAAATCCAACTTGCATCTTCATTAAACTCCACATCT
CTACTGATCATGATATTCCCAGTGTCAAGATTGAAAATTCGGTAGCCTTTGGCTTGAGAATCATA
TCTAGT
Found at i:2569978 original size:13 final size:13
Alignment explanation
Indices: 2569960--2570006 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
2569950 TGTCATTTTA
2569960 TTTCTATATCTAT
1 TTTCTATATCTAT
* *
2569973 TTTCTACAATTTAT
1 TTTCTA-TATCTAT
2569987 GTTTCTATATCTAT
1 -TTTCTATATCTAT
2570001 TTTCTA
1 TTTCTA
2570007 CAATTTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 12 0.43
14 10 0.36
15 6 0.21
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTCTATATCTAT
Found at i:2569993 original size:28 final size:28
Alignment explanation
Indices: 2569960--2570018 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
2569950 TGTCATTTTA
2569960 TTTCTATATCTATTTTCTACAATTTATG
1 TTTCTATATCTATTTTCTACAATTTATG
2569988 TTTCTATATCTATTTTCTACAATTTATG
1 TTTCTATATCTATTTTCTACAATTTATG
2570016 TTT
1 TTT
2570019 GAAATTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.24, C:0.14, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTCTATATCTATTTTCTACAATTTATG
Found at i:2573553 original size:25 final size:25
Alignment explanation
Indices: 2573524--2573572 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2573514 ACGAGAATAA
* *
2573524 AAAAATATTATAGAAATGATTCATT
1 AAAAATATTATACAAATAATTCATT
2573549 AAAAATATTATACAAATAATTCAT
1 AAAAATATTATACAAATAATTCAT
2573573 GAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAATATTATACAAATAATTCATT
Found at i:2574889 original size:24 final size:21
Alignment explanation
Indices: 2574857--2574909 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
2574847 AATGTGATTT
*
2574857 AAATTGAAAACAGAAGAATCCCAG
1 AAATGGAAAACA-AA-AA-CCCAG
* *
2574881 AAATGGAAAGCAAAAAGCCAG
1 AAATGGAAAACAAAAACCCAG
2574902 AAATGGAA
1 AAATGGAA
2574910 TGAAATAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 12 0.46
22 2 0.08
23 2 0.08
24 10 0.38
ACGTcount: A:0.57, C:0.13, G:0.21, T:0.09
Consensus pattern (21 bp):
AAATGGAAAACAAAAACCCAG
Found at i:2580724 original size:20 final size:20
Alignment explanation
Indices: 2580699--2580738 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2580689 GGAATAGTAC
*
2580699 AATATTAAATTATGTTTTTA
1 AATATTAAATTATGGTTTTA
*
2580719 AATATTACATTATGGTTTTA
1 AATATTAAATTATGGTTTTA
2580739 TGCGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
AATATTAAATTATGGTTTTA
Found at i:2581124 original size:2 final size:2
Alignment explanation
Indices: 2581117--2581153 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2581107 TAGGTTTGAA
*
2581117 AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2581154 ACAATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2584994 original size:15 final size:15
Alignment explanation
Indices: 2584974--2585003 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2584964 TTTAGCTGGA
2584974 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
2584989 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
2585004 TGGGTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.67, T:0.07
Consensus pattern (15 bp):
CGGGCGGATGCGGGG
Found at i:2585266 original size:2 final size:2
Alignment explanation
Indices: 2585259--2585285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2585249 TTGGATGGAG
2585259 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
2585286 GGATTGTTGG
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:2586568 original size:60 final size:60
Alignment explanation
Indices: 2586500--2586709 Score: 204
Period size: 60 Copynumber: 3.4 Consensus size: 60
2586490 CTGGAGCTTC
2586500 TGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAGCAGG
1 TGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAGCAGG
* * * ** * ** * *
2586560 TGGATATGGAGGTGGCGGCGGCAAAGGTGGTGGTGGAGGTGCTGCAGGTGGATATGGAGGAGGAG
1 TGGATATGGAAGTGGAGGTGGTGAA---GGAGGTGGA---GCTGGTGGTGGGTATGGAGGAGCAG
*
2586625 CTTC
60 ---G
*
2586629 TGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAGCAGG
1 TGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAGCAGG
* * *
2586689 TGGACATGGAGGTGGCGGTGG
1 TGGATATGGAAGTGGAGGTGG
2586710 AAGTGGTGGT
Statistics
Matches: 114, Mismatches: 27, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
60 37 0.32
63 29 0.25
66 29 0.25
69 19 0.17
ACGTcount: A:0.20, C:0.07, G:0.54, T:0.20
Consensus pattern (60 bp):
TGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGGTATGGAGGAGCAGG
Done.