Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 17 of 20
Found at i:6895993 original size:60 final size:60
Alignment explanation
Indices: 6895896--6896016 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
6895886 CTGGAACGGA
*
6895896 AGGTCCTTGGCTCCTTATAAGCAGGTGTGCTGTACACCCCTATAAGCACGTTTGCTGGGG
1 AGGTCCTTGGCTCCTTATAAGCAGGTGTGCTGCACACCCCTATAAGCACGTTTGCTGGGG
*
6895956 AGGTCCTTGGCTCCTTATAAGCAGGTGTGCTGCACACCCTTATAAGCACGTTTGCTGGGG
1 AGGTCCTTGGCTCCTTATAAGCAGGTGTGCTGCACACCCCTATAAGCACGTTTGCTGGGG
6896016 A
1 A
6896017 AAAGGTAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (60 bp):
AGGTCCTTGGCTCCTTATAAGCAGGTGTGCTGCACACCCCTATAAGCACGTTTGCTGGGG
Found at i:6897819 original size:11 final size:11
Alignment explanation
Indices: 6897803--6897832 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
6897793 AATCGATAAA
6897803 GTTCATCTATT
1 GTTCATCTATT
6897814 GTTCATCTATT
1 GTTCATCTATT
6897825 GTTCATCT
1 GTTCATCT
6897833 TGATTCAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.10, T:0.53
Consensus pattern (11 bp):
GTTCATCTATT
Found at i:6905592 original size:13 final size:13
Alignment explanation
Indices: 6905574--6905606 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6905564 AACTTCGGAC
6905574 AAAAAAAAACAGA
1 AAAAAAAAACAGA
*
6905587 AAAAAAAAAGAGA
1 AAAAAAAAACAGA
6905600 AAAAAAA
1 AAAAAAA
6905607 TGGGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAGA
Found at i:6919535 original size:18 final size:17
Alignment explanation
Indices: 6919508--6919550 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
6919498 TTTTTAATTT
*
6919508 TATTTTTAATCAAATAAA
1 TATTTATAAT-AAATAAA
* *
6919526 TATTTATAATTAATAAT
1 TATTTATAATAAATAAA
6919543 TATTTATA
1 TATTTATA
6919551 TTTTATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTTATAATAAATAAA
Found at i:6922869 original size:15 final size:16
Alignment explanation
Indices: 6922849--6922883 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6922839 TTGTGATTTC
6922849 TTTTTTTTGTTTTGT-
1 TTTTTTTTGTTTTGTG
*
6922864 TTTTTTTTTTTTTGTG
1 TTTTTTTTGTTTTGTG
6922880 TTTT
1 TTTT
6922884 CAGTTACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (16 bp):
TTTTTTTTGTTTTGTG
Found at i:6922871 original size:17 final size:17
Alignment explanation
Indices: 6922839--6922883 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
6922829 ACATGGTATC
6922839 TTGTGATTTCTTTTTTTTGT
1 TTGTG-TTT-TTTTTTTT-T
6922859 TT-TGTTTTTTTTTTTT
1 TTGTGTTTTTTTTTTTT
6922875 TTGTGTTTT
1 TTGTGTTTT
6922884 CAGTTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 14 0.58
18 3 0.12
19 2 0.08
20 2 0.08
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.82
Consensus pattern (17 bp):
TTGTGTTTTTTTTTTTT
Found at i:6924748 original size:2 final size:2
Alignment explanation
Indices: 6924741--6924773 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6924731 TAATTAGGAA
6924741 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
6924774 AAATTTTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6932569 original size:14 final size:14
Alignment explanation
Indices: 6932550--6932578 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6932540 GAATGACTGG
6932550 TTTATGCATGTCAT
1 TTTATGCATGTCAT
6932564 TTTATGCATGTCAT
1 TTTATGCATGTCAT
6932578 T
1 T
6932579 AGCAACATTG
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:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTATGCATGTCAT
Found at i:6956640 original size:3 final size:3
Alignment explanation
Indices: 6956634--6956673 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
6956624 ACTACTAAAA
6956634 TCT TCT T-T TC- TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
6956674 CTCTCTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:6962976 original size:39 final size:39
Alignment explanation
Indices: 6962920--6962999 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
6962910 ATACACGATT
*
6962920 AATTGATGCAAACGTAGAAAAGCCAAAGAGCGATGATAA
1 AATTGATGCAAAAGTAGAAAAGCCAAAGAGCGATGATAA
6962959 AATTGATGCAAAAGTAGAAAAGCCAAAGAGCGATGATAA
1 AATTGATGCAAAAGTAGAAAAGCCAAAGAGCGATGATAA
6962998 AA
1 AA
6963000 AGATCAGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.51, C:0.11, G:0.23, T:0.15
Consensus pattern (39 bp):
AATTGATGCAAAAGTAGAAAAGCCAAAGAGCGATGATAA
Found at i:6963760 original size:35 final size:35
Alignment explanation
Indices: 6963714--6963785 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
6963704 GTTCTCTTTC
6963714 ATTGCTTTACTATTTTCCCATTTCCTCCCTTATCA
1 ATTGCTTTACTATTTTCCCATTTCCTCCCTTATCA
*
6963749 ATTGCTTTACTATTTTTCCATTTCCTCCCTTATCA
1 ATTGCTTTACTATTTTCCCATTTCCTCCCTTATCA
6963784 AT
1 AT
6963786 CTCAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.18, C:0.29, G:0.03, T:0.50
Consensus pattern (35 bp):
ATTGCTTTACTATTTTCCCATTTCCTCCCTTATCA
Found at i:6977757 original size:2 final size:2
Alignment explanation
Indices: 6977752--6977813 Score: 90
Period size: 2 Copynumber: 31.0 Consensus size: 2
6977742 TTATAGTGTG
6977752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
6977794 TC TCA AA T- TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA
6977814 ATAAAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6985048 original size:35 final size:35
Alignment explanation
Indices: 6984997--6985097 Score: 157
Period size: 35 Copynumber: 2.9 Consensus size: 35
6984987 CAAAGCTCCC
*
6984997 AGTTCCTACTCCATTCTTGTTAGATTGTATCCCTT
1 AGTTCCTACTCAATTCTTGTTAGATTGTATCCCTT
* *
6985032 AGTTCCTACTCAATTCTTGTCAGATTGTATCCGTT
1 AGTTCCTACTCAATTCTTGTTAGATTGTATCCCTT
* *
6985067 AGTTCCTACTCTATTATTGTTAGATTGTATC
1 AGTTCCTACTCAATTCTTGTTAGATTGTATC
6985098 TCATGCTCCC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.46
Consensus pattern (35 bp):
AGTTCCTACTCAATTCTTGTTAGATTGTATCCCTT
Found at i:7030392 original size:2 final size:2
Alignment explanation
Indices: 7030385--7030415 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7030375 TTAGGGCTTG
7030385 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
7030416 GACTATTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:7031477 original size:134 final size:136
Alignment explanation
Indices: 7031285--7031536 Score: 341
Period size: 134 Copynumber: 1.9 Consensus size: 136
7031275 GATTTTTTAA
* * *
7031285 AAAAATAAAAAAGTGAAATGCAAGTGTAATGTCGTACTAAGTCTGTAATTGATTTTATCTATGAC
1 AAAAATAAAAAAGTGAAATGCAAGTGCAATGTCGTACGAAGTCTGTAATTGACTTTATCTATGAC
*
7031350 AACAGACTTGAATTGATATTCATGTAATCTTTTTCTA-TCAATCAATGACTTATACTTCGTTCTT
66 AACAGACTTGAATTGATATTCATGTAATCTCTTTC-AGTCAATCAATGACTTATACTTCGTTCTT
7031414 TTTTTTT
130 TTTTTTT
* * * * *
7031421 AAAAA-AAAAAA-TGAAATGTAATTGCAATGTCGTATCGAA-TTTGTGATTGACTTTATCTATTA
1 AAAAATAAAAAAGTGAAATGCAAGTGCAATGTCGTA-CGAAGTCTGTAATTGACTTTATCTATGA
* * * *
7031483 TAGCAGATTTGAATTGATATTCATGTAATCTCTTTCAGTGAATCAATGACTTAT
65 CAACAGACTTGAATTGATATTCATGTAATCTCTTTCAGTCAATCAATGACTTAT
7031537 GCTTTTTTTG
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
133 1 0.01
134 86 0.85
135 9 0.09
136 5 0.05
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (136 bp):
AAAAATAAAAAAGTGAAATGCAAGTGCAATGTCGTACGAAGTCTGTAATTGACTTTATCTATGAC
AACAGACTTGAATTGATATTCATGTAATCTCTTTCAGTCAATCAATGACTTATACTTCGTTCTTT
TTTTTT
Found at i:7035747 original size:15 final size:16
Alignment explanation
Indices: 7035721--7035754 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
7035711 GCAGACTCTT
7035721 TGGCTAAAGCTTGGTG
1 TGGCTAAAGCTTGGTG
7035737 TGGCT-AAGCTTGGTG
1 TGGCTAAAGCTTGGTG
7035752 TGG
1 TGG
7035755 ACAGGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.15, C:0.12, G:0.41, T:0.32
Consensus pattern (16 bp):
TGGCTAAAGCTTGGTG
Found at i:7037966 original size:2 final size:2
Alignment explanation
Indices: 7037953--7037987 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7037943 ATTTTGGACC
*
7037953 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7037988 GGTTGTGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7042694 original size:228 final size:227
Alignment explanation
Indices: 7042232--7042663 Score: 512
Period size: 227 Copynumber: 1.9 Consensus size: 227
7042222 CTCCGTCTTT
* * * * * * **
7042232 GTGGTGGTATGCAGATTTTTGTGAAGACGCTGACTGGTAAGACCATTACTTTGCAAGTTGAAAGC
1 GTGGTGGGATGCAAATTTTTATGAAGACGCTGACAGGAAAGACCATCACCCTGCAAGTTGAAAGC
* * * *
7042297 TCCAACACAGTTGACAATGTCAAGGCCAAAATTCAAGACAATGAAGGTATCCTCCAGACCAGCAG
66 TCCAACACAGTTGACAATGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCCCAGACCAGCAG
* * * * * * *
7042362 AGGCTTATTTTTGCTGGTAAGCAGCTTAAGGATGGGAAGACCCTTGCAGATTACAACATTCAAAA
131 AGGCTGATCTTTGCAGGGAAGCAACTTAAGGATGGGAAGACCCTGGCAGACTACAACATTCAAAA
* * *
7042427 GGAGTCAACCCTCCACTTGGTGTTGCGCCTTC
196 GGAATCAACCCTCCACTTGGTCTTGCGCCTCC
*
7042459 GTGGTGGGATGCAAATTTTTATGAAGAC-CTTGACAGGAAAGACCATCACCCTGGAAGTTGAAAG
1 GTGGTGGGATGCAAATTTTTATGAAGACGC-TGACAGGAAAGACCATCACCCTGCAAGTTGAAAG
* * * * * *
7042523 -TTCAGACACCA-TTGATAATGTTAAGGCCAAGATCCAGGATAAGGAAGGGATCCCCCAAGACCA
65 CTCCA-ACA-CAGTTGACAATGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCCC-AGACCA
*
7042586 GCAGAGGCTGATCTTTGCAGGGAAGCAACTTGAA-GATGGGAGGACCCTGGCAGACTACAACATT
127 GCAGAGGCTGATCTTTGCAGGGAAGCAACTT-AAGGATGGGAAGACCCTGGCAGACTACAACATT
*
7042650 CAGAAGGAATCAAC
191 CAAAAGGAATCAAC
7042664 TTGGCACCTT
Statistics
Matches: 171, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
226 4 0.02
227 92 0.54
228 73 0.43
229 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (227 bp):
GTGGTGGGATGCAAATTTTTATGAAGACGCTGACAGGAAAGACCATCACCCTGCAAGTTGAAAGC
TCCAACACAGTTGACAATGTCAAGGCCAAAATCCAAGACAAGGAAGGGATCCCCCAGACCAGCAG
AGGCTGATCTTTGCAGGGAAGCAACTTAAGGATGGGAAGACCCTGGCAGACTACAACATTCAAAA
GGAATCAACCCTCCACTTGGTCTTGCGCCTCC
Found at i:7046348 original size:227 final size:226
Alignment explanation
Indices: 7045511--7046553 Score: 864
Period size: 227 Copynumber: 4.6 Consensus size: 226
7045501 TTGACAACAG
* * * * * *
7045511 ATGCAGATCTTTGTGAAAACCTT-ACTGGCAAGACCATCACCCTCGAGGTGGAAAGCTCTGACAC
1 ATGCAGATTTTTGTGAAAACCTTCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACAC
* * * *
7045575 TATGTGATAATGTCAAAGCCAAGATCCA-GACAA-GAGGG-ATCCCGCCAGACCAACAGAGGCTT
66 CAT-TGACAATGTCAAAGCAAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGG-TT
* * * * * * * * * *
7045637 -ATCTTTGCTGGTAACAGCTAGAGGATGGCCGCACCCTTGCTGATTACAATAT-CAGAAGGAGTC
129 GATCTTTGCTGGAAACAGCTAGAAGATGGCAGGACACTTGCAGACTACAACATCCAAAAAGAGTC
* * *
7045700 CACCCTCCCACCTT-GTCCTT-CGTCT--TAGGTGGC
194 AACCCT-CCA-TTTGGT-CTTGCGTCTCGT-GGAGGC
* * * * * *
7045733 ATGCAGATATTTGTGAAAA-CTCTCACCGGGAAAACCATCCACTTTGGAGGTGGAGAGTTCGGAT
1 ATGCAGATTTTTGTGAAAACCT-TCACTGGGAAAACCAT-CACCTTGGAGGTGGAGAGCTCTGAC
* * * * *
7045797 ACCATCGACAATGTGAAGGCAAAGATTCAGGACAAGGAGGGTATCCCACCAGACCAGCAGAGGTT
64 ACCATTGACAATGTCAAAGCAAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTT
* * * * * * * *
7045862 AATTTTTGCTGGAAAACAGCTTGAAGATGGCAGAACCCTTGCAGACTATAACATCCAGAAGGAGT
129 GATCTTTGCTGG-AAACAGCTAGAAGATGGCAGGACACTTGCAGACTACAACATCCAAAAAGAGT
* * *
7045927 CAACCCTCCATTTGGTTTTGCGACTCCGTGGTGGC
193 CAACCCTCCATTTGGTCTTGCGTCT-CGTGGAGGC
* * ** * * * * * * *
7045962 ATGCAAATTTTGTGTCAAGCCCCTCACT--GAAAGACTATTACCTTGGAAGTTGAGAGTTCTGAT
1 ATGCAGATTTT-TGTGAAAACCTTCACTGGGAAA-ACCATCACCTTGGAGGTGGAGAGCTCTGAC
* * * * * *
7046025 ACCATTGACAATGTAAAAGCTAAGATCCAGGACAAGGAAGGTATCCCTCCAGATCAACAGAGGCT
64 ACCATTGACAATGTCAAAGCAAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTT
* * * * * * * *
7046090 GATATTTGCCGGCAAACAGTTGGAGGATGGGAGGACACTTGCAGATTACAATATCCAAAAAGAGT
129 GATCTTTGCTGG-AAACAGCTAGAAGATGGCAGGACACTTGCAGACTACAACATCCAAAAAGAGT
* *
7046155 CAACCCTCCATTTGG-CTGGCGTCTGCGTGGAGGA
193 CAACCCTCCATTTGGTCTTGCGTCT-CGTGGAGGC
* * *
7046189 ATGCAGATTTTTGTGAAAACCTTGACTGGTAAAACCATCACTTTGGAGGTGGAGAGCTCTGACAC
1 ATGCAGATTTTTGTGAAAACCTTCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACAC
* * * * * *
7046254 AATTGACAACGTCAAAGCCAAGATCCAAGATAAGGAGGGTATCCCACCTGACCAACAGAGGTTGA
66 CATTGACAATGTCAAAGCAAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTGA
* * *
7046319 T-TTTCGCTGGAAAGCAGCTCGAAGATGGGAGGACACTTGCAGACTATAACATCC-AAAAGA-TC
131 TCTTT-GCTGGAAA-CAGCTAGAAGATGGCAGGACACTTGCAGACTACAACATCCAAAAAGAGTC
* * * * * *
7046381 AACCCTGCATTTGGTTTTGCGCCTTAGAGGAGGG
194 AACCCTCCATTTGGTCTTGCGTC-TCGTGGAGGC
* * * * * *
7046415 ATGCAGATATTTT-TCAAGACCTTGACTGGGAAAACCATCACCCTGGAGGTTGA-AGCTCAGACA
1 ATGCAGAT-TTTTGTGAAAACCTTCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACA
* * * * * * *
7046478 CGATTGACAATGTGAAAGCAAAGATTCAGGACAAGGAGGGGATTCCTCCAGACCAGCAGAGGTTG
65 CCATTGACAATGTCAAAGCAAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTG
7046543 ATCTTTGCTGG
130 ATCTTTGCTGG
7046554 CAAGCATTGG
Statistics
Matches: 660, Mismatches: 136, Indels: 47
0.78 0.16 0.06
Matches are distributed among these distances:
221 2 0.00
222 19 0.03
223 29 0.04
224 27 0.04
225 91 0.14
226 112 0.17
227 187 0.28
228 163 0.25
229 19 0.03
230 10 0.02
231 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (226 bp):
ATGCAGATTTTTGTGAAAACCTTCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACAC
CATTGACAATGTCAAAGCAAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTGA
TCTTTGCTGGAAACAGCTAGAAGATGGCAGGACACTTGCAGACTACAACATCCAAAAAGAGTCAA
CCCTCCATTTGGTCTTGCGTCTCGTGGAGGC
Found at i:7052793 original size:228 final size:226
Alignment explanation
Indices: 7052396--7053503 Score: 953
Period size: 228 Copynumber: 4.9 Consensus size: 226
7052386 TTGACAACAG
* * * * * *
7052396 ATGCAGATCTTTGTGAAAACCCTTACTGGCAAGACCATCACCCTT-GAGGTGGAAAGCTCTGACA
1 ATGCAGATATTTGTGAAGA-CCTCACTGGGAAAACCATCA-CCTTGGAGGTGGAGAGCTCTGACA
* * * * *
7052460 CTATTGATAATGTCAAAGCCAAGATCCAAGACAAGGAGGGGATCCCGCCAGACCAACAGAGGCTT
64 CCATTGACAATGTCAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGG-TT
* * * * * *
7052525 -ATCTTTGCTGGTAAACAGCTAGAGGATGGCCGCACCCTTGCTGATTACAATATCCAGAAGGAGT
128 GATCTTTGCTGGCAAACAGCTTGAGGATGGCAGCACACTTGCAGACTACAATATCCAGAAGGAGT
* * *
7052589 CCACCCTCCACCTT-GTCCTTCGTCTTAGGGGTGGC
193 CAACCCTCCA-CTTGGT-CTTCGTCTTAGTGGAGGC
* * * * * *
7052624 ATGCAGATATTTGTGAAAACTCTCACTGGGAAAACCATCACTTTAGAGGTGGAGAGTTCAGATAC
1 ATGCAGATATTTGTGAAGAC-CTCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACAC
* * * * * * * *
7052689 CATCGATAATGTGAAGGCGAAGATTCAGGACAAGGAGGGTATCCCACCAGACCAGCAGAGGTTAA
65 CATTGACAATGTCAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTGA
* * * * * * * * *
7052754 TTTTTGCCGGAAAACAGCTTGAAGATGGCAGAACCCTTGCAGACTATAACATTCAGAAGGAGTCA
130 TCTTTGCTGGCAAACAGCTTGAGGATGGCAGCACACTTGCAGACTACAATATCCAGAAGGAGTCA
* * * ** *
7052819 ACCCTCCATTTGGTTTTGCGGCTCCGTGGTGGC
195 ACCCTCCACTTGGTCTT-CGTCTTAGTGGAGGC
* * * * * * * * *
7052852 ATGCAAATTTTTGTCAAGACCCTCACT-GGAAAGACTATTACCTTGGAAGTTGAGAGTTCTGATA
1 ATGCAGATATTTGTGAAGA-CCTCACTGGGAAA-ACCATCACCTTGGAGGTGGAGAGCTCTGACA
* * * * * *
7052916 CCATTGACAATGTAAAAGCTAAGATCCAGGACAAGGAAGGTATCCCTCCAGATCAACAGAGGCTG
64 CCATTGACAATGTCAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTG
* * * * * *
7052981 ATATTTGCTGGCAAACAG-TTGGAGGATGGGAGGACACTTGCAGATTACAATATCCAAAAAGAGT
129 ATCTTTGCTGGCAAACAGCTT-GAGGATGGCAGCACACTTGCAGACTACAATATCCAGAAGGAGT
* ** *
7053045 CAACCCTCCACTTGGTGCTGCGTCTGCGTGGAGGA
193 CAACCCTCCACTTGGT-CTTCGTCTTAGTGGAGGC
* * * *
7053080 ATGCAGAT-TTTGTGAAGACCTTGACTGGTAAAACCATTACTTTGGAGGTGGAGAGCTCTGACAC
1 ATGCAGATATTTGTGAAGACC-TCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACAC
* * * * *
7053144 CAATTGACAACGTCAAAGCCAAGATCCAAGATAAGGA-GGTATCCCACCTGACCAACAAAGGTTG
65 C-ATTGACAATGTCAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTG
* * * * * * * *
7053208 ATTTTTGCTGGGAAGCAGCTTGAAGATGG-AGGACACTTGCAGACTATAACATCCAAAAGGAGTC
129 ATCTTTGCTGGCAAACAGCTTGAGGATGGCAGCACACTTGCAGACTACAATATCCAGAAGGAGTC
* * * * * *
7053272 AACCCTGCATTTGGTTTTGCGCCTTAGAGGAGGG
194 AACCCTCCACTTGGTCTT-CGTCTTAGTGGAGGC
* * * * *
7053306 ATGCAGATATTTGTCAAGACCTTGA-TGGGAAAACCATCACCCTGGAGGTTGAGAGCTCAGACAC
1 ATGCAGATATTTGTGAAGACC-TCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACAC
* * * * * * *
7053370 GATTGACAATGTGAAAGCAAAGATTCAGGACAAGGAGGG-ATTCCTCCAGACCAGCAGAGGTTGA
65 CATTGACAATGTCAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTGA
* * * *
7053434 TCTTTGCTGGCAAGCAG-TTGGAGGATGGTC-GCACTCTGGCTGACTACAATATCCAGAAGGAGT
130 TCTTTGCTGGCAAACAGCTT-GAGGATGG-CAGCACACTTGCAGACTACAATATCCAGAAGGAGT
*
7053497 CCACCCT
193 CAACCCT
7053504 GCATCTTGTC
Statistics
Matches: 713, Mismatches: 148, Indels: 40
0.79 0.16 0.04
Matches are distributed among these distances:
224 2 0.00
225 72 0.10
226 131 0.18
227 116 0.16
228 390 0.55
229 2 0.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (226 bp):
ATGCAGATATTTGTGAAGACCTCACTGGGAAAACCATCACCTTGGAGGTGGAGAGCTCTGACACC
ATTGACAATGTCAAAGCCAAGATCCAGGACAAGGAGGGTATCCCACCAGACCAACAGAGGTTGAT
CTTTGCTGGCAAACAGCTTGAGGATGGCAGCACACTTGCAGACTACAATATCCAGAAGGAGTCAA
CCCTCCACTTGGTCTTCGTCTTAGTGGAGGC
Found at i:7053727 original size:21 final size:23
Alignment explanation
Indices: 7053684--7053727 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
7053674 ATTAAATAAA
7053684 GTTCTATCTCGTTCTAAAATTAT
1 GTTCTATCTCGTTCTAAAATTAT
7053707 GTTCTA-CTC-TT-TAAGAATTAT
1 GTTCTATCTCGTTCTAA-AATTAT
7053728 TTTGCCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 3 0.15
23 6 0.30
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (23 bp):
GTTCTATCTCGTTCTAAAATTAT
Found at i:7058262 original size:30 final size:30
Alignment explanation
Indices: 7058228--7058286 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
7058218 TGATAATATT
* * *
7058228 AAAATTATAATTTTATTTTTATTAATTTTA
1 AAAATTATAATATAATTATTATTAATTTTA
*
7058258 AAAATTATTATATAATTATTATTAATTTT
1 AAAATTATAATATAATTATTATTAATTTT
7058287 TTTATTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
AAAATTATAATATAATTATTATTAATTTTA
Found at i:7061775 original size:40 final size:40
Alignment explanation
Indices: 7061720--7061800 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
7061710 ACAAAATAAG
7061720 TAAGCAAGTTTCAATCAGAACAAATGGCATATGGCTCTGT
1 TAAGCAAGTTTCAATCAGAACAAATGGCATATGGCTCTGT
7061760 TAAGCAAGTTTCAATCAGAACAAATGGCATATGGCTCTGT
1 TAAGCAAGTTTCAATCAGAACAAATGGCATATGGCTCTGT
7061800 T
1 T
7061801 TCATGAGCGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (40 bp):
TAAGCAAGTTTCAATCAGAACAAATGGCATATGGCTCTGT
Found at i:7076282 original size:22 final size:25
Alignment explanation
Indices: 7076254--7076300 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 25
7076244 GAAAAGCCCA
*
7076254 ATATTAC-TATTT-TTATTT-TTTT
1 ATATTACAAATTTATTATTTGTTTT
7076276 ATATTACAAATTTATTATTTGTTTT
1 ATATTACAAATTTATTATTTGTTTT
7076301 TTTTTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 4 0.19
24 6 0.29
25 4 0.19
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (25 bp):
ATATTACAAATTTATTATTTGTTTT
Found at i:7076323 original size:29 final size:30
Alignment explanation
Indices: 7076261--7076320 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
7076251 CCAATATTAC
*
7076261 TATTTTTATTTTTTTATATTACAAATTTAT
1 TATTTTTATTTTTTTATATTACAAATCTAT
*
7076291 TATTTGTT-TTTTTTTCATATTA-ACATCTAT
1 TATTT-TTATTTTTTT-ATATTACAAATCTAT
7076321 ATTATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.65
Consensus pattern (30 bp):
TATTTTTATTTTTTTATATTACAAATCTAT
Found at i:7100846 original size:28 final size:30
Alignment explanation
Indices: 7100813--7100888 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
7100803 ATTTAAAGAT
*
7100813 ATTTAAATAAATTTTTAT-TTTTTA-TTAC
1 ATTTAAATAAATTTTTATATTTTTATTTAA
* *
7100841 ATTT-AATTAAGTTTTATATTTTTATTTAA
1 ATTTAAATAAATTTTTATATTTTTATTTAA
* *
7100870 AGTCAAATAAATTTTTATA
1 ATTTAAATAAATTTTTATA
7100889 ATTAATGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 11 0.29
28 10 0.26
29 5 0.13
30 12 0.32
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (30 bp):
ATTTAAATAAATTTTTATATTTTTATTTAA
Found at i:7101890 original size:29 final size:30
Alignment explanation
Indices: 7101838--7101894 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
7101828 TAATATTTTA
7101838 AAAAATAAAGTTATAAAATTTTTAAAATAT
1 AAAAATAAAGTTATAAAATTTTTAAAATAT
7101868 AAAAATAAA-TTAATAAAA-TTTTAAAAT
1 AAAAATAAAGTT-ATAAAATTTTTAAAAT
7101895 TTTATGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAATAAAGTTATAAAATTTTTAAAATAT
Found at i:7110317 original size:155 final size:155
Alignment explanation
Indices: 7110035--7110397 Score: 593
Period size: 155 Copynumber: 2.3 Consensus size: 155
7110025 GGGCAACCAT
* * * *
7110035 CTGCATCAGCCCGACGGAAAGAAACAACCAAAACAACAACCTGCATCAAAACCATATGTAGTAAT
1 CTGCATCAGCCCAACGAAAATAAACAACCAAAACAACAACCTGCATCAAAACCAAATGTAGTAAT
* * *
7110100 CATGTTGAGTTTCATTAATGGCAGAATAGGCATCAACAAAAAGCAAGGGCCGGCAAGCTGCATCA
66 CATGTTGAGTTTCATTAATAGCAGAATAGACATCAACAAAAAGCAAGGGACGGCAAGCTGCATCA
7110165 TAGCAATGAAAATCAATACCGCAAG
131 TAGCAATGAAAATCAATACCGCAAG
*
7110190 CTGCATCAGCCCAATGAAAATAAACAACCAAAACAGA-AACCTGCATCAAAACCAAATGTAGTAA
1 CTGCATCAGCCCAACGAAAATAAACAACCAAAACA-ACAACCTGCATCAAAACCAAATGTAGTAA
* *
7110254 TCATGTTGAGTTTCATTAATAGCATAATAGACATCAACACAAAGCAAGGGACGGCAAGCTGCATC
65 TCATGTTGAGTTTCATTAATAGCAGAATAGACATCAACAAAAAGCAAGGGACGGCAAGCTGCATC
*
7110319 ATAGCAATGAAAATCAATACTGCAAG
130 ATAGCAATGAAAATCAATACCGCAAG
* *
7110345 CTGCATCAGCCCAACGAAAATAAACAACCAAAACAACCACCTGGATCAAAACC
1 CTGCATCAGCCCAACGAAAATAAACAACCAAAACAACAACCTGCATCAAAACC
7110398 GTTAGACAGT
Statistics
Matches: 192, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
154 1 0.01
155 190 0.99
156 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.17
Consensus pattern (155 bp):
CTGCATCAGCCCAACGAAAATAAACAACCAAAACAACAACCTGCATCAAAACCAAATGTAGTAAT
CATGTTGAGTTTCATTAATAGCAGAATAGACATCAACAAAAAGCAAGGGACGGCAAGCTGCATCA
TAGCAATGAAAATCAATACCGCAAG
Found at i:7111919 original size:26 final size:26
Alignment explanation
Indices: 7111888--7111965 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 26
7111878 TTCCCCTCGG
* *
7111888 CCCCCCTTCCACGAGTCCGATTCCC-
1 CCCCCCCTCCACGAGTCCGACTCCCA
7111913 CCCCCCC-CCACTCGAGTCCCGACTCCCGA
1 CCCCCCCTCCA--CGAGT-CCGACTCCC-A
7111942 CCCCCCCCTCCACGAGTCCCGACT
1 -CCCCCCCTCCACGAGT-CCGACT
7111966 GTGGATCCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
24 3 0.07
25 6 0.14
26 5 0.11
27 8 0.18
29 12 0.27
30 7 0.16
31 3 0.07
ACGTcount: A:0.13, C:0.60, G:0.13, T:0.14
Consensus pattern (26 bp):
CCCCCCCTCCACGAGTCCGACTCCCA
Found at i:7111975 original size:29 final size:27
Alignment explanation
Indices: 7111896--7111995 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
7111886 GGCCCCCCTT
*
7111896 CCACGAGT-CCGATTCCC--CCCCCCC
1 CCACGAGTCCCGACTCCCGACCCCCCC
7111920 CCACTCGAGTCCCGACTCCCGACCCCCCCC
1 CCA--CGAGTCCCGACTCCCGA-CCCCCCC
*** * *
7111950 TCCACGAGTCCCGACTGTGGATCCCCTC
1 -CCACGAGTCCCGACTCCCGACCCCCCC
*
7111978 CCACGAGTCCCGATTCCC
1 CCACGAGTCCCGACTCCC
7111996 CCGCCGAAAC
Statistics
Matches: 59, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
24 3 0.05
26 5 0.08
27 22 0.37
28 5 0.08
29 14 0.24
30 7 0.12
31 3 0.05
ACGTcount: A:0.14, C:0.55, G:0.16, T:0.15
Consensus pattern (27 bp):
CCACGAGTCCCGACTCCCGACCCCCCC
Found at i:7115178 original size:144 final size:143
Alignment explanation
Indices: 7114914--7115422 Score: 552
Period size: 144 Copynumber: 3.6 Consensus size: 143
7114904 AAGGTCTTTG
* * *
7114914 AGGGAAGTGAGATTGAGTATCCAGTCTGGCAAAGCCCTCAAATTATGGC-A--G-CAAACATATA
1 AGGGAAGTGAGATTGAGTATCCAGTCAGGCAAAGCCCTCAGATTATGGCAATTGCCAAACAGATA
* * *
7114975 ATTCTTCTAAAGATGTAAAGCGAGGCGTCCCTTTTGGCATGTGCTGTAATTCAAGGCACTCCCAA
66 ATTCTTCTAAAGAGGT-AAGTGAGGCGTCCCTTCTGGCATGTGCTGTAATTCAAGGCACT-CCAA
7115040 ATTTCAAGTGTTTTA
129 ATTTCAAGTGTTTTA
* * * *
7115055 AGGGAAGTGAGATTGAGTATCCAGTCAGGCAAAGCCCTCAGATTAGGGCAATTGCCTACCA-ACA
1 AGGGAAGTGAGATTGAGTATCCAGTCAGGCAAAGCCCTCAGATTATGGCAATTGCCAAACAGATA
* * * *
7115119 ATTCTTTTAAAGAGGTAAGTTGATGCGTCCCTCCTGGCATGTGCTGTAATTCAAAGCACTCCACA
66 ATTCTTCTAAAGAGGTAAG-TGAGGCGTCCCTTCTGGCATGTGCTGTAATTCAAGGCACTCCA-A
*
7115184 ATTTGAAGTGTTTTA
129 ATTTCAAGTGTTTTA
* * * **
7115199 AGGGAAGTGAGATTGAGTATCCAGTCAGGTAAAGCCCCCA-ACTTATGACAGCT-CCAAACAGAT
1 AGGGAAGTGAGATTGAGTATCCAGTCAGGCAAAGCCCTCAGA-TTATGGCAATTGCCAAACAGAT
* * * *
7115262 AATTCTTCTAAAGATGTAAGCTGAGGCGTCCCTTCTGGAATG-GACCGTAATTCAAGGCACT-TA
65 AATTCTTCTAAAGAGGTAAG-TGAGGCGTCCCTTCTGGCATGTG-CTGTAATTCAAGGCACTCCA
* *
7115325 TGAATTTCAAGTCTTCTA
128 --AATTTCAAGTGTTTTA
* * * * ** * *
7115343 AGGGAAGTGAGATTGAGTATCCAATCCGGCAAACCCCTCAGATTACGGCAATTTTC-AACCGAAA
1 AGGGAAGTGAGATTGAGTATCCAGTCAGGCAAAGCCCTCAGATTATGGCAATTGCCAAACAGATA
*
7115407 ATTCTTGTAAAGAGGT
66 ATTCTTCTAAAGAGGT
7115423 GAGGCAGCTC
Statistics
Matches: 306, Mismatches: 50, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
141 46 0.15
142 1 0.00
143 14 0.05
144 239 0.78
145 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (143 bp):
AGGGAAGTGAGATTGAGTATCCAGTCAGGCAAAGCCCTCAGATTATGGCAATTGCCAAACAGATA
ATTCTTCTAAAGAGGTAAGTGAGGCGTCCCTTCTGGCATGTGCTGTAATTCAAGGCACTCCAAAT
TTCAAGTGTTTTA
Found at i:7115667 original size:6 final size:6
Alignment explanation
Indices: 7115656--7115682 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7115646 CTGGCCTCAA
7115656 TCATCT TCATCT TCATCT TCATCT TCA
1 TCATCT TCATCT TCATCT TCATCT TCA
7115683 ATGTTTGTTG
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:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
TCATCT
Found at i:7118869 original size:20 final size:20
Alignment explanation
Indices: 7118844--7118884 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
7118834 TGTGTTCATA
7118844 GTTTTAATTAAAGATCACTT
1 GTTTTAATTAAAGATCACTT
7118864 GTTTTAATTAAAGATCACTT
1 GTTTTAATTAAAGATCACTT
7118884 G
1 G
7118885 AATCTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
GTTTTAATTAAAGATCACTT
Found at i:7123387 original size:5 final size:5
Alignment explanation
Indices: 7123377--7123413 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
7123367 TTGATCAACC
7123377 AAAA- AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
7123414 AGTTTCAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:7128329 original size:69 final size:69
Alignment explanation
Indices: 7128218--7128359 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 69
7128208 ATCTTCCACG
* * *
7128218 TGTTCTAAAACATGGAACCCGTGAAGAGTAAGAGACTCGAGAGATGAAAGATGATCCAAGGGTGG
1 TGTTCTAAAACATGAAACCCCTGAAGAGTAAGAGACTCGAGAGATGAAAGATGATCCAAGCGTGG
7128283 CAGC
66 CAGC
*
7128287 TGTTCTAAAACATGAAACCCCTGAAGAGTAAGAGACTTGAGAGATGAAAGATGATCCAAGCGTGG
1 TGTTCTAAAACATGAAACCCCTGAAGAGTAAGAGACTCGAGAGATGAAAGATGATCCAAGCGTGG
*
7128352 CAGG
66 CAGC
7128356 TGTT
1 TGTT
7128360 GGCAATTCCA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (69 bp):
TGTTCTAAAACATGAAACCCCTGAAGAGTAAGAGACTCGAGAGATGAAAGATGATCCAAGCGTGG
CAGC
Found at i:7136620 original size:3 final size:3
Alignment explanation
Indices: 7136612--7136637 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7136602 ACGATGGCAG
7136612 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
7136638 CTTCTGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:7139930 original size:28 final size:27
Alignment explanation
Indices: 7139880--7139934 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
7139870 AAAGGAATGT
7139880 TAAGAATATTTTTAATTATTTTGGTAG
1 TAAGAATATTTTTAATTATTTTGGTAG
7139907 TAAGAATATATTTTAA-TATATTTGGTAG
1 TAAGAATAT-TTTTAATTAT-TTTGGTAG
7139935 GAATGTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (27 bp):
TAAGAATATTTTTAATTATTTTGGTAG
Found at i:7154488 original size:34 final size:35
Alignment explanation
Indices: 7154437--7154504 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
7154427 AAAAAGATAC
*
7154437 CCAAAATTAATGTTTTTTTCATTCATAAAGAAAAT
1 CCAAAAATAATGTTTTTTTCATTCATAAAGAAAAT
*
7154472 CCAAAAATAATG-TTTTTTGATTCATAAAGAAAA
1 CCAAAAATAATGTTTTTTTCATTCATAAAGAAAA
7154505 GTAGTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 20 0.65
35 11 0.35
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (35 bp):
CCAAAAATAATGTTTTTTTCATTCATAAAGAAAAT
Found at i:7157042 original size:3 final size:3
Alignment explanation
Indices: 7157034--7157075 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
7157024 TGAAAACAAT
7157034 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AA
7157076 AGCTTATAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7157869 original size:3 final size:3
Alignment explanation
Indices: 7157861--7157890 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7157851 TTGAAAATCT
7157861 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
7157891 AGTCATCCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:7160730 original size:2 final size:2
Alignment explanation
Indices: 7160723--7160758 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7160713 ACTAGTTTTA
7160723 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7160759 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:7161940 original size:2 final size:2
Alignment explanation
Indices: 7161933--7161964 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7161923 AGATAATCTT
7161933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7161965 AACCTTTTAA
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):
TA
Found at i:7162671 original size:92 final size:90
Alignment explanation
Indices: 7162470--7162689 Score: 237
Period size: 92 Copynumber: 2.4 Consensus size: 90
7162460 GTAAATTTGT
* * ** * ** *
7162470 AAATTTTAAGTACCAATTGGTAAATTAGTAAGATTTATGAGAGATAAAGATAGGGTAAAACTTGA
1 AAATTTTAAGTACTAATTGGTAAATGA-TAAGATTTACAAGAAATAAAGATAGGACAAAACATGA
*
7162535 ATAAACTTCGTAAGATTTTTCATTAA
65 AAAAACTTCGTAAGATTTTTCATTAA
* * *
7162561 AAGTTTTAAGTA-TCAATTGGTAAACTGATAAGATTTACAAGAAATAAAGATCATGACAAGACAT
1 AAATTTTAAGTACT-AATTGGTAAA-TGATAAGATTTACAAGAAATAAAGAT-AGGACAAAACAT
* *
7162625 GAAAAAAGTTCGTATG-TTCTTTCATTAA
63 GAAAAAACTTCGTAAGATT-TTTCATTAA
*
7162653 AAATTTTAAGTACTAATTGGTAAATTGGTAAGATTTA
1 AAATTTTAAGTACTAATTGGTAAA-TGATAAGATTTA
7162690 TGGGAGACAA
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
91 43 0.40
92 63 0.59
93 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (90 bp):
AAATTTTAAGTACTAATTGGTAAATGATAAGATTTACAAGAAATAAAGATAGGACAAAACATGAA
AAAACTTCGTAAGATTTTTCATTAA
Found at i:7163452 original size:80 final size:81
Alignment explanation
Indices: 7163354--7163513 Score: 209
Period size: 81 Copynumber: 2.0 Consensus size: 81
7163344 AAAAAAATAA
* * * * *
7163354 TTTCTTGAGATTGGATTGACTTCGGAAATGT-AACA-TAATATCAAATTTGACTTAAAACTGCAT
1 TTTCATGAGATTGGATTGACTTCGAAAATATAAACACT-ATAACAAATTTGACTTAAAACTACAT
*
7163417 AATTT-ACAAATGTATTC
65 -ATTTCACAAATATATTC
* *
7163434 TTTCATGAGATTGGATTGACTTCGAAAATATAAACACTATAACAAATTTGATTTAAAATTACATA
1 TTTCATGAGATTGGATTGACTTCGAAAATATAAACACTATAACAAATTTGACTTAAAACTACATA
7163499 TTTCACAAATATATT
66 TTTCACAAATATATT
7163514 ATTAAATATG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
80 32 0.46
81 36 0.52
82 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (81 bp):
TTTCATGAGATTGGATTGACTTCGAAAATATAAACACTATAACAAATTTGACTTAAAACTACATA
TTTCACAAATATATTC
Found at i:7166622 original size:86 final size:86
Alignment explanation
Indices: 7166477--7166648 Score: 317
Period size: 86 Copynumber: 2.0 Consensus size: 86
7166467 GGAGCTATGA
7166477 CGGGAGGGTTCAAGTGGTAAACCTAAAAATCATCTATATTTTATCTCTTTCATTCGAAATGCAAT
1 CGGGAGGGTTCAAGTGGTAAACCTAAAAATCATCTATATTTTATCTCTTTCATTCGAAATGCAAT
7166542 AATGAACTCGTCACTTGATTT
66 AATGAACTCGTCACTTGATTT
* *
7166563 CGGGAGGGTTCAAGTGGTAAACCTAAAAATTATCTATATTTTATCTCTTTCATTCGAAATGTAAT
1 CGGGAGGGTTCAAGTGGTAAACCTAAAAATCATCTATATTTTATCTCTTTCATTCGAAATGCAAT
*
7166628 AATGAACTTGTCACTTGATTT
66 AATGAACTCGTCACTTGATTT
7166649 ATTAACGTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (86 bp):
CGGGAGGGTTCAAGTGGTAAACCTAAAAATCATCTATATTTTATCTCTTTCATTCGAAATGCAAT
AATGAACTCGTCACTTGATTT
Found at i:7167595 original size:16 final size:15
Alignment explanation
Indices: 7167574--7167604 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
7167564 ATAGACATTG
7167574 TCAATGGCTAGCAACT
1 TCAATGGCTAG-AACT
7167590 TCAATGGCTAGAACT
1 TCAATGGCTAGAACT
7167605 AGTCCAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (15 bp):
TCAATGGCTAGAACT
Found at i:7192445 original size:60 final size:60
Alignment explanation
Indices: 7192333--7192446 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
7192323 GAGAAGTAAA
* * * *
7192333 AAAGACAAGATGAAATCTGAAATCCAGAAAATATGTGAAGTGCATGATGATGATTCTGGT
1 AAAGACAACATGAAATCCGAAATCCAGAAAATATGTGAAGTCCATGAAGATGATTCTGGT
* *
7192393 AAAGACAACATGAAATCCGAAATCCGGAATCA-ATGTGAAGTCCA-GCAAGATGAT
1 AAAGACAACATGAAATCCGAAATCCAGAA-AATATGTGAAGTCCATG-AAGATGAT
7192447 GATTTGGGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 44 0.96
61 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (60 bp):
AAAGACAACATGAAATCCGAAATCCAGAAAATATGTGAAGTCCATGAAGATGATTCTGGT
Found at i:7208156 original size:53 final size:53
Alignment explanation
Indices: 7208088--7208241 Score: 186
Period size: 53 Copynumber: 2.9 Consensus size: 53
7208078 GTTTCAAATG
*
7208088 AAACCCTATTAGTGAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAGGATA-
1 AAACCCTATTGGTGAATTAATAAAGAATATAAAGAGAAAGAGGTTCTA-GATAT
* *
7208141 AAACCCTATTGGTGAATTAATAAAGAATATCAAGAGAAAGAGGTTTTA-ATAT
1 AAACCCTATTGGTGAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAGATAT
****** **
7208193 TTTGGTTATTGACGAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAG
1 AAACCCTATTGGTGAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAG
7208242 TATTTTGGCT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 3 0.03
52 38 0.44
53 45 0.52
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.28
Consensus pattern (53 bp):
AAACCCTATTGGTGAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAGATAT
Found at i:7208228 original size:52 final size:52
Alignment explanation
Indices: 7208101--7208251 Score: 178
Period size: 52 Copynumber: 2.9 Consensus size: 52
7208091 CCCTATTAGT
***** **
7208101 GAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAGGATA-AAACCCTATTGGT
1 GAATTAATAAAGAATATAAAGAGAAAGAGGTTCTA--ATATTTTGGCTATTGAC
* * *
7208154 GAATTAATAAAGAATATCAAGAGAAAGAGGTTTTAATATTTTGGTTATTGAC
1 GAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAATATTTTGGCTATTGAC
*
7208206 GAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAGTATTTTGGCT
1 GAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAATATTTTGGCT
7208252 TGGTCAATTA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
51 3 0.04
52 47 0.57
53 33 0.40
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (52 bp):
GAATTAATAAAGAATATAAAGAGAAAGAGGTTCTAATATTTTGGCTATTGAC
Found at i:7210691 original size:22 final size:22
Alignment explanation
Indices: 7210666--7210724 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 22
7210656 CTAACTGTAA
7210666 ATGTCTTGTAGTCTAGCTATAT
1 ATGTCTTGTAGTCTAGCTATAT
7210688 ATGTCTTGTGTATCAGTCTAGCTATAT
1 ATGTC-T-TG--T-AGTCTAGCTATAT
7210715 ATGTCTTGTA
1 ATGTCTTGTA
7210725 TGTGCTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 6 0.19
23 2 0.06
24 2 0.06
25 2 0.06
26 2 0.06
27 18 0.56
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (22 bp):
ATGTCTTGTAGTCTAGCTATAT
Found at i:7211051 original size:13 final size:13
Alignment explanation
Indices: 7211033--7211057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7211023 TTCGTTGGTA
7211033 GAAAATATTTTTG
1 GAAAATATTTTTG
7211046 GAAAATATTTTT
1 GAAAATATTTTT
7211058 CAGTATCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
GAAAATATTTTTG
Found at i:7211132 original size:31 final size:33
Alignment explanation
Indices: 7211073--7211142 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
7211063 TCACAAATGG
* * *
7211073 AAAACATTTTCTATTGTTTATATTATCTCGT-GA
1 AAAATATTTTCTA-TGTTTAAATCATCTCGTGGA
7211106 AAAATATTTTCTA-GTTTAAATCATCTCGTGGA
1 AAAATATTTTCTATGTTTAAATCATCTCGTGGA
7211138 AAAAT
1 AAAAT
7211143 GGAGTTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 14 0.42
32 7 0.21
33 12 0.36
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (33 bp):
AAAATATTTTCTATGTTTAAATCATCTCGTGGA
Found at i:7211916 original size:28 final size:28
Alignment explanation
Indices: 7211885--7211980 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 28
7211875 TAAGACATGC
7211885 AAAACTTATATTTATGTGTATTCACTAT
1 AAAACTTATATTTATGTGTATTCACTAT
* ** *
7211913 AAAAATGTCAATATTTAACAATTGTGTA-AGACATCT
1 AAAACT-T--ATATTT----A-TGTGTATTCAC-TAT
7211949 AAAACTTATATTTATGTGTATTCACTAT
1 AAAACTTATATTTATGTGTATTCACTAT
7211977 AAAA
1 AAAA
7211981 ATATCAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
28 17 0.34
29 4 0.08
31 6 0.12
33 6 0.12
35 4 0.08
36 13 0.26
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (28 bp):
AAAACTTATATTTATGTGTATTCACTAT
Found at i:7211928 original size:64 final size:63
Alignment explanation
Indices: 7211848--7212023 Score: 289
Period size: 64 Copynumber: 2.7 Consensus size: 63
7211838 ACCCTAAATC
*
7211848 TAAAAATATCAATATTTATCAATTTTGTAAGACATGCAAAACTTATATTTATGTGTATTCACTA
1 TAAAAATATCAATATTTATCAATTGTGTAAGACAT-CAAAACTTATATTTATGTGTATTCACTA
* *
7211912 TAAAAATGTCAATATTTAACAATTGTGTAAGACATCTAAAACTTATATTTATGTGTATTCACTA
1 TAAAAATATCAATATTTATCAATTGTGTAAGACATC-AAAACTTATATTTATGTGTATTCACTA
*
7211976 TAAAAATATCAATATTTATAAATTGTGTAAGACATCCAAAACTTATAT
1 TAAAAATATCAATATTTATCAATTGTGTAAGACAT-CAAAACTTATAT
7212024 ATACTAATAT
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
63 1 0.01
64 102 0.98
65 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.39
Consensus pattern (63 bp):
TAAAAATATCAATATTTATCAATTGTGTAAGACATCAAAACTTATATTTATGTGTATTCACTA
Found at i:7212183 original size:15 final size:18
Alignment explanation
Indices: 7212145--7212184 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
7212135 ATATTTTTTA
7212145 ATTTTAATAGTATTGAAT
1 ATTTTAATAGTATTGAAT
*
7212163 AATTTAA-A-TATT-AAT
1 ATTTTAATAGTATTGAAT
7212178 ATTTTAA
1 ATTTTAA
7212185 GTTAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTAATAGTATTGAAT
Found at i:7212451 original size:13 final size:13
Alignment explanation
Indices: 7212433--7212458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7212423 AGTATAAGTC
7212433 TTTAAAATATTTT
1 TTTAAAATATTTT
7212446 TTTAAAATATTTT
1 TTTAAAATATTTT
7212459 ATATCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAAAATATTTT
Found at i:7214450 original size:20 final size:20
Alignment explanation
Indices: 7214425--7214489 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
7214415 AATCGAAATA
7214425 TAATTCAATATAATTTGTTC
1 TAATTCAATATAATTTGTTC
7214445 TAATTCCATATAATATGATTTGTTC
1 TAATT-CA-AT-ATA--ATTTGTTC
* *
7214470 TAAATCCATATAATTTGTTC
1 TAATTCAATATAATTTGTTC
7214490 AGGTCAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 13 0.34
21 2 0.05
22 5 0.13
23 5 0.13
24 1 0.03
25 12 0.32
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (20 bp):
TAATTCAATATAATTTGTTC
Found at i:7214459 original size:25 final size:25
Alignment explanation
Indices: 7214431--7214483 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
7214421 AATATAATTC
*
7214431 AATATAATTTGTTCTAATTCCATAT
1 AATATAATTTGTTCTAAATCCATAT
*
7214456 AATATGATTTGTTCTAAATCCATAT
1 AATATAATTTGTTCTAAATCCATAT
7214481 AAT
1 AAT
7214484 TTGTTCAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (25 bp):
AATATAATTTGTTCTAAATCCATAT
Found at i:7222465 original size:23 final size:23
Alignment explanation
Indices: 7222420--7222465 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7222410 TTCAATGTTT
* * *
7222420 TCAACAGACACATCTATTGAAAC
1 TCAACAAACACATATATTAAAAC
*
7222443 TCAACAAACACATATGTTAAAAC
1 TCAACAAACACATATATTAAAAC
7222466 ATATTCAGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (23 bp):
TCAACAAACACATATATTAAAAC
Found at i:7232104 original size:81 final size:80
Alignment explanation
Indices: 7231939--7232176 Score: 431
Period size: 81 Copynumber: 3.0 Consensus size: 80
7231929 GAAATGCATG
*
7231939 TGGAAAAGCTACTTGCAGGGTTAATATAAACCCTCCATTAGCATGTGAGCATGTCTCTCCATGCC
1 TGGAAAAGCTACTTGCAGGGTTAATTTAAACCCTCCATTAGCATGTGAGCATGTCTCTCCATGCC
7232004 CTGGAAAAGATTATT
66 CTGGAAAAGATTATT
* *
7232019 TGGAAAAGCTACTTGCAGGGTTAATTTAACCCCTCCATTATCATGTTGAGCATGTCTCTCCATGC
1 TGGAAAAGCTACTTGCAGGGTTAATTTAAACCCTCCATTAGCATG-TGAGCATGTCTCTCCATGC
7232084 CCTGGAAAAGATTATT
65 CCTGGAAAAGATTATT
*
7232100 TGGAAAAGCTACTTGCAGGGTTAATTTAAACCCTCCATTAGCATGTGAGCATGTCTCTTCATGCC
1 TGGAAAAGCTACTTGCAGGGTTAATTTAAACCCTCCATTAGCATGTGAGCATGTCTCTCCATGCC
7232165 CTGGAAAAGATT
66 CTGGAAAAGATT
7232177 TTGAAAGCAT
Statistics
Matches: 151, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
80 73 0.48
81 78 0.52
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (80 bp):
TGGAAAAGCTACTTGCAGGGTTAATTTAAACCCTCCATTAGCATGTGAGCATGTCTCTCCATGCC
CTGGAAAAGATTATT
Found at i:7233299 original size:2 final size:2
Alignment explanation
Indices: 7233292--7233322 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7233282 AATCATAAAG
7233292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7233323 CACATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7243497 original size:32 final size:32
Alignment explanation
Indices: 7243451--7243513 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
7243441 AAACCAAGTG
*
7243451 GAATGATTCCCAACTCCACTGTTCAGCAACAA
1 GAATCATTCCCAACTCCACTGTTCAGCAACAA
7243483 GAATCATTCCCAACTCCACTGTTCAGCAACA
1 GAATCATTCCCAACTCCACTGTTCAGCAACA
7243514 TAAAGAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.22
Consensus pattern (32 bp):
GAATCATTCCCAACTCCACTGTTCAGCAACAA
Found at i:7248337 original size:2 final size:2
Alignment explanation
Indices: 7248330--7248356 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7248320 TCATAACAAG
7248330 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7248357 ACCCCATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7261680 original size:2 final size:2
Alignment explanation
Indices: 7261675--7261733 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
7261665 CCCCGCCCCC
* *
7261675 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CC CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
7261716 CT CC CT CC CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
7261734 GTGTATTCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (2 bp):
CT
Found at i:7270584 original size:24 final size:23
Alignment explanation
Indices: 7270553--7270614 Score: 97
Period size: 24 Copynumber: 2.7 Consensus size: 23
7270543 TTATAGAAGC
7270553 ATGGATAATCTGAATGCTTAGTA
1 ATGGATAATCTGAATGCTTAGTA
*
7270576 ATGGCATAACCTGAATGCTTAGTA
1 ATGG-ATAATCTGAATGCTTAGTA
*
7270600 ATGAATAATCTGAAT
1 ATGGATAATCTGAAT
7270615 TTCATTGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 14 0.40
24 21 0.60
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (23 bp):
ATGGATAATCTGAATGCTTAGTA
Found at i:7276362 original size:3 final size:3
Alignment explanation
Indices: 7276354--7276380 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7276344 GTAGCAACTC
7276354 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
7276381 TAGGAGGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:7287320 original size:2 final size:2
Alignment explanation
Indices: 7287313--7287393 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
7287303 TCATCTAGAT
7287313 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
7287355 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
7287394 TTCATGAGGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7295777 original size:27 final size:27
Alignment explanation
Indices: 7295737--7295790 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
7295727 CTGTTTCCTC
*
7295737 CTTCTTCTGCACCCTTGTTTGCTGTTA
1 CTTCTTCTGCACCCTTGTTTGCAGTTA
*
7295764 CTTCTTCTGGACCCTTGTTTGCAGTTA
1 CTTCTTCTGCACCCTTGTTTGCAGTTA
7295791 GGTACTCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.09, C:0.28, G:0.17, T:0.46
Consensus pattern (27 bp):
CTTCTTCTGCACCCTTGTTTGCAGTTA
Found at i:7317770 original size:18 final size:18
Alignment explanation
Indices: 7317747--7317784 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
7317737 ATCTTCATTA
*
7317747 TCAAAATAGTCAAGAATG
1 TCAAAATAGCCAAGAATG
7317765 TCAAAATAGCCAAGAATG
1 TCAAAATAGCCAAGAATG
7317783 TC
1 TC
7317785 CATTTCTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (18 bp):
TCAAAATAGCCAAGAATG
Found at i:7318534 original size:20 final size:22
Alignment explanation
Indices: 7318505--7318553 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
7318495 GGATGCAAAC
*
7318505 TTTTATTAAAAAAAT-A-ATTT
1 TTTTAATAAAAAAATGACATTT
7318525 TTTTAATAAAAAAATGACATTT
1 TTTTAATAAAAAAATGACATTT
*
7318547 GTTTAAT
1 TTTTAAT
7318554 CAACAACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.56
21 1 0.04
22 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTAATAAAAAAATGACATTT
Found at i:7322272 original size:9 final size:9
Alignment explanation
Indices: 7322240--7322272 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
7322230 CCGACCAAGC
7322240 ACCGAA-GA
1 ACCGAATGA
*
7322248 ACCGAACGA
1 ACCGAATGA
7322257 ACCGAATGA
1 ACCGAATGA
7322266 ACCGAAT
1 ACCGAAT
7322273 TCAAACATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.45, C:0.27, G:0.21, T:0.06
Consensus pattern (9 bp):
ACCGAATGA
Found at i:7330293 original size:2 final size:2
Alignment explanation
Indices: 7330286--7330322 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
7330276 TCCTTTTACC
7330286 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7330323 GCAACAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:7331068 original size:14 final size:16
Alignment explanation
Indices: 7331049--7331080 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
7331039 TCTCTTTCAT
7331049 TTTTGA-GCAT-TTTC
1 TTTTGATGCATGTTTC
7331063 TTTTGATGCATGTTTC
1 TTTTGATGCATGTTTC
7331079 TT
1 TT
7331081 AAGTTGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (16 bp):
TTTTGATGCATGTTTC
Found at i:7335823 original size:29 final size:29
Alignment explanation
Indices: 7335781--7335842 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
7335771 TTTATTATGT
* *
7335781 TTAATTAAAATTTTATAATTTAT-TTTAAA
1 TTAAATAAAATTTTATAATTAATATTT-AA
* *
7335810 TTAAATAAATTTTTATGATTAATATTTAA
1 TTAAATAAAATTTTATAATTAATATTTAA
7335839 TTAA
1 TTAA
7335843 TTATTGATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAAATAAAATTTTATAATTAATATTTAA
Found at i:7343650 original size:49 final size:49
Alignment explanation
Indices: 7343590--7343688 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
7343580 ATATGAGTTA
7343590 ATGATCTGAGACTCAGTTTCATGTAGAATGTACATAGATAATGGAGCAT
1 ATGATCTGAGACTCAGTTTCATGTAGAATGTACATAGATAATGGAGCAT
7343639 ATGATCTGAGACTCAGTTTCATGTAGAATGTACATAGATAATGGAGCAT
1 ATGATCTGAGACTCAGTTTCATGTAGAATGTACATAGATAATGGAGCAT
7343688 A
1 A
7343689 ACAATATAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (49 bp):
ATGATCTGAGACTCAGTTTCATGTAGAATGTACATAGATAATGGAGCAT
Found at i:7349729 original size:16 final size:16
Alignment explanation
Indices: 7349704--7349735 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7349694 TTGCGGCCGG
*
7349704 CTTCTTTCTATTTCTT
1 CTTCTCTCTATTTCTT
7349720 CTTCTCTCTATTTCTT
1 CTTCTCTCTATTTCTT
7349736 TTTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTCTCTCTATTTCTT
Found at i:7355273 original size:2 final size:2
Alignment explanation
Indices: 7355268--7355301 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7355258 ATACATACAT
7355268 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
7355302 GCAAGATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:7370766 original size:14 final size:14
Alignment explanation
Indices: 7370747--7370773 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7370737 CCTAAAATGG
7370747 TTGGTTGATATTGT
1 TTGGTTGATATTGT
7370761 TTGGTTGATATTG
1 TTGGTTGATATTG
7370774 GTGCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (14 bp):
TTGGTTGATATTGT
Found at i:7372722 original size:65 final size:63
Alignment explanation
Indices: 7372590--7372775 Score: 239
Period size: 65 Copynumber: 2.9 Consensus size: 63
7372580 TGTTTTCTGT
* * * * *
7372590 CTCAAACATTGAATGCATTCGTTCCTTTTATTTTACCCATAATAAATCGTTACCTTTTTGTTTG
1 CTCAAACATTGAATGCATTCATACCTTTTATTTTACCCATAATAAAAC-CTGCCTTTTTGTTTG
* *
7372654 CTCAAATATTAAATGCATTCATACCTTTTATTTT-CTTCCATAATAAAACCTGCCCTTTTTGTTT
1 CTCAAACATTGAATGCATTCATACCTTTTATTTTAC--CCATAATAAAACCTG-CCTTTTTGTTT
7372718 G
63 G
* * *
7372719 CTCAAACATTGAATGCCTTCATACCTTTTATTTTGCCCATATTAAAACCTGCCTTTT
1 CTCAAACATTGAATGCATTCATACCTTTTATTTTACCCATAATAAAACCTGCCTTTT
7372776 GTCACGAGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
63 7 0.07
64 45 0.42
65 54 0.50
66 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (63 bp):
CTCAAACATTGAATGCATTCATACCTTTTATTTTACCCATAATAAAACCTGCCTTTTTGTTTG
Found at i:7373795 original size:2 final size:2
Alignment explanation
Indices: 7373788--7373814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7373778 GGAATATCGT
7373788 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7373815 TGCAAGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7379428 original size:2 final size:2
Alignment explanation
Indices: 7379421--7379451 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7379411 TAGTGTCATT
7379421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7379452 GATTAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7379906 original size:3 final size:3
Alignment explanation
Indices: 7379893--7379932 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
7379883 GTTTGGGACA
*
7379893 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
7379933 TGAAAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:7380048 original size:2 final size:2
Alignment explanation
Indices: 7380041--7380065 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7380031 CCAACAATTC
7380041 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7380066 TACGACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7414074 original size:21 final size:20
Alignment explanation
Indices: 7414046--7414085 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
7414036 ACCAGCTTGA
* *
7414046 TGCTTTTATGTTTTTTTTTT
1 TGCTTTTATATTTTATTTTT
7414066 TGCTATTTATATTTTATTTT
1 TGCT-TTTATATTTTATTTT
7414086 CTTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.75
Consensus pattern (20 bp):
TGCTTTTATATTTTATTTTT
Found at i:7422554 original size:25 final size:25
Alignment explanation
Indices: 7422526--7422576 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
7422516 CAAACATGAA
7422526 AAATCAAATAACCACCAAATAAAAG
1 AAATCAAATAACCACCAAATAAAAG
* * *
7422551 AAATTAAATAACCATCAAGTAAAAG
1 AAATCAAATAACCACCAAATAAAAG
7422576 A
1 A
7422577 CATGTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.16, G:0.06, T:0.16
Consensus pattern (25 bp):
AAATCAAATAACCACCAAATAAAAG
Found at i:7436291 original size:26 final size:26
Alignment explanation
Indices: 7436255--7436306 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
7436245 TCAATCTTTG
* *
7436255 TCCACATTTAAGTTGTGGCAGGACAA
1 TCCACACTTAAGATGTGGCAGGACAA
*
7436281 TCCACACTTAAGATGTGGTAGGACAA
1 TCCACACTTAAGATGTGGCAGGACAA
7436307 ATCTTGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (26 bp):
TCCACACTTAAGATGTGGCAGGACAA
Found at i:7442087 original size:26 final size:23
Alignment explanation
Indices: 7442058--7442115 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 23
7442048 TCAATTAATT
7442058 TAATTATTTTTATATAAAAATTTAA
1 TAATTATTTTT-T-TAAAAATTTAA
*
7442083 CTAATT-TAATTTTTAAAAATTTAA
1 -TAATTAT-TTTTTTAAAAATTTAA
7442107 -AATTATTTT
1 TAATTATTTT
7442116 AATCGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 6 0.21
23 1 0.04
24 11 0.39
25 2 0.07
26 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATTATTTTTTTAAAAATTTAA
Found at i:7447630 original size:10 final size:10
Alignment explanation
Indices: 7447611--7447674 Score: 74
Period size: 10 Copynumber: 6.1 Consensus size: 10
7447601 CACAATATTA
7447611 AAAAAAATTT
1 AAAAAAATTT
*
7447621 AAAAATATTTTT
1 AAAAA-A-ATTT
7447633 AAAAAAATTT
1 AAAAAAATTT
*
7447643 AAAAAATTTTT
1 AAAAAA-ATTT
7447654 AAAAAAATTT
1 AAAAAAATTT
*
7447664 AAAAAATTTT
1 AAAAAAATTT
7447674 A
1 A
7447675 TTTTATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
10 27 0.59
11 11 0.24
12 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:7447633 original size:12 final size:11
Alignment explanation
Indices: 7447608--7447673 Score: 73
Period size: 11 Copynumber: 6.1 Consensus size: 11
7447598 AGACACAATA
**
7447608 TTAAAAAAAAT
1 TTAAAAAATTT
7447619 TTAAAAATATTT
1 TTAAAAA-ATTT
*
7447631 TTAAAAAA-AT
1 TTAAAAAATTT
7447641 TTAAAAAATTT
1 TTAAAAAATTT
*
7447652 TTAAAAAA-AT
1 TTAAAAAATTT
7447662 TTAAAAAATTT
1 TTAAAAAATTT
7447673 T
1 T
7447674 ATTTTATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
10 18 0.39
11 19 0.41
12 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAAAAATTT
Found at i:7447636 original size:21 final size:21
Alignment explanation
Indices: 7447611--7447673 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
7447601 CACAATATTA
7447611 AAAAAAATTTAAAAATATTTTT
1 AAAAAAATTTAAAAA-ATTTTT
7447633 AAAAAAATTTAAAAAATTTTT
1 AAAAAAATTTAAAAAATTTTT
7447654 AAAAAAATTTAAAAAATTTT
1 AAAAAAATTTAAAAAATTTT
7447674 ATTTTATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 26 0.63
22 15 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAAATTTAAAAAATTTTT
Found at i:7466901 original size:2 final size:2
Alignment explanation
Indices: 7466894--7466948 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
7466884 TTGGAATTAG
7466894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7466936 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
7466949 TATTCGAAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7468593 original size:28 final size:28
Alignment explanation
Indices: 7468557--7468614 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
7468547 TTTATGAAAC
*
7468557 TATAATTAGAGTTATTATACAATCCTAT
1 TATAATTAGAGTTATTATACAATACTAT
7468585 TATAATTAGAGTTATTATACAATACTAT
1 TATAATTAGAGTTATTATACAATACTAT
7468613 TA
1 TA
7468615 CCTAGTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (28 bp):
TATAATTAGAGTTATTATACAATACTAT
Found at i:7469262 original size:18 final size:18
Alignment explanation
Indices: 7469239--7469273 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7469229 GCCATTTAGT
7469239 TAGATCAAATAAGATAGG
1 TAGATCAAATAAGATAGG
*
7469257 TAGATCAAGTAAGATAG
1 TAGATCAAATAAGATAG
7469274 TTGCTGAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (18 bp):
TAGATCAAATAAGATAGG
Found at i:7470339 original size:2 final size:2
Alignment explanation
Indices: 7470332--7470362 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7470322 AGTCTGGTCC
*
7470332 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7470363 TTGTTTTGGA
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:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7471916 original size:27 final size:27
Alignment explanation
Indices: 7471886--7471939 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
7471876 TGAAGTTATG
7471886 GAGAGTCTTACTATTACCTTGAGTAAA
1 GAGAGTCTTACTATTACCTTGAGTAAA
7471913 GAGAGTCTTACTATTACCTTGAGTAAA
1 GAGAGTCTTACTATTACCTTGAGTAAA
7471940 CATCAACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (27 bp):
GAGAGTCTTACTATTACCTTGAGTAAA
Found at i:7476683 original size:9 final size:9
Alignment explanation
Indices: 7476669--7476699 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
7476659 TTCAAGCCTT
7476669 AGCCTTCAA
1 AGCCTTCAA
7476678 AGCCTTCAA
1 AGCCTTCAA
7476687 AGCCTTCAA
1 AGCCTTCAA
7476696 AGCC
1 AGCC
7476700 AAGCCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.19
Consensus pattern (9 bp):
AGCCTTCAA
Found at i:7482117 original size:3 final size:3
Alignment explanation
Indices: 7482109--7482137 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7482099 TTAATTTTTA
7482109 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
7482138 ATGTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7485761 original size:21 final size:22
Alignment explanation
Indices: 7485730--7485770 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
7485720 GGAGAAGGAG
7485730 GAGGATGGTGGT-GGTGGACGGA
1 GAGGATGGTGGTCGG-GGACGGA
7485752 GAGG-TGGTGGTCGGGGACG
1 GAGGATGGTGGTCGGGGACG
7485771 ACGGAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.15, C:0.07, G:0.61, T:0.17
Consensus pattern (22 bp):
GAGGATGGTGGTCGGGGACGGA
Found at i:7500521 original size:210 final size:211
Alignment explanation
Indices: 7500143--7500539 Score: 573
Period size: 210 Copynumber: 1.9 Consensus size: 211
7500133 TTGGTCGGTT
* * *
7500143 TTTAATTTATACATAAAAATTACTATAACTTATAATAGACTTTATTTATATGATTACACTTAATA
1 TTTAATTTATACATAAAAATTACTACAACTTATAATAAACTTTATGTATATGATTACACTTAATA
* ** * * *
7500208 ACTTTATTAGTTATCATTTTAGATTTTATAACATATTATTTATAATTAATTATTATTTATACAAG
66 ACTTTATTAGCTATCACCTTAGATGTTATAACATATTATTTATAATGAATTATTATTTATACAAA
* * * *
7500273 TTTTGGTATAAAACAGTTGAACCTATAATTTGTATCATTAATTATATATATA-ATAAAGTAATAT
131 CTTTGATATAAAACAGTTGAACCTATAAGTTATATCATTAATTATATATATATATAAAGTAATAT
7500337 ATTACAAATACATATA
196 ATTACAAATACATATA
** *
7500353 TTTAATTTATACATAAGCATTATTACAACTTATAATAAACTTTATGTATATGATTACACTTAATA
1 TTTAATTTATACATAAAAATTACTACAACTTATAATAAACTTTATGTATATGATTACACTTAATA
* * * *
7500418 AGTTTATTAGCTATCACCTTAGATGTTATAATATATTGTTTATAATGAGTTATTATTTATACAAA
66 ACTTTATTAGCTATCACCTTAGATGTTATAACATATTATTTATAATGAATTATTATTTATACAAA
* *
7500483 CTTTGATATAAAACA-TTATAACGTATAAGTTATATCATTAATTATATATATATATAA
131 CTTTGATATAAAACAGTT-GAACCTATAAGTTATATCATTAATTATATATATATATAA
7500540 TTATTGATGA
Statistics
Matches: 163, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
209 2 0.01
210 157 0.96
211 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (211 bp):
TTTAATTTATACATAAAAATTACTACAACTTATAATAAACTTTATGTATATGATTACACTTAATA
ACTTTATTAGCTATCACCTTAGATGTTATAACATATTATTTATAATGAATTATTATTTATACAAA
CTTTGATATAAAACAGTTGAACCTATAAGTTATATCATTAATTATATATATATATAAAGTAATAT
ATTACAAATACATATA
Found at i:7501443 original size:15 final size:15
Alignment explanation
Indices: 7501423--7501453 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
7501413 TCGAAACAAA
7501423 CAAATTTCATTCATG
1 CAAATTTCATTCATG
7501438 CAAATTTCATTCATG
1 CAAATTTCATTCATG
7501453 C
1 C
7501454 GAGAGTGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (15 bp):
CAAATTTCATTCATG
Found at i:7513967 original size:20 final size:21
Alignment explanation
Indices: 7513930--7513969 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7513920 AGAAATTAAA
*
7513930 TTTTTTATTATAAGATTTTAT
1 TTTTTTATAATAAGATTTTAT
*
7513951 TTTTTTATAATTA-ATTTTA
1 TTTTTTATAATAAGATTTTA
7513970 CAATCCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTTTATAATAAGATTTTAT
Found at i:7516271 original size:24 final size:23
Alignment explanation
Indices: 7516235--7516282 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
7516225 GTTTATGATT
*
7516235 TTTTTTTCAAAAAAGTAGTTGAA
1 TTTTTTTCAAAAAAATAGTTGAA
*
7516258 TTTTTTTCTTAAAAAATAGTTGAA
1 TTTTTTTC-AAAAAAATAGTTGAA
7516282 T
1 T
7516283 ATAGGTCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (23 bp):
TTTTTTTCAAAAAAATAGTTGAA
Found at i:7516271 original size:25 final size:24
Alignment explanation
Indices: 7516232--7516282 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
7516222 CAGGTTTATG
7516232 ATTTTTTTTTCAAAAAAGTAGTTGA
1 ATTTTTTTTTCAAAAAA-TAGTTGA
7516257 ATTTTTTTCTT-AAAAAATAGTTGA
1 ATTTTTTT-TTCAAAAAATAGTTGA
7516281 AT
1 AT
7516283 ATAGGTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.36
25 14 0.56
26 2 0.08
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
ATTTTTTTTTCAAAAAATAGTTGA
Found at i:7526926 original size:7 final size:7
Alignment explanation
Indices: 7526916--7526945 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
7526906 AAAAATATTG
7526916 GCAGACA
1 GCAGACA
7526923 GCAGACA
1 GCAGACA
7526930 GCAGACA
1 GCAGACA
7526937 GCAGACA
1 GCAGACA
7526944 GC
1 GC
7526946 TAATGGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.30, G:0.30, T:0.00
Consensus pattern (7 bp):
GCAGACA
Found at i:7539807 original size:187 final size:184
Alignment explanation
Indices: 7539355--7539858 Score: 620
Period size: 184 Copynumber: 2.7 Consensus size: 184
7539345 GATGATCGAT
* * * *
7539355 TAGGTTGATAGTTCCATCCTATGGGTGATGT-ATGCATTATCAGTTGTTTCCCTAAGGTTATAGT
1 TAGGTTGATAGTTCCATCCTATGGATGAT-TAATGCATTATCATTTGTTTCCCTAGGGTTTTAGT
* * * *
7539419 TCGATTCAGTCGGTTAGGAGAATCATAGTTTATTCGTTGTTGAATTGCTTAATGATATGTTATCA
65 TTGATTCATTCGGTTAGGAGAATCATAGTTTATTCGGTATTGAATTGCTTAATGATATGTTATCA
* * * * *
7539484 ATTCATCCTTTCATTTCTTTCGAGTTGATGATGATTTTGTTAACAATTTGTTGCT
130 ATTCATCCTTTCATTCCTTTCAAGTTGATGATGATTTTGTAAACAAATTGTTGCA
* *
7539539 TAGGTTGATAGTTCCATCCTATGGATGATTAACGCCTTATCATTTGTTTCCCTAGGGTTATT-GT
1 TAGGTTGATAGTTCCATCCTATGGATGATTAATGCATTATCATTTGTTTCCCTAGGGTT-TTAGT
* * * *
7539603 CTGATTCATTGGGTTAGGAGAATCATAGTTTATTTGGTATTGAATTGCTTAATGATATGTTATTA
65 TTGATTCATTCGGTTAGGAGAATCATAGTTTATTCGGTATTGAATTGCTTAATGATATGTTATCA
**
7539668 ATTCATCCTTTTGTTCCTTTCAAGTTGATGATGATGAATTTGTAAACAACATT-TTGCA
130 ATTCATCCTTTCATTCCTTTCAAGTTGATGATGAT---TTTGTAAACAA-ATTGTTGCA
* **
7539726 TAGGTTGATAGTTCCATCTTATCAATGATTAATGCATTATCATTTGTTTCCCTAGGGTTTTAGTT
1 TAGGTTGATAGTTCCATCCTATGGATGATTAATGCATTATCATTTGTTTCCCTAGGGTTTTAGTT
* ** * ** * * *
7539791 TGATTCATTTGGTTAGGAGAATTGTAGTTTATCCATTGTTGAATTGCTTAACGGTATGTT-TCCA
66 TGATTCATTCGGTTAGGAGAATCATAGTTTATTCGGTATTGAATTGCTTAATGATATGTTAT-CA
7539855 ATTC
130 ATTC
7539859 GATATCTAGA
Statistics
Matches: 274, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
183 1 0.00
184 142 0.52
185 1 0.00
186 3 0.01
187 125 0.46
188 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (184 bp):
TAGGTTGATAGTTCCATCCTATGGATGATTAATGCATTATCATTTGTTTCCCTAGGGTTTTAGTT
TGATTCATTCGGTTAGGAGAATCATAGTTTATTCGGTATTGAATTGCTTAATGATATGTTATCAA
TTCATCCTTTCATTCCTTTCAAGTTGATGATGATTTTGTAAACAAATTGTTGCA
Found at i:7542338 original size:2 final size:2
Alignment explanation
Indices: 7542331--7542372 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7542321 CATAAAACAC
7542331 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7542373 GAAAGGAGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7546184 original size:33 final size:35
Alignment explanation
Indices: 7546147--7546228 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 35
7546137 CCCTCTGCTA
7546147 TTCTCATC-T-GACTTTACGACTTCAGTTTCTGCC
1 TTCTCATCATAGACTTTACGACTTCAGTTTCTGCC
*
7546180 TTCTCATCATCAACAGACTTTACGACTTCAGTTTCTGCT
1 TTCTCATCAT----AGACTTTACGACTTCAGTTTCTGCC
7546219 TTCTCATCAT
1 TTCTCATCAT
7546229 CAACAGTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
33 8 0.19
34 1 0.02
39 33 0.79
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (35 bp):
TTCTCATCATAGACTTTACGACTTCAGTTTCTGCC
Found at i:7546201 original size:39 final size:39
Alignment explanation
Indices: 7546156--7546234 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
7546146 ATTCTCATCT
7546156 GACTTTACGACTTCAGTTTCTGCCTTCTCATCATCAACA
1 GACTTTACGACTTCAGTTTCTGCCTTCTCATCATCAACA
*
7546195 GACTTTACGACTTCAGTTTCTGCTTTCTCATCATCAACA
1 GACTTTACGACTTCAGTTTCTGCCTTCTCATCATCAACA
7546234 G
1 G
7546235 TAGAAGATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (39 bp):
GACTTTACGACTTCAGTTTCTGCCTTCTCATCATCAACA
Found at i:7546996 original size:99 final size:99
Alignment explanation
Indices: 7546819--7547029 Score: 343
Period size: 99 Copynumber: 2.1 Consensus size: 99
7546809 GTTAGAGGAC
*
7546819 TCATTCTGTTCAGGCTTGGAAACTTCTGAAACAATATCCTCCACGCTTTCAGCAGGTAAACAATC
1 TCATTCTGTTCAGGCTTGGAAACTTCTGAAACAATATCCTCCACGATTTCAGCAGGTAAACAATC
*
7546884 CCCATTAGGATCAGAGACAGAGACAGGAACACCA
66 CCCATTACGATCAGAGACAGAGACAGGAACACCA
* *
7546918 TCATTCTGTTCAGGCTTGGAAACTTCTGAAACAGTATCTTCCAC-ATTATCAGCAGGTAAACAAT
1 TCATTCTGTTCAGGCTTGGAAACTTCTGAAACAATATCCTCCACGATT-TCAGCAGGTAAACAAT
* * *
7546982 TCCCATTACTATCAGAGACAGAGAGAGGAACACCA
65 CCCCATTACGATCAGAGACAGAGACAGGAACACCA
7547017 TCATTCTGTTCAG
1 TCATTCTGTTCAG
7547030 CCCCGGAATC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 2 0.02
99 102 0.98
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (99 bp):
TCATTCTGTTCAGGCTTGGAAACTTCTGAAACAATATCCTCCACGATTTCAGCAGGTAAACAATC
CCCATTACGATCAGAGACAGAGACAGGAACACCA
Found at i:7547395 original size:105 final size:105
Alignment explanation
Indices: 7547231--7547454 Score: 371
Period size: 105 Copynumber: 2.1 Consensus size: 105
7547221 GCTAAAGCAT
* *
7547231 CTCCATTGCTATCACCATCATCAGGTACAGCCGTTTCAGAGTCCTCATTCTCTTGTGACCTGGAA
1 CTCCATTACTATCACCATCATCAGCTACAGCCGTTTCAGAGTCCTCATTCTCTTGTGACCTGGAA
7547296 TCGACAACACTGTC-TCTGAAACTATCATTAGCCAAACTAC
66 TCGACAACACTGTCTTC-GAAACTATCATTAGCCAAACTAC
*
7547336 CTCCATTACTATCACCATCATCAGCTACAGCCGTTTCAGAGTCCTCATT-TGCTTTTGACCTGGA
1 CTCCATTACTATCACCATCATCAGCTACAGCCGTTTCAGAGTCCTCATTCT-CTTGTGACCTGGA
* *
7547400 ATCGACAACACTGTCTTCGACACTGTCATTAGCCAAACTAC
65 ATCGACAACACTGTCTTCGAAACTATCATTAGCCAAACTAC
7547441 CTCCATTACTATCA
1 CTCCATTACTATCA
7547455 GAGACAGAGA
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
104 1 0.01
105 109 0.97
106 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.29
Consensus pattern (105 bp):
CTCCATTACTATCACCATCATCAGCTACAGCCGTTTCAGAGTCCTCATTCTCTTGTGACCTGGAA
TCGACAACACTGTCTTCGAAACTATCATTAGCCAAACTAC
Found at i:7548886 original size:17 final size:16
Alignment explanation
Indices: 7548863--7548901 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
7548853 TTTTTTTAAT
7548863 TATTTTTATATATAAATA
1 TATTTTT-T-TATAAATA
7548881 -ATTTTTTTATAAATA
1 TATTTTTTTATAAATA
7548896 TATTTT
1 TATTTT
7548902 GAAAATGTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTTTTATAAATA
Found at i:7558370 original size:29 final size:29
Alignment explanation
Indices: 7558337--7558398 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
7558327 GAAATGTCTG
** *
7558337 ATGTGGTAACTGCACTAACAAAATGTTCA
1 ATGTGGTAACCACACTAAAAAAATGTTCA
* *
7558366 ATGTGGTATCCATACTAAAAAAATGTTCA
1 ATGTGGTAACCACACTAAAAAAATGTTCA
7558395 ATGT
1 ATGT
7558399 AGTACCCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (29 bp):
ATGTGGTAACCACACTAAAAAAATGTTCA
Found at i:7562033 original size:18 final size:17
Alignment explanation
Indices: 7562010--7562045 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
7562000 ATTGAAACTT
*
7562010 TTTATTTTTTACTTTTTA
1 TTTATTATTTA-TTTTTA
7562028 TTTATTATTTATTTTTA
1 TTTATTATTTATTTTTA
7562045 T
1 T
7562046 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTATTTATTTTTA
Found at i:7585885 original size:12 final size:15
Alignment explanation
Indices: 7585854--7585886 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
7585844 TATCCATGGC
7585854 ATGATGATGAGGGTG
1 ATGATGATGAGGGTG
*
7585869 ATGATGATGGGGGTG
1 ATGATGATGAGGGTG
7585884 ATG
1 ATG
7585887 GCTATGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.27
Consensus pattern (15 bp):
ATGATGATGAGGGTG
Found at i:7585953 original size:15 final size:15
Alignment explanation
Indices: 7585933--7585975 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
7585923 TTGGAGAGAG
7585933 TGATGATGAAGAAGA
1 TGATGATGAAGAAGA
7585948 TGATGAT-AGAGAAGA
1 TGATGATGA-AGAAGA
*
7585963 GGATGATGAAGAA
1 TGATGATGAAGAA
7585976 TACAATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.19
Consensus pattern (15 bp):
TGATGATGAAGAAGA
Found at i:7588086 original size:177 final size:177
Alignment explanation
Indices: 7587769--7588661 Score: 1385
Period size: 177 Copynumber: 5.0 Consensus size: 177
7587759 TGAGTTTGAA
* * * *
7587769 GAACTCATATCACACAACAACAACCATTTGTTCTTGTGAACCAGAAACATCATAGTATTGGTATA
1 GAACTCATA-C-CAC-ACAACAATCATTTGTTCTTGTGAATCAGAAACATCATGGTATTGGTCTA
* *
7587834 AGATTTTGCCTTCCACAAGCTGCAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACAC
63 AGATTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACAC
* * *
7587899 CCAGTTCTCTTCATTGTTCAAATCCTGGAAAACGATCACTGATAACACTG
128 CCACTTCTCTTCATTGTTCAAATCCTGGAAAACTATCACTGATAACATTG
* *
7587949 GAACTCATACCAAACAACAATCATTTGTTCTTGTGAATCAGAAACATCATGGTATTGGTCTAGGA
1 GAACTCATACCACACAACAATCATTTGTTCTTGTGAATCAGAAACATCATGGTATTGGTCTAAGA
* * *
7588014 TTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTCAACCAAACCCA
66 TTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACACCCA
* *
7588079 CTTCTCTTCATTGTTCAAATCCTGGAAAACTATTACTGATCACATTG
131 CTTCTCTTCATTGTTCAAATCCTGGAAAACTATCACTGATAACATTG
* *
7588126 GAACTCATACCACACAACAATCATTTGTTCTTGTGAATCAAAAACATCATATAGTATTGGTCTAA
1 GAACTCATACCACACAACAATCATTTGTTCTTGTGAATCAGAAACATC--ATGGTATTGGTCTAA
*
7588191 GATTATGCCTTCCACAAGCTACAAAATGTAAACAAATTCATTAACAAGATTATTTGATCCACACC
64 GATTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACACC
** * *
7588256 CTGTTCTCCTCATTGTTCAAATCCTGGAAAACAATCACTGATAACATTG
129 CACTTCTCTTCATTGTTCAAATCCTGGAAAACTATCACTGATAACATTG
* * * *
7588305 GAACTCAAACCACACAACAATCATTTGTTCTTGTGAATCAGAAACGTCACGGTATTAGTCTAAAG
1 GAACTCATACCACACAACAATCATTTGTTCTTGTGAATCAGAAACATCATGGTATTGGTCT-AAG
* *
7588370 ATTAAGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTGTTTGATCCGA-ACC
65 ATTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCC-ACACC
*
7588434 CACTTCTCTTCATTGTTAAAATCCTGGAAAACTATCACTGATCAA-ATTG
129 CACTTCTCTTCATTGTTCAAATCCTGGAAAACTATCACTGAT-AACATTG
*
7588483 GAACTCATACCACACAACAATCATTTGTTCTTGTGAATTAGAAACATCATGGTATTGGTCTAAGA
1 GAACTCATACCACACAACAATCATTTGTTCTTGTGAATCAGAAACATCATGGTATTGGTCTAAGA
*
7588548 TTAGGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACACCCA
66 TTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACACCCA
* * *
7588613 CTTCTCTTTATTGTTCAAATCCTGGAAAACTATCACTCATCACATTG
131 CTTCTCTTCATTGTTCAAATCCTGGAAAACTATCACTGATAACATTG
7588660 GA
1 GA
7588662 CAAATACCAA
Statistics
Matches: 651, Mismatches: 55, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
176 2 0.00
177 313 0.48
178 161 0.25
179 166 0.25
180 9 0.01
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (177 bp):
GAACTCATACCACACAACAATCATTTGTTCTTGTGAATCAGAAACATCATGGTATTGGTCTAAGA
TTATGCCTTCCACAAGCTACAAAATGTGAACAAATTCATTAACAAGATTATTTGATCCACACCCA
CTTCTCTTCATTGTTCAAATCCTGGAAAACTATCACTGATAACATTG
Found at i:7591121 original size:51 final size:51
Alignment explanation
Indices: 7591062--7591166 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
7591052 TATGATCTCT
7591062 ATTTTTTTTCCCTTAAAACAATTAATTAATAAATATTATTAAAAGTTTTAG
1 ATTTTTTTTCCCTTAAAACAATTAATTAATAAATATTATTAAAAGTTTTAG
7591113 ATTTTTTTTCCCTTAAAACAATTAATTAATAAATATTATTAAAAGTTTTAG
1 ATTTTTTTTCCCTTAAAACAATTAATTAATAAATATTATTAAAAGTTTTAG
7591164 ATT
1 ATT
7591167 GCGATAAGCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.48
Consensus pattern (51 bp):
ATTTTTTTTCCCTTAAAACAATTAATTAATAAATATTATTAAAAGTTTTAG
Found at i:7592282 original size:204 final size:202
Alignment explanation
Indices: 7591913--7592285 Score: 473
Period size: 204 Copynumber: 1.8 Consensus size: 202
7591903 TAATTTATAT
* * * *
7591913 ATTATAATATTTTAATTTTTATATAAAAATTTGTATAAATAATAATCGATTACAAACAATATCTT
1 ATTATAATATTATAATTTTTATATAAAAATTTATATAAATAATAATCAATAACAAACAATATCTT
* * * * *
7591978 ATAAAATTAAAATGATAATTAATACAATTATTAAGTGTAGTCATATAAATAAAGTCTATTATAAG
66 ATAAAACTAAAATGATAATTAATAAAATCATTAAGTGTAATCATATAAATAAAATCTATTATAAG
* * * *
7592043 TTATAGTAATACTTATGTGTATAAATTTAATATATATAATATCACTTTATTATATATATAATTAA
131 TCATAATAATA-TTATATCTATAAATTTAATATATATAATATCACTTTATTATATATATAATTAA
7592108 TGACATAA
195 TGACATAA
* * * * *
7592116 ATTAT-ATATTATAATATTTTATATCAAATTTTATATAAATAATAA-CTAATAATAAATAATATG
1 ATTATAATATTATAAT-TTTTATATAAAAATTTATATAAATAATAATC-AATAACAAACAATATC
** *
7592179 TTATAAAAACTAAGGTGATAATTAATAAAATCATTAAGTGTAATCATATAAATAAAATTTATTAT
64 TTAT-AAAACTAAAATGATAATTAATAAAATCATTAAGTGTAATCATATAAATAAAATCTATTAT
*
7592244 AAGTCATAATAAT-TTTTATCTATAAATTATATATATATATAA
128 AAGTCATAATAATATTATATCTATAAATT-TA-ATATATATAA
7592286 AATAGTGATA
Statistics
Matches: 143, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
202 22 0.15
203 48 0.34
204 73 0.51
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (202 bp):
ATTATAATATTATAATTTTTATATAAAAATTTATATAAATAATAATCAATAACAAACAATATCTT
ATAAAACTAAAATGATAATTAATAAAATCATTAAGTGTAATCATATAAATAAAATCTATTATAAG
TCATAATAATATTATATCTATAAATTTAATATATATAATATCACTTTATTATATATATAATTAAT
GACATAA
Found at i:7593265 original size:17 final size:17
Alignment explanation
Indices: 7593243--7593279 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7593233 CAGTAATATT
*
7593243 TATGTATAAATTAAATA
1 TATGTATAAATAAAATA
*
7593260 TATGTATATATAAAATA
1 TATGTATAAATAAAATA
7593277 TAT
1 TAT
7593280 TATTTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
TATGTATAAATAAAATA
Found at i:7593443 original size:213 final size:217
Alignment explanation
Indices: 7593062--7593482 Score: 548
Period size: 213 Copynumber: 1.9 Consensus size: 217
7593052 ATAATCTCAC
* * * *
7593062 TTTATTATATATATGAAATTAATGATACAATTTATATGTTATAATATTTTATTTTTTAATTCAAA
1 TTTATTATATATATAAAATTAATGACACAACTTATATGTTATAATATTTTA----TTAATCCAAA
** * * *
7593127 ATTTGTATAAATAATAACTAATTATAAACTGTATGTTATAAAAATTAAGGCGATAACTAACAAAA
62 ATTTGTATAAATAATAACTAATTATAAACAATATGCTATAAAAACTAAAGCGATAACTAACAAAA
*
7593192 TTATTAAGCATAATCATATAAATAAAGTTTACTATAAGTTACAGTAATAT-TTATGTATAAATTA
127 TTATTAAACATAATCATATAAATAAAGTTTACTATAAGTTACAGTAAT-TCTTATGTATAAATTA
*
7593256 AATATATGTATATATAAAATATATTAT
191 AATATATATATATATAAAATATATTAT
* *
7593283 TTTATTATATATATAAAATTAATGACACAACTTATATGTTCTAATGTTTTA-T-A-CCAAAATTT
1 TTTATTATATATATAAAATTAATGACACAACTTATATGTTATAATATTTTATTAATCCAAAATTT
* * *
7593345 GTATAAATAATAACTAA-TATAAACAATATGCTATAAAAACTAAAGTGATAATTAATAAAGA-TA
66 GTATAAATAATAACTAATTATAAACAATATGCTATAAAAACTAAAGCGATAACTAACAAA-ATTA
** * * * *
7593408 TTAAATGTAATCATATAAATAAAGTTTATTATAAGTTATAGTAGTTCTTATGTTTAAATTAAATA
130 TTAAACATAATCATATAAATAAAGTTTACTATAAGTTACAGTAATTCTTATGTATAAATTAAATA
7593473 TATATATATA
195 TATATATATA
7593483 ATAGCTATAC
Statistics
Matches: 176, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
212 1 0.01
213 101 0.57
214 26 0.15
215 1 0.01
216 1 0.01
221 46 0.26
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (217 bp):
TTTATTATATATATAAAATTAATGACACAACTTATATGTTATAATATTTTATTAATCCAAAATTT
GTATAAATAATAACTAATTATAAACAATATGCTATAAAAACTAAAGCGATAACTAACAAAATTAT
TAAACATAATCATATAAATAAAGTTTACTATAAGTTACAGTAATTCTTATGTATAAATTAAATAT
ATATATATATAAAATATATTAT
Done.