Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 99 of 211
Found at i:31099967 original size:5 final size:5
Alignment explanation
Indices: 31099957--31099985 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31099947 TCAGACACTA
31099957 AATCT AATCT AATCT AATCT AATCT AATC
1 AATCT AATCT AATCT AATCT AATCT AATC
31099986 ATTTTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
AATCT
Found at i:31103309 original size:21 final size:21
Alignment explanation
Indices: 31103285--31103334 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
31103275 AGGGTCTAGG
31103285 CCGTGTGACTGAGGAACACAC
1 CCGTGTGACTGAGGAACACAC
* ** *
31103306 CCGTATGACTGAGGGTCACGC
1 CCGTGTGACTGAGGAACACAC
31103327 CCGTGTGA
1 CCGTGTGA
31103335 GCAAGCTGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (21 bp):
CCGTGTGACTGAGGAACACAC
Found at i:31106508 original size:21 final size:21
Alignment explanation
Indices: 31106482--31106522 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31106472 CGACGGTATG
* *
31106482 GCCAAGACACATGCTTGTGTA
1 GCCAAGAAACATGCTCGTGTA
31106503 GCCAAGAAACATGCTCGTGT
1 GCCAAGAAACATGCTCGTGT
31106523 GCACTATCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
GCCAAGAAACATGCTCGTGTA
Found at i:31108265 original size:15 final size:18
Alignment explanation
Indices: 31108232--31108289 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 18
31108222 AAATGTACCT
31108232 TTCTTCTTTCCTTTCTTG
1 TTCTTCTTTCCTTTCTTG
31108250 TTCTTC-TTCC-TT-TTG
1 TTCTTCTTTCCTTTCTTG
* *
31108265 TTCTT-TTT-TTTTCTTT
1 TTCTTCTTTCCTTTCTTG
31108281 TTCTTCTTT
1 TTCTTCTTT
31108290 TCTCTTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 12 0.35
16 9 0.26
17 7 0.21
18 6 0.18
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.74
Consensus pattern (18 bp):
TTCTTCTTTCCTTTCTTG
Found at i:31117976 original size:8 final size:8
Alignment explanation
Indices: 31117954--31117988 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
31117944 TGAGTGTCTT
31117954 TAAAA-GG
1 TAAAATGG
*
31117961 TAACATGG
1 TAAAATGG
31117969 TAAAATGG
1 TAAAATGG
31117977 TAAAATGG
1 TAAAATGG
31117985 TAAA
1 TAAA
31117989 TAAGGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.16
8 21 0.84
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (8 bp):
TAAAATGG
Found at i:31120051 original size:12 final size:12
Alignment explanation
Indices: 31120034--31120063 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31120024 TCAATTTGTT
31120034 ACACGGCCTAGC
1 ACACGGCCTAGC
*
31120046 ACACGGCCTGGC
1 ACACGGCCTAGC
31120058 ACACGG
1 ACACGG
31120064 GCGTGTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:31120108 original size:13 final size:13
Alignment explanation
Indices: 31120058--31120111 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
31120048 ACGGCCTGGC
*
31120058 ACACGGGCGTGTG
1 ACACGGTCGTGTG
* *
31120071 ACCCAGG-CGTGAG
1 ACAC-GGTCGTGTG
*
31120084 ACACGATCGTGTG
1 ACACGGTCGTGTG
31120097 ACACGGTCGTGTG
1 ACACGGTCGTGTG
31120110 AC
1 AC
31120112 CCTACTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 1 0.03
13 30 0.91
14 2 0.06
ACGTcount: A:0.20, C:0.26, G:0.37, T:0.17
Consensus pattern (13 bp):
ACACGGTCGTGTG
Found at i:31121299 original size:31 final size:30
Alignment explanation
Indices: 31121261--31121557 Score: 149
Period size: 30 Copynumber: 9.9 Consensus size: 30
31121251 GATCATTGGC
*
31121261 TAATGAAAAGGGATAGCATCGGTTATCAAAA
1 TAATGAAAAGGGATAGCATCGGCTATC-AAA
* *
31121292 TAATGAAAAGGGATTGCCTCGGCTATCAAA
1 TAATGAAAAGGGATAGCATCGGCTATCAAA
* * * * *
31121322 TTATGAAAAGGGATGGTAACGAAAC-ATC-AA
1 TAATGAAAAGGGATAGCATCG--GCTATCAAA
* * * * *
31121352 TAATGAAAAGGGATGGTGA-CGACCATCGAA
1 TAATGAAAAGGGATAG-CATCGGCTATCAAA
* *
31121382 CAATGAAAAGGGATAGC-TCCGGCTATCGAA
1 TAATGAAAAGGGATAGCAT-CGGCTATCAAA
** * * * * *
31121412 TTGTGATAAGGGATAGCTTCAGTTATCGAA
1 TAATGAAAAGGGATAGCATCGGCTATCAAA
** * * *
31121442 TTGTGAAAAGGGATAACTTCAGCTATCAAA
1 TAATGAAAAGGGATAGCATCGGCTATCAAA
* * * *
31121472 TTATGAAAAGGGATGGTGAT-GGCCATC-AA
1 TAATGAAAAGGGATAG-CATCGGCTATCAAA
* * * *
31121501 TAATGAAAAGGGATGGTGA-CGACCATCAAA
1 TAATGAAAAGGGATAG-CATCGGCTATCAAA
* *
31121531 TAATGAAAAGGGATAGCTTCGACTATC
1 TAATGAAAAGGGATAGCATCGGCTATC
31121558 GAGTTGCTGA
Statistics
Matches: 215, Mismatches: 39, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 29 0.13
30 153 0.71
31 30 0.14
32 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (30 bp):
TAATGAAAAGGGATAGCATCGGCTATCAAA
Found at i:31121330 original size:30 final size:31
Alignment explanation
Indices: 31121261--31121335 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
31121251 GATCATTGGC
*
31121261 TAATGAAAAGGGATAGCATCGGTTATCAAAA
1 TAATGAAAAGGGATAGCATCGGCTATCAAAA
* *
31121292 TAATGAAAAGGGATTGCCTCGGCTATC-AAA
1 TAATGAAAAGGGATAGCATCGGCTATCAAAA
*
31121322 TTATGAAAAGGGAT
1 TAATGAAAAGGGAT
31121336 GGTAACGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 16 0.40
31 24 0.60
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (31 bp):
TAATGAAAAGGGATAGCATCGGCTATCAAAA
Found at i:31121410 original size:30 final size:30
Alignment explanation
Indices: 31121384--31121602 Score: 137
Period size: 30 Copynumber: 7.3 Consensus size: 30
31121374 CCATCGAACA
* *
31121384 ATGAAAAGGGATAGCTCCGGCTATCGAATT
1 ATGAAAAGGGATAGCTTCAGCTATCGAATT
* * *
31121414 GTGATAAGGGATAGCTTCAGTTATCGAATT
1 ATGAAAAGGGATAGCTTCAGCTATCGAATT
* * *
31121444 GTGAAAAGGGATAACTTCAGCTATCAAATT
1 ATGAAAAGGGATAGCTTCAGCTATCGAATT
* * * *
31121474 ATGAAAAGGGAT-GGTGAT-GGCCATC-AATA
1 ATGAAAAGGGATAGCT--TCAGCTATCGAATT
* * * * *
31121503 ATGAAAAGGGAT-G-GTGACGACCATCAAATA
1 ATGAAAAGGGATAGCTTCA-G-CTATCGAATT
*
31121533 ATGAAAAGGGATAGCTTC-GACTATCGAGTT
1 ATGAAAAGGGATAGCTTCAG-CTATCGAATT
* * **
31121563 GCTG-AAAGGGATAGCTTCAGGTATCGAGCT
1 -ATGAAAAGGGATAGCTTCAGCTATCGAATT
31121593 ATGAAAAGGG
1 ATGAAAAGGG
31121603 TTGGGACAAC
Statistics
Matches: 151, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.01
28 1 0.01
29 24 0.16
30 119 0.79
31 5 0.03
32 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.24
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCAGCTATCGAATT
Found at i:31121515 original size:29 final size:30
Alignment explanation
Indices: 31121466--31121544 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 30
31121456 AACTTCAGCT
* * *
31121466 ATCAAATTATGAAAAGGGATGGTGATGGCC
1 ATCAAATAATGAAAAGGGATGGTGACGACC
31121496 ATC-AATAATGAAAAGGGATGGTGACGACC
1 ATCAAATAATGAAAAGGGATGGTGACGACC
31121525 ATCAAATAATGAAAAGGGAT
1 ATCAAATAATGAAAAGGGAT
31121545 AGCTTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.58
30 19 0.42
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (30 bp):
ATCAAATAATGAAAAGGGATGGTGACGACC
Found at i:31121540 original size:149 final size:150
Alignment explanation
Indices: 31121267--31121602 Score: 444
Period size: 149 Copynumber: 2.2 Consensus size: 150
31121257 TGGCTAATGA
* * * ** *
31121267 AAAGGGATAGCATCGGTTATCAAAATAATGAAAAGGGATTGCCTCGGCTATCAAATTATGAAAAG
1 AAAGGGATAGCTTCAGTTATC-GAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAG
*
31121332 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATA
65 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATA
*
31121397 GCTCCGGCTATCGAATTG-TG
130 GCTCCGACTATCGAATTGCTG
** *
31121417 ATAAGGGATAGCTTCAGTTATCGAATTGTGAAAAGGGATAACTTCAGCTATCAAATTATGAAAAG
1 A-AAGGGATAGCTTCAGTTATCGAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAG
* * ** *
31121482 GGATGGTGATG-GCCATCAATAATGAAAAGGGATGGTGACGACCATCAAATAATGAAAAGGGATA
65 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATA
* *
31121546 GCTTCGACTATCGAGTTGCTG
130 GCTCCGACTATCGAATTGCTG
* *
31121567 AAAGGGATAGCTTCAGGTATCGAGCT-ATGAAAAGGG
1 AAAGGGATAGCTTCAGTTATCGA-ATAATGAAAAGGG
31121603 TTGGGACAAC
Statistics
Matches: 162, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
149 94 0.58
150 50 0.31
151 18 0.11
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (150 bp):
AAAGGGATAGCTTCAGTTATCGAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAGG
GATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATAG
CTCCGACTATCGAATTGCTG
Found at i:31130736 original size:13 final size:13
Alignment explanation
Indices: 31130720--31130754 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
31130710 AAAAAAAACG
31130720 AAAAGAAAAGAA-A
1 AAAAGAAAA-AAGA
31130733 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
31130746 AAAAGAAAA
1 AAAAGAAAA
31130755 CCCAAAACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 19 0.90
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:31138114 original size:16 final size:16
Alignment explanation
Indices: 31138088--31138126 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
31138078 TTATTTCCCA
31138088 ATTTAATTTAATTTTTG
1 ATTT-ATTTAATTTTTG
*
31138105 ATTTATTTAATTTTTT
1 ATTTATTTAATTTTTG
31138121 ATTTAT
1 ATTTAT
31138127 GCTATTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTATTTAATTTTTG
Found at i:31140919 original size:21 final size:22
Alignment explanation
Indices: 31140877--31140926 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
31140867 TTTGATTCTG
*
31140877 ATCTATTCTGCATCCGTATCTA
1 ATCTGTTCTGCATCCGTATCTA
*
31140899 ATCTGTTCTGCAT-CTTATCTA
1 ATCTGTTCTGCATCCGTATCTA
*
31140920 AACTGTT
1 ATCTGTT
31140927 ACGATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (22 bp):
ATCTGTTCTGCATCCGTATCTA
Found at i:31143933 original size:14 final size:14
Alignment explanation
Indices: 31143914--31143942 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31143904 TAGAAAAAAA
31143914 AAGACTAAATGCTT
1 AAGACTAAATGCTT
31143928 AAGACTAAATGCTT
1 AAGACTAAATGCTT
31143942 A
1 A
31143943 CTCAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AAGACTAAATGCTT
Found at i:31144541 original size:106 final size:106
Alignment explanation
Indices: 31144356--31144567 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
31144346 TTGGTACTTC
31144356 TTTTCAACTGCCCCAAACTTATTTTTAAAGAATATTCTGAATAGTACTGAGTCTAGTATTTGAGA
1 TTTTCAACTGCCCCAAACTTATTTTTAAAGAATATTCTGAATAGTACTGAGTCTAGTATTTGAGA
31144421 CAATTAAAAGATGATTAAGAGAGAAGTGATGGCTGAATATT
66 CAATTAAAAGATGATTAAGAGAGAAGTGATGGCTGAATATT
31144462 TTTTCAACTGCCCCAAACTTATTTTTAAAGAATATTCTGAATAGTACTGAGTCTAGTATTTGAGA
1 TTTTCAACTGCCCCAAACTTATTTTTAAAGAATATTCTGAATAGTACTGAGTCTAGTATTTGAGA
31144527 CAATTAAAAGATGATTAAGAGAGAAGTGATGGCTGAATATT
66 CAATTAAAAGATGATTAAGAGAGAAGTGATGGCTGAATATT
31144568 GCAAAGGTTC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (106 bp):
TTTTCAACTGCCCCAAACTTATTTTTAAAGAATATTCTGAATAGTACTGAGTCTAGTATTTGAGA
CAATTAAAAGATGATTAAGAGAGAAGTGATGGCTGAATATT
Found at i:31146371 original size:25 final size:25
Alignment explanation
Indices: 31146342--31146397 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
31146332 TTAATTAGTA
* *
31146342 TAAAATATTAATAATTCAAT-AAAT
1 TAAAATATAAATAATTAAATAAAAT
*
31146366 TGAAAAAATAAATAATTAAATAAAAT
1 T-AAAATATAAATAATTAAATAAAAT
31146392 TAAAAT
1 TAAAAT
31146398 TTAGGAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 20 0.77
26 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAAATATAAATAATTAAATAAAAT
Found at i:31158821 original size:24 final size:24
Alignment explanation
Indices: 31158789--31158871 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
31158779 TCCTGAAACC
31158789 ATGAAAAGGTTGAAAAGGAT-CCGA
1 ATGAAAAGGTTGAAAAGGATACC-A
* *
31158813 ATGAAAAGGCTGAAAAGGTTACCA
1 ATGAAAAGGTTGAAAAGGATACCA
* ** *
31158837 TTGAAAAGGTCAAAAAGGATATCA
1 ATGAAAAGGTTGAAAAGGATACCA
*
31158861 ATGAAATGGTT
1 ATGAAAAGGTT
31158872 ATTATATCAA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.20
Consensus pattern (24 bp):
ATGAAAAGGTTGAAAAGGATACCA
Found at i:31161605 original size:15 final size:15
Alignment explanation
Indices: 31161585--31161613 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31161575 CAACCCAAAT
31161585 AATCAATAATAATTA
1 AATCAATAATAATTA
31161600 AATCAATAATAATT
1 AATCAATAATAATT
31161614 GAACTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AATCAATAATAATTA
Found at i:31167842 original size:26 final size:27
Alignment explanation
Indices: 31167784--31167846 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
31167774 CTACCTACAG
31167784 TAGTTTCAGAATATCATAACATATAAC
1 TAGTTTCAGAATATCATAACATATAAC
* * *
31167811 -AATTTCAGAATATCATAGCATGT-AC
1 TAGTTTCAGAATATCATAACATATAAC
31167836 TAGTTTCAGAA
1 TAGTTTCAGAA
31167847 CACTTACAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (27 bp):
TAGTTTCAGAATATCATAACATATAAC
Found at i:31175751 original size:24 final size:24
Alignment explanation
Indices: 31175719--31175774 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
31175709 ATTTCCGAAA
31175719 CAATGAAAAGGTCGAAAAGGATAC
1 CAATGAAAAGGTCGAAAAGGATAC
*
31175743 CAATGAAAAGGTCGAAAAGGATAT
1 CAATGAAAAGGTCGAAAAGGATAC
*
31175767 TAATGAAA
1 CAATGAAA
31175775 TGGTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (24 bp):
CAATGAAAAGGTCGAAAAGGATAC
Found at i:31176098 original size:18 final size:18
Alignment explanation
Indices: 31176077--31176117 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
31176067 TTGGTTTGGT
31176077 GTTTGTGTTTGATACTTA
1 GTTTGTGTTTGATACTTA
31176095 GTTTGTGTTTGATACTTA
1 GTTTGTGTTTGATACTTA
31176113 GTTTG
1 GTTTG
31176118 GTGACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.05, G:0.24, T:0.56
Consensus pattern (18 bp):
GTTTGTGTTTGATACTTA
Found at i:31177896 original size:46 final size:46
Alignment explanation
Indices: 31177822--31177936 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
31177812 GGTGTTATTG
*
31177822 ATCAGTGGTAGCTTCGACTACATCTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTACGGCTACAT
* * * *
31177868 ATCGGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTATGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTACGGCTACAT
*
31177914 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31177937 ATCAATGTGG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATCTCAGTGGTAGCTACGGCTACAT
Found at i:31177943 original size:23 final size:23
Alignment explanation
Indices: 31177822--31177940 Score: 159
Period size: 23 Copynumber: 5.2 Consensus size: 23
31177812 GGTGTTATTG
*
31177822 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
31177845 CTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
31177868 ATCGGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
31177891 TTCAGTGGTAGCTAT-GGCTACGT
1 ATCAGTGGTAGCT-TCGGCTACAT
*
31177914 ATCAATGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
31177937 ATCA
1 ATCA
31177941 ATGTGGCACT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.98
24 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:31179740 original size:27 final size:27
Alignment explanation
Indices: 31179710--31180152 Score: 502
Period size: 27 Copynumber: 16.4 Consensus size: 27
31179700 GGTATAACAA
* *
31179710 TCATTTTACCCTAT-GGGGGTATTTTAG
1 TCATTTTACCCT-TCGAGGGTATTTCAG
* *
31179737 TCATTTTACCCTTCAAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
31179764 TCATTTTCCCCTTCGAGGGTATTTC-G
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
31179790 ATCATTTTACCTTTCGAGGGTATTT-TG
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* * *
31179817 ATCATTTTATCCTTCGGGGGTATTTCAA
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* *
31179845 TTATTTTACCCTTCGGGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
31179872 TTATTTTACCCTTCAAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * *
31179899 CCATTTTACCCTTCAAGGGTATTTTAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
31179926 TCATTTTACCTTTCGAGGGTATTGCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
31179953 TCATTTTACCCTTCGAGGGTATTTC-G
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
31179979 ATCATTTCACCCTTCAAGGGTATTTC-G
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* *
31180006 ATCATTTTATCCTTCGGGGGTATTTCAG
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* **
31180034 TCATTTTACCCTT-TAGGGGTATTTTGG
1 TCATTTTACCCTTCGA-GGGTATTTCAG
*
31180061 TCATTTTACCCCTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
31180088 TCATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
31180115 TCATTTTACCCTTCGGGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
31180142 TCATTTTACCC
1 TCATTTTACCC
31180153 ATGAATCGTA
Statistics
Matches: 356, Mismatches: 52, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.01
27 352 0.99
28 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCAG
Found at i:31182602 original size:19 final size:18
Alignment explanation
Indices: 31182578--31182631 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
31182568 CATGTGGCAG
*
31182578 AAAATATAAAAAAATGCTA
1 AAAATATAAAAAAAT-ATA
*
31182597 AAAATATAAAAGAATATA
1 AAAATATAAAAAAATATA
31182615 AAAATATTAGAAAAAAT
1 AAAATA-TA-AAAAAAT
31182632 TATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 16 0.53
20 6 0.20
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAATATAAAAAAATATA
Found at i:31184388 original size:6 final size:6
Alignment explanation
Indices: 31184377--31184402 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31184367 CATACATATC
31184377 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
31184403 AAGAAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:31197089 original size:47 final size:47
Alignment explanation
Indices: 31197026--31197329 Score: 409
Period size: 47 Copynumber: 6.4 Consensus size: 47
31197016 CCCTTCGGGA
* *
31197026 CTTATCACACT-TATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACA-TATATACACTTTCACATTCATCACATTGGCCATTCGGC
31197073 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
31197120 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
31197167 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
31197214 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
31197261 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
31197310 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
31197330 GTACATCAAT
Statistics
Matches: 237, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
46 2 0.01
47 194 0.82
49 40 0.17
50 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:31202801 original size:22 final size:22
Alignment explanation
Indices: 31202776--31202828 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
31202766 TAATTAAAAT
* * *
31202776 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
31202798 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
31202820 TAAAATTAA
1 TAAAATTAA
31202829 TTATTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:31202841 original size:16 final size:16
Alignment explanation
Indices: 31202804--31202843 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31202794 TTAATAAAAT
* * *
31202804 TAAAACTAATTGTTAT
1 TAAAATTAATTATTAG
31202820 TAAAATTAATTATTAG
1 TAAAATTAATTATTAG
31202836 TAAAATTA
1 TAAAATTA
31202844 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:31202922 original size:59 final size:59
Alignment explanation
Indices: 31202854--31202993 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
31202844 TCAAATTATT
*
31202854 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
31202913 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
31202972 AATTATTATTTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
31202994 ATTAATTGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:31203139 original size:22 final size:24
Alignment explanation
Indices: 31203099--31203142 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
31203089 AAATAAACTT
31203099 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
31203123 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
31203143 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:31209195 original size:25 final size:25
Alignment explanation
Indices: 31209162--31209250 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 25
31209152 TGTTTGATTG
31209162 AAAAGAACTGAAAAGAACACGAATA
1 AAAAGAACTGAAAAGAACACGAATA
*
31209187 AAAAGAACTG-AAA-ATCTAC-AA-A
1 AAAAGAACTGAAAAGAAC-ACGAATA
** ** **
31209209 TCAAGTTCTTCAAAGAACACGAATA
1 AAAAGAACTGAAAAGAACACGAATA
31209234 AAAAGAACTGAAAAGAA
1 AAAAGAACTGAAAAGAA
31209251 ATCTAAAACC
Statistics
Matches: 46, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
22 6 0.13
23 9 0.20
24 9 0.20
25 22 0.48
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (25 bp):
AAAAGAACTGAAAAGAACACGAATA
Found at i:31213703 original size:41 final size:42
Alignment explanation
Indices: 31213641--31213746 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 42
31213631 TTGTGTTTAC
* * * *
31213641 GTGTAAGACCATGTCTGGGACATTAGCATCG-TATTTGATTT
1 GTGTAAGACCATATCTAGGACAGTAGCATCGATATGTGATTT
* * *
31213682 GTGTAAGACCCTATCTAGGACAGTGGCATCGATATGTGATTAC
1 GTGTAAGACCATATCTAGGACAGTAGCATCGATATGTGATT-T
* * *
31213725 ATGTAAGACCATGTCTGGGACA
1 GTGTAAGACCATATCTAGGACA
31213747 TTTGCATTGT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 26 0.50
42 8 0.15
43 18 0.35
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATATCTAGGACAGTAGCATCGATATGTGATTT
Found at i:31213746 original size:43 final size:43
Alignment explanation
Indices: 31213583--31213746 Score: 165
Period size: 43 Copynumber: 3.9 Consensus size: 43
31213573 ACATAGAATT
* * * *
31213583 TCGATATGTGTTTTCGTGCAAGACCACGTCTGGGAC-GTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACAG-TGGCA
* * *
31213626 TCGACT-TGTGTTTACGTGTAAGACCATGTCTGGGACATTAGCA
1 TCGA-TATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCA
* * * * *
31213669 TCG-TATTTGATT-TGTGTAAGACCCTATCTAGGACAGTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCA
*
31213710 TCGATATGTGATTACATGTAAGACCATGTCTGGGACA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACA
31213747 TTTGCATTGT
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 27 0.28
42 13 0.13
43 56 0.58
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCA
Found at i:31213901 original size:16 final size:17
Alignment explanation
Indices: 31213872--31213903 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31213862 TGAATTGATG
31213872 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
31213889 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
31213904 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:31224008 original size:236 final size:237
Alignment explanation
Indices: 31223586--31224068 Score: 799
Period size: 236 Copynumber: 2.0 Consensus size: 237
31223576 AAAGATTGTC
* *
31223586 CTTTAAAT-GACCTACAAGTATCGAGAGAAACATAGAAGATAATCCTATACAAATACTATTTGAC
1 CTTTAAATAGACCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACAAATACTATTTGAC
* * *
31223650 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACTTGCTTGACACAGTGTTCAAGC
66 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
* * **
31223715 AAACTAGGCATACTATACATTTGGCGGTAACCTTTGTAACACCTCAAACTTGTCTTCGTCTCTAG
131 AAACTAGGCATACTATACATTTGGCGGTAACCTTTGCAACACCCCAAACCCGTCTTCGTCTCTAG
*
31223780 ATTAGGGTTACAAAGTATTACATTACAAATCAGAACATTTAA
196 ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
*
31223822 CTTTAAATAG-CCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACATATACTATTTGAC
1 CTTTAAATAGACCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACAAATACTATTTGAC
31223886 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
66 CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
* * * *
31223951 AAACTAGGCATACTATACCTTTGGCGGTAACCTTTGCAACACCCCTAACCCGTCTTCGTCTTTGG
131 AAACTAGGCATACTATACATTTGGCGGTAACCTTTGCAACACCCCAAACCCGTCTTCGTCTCTAG
* *
31224016 ATTAGGGTTACGAAGTATTACAGTACAAATTAGAACATTTAA
196 ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
31224058 CTTTAAATAGA
1 CTTTAAATAGA
31224069 AAGAAATATG
Statistics
Matches: 228, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
236 227 1.00
237 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (237 bp):
CTTTAAATAGACCTACAAGTACCGAGAGAAACATAAAAGATAATCCTATACAAATACTATTTGAC
CAGTCAATTCTGTTGGTTCCTAACCAGATCTCATTACCAAAACCTACTTGACACAGCGTTCAAGC
AAACTAGGCATACTATACATTTGGCGGTAACCTTTGCAACACCCCAAACCCGTCTTCGTCTCTAG
ATTAGGGTTACAAAGTATTACAGTACAAATCAGAACATTTAA
Found at i:31231346 original size:14 final size:14
Alignment explanation
Indices: 31231324--31231353 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31231314 AAGCAACATG
*
31231324 GAAGCAACCATGAT
1 GAAGAAACCATGAT
31231338 GAAGAAACCATGAT
1 GAAGAAACCATGAT
31231352 GA
1 GA
31231354 GATGTGATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (14 bp):
GAAGAAACCATGAT
Found at i:31234335 original size:28 final size:29
Alignment explanation
Indices: 31234278--31234341 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
31234268 TTTTATTAAT
*
31234278 ATAATATAAATAAAAAATTAATTACTAAA
1 ATAATATAAATAAAAAATTAATTACCAAA
*
31234307 ATAATATAGAT-AAAAATT-ATTCACCAAA
1 ATAATATAAATAAAAAATTAATT-ACCAAA
31234335 ATAATAT
1 ATAATAT
31234342 GTTTTGAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 3 0.09
28 19 0.59
29 10 0.31
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (29 bp):
ATAATATAAATAAAAAATTAATTACCAAA
Found at i:31234611 original size:116 final size:116
Alignment explanation
Indices: 31234488--31234719 Score: 410
Period size: 116 Copynumber: 2.0 Consensus size: 116
31234478 CAAGCAGAAT
* * *
31234488 GAAATTCGAGTCGAACTAGTGAAATTGTTTGAGTTAAATTAAAAAAATTAAACATGTCAAATTAA
1 GAAATTCGAGTCGAACGAGTGAAATTGTTTGAGTTAAATTAAAAAAAGTAAACATGTCAAACTAA
* *
31234553 AATCTTGTTACAGTATAACTAATTTCATTTTAAAGCACATAAATTCAAAAC
66 AATCTTGTTACAATATAACTAATTTCATGTTAAAGCACATAAATTCAAAAC
*
31234604 GAAATTCGAGTCGAACGAGTGAAATTGTTTGAGTTAAATTAAAAATAGTAAACATGTCAAACTAA
1 GAAATTCGAGTCGAACGAGTGAAATTGTTTGAGTTAAATTAAAAAAAGTAAACATGTCAAACTAA
31234669 AATCTTGTTACAATATAACTAATTTCATGTTAAAGCACATAAATTCAAAAC
66 AATCTTGTTACAATATAACTAATTTCATGTTAAAGCACATAAATTCAAAAC
31234720 CATATTTCAA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (116 bp):
GAAATTCGAGTCGAACGAGTGAAATTGTTTGAGTTAAATTAAAAAAAGTAAACATGTCAAACTAA
AATCTTGTTACAATATAACTAATTTCATGTTAAAGCACATAAATTCAAAAC
Found at i:31234866 original size:30 final size:30
Alignment explanation
Indices: 31234832--31234918 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
31234822 TTTTTTAAAA
*
31234832 TTTTTTATATATTCTTTAGATTTTTAATCT
1 TTTTTTATATATTATTTAGATTTTTAATCT
* * * * *
31234862 TTTTTTATATACTATATAGAATTTTAGTTT
1 TTTTTTATATATTATTTAGATTTTTAATCT
* *
31234892 TTTTTTATA-ATTTTTTTATATTTTTAA
1 TTTTTTATATA-TTATTTAGATTTTTAA
31234919 AATATGAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 43 0.98
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTTTTATATATTATTTAGATTTTTAATCT
Found at i:31242036 original size:47 final size:47
Alignment explanation
Indices: 31241949--31242452 Score: 828
Period size: 47 Copynumber: 10.6 Consensus size: 47
31241939 GTATATTTGA
31241949 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
* *
31241998 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
31242045 ATGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
31242092 ATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
31242139 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTG
*
31242188 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
31242235 ATGAATGTGAAAGTGTGTATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
31242282 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
31242329 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* * * * * * *
31242376 ATGAATGTGAAAGTGTATATATGTGACAGGGTCGAGTGGCCAACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
* *
31242423 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
31242453 TCCCGAAGGG
Statistics
Matches: 428, Mismatches: 25, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
47 368 0.86
49 60 0.14
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
Found at i:31242272 original size:190 final size:190
Alignment explanation
Indices: 31241949--31242452 Score: 877
Period size: 190 Copynumber: 2.7 Consensus size: 190
31241939 GTATATTTGA
31241949 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
31242014 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGCCT
66 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGCCT
31242079 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
131 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
31242139 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * *
31242204 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGCCT
66 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGCCT
* *
31242269 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
131 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
31242329 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * * * * * * *
31242392 ATATATGTGACAGGGTCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAG
31242453 TCCCGAAGGG
Statistics
Matches: 298, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 98 0.33
190 200 0.67
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (190 bp):
ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG
Found at i:31242621 original size:37 final size:37
Alignment explanation
Indices: 31242571--31242715 Score: 227
Period size: 37 Copynumber: 3.9 Consensus size: 37
31242561 CCGAGCTCTA
* *
31242571 AAGACCCGATGACTACGTGTGGAGAGTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
31242608 AAGACCCGATGACTACGTGTGGAGATTTTGCCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
*
31242645 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGA
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
* * *
31242682 AAGACCCGATAACTTCGTGTGGAGATTTCGTCCG
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCG
31242716 AGCTAAAGGT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 100 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
Found at i:31244342 original size:40 final size:40
Alignment explanation
Indices: 31243979--31244330 Score: 596
Period size: 40 Copynumber: 8.8 Consensus size: 40
31243969 GAGAATTGAG
31243979 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
31244019 AGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
31244059 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
31244099 AGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
31244139 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
31244179 AGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
31244219 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* ** *
31244259 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * * *
31244299 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCA
31244331 ACCATGCTGG
Statistics
Matches: 294, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 294 1.00
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
Found at i:31263824 original size:19 final size:19
Alignment explanation
Indices: 31263800--31263837 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31263790 AGAACAAGTA
31263800 TATGCCTTGTTCTCTAAAC
1 TATGCCTTGTTCTCTAAAC
31263819 TATGCCTTGTTCTCTAAAC
1 TATGCCTTGTTCTCTAAAC
31263838 AGAAATTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (19 bp):
TATGCCTTGTTCTCTAAAC
Found at i:31265036 original size:16 final size:16
Alignment explanation
Indices: 31265015--31265049 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31265005 TGAATTACTT
*
31265015 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTCC
*
31265031 ATTACATCTCTATTCC
1 ATTACAGCTCTATTCC
31265047 ATT
1 ATT
31265050 CACCCTAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.46
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:31268013 original size:25 final size:26
Alignment explanation
Indices: 31267980--31268087 Score: 120
Period size: 25 Copynumber: 4.3 Consensus size: 26
31267970 AATTATTATT
* *
31267980 TTTATTTTTATAATTTTCATATGTA-A
1 TTTATTTTTTTAATTAT-ATATGTATA
31268006 -TTATTTTTTTAA-TATATATGTATA
1 TTTATTTTTTTAATTATATATGTATA
31268030 TTTATTTTTTTAA-TATATATGTATA
1 TTTATTTTTTTAATTATATATGTATA
* *
31268055 TTTATTTTTTT-ATGTACATATTTATA
1 TTTATTTTTTTAAT-TATATATGTATA
31268081 TTT-TTTT
1 TTTATTTT
31268088 AAACTAATAT
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.09
24 4 0.05
25 50 0.68
26 13 0.18
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTATTTTTTTAATTATATATGTATA
Found at i:31274549 original size:44 final size:45
Alignment explanation
Indices: 31274478--31275604 Score: 1022
Period size: 44 Copynumber: 25.5 Consensus size: 45
31274468 GCAGGCTAAA
* * * *
31274478 AAGA-AGCAGATCTTGCCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * *
31274521 AAGATAGCAGATCCTGTCTTTCTATATTGGTAG-GAATTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* *
31274565 AAGAT-GCAGATCTTGTCTTCGC-ATACTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTC-CTATATTGGTCGCGAAGTAGATCG
* * * *
31274609 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * *
31274653 AAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31274698 AAGATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31274742 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31274786 AAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * *
31274831 AAGATA-CAGATCTTGTCTTCCTATACTGGTGGCGAAGAAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * *
31274875 AAGAAAGTAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31274919 AAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31274964 AAGATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * *
31275008 AAGAAAGCAGATCTTGCCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31275052 AAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31275097 AAGATA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * * * ** *
31275141 AAGAAAGTAGATATTATCTTCATGTATTGG-CATGAACTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31275185 AAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * *
31275230 AAGATA-CAGATCTTATCTTCCCATACTGGTGGCGAAGTAAATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* ** * * ** *
31275274 AAGAAAGCAGATCTCATCTTCATGTATTGG-CATGAAGTAAATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31275318 AAGGTAGCAGATCATGTCTTCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * *
31275362 AAGAT-GTAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * ** *
31275406 AAGAAAGCAGATCTTGTCTTCATGTATTGG-CATGAAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31275450 AAGATAACAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * *
31275494 AAGAT-GTAGATCTTGTCTTCCCACATTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
* * * * ** * *
31275538 AAGAAAGCAGATCTTATCTTCTTGTATTGG-CATGAAATGGATCGG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATC-G
*
31275583 AA-ATAGCAGATCTTGCCTTCCT
1 AAGATAGCAGATCTTGTCTTCCT
31275605 GTACTAATAG
Statistics
Matches: 857, Mismatches: 204, Indels: 45
0.77 0.18 0.04
Matches are distributed among these distances:
43 69 0.08
44 554 0.65
45 234 0.27
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (45 bp):
AAGATAGCAGATCTTGTCTTCCTATATTGGTCGCGAAGTAGATCG
Found at i:31274756 original size:133 final size:133
Alignment explanation
Indices: 31274481--31275604 Score: 1808
Period size: 133 Copynumber: 8.5 Consensus size: 133
31274471 GGCTAAAAAG
* * *
31274481 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTTCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
* * * *
31274546 ATTGGTAG-GAATTGGATCGAAGATGCAGATCTTGTCTTCGCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31274610 AGA
131 AGA
31274613 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
*
31274678 ATTGGTAGCGAAGTGGATCAAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31274743 AGA
131 AGA
31274746 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
*
31274811 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCTATACTGGTGGCGAAGAAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31274876 AGA
131 AGA
*
31274879 AAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
31274944 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31275009 AGA
131 AGA
*
31275012 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
31275077 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31275142 AGA
131 AGA
* * * * *
31275145 AAGTAGATATTATCTTCATGTATTGGCATGAACTAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
*
31275210 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTATCTTCCCATACTGGTGGCGAAGTAA-ATCG
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAG-AAGATCG
31275274 AAGA
130 AAGA
** * * * * *
31275278 AAGCAGATCTCATCTTCATGTATTGGCATGAAGTAAATCGAAGGTAGCAGATCATGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
** * *
31275343 ATTGGTAG-GAAGTGGATCGAAGATGTAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31275407 AGA
131 AGA
* *
31275410 AAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGATCGAAGATAACAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
** * * *
31275475 ATTGGTAG-GAAGTGGATCGAAGATGTAGATCTTGTCTTCCCACATTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
31275539 AGA
131 AGA
* * * * * * * *
31275542 AAGCAGATCTTATCTTCTTGTATTGGCATGAAATGGATCGGAA-ATAGCAGATCTTGCCTTCCT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC-GAAGATAACAGATCCTGTCTTCCT
31275605 GTACTAATAG
Statistics
Matches: 940, Mismatches: 48, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 299 0.32
133 638 0.68
134 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (133 bp):
AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGAAGATCGA
AGA
Found at i:31275734 original size:88 final size:87
Alignment explanation
Indices: 31275585--31275897 Score: 455
Period size: 88 Copynumber: 3.6 Consensus size: 87
31275575 TGGATCGGAA
* *
31275585 ATAGCAGATCTTGCCTTCCTGTACTAATAGTGAAGCAGATTGAAGACACTAGCATTGCCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
*
31275650 AGTGGCAGCGGAGCAGGTTAAAG
66 -GTGGCAGTGGAGCAGGTTAAAG
* * *
31275673 ATAGCAGATCTTGTCTTCTTGTACTAACAGTGAAGCAGATTGACGACACTAGCCTTGCCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
31275738 GATGGCAGTGGAGCAGGTTAAAG
66 G-TGGCAGTGGAGCAGGTTAAAG
* * * * *
31275761 ATAGCAGATCTTGCCTTTCTGTACTGACAGTGAAGCAGATTGAAGATACTAGCCCTACCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
31275826 GGTGGCAGTGGAGCAGGTTAAAG
66 -GTGGCAGTGGAGCAGGTTAAAG
* * * **
31275849 ATAGCAAATCTTGCCTTCCTGTACTGACAGTGAAACAGATCAAAGACAC
1 ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACAC
31275898 CAGTCTTATC
Statistics
Matches: 203, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
87 1 0.00
88 201 0.99
89 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
ATAGCAGATCTTGCCTTCCTGTACTAACAGTGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTC
GTGGCAGTGGAGCAGGTTAAAG
Found at i:31275798 original size:45 final size:45
Alignment explanation
Indices: 31275585--31275882 Score: 161
Period size: 43 Copynumber: 6.8 Consensus size: 45
31275575 TGGATCGGAA
* * * *
31275585 ATAGCAGATCTTGCCTTCCTGTACTAATAGTGAAGCAGATTGAAG
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGGTTAAAG
* * * * * * *
31275630 ACA-CTAG--CATTGCCTCCCT-CAGTGGCAGCGGAGCAGGTTAAAG
1 ATAGC-AGATC-TTGCCTTCCTGTACTGACAGTGAAGCAGGTTAAAG
* * * * * *
31275673 ATAGCAGATCTTGTCTTCTTGTACTAACAGTGAAGCAGATTGACG
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGGTTAAAG
* * * * *
31275718 ACA-CTAG-CCTTGCCTCCCTCG-A-TGGCAGTGGAGCAGGTTAAAG
1 ATAGC-AGATCTTGCCTTCCT-GTACTGACAGTGAAGCAGGTTAAAG
* * *
31275761 ATAGCAGATCTTGCCTTTCTGTACTGACAGTGAAGCAGATTGAAG
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGGTTAAAG
* * * * * * *
31275806 ATA-CTAG-CCCTACCTCCCTCG--GTGGCAGTGGAGCAGGTTAAAG
1 ATAGC-AGATCTTGCCTTCCT-GTACTGACAGTGAAGCAGGTTAAAG
*
31275849 ATAGCAAATCTTGCCTTCCTGTACTGACAGTGAA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGTGAA
31275883 ACAGATCAAA
Statistics
Matches: 174, Mismatches: 61, Indels: 36
0.64 0.23 0.13
Matches are distributed among these distances:
43 62 0.36
44 56 0.32
45 56 0.32
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (45 bp):
ATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGGTTAAAG
Found at i:31277865 original size:25 final size:26
Alignment explanation
Indices: 31277811--31277870 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
31277801 AATTATTATT
* *
31277811 TTTATTTTTATAATTTTCATATGTAA
1 TTTATTTTTTTAATTATCATATGTAA
31277837 -TTATTTTTTTAA-TAT-ATATGTATA
1 TTTATTTTTTTAATTATCATATGTA-A
31277861 TTTATTTTTT
1 TTTATTTTTT
31277871 ATGTACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
25 20 0.67
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTATTTTTTTAATTATCATATGTAA
Found at i:31277880 original size:25 final size:25
Alignment explanation
Indices: 31277828--31277893 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
31277818 TTATAATTTT
31277828 CATATGTA-A-TTATTTTTTTAATA
1 CATATGTATATTTATTTTTTTAATA
* *
31277851 TATATGTATATTTA-TTTTTTATGTA
1 CATATGTATATTTATTTTTTTA-ATA
*
31277876 CATATTTATATTT-TTTTT
1 CATATGTATATTTATTTTT
31277894 AAACTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 7 0.20
24 8 0.23
25 20 0.57
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (25 bp):
CATATGTATATTTATTTTTTTAATA
Found at i:31277993 original size:26 final size:28
Alignment explanation
Indices: 31277940--31277993 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
31277930 TATTCTTTTC
*
31277940 ATTTAATTAATTTTGGTAATGTAGATATT
1 ATTTAATTAATTTT-GTAATCTAGATATT
*
31277969 ATTTAATT-ATTTT-TAATCTATATAT
1 ATTTAATTAATTTTGTAATCTAGATAT
31277994 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
28 5 0.22
29 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (28 bp):
ATTTAATTAATTTTGTAATCTAGATATT
Found at i:31283212 original size:14 final size:14
Alignment explanation
Indices: 31283193--31283224 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
31283183 AGGTCATTTA
31283193 GCCCAACCAAACTG
1 GCCCAACCAAACTG
31283207 GCCCAACCAAACTG
1 GCCCAACCAAACTG
31283221 GCCC
1 GCCC
31283225 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:31288850 original size:68 final size:71
Alignment explanation
Indices: 31288760--31288897 Score: 201
Period size: 72 Copynumber: 2.0 Consensus size: 71
31288750 TTTAATAAAT
* * * *
31288760 TTAATATTTAATTTAATTTAATATTTATC-CTA-AT-ATTATTTTATTAATTTAATATTAAAGTG
1 TTAATATTAAATTTAATTTAATATTTATCTCTAGATAAATATTCTATTAATTTAATATCAAAGTG
31288822 ATTATC
66 ATTATC
*
31288828 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTCTATTAATTTAATATCAAAGT
1 TTAATATTAAATTTAATTTAATATTTATC-TCTAGATAAATATTCTATTAATTTAATATCAAAGT
31288893 GATTA
65 GATTA
31288898 AGTTTAATCA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 28 0.46
70 2 0.03
71 2 0.03
72 29 0.48
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (71 bp):
TTAATATTAAATTTAATTTAATATTTATCTCTAGATAAATATTCTATTAATTTAATATCAAAGTG
ATTATC
Found at i:31291062 original size:21 final size:20
Alignment explanation
Indices: 31291036--31291078 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
31291026 AGAGACTCTT
* *
31291036 TTAAAATGTTTTCAATATGAA
1 TTAAAATGTATT-AAAATGAA
31291057 TTAAAATGTATTAAAATGAA
1 TTAAAATGTATTAAAATGAA
31291077 TT
1 TT
31291079 TTGATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (20 bp):
TTAAAATGTATTAAAATGAA
Found at i:31296903 original size:23 final size:23
Alignment explanation
Indices: 31296849--31296905 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
31296839 TATCTTTTTC
* *
31296849 TAAAAAATAATTTTTATAAAAAA
1 TAAAAATTTATTTTTATAAAAAA
* *
31296872 TCATAATTTATTTTTA-AAAAAA
1 TAAAAATTTATTTTTATAAAAAA
31296894 TAAAATATTTAT
1 TAAAA-ATTTAT
31296906 ATCAAGTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAAAATTTATTTTTATAAAAAA
Found at i:31297595 original size:26 final size:25
Alignment explanation
Indices: 31297564--31297655 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 25
31297554 ATATTTTATT
31297564 TTTATTAAATTATATTTAATAATAA
1 TTTATTAAATTATATTTAATAATAA
* * * *
31297589 TTATATTAGAATATGATTAGATTATTTATTAT
1 TT-TATTA-AAT-T-A-TA-TTTA-ATAATAA
*
31297621 TTTATTAAATTATTTTTAATAATAA
1 TTTATTAAATTATATTTAATAATAA
31297646 TCTTATTAAA
1 T-TTATTAAA
31297656 ATTTAATAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
25 7 0.14
26 16 0.32
27 4 0.08
28 2 0.04
29 2 0.04
30 5 0.10
31 8 0.16
32 6 0.12
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (25 bp):
TTTATTAAATTATATTTAATAATAA
Found at i:31299301 original size:45 final size:45
Alignment explanation
Indices: 31299236--31299391 Score: 167
Period size: 45 Copynumber: 3.5 Consensus size: 45
31299226 TATACACCTA
*
31299236 AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCAGGACA-
1 AAATGAGTAAGACCATAGCTGAAAGACGCTATGACATCAGGACAT
* * * *
31299280 AGAATGATTAAAACCATAGCTGAAAGACGCTATGGCATCATGACAT
1 A-AATGAGTAAGACCATAGCTGAAAGACGCTATGACATCAGGACAT
* *
31299326 AAATGAGTAAGACCATAGCTAAAAGACACTATGGA-ATCATGGTA-A-
1 AAATGAGTAAGACCATAGCTGAAAGACGCTAT-GACATCA-GG-ACAT
* *
31299371 AAAGGACTAAGACCATAGCTG
1 AAATGAGTAAGACCATAGCTG
31299392 GGAGACACTA
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
44 1 0.01
45 87 0.94
46 4 0.04
47 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGACGCTATGACATCAGGACAT
Found at i:31299389 original size:90 final size:90
Alignment explanation
Indices: 31299236--31299408 Score: 217
Period size: 90 Copynumber: 1.9 Consensus size: 90
31299226 TATACACCTA
* ** * *
31299236 AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCAGGACAAGAATGATTAAAACCATAGCT
1 AAATGAGTAAGACCATAGCTAAAAGACACTATGACATCAGGACAAGAAGGACTAAAACCATAGCT
*
31299301 GAAAGACGCTATGGCATCATGACAT
66 GAAAGACACTATGGCATCATGACAT
*
31299326 AAATGAGTAAGACCATAGCTAAAAGACACTATGGA-ATCATGGTA-AA-AAGGACTAAGACCATA
1 AAATGAGTAAGACCATAGCTAAAAGACACTAT-GACATCA-GG-ACAAGAAGGACTAAAACCATA
**
31299388 GCTGGGAGACACTATGGCATC
63 GCTGAAAGACACTATGGCATC
31299409 CTTTGATGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 64 0.90
91 6 0.08
92 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (90 bp):
AAATGAGTAAGACCATAGCTAAAAGACACTATGACATCAGGACAAGAAGGACTAAAACCATAGCT
GAAAGACACTATGGCATCATGACAT
Found at i:31300843 original size:27 final size:27
Alignment explanation
Indices: 31300812--31300868 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
31300802 AATATTTGTG
31300812 ACTATTATATAATAATCCAAGAAACAT
1 ACTATTATATAATAATCCAAGAAACAT
31300839 ACTATTATATAATAATCCAAGAAACAT
1 ACTATTATATAATAATCCAAGAAACAT
31300866 ACT
1 ACT
31300869 CATTGCGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.30
Consensus pattern (27 bp):
ACTATTATATAATAATCCAAGAAACAT
Found at i:31308317 original size:15 final size:15
Alignment explanation
Indices: 31308297--31308335 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
31308287 TTTTAAATTT
31308297 TATTATTATAACATA
1 TATTATTATAACATA
*
31308312 TATTATTATAACTTA
1 TATTATTATAACATA
31308327 TATATATTA
1 TAT-TATTA
31308336 AGTTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTATTATAACATA
Found at i:31313731 original size:23 final size:24
Alignment explanation
Indices: 31313680--31313724 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
31313670 TTCATAAAAA
*
31313680 ATAAAAAAAATATTTTAAAAATTC
1 ATAAAAAAAATATATTAAAAATTC
31313704 A-AAAAATAAATA-ATTAAAAAT
1 ATAAAAA-AAATATATTAAAAAT
31313725 GATAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
ATAAAAAAAATATATTAAAAATTC
Found at i:31328530 original size:19 final size:18
Alignment explanation
Indices: 31328487--31328534 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
31328477 TGTTAAAATT
*
31328487 ATAATTTTAATAATTTTT
1 ATAATTTTAATAATTTTA
*
31328505 TTCAATTTTAATAATTTTAA
1 AT-AATTTTAATAATTTT-A
31328525 ATAATTTTAA
1 ATAATTTTAA
31328535 ACAATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATTTTAATAATTTTA
Found at i:31328535 original size:10 final size:9
Alignment explanation
Indices: 31328487--31328534 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
31328477 TGTTAAAATT
31328487 ATAATTTTA
1 ATAATTTTA
*
31328496 ATAATTTTT
1 ATAATTTTA
*
31328505 TTCAATTTTA
1 AT-AATTTTA
31328515 ATAATTTTAA
1 ATAATTTT-A
31328525 ATAATTTTA
1 ATAATTTTA
31328534 A
1 A
31328535 ACAATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATTTTA
Found at i:31328956 original size:21 final size:21
Alignment explanation
Indices: 31328918--31328961 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
31328908 AATAACAGTG
* * *
31328918 ACAATGAGATTAATTATTGTA
1 ACAATGAAATTAAGTATTATA
*
31328939 ACAATGAAATTGAGTATTATA
1 ACAATGAAATTAAGTATTATA
31328960 AC
1 AC
31328962 GGTAAGATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (21 bp):
ACAATGAAATTAAGTATTATA
Found at i:31331058 original size:22 final size:23
Alignment explanation
Indices: 31331039--31331081 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
31331029 TAAAAAAATA
31331039 TCCTATAAAAAT-TTTGAAAAGT
1 TCCTATAAAAATCTTTGAAAAGT
* *
31331061 TCCTGTCAAAATCTTTGAAAA
1 TCCTATAAAAATCTTTGAAAA
31331082 ATAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (23 bp):
TCCTATAAAAATCTTTGAAAAGT
Found at i:31333881 original size:19 final size:19
Alignment explanation
Indices: 31333841--31333882 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
31333831 AAACATTAAA
* *
31333841 ATAATTTAAAATATATGTT
1 ATAATTAAAAATATATGAT
31333860 ATAATTAAATAATATAT-AT
1 ATAATTAAA-AATATATGAT
31333879 ATAA
1 ATAA
31333883 AAGAAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAATTAAAAATATATGAT
Found at i:31334687 original size:43 final size:44
Alignment explanation
Indices: 31334595--31334690 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 44
31334585 GCAACTTGAT
*
31334595 TGTGTTTGGAAGGAATACACTATTAGTGCAATATAATATATGGT
1 TGTGTTTGGAAGGAATACACTATTAGTGCAATATAATATATGGG
* *
31334639 TGTGTTTGGATGG-ATGCACT-TCTAGTG-AA-ATAATTATATGTGG
1 TGTGTTTGGAAGGAATACACTAT-TAGTGCAATATAA-TATATG-GG
31334682 TGTGTTTGG
1 TGTGTTTGG
31334691 TTAGAATTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
41 4 0.09
42 9 0.20
43 21 0.46
44 12 0.26
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (44 bp):
TGTGTTTGGAAGGAATACACTATTAGTGCAATATAATATATGGG
Found at i:31334899 original size:42 final size:42
Alignment explanation
Indices: 31334840--31334927 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
31334830 GCTATTATTC
31334840 ATTAATATTTAATAATTTAGTGTTAAGAAATTGAAATTAGAA
1 ATTAATATTTAATAATTTAGTGTTAAGAAATTGAAATTAGAA
31334882 ATTAATATTTAATAATTTAGTGTTAAGAAATTGAAATTAGAA
1 ATTAATATTTAATAATTTAGTGTTAAGAAATTGAAATTAGAA
31334924 ATTA
1 ATTA
31334928 GAATTGAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (42 bp):
ATTAATATTTAATAATTTAGTGTTAAGAAATTGAAATTAGAA
Found at i:31338625 original size:72 final size:72
Alignment explanation
Indices: 31338508--31338656 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
31338498 TTTAAATTTC
31338508 ATTTTGGGCAATTAAAGACATAATTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
1 ATTTTGGGCAATTAAAGACATAATTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
31338573 TTTAAAT
66 TTTAAAT
*
31338580 ATTTTGGGCAATTAAAGACATAGTTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
1 ATTTTGGGCAATTAAAGACATAATTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
31338645 TTTAAAT
66 TTTAAAT
31338652 ATTTT
1 ATTTT
31338657 TAATGTTTGA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (72 bp):
ATTTTGGGCAATTAAAGACATAATTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
TTTAAAT
Found at i:31338766 original size:13 final size:13
Alignment explanation
Indices: 31338748--31338843 Score: 104
Period size: 13 Copynumber: 7.2 Consensus size: 13
31338738 ATATTAAAAG
*
31338748 TTAAAACATTATA
1 TTAAAACAGTATA
*
31338761 TTAAAATAGTATA
1 TTAAAACAGTATA
*
31338774 TATATAACAGTATA
1 T-TAAAACAGTATA
*
31338788 TTAAAACAATATA
1 TTAAAACAGTATA
31338801 TTAAAA-AGGTATA
1 TTAAAACA-GTATA
* *
31338814 TTTATAATAGTATA
1 -TTAAAACAGTATA
31338828 TTAAAACAGTATA
1 TTAAAACAGTATA
31338841 TTA
1 TTA
31338844 CATTAAAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
12 1 0.01
13 46 0.67
14 21 0.30
15 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (13 bp):
TTAAAACAGTATA
Found at i:31338787 original size:27 final size:25
Alignment explanation
Indices: 31338751--31338843 Score: 96
Period size: 27 Copynumber: 3.5 Consensus size: 25
31338741 TTAAAAGTTA
*
31338751 AAACATTATATTAAAATAGTATATAT
1 AAACAGTATATTAAAATAGTATAT-T
* *
31338777 ATAACAGTATATTAAAACAATATATT
1 A-AACAGTATATTAAAATAGTATATT
* *
31338803 AAAAAGGTATATTTATAATAGTATATT
1 AAACA-GTATA-TTAAAATAGTATATT
31338830 AAAACAGTATATTA
1 -AAACAGTATATTA
31338844 CATTAAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
25 3 0.05
26 11 0.20
27 37 0.67
28 4 0.07
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (25 bp):
AAACAGTATATTAAAATAGTATATT
Found at i:31338792 original size:40 final size:40
Alignment explanation
Indices: 31338748--31338843 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
31338738 ATATTAAAAG
*
31338748 TTAAAACATTATATTAAAATA-GTATATATATAACAGTATA
1 TTAAAACAATATATTAAAA-AGGTATATATATAACAGTATA
* *
31338788 TTAAAACAATATATTAAAAAGGTATATTTATAATAGTATA
1 TTAAAACAATATATTAAAAAGGTATATATATAACAGTATA
*
31338828 TTAAAACAGTATATTA
1 TTAAAACAATATATTA
31338844 CATTAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.02
40 50 0.98
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (40 bp):
TTAAAACAATATATTAAAAAGGTATATATATAACAGTATA
Found at i:31341590 original size:43 final size:42
Alignment explanation
Indices: 31341530--31341783 Score: 282
Period size: 43 Copynumber: 6.0 Consensus size: 42
31341520 GGCGCTTACA
*
31341530 GAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
* * *
31341573 AAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGAGCTTG
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
*
31341615 CGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTG
1 -GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
* * * *
31341658 TG-CAAAAACGCCGCTAAATAACATGATCTTTAGCGGCGCTTGG
1 -GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G
* *
31341701 GAAAAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTG
1 GAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTG
* * * *
31341743 GTAGAAAATGCCGCTAAA-AGT-ACTGTTCTTTAGCAGCGCTT
1 GAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTT
31341784 CATCTACAAA
Statistics
Matches: 182, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 72 0.40
43 109 0.60
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (42 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG
Found at i:31341699 original size:85 final size:84
Alignment explanation
Indices: 31341518--31341783 Score: 302
Period size: 85 Copynumber: 3.1 Consensus size: 84
31341508 GCTAACGTTT
* * *
31341518 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAAAAATG
1 GCGGCGCTTGC-GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-G-GAAAAAATG
* *
31341583 CCGCTAAAGATCATGTTCTTTA
63 CCGCTAAAGAACATGATCTTTA
* * * *
31341605 GCGGAGCTTGCGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTGTGCAAAAACGCC
1 GCGGCGCTTGCGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTG-GAAAAAATGCC
*
31341670 GCTAAATAACATGATCTTTA
65 GCTAAAGAACATGATCTTTA
* * * *
31341690 GCGGCGCTTGGGAAAAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTTGGTAGAAAATGC
1 GCGGCGCTTGCGAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTGG-AAAAAATGC
* *
31341754 CGCTAAAAGTAC-TGTTCTTTA
64 CGCT-AAAGAACATGATCTTTA
*
31341775 GCAGCGCTT
1 GCGGCGCTT
31341784 CATCTACAAA
Statistics
Matches: 153, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
84 2 0.01
85 98 0.64
86 44 0.29
87 9 0.06
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (84 bp):
GCGGCGCTTGCGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGGAAAAAATGCCG
CTAAAGAACATGATCTTTA
Found at i:31341718 original size:128 final size:127
Alignment explanation
Indices: 31341533--31341776 Score: 314
Period size: 128 Copynumber: 1.9 Consensus size: 127
31341523 GCTTACAGAA
** * * *
31341533 AAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAAAAATGCCGCT-AAAGATCAT
1 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAG-TAAT
*
31341597 GTTCTTTAGCGGAGCTTGCGAAAAAAACGCCGCT-AAAG-ATCATGTTCTTTAGCGGCACTTGTG
65 GTTCTATAGCGGAGCTTG-GAAAAAAACGCCGCTAAAAGTA-C-TGTTCTTTAGCGGCACTTGTG
31341660 C
127 C
* * *
31341661 AAAAACGCCGCTAAATAACATGATCTTTAGCGGCGCTTGGGAAAAAAACGCCGCTAAAAGTAATG
1 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAGTAATG
* * * *
31341726 TTCTATAGCGGCGCTTGGTAGAAAATGCCGCTAAAAGTACTGTTCTTTAGC
66 TTCTATAGCGGAGCTTGGAAAAAAACGCCGCTAAAAGTACTGTTCTTTAGC
31341777 AGCGCTTCAT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
127 23 0.23
128 72 0.72
129 5 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (127 bp):
AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAAGTAATG
TTCTATAGCGGAGCTTGGAAAAAAACGCCGCTAAAAGTACTGTTCTTTAGCGGCACTTGTGC
Found at i:31341840 original size:43 final size:42
Alignment explanation
Indices: 31341518--31341827 Score: 265
Period size: 43 Copynumber: 7.2 Consensus size: 42
31341508 GCTAACGTTT
* *
31341518 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGGTCATGTTCTTTA
1 GCGGCGCTTA-GGAAAAAAACGCCGCTAAAAGT-ATGTTCTTTA
* *
31341562 GCGGCGCTTAGAAAAAAAATGCCGCT-AAAGATCATGTTCTTTA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAAAAG-T-ATGTTCTTTA
*
31341605 GCGGAGCTT-GCGAAAAAAACGCCGCT-AAAGATCATGTTCTTTA
1 GCGGCGCTTAG-GAAAAAAACGCCGCTAAAAG-T-ATGTTCTTTA
* * ** *
31341648 GCGGCACTT-GTG-CAAAAACGCCGCTAAATAACATGATCTTTA
1 GCGGCGCTTAG-GAAAAAAACGCCGCTAAA-AGTATGTTCTTTA
* *
31341690 GCGGCGCTTGGGAAAAAAACGCCGCTAAAAGTAATGTTCTATA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAAAAGT-ATGTTCTTTA
* * *
31341733 GCGGCGCTT-GGTAGAAAATGCCGCTAAAAGTACTGTTCTTTA
1 GCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTA-TGTTCTTTA
* *** * *
31341775 GCAGCGCTTCA-TCTACAAACGCCGCTAAAAGTAGTGTGCTTTA
1 GCGGCGCTT-AGGAAAAAAACGCCGCTAAAAGTA-TGTTCTTTA
31341818 GCGGCGCTTA
1 GCGGCGCTTA
31341828 TTTAAAAAAC
Statistics
Matches: 222, Mismatches: 34, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.00
42 71 0.32
43 139 0.63
44 11 0.05
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (42 bp):
GCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTATGTTCTTTA
Found at i:31341840 original size:128 final size:126
Alignment explanation
Indices: 31341533--31341827 Score: 312
Period size: 128 Copynumber: 2.3 Consensus size: 126
31341523 GCTTACAGAA
* * *
31341533 AAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAGAAAAAAAATGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAAGT-ATG-TCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGATAATG
* * *
31341598 TTCTTTAGCGGAGCTTGCGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTGTGC
64 TTCTATAGCGGAGCTTGCGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCACTTATGC
** * *
31341661 AAAAACGCCGCTAAATAACATGATCTTTAGCGGCGCTTGGGAAAAAAACGCCGCTAAA-AGTAAT
1 AAAAACGCCGCTAAA-AGTATG-TCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGA-TAAT
* * * * *
31341725 GTTCTATAGCGGCGCTTG-GTAGAAAATGCCGCTAAA-AGT-ACTGTTCTTTAGCAGCGCTTCAT
63 GTTCTATAGCGGAGCTTGCGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCAGCACTT-AT
31341787 -C
125 GC
*
31341788 TACAAACGCCGCTAAAAGTAGTGTGCTTTAGCGGCGCTTA
1 -AAAAACGCCGCTAAAAGTA-TGT-CTTTAGCGGCGCTTA
31341828 TTTAAAAAAC
Statistics
Matches: 139, Mismatches: 20, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
126 2 0.01
127 37 0.27
128 100 0.72
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (126 bp):
AAAAACGCCGCTAAAAGTATGTCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGATAATGTT
CTATAGCGGAGCTTGCGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCACTTATGC
Found at i:31342283 original size:12 final size:12
Alignment explanation
Indices: 31342266--31342290 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31342256 TGAACATCTA
31342266 CTTCTCTCGCTG
1 CTTCTCTCGCTG
31342278 CTTCTCTCGCTG
1 CTTCTCTCGCTG
31342290 C
1 C
31342291 AGCCTCTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.16, T:0.40
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:31342304 original size:21 final size:21
Alignment explanation
Indices: 31342278--31342323 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
31342268 TCTCTCGCTG
*
31342278 CTTCTCTCGCTGCAGCCTCTA
1 CTTCTCTCACTGCAGCCTCTA
*
31342299 CTTCTCTCACTGCAGCCTCTG
1 CTTCTCTCACTGCAGCCTCTA
31342320 CTTC
1 CTTC
31342324 CCTCCCTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.43, G:0.13, T:0.35
Consensus pattern (21 bp):
CTTCTCTCACTGCAGCCTCTA
Found at i:31347870 original size:9 final size:9
Alignment explanation
Indices: 31347856--31348058 Score: 165
Period size: 9 Copynumber: 23.2 Consensus size: 9
31347846 TTTTTATGTA
31347856 TTATGTAAG
1 TTATGTAAG
*
31347865 TTATGTAAC
1 TTATGTAAG
*
31347874 TTACGTAAG
1 TTATGTAAG
* *
31347883 TTAT-CAAA
1 TTATGTAAG
*
31347891 TTAATGTATG
1 TT-ATGTAAG
31347901 TTATGTAAG
1 TTATGTAAG
31347910 -T-TGTAAG
1 TTATGTAAG
31347917 TTATGTAAG
1 TTATGTAAG
31347926 TTATGTAAG
1 TTATGTAAG
31347935 TTATGT-A-
1 TTATGTAAG
*
31347942 TTATGTAGG
1 TTATGTAAG
31347951 TTATGTAAG
1 TTATGTAAG
*
31347960 TTGTGTAAG
1 TTATGTAAG
* *
31347969 ATATTTAAG
1 TTATGTAAG
31347978 TTATGTAAG
1 TTATGTAAG
*
31347987 TTCTGTAA-
1 TTATGTAAG
31347995 -TATGTAAG
1 TTATGTAAG
*
31348003 TTATGTATG
1 TTATGTAAG
*
31348012 CTATGT-A-
1 TTATGTAAG
*
31348019 TAATGTAAGTTG
1 TTATGTAA---G
*
31348031 TTATGTTA-
1 TTATGTAAG
31348039 TTATGTAAG
1 TTATGTAAG
*
31348048 TTATGCAAG
1 TTATGTAAG
31348057 TT
1 TT
31348059 TAAATATAAG
Statistics
Matches: 151, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
7 22 0.15
8 15 0.10
9 105 0.70
10 3 0.02
12 6 0.04
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:31347967 original size:52 final size:50
Alignment explanation
Indices: 31347859--31348009 Score: 176
Period size: 52 Copynumber: 2.9 Consensus size: 50
31347849 TTATGTATTA
* * ** *
31347859 TGTAAGTTATGTAACTTACGTAAGTTATCAAATTAATGTATGTTATGTAAGT
1 TGTAAGTTATGTAAGTTATGTAAGTTAT-GTATT-ATGTAAGTTATGTAAGT
*
31347911 TGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAGGTTATGTAAGTT
1 TGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAG-T
* * * *
31347962 GTGTAAGATATTTAAGTTATGTAAGTTCTGTAATATGTAAGTTATGTA
1 -TGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTA
31348010 TGCTATGTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
50 15 0.17
51 4 0.05
52 68 0.78
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (50 bp):
TGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTAAGT
Found at i:31348018 original size:25 final size:25
Alignment explanation
Indices: 31347894--31348029 Score: 134
Period size: 25 Copynumber: 5.4 Consensus size: 25
31347884 TATCAAATTA
*
31347894 ATGTATGTTATGTAAG-T-TGTAAGTT
1 ATGTAAGTTATGTAAGTTATGTAA--T
*
31347919 ATGTAAGTTATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTATGTAAT
* *
31347944 ATGTAGGTTATGTAAGTTGTGTAAGAT
1 ATGTAAGTTATGTAAGTTATGT-A-AT
* *
31347971 ATTTAAGTTATGTAAGTTCTGTAAT
1 ATGTAAGTTATGTAAGTTATGTAAT
* *
31347996 ATGTAAGTTATGTATGCTATGT-AT
1 ATGTAAGTTATGTAAGTTATGTAAT
31348020 AATGTAAGTT
1 -ATGTAAGTT
31348030 GTTATGTTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
24 2 0.02
25 65 0.69
26 3 0.03
27 24 0.26
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (25 bp):
ATGTAAGTTATGTAAGTTATGTAAT
Found at i:31348190 original size:13 final size:15
Alignment explanation
Indices: 31348171--31348211 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
31348161 CATATAAGTT
31348171 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
31348185 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
31348199 TTATGTAAGTTAT
1 -TATGTAAGTTAT
31348212 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:31348206 original size:16 final size:16
Alignment explanation
Indices: 31348170--31348248 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
31348160 ACATATAAGT
31348170 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
31348185 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
31348199 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
31348217 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
31348233 TTATATAAGTCATGTA
1 TTATGTAAGTTATGTA
31348249 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 12 0.23
14 1 0.02
16 26 0.50
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:31348324 original size:21 final size:21
Alignment explanation
Indices: 31348285--31348324 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31348275 GATATGATTG
*
31348285 ATAAAATTTTCAAATATATCA
1 ATAAAATTTTCAAAAATATCA
31348306 ATAAAATTTT-AATAAATAT
1 ATAAAATTTTCAA-AAATAT
31348325 ATTAAAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAATTTTCAAAAATATCA
Found at i:31351486 original size:56 final size:56
Alignment explanation
Indices: 31351400--31351575 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
31351390 ACAAGGGATG
*
31351400 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
31351456 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
31351512 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
31351568 ATGGGCAA
1 ATGGGCAA
31351576 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:31352938 original size:40 final size:40
Alignment explanation
Indices: 31352700--31352924 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
31352690 TCGAATGATG
* * * *
31352700 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
31352740 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31352780 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31352819 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31352859 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31352900 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31352925 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31352946 original size:119 final size:119
Alignment explanation
Indices: 31352700--31352957 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
31352690 TCGAATGATG
* *
31352700 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
31352765 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * **
31352819 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
31352882 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
31352939 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
31352958 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 84 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:31359531 original size:56 final size:55
Alignment explanation
Indices: 31359424--31359556 Score: 250
Period size: 56 Copynumber: 2.4 Consensus size: 55
31359414 CATGATGAAA
31359424 AATAAAATAAGAAGCAT-GGCAAAACATGTCATGAACATGTTGTGTTAATGGAAG
1 AATAAAATAAGAAGCATGGGCAAAACATGTCATGAACATGTTGTGTTAATGGAAG
31359478 AATAAAATAAGAAGCATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAG
1 AATAAAATAAGAAGCATGGGCAAAACATGTCATG-AACATGTTGTGTTAATGGAAG
31359534 AATAAAATAAGAAGCATGGGCAA
1 AATAAAATAAGAAGCATGGGCAA
31359557 TAAACTAATA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 17 0.22
55 16 0.21
56 44 0.57
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.22
Consensus pattern (55 bp):
AATAAAATAAGAAGCATGGGCAAAACATGTCATGAACATGTTGTGTTAATGGAAG
Found at i:31360807 original size:40 final size:40
Alignment explanation
Indices: 31360689--31360913 Score: 291
Period size: 40 Copynumber: 5.7 Consensus size: 40
31360679 TCGAATGATG
* * * *
31360689 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
31360729 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
31360769 TTCCGGTGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 -TCCGG-GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31360809 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31360849 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-AGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31360889 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31360914 AACGAGTAGC
Statistics
Matches: 168, Mismatches: 9, Indels: 17
0.87 0.05 0.09
Matches are distributed among these distances:
38 5 0.03
39 46 0.27
40 90 0.54
41 22 0.13
42 5 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31362670 original size:18 final size:19
Alignment explanation
Indices: 31362630--31362672 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
31362620 AACCCCGGCC
*
31362630 AAACCCTTAAAACCTCTCT
1 AAACCCTTAAAACCTCCCT
*
31362649 -AACCCTTAAATCC-CCCT
1 AAACCCTTAAAACCTCCCT
31362666 AAACCCT
1 AAACCCT
31362673 AATTAACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (19 bp):
AAACCCTTAAAACCTCCCT
Found at i:31364739 original size:41 final size:40
Alignment explanation
Indices: 31364675--31364914 Score: 203
Period size: 41 Copynumber: 5.9 Consensus size: 40
31364665 TTTTGTTACT
**
31364675 ATTAGCGGCGCTTC-GGCAAAAACGCCGCTAAAGGTAAATGC
1 ATTAGCGGCGC-TCAGATAAAAACGCCGCTAAAGGTAAA-GC
* * * * * *
31364716 ATTAGCAGCGCTTAGATATAAACGCCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGG-TAAAGC
* * * * **
31364757 ATTAGTGGCGCTCAGATAAATACGCCACTAAAGATCCGAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGT-AAAGC
* * * * *
31364798 ATTAGCGGCGCTTAGACAAAAACGCCGCTAACGGTCATAGG
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGT-AAAGC
* * * *
31364839 ATTAGCAGCGCTCAGATAAAAACGCTGCTAAAGATCCAAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGT-AAAGC
*
31364880 ATTAGCGGCGCTCAAATAAAAACGCCGCTAAAGGT
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGT
31364915 TTAAAAATTG
Statistics
Matches: 155, Mismatches: 41, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
40 1 0.01
41 152 0.98
42 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (40 bp):
ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTAAAGC
Found at i:31364812 original size:82 final size:82
Alignment explanation
Indices: 31364692--31364913 Score: 266
Period size: 82 Copynumber: 2.7 Consensus size: 82
31364682 GCGCTTCGGC
* * * * *
31364692 AAAAACGCCGCTAAAGGT-AAATGCATTAGCAGCGCTTAGATATAAACGCCGCTAAAGGCCAGAG
1 AAAAACGCCACTAAAGATCCAA-GCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAG
**
31364756 AATTAGTGGCGCTCAGAT
65 AATTAGCAGCGCTCAGAT
* * * * * * *
31364774 AAATACGCCACTAAAGATCCGAGCATTAGCGGCGCTTAGACAAAAACGCCGCTAACGGTCATAGG
1 AAAAACGCCACTAAAGATCCAAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGA
31364839 ATTAGCAGCGCTCAGAT
66 ATTAGCAGCGCTCAGAT
** * *
31364856 AAAAACGCTGCTAAAGATCCAAGCATTAGCGGCGCTCAAATAAAAACGCCGCTAAAGG
1 AAAAACGCCACTAAAGATCCAAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGG
31364914 TTTAAAAATT
Statistics
Matches: 117, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 116 0.99
83 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (82 bp):
AAAAACGCCACTAAAGATCCAAGCATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGGCCAGAGA
ATTAGCAGCGCTCAGAT
Found at i:31364899 original size:123 final size:123
Alignment explanation
Indices: 31364675--31364912 Score: 318
Period size: 123 Copynumber: 1.9 Consensus size: 123
31364665 TTTTGTTACT
* * * *
31364675 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTAAATGCATTAGCAGCGCTTAGATATAAACG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTAAATGCATTAGCAGCGCTCAGATAAAAACG
* * *
31364740 CCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAATACGCCACTAAAGATCCGAGC
66 CCGCTAAAGGCCAGAGAATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCGAGC
* * *
31364798 ATTAGCGGCGCTTAGACAAAAACGCCGCTAACGGT-CATAGGATTAGCAGCGCTCAGATAAAAAC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTAAAT-GCATTAGCAGCGCTCAGATAAAAAC
* * * *
31364862 GCTGCTAAAGATCCA-AGCATTAGCGGCGCTCAAATAAAAACGCCGCTAAAG
65 GCCGCTAAAG-GCCAGAGAATTAGCGGCGCTCAAATAAAAACGCCACTAAAG
31364913 GTTTAAAAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
122 2 0.02
123 94 0.95
124 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (123 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGGTAAATGCATTAGCAGCGCTCAGATAAAAACG
CCGCTAAAGGCCAGAGAATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCGAGC
Found at i:31366334 original size:31 final size:30
Alignment explanation
Indices: 31366299--31366419 Score: 174
Period size: 30 Copynumber: 4.0 Consensus size: 30
31366289 CCCTCAAACA
31366299 TTCTCAC-TTTTCCCATCAAAACTTTGACTCC
1 TTCTCACTTTTTCCC--CAAAACTTTGACTCC
*
31366330 TTCTCACTTTTTCCCCAAAACTTTGACTCA
1 TTCTCACTTTTTCCCCAAAACTTTGACTCC
*
31366360 TTCTCAC-TTTCCCACCAAAACTTTGACTCC
1 TTCTCACTTTTTCC-CCAAAACTTTGACTCC
*
31366390 TTCTCACTTTTTCCCCAAAACTTTTACTCC
1 TTCTCACTTTTTCCCCAAAACTTTGACTCC
31366420 CTTCCCATCC
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
29 5 0.06
30 58 0.71
31 12 0.15
32 7 0.09
ACGTcount: A:0.22, C:0.36, G:0.02, T:0.39
Consensus pattern (30 bp):
TTCTCACTTTTTCCCCAAAACTTTGACTCC
Found at i:31366350 original size:61 final size:60
Alignment explanation
Indices: 31366276--31366410 Score: 189
Period size: 60 Copynumber: 2.2 Consensus size: 60
31366266 ATATTTTACA
* * *
31366276 TTTTTACCTAAAACCCTCAAACATTCTCACTTTTCCCATCAAAACTTTGACTCCTTCTCAC
1 TTTTTCCCCAAAACCCTCAAACATTCTCAC-TTTCCCACCAAAACTTTGACTCCTTCTCAC
** * **
31366337 TTTTTCCCCAAAACTTTGACTCATTCTCACTTTCCCACCAAAACTTTGACTCCTTCTCAC
1 TTTTTCCCCAAAACCCTCAAACATTCTCACTTTCCCACCAAAACTTTGACTCCTTCTCAC
31366397 TTTTTCCCCAAAAC
1 TTTTTCCCCAAAAC
31366411 TTTTACTCCC
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 43 0.65
61 23 0.35
ACGTcount: A:0.26, C:0.36, G:0.02, T:0.36
Consensus pattern (60 bp):
TTTTTCCCCAAAACCCTCAAACATTCTCACTTTCCCACCAAAACTTTGACTCCTTCTCAC
Found at i:31366389 original size:60 final size:61
Alignment explanation
Indices: 31366297--31366418 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 61
31366287 AACCCTCAAA
*
31366297 CATTCTCACTTTTCCCATCAAAACTTTGACTCCTTCTCACTTTTTCCCCAAAACTTTGACT
1 CATTCTCACTTTTCCCACCAAAACTTTGACTCCTTCTCACTTTTTCCCCAAAACTTTGACT
*
31366358 CATTCTCAC-TTTCCCACCAAAACTTTGACTCCTTCTCACTTTTTCCCCAAAACTTTTACT
1 CATTCTCACTTTTCCCACCAAAACTTTGACTCCTTCTCACTTTTTCCCCAAAACTTTGACT
31366418 C
1 C
31366419 CCTTCCCATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 50 0.85
61 9 0.15
ACGTcount: A:0.23, C:0.36, G:0.02, T:0.39
Consensus pattern (61 bp):
CATTCTCACTTTTCCCACCAAAACTTTGACTCCTTCTCACTTTTTCCCCAAAACTTTGACT
Found at i:31366603 original size:30 final size:30
Alignment explanation
Indices: 31366556--31366615 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
31366546 AACTTTTTAT
* *
31366556 TTTCTCCCAAAATTTTTACT-CCCTCCCAC
1 TTTCCCCCAAAACTTTTACTCCCCTCCCAC
31366585 TTTCCCCCTAAAACTTTTACTCCCCTCCCAC
1 TTTCCCCC-AAAACTTTTACTCCCCTCCCAC
31366616 CCCCATCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 11 0.41
31 9 0.33
ACGTcount: A:0.20, C:0.45, G:0.00, T:0.35
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTCCCCTCCCAC
Found at i:31369896 original size:6 final size:6
Alignment explanation
Indices: 31369887--31369913 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31369877 ATAGTGATAT
31369887 TGAAGA TGAAGA TGAAGA TGAAGA TGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGA
31369914 GAATGCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAGA
Found at i:31371766 original size:21 final size:21
Alignment explanation
Indices: 31371740--31371779 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31371730 GTGCTTTTGA
*
31371740 AAAGCACTTCTGAAAAGGAGC
1 AAAGCACATCTGAAAAGGAGC
31371761 AAAGCACATCTGAAAAGGA
1 AAAGCACATCTGAAAAGGA
31371780 CTTTTGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.12
Consensus pattern (21 bp):
AAAGCACATCTGAAAAGGAGC
Found at i:31374105 original size:44 final size:44
Alignment explanation
Indices: 31374056--31374144 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
31374046 TGTAAGTGGA
31374056 TTCCTCCCTTATCTTTTGATGATTTTATAATTTGAAATATAAAG
1 TTCCTCCCTTATCTTTTGATGATTTTATAATTTGAAATATAAAG
31374100 TTCCTCCCTTATCTTTTGATGATTTTATAATTTGAAATATAAAG
1 TTCCTCCCTTATCTTTTGATGATTTTATAATTTGAAATATAAAG
31374144 T
1 T
31374145 CAAACATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.48
Consensus pattern (44 bp):
TTCCTCCCTTATCTTTTGATGATTTTATAATTTGAAATATAAAG
Found at i:31374559 original size:27 final size:27
Alignment explanation
Indices: 31374514--31374574 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
31374504 ATCATAGTAG
*
31374514 TTTTTTCGTCTGCCGTTTTGGCACGCAA
1 TTTTTTCGTCTGCCGTTTTGACACG-AA
* * *
31374542 TTTTTTCGTTTGTC-TTTTGACACGAT
1 TTTTTTCGTCTGCCGTTTTGACACGAA
31374568 TTTTTTC
1 TTTTTTC
31374575 TAGGGCTCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.28
27 9 0.31
28 12 0.41
ACGTcount: A:0.10, C:0.20, G:0.16, T:0.54
Consensus pattern (27 bp):
TTTTTTCGTCTGCCGTTTTGACACGAA
Found at i:31375977 original size:26 final size:26
Alignment explanation
Indices: 31375941--31375992 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31375931 GTTGTGTGGT
31375941 TAGTTTGCAAAGCTATTCGCAGTATC
1 TAGTTTGCAAAGCTATTCGCAGTATC
31375967 TAGTTTGCAAAGCTATTCGCAGTATC
1 TAGTTTGCAAAGCTATTCGCAGTATC
31375993 ATATTGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
TAGTTTGCAAAGCTATTCGCAGTATC
Found at i:31383756 original size:33 final size:33
Alignment explanation
Indices: 31383718--31383789 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
31383708 GATTACTCTC
31383718 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* * *
31383751 TTCACTTGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
31383784 TCCACT
1 TTCACT
31383790 TTCGTTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.11, C:0.26, G:0.07, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:31383790 original size:33 final size:34
Alignment explanation
Indices: 31383726--31383790 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
31383716 TCTTCACTCG
*
31383726 TTTCTTTTACAGACTCTCTTTCTTTTTCACTTGA
1 TTTCTTTTACAGACTCTCTTTCTTTTCCACTTGA
* *
31383760 TTTCTTTT-CAGGCTCTTTTTCTTTTCCACTT
1 TTTCTTTTACAGACTCTCTTTCTTTTCCACTT
31383791 TCGTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 20 0.71
34 8 0.29
ACGTcount: A:0.11, C:0.25, G:0.06, T:0.58
Consensus pattern (34 bp):
TTTCTTTTACAGACTCTCTTTCTTTTCCACTTGA
Found at i:31384994 original size:10 final size:10
Alignment explanation
Indices: 31384983--31385029 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
31384973 ATTTTTGAAA
31384983 TTTTTTCTAAT
1 TTTTTTC-AAT
**
31384994 TTTTTTTTAT
1 TTTTTTCAAT
31385004 TTTTTTCAAT
1 TTTTTTCAAT
*
31385014 TTTTTTGAAT
1 TTTTTTCAAT
31385024 TTTTTT
1 TTTTTT
31385030 TACAATGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
10 25 0.81
11 6 0.19
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTTCAAT
Found at i:31385005 original size:20 final size:20
Alignment explanation
Indices: 31384983--31385029 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
31384973 ATTTTTGAAA
31384983 TTTTTTCTAATTTTTTTTTAT
1 TTTTTTC-AATTTTTTTTTAT
**
31385004 TTTTTTCAATTTTTTTGAAT
1 TTTTTTCAATTTTTTTTTAT
31385024 TTTTTT
1 TTTTTT
31385030 TACAATGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTTCAATTTTTTTTTAT
Found at i:31385008 original size:30 final size:30
Alignment explanation
Indices: 31384974--31385030 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31384964 AATAAAAAAA
31384974 TTTTTGAAATTTTTTCT-AATTTTTTTTTAT
1 TTTTTGAAATTTTTT-TGAATTTTTTTTTAT
**
31385004 TTTTTTCAATTTTTTTGAATTTTTTTT
1 TTTTTGAAATTTTTTTGAATTTTTTTT
31385031 ACAATGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (30 bp):
TTTTTGAAATTTTTTTGAATTTTTTTTTAT
Found at i:31391711 original size:21 final size:21
Alignment explanation
Indices: 31391680--31391738 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
31391670 TATTTTTGAA
*
31391680 ATTTTTAAAATTTAT-TTAAT
1 ATTTTTAAAATTTATAATAAT
31391700 ATTTTTATAAATTT-TAATAAT
1 ATTTTTA-AAATTTATAATAAT
*
31391721 GTTTTTAAAAATTTATAA
1 ATTTTT-AAAATTTATAA
31391739 AATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 8 0.24
21 21 0.64
22 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTAAAATTTATAATAAT
Found at i:31391873 original size:10 final size:11
Alignment explanation
Indices: 31391856--31391883 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31391846 CAATTTTTTT
31391856 TTATTTTTGAA
1 TTATTTTTGAA
31391867 TTATTTTTGAA
1 TTATTTTTGAA
31391878 TTATTT
1 TTATTT
31391884 ATTTTTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (11 bp):
TTATTTTTGAA
Found at i:31395430 original size:29 final size:29
Alignment explanation
Indices: 31395397--31395453 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
31395387 TCTATGACTT
31395397 GATCAAATTAATATTTCTACTATTAAATG
1 GATCAAATTAATATTTCTACTATTAAATG
* * * *
31395426 GATCAATTTAATCTTTGTACTGTTAAAT
1 GATCAAATTAATATTTCTACTATTAAAT
31395454 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (29 bp):
GATCAAATTAATATTTCTACTATTAAATG
Found at i:31401593 original size:50 final size:50
Alignment explanation
Indices: 31401481--31401671 Score: 184
Period size: 50 Copynumber: 3.7 Consensus size: 50
31401471 ATTTGGGTAA
* * *
31401481 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTAGCA-C--CGAG---ATG
* * *
31401537 TGAGGTCCCATGTAAGAACATGCCTGGGACATGGCGTTAGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTAGCACCGAGATG
*** * * *
31401587 AGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGAGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTAGCACCGAGATG
** * *
31401637 AGAACTCCCATGTAAGACCATATCTGGGATATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
31401672 ATTGGCAGTA
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 72 0.64
53 3 0.03
55 1 0.01
56 37 0.33
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTAGCACCGAGATG
Found at i:31401672 original size:50 final size:50
Alignment explanation
Indices: 31401542--31401720 Score: 159
Period size: 50 Copynumber: 3.6 Consensus size: 50
31401532 TTATGTGAGG
* * * * **
31401542 TCCCATGTAAGAACATGCCTGGGACATGGCGTTAGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGAGCACCGAGATGAGAAC
*** *
31401592 TCCCCCATAAGACCATGTCTGGGACATGGCATGAGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGAGCACCGAGATGAGAAC
* * * *
31401642 TCCCATGTAAGACCATATCTGGGATATGGCATTG-GCA--GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCA-TGAGCACCG-AGATGAGAAC
* *
31401690 ATCCCATGTAATACCATGTCTAGGACATGGC
1 -TCCCATGTAAGACCATGTCTGGGACATGGC
31401721 TTTGGCATGT
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
48 4 0.04
49 30 0.29
50 69 0.66
51 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGAGCACCGAGATGAGAAC
Found at i:31421726 original size:6 final size:6
Alignment explanation
Indices: 31421715--31421764 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
31421705 TGACTCTCTG
31421715 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
31421763 GT
1 GT
31421765 CAGTCATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:31423411 original size:15 final size:14
Alignment explanation
Indices: 31423376--31423412 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
31423366 AAATATTTTG
31423376 AAATATAT-ATATA
1 AAATATATAATATA
31423389 AAAT-TATAATATA
1 AAATATATAATATA
31423402 TAAATATATAA
1 -AAATATATAA
31423413 AAGAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 9 0.43
14 4 0.19
15 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATATAATATA
Done.