Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009620.1 Hibiscus syriacus cultivar Beakdansim tig00117009_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: 1051670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:718012 original size:14 final size:14
Alignment explanation
Indices: 717993--718057 Score: 87
Period size: 14 Copynumber: 4.6 Consensus size: 14
717983 AAGTCAAAGG
717993 GTTGACTCAGACGA
1 GTTGACTCAGACGA
*
718007 GTTGACTCAGACGG
1 GTTGACTCAGACGA
718021 GTTGACTCAGACCGA
1 GTTGACTCAGA-CGA
*
718036 GTTGACTTAGAC-A
1 GTTGACTCAGACGA
718049 GGTTGACTC
1 -GTTGACTC
718058 GGACCGAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
13 1 0.02
14 32 0.71
15 12 0.27
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:718047 original size:29 final size:29
Alignment explanation
Indices: 717991--718064 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
717981 CAAAGTCAAA
717991 GGGTTGACTCAGA-CGAGTTGACTCAGAC
1 GGGTTGACTCAGACCGAGTTGACTCAGAC
*
718019 GGGTTGACTCAGACCGAGTTGACTTAGAC
1 GGGTTGACTCAGACCGAGTTGACTCAGAC
* *
718048 AGGTTGACTCGGACCGA
1 GGGTTGACTCAGACCGA
718065 ATCAGGTAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 13 0.31
29 29 0.69
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (29 bp):
GGGTTGACTCAGACCGAGTTGACTCAGAC
Found at i:722559 original size:7 final size:7
Alignment explanation
Indices: 722547--722587 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
722537 TTGACTTTTT
722547 GGTCAAC
1 GGTCAAC
722554 GGTCAAC
1 GGTCAAC
722561 GGTCAAC
1 GGTCAAC
*
722568 GGTCAAT
1 GGTCAAC
* *
722575 AGTCAAT
1 GGTCAAC
722582 GGTCAA
1 GGTCAA
722588 AGTTAACCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (7 bp):
GGTCAAC
Found at i:722616 original size:14 final size:14
Alignment explanation
Indices: 722593--722683 Score: 85
Period size: 14 Copynumber: 6.4 Consensus size: 14
722583 GTCAAAGTTA
*
722593 ACCGGTTGACTCGG
1 ACCGGTTGACTCAG
*
722607 A-CGAGTTGACTTAG
1 ACCG-GTTGACTCAG
*
722621 ACGGGTTGACTCAG
1 ACCGGTTGACTCAG
*
722635 ACCGGTTTGACTCAA
1 ACCGG-TTGACTCAG
*
722650 ACCGGGTTGACTCGG
1 ACC-GGTTGACTCAG
* *
722665 ACCGGCTGACTCGG
1 ACCGGTTGACTCAG
722679 ACCGG
1 ACCGG
722684 ACCAGGCGGG
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
13 2 0.03
14 38 0.59
15 22 0.34
16 2 0.03
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (14 bp):
ACCGGTTGACTCAG
Found at i:732623 original size:22 final size:22
Alignment explanation
Indices: 732598--732640 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
732588 AATATATTTA
732598 TTATAAAACATAT-TATAAAATG
1 TTATAAAA-ATATATATAAAATG
*
732620 TTATAAAAATATATCTAAAAT
1 TTATAAAAATATATATAAAAT
732641 TAATTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TTATAAAAATATATATAAAATG
Found at i:732754 original size:16 final size:18
Alignment explanation
Indices: 732729--732774 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
732719 GTGAAAATAT
732729 AATA-AATATACA-T-TA
1 AATATAATATACATTATA
* *
732744 ATTATAATATAAATTATA
1 AATATAATATACATTATA
732762 AATATAATATACA
1 AATATAATATACA
732775 AATATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 7 0.29
17 1 0.04
18 13 0.54
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATAATATACATTATA
Found at i:732828 original size:24 final size:24
Alignment explanation
Indices: 732747--732828 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 24
732737 TACATTAATT
732747 ATAATATAAATTATAAAT-ATAATATA
1 ATAATAT--ATTATAAATAATAATA-A
*
732773 CA-AATATATTTATAACATAGTATATAA
1 -ATAATATA-TTATAA-ATAATA-ATAA
*
732800 TTAATATATTATAAATAATAATAA
1 ATAATATATTATAAATAATAATAA
732824 ATAAT
1 ATAAT
732829 TGGAGGGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
24 9 0.20
25 11 0.24
26 13 0.28
27 10 0.22
28 3 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (24 bp):
ATAATATATTATAAATAATAATAA
Found at i:756545 original size:65 final size:62
Alignment explanation
Indices: 756463--756607 Score: 184
Period size: 61 Copynumber: 2.3 Consensus size: 62
756453 GTAGGTTTAT
* *
756463 ATTAGCACTAGTGTGTAAGGACACTAAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAG
1 ATTAGCACTAGAGTGTAA-GACA-T-AGTGCAGATGGTGGGCACAACCTTATGTGTCATATCCAG
* * * * *
756528 ATTAACACTAGAGTGTAA-ATATAGTGTAGATGGTGGGCACGACCTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAAGACATAGTGCAGATGGTGGGCACAACCTTATGTGTCATATCCAG
*
756589 ATTAGCACTAGAGCGTAAG
1 ATTAGCACTAGAGTGTAAG
756608 CTTAGTGTAG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
61 51 0.73
62 1 0.01
63 2 0.03
65 16 0.23
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (62 bp):
ATTAGCACTAGAGTGTAAGACATAGTGCAGATGGTGGGCACAACCTTATGTGTCATATCCAG
Found at i:757105 original size:16 final size:15
Alignment explanation
Indices: 757080--757113 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
757070 CTGCAATTTC
*
757080 TTAATATAATTATTA
1 TTAATATAATTAATA
757095 TTAATTATAATTAATA
1 TTAA-TATAATTAATA
757111 TTA
1 TTA
757114 TGATATTAAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:764729 original size:6 final size:6
Alignment explanation
Indices: 764664--764728 Score: 121
Period size: 6 Copynumber: 10.8 Consensus size: 6
764654 TATTATTATT
764664 AGTATC AGTATC AGTATC AGTATC AGTATC AGTATC AGTATC AGTATC
1 AGTATC AGTATC AGTATC AGTATC AGTATC AGTATC AGTATC AGTATC
*
764712 AGTATC AGTATT AGTAT
1 AGTATC AGTATC AGTAT
764729 TTATTGCAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (6 bp):
AGTATC
Found at i:767077 original size:130 final size:131
Alignment explanation
Indices: 766821--767184 Score: 511
Period size: 131 Copynumber: 2.8 Consensus size: 131
766811 ATTAATATTG
* * * * * *
766821 AAAATAGTAATATCTTTTCATTTCGGGTT-GAGTAGTAAATGACTGCTTAAAGGCATGAGAGATC
1 AAAATAGTGATATCTCTTCATTTC-GATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTC
* *
766885 ATTTTATTCTCGATTGGAAATAATTAGATATTA-CGGTTTTCTCTCGAATTAATATTGAATTTTA
65 A-TTTATTCTCGATTGGAAATAATTAGATATTATC-GTTTTCTCTCAAATCAATATTGAATTTTA
766949 AGAC
128 AGAC
766953 AAAATAGTGATA-CTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* *
767017 -TTATTTCTCGATTAGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGCATTTTAAG
66 TTTA-TTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTTAAG
*
767081 AT
130 AC
* * * * *
767083 GAAATAGTGATATATCTTCATTTCGATTGTAGTAATAAATGACTGCTTTAAGGCATTAGATGTCA
1 AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
*
767148 TTTATTCTCGATTGGAAATAATTAGATATTATAGTTT
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTT
767185 CCTTTTTTAA
Statistics
Matches: 209, Mismatches: 18, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
129 3 0.01
130 69 0.33
131 123 0.59
132 14 0.07
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
AAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCAAATCAATATTGAATTTTAAGA
C
Found at i:783339 original size:13 final size:13
Alignment explanation
Indices: 783307--783331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
783297 ATACTTATAT
783307 ATATATATATGCC
1 ATATATATATGCC
783320 ATATATATATGC
1 ATATATATATGC
783332 ATGTTATACT
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:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
ATATATATATGCC
Found at i:785362 original size:18 final size:18
Alignment explanation
Indices: 785336--785375 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
785326 TGAACTTATG
* *
785336 TTATTGTTTTAAATTGTT
1 TTATAGTTTTAAATAGTT
785354 TTATAGTTTTAAATAGTT
1 TTATAGTTTTAAATAGTT
785372 TTAT
1 TTAT
785376 GAACTTTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (18 bp):
TTATAGTTTTAAATAGTT
Found at i:787442 original size:24 final size:24
Alignment explanation
Indices: 787398--787447 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
787388 ATAAAGAACC
*
787398 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
787422 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
787446 AA
1 AA
787448 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:790770 original size:19 final size:20
Alignment explanation
Indices: 790755--790805 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
790745 AAGTTAAAAT
790755 GAAAGAGAAAAATTAATAAA
1 GAAAGAGAAAAATTAATAAA
790775 GAAAGAGAAAAATTAATAAA
1 GAAAGAGAAAAATTAATAAA
790795 GAAAGAGAAAA
1 GAAAGAGAAAA
790806 GAAAAAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.12
Consensus pattern (20 bp):
GAAAGAGAAAAATTAATAAA
Found at i:797700 original size:24 final size:24
Alignment explanation
Indices: 797656--797705 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
797646 ATAAAGAACC
*
797656 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
797680 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
797704 AA
1 AA
797706 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:808047 original size:182 final size:185
Alignment explanation
Indices: 807715--808059 Score: 628
Period size: 182 Copynumber: 1.9 Consensus size: 185
807705 ATTTGAAAAT
807715 ATCGAGGATTTATTGAATTATTTTTAAATTAAGACTAATTTGATATAATGTATAAGTTTTAGAGA
1 ATCGAGGATTTATTGAATTATTTTTAAATTAAGACTAATTTGA-ATAATGTATAAGTTTTAGAGA
807780 CTAAATCTAGATTATACGCATGTCACACCACCTTTTCCATTGAATTAGGACTAATTTGATACAAT
65 CTAAATCTAGATTATACGCATGTCACACCACCTTTTCCATTGAATTAGGACTAATTTGATACAAT
807845 GTATAAGTATGAGAGACTAAAACTATATAATACCCGTGTCACATCGTGTTTTCCGAAA
130 GTATAAGTATGAGAGACT-AAACTATAT-ATACCCGTGTCACATCGTGTTTTCCGAAA
807903 ATCGAGGATTTATTGAATTATTTTTAAATTAAGACTAATTTG-AT-ATGTATAAG-TTTAGAGAC
1 ATCGAGGATTTATTGAATTATTTTTAAATTAAGACTAATTTGAATAATGTATAAGTTTTAGAGAC
807965 TAAATCTAGATTATACGCATGTCACACCACC-TTTCCA-TGAATTAGGACTAATTTGATACAATG
66 TAAATCTAGATTATACGCATGTCACACCACCTTTTCCATTGAATTAGGACTAATTTGATACAATG
808028 TATAAGTATGAGAGACTAAACTATATATACCC
131 TATAAGTATGAGAGACTAAACTATATATACCC
808060 CGTTAAGTCA
Statistics
Matches: 157, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
180 6 0.04
181 9 0.06
182 43 0.27
183 6 0.04
184 40 0.25
185 9 0.06
186 2 0.01
188 42 0.27
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (185 bp):
ATCGAGGATTTATTGAATTATTTTTAAATTAAGACTAATTTGAATAATGTATAAGTTTTAGAGAC
TAAATCTAGATTATACGCATGTCACACCACCTTTTCCATTGAATTAGGACTAATTTGATACAATG
TATAAGTATGAGAGACTAAACTATATATACCCGTGTCACATCGTGTTTTCCGAAA
Found at i:809132 original size:19 final size:19
Alignment explanation
Indices: 809105--809148 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
809095 ATCTCAAATT
*
809105 ACAACAAAAATTTACAATC
1 ACAATAAAAATTTACAATC
809124 ACAATAAAAATTTACAATC
1 ACAATAAAAATTTACAATC
809143 ACAATA
1 ACAATA
809149 GTAAATTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.23
Consensus pattern (19 bp):
ACAATAAAAATTTACAATC
Found at i:821881 original size:36 final size:36
Alignment explanation
Indices: 821832--821936 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
821822 TTCTCAAGTT
821832 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
* *
821868 AATCAAGCATTCACAAAAGAGTAGTGAAACAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
821904 AATCAAGCCTTCACAAAAAGAGTAGTGAAGCAA
1 AATCAAGCCTTCAC-AAAAGAGTAGTGAAGCAA
821937 GATCAGATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 47 0.73
37 17 0.27
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
Found at i:823386 original size:19 final size:18
Alignment explanation
Indices: 823344--823388 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
823334 TATTTTACAT
823344 TTTAAT-TTATATAATAA
1 TTTAATATTATATAATAA
*
823361 TTT--TATTAGTATAGTAA
1 TTTAATATTA-TATAATAA
823378 TTTAATATTAT
1 TTTAATATTAT
823389 TTTGAGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 13 0.57
18 1 0.04
19 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTAATATTATATAATAA
Found at i:825275 original size:2 final size:2
Alignment explanation
Indices: 825268--825300 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
825258 GAATGGGCCA
825268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
825301 AAAACTTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:833465 original size:24 final size:24
Alignment explanation
Indices: 833403--833471 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
833393 TTGATTTAGT
*
833403 AAAATATTAATAATTTTTAGA-ATTA
1 AAAATATTTAT-ATTTTTA-ATATTA
833428 AAAATATTTATATTTTTAATATTA
1 AAAATATTTATATTTTTAATATTA
* *
833452 AATAT-TTTACTATTTATAAT
1 AAAATATTTA-TATTTTTAAT
833472 TTTATGGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 5 0.13
24 24 0.62
25 10 0.26
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (24 bp):
AAAATATTTATATTTTTAATATTA
Found at i:833563 original size:17 final size:17
Alignment explanation
Indices: 833541--833573 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
833531 TACTACCATA
*
833541 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
833558 ATATTATATTTTATAT
1 ATATTATATTTTATAT
833574 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:836542 original size:63 final size:63
Alignment explanation
Indices: 836420--836543 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
836410 TACTTTGAGT
* * ** *
836420 ATTAAACAAATTTATCACAATTTTTATTGATAATAGAGTCGAACATTTGGTCACTAAAAAATA
1 ATTAAACAAATTCATCACAATTTATATTGATAATAGAGTCGAACAGATGATCACTAAAAAATA
* *
836483 ATTAAACAAATTCATCACAATTTATATTGATAATTGTA-TCGAATAGATGATCA-TAAAAAAT
1 ATTAAACAAATTCATCACAATTTATATTGATAATAG-AGTCGAACAGATGATCACTAAAAAAT
836544 GAACAATTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 8 0.15
63 44 0.83
64 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (63 bp):
ATTAAACAAATTCATCACAATTTATATTGATAATAGAGTCGAACAGATGATCACTAAAAAATA
Found at i:854799 original size:14 final size:14
Alignment explanation
Indices: 854774--854814 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
854764 TTTGATAGGT
854774 GAAAATTGTTTTCAG
1 GAAAA-TGTTTTCAG
*
854789 GAAAATGTTTTTAG
1 GAAAATGTTTTCAG
854803 GAAAATGTTTTC
1 GAAAATGTTTTC
854815 CTCATTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (14 bp):
GAAAATGTTTTCAG
Found at i:855114 original size:17 final size:17
Alignment explanation
Indices: 855092--855125 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
855082 TAATATACAT
855092 ATATTAGAATTTTAATA
1 ATATTAGAATTTTAATA
* *
855109 ATATTATATTTTTAATA
1 ATATTAGAATTTTAATA
855126 TTTTATTAAT
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATTAGAATTTTAATA
Found at i:855116 original size:22 final size:23
Alignment explanation
Indices: 855061--855164 Score: 74
Period size: 23 Copynumber: 4.6 Consensus size: 23
855051 TTTTAATAAA
855061 AATAATAAT-TATTAAAATATTT
1 AATAATAATATATTAAAATATTT
*
855083 AAT-ATACATATATTAGAAT-TTT
1 AATAATA-ATATATTAAAATATTT
* **
855105 AATAATATTATATTTTTAATATTTT
1 AATAATAATATA-TTAAAATA-TTT
* * *
855130 ATTAAT-ATATACTCAAATATATT
1 AATAATAATATATTAAAATAT-TT
855153 -ATAATAATATAT
1 AATAATAATATAT
855165 GATATTATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
21 3 0.05
22 20 0.32
23 28 0.44
24 4 0.06
25 8 0.13
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (23 bp):
AATAATAATATATTAAAATATTT
Found at i:855596 original size:29 final size:30
Alignment explanation
Indices: 855554--855640 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
855544 CAAAAAATGC
*
855554 AATTCATTTTACGTAAAACAATTTTC-GGT
1 AATTCATTTTACGTAAAACAGTTTTCAGGT
* * *
855583 AATTCACTTTACGTAAAATAGTTTTCATGT
1 AATTCATTTTACGTAAAACAGTTTTCAGGT
* *
855613 AATTCTTTTTACGTAAATCAGTTTTCAG
1 AATTCATTTTACGTAAAACAGTTTTCAG
855641 AAAATCAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (30 bp):
AATTCATTTTACGTAAAACAGTTTTCAGGT
Found at i:855617 original size:30 final size:30
Alignment explanation
Indices: 855554--855640 Score: 106
Period size: 29 Copynumber: 2.9 Consensus size: 30
855544 CAAAAAATGC
* *
855554 AATTCATTTTACGTAAAACAATTTTC-GGT
1 AATTCATTTTACGTAAAATAGTTTTCAGGT
* *
855583 AATTCACTTTACGTAAAATAGTTTTCATGT
1 AATTCATTTTACGTAAAATAGTTTTCAGGT
*
855613 AATTCTTTTTACGT-AAATCAGTTTTCAG
1 AATTCATTTTACGTAAAAT-AGTTTTCAG
855641 AAAATCAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 27 0.55
30 22 0.45
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (30 bp):
AATTCATTTTACGTAAAATAGTTTTCAGGT
Found at i:856325 original size:51 final size:50
Alignment explanation
Indices: 856258--856359 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 50
856248 AGGGTCGCGC
* *
856258 CTTACCTTTAATTCTGACATAATTATGTAAGGCGCGATGCAGGTACCGCTG
1 CTTACCTTTAACTCTGACACAATTATGTAAGGCGCGATGCAGGTACC-CTG
* * *
856309 CTTAGCTTTAACTCTGATACAATTATGTAAGGCGCGGTGCAGGTACCCTG
1 CTTACCTTTAACTCTGACACAATTATGTAAGGCGCGATGCAGGTACCCTG
856359 C
1 C
856360 CTTGTATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 4 0.09
51 42 0.91
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (50 bp):
CTTACCTTTAACTCTGACACAATTATGTAAGGCGCGATGCAGGTACCCTG
Found at i:856426 original size:15 final size:15
Alignment explanation
Indices: 856408--856437 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
856398 TATCTCATAC
856408 CTTCCTCTCTCACAT
1 CTTCCTCTCTCACAT
856423 CTTCCTCTCTCACAT
1 CTTCCTCTCTCACAT
856438 ATTTCTCTCA
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:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTCCTCTCTCACAT
Found at i:856445 original size:15 final size:15
Alignment explanation
Indices: 856409--856446 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
856399 ATCTCATACC
*
856409 TTCCTCTCTCACATC
1 TTCCTCTCTCACATA
856424 TTCCTCTCTCACATA
1 TTCCTCTCTCACATA
*
856439 TTTCTCTC
1 TTCCTCTC
856447 AATGAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (15 bp):
TTCCTCTCTCACATA
Found at i:859732 original size:32 final size:33
Alignment explanation
Indices: 859668--859754 Score: 108
Period size: 32 Copynumber: 2.6 Consensus size: 33
859658 GTAATAAACA
*
859668 AAATTAACCAAAA-AATATTAACAAAATGTCCAAC
1 AAATTAA-CAAAATAA-ATTAACAAAATATCCAAC
859702 AATATTAACAAAATAAATTAA-AAAA-ATCCAACC
1 AA-ATTAACAAAATAAATTAACAAAATATCCAA-C
859735 AAATTAACAAAATAAATTAA
1 AAATTAACAAAATAAATTAA
859755 GTATTAAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
32 23 0.47
33 7 0.14
34 12 0.24
35 7 0.14
ACGTcount: A:0.63, C:0.14, G:0.01, T:0.22
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAACAAAATATCCAAC
Found at i:863523 original size:19 final size:19
Alignment explanation
Indices: 863499--863541 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
863489 TAACAACTAA
863499 TAGAGTATTATAAGTGTAT
1 TAGAGTATTATAAGTGTAT
863518 TAGAGTATTATAAGTGTAT
1 TAGAGTATTATAAGTGTAT
863537 TAGAG
1 TAGAG
863542 GATTGTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (19 bp):
TAGAGTATTATAAGTGTAT
Found at i:864776 original size:29 final size:30
Alignment explanation
Indices: 864718--864777 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
864708 AAATCATACG
864718 ATTTTTTGAAAATATAATATATATTATATA
1 ATTTTTTGAAAATATAATATATATTATATA
*
864748 ATTTTTT-AAATATATATATATATAGTATAT
1 ATTTTTTGAAA-ATATA-ATATATATTATAT
864778 TATTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.11
30 12 0.44
31 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTTTGAAAATATAATATATATTATATA
Found at i:875536 original size:19 final size:19
Alignment explanation
Indices: 875512--875548 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
875502 CGTTGTACAA
875512 GGGGGGAATCGGTACCCTT
1 GGGGGGAATCGGTACCCTT
*
875531 GGGGGGAATCGGTTCCCT
1 GGGGGGAATCGGTACCCT
875549 CCGAGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.22
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCTT
Found at i:875620 original size:76 final size:76
Alignment explanation
Indices: 875511--875700 Score: 280
Period size: 76 Copynumber: 2.5 Consensus size: 76
875501 CCGTTGTACA
* *
875511 AGGGGGGAATCGG-TAC-CCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG-G
* ** *
875573 TA-AAACTGTTT
65 GACAAACCATTC
*
875584 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGGG
875649 ACAAACCATTC
66 ACAAACCATTC
875660 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCT
875701 GAGCAATCTA
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
73 13 0.12
74 2 0.02
75 5 0.05
76 86 0.81
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGGG
ACAAACCATTC
Found at i:876324 original size:17 final size:16
Alignment explanation
Indices: 876304--876345 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
876294 CACCATTCAT
876304 AAATCCAACAATCCACA
1 AAATCCAACAATCCA-A
*
876321 AAATCAAACAATCCAA
1 AAATCCAACAATCCAA
876337 AATATCCAA
1 AA-ATCCAA
876346 AATGTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (16 bp):
AAATCCAACAATCCAA
Found at i:878434 original size:20 final size:21
Alignment explanation
Indices: 878388--878448 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
878378 TCCCCTGTGG
878388 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
878411 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
878431 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
878449 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:880832 original size:34 final size:34
Alignment explanation
Indices: 880786--880853 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
880776 AACTCCATTT
880786 GTTGAGGGTCTAGGTGCTGAAAAATTGTGGCTAA
1 GTTGAGGGTCTAGGTGCTGAAAAATTGTGGCTAA
*
880820 GTTGAGGTTCTAGGTGCTGAAAAATTGTGGCTAA
1 GTTGAGGGTCTAGGTGCTGAAAAATTGTGGCTAA
880854 TACCATTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (34 bp):
GTTGAGGGTCTAGGTGCTGAAAAATTGTGGCTAA
Found at i:884147 original size:75 final size:76
Alignment explanation
Indices: 883976--884180 Score: 290
Period size: 75 Copynumber: 2.7 Consensus size: 76
883966 CCGTTGTACA
* * *
883976 AGGGGGGAATCGGTACC-CCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
* ** *
884039 TAAAACTGTTT
66 CAAAACCATTC
*
884050 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
*
884115 CCAAACCATTC
66 CAAAACCATTC
* *
884126 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
884181 GTTTTGGCTT
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
74 16 0.14
75 55 0.47
76 47 0.40
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
CAAAACCATTC
Found at i:893784 original size:20 final size:20
Alignment explanation
Indices: 893761--893806 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
893751 TGTTGGTACT
*
893761 GATACTGGCCTCTCG-GTATC
1 GATACTGACC-CTCGAGTATC
*
893781 GATACTGACCCTTGAGTATC
1 GATACTGACCCTCGAGTATC
893801 GATACT
1 GATACT
893807 CCCCTTAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (20 bp):
GATACTGACCCTCGAGTATC
Found at i:893819 original size:20 final size:19
Alignment explanation
Indices: 893775--893827 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
893765 CTGGCCTCTC
*
893775 GGTATCGATACTGACCCTTG
1 GGTATCGATACT-CCCCTTG
*
893795 AGTATCGATACTCCCCTTAG
1 GGTATCGATACTCCCCTT-G
893815 GGTATCGATACTC
1 GGTATCGATACTC
893828 TACTACTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 5 0.17
20 24 0.83
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (19 bp):
GGTATCGATACTCCCCTTG
Found at i:894036 original size:18 final size:19
Alignment explanation
Indices: 893993--894042 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
893983 CTCCTATAGG
*
893993 GAGTAACGATACTCAACCTT
1 GAGTATCGATACTC-ACCTT
*
894013 GGGTATCGATACTC-CCTT
1 GAGTATCGATACTCACCTT
894031 GAGTATCGATAC
1 GAGTATCGATAC
894043 CAAATATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
20 12 0.44
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (19 bp):
GAGTATCGATACTCACCTT
Found at i:906206 original size:20 final size:20
Alignment explanation
Indices: 906181--906218 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
906171 AATTCAAACA
906181 TGTTTAAAGTGTTTAAAATG
1 TGTTTAAAGTGTTTAAAATG
* *
906201 TGTTTAATGTTTTTAAAA
1 TGTTTAAAGTGTTTAAAA
906219 CACGGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TGTTTAAAGTGTTTAAAATG
Found at i:906316 original size:19 final size:19
Alignment explanation
Indices: 906288--906361 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
906278 CACTGTTCAT
*
906288 AGTTTGGAAACTTTGTAAA
1 AGTTTCGAAACTTTGTAAA
*
906307 AGTTTTGAAACTTT-TATTAA
1 AGTTTCGAAACTTTGTA--AA
* **
906327 GAGTTTCAAAACTTTACAAA
1 -AGTTTCGAAACTTTGTAAA
906347 AGTTTCGAAACTTTG
1 AGTTTCGAAACTTTG
906362 AACCCAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.04
19 26 0.58
20 4 0.09
21 12 0.27
22 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (19 bp):
AGTTTCGAAACTTTGTAAA
Found at i:906476 original size:19 final size:19
Alignment explanation
Indices: 906454--906511 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
906444 TAAAATTTTT
906454 GATACTTTCAAAAAGTTTC
1 GATACTTTCAAAAAGTTTC
* *
906473 GATACTTTCACAAGGTTTC
1 GATACTTTCAAAAAGTTTC
* *
906492 GAAACTTTCTCAAAAGTTTC
1 GATACTTTC-AAAAAGTTTC
906512 AAAACATTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 25 0.78
20 7 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (19 bp):
GATACTTTCAAAAAGTTTC
Found at i:906516 original size:20 final size:19
Alignment explanation
Indices: 906465--906530 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
906455 ATACTTTCAA
* *
906465 AAAGTTTCGATACTTTCAC
1 AAAGTTTCGAAACTTTCTC
*
906484 AAGGTTTCGAAACTTTCTC
1 AAAGTTTCGAAACTTTCTC
* *
906503 AAAAGTTTCAAAACATTCTTC
1 -AAAGTTTCGAAACTTTC-TC
906524 AAAGTTT
1 AAAGTTT
906531 TGGAACTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.41
20 21 0.54
21 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (19 bp):
AAAGTTTCGAAACTTTCTC
Found at i:917126 original size:16 final size:17
Alignment explanation
Indices: 917082--917133 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 17
917072 ATGATGGACT
917082 TAAGAAATGGATAATAATAA
1 TAAGAAATGGA-AAT-A-AA
*
917102 TAAGTAATGGAAATAAA
1 TAAGAAATGGAAATAAA
917119 -AAGAAAT-GAAATAAA
1 TAAGAAATGGAAATAAA
917134 GATATAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 8 0.27
16 6 0.20
17 2 0.07
18 1 0.03
19 3 0.10
20 10 0.33
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
TAAGAAATGGAAATAAA
Found at i:921422 original size:29 final size:29
Alignment explanation
Indices: 921380--921438 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
921370 ATTTTCACCT
921380 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
*
921409 AACTAAATTGATGTAAGTAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
921438 A
1 A
921439 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:926106 original size:29 final size:29
Alignment explanation
Indices: 926064--926122 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
926054 ATTTTCACCT
926064 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
*
926093 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
926122 A
1 A
926123 TTAATTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:935382 original size:81 final size:81
Alignment explanation
Indices: 935246--935722 Score: 760
Period size: 81 Copynumber: 5.9 Consensus size: 81
935236 TGTTGTTGTT
*
935246 GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAAGCCATT
1 GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATT
935311 AATCTTTTACTCAAAG
66 AATCTTTTACTCAAAG
* * * * *
935327 GTATTTAAACTTTCATCTAACTAGCACAATTGATACCTTTCTGTCAAATGTACAACTAGGCCATT
1 GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATT
935392 AATCTTTTACTCAAAG
66 AATCTTTTACTCAAAG
* * *
935408 GTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAAAT-CACAGCTAGGTCAT
1 GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTC-AAATGCACAACTAGGCCAT
* *
935472 TAATCTTTTATTTAAAG
65 TAATCTTTTACTCAAAG
* *
935489 GTATTTAACATTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATT
1 GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATT
935554 AATCTTTTACTCAAAG
66 AATCTTTTACTCAAAG
935570 GTATTTAACCTTTCATCTAACTAGCATAATTGAC-CACTTTCTGTCAAATGCACAACTAGGCCAT
1 GTATTTAACCTTTCATCTAACTAGCATAATTGACACA-TTTCTGTCAAATGCACAACTAGGCCAT
** *
935634 TGGTCTTTTACTCAAAT
65 TAATCTTTTACTCAAAG
* *
935651 GTATTTAACCTTTCATCTAACTAGCATAATTGACATATTTCTGTCAAATGCACAGCTAGGCCATT
1 GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATT
935716 AATCTTT
66 AATCTTT
935723 CACTTTAAAA
Statistics
Matches: 360, Mismatches: 32, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
80 5 0.01
81 350 0.97
82 5 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (81 bp):
GTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATT
AATCTTTTACTCAAAG
Found at i:938959 original size:27 final size:26
Alignment explanation
Indices: 938929--939001 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
938919 CTTGGATAAG
* **
938929 AAATTAAGAAAATATCCTTTTGAGGTA
1 AAATTAAGAAAATACCCTTAAG-GGTA
* *
938956 AAATTACGAAAATACCCATAAGGGTA
1 AAATTAAGAAAATACCCTTAAGGGTA
*
938982 AAATTAAAAAAATACCCTTA
1 AAATTAAGAAAATACCCTTA
939002 CATTGTAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (26 bp):
AAATTAAGAAAATACCCTTAAGGGTA
Found at i:940321 original size:32 final size:33
Alignment explanation
Indices: 940269--940391 Score: 117
Period size: 32 Copynumber: 3.8 Consensus size: 33
940259 GTAGGCCCCT
* * * *
940269 AGGCCCCAAGGTAATTCCTT-GGTTAGGCTCTT
1 AGGCCCCAAGATACTCCCTTAGGTTAGGCTCTA
* *
940301 AGGCCCCAAGATACTCCCTT-GGGTAGGATCTA
1 AGGCCCCAAGATACTCCCTTAGGTTAGGCTCTA
** * *
940333 AAACCCCAAGGTACACCCTTAGG-TAGGCTCTA
1 AGGCCCCAAGATACTCCCTTAGGTTAGGCTCTA
* *
940365 AGTCCCGAAGATACTCCCTTAGGTTAG
1 AGGCCCCAAGATACTCCCTTAGGTTAG
940392 CTCCTACGCC
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
32 68 0.93
33 5 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (33 bp):
AGGCCCCAAGATACTCCCTTAGGTTAGGCTCTA
Found at i:943881 original size:23 final size:23
Alignment explanation
Indices: 943843--943889 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
943833 AGTCCATACC
*
943843 CTAAAATAATTCAGAAAATATTT
1 CTAAAATAATTAAGAAAATATTT
*
943866 CTAAAATCATTAAGAAAATATTT
1 CTAAAATAATTAAGAAAATATTT
943889 C
1 C
943890 AGTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (23 bp):
CTAAAATAATTAAGAAAATATTT
Found at i:949541 original size:54 final size:53
Alignment explanation
Indices: 949454--949686 Score: 322
Period size: 54 Copynumber: 4.3 Consensus size: 53
949444 CTATGTGTAC
** *
949454 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATAAACGACCG
1 TATC-GCACTAAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
*
949508 TATCAGCACTAAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGATCG
1 TATC-GCACTAAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
* * *
949562 TATCGGCACTAAGTATGCAATCCACCGAATTCATAATATGTTTATGAACGACCG
1 TATC-GCACTAAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
* * *
949616 TATCGACTCTAAGTGTGCAACCCACGAAATTCGTAATATGTTTATGAACGACCG
1 TATCG-CACTAAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
*
949670 TATCGACACTATGTGTG
1 TATCG-CACTAAGTGTG
949687 TAGCCTAAAT
Statistics
Matches: 160, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.01
54 159 0.99
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (53 bp):
TATCGCACTAAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
Found at i:949646 original size:108 final size:108
Alignment explanation
Indices: 949454--949680 Score: 357
Period size: 108 Copynumber: 2.1 Consensus size: 108
949444 CTATGTGTAC
* *
949454 TATCGGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATAAACGACCGTATCAGCACTA
1 TATCGGCACTAAGTATGCAACCCACCGAATTCATAATATGTTTATAAACGACCGTATCAGCACTA
*
949519 AGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGATCG
66 AGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
* * *
949562 TATCGGCACTAAGTATGCAATCCACCGAATTCATAATATGTTTATGAACGACCGTATC-GACTCT
1 TATCGGCACTAAGTATGCAACCCACCGAATTCATAATATGTTTATAAACGACCGTATCAG-CACT
* *
949626 AAGTGTGCAACCCACGAAATTCGTAATATGTTTATGAACGACCG
65 AAGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
*
949670 TATCGACACTA
1 TATCGGCACTA
949681 TGTGTGTAGC
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
107 1 0.01
108 108 0.99
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (108 bp):
TATCGGCACTAAGTATGCAACCCACCGAATTCATAATATGTTTATAAACGACCGTATCAGCACTA
AGTGTGCAACCCACCAAATTCATAATATGTTTATGAACGACCG
Found at i:960026 original size:12 final size:12
Alignment explanation
Indices: 960009--960033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
959999 ACAAAGCACC
960009 ATTTGGTGCCTA
1 ATTTGGTGCCTA
960021 ATTTGGTGCCTA
1 ATTTGGTGCCTA
960033 A
1 A
960034 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:963896 original size:149 final size:149
Alignment explanation
Indices: 963626--963923 Score: 596
Period size: 149 Copynumber: 2.0 Consensus size: 149
963616 CTACTATTTT
963626 ATAGCTTAAGGATGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGTGTCCCGTCACTAAAG
1 ATAGCTTAAGGATGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGTGTCCCGTCACTAAAG
963691 TAGATCCTGACATCCGAAGAGTGTACAATTTCCTCTGAAGGAAAATTTTATTGTGCAATGATGTG
66 TAGATCCTGACATCCGAAGAGTGTACAATTTCCTCTGAAGGAAAATTTTATTGTGCAATGATGTG
963756 GCCTCGTACAATTTGGTGA
131 GCCTCGTACAATTTGGTGA
963775 ATAGCTTAAGGATGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGTGTCCCGTCACTAAAG
1 ATAGCTTAAGGATGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGTGTCCCGTCACTAAAG
963840 TAGATCCTGACATCCGAAGAGTGTACAATTTCCTCTGAAGGAAAATTTTATTGTGCAATGATGTG
66 TAGATCCTGACATCCGAAGAGTGTACAATTTCCTCTGAAGGAAAATTTTATTGTGCAATGATGTG
963905 GCCTCGTACAATTTGGTGA
131 GCCTCGTACAATTTGGTGA
963924 GATGATCCCA
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (149 bp):
ATAGCTTAAGGATGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGTGTCCCGTCACTAAAG
TAGATCCTGACATCCGAAGAGTGTACAATTTCCTCTGAAGGAAAATTTTATTGTGCAATGATGTG
GCCTCGTACAATTTGGTGA
Found at i:964801 original size:12 final size:12
Alignment explanation
Indices: 964784--964808 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
964774 TGACAAAACC
964784 ATTTGGTGCCTA
1 ATTTGGTGCCTA
964796 ATTTGGTGCCTA
1 ATTTGGTGCCTA
964808 A
1 A
964809 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:970730 original size:2 final size:2
Alignment explanation
Indices: 970723--970830 Score: 202
Period size: 2 Copynumber: 55.0 Consensus size: 2
970713 TGTACCTGTC
970723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
970764 AT AT AT AT AT AT AT AT AT AT A- 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
970805 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
970831 TCAGTTCATA
Statistics
Matches: 104, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 102 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:971194 original size:24 final size:23
Alignment explanation
Indices: 971119--971206 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 23
971109 GTATATGAAT
* *
971119 GTACTAAAACAGGAGTACCCAAAG
1 GTACTAATACAGGAGTA-CCATAG
* ** * *
971143 GTATTAATACAGGAGCGCCTTCAT
1 GTACTAATACAGGAGTACCAT-AG
971167 GTACTAATACAGGAGTACACATAG
1 GTACTAATACAGGAGTAC-CATAG
* *
971191 GTACTATTATAGGAGT
1 GTACTAATACAGGAGT
971207 GCACGAATGC
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
23 2 0.04
24 44 0.92
25 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (23 bp):
GTACTAATACAGGAGTACCATAG
Found at i:971229 original size:24 final size:23
Alignment explanation
Indices: 971202--971292 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 23
971192 TACTATTATA
*
971202 GGAGTGC-ACGAATGCACTGTTACT
1 GGAGTGCAAC-AATGCACT-ATACT
* * *
971226 GGAGTGCAACAAGGCACTAAACA
1 GGAGTGCAACAATGCACTATACT
*
971249 GGAGTGCAACAATTGCAGTAATACT
1 GGAGTGCAACAA-TGCACT-ATACT
971274 GGAGTGC-ACGAATGCACTA
1 GGAGTGCAAC-AATGCACTA
971293 AATAGGATCG
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
23 15 0.28
24 25 0.46
25 14 0.26
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (23 bp):
GGAGTGCAACAATGCACTATACT
Found at i:972618 original size:19 final size:20
Alignment explanation
Indices: 972567--972619 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
972557 TTGTTGTACC
*
972567 ATGTTGAGAATTAATGTTAGA
1 ATGTTGA-AATTGATGTTAGA
*
972588 ATGTTTAAATTGATGTTAGA
1 ATGTTGAAATTGATGTTAGA
*
972608 GTG-TGAAATTGA
1 ATGTTGAAATTGA
972620 ACCACTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.40
Consensus pattern (20 bp):
ATGTTGAAATTGATGTTAGA
Found at i:974057 original size:45 final size:45
Alignment explanation
Indices: 973992--974159 Score: 195
Period size: 45 Copynumber: 3.8 Consensus size: 45
973982 GTGTTATTGG
* *
973992 AGTAGTACATTTGTTTTACTATGGCACTAAGTGCGCAAAGATGGT
1 AGTAGTACATTTGTTGTACTATGGCACTAAGTGTGCAAAGATGGT
* **
974037 AGTAGTACATTTGTTGTACTATGGCACTATGTGTGCAAAGATAAT
1 AGTAGTACATTTGTTGTACTATGGCACTAAGTGTGCAAAGATGGT
*
974082 AGTAATACATTTGTTGTAC--T---ACTATA-TGTGCAAAGATGGT
1 AGTAGTACATTTGTTGTACTATGGCACTA-AGTGTGCAAAGATGGT
* * **
974122 AGTAGTACATTTTTTGTACCATGGCACTGTGTGTGCAA
1 AGTAGTACATTTGTTGTACTATGGCACTAAGTGTGCAA
974160 GAATTGTGTT
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
40 33 0.32
42 1 0.01
43 1 0.01
45 68 0.66
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (45 bp):
AGTAGTACATTTGTTGTACTATGGCACTAAGTGTGCAAAGATGGT
Found at i:975179 original size:16 final size:16
Alignment explanation
Indices: 975158--975196 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
975148 ATTGTTTTAA
975158 ATAAAAATATAATGAT
1 ATAAAAATATAATGAT
* *
975174 AT-AAAATATTATGGT
1 ATAAAAATATAATGAT
975189 ATAAAAAT
1 ATAAAAAT
975197 CATCTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (16 bp):
ATAAAAATATAATGAT
Found at i:983104 original size:17 final size:15
Alignment explanation
Indices: 983091--983162 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 15
983081 CGGTCAACGG
983091 TCGGGTCGGGTCAA-
1 TCGGGTCGGGTCAAC
*
983105 -CGGGTCGGGTTAA-
1 TCGGGTCGGGTCAAC
983118 -CGGGTCGGGTCAAC
1 TCGGGTCGGGTCAAC
983132 GGTCGGGTCGGGTCAAC
1 --TCGGGTCGGGTCAAC
983149 TATCGGGTCGGGTC
1 --TCGGGTCGGGTC
983163 GTGACCGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
13 24 0.48
17 26 0.52
ACGTcount: A:0.12, C:0.22, G:0.44, T:0.21
Consensus pattern (15 bp):
TCGGGTCGGGTCAAC
Found at i:983110 original size:13 final size:13
Alignment explanation
Indices: 983092--983140 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
983082 GGTCAACGGT
983092 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
983105 CGGGTCGGGTTAA
1 CGGGTCGGGTCAA
983118 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
983131 C-GGTCGGGTC
1 CGGGTCGGGTC
983141 GGGTCAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 9 0.26
13 25 0.74
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:990339 original size:17 final size:15
Alignment explanation
Indices: 990326--990397 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 15
990316 CGGTCAACGG
990326 TCGGGTCGGGTCAA-
1 TCGGGTCGGGTCAAC
*
990340 -CGGGTCGGGTTAA-
1 TCGGGTCGGGTCAAC
990353 -CGGGTCGGGTCAAC
1 TCGGGTCGGGTCAAC
990367 GGTCGGGTCGGGTCAAC
1 --TCGGGTCGGGTCAAC
990384 TATCGGGTCGGGTC
1 --TCGGGTCGGGTC
990398 GTGACCGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
13 24 0.48
17 26 0.52
ACGTcount: A:0.12, C:0.22, G:0.44, T:0.21
Consensus pattern (15 bp):
TCGGGTCGGGTCAAC
Found at i:990345 original size:13 final size:13
Alignment explanation
Indices: 990327--990375 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
990317 GGTCAACGGT
990327 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
990340 CGGGTCGGGTTAA
1 CGGGTCGGGTCAA
990353 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
990366 C-GGTCGGGTC
1 CGGGTCGGGTC
990376 GGGTCAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
12 9 0.26
13 25 0.74
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:992921 original size:42 final size:43
Alignment explanation
Indices: 992875--992955 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
992865 CAGTACATCA
*
992875 AACAAAACTTTACATATA-GGGATAACTTTCACTCCTAACTTC
1 AACAAAACTTTACATATAGGGGATAACTGTCACTCCTAACTTC
992917 AACAAAACTTTACATATAGGGGATAACTGTCACTCCTAA
1 AACAAAACTTTACATATAGGGGATAACTGTCACTCCTAA
992956 TTTCTCTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 18 0.49
43 19 0.51
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGATAACTGTCACTCCTAACTTC
Found at i:995849 original size:30 final size:30
Alignment explanation
Indices: 995813--995876 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
995803 TAACCAAAAT
*
995813 AAAATAATTAAAA-TTATAGGAATAAATTAA
1 AAAATAA-TAAAACTTATAGGAAAAAATTAA
*
995843 AAAATAATAAAACTTATAGTAAAAAATTAA
1 AAAATAATAAAACTTATAGGAAAAAATTAA
995873 AAAA
1 AAAA
995877 ATTACTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAATAATAAAACTTATAGGAAAAAATTAA
Found at i:997062 original size:3 final size:3
Alignment explanation
Indices: 997056--997084 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
997046 TATTATTTTT
997056 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
997085 TGGGACAAAA
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:997866 original size:3 final size:3
Alignment explanation
Indices: 997858--997945 Score: 160
Period size: 3 Copynumber: 29.7 Consensus size: 3
997848 AGTATGAAAG
997858 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
997906 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAG TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
997946 CAAAAGACTT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:999509 original size:16 final size:16
Alignment explanation
Indices: 999482--999551 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
999472 GGCGAGCAAT
*
999482 GAGCATCGAGCTTAAC
1 GAGCAACGAGCTTAAC
** *
999498 GAATAACGAGCTTAAT
1 GAGCAACGAGCTTAAC
*
999514 GAGCAACGAGCTTAAT
1 GAGCAACGAGCTTAAC
999530 GAGCAACGAGCTTAAC
1 GAGCAACGAGCTTAAC
999546 GAGCAA
1 GAGCAA
999552 TAAGTCGAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (16 bp):
GAGCAACGAGCTTAAC
Found at i:999546 original size:9 final size:9
Alignment explanation
Indices: 999488--999549 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 9
999478 CAATGAGCAT
999488 CGAGCTTAA
1 CGAGCTTAA
*
999497 CGA--ATAA
1 CGAGCTTAA
999504 CGAGCTTAA
1 CGAGCTTAA
*
999513 TGAGC--AA
1 CGAGCTTAA
999520 CGAGCTTAA
1 CGAGCTTAA
*
999529 TGAGC--AA
1 CGAGCTTAA
999536 CGAGCTTAA
1 CGAGCTTAA
999545 CGAGC
1 CGAGC
999550 AATAAGTCGA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
7 18 0.44
9 23 0.56
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (9 bp):
CGAGCTTAA
Found at i:1004920 original size:5 final size:5
Alignment explanation
Indices: 1004851--1004917 Score: 107
Period size: 5 Copynumber: 13.4 Consensus size: 5
1004841 GTTTAATAAT
1004851 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC
1 ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC ATGAC
* * *
1004901 ATAAC ATAAC ATAAC AT
1 ATGAC ATGAC ATGAC AT
1004918 AACTTAACAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 61 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (5 bp):
ATGAC
Found at i:1004925 original size:5 final size:5
Alignment explanation
Indices: 1004854--1004928 Score: 60
Period size: 5 Copynumber: 15.0 Consensus size: 5
1004844 TAATAATATG
* * * * * * * * *
1004854 ACATG ACATG ACATG ACATG ACATG ACATG ACATG ACATG ACATG ACATA
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA
*
1004904 ACATA ACATA ACATA ACTTA ACATA
1 ACATA ACATA ACATA ACATA ACATA
1004929 TACTTATATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 67 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.21
Consensus pattern (5 bp):
ACATA
Found at i:1006471 original size:18 final size:17
Alignment explanation
Indices: 1006431--1006472 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1006421 TGAAAATTAA
1006431 CTTTTTCTCAAATCGTG
1 CTTTTTCTCAAATCGTG
*
1006448 CCTTTTCTCGAATAT-GTG
1 CTTTTTCTC-AA-ATCGTG
1006466 CTTTTTC
1 CTTTTTC
1006473 GGGTCATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 11 0.52
19 2 0.10
ACGTcount: A:0.14, C:0.24, G:0.12, T:0.50
Consensus pattern (17 bp):
CTTTTTCTCAAATCGTG
Found at i:1012956 original size:19 final size:20
Alignment explanation
Indices: 1012913--1012956 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1012903 TTACTTAAAT
*
1012913 TTATTTCATTTAAATTTCTA
1 TTATTTCATTTAAATTTCCA
* *
1012933 ATATTTCCTTT-AATTTCCA
1 TTATTTCATTTAAATTTCCA
1012952 TTATT
1 TTATT
1012957 GCATCCATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.27, C:0.14, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATTTCATTTAAATTTCCA
Found at i:1014879 original size:117 final size:117
Alignment explanation
Indices: 1014673--1014953 Score: 388
Period size: 117 Copynumber: 2.4 Consensus size: 117
1014663 GTATTGTAGT
**
1014673 ATACCATCCTTGCACACAAAGTGCACCCAATAAGCACCTAAGTGCCACAATGATGTATAGGTTAT
1 ATACCATCCTTGCACACAAAGTGCACCCAATAAGCACCTAAGTGCCACAATGACATATAGGTTAT
*
1014738 ATAGTATACAACAACACTATACTAACAAGTT-TAGAGTGGTAATTAATTATGA
66 ATAGTATACAACAACACTATACTAACAA-TTCAAGAGTGGTAATTAATTATGA
* **
1014790 ATACCATCCTTTCACACAAAGAACACCCAATAAGCACCTAAGTGCCACAATGACATATAGG-TAC
1 ATACCATCCTTGCACACAAAGTGCACCCAATAAGCACCTAAGTGCCACAATGACATATAGGTTA-
* * * *
1014854 TGTAGTATA-AATCGATACTATACTAACAATTCAAGAGTGGTAATTCATTATGA
65 TATAGTATACAA-CAACACTATACTAACAATTCAAGAGTGGTAATTAATTATGA
* * * *
1014907 ATACCATCCTTGCACACAAATTGCTCCCAATAAGTACCAAAGTGCCA
1 ATACCATCCTTGCACACAAAGTGCACCCAATAAGCACCTAAGTGCCA
1014954 GAGTACAACA
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
116 6 0.04
117 138 0.96
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (117 bp):
ATACCATCCTTGCACACAAAGTGCACCCAATAAGCACCTAAGTGCCACAATGACATATAGGTTAT
ATAGTATACAACAACACTATACTAACAATTCAAGAGTGGTAATTAATTATGA
Found at i:1015081 original size:26 final size:26
Alignment explanation
Indices: 1015044--1015100 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1015034 TATAGTTTCC
*
1015044 TTTATCACTTGCACTCGAAAGTGCCA
1 TTTATCAATTGCACTCGAAAGTGCCA
* * *
1015070 TTTATCAATTGCACTTGAAGGTGTCA
1 TTTATCAATTGCACTCGAAAGTGCCA
1015096 TTTAT
1 TTTAT
1015101 ACCAAAGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (26 bp):
TTTATCAATTGCACTCGAAAGTGCCA
Found at i:1016369 original size:20 final size:20
Alignment explanation
Indices: 1016331--1016378 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1016321 CACAGTGACC
1016331 CAATTTC-ACACTTTAACAT
1 CAATTTCAACACTTTAACAT
1016350 CAATTTCAACA-TTCTAACAT
1 CAATTTCAACACTT-TAACAT
*
1016370 AAATTTCAA
1 CAATTTCAA
1016379 ACATAGTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTTTAACAT
Found at i:1017572 original size:27 final size:28
Alignment explanation
Indices: 1017526--1017587 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
1017516 AAATACATAT
1017526 CTTTTGAAAATTACACTTT-TCCCTAAA
1 CTTTTGAAAATTACACTTTGTCCCTAAA
**
1017553 CTTTTGAAAATTATCTTTTTGGTCCCTAAA
1 CTTTTGAAAATTA-CACTTT-GTCCCTAAA
1017583 CTTTT
1 CTTTT
1017588 CCAAACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 13 0.43
28 4 0.13
30 13 0.43
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.47
Consensus pattern (28 bp):
CTTTTGAAAATTACACTTTGTCCCTAAA
Found at i:1029779 original size:15 final size:15
Alignment explanation
Indices: 1029759--1029790 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1029749 ATACAAAAAT
*
1029759 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
1029774 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
1029789 AA
1 AA
1029791 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:1029957 original size:2 final size:2
Alignment explanation
Indices: 1029950--1029982 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1029940 AAGATAATTA
1029950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1029983 ATAAGAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1031535 original size:110 final size:110
Alignment explanation
Indices: 1031400--1031606 Score: 299
Period size: 110 Copynumber: 1.9 Consensus size: 110
1031390 GCTCTGGAAA
* * * *
1031400 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGACCTTATGTTGTCTCGAGTTCAATA
1 TTGTTTGATGACAATCAGTCGCCCCTTCGCTGTGAAATTGACCTTATGTTGTCTCGAGTCCAATA
* *
1031465 TCCTTCGCTGTGAAGTTGAAATT-GACTCTGAATAAAACTAAAAAG
66 TCCCTCGCTGTGAAATTGAAATTAG-CTCTGAATAAAACTAAAAAG
* * * * *
1031510 TTGTTTGATGACAATCAGTTGCCCCTTCGTTGTGAAATTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGATGACAATCAGTCGCCCCTTCGCTGTGAAATTGACCTTATGTTGTCTCGAGTCCAATA
1031575 TCCCTCGCTGTGAAATTGAAATTAGCTCTGAA
66 TCCCTCGCTGTGAAATTGAAATTAGCTCTGAA
1031607 ACTGGGAAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 84 0.99
111 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (110 bp):
TTGTTTGATGACAATCAGTCGCCCCTTCGCTGTGAAATTGACCTTATGTTGTCTCGAGTCCAATA
TCCCTCGCTGTGAAATTGAAATTAGCTCTGAATAAAACTAAAAAG
Found at i:1032657 original size:18 final size:17
Alignment explanation
Indices: 1032618--1032659 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1032608 AACCCACCTT
*
1032618 ATTTTTTGTTTTTTTCT
1 ATTTTTTGTTTTTTTCA
*
1032635 CTTTTTTGTCTTTTTTCA
1 ATTTTTTGT-TTTTTTCA
1032653 ATTTTTT
1 ATTTTTT
1032660 CAATTTAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.79
Consensus pattern (17 bp):
ATTTTTTGTTTTTTTCA
Found at i:1043108 original size:29 final size:29
Alignment explanation
Indices: 1043050--1043112 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1043040 AAAAATGTAG
* *
1043050 TAAAAATGAATAAAATAAAGAAGGTGAAA
1 TAAAAATAAATAAAATAAAGAAGGTAAAA
* *
1043079 TAAAAATAAATACAATAAAGTAGAG-AAAA
1 TAAAAATAAATAAAATAAAGAAG-GTAAAA
1043108 TAAAA
1 TAAAA
1043113 CAGATAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (29 bp):
TAAAAATAAATAAAATAAAGAAGGTAAAA
Found at i:1043261 original size:15 final size:15
Alignment explanation
Indices: 1043241--1043272 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1043231 ATACAAAAAT
*
1043241 AAAAATAGAAGATAA
1 AAAAATAAAAGATAA
1043256 AAAAATAAAAGATAA
1 AAAAATAAAAGATAA
1043271 AA
1 AA
1043273 TGAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAGATAA
Found at i:1043296 original size:16 final size:17
Alignment explanation
Indices: 1043275--1043338 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
1043265 AGATAAAATG
1043275 AAATATATA-AAATAAT
1 AAATATATAGAAATAAT
*
1043291 AAATATATA-ACAT-AT
1 AAATATATAGAAATAAT
*
1043306 -AAT-TATAGTAATAA-
1 AAATATATAGAAATAAT
*
1043320 AAATATATATAAATAAT
1 AAATATATAGAAATAAT
1043337 AA
1 AA
1043339 TGATATATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.11
14 5 0.13
15 6 0.16
16 21 0.55
17 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATATATAGAAATAAT
Found at i:1043336 original size:19 final size:19
Alignment explanation
Indices: 1043314--1043370 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1043304 ATAATTATAG
1043314 TAATAAAAATATATATAAA
1 TAATAAAAATATATATAAA
** *
1043333 TAATAATGATATATGAAAAA
1 TAATAAAAATATAT-ATAAA
* *
1043353 GAATTAAAAGTATATATA
1 TAA-TAAAAATATATATA
1043371 TATATATAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
19 12 0.43
20 8 0.29
21 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
TAATAAAAATATATATAAA
Found at i:1045195 original size:17 final size:17
Alignment explanation
Indices: 1045175--1045213 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1045165 AAATATATAT
1045175 ATAATTTAAAATAAAAA
1 ATAATTTAAAATAAAAA
* *
1045192 ATAATTTTATATAAAAA
1 ATAATTTAAAATAAAAA
1045209 ATAAT
1 ATAAT
1045214 ATTATATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATTTAAAATAAAAA
Found at i:1045218 original size:17 final size:17
Alignment explanation
Indices: 1045185--1045220 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1045175 ATAATTTAAA
*
1045185 ATAAAAAATAATTTTAT
1 ATAAAAAATAATATTAT
1045202 ATAAAAAATAATATTAT
1 ATAAAAAATAATATTAT
1045219 AT
1 AT
1045221 TGTTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAAATAATATTAT
Found at i:1045958 original size:171 final size:169
Alignment explanation
Indices: 1045589--1046339 Score: 640
Period size: 171 Copynumber: 4.4 Consensus size: 169
1045579 GGTATTTGTT
* * * * * * *
1045589 TCACATAATCAAACATAACATGTATACACTACTCGTTTTACTTTTCAAAAATTTCCACTTAATTC
1 TCACATAATCAAGCAAAAAAGGTATACACTATTCGTTTTACTTTTCAAAAATTTCCCCTTAATTT
* * * * ** *** * * * *
1045654 TTTATTATC-AAATTACATTTGCTGGGAGTTGAATTTGGGTCTATTGCTTGTAAGACAATTATCC
66 TTTACTATCGAAATT--GTTTTCTAGGAGTCAAACCAGAGTATATTGCTTGGAAGGCAATTATCC
* * ** * * *
1045718 TAACTATTGGACTACAAATGCCTCTTTTTTACATTATTCGT
129 AAACTATTAGACTACAAACACCTCTTCTTTACACTATTCGC
* * * **
1045759 TTACATAATCAAGCAAAAACACGTATACACTA-CCGGTTTTACTTTTCAAATTTTTCCCCTTAAT
1 TCACATAATCAAGCAAAAA-AGGTATACACTATTC-GTTTTACTTTTCAAAAATTTCCCCTTAAT
* * * * *
1045823 TTTTTACAATCGTAATTGTGTCTTCTTGGAGTCGAA-CATGAGTATATTGCTTAGAAGGCAATTA
64 TTTTTACTATCGAAATTGT-T-TTCTAGGAGTCAAACCA-GAGTATATTGCTTGGAAGGCAATTA
**
1045887 TCCAAACCGTTAGACTACAAACACCTCTTCTTTACACTATTCGC
126 TCCAAACTATTAGACTACAAACACCTCTTCTTTACACTATTCGC
* **
1045931 TCACATAATCAAGCACAAAAGGTATACACTATTCGTTAAACTTTTCAAAAATTTCCCCTTAATTT
1 TCACATAATCAAGCAAAAAAGGTATACACTATTCGTTTTACTTTTCAAAAATTTCCCCTTAATTT
*
1045996 TTTACTATCGAAATTGCATTTGCTAGGAGTCAAACCA-AGGTATATTGCTTGGAAGGCAATTAT-
66 TTTACTATCGAAATTG--TTTTCTAGGAGTCAAACCAGA-GTATATTGCTTGGAAGGCAATTATC
* * *
1046059 CATAACTATTAGACAACAAACACCTCTTCTTGACAATATTCGC
128 CA-AACTATTAGACTACAAACACCTCTTCTTTACACTATTCGC
* * * * * * * * *
1046102 TTCTCATAATCATGCAAAAAATGTTTACACTATTTGGTTTATTTTTAAAAAAATT-CCCTTAA-T
1 -TCACATAATCAAGCAAAAAAGGTATACACTATTCGTTTTACTTTTCAAAAATTTCCCCTTAATT
* * * *
1046165 TTTTACTATTGAAATTGCTTTTGTCGGGAGTCAAACCA-AGCTATATTGCTTGGAAGGCAACTAT
65 TTTTACTATCGAAATTG-TTTTCT-AGGAGTCAAACCAGAG-TATATTGCTTGGAAGGCAATTAT
* * * * * * *
1046229 CCTAACTGTTGGACTACAAACGCCTCTTCTTTAAACTATTTGTT
127 CCAAACTATTAGACTACAAACACCTCTTCTTTACACTATTCG-C
* * * *
1046273 TCACATAAACGAG-AACGAAAGGTATACACTATTCGTTTTACTTTTC-AAAATTTCTCCCTTCAT
1 TCACATAATCAAGCAA-AAAAGGTATACACTATTCGTTTTACTTTTCAAAAATTTC-CCCTTAAT
1046336 TTTT
64 TTTT
1046340 ATTATGTAAT
Statistics
Matches: 467, Mismatches: 93, Indels: 40
0.78 0.16 0.07
Matches are distributed among these distances:
169 13 0.03
170 135 0.29
171 181 0.39
172 137 0.29
173 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (169 bp):
TCACATAATCAAGCAAAAAAGGTATACACTATTCGTTTTACTTTTCAAAAATTTCCCCTTAATTT
TTTACTATCGAAATTGTTTTCTAGGAGTCAAACCAGAGTATATTGCTTGGAAGGCAATTATCCAA
ACTATTAGACTACAAACACCTCTTCTTTACACTATTCGC
Found at i:1046557 original size:341 final size:341
Alignment explanation
Indices: 1045581--1046768 Score: 979
Period size: 341 Copynumber: 3.5 Consensus size: 341
1045571 TTCCAAATGG
*
1045581 TATTTGTTTCACATAATC-A-AACATAACATGTATACACTACTCGTTTTACTTTTCAAAAATTTC
1 TATTTGTTTCACATAATCAAGAACA-AA-AGGTATACACTACTCGTTTTACTTTTCAAAAATTTC
* * * * * ** * ** *
1045644 CACTTAATTCTTTATTATCAAATTACATTTGCTGGGAGTTGAAT-TTGGGTCTATTGCTTGTAAG
64 CCCTTAATTTTTTACTATGAAATTGCATTTGCCAGGAG-TCAATCCCGGGTCTATTGCTTGGAAG
* *
1045708 ACAATTATCCTAACTATTGGACTACAAATGCCTCTTTTTTACATTATTCGTTT-ACATAATCAAG
128 ACAATTATCCTAACTATTGGACTACAAACGCCTCTTTTTTACAATATTCGTTTCACATAATCAAG
* *
1045772 CAAAAACACGTATACACTAC-CGGTTTTACTTTTCAAATTTTTCCCCTTAATTTTTTACA-ATCG
193 C-AAAACACGTATACACTACTC-TTTTTACTTTTCAAA--TTTCCCCTTAATTTTTTAAATATCG
* ** * * * * * * *
1045835 TAATTGTGTCTTCTTGGAGTCGAACATGAGTATATTGCTTAGAAGGCAATTATCCAAACCGTTAG
254 TAATTGTGT-TTCCTGGAGTCGAACCCGAATCTTTTGCTTGGAAGGCAATTATCCTAACTGTTGG
* *
1045900 ACTACAAACACCTCTTCTTTACAC
318 ACTACAAACGCCTCTTCTTTAAAC
* * * * **
1045924 TATTCG-CTCACATAATCAAGCACAAAAGGTATACACTATTCGTTAAACTTTTCAAAAATTTCCC
1 TATTTGTTTCACATAATCAAGAACAAAAGGTATACACTACTCGTTTTACTTTTCAAAAATTTCCC
* * ** * *
1045988 CTTAATTTTTTACTATCGAAATTGCATTTGCTAGGAGTCAAACCAAGGTATATTGCTTGGAAGGC
66 CTTAATTTTTTACTAT-GAAATTGCATTTGCCAGGAGTCAATCCCGGGTCTATTGCTTGGAAGAC
* * * * * * * * *
1046053 AATTATCATAACTATTAGACAACAAACACCTCTTCTTGACAATATTCGCTTCTCATAATCATGCA
130 AATTATCCTAACTATTGGACTACAAACGCCTCTTTTTTACAATATTCGTTTCACATAATCAAGCA
* * * * * * * * *
1046118 AAAAATGTTTACACTA-T-TTGGTTTATTTTTAAAAAAATT-CCCTTAA-TTTTT-ACTATTGAA
195 AAACACGTATACACTACTCTT--TTTACTTTT--CAAATTTCCCCTTAATTTTTTAAATATCGTA
* * * * *
1046178 ATTGCT-TTTGTCGGGAGTC-AAACC-AAGCTATATTGCTTGGAAGGCAACTATCCTAACTGTTG
256 ATTG-TGTTT-CCTGGAGTCGAACCCGAATCT-T-TTGCTTGGAAGGCAATTATCCTAACTGTTG
1046240 GACTACAAACGCCTCTTCTTTAAAC
317 GACTACAAACGCCTCTTCTTTAAAC
* * * *
1046265 TATTTGTTTCACATAAACGAGAACGAAAGGTATACACTATTCGTTTTACTTTTC-AAAATTTCTC
1 TATTTGTTTCACATAATCAAGAACAAAAGGTATACACTACTCGTTTTACTTTTCAAAAATTTC-C
* * * * * *
1046329 CCTTCA-TTTTTATTATGTAATTGCATTTGCCAAGACTCAATCCCGGGTCTA-TGCTTGGAAGGC
65 CCTTAATTTTTTACTATGAAATTGCATTTGCCAGGAGTCAATCCCGGGTCTATTGCTTGGAAGAC
** * * *
1046392 AATTATCCTAACCGTTGGATTACAAACGCCT-TTTTTTACACT-TT-GTTTCAAATAATCAAAAG
130 AATTATCCTAACTATTGGACTACAAACGCCTCTTTTTTACAATATTCGTTTCACATAATC--AAG
* *
1046454 -AACAACACCTATACACTACTCTTTTTACTTATCAACATTTCCCCCTTAATTTTTTAAATATCGT
193 CAA-AACACGTATACACTACTCTTTTTACTTTTCAA-ATTT-CCCCTTAATTTTTTAAATATCGT
* * * *
1046518 AATTGTGTTTACCTGGAGTCGAACCCGATTCTTTTGCTTGGAAGGAAATTATCCTAATTATTGGA
255 AATTGTGTTT-CCTGGAGTCGAACCCGAATCTTTTGCTTGGAAGGCAATTATCCTAACTGTTGGA
* * * * * *
1046583 -TGAAAAATGCATCCTATTTAAGC
319 CT-ACAAACGCCTCTTCTTTAAAC
* * * *
1046606 TATTTGTTTCACATAATCAAGAACTACACAA--TATACACTACACGTTTTACTTATCAACATTTT
1 TATTTGTTTCACATAATCAAGAAC-A-A-AAGGTATACACTACTCGTTTTACTTTTCAAAAATTT
* ** * * * * *
1046669 CCTCTTAATTTTTTACTATTGTGATTGCGTTTGTCGGGAGTCGAA-CCCGAGTCTATTGATTGGA
63 CCCCTTAATTTTTTACTA-TGAAATTGCATTTGCCAGGAGTC-AATCCCGGGTCTATTGCTTGGA
* * *
1046733 AGAAAATTATCCTAACTGTTGGACTACAAATGCCTC
126 AGACAATTATCCTAACTATTGGACTACAAACGCCTC
1046769 ATCTTTACTT
Statistics
Matches: 662, Mismatches: 143, Indels: 77
0.75 0.16 0.09
Matches are distributed among these distances:
336 12 0.02
337 7 0.01
338 28 0.04
339 46 0.07
340 40 0.06
341 176 0.27
342 145 0.22
343 125 0.19
344 41 0.06
345 42 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (341 bp):
TATTTGTTTCACATAATCAAGAACAAAAGGTATACACTACTCGTTTTACTTTTCAAAAATTTCCC
CTTAATTTTTTACTATGAAATTGCATTTGCCAGGAGTCAATCCCGGGTCTATTGCTTGGAAGACA
ATTATCCTAACTATTGGACTACAAACGCCTCTTTTTTACAATATTCGTTTCACATAATCAAGCAA
AACACGTATACACTACTCTTTTTACTTTTCAAATTTCCCCTTAATTTTTTAAATATCGTAATTGT
GTTTCCTGGAGTCGAACCCGAATCTTTTGCTTGGAAGGCAATTATCCTAACTGTTGGACTACAAA
CGCCTCTTCTTTAAAC
Found at i:1046572 original size:172 final size:172
Alignment explanation
Indices: 1046208--1046768 Score: 494
Period size: 173 Copynumber: 3.3 Consensus size: 172
1046198 AACCAAGCTA
* * * * * * *
1046208 TATTGCTTGGAAGGCAACTATCCTAACTGTTGGACTACAAACGCCTCTTCTTTAAACTATTTGTT
1 TATTGCTTGGAAGGAAATTATCCTAACTGTTGGATTACAAATGCCTCCTATTTAAGC-ATTTGTT
* * * ** ** * * * *
1046273 TCACATAAACGAGAACGAA-A-GGTATACACTATTCGTTTTACTTTTCAAAATTTCTCCCTTCA-
65 TCAAATAATCAAGAAC-AACACAATATACACTACACGTTTTACTTATCAACATTTCCCCCTTAAT
* * * ** * *
1046335 TTTTTATTAT-GTAATTGCATTTGCCAAGACTC-AATCCCGGGTC
129 TTTTTAATATCGTAATTGCGTTTACCGGGAGTCGAA-CCCGAGTC
* * * * *
1046378 TA-TGCTTGGAAGGCAATTATCCTAACCGTTGGATTACAAACGCCT--TTTTTTA-CACTTTGTT
1 TATTGCTTGGAAGGAAATTATCCTAACTGTTGGATTACAAATGCCTCCTATTTAAGCA-TTTGTT
* * *
1046439 TCAAATAATCAAAAGAACAACAC-CTATACACTACTCTTTTTACTTATCAACATTTCCCCCTTAA
65 TCAAATAATC--AAGAACAACACAATATACACTACACGTTTTACTTATCAACATTTCCCCCTTAA
* * *
1046503 TTTTTTAAATATCGTAATTGTGTTTACCTGGAGTCGAACCCGATTC
128 TTTTTT-AATATCGTAATTGCGTTTACCGGGAGTCGAACCCGAGTC
* * * * * *
1046549 TTTTGCTTGGAAGGAAATTATCCTAATTATTGGATGAAAAATGCATCCTATTTAAGCTATTTGTT
1 TATTGCTTGGAAGGAAATTATCCTAACTGTTGGATTACAAATGCCTCCTATTTAAGC-ATTTGTT
* * * *
1046614 TCACATAATCAAGAACTACACAATATACACTACACGTTTTACTTATCAACATTTTCCTCTTAATT
65 TCAAATAATCAAGAACAACACAATATACACTACACGTTTTACTTATCAACATTTCCCCCTTAATT
* * * **
1046679 TTTTACTATTGTGATTGCGTTTGTCGGGAGTCGAACCCGAGTC
130 TTTTAATATCGTAATTGCGTTTACCGGGAGTCGAACCCGAGTC
* * *
1046722 TATTGATTGGAAGAAAATTATCCTAACTGTTGGACTACAAATGCCTC
1 TATTGCTTGGAAGGAAATTATCCTAACTGTTGGATTACAAATGCCTC
1046769 ATCTTTACTT
Statistics
Matches: 317, Mismatches: 59, Indels: 27
0.79 0.15 0.07
Matches are distributed among these distances:
165 1 0.00
166 15 0.05
167 7 0.02
168 40 0.13
169 45 0.14
170 6 0.02
171 23 0.07
172 37 0.12
173 79 0.25
174 47 0.15
175 16 0.05
176 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (172 bp):
TATTGCTTGGAAGGAAATTATCCTAACTGTTGGATTACAAATGCCTCCTATTTAAGCATTTGTTT
CAAATAATCAAGAACAACACAATATACACTACACGTTTTACTTATCAACATTTCCCCCTTAATTT
TTTAATATCGTAATTGCGTTTACCGGGAGTCGAACCCGAGTC
Found at i:1046865 original size:110 final size:110
Alignment explanation
Indices: 1046667--1046872 Score: 340
Period size: 110 Copynumber: 1.9 Consensus size: 110
1046657 TATCAACATT
* *
1046667 TTCCTCTTAATTTTTTACTATTGTGATTGCGTTTGTCGGGAGTCGAACCCGAGTCTATTGATTGG
1 TTCCCCTTAATTTTTTACTATTGTGATTGCATTTGTCGGGAGTCGAACCCGAGTCTATTGATTGG
*
1046732 AAGAAAATTATCCTAACTGTTGGACTACAAATGCCTCATCTTTAC
66 AAGAAAATTATCCTAACCGTTGGACTACAAATGCCTCATCTTTAC
* * *
1046777 TTCCCCTTAATTTTTTACTATTGTGATTGCATTTGTCGGGAGTCGAACCTGGGTCTATTGCTTGG
1 TTCCCCTTAATTTTTTACTATTGTGATTGCATTTGTCGGGAGTCGAACCCGAGTCTATTGATTGG
**
1046842 AAGGCAATTATCCTAACCGTTGGACTACAAA
66 AAGAAAATTATCCTAACCGTTGGACTACAAA
1046873 CACCTATTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 88 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (110 bp):
TTCCCCTTAATTTTTTACTATTGTGATTGCATTTGTCGGGAGTCGAACCCGAGTCTATTGATTGG
AAGAAAATTATCCTAACCGTTGGACTACAAATGCCTCATCTTTAC
Found at i:1047299 original size:120 final size:120
Alignment explanation
Indices: 1047083--1047306 Score: 283
Period size: 120 Copynumber: 1.9 Consensus size: 120
1047073 TAAAAGGTAA
* * ** * *
1047083 ACACTATTTGTTTTACTTTTCAGAATTTTCCCCTTATTTTTTTACTATCGAAATTTCCTTTTTCG
1 ACACTATTTGTGTTACTTTTCAAAATTTTCCCCTTAAATTTTTACTATCGAAATATCCTTTGTCG
* * * * *
1047148 CTAGTCGAACCCATGTTTATTGCTTGTAAGGCAATTATCCTAGTGGTTGGAAGAC
66 CGAGTCCAACCCAGGTCTATTGCTTGGAAGGCAATTATCCTAGTGGTTGGAAGAC
* *
1047203 ACACTATTTGTGTTACTTTTCAAAATTTTCCCTTTAAATTTTTACTATC-ATAATAAT-GTTTGT
1 ACACTATTTGTGTTACTTTTCAAAATTTTCCCCTTAAATTTTTACTATCGA-AAT-ATCCTTTGT
1047266 CG-GAGTCCAACCCAGGTCCTATTGCTTGGAAGGCAATTATC
64 CGCGAGTCCAACCCAGGT-CTATTGCTTGGAAGGCAATTATC
1047307 GTACTTCTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
119 13 0.15
120 74 0.84
121 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (120 bp):
ACACTATTTGTGTTACTTTTCAAAATTTTCCCCTTAAATTTTTACTATCGAAATATCCTTTGTCG
CGAGTCCAACCCAGGTCTATTGCTTGGAAGGCAATTATCCTAGTGGTTGGAAGAC
Found at i:1047812 original size:172 final size:171
Alignment explanation
Indices: 1047322--1048226 Score: 822
Period size: 172 Copynumber: 5.3 Consensus size: 171
1047312 TCTTTTCACA
*
1047322 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTAC-TTTTCAAAATTATCCC
1 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTTAAAAATT-TCCC
* ** * *
1047386 CTT-ATTTTTTTCTATCGTAATTGTGTTTGTTGGGAGTCGAATCCGAGTCTATTGATTGGAAGGG
65 CTTAATTTTTTTCTATCGTAATTG-ATTTGCCGGGAGTCGAACCCGAGTCTATTGCTTGGAA--G
* * * * * * *
1047450 GCAATTATCCTAACTG-TAGGACTACGAACGCATCATCTTCACACT
127 GCAATTATTCTAACAGCT-GGACTACAAACGCCTCTTATTTACACT
*
1047495 ATTTGTTTCACATAATCAAGAACAACA--TGT--A-TACTCGTTTTACTTTTT-AAAATTTCCCC
1 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTTAAAAATTT-CCC
*** * * * * * *
1047554 CTTAATTTTTTAAGATCGCGATAGTGA-TTGCCGGGAGTCGAACCCGGGTCCATCGCTTGAAAGG
65 CTTAATTTTTTTCTATCG-TA-ATTGATTTGCCGGGAGTCGAACCCGAGTCTATTGCTTGGAAGG
* * *
1047618 CAATTATCCTAACCGTTGGACTACAAACGCCTCTTATTTACACT
128 CAATTATTCTAACAGCTGGACTACAAACGCCTCTTATTTACACT
* * * **
1047662 ATTTGTTTCACATAATGAAGAAAAACACGTATACACTAATCGTTTTACTTTTTAAAAATTTCCTA
1 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTTAAAAATTTCCCC
* * * * * * *
1047727 ATAATTTTTTTCCTAACGTAATTCATTTGCCGGGAGTCAAACCCGAGTCTATTGCTTAGAAAGTA
66 TTAATTTTTTT-CTATCGTAATTGATTTGCCGGGAGTCGAACCCGAGTCTATTGCTTGGAAGGCA
*
1047792 ATTATTCTAAGAGCTGGACTACAAACGCCTCTTATTTACACT
130 ATTATTCTAACAGCTGGACTACAAACGCCTCTTATTTACACT
* * * * * *
1047834 ATTAGTTTCACATAATCAAGAACAACACCTATACACTACTTGTTCTACTTTTCAAAATTTTCCCC
1 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTTAAAAATTTCCCC
* * * * * *
1047899 TTAATTTTTTACTATCGTAATTGAGTTTTCCCGGAGTCGAA-TCGGGTCTACTGCTTGGAAGGCA
66 TTAATTTTTTTCTATCGTAATTGA-TTTGCCGGGAGTCGAACCCGAGTCTATTGCTTGGAAGGCA
* * * *
1047963 ATTA-TCTTAACCA-CTGGACTAAAAACGCATCTTCTTTAAACT
130 ATTATTC-TAA-CAGCTGGACTACAAACGCCTCTTATTTACACT
* * * * * * *
1048005 ATTTGCTTCACATAATTAGGAATAACACATATACATTACTCGTTTTAC-TTTTAAACATTTCCCC
1 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTTAAAAATTTCCCC
* * ** * * *
1048069 TTAATTTTTTT-TACATTTGTAATTGTGTTTATCGGGAGTCGTACCTGCA-TCTTTTGCTTGGAA
66 TTAATTTTTTTCT--A-TCGTAATTG-ATTTGCCGGGAGTCGAACCCG-AGTCTATTGCTTGGAA
* ** *
1048132 GGAAATTATATCCTAATTGTTGGAC-A-AAACGCCTCTTATTTA-AGCT
126 GGCAATTAT-T-CTAACAGCTGGACTACAAACGCCTCTTATTTACA-CT
* *
1048178 ATTTGTTTCACATAGTGAAGAACAACACGTATACACTACTCGTTTTACT
1 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACT
1048227 ATCGTAATTA
Statistics
Matches: 590, Mismatches: 113, Indels: 57
0.78 0.15 0.08
Matches are distributed among these distances:
167 64 0.11
168 25 0.04
169 46 0.08
170 26 0.04
171 109 0.18
172 195 0.33
173 114 0.19
174 1 0.00
175 9 0.02
176 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (171 bp):
ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTTAAAAATTTCCCC
TTAATTTTTTTCTATCGTAATTGATTTGCCGGGAGTCGAACCCGAGTCTATTGCTTGGAAGGCAA
TTATTCTAACAGCTGGACTACAAACGCCTCTTATTTACACT
Found at i:1048080 original size:343 final size:338
Alignment explanation
Indices: 1047322--1048079 Score: 844
Period size: 343 Copynumber: 2.2 Consensus size: 338
1047312 TCTTTTCACA
*
1047322 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTATCCCC
1 ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTACTTTT-AAAATT-TCCCC
* ** ** * * * *
1047387 TT-ATTTTTTTCTATCGTAATTGTGTTTGTTGGGAGTCGAATCCGAGTCTATTGATTGGAAGGGG
64 TTAATTTTTTTCTAACGTAATTGCATTTGCCGGGAGTCAAACCCGAGTCTATTGATTAGAA-GAG
* * * *
1047451 CAATTATCCTAACTGTAGGACTACGAACGCATCATCTTCACACTATTTGTTTCACATAATCAAGA
128 CAATTATCCTAACAGTAGGACTACAAACGCATCATATTCACACTATTAGTTTCACATAATCAAGA
* * * * *
1047516 ACAACATGTATACTCGTTTTACTTTTTAAAATTTCCCCCTTAATTTTTTAAGATCGCGATAGTGA
193 ACAACATATATACTCGTTCTACTTTTCAAAATTTCCCCCTTAATTTTTTAAGATCGCAATAGAGA
* ** *
1047581 TTGCCGGGAGTCGAACCCGGGTCCATCGCTTGAAAGGCAATTATCCTAACCGTTGGACTACAAAC
258 TTGCCCGGAGTCGAACCCGGGTCCATCGCTTGAAAGGCAATTATCCTAACCACTGGACTAAAAAC
* *
1047646 GCCTCTTATTTACACT
323 GCATCTTATTTAAACT
* * **
1047662 ATTTGTTTCACATAATGAAGAAAAACACGTATACACTAATCGTTTTACTTTTTAAAAATTTCCTA
1 ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTAC-TTTT-AAAATTTCCCC
* *
1047727 ATAATTTTTTTCCTAACGTAATT-CATTTGCCGGGAGTCAAACCCGAGTCTATTGCTTAGAA-AG
64 TTAATTTTTTT-CTAACGTAATTGCATTTGCCGGGAGTCAAACCCGAGTCTATTGATTAGAAGAG
* * * * * *
1047790 TAATTATTCTAAGAGCT-GGACTACAAACGCCTCTTATTTACACTATTAGTTTCACATAATCAAG
128 CAATTATCCTAACAG-TAGGACTACAAACGCATCATATTCACACTATTAGTTTCACATAATCAAG
* * ** *
1047854 AACAACACCTATACACTACTTGTTCTACTTTTCAAAATTTTCCCCTTAATTTTTTACTATCGTAA
192 AACAACA--TAT--A-TACTCGTTCTACTTTTCAAAATTTCCCCCTTAATTTTTTAAGATCGCAA
* * * * * * *
1047919 TTGAGTTTTCCCGGAGTCGAA-TCGGGTCTA-CTGCTTGGAAGGCAATTATCTTAACCACTGGAC
252 TAGAGATTGCCCGGAGTCGAACCCGGGTCCATC-GCTTGAAAGGCAATTATCCTAACCACTGGAC
*
1047982 TAAAAACGCATCTTCTTTAAACT
316 TAAAAACGCATCTTATTTAAACT
* * * * * *
1048005 ATTTGCTTCACATAATTAGGAATAACACATATACATTACTCGTTTTACTTTTAAACATTTCCCCT
1 ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTACTTTTAAA-ATTTCCCCT
1048070 TAATTTTTTT
65 TAATTTTTTT
1048080 TACATTTGTA
Statistics
Matches: 346, Mismatches: 61, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
339 60 0.17
340 50 0.14
341 53 0.15
342 31 0.09
343 95 0.27
344 57 0.16
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (338 bp):
ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTACTTTTAAAATTTCCCCTT
AATTTTTTTCTAACGTAATTGCATTTGCCGGGAGTCAAACCCGAGTCTATTGATTAGAAGAGCAA
TTATCCTAACAGTAGGACTACAAACGCATCATATTCACACTATTAGTTTCACATAATCAAGAACA
ACATATATACTCGTTCTACTTTTCAAAATTTCCCCCTTAATTTTTTAAGATCGCAATAGAGATTG
CCCGGAGTCGAACCCGGGTCCATCGCTTGAAAGGCAATTATCCTAACCACTGGACTAAAAACGCA
TCTTATTTAAACT
Found at i:1048168 original size:344 final size:344
Alignment explanation
Indices: 1047322--1048226 Score: 927
Period size: 344 Copynumber: 2.6 Consensus size: 344
1047312 TCTTTTCACA
*
1047322 ATTTGTTTCACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTATCCCC
1 ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTACTTTT-AAAATT-TCCCC
* *
1047387 TT-A-TTTTTTT-C-TATCGTAATTGTGTTTGTTGGGAGTCGAATCCGAGTCTATTGATTGGAAG
64 TTAATTTTTTTTACAT-TCGTAATTGTGTTTGTCGGGAGTCGAA-CCGAGTCTATTGCTTGGAA-
* * * * * * *
1047448 GGGCAA-T-TATCCTAACTGTAGGACTACGAACGCATCATCTTCACACTATTTGTTTCACATAAT
126 -GGAAATTATATCCTAACTGTTGGACTACAAACGCCTCTTATTTACACTATTTGTTTCACATAAT
* *
1047511 CAAGAACAACA-TGT--A-TACTCGTTTTACTTTTTAAAATTTCCCCCTTAATTTTTTAAGATCG
190 CAAGAACAACACTATACACTACTCGTTTTACTTTTCAAAATTTCCCCCTTAATTTTTTAAGATCG
* * * **
1047572 CGATAGTGATTGCCGGGAGTCGAACCCGGGTCCATCGCTTGAAAGGCAATTATCCTAACCGTTGG
255 CAATAGAGATTGCCCGGAGTCGAACCCGGGTCCATCGCTTGAAAGGCAATTATCCTAACCACTGG
* * *
1047637 ACTACAAACGCCTCTTATTTACACT
320 ACTAAAAACGCATCTTATTTAAACT
* * **
1047662 ATTTGTTTCACATAATGAAGAAAAACACGTATACACTAATCGTTTTACTTTTTAAAAATTTCCTA
1 ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTAC-TTTT-AAAATTTCCCC
* ** * * *
1047727 ATAATTTTTTTCCTA-A--CGTAATT-CATTTGCCGGGAGTCAAACCCGAGTCTATTGCTTAGAA
64 TTAATTTTTTT--TACATTCGTAATTGTGTTTGTCGGGAGTCGAA-CCGAGTCTATTGCTTGGAA
* * ** * *
1047788 AGTAATTAT-T-CTAAGAGCTGGACTACAAACGCCTCTTATTTACACTATTAGTTTCACATAATC
126 GGAAATTATATCCTAACTGTTGGACTACAAACGCCTCTTATTTACACTATTTGTTTCACATAATC
* * * **
1047851 AAGAACAACACCTATACACTACTTGTTCTACTTTTCAAAATTTTCCCCTTAATTTTTTACTATCG
191 AAGAACAACA-CTATACACTACTCGTTTTACTTTTCAAAATTTCCCCCTTAATTTTTTAAGATCG
* * * * * * * *
1047916 TAATTGAGTTTTCCCGGAGTCGAA-TCGGGTCTA-CTGCTTGGAAGGCAATTATCTTAACCACTG
255 CAATAGAGATTGCCCGGAGTCGAACCCGGGTCCATC-GCTTGAAAGGCAATTATCCTAACCACTG
*
1047979 GACTAAAAACGCATCTTCTTTAAACT
319 GACTAAAAACGCATCTTATTTAAACT
* * * * * *
1048005 ATTTGCTTCACATAATTAGGAATAACACATATACATTACTCGTTTTACTTTTAAACATTTCCCCT
1 ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTACTTTTAAA-ATTTCCCCT
* * * *
1048070 TAATTTTTTTTACATTTGTAATTGTGTTTATCGGGAGTCGTACCTGCA-TCTTTTGCTTGGAAGG
65 TAATTTTTTTTACATTCGTAATTGTGTTTGTCGGGAGTCGAACC-G-AGTCTATTGCTTGGAAGG
* * *
1048134 AAATTATATCCTAATTGTTGGAC-A-AAACGCCTCTTATTTA-AGCTATTTGTTTCACATAGTGA
128 AAATTATATCCTAACTGTTGGACTACAAACGCCTCTTATTTACA-CTATTTGTTTCACATAATCA
1048196 AGAACAACACGTATACACTACTCGTTTTACT
192 AGAACAACAC-TATACACTACTCGTTTTACT
1048227 ATCGTAATTA
Statistics
Matches: 459, Mismatches: 80, Indels: 48
0.78 0.14 0.08
Matches are distributed among these distances:
339 56 0.12
340 53 0.12
341 48 0.10
342 34 0.07
343 105 0.23
344 150 0.33
345 3 0.01
346 10 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (344 bp):
ATTTGTTTCACATAATCAAGAAAAACACGTATACACTACTCGTTTTACTTTTAAAATTTCCCCTT
AATTTTTTTTACATTCGTAATTGTGTTTGTCGGGAGTCGAACCGAGTCTATTGCTTGGAAGGAAA
TTATATCCTAACTGTTGGACTACAAACGCCTCTTATTTACACTATTTGTTTCACATAATCAAGAA
CAACACTATACACTACTCGTTTTACTTTTCAAAATTTCCCCCTTAATTTTTTAAGATCGCAATAG
AGATTGCCCGGAGTCGAACCCGGGTCCATCGCTTGAAAGGCAATTATCCTAACCACTGGACTAAA
AACGCATCTTATTTAAACT
Found at i:1049390 original size:171 final size:171
Alignment explanation
Indices: 1048220--1049391 Score: 965
Period size: 172 Copynumber: 6.8 Consensus size: 171
1048210 ACACTACTCG
* * * * * ** *
1048220 TTTTACTATCGTAATTACGTTTTCTA-AGAGTCGAACCCGAGTCTATTACTTTAAAGGAAATTAT
1 TTTTACAATCGTAATTGCATTTAC-AGAGAGTCGAACCCG-GTCTATTGCTTGGAAGGCAATTAT
* * * * *
1048284 CCTAACCGTTAGACTACTAAA-GCCTCTTCTTTACACAATTCGTTTCACAAAATCAAGCACGAAA
64 CCTAACCGTTGGACTAC-AAACGCCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAAA
* * * * *
1048348 GGTAAACATTTTTCGTTTTACTTTT-TAAATTTTCCCCTTTAATT
128 GGTATACACTATTCGTTTTACTTTTCAAAATTTTCCCC-TTAATA
* * * * * *
1048392 TTTTA-ATATCGTAATTACATTTACCGAGAGTCAAACTCTGATCTATTGCATGGAAGGCAATTAT
1 TTTTACA-ATCGTAATTGCATTTACAGAGAGTCGAAC-CCGGTCTATTGCTTGGAAGGCAATTAT
* * * ** * * * *
1048456 CCAAACCGTTGGACTACAAAGGCCTCTTCTTTAAACTATTTGTTTCATATAATCAAGAACAACAC
64 CCTAACCGTTGGACTACAAACGCCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAAAG
* * * *
1048521 GTATACACTACTCGTTTTACTTTTCAAAATTTTTCCTTTGAT-
129 GTATACACTATTCGTTTTACTTTTCAAAATTTTCCCCTTAATA
* * * * *** * * * *
1048563 TTATAACTATCCTATTTTTTTTTGCCAG-GAGTAGAACCCGGGTCTATTGCTTGGAAAGAAATTA
1 TT-TTACAATCGTAATTGCATTT-ACAGAGAGTCGAACCC-GGTCTATTGCTTGGAAGGCAATTA
* * * * * * *
1048627 TCCTAATCGTTAGACAATAAATGCCTCTTCTTTACACTATTCATTTCACATAATCAAGAACAACA
63 TCCTAACCGTTGGACTACAAACGCCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAAA
* * * * *
1048692 TGTATACACTAGTT-GTTCTACTTTCCAAAATTTTACCTTTAATTA
128 GGTATACACTA-TTCGTTTTACTTTTCAAAATTTTCCCCTTAA-TA
* * * * * * * *** *
1048737 TTTTACTATTGTGATTG-AGTTTGCCGGGAGTCGAACCTGAGTCTATTGCTCAAAAGGCAATTTT
1 TTTTACAATCGTAATTGCA-TTTACAGAGAGTCGAACCCG-GTCTATTGCTTGGAAGGCAATTAT
* * * *
1048801 CCTAACCGTTGGACTACAAACGCCTCTTATTCACACTATTTC-TTTCACATAATCAAGAACAACA
64 CCTAACCGTTGGACTACAAACGCCTCTTCTTTACACTA-TTCATTTCACATAATCAAGCACAAAA
* *
1048865 CGTATACACTACTCGTTTTACTTTTCAAAATTTTCCCCTTAATA
128 GGTATACACTATTCGTTTTACTTTTCAAAATTTTCCCCTTAATA
* * * *
1048909 TTTTACAATCGTAATT-CATTTGTC-GAGAGTCGAACCTGGGTTTATTGCTTGGAAGGTAATTA-
1 TTTTACAATCGTAATTGCATTT-ACAGAGAGTCGAACC-CGGTCTATTGCTTGGAAGGCAATTAT
* ** * * * * * *
1048971 CCGTAACCGTTGGACTATAAATACCTATTCTTTATGA-TGTTCGTTTCACGTAATCAAGCACGAA
64 CC-TAACCGTTGGACTACAAACGCCTCTTCTTTA-CACTATTCATTTCACATAATCAAGCACAAA
* * *
1049035 AGGTAAACACTATTCGTTTCACTTTTCAAAATTTTCCCCTTAATT
127 AGGTATACACTATTCGTTTTACTTTTCAAAATTTTCCCCTTAATA
* * * ** * * ** *
1049080 TTTTACTATGGTGATTGTGTTTGCTGAGAGTTAAACCCGAGTCTATTTCTTGGAAGGCACA-TAT
1 TTTTACAATCGTAATTGCATTTACAGAGAGTCGAACCCG-GTCTATTGCTTGGAAGGCA-ATTAT
* * * *
1049144 CCTAACCGTTGGATTACATACGTCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAATG
64 CCTAACCGTTGGACTACAAACGCCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAAAG
* * *
1049209 GTTTACACTATTCGTTTTATTTTTTAAAATTTT-CCCTTAATA
129 GTATACACTATTCGTTTTACTTTTCAAAATTTTCCCCTTAATA
* *
1049251 TTTTACAATTGTAATTGCACTTACAGCA-AGTCGAACCCAGGTCTATTGCTTGGAAGGCAATTA-
1 TTTTACAATCGTAATTGCATTTACAG-AGAGTCGAACCC-GGTCTATTGCTTGGAAGGCAATTAT
* * * * *
1049314 CCATAACTGTTAGACAACAAACGCCTCTTCTTTACACTATTCACTTCTCATAATCAAGCACAAAA
64 CC-TAACCGTTGGACTACAAACGCCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAAA
1049379 GGTATACACTATT
128 GGTATACACTATT
1049392 TGGTTTATTT
Statistics
Matches: 793, Mismatches: 174, Indels: 67
0.77 0.17 0.06
Matches are distributed among these distances:
170 8 0.01
171 255 0.32
172 381 0.48
173 144 0.18
174 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (171 bp):
TTTTACAATCGTAATTGCATTTACAGAGAGTCGAACCCGGTCTATTGCTTGGAAGGCAATTATCC
TAACCGTTGGACTACAAACGCCTCTTCTTTACACTATTCATTTCACATAATCAAGCACAAAAGGT
ATACACTATTCGTTTTACTTTTCAAAATTTTCCCCTTAATA
Found at i:1049427 original size:343 final size:339
Alignment explanation
Indices: 1048246--1049402 Score: 1066
Period size: 343 Copynumber: 3.4 Consensus size: 339
1048236 ACGTTTTCTA
* * ** * *
1048246 AGAGTCGAACCCGAGTCTATTACTTTAAAGGAAATTATCCTAACCGTTAGACTACTAAA-GCCTC
1 AGAGTCGAACCCGGGTCTATTGCTTGGAAGGAAATTA-CCTAACTGTTAGAC-AATAAATGCCTC
* * * * * * * *
1048310 TTCTTTACACAATTCGTTTCACAAAATCAAGCACGAAAGGTAAACATTTTTCGTTTTACTTTT-T
64 TTCTTTACACTATTCATTTCACATAATCAAGCACAAAAGGTATACACTATT-G-TTTA-TTTTCA
* * * * * * *
1048374 AAATTTTCCCCTTTAATTTTTTAATATCGTAATT-ACATTTACCGAGAGTCAAACTCTGA-TCTA
126 AAATTTTACCC-TTAATTTTTTACTATGGTGATTGA-GTTTGCCGAGAGTCAAAC-CCGAGTCTA
** * * * * * *
1048437 TTGCAT-GGAAGGCAATTATCCAAACCGTTGGACTACAAAGGCCTCTTCTTTAAACTATTTGTTT
188 TTGC-TCAAAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTCTTATTCACACTATTTCTTT
* * * *
1048501 CATATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTTTTCCTTTGAT-TT
252 CACATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTTTCCCCTTAATATT
* * * * *** *
1048565 ATAACTATCCTATTTTTTTTTG-CC
317 -TTACAATCGTA-ATTCACTTGACG
* *
1048589 AGGAGTAGAACCCGGGTCTATTGCTTGGAAAGAAATTATCCTAA-TCGTTAGACAATAAATGCCT
1 A-GAGTCGAACCCGGGTCTATTGCTTGGAAGGAAATTA-CCTAACT-GTTAGACAATAAATGCCT
* * * *
1048653 CTTCTTTACACTATTCATTTCACATAATCAAGAACAACATGTATACACTAGTTGTTCTACTTTCC
63 CTTCTTTACACTATTCATTTCACATAATCAAGCACAAAAGGTATACACTA-TTGTT-TA-TTTTC
* * * * *
1048718 AAAATTTTACCTTTAATTATTTTACTATTGTGATTGAGTTTGCCGGGAGTCGAACCTGAGTCTAT
125 AAAATTTTACCCTTAATT-TTTTACTATGGTGATTGAGTTTGCCGAGAGTCAAACCCGAGTCTAT
*
1048783 TGCTCAAAAGGCAATTTTCCTAACCGTTGGACTACAAACGCCTCTTATTCACACTATTTCTTTCA
189 TGCTCAAAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTCTTATTCACACTATTTCTTTCA
1048848 CATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTTTCCCCTTAATATTTT
254 CATAATCAAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTTTCCCCTTAATATTTT
* *
1048913 ACAATCGTAATTCATTTGTCG
319 ACAATCGTAATTCACTTGACG
* * * * * * * *
1048934 AGAGTCGAACCTGGGTTTATTGCTTGGAAGGTAATTACCGTAACCGTTGGACTATAAATACCTAT
1 AGAGTCGAACCCGGGTCTATTGCTTGGAAGGAAATTACC-TAACTGTTAGACAATAAATGCCTCT
* * * * * *
1048999 TCTTTATGA-TGTTCGTTTCACGTAATCAAGCACGAAAGGTAAACACTATTCGTTTCACTTTTCA
65 TCTTTA-CACTATTCATTTCACATAATCAAGCACAAAAGGTATACACTATT-GTTT-A-TTTTCA
* * * * *
1049063 AAATTTTCCCCTTAATTTTTTACTATGGTGATTGTGTTTGCTGAGAGTTAAACCCGAGTCTATTT
126 AAATTTTACCCTTAATTTTTTACTATGGTGATTGAGTTTGCCGAGAGTCAAACCCGAGTCTATTG
*** * * * * *
1049128 CTTGGAAGGCACA-TATCCTAACCGTTGGATTACATACGTCTCTTCTTTACACTA-TTCATTTCA
191 CTCAAAAGGCA-ATTATCCTAACCGTTGGACTACAAACGCCTCTTATTCACACTATTTC-TTTCA
* * * * * *
1049191 CATAATCAAGCACAA-ATGGTTTACACTATTCGTTTTATTTTTTAAAATTTT-CCCTTAATATTT
254 CATAATCAAGAACAACA-CGTATACACTACTCGTTTTACTTTTCAAAATTTTCCCCTTAATATTT
*
1049254 TACAATTGTAATTGCACTT-AC-
318 TACAATCGTAATT-CACTTGACG
* * * *
1049275 AGCAAGTCGAACCCAGGTCTATTGCTTGGAAGGCAATTACCATAACTGTTAGACAACAAACGCCT
1 AG--AGTCGAACCCGGGTCTATTGCTTGGAAGGAAATTACC-TAACTGTTAGACAATAAATGCCT
* *
1049340 CTTCTTTACACTATTCACTTCTCATAATCAAGCACAAAAGGTATACACTATTTGGTTTATTTT
63 CTTCTTTACACTATTCATTTCACATAATCAAGCACAAAAGGTATACACTA-TT-GTTTATTTT
1049403 TTAAAAAAAA
Statistics
Matches: 671, Mismatches: 118, Indels: 51
0.80 0.14 0.06
Matches are distributed among these distances:
341 2 0.00
342 34 0.05
343 238 0.35
344 230 0.34
345 164 0.24
346 3 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (339 bp):
AGAGTCGAACCCGGGTCTATTGCTTGGAAGGAAATTACCTAACTGTTAGACAATAAATGCCTCTT
CTTTACACTATTCATTTCACATAATCAAGCACAAAAGGTATACACTATTGTTTATTTTCAAAATT
TTACCCTTAATTTTTTACTATGGTGATTGAGTTTGCCGAGAGTCAAACCCGAGTCTATTGCTCAA
AAGGCAATTATCCTAACCGTTGGACTACAAACGCCTCTTATTCACACTATTTCTTTCACATAATC
AAGAACAACACGTATACACTACTCGTTTTACTTTTCAAAATTTTCCCCTTAATATTTTACAATCG
TAATTCACTTGACG
Found at i:1049799 original size:169 final size:170
Alignment explanation
Indices: 1049501--1050169 Score: 439
Period size: 171 Copynumber: 3.9 Consensus size: 170
1049491 AAGCTAGTCT
* * * * * * *
1049501 TTTTATTTTTCAAAATTTTCCCATGAAGTTTTTTACTTTTGTAATTGCATTTGACGGGAGTCGAA
1 TTTTACTTTTCAAAATTTT-CC-TTAA-TTTTTTACTATCGTAATTCCATTTGACGGCAGTCAAA
* * * *
1049566 CCCGGCTCTATTACTTGGAAGGCCATTATCCTAACCGTTGTAATACAAACGTCTCATCTTTACAC
63 CCCAGCTCTATTACTTGAAAGGCCATTATCCTAACCATTGTAATACAAACGCCTCATCTTTACAC
* *
1049631 TATTTGTTTCACTTAATCTAGAACAAGACG-TATACACGACTCG
128 TATTTGTTTCACATAATCAAGAACAA-ACGTTATACACGACTCG
*
1049674 TTTTACTTTTCAAAATTTTTCTTAATTTTTTACTATCGTAATT-CATTT-ACTGGCAGTCAAACC
1 TTTTACTTTTCAAAATTTTCCTTAATTTTTTACTATCGTAATTCCATTTGAC-GGCAGTCAAACC
* * *
1049737 CAAG-TCTATTACTTGAAAGG-TATTCATCCTAACCATTG-AACTACAAACGCCTCCTTTTTACA
65 C-AGCTCTATTACTTGAAAGGCCATT-ATCCTAACCATTGTAA-TACAAACGCCTCATCTTTACA
* * * * * *
1049799 CTATTTGTTTCACATAATCAAGCACAAATGTTATATACTATTTG
127 CTATTTGTTTCACATAATCAAGAACAAACGTTATACACGACTCG
* * * * ** * *
1049843 TTATACTTTTCAAAAATTTCTCCATAATTTTTTACAATCATAATTCCATTTTCCAGAAGTCAAAC
1 TTTTACTTTTC-AAAATTT-TCCTTAATTTTTTACTATCGTAATTCCATTTGACGGCAGTCAAAC
* * * ** * * *
1049908 CCGGGC-CTATTGCTTGCAAGGAAATTATCCTAGA--AGTTGGACA-ACAAGA-GCCACTTCTTT
64 CC-AGCTCTATTACTTGAAAGGCCATTATCCTA-ACCA-TTGTA-ATACAA-ACGCCTCATCTTT
* * * ** * * * * *
1049968 AGAGTGTGCGCTCCACATAATCAAGAACAAAAGGTATA-ACGCTAATCG
124 ACACTATTTGTTTCACATAATCAAGAACAAACGTTATACACG--ACTCG
* * * * ** ** **
1050016 TTTTACTTTACCAAATTTTCCTTAATTTGTTACTATTGTAATTGTATTTG-CATCAAGTTGAACC
1 TTTTACTTTTCAAAATTTTCCTTAATTTTTTACTATCGTAATTCCATTTGACGGC-AGTCAAACC
* * * * * * * *
1050080 CGAG-TCTATTGCTTGGAAGGCAATCATCCTAACCGTTGGACTACAAACGCCTCTTCTTTACACT
65 C-AGCTCTATTACTTGAAAGGCCATTATCCTAACCATTGTAATACAAACGCCTCATCTTTACACT
* * *
1050144 ATTTGTTTCATATAAACAAGCACAAA
129 ATTTGTTTCACATAATCAAGAACAAA
1050170 AGGTATATAT
Statistics
Matches: 389, Mismatches: 83, Indels: 50
0.75 0.16 0.10
Matches are distributed among these distances:
168 9 0.02
169 104 0.27
170 28 0.07
171 124 0.32
172 86 0.22
173 37 0.10
174 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (170 bp):
TTTTACTTTTCAAAATTTTCCTTAATTTTTTACTATCGTAATTCCATTTGACGGCAGTCAAACCC
AGCTCTATTACTTGAAAGGCCATTATCCTAACCATTGTAATACAAACGCCTCATCTTTACACTAT
TTGTTTCACATAATCAAGAACAAACGTTATACACGACTCG
Done.