Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 23
Found at i:5238470 original size:23 final size:23
Alignment explanation
Indices: 5238444--5238487 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5238434 TAAATTGAAA
*
5238444 TAAAATAAAATTGGGGGTGAATT
1 TAAAAGAAAATTGGGGGTGAATT
* *
5238467 TAAAAGGAAATTTGGGGTGAA
1 TAAAAGAAAATTGGGGGTGAA
5238488 ATCGAACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (23 bp):
TAAAAGAAAATTGGGGGTGAATT
Found at i:5238772 original size:20 final size:20
Alignment explanation
Indices: 5238747--5238786 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5238737 TAAGATATGT
5238747 ATGATATATATATATAAGGG
1 ATGATATATATATATAAGGG
5238767 ATGATATATATATATAAGGG
1 ATGATATATATATATAAGGG
5238787 GCAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (20 bp):
ATGATATATATATATAAGGG
Found at i:5243540 original size:36 final size:36
Alignment explanation
Indices: 5243493--5243855 Score: 326
Period size: 36 Copynumber: 10.4 Consensus size: 36
5243483 TTTTAATTTA
* * *
5243493 TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* *
5243529 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAAAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* * * * **
5243565 TTTCTCTTTAAACACAAATATG------TT-AGACCG
1 TTTCCCTTGAAACA-AATTTTGTCTCTCTTGAGATAG
* *
5243595 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
*
5243631 TTTCCCTTGAAAC-AATTTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGATAG
* *
5243667 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATGG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGATAG
* * * *
5243704 TTTCCCTCGAAATAAA------ATCT-TTCA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA-G
* *
5243733 TTTCCCTTGAAACAAATTTCGCCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
*
5243769 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGATAG
* * * *
5243806 TTTCCCTTAAAACGAATTTTGTCTCTCTTGAGACAT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
5243842 TTTCCCTTGAAACA
1 TTTCCCTTGAAACA
5243856 TCAACCTTTG
Statistics
Matches: 265, Mismatches: 41, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 23 0.09
30 18 0.07
31 2 0.01
35 11 0.04
36 137 0.52
37 68 0.26
38 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
Found at i:5243617 original size:102 final size:102
Alignment explanation
Indices: 5243493--5243680 Score: 306
Period size: 102 Copynumber: 1.8 Consensus size: 102
5243483 TTTTAATTTA
5243493 TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAGTTTCCCTTGAAACAAATTTT-GTCTCCCT
1 TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAGTTTCCCTTGAAAC-AATTTTCGTCTCCCT
*
5243557 TGAGAAAGTTTCTCTTTAAACACAAATATGTTAGACCG
65 TGAGAAAGTTTCTCTTGAAACACAAATATGTTAGACCG
* * * *
5243595 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAATTTTCGTCTCTCTT
1 TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAGTTTCCCTTGAAACAATTTTCGTCTCCCTT
*
5243660 GAGACAGTTTCTCTTGAAACA
66 GAGAAAGTTTCTCTTGAAACA
5243681 AAGTTTTGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 6 0.08
102 73 0.92
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAGTTTCCCTTGAAACAATTTTCGTCTCCCTT
GAGAAAGTTTCTCTTGAAACACAAATATGTTAGACCG
Found at i:5243707 original size:37 final size:35
Alignment explanation
Indices: 5243493--5243920 Score: 277
Period size: 36 Copynumber: 12.4 Consensus size: 35
5243483 TTTTAATTTA
* * *
5243493 TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAG
1 TTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAG
* *
5243529 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAAAG
1 TTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAG
* * * * **
5243565 TTTCTCTTTAAACACAAATATG------TT-AGACCG
1 TTTC-CCTTGAA-ACAATTTTGTCTCTCTTGAGATAG
*
5243595 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAG
*
5243631 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAATTTT-GTCTCTCTTGAGATAG
* *
5243667 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATGG
1 TTTCCCTTGAAAC-AA-TTTTGTCTCTCTTGAGATAG
* * ** *
5243704 TTTCCCTCGAAATAA-----AATCT-TTCA-ATATG
1 TTTCCCTTGAAACAATTTTGTCTCTCTTGAGATA-G
* *
5243733 TTTCCCTTGAAACAAATTTCGCCTCTCTTGAGATAG
1 TTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAG
*
5243769 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAC-AA-TTTTGTCTCTCTTGAGATAG
* * *
5243806 TTTCCCTTAAAACGAATTTTGTCTCTCTTGAGACAT
1 TTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAG
*** *
5243842 TTTCCCTTGAAAC-A--TCAAC-CT-TTGAGATTG
1 TTTCCCTTGAAACAATTTTGTCTCTCTTGAGATAG
*
5243872 TTTCCCTT-AAACCATGTTTTGTCTCTCTTGAGAT-G
1 TTTCCCTTGAAA-CA-ATTTTGTCTCTCTTGAGATAG
*
5243907 ATTTCTCTTGAAAC
1 -TTTCCCTTGAAAC
5243921 CATCATACCC
Statistics
Matches: 308, Mismatches: 52, Indels: 64
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.01
29 28 0.09
30 28 0.09
31 4 0.01
32 2 0.01
34 3 0.01
35 14 0.05
36 146 0.47
37 73 0.24
38 6 0.02
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTCCCTTGAAACAATTTTGTCTCTCTTGAGATAG
Found at i:5243741 original size:138 final size:138
Alignment explanation
Indices: 5243493--5243855 Score: 428
Period size: 138 Copynumber: 2.6 Consensus size: 138
5243483 TTTTAATTTA
* * * *
5243493 TTTCCCTTGAAACAAAGTTTGTCTCCCTAGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
* ** * * * *
5243558 GAGAAAGTTTCTCTTTAAACACAAATATGTTAGACCGTTTCCCTTGAAACGAATTTTGTCTCCCT
66 GAGAAAGTTTCCCTCGAAACACAAATATGTTAGAACGTTTCCCTTGAAACAAATTTCGCCTCCCT
5243623 TGAGATAG
131 TGAGATAG
* *
5243631 TTTCCCTTGAAAC-AATTTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTC
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGATAGTTTCCCTTGAAACAAA-TTTTGTCTCTC
** * * *
5243695 TTGAGATGGTTTCCCTCGAAATA-AAATCT-TTCA-ATATGTTTCCCTTGAAACAAATTTCGCCT
64 TTGAGAAAGTTTCCCTCGAAACACAAATATGTT-AGA-ACGTTTCCCTTGAAACAAATTTCGCCT
*
5243757 CTCTTGAGATAG
127 CCCTTGAGATAG
* * *
5243769 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTAAAACGAATTTTGTCTCTCT
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCT
* * *
5243834 TGAGACATTTTCCCTTGAAACA
65 TGAGAAAGTTTCCCTCGAAACA
5243856 TCAACCTTTG
Statistics
Matches: 190, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
137 8 0.04
138 121 0.64
139 57 0.30
140 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (138 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
GAGAAAGTTTCCCTCGAAACACAAATATGTTAGAACGTTTCCCTTGAAACAAATTTCGCCTCCCT
TGAGATAG
Found at i:5243917 original size:66 final size:67
Alignment explanation
Indices: 5243797--5243925 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
5243787 TTTGTCTCTC
*
5243797 TTGAGATAGTTTCCCTTAAAACGAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAA-CATCAAC
1 TTGAGATAGTTTCCCTTAAAACCAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAACCATCAAC
5243861 CT
66 CT
* * * *
5243863 TTGAGATTGTTTCCCTT-AAACCATGTTTTGTCTCTCTTGAGATGA-TTTCTCTTGAAACCATCA
1 TTGAGATAGTTTCCCTTAAAACCA-ATTTTGTCTCTCTTGAGA-CATTTTCCCTTGAAACCATCA
5243926 TACCCTTAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
65 5 0.09
66 44 0.80
67 6 0.11
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (67 bp):
TTGAGATAGTTTCCCTTAAAACCAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAACCATCAAC
CT
Found at i:5247384 original size:3 final size:3
Alignment explanation
Indices: 5247372--5247444 Score: 85
Period size: 3 Copynumber: 23.0 Consensus size: 3
5247362 AAAAATACTA
*
5247372 ATT ATAT ATT ATT ATA ATT ATAT ATT ATT AATT ATAT ATT ATT AATT
1 ATT AT-T ATT ATT ATT ATT AT-T ATT ATT -ATT AT-T ATT ATT -ATT
5247419 A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5247445 TTACATTTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
2 2 0.03
3 45 0.73
4 15 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5247403 original size:14 final size:14
Alignment explanation
Indices: 5247370--5247442 Score: 105
Period size: 14 Copynumber: 5.1 Consensus size: 14
5247360 AAAAAAATAC
5247370 TAATTATATATTATT
1 TAATTATATATTA-T
5247385 ATAATTATATATTAT
1 -TAATTATATATTAT
5247400 TAATTATATATTAT
1 TAATTATATATTAT
5247414 TAATTATATTATTAT
1 TAATTATA-TATTAT
5247429 T-ATTAT-TATTAT
1 TAATTATATATTAT
5247441 TA
1 TA
5247443 TTTTACATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.13
14 27 0.49
15 8 0.15
16 13 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATATTAT
Found at i:5250824 original size:33 final size:33
Alignment explanation
Indices: 5250778--5250860 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
5250768 TTAAAAAAAA
*
5250778 TCGGGTTCAGGTCGGGTTTTTTTAAGTT-TGATAT
1 TCGGG-TCGGGTCGGGTTTTTTTAA-TTGTGATAT
*
5250812 TCGGGTCGGGTCGAG-TTTTTTAATTGTGATAT
1 TCGGGTCGGGTCGGGTTTTTTTAATTGTGATAT
*
5250844 TTGGGTCGGGTTCGGGT
1 TCGGGTCGGG-TCGGGT
5250861 CGGGTCGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 2 0.05
32 23 0.55
33 12 0.29
34 5 0.12
ACGTcount: A:0.12, C:0.10, G:0.35, T:0.43
Consensus pattern (33 bp):
TCGGGTCGGGTCGGGTTTTTTTAATTGTGATAT
Found at i:5250894 original size:28 final size:27
Alignment explanation
Indices: 5250855--5250909 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
5250845 TGGGTCGGGT
* * *
5250855 TCGGGTCGGGTCGGTTTTTAAAAAAAA
1 TCGGGTCGGGTCAGATTTAAAAAAAAA
5250882 TCGGGATCGGGTCAGATTTAAAAAAAAA
1 TCGGG-TCGGGTCAGATTTAAAAAAAAA
5250910 AATTAGGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.25
Consensus pattern (27 bp):
TCGGGTCGGGTCAGATTTAAAAAAAAA
Found at i:5250970 original size:32 final size:33
Alignment explanation
Indices: 5250918--5251027 Score: 125
Period size: 33 Copynumber: 3.4 Consensus size: 33
5250908 AAAATTAGGG
*
5250918 GTCGGGTCGGG-CTTTTTAAGTTTGATATTC-A
1 GTCGGGTCGGGTCTTTTTAAGTGTGATATTCGA
*
5250949 GTCGGGTCGGGTCTTTTTAAGTGTGATATTCGG
1 GTCGGGTCGGGTCTTTTTAAGTGTGATATTCGA
** * * *
5250982 GTCGGGTTAGATTTTTTTAAGTGTGATATTCGG
1 GTCGGGTCGGGTCTTTTTAAGTGTGATATTCGA
*
5251015 GTCAGGTTCGGGT
1 GTC-GGGTCGGGT
5251028 TTAGGGTGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
31 11 0.17
32 18 0.27
33 32 0.48
34 5 0.08
ACGTcount: A:0.15, C:0.11, G:0.34, T:0.41
Consensus pattern (33 bp):
GTCGGGTCGGGTCTTTTTAAGTGTGATATTCGA
Found at i:5252562 original size:22 final size:24
Alignment explanation
Indices: 5252537--5252583 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5252527 CAAGTTTATC
*
5252537 ACTTTTTA-C-ATTTGATATCTAT
1 ACTTTTTATCAATTTGATACCTAT
5252559 ACTTTTTATCAATTTGATACCTAT
1 ACTTTTTATCAATTTGATACCTAT
5252583 A
1 A
5252584 TTTAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 1 0.05
24 13 0.59
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (24 bp):
ACTTTTTATCAATTTGATACCTAT
Found at i:5252665 original size:29 final size:30
Alignment explanation
Indices: 5252623--5252679 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
5252613 AATTGATCAC
* *
5252623 TTTTACAAATTTGGTACCTTTTTTTTTCTT
1 TTTTACAAATTTGGTACCTATATTTTTCTT
*
5252653 TTTTACCAA-TTGGTACCTATATTTTTC
1 TTTTACAAATTTGGTACCTATATTTTTC
5252680 AGACATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.19, C:0.16, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTTACAAATTTGGTACCTATATTTTTCTT
Found at i:5256960 original size:3 final size:3
Alignment explanation
Indices: 5256952--5257031 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
5256942 TTAATATATT
* * * *
5256952 TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5257000 TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5257032 TTTATAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5257036 original size:18 final size:18
Alignment explanation
Indices: 5256952--5257040 Score: 89
Period size: 18 Copynumber: 5.1 Consensus size: 18
5256942 TTAATATATT
* *
5256952 TAATAATAATAATGATAA
1 TAATAATAATATTTATAA
*
5256970 TGATAATAATA---ATAA
1 TAATAATAATATTTATAA
*
5256985 TAATAATAAT-TATAGTAA
1 TAATAATAATATTTA-TAA
5257003 TAATAATAAT-TATTATAA
1 TAATAATAATAT-TTATAA
5257021 TAATAATAATATTTATAA
1 TAATAATAATATTTATAA
5257039 TA
1 TA
5257041 TGGGTAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
15 13 0.21
17 1 0.02
18 45 0.73
19 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TAATAATAATATTTATAA
Found at i:5257487 original size:112 final size:113
Alignment explanation
Indices: 5257342--5257565 Score: 353
Period size: 112 Copynumber: 2.0 Consensus size: 113
5257332 CTATCTCCTG
*
5257342 TGATAGAATTATGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATAGAATTATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* ** *
5257407 TGAGTTCTTCTCATTATGATC-TTCTCTGGAAATTCTGATCGATCAAT
66 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAT
* *
5257454 TGAT-GAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 TGATAGAATT-ATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
5257518 ATGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAA
65 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAA
5257566 GTGAGTTCTT
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
111 5 0.05
112 76 0.75
113 21 0.21
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (113 bp):
TGATAGAATTATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAT
Found at i:5257590 original size:48 final size:48
Alignment explanation
Indices: 5257519--5257617 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
5257509 CTTCTTCAGA
5257519 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAG
1 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAG
5257567 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAG
1 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAG
5257615 TGA
1 TGA
5257618 TGGATTTGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (48 bp):
TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAG
Found at i:5257635 original size:160 final size:159
Alignment explanation
Indices: 5257407--5257729 Score: 488
Period size: 160 Copynumber: 2.0 Consensus size: 159
5257397 CTTCTTCAGA
* ** * *
5257407 TGAGTTCTTCTCATTATGATCTTCTCTGGAAATTCTGATCGATCAATTGATGAATTCATGTAAAA
1 TGAGTTCTTCTCATTATGAACTTCTCTGGAAAAACTGATCCATCAAGTGATGAATT-ATGTAAAA
*
5257472 GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
65 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
*
5257537 AACTTTCTTTGGAAAAACTGATCCATCAAG
130 AACTTTCTCTGGAAAAACTGATCCATCAAG
* *
5257567 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAGTGATGGATT-TG-AGCA
1 TGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAACTGATCCATCAAGTGATGAATTATGTA--A
* *
5257630 AAGGTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
63 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
5257695 TGAACTTTCTCTGGAAAAGCTGATCCATCAAG
128 TGAACTTTCTCTGGAAAAACTGATCCATCAAG
5257727 TGA
1 TGA
5257730 TGGATTTGAG
Statistics
Matches: 148, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
158 1 0.01
159 2 0.01
160 116 0.78
161 29 0.20
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (159 bp):
TGAGTTCTTCTCATTATGAACTTCTCTGGAAAAACTGATCCATCAAGTGATGAATTATGTAAAAG
GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTCTCTGGAAAAACTGATCCATCAAG
Found at i:5257767 original size:112 final size:112
Alignment explanation
Indices: 5257567--5258186 Score: 1177
Period size: 112 Copynumber: 5.5 Consensus size: 112
5257557 ATCCATCAAG
* *
5257567 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAACTGATCCATCAAGTGATGGATTTGAGCAAA
1 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
*
5257632 GGTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTTCTTCAGA
66 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
5257679 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
1 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
*
5257744 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
66 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
*
5257791 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
1 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
*
5257856 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCATA
66 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
5257903 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
1 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
5257968 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
66 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
*
5258015 TGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
1 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
5258080 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
66 GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
5258127 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
1 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
5258187 ATCTTTGCTA
Statistics
Matches: 497, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 497 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (112 bp):
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAA
GGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGA
Found at i:5259049 original size:83 final size:83
Alignment explanation
Indices: 5258907--5259367 Score: 814
Period size: 83 Copynumber: 5.6 Consensus size: 83
5258897 TAGTTCCTAC
* * * *
5258907 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAACACATTTATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
*
5258972 TTCAATGATTGGTTCTGC
66 TTCAATGATTGGTTCTGT
* * * *
5258990 CAAACCAGATCAGATAACTCAAAGAACACTTCGAGAAGATGCTATGAACACATTCATCTTCTAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
5259055 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
*
5259073 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGATGATGCTATTAATACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
5259138 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
5259156 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
5259221 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
* *
5259239 CAAACCAGATCAGATAACTCAAAGAGCACTTCCAGAAGATGATATTAATACATTCATCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
5259304 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
5259322 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
5259368 GGCCAATTTA
Statistics
Matches: 363, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 363 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAATACATTCATCTTCCAAA
TTCAATGATTGGTTCTGT
Found at i:5260539 original size:10 final size:10
Alignment explanation
Indices: 5260526--5260575 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
5260516 CCCTTTTTTC
5260526 TTTTTTCTTT
1 TTTTTTCTTT
5260536 TTTTTTCTTT
1 TTTTTTCTTT
*
5260546 CTTTTTC-TT
1 TTTTTTCTTT
* *
5260555 TTCTCTC-TT
1 TTTTTTCTTT
5260564 TTTTTTCTTT
1 TTTTTTCTTT
5260574 TT
1 TT
5260576 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 13 0.39
10 20 0.61
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:5260550 original size:27 final size:28
Alignment explanation
Indices: 5260520--5260573 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
5260510 TGACCCCCCT
*
5260520 TTTTTCTTTTTTCT-TTTTTTTTCTTTC
1 TTTTTCTTTTCTCTCTTTTTTTTCTTTC
5260547 TTTTTCTTTTCTCTCTTTTTTTTCTTT
1 TTTTTCTTTTCTCTCTTTTTTTTCTTT
5260574 TTCTTCAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTTTCTTTTCTCTCTTTTTTTTCTTTC
Found at i:5271205 original size:15 final size:13
Alignment explanation
Indices: 5271173--5271210 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
5271163 TTTGACAGTA
5271173 AAAT-AAATAATG
1 AAATAAAATAATG
5271185 AAATAAAATAATTG
1 AAATAAAATAA-TG
5271199 CAAATAAAATAA
1 -AAATAAAATAA
5271211 AATAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:5273350 original size:3 final size:3
Alignment explanation
Indices: 5273342--5273421 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
5273332 TTAATATATT
* * * *
5273342 TAA TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5273390 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5273422 TTTATAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5273428 original size:18 final size:18
Alignment explanation
Indices: 5273368--5273430 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
5273358 AATGATAATA
*
5273368 ATAATAATAATAATAATT
1 ATAATAATAATAATATTT
*
5273386 ATAGTAATAATAATAATTAT
1 ATAATAATAATAAT-ATT-T
5273406 AATAATAATAATAATATTT
1 -ATAATAATAATAATATTT
5273425 ATAATA
1 ATAATA
5273431 TGGGTAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 19 0.49
19 3 0.08
20 4 0.10
21 13 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATAATAATAATATTT
Found at i:5273430 original size:15 final size:15
Alignment explanation
Indices: 5273333--5273417 Score: 100
Period size: 15 Copynumber: 5.5 Consensus size: 15
5273323 TATATGTATT
5273333 TAATATATT-TAATAA
1 TAATA-ATTATAATAA
* *
5273348 TAATAATGATAATGA
1 TAATAATTATAATAA
*
5273363 TAATAATAATAATAA
1 TAATAATTATAATAA
5273378 TAATAATTATAGTAATAA
1 TAATAA-T-TA-TAATAA
5273396 TAATAATTATAATAA
1 TAATAATTATAATAA
5273411 TAATAAT
1 TAATAAT
5273418 AATATTTATA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
14 2 0.03
15 42 0.69
16 3 0.05
17 2 0.03
18 12 0.20
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (15 bp):
TAATAATTATAATAA
Found at i:5284751 original size:12 final size:12
Alignment explanation
Indices: 5284718--5284750 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5284708 TAAATAAACA
5284718 AATACATAAAAT
1 AATACATAAAAT
5284730 AATA-ATAAAAT
1 AATACATAAAAT
5284741 -ATACATAAAA
1 AATACATAAAA
5284751 AACTAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 13 0.65
12 4 0.20
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
AATACATAAAAT
Found at i:5284781 original size:3 final size:3
Alignment explanation
Indices: 5284773--5284812 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5284763 ACCAAAACAC
5284773 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5284813 CCTAATTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5285919 original size:26 final size:26
Alignment explanation
Indices: 5285883--5285942 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
5285873 ACGAGCCGTT
5285883 TTCATTCTCTTCTTGTTTTGTTCGTC
1 TTCATTCTCTTCTTGTTTTGTTCGTC
5285909 TTCATTCTCTTCTTGTTTTGTTCGTC
1 TTCATTCTCTTCTTGTTTTGTTCGTC
5285935 TTCATTCT
1 TTCATTCT
5285943 TTTTTGACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.05, C:0.23, G:0.10, T:0.62
Consensus pattern (26 bp):
TTCATTCTCTTCTTGTTTTGTTCGTC
Found at i:5285942 original size:21 final size:22
Alignment explanation
Indices: 5285892--5285948 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 22
5285882 TTTCATTCTC
5285892 TTCTTGTTTTGTTCGTCTTCATTCT
1 TTCTTGTTTTGTTCGTCTTCA---T
5285917 CTTCTTGTTTTGTTCGTCTTCA-
1 -TTCTTGTTTTGTTCGTCTTCAT
5285939 TTCTT-TTTTG
1 TTCTTGTTTTG
5285949 ACACCTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
26 21 0.68
ACGTcount: A:0.04, C:0.19, G:0.12, T:0.65
Consensus pattern (22 bp):
TTCTTGTTTTGTTCGTCTTCAT
Found at i:5286151 original size:25 final size:24
Alignment explanation
Indices: 5286096--5286202 Score: 92
Period size: 25 Copynumber: 4.4 Consensus size: 24
5286086 TTTCAAAAGG
* *
5286096 TGAAAAAGTTCAATG-AATAAGTTT
1 TGAAAATGTTTAATGAAATAA-TTT
* *
5286120 TGAAAATATTTTATGAAATAATTT
1 TGAAAATGTTTAATGAAATAATTT
* *
5286144 TGAGAAATGTTTAACGAAAGAATTT
1 TGA-AAATGTTTAATGAAATAATTT
* *
5286169 TGAAAAATGTTTGATGAAA-AAATT
1 TG-AAAATGTTTAATGAAATAATTT
*
5286193 GGAAAATGTT
1 TGAAAATGTT
5286203 GTCATTTACT
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
23 8 0.12
24 22 0.32
25 37 0.54
26 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.36
Consensus pattern (24 bp):
TGAAAATGTTTAATGAAATAATTT
Found at i:5289639 original size:15 final size:16
Alignment explanation
Indices: 5289613--5289643 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5289603 CAAAATAGAA
5289613 ATACTAGAATAGGTAG
1 ATACTAGAATAGGTAG
5289629 ATACT-GAATAGGTAG
1 ATACTAGAATAGGTAG
5289644 TTTATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
ATACTAGAATAGGTAG
Found at i:5294769 original size:3 final size:3
Alignment explanation
Indices: 5294761--5294860 Score: 146
Period size: 3 Copynumber: 33.3 Consensus size: 3
5294751 TTAATATATT
* * * *
5294761 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5294809 TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5294857 TAA T
1 TAA T
5294861 GACCAAACGA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5296165 original size:15 final size:13
Alignment explanation
Indices: 5296145--5296182 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
5296135 ATGTTTCATT
5296145 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
5296160 TTATTTTATTTCA
1 TTATTTTATTTCA
5296173 TTA-TTTATTT
1 TTATTTTATTT
5296183 TTCTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:5306789 original size:23 final size:23
Alignment explanation
Indices: 5306763--5306841 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
5306753 ATTATGCTTG
* *
5306763 AAGAAAAAAGAGAAGAAAGAAAA
1 AAGAAAAAAGAAAAGAAAAAAAA
* *
5306786 AAGAAAGAAAATAAAATTAAAAAAAA
1 AAG-AA-AAAAGAAAA-GAAAAAAAA
5306812 AAG-AAAAAGAAAAAGAAAAAAAA
1 AAGAAAAAAG-AAAAGAAAAAAAA
5306835 AAGAAAA
1 AAGAAAA
5306842 GAGGGGGGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 18 0.40
24 10 0.22
25 7 0.16
26 10 0.22
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (23 bp):
AAGAAAAAAGAAAAGAAAAAAAA
Found at i:5306813 original size:12 final size:11
Alignment explanation
Indices: 5306778--5306841 Score: 83
Period size: 11 Copynumber: 5.7 Consensus size: 11
5306768 AAAAGAGAAG
*
5306778 AAAGAAAAAAG
1 AAAGAAAAAAA
*
5306789 AAAGAAAATAA
1 AAAGAAAAAAA
**
5306800 AATTAAAAAAA
1 AAAGAAAAAAA
5306811 AAAGAAAAAGAA
1 AAAGAAAAA-AA
5306823 AAAGAAAAAAA
1 AAAGAAAAAAA
5306834 AAAGAAAA
1 AAAGAAAA
5306842 GAGGGGGGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 34 0.76
12 11 0.24
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:5306814 original size:22 final size:22
Alignment explanation
Indices: 5306773--5306843 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 22
5306763 AAGAAAAAAG
*
5306773 AGAAGAAAGAAAAAAGAAAGAAA
1 AGAA-AAAGAAAAAAAAAAGAAA
* **
5306796 ATAAAATTAAAAAAAAAAGAAAA
1 AGAAAAAGAAAAAAAAAAG-AAA
5306819 AGAAAAAGAAAAAAAAAAGAAA
1 AGAAAAAGAAAAAAAAAAGAAA
5306841 AGA
1 AGA
5306844 GGGGGGATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 18 0.45
23 22 0.55
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (22 bp):
AGAAAAAGAAAAAAAAAAGAAA
Found at i:5306841 original size:16 final size:16
Alignment explanation
Indices: 5306766--5306843 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 16
5306756 ATGCTTGAAG
* *
5306766 AAAAAAGAGAAGAAAG
1 AAAAAAGAAAAGAAAA
5306782 AAAAAAG-AAAGAAAA
1 AAAAAAGAAAAGAAAA
* ** *
5306797 TAAAATTAAAAAAAAA
1 AAAAAAGAAAAGAAAA
5306813 AGAAAAAGAAAAAGAAAA
1 A-AAAAAG-AAAAGAAAA
5306831 AAAAAAGAAAAGA
1 AAAAAAGAAAAGA
5306844 GGGGGGATCA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
15 10 0.20
16 20 0.41
17 10 0.20
18 9 0.18
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAA
Found at i:5308122 original size:83 final size:83
Alignment explanation
Indices: 5307997--5308705 Score: 1283
Period size: 83 Copynumber: 8.5 Consensus size: 83
5307987 TAAATTGGCC
5307997 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
* *
5308062 TTGGAAGATGAATTTGCT
66 TTGGAAGATGAATGTGTT
5308080 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
*
5308145 TTGGAAGATGAATGTATT
66 TTGGAAGATGAATGTGTT
5308163 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
*
5308228 TTGGAAGATGAATGTATT
66 TTGGAAGATGAATGTGTT
*
5308246 AATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
*
5308311 TTGGAAGATGAATGTATT
66 TTGGAAGATGAATGTGTT
5308329 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
*
5308394 TTGGAAGATGAATGTATT
66 TTGGAAGATGAATGTGTT
*
5308412 AATAGCATCTTCTGGAAGTGTTCTGTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
* *
5308477 TTGGAAGATGAATTTGCT
66 TTGGAAGATGAATGTGTT
5308495 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
*
5308560 TTGGAAGATAAATGTGTT
66 TTGGAAGATGAATGTGTT
*
5308578 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
* *
5308643 TTGGAAGATGAATTTGCT
66 TTGGAAGATGAATGTGTT
*
5308661 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
5308706 AGGTAAGAAC
Statistics
Matches: 607, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 607 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAAT
TTGGAAGATGAATGTGTT
Found at i:5310322 original size:112 final size:111
Alignment explanation
Indices: 5309433--5310311 Score: 1299
Period size: 112 Copynumber: 7.9 Consensus size: 111
5309423 TAGCAAAGAT
* * * * *
5309433 TCAAATCTATCATTTGATGGAT-TGACATTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTG
1 TCAAATCCATCACTTGATGGATCAG-CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * **
5309497 AAGGAGGAAGAAGAAA-TTCATAATAAGAAGAATTTGTTCAACCTTT-
65 AAGAAGGAAGAA-AAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTC
* * * *
5309543 TACATGAATTCATCAATTGATCGATCAGCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATC
1 T-CA--AATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
5309607 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGC
63 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT-C
*
5309657 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
5309721 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT-C
* *
5309768 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTTATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
5309833 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT-C
*
5309880 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
5309945 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT-C
5309992 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
5310057 AGAAGGAAGAGAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTT-C
*
5310105 TCAAATCCATCA-TTAGATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
5310169 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT-
65 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTC
* * * *
5310215 TACATGAATTCATCAATTGATGGATCAACATTTT-CAGAG-AAGTTCATAATGAGTAGAACTCAT
1 T-CA--AATCCATCACTTGATGGATCAGC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCAT
* * *
5310278 CTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
62 CTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGA
5310312 ATTTTTTCAA
Statistics
Matches: 723, Mismatches: 30, Indels: 30
0.92 0.04 0.04
Matches are distributed among these distances:
110 2 0.00
111 145 0.20
112 413 0.57
113 156 0.22
114 7 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (111 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTC
Found at i:5310659 original size:3 final size:3
Alignment explanation
Indices: 5310653--5310745 Score: 123
Period size: 3 Copynumber: 31.0 Consensus size: 3
5310643 CCATATTAAT
* * * *
5310653 TTA TTA TTA TTA TTA TTA TAA TTA TAA TTA TAA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
5310701 TAA TAA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5310746 AATATATTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5310682 original size:21 final size:21
Alignment explanation
Indices: 5310674--5310754 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
5310664 ATTATTATAA
5310674 TTATAATTATAATTATTATTA
1 TTATAATTATAATTATTATTA
*
5310695 TTATAATAATAATTATTATTA
1 TTATAATTATAATTATTATTA
* * *
5310716 TTATTATCATTATTATTATTA
1 TTATAATTATAATTATTATTA
*
5310737 TTATTATTA-AATATATTA
1 TTATAATTATAAT-TATTA
5310755 AATACATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 2 0.04
21 51 0.96
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATAATTATAATTATTATTA
Found at i:5314594 original size:24 final size:27
Alignment explanation
Indices: 5314561--5314613 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
5314551 AGCTCGACTT
*
5314561 AAGTAGAAAAT-CCAA-AAAAAA-AAG
1 AAGTAAAAAATGCCAAGAAAAAACAAG
*
5314585 AAGTAAAAAATGCTAAGAAAAAACAAG
1 AAGTAAAAAATGCCAAGAAAAAACAAG
5314612 AA
1 AA
5314614 ATCATTCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 3 0.12
26 6 0.25
27 5 0.21
ACGTcount: A:0.70, C:0.08, G:0.13, T:0.09
Consensus pattern (27 bp):
AAGTAAAAAATGCCAAGAAAAAACAAG
Found at i:5319833 original size:8 final size:8
Alignment explanation
Indices: 5319820--5319860 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5319810 CTCATTTTCA
5319820 GAGAATTT
1 GAGAATTT
5319828 GAGAATTT
1 GAGAATTT
*
5319836 -AGAGTTT
1 GAGAATTT
*
5319843 GGGAATTT
1 GAGAATTT
5319851 GAGAATTT
1 GAGAATTT
5319859 GA
1 GA
5319861 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:5320158 original size:128 final size:128
Alignment explanation
Indices: 5319931--5320302 Score: 615
Period size: 128 Copynumber: 2.9 Consensus size: 128
5319921 TAATCAGAGT
* * *
5319931 ACTATTCACATGAAGGCGCGTT-CCGAGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
5319995 CATTTCCCTATTATGTCACTCATATCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
5320058 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
5320123 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* ***
5320186 TC-AGGGGACT-TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
1 ACTA-TTCA-TATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
5320249 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
64 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
5320303 AATCAGGTAA
Statistics
Matches: 231, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
127 22 0.10
128 208 0.90
129 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (128 bp):
ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:5320536 original size:14 final size:14
Alignment explanation
Indices: 5320517--5320546 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5320507 CATAAGTTGA
*
5320517 TTTTAATGTATATG
1 TTTTAATATATATG
5320531 TTTTAATATATATG
1 TTTTAATATATATG
5320545 TT
1 TT
5320547 AATGATAAAA
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:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:5320695 original size:28 final size:28
Alignment explanation
Indices: 5320653--5320756 Score: 93
Period size: 28 Copynumber: 3.5 Consensus size: 28
5320643 ATTAAGTTGA
* *
5320653 AATTTA-ATGTTAAATTTTGAATACTAT
1 AATTTATATTTTAAATTTTGAATAATAT
5320680 AATTTATATTTTAAATTTAAATTTTGAATAATAT
1 AATTTATA---T---TTTAAATTTTGAATAATAT
* * *
5320714 TATTTTTATTTTAAATTTCGAATAATAT
1 AATTTATATTTTAAATTTTGAATAATAT
*
5320742 AATTTGTATTTTAAA
1 AATTTATATTTTAAA
5320757 AACATTTATC
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.10
28 32 0.51
31 2 0.03
34 23 0.37
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (28 bp):
AATTTATATTTTAAATTTTGAATAATAT
Found at i:5320700 original size:34 final size:34
Alignment explanation
Indices: 5320662--5320731 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
5320652 AAATTTAATG
*
5320662 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* *
5320696 TTAAATTTTGAATAATATTATTTTTATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
5320730 TT
1 TT
5320732 CGAATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:5321287 original size:21 final size:20
Alignment explanation
Indices: 5321260--5321329 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
5321250 GGTATAAAAC
*
5321260 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
5321280 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
5321301 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
5321322 CCCTGCGG
1 -CCTGCGG
5321330 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:5321359 original size:21 final size:21
Alignment explanation
Indices: 5321333--5321380 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5321323 CCTGCGGAGA
*
5321333 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
5321354 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
5321375 GGGCAT
1 TGGCAT
5321381 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:5323146 original size:35 final size:32
Alignment explanation
Indices: 5323105--5323189 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
5323095 AATTCTAAAT
5323105 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTATATAAATA-TA--TTAATAAAAA
* * *
5323140 AAATAATATTTACATAAATATATTAATATAAA
1 AAATAATAATTATATAAATATATTAATAAAAA
* * *
5323172 ATATAATAACTATTTAAA
1 AAATAATAATTATATAAA
5323190 AAAATACTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 22 0.52
34 2 0.05
35 18 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATAATAATTATATAAATATATTAATAAAAA
Found at i:5323166 original size:32 final size:34
Alignment explanation
Indices: 5323105--5323180 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 34
5323095 AATTCTAAAT
*
5323105 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTACATAAATATTA-TTTAATAAAAA
* *
5323140 AAATAATATTTACATAAATA-TA-TTAATATAAA
1 AAATAATAATTACATAAATATTATTTAATAAAAA
*
5323172 ATATAATAA
1 AAATAATAA
5323181 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 16 0.44
34 2 0.06
35 18 0.50
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATAATAATTACATAAATATTATTTAATAAAAA
Found at i:5323205 original size:34 final size:34
Alignment explanation
Indices: 5323133--5323210 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
5323123 TATTATTTTA
* * * *
5323133 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAAAATACTAAC
5323167 ATAAAATATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTACATAAAAATACTAAC
5323201 ATAAAAATAA
1 ATAAAAATAA
5323211 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 21 0.55
35 7 0.18
36 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAAAATACTAAC
Found at i:5324387 original size:59 final size:59
Alignment explanation
Indices: 5324268--5324412 Score: 150
Period size: 59 Copynumber: 2.4 Consensus size: 59
5324258 GAATATATGA
* * * * ***
5324268 ATAGTTGGTGATCATTTTGTAACTTTTAATAGTCAGAGAACTCAACAAAGTAATGTCCT
1 ATAGTTGGAGACCATTTTGTAACTTTTAATAGTCAAAGAACTCAACAAAATAACACCCT
* *
5324327 ATAGTTGGAGACCATTTTGTAACTTTTAATAATTGAAAG-ACTCAACAAAATAACACCCT
1 ATAGTTGGAGACCATTTTGTAACTTTTAAT-AGTCAAAGAACTCAACAAAATAACACCCT
* *
5324386 ATAATTGAGAGACTA-TTTGTGAACTTT
1 ATAGTTG-GAGACCATTTTGT-AACTTT
5324413 ACCCTAAATT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 55 0.76
60 17 0.24
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (59 bp):
ATAGTTGGAGACCATTTTGTAACTTTTAATAGTCAAAGAACTCAACAAAATAACACCCT
Found at i:5328031 original size:11 final size:11
Alignment explanation
Indices: 5328015--5328051 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5328005 CAATTTCTTG
5328015 TTTTAAAATAT
1 TTTTAAAATAT
5328026 TTTTAAAATA-
1 TTTTAAAATAT
5328036 -TTTAAAATTAT
1 TTTTAAAA-TAT
5328047 TTTTA
1 TTTTA
5328052 TTTATTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 10 0.43
12 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5332034 original size:35 final size:35
Alignment explanation
Indices: 5331988--5332071 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
5331978 CCAAAGGGAA
*
5331988 GGTATCGATACCATTTTAAAACAGAATGTAAAAAT
1 GGTATCGATACCATTTCAAAACAGAATGTAAAAAT
*
5332023 GGTATCAATACCATTTCAAAACAGAATGTAAAAAT
1 GGTATCGATACCATTTCAAAACAGAATGTAAAAAT
5332058 GGTATCGATACCAT
1 GGTATCGATACCAT
5332072 AGTATGGAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (35 bp):
GGTATCGATACCATTTCAAAACAGAATGTAAAAAT
Found at i:5332105 original size:20 final size:22
Alignment explanation
Indices: 5332059--5332110 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
5332049 TGTAAAAATG
* *
5332059 GTATCGATACCATAGTATGGAA
1 GTATCGATACCATAGGAAGGAA
5332081 GTATCGATACCAT-GGAAGG-A
1 GTATCGATACCATAGGAAGGAA
5332101 GTATCGATAC
1 GTATCGATAC
5332111 TGAAGAGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.39
21 4 0.14
22 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (22 bp):
GTATCGATACCATAGGAAGGAA
Found at i:5332583 original size:59 final size:59
Alignment explanation
Indices: 5332427--5332887 Score: 746
Period size: 59 Copynumber: 7.8 Consensus size: 59
5332417 ATGGCACTAA
* *
5332427 GTGTGCAAAAATTTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
5332486 GTGTG-AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
5332544 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
5332603 GTGTGTAAAAATGTTAAGAAATTCATACTAAGTGTATGGATTTCCCTATTGGGCACTTT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* **
5332662 GTGTGCAAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTTTGTATTGGGCACTTT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
5332721 GTGTGAAAAAAATGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGACACTCT
1 GTGTG-CAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
5332781 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
5332840 ATTTGCAAAAAT-ATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
5332888 GAGAAATATA
Statistics
Matches: 373, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
58 91 0.24
59 230 0.62
60 52 0.14
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (59 bp):
GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:5332795 original size:178 final size:177
Alignment explanation
Indices: 5332427--5332887 Score: 746
Period size: 178 Copynumber: 2.6 Consensus size: 177
5332417 ATGGCACTAA
* *
5332427 GTGTGCAAAAATTTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTTGTGTG-
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGC
* *
5332491 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTTGTGTGCAAAAAT
66 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGAAAAAAT
* * *
5332556 GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
131 GTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGACACTCT
* * *
5332603 GTGTGTAAAAATGTTAAGAAATTCATACTAAGTGTATGGATTTCCCTATTGGGCACTTTGTGTGC
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGC
* **
5332668 AAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTTTGTATTGGGCACTTTGTGTGAAAAAAA
66 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTG-AAAAAA
5332733 TGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGACACTCT
130 TGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGACACTCT
* * *
5332781 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTTATTTGC
1 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGC
*
5332846 AAAAAT-ATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
66 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
5332888 GAGAAATATA
Statistics
Matches: 260, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
176 59 0.23
177 86 0.33
178 115 0.44
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (177 bp):
GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGC
AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGAAAAAAT
GTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGACACTCT
Found at i:5336108 original size:2 final size:2
Alignment explanation
Indices: 5336101--5336132 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5336091 ATCCCTTTAC
5336101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5336133 CATTCATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5337294 original size:23 final size:23
Alignment explanation
Indices: 5337268--5337336 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
5337258 CACCACAGCT
*
5337268 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
5337291 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
5337314 CATAGAATTGCACC-AGAGTGCCA
1 CGTAGAATTGCACCGA-AGTGCCA
5337337 TATAATAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:5344319 original size:23 final size:23
Alignment explanation
Indices: 5344263--5344322 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
5344253 CAGCTTGTAT
*
5344263 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
5344286 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
5344309 AATTGCACCGGAGT
1 AATTGCACCGGAGT
5344323 TCCATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:5348869 original size:42 final size:41
Alignment explanation
Indices: 5348811--5348901 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 41
5348801 ATACTTTGCC
* **
5348811 TAAAAAAACTTAGAGTGAAAACCCGTAAAGGGCGCTCTAGG
1 TAAAAAAAATTAGAGTGAAAACCCACAAAGGGCGCTCTAGG
* *
5348852 TAAAAAACAATTAGAGTGAAAATCCACAAAGGGCTCTCTAGG
1 TAAAAAA-AATTAGAGTGAAAACCCACAAAGGGCGCTCTAGG
5348894 TAAAAAAA
1 TAAAAAAA
5348902 GAAAAAGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 8 0.18
42 36 0.82
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (41 bp):
TAAAAAAAATTAGAGTGAAAACCCACAAAGGGCGCTCTAGG
Found at i:5350725 original size:2 final size:2
Alignment explanation
Indices: 5350714--5350780 Score: 50
Period size: 2 Copynumber: 34.0 Consensus size: 2
5350704 ATCCCATTTG
* * * *
5350714 TA TA TA -A TA TA TA TA TA TA TA TA TT TA AA TA TA TA TT TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
5350756 TT TGA -A TA TA TA TA TA TA TA -A TA TA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA
5350781 GTTTTTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
1 3 0.06
2 48 0.92
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5350764 original size:29 final size:28
Alignment explanation
Indices: 5350732--5350798 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
5350722 ATATATATAT
* *
5350732 ATATATTTAAATATATATTTAGTTTTTGA
1 ATATATATAAATATA-ATATAGTTTTTGA
* *
5350761 ATATATATATATATAATATAGTTTTTAA
1 ATATATATAAATATAATATAGTTTTTGA
*
5350789 AAATATATAA
1 ATATATATAA
5350799 TACATATAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
ATATATATAAATATAATATAGTTTTTGA
Found at i:5350794 original size:28 final size:27
Alignment explanation
Indices: 5350742--5350808 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
5350732 ATATATTTAA
* * *
5350742 ATATATATTTAGTTTTTGAATATATAT
1 ATATATATATAGTTTTTAAAAATATAT
5350769 ATATATAATATAGTTTTTAAAAATATAT
1 ATATAT-ATATAGTTTTTAAAAATATAT
*
5350797 A-ATACATATAGT
1 ATATATATATAGT
5350809 GAAACTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.20
27 9 0.26
28 19 0.54
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (27 bp):
ATATATATATAGTTTTTAAAAATATAT
Found at i:5350805 original size:26 final size:28
Alignment explanation
Indices: 5350742--5350808 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
5350732 ATATATTTAA
* *
5350742 ATATAT-ATTTAGTTTTTGAATATATAT
1 ATATATAATATAGTTTTTGAATAAATAT
5350769 ATATATAATATAGTTTTT-AA-AAATAT
1 ATATATAATATAGTTTTTGAATAAATAT
5350795 ATA-ATACATATAGT
1 ATATATA-ATATAGT
5350809 GAAACTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 3 0.08
26 15 0.42
27 8 0.22
28 10 0.28
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (28 bp):
ATATATAATATAGTTTTTGAATAAATAT
Found at i:5361591 original size:19 final size:19
Alignment explanation
Indices: 5361567--5361607 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5361557 TGGATTAATT
*
5361567 GACTATTTTTTCTTAATGA
1 GACTATTTTTCCTTAATGA
5361586 GACTATTTTTCCTTAATGA
1 GACTATTTTTCCTTAATGA
5361605 GAC
1 GAC
5361608 CTTTGGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (19 bp):
GACTATTTTTCCTTAATGA
Found at i:5363450 original size:55 final size:55
Alignment explanation
Indices: 5363350--5363884 Score: 811
Period size: 55 Copynumber: 9.7 Consensus size: 55
5363340 CCCACTACCA
* * * * *
5363350 ATACGAAAATTTATACACTTAGTATGAATTTCCT-AGTTTTGCACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATATAGTGCCC
* * * *
5363405 ATACAGAAATTTATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGTCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
* * * *
5363460 ATACAGAAATTCATCCACTTAATATAAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
* * *
5363515 ATGCGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACCCATACAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
**
5363570 ATATAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
*
5363625 ATACGGAAATTCATCCATTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
*
5363680 ATACGGAAATTCATCCACTTAATATGAATTTCTTAAGTTTACACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
* * * *
5363735 ATACGGAAATTCATACACTAATTATGAATTTCTTAAGTTTACACATATAGTGTCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
**
5363790 ATACAAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
*
5363845 ATACGGAAATTCATCCACTTAGTATAAATTTCTTAAGTTT
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
5363885 TTGCACACTT
Statistics
Matches: 439, Mismatches: 40, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
55 437 1.00
56 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCC
Found at i:5364369 original size:20 final size:21
Alignment explanation
Indices: 5364318--5364369 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
5364308 TGTTTTGAAT
* *
5364318 GGTATCGATAC-CTTCCCTTT
1 GGTATCGATACTCTCCCCTTC
5364338 GGTATCGATACTC-CCCCTTC
1 GGTATCGATACTCTCCCCTTC
5364358 GGTATCGATACT
1 GGTATCGATACT
5364370 GATTGCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTCTCCCCTTC
Found at i:5369655 original size:54 final size:54
Alignment explanation
Indices: 5369573--5369680 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
5369563 ATCGAATTCA
*
5369573 CAATTTTCACCACTACGACAACGTATAAGAGATTAATGGCCTAACTCTCTAACC
1 CAATTTTCACCACTACGACAACATATAAGAGATTAATGGCCTAACTCTCTAACC
* * * *
5369627 CAATTTTTACCACTATGACAACATATAAGCGATTAATGGTCTAACTCTCTAACC
1 CAATTTTCACCACTACGACAACATATAAGAGATTAATGGCCTAACTCTCTAACC
5369681 AGTCCCCAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (54 bp):
CAATTTTCACCACTACGACAACATATAAGAGATTAATGGCCTAACTCTCTAACC
Found at i:5370239 original size:25 final size:25
Alignment explanation
Indices: 5370211--5370276 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
5370201 TATTCGAATA
* *
5370211 AAAAGAAAATAAATATATG-CATAAT
1 AAAATAAAATAAATATAAGCCAT-AT
5370236 AAAATAAGAATAAA-ATAAGCCATAT
1 AAAATAA-AATAAATATAAGCCATAT
5370261 AAAATAAAATAAATAT
1 AAAATAAAATAAATAT
5370277 GCTCTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
24 6 0.17
25 21 0.58
26 9 0.25
ACGTcount: A:0.67, C:0.05, G:0.06, T:0.23
Consensus pattern (25 bp):
AAAATAAAATAAATATAAGCCATAT
Found at i:5370285 original size:24 final size:25
Alignment explanation
Indices: 5370234--5370295 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
5370224 TATATGCATA
5370234 ATAAAATAAGAATAAAATAAGCCAT
1 ATAAAATAAGAATAAAATAAGCCAT
* *
5370259 ATAAAATAA-AAT-AAATATGCTCTT
1 ATAAAATAAGAATAAAATAAGC-CAT
5370283 ATAAAA-AAGAATA
1 ATAAAATAAGAATA
5370296 TATAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.28
24 14 0.44
25 9 0.28
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (25 bp):
ATAAAATAAGAATAAAATAAGCCAT
Found at i:5370415 original size:23 final size:23
Alignment explanation
Indices: 5370389--5370434 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5370379 AACATTAAGC
5370389 TATGAAACTTATTATTATTCATT
1 TATGAAACTTATTATTATTCATT
5370412 TATGAAACTTATTATTATTCATT
1 TATGAAACTTATTATTATTCATT
5370435 ATATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (23 bp):
TATGAAACTTATTATTATTCATT
Found at i:5374740 original size:19 final size:21
Alignment explanation
Indices: 5374716--5374758 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5374706 AACAATTGAA
5374716 AAACAA-AATTAAGAAAAG-G
1 AAACAAGAATTAAGAAAAGAG
*
5374735 AAACAAGAATTAATAAAAGAG
1 AAACAAGAATTAAGAAAAGAG
5374756 AAA
1 AAA
5374759 AGGAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.12
Consensus pattern (21 bp):
AAACAAGAATTAAGAAAAGAG
Found at i:5374766 original size:21 final size:21
Alignment explanation
Indices: 5374721--5374771 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
5374711 TTGAAAAACA
5374721 AAATTAAGAAAAGGAAACAAG
1 AAATTAAGAAAAGGAAACAAG
* *
5374742 -AATTAATAAAAGAGAAA-AGG
1 AAATTAAGAAAAG-GAAACAAG
5374762 AAATTGAAGA
1 AAATT-AAGA
5374772 GGAGAAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 13 0.54
21 8 0.33
22 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.20, T:0.14
Consensus pattern (21 bp):
AAATTAAGAAAAGGAAACAAG
Found at i:5375080 original size:18 final size:19
Alignment explanation
Indices: 5375046--5375081 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5375036 TAGTAAAATT
*
5375046 AAATTATTAATTTCCAAAA
1 AAATTAATAATTTCCAAAA
5375065 AAATTAATAA-TTCCAAA
1 AAATTAATAATTTCCAAA
5375082 CCATTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTAATAATTTCCAAAA
Found at i:5381028 original size:15 final size:15
Alignment explanation
Indices: 5381008--5381045 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
5380998 CAATTTATGA
*
5381008 ATTTGTATTTAGTAC
1 ATTTGTACTTAGTAC
5381023 ATTTGTACTTAGTAC
1 ATTTGTACTTAGTAC
5381038 ATTTGTAC
1 ATTTGTAC
5381046 ATGACTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (15 bp):
ATTTGTACTTAGTAC
Found at i:5387755 original size:2 final size:2
Alignment explanation
Indices: 5387716--5387741 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5387706 AAGGGTAAAT
5387716 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5387742 CACACACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5390790 original size:124 final size:124
Alignment explanation
Indices: 5390442--5390790 Score: 562
Period size: 123 Copynumber: 2.8 Consensus size: 124
5390432 TGAGGACGGC
* * * *
5390442 TGGTTAT-CAGGGATGACACGGTTCCTACGTGATGAGGACG-GCTGGTCGGGGATGACATTGCTC
1 TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGA-GATCTGGTCGGGGATGACACTGCTC
* * *
5390505 ATACTATGATAAGTCTTAGCCATCTAAGGGTGATAAAACTGCTCATACTATGATGAATCT
65 ATACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATAT
* *
5390565 TGGTTATCCATGGTTGACACGGCTCCTACGTGATGA-GAGATCTAGTCGGGGATGACACTGCTCA
1 TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGATGACACTGCTCA
5390629 TACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATAT
66 TACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATAT
*
5390688 TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACTGCTCA
1 TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGATGACACTGCTCA
5390753 TACTATGATGAA-TCTTGGCCATCTAAGGGTGATAACAC
66 TACTATGAT-AAGTCTTGGCCATCTAAGGGTGATAACAC
5390791 AGTTCATGTG
Statistics
Matches: 210, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
122 1 0.00
123 121 0.58
124 86 0.41
125 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (124 bp):
TGGTTATCCAGGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGATGACACTGCTCA
TACTATGATAAGTCTTGGCCATCTAAGGGTGATAACACTGCTCATACTATGATGAATAT
Found at i:5392310 original size:42 final size:42
Alignment explanation
Indices: 5392258--5392337 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
5392248 ATTCTTGTCC
*
5392258 CTTTTTATTTGCTTT-TCTTTTTCTGATTTTTCTTTGTTTTTT
1 CTTTTCATTTGCTTTCTCTTTTTCT-ATTTTTCTTTGTTTTTT
* *
5392300 CTTTTCATTTGCTTTCTCTTTTTCTCTTTTTTTTTGTT
1 CTTTTCATTTGCTTTCTCTTTTTCTATTTTTCTTTGTT
5392338 CTGATTAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 25 0.74
43 9 0.26
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (42 bp):
CTTTTCATTTGCTTTCTCTTTTTCTATTTTTCTTTGTTTTTT
Found at i:5393583 original size:13 final size:13
Alignment explanation
Indices: 5393565--5393609 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
5393555 CTTAAAAATG
5393565 AAATGCAGATGCA
1 AAATGCAGATGCA
*
5393578 AAATGCAAAGACGC-
1 AAATGC--AGATGCA
5393592 AAATGCAGATGCA
1 AAATGCAGATGCA
5393605 AAATG
1 AAATG
5393610 TTGATCCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.19
13 11 0.41
14 6 0.22
15 5 0.19
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:5395862 original size:2 final size:2
Alignment explanation
Indices: 5395855--5395885 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5395845 GGGTAAATTA
*
5395855 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5395886 CAATGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5399295 original size:23 final size:23
Alignment explanation
Indices: 5399265--5399321 Score: 98
Period size: 22 Copynumber: 2.5 Consensus size: 23
5399255 TAGCACGACT
5399265 TCTGCTTTTTAGCATGATCCATC
1 TCTGCTTTTTAGCATGATCCATC
5399288 TCTGC-TTTTAGCATGATCCATC
1 TCTGCTTTTTAGCATGATCCATC
*
5399310 TCTGCTTGTTAG
1 TCTGCTTTTTAG
5399322 ACACGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.44
Consensus pattern (23 bp):
TCTGCTTTTTAGCATGATCCATC
Found at i:5402476 original size:3 final size:3
Alignment explanation
Indices: 5402459--5402501 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
5402449 CAAACATATG
*
5402459 TAA TAA -AA TTAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5402502 TATATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 30 0.86
4 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:5402645 original size:28 final size:28
Alignment explanation
Indices: 5402550--5402645 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 28
5402540 GGCTCTGTCG
* *
5402550 CCTAAATAATATATAGTCGATTA-TACCA
1 CCTAAATAATATATGGTCGA-CACTACCA
* * **
5402578 CCTGATTAATATATGGTCGACACTATTA
1 CCTAAATAATATATGGTCGACACTACCA
* * * *
5402606 ACTAAATGATATATGGTTGACCCTACCA
1 CCTAAATAATATATGGTCGACACTACCA
*
5402634 CCTAAGTAATAT
1 CCTAAATAATAT
5402646 TGTGATTATA
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
27 1 0.02
28 49 0.98
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (28 bp):
CCTAAATAATATATGGTCGACACTACCA
Found at i:5403793 original size:9 final size:9
Alignment explanation
Indices: 5403760--5403792 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5403750 TTGATAATAT
5403760 ATTTTTTAA
1 ATTTTTTAA
*
5403769 AATTTTTAA
1 ATTTTTTAA
5403778 ATTTTTT-A
1 ATTTTTTAA
5403786 ATTTTTT
1 ATTTTTT
5403793 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:5404172 original size:23 final size:23
Alignment explanation
Indices: 5404142--5404201 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
5404132 TAGCACGACT
5404142 TCTGCTTTTTAGCATGATCCATC
1 TCTGCTTTTTAGCATGATCCATC
5404165 TCTGCTTTTTAGCATGATCCATC
1 TCTGCTTTTTAGCATGATCCATC
*
5404188 TCTGCTTGTTAGCA
1 TCTGCTTTTTAGCA
5404202 CGATTTTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (23 bp):
TCTGCTTTTTAGCATGATCCATC
Found at i:5416970 original size:44 final size:44
Alignment explanation
Indices: 5416920--5417004 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
5416910 AACTGTACTT
* *
5416920 TAGTGTATTTTTATACACTAGTATCGGTAC-TAGTATCGATATTG
1 TAGTGTATTTTTACACACTAGTATCGATACAT-GTATCGATATTG
* *
5416964 TAGTGTATTTTTACACATTGGTATCGATACATGTATCGATA
1 TAGTGTATTTTTACACACTAGTATCGATACATGTATCGATA
5417005 CCACTTGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (44 bp):
TAGTGTATTTTTACACACTAGTATCGATACATGTATCGATATTG
Found at i:5419866 original size:20 final size:20
Alignment explanation
Indices: 5419812--5419879 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
5419802 ATACTCTTAA
5419812 CGATACTATAAGAACAATAT
1 CGATACTATAAGAACAATAT
* *
5419832 C-AGTACT-TGACGAACATTAT
1 CGA-TACTAT-AAGAACAATAT
* *
5419852 CGATACTATATGAACAATAG
1 CGATACTATAAGAACAATAT
5419872 CGATACTA
1 CGATACTA
5419880 AATGCACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
CGATACTATAAGAACAATAT
Found at i:5429589 original size:20 final size:22
Alignment explanation
Indices: 5429548--5429589 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5429538 ATGATGTAAT
5429548 ATGTTGGAATTTAGAAGCTAGA
1 ATGTTGGAATTTAGAAGCTAGA
*
5429570 ATGTT-GAATTT-GATGCTAGA
1 ATGTTGGAATTTAGAAGCTAGA
5429590 GTGTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (22 bp):
ATGTTGGAATTTAGAAGCTAGA
Found at i:5430829 original size:65 final size:65
Alignment explanation
Indices: 5430725--5431165 Score: 603
Period size: 65 Copynumber: 6.8 Consensus size: 65
5430715 ATGATACGAC
* * * *
5430725 ACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGATGGATTAATAATTGAATACTGT
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
* * * *
5430790 ACAGACCACGCATATGATTCATGTATCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTAT
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
* * * * * *
5430855 ACAAACTACTCATATGAATCATGTACCTTTGTGGTGTATGAGGTGGAGTGATAATTGAAAATTGT
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
* *
5430920 ACAGACTACTCATATGACTCATGTACCTTTGTGGTGCATGAAGTGGAGTGATAATTGAATACTGT
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
* * * *
5430985 ACAGACCACTCATATGACTCATGTTCCTTTGTGTTGCATGAAGTAGAGTGATAATTGAATACTGT
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
* * ** * *
5431050 ACAAACCACTCATATGACTCATGTGCCTTCATGGTGCATGAGGTGGAGTGATACTTGAATATTGT
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
** * * *
5431115 ATTGACCACTCATATGGCTCATGTACCATTGTGATGCATGAGGTGGAGTGA
1 ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGA
5431166 CTATATGATA
Statistics
Matches: 331, Mismatches: 45, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 331 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (65 bp):
ACAGACCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGT
Found at i:5431225 original size:25 final size:25
Alignment explanation
Indices: 5431197--5431276 Score: 151
Period size: 25 Copynumber: 3.2 Consensus size: 25
5431187 GGCACCTATG
5431197 GTGCAATTCTAAGAAGCACTTTTAA
1 GTGCAATTCTAAGAAGCACTTTTAA
5431222 GTGCAATTCTAAGAAGCACTTTTAA
1 GTGCAATTCTAAGAAGCACTTTTAA
*
5431247 GTGCAATTCTACGAAGCACTTTTAA
1 GTGCAATTCTAAGAAGCACTTTTAA
5431272 GTGCA
1 GTGCA
5431277 TACAAGTGTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (25 bp):
GTGCAATTCTAAGAAGCACTTTTAA
Found at i:5434193 original size:12 final size:12
Alignment explanation
Indices: 5434151--5434202 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
5434141 AACTCAAAGC
* *
5434151 AAAAAACAAAAG
1 AAAATACAAGAG
5434163 AAATATAC-A-AG
1 AAA-ATACAAGAG
*
5434174 AAACTACAAGAG
1 AAAATACAAGAG
5434186 AAAATACAAGAG
1 AAAATACAAGAG
5434198 AAAAT
1 AAAAT
5434203 CAGAGCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.09
11 6 0.18
12 22 0.65
13 3 0.09
ACGTcount: A:0.69, C:0.10, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAATACAAGAG
Found at i:5434200 original size:35 final size:35
Alignment explanation
Indices: 5434130--5434200 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
5434120 CTAGGACTAT
*
5434130 ATATGCAAGTAAACTCAAAGCAAAAAACAAAAGAA
1 ATATACAAGTAAACTCAAAGCAAAAAACAAAAGAA
* *
5434165 ATATACAAG-AAACTACAAGAG-AAAATACAAGAGAA
1 ATATACAAGTAAACT-CAA-AGCAAAAAACAAAAGAA
5434200 A
1 A
5434201 ATCAGAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 5 0.16
35 24 0.77
36 2 0.06
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (35 bp):
ATATACAAGTAAACTCAAAGCAAAAAACAAAAGAA
Found at i:5434801 original size:18 final size:17
Alignment explanation
Indices: 5434780--5434836 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
5434770 TTTAATTCCC
5434780 ATTTTAATTTAATTTTTT
1 ATTTT-ATTTAATTTTTT
*
5434798 ATTTTATTTTATTTTTT
1 ATTTTATTTAATTTTTT
5434815 AATTATT-TTT-ATTTCTTT
1 -ATT-TTATTTAATTT-TTT
5434833 ATTT
1 ATTT
5434837 CTTATTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 1 0.03
17 18 0.51
18 14 0.40
19 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTATTTAATTTTTT
Found at i:5434920 original size:19 final size:21
Alignment explanation
Indices: 5434896--5434940 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
5434886 AATTTAGCCA
5434896 TTTTTCTCTTTTT-ATTC-AT
1 TTTTTCTCTTTTTAATTCAAT
*
5434915 TTTTTCTTTTTTTAATTCAAT
1 TTTTTCTCTTTTTAATTCAAT
5434936 TTTTT
1 TTTTT
5434941 ATTTCTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 4 0.17
21 7 0.30
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCTCTTTTTAATTCAAT
Found at i:5434927 original size:20 final size:21
Alignment explanation
Indices: 5434904--5434964 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
5434894 CATTTTTCTC
*
5434904 TTTTTATTC-ATTTTTTCTTT
1 TTTTTATTCAATTTTTTATTT
*
5434924 TTTTAATTCAATTTTTTATTT
1 TTTTTATTCAATTTTTTATTT
* **
5434945 CTTTTACTTTTATTTTTTAT
1 TTTTTA-TTCAATTTTTTAT
5434965 CTACATTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 8 0.24
21 14 0.42
22 11 0.33
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTATTCAATTTTTTATTT
Found at i:5434949 original size:22 final size:21
Alignment explanation
Indices: 5434902--5434964 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
5434892 GCCATTTTTC
* *
5434902 TCTTTTTATTCATTTTTTCTT
1 TCTTTTAATTCATTTTTTATT
5434923 T-TTTTAATTCAATTTTTTATT
1 TCTTTTAATTC-ATTTTTTATT
* *
5434944 TCTTTTACTTTTATTTTTTAT
1 TCTTTTA-ATTCATTTTTTAT
5434965 CTACATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.23
21 11 0.31
22 14 0.40
23 2 0.06
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (21 bp):
TCTTTTAATTCATTTTTTATT
Found at i:5441899 original size:21 final size:21
Alignment explanation
Indices: 5441875--5441923 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
5441865 CACAGCGTTG
*
5441875 AGGAGGCAACTTAGGAAACCA
1 AGGAGGAAACTTAGGAAACCA
5441896 AGGAGGAAACTTAGGAAACCA
1 AGGAGGAAACTTAGGAAACCA
5441917 AGGAGGA
1 AGGAGGA
5441924 CATACAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.14, G:0.33, T:0.08
Consensus pattern (21 bp):
AGGAGGAAACTTAGGAAACCA
Found at i:5444463 original size:5 final size:5
Alignment explanation
Indices: 5444453--5444504 Score: 70
Period size: 5 Copynumber: 10.0 Consensus size: 5
5444443 TAATAAAAAT
5444453 TAATA TAATA TAATA TACAT- TATATA TAAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TA-ATA TA-ATA T-AATA TAATA TAATA TAATA
5444500 TAATA
1 TAATA
5444505 AGCAAATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
5 35 0.81
6 7 0.16
7 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:5444487 original size:22 final size:20
Alignment explanation
Indices: 5444451--5444504 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
5444441 AGTAATAAAA
5444451 ATTAATATAATATAATATAC
1 ATTAATATAATATAATATAC
5444471 ATTATATATAAATATAATATA-
1 ATTA-ATAT-AATATAATATAC
5444492 ATATAATATAATA
1 AT-TAATATAATA
5444505 AGCAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.26
21 10 0.32
22 13 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTAATATAATATAATATAC
Found at i:5445972 original size:9 final size:9
Alignment explanation
Indices: 5445958--5445985 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5445948 ATTATAGTGA
5445958 ATTTAATTT
1 ATTTAATTT
5445967 ATTTAATTT
1 ATTTAATTT
5445976 ATTTAATTT
1 ATTTAATTT
5445985 A
1 A
5445986 ACCCCTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTAATTT
Found at i:5446137 original size:20 final size:20
Alignment explanation
Indices: 5446095--5446137 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5446085 TTTAAACCCC
*
5446095 AAATCTCAAACCTATACCAT
1 AAATCTCAAACCTAAACCAT
*
5446115 AAATCTTAAACCTTAAACC-T
1 AAATCTCAAACC-TAAACCAT
5446135 AAA
1 AAA
5446138 AATTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATCTCAAACCTAAACCAT
Found at i:5446626 original size:12 final size:12
Alignment explanation
Indices: 5446609--5446638 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5446599 GAACAAACTT
*
5446609 GTTTATGAGGTC
1 GTTTATGAGCTC
5446621 GTTTATGAGCTC
1 GTTTATGAGCTC
5446633 GTTTAT
1 GTTTAT
5446639 CGACTCTTTC
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:0.17, C:0.10, G:0.27, T:0.47
Consensus pattern (12 bp):
GTTTATGAGCTC
Found at i:5468485 original size:30 final size:30
Alignment explanation
Indices: 5468427--5468519 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
5468417 AAATGCTACG
*
5468427 CTCTCAACCCGTAAA-ATCACACATCAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
* *
5468456 CTCTCAACCCGAAAACATTACACAACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
* * * *
5468486 CTCTTAACTCGTAAACATCACCCGACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
5468516 CTCT
1 CTCT
5468520 TATCTTTGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 14 0.26
30 40 0.74
ACGTcount: A:0.37, C:0.38, G:0.04, T:0.22
Consensus pattern (30 bp):
CTCTCAACCCGTAAACATCACACAACAATC
Found at i:5468582 original size:16 final size:15
Alignment explanation
Indices: 5468561--5468592 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5468551 CGTTGCAAGG
5468561 TAATTTTTTTAATATA
1 TAATTTTTTT-ATATA
5468577 TAATTTTTTTATATA
1 TAATTTTTTTATATA
5468592 T
1 T
5468593 GAATATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTATATA
Found at i:5474402 original size:20 final size:20
Alignment explanation
Indices: 5474379--5474445 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
5474369 ATAACTGCAA
5474379 AAAAAATTAAATAAAATACT
1 AAAAAATTAAATAAAATACT
5474399 AAAAAA-TAAAT--AATAC-
1 AAAAAATTAAATAAAATACT
*
5474415 -AATAATTAAA-AAAATACT
1 AAAAAATTAAATAAAATACT
5474433 AAAAAAATTAAAT
1 -AAAAAATTAAAT
5474446 GGAATATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
15 4 0.11
16 4 0.11
17 10 0.26
19 5 0.13
20 15 0.39
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATTAAATAAAATACT
Found at i:5474828 original size:51 final size:51
Alignment explanation
Indices: 5474731--5474838 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
5474721 CCATGCACCG
* * *
5474731 CGCCTTACCTCACGTGGCGCCACATCAGCGTAATACGCGATGCATGAGCCA
1 CGCCTTACCTCACGTGGCGACACATCAGCGTAAGACGCGATACATGAGCCA
* * * * *
5474782 CGCCTTAACC-CACGTGGCGACACATTAGCGTAAGGCGCGGTACATGAGTCG
1 CGCCTT-ACCTCACGTGGCGACACATCAGCGTAAGACGCGATACATGAGCCA
5474833 CGCCTT
1 CGCCTT
5474839 TCTAAAGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 45 0.94
52 3 0.06
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (51 bp):
CGCCTTACCTCACGTGGCGACACATCAGCGTAAGACGCGATACATGAGCCA
Found at i:5488025 original size:30 final size:30
Alignment explanation
Indices: 5487966--5488055 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
5487956 GACTAAACAA
* *
5487966 CAAAAATAGAAAATTTAAAGGATTAAAATAG
1 CAAAAATAGAAAATTT-AGGGACTAAAATAG
*
5487997 CAAAAATAAAAAATTTAGGGACTAAAATAG
1 CAAAAATAGAAAATTTAGGGACTAAAATAG
* * *
5488027 -ATAAAATAGAAACTTAAGGGACCAAAATA
1 CA-AAAATAGAAAATTTAGGGACTAAAATA
5488056 TAAAATAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.02
30 35 0.69
31 15 0.29
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (30 bp):
CAAAAATAGAAAATTTAGGGACTAAAATAG
Found at i:5489169 original size:11 final size:12
Alignment explanation
Indices: 5489144--5489179 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
5489134 ATGCTCCTGG
5489144 TGGGCTTGTAAT
1 TGGGCTTGTAAT
5489156 TGGGCTTG-AAT
1 TGGGCTTGTAAT
5489167 TGGTGCTTGTAAT
1 TGG-GCTTGTAAT
5489180 ATAGGCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 13 0.59
13 3 0.14
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (12 bp):
TGGGCTTGTAAT
Found at i:5489245 original size:3 final size:3
Alignment explanation
Indices: 5489229--5489305 Score: 104
Period size: 3 Copynumber: 25.7 Consensus size: 3
5489219 ATGTAAAATG
5489229 TAA TAA TCAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5489274 TAA TAA TAA TAA TTA TAT TAA TTAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TA
5489306 TAAAAAAGAC
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 57 0.86
4 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5489745 original size:129 final size:129
Alignment explanation
Indices: 5489611--5489847 Score: 341
Period size: 129 Copynumber: 1.8 Consensus size: 129
5489601 TTCCTACACA
* * * *
5489611 ATGAGGACTGCTGGTTATCTAGGGGTGACACGGCTTCTACG-GATGAGGAGGTCTGGTCGGGGAT
1 ATGAGGAC-GCTGGTTATCTAGGGGTGACACGGATCCTACGTGATGAGGAGGTCTAGTCAGGGAT
* *
5489675 GACACGGTTCCTACGCGATGAGGAAGGCATACCATCTTTAGGAATGATAACACTGTTCCTACGTG
65 GACACAGTTCCTACGCGATGAGGAAGACATACCATCTTTAGGAATGATAACACTGTTCCTACGTG
* * *
5489740 ATGAGGACGCTGTTTATCTAGGGTTGACGCGGATCCTACGTGATGAGGAGGTCTAGTCAGGGATG
1 ATGAGGACGCTGGTTATCTAGGGGTGACACGGATCCTACGTGATGAGGAGGTCTAGTCAGGGATG
* * * *
5489805 ACACAGTTCCTGCGTGATGAGGACGACATGCCATCTTTAGGAA
66 ACACAGTTCCTACGCGATGAGGAAGACATACCATCTTTAGGAA
5489848 GGGATTTTGG
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
128 27 0.29
129 67 0.71
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (129 bp):
ATGAGGACGCTGGTTATCTAGGGGTGACACGGATCCTACGTGATGAGGAGGTCTAGTCAGGGATG
ACACAGTTCCTACGCGATGAGGAAGACATACCATCTTTAGGAATGATAACACTGTTCCTACGTG
Found at i:5490020 original size:64 final size:64
Alignment explanation
Indices: 5489889--5490028 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
5489879 AGATGATGCT
* *
5489889 TCAAGAGAGACAAAATTCGTTTCAAGGAAACGACTCAAAGATATGTGTTTCATGAGAAACTACC
1 TCAAGAGAGACAAAATTCGTTTCAAGGAAACGACTCAAAGATATGTGTTTCAAGAAAAACTACC
* * * * * * **
5489953 TCAAGGGAGACAAGATTTGTTTCAAATGAAACAGACTCAAAGAT-T-TTTTTCAAGAAAAATTGT
1 TCAAGAGAGACAAAATTCGTTTC-AAGGAAAC-GACTCAAAGATATGTGTTTCAAGAAAAACTAC
5490016 C
64 C
5490017 TCAAGAGAGACA
1 TCAAGAGAGACA
5490029 GACTCAAAGA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
64 44 0.70
65 8 0.13
66 11 0.17
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (64 bp):
TCAAGAGAGACAAAATTCGTTTCAAGGAAACGACTCAAAGATATGTGTTTCAAGAAAAACTACC
Found at i:5498026 original size:30 final size:30
Alignment explanation
Indices: 5497992--5498049 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5497982 AAACCCTAAA
*
5497992 GGACTAAAATAGCCAAAAACAAAAACTTAG
1 GGACTAAAATAGCAAAAAACAAAAACTTAG
* *
5498022 GGACTAAAATAGTAAAAAACCAAAACTT
1 GGACTAAAATAGCAAAAAACAAAAACTT
5498050 CATGGGCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.16
Consensus pattern (30 bp):
GGACTAAAATAGCAAAAAACAAAAACTTAG
Found at i:5498062 original size:31 final size:30
Alignment explanation
Indices: 5497992--5498062 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
5497982 AAACCCTAAA
* *
5497992 GGACTAAAATAGCCAAAAACAAAAACTTAG
1 GGACCAAAATAGCAAAAAACAAAAACTTAG
* * *
5498022 GGACTAAAATAGTAAAAAACCAAAACTTCATG
1 GGACCAAAATAGCAAAAAACAAAAACTT-A-G
5498054 GG-CCAAAAT
1 GGACCAAAAT
5498063 GGATACAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 25 0.71
31 7 0.20
32 3 0.09
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.15
Consensus pattern (30 bp):
GGACCAAAATAGCAAAAAACAAAAACTTAG
Found at i:5499521 original size:12 final size:12
Alignment explanation
Indices: 5499504--5499560 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
5499494 ATGCTCCTGG
5499504 TGGGCTTGTAAT
1 TGGGCTTGTAAT
5499516 TGGGCTTG-AAT
1 TGGGCTTGTAAT
*
5499527 TAGTGCTTGTAAT
1 T-GGGCTTGTAAT
*
5499540 CTGGGCCTGTGTATT
1 -TGGG-CT-TGTAAT
5499555 TGGGCT
1 TGGGCT
5499561 CCAGGTGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.11
12 14 0.38
13 7 0.19
14 7 0.19
15 5 0.14
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.40
Consensus pattern (12 bp):
TGGGCTTGTAAT
Found at i:5499603 original size:3 final size:3
Alignment explanation
Indices: 5499588--5499642 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
5499578 AATGTAAAAT
* *
5499588 ATA ATA ATCA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA GTT
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
5499635 ATA ATA AT
1 ATA ATA AT
5499643 TAATTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5499653 original size:13 final size:12
Alignment explanation
Indices: 5499588--5499654 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
5499578 AATGTAAAAT
*
5499588 ATAATAATCAATA
1 ATAATAATTAA-A
5499601 ATAATAA-TAATA
1 ATAATAATTAA-A
*
5499613 ATAATAATAATAA
1 ATAATAATTA-AA
* *
5499626 ATAATAGTTATA
1 ATAATAATTAAA
5499638 ATAATTAATTAAA
1 ATAA-TAATTAAA
5499651 ATAA
1 ATAA
5499655 AATAGAAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 16 0.36
13 27 0.61
14 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (12 bp):
ATAATAATTAAA
Done.