Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009638.1 Hibiscus syriacus cultivar Beakdansim tig00117047_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: 894601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:291892 original size:73 final size:73
Alignment explanation
Indices: 291800--291945 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 73
291790 GCATCATGCG
* * *
291800 TGTCAAATATACGTAATTATACGAGTTAGACGGTGATGATGTATGTGCATTAGTTTATATTGAAT
1 TGTCAAACATACGTAATTATACGAGTCAGACGGTGATGATATATGTGCATTAGTTTATATTGAAT
291865 AAGTCAAT
66 AAGTCAAT
*
291873 TGTCAAACATACGTAATTATACGAGTCAGGCGGTGATGATATATGTGCATTAGTTTATATTGAAT
1 TGTCAAACATACGTAATTATACGAGTCAGACGGTGATGATATATGTGCATTAGTTTATATTGAAT
*
291938 CAGTCAAT
66 AAGTCAAT
291946 AAATATATGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (73 bp):
TGTCAAACATACGTAATTATACGAGTCAGACGGTGATGATATATGTGCATTAGTTTATATTGAAT
AAGTCAAT
Found at i:293019 original size:19 final size:19
Alignment explanation
Indices: 292967--293020 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
292957 AATTCAAATA
292967 TAACAATTCAATAATACATT
1 TAACAATTCAA-AATACATT
**
292987 TAACAATTTC-AAATTTATT
1 TAACAA-TTCAAAATACATT
*
293006 TATCAATTCAAAATA
1 TAACAATTCAAAATA
293021 TTCAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 7 0.25
21 3 0.11
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (19 bp):
TAACAATTCAAAATACATT
Found at i:297684 original size:21 final size:21
Alignment explanation
Indices: 297660--297704 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
297650 GTTTTTGAAA
* *
297660 AAAATTGAAAGTTTAGTTACT
1 AAAACTGAAAGTTTAGGTACT
*
297681 AAAACTGATAGTTTAGGTACT
1 AAAACTGAAAGTTTAGGTACT
297702 AAA
1 AAA
297705 CATGTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGGTACT
Found at i:298309 original size:385 final size:383
Alignment explanation
Indices: 297726--298672 Score: 1386
Period size: 385 Copynumber: 2.5 Consensus size: 383
297716 CCGTAACAAT
* * * * *
297726 TACACCAAATGTTATTGAACAATGTTTAAATCATTGTTTTGGTAACTGAACTTACAAAAGTCATA
1 TACACCCAAGGTTATTGAACAATGTTTAAATCATTGTTTTGGTCATTGAACTTACAAAAGTTATA
* * *
297791 AAATGATCATTAAATTTATCGTGTTGTTATAAAATGATTACTATAGTACTATAAAAATGTAATC-
66 AAATGATCATTAAATTTATCGAGTTGTTAT-AAATGATTACTATAATATTATAAAAATGTAA-CA
* * * *
297855 GTTCGATAAAACTTAAAGAACATTC-TGCAATAATTCGATAAATTTAATGATTATTTTGTAACTT
129 GTTCGATAAAAATTAAAGATCATTCTTTC-ATAATTCGATAAATTTAATGATTAATTTGTAACTT
* ** *
297919 TTGAAACTTTAGTGACCAAAATGATTGTTTGAGTGTATTTTAATGATCTCTAGCATGTTTTACCC
193 TTGAAACTTTAGTGACCAAAATGATTGTTTGAGCGTAACTTAATGATCTCTAGCATATTTTACCC
* *
297984 TAAATTTTTTAAACTA-TTTTGTTTGAGTCCTTAAAATGTCAATTTCTTATATAGTTTAGGGTTA
258 TAAACTTTTTAAACTATTTTTGTTTGAGTCCTTAAAATGTCAATCTC-T-TATAGTTTAGGGTTA
* ** *
298048 CTTAACTCTAATCATAAAGTGGTAAGTCCCTCCCCCCTAATTTGGCCATAAAAAATTGAGTGAG
321 CTTAACTCGAATCATAAAGTGGTAAGTCCCT-CCCCCTAATTTGGCCATAAAAAATTGAGCAAA
298112 TACACCCAAGGTTATTGAACAATG-TTAAATCATTGTTTTGGTCATTGAACTTACAAAAGTTATA
1 TACACCCAAGGTTATTGAACAATGTTTAAATCATTGTTTTGGTCATTGAACTTACAAAAGTTATA
*
298176 AAATGATCATTAAATTCATCGAGTTGTTATAAAGTGATTACTATAATATTATAAAAATGTAACAG
66 AAATGATCATTAAATTTATCGAGTTGTTATAAA-TGATTACTATAATATTATAAAAATGTAACAG
298241 TTCGATAAAAATTAAAGATCATTCTTTCATAATTCGATAAATTTAATGATTAATTTGTAACTTTT
130 TTCGATAAAAATTAAAGATCATTCTTTCATAATTCGATAAATTTAATGATTAATTTGTAACTTTT
* * * *
298306 GAAATTTTAGTGACCAAAATTATTGTTTGAGCGTAACTTAGTGATCTCTAGCATATTTTATCCTA
195 GAAACTTTAGTGACCAAAATGATTGTTTGAGCGTAACTTAATGATCTCTAGCATATTTTACCCTA
*
298371 GACTTTTTAAACTATTTTTGTTTGAGTCCTTAAAATGTCAATCTCTTATAGTTTAGGGTTACTTA
260 AACTTTTTAAACTATTTTTGTTTGAGTCCTTAAAATGTCAATCTCTTATAGTTTAGGGTTACTTA
* * * * * * *
298436 ACTCGAATTATCAAGTGGTAAGTCCCTTCCCCTAGTTTGGTCATCAAAATTTGAGCAAA
325 ACTCGAATCATAAAGTGGTAAGTCCCTCCCCCTAATTTGGCCATAAAAAATTGAGCAAA
* * *
298495 TACACCCAAGGTTATTGAACAATGTTTAAA-CATTATTTTGGTCATTGAACTTATAAAAATTATA
1 TACACCCAAGGTTATTGAACAATGTTTAAATCATTGTTTTGGTCATTGAACTTACAAAAGTTATA
* *
298559 AAATGGTCATTAAATTTATCGAGCTGTT-TCAAATGATTACTATAATATTATAAAAATGTAACAG
66 AAATGATCATTAAATTTATCGAGTTGTTAT-AAATGATTACTATAATATTATAAAAATGTAACAG
* *
298623 TTCGATAAAAATTAAAGATCATTATGT-ACTAATTCGATAAATTTAATGAT
130 TTCGATAAAAATTAAAGATCATTCTTTCA-TAATTCGATAAATTTAATGAT
298673 CATTTTAATG
Statistics
Matches: 511, Mismatches: 43, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
381 1 0.00
382 78 0.15
383 107 0.21
384 52 0.10
385 220 0.43
386 53 0.10
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (383 bp):
TACACCCAAGGTTATTGAACAATGTTTAAATCATTGTTTTGGTCATTGAACTTACAAAAGTTATA
AAATGATCATTAAATTTATCGAGTTGTTATAAATGATTACTATAATATTATAAAAATGTAACAGT
TCGATAAAAATTAAAGATCATTCTTTCATAATTCGATAAATTTAATGATTAATTTGTAACTTTTG
AAACTTTAGTGACCAAAATGATTGTTTGAGCGTAACTTAATGATCTCTAGCATATTTTACCCTAA
ACTTTTTAAACTATTTTTGTTTGAGTCCTTAAAATGTCAATCTCTTATAGTTTAGGGTTACTTAA
CTCGAATCATAAAGTGGTAAGTCCCTCCCCCTAATTTGGCCATAAAAAATTGAGCAAA
Found at i:300839 original size:16 final size:16
Alignment explanation
Indices: 300818--300851 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
300808 TCAGCACCTC
300818 GGTTCCTGCTTGAGAT
1 GGTTCCTGCTTGAGAT
300834 GGTTCCTGCTTGAGAT
1 GGTTCCTGCTTGAGAT
300850 GG
1 GG
300852 ATCCAGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (16 bp):
GGTTCCTGCTTGAGAT
Found at i:300860 original size:16 final size:16
Alignment explanation
Indices: 300825--300860 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
300815 CTCGGTTCCT
* *
300825 GCTTGAGATGGTTCCT
1 GCTTGAGATGGATCCA
300841 GCTTGAGATGGATCCA
1 GCTTGAGATGGATCCA
300857 GCTT
1 GCTT
300861 TGCGAGCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (16 bp):
GCTTGAGATGGATCCA
Found at i:305755 original size:30 final size:30
Alignment explanation
Indices: 305719--305844 Score: 87
Period size: 30 Copynumber: 4.2 Consensus size: 30
305709 TATTCTAATG
305719 TTGCTGCTACTAAGAACAAAACTGAAGTTA
1 TTGCTGCTACTAAGAACAAAACTGAAGTTA
* * *
305749 TTGCTGCTGTCT-CGAACAAAGCTGAAGTTA
1 TTGCTGCT-ACTAAGAACAAAACTGAAGTTA
* * * * * *
305779 CTGCTGCT-GTCACGATCAAAGCTGATA-TTG
1 TTGCTGCTACT-AAGAACAAAACTGA-AGTTA
* * *
305809 TTGCTGCTATTAAGAACAAAACCGAAGATA
1 TTGCTGCTACTAAGAACAAAACTGAAGTTA
*
305839 CTGCTG
1 TTGCTG
305845 TTGTCCCAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 68 0.92
31 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (30 bp):
TTGCTGCTACTAAGAACAAAACTGAAGTTA
Found at i:305816 original size:33 final size:30
Alignment explanation
Indices: 305732--305803 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
305722 CTGCTACTAA
* * *
305732 GAACAAAACTGAAGTTATTGCTGCTGTCTC
1 GAACAAAGCTGAAGTTACTGCTGCTGTCAC
305762 GAACAAAGCTGAAGTTACTGCTGCTGTCAC
1 GAACAAAGCTGAAGTTACTGCTGCTGTCAC
*
305792 GATCAAAGCTGA
1 GAACAAAGCTGA
305804 TATTGTTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (30 bp):
GAACAAAGCTGAAGTTACTGCTGCTGTCAC
Found at i:311118 original size:15 final size:15
Alignment explanation
Indices: 311098--311130 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
311088 TTAAAAAATA
311098 TATTATTTATTTT-TT
1 TATTATTT-TTTTCTT
311113 TATTATTTTTTTCTT
1 TATTATTTTTTTCTT
311128 TAT
1 TAT
311131 CTTCTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTATTTTTTTCTT
Found at i:314967 original size:52 final size:52
Alignment explanation
Indices: 314889--314991 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
314879 TTATAATATT
314889 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
314941 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
314992 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:319564 original size:52 final size:52
Alignment explanation
Indices: 319486--319588 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
319476 TTATAATATT
319486 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
319538 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
319589 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:323258 original size:59 final size:58
Alignment explanation
Indices: 323166--323276 Score: 141
Period size: 59 Copynumber: 1.9 Consensus size: 58
323156 TTAAGGGCAT
* * ** *
323166 ATATAGAATATCTTAAAGTTTATGGACCAATTTAAAATGATGTCATAATTTGAAGACCG
1 ATATAGAATATCTTAAAGCTCAAAGACCAATTTAAAAT-AAGTCATAATTTGAAGACCG
* * *
323225 ATATAGAATATTTTAAAGCTCAAAGACTAATTTAAAATAAGTCGTAATTTGA
1 ATATAGAATATCTTAAAGCTCAAAGACCAATTTAAAATAAGTCATAATTTGA
323277 GGATATCCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
58 12 0.27
59 32 0.73
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (58 bp):
ATATAGAATATCTTAAAGCTCAAAGACCAATTTAAAATAAGTCATAATTTGAAGACCG
Found at i:324909 original size:60 final size:61
Alignment explanation
Indices: 324820--324992 Score: 144
Period size: 60 Copynumber: 2.9 Consensus size: 61
324810 ATGAAATTGG
*
324820 AATGCTCAAAAAGTTTGGAGACCAATTTAGAA-AGAGGGTCATAGTTTAAGGATGAAATCAA
1 AATGCTCAAAAAGTTTGGAGACCAATTTAGAATA-AGAGTCATAGTTTAAGGATGAAATCAA
* * * * * *
324881 AATGTTCAAAAA-TTT-GAGGACTAATTTAGAATAATATTCATAGTTTAGGGATGAAATTGAA
1 AATGCTCAAAAAGTTTGGA-GACCAATTTAGAATAAGAGTCATAGTTTAAGGATGAAA-TCAA
* * * * *
324942 ACAT--T-AAGAAGTTTAGGA-ACCAATTTAAAATGAGAGTAATAGTTTGAGGAT
1 A-ATGCTCAAAAAGTTT-GGAGACCAATTTAGAATAAGAGTCATAGTTTAAGGAT
324993 ATACGATGCA
Statistics
Matches: 89, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
59 6 0.07
60 63 0.71
61 16 0.18
62 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (61 bp):
AATGCTCAAAAAGTTTGGAGACCAATTTAGAATAAGAGTCATAGTTTAAGGATGAAATCAA
Found at i:325018 original size:2 final size:2
Alignment explanation
Indices: 325011--325039 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
325001 CAATTAATTC
325011 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 A
325040 AACACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:328976 original size:15 final size:15
Alignment explanation
Indices: 328958--328986 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
328948 ATTTTTTTTG
328958 TTTTT-AAATTTTAA
1 TTTTTAAAATTTTAA
328972 TTTTTAAAATTTTAA
1 TTTTTAAAATTTTAA
328987 ATAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATTTTAA
Found at i:329792 original size:20 final size:18
Alignment explanation
Indices: 329767--329810 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 18
329757 AAAACCGATC
329767 ATTTAAATATTACACACATA
1 ATTTAAATATTA-ACA-ATA
329787 ATTTAAAATATTAACAATA
1 ATTT-AAATATTAACAATA
329806 ATTTA
1 ATTTA
329811 CTTAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.04
19 7 0.30
20 7 0.30
21 8 0.35
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAAATATTAACAATA
Found at i:329808 original size:19 final size:21
Alignment explanation
Indices: 329767--329810 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
329757 AAAACCGATC
329767 ATTT-AAATATTACACACATA
1 ATTTAAAATATTACACACATA
329787 ATTTAAAATATTA-ACA-ATA
1 ATTTAAAATATTACACACATA
329806 ATTTA
1 ATTTA
329811 CTTAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTAAAATATTACACACATA
Found at i:331426 original size:2 final size:2
Alignment explanation
Indices: 331419--331447 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
331409 TATGTTAAAG
331419 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 A
331448 ACCATGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:331587 original size:39 final size:39
Alignment explanation
Indices: 331533--331608 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
331523 AGAACAAAGG
331533 TTACTTGATCCATAACCATGACTAAATAGGGATCAAACA
1 TTACTTGATCCATAACCATGACTAAATAGGGATCAAACA
331572 TTACTTGATCCATAACCATGACTAAATAGGGATCAAA
1 TTACTTGATCCATAACCATGACTAAATAGGGATCAAA
331609 AATTGTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (39 bp):
TTACTTGATCCATAACCATGACTAAATAGGGATCAAACA
Found at i:332905 original size:19 final size:20
Alignment explanation
Indices: 332883--332970 Score: 54
Period size: 22 Copynumber: 4.2 Consensus size: 20
332873 ATTAAGTTAA
332883 TAAAAAT-AAAATTATTA-T
1 TAAAAATAAAAATTATTACT
* *
332901 TTAAATTAAAAATTATTACT
1 TAAAAATAAAAATTATTACT
*
332921 TAAATATATATAAGGAATTATTAAT
1 TAAA-A-ATA-AA--AATTATTACT
* *
332946 AAAAAAATTTAAAATTATTACT
1 -TAAAAA-TAAAAATTATTACT
332968 TAA
1 TAA
332971 GTTATACAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
18 5 0.10
19 10 0.19
20 4 0.08
21 3 0.06
22 11 0.21
23 2 0.04
24 3 0.06
25 11 0.21
26 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAAATAAAAATTATTACT
Found at i:333560 original size:17 final size:16
Alignment explanation
Indices: 333538--333569 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
333528 ATACATTCTA
333538 TTAATTTGATCTTAATT
1 TTAATTTGAT-TTAATT
333555 TTAATTTGATTTAAT
1 TTAATTTGATTTAAT
333570 AAATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TTAATTTGATTTAATT
Found at i:334130 original size:2 final size:2
Alignment explanation
Indices: 334123--334164 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
334113 TATGTAAGTT
334123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
334165 AGTTTAATTA
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):
TA
Found at i:335469 original size:21 final size:21
Alignment explanation
Indices: 335445--335491 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
335435 CAGGGCATGA
335445 GACCCGAACTCAATGGGCTCC
1 GACCCGAACTCAATGGGCTCC
* *
335466 GACCCGAACTCGATGGGTTCC
1 GACCCGAACTCAATGGGCTCC
335487 GACCC
1 GACCC
335492 AACCGGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (21 bp):
GACCCGAACTCAATGGGCTCC
Found at i:337099 original size:33 final size:33
Alignment explanation
Indices: 337057--337122 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
337047 ACACTTACGT
*
337057 GAAAAAACCGACGTTAATCGAGACAAATAACAC
1 GAAAAAACCGACGATAATCGAGACAAATAACAC
337090 GAAAAAACCGACGATAATCGAGACAAATAACAC
1 GAAAAAACCGACGATAATCGAGACAAATAACAC
337123 AATCTTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.21, G:0.15, T:0.11
Consensus pattern (33 bp):
GAAAAAACCGACGATAATCGAGACAAATAACAC
Found at i:342935 original size:60 final size:58
Alignment explanation
Indices: 342827--343004 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 58
342817 TTTGAGATGA
* ** *
342827 AATTGAAATGTTCAAAAAGCTTGGGGACTAATTTAGGGTGAAGGTCATAGTTTGAGGATAG
1 AATTGAAATGTTC-AAAAG-TTTGGGACTAATTTAGAATGAA-ATCATAGTTTGAGGATAG
* * *
342888 AATTGAAATGTTCAAAAGTTTGGAAACTAATTTAGAATGACAATCATAGTTTAAGGATAT
1 AATTGAAATGTTCAAAAGTTTGG-GACTAATTTAGAATGA-AATCATAGTTTGAGGATAG
* * * * * * *
342948 AATTGGAATATTTAAGAGTTTAGGGACTAATCTAGAATGAGAATCGTAATTTGAGGA
1 AATTGAAATGTTCAAAAGTTT-GGGACTAATTTAGAATGA-AATCATAGTTTGAGGA
343005 CATGTGATGC
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
59 4 0.04
60 77 0.79
61 16 0.16
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (58 bp):
AATTGAAATGTTCAAAAGTTTGGGACTAATTTAGAATGAAATCATAGTTTGAGGATAG
Found at i:343130 original size:11 final size:11
Alignment explanation
Indices: 343108--343161 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
343098 TGAAATGATC
343108 ATTAAATT-TT
1 ATTAAATTATT
343118 ATTAAATTATT
1 ATTAAATTATT
* * *
343129 ATAAAATAATC
1 ATTAAATTATT
343140 ATTAAATT-TT
1 ATTAAATTATT
343150 ATTGAAA-TATT
1 ATT-AAATTATT
343161 A
1 A
343162 GGTATTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 13 0.37
11 22 0.63
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
ATTAAATTATT
Found at i:343141 original size:32 final size:32
Alignment explanation
Indices: 343100--343161 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
343090 AATTCATATG
*
343100 AAATGATCATTAAATTTTATT-AAATTATTATA
1 AAATAATCATTAAATTTTATTGAAA-TATTATA
343132 AAATAATCATTAAATTTTATTGAAATATTA
1 AAATAATCATTAAATTTTATTGAAATATTA
343162 GGTATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (32 bp):
AAATAATCATTAAATTTTATTGAAATATTATA
Found at i:350218 original size:3 final size:3
Alignment explanation
Indices: 350210--350246 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
350200 AAATGTAAAT
* *
350210 TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
350247 GGAAACCCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:351835 original size:31 final size:30
Alignment explanation
Indices: 351797--351856 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
351787 TTCCCTCGAC
351797 TACTTATATAATTCAGCCCTAATTTATTTTT
1 TACTTATATAATTCAGCCCTAATTT-TTTTT
* *
351828 TACTTATATAATTTAGTCCTAATTTTTTT
1 TACTTATATAATTCAGCCCTAATTTTTTT
351857 AATCTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.55
Consensus pattern (30 bp):
TACTTATATAATTCAGCCCTAATTTTTTTT
Found at i:351966 original size:44 final size:42
Alignment explanation
Indices: 351824--351967 Score: 146
Period size: 45 Copynumber: 3.3 Consensus size: 42
351814 CCTAATTTAT
* *
351824 TTTTTACTTATATAATTTAG-TCCTAATTTTTTTAATCTCAC
1 TTTTTACTTTTATAATTGAGCTCCTAATTTTTTTAATCTCAC
* * * *
351865 ATTTTACTTTTAAAATTGGGGGCCCCTAATTTTTTTTAATCTCAC
1 TTTTTACTTTTATAATT--GAGCTCCTAA-TTTTTTTAATCTCAC
* * * *
351910 TTTCTACCTTTATAATTGAGCTCCGTAATTTTTTAAATCACAC
1 TTTTTACTTTTATAATTGAGCTCC-TAATTTTTTTAATCTCAC
351953 TTTTTTACTTTTATA
1 -TTTTTACTTTTATA
351968 GTTTAATCCC
Statistics
Matches: 81, Mismatches: 16, Indels: 9
0.76 0.15 0.08
Matches are distributed among these distances:
41 14 0.17
43 19 0.23
44 20 0.25
45 28 0.35
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (42 bp):
TTTTTACTTTTATAATTGAGCTCCTAATTTTTTTAATCTCAC
Found at i:358564 original size:29 final size:29
Alignment explanation
Indices: 358522--358605 Score: 159
Period size: 29 Copynumber: 2.9 Consensus size: 29
358512 CGACCTACTC
358522 CGACCTTGTAGGTCGCCATGCACTCCGGG
1 CGACCTTGTAGGTCGCCATGCACTCCGGG
*
358551 CGACCTTGTAGGTCGCCATGCACTCCTGG
1 CGACCTTGTAGGTCGCCATGCACTCCGGG
358580 CGACCTTGTAGGTCGCCATGCACTCC
1 CGACCTTGTAGGTCGCCATGCACTCC
358606 CTCCTGCTCC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.14, C:0.36, G:0.27, T:0.23
Consensus pattern (29 bp):
CGACCTTGTAGGTCGCCATGCACTCCGGG
Found at i:358666 original size:13 final size:14
Alignment explanation
Indices: 358645--358699 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
358635 CTCGGATGCC
*
358645 CTCGCATAG-CTCG
1 CTCGGATAGCCTCG
358658 CTCGGATAGCCTCG
1 CTCGGATAGCCTCG
*
358672 ATCGGAT-GCCCTCG
1 CTCGGATAG-CCTCG
* *
358686 GTCGGATGGCCTCG
1 CTCGGATAGCCTCG
358700 GATACCCAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.25
14 26 0.72
15 1 0.03
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.22
Consensus pattern (14 bp):
CTCGGATAGCCTCG
Found at i:358700 original size:14 final size:14
Alignment explanation
Indices: 358654--358700 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
358644 CCTCGCATAG
* *
358654 CTCGCTCGGATAGC
1 CTCGGTCGGATGGC
* *
358668 CTCGATCGGATGCC
1 CTCGGTCGGATGGC
358682 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
358696 CTCGG
1 CTCGG
358701 ATACCCAGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:358795 original size:29 final size:29
Alignment explanation
Indices: 358762--358831 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
358752 GTCGGGAAGA
* *
358762 CATGGCGACCTAGTAGGTCGCCCGGATGG
1 CATGGCGACCTAGTAGGTCACCCGGATAG
358791 CATGGCGACCTAGTAGGTCACCCGGATAG
1 CATGGCGACCTAGTAGGTCACCCGGATAG
358820 CATGGCGACCTA
1 CATGGCGACCTA
358832 CGATCAACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (29 bp):
CATGGCGACCTAGTAGGTCACCCGGATAG
Found at i:360719 original size:34 final size:34
Alignment explanation
Indices: 360676--360758 Score: 134
Period size: 32 Copynumber: 2.5 Consensus size: 34
360666 CCTGAACCCG
* *
360676 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAA
360710 AAAATA-T-TATATATAATTAATATAAAAAATAA
1 AAAATATTATATATATAATTAATATAAAAAATAA
360742 AAAATATTATATATATA
1 AAAATATTATATATATA
360759 TATTTGGGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 29 0.64
33 2 0.04
34 14 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAA
Found at i:365806 original size:124 final size:125
Alignment explanation
Indices: 365578--365814 Score: 298
Period size: 124 Copynumber: 1.9 Consensus size: 125
365568 TATACTTAAT
* * **
365578 GTTTAATTTTTATTTCATTTTAGTATCTCGTCGTTAAAAACTTAACGCGTTTAGTACCTAGCCTA
1 GTTTAATTTTTATTTCATTTTAGTATCTCATCATTAAAAACTTAACGCGTTTAGTACCTAAACTA
*
365643 TCAGTTTTGGTCCGATTTAGTACCAAAACTTTTAATTTTTTTTTAAAAATCATGTCTAAC
66 TCAGTTTTGGTCCGATTTAGTACCAAAACTTTTAATTTTTTTTCAAAAATCATGTCTAAC
* * * * * *
365703 GTTTAGTTTTTGTTTCATTTTAGTATC-CATCATTGAAAATTTAATGTGTTTAGTACCTAAACTA
1 GTTTAATTTTTATTTCATTTTAGTATCTCATCATTAAAAACTTAACGCGTTTAGTACCTAAACTA
* * * ** *
365767 TTAGTTTTGGT-TGTTTTAGTACTTAAATTTTTAATTTTTTTTTCAAAA
66 TCAGTTTTGGTCCGATTTAGTACCAAAACTTTTAA-TTTTTTTTCAAAA
365815 CTTAACGTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
123 18 0.19
124 51 0.54
125 25 0.27
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.49
Consensus pattern (125 bp):
GTTTAATTTTTATTTCATTTTAGTATCTCATCATTAAAAACTTAACGCGTTTAGTACCTAAACTA
TCAGTTTTGGTCCGATTTAGTACCAAAACTTTTAATTTTTTTTCAAAAATCATGTCTAAC
Found at i:374987 original size:16 final size:16
Alignment explanation
Indices: 374963--374996 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
374953 TATCGCCGAC
*
374963 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
374979 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
374995 CG
1 CG
374997 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:391546 original size:2 final size:2
Alignment explanation
Indices: 391541--391607 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
391531 CATACGTGTG
391541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
391583 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 T
391608 GTCGTATACG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:391935 original size:29 final size:29
Alignment explanation
Indices: 391893--391950 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
391883 ACAGGAACGA
391893 ATGCACTAAACTCCTTAAGGAGATCAAGC
1 ATGCACTAAACTCCTTAAGGAGATCAAGC
391922 ATGCACTAAACTCCTTAAGGAGATCAAGC
1 ATGCACTAAACTCCTTAAGGAGATCAAGC
391951 GCATCCCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (29 bp):
ATGCACTAAACTCCTTAAGGAGATCAAGC
Found at i:394134 original size:4 final size:4
Alignment explanation
Indices: 394125--394155 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
394115 GAAACAATTA
394125 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
394156 TATATACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:395978 original size:2 final size:2
Alignment explanation
Indices: 395973--396001 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
395963 AGAAAAGGCA
395973 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 A
396002 AAGCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:396020 original size:10 final size:10
Alignment explanation
Indices: 396009--396083 Score: 88
Period size: 10 Copynumber: 7.9 Consensus size: 10
395999 ATAAAGCTAT
*
396009 GAAAGAGAAT
1 GAAAGAGAAA
*
396019 GAAACAGAAA
1 GAAAGAGAAA
396029 GAAAGAGAAA
1 GAAAGAGAAA
396039 GAAAGAGAAA
1 GAAAGAGAAA
396049 G--AGA-AAGA
1 GAAAGAGAA-A
396057 GAAAGAGAAA
1 GAAAGAGAAA
396067 G-AA-AGAAA
1 GAAAGAGAAA
396075 GAAAGAGAA
1 GAAAGAGAA
396084 GCCCCAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
7 2 0.04
8 11 0.20
9 4 0.07
10 37 0.66
11 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.29, T:0.01
Consensus pattern (10 bp):
GAAAGAGAAA
Found at i:396030 original size:16 final size:15
Alignment explanation
Indices: 396026--396083 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 15
396016 AATGAAACAG
396026 AAAGAAAGAGAAAGA
1 AAAGAAAGAGAAAGA
396041 AAGAGAAAGAGAAAGA
1 AA-AGAAAGAGAAAGA
396057 GAAAGAGAA-AGAAAG-
1 -AAAGA-AAGAGAAAGA
396072 AAAGAAAGAGAA
1 AAAGAAAGAGAA
396084 GCCCCAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.05
14 9 0.23
15 2 0.05
16 22 0.56
17 4 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAGAAAGA
Found at i:396033 original size:4 final size:4
Alignment explanation
Indices: 396024--396080 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
396014 AGAATGAAAC
* *
396024 AGAA AGAA AG-- AGAA AGAA AGAGA A-AG AGAA AGAGA A-AG AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA AGA-A AGAA AGAA AGAA
396070 AGAA AGAA AGA
1 AGAA AGAA AGA
396081 GAAGCCCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
2 2 0.05
3 2 0.05
4 35 0.81
5 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:396034 original size:20 final size:19
Alignment explanation
Indices: 396009--396083 Score: 84
Period size: 18 Copynumber: 3.9 Consensus size: 19
395999 ATAAAGCTAT
* *
396009 GAAAGAGAATGAAACAGAAA
1 GAAA-AGAAAGAAAGAGAAA
396029 GAAAGAGAAAGAAAGAGAAA
1 GAAA-AGAAAGAAAGAGAAA
396049 GAGAAAG--AGAAAGAGAAA
1 GA-AAAGAAAGAAAGAGAAA
396067 G-AAAGAAAGAAAGAGAA
1 GAAAAGAAAGAAAGAGAA
396084 GCCCCAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.08
18 22 0.44
20 22 0.44
21 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.29, T:0.01
Consensus pattern (19 bp):
GAAAAGAAAGAAAGAGAAA
Found at i:396037 original size:6 final size:6
Alignment explanation
Indices: 396028--396083 Score: 73
Period size: 6 Copynumber: 9.7 Consensus size: 6
396018 TGAAACAGAA
*
396028 AGAAAG AG-AA- AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG A-AAGAA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAA-AG
396074 AGAAAG AGAA
1 AGAAAG AGAA
396084 GCCCCAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 34 0.77
7 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:398768 original size:22 final size:21
Alignment explanation
Indices: 398722--398781 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
398712 ACATTCACGA
*
398722 TGGTACCGATACT--CCTCCT
1 TGGTATCGATACTCCCCTCCT
398741 TAGGTATCGATACTCCCCTCCT
1 T-GGTATCGATACTCCCCTCCT
*
398763 GTGGTATCAATACTTCCCC
1 -TGGTATCGATAC-TCCCC
398782 AAGTATCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 11 0.32
22 16 0.47
23 6 0.18
ACGTcount: A:0.18, C:0.35, G:0.15, T:0.32
Consensus pattern (21 bp):
TGGTATCGATACTCCCCTCCT
Found at i:400287 original size:29 final size:30
Alignment explanation
Indices: 400245--400316 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
400235 GTACCCATAT
*
400245 AGGTCGCCATGCACGCCCAGCTACCTA-CC
1 AGGTCGCCATGCACGCCCAGCGACCTAGCC
**
400274 AGGTCGCCATGCACGCCCAGCGACCTAGGT
1 AGGTCGCCATGCACGCCCAGCGACCTAGCC
400304 AGGTCGCCATGCA
1 AGGTCGCCATGCA
400317 ATCCATGCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.14
Consensus pattern (30 bp):
AGGTCGCCATGCACGCCCAGCGACCTAGCC
Found at i:400422 original size:23 final size:23
Alignment explanation
Indices: 400363--400423 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
400353 TCGCTCGGTT
*
400363 GCTCGGATTCCCTCGCATAGCTC
1 GCTCGGATGCCCTCGCATAGCTC
*
400386 GCTCGGTTGCCCTCGCATAGCTC
1 GCTCGGATGCCCTCGCATAGCTC
* *
400409 GTTCGGATGGCCTCG
1 GCTCGGATGCCCTCG
400424 GTCGGATGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.10, C:0.36, G:0.28, T:0.26
Consensus pattern (23 bp):
GCTCGGATGCCCTCGCATAGCTC
Found at i:401745 original size:141 final size:141
Alignment explanation
Indices: 401458--401795 Score: 428
Period size: 141 Copynumber: 2.4 Consensus size: 141
401448 GGTTCATTTA
* * * * * *
401458 GATTATTTGATTCAATAAATGAATAAAAATAACTATGATTAATATTAGAGCCTTCACTTTAGATT
1 GATTATTCGATTCAATAATTGGATAAAAATGACTATGATTAATATTAGAGCCTCCACTTTAGACT
* *
401523 TAATTTCACTTTACTCCTTTAATTTAGGGAATAATTCGATTTGACTTTCACATTAAAATACCCGA
66 TAATTTCACTTTACTCCCTTAATTTAGGGAATAATTCGATTTGACTTTCACATTAAAATACCAGA
* * *
401588 TGGTTCACGTT
131 GGGTCCACATT
* * *
401599 GATTATTCGATTTAATAATTGGATAAAAATGACTAGGATTAATATTAGAGCCTCCACTTTAGGCT
1 GATTATTCGATTCAATAATTGGATAAAAATGACTATGATTAATATTAGAGCCTCCACTTTAGACT
* * **
401664 TAATTTCACTTTAGTCCCTTAATTTAGGGAATAATTCGATTTGATCTTT-GCATTAAAATGTCAG
66 TAATTTCACTTTACTCCCTTAATTTAGGGAATAATTCGATTTGA-CTTTCACATTAAAATACCAG
401728 AGGGTCCACATT
130 AGGGTCCACATT
* * * * * *
401740 TATTATTCAACTCAATAATT-GTTTAAAATCGATTATGATTAATATTAGAGCCTCCA
1 GATTATTCGATTCAATAATTGGATAAAAAT-GACTATGATTAATATTAGAGCCTCCA
401796 TTTTTAGGTT
Statistics
Matches: 169, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
140 7 0.04
141 158 0.93
142 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (141 bp):
GATTATTCGATTCAATAATTGGATAAAAATGACTATGATTAATATTAGAGCCTCCACTTTAGACT
TAATTTCACTTTACTCCCTTAATTTAGGGAATAATTCGATTTGACTTTCACATTAAAATACCAGA
GGGTCCACATT
Found at i:403701 original size:31 final size:31
Alignment explanation
Indices: 403663--403728 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
403653 AACGTGGAAG
*
403663 TTAGGTATTAAAACAGATCAAAATTGATAAT
1 TTAGGTATTAAAACAGATCAAAATGGATAAT
* * *
403694 TTAGGTATTAAAATATATCAAAATGGATAGT
1 TTAGGTATTAAAACAGATCAAAATGGATAAT
403725 TTAG
1 TTAG
403729 AATCAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (31 bp):
TTAGGTATTAAAACAGATCAAAATGGATAAT
Found at i:403735 original size:20 final size:20
Alignment explanation
Indices: 403710--403748 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
403700 ATTAAAATAT
403710 ATCAAAATGGATAGTTTAGA
1 ATCAAAATGGATAGTTTAGA
*
403730 ATCAAAATTGATAGTTTAG
1 ATCAAAATGGATAGTTTAG
403749 GTACTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (20 bp):
ATCAAAATGGATAGTTTAGA
Found at i:403779 original size:2 final size:2
Alignment explanation
Indices: 403772--403799 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
403762 AATTTACCTA
403772 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
403800 TCATACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411909 original size:60 final size:59
Alignment explanation
Indices: 411800--411912 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
411790 TTGGATGACC
* *
411800 ATTTTGTAACTTTTAATAGTTAAGAGACTCAACAAAGCAATTTCCTATAGTCAGGGGACT
1 ATTTTGTAAATTTTAATAGTAAAGAGACTCAACAAAGCAATTT-CTATAGTCAGGGGACT
* *
411860 ATTTTGTAAATTTTTATAGTAAATGA-ACTCAATAAAGCATTATTT-TATAGTCA
1 ATTTTGTAAATTTTAATAGTAAA-GAGACTCAACAAAGCA--ATTTCTATAGTCA
411913 AAGGATCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
60 40 0.87
61 2 0.04
62 4 0.09
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (59 bp):
ATTTTGTAAATTTTAATAGTAAAGAGACTCAACAAAGCAATTTCTATAGTCAGGGGACT
Found at i:413422 original size:12 final size:12
Alignment explanation
Indices: 413407--413450 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
413397 TTTTTTGGTC
413407 TTTTAAATATAA
1 TTTTAAATATAA
* *
413419 TTTTAATTTTTAA
1 TTTTAA-ATATAA
*
413432 TTTTAAATAAAA
1 TTTTAAATATAA
413444 TTTTAAA
1 TTTTAAA
413451 ATTATCATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTAAATATAA
Found at i:428148 original size:21 final size:22
Alignment explanation
Indices: 428101--428148 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
428091 AAAAATCATA
428101 ATTTTTGATAAGTTTAAGAATC
1 ATTTTTGATAAGTTTAAGAATC
*
428123 GTTTTT-ATAAGTTTAATG-ATC
1 ATTTTTGATAAGTTTAA-GAATC
428144 ATTTT
1 ATTTT
428149 ATATTTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (22 bp):
ATTTTTGATAAGTTTAAGAATC
Found at i:429394 original size:17 final size:17
Alignment explanation
Indices: 429369--429402 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
429359 CCAGTTCCCC
* *
429369 AGAAGAACACGACATCA
1 AGAAAAACACAACATCA
429386 AGAAAAACACAACATCA
1 AGAAAAACACAACATCA
429403 TCCGAGTAAA
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:0.59, C:0.24, G:0.12, T:0.06
Consensus pattern (17 bp):
AGAAAAACACAACATCA
Found at i:433047 original size:31 final size:32
Alignment explanation
Indices: 432990--433059 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
432980 CCATTCGAAT
* *
432990 TCGATCTGACTCAAAAATTATATATCATCCAC
1 TCGATCTGACCCAAAAATCATATATCATCCAC
433022 TCGATCTGACCCAAAAA-CATATATCATCCAC
1 TCGATCTGACCCAAAAATCATATATCATCCAC
*
433053 TAGATCT
1 TCGATCT
433060 CAACTTGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 19 0.54
32 16 0.46
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (32 bp):
TCGATCTGACCCAAAAATCATATATCATCCAC
Found at i:433478 original size:28 final size:29
Alignment explanation
Indices: 433436--433492 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
433426 AAGAAAAATA
433436 TAAATAAAAATATTATTATA-ATTATTTT
1 TAAATAAAAATATTATTATACATTATTTT
433464 TAAATATAAAA-ATTATTATACTATTATTT
1 TAAATA-AAAATATTATTATAC-ATTATTT
433493 CGCATCGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 15 0.58
29 4 0.15
30 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAATAAAAATATTATTATACATTATTTT
Found at i:438809 original size:29 final size:30
Alignment explanation
Indices: 438767--438840 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
438757 AAGGATATTG
438767 AATATGGAGTCAATTGTTAAT-AAAAAACA
1 AATATGGAGTCAATTGTTAATAAAAAAACA
438796 AATATGGAGTCAATTGTTAATAAAAAAACA
1 AATATGGAGTCAATTGTTAATAAAAAAACA
438826 AATATGGAGTCAATT
1 AATATGGAGTCAATT
438841 ACAAACATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (30 bp):
AATATGGAGTCAATTGTTAATAAAAAAACA
Found at i:439486 original size:23 final size:23
Alignment explanation
Indices: 439460--439505 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
439450 TACCCTCGAA
439460 TTTAAT-TATATTTAAATAATTAT
1 TTTAATATATATTTAAA-AATTAT
* *
439483 TTTAATATTTTTTTAAAAATTAT
1 TTTAATATATATTTAAAAATTAT
439506 AAAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAATATATATTTAAAAATTAT
Found at i:442945 original size:11 final size:11
Alignment explanation
Indices: 442929--442967 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
442919 ATTTATCCTT
442929 TTAATATTTAC
1 TTAATATTTAC
*
442940 TTAATATCTT-T
1 TTAATAT-TTAC
442951 TTAATATTTAC
1 TTAATATTTAC
442962 TTAATA
1 TTAATA
442968 AAGATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATATTTAC
Found at i:442947 original size:22 final size:22
Alignment explanation
Indices: 442922--442967 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
442912 GCGTGTAATT
442922 TATCCTTTTAATATTTACTTAA
1 TATCCTTTTAATATTTACTTAA
*
442944 TATCTTTTTAATATTTACTTAA
1 TATCCTTTTAATATTTACTTAA
442966 TA
1 TA
442968 AAGATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (22 bp):
TATCCTTTTAATATTTACTTAA
Found at i:444621 original size:2 final size:2
Alignment explanation
Indices: 444614--444649 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
444604 AAACATGGTG
444614 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
444650 AACTGAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:448739 original size:59 final size:59
Alignment explanation
Indices: 448666--448784 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
448656 GAACTAACGT
* * *
448666 CTTCTAACGATACCCAGGGTCGTATTTGGGCTTGGGTAGGAGGGGCACTTGCCCAGGGC
1 CTTCTAACGATACCCAAGGTCGTATTTGGGCTTGGGCAGGAGAGGCACTTGCCCAGGGC
* * *
448725 CTTCTAATGATACCCAAGGTCGTATTTGGGCTTGGGCAGGAGAGGTACTTGCCTAGGGC
1 CTTCTAACGATACCCAAGGTCGTATTTGGGCTTGGGCAGGAGAGGCACTTGCCCAGGGC
448784 C
1 C
448785 GTAATTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.18, C:0.23, G:0.34, T:0.25
Consensus pattern (59 bp):
CTTCTAACGATACCCAAGGTCGTATTTGGGCTTGGGCAGGAGAGGCACTTGCCCAGGGC
Found at i:448894 original size:30 final size:31
Alignment explanation
Indices: 448823--448903 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 31
448813 TAAAAAATGA
* *
448823 TTTTTAATATTTGTTATTAAGGGTTTGCTTTT
1 TTTTTAATATTTATTATTAAGGGTTTGC-ATT
*
448855 GTTTTTAATATTTATTATTATGGG-TT-CATT
1 -TTTTTAATATTTATTATTAAGGGTTTGCATT
448885 TTTTCTAATATTTATTATT
1 TTTT-TAATATTTATTATT
448904 GGAGACTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 4 0.09
30 16 0.36
31 1 0.02
32 2 0.05
33 21 0.48
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.63
Consensus pattern (31 bp):
TTTTTAATATTTATTATTAAGGGTTTGCATT
Found at i:449003 original size:30 final size:30
Alignment explanation
Indices: 448967--449035 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
448957 TTTTGTCATC
** *
448967 ATTTTTTTAACATTTGTTATTAAGGGTCTA
1 ATTTTTTTAACACCTGTTATCAAGGGTCTA
* *
448997 ATTTTTTCAATACCTGTTATCAAGGGTCTA
1 ATTTTTTTAACACCTGTTATCAAGGGTCTA
449027 ATTTTTTTA
1 ATTTTTTTA
449036 GTATTTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (30 bp):
ATTTTTTTAACACCTGTTATCAAGGGTCTA
Found at i:452216 original size:23 final size:23
Alignment explanation
Indices: 452169--452216 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
452159 TAGTATTTAG
* *
452169 ATAAATTTATTAATAATTTTTTA
1 ATAAATTTAATAATAATTTTATA
452192 ATAAATTTAATAAGT-ATTTTATA
1 ATAAATTTAATAA-TAATTTTATA
452215 AT
1 AT
452217 TTTTTAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATAAATTTAATAATAATTTTATA
Found at i:458989 original size:2 final size:2
Alignment explanation
Indices: 458984--459016 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
458974 TATAATTCTT
458984 TC TC TC TC 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 TC TC TC TC T
459017 TCATTTATGG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:459115 original size:19 final size:18
Alignment explanation
Indices: 459078--459112 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
459068 ATTTTTATTA
* *
459078 TCATAATTTTCTATTTTC
1 TCATAAATTTATATTTTC
459096 TCATAAATTTATATTTT
1 TCATAAATTTATATTTT
459113 TCTAAAAACA
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:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TCATAAATTTATATTTTC
Found at i:462894 original size:274 final size:274
Alignment explanation
Indices: 462405--462953 Score: 1071
Period size: 274 Copynumber: 2.0 Consensus size: 274
462395 CTTAATTTTT
462405 CAAAAGAAATAATAATTATTTTTTATTGAATATAATAAAGAAAATAATTTGATAAAATGAAATAT
1 CAAAAGAAATAATAATTATTTTTTATTGAATATAATAAAGAAAATAATTTGATAAAATGAAATAT
462470 ATTGAGCAAAAATGACAAATATAAATTAAATTTAAATTAAGAGCAGTTAAAAATTTCATTTTTAA
66 ATTGAGCAAAAATGACAAATATAAATTAAATTTAAATTAAGAGCAGTTAAAAATTTCATTTTTAA
*
462535 ACTTTCAATTTTTTAAGACCATACCTAATGTTTAGTTTTTGTTTTATTTTAGTACAAGCCACTAA
131 ACTTTCAATTTTTTAAGACCATACCTAATGTTTAGTTTTTATTTTATTTTAGTACAAGCCACTAA
462600 AAATTTAGCATGTTTAGTACCTAACCCATCCGTTTTGGTACGTTTTAGTACCTAAACTTTAAAAA
196 AAATTTAGCATGTTTAGTACCTAACCCATCCGTTTTGGTACGTTTTAGTACCTAAACTTTAAAAA
462665 AAATAAAAATGTAA
261 AAATAAAAATGTAA
462679 CAAAAGAAATAATAATTATTTTTTATTGAATATAATAAAGAAAATAATTTGATAAAATGAAATAT
1 CAAAAGAAATAATAATTATTTTTTATTGAATATAATAAAGAAAATAATTTGATAAAATGAAATAT
462744 ATTGAGCAAAAATGACAAATATAAATTAAATTTAAATTAAGAGCAGTTAAAAATTTCATTTTTAA
66 ATTGAGCAAAAATGACAAATATAAATTAAATTTAAATTAAGAGCAGTTAAAAATTTCATTTTTAA
*
462809 ACTTTCAATTTTTTAAGACCATACCTAATGTTTAGTTTTTATTTTATTTTAGTACAAGCCATTAA
131 ACTTTCAATTTTTTAAGACCATACCTAATGTTTAGTTTTTATTTTATTTTAGTACAAGCCACTAA
*
462874 AAATTTAGCATGTTTAGTACCTAACCCATCCGTTTTGGTCCGTTTTAGTACCTAAACTTTAAAAA
196 AAATTTAGCATGTTTAGTACCTAACCCATCCGTTTTGGTACGTTTTAGTACCTAAACTTTAAAAA
462939 AAATAAAAATGTAA
261 AAATAAAAATGTAA
462953 C
1 C
462954 GTTAAGTTTT
Statistics
Matches: 272, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
274 272 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (274 bp):
CAAAAGAAATAATAATTATTTTTTATTGAATATAATAAAGAAAATAATTTGATAAAATGAAATAT
ATTGAGCAAAAATGACAAATATAAATTAAATTTAAATTAAGAGCAGTTAAAAATTTCATTTTTAA
ACTTTCAATTTTTTAAGACCATACCTAATGTTTAGTTTTTATTTTATTTTAGTACAAGCCACTAA
AAATTTAGCATGTTTAGTACCTAACCCATCCGTTTTGGTACGTTTTAGTACCTAAACTTTAAAAA
AAATAAAAATGTAA
Found at i:463427 original size:34 final size:32
Alignment explanation
Indices: 463373--463444 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
463363 ACCTTACAAA
*
463373 CTCCCTAGTTTTTCCGGGCTAAACTAGAACCT
1 CTCCCTAGTTTTACCGGGCTAAACTAGAACCT
* *
463405 TTCCCTAGCTTTTACACGGGCTAAGCTAGAACCT
1 CTCCCTAG-TTTTAC-CGGGCTAAACTAGAACCT
463439 CTCCCT
1 CTCCCT
463445 TTTACAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (32 bp):
CTCCCTAGTTTTACCGGGCTAAACTAGAACCT
Found at i:465553 original size:22 final size:20
Alignment explanation
Indices: 465501--465555 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
465491 CGTTAGACAA
*
465501 GGGGGAATCGATACCCCCTG
1 GGGGGAATCGGTACCCCCTG
465521 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
465541 GGTGGTGAATCGGTA
1 GG-GG-GAATCGGTA
465556 TCCCATACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 21 0.66
21 2 0.06
22 9 0.28
ACGTcount: A:0.18, C:0.24, G:0.40, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:465597 original size:18 final size:18
Alignment explanation
Indices: 465564--465598 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
465554 TATCCCATAC
* *
465564 AGGGGGAATTTGTACCCT
1 AGGGGGAATATATACCCT
465582 AGGGGGAATATATACCC
1 AGGGGGAATATATACCC
465599 CTGGACAATC
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:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (18 bp):
AGGGGGAATATATACCCT
Found at i:467485 original size:2 final size:2
Alignment explanation
Indices: 467480--467523 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
467470 CAAAAAAAAG
467480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
467522 TA
1 TA
467524 GAAAGAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:472116 original size:60 final size:60
Alignment explanation
Indices: 472015--472161 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 60
472005 ATCATATTTT
* * *
472015 CTCAAACTATGAC-CATCATTTTAAATTAGTCCTTAAACTTTTAAATAGTTC-AATTTCATC
1 CTCAAACCATGACTC-TCATTTTAAATTAGTACTTAAACTTTTAAACA-TTCTAATTTCATC
472075 C-CTAAACCATGACTCTCATTTTAAATTAGTACTTAAACTTTTAAACATTCTAATTTCATC
1 CTC-AAACCATGACTCTCATTTTAAATTAGTACTTAAACTTTTAAACATTCTAATTTCATC
** * *
472135 CTCAAATTATGACTCTCAATCTAAATT
1 CTCAAACCATGACTCTCATTTTAAATT
472162 GGTTCCAAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
59 4 0.05
60 70 0.92
61 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.39
Consensus pattern (60 bp):
CTCAAACCATGACTCTCATTTTAAATTAGTACTTAAACTTTTAAACATTCTAATTTCATC
Found at i:475680 original size:21 final size:21
Alignment explanation
Indices: 475656--475700 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
475646 CTGCTATGGG
475656 ATGCTTAACAAGCTCAATGAC
1 ATGCTTAACAAGCTCAATGAC
475677 ATGCTTAACAAGCTCAATGAC
1 ATGCTTAACAAGCTCAATGAC
475698 ATG
1 ATG
475701 AAGATCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (21 bp):
ATGCTTAACAAGCTCAATGAC
Found at i:482414 original size:31 final size:28
Alignment explanation
Indices: 482354--482457 Score: 111
Period size: 28 Copynumber: 3.6 Consensus size: 28
482344 TCACTAGTAA
*
482354 AAGTACCTAAAATATTTTTTGATCAAAAT
1 AAGTACCTAAAGTATTTTTTG-TCAAAAT
*
482383 AAGTACCTATAGTTATAATTTTTGTCAAAAT
1 AAGTACCTAAAG-TAT--TTTTTGTCAAAAT
* *
482414 ATGTATCTAAAGTATTTTTTGGTCAAAAT
1 AAGTACCTAAAGTATTTTTT-GTCAAAAT
*
482443 -AGTAACTAAAGTATT
1 AAGTACCTAAAGTATT
482458 CAATTTTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.28
29 18 0.28
30 6 0.09
31 16 0.25
32 6 0.09
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (28 bp):
AAGTACCTAAAGTATTTTTTGTCAAAAT
Found at i:484813 original size:2 final size:2
Alignment explanation
Indices: 484806--484881 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
484796 TAACCATTAC
484806 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
484848 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
484882 GCAGCCAATG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:485464 original size:29 final size:29
Alignment explanation
Indices: 485429--485510 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
485419 AAACTAAATT
*
485429 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
485458 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
485487 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
485511 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:490235 original size:29 final size:29
Alignment explanation
Indices: 490200--490281 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
490190 AAACTAAATT
*
490200 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
490229 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
490258 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
490282 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:500362 original size:2 final size:2
Alignment explanation
Indices: 500355--500384 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
500345 TTAATCCAAC
500355 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
500385 GTTAGGATTC
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:503652 original size:2 final size:2
Alignment explanation
Indices: 503647--503686 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
503637 CTGATTTAAG
503647 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
503687 TCAGGTAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:504689 original size:21 final size:22
Alignment explanation
Indices: 504659--504701 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
504649 GTGTAAACAC
504659 CAAAACAATCACA-AATATATA
1 CAAAACAATCACACAATATATA
*
504680 CAAAATAATCACATCAATATAT
1 CAAAACAATCACA-CAATATAT
504702 TTTTCATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (22 bp):
CAAAACAATCACACAATATATA
Found at i:507616 original size:29 final size:29
Alignment explanation
Indices: 507583--507660 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
507573 TAAATTGATA
*
507583 TCATTGCTTACATCATTTAATTAAAGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
* *
507612 TCATTGCTTACATCATTTACGTAATGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
507641 TCATTGCTTACATCAATTTA
1 TCATTGCTTACATC-ATTTA
507661 GTTAGGTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAGATG
Found at i:508909 original size:24 final size:24
Alignment explanation
Indices: 508882--508932 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
508872 AACGTGGCCA
508882 AGGTAG-AGATAGAGGCCATGGACG
1 AGGTAGAAG-TAGAGGCCATGGACG
* * *
508906 AGGTGGAAGTCGAGGTCATGGACG
1 AGGTAGAAGTAGAGGCCATGGACG
508930 AGG
1 AGG
508933 CTGGAATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.29, C:0.12, G:0.45, T:0.14
Consensus pattern (24 bp):
AGGTAGAAGTAGAGGCCATGGACG
Found at i:512373 original size:29 final size:29
Alignment explanation
Indices: 512340--512417 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
512330 TAAATTGATA
* *
512340 TCATTACTTACATCATTTAATTAAAGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
*
512369 TCATTGCTTACATCATTTAAGTAATGATG
1 TCATTGCTTACATCATTTAAGTAAAGATG
512398 TCATTGCTTACATCAATTTA
1 TCATTGCTTACATC-ATTTA
512418 GTTAGGTGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAGATG
Found at i:513038 original size:15 final size:14
Alignment explanation
Indices: 513018--513051 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
513008 TATTTTAAAT
513018 ATTTTAAACAAATAC
1 ATTTTAAA-AAATAC
*
513033 ATTTTATAAAATAC
1 ATTTTAAAAAATAC
513047 ATTTT
1 ATTTT
513052 TTATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAAAATAC
Found at i:513197 original size:14 final size:14
Alignment explanation
Indices: 513163--513201 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
513153 TGATTATTTT
513163 ATTTTAAAATGATA
1 ATTTTAAAATGATA
513177 ATCTTTAAATAT-ATA
1 AT-TTTAAA-ATGATA
513192 ATTTTAAAAT
1 ATTTTAAAAT
513202 TGTTGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.09
14 8 0.35
15 11 0.48
16 2 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (14 bp):
ATTTTAAAATGATA
Found at i:513483 original size:108 final size:108
Alignment explanation
Indices: 513361--513576 Score: 396
Period size: 108 Copynumber: 2.0 Consensus size: 108
513351 AAAACAAAAC
*
513361 TAGTAACTTAAGATTACATAAGGACAGTATAAAGAAATATTAAATTTAACCAAGAAACTCGAACA
1 TAGTAACTTAAGATTACATAAGAACAGTATAAAGAAATATTAAATTTAACCAAGAAACTCGAACA
* *
513426 AAAATACATATAAACAAATCTGATCGTATGGACAAACGAACTA
66 AAAATACATATAAACAAATCTGATCGTATGAACAAACAAACTA
513469 TAGTAACTTAAGATTACATAAGAACAGTATAAAGAAATATTAAATTTAACCAAGAAACTCGAACA
1 TAGTAACTTAAGATTACATAAGAACAGTATAAAGAAATATTAAATTTAACCAAGAAACTCGAACA
*
513534 AAAATACATATAAACAAATCTGATTGTATGAACAAACAAACTA
66 AAAATACATATAAACAAATCTGATCGTATGAACAAACAAACTA
513577 CAAAAGAGAA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (108 bp):
TAGTAACTTAAGATTACATAAGAACAGTATAAAGAAATATTAAATTTAACCAAGAAACTCGAACA
AAAATACATATAAACAAATCTGATCGTATGAACAAACAAACTA
Found at i:515048 original size:66 final size:66
Alignment explanation
Indices: 514942--515072 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
514932 GGCATCTTTG
* *
514942 TTTGATGTGAATGTTGATTACAGGAGGAACAGGTTCAGTGATCATGAGAAGGATCCGTATAAAAC
1 TTTGATGTGAATGTTGATTACAGGAGAAACAGGTTCAGTGATCATGAGAAGGAGCCGTATAAAAC
515007 A
66 A
*
515008 TTTGATGTGAATGTTGATTACTGGAGAAACAGGTTCAGTGATCATGAGAAGGAGCCGTATAAAAC
1 TTTGATGTGAATGTTGATTACAGGAGAAACAGGTTCAGTGATCATGAGAAGGAGCCGTATAAAAC
515073 GTTGCCGGGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.27
Consensus pattern (66 bp):
TTTGATGTGAATGTTGATTACAGGAGAAACAGGTTCAGTGATCATGAGAAGGAGCCGTATAAAAC
A
Found at i:525133 original size:2 final size:2
Alignment explanation
Indices: 525126--525166 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
525116 TAAGATATTC
525126 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 A
525167 ATCTAAAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:525529 original size:15 final size:15
Alignment explanation
Indices: 525511--525585 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
525501 TGTGAAATTC
525511 AAATTATTTAAATAA
1 AAATTATTTAAATAA
*
525526 AAATTATTTATATAA
1 AAATTATTTAAATAA
*
525541 AAATTCA--TCAAT-A
1 AAATT-ATTTAAATAA
*
525554 ATA-TATTTAAATAA
1 AAATTATTTAAATAA
*
525568 AAATTATTTATATAA
1 AAATTATTTAAATAA
525583 AAA
1 AAA
525586 ATCATTGGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 7 0.15
14 6 0.12
15 32 0.67
16 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTATTTAAATAA
Found at i:525541 original size:19 final size:19
Alignment explanation
Indices: 525514--525583 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
525504 GAAATTCAAA
*
525514 TTATTTAAATAAAAATTAT
1 TTATATAAATAAAAATTAT
*
525533 TTATATAAA-AATTCATCAATAAT
1 TTATATAAATAA---A--AATTAT
* *
525556 ATATTTAAATAAAAATTAT
1 TTATATAAATAAAAATTAT
525575 TTATATAAA
1 TTATATAAA
525584 AAATCATTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
21 2 0.05
23 12 0.32
24 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
TTATATAAATAAAAATTAT
Found at i:525544 original size:21 final size:21
Alignment explanation
Indices: 525520--525585 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
525510 CAAATTATTT
525520 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
** * **
525541 AAATTCATCAA-TA-ATATATTT
1 AAA-T-AAAAATTATTTATATAA
525562 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
525583 AAA
1 AAA
525586 ATCATTGGTA
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 19 0.61
22 3 0.10
23 3 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAAAAATTATTTATATAA
Found at i:528878 original size:22 final size:22
Alignment explanation
Indices: 528833--528899 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
528823 CTCGTATAAA
528833 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
528856 TGCACCGAAGTGCCCATAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
528878 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
528900 GATGTCCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 29 0.71
23 12 0.29
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:530586 original size:21 final size:21
Alignment explanation
Indices: 530562--530606 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
530552 TCTTGTTCGT
* *
530562 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
530583 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
530604 TTG
1 TTG
530607 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:533729 original size:22 final size:22
Alignment explanation
Indices: 533684--533750 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
533674 CTCGTATAAA
*
533684 TGCACCGAAGTGCCCCATAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
533707 TGCATCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
533729 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
533751 GATGTCCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 29 0.73
23 11 0.28
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:535420 original size:21 final size:21
Alignment explanation
Indices: 535396--535440 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
535386 TCTTGTTCGT
* *
535396 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
535417 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
535438 TTG
1 TTG
535441 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:536372 original size:23 final size:23
Alignment explanation
Indices: 536345--536389 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
536335 TGCCAAACAT
*
536345 AGAGATGAGAAGAACAGAAAAAC
1 AGAGATGAGAAGAACAAAAAAAC
536368 AGAGATGAGAAGAACAAAAAAA
1 AGAGATGAGAAGAACAAAAAAA
536390 ATTGAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.64, C:0.07, G:0.24, T:0.04
Consensus pattern (23 bp):
AGAGATGAGAAGAACAAAAAAAC
Found at i:536848 original size:15 final size:15
Alignment explanation
Indices: 536817--536845 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
536807 ACTCAAAAAG
536817 TTTTTAGAAAAATAA
1 TTTTTAGAAAAATAA
536832 TTTTT-GAAAAATAA
1 TTTTTAGAAAAATAA
536846 ATTATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTTTAGAAAAATAA
Found at i:537225 original size:17 final size:16
Alignment explanation
Indices: 537164--537228 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
537154 TTAAATATCT
*
537164 TTATTAAAATATTATTA
1 TTATTAATA-ATTATTA
537181 GTTATTATATAA-TATTAA
1 -TTATTA-ATAATTATT-A
*
537199 TATATAAATAATTATTCA
1 T-TATTAATAATTATT-A
537217 TTATTAATAATT
1 TTATTAATAATT
537229 TAGTAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 19 0.49
18 18 0.46
19 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
TTATTAATAATTATTA
Found at i:537329 original size:18 final size:17
Alignment explanation
Indices: 537306--537359 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
537296 AAAATAAAAA
537306 TATAATATCTTATATTAT
1 TATAATAT-TTATATTAT
* *
537324 TATAATATAATATTTTAT
1 TATAATAT-TTATATTAT
537342 TATAATA-TTATATTAT
1 TATAATATTTATATTAT
537358 TA
1 TA
537360 GAAATATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 9 0.29
18 22 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAATATTTATATTAT
Found at i:537334 original size:23 final size:21
Alignment explanation
Indices: 537299--537358 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
537289 CATTATTAAA
*
537299 ATAAAAATATAATATCTTATATT
1 ATAATAATATAATAT-TT-TATT
*
537322 ATTATAATATAATATTTTATT
1 ATAATAATATAATATTTTATT
* *
537343 ATAATATTATATTATT
1 ATAATAATATAATATT
537359 AGAAATATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 17 0.53
22 2 0.06
23 13 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATAATATAATATTTTATT
Found at i:537355 original size:13 final size:13
Alignment explanation
Indices: 537315--537357 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
537305 ATATAATATC
*
537315 TTATATTATTATA
1 TTATAATATTATA
* *
537328 ATATAATATTTTA
1 TTATAATATTATA
537341 TTATAATATTATA
1 TTATAATATTATA
537354 TTAT
1 TTAT
537358 TAGAAATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATAATATTATA
Found at i:546866 original size:51 final size:51
Alignment explanation
Indices: 546804--546906 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
546794 CGAGGCAGGC
* *
546804 CTTCGAGTGTCTTGATGAGCTCGAATCCTCGGAGGAAGGATCATCGAACTT
1 CTTCGACTGTCTTGATGAGCTCAAATCCTCGGAGGAAGGATCATCGAACTT
546855 CTTCGACTGTCTTGATGAGCTCAAATCCTCGGAGGAAGGATCATCGAACTT
1 CTTCGACTGTCTTGATGAGCTCAAATCCTCGGAGGAAGGATCATCGAACTT
546906 C
1 C
546907 GTGGAGGCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (51 bp):
CTTCGACTGTCTTGATGAGCTCAAATCCTCGGAGGAAGGATCATCGAACTT
Found at i:547662 original size:87 final size:87
Alignment explanation
Indices: 547516--547886 Score: 697
Period size: 87 Copynumber: 4.3 Consensus size: 87
547506 ACGCTATTTG
* *
547516 GAAAAAGATGAAAACCATGTATCTGAGGAACACCAAAGCAACATTAAATTTAAGAAACAACAAGA
1 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
547581 GTGGAGACCGAAATCGGAAGTA
66 GTGGAGACCGAAATCGGAAGTA
547603 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
1 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
547668 GTGGAGACCGAAATCGGAAGTA
66 GTGGAGACCGAAATCGGAAGTA
547690 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
1 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
547755 GTGGAGACCGAAATCGGAAGTA
66 GTGGAGACCGAAATCGGAAGTA
547777 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
1 GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
*
547842 GTGGAGACCAAAATCGGAAGTA
66 GTGGAGACCGAAATCGGAAGTA
* *
547864 GAAAAAGATGAAACCCATATATC
1 GAAAAAGATGAAAACCATGTATC
547887 CGAGAAATCC
Statistics
Matches: 279, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 279 1.00
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (87 bp):
GAAAAAGATGAAAACCATGTATCTGAGGAACCCCAAAGCAACAATAAATTTAAGAAACAACAAGA
GTGGAGACCGAAATCGGAAGTA
Found at i:548830 original size:3 final size:3
Alignment explanation
Indices: 548815--548867 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
548805 TTTTTACCCA
* *
548815 TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
548863 TAT TA
1 TAT TA
548868 AATATATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:549306 original size:17 final size:17
Alignment explanation
Indices: 549284--549323 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
549274 CCAAAAAAAA
*
549284 AAAAGAGAGACAGAGAG
1 AAAAGAGAGACAGAAAG
*
549301 AAAAGAGAGAGAGAAAG
1 AAAAGAGAGACAGAAAG
549318 AAAAGA
1 AAAAGA
549324 AAAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.65, C:0.03, G:0.33, T:0.00
Consensus pattern (17 bp):
AAAAGAGAGACAGAAAG
Found at i:550268 original size:13 final size:13
Alignment explanation
Indices: 550252--550298 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
550242 ATATAATAAA
550252 TAAATATTTATTT
1 TAAATATTTATTT
*
550265 TAAATAAATTATTT
1 TAAAT-ATTTATTT
550279 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
550292 TCAATAT
1 TAAATAT
550299 CAAGAACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:561474 original size:1 final size:1
Alignment explanation
Indices: 561468--561520 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
561458 ATTATGCTTG
* * * * *
561468 AAAAAAAAAAGAAAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAGAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
561521 GGGGTCAAGG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:561484 original size:10 final size:10
Alignment explanation
Indices: 561469--561520 Score: 74
Period size: 10 Copynumber: 5.5 Consensus size: 10
561459 TTATGCTTGA
561469 AAAAAAAAAG
1 AAAAAAAAAG
561479 AAAAAAAAAG
1 AAAAAAAAAG
561489 --AAAAAAAG
1 AAAAAAAAAG
561497 AAAAAAAAA-
1 AAAAAAAAAG
*
561506 AAAAAGAAAG
1 AAAAAAAAAG
561516 AAAAA
1 AAAAA
561521 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
8 8 0.21
9 8 0.21
10 22 0.58
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:561494 original size:19 final size:18
Alignment explanation
Indices: 561468--561520 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
561458 ATTATGCTTG
561468 AAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAGAAAAAAA
*
561486 AAGAAAAAAAGAAAAAAA
1 AAAAAAAAAAGAAAAAAA
561504 AAAAAAAGAAAGAAAAA
1 AAAAAAA-AAAGAAAAA
561521 GGGGTCAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 23 0.72
19 9 0.28
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAA
Found at i:561521 original size:10 final size:9
Alignment explanation
Indices: 561470--561520 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
561460 TATGCTTGAA
561470 AAAAAAAAG
1 AAAAAAAAG
561479 AAAAAAAA-
1 AAAAAAAAG
561487 AGAAAAAAAG
1 A-AAAAAAAG
*
561497 AAAAAAAAA
1 AAAAAAAAG
561506 AAAAAGAAAG
1 AAAAA-AAAG
561516 AAAAA
1 AAAAA
561521 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
8 1 0.03
9 27 0.73
10 9 0.24
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:563063 original size:248 final size:249
Alignment explanation
Indices: 562624--563082 Score: 746
Period size: 248 Copynumber: 1.8 Consensus size: 249
562614 GAAAGAGACT
* *
562624 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATATTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGACAGAACCAATCATTGAA
* *
562689 TTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTGG
66 TTTAGAAGATGAATGTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
*
562754 ACAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGA
131 ACAGAACCAATCATTGAATTTAGAAGATGAATGTGCCAATAGCATCTTCTGGAAGTGTTCTTTGA
562819 GTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTTTAGAAGATGAATTTGC
196 GTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTTTAGAAGATGAATTTGC
* * *
562873 CAATAGCATATTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACCAATCATT-AA
1 CAATAGCATATTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGACAGAACCAATCATTGAA
* *
562937 TTTGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
66 TTTAGAAGATGAATGTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TT
* * *
563001 GG-CAGAACCAATCATTGAATTTGGAAGATGAATGTGTTC-ATAGCATCTTTTGGAAGTGTTCTT
129 GGACAGAACCAATCATTGAATTTAGAAGATGAATGTG-CCAATAGCATCTTCTGGAAGTGTTCTT
563064 TGAGTTATCTGATCTGGTT
193 TGAGTTATCTGATCTGGTT
563083 TGGTAGGAAC
Statistics
Matches: 194, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
248 130 0.67
249 64 0.33
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (249 bp):
CAATAGCATATTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGACAGAACCAATCATTGAA
TTTAGAAGATGAATGTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
ACAGAACCAATCATTGAATTTAGAAGATGAATGTGCCAATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTTTAGAAGATGAATTTGC
Found at i:563085 original size:83 final size:83
Alignment explanation
Indices: 562624--563082 Score: 737
Period size: 83 Copynumber: 5.5 Consensus size: 83
562614 GAAAGAGACT
* *
562624 CAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
562689 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
*
562707 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
562772 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
*
562790 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
562855 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
* * *
562873 CAATAGCATATTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACCAATCATT-AA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
* * *
562937 TTTGGAAGATGAATGTGTT
66 TTTAGAAGATGAATTTG-C
562956 C-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGA
* * *
563019 ATTTGGAAGATGAATGTGTT
65 ATTTAGAAGATGAATTTG-C
*
563039 C-ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
563083 TGGTAGGAAC
Statistics
Matches: 357, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
82 71 0.20
83 286 0.80
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
TTTAGAAGATGAATTTGC
Found at i:564009 original size:113 final size:109
Alignment explanation
Indices: 563812--564364 Score: 668
Period size: 113 Copynumber: 4.9 Consensus size: 109
563802 GATTCAAATC
* *
563812 CATCACTTGATGGATCAACATTGCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATC-ACTTTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
563876 AGGAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTTGCCTGAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATC-TTTTG---GAATT
* *
563924 CATCACTTGATGGATTAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCA-CTTTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
563989 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG---GAATT
* * * * *
564037 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATTAGAAGAACTCGTTATCTGAAGAA
1 CATCACTTGATGGATCA-CTTTGCCAGAAAAAGTTCATAATGAGAAGAACTC---ATCTGAAGAA
564102 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGGAATT
62 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGGAATT
* * * *
564150 CATCA-TTGGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAA
1 CATCACTT-GATGGATC-ACTTTGCCAGA-AAAAGTTCATAATGAGAAGAA--C-TCATCTGAAG
564213 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGGAATT
60 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGGAATT
* * *
564263 CATCA-TTGGATGGATCAATATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 CATCACTT-GATGGATCACT-TTGCCAGA-AAAAGTTCATAATGAGAAGAA--C-TCATCTGAAG
564326 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAT
60 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAT
564365 AATTCTATCA
Statistics
Matches: 402, Mismatches: 26, Indels: 25
0.89 0.06 0.06
Matches are distributed among these distances:
111 1 0.00
112 26 0.06
113 319 0.79
114 2 0.00
115 1 0.00
116 53 0.13
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (109 bp):
CATCACTTGATGGATCACTTTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGGAATT
Found at i:564219 original size:229 final size:224
Alignment explanation
Indices: 563812--564364 Score: 766
Period size: 226 Copynumber: 2.5 Consensus size: 224
563802 GATTCAAATC
*
563812 CATCACTTGATGGATCAACATTGCCAGAGAA-GTTCATAATGAGAAGAACTC--ATCTGAAGAAG
1 CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTATCTGAAGAAG
*
563874 GAAGGAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTTGCCTGAATTCATCACTTGATGGA
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTG-C-GAATTCATCACTTGATGGA
* * * * *
563938 TTAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
129 TCAACATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATA
*
564003 ATGAGAAGAATTTGTTCAACCTTTTGTCTGAATT
194 ATGAGAAGAACTTGTTCAACCTTTTG---GAATT
* * * *
564037 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATTAGAAGAACTCGTTATCTGAAGAA
1 CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCG-TATCTGAAGAA
564102 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATC-TTTTG-GAATTCATCA-TTGGATGGA
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTGCGAATTCATCACTT-GATGGA
* *
564164 TCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTT
129 TCAACATTGCCAGA-AAAAGTTCATAATGAGAAGAA--C-TCATCTGAAAAAGGAAGAAGAAGTT
*
564228 CATAATGAGAAGAACTTGTTCAATCTTTTGGAATT
190 CATAATGAGAAGAACTTGTTCAACCTTTTGGAATT
*
564263 CATCA-TTGGATGGATCAATATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 CATCACTT-GATGGATCAATATTGCCAGAGAAG-GTTCATAATGAGAAGAACTCGT-ATCTGAAG
564326 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAT
63 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAT
564365 AATTCTATCA
Statistics
Matches: 295, Mismatches: 20, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
225 37 0.13
226 154 0.52
228 1 0.00
229 102 0.35
230 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (224 bp):
CATCACTTGATGGATCAATATTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTGCGAATTCATCACTTGATGGATC
AACATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGGAATT
Found at i:564694 original size:3 final size:3
Alignment explanation
Indices: 564679--564722 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
564669 TTTTTACCCA
* *
564679 TAT TAT AAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
564723 AATATATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:566143 original size:13 final size:13
Alignment explanation
Indices: 566127--566173 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
566117 ATATAATAAA
566127 TAAATATTTATTT
1 TAAATATTTATTT
*
566140 TAAATAAATTATTT
1 TAAAT-ATTTATTT
566154 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
566167 TCAATAT
1 TAAATAT
566174 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Done.