Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009065.1 Hibiscus syriacus cultivar Beakdansim tig00112488_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: 1198333
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:898553 original size:42 final size:42
Alignment explanation
Indices: 898471--898559 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
898461 TGCTCGGACG
* * * *
898471 TCGACTCGGGTACTGGTATAAGTCGAACATTTAACCTCTCAC
1 TCGACTCGGATACGGGTATAAGTAGAACACTTAACCTCTCAC
* * * * *
898513 TCGATTCGGATACGGGTATACGTAGAACACTTGACGTCTCAT
1 TCGACTCGGATACGGGTATAAGTAGAACACTTAACCTCTCAC
898555 TCGAC
1 TCGAC
898560 AAACCACTAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (42 bp):
TCGACTCGGATACGGGTATAAGTAGAACACTTAACCTCTCAC
Found at i:899468 original size:18 final size:18
Alignment explanation
Indices: 899445--899479 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
899435 AGTGACAAAC
*
899445 TATATATATACATACACA
1 TATATATATACACACACA
*
899463 TATATATTTACACACAC
1 TATATATATACACACAC
899480 GGGCATACAT
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:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
TATATATATACACACACA
Found at i:901640 original size:23 final size:23
Alignment explanation
Indices: 901610--901655 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
901600 AAGACATGTG
901610 TACTGAAATGAAATAAT-AACTAA
1 TACTGAAATGAAAT-ATGAACTAA
901633 TACTGAAATGAAATATGAACTAA
1 TACTGAAATGAAATATGAACTAA
901656 ATGTTAGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (23 bp):
TACTGAAATGAAATATGAACTAA
Found at i:909451 original size:21 final size:21
Alignment explanation
Indices: 909377--909459 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 21
909367 TATTTGGCAG
* *
909377 AGGGAATCGATACCCCC-ATA
1 AGGGAACCGATACCCCCTGTA
* *
909397 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATACCCCCTGT-A
*
909419 ATGGGAACCGATTCCCCCTGTA
1 A-GGGAACCGATACCCCCTGTA
* *
909441 GGGGAATCGATACCCCCTG
1 AGGGAACCGATACCCCCTG
909460 GGGTTCTGGA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
20 15 0.28
21 17 0.32
22 3 0.06
23 18 0.34
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.19
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTGTA
Found at i:916248 original size:216 final size:216
Alignment explanation
Indices: 915874--916305 Score: 783
Period size: 216 Copynumber: 2.0 Consensus size: 216
915864 AGATCTAAAT
915874 GGCCAAAGGGCCCAAAACACTCGTGGAAGCGAGTTACAACCGGAGTAACCATAGCTGACATAATA
1 GGCCAAAGGGCCCAAAACACTCGTGGAAGCGAGTTACAACCGGAGTAACCATAGCTGACATAATA
* *
915939 CGATTATGTTTCTTCAGCCAAGCACGTAGCAAGTATATAAAAATAAAATATCATTATAGAGGATG
66 CGATTATGTTTCTTCAACCAAGCACGTAGCAAGTATATAAAAATAAAATACCATTATAGAGGATG
* *
916004 TACTAACAAACGGTATGACGAATACTGCTAGAATAATCATGGATGATGAATGTATTGGTGTCCCT
131 TACCAACAAACGGTATGACAAATACTGCTAGAATAATCATGGATGATGAATGTATTGGTGTCCCT
916069 CTAATTCAAGGACAATTGGGA
196 CTAATTCAAGGACAATTGGGA
*
916090 GGCCAAAGGGCCCAAAACACTCGTGGAAGCGAGTTACAATCGGAGTAACCATAGCTGACATAATA
1 GGCCAAAGGGCCCAAAACACTCGTGGAAGCGAGTTACAACCGGAGTAACCATAGCTGACATAATA
* *
916155 CGATTATGTTTCTTCAACCAAGCACGTATCAAGTATATAAGAATAAAATACCATTATAGAGGATG
66 CGATTATGTTTCTTCAACCAAGCACGTAGCAAGTATATAAAAATAAAATACCATTATAGAGGATG
*
916220 TACCAACAAATGGTATGACAAATACTGCTAGAATAATCATGGATGATGAATGTATTGGTGTCCCT
131 TACCAACAAACGGTATGACAAATACTGCTAGAATAATCATGGATGATGAATGTATTGGTGTCCCT
*
916285 CTAATTCAAGGACGATTGGGA
196 CTAATTCAAGGACAATTGGGA
916306 AAAACATATT
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 207 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (216 bp):
GGCCAAAGGGCCCAAAACACTCGTGGAAGCGAGTTACAACCGGAGTAACCATAGCTGACATAATA
CGATTATGTTTCTTCAACCAAGCACGTAGCAAGTATATAAAAATAAAATACCATTATAGAGGATG
TACCAACAAACGGTATGACAAATACTGCTAGAATAATCATGGATGATGAATGTATTGGTGTCCCT
CTAATTCAAGGACAATTGGGA
Found at i:926671 original size:32 final size:32
Alignment explanation
Indices: 926625--926686 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
926615 AGATTTTTTT
926625 GGCGTCTTGCTTGGGATCTCCCGACGTCTTCA
1 GGCGTCTTGCTTGGGATCTCCCGACGTCTTCA
* * *
926657 GGCGTTTTGTTTGGGATCTCCCGGCGTCTT
1 GGCGTCTTGCTTGGGATCTCCCGACGTCTT
926687 GAGGGTGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.06, C:0.27, G:0.31, T:0.35
Consensus pattern (32 bp):
GGCGTCTTGCTTGGGATCTCCCGACGTCTTCA
Found at i:928009 original size:11 final size:10
Alignment explanation
Indices: 927983--928012 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
927973 ATTTAATTTT
927983 TTAAAAATAA
1 TTAAAAATAA
*
927993 TTAAAAATAC
1 TTAAAAATAA
928003 TTAAAAATAA
1 TTAAAAATAA
928013 ATTTGAGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:929332 original size:19 final size:19
Alignment explanation
Indices: 929296--929332 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
929286 TTGAAAATTT
*
929296 AAAATAATTATTTATTTTA
1 AAAATAATTAGTTATTTTA
*
929315 AAAATAATTAGTTGTTTT
1 AAAATAATTAGTTATTTT
929333 GGTTGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
AAAATAATTAGTTATTTTA
Found at i:930802 original size:19 final size:20
Alignment explanation
Indices: 930777--930865 Score: 101
Period size: 19 Copynumber: 4.3 Consensus size: 20
930767 CTTATTTTGG
930777 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
930797 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
930817 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
930841 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
930860 ATTTTT
1 ATTTTT
930866 TAAAATCGCG
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
19 30 0.51
20 6 0.10
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:931675 original size:20 final size:20
Alignment explanation
Indices: 931652--931689 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
931642 GAAGATGACC
931652 AAAATTCTA-AGGAACGAACT
1 AAAATTCTAGAGG-ACGAACT
931672 AAAATTCTAGAGGACGAA
1 AAAATTCTAGAGGACGAA
931690 ACAGATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATTCTAGAGGACGAACT
Found at i:933373 original size:7 final size:7
Alignment explanation
Indices: 933361--933390 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
933351 GTGCTAATTG
933361 ACCTGCT
1 ACCTGCT
933368 ACCTGCT
1 ACCTGCT
933375 ACCTGCT
1 ACCTGCT
933382 ACCTGCT
1 ACCTGCT
933389 AC
1 AC
933391 AGTTGACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.43, G:0.13, T:0.27
Consensus pattern (7 bp):
ACCTGCT
Found at i:935628 original size:5 final size:5
Alignment explanation
Indices: 935618--935650 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
935608 AATCTCTCAC
*
935618 TATAT TATAT TATAT TATAT TATAA TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
935651 CACATGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:936785 original size:38 final size:38
Alignment explanation
Indices: 936724--936844 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 38
936714 TTTTGTTCGG
936724 GTCGGGTCGA-GTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGAGGTTTTTTAAGTGTGATATTCGGGTCGA
936761 GTCGGGTCGAGGTTTTTTAAGTGTGATATTCGGGTC-A
1 GTCGGGTCGAGGTTTTTTAAGTGTGATATTCGGGTCGA
* * *
936798 ----GATCGAGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGAGGTTTTTTAAGTGTGATATTCGGGTCGA
*
936832 GTCGAGTCG-GGTT
1 GTCGGGTCGAGGTT
936845 CGGGTTTAGG
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
33 30 0.42
37 14 0.19
38 28 0.39
ACGTcount: A:0.16, C:0.11, G:0.36, T:0.38
Consensus pattern (38 bp):
GTCGGGTCGAGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:938508 original size:31 final size:31
Alignment explanation
Indices: 938473--938535 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
938463 AATTAAGGAT
938473 TAAATGAACAAAGCATTCAGTGAATTGTTCA
1 TAAATGAACAAAGCATTCAGTGAATTGTTCA
*
938504 TAAATGAACAAAGTATTCAGTGAATTGTTCA
1 TAAATGAACAAAGCATTCAGTGAATTGTTCA
938535 T
1 T
938536 GAATAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (31 bp):
TAAATGAACAAAGCATTCAGTGAATTGTTCA
Found at i:938950 original size:23 final size:24
Alignment explanation
Indices: 938906--939004 Score: 94
Period size: 23 Copynumber: 4.2 Consensus size: 24
938896 TAAACAAAGC
* * * *
938906 TAAACGAACGTGTTTGTAAACAT-
1 TAAATGAACATGTTCGTGAACATA
* *
938929 TAAATAAACATATTCGTGAACATA
1 TAAATGAACATGTTCGTGAACATA
* * *
938953 TAAACGAACTTGTTCATGAACAT-
1 TAAATGAACATGTTCGTGAACATA
*
938976 TAAATGAATATGTTCGTGAACATA
1 TAAATGAACATGTTCGTGAACATA
939000 TAAAT
1 TAAAT
939005 TGTAACACCT
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
23 36 0.61
24 23 0.39
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (24 bp):
TAAATGAACATGTTCGTGAACATA
Found at i:938960 original size:47 final size:47
Alignment explanation
Indices: 938906--939003 Score: 133
Period size: 47 Copynumber: 2.1 Consensus size: 47
938896 TAAACAAAGC
**
938906 TAAACGAACGTGTTTGTAAACATTAAATAAACATATTCGTGAACATA
1 TAAACGAACGTGTTCATAAACATTAAATAAACATATTCGTGAACATA
* * * * *
938953 TAAACGAACTTGTTCATGAACATTAAATGAATATGTTCGTGAACATA
1 TAAACGAACGTGTTCATAAACATTAAATAAACATATTCGTGAACATA
939000 TAAA
1 TAAA
939004 TTGTAACACC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (47 bp):
TAAACGAACGTGTTCATAAACATTAAATAAACATATTCGTGAACATA
Found at i:939937 original size:18 final size:18
Alignment explanation
Indices: 939914--939948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
939904 GCGTAGAATT
* *
939914 TGTCCCGTAGGGCCACTA
1 TGTCCCGAAGGACCACTA
939932 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
939949 GATAATCCCT
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:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:941399 original size:31 final size:31
Alignment explanation
Indices: 941358--941453 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
941348 AAACCTCGAC
* *
941358 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * **
941389 AATTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
941420 AACTATCAATATATCCCGAAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
941451 AAC
1 AAC
941454 CCTCTACTCT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:942446 original size:66 final size:67
Alignment explanation
Indices: 942376--942501 Score: 163
Period size: 66 Copynumber: 1.9 Consensus size: 67
942366 ACCCTGATAA
*
942376 CATTCTGGAAATTTTTATC-TTC-AGAG-AGGTATCGATAACCCC-T-ATAGGGTATCGATACCA
1 CATTCT-GAAA-TTTT-TCGTTCAAGAGAAGGTATCGAT-ACCCCTTCATAGGGTACCGATACCA
942436 TACTGG
62 TACTGG
*
942442 CATTCTGTAATTTTTCGTTCAAGAGAAGGTATCGATACCCCTTCATAGGGTACCGATACC
1 CATTCTGAAATTTTTCGTTCAAGAGAAGGTATCGATACCCCTTCATAGGGTACCGATACC
942502 CTTTGCCCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
63 2 0.04
64 7 0.13
65 12 0.23
66 17 0.32
67 15 0.28
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (67 bp):
CATTCTGAAATTTTTCGTTCAAGAGAAGGTATCGATACCCCTTCATAGGGTACCGATACCATACT
GG
Found at i:947772 original size:36 final size:36
Alignment explanation
Indices: 947725--947809 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
947715 GATACAATCT
947725 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
947761 GTCCATCACCATTATCACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
947797 TTCCATTACCATT
1 GTCCATCACCATT
947810 TCATCACCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:953437 original size:36 final size:36
Alignment explanation
Indices: 953390--953474 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
953380 GATACAATCT
953390 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
953426 GTCCATCACCATTATCACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
953462 TTCCATTACCATT
1 GTCCATCACCATT
953475 TCATCACCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:953823 original size:23 final size:23
Alignment explanation
Indices: 953793--953856 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
953783 CATCTCATAT
953793 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
953816 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
953839 AATTGTACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
953857 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:954043 original size:103 final size:104
Alignment explanation
Indices: 953872--954074 Score: 363
Period size: 103 Copynumber: 2.0 Consensus size: 104
953862 TAATGTCCAT
* *
953872 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
953937 GACTTCACACATGTTCCAAAGAATACATA-TATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATAGTATGTCCCG
* *
953975 AAGGACCACATATCATTCCTTAAGAATCATTTACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
954040 GACTTCACACATGTTCCAAAGAATACATAGTATGT
66 GACTTCACACATGTTCCAAAGAATACATAGTATGT
954075 GTCTCACCAG
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 90 0.95
104 5 0.05
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (104 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATAGTATGTCCCG
Found at i:954087 original size:44 final size:44
Alignment explanation
Indices: 954024--954117 Score: 181
Period size: 44 Copynumber: 2.2 Consensus size: 44
954014 CCAAGGATCA
954024 AGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACAT
1 AGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACAT
954068 AGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACAT
1 AGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACAT
954112 A-TATGT
1 AGTATGT
954118 CCCGAAGGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 5 0.10
44 45 0.90
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (44 bp):
AGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATACAT
Found at i:954993 original size:64 final size:64
Alignment explanation
Indices: 954885--955108 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 64
954875 TAATGAAGGT
* ** * * * * *
954885 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCAATACACAAATTGCATTCGATGTT-TCATTATTAATGGG
* * * *
954949 ATGCATCGATGCA-TGACTTATGCATCAATATACTAATTGCATTCGATGTTTCCTTATTAATGTG
1 ATGCATCGATGCACT-ACTTATGCATCAATACACAAATTGCATTCGATGTTTCATTATTAATGGG
* * * **
955013 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGA-GTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCAATACACAAATTGCATTCGATGT-TTCATTATTAATGGG
** *
955075 AGTGCATCGATGCACTACCAATGCATCGATACAC
1 A-TGCATCGATGCACTACTTATGCATCAATACAC
955109 CTTCAAACAA
Statistics
Matches: 132, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
62 2 0.02
63 37 0.28
64 92 0.70
65 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCAATACACAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:956500 original size:18 final size:18
Alignment explanation
Indices: 956477--956529 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
956467 TCGTAGAATT
*
956477 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
956495 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
956513 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
956530 GATAATCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:956992 original size:22 final size:21
Alignment explanation
Indices: 956967--957008 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
956957 ATAGATCATT
*
956967 ATCATATAACACATAAATGCAC
1 ATCACATAACACAT-AATGCAC
*
956989 ATCACATAACATATAATGCA
1 ATCACATAACACATAATGCA
957009 AGCATGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (21 bp):
ATCACATAACACATAATGCAC
Found at i:957547 original size:24 final size:24
Alignment explanation
Indices: 957519--957585 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
957509 ATGTTACATA
*
957519 AATGAACTTGTTCGTGAACATATT
1 AATGAACATGTTCGTGAACATATT
**
957543 AATGAACATGTTCACG-A-ATATT
1 AATGAACATGTTCGTGAACATATT
*
957565 AAGCGAACATGTTCGTGAACA
1 AA-TGAACATGTTCGTGAACA
957586 ATAAATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 7 0.21
23 12 0.35
24 14 0.41
25 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (24 bp):
AATGAACATGTTCGTGAACATATT
Found at i:959604 original size:20 final size:21
Alignment explanation
Indices: 959579--959617 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
959569 TTTAAACCCT
959579 ATTCT-AAATACTTCAATTAA
1 ATTCTAAAATACTTCAATTAA
959599 ATTCTAAAATACTTCAATT
1 ATTCTAAAATACTTCAATT
959618 TAAGGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTCTAAAATACTTCAATTAA
Found at i:959726 original size:14 final size:14
Alignment explanation
Indices: 959707--959733 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
959697 TGTATGAATC
959707 ATTTTATTTTTAAT
1 ATTTTATTTTTAAT
959721 ATTTTATTTTTAA
1 ATTTTATTTTTAA
959734 ATTAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTTTTAAT
Found at i:967980 original size:109 final size:109
Alignment explanation
Indices: 967789--968008 Score: 440
Period size: 109 Copynumber: 2.0 Consensus size: 109
967779 CTACGGTAGT
967789 ACTCCCTACTTATAAAAAAGTACATTTTATAACAGTGTTGATGCAATTCTATTAAATTTAAACTT
1 ACTCCCTACTTATAAAAAAGTACATTTTATAACAGTGTTGATGCAATTCTATTAAATTTAAACTT
967854 AAATCGAGATTAAATTTGAAAATCGAAAGAGTAGAGGATGTGAA
66 AAATCGAGATTAAATTTGAAAATCGAAAGAGTAGAGGATGTGAA
967898 ACTCCCTACTTATAAAAAAGTACATTTTATAACAGTGTTGATGCAATTCTATTAAATTTAAACTT
1 ACTCCCTACTTATAAAAAAGTACATTTTATAACAGTGTTGATGCAATTCTATTAAATTTAAACTT
967963 AAATCGAGATTAAATTTGAAAATCGAAAGAGTAGAGGATGTGAA
66 AAATCGAGATTAAATTTGAAAATCGAAAGAGTAGAGGATGTGAA
968007 AC
1 AC
968009 CTAAATTTAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 111 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (109 bp):
ACTCCCTACTTATAAAAAAGTACATTTTATAACAGTGTTGATGCAATTCTATTAAATTTAAACTT
AAATCGAGATTAAATTTGAAAATCGAAAGAGTAGAGGATGTGAA
Found at i:983140 original size:138 final size:135
Alignment explanation
Indices: 982890--983161 Score: 492
Period size: 138 Copynumber: 2.0 Consensus size: 135
982880 CATGCATAAT
982890 TTTTATTGGGGTAGAGTTCAAGATTATCGTTTAATAAATCCTTATTCACCTCATTCCTAAGAAGG
1 TTTTATTGGGGTAGAGTTCAAGATTATCGTTTAATAAATCCTTATTCACCTCATTCCTAAGAAGG
982955 TGGAGGCTTGTATCCGAGGATTTTAGACCGATTTCGTTGGTGGGTAGTTTGTATAAG-ATTATCT
66 TGGAGGCTTGTATCCGAGGATTTTAGACCGATTTCGTTGGTGGGTAGTTTGTATAAGAATTATCT
983019 AGAAA
131 AGAAA
983024 TTTTATTGGGGTAGAGTTCAAGATTTATCGTTTAATAAATCCTTTATTCACCTCATTCCTAAGAA
1 TTTTATTGGGGTAGAGTTCAAGA-TTATCGTTTAATAAATCC-TTATTCACCTCATTCCTAAGAA
983089 GGTGGAGGCTTTGTATCCGGAGGATTTTAGACCGATTTCGTTGGTGGGTAGTTTGTATAAGATAT
64 GGTGGAGGC-TTGTATCC-GAGGATTTTAGACCGATTTCGTTGGTGGGTAGTTTGTATAAGA-AT
983154 TATCTAGA
126 TATCTAGA
983162 GTTTTAGCCA
Statistics
Matches: 132, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
134 23 0.17
135 18 0.14
136 31 0.23
137 8 0.06
138 42 0.32
140 10 0.08
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (135 bp):
TTTTATTGGGGTAGAGTTCAAGATTATCGTTTAATAAATCCTTATTCACCTCATTCCTAAGAAGG
TGGAGGCTTGTATCCGAGGATTTTAGACCGATTTCGTTGGTGGGTAGTTTGTATAAGAATTATCT
AGAAA
Found at i:989798 original size:52 final size:53
Alignment explanation
Indices: 989735--989835 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 53
989725 TTGAAATCTG
* * *
989735 AATTTTTTTATACTAATTATTTATTTTACTG-AAGGTGCCCACCCTGAATTCA
1 AATTTCTTTATACTAATTATTCATTTTACTGAAAAGTGCCCACCCTGAATTCA
* * *
989787 AATTTCTTTATATTAGTTGTTCATTTTACTGAAAAGTGCCCACCCTGAA
1 AATTTCTTTATACTAATTATTCATTTTACTGAAAAGTGCCCACCCTGAA
989836 ATTTTATTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 26 0.62
53 16 0.38
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.43
Consensus pattern (53 bp):
AATTTCTTTATACTAATTATTCATTTTACTGAAAAGTGCCCACCCTGAATTCA
Found at i:998211 original size:22 final size:22
Alignment explanation
Indices: 998152--998200 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
998142 GATACTGAAT
998152 GAACAATATCGATACTAAACAA
1 GAACAATATCGATACTAAACAA
998174 GAACAATATCGATACTAAACAA
1 GAACAATATCGATACTAAACAA
998196 GAACA
1 GAACA
998201 TTATTGGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.16
Consensus pattern (22 bp):
GAACAATATCGATACTAAACAA
Found at i:1004076 original size:21 final size:23
Alignment explanation
Indices: 1004050--1004109 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
1004040 CTAAAGGAGC
*
1004050 AGTATCGGTACCATAACTC-AG-
1 AGTATCGATACCATAACTCAAGT
1004071 AGTATCGATACCACT-ACTCTAAGT
1 AGTATCGATACCA-TAACTC-AAGT
1004095 AGTATCGATACCATA
1 AGTATCGATACCATA
1004110 TATGGTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (23 bp):
AGTATCGATACCATAACTCAAGT
Found at i:1004768 original size:30 final size:30
Alignment explanation
Indices: 1004732--1004804 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
1004722 AAGTCGAGTA
*
1004732 ACCATTTTGTAACAAACGATAACGTTGGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
* *
1004762 ACCATTTTGTAACAAATGATGACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
1004792 ACCGA-TTTGTAAC
1 ACC-ATTTTGTAAC
1004805 TTTTCAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (30 bp):
ACCATTTTGTAACAAACGATAACGTTAGTG
Found at i:1032475 original size:37 final size:38
Alignment explanation
Indices: 1032425--1032498 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 38
1032415 ACTTAAACGT
*
1032425 TAAATTTTGAACGG-G-GTACCAAAATGAAATAAAAGC
1 TAAATTTTGAACGGAGTGTACCAAAATGAAACAAAAGC
* *
1032461 TAAAGTTTTTAACGGATGTGTACTAAAATGAAACAAAA
1 TAAA-TTTTGAACGGA-GTGTACCAAAATGAAACAAAA
1032499 AATGAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 4 0.13
37 9 0.29
39 1 0.03
40 17 0.55
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (38 bp):
TAAATTTTGAACGGAGTGTACCAAAATGAAACAAAAGC
Found at i:1037661 original size:5 final size:5
Alignment explanation
Indices: 1037651--1037682 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1037641 TAAAGGGATC
1037651 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
1037683 CAAACTCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:1039446 original size:163 final size:163
Alignment explanation
Indices: 1039176--1039506 Score: 583
Period size: 163 Copynumber: 2.0 Consensus size: 163
1039166 TGAATGAATA
* *
1039176 AATTTGAACCTGATTGAAGACTTCCTTTAAAGGCGCCAAGGCCAAGATGATTTCTCAAGAGATAG
1 AATTTGAAACTGATTGAAGACTTCCTTTAAAGGCACCAAGGCCAAGATGATTTCTCAAGAGATAG
* * *
1039241 ATACAATCATACCAATGACGAGAAGACGTTTCACAAAGACATGAAGACCACTTCGTACTAGAAGT
66 ATACAATCATACCAATGACGAGAAGACCTTTCACAAAGACATGAAGACCACTTCGCACTAAAAGT
*
1039306 AAAAAATGGAGATCTCAAGATTCAACCATAAAT
131 AAAAAATAGAGATCTCAAGATTCAACCATAAAT
1039339 AATTTGAAACTGATTGAAGACTTCCTTTAAAGGCACCAAGGCCAAGATG-TTTCCTCAAGAGATA
1 AATTTGAAACTGATTGAAGACTTCCTTTAAAGGCACCAAGGCCAAGATGATTT-CTCAAGAGATA
*
1039403 GATACAATCATACCAATGACGAGAAGACCTTTCACGAAGACATGAAGACCACTTCGCACTAAAAG
65 GATACAATCATACCAATGACGAGAAGACCTTTCACAAAGACATGAAGACCACTTCGCACTAAAAG
1039468 TAAAAAATAGAGATCTCAAGATTCAACCATAAAT
130 TAAAAAATAGAGATCTCAAGATTCAACCATAAAT
1039502 AATTT
1 AATTT
1039507 AAGGACATTA
Statistics
Matches: 160, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
162 3 0.02
163 157 0.98
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (163 bp):
AATTTGAAACTGATTGAAGACTTCCTTTAAAGGCACCAAGGCCAAGATGATTTCTCAAGAGATAG
ATACAATCATACCAATGACGAGAAGACCTTTCACAAAGACATGAAGACCACTTCGCACTAAAAGT
AAAAAATAGAGATCTCAAGATTCAACCATAAAT
Found at i:1044348 original size:20 final size:20
Alignment explanation
Indices: 1044325--1044379 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1044315 TCCAAAATTG
* *
1044325 GTAAGTCCTTCGGGCTATCA
1 GTAAGTCCTTCGAGCCATCA
*
1044345 GTAAGTCCTTTGAGCCATCA
1 GTAAGTCCTTCGAGCCATCA
1044365 GTAAGTCCTTCGAGC
1 GTAAGTCCTTCGAGC
1044380 ATGATGATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (20 bp):
GTAAGTCCTTCGAGCCATCA
Found at i:1047068 original size:21 final size:21
Alignment explanation
Indices: 1047005--1047093 Score: 82
Period size: 20 Copynumber: 4.4 Consensus size: 21
1046995 GGAAGAACAA
1047005 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
* * *
1047026 TAT-GA-ATCGGA-TGAA-CAA
1 TATCGATA-CTGATTGAAGTAG
1047044 TATCGATACTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
*
1047065 TATCGATACTGATGTGGAG--G
1 TATCGATACTGAT-TGAAGTAG
1047085 TATCGATAC
1 TATCGATAC
1047094 CAAGAGTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
18 4 0.07
19 10 0.18
20 20 0.36
21 17 0.31
22 4 0.07
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (21 bp):
TATCGATACTGATTGAAGTAG
Found at i:1047641 original size:15 final size:15
Alignment explanation
Indices: 1047579--1047641 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
1047569 ATTTTATTAG
*
1047579 TATGTGAAAT-TGTTA
1 TATGTG-AATGTGTTC
1047594 TATGTGAATGTGTTC
1 TATGTGAATGTGTTC
** ** *
1047609 TACATGAAACTGCTC
1 TATGTGAATGTGTTC
1047624 TATGTGAATGTGTTC
1 TATGTGAATGTGTTC
1047639 TAT
1 TAT
1047642 ATGGATAAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
14 3 0.08
15 33 0.92
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (15 bp):
TATGTGAATGTGTTC
Found at i:1047797 original size:23 final size:23
Alignment explanation
Indices: 1047771--1047828 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1047761 CCCTTGGGAT
1047771 AATTCTATGTGGTCATTTAGGAC
1 AATTCTATGTGGTCATTTAGGAC
* * * *
1047794 AATTCTACGCGATCCTTTAGGAC
1 AATTCTATGTGGTCATTTAGGAC
*
1047817 AAATCTATGTGG
1 AATTCTATGTGG
1047829 CACTTCAGTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (23 bp):
AATTCTATGTGGTCATTTAGGAC
Found at i:1047852 original size:24 final size:24
Alignment explanation
Indices: 1047816--1047873 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1047806 TCCTTTAGGA
*
1047816 CAAA-TCTATGTGGCACTTCAGTG
1 CAAATTCTACGTGGCACTTCAGTG
*
1047839 CATATTCTACGTGGCACTTCAGTG
1 CAAATTCTACGTGGCACTTCAGTG
1047863 CAAATTCTACG
1 CAAATTCTACG
1047874 CAGCAGTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCAGTG
Found at i:1058516 original size:21 final size:21
Alignment explanation
Indices: 1058491--1058545 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1058481 GTACTCATAG
1058491 GGGTATCGATACTTGACCCTA
1 GGGTATCGATACTTGACCCTA
*
1058512 GGGTATTGATACTTGACCCTA
1 GGGTATCGATACTTGACCCTA
*
1058533 GAGTATCGATACT
1 GGGTATCGATACT
1058546 AACCTCTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (21 bp):
GGGTATCGATACTTGACCCTA
Found at i:1059675 original size:32 final size:32
Alignment explanation
Indices: 1059597--1059677 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
1059587 ACAAAGTCAG
*
1059597 TATTGCATTCAGATAATGCACAGCAGAATCAA
1 TATTGCATTCAGATAATGCACAGCAGAACCAA
* * * *
1059629 TAATGTATTCAGATAATGCACAGTAGAGCCAA
1 TATTGCATTCAGATAATGCACAGCAGAACCAA
1059661 TATTGCATAT-AGATAAT
1 TATTGCAT-TCAGATAAT
1059678 ACGTAGTAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (32 bp):
TATTGCATTCAGATAATGCACAGCAGAACCAA
Found at i:1060614 original size:13 final size:13
Alignment explanation
Indices: 1060596--1060620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1060586 AATGAATTTT
1060596 AAGATTTTCTAAA
1 AAGATTTTCTAAA
1060609 AAGATTTTCTAA
1 AAGATTTTCTAA
1060621 GTATATTCGA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:1066300 original size:19 final size:20
Alignment explanation
Indices: 1066276--1066331 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
1066266 TATTTGGCAG
1066276 AGGGAATCGATACCCC-ATA
1 AGGGAATCGATACCCCTATA
* *
1066295 AGGGAA-CTGATTCCCCCTGTA
1 AGGGAATC-GA-TACCCCTATA
*
1066316 GGGGAATCGATACCCC
1 AGGGAATCGATACCCC
1066332 CATGGGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.03
19 8 0.28
20 10 0.34
21 9 0.31
22 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (20 bp):
AGGGAATCGATACCCCTATA
Found at i:1066331 original size:21 final size:20
Alignment explanation
Indices: 1066276--1066334 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1066266 TATTTGGCAG
1066276 AGGGAATCGATA-CCCCATA
1 AGGGAATCGATACCCCCATA
* *
1066295 AGGGAA-CTGATTCCCCCTGTA
1 AGGGAATC-GATACCCCC-ATA
*
1066316 GGGGAATCGATACCCCCAT
1 AGGGAATCGATACCCCCAT
1066335 GGGGTTCTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 9 0.29
20 5 0.16
21 15 0.48
22 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (20 bp):
AGGGAATCGATACCCCCATA
Found at i:1068463 original size:21 final size:21
Alignment explanation
Indices: 1068430--1068471 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1068420 TCCAGAATGT
1068430 CTAGAGGGAACCGATTCCCCC
1 CTAGAGGGAACCGATTCCCCC
* *
1068451 CTAGGGGGTACCGATTCCCCC
1 CTAGAGGGAACCGATTCCCCC
1068472 TGAATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.26, T:0.17
Consensus pattern (21 bp):
CTAGAGGGAACCGATTCCCCC
Found at i:1070262 original size:42 final size:42
Alignment explanation
Indices: 1070226--1070488 Score: 449
Period size: 42 Copynumber: 6.3 Consensus size: 42
1070216 TCCAAGTTCG
*
1070226 CGTTGAGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1070266 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
1070308 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1070350 CGTTGCGATAGTCGAAGTTCGCGTTTCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1070392 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1070434 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
1070476 CGTTACGATAGTC
1 CGTTGCGATAGTC
1070489 CAAAATCGCA
Statistics
Matches: 209, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 27 0.13
41 2 0.01
42 180 0.86
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:1071481 original size:16 final size:15
Alignment explanation
Indices: 1071456--1071489 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1071446 TTGAATTCTC
1071456 TCTTCTTTCTCTAAA
1 TCTTCTTTCTCTAAA
*
1071471 TCTTCTCTTCTCTCAA
1 TCTTCT-TTCTCTAAA
1071487 TCT
1 TCT
1071490 CTATTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.32, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTTCTTTCTCTAAA
Found at i:1072688 original size:15 final size:15
Alignment explanation
Indices: 1072670--1072699 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1072660 ATCCTAAAAA
*
1072670 TTCTATTTCTGTTTT
1 TTCTATTTCTATTTT
1072685 TTCTATTTCTATTTT
1 TTCTATTTCTATTTT
1072700 CTTATGACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.73
Consensus pattern (15 bp):
TTCTATTTCTATTTT
Found at i:1073199 original size:15 final size:15
Alignment explanation
Indices: 1073179--1073209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1073169 TATCAGTTTG
1073179 TTCTAATAATACTTT
1 TTCTAATAATACTTT
*
1073194 TTCTAATAATTCTTT
1 TTCTAATAATACTTT
1073209 T
1 T
1073210 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TTCTAATAATACTTT
Found at i:1073817 original size:2 final size:2
Alignment explanation
Indices: 1073810--1073835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1073800 CAAAACACTA
1073810 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
1073836 TGAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1079584 original size:58 final size:56
Alignment explanation
Indices: 1079474--1079761 Score: 255
Period size: 58 Copynumber: 5.1 Consensus size: 56
1079464 CCCAAACAAT
* * * *
1079474 ATGATATTTTCAAAAGACTTTTTAAAGAAACTAAGCCTGATTTTTAGGGGGTTTCTTG
1 ATGATA-TTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTA-AGGGTTTCTTG
** *
1079532 ATGATGATTTTTAATGAATTTTTAAAAGAAACTAATCCTAATTTTTAAGGGTTTCTTG
1 ATGAT-ATTTCAAATGAATTTTT-AAAGAAACTAAGCCTAATTTTTAAGGGTTTCTTG
* * * *
1079590 ATG-T-TTTCAAATGAGTTTTT--AGAAACTAAGCTTGATTTTCAAGGGTTTCTTG
1 ATGATATTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAAGGGTTTCTTG
* * *
1079642 ATGATTATTTCCAAA-GAATTTTTTTAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTG
1 ATGA-TATTT-CAAATGAA-TTTTTAAAGAAACTAAGCCTAATTTTTAAGGGTTTCTTG
* ** * * * *
1079700 ATGATAACTGAAAATGAAAGATTTT-AAGAAACTAAGCTTGATTTTCAAGGGTTTCTTG
1 ATGAT-ATTTCAAATG-AA-TTTTTAAAGAAACTAAGCCTAATTTTTAAGGGTTTCTTG
1079758 ATGA
1 ATGA
1079762 GTAAGTCCTT
Statistics
Matches: 188, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
52 31 0.16
54 1 0.01
55 18 0.10
56 9 0.05
57 5 0.03
58 96 0.51
59 28 0.15
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (56 bp):
ATGATATTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAAGGGTTTCTTG
Found at i:1079682 original size:110 final size:110
Alignment explanation
Indices: 1079475--1079761 Score: 322
Period size: 110 Copynumber: 2.5 Consensus size: 110
1079465 CCAAACAATA
* * * * * *
1079475 TGATATTTTCAAAAGACTTTTTAAAGAAACTAAGCCTGATTTTTAGGGGGTTTCTTGATGATGAT
1 TGATGTTTTCAAATGAGTTTTT--AGAAACTAAGCTTGATTTTCA-AGGGTTTCTTGATGATGAT
** * *
1079540 TTTTAATGAATTTTTAAAAGAAACTAATCCTAATTTTTAAGGGTTTCT
63 TTCCAAAGAATTTTTAAAAGAAACTAAGCCTAATTTTTAAGGGTTTCT
*
1079588 TGATGTTTTCAAATGAGTTTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTC
1 TGATGTTTTCAAATGAGTTTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGATGATTTC
** * *
1079653 CAAAGAATTTTTTTAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
66 CAAAGAATTTTTAAAAGAAACTAAGCCTAATTTTTAAGGGTTTCT
* ** *
1079698 TGATGATAACTGAAAATGAAAGATTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 TGATG-T--TTTCAAATG--AG-TTTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1079762 GTAAGTCCTT
Statistics
Matches: 149, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
110 62 0.42
111 20 0.13
113 25 0.17
115 2 0.01
116 40 0.27
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (110 bp):
TGATGTTTTCAAATGAGTTTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGATGATTTC
CAAAGAATTTTTAAAAGAAACTAAGCCTAATTTTTAAGGGTTTCT
Found at i:1079869 original size:41 final size:41
Alignment explanation
Indices: 1079757--1079869 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
1079747 AGGGTTTCTT
* *
1079757 GATGAGTAAGTCCTTTGGGCCAT-CAGTAAGTCTTTTGAGCAT
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTTGAGCAA
* * * *
1079799 GATGCTTAAATCCTTCGGGTCATCTATAAGT-TTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTT-GAGCAA
1079841 GATGATAAGTCCTTCGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCATCCATAAG
1079870 ACCTTCGGGC
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
41 25 0.43
42 32 0.55
43 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTTGAGCAA
Found at i:1080344 original size:134 final size:136
Alignment explanation
Indices: 1080056--1080423 Score: 535
Period size: 134 Copynumber: 2.7 Consensus size: 136
1080046 TTTCAAGTGG
* *
1080056 AGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAAGATCATAATGAGAAGAG-TTAG
1 AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTT-G
* * *** * *
1080120 TTCAACCTATCACTCGATTCACGGCATTTTGAATTGGTGACGCCTCGCTTGAGGGATTGAAATTT
65 TTCAACCTATCACTCGATTCACGACATTTCGAATCAATGACGCCTCACTTGAGAGATTGAAATTT
*
1080185 CCAATGG
130 CCAATGA
1080192 AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
*
1080257 TCAA-CTATCACT-GATTCATGACATTTCGAATCAATGACGCCTCACTTGAGAGATTGAAATTTC
66 TCAACCTATCACTCGATTCACGACATTTCGAATCAATGACGCCTCACTTGAGAGATTGAAATTTC
1080320 CAATGA
131 CAATGA
* *
1080326 AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGGAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
* ** * * *
1080391 TCGACCTATTGCTAGATTCACAACACTTCGAAT
66 TCAACCTATCACTCGATTCACGACATTTCGAAT
1080424 TAGCACTGCT
Statistics
Matches: 210, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
134 114 0.54
135 14 0.07
136 80 0.38
137 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (136 bp):
AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
TCAACCTATCACTCGATTCACGACATTTCGAATCAATGACGCCTCACTTGAGAGATTGAAATTTC
CAATGA
Found at i:1080514 original size:39 final size:40
Alignment explanation
Indices: 1080459--1080655 Score: 284
Period size: 39 Copynumber: 5.1 Consensus size: 40
1080449 CATCCCGCTG
*
1080459 GAGATATTTTCACTCGAAACAGAAGATTTTATCTCAG-TT
1 GAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAGCTT
* *
1080498 TAGATAGTTTCACTCGAAATAGAAGATTTTATCTC-GCTT
1 GAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAGCTT
*
1080537 GAGATAGTTTCACTCGAAACAGAAGATTTTATCTTA-CTT
1 GAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAGCTT
1080576 GAGATAGTTTCACTCGAAAC--AAGATTTTATCTC-GCTT
1 GAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAGCTT
* *
1080613 GAGATAATTTCACTCGAAACGGAAGA-TTTATCTCA-CTT
1 GAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAGCTT
1080651 GAGAT
1 GAGAT
1080656 TGTTCTTCTT
Statistics
Matches: 144, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
37 34 0.24
38 17 0.12
39 93 0.65
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (40 bp):
GAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAGCTT
Found at i:1080797 original size:61 final size:60
Alignment explanation
Indices: 1080679--1080797 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
1080669 ACAAACAACA
* * * *
1080679 CCCCACCAGAGGGGTTAACATTTCCTATTGTTCTATTCACAACACTTCGAATCAGCAATG
1 CCCCACCAGAGAGGATAACATTTCCTATTGCTCAATTCACAACACTTCGAATCAGCAATG
* *
1080739 CCCCACCAGAGAGGATAACATTT-CTTTTGCTCAATTCACACAACTCTTCGAATCAGCAA
1 CCCCACCAGAGAGGATAACATTTCCTATTGCTCAATT--CACAACACTTCGAATCAGCAA
1080798 CGCATCACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 10 0.20
60 21 0.41
61 20 0.39
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.27
Consensus pattern (60 bp):
CCCCACCAGAGAGGATAACATTTCCTATTGCTCAATTCACAACACTTCGAATCAGCAATG
Found at i:1081922 original size:25 final size:25
Alignment explanation
Indices: 1081883--1081933 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1081873 TATTTTTTTC
* *
1081883 AAAAAAAATGCAAAATGAAAATTTGT
1 AAAAAAAATG-AAAAAGAAAAATTGT
1081909 AAAAAAAA-GAAAAAGAAAAATTGT
1 AAAAAAAATGAAAAAGAAAAATTGT
1081933 A
1 A
1081934 TTTATAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 1 0.04
26 8 0.35
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.18
Consensus pattern (25 bp):
AAAAAAAATGAAAAAGAAAAATTGT
Found at i:1084616 original size:18 final size:18
Alignment explanation
Indices: 1084593--1084629 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1084583 TTTGGTTCAA
1084593 AGATTCTACTTCAGCTGT
1 AGATTCTACTTCAGCTGT
1084611 AGATTCTACTTCAGCTGT
1 AGATTCTACTTCAGCTGT
1084629 A
1 A
1084630 TTAGTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (18 bp):
AGATTCTACTTCAGCTGT
Found at i:1090091 original size:31 final size:32
Alignment explanation
Indices: 1090026--1090091 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
1090016 TTGAAAGGGA
* *
1090026 GTACTAAAATGGAACAAAAACTAAAGTTTTAG
1 GTACTAAAATGAAACAAAAACTAAAGCTTTAG
*
1090058 GTACTAAAATGAAACGAAAACTAAA-CTTTAG
1 GTACTAAAATGAAACAAAAACTAAAGCTTTAG
1090089 GTA
1 GTA
1090092 TGATTTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (32 bp):
GTACTAAAATGAAACAAAAACTAAAGCTTTAG
Found at i:1091974 original size:21 final size:21
Alignment explanation
Indices: 1091879--1091964 Score: 145
Period size: 21 Copynumber: 4.1 Consensus size: 21
1091869 GTTTCCAGAT
* *
1091879 TCGCAAGGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
1091900 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1091921 TCGCAATGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
1091942 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1091963 TC
1 TC
1091965 ACATTACGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1092049 original size:21 final size:21
Alignment explanation
Indices: 1091995--1092049 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1091985 GCGACACATA
*
1091995 TTCGCAATGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
1092016 TTCGCATTACGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
1092037 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
1092050 TTATTCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:1092113 original size:21 final size:21
Alignment explanation
Indices: 1092068--1092155 Score: 83
Period size: 21 Copynumber: 4.2 Consensus size: 21
1092058 AATTCGACTA
* * *
1092068 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
*
1092088 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
*
1092109 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
1092132 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
1092151 TCGCA
1 TCGCA
1092156 ACGACTGGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
19 11 0.20
20 12 0.22
21 21 0.38
23 11 0.20
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:1092155 original size:42 final size:40
Alignment explanation
Indices: 1092067--1092155 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 40
1092057 AAATTCGACT
* *
1092067 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATTTACAAATTCG-ATTGCGATAGTCCAAA
*
1092108 TTCGCATTGCGATTTATTCCAAATTCG-TTGCGATAGTCCAAA
1 ATCGCATTGCGATTTA---CAAATTCGATTGCGATAGTCCAAA
1092150 ATCGCA
1 ATCGCA
1092156 ACGACTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 15 0.37
42 19 0.46
44 7 0.17
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (40 bp):
ATCGCATTGCGATTTACAAATTCGATTGCGATAGTCCAAA
Found at i:1092249 original size:6 final size:6
Alignment explanation
Indices: 1092238--1092330 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
1092228 GACACGTATT
1092238 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1092286 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1092331 CGAGACGAGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1092854 original size:6 final size:6
Alignment explanation
Indices: 1092843--1092874 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1092833 TCTCATCTCG
1092843 GGTCGT GGTCGT -GTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1092875 AATAAGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GGTCGT
Found at i:1092860 original size:11 final size:12
Alignment explanation
Indices: 1092843--1092874 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
1092833 TCTCATCTCG
1092843 GGTCGTGGTCGT
1 GGTCGTGGTCGT
1092855 -GTCGTGGTCGT
1 GGTCGTGGTCGT
1092866 GGTCGTGGT
1 GGTCGTGGT
1092875 AATAAGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (12 bp):
GGTCGTGGTCGT
Found at i:1093020 original size:42 final size:42
Alignment explanation
Indices: 1092971--1093082 Score: 197
Period size: 42 Copynumber: 2.7 Consensus size: 42
1092961 ATTTTGGACT
*
1092971 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACAAATTTGGAATAA
1093013 ATCGCAACGCGAACTTCGACTATCGCAACAAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACAAATTTGGAATAA
* *
1093055 ATCGCAATGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
1093083 TGCGAATATG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACAAATTTGGAATAA
Found at i:1093079 original size:21 final size:20
Alignment explanation
Indices: 1092964--1093088 Score: 101
Period size: 21 Copynumber: 6.0 Consensus size: 20
1092954 CGTTGCGATT
1092964 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA-GCGAAC
* *
1092985 TTCGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
1093004 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* * *
1093027 TTCGACTATCGCAA-CAAAT
1 TTGGACTATCGCAAGCGAAC
*
1093046 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
1093069 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
1093089 TATGTAAATC
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
19 17 0.21
21 47 0.57
23 18 0.22
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:1093101 original size:20 final size:20
Alignment explanation
Indices: 1093052--1093107 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1093042 AAATTTGGAA
1093052 TAAATCGCAATGCGAACTTG
1 TAAATCGCAATGCGAACTTG
* *
1093072 GACTATCGCAATGCGAA-TATG
1 TA-AATCGCAATGCGAACT-TG
1093093 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
1093108 TAGTCGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:1093150 original size:21 final size:21
Alignment explanation
Indices: 1093126--1093200 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
1093116 TTTGGAATAA
*
1093126 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
1093147 ATCGTAATGCGAACTTTGACT
1 ATCGCAATGCGAACTTCGACT
* *
1093168 ATCACAATGCGAACTTCGATT
1 ATCGCAATGCGAACTTCGACT
*
1093189 ATCGCATTGCGA
1 ATCGCAATGCGA
1093201 TTTACATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1093235 original size:21 final size:21
Alignment explanation
Indices: 1093209--1093262 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1093199 GATTTACATA
1093209 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1093230 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1093251 TTCACGTTGCGA
1 TTCGCATTGCGA
1093263 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1095095 original size:37 final size:37
Alignment explanation
Indices: 1095022--1095093 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
1095012 TGGAAAATAA
* *
1095022 TTATATATTTTCTTTAAAAAATTTAAATTCATAAAAT
1 TTATATATTTTCTTTAAAAAATTGAAAATCATAAAAT
*
1095059 TTATATAATTTT-TTTACAAAATTGAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAAA
1095094 ATGTTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 20 0.65
38 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
TTATATATTTTCTTTAAAAAATTGAAAATCATAAAAT
Found at i:1098416 original size:94 final size:94
Alignment explanation
Indices: 1098255--1098443 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
1098245 TCAGTGGAAA
1098255 TCGTGATCGTATCTCTTTGATACTATCAAATGAGACATTGTGACTTCCATCTGTTTACTATTACA
1 TCGTGATCGTATCTCTTTGATACTATCAAATGAGACATTGTGACTTCCATCTGTTTACTATTACA
1098320 TAGTGTTAATCATGTTAAAATTTTCAATT
66 TAGTGTTAATCATGTTAAAATTTTCAATT
1098349 TCGTGATCGTATCTCTTTGATACTATCAAATGAGACATTGTGACTTCCATCTGTTTACTATTACA
1 TCGTGATCGTATCTCTTTGATACTATCAAATGAGACATTGTGACTTCCATCTGTTTACTATTACA
1098414 TAGTGTTAATCATGTTAAAATTTTCAATT
66 TAGTGTTAATCATGTTAAAATTTTCAATT
1098443 T
1 T
1098444 GAGAGTTGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (94 bp):
TCGTGATCGTATCTCTTTGATACTATCAAATGAGACATTGTGACTTCCATCTGTTTACTATTACA
TAGTGTTAATCATGTTAAAATTTTCAATT
Found at i:1105423 original size:80 final size:80
Alignment explanation
Indices: 1105326--1105485 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
1105316 AATTTACCCC
1105326 TAAGAATGATGTTTATGTGGGAATCAATTTTTTTTACGGATTTGATATTAAAAGCTATAAAGTGA
1 TAAGAATGATGTTTATGTGGGAATCAATTTTTTTTACGGATTTGATATTAAAAGCTATAAAGTGA
1105391 TAAAGTCCGGTAAAA
66 TAAAGTCCGGTAAAA
1105406 TAAGAATGATGTTTATGTGGGAATCAATTTTTTTTACGGATTTGATATTAAAAGCTATAAAGTGA
1 TAAGAATGATGTTTATGTGGGAATCAATTTTTTTTACGGATTTGATATTAAAAGCTATAAAGTGA
1105471 TAAAGTCCGGTAAAA
66 TAAAGTCCGGTAAAA
1105486 ATTCGGTAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (80 bp):
TAAGAATGATGTTTATGTGGGAATCAATTTTTTTTACGGATTTGATATTAAAAGCTATAAAGTGA
TAAAGTCCGGTAAAA
Found at i:1120159 original size:163 final size:159
Alignment explanation
Indices: 1119904--1120304 Score: 527
Period size: 163 Copynumber: 2.5 Consensus size: 159
1119894 GTTTCATGTT
* * * * * * * *
1119904 TATTCTATTGTGGTATATGAGCATGTGGTTAAAATTTGGTAAAAAATGACTTAAAATAAATCACA
1 TATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAGGACTTAAAATAAATGACG
* ** ***
1119969 AATTGAAGGAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAA-TTTTGTT
66 AATTGAAGAAATAAGGAGATTATGAAAAATTGAAAAACTAAATTGAAAAATAAAAAACAAATGTT
*
1120033 ATCAAAAAGAGGAATTGAAAGTACATATG
131 ATCAAAAAGAGGAATTGAAAGTACACATG
*
1120062 TATTTTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAAAGGGGGACTTAAAATAAA
1 TATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGT--AAAAAA---GGACTTAAAATAAA
*
1120127 TGATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAAAACTAAATTGAAAAATAAAAAACAA
61 TGACGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAAAACTAAATTGAAAAATAAAAAACAA
* *
1120192 ATGTTATCGAAAAGAGGAATTGAAGGTACACATG
126 ATGTTATCAAAAAGAGGAATTGAAAGTACACATG
* * * *
1120226 TATTCTACTATTGTTTAGGAGCATGTGGTTCAAATTTGG-AAAAAATGGACTTAAAATGAAGGAG
1 TATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAA-GGACTTAAAATAAATGAC
1120290 GAATTGAAGAAATAA
65 GAATTGAAGAAATAA
1120305 TGAAATCATG
Statistics
Matches: 212, Mismatches: 25, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
158 34 0.16
159 30 0.14
160 6 0.03
161 6 0.03
163 69 0.33
164 67 0.32
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.28
Consensus pattern (159 bp):
TATTCTACTATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAAGGACTTAAAATAAATGACG
AATTGAAGAAATAAGGAGATTATGAAAAATTGAAAAACTAAATTGAAAAATAAAAAACAAATGTT
ATCAAAAAGAGGAATTGAAAGTACACATG
Found at i:1124686 original size:41 final size:41
Alignment explanation
Indices: 1124629--1124714 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
1124619 GCGGTGTTTT
1124629 TAGCGGCGTTTGGAGAGTAAACGCCACAAAAGTTAAACATA
1 TAGCGGCGTTTGGAGAGTAAACGCCACAAAAGTTAAACATA
1124670 TAGCGGCGTTTGGAGAGTAAACGCCACAAAAGTTAAACATA
1 TAGCGGCGTTTGGAGAGTAAACGCCACAAAAGTTAAACATA
1124711 TAGC
1 TAGC
1124715 AGTGTTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
TAGCGGCGTTTGGAGAGTAAACGCCACAAAAGTTAAACATA
Found at i:1125070 original size:42 final size:41
Alignment explanation
Indices: 1124932--1125070 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 41
1124922 TTTATAATGA
*
1124932 AAACGCCGCAAT-TGAGTGTTAATTTAGCGGCGTTTATACCAC
1 AAACGCCGCAATAT-AGTG-TAAATTAGCGGCGTTTATACCAC
* * * **
1124974 AAACGCCGTAATAGATTTGTAAATTAGTTGCGTTTATACCAC
1 AAACGCCGCAATATA-GTGTAAATTAGCGGCGTTTATACCAC
* *
1125016 AAACGCCGCAATATAGTGATAAATTAGCGGTGTTTATATCTA-
1 AAACGCCGCAATATAGTG-TAAATTAGCGGCGTTTATA-CCAC
1125058 AAACGCCGCAATA
1 AAACGCCGCAATA
1125071 AATAATACTT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.03
42 74 0.93
43 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
AAACGCCGCAATATAGTGTAAATTAGCGGCGTTTATACCAC
Found at i:1126454 original size:42 final size:41
Alignment explanation
Indices: 1126402--1126483 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
1126392 CACAGTAGGT
*
1126402 TTCATCAATAGTGGCGTTTGTATCTAG-AAACGCCGCAATAAG
1 TTCATCAATAGTGGCATTT-TA-CTAGCAAACGCCGCAATAAG
* * *
1126444 TTCATTAATAGTGTCATTTTAGTAGCAAACGCCGCAATAA
1 TTCATCAATAGTGGCATTTTACTAGCAAACGCCGCAATAA
1126484 AGTTTACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 3 0.09
41 16 0.46
42 16 0.46
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (41 bp):
TTCATCAATAGTGGCATTTTACTAGCAAACGCCGCAATAAG
Found at i:1126762 original size:195 final size:187
Alignment explanation
Indices: 1126433--1126813 Score: 564
Period size: 195 Copynumber: 2.0 Consensus size: 187
1126423 ATCTAGAAAC
* * * * *
1126433 GCCGCAATAAGTTCATTAATAGTGTCATTTTAGTAGCAAACGCCGCAATAAAGTTTACTTTAGCG
1 GCCGCAATAAGTTCATTAATAGTGGCATTTTAGTAACAAACGCCACAATAAAGTGTACGTTAGCG
* * *
1126498 GCGTTTGTCAAACGCTGCGATAGGCTTTATCAATCGTGGCGTTTTTATAAAAAAACGCCGCAATA
66 ACGTTTGTCAAACGCCGCGATAGGCTTTATCAATCGTGGCGTTTTTACAAAAAAACGCCGCAATA
1126563 GGTACATACATACATTTAATTTAATTTAATGTTTATCAAATAGCGGCGTTTCTTCAAAAAAT
131 GGTACATACATAC-----ATTTAATTTAATGTTTATCAAATAGCGGCGTTTCTTCAAAAAAT
* * *
1126625 GCCGCAATAGGTTTATTAATAGTGGCATTTTAGTAACAAACGTCACAATAAAGTGTACGTTAGCG
1 GCCGCAATAAGTTCATTAATAGTGGCATTTTAGTAACAAACGCCACAATAAAGTGTACGTTAGCG
* *
1126690 ACGTTTGTCTTCAAACGCCGCGATAGGCTTTATCAATCGTGGCGTTTTTACAAAAAAACGCTGCG
66 ACGTTTG---TCAAACGCCGCGATAGGCTTTATCAATCGTGGCGTTTTTACAAAAAAACGCCGCA
*
1126755 ATAGGTACGTACATACATTTAATTTAATGTTTATCAAATAGCGGCGTTTCTTCAAAAAA
128 ATAGGTACATACATACATTTAATTTAATGTTTATCAAATAGCGGCGTTTCTTCAAAAAA
1126814 CGCAGCGATA
Statistics
Matches: 172, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
190 43 0.25
192 63 0.37
195 66 0.38
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (187 bp):
GCCGCAATAAGTTCATTAATAGTGGCATTTTAGTAACAAACGCCACAATAAAGTGTACGTTAGCG
ACGTTTGTCAAACGCCGCGATAGGCTTTATCAATCGTGGCGTTTTTACAAAAAAACGCCGCAATA
GGTACATACATACATTTAATTTAATGTTTATCAAATAGCGGCGTTTCTTCAAAAAAT
Found at i:1129315 original size:18 final size:17
Alignment explanation
Indices: 1129287--1129323 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
1129277 AGTGGTATAG
1129287 TTTGTTTGTTGTCTTAT
1 TTTGTTTGTTGTCTTAT
1129304 TTTGTATTGTTGTCTTAT
1 TTTGT-TTGTTGTCTTAT
1129322 TT
1 TT
1129324 CATTTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.70
Consensus pattern (17 bp):
TTTGTTTGTTGTCTTAT
Found at i:1135461 original size:59 final size:59
Alignment explanation
Indices: 1135362--1135495 Score: 160
Period size: 59 Copynumber: 2.3 Consensus size: 59
1135352 CAGCAAACTA
** * ** * *
1135362 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTATGTGT
1 CATATTCGGGAATGTACTAAAGGATACCTACTACAGATGGTGGACACAACCTTATGTGT
* * *
1135421 CATATTCGGGACTGTACTTAAGGATACCTACTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATGTACTAAAGGATACCTACTACAGATGGTGGACACAACCTTATGTGT
* *
1135480 CATACTCGGGATTGTA
1 CATATTCGGGAATGTA
1135496 TTACGGTGCA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATGTACTAAAGGATACCTACTACAGATGGTGGACACAACCTTATGTGT
Found at i:1138027 original size:23 final size:23
Alignment explanation
Indices: 1137997--1138048 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
1137987 TTATGCATAG
1137997 ACTATCGATAGTTAAACAGAGTA
1 ACTATCGATAGTTAAACAGAGTA
1138020 ACTATCGATAGTTAAACAGAGTA
1 ACTATCGATAGTTAAACAGAGTA
1138043 ACTATC
1 ACTATC
1138049 AAGAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (23 bp):
ACTATCGATAGTTAAACAGAGTA
Found at i:1138965 original size:59 final size:59
Alignment explanation
Indices: 1138866--1138987 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 59
1138856 CAGCAGGCTA
* ** * *
1138866 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTATGTGT
1 CATATCCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
* * * *
1138925 CATATCCGGGACTATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATCCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
1138984 CATA
1 CATA
1138988 CTCGGGATTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (59 bp):
CATATCCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
Found at i:1150111 original size:21 final size:21
Alignment explanation
Indices: 1150087--1150134 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1150077 CAGCCAGAGC
*
1150087 AGCAGCGGAAGCATAGAAAGA
1 AGCAGCGGAAGCACAGAAAGA
* *
1150108 AGCAGCGGCAGCACAGAGAGA
1 AGCAGCGGAAGCACAGAAAGA
1150129 AGCAGC
1 AGCAGC
1150135 ATATCATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.35, T:0.02
Consensus pattern (21 bp):
AGCAGCGGAAGCACAGAAAGA
Found at i:1150135 original size:24 final size:21
Alignment explanation
Indices: 1150052--1150135 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 21
1150042 ATGAAGCAAG
* *
1150052 GGAAGTAGAGAGAG-AGCAGC
1 GGAAGCAGAGAAAGCAGCAGC
* ** *
1150072 AGAAGCAGCCAGAGCAGCAGC
1 GGAAGCAGAGAAAGCAGCAGC
* *
1150093 GGAAGCATAGAAAGAAGCAGC
1 GGAAGCAGAGAAAGCAGCAGC
*
1150114 GGCAGCACAGAGAGAAGCAGCA
1 GGAAG--CAGAGA-AAGCAGCA
1150136 TATCATCAGA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 10 0.21
21 25 0.53
23 5 0.11
24 7 0.15
ACGTcount: A:0.42, C:0.19, G:0.37, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAAAGCAGCAGC
Found at i:1150648 original size:85 final size:85
Alignment explanation
Indices: 1150546--1150742 Score: 209
Period size: 85 Copynumber: 2.3 Consensus size: 85
1150536 CATTTTTAGC
* * * * * *
1150546 AAAAACGCCGCAAAACATCAACACTTACTGC-GACGTTTGTGGGAAAACGCCGCAAAACATCAAC
1 AAAAACGCCGCTAAACATCAACACCTACTGCAG-CGTTTATCGAAAAACGCCACAAAACATCAAC
*
1150610 ACCTATTGCGGCGTTTGTGAG
65 ACCTATTGCGGCGTTTGTCAG
* * * * * *
1150631 AAAAATGCCGCTAAACATCATA-ACCTATTGCAGTGTTTATCTAAAAACGCCACTAAATATCAAC
1 AAAAACGCCGCTAAACATCA-ACACCTACTGCAGCGTTTATCGAAAAACGCCACAAAACATCAAC
* *
1150695 ACCTATTGCGGCGTTTTTCTG
65 ACCTATTGCGGCGTTTGTCAG
* *
1150716 ACAAACGCCGCTAAATATCAACACCTA
1 AAAAACGCCGCTAAACATCAACACCTA
1150743 TTACGGCGTT
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
84 1 0.01
85 88 0.97
86 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.23
Consensus pattern (85 bp):
AAAAACGCCGCTAAACATCAACACCTACTGCAGCGTTTATCGAAAAACGCCACAAAACATCAACA
CCTATTGCGGCGTTTGTCAG
Found at i:1150657 original size:43 final size:43
Alignment explanation
Indices: 1150546--1150788 Score: 231
Period size: 43 Copynumber: 5.7 Consensus size: 43
1150536 CATTTTTAGC
* * * * *
1150546 AAAAACGCCGCAAAACATCAACACTTACTGCGACGTTTGT-GG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCAG
* * *
1150588 GAAAACGCCGCAAAACATCAACACCTATTGCGGCGTTTGTGAG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCAG
* * * * *
1150631 AAAAATGCCGCTAAACATCATA-ACCTATTGCAGTGTTTATC-T
1 AAAAACGCCGCTAAACATCA-ACACCTATTGCGGCGTTTGTCAG
* * * *
1150673 AAAAACGCCACTAAATATCAACACCTATTGCGGCGTTTTTCTG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCAG
* * * *
1150716 ACAAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTCAC
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCAG
* * * *
1150759 ACAAACGCCGCTAAATAACAATACCTATTG
1 AAAAACGCCGCTAAACATCAACACCTATTG
1150789 AGGCATTTTT
Statistics
Matches: 168, Mismatches: 29, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
41 1 0.01
42 69 0.41
43 97 0.58
44 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCAG
Found at i:1150743 original size:85 final size:85
Alignment explanation
Indices: 1150589--1150798 Score: 226
Period size: 85 Copynumber: 2.5 Consensus size: 85
1150579 CGTTTGTGGG
* * * * *
1150589 AAAACGCCGCAAAACATCAACACCTATTGCGGCGTTTGTGAGAAAAATGCCGCTAAACATCATAA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCAGAAAAACGCCGCTAAACATCATAA
* *
1150654 CCTATTGCAGTGTTTATCTA-
66 CCTATTACAGCGTTTATC-AC
* * * *
1150674 AAAACGCCACTAAATATCAACACCTATTGCGGCGTTTTTCTGACAAACGCCGCTAAATATCA-AC
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCAGAAAAACGCCGCTAAACATCATA-
* *
1150738 ACCTATTACGGCGTTTGTCAC
65 ACCTATTACAGCGTTTATCAC
* * * *
1150759 ACAAACGCCGCTAAATAACAATACCTATTGAGGCATTTTT
1 A-AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
1150799 TTTTAAAACG
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
84 2 0.02
85 69 0.66
86 33 0.32
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (85 bp):
AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCAGAAAAACGCCGCTAAACATCATAA
CCTATTACAGCGTTTATCAC
Found at i:1152510 original size:40 final size:40
Alignment explanation
Indices: 1152460--1152563 Score: 174
Period size: 40 Copynumber: 2.6 Consensus size: 40
1152450 CAAGGGTGCT
*
1152460 AAAATGAAACAAAAACTAAAGCTTTTAATGATGAGGTACC
1 AAAATAAAACAAAAACTAAAGCTTTTAATGATGAGGTACC
*
1152500 ACAATAAAACAAAAACTAAAGCTTTTAATGATGAGGTACC
1 AAAATAAAACAAAAACTAAAGCTTTTAATGATGAGGTACC
*
1152540 AAAATGAAACAAAAACTAAA-CTTT
1 AAAATAAAACAAAAACTAAAGCTTT
1152564 AGGCGTGATT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 4 0.07
40 56 0.93
ACGTcount: A:0.53, C:0.13, G:0.12, T:0.22
Consensus pattern (40 bp):
AAAATAAAACAAAAACTAAAGCTTTTAATGATGAGGTACC
Found at i:1154518 original size:15 final size:15
Alignment explanation
Indices: 1154485--1154519 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1154475 ATTTAGCTGG
* *
1154485 GCGGGCGGATGTGGG
1 GCGGGCGGATGCGGA
1154500 GCGGGCGGATGCGGA
1 GCGGGCGGATGCGGA
1154515 GCGGG
1 GCGGG
1154520 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.17, G:0.66, T:0.09
Consensus pattern (15 bp):
GCGGGCGGATGCGGA
Found at i:1156399 original size:19 final size:18
Alignment explanation
Indices: 1156362--1156406 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1156352 ATATAGAAAT
*
1156362 ATTTTAAAATAAGTTTTA
1 ATTTTAAAACAAGTTTTA
*
1156380 ATTTTAACAACAATTTTTA
1 ATTTTAA-AACAAGTTTTA
*
1156399 ATTATAAA
1 ATTTTAAA
1156407 TATTTCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTAAAACAAGTTTTA
Found at i:1157389 original size:23 final size:27
Alignment explanation
Indices: 1157339--1157392 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
1157329 TTTATATGCT
1157339 TAAATATATATATTTTTGATATTGTAA
1 TAAATATATATATTTTTGATATTGTAA
*
1157366 TAAAT-TAT-TATTTTTTA-ATT-TAA
1 TAAATATATATATTTTTGATATTGTAA
1157389 TAAA
1 TAAA
1157393 AAATTCTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 3 0.12
25 8 0.31
26 3 0.12
27 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TAAATATATATATTTTTGATATTGTAA
Found at i:1157565 original size:54 final size:54
Alignment explanation
Indices: 1157485--1157594 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
1157475 GGCTCATTTT
* * * * *
1157485 TTTTTATTTTTGCCCCGAGTCAAGAAATAATTAGGACTGATCCTGCATGTGACA
1 TTTTTATTTTCGCCCCAAGTCAAGAAATAATCAAGACTGACCCTGCATGTGACA
*
1157539 TTTTTATTTTCGCCCCAAGTCAAGAAATAATCAAGAGTGACCCTGCATGTGACA
1 TTTTTATTTTCGCCCCAAGTCAAGAAATAATCAAGACTGACCCTGCATGTGACA
1157593 TT
1 TT
1157595 GAACGCTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (54 bp):
TTTTTATTTTCGCCCCAAGTCAAGAAATAATCAAGACTGACCCTGCATGTGACA
Found at i:1158410 original size:21 final size:20
Alignment explanation
Indices: 1158385--1158423 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1158375 ATATATATAT
*
1158385 AATAACAAAAATTTTAAAATA
1 AATAA-AAAAATTTGAAAATA
*
1158406 AATAAAAAACTTTGAAAA
1 AATAAAAAAATTTGAAAA
1158424 CCTTCATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAAAAAAATTTGAAAATA
Found at i:1160287 original size:19 final size:20
Alignment explanation
Indices: 1160246--1160287 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 20
1160236 TGCATCTATG
1160246 TATCTTTCTTAATATCACACATC
1 TATCTTTCTTAATAT---ACATC
1160269 TATCTTTCTTAATAT-CATC
1 TATCTTTCTTAATATACATC
1160288 CTATTTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.21
23 15 0.79
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.48
Consensus pattern (20 bp):
TATCTTTCTTAATATACATC
Found at i:1165295 original size:27 final size:27
Alignment explanation
Indices: 1165257--1165319 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1165247 ATAATGACTC
1165257 TGAATCATTTAGAATGTACTTCTGTGT
1 TGAATCATTTAGAATGTACTTCTGTGT
1165284 TGAATCATTTAGAATGTACTTCTGTGT
1 TGAATCATTTAGAATGTACTTCTGTGT
1165311 TGAATCATT
1 TGAATCATT
1165320 CAGTACTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.44
Consensus pattern (27 bp):
TGAATCATTTAGAATGTACTTCTGTGT
Found at i:1167620 original size:21 final size:21
Alignment explanation
Indices: 1167596--1167649 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1167586 CAGCCATTTT
*
1167596 AGATGCCACCGTAGCAGGGTC
1 AGATGCCACCGCAGCAGGGTC
* * *
1167617 AGATGTCACCGCAGCTGGTTC
1 AGATGCCACCGCAGCAGGGTC
*
1167638 AGATACCACCGC
1 AGATGCCACCGC
1167650 CGTAGGGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.28, T:0.17
Consensus pattern (21 bp):
AGATGCCACCGCAGCAGGGTC
Found at i:1170389 original size:23 final size:22
Alignment explanation
Indices: 1170359--1170446 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 22
1170349 TTGGGATAAA
1170359 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAA-C
*
1170382 TATGTGGCACTTTGGTGCAAAAC
1 TATGTGGCACTTCGGTGC-AAAC
* * *
1170405 TATATGGTCA-TTCAG-G-ACAAT
1 TATGTGG-CACTTCGGTGCA-AAC
1170426 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
1170447 TTACGAGCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 3 0.06
21 12 0.23
22 4 0.08
23 28 0.54
24 5 0.10
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAC
Found at i:1180017 original size:23 final size:23
Alignment explanation
Indices: 1179988--1180070 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
1179978 GCAAATATGC
*
1179988 GGCACTTCGGTGCAAACCTATAT
1 GGCACTTCGGTGCAAAACTATAT
*
1180011 GGCACTTCGGTGCAAAACTATGT
1 GGCACTTCGGTGCAAAACTATAT
* * *
1180034 GGTCA-TTCGG-G-ACAATTATGT
1 GG-CACTTCGGTGCAAAACTATAT
*
1180055 GGCACTTCGATGCAAA
1 GGCACTTCGGTGCAAA
1180071 TTACGAGCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 2 0.04
21 14 0.28
22 2 0.04
23 30 0.60
24 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAAAACTATAT
Found at i:1183143 original size:17 final size:17
Alignment explanation
Indices: 1183121--1183156 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1183111 CCATAAATCC
*
1183121 AAAATCCAACAATCCAA
1 AAAATCAAACAATCCAA
*
1183138 AAAATCAAACAATTCAA
1 AAAATCAAACAATCCAA
1183155 AA
1 AA
1183157 TGTTGAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.22, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATCAAACAATCCAA
Found at i:1185151 original size:20 final size:21
Alignment explanation
Indices: 1185097--1185159 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1185087 GATTCCCCTG
1185097 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1185121 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1185141 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1185160 TACACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1189005 original size:22 final size:21
Alignment explanation
Indices: 1188963--1189002 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1188953 GAGTTTGTTT
*
1188963 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1188984 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1189003 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1196475 original size:19 final size:19
Alignment explanation
Indices: 1196451--1196493 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1196441 CAGACAATGG
*
1196451 CCACAGGAGCTGACTACAC
1 CCACAGGAGCCGACTACAC
*
1196470 CCACAGGAGCCGACTACGC
1 CCACAGGAGCCGACTACAC
1196489 CCACA
1 CCACA
1196494 AAAGACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.42, G:0.21, T:0.07
Consensus pattern (19 bp):
CCACAGGAGCCGACTACAC
Found at i:1197510 original size:34 final size:34
Alignment explanation
Indices: 1197472--1197545 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
1197462 CAAAACATCC
*
1197472 TCAATTTCATTCTAAACCCCAATTTCCAAAGT-AT
1 TCAATTTCATTCTAAACCCCAA-TTCCAAAATAAT
* *
1197506 TCAATTTCATTCTCAACCCTAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAATTCCAAAATAAT
1197540 TCAATT
1 TCAATT
1197546 AAATTCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCCAATTCCAAAATAAT
Found at i:1198073 original size:129 final size:124
Alignment explanation
Indices: 1197929--1198169 Score: 358
Period size: 129 Copynumber: 1.9 Consensus size: 124
1197919 TATTTATATA
* ** *
1197929 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTG-CATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA-GATCTGACATATG
*
1197993 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTCACCACCTAATTATTTATATATGCT
65 TTA-CACATGATCATGACA--TGTCATTGGTGACA--TGTCACCACCGAATTATTTATATATGCT
1198058 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGATCTGACATATGT
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGATCTGACATATGT
* *
1198123 TACACATGATCATGATATGTTATTGGTGACATGTCACCACCGAATTA
66 TACACATGATCATGACATGTCATTGGTGACATGTCACCACCGAATTA
1198170 AAGAAAATTA
Statistics
Matches: 104, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
124 15 0.14
126 13 0.12
128 20 0.19
129 56 0.54
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (124 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGATCTGACATATGT
TACACATGATCATGACATGTCATTGGTGACATGTCACCACCGAATTATTTATATATGCT
Done.