Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 21
Found at i:3252021 original size:10 final size:10
Alignment explanation
Indices: 3252006--3252045 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
3251996 TCCAGCAAAG
3252006 AAAAAAGAAA
1 AAAAAAGAAA
3252016 AAAAAAGAAAA
1 AAAAAAG-AAA
3252027 AAGAAAAGAAA
1 AA-AAAAGAAA
3252038 AAAAAAGA
1 AAAAAAGA
3252046 GAAGAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 13 0.46
11 10 0.36
12 5 0.18
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:3252024 original size:17 final size:18
Alignment explanation
Indices: 3252002--3252063 Score: 83
Period size: 17 Copynumber: 3.4 Consensus size: 18
3251992 CTCATCCAGC
3252002 AAAGAAAAAAGAAAA-AA
1 AAAGAAAAAAGAAAAGAA
3252019 AAAGAAAAAAGAAAAGAA
1 AAAGAAAAAAGAAAAGAA
*
3252037 AAA-AAAAGAGAAGAAGAA
1 AAAGAAAAAAGAA-AAGAA
3252055 AAAGGAAAA
1 AAA-GAAAA
3252064 TTGAATCAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 23 0.57
18 13 0.32
20 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAGAA
Found at i:3252028 original size:12 final size:12
Alignment explanation
Indices: 3252013--3252063 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
3252003 AAGAAAAAAG
3252013 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
3252025 AAAAGAAAAGAA
1 AAAAAAAAAGAA
*
3252037 AAAAAAAGAGAA
1 AAAAAAAAAGAA
* *
3252049 GAAGAAAAAGGAA
1 -AAAAAAAAAGAA
3252062 AA
1 AA
3252064 TTGAATCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:3252036 original size:22 final size:23
Alignment explanation
Indices: 3252008--3252056 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
3251998 CAGCAAAGAA
3252008 AAAAGAAAAAAAAAGA-AAAAAG
1 AAAAGAAAAAAAAAGAGAAAAAG
*
3252030 AAAAGAAAAAAAAAGAGAAGAAG
1 AAAAGAAAAAAAAAGAGAAAAAG
3252053 AAAA
1 AAAA
3252057 AGGAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAAAAAGAGAAAAAG
Found at i:3252040 original size:24 final size:23
Alignment explanation
Indices: 3252002--3252063 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
3251992 CTCATCCAGC
3252002 AAAGAAAAAAGAAAAAAAAAGAA
1 AAAGAAAAAAGAAAAAAAAAGAA
*
3252025 AAA-AGAAAAGAAAAAAAAAGAGA
1 AAAGAAAAAAGAAAAAAAAAGA-A
*
3252048 AGAAGAAAAAGGAAAA
1 A-AAGAAAAAAGAAAA
3252064 TTGAATCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 17 0.52
23 5 0.15
24 2 0.06
25 9 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAGAAAAAAAAAGAA
Found at i:3254488 original size:93 final size:93
Alignment explanation
Indices: 3254344--3254722 Score: 575
Period size: 93 Copynumber: 4.1 Consensus size: 93
3254334 ATAAGAAGAC
*
3254344 CTCATAGCATCTTCTGGAAG-AGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAA
1 CTCATAGCACCTTCTGGAAGTA-TTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAA
*
3254408 CCAATCATTGAATTTAGAAGATGAATGTG
65 CCAATCATTGAATTTGGAAGATGAATGTG
3254437 CTCATAGCACCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAAC
1 CTCATAGCACCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAAC
3254502 CAATCATTGAATTTGGAAGATGAATGTG
66 CAATCATTGAATTTGGAAGATGAATGTG
* * *
3254530 CTCATAGCACCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAATCATAGAAC
1 CTCATAGCACCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAAC
*
3254595 CAATCATTGAATTTGGAAGATGAATGTT
66 CAATCATTGAATTTGGAAGATGAATGTG
* * * * *
3254623 CTCATAGCATCTTGTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACTC-CAAAA
1 CTCATAGCACCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAGAA
* * * *
3254686 TCAATCATTGGATTTGAAAGATGAATTTTG
65 CCAATCATTGAATTTGGAAGATGAA-TGTG
3254716 CTCATAG
1 CTCATAG
3254723 TAGAAATAAT
Statistics
Matches: 266, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
92 27 0.10
93 238 0.89
94 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (93 bp):
CTCATAGCACCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAAC
CAATCATTGAATTTGGAAGATGAATGTG
Found at i:3257242 original size:22 final size:22
Alignment explanation
Indices: 3257205--3257259 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3257195 ATCTACACTC
*
3257205 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
* *
3257227 TTTAAAGCTGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3257249 TTCAAAGATGA
1 TTCAAAGATGA
3257260 AAGCTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:3258022 original size:76 final size:76
Alignment explanation
Indices: 3257940--3258193 Score: 481
Period size: 76 Copynumber: 3.3 Consensus size: 76
3257930 CTATTTCCTA
*
3257940 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3258005 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3258016 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3258081 AGCCTTCGGGT
66 AGCCTTCGGGT
*
3258092 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3258157 AGCCTTCGGGT
66 AGCCTTCGGGT
3258168 CATCTGTAAGCCCTTCAGTGCATGAT
1 CATCTGTAAGCCCTTCAGTGCATGAT
3258194 CCAGCCTTTT
Statistics
Matches: 173, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 173 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:3258212 original size:59 final size:59
Alignment explanation
Indices: 3258140--3258252 Score: 217
Period size: 59 Copynumber: 1.9 Consensus size: 59
3258130 CCTTCGGGAG
3258140 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATCCAGC
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATCCAGC
*
3258199 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGAT
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
3258253 GTTTCCAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (59 bp):
CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATCCAGC
Found at i:3258817 original size:76 final size:76
Alignment explanation
Indices: 3258199--3258783 Score: 1072
Period size: 76 Copynumber: 7.8 Consensus size: 76
3258189 ATGATCCAGC
3258199 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
3258264 GCCTTCGGGAG
66 GCCTTCGGGAG
3258275 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
3258340 GCCTTCGGGAG
66 GCCTTCGGGAG
*
3258351 CTTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
3258415 GCCTTC--G-G
66 GCCTTCGGGAG
*
3258423 C-TTTTGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
3258487 GCCTTCGGGAG
66 GCCTTCGGGAG
*
3258498 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
*
3258563 GCCTTCAGGAG
66 GCCTTCGGGAG
3258574 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
*
3258639 GCCTTCAGGAG
66 GCCTTCGGGAG
* *
3258650 CTTTTAGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
3258715 GCCTTCGGGAG
66 GCCTTCGGGAG
3258726 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
3258784 TTAAGACCTC
Statistics
Matches: 493, Mismatches: 11, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
71 22 0.04
72 47 0.10
73 1 0.00
74 1 0.00
75 47 0.10
76 375 0.76
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
GCCTTCGGGAG
Found at i:3258940 original size:9 final size:9
Alignment explanation
Indices: 3258926--3258964 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3258916 GTAAACACTA
*
3258926 ATTTTTTTT
1 ATTTTTATT
3258935 ATTTTTATT
1 ATTTTTATT
*
3258944 ATTATTATT
1 ATTTTTATT
*
3258953 ATTATTATT
1 ATTTTTATT
3258962 ATT
1 ATT
3258965 AAATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTATT
Found at i:3258945 original size:3 final size:3
Alignment explanation
Indices: 3258933--3258985 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
3258923 CTAATTTTTT
* *
3258933 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
3258979 -TA TTA TT
1 TTA TTA TT
3258986 TACAAACAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3259028 original size:26 final size:26
Alignment explanation
Indices: 3258992--3259046 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
3258982 TATTTACAAA
* * *
3258992 CAGTTACAAACCAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
3259018 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
3259044 CAG
1 CAG
3259047 ACCAACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.33, G:0.18, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:3260373 original size:13 final size:13
Alignment explanation
Indices: 3260357--3260396 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
3260347 ATATAATAAA
3260357 TAAATATTTATTT
1 TAAATATTTATTT
*
3260370 TAAATAAATTATTT
1 TAAAT-ATTTATTT
3260384 T-AATATTTATTT
1 TAAATATTTATTT
3260396 T
1 T
3260397 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:3268448 original size:18 final size:19
Alignment explanation
Indices: 3268425--3268460 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3268415 CCCTTTGGGA
3268425 TTAGACTTT-CCATTACCC
1 TTAGACTTTGCCATTACCC
3268443 TTAGACTTTGCCATTACC
1 TTAGACTTTGCCATTACC
3268461 TTATTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.31, G:0.08, T:0.39
Consensus pattern (19 bp):
TTAGACTTTGCCATTACCC
Found at i:3270111 original size:91 final size:91
Alignment explanation
Indices: 3269956--3270137 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
3269946 AGAAATACAA
3269956 CAGAAGTATAGGAAAGTAAGACACGCATGCCGTATTTAAAAATGACAACCATTGCAAAGAAAGGG
1 CAGAAGTATAGGAAAGTAAGACACGCATGCCGTATTTAAAAATGACAACCATTGCAAAGAAAGGG
3270021 TTGTAACCATGCATGTCAAACATCGT
66 TTGTAACCATGCATGTCAAACATCGT
3270047 CAGAAGTATAGGAAAGTAAGACACGCATGCCGTATTTAAAAATGACAACCATTGCAAAGAAAGGG
1 CAGAAGTATAGGAAAGTAAGACACGCATGCCGTATTTAAAAATGACAACCATTGCAAAGAAAGGG
3270112 TTGTAACCATGCATGTCAAACATCGT
66 TTGTAACCATGCATGTCAAACATCGT
3270138 ACATATCATA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (91 bp):
CAGAAGTATAGGAAAGTAAGACACGCATGCCGTATTTAAAAATGACAACCATTGCAAAGAAAGGG
TTGTAACCATGCATGTCAAACATCGT
Found at i:3273221 original size:204 final size:208
Alignment explanation
Indices: 3272861--3273273 Score: 798
Period size: 204 Copynumber: 2.0 Consensus size: 208
3272851 AGAGAAGGGA
3272861 TTGATCTTTTTTCAAGAGGGACCGATTCTTTGCATAATAGTAAGTTTGGGATTGATCTTTCTGAC
1 TTGATCTTTTTTCAAGAGGGACCGATTCTTTGCATAATAGTAAGTTTGGGATTGATCTTTCTGAC
3272926 CAAGGGATCAATCTTTTTTGAAAAGGGATCGATCCATTCCCCTAAGGGTTCAATCCTTTTTCTGG
66 CAAGGGATCAATCTTTTTTGAAAAGGGATCGATCCATTCCCCTAAGGGTTCAATCCTTTTTCTGG
3272991 AAAAGTATCAAATTCTCAAGAACTTGCATAAATGAGTTACGAATCTTCCACTTAATGAATCCTAC
131 AAAAGTATCAAATTCTCAAGAACTTGCATAAATGAGTTACGAATCTTCCACTTAATGAATCCTAC
3273056 AAACTAGATACAT
196 AAACTAGATACAT
3273069 TTGATC-TTTTTCAAGAGGGACCGATTCTTTGCATAATAGTAAGTTT-GGATTGATCTTTC-GAC
1 TTGATCTTTTTTCAAGAGGGACCGATTCTTTGCATAATAGTAAGTTTGGGATTGATCTTTCTGAC
3273131 CAAGGGATCAATC-TTTTTGAAAAGGGATCGATCCATTCCCCTAAGGGTTCAATCCTTTTTCTGG
66 CAAGGGATCAATCTTTTTTGAAAAGGGATCGATCCATTCCCCTAAGGGTTCAATCCTTTTTCTGG
3273195 AAAAGTATCAAATTCTCAAGAACTTGCATAAATGAGTTACGAATCTTCCACTTAATGAATCCTAC
131 AAAAGTATCAAATTCTCAAGAACTTGCATAAATGAGTTACGAATCTTCCACTTAATGAATCCTAC
3273260 AAACTAGATACAT
196 AAACTAGATACAT
3273273 T
1 T
3273274 CTTAAACACT
Statistics
Matches: 205, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
204 130 0.63
205 16 0.08
206 13 0.06
207 40 0.20
208 6 0.03
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (208 bp):
TTGATCTTTTTTCAAGAGGGACCGATTCTTTGCATAATAGTAAGTTTGGGATTGATCTTTCTGAC
CAAGGGATCAATCTTTTTTGAAAAGGGATCGATCCATTCCCCTAAGGGTTCAATCCTTTTTCTGG
AAAAGTATCAAATTCTCAAGAACTTGCATAAATGAGTTACGAATCTTCCACTTAATGAATCCTAC
AAACTAGATACAT
Found at i:3273919 original size:31 final size:31
Alignment explanation
Indices: 3273884--3273981 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
3273874 TTACATGCAA
3273884 ATACTTCTCACTTGTTTTTACCCCAACATTC
1 ATACTTCTCACTTGTTTTTACCCCAACATTC
** * ****** *
3273915 ATACTATCATGTCTTGCTTTTATATTTGCA--A
1 ATACT-TC-TCACTTGTTTTTACCCCAACATTC
3273946 ATACTTCTCACTTGTTTTTACCCCAACATTC
1 ATACTTCTCACTTGTTTTTACCCCAACATTC
3273977 ATACT
1 ATACT
3273982 ATCATGTCTT
Statistics
Matches: 43, Mismatches: 20, Indels: 8
0.61 0.28 0.11
Matches are distributed among these distances:
29 12 0.28
30 2 0.05
31 15 0.35
32 2 0.05
33 12 0.28
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (31 bp):
ATACTTCTCACTTGTTTTTACCCCAACATTC
Found at i:3273936 original size:33 final size:33
Alignment explanation
Indices: 3273894--3273998 Score: 83
Period size: 33 Copynumber: 3.3 Consensus size: 33
3273884 ATACTTCTCA
*
3273894 CTTGTTTTTACCCCAACATTCATACTATCATGT
1 CTTGCTTTTACCCCAACATTCATACTATCATGT
****** * **
3273927 CTTGCTTTTATATTTGCA--AATACT-TC-TCA
1 CTTGCTTTTACCCCAACATTCATACTATCATGT
*
3273956 CTTGTTTTTACCCCAACATTCATACTATCATGT
1 CTTGCTTTTACCCCAACATTCATACTATCATGT
3273989 CTTGCTTTTA
1 CTTGCTTTTA
3273999 TATTCACATA
Statistics
Matches: 47, Mismatches: 21, Indels: 8
0.62 0.28 0.11
Matches are distributed among these distances:
29 12 0.26
30 2 0.04
31 10 0.21
32 2 0.04
33 21 0.45
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.46
Consensus pattern (33 bp):
CTTGCTTTTACCCCAACATTCATACTATCATGT
Found at i:3273976 original size:62 final size:62
Alignment explanation
Indices: 3273879--3274002 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
3273869 CAACCTTACA
3273879 TGCAAATACTTCTCACTTGTTTTTACCCCAACATTCATACTATCATGTCTTGCTTTTATATT
1 TGCAAATACTTCTCACTTGTTTTTACCCCAACATTCATACTATCATGTCTTGCTTTTATATT
3273941 TGCAAATACTTCTCACTTGTTTTTACCCCAACATTCATACTATCATGTCTTGCTTTTATATT
1 TGCAAATACTTCTCACTTGTTTTTACCCCAACATTCATACTATCATGTCTTGCTTTTATATT
3274003 CACATATTCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (62 bp):
TGCAAATACTTCTCACTTGTTTTTACCCCAACATTCATACTATCATGTCTTGCTTTTATATT
Found at i:3284535 original size:9 final size:9
Alignment explanation
Indices: 3284521--3284555 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3284511 GCGTTGGATA
3284521 GTCAAATTG
1 GTCAAATTG
3284530 GTCAAATT-
1 GTCAAATTG
*
3284538 GTCAAGTTG
1 GTCAAATTG
3284547 GTCAAATTG
1 GTCAAATTG
3284556 CTGCGGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (9 bp):
GTCAAATTG
Found at i:3284547 original size:17 final size:17
Alignment explanation
Indices: 3284521--3284555 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3284511 GCGTTGGATA
3284521 GTCAAATTGGTCAAATT
1 GTCAAATTGGTCAAATT
*
3284538 GTCAAGTTGGTCAAATT
1 GTCAAATTGGTCAAATT
3284555 G
1 G
3284556 CTGCGGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
GTCAAATTGGTCAAATT
Found at i:3294289 original size:30 final size:30
Alignment explanation
Indices: 3294246--3294312 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
3294236 AGACTTATAA
* *
3294246 AAAAGTTGGGGACCATTAT-ATAATTTTTG
1 AAAAGTTGGGGACCATTATAACAATTTTGG
*
3294275 AAAAGTTGGGGGACCATTTTAACAATTTTGG
1 AAAAGTT-GGGGACCATTATAACAATTTTGG
3294306 AAAAGTT
1 AAAAGTT
3294313 ATAAATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 7 0.21
30 11 0.33
31 15 0.45
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.34
Consensus pattern (30 bp):
AAAAGTTGGGGACCATTATAACAATTTTGG
Found at i:3300072 original size:30 final size:30
Alignment explanation
Indices: 3299985--3300072 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
3299975 AATATAAATA
* *
3299985 GTGACCAAAATGG-AAATTTTGAAAGTTTG
1 GTGACCAAAATGGTAATTTTTAAAAGTTTG
* *
3300014 GTGACCAAAGT-ATAATCTTTTGAAAAGTTTAG
1 GTGACCAAAATGGTAAT-TTTT-AAAAGTTT-G
3300046 G-GACCAAAATGGTAATTTTTAAAAGTT
1 GTGACCAAAATGGTAATTTTTAAAAGTT
3300073 ATATTTTGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
29 12 0.25
30 11 0.23
31 19 0.40
32 6 0.12
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (30 bp):
GTGACCAAAATGGTAATTTTTAAAAGTTTG
Found at i:3300564 original size:11 final size:11
Alignment explanation
Indices: 3300550--3300577 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3300540 TTTAATATTC
3300550 ATTTAAGGTAA
1 ATTTAAGGTAA
3300561 ATTTAAGGTAA
1 ATTTAAGGTAA
3300572 ATTTAA
1 ATTTAA
3300578 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (11 bp):
ATTTAAGGTAA
Found at i:3306713 original size:21 final size:21
Alignment explanation
Indices: 3306687--3306739 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
3306677 TTAACATATT
3306687 TATACTCCTCGAAGAAGTACC
1 TATACTCCTCGAAGAAGTACC
*
3306708 TATACTCCTCGAAGGAGTACC
1 TATACTCCTCGAAGAAGTACC
*
3306729 GATACTCCTCG
1 TATACTCCTCG
3306740 TTTAGTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (21 bp):
TATACTCCTCGAAGAAGTACC
Found at i:3308168 original size:3 final size:3
Alignment explanation
Indices: 3308160--3308187 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3308150 GAATAGGGTT
3308160 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
3308188 GCTTCATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:3310195 original size:46 final size:46
Alignment explanation
Indices: 3310121--3310316 Score: 216
Period size: 46 Copynumber: 4.3 Consensus size: 46
3310111 AAATGAATGA
* *
3310121 ATAAATGAAAATGCATAATGGTGAATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAATAGTGCATTATCGGCATGAAAGGATGCC
*
3310167 ATAAATGAAAATGCATAATATTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAATAGTGCATTATCGGCATGAAAGGATGCC
* * ** * * * * *
3310213 GTAAATTAAAATGCGCAA-CGATGTATTATCGGCCTGAAATGATGTC
1 ATAAATGAAAATGCATAATAG-TGCATTATCGGCATGAAAGGATGCC
* ** *
3310259 ATAAATGAAAATGCATAATGGTGCATTATTTGCATGAAAAGA-GACC
1 ATAAATGAAAATGCATAATAGTGCATTATCGGCATGAAAGGATG-CC
3310305 ATAAATGAAAAT
1 ATAAATGAAAAT
3310317 AAAGAATAAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
45 1 0.01
46 121 0.98
47 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (46 bp):
ATAAATGAAAATGCATAATAGTGCATTATCGGCATGAAAGGATGCC
Found at i:3310310 original size:92 final size:92
Alignment explanation
Indices: 3310121--3310316 Score: 241
Period size: 92 Copynumber: 2.1 Consensus size: 92
3310111 AAATGAATGA
** * * *
3310121 ATAAATGAAAATGCATAATGGTGAATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
1 ATAAATGAAAATGCGCAACGATGTATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
* *
3310186 ATTGCATTATCGGCATGAAAGGATGCC
66 AGTGCATTATCGGCATGAAAAGATGCC
* * * * *
3310213 GTAAATTAAAATGCGCAACGATGTATTATCGGCCTGAAATGATGTCATAAATGAAAATGCATAAT
1 ATAAATGAAAATGCGCAACGATGTATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
* **
3310278 GGTGCATTATTTGCATGAAAAGA-GACC
66 AGTGCATTATCGGCATGAAAAGATG-CC
3310305 ATAAATGAAAAT
1 ATAAATGAAAAT
3310317 AAAGAATAAT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
91 1 0.01
92 85 0.99
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (92 bp):
ATAAATGAAAATGCGCAACGATGTATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAT
AGTGCATTATCGGCATGAAAAGATGCC
Found at i:3313155 original size:57 final size:57
Alignment explanation
Indices: 3313011--3314863 Score: 2714
Period size: 57 Copynumber: 32.6 Consensus size: 57
3313001 TCTAATACAT
* * *
3313011 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAATGCCATATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3313068 -AATTCATACACTTAATATGATTTCTTAACATTTTAGCATACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
3313124 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * ** *
3313181 AAATTCAAACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAATACCATATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
3313238 -AATTCATACACTTAATATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
3313294 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * * *
3313351 AAATTCAAACACTTAGTATGATATCTTAACAATTTAGCGTATGAAATGTCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3313408 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCGCTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3313465 AAATTCATATACTTAGTATGATTTCTTAATATTTTAGCGTACGAAACACACTACCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3313522 AAATTCATACACTTAGAATCATTTCTTAACATTTTAGCGTACGAAACACCATATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3313579 GAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3313636 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACTAAACGCCTTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3313693 AAATTTATACACTTAATATGATTTCTTAACATTTTAACATACGAAAAGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
3313750 AAATTCATACAATTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3313807 AAATTCATATACTTAGTATGATTTCTTAATATTTTAGCGTACGAAATGCACTACCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3313864 AAATTCATACACTAAGAATGATTTCTTAACATTTTAGCGTACGAAACGCGCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3313921 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3313978 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACTAAACGCCTTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3314035 AAATTTATACACTTAATATGATTTCTTAACATTTTAGCATACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
3314092 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3314149 AAATTCATATACTTAGTATGATTTCTTAACATTTTAGCGTACGAAATGTCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3314206 AAATTCATACACTTTGTATGATTTCTTAATATTTTAGCATACAAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3314263 AAATTCATACACTTAGTATGATTTCTTAATATTTTAGCGTACAAAATGCCCAACCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3314320 AAATTCATACACTTAGAATGATTTCTTAACATTTTA---T--GAAATGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3314372 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3314429 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACTAAACGCCTTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * *
3314486 AAATCCATACACTTAGTATGATTTCATAATATTTTAGCATACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * * *
3314543 TAATTCATACACTTAGTATTATTTCTTAACATTTTAGCATATGAAACGGCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * **
3314600 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAATGCCCTATCCA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * ** *
3314657 AAATTAATACACTAAGTATGATTTCTTTACATTTTAGCGTAC-AAAAACCCTATCCG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* ** *
3314713 AAATTCATACACTAAGTATGATTTCTTAACATTTTAGCGTATAAAACCCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
3314770 AAATTTATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
3314827 AAATTCATACACTTTGTATGATTTATTAAAATTTTAG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAG
3314864 ACAATTAGTG
Statistics
Matches: 1617, Mismatches: 171, Indels: 16
0.90 0.09 0.01
Matches are distributed among these distances:
52 46 0.03
54 1 0.00
55 1 0.00
56 151 0.09
57 1418 0.88
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:3315315 original size:20 final size:20
Alignment explanation
Indices: 3315290--3315347 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 20
3315280 ATATTGCTTA
3315290 GTATCGATACCCTTATTATG
1 GTATCGATACCCTTATTATG
*
3315310 GTATCGATACTACTATATATTATG
1 GTATCGATAC--C-CT-TATTATG
*
3315334 GTATCTATACCCTT
1 GTATCGATACCCTT
3315348 TCCGGTATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 11 0.35
21 1 0.03
22 2 0.06
23 1 0.03
24 16 0.52
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (20 bp):
GTATCGATACCCTTATTATG
Found at i:3315347 original size:95 final size:95
Alignment explanation
Indices: 3315193--3315418 Score: 249
Period size: 96 Copynumber: 2.4 Consensus size: 95
3315183 TCTGGCTCTA
* * * * **
3315193 TAGTATTGATTCCCCTATCATGGTATCGATACTACTATACTATGGTATCAATACCCCCTTCTTGT
1 TAGTATCGATACCCTTATCATGGTATCGATACTACTATACTATGGTATCAATACCCCTTTCCGGT
* ** **
3315258 ATCGATACTAATTTTTTATTCGATAT-TGC
66 ATCGATACCAATTTTAGATTCGATATAAAC
* * *
3315287 TTAGTATCGATACCCTTATTATGGTATCGATACTACTATATATTATGGTATCTATA-CCCTTTCC
1 -TAGTATCGATACCCTTATCATGGTATCGATACTAC--TATACTATGGTATCAATACCCCTTTCC
* *
3315351 GGTATCGATACCCATTTTAGATTCGATGTAAAC
63 GGTATCGATACCAATTTTAGATTCGATATAAAC
* *
3315384 TGGTATCGATACCCTTACCATGGTATCGATACTAC
1 TAGTATCGATACCCTTATCATGGTATCGATACTAC
3315419 CTTTTCGGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
95 31 0.28
96 61 0.56
97 17 0.16
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (95 bp):
TAGTATCGATACCCTTATCATGGTATCGATACTACTATACTATGGTATCAATACCCCTTTCCGGT
ATCGATACCAATTTTAGATTCGATATAAAC
Found at i:3319311 original size:46 final size:46
Alignment explanation
Indices: 3319240--3319480 Score: 292
Period size: 46 Copynumber: 5.3 Consensus size: 46
3319230 AAATGAATGA
* * *
3319240 ATAAATGAAAATGCAT-ATGGTGCATTATCGGAATGAAAAGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAAGATGCC
* *
3319285 ATAAAT-AAAAGTGTATAACGATGCATTATCGGCATGAAAAGATGTC
1 ATAAATGAAAA-TGCATAACGATGCATTATCGGCATGAAAAGATGCC
* * * *
3319331 ATAAATGAAAATGCATTACGGTGCATTATCTGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAAGATGCC
* *
3319377 ATAAATGAAAATGCATAA-TAGTGCATTATCGACAT-AAAAGGATGCC
1 ATAAATGAAAATGCATAACGA-TGCATTATCGGCATGAAAA-GATGCC
* * * *
3319423 ATAAATAAAAATGCATAACGGTGCATTATAGGCATGAAACGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAAGATGCC
3319469 ATAAATGAAAAT
1 ATAAATGAAAAT
3319481 AAAGAATAAT
Statistics
Matches: 165, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
44 4 0.02
45 13 0.08
46 141 0.85
47 7 0.04
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAAGATGCC
Found at i:3332183 original size:24 final size:24
Alignment explanation
Indices: 3332151--3332198 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3332141 AGTCTTCCTG
3332151 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
3332175 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
3332199 CATGTCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:3338404 original size:24 final size:24
Alignment explanation
Indices: 3338370--3338438 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
3338360 TCTTCCTGAT
*
3338370 GATGTACAAAACATCTATGTAAAC
1 GATGTATAAAACATCTATGTAAAC
3338394 GATGTATAAAACATCTATGTAAAC
1 GATGTATAAAACATCTATGTAAAC
* *
3338418 AATATATAAAACATCTATGTA
1 GATGTATAAAACATCTATGTA
3338439 CCTTGTCATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTAAAC
Found at i:3339030 original size:30 final size:31
Alignment explanation
Indices: 3338976--3339034 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3338966 AACCATTCAC
* *
3338976 AACTTTTCCAAAATTGTTAAAATGGTCCCTT
1 AACTTTTCAAAAATTGATAAAATGGTCCCTT
*
3339007 AACTTTTCAAAAATT-ATAGAATGGTCCC
1 AACTTTTCAAAAATTGATAAAATGGTCCC
3339035 AAATTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (31 bp):
AACTTTTCAAAAATTGATAAAATGGTCCCTT
Found at i:3342237 original size:2 final size:2
Alignment explanation
Indices: 3342230--3342258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3342220 CAAAAATTAT
3342230 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 T
3342259 TGTTATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3345151 original size:49 final size:49
Alignment explanation
Indices: 3345076--3345360 Score: 354
Period size: 49 Copynumber: 5.8 Consensus size: 49
3345066 AGTGCTAAAA
* * * * * * *
3345076 TAAATGCATAGCAGTGCATTCCAGCATAAAAGTTGCCAATAATAAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
* * * ** * * *
3345125 TAAATGTATAACGATGTATTTTAGCATAAAAGGTTCCACTAATAAAAAT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
** * *
3345174 TAAATGCATAGTGGTGCATTTCGACATAAACGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
*
3345223 TAAATGCATAACGGTGTATTTCGGCATAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
* * * *
3345272 TAAATGTAAAACAGTGCATTTCGGCATAAAAGGTGCAACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
3345321 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
3345361 CATGGTATTC
Statistics
Matches: 199, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 199 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGT
Found at i:3352186 original size:49 final size:49
Alignment explanation
Indices: 3352129--3352463 Score: 456
Period size: 49 Copynumber: 6.8 Consensus size: 49
3352119 GGTACTAAAA
* **
3352129 TAAATGCATAACGGTGTATTTCAACATAAAAGGTGCCACTAATAAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGT
* * *
3352178 TAAGTGCATAACAGTGCATTTCGACATAAAAGGTGCCACTAATAAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGT
* *
3352227 T-AATGCATAAAGGTGCATTTCGGCATAAAAAAGGTGCCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCAT--AAAAGGTGCCACTAATAAAAGT
**
3352277 TAAATGCATAACGGTGCATTTTAGCATAAAAGGTGCCACTAATAAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGT
* * * *
3352326 TAAATACATAATGGTGTATTTCGGCATAAAAGGTGCCACTAATTAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGT
* * *
3352375 TAAATGCATAACAGTGCATTTCGGCATAAAAGGTACCACTAATGAAAGT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGT
* * * *
3352424 TAAATGTATAATGGTGCATTTCGGCATAAAATGTGTCACT
1 TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
3352464 TATGGTATTC
Statistics
Matches: 252, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
48 21 0.08
49 187 0.74
50 22 0.09
51 22 0.09
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (49 bp):
TAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAAGT
Found at i:3352508 original size:147 final size:146
Alignment explanation
Indices: 3352129--3352463 Score: 413
Period size: 148 Copynumber: 2.3 Consensus size: 146
3352119 GGTACTAAAA
* * *** ** **
3352129 TAAATGCATAACGGTGTATTTCAACATAAAAGGTGCCACTAATAAAAGTTAAGTGCATAACAGTG
1 TAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTAATAAAAGTTAAAAACATAATGGAC
3352194 CATTTCGACATAAAAGGTGCCACTAATAAAAGTTAATGCATAAAGGTGCATTTCGGCATAAAAAA
66 CATTTCGACAT-AAAGGTGCCACTAATAAAAGTTAATGCATAAAGGTGCATTTCGGCAT-AAAAA
*
3352259 GGTGCCACTAATGAAAGT
129 GGTACCACTAATGAAAGT
* * **
3352277 TAAATGCATAACGGTGCATTTTAGCATAAAAGGTGCCACTAATAAAAGTTAAATACATAATGGTG
1 TAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTAATAAAAGTTAAAAACATAATGGAC
* * *
3352342 TATTTCGGCATAAAAGGTGCCACTAATTAAAGTTAAATGCATAACA-GTGCATTTCGGCAT-AAA
66 CATTTCGACAT-AAAGGTGCCACTAATAAAAGTT-AATGCATAA-AGGTGCATTTCGGCATAAAA
3352405 AGGTACCACTAATGAAAGT
128 AGGTACCACTAATGAAAGT
* * * * *
3352424 TAAATGTATAATGGTGCATTTCGGCATAAAATGTGTCACT
1 TAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
3352464 TATGGTATTC
Statistics
Matches: 168, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
147 55 0.33
148 89 0.53
149 23 0.14
150 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (146 bp):
TAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTAATAAAAGTTAAAAACATAATGGAC
CATTTCGACATAAAGGTGCCACTAATAAAAGTTAATGCATAAAGGTGCATTTCGGCATAAAAAGG
TACCACTAATGAAAGT
Found at i:3355783 original size:3 final size:3
Alignment explanation
Indices: 3355775--3355831 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
3355765 CTATGCTTTA
3355775 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3355823 ATT ATT ATT
1 ATT ATT ATT
3355832 TTCTTAAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3357468 original size:23 final size:23
Alignment explanation
Indices: 3357442--3357486 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3357432 ATGATAATTT
*
3357442 ATTTAGAAAAAATAACAAATTAA
1 ATTTAGAAAAAATAAAAAATTAA
**
3357465 ATTTAGTTAAAATAAAAAATTA
1 ATTTAGAAAAAATAAAAAATTA
3357487 TATCAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTTAGAAAAAATAAAAAATTAA
Found at i:3357717 original size:45 final size:45
Alignment explanation
Indices: 3357662--3357752 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3357652 AACATATTAA
* ** *
3357662 ATTTTGTCAAAATAA-AAATTTATGTTAAATTTATTTCGTCACAAT
1 ATTTTATCAAAATAACAAATTT-TGACAAATTTATTTAGTCACAAT
*
3357707 ATTTTATCAAAATAACAAATTTTGACAAATTTATTTAGTCATAAT
1 ATTTTATCAAAATAACAAATTTTGACAAATTTATTTAGTCACAAT
3357752 A
1 A
3357753 ACAATTTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 34 0.85
46 6 0.15
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (45 bp):
ATTTTATCAAAATAACAAATTTTGACAAATTTATTTAGTCACAAT
Found at i:3357767 original size:32 final size:31
Alignment explanation
Indices: 3357709--3357841 Score: 79
Period size: 33 Copynumber: 4.1 Consensus size: 31
3357699 GTCACAATAT
*
3357709 TTTATCAAAATAACAAATTTTGACAAATTTA
1 TTTATCAAAATAACAAATTTTAACAAATTTA
*
3357740 TTTAGTCATAATAAC-AATTTGTAACAAATATTAA
1 TTTA-TCAAAATAACAAATTT-TAACAAAT-TT-A
** * * * * **
3357774 TTCCTCAATATAAAAAATTATGACAAATAAAA
1 TTTATCAAAATAACAAATTTTAACAAAT-TTA
* * * *
3357806 TTCTTTCACAATAACAAAGTGTAACAAATTTA
1 TT-TATCAAAATAACAAATTTTAACAAATTTA
3357838 TTTA
1 TTTA
3357842 GGTACAATAA
Statistics
Matches: 74, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
31 10 0.14
32 22 0.30
33 35 0.47
34 7 0.09
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (31 bp):
TTTATCAAAATAACAAATTTTAACAAATTTA
Found at i:3357772 original size:197 final size:196
Alignment explanation
Indices: 3357437--3358233 Score: 924
Period size: 197 Copynumber: 4.1 Consensus size: 196
3357427 AAATTATGAT
* * * * * *
3357437 AATTTATTTAGAAAAAATAACAAATTAAATTTAGTTAAAATAAAAAATTATATCAAATTTATTTA
1 AATTTATTTAGTAACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTA
* ** * ** * * * *
3357502 GTCAAAATATTTCCTCAAAATAACAAATTATGACAAATTTAAATAGTTATAATAACAAATTATAA
66 GTC-CAATATTTTATCAAAATAA-AAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAA
* * *
3357567 TAAATATTAATTTCTCAATATAAAAAGTTATGAAAAATAATATT-TTTCACAATAATC-AATTAT
129 CAAATATTAATTTCTCAATATAAAAAGTTATGACAAATAATATTCTTTCACAATAA-CAAATTGT
3357630 AACA
193 AACA
* * * *
3357634 AATTTATTTAGTCACAATAACATATTAAATTTTGTCAAAATAAAAATTTATGTTAAATTTATTTC
1 AATTTATTTAGTAACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTA
* * *
3357699 GTCACAATATTTTATCAAAATAACAAATTTTGACAAATTTATTTAGTCATAATAACAATTTGTAA
66 GTC-CAATATTTTATCAAAATAA-AAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAA
* * * *
3357764 CAAATATTAATTCCTCAATATAAAAAATTATGACAAATAAAATTCTTTCACAATAACAAAGTGTA
129 CAAATATTAATTTCTCAATATAAAAAGTTATGACAAATAATATTCTTTCACAATAACAAATTGTA
3357829 ACA
194 ACA
* *
3357832 AATTTATTTAGGT-ACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCCAATTTACTT
1 AATTTATTTA-GTAACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTA-TT
* *
3357896 T-GT-CAA-A----AT----A-AAAAATTGTGACAAATTTATTTAATCAAAATAATAATTTATAA
64 TAGTCCAATATTTTATCAAAATAAAAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAA
* * * * *
3357949 CAAATATTAATTTCTCAATATAGAAATTTGTGACAAGTAGTATTCTTTCACAATAACAAATTGTA
129 CAAATATTAATTTCTCAATATAAAAAGTTATGACAAATAATATTCTTTCACAATAACAAATTGTA
*
3358014 AAA
194 ACA
* * ** * *
3358017 AAATGATTTAGTAACAATAACACGTTAAATTTAGTC-AAAGAAAATTTTATGTCAAATTTATTTA
1 AATTTATTTAGTAACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTA
*
3358081 GTCCTAATATTTTGTCAAAATAAAAATTTGTGACAAATTTATTTAATCAAAATAACAATTTATAA
66 GTCC-AATATTTTATCAAAATAAAAATTT-TGACAAATTTATTTAATCAAAATAACAATTTATAA
* * * *
3358146 CAAATATTAATTTCTCATTATAAAAAGTTGTGACAAATAATATTCTGTCACAATAAGAAATTGTA
129 CAAATATTAATTTCTCAATATAAAAAGTTATGACAAATAATATTCTTTCACAATAACAAATTGTA
3358211 ACA
194 ACA
* *
3358214 AAATTATTTAGTCACAATAA
1 AATTTATTTAGTAACAATAA
3358234 AAAGTTATAA
Statistics
Matches: 516, Mismatches: 65, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
183 3 0.01
184 25 0.05
185 124 0.24
186 4 0.01
187 2 0.00
191 3 0.01
195 2 0.00
196 10 0.02
197 263 0.51
198 75 0.15
199 5 0.01
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (196 bp):
AATTTATTTAGTAACAATAACATATTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTA
GTCCAATATTTTATCAAAATAAAAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAACA
AATATTAATTTCTCAATATAAAAAGTTATGACAAATAATATTCTTTCACAATAACAAATTGTAAC
A
Found at i:3357851 original size:98 final size:97
Alignment explanation
Indices: 3357520--3358251 Score: 317
Period size: 98 Copynumber: 7.6 Consensus size: 97
3357510 ATTTCCTCAA
* * ** * * * * *
3357520 AATAACAAATTATGACAAATTTAAATAGTTATAATAACAAATTATAATAAATATTAATTTCTCAA
1 AATAACAAATTGTAACAAATTTATTTAGTCACAATAACAATTTGTAACAAATATTAA-TTCTCAA
* * *
3357585 TATAAAAAGTTATGAAAAATAATATT-TTTCAC
65 TATAAAAATTTATGACAAATAAAATTCTTTCAC
* * **
3357617 AATAATC-AATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTTGTCA-AAATAAAAA
1 AATAA-CAAATTGTAACAAATTTATTTAGTCACAATAAC------AA-TTTGTAACAAATATTAA
* * ** ** * * *
3357680 TT-T--ATGT-TAAATTTATTTCGTCACAATATT-TTATCAA
58 TTCTCAATATAAAAATTTATGAC-AAATAAAATTCTT-TCAC
* * *
3357717 AATAACAAATTTTGACAAATTTATTTAGTCATAATAACAATTTGTAACAAATATTAATTCCTCAA
1 AATAACAAATTGTAACAAATTTATTTAGTCACAATAACAATTTGTAACAAATATTAATT-CTCAA
*
3357782 TATAAAAAATTATGACAAATAAAATTCTTTCAC
65 TATAAAAATTTATGACAAATAAAATTCTTTCAC
* * *
3357815 AATAACAAAGTGTAACAAATTTATTTAGGT-ACAATAAC-A-TAGT---AAAT-TT-A--GTCAA
1 AATAACAAATTGTAACAAATTTATTTA-GTCACAATAACAATTTGTAACAAATATTAATTCTCAA
* * * ** * * *
3357870 AATAAAAATTTATGTCCAATTTACTT-TGTCAA
65 TATAAAAATTTATGACAAATAAAATTCTTTCAC
* * * * * *
3357902 AATAAAAAATTGTGACAAATTTATTTAATCAAAATAATAATTTATAACAAATATTAATTTCTCAA
1 AATAACAAATTGTAACAAATTTATTTAGTCACAATAACAATTTGTAACAAATATTAA-TTCTCAA
* * * **
3357967 TATAGAAATTTGTGACAAGTAGTATTCTTTCAC
65 TATAAAAATTTATGACAAATAAAATTCTTTCAC
* * * * * * * * *
3358000 AATAACAAATTGTAAAAAAATGATTTAGTAACAATAACACGTTAAATTTAGTCAAAGA-AAATT-
1 AATAACAAATTGTAACAAATTTATTTAGTCACAATAACA-ATT---TGTA-ACAAATATTAATTC
* * * * **** * *
3358063 T-TATGT-CAAATTTATTTAGTCCTAATATT-TTGTCAA
61 TCAATATAAAAATTTA-TGACAAATAAAATTCTT-TCAC
* * * *
3358099 AATAA-AAATTTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCA
1 AATAACAAA-TTGTAACAAATTTATTTAGTCACAATAACAATTTGTAACAAATATTAA-TTCTCA
* * * * *
3358163 TTATAAAAAGTTGTGACAAATAATATTCTGTCAC
64 ATATAAAAATTTATGACAAATAAAATTCTTTCAC
* * * * * *
3358197 AATAAGAAATTGTAACAAAATTATTTAGTCACAATAAAAAGTTATAAAAAATATT
1 AATAACAAATTGTAACAAATTTATTTAGTCACAATAACAATTTGTAACAAATATT
3358252 TAGTGACGAC
Statistics
Matches: 460, Mismatches: 129, Indels: 91
0.68 0.19 0.13
Matches are distributed among these distances:
86 1 0.00
87 34 0.07
88 24 0.05
89 2 0.00
91 1 0.00
92 6 0.01
93 12 0.03
94 17 0.04
95 5 0.01
96 6 0.01
97 53 0.12
98 156 0.34
99 78 0.17
100 37 0.08
101 3 0.01
102 7 0.02
103 14 0.03
104 4 0.01
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (97 bp):
AATAACAAATTGTAACAAATTTATTTAGTCACAATAACAATTTGTAACAAATATTAATTCTCAAT
ATAAAAATTTATGACAAATAAAATTCTTTCAC
Found at i:3357902 original size:32 final size:32
Alignment explanation
Indices: 3357860--3357984 Score: 110
Period size: 32 Copynumber: 3.9 Consensus size: 32
3357850 AACATAGTAA
* *
3357860 ATTTAGTCAAAATAAAAATTTATGTCCAATTT
1 ATTTAGTCAAAATAAAAATTTATGACAAATTT
* *
3357892 ACTTT-GTCAAAATAAAAAATTGTGACAAATTT
1 A-TTTAGTCAAAATAAAAATTTATGACAAATTT
* * *
3357924 ATTTAATCAAAATAATAATTTATAACAAATATT
1 ATTTAGTCAAAATAAAAATTTATGACAAAT-TT
* * * *
3357957 AATTT-CTCAATATAGAAATTTGTGACAA
1 -ATTTAGTCAAAATAAAAATTTATGACAA
3357985 GTAGTATTCT
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
31 3 0.04
32 45 0.61
33 22 0.30
34 4 0.05
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (32 bp):
ATTTAGTCAAAATAAAAATTTATGACAAATTT
Found at i:3358076 original size:382 final size:382
Alignment explanation
Indices: 3357516--3358233 Score: 987
Period size: 382 Copynumber: 1.9 Consensus size: 382
3357506 AAATATTTCC
* * * * *
3357516 TCAAAATAACAAATTATGACAAATTTAAATAGTTATAATAACAAATTATAATAAATATTAATTTC
1 TCAAAATAAAAAATTATGACAAATTTAAATAATCAAAATAACAAATTATAACAAATATTAATTTC
* * *
3357581 TCAATATAAAAAGTTATGAAAAATAATATTTTTCACAATAATCAATTATAACAAATTTATTTAGT
66 TCAATATAAAAAGTTATGAAAAATAATATTTTTCACAATAATCAATTATAAAAAAATGATTTAGT
* * * * * *
3357646 CACAATAACATATTAAATTTTGTCAAAATAAAAATTTATGTTAAATTTATTTCGTCAC-AATATT
131 AACAATAACACATTAAATTTAGTCAAAAGAAAAATTTATGTCAAATTTATTTAGTC-CTAATATT
* * *
3357710 TTATCAAAATAACAAATTT-TGACAAATTTATTTAGTCATAATAACAATTTGTAACAAATATTAA
195 TTATCAAAATAA-AAATTTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAA
* *
3357774 TTCCTCAATATAAAAAATTATGACAAATAAAATTCTTTCACAATAACAAAGTGTAACAAATTTAT
259 TTCCTCAATATAAAAAATTATGACAAATAAAATTCTGTCACAATAACAAAGTGTAACAAAATTAT
3357839 TTAGGT-ACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCCAATTTACTTTG
324 TTA-GTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCCAATTTACTTTG
* ** * *
3357898 TCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAATAATTTATAACAAATATTAATTTC
1 TCAAAATAAAAAATTATGACAAATTTAAATAATCAAAATAACAAATTATAACAAATATTAATTTC
* * * * * * *
3357963 TCAATATAGAAATTTGTGACAAGTAGTATTCTTTCACAATAA-CAAATTGTAAAAAAATGATTTA
66 TCAATATAAAAAGTTATGAAAAATAATATT-TTTCACAATAATC-AATTATAAAAAAATGATTTA
* *
3358027 GTAACAATAACACGTTAAATTTAGTC-AAAGAAAATTTTATGTCAAATTTATTTAGTCCTAATAT
129 GTAACAATAACACATTAAATTTAGTCAAAAGAAAAATTTATGTCAAATTTATTTAGTCCTAATAT
*
3358091 TTTGTCAAAATAAAAATTTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAA
194 TTTATCAAAATAAAAATTTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAA
* * * * * * *
3358156 TTTCTCATTATAAAAAGTTGTGACAAATAATATTCTGTCACAATAAGAAATTGTAACAAAATTAT
259 TTCCTCAATATAAAAAATTATGACAAATAAAATTCTGTCACAATAACAAAGTGTAACAAAATTAT
3358221 TTAGTCACAATAA
324 TTAGTCACAATAA
3358234 AAAGTTATAA
Statistics
Matches: 290, Mismatches: 41, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
381 9 0.03
382 232 0.80
383 49 0.17
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.36
Consensus pattern (382 bp):
TCAAAATAAAAAATTATGACAAATTTAAATAATCAAAATAACAAATTATAACAAATATTAATTTC
TCAATATAAAAAGTTATGAAAAATAATATTTTTCACAATAATCAATTATAAAAAAATGATTTAGT
AACAATAACACATTAAATTTAGTCAAAAGAAAAATTTATGTCAAATTTATTTAGTCCTAATATTT
TATCAAAATAAAAATTTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATT
CCTCAATATAAAAAATTATGACAAATAAAATTCTGTCACAATAACAAAGTGTAACAAAATTATTT
AGTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCCAATTTACTTTG
Found at i:3358131 original size:32 final size:32
Alignment explanation
Indices: 3358091--3358251 Score: 121
Period size: 32 Copynumber: 5.0 Consensus size: 32
3358081 GTCCTAATAT
*
3358091 TTTGTCAAAATAAAAATTTGTGACAAAT-TTA
1 TTTGTCAAAATAAAAATTTGTAACAAATATTA
* * *
3358122 TTTAATCAAAATAACAATTTATAACAAATATTAA
1 TTT-GTCAAAATAAAAATTTGTAACAAATATT-A
* ** * * *
3358156 TTTCTCATTATAAAAAGTTGTGACAAATAATA
1 TTTGTCAAAATAAAAATTTGTAACAAATATTA
*
3358188 TTCTGTCACAATAAGAAA-TTGTAACAAA-ATTA
1 TT-TGTCAAAATAA-AAATTTGTAACAAATATTA
* * * *
3358220 TTTAGTCACAATAAAAAGTTATAAAAAATATT
1 TTT-GTCAAAATAAAAATTTGTAACAAATATT
3358252 TAGTGACGAC
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
31 7 0.07
32 47 0.46
33 42 0.41
34 7 0.07
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (32 bp):
TTTGTCAAAATAAAAATTTGTAACAAATATTA
Found at i:3359287 original size:42 final size:42
Alignment explanation
Indices: 3359156--3359732 Score: 586
Period size: 42 Copynumber: 13.7 Consensus size: 42
3359146 TTTAGGAAAA
* * * * *
3359156 AAACGTCGCAATAGGTCAATATCTATAGCGGCGTTTTTGGAAA
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGAAC
* * * *
3359199 AAACACCGTAAAAGGTCGATATCTATAG-AATCGTTTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGA-CG--TTTTTGGAAC
* * *
3359244 AAACGCCGCAAAAGGTCACATCTAAAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * * * *
3359286 AAACGACGCAAAAGGTTAGATTTATAGCGACATTTTTGCAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * *
3359328 AAACGCTGCAAAAGGTC-GTATCTATAGTGACATTTTTGGAAC
1 AAACGCCGCAAAAGGTCAG-ATCTATAGCGACGTTTTTGGAAC
* * *
3359370 AAACGCCGTAAAAGGTCAGATCTATAGTGACGTTTTT-TAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * * *
3359411 AAACACCGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * * * *
3359453 AAACGTCGCAAAAGGTCAGATTTATAGCGACATTTTTGTAAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * *
3359495 AAACGCTGCAAAAGGTCAGATCTATAGTGACATTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
**
3359537 AAACGCC-CAAAAGGTCAGATCTATAGCGACGTTTTTTTAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * *
3359578 AAACGTCGTAAAAGGTCAGATCTATAGCGACGTTTTTGAAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * **
3359620 AAACGCCGTAAAAGGTCAGATCTATAGCAATATTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
* * ** * ** * *
3359662 AAACGCTGCAAAATGTTTGATTTATAATGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
*
3359704 AAACGCCACAAAAGGTCAGATCTATAGCG
1 AAACGCCGCAAAAGGTCAGATCTATAGCG
3359733 GCATTTTTTG
Statistics
Matches: 439, Mismatches: 87, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
41 73 0.17
42 306 0.70
43 26 0.06
44 10 0.02
45 24 0.05
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAAC
Found at i:3359455 original size:167 final size:167
Alignment explanation
Indices: 3359175--3359730 Score: 706
Period size: 167 Copynumber: 3.3 Consensus size: 167
3359165 AATAGGTCAA
* * * * * * * *
3359175 TATCTATAGCGGCGTTTTTGGAAAAAACACCGTAAAAGGTCGATATCTATAGAATCGTTTTTTTG
1 TATCTATAGTGACATTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGGA-CGTTTTTTT-
* * *
3359240 GAACAAACGCCGCAAAAGGTCACATCTAAAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTTAG
63 -AACAAACGCCGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTCAG
3359305 ATTTATAGCGACATTTTTGCAACAAACGCTGCAAAAGGTCG
127 ATTTATAGCGACATTTTTGCAACAAACGCTGCAAAAGGTCG
*
3359346 TATCTATAGTGACATTTTTGGAACAAACGCCGTAAAAGGTCAGATCTATAGTGACG-TTTTTTAA
1 TATCTATAGTGACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAG-GACGTTTTTTTAA
* *
3359410 CAAACACCGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCAGATT
65 CAAACGCCGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATT
* *
3359475 TATAGCGACATTTTTGTAATAAACGCTGCAAAAGGTCAG
130 TATAGCGACATTTTTGCAACAAACGCTGCAAAAGGTC-G
3359514 -ATCTATAGTGACATTTTTGGAACAAACGCC-CAAAAGGTCAGATCTATAGCGACGTTTTTTTAA
1 TATCTATAGTGACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAG-GACGTTTTTTTAA
* * * * * * *
3359577 CAAACGTCGTAAAAGGTCAGATCTATAGCGACGTTTTTGAAACAAACGCCGTAAAAGGTCAGATC
65 CAAACGCCGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATT
* * * * *
3359642 TATAGCAATATTTTTGGAACAAACGCTGCAAAATGT-T
130 TATAGCGACATTTTTGCAACAAACGCTGCAAAAGGTCG
* * * * * *
3359679 TGATTTATAATGGCGTTTTTGGAATAAACGCCACAAAAGGTCAGATCTATAG
1 T-ATCTATAGTGACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAG
3359731 CGGCATTTTT
Statistics
Matches: 344, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
166 22 0.06
167 248 0.72
168 20 0.06
169 6 0.02
170 11 0.03
171 37 0.11
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (167 bp):
TATCTATAGTGACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGGACGTTTTTTTAAC
AAACGCCGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATTT
ATAGCGACATTTTTGCAACAAACGCTGCAAAAGGTCG
Found at i:3359464 original size:125 final size:126
Alignment explanation
Indices: 3359162--3359749 Score: 567
Period size: 125 Copynumber: 4.6 Consensus size: 126
3359152 AAAAAAACGT
* * * * ** * *
3359162 CGCAATAGGTCAATATCTATAGCGGCGTTTTTGGAAAAAACACCGTAAAAGGTCGATATCTATAG
1 CGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGAACAAACGTCGCAAAAGGTC-AGATCTATAG
** * * * *
3359227 AATCG-TTTTTTTGGAACAAACGCCGCAAAAGGTCACATCTAAAGCGGCGTTTTTGGAACAAACG
64 ---CGACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGTGACGTTTTTGGAACAAAC-
3359291 A-
125 AC
* * * *
3359292 CGCAAAAGGTTAGATTTATAGCGACATTTTTGCAACAAACG-CTGCAAAAGGTC-GTATCTATAG
1 CGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTC-GCAAAAGGTCAG-ATCTATAG
* * *
3359355 TGACATTTTTGGAACAAACGCCGTAAAAGGTCAGATCTATAGTGACGTTTTT-TAACAAACAC
64 CGACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGTGACGTTTTTGGAACAAACAC
* * * *
3359417 CGTAAAAGGTCACATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCAGATTTATAGCG
1 CGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCG
* * * * *
3359482 ACATTTTTGTAATAAACGCTGCAAAAGGTCAGATCTATAGTGACATTTTTGGAACAAACGC
66 ACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGTGACGTTTTTGGAACAAACAC
** *
3359543 C-CAAAAGGTCAGATCTATAGCGACGTTTTTTTAACAAACGTCGTAAAAGGTCAGATCTATAGCG
1 CGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCG
* * * ** ** *
3359607 ACGTTTTTGAAACAAACGCCGTAAAAGGTCAGATCTATAGCAATATTTTTGGAACAAACGC
66 ACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGTGACGTTTTTGGAACAAACAC
* * ** * ** * * * *
3359668 TGCAAAATGTTTGATTTATAATGGCGTTTTTGGAATAAACGCCACAAAAGGTCAGATCTATAGCG
1 CGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCG
* *
3359733 GCATTTTTTGATACAAA
66 ACATTTTTGGA-ACAAA
3359750 AGACGCTAAT
Statistics
Matches: 380, Mismatches: 69, Indels: 21
0.81 0.15 0.04
Matches are distributed among these distances:
124 1 0.00
125 214 0.56
126 110 0.29
127 5 0.01
128 9 0.02
129 32 0.08
130 9 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (126 bp):
CGCAAAAGGTCAGATCTATAGCGACGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCG
ACATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGTGACGTTTTTGGAACAAACAC
Found at i:3361331 original size:40 final size:41
Alignment explanation
Indices: 3361253--3361554 Score: 187
Period size: 40 Copynumber: 7.6 Consensus size: 41
3361243 AAAAATAAAG
** * *
3361253 ACTAAAGTACAAGTATTTAGCGGTGTTTGTATACAAATGCC
1 ACTAAAGTACAAGTATTTAGCGGCATTTATATAAAAATGCC
* *
3361294 CCTAAAGTACAA-TATTTAGCGACATTTATATAAAAATGCC
1 ACTAAAGTACAAGTATTTAGCGGCATTTATATAAAAATGCC
* * *
3361334 ACTAAAGTA-AAGTTTTTAGTGGCATTTATATAAAAACGCC
1 ACTAAAGTACAAGTATTTAGCGGCATTTATATAAAAATGCC
* * * * *
3361374 ACT--AG----AGTA--TAACGACATTTATGCTTAAAATACC
1 ACTAAAGTACAAGTATTTAGCGGCATTTAT-ATAAAAATGCC
* ** * *
3361408 ACTAAAGTACGAGCCTTTAGCGGCGTTTGTA-AAAAATGCC
1 ACTAAAGTACAAGTATTTAGCGGCATTTATATAAAAATGCC
* ** * * * *
3361448 ACTAAATTACAAGTATTTAGCGGTGTTTGTGCTTAAAACGCC
1 ACTAAAGTACAAGTATTTAGCGGCATTTAT-ATAAAAATGCC
* * ** * * *
3361490 ACTAAAGTAAAAGTATTTAGCAGTGTTTGTACAAAAACGCC
1 ACTAAAGTACAAGTATTTAGCGGCATTTATATAAAAATGCC
* *
3361531 ACTAAACTACAA-TATTTTGCGGCA
1 ACTAAAGTACAAGTATTTAGCGGCA
3361555 AACGCCGCTA
Statistics
Matches: 201, Mismatches: 48, Indels: 25
0.73 0.18 0.09
Matches are distributed among these distances:
33 10 0.05
34 10 0.05
35 3 0.01
36 2 0.01
38 2 0.01
39 2 0.01
40 100 0.50
41 29 0.14
42 43 0.21
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (41 bp):
ACTAAAGTACAAGTATTTAGCGGCATTTATATAAAAATGCC
Found at i:3361443 original size:74 final size:73
Alignment explanation
Indices: 3361313--3361451 Score: 163
Period size: 74 Copynumber: 1.9 Consensus size: 73
3361303 CAATATTTAG
* ** *
3361313 CGACATTTATATAAAAATGCCACTAAAGTAAAGTTTTTAGTGGCATTTATATAAAAACGCCACTA
1 CGACATTTATATAAAAATACCACTAAAGTAAAGCCTTTAGCGGCATTTATATAAAAACGCCACTA
3361378 GAGTATAA
66 GAGTATAA
* * * * * *
3361386 CGACATTTATGCTTAAAATACCACTAAAGTACGAGCCTTTAGCGGCGTTTGTA-AAAAATGCCAC
1 CGACATTTAT-ATAAAAATACCACTAAAGTA-AAGCCTTTAGCGGCATTTATATAAAAACGCCAC
3361450 TA
64 TA
3361452 AATTACAAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
73 10 0.19
74 29 0.54
75 15 0.28
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (73 bp):
CGACATTTATATAAAAATACCACTAAAGTAAAGCCTTTAGCGGCATTTATATAAAAACGCCACTA
GAGTATAA
Found at i:3361504 original size:42 final size:41
Alignment explanation
Indices: 3361423--3361536 Score: 140
Period size: 42 Copynumber: 2.8 Consensus size: 41
3361413 AGTACGAGCC
* * * * *
3361423 TTTAGCGGCGTTTGTA-AAAAATGCCACTAAATTACAAGTA
1 TTTAGCAGTGTTTGTACAAAAACGCCACTAAAGTAAAAGTA
* * *
3361463 TTTAGCGGTGTTTGTGCTTAAAACGCCACTAAAGTAAAAGTA
1 TTTAGCAGTGTTTGTAC-AAAAACGCCACTAAAGTAAAAGTA
3361505 TTTAGCAGTGTTTGTACAAAAACGCCACTAAA
1 TTTAGCAGTGTTTGTACAAAAACGCCACTAAA
3361537 CTACAATATT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 14 0.22
41 14 0.22
42 35 0.56
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (41 bp):
TTTAGCAGTGTTTGTACAAAAACGCCACTAAAGTAAAAGTA
Found at i:3361547 original size:82 final size:82
Alignment explanation
Indices: 3361395--3361552 Score: 201
Period size: 82 Copynumber: 1.9 Consensus size: 82
3361385 ACGACATTTA
* ** * * * *
3361395 TGCTTAAAATACCACTAAAGTACGAGCCTTTAGCGGCGTTTGTAAAAAATGCCACTAAATTACAA
1 TGCTTAAAACACCACTAAAGTAAAAGCATTTAGCAGCGTTTGTAAAAAACGCCACTAAACTACAA
3361460 GTATTTAGCGGTGTTTG
66 GTATTTAGCGGTGTTTG
* * *
3361477 TGCTTAAAACGCCACTAAAGTAAAAGTATTTAGCAGTGTTTGTACAAAAACGCCACTAAACTACA
1 TGCTTAAAACACCACTAAAGTAAAAGCATTTAGCAGCGTTTGTA-AAAAACGCCACTAAACTACA
*
3361542 A-TATTTTGCGG
65 AGTATTTAGCGG
3361553 CAAACGCCGC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 45 0.70
83 19 0.30
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (82 bp):
TGCTTAAAACACCACTAAAGTAAAAGCATTTAGCAGCGTTTGTAAAAAACGCCACTAAACTACAA
GTATTTAGCGGTGTTTG
Found at i:3361825 original size:16 final size:16
Alignment explanation
Indices: 3361806--3361837 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3361796 TAATAAAGAT
3361806 AAAAAATAAGTAACTC
1 AAAAAATAAGTAACTC
3361822 AAAAAATAAGTAACTC
1 AAAAAATAAGTAACTC
3361838 TAATTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAAATAAGTAACTC
Found at i:3363173 original size:20 final size:20
Alignment explanation
Indices: 3363148--3363187 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3363138 GAAGACAATA
3363148 TTGAACTCCCTTAAATTGGT
1 TTGAACTCCCTTAAATTGGT
*
3363168 TTGAACTCCTTTAAATTGGT
1 TTGAACTCCCTTAAATTGGT
3363188 CCTGATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGAACTCCCTTAAATTGGT
Found at i:3365328 original size:15 final size:15
Alignment explanation
Indices: 3365308--3365339 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3365298 TACTTTCGAG
3365308 CCACATGTTTTTCTA
1 CCACATGTTTTTCTA
3365323 CCACATGTTTTTCTA
1 CCACATGTTTTTCTA
3365338 CC
1 CC
3365340 GTCTTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (15 bp):
CCACATGTTTTTCTA
Found at i:3365419 original size:2 final size:2
Alignment explanation
Indices: 3365414--3365442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3365404 TGTGTGTGTG
3365414 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 T
3365443 TTATCATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3366204 original size:56 final size:56
Alignment explanation
Indices: 3366144--3366282 Score: 260
Period size: 56 Copynumber: 2.5 Consensus size: 56
3366134 AAAAGAAAAG
*
3366144 AGTTTAACTTATCCAAGTTGTTACATTGATAGTTGTAAGTTTAAATAGTGTTGTAA
1 AGTTTAACATATCCAAGTTGTTACATTGATAGTTGTAAGTTTAAATAGTGTTGTAA
3366200 AGTTTAACATATCCAAGTTGTTACATTGATAGTTGTAAGTTTAAATAGTGTTGTAA
1 AGTTTAACATATCCAAGTTGTTACATTGATAGTTGTAAGTTTAAATAGTGTTGTAA
*
3366256 AGTTTAACATATCCAAGTTATTACATT
1 AGTTTAACATATCCAAGTTGTTACATT
3366283 CAAAGATGGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 81 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (56 bp):
AGTTTAACATATCCAAGTTGTTACATTGATAGTTGTAAGTTTAAATAGTGTTGTAA
Found at i:3366606 original size:56 final size:56
Alignment explanation
Indices: 3366528--3366778 Score: 184
Period size: 56 Copynumber: 4.5 Consensus size: 56
3366518 CAAAGTGTTT
*** * **
3366528 GTTAAGACATTACAACATTATTTGAACCTTCATCTTTTTATGTAACCACCTGGATACA
1 GTTAA-ACATTACAATGCTATTTAAACCTTCATCTTTGAATGTAACCACCTGGATA-A
* * * *
3366586 -TTAAACATTACAATGCTATTTAAACTTTCGTCTTTGAATGTAACGACTTGGATAA
1 GTTAAACATTACAATGCTATTTAAACCTTCATCTTTGAATGTAACCACCTGGATAA
* ** * * * *
3366641 GTTAAATATTACAACACTATTCAAA-CTTCCATCTTTGAATGTAACAACTTGGATGA
1 GTTAAACATTACAATGCTATTTAAACCTT-CATCTTTGAATGTAACCACCTGGATAA
* * * * * * **
3366697 GTTAATCATTACAACGGTATTCAAA-CTTCCATCTCTGAATGTAACAAGTTGGATAA
1 GTTAAACATTACAATGCTATTTAAACCTT-CATCTTTGAATGTAACCACCTGGATAA
* * * *
3366753 GTTAAACAATATAACGCTATTCAAAC
1 GTTAAACATTACAATGCTATTTAAAC
3366779 TTCTAACTAT
Statistics
Matches: 161, Mismatches: 29, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
55 3 0.02
56 154 0.96
57 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (56 bp):
GTTAAACATTACAATGCTATTTAAACCTTCATCTTTGAATGTAACCACCTGGATAA
Found at i:3366779 original size:56 final size:56
Alignment explanation
Indices: 3366558--3366781 Score: 270
Period size: 56 Copynumber: 4.0 Consensus size: 56
3366548 TTTGAACCTT
** * * * * *
3366558 CATCTTTTTATGTAACCACCTGGATACA-TTAAACATTACAATGCTATTTAAACTTT
1 CATCTTTGAATGTAACAACTTGGATA-AGTTAAACATTACAACGCTATTCAAACTTC
* * * *
3366614 CGTCTTTGAATGTAACGACTTGGATAAGTTAAATATTACAACACTATTCAAACTTC
1 CATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTATTCAAACTTC
* * *
3366670 CATCTTTGAATGTAACAACTTGGATGAGTTAATCATTACAACGGTATTCAAACTTC
1 CATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTATTCAAACTTC
* * * *
3366726 CATCTCTGAATGTAACAAGTTGGATAAGTTAAACAATATAACGCTATTCAAACTTC
1 CATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTATTCAAACTTC
3366782 TAACTATCAA
Statistics
Matches: 143, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
55 1 0.01
56 142 0.99
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (56 bp):
CATCTTTGAATGTAACAACTTGGATAAGTTAAACATTACAACGCTATTCAAACTTC
Found at i:3367095 original size:56 final size:56
Alignment explanation
Indices: 3367002--3367246 Score: 260
Period size: 56 Copynumber: 4.4 Consensus size: 56
3366992 TATAAACGAA
* * *
3367002 AATGGTTAACTTATCCAAGTTATTACATTGATTGTTGGAAGTTGGAATAG-GTTTGT
1 AATGTTTAACTTATCCAAGTTGTTACATTGATAGTTGGAAGTTGGAATAGAG-TTGT
* * * * * *
3367058 AATGTTTAACTTATCCAATTTGTCATATAGATAGTTGGAAGTTTGAATAGAGTTTT
1 AATGTTTAACTTATCCAAGTTGTTACATTGATAGTTGGAAGTTGGAATAGAGTTGT
* * * * * * *
3367114 AATGTTTAGCTTATCCAAGTTGTTACATTCAAAGATAGAAGTTTGAATATAGTTGT
1 AATGTTTAACTTATCCAAGTTGTTACATTGATAGTTGGAAGTTGGAATAGAGTTGT
* ** *
3367170 AGTGTTTAACTTATCCAAGTTGTTACATTGATAGTTGTTAGTTTGG-ATAGCGTTGT
1 AATGTTTAACTTATCCAAGTTGTTACATTGATAGTTGGAAG-TTGGAATAGAGTTGT
* *
3367226 AATGTTTAAATTATTCAAGTT
1 AATGTTTAACTTATCCAAGTT
3367247 ATTATATTCA
Statistics
Matches: 153, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
56 149 0.97
57 4 0.03
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (56 bp):
AATGTTTAACTTATCCAAGTTGTTACATTGATAGTTGGAAGTTGGAATAGAGTTGT
Found at i:3367176 original size:112 final size:112
Alignment explanation
Indices: 3367002--3367285 Score: 286
Period size: 112 Copynumber: 2.5 Consensus size: 112
3366992 TATAAACGAA
* * * ** * * * *
3367002 AATGGTTAACTTATCCAAGTTATTACATTGATTGTTGGAAGTTGGAATA-GGTTTGTAATGTTTA
1 AATGTTTAAATTATCCAAGTTATTACATTCAAAGATAGAAGTTTGAATATAG-TTGTAATGTTTA
* * *
3367066 ACTTATCCAATTTGTCATATAGATAGTTGGAAGTTTGAATAGAGTTTT
65 ACTTATCCAAGTTGTCACATAGATAGTTGGAAGTTTGAATAGAGTTGT
** * *
3367114 AATGTTTAGCTTATCCAAGTTGTTACATTCAAAGATAGAAGTTTGAATATAGTTGTAGTGTTTAA
1 AATGTTTAAATTATCCAAGTTATTACATTCAAAGATAGAAGTTTGAATATAGTTGTAATGTTTAA
* * ** * *
3367179 CTTATCCAAGTTGTTACATTGATAGTTGTTAGTTTGGATAGCGTTGT
66 CTTATCCAAGTTGTCACATAGATAGTTGGAAGTTTGAATAGAGTTGT
* * * *
3367226 AATGTTTAAATTATTCAAGTTATTATATTCAAAAATTA-ATGTTTGAATAGT-GTTGTAATG
1 AATGTTTAAATTATCCAAGTTATTACATTCAAAGA-TAGAAGTTTGAATA-TAGTTGTAATG
3367286 CTTACAAATG
Statistics
Matches: 141, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
112 137 0.97
113 4 0.03
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (112 bp):
AATGTTTAAATTATCCAAGTTATTACATTCAAAGATAGAAGTTTGAATATAGTTGTAATGTTTAA
CTTATCCAAGTTGTCACATAGATAGTTGGAAGTTTGAATAGAGTTGT
Found at i:3367892 original size:57 final size:57
Alignment explanation
Indices: 3367821--3367941 Score: 170
Period size: 57 Copynumber: 2.1 Consensus size: 57
3367811 AATAACTCAT
* *
3367821 ATAAGTTAATACATTACAGTGCTATTCAAACCTCCATCAATCAATGAAACAACATGG
1 ATAAGTTAAGACATTACAATGCTATTCAAACCTCCATCAATCAATGAAACAACATGG
* * * ***
3367878 ATAAGTTAAGACATTACAATGCTATTCAAACTTCCATCTATCAATGTAATGCCATGG
1 ATAAGTTAAGACATTACAATGCTATTCAAACCTCCATCAATCAATGAAACAACATGG
3367935 ATAAGTT
1 ATAAGTT
3367942 TGTAGGTCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (57 bp):
ATAAGTTAAGACATTACAATGCTATTCAAACCTCCATCAATCAATGAAACAACATGG
Found at i:3369720 original size:93 final size:93
Alignment explanation
Indices: 3369580--3369753 Score: 251
Period size: 93 Copynumber: 1.9 Consensus size: 93
3369570 TTTGATGTTA
* *
3369580 AGACATTAAAATGCTATTCAAACTTCCAACTATCATTGTAATAACTTGGATAAGTTAAAATCA-T
1 AGACATTAAAATGCTATTCAAACATCCAACTATCAATGTAATAACTTGGATAAGTTAAAAT-ATT
*
3369644 TAGTTTGTAAACATCAAAATGTTTTGATT
65 TAGATTGTAAACATCAAAATGTTTTGATT
* * * * * *
3369673 AGACATTAAAATGCTATTCAAACATCCATCTTTGAATGTAATGACTTGTATAAGTTAAACTATTT
1 AGACATTAAAATGCTATTCAAACATCCAACTATCAATGTAATAACTTGGATAAGTTAAAATATTT
3369738 AGATTGTAAACATCAA
66 AGATTGTAAACATCAA
3369754 GTTGCTACAC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (93 bp):
AGACATTAAAATGCTATTCAAACATCCAACTATCAATGTAATAACTTGGATAAGTTAAAATATTT
AGATTGTAAACATCAAAATGTTTTGATT
Found at i:3369903 original size:56 final size:55
Alignment explanation
Indices: 3369768--3369923 Score: 145
Period size: 56 Copynumber: 2.8 Consensus size: 55
3369758 CTACACTTGC
* * *
3369768 ATAATATCATAATTTATCCAAGTTGTTACATTCAAAGATGAAAGATATATTAGCATT
1 ATAATAT--TAATTTATCCAAGTTGTTACATTCAAAAATGAAAGATATAATAACATT
* * * * * *
3369825 GTAATTTTTAACTTAACAAAGTTGTTACATTCAAAAAAT-AGAAG-TTTGAATAACATT
1 ATAA-TATTAATTTATCCAAGTTGTTACATTC-AAAAATGA-AAGATAT-AATAACATT
* *
3369882 ATAATATTAATTTATCCAAGTTGTTACATTTAAAGATGAAAG
1 ATAATATTAATTTATCCAAGTTGTTACATTCAAAAATGAAAG
3369924 TTGAACAACT
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
55 8 0.10
56 47 0.60
57 21 0.27
58 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (55 bp):
ATAATATTAATTTATCCAAGTTGTTACATTCAAAAATGAAAGATATAATAACATT
Found at i:3370155 original size:56 final size:57
Alignment explanation
Indices: 3370054--3370169 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 57
3370044 AAGTGTTATA
** * * * *
3370054 TTAAGACATTACAACGCTATTGTAACTTTCATCTTCGAATTTAACAATTTGGATAAG
1 TTAAGACATTACAACGCTATTCAAACTTCCAACTTCGAATGTAACAACTTGGATAAG
*
3370111 TTAA-ACATTACAATGCTATTCAAACTTCCAACTGTC-AATGTAACAACTTGGATAAG
1 TTAAGACATTACAACGCTATTCAAACTTCCAACT-TCGAATGTAACAACTTGGATAAG
3370167 TTA
1 TTA
3370170 CACTCTTTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 45 0.88
57 6 0.12
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (57 bp):
TTAAGACATTACAACGCTATTCAAACTTCCAACTTCGAATGTAACAACTTGGATAAG
Found at i:3370318 original size:92 final size:91
Alignment explanation
Indices: 3370111--3370356 Score: 282
Period size: 92 Copynumber: 2.7 Consensus size: 91
3370101 TTTGGATAAG
* * * *
3370111 TTAA-ACATTACAATGCTATTCAAACTTCCAACTGTCAATGTAACAACTTGGATAAGTTACACTC
1 TTAAGACATTACAATGCTATTCCAACTTCC-ATTTTCAATGTAACAACTTGGATAAGTTAAACTC
3370175 TTTAGTTTGTAAACATCAAAGTATTTA
65 TTTAGTTTGTAAACATCAAAGTATTTA
* ** * * **
3370202 CTTAAGACATTAAAACACTA-TCCAACTTTCATTTATCATTGTAACAACTTTAATAAGTTAAACT
1 -TTAAGACATTACAATGCTATTCCAACTTCCATTT-TCAATGTAACAACTTGGATAAGTTAAACT
* *
3370266 CTTTAGTTTTTAAACATCAAAGTGCTTT-
64 CTTTAGTTTGTAAACATCAAAGT-ATTTA
* * *
3370294 TTAAGATATTACAATGTTATTCCAACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAAC
1 TTAAGACATTACAATGCTATTCCAACTTCCAT-TTTCAATGTAACAACTTGGATAAGTTAAAC
3370357 ATTACAACAC
Statistics
Matches: 126, Mismatches: 23, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
91 16 0.13
92 94 0.75
93 16 0.13
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (91 bp):
TTAAGACATTACAATGCTATTCCAACTTCCATTTTCAATGTAACAACTTGGATAAGTTAAACTCT
TTAGTTTGTAAACATCAAAGTATTTA
Found at i:3370387 original size:56 final size:56
Alignment explanation
Indices: 3370317--3370475 Score: 194
Period size: 56 Copynumber: 2.8 Consensus size: 56
3370307 ATGTTATTCC
3370317 AACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAACACTATAAA
1 AACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAACACTATAAA
* * * * * * * **
3370373 AACTTCCATTTTTGAATGTAGCAACTTGTACAAGTTTAACATTACGACGCTATTCA
1 AACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAACACTATAAA
* * *
3370429 AACTTCAATGA-ATCAATGTAACAACTTGGATAAGTTAAACATTACAA
1 AACTTCCAT-ATTTGAATGTAACAACTTGGATAAGTTAAACATTACAA
3370476 AGCTATTCAA
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
56 84 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (56 bp):
AACTTCCATATTTGAATGTAACAACTTGGATAAGTTAAACATTACAACACTATAAA
Found at i:3375542 original size:2 final size:2
Alignment explanation
Indices: 3375537--3375582 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3375527 TTTTTTGATT
* * * *
3375537 TA TA TA TG TA TG TA TA TA TA TA TA TG TA TG 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
3375579 TA TA
1 TA TA
3375583 AGTTTATCGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3375556 original size:14 final size:14
Alignment explanation
Indices: 3375537--3375582 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
3375527 TTTTTTGATT
*
3375537 TATATATGTATGTA
1 TATATATATATGTA
3375551 TATATATATATGTA
1 TATATATATATGTA
* *
3375565 TGTATATATATATA
1 TATATATATATGTA
3375579 TATA
1 TATA
3375583 AGTTTATCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
TATATATATATGTA
Found at i:3375560 original size:18 final size:18
Alignment explanation
Indices: 3375537--3375579 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
3375527 TTTTTTGATT
3375537 TATATATGTATGTATATA
1 TATATATGTATGTATATA
3375555 TATATATGTATGTATATA
1 TATATATGTATGTATATA
3375573 TATATAT
1 TATATAT
3375580 ATAAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TATATATGTATGTATATA
Found at i:3375567 original size:22 final size:22
Alignment explanation
Indices: 3375541--3375582 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3375531 TTGATTTATA
*
3375541 TATGTATGTATATATATATATG
1 TATGTATATATATATATATATG
3375563 TATGTATATATATATATATA
1 TATGTATATATATATATATA
3375583 AGTTTATCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
TATGTATATATATATATATATG
Found at i:3376712 original size:263 final size:263
Alignment explanation
Indices: 3376245--3376772 Score: 1056
Period size: 263 Copynumber: 2.0 Consensus size: 263
3376235 TTCCGTTCAA
3376245 GGGCATTACTAGTGGACATTCGAATGACGTTGAGTATTGGTTGGAGGATATAAAGAGGATTATGG
1 GGGCATTACTAGTGGACATTCGAATGACGTTGAGTATTGGTTGGAGGATATAAAGAGGATTATGG
3376310 ATGAGATGGACCTGAGACCTACTTAAAAGATAAAGGGGCCTTGTCTATGTTGAAGAAAGAGAGTT
66 ATGAGATGGACCTGAGACCTACTTAAAAGATAAAGGGGCCTTGTCTATGTTGAAGAAAGAGAGTT
3376375 TTGGATGGTGATAATCGATTTTTGGTAGTATTATGGGGAATTAGTTTACTTGGGATCTTTTCAAT
131 TTGGATGGTGATAATCGATTTTTGGTAGTATTATGGGGAATTAGTTTACTTGGGATCTTTTCAAT
3376440 GCACGTTTTTTTAGTTACTACATCGGAGAGAGATACTTGCAGTAGATATGCCAAAAGTTTTAAAA
196 GCACGTTTTTTTAGTTACTACATCGGAGAGAGATACTTGCAGTAGATATGCCAAAAGTTTTAAAA
3376505 TTT
261 TTT
3376508 GGGCATTACTAGTGGACATTCGAATGACGTTGAGTATTGGTTGGAGGATATAAAGAGGATTATGG
1 GGGCATTACTAGTGGACATTCGAATGACGTTGAGTATTGGTTGGAGGATATAAAGAGGATTATGG
3376573 ATGAGATGGACCTGAGACCTACTTAAAAGATAAAGGGGCCTTGTCTATGTTGAAGAAAGAGAGTT
66 ATGAGATGGACCTGAGACCTACTTAAAAGATAAAGGGGCCTTGTCTATGTTGAAGAAAGAGAGTT
3376638 TTGGATGGTGATAATCGATTTTTGGTAGTATTATGGGGAATTAGTTTACTTGGGATCTTTTCAAT
131 TTGGATGGTGATAATCGATTTTTGGTAGTATTATGGGGAATTAGTTTACTTGGGATCTTTTCAAT
3376703 GCACGTTTTTTTAGTTACTACATCGGAGAGAGATACTTGCAGTAGATATGCCAAAAGTTTTAAAA
196 GCACGTTTTTTTAGTTACTACATCGGAGAGAGATACTTGCAGTAGATATGCCAAAAGTTTTAAAA
3376768 TTT
261 TTT
3376771 GG
1 GG
3376773 AGCAGGGTGA
Statistics
Matches: 265, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
263 265 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (263 bp):
GGGCATTACTAGTGGACATTCGAATGACGTTGAGTATTGGTTGGAGGATATAAAGAGGATTATGG
ATGAGATGGACCTGAGACCTACTTAAAAGATAAAGGGGCCTTGTCTATGTTGAAGAAAGAGAGTT
TTGGATGGTGATAATCGATTTTTGGTAGTATTATGGGGAATTAGTTTACTTGGGATCTTTTCAAT
GCACGTTTTTTTAGTTACTACATCGGAGAGAGATACTTGCAGTAGATATGCCAAAAGTTTTAAAA
TTT
Found at i:3407640 original size:15 final size:14
Alignment explanation
Indices: 3407610--3407645 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
3407600 TATCTACTCA
3407610 TTTTTTATTTACTG
1 TTTTTTATTTACTG
*
3407624 TTTATTTATTTATTG
1 TTT-TTTATTTACTG
3407639 TTTTTTA
1 TTTTTTA
3407646 CCATTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTTATTTACTG
Found at i:3427434 original size:141 final size:137
Alignment explanation
Indices: 3427201--3427500 Score: 369
Period size: 141 Copynumber: 2.2 Consensus size: 137
3427191 GAGACACGAT
* * **
3427201 TCCTACGTGATGAGGAAATCT-G--GTCAAGGGATGACACGGCTCATACGCGATGAAGAGTTCTG
1 TCCTACGTGATGAGGAAGTCTGGTCGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
*
3427263 GTCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATGAGGACGGCTGATTAT-CTAAGGTT
66 GCCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATGAGGACGGCTGATTATCCTAAGGTT
3427327 GACACGGC
131 GACAC-GC
* * *
3427335 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACATGATGAAGAAC
1 TCCTACGTGATGAGGAAGTCTGGTCGTC-AA-GG--GATGACACGGCTCATACACGATGAAGAAC
* * * *
3427400 TCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAA
62 TCTGGCCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATGAGGACGGCTGATTATCCTAA
* *
3427465 TGTTGACACTC
127 GGTTGACACGC
3427476 TCCTACGTG-TCGAGG-AGATCTGGTC
1 TCCTACGTGAT-GAGGAAG-TCTGGTC
3427501 AGTTGATGTT
Statistics
Matches: 142, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
134 20 0.14
135 1 0.01
137 3 0.02
138 2 0.01
139 2 0.01
140 3 0.02
141 99 0.70
142 12 0.08
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (137 bp):
TCCTACGTGATGAGGAAGTCTGGTCGTCAAGGGATGACACGGCTCATACACGATGAAGAACTCTG
GCCATCTTTAAGAAGGGTGATAACTAGGTTCCTACGTAATGAGGACGGCTGATTATCCTAAGGTT
GACACGC
Found at i:3428469 original size:23 final size:23
Alignment explanation
Indices: 3428443--3428492 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3428433 ACCCTCCTTT
3428443 ATTTAT-TTTTTCTTCTTTTTTTC
1 ATTTATCTTTTTCTTC-TTTTTTC
*
3428466 ATTTTTCTTTTTCTTCTTTTTTC
1 ATTTATCTTTTTCTTCTTTTTTC
3428489 ATTT
1 ATTT
3428493 TTCCATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (23 bp):
ATTTATCTTTTTCTTCTTTTTTC
Found at i:3428493 original size:23 final size:24
Alignment explanation
Indices: 3428449--3428495 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
3428439 CTTTATTTAT
3428449 TTTTTCTTCTTTTTTTCATTTTTC
1 TTTTTCTTCTTTTTTTCATTTTTC
3428473 TTTTTCTTC-TTTTTTCATTTTTC
1 TTTTTCTTCTTTTTTTCATTTTTC
3428496 CATCATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTCTTCTTTTTTTCATTTTTC
Found at i:3428529 original size:35 final size:34
Alignment explanation
Indices: 3428464--3428530 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
3428454 CTTCTTTTTT
*
3428464 TCATTTTTCTTTTTCTTCTTTTTTCATTTTTCCA
1 TCATTTTTCTTTTTCTTCTTTTTACATTTTTCCA
*
3428498 TCATATTTTCATTTTT-TTCCTTTTTACTTTTTT
1 TCAT-TTTTC-TTTTTCTT-CTTTTTACATTTTT
3428531 TTAAGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 7 0.25
36 17 0.61
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (34 bp):
TCATTTTTCTTTTTCTTCTTTTTACATTTTTCCA
Found at i:3435674 original size:30 final size:30
Alignment explanation
Indices: 3435639--3435701 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3435629 TTAAATTCGA
**
3435639 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
3435669 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
3435699 ATG
1 ATG
3435702 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:3442047 original size:3 final size:3
Alignment explanation
Indices: 3442039--3442075 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3442029 ACATGTATAT
3442039 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3442076 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3447554 original size:21 final size:21
Alignment explanation
Indices: 3447528--3447582 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
3447518 CCCATAATAG
3447528 GGTGTATCGGTACACTATCAA
1 GGTGTATCGGTACACTATCAA
3447549 GGTGTATCGGTACACTATCAA
1 GGTGTATCGGTACACTATCAA
3447570 GGTGTATCGGTAC
1 GGTGTATCGGTAC
3447583 CCCTTCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (21 bp):
GGTGTATCGGTACACTATCAA
Found at i:3447761 original size:20 final size:20
Alignment explanation
Indices: 3447746--3447784 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3447736 ATAATACAGT
3447746 TACTATTCATACAATACATG
1 TACTATTCATACAATACATG
3447766 TACTATTCATA-AA-ACATG
1 TACTATTCATACAATACATG
3447784 T
1 T
3447785 TGTGCTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAATACATG
Found at i:3448008 original size:21 final size:21
Alignment explanation
Indices: 3447979--3448042 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
3447969 AATAAAATGT
3447979 TTAATGAAAAAGATACCAATTG
1 TTAA-GAAAAAGATACCAATTG
* *
3448001 TTAAGAAAATGATATCAATTG
1 TTAAGAAAAAGATACCAATTG
3448022 TT---AAAAAGATACCAATTG
1 TTAAGAAAAAGATACCAATTG
3448040 TTA
1 TTA
3448043 CCAATTGTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 16 0.43
21 17 0.46
22 4 0.11
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (21 bp):
TTAAGAAAAAGATACCAATTG
Found at i:3448032 original size:18 final size:18
Alignment explanation
Indices: 3447985--3448042 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
3447975 ATGTTTAATG
3447985 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
3448003 AAGAAAATGATATCAATTGTT
1 -A-AAAA-GATACCAATTGTT
3448024 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
3448042 A
1 A
3448043 CCAATTGTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
20 5 0.14
21 12 0.34
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:3452815 original size:20 final size:20
Alignment explanation
Indices: 3452767--3452807 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3452757 TGATACTTTT
*
3452767 CAAGAGTTTTGAAACTATCT
1 CAAGAGTTTTGAAACTATCC
*
3452787 CAAGAGTTTTGAAACTTTCC
1 CAAGAGTTTTGAAACTATCC
3452807 C
1 C
3452808 TAAAGTTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (20 bp):
CAAGAGTTTTGAAACTATCC
Found at i:3452989 original size:21 final size:21
Alignment explanation
Indices: 3452965--3453008 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3452955 TTCCAACATA
3452965 TAAAAACAAGTT-CAAAACACT
1 TAAAAA-AAGTTACAAAACACT
* *
3452986 TAAAGAAGGTTACAAAACACT
1 TAAAAAAAGTTACAAAACACT
3453007 TA
1 TA
3453009 TCGAAGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (21 bp):
TAAAAAAAGTTACAAAACACT
Found at i:3453022 original size:21 final size:22
Alignment explanation
Indices: 3452976--3453022 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
3452966 AAAAACAAGT
*
3452976 TCAAAACACTTAAAGAAGGTTA
1 TCAAAACACTTAAAGAAGGTAA
**
3452998 -CAAAACACTTATCGAA-GTAA
1 TCAAAACACTTAAAGAAGGTAA
3453018 TCAAA
1 TCAAA
3453023 CACAAGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (22 bp):
TCAAAACACTTAAAGAAGGTAA
Found at i:3453474 original size:20 final size:20
Alignment explanation
Indices: 3453449--3453500 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3453439 TAAGCTCCTC
3453449 GATATCGATAC-AAGCCTTTG
1 GATATCGATACTAA-CCTTTG
*
3453469 GGTATCGATACTAACCTTTG
1 GATATCGATACTAACCTTTG
*
3453489 GATATCAATACT
1 GATATCGATACT
3453501 GCTAACTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (20 bp):
GATATCGATACTAACCTTTG
Found at i:3461673 original size:40 final size:40
Alignment explanation
Indices: 3461616--3461725 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
3461606 ATAGTACAAG
*
3461616 TTATGTGGACAAGGCTCGACCTCAGCACTACGATGCATAA
1 TTATGTGGGCAAGGCTCGACCTCAGCACTACGATGCATAA
* * * *
3461656 TTATGTGGGCAACGCTCGATCTCAGCACTATGATGCATTA
1 TTATGTGGGCAAGGCTCGACCTCAGCACTACGATGCATAA
* * * *
3461696 TTAGGTGAGTAAGGCTCGACCTCAACACTA
1 TTATGTGGGCAAGGCTCGACCTCAGCACTA
3461726 TTTTTCAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (40 bp):
TTATGTGGGCAAGGCTCGACCTCAGCACTACGATGCATAA
Found at i:3469230 original size:18 final size:18
Alignment explanation
Indices: 3469196--3469229 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3469186 AGGGAGAGAC
3469196 AACAAGATAAAGAAAAAT
1 AACAAGATAAAGAAAAAT
3469214 AACAAGA-AAAGAAAAA
1 AACAAGATAAAGAAAAA
3469230 AATTGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (18 bp):
AACAAGATAAAGAAAAAT
Found at i:3475954 original size:20 final size:20
Alignment explanation
Indices: 3475925--3475968 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3475915 TTTTGTCCCA
3475925 ATTA-ATTATTAATA-TATAT
1 ATTATATTATTAATATTAT-T
3475944 ATTATATTATTAATATTATT
1 ATTATATTATTAATATTATT
3475964 ATTAT
1 ATTAT
3475969 TAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTATATTATTAATATTATT
Found at i:3489919 original size:81 final size:81
Alignment explanation
Indices: 3489780--3490872 Score: 1364
Period size: 81 Copynumber: 13.5 Consensus size: 81
3489770 CAATTCAAAA
* * * * *
3489780 TACCCGAAAAAGATGAACAAATGAAGTCTAATCT-CCCTAAAAGAATAGTGGAGGAGACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3489844 TCCAAAATTGATCTGAG
65 TCCAAAATTGATCTGAC
* * *
3489861 TACCC-AAAATAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGTGGGAAGACTCGTTT
1 TACCCGAAAA-AGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGTGAGCAGACTCGTCT
* *
3489925 TCCAAAATTGATTTGAG
65 TCCAAAATTGATCTGAC
* *
3489942 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCTCTGAAAGAATAGTGGAGCAGACTCATCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
* *
3490007 TCC-AAATTGATATGAA
65 TCCAAAATTGATCTGAC
* * * * *
3490023 TACCCAAAAAAGAGGAAAAAATCAAGTCT-TTCTCCCCTAAAAGAATAGTGGAGCAGACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3490087 TCCAAAATAGATCTGAC
65 TCCAAAATTGATCTGAC
* * * *
3490104 TACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCTTGAAAGAAGAGATGAGCAGACTCGTCC
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAG-TGAGCAGACTCGTCT
*
3490169 TCCAAAATTAATCTGAC
65 TCCAAAATTGATCTGAC
* * * *
3490186 TACCTGAAAAAAATGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGTAGCGCAGACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3490251 TCC-AAATTGACCTGAC
65 TCCAAAATTGATCTGAC
* * * * * * *
3490267 TACCCGAAAAAGAGGAACATATCAAGTCTGATATCCCCTGAAAGAAGAGAAGAGTAGACCCATCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAG-TGAGCAGACTCGTCT
*
3490332 TCTAAAATTGATCTGAC
65 TCCAAAATTGATCTGAC
* * * *
3490349 TACCCAAAAAAGA-GAATAGATCAAGTCTGATCTCCCCTGAAAGAATAGTAGAGCAGACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3490413 TCCAAAATTTATCTGAC
65 TCCAAAATTGATCTGAC
*
3490430 TACCCGAAAAAGAGGAACATATCAAGTCT-ATCTCCCCTGAAAGAATAGTAGAGCATACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
* * *
3490494 TCAAAAATTTATCTAAC
65 TCCAAAATTGATCTGAC
* * ** * * *
3490511 TACCCAAAAAAGAGGAACAAATCAAGTCTGGTCTCCCCTGAAAGAATGGTGGAGTATACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3490576 TCCAAAATTGATATGAC
65 TCCAAAATTGATCTGAC
* * *
3490593 TACCTGAAAAAGAGGAACATATCAAGTCTAATCT--CCTAAAAGAATAGTAGAGTAGACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3490656 TCCAAAATTGATATGAC
65 TCCAAAATTGATCTGAC
* * *
3490673 TACCCGAAAAATAGAAACATTTCAAGTCTAATCTCCCCTGAAAGAATAGTAGAGCAGAC-CGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGT-GAGCAGACTCGTCT
*
3490737 TCCAAAATTGATCTGAT
65 TCCAAAATTGATCTGAC
* * * *
3490754 TACCCGAAAAAGAGGAACATATCAAGTTTGATCT--CCTGAAAGAATAGAAGAGCAAACTCGTCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAG-TGAGCAGACTCGTCT
3490817 TCCAAAATTGATCTGAC
65 TCCAAAATTGATCTGAC
*
3490834 TACCCGAAAAAGAGGAACATATCAAGTCTGATCTCCCCT
1 TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCT
3490873 AAGGGAAGAG
Statistics
Matches: 883, Mismatches: 110, Indels: 37
0.86 0.11 0.04
Matches are distributed among these distances:
79 20 0.02
80 164 0.19
81 432 0.49
82 266 0.30
83 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (81 bp):
TACCCGAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATAGTGAGCAGACTCGTCTT
CCAAAATTGATCTGAC
Found at i:3490293 original size:244 final size:245
Alignment explanation
Indices: 3489780--3490872 Score: 1452
Period size: 244 Copynumber: 4.5 Consensus size: 245
3489770 CAATTCAAAA
* * * * *
3489780 TACCCGAAAAAGATGAACAAATGAAGTCTAATCT-CCCTAAAAGAATAGTGGAGGAGACTCGTCT
1 TACCCGAAAAAGAGGAACAAATCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCT
* *
3489844 TCCAAAATTGATCTGAGTACCCAAAATAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATA
66 TCCAAAATTGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATA
* * * * *
3489909 GT-GGGAAGACTCGTTTTCCAAAATTGATTTGAGTACCCGAAAAAGAGGAACATATCAAGTCTAA
131 GTAGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATCAAGTCTAA
* * * * *
3489973 TCTCCTCTGAAAGAATAGTGGAGCAGACTCATCTTCCAAATTGATATGAA
196 TCTCCCCTGAAAGAATAGTAGAGCAGACTCGTCTTCCAAATTGATCTGAC
* * * *
3490023 TACCCAAAAAAGAGGAAAAAATCAAGTCT-TTCTCCCCTAAAAGAATAGTGGAGCAGACTCGTCT
1 TACCCGAAAAAGAGGAACAAATCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCT
* * *
3490087 TCCAAAATAGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCTTGAAAGAAGA
66 TCCAAAATTGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATA
* * * * *
3490152 G-ATGAGCAGACTCGTCCTCCAAAATTAATCTGACTACCTGAAAAAAATGAACATATCAAGTCTA
131 GTA-GAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATCAAGTCTA
* *
3490216 ATCTCCCCTGAAAGAATAGTAGCGCAGACTCGTCTTCCAAATTGACCTGAC
195 ATCTCCCCTGAAAGAATAGTAGAGCAGACTCGTCTTCCAAATTGATCTGAC
* * * ** * * *
3490267 TACCCGAAAAAGAGGAACATATCAAGTCTGATATCCCCTGAAAGAAGAGAAGAGTAGACCCATCT
1 TACCCGAAAAAGAGGAACAAATCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCT
* * * *
3490332 TCTAAAATTGATCTGACTACCCAAAAAAGA-GAATAGATCAAGTCTGATCTCCCCTGAAAGAATA
66 TCCAAAATTGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATA
*
3490396 GTAGAGCAGACTCGTCTTCCAAAATTTATCTGACTACCCGAAAAAGAGGAACATATCAAGTCT-A
131 GTAGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATCAAGTCTAA
* * * *
3490460 TCTCCCCTGAAAGAATAGTAGAGCATACTCGTCTTCAAAAATTTATCTAAC
196 TCTCCCCTGAAAGAATAGTAGAGCAGACTCGTCTTC-CAAATTGATCTGAC
* * * * *
3490511 TACCCAAAAAAGAGGAACAAATCAAGTCTGGTCTCCCCTGAAAGAATGGTGGAGTATACTCGTCT
1 TACCCGAAAAAGAGGAACAAATCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCT
* ** *
3490576 TCCAAAATTGATATGACTACCTGAAAAAGAGGAACATATCAAGTCTAATCT--CCTAAAAGAATA
66 TCCAAAATTGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATA
* * * * *
3490639 GTAGAGTAGACTCGTCTTCCAAAATTGATATGACTACCCGAAAAATAGAAACATTTCAAGTCTAA
131 GTAGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATCAAGTCTAA
*
3490704 TCTCCCCTGAAAGAATAGTAGAGCAGAC-CGTCTTCCAAAATTGATCTGAT
196 TCTCCCCTGAAAGAATAGTAGAGCAGACTCGTCTTCC-AAATTGATCTGAC
* * ** *
3490754 TACCCGAAAAAGAGGAACATATCAAGTTTGATCT--CCTGAAAGAATAGAAGAGCAAACTCGTCT
1 TACCCGAAAAAGAGGAACAAATCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCT
* *
3490817 TCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATCAAGTCTGATCTCCCCT
66 TCCAAAATTGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCCT
3490873 AAGGGAAGAG
Statistics
Matches: 739, Mismatches: 100, Indels: 22
0.86 0.12 0.03
Matches are distributed among these distances:
241 72 0.10
242 3 0.00
243 268 0.36
244 324 0.44
245 72 0.10
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (245 bp):
TACCCGAAAAAGAGGAACAAATCAAGTCTGATCTCCCCTGAAAGAATAGTGGAGCAGACTCGTCT
TCCAAAATTGATCTGACTACCCAAAAAAGAGGAACATATCAAGTCTAATCTCCCCTGAAAGAATA
GTAGAGCAGACTCGTCTTCCAAAATTGATCTGACTACCCGAAAAAGAGGAACATATCAAGTCTAA
TCTCCCCTGAAAGAATAGTAGAGCAGACTCGTCTTCCAAATTGATCTGAC
Found at i:3491037 original size:18 final size:19
Alignment explanation
Indices: 3491002--3491043 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3490992 TAAATAGTAG
3491002 TTTTATCTTAATTAATTAT
1 TTTTATCTTAATTAATTAT
* *
3491021 TTTTATTTTTATT-ATTAT
1 TTTTATCTTAATTAATTAT
3491039 TTTTA
1 TTTTA
3491044 AATAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATCTTAATTAATTAT
Found at i:3491126 original size:24 final size:25
Alignment explanation
Indices: 3491099--3491154 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
3491089 AGACCCAGTT
*
3491099 ACAAAACCCAG-GGCCCAATTAACA
1 ACAAAACCCAGAAGCCCAATTAACA
*
3491123 ACAAAA-CCTGAAGCCCAATTAACA
1 ACAAAACCCAGAAGCCCAATTAACA
3491147 ACAAAACC
1 ACAAAACC
3491155 GGACTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 24 0.86
25 1 0.04
ACGTcount: A:0.50, C:0.32, G:0.09, T:0.09
Consensus pattern (25 bp):
ACAAAACCCAGAAGCCCAATTAACA
Found at i:3493624 original size:100 final size:98
Alignment explanation
Indices: 3493504--3493852 Score: 314
Period size: 100 Copynumber: 3.5 Consensus size: 98
3493494 TGTTATAAAT
** *
3493504 TGTTATTAAGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAAAATATTGTGATGAAATATA
1 TGTTATTGTGACTAAATAAATTTGTCAAAAGTTGTTATTGTGA-AAAATATTGTGATGAAATATA
3493569 TTTAACATAAATTTTTATTTTGACTAAATTTACTA
65 TTTAACATAAATTTTTATTTTGACTAAATTTA-TA
* * * * * **
3493604 TGTTATTGTAACTAAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTGT-TTGTCATAAT
1 TGTTATTGTGACTAAATAAATTTGTCAAAAGTTGTTATTGTGAAA-AATATTGTGATGAAAT-AT
* * * *** * *
3493668 TTTTTATATTGAAAAAATAATATTTG-TTATAA---AT-
64 ATTTAACA-T-AAATTTTTAT-TTTGACTA-AATTTATA
* * * *
3493702 TGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTAAGAAAATATTGTGATGAAATAAA
1 TGTTATTGTGACTAAATAAATTTGTCAAAAGTTGTTATTGTGA-AAAATATTGTGATGAAATATA
* * *
3493767 TTTAACATAATTTTTTATTTTTACTAATTTTAATA
65 TTTAACATAAATTTTTATTTTGACTAAATTT-ATA
* * *
3493802 TGTTATTGCGACTAAATAAATTTGTTAAAAGTTATTATTGTGAAAAATATT
1 TGTTATTGTGACTAAATAAATTTGTCAAAAGTTGTTATTGTGAAAAATATT
3493853 ATTTTTCATA
Statistics
Matches: 189, Mismatches: 46, Indels: 29
0.72 0.17 0.11
Matches are distributed among these distances:
95 4 0.02
96 7 0.04
97 1 0.01
98 50 0.26
99 23 0.12
100 89 0.47
101 1 0.01
102 8 0.04
103 6 0.03
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (98 bp):
TGTTATTGTGACTAAATAAATTTGTCAAAAGTTGTTATTGTGAAAAATATTGTGATGAAATATAT
TTAACATAAATTTTTATTTTGACTAAATTTATA
Found at i:3493669 original size:33 final size:32
Alignment explanation
Indices: 3493617--3493751 Score: 103
Period size: 33 Copynumber: 4.2 Consensus size: 32
3493607 TATTGTAACT
* *
3493617 AAATAA-ATTTGTTACAATTTGTTATTGTGAAA
1 AAATAATATTTGTCATAATTTGTTATT-TGAAA
* * * *
3493649 GAATATTGTTTGTCATAATTTTTTATATTGAAA
1 AAATAATATTTGTCATAATTTGTTAT-TTGAAA
* * **
3493682 AAATAATATTTGTTATAAATTGTTATTATGACT
1 AAATAATATTTGTCATAATTTGTTATT-TGAAA
* * *
3493715 AAATAA-ATTTGTCAAAAGTTGTTATTTTAAGA
1 AAATAATATTTGTCATAATTTGTTATTTGAA-A
3493747 AAATA
1 AAATA
3493752 TTGTGATGAA
Statistics
Matches: 79, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
31 2 0.03
32 27 0.34
33 49 0.62
34 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (32 bp):
AAATAATATTTGTCATAATTTGTTATTTGAAA
Found at i:3493842 original size:198 final size:188
Alignment explanation
Indices: 3493492--3494014 Score: 643
Period size: 198 Copynumber: 2.7 Consensus size: 188
3493482 TGTTATCATG
*
3493492 TTTGTTATAAATTGTTATTAAGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAAAATATTG
1 TTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAAAATATTG
* * * * *
3493557 TGATGAAATATATTTAACATAAATTTTTATTTTGACTAAATTTACTATGTTATTGTAACTAAATA
66 TGATGAAATAAATTTAACATAATTTTTTATTTTAACTAAATTTAATATGTTATTGTGACTAAATA
* * * *
3493622 AATTTGTTACAATTTGTTATTGTGAAAGAATATTGTTTGTCATAATTTTTTATATTGAAAAAATA
131 AATTTGTTAAAAGTTATTATTGTGAAA-AATATTATTTGTCATAA-TTTTTATA-T-------TA
3493687 ATA
186 ATA
*
3493690 TTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTAAGAAAATATTG
1 TTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAAAATATTG
* * *
3493755 TGATGAAATAAATTTAACATAATTTTTTATTTTTACTAATTTTAATATGTTATTGCGACTAAATA
66 TGATGAAATAAATTTAACATAATTTTTTATTTTAACTAAATTTAATATGTTATTGTGACTAAATA
*
3493820 AATTTGTTAAAAGTTATTATTGTGAAAAATATTATTTTTCATAATTTTTATATTAATA
131 AATTTGTTAAAAGTTATTATTGTGAAAAATATTATTTGTCATAATTTTTATATTAATA
* * * ** * * * * *
3493878 TTTATTATAAATTATTATTATAACTATTTAAATTTGTCATAATTTTTTATTTTGAGAAAATGTTT
1 TTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAAAATATTG
* * * * *
3493943 TGACT-AAAGAAATTTAGCATATATATTTTTAATTTTAACTAAATTTAATTTGTTATCGTGTCTA
66 TGA-TGAAATAAATTTAACATA-AT-TTTTT-ATTTTAACTAAATTTAATATGTTATTGTGACTA
3494007 AATAAATT
127 AATAAATT
3494015 ACCATAATTT
Statistics
Matches: 288, Mismatches: 33, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
188 76 0.26
189 3 0.01
190 5 0.02
191 35 0.12
195 1 0.00
196 8 0.03
197 15 0.05
198 145 0.50
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.48
Consensus pattern (188 bp):
TTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTGTTATTTTGAGAAAATATTG
TGATGAAATAAATTTAACATAATTTTTTATTTTAACTAAATTTAATATGTTATTGTGACTAAATA
AATTTGTTAAAAGTTATTATTGTGAAAAATATTATTTGTCATAATTTTTATATTAATA
Found at i:3501314 original size:38 final size:37
Alignment explanation
Indices: 3501218--3501493 Score: 248
Period size: 38 Copynumber: 7.4 Consensus size: 37
3501208 GATTATTTAG
**
3501218 TATATATTAATATAATAGAGTTTTGAAATTATTTTTGAAAAA
1 TATATA-TAATAT-AT--AGTTTTGAAAACA-TTTTGAAAAA
*
3501260 -ATATA-AATATA-A-TTTTGAAAACGATTTTCAAAAA
1 TATATATAATATATAGTTTTGAAAAC-ATTTTGAAAAA
* *
3501294 TATATATATTATATAGTTTTGAAAATTATTTTTG---AA
1 TATATATAATATATAGTTTTGAAAA-CA-TTTTGAAAAA
**
3501330 TATATAT-AT-TATAGTTTCAAAAACATTTTGAAAACA
1 TATATATAATATATAGTTTTGAAAACATTTTGAAAA-A
* * *
3501366 TATATATAATACATAGTTTTTAAAATATTTTG-AAAA
1 TATATATAATATATAGTTTTGAAAACATTTTGAAAAA
3501402 TATATATAATATATAGTTTTTGAAAACATTTTGAAAACA
1 TATATATAATATATAG-TTTTGAAAACATTTTGAAAA-A
* * *
3501441 AATATATAATATATGGTTTTTGAAAACATTTTGGAAAA
1 TATATATAATATATAG-TTTTGAAAACATTTTGAAAAA
*
3501479 TAAATATAATATATA
1 TATATATAATATATA
3501494 TATATATTAA
Statistics
Matches: 195, Mismatches: 23, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
32 5 0.03
33 1 0.01
34 29 0.15
35 9 0.05
36 38 0.19
37 20 0.10
38 44 0.23
39 44 0.23
41 5 0.03
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (37 bp):
TATATATAATATATAGTTTTGAAAACATTTTGAAAAA
Found at i:3501339 original size:36 final size:35
Alignment explanation
Indices: 3501227--3501427 Score: 119
Period size: 36 Copynumber: 5.6 Consensus size: 35
3501217 GTATATATTA
* * *
3501227 ATATA-ATAGAGTTTTG-AAATTATTTTTGAAAAA
1 ATATATATATAGTTTTGAAAATTATTTTTGAATAT
* * ** **
3501260 ATATAAATATAATTTTGAAAACGATTTTCAAAAATAT
1 ATATATATATAGTTTTGAAAATTATTTT--TGAATAT
3501297 ATATATTATATAGTTTTGAAAATTATTTTTGAATAT
1 ATATA-TATATAGTTTTGAAAATTATTTTTGAATAT
* **
3501333 ATATAT-TATAG-TTTCAAAAACA-TTTTGAAAACATAT
1 ATATATATATAGTTTTGAAAATTATTTTTG---A-ATAT
* *
3501369 ATATAATACATAGTTTTTAAAA-TA-TTTTGAAAATAT
1 ATAT-ATATATAGTTTTGAAAATTATTTTTG--AATAT
3501405 ATATAATATATAGTTTTTGAAAA
1 ATAT-ATATATAG-TTTTGAAAA
3501428 CATTTTGAAA
Statistics
Matches: 133, Mismatches: 22, Indels: 22
0.75 0.12 0.12
Matches are distributed among these distances:
32 5 0.04
33 13 0.10
34 14 0.11
35 10 0.08
36 34 0.26
37 21 0.16
38 29 0.22
39 7 0.05
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATATATAGTTTTGAAAATTATTTTTGAATAT
Found at i:3501369 original size:72 final size:73
Alignment explanation
Indices: 3501218--3501466 Score: 265
Period size: 72 Copynumber: 3.3 Consensus size: 73
3501208 GATTATTTAG
* * * *
3501218 TATATATTAATATAATAGAGTTTTG-AAATTATTTTTGAAAAAATATAAATATAATTTTGAAAAC
1 TATATA-TAATAT-AT--AGTTTTGAAAATTATTTTTGAATATATATAATTATAGTTTTGAAAAC
*
3501282 GATTTTCAAAA-A
62 -ATTTTGAAAACA
* **
3501294 TATATATATTATATAGTTTTGAAAATTATTTTTGAATATATAT-ATTATAGTTTCAAAAACATTT
1 TATATATAATATATAGTTTTGAAAATTATTTTTGAATATATATAATTATAGTTTTGAAAACATTT
3501358 TGAAAACA
66 TGAAAACA
* *
3501366 TATATATAATACATAGTTTTTAAAA-TA-TTTTGAAAATATATATAATATATAGTTTTTGAAAAC
1 TATATATAATATATAGTTTTGAAAATTATTTTTG--AATATATATAAT-TATAG-TTTTGAAAAC
3501429 ATTTTGAAAACA
62 ATTTTGAAAACA
* *
3501441 AATATATAATATATGGTTTTTGAAAA
1 TATATATAATATATAG-TTTTGAAAA
3501467 CATTTTGGAA
Statistics
Matches: 148, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
70 5 0.03
71 11 0.07
72 52 0.35
73 21 0.14
74 7 0.05
75 38 0.26
76 14 0.09
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (73 bp):
TATATATAATATATAGTTTTGAAAATTATTTTTGAATATATATAATTATAGTTTTGAAAACATTT
TGAAAACA
Found at i:3501531 original size:17 final size:16
Alignment explanation
Indices: 3501509--3501548 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3501499 ATTAAATAAA
3501509 ATTATTATTATTATTAT
1 ATTATTATT-TTATTAT
*
3501526 ATTATTTATTTTTTTAT
1 ATTA-TTATTTTATTAT
3501543 ATTATT
1 ATTATT
3501549 GTTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 14 0.67
18 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATTATTTTATTAT
Found at i:3502875 original size:41 final size:38
Alignment explanation
Indices: 3502799--3502900 Score: 100
Period size: 41 Copynumber: 2.6 Consensus size: 38
3502789 TAACTTTAAA
* *
3502799 ATTTAACATTTTTTTATTTTTTATTTTTTCCCCTTTGATTT
1 ATTTAATATTTTTTTATTTTTTATTTTTT-CCCTTT--TTG
3502840 ATTTAATATTTTTTTATTTTATT-TTTCCTTT-CCTTTTTG
1 ATTTAATATTTTTTTATTTT-TTATTT--TTTCCCTTTTTG
*
3502879 ATTTAATTTTTTATTTATTTTT
1 ATTTAATATTTT-TTTATTTTT
3502901 CTTTGATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
39 14 0.26
40 8 0.15
41 27 0.50
42 2 0.04
43 3 0.06
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.72
Consensus pattern (38 bp):
ATTTAATATTTTTTTATTTTTTATTTTTTCCCTTTTTG
Found at i:3502900 original size:24 final size:24
Alignment explanation
Indices: 3502846--3502900 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
3502836 ATTTATTTAA
* * *
3502846 TATTTTTTTATTTTATTTTTCCTT
1 TATTTTTTGATTTAATTTTTCATT
** *
3502870 TCCTTTTTGATTTAATTTTTTATT
1 TATTTTTTGATTTAATTTTTCATT
3502894 TATTTTT
1 TATTTTT
3502901 CTTTGATTTA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (24 bp):
TATTTTTTGATTTAATTTTTCATT
Found at i:3502929 original size:36 final size:36
Alignment explanation
Indices: 3502817--3502930 Score: 103
Period size: 36 Copynumber: 3.2 Consensus size: 36
3502807 TTTTTTTATT
**
3502817 TTTTATTT-TTTCCCCTTTGATTTATTTAATATTT-
1 TTTTATTTATTTTTCCTTTGATTTATTTAATATTTA
** * * *
3502851 TTTTATTTTATTTTTCCTTTCCTTT-TTGATTTAATT-
1 TTTTA-TTTATTTTTCCTTTGATTTATTTA-ATATTTA
3502887 TTTTATTTATTTTT-CTTTGATTTATTTAATATTTA
1 TTTTATTTATTTTTCCTTTGATTTATTTAATATTTA
3502922 TTATTATTT
1 TT-TTATTT
3502931 CTTATAATAT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
34 16 0.26
35 20 0.32
36 26 0.42
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (36 bp):
TTTTATTTATTTTTCCTTTGATTTATTTAATATTTA
Found at i:3506822 original size:99 final size:100
Alignment explanation
Indices: 3506701--3506889 Score: 317
Period size: 100 Copynumber: 1.9 Consensus size: 100
3506691 ATATATAGAT
3506701 AATAAAGCATGAGCTGTACCTCTAGAGCAATTAGTTAAAA-GCCCCAGCTTTATGGATAAGATTC
1 AATAAAGCATGAGCTGTACCTCTAGAGCAATTAGTTAAAACGCCCCAGCTTTATGGATAAGATTC
3506765 AACTAGCCTGATAAAGGTGATTATAATACATATAC
66 AACTAGCCTGATAAAGGTGATTATAATACATATAC
* * * * *
3506800 AATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAACGCCCCGGCTTTATGGATAAGATTC
1 AATAAAGCATGAGCTGTACCTCTAGAGCAATTAGTTAAAACGCCCCAGCTTTATGGATAAGATTC
*
3506865 AGCTAGCCTGATAAAGGTGATTATA
66 AACTAGCCTGATAAAGGTGATTATA
3506890 GTATTGAGGT
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 36 0.43
100 47 0.57
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (100 bp):
AATAAAGCATGAGCTGTACCTCTAGAGCAATTAGTTAAAACGCCCCAGCTTTATGGATAAGATTC
AACTAGCCTGATAAAGGTGATTATAATACATATAC
Found at i:3508171 original size:22 final size:21
Alignment explanation
Indices: 3508146--3508190 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3508136 ATTTTGAAAA
3508146 TTACTCAAAAAATTACTCCCCC
1 TTACT-AAAAAATTACTCCCCC
* * *
3508168 TTACTATAAGATTTCTCCCCC
1 TTACTAAAAAATTACTCCCCC
3508189 TT
1 TT
3508191 TTTGTTAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (21 bp):
TTACTAAAAAATTACTCCCCC
Found at i:3512134 original size:85 final size:85
Alignment explanation
Indices: 3511963--3512387 Score: 541
Period size: 85 Copynumber: 5.0 Consensus size: 85
3511953 GAATTATTCG
* * *
3511963 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTTAGCAA-AAAAATCTTCGAGTTCGATTCCATTC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTG-T--CAACCAAAACCTTCGAGTTCGATTACATTC
* *
3512027 ATCTTAAGGGCATATCAAATTTA
63 AGCTCAAGGGCATATCAAATTTA
* * *
3512050 CAGCATAGCTCAAGGCGAGAAGGGCAATCTGTCAACCAAAACCTTCGAGTTCAATTTCATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGC
* * *
3512115 TTAAGGGTATATTAAATTTA
66 TCAAGGGCATATCAAATTTA
* * * *
3512135 CAGTATAGCTCAAGGCGAGAAGGGTTATATGTCAACCAAAACCTTCGAGTTTGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGC
** *
3512200 TCAAGTACATATTAAATTTA
66 TCAAGGGCATATCAAATTTA
** *
3512220 CAGCATAGCTCAAGGAAAGAAGGGCTATATGTCAACCAAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGC
* *
3512285 TCAAGGACATATCAAATTTG
66 TCAAGGGCATATCAAATTTA
* * * **
3512305 CAGCATAACTCAA-G-GAAAAGGGTTATCTGTCAATAAAAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGC
*
3512368 TCAAGGGTATATCAAATTTA
66 TCAAGGGCATATCAAATTTA
3512388 GCAACAAGGC
Statistics
Matches: 300, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
83 60 0.20
84 4 0.01
85 205 0.68
86 1 0.00
87 30 0.10
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (85 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGC
TCAAGGGCATATCAAATTTA
Found at i:3513366 original size:38 final size:38
Alignment explanation
Indices: 3513246--3513394 Score: 187
Period size: 38 Copynumber: 4.0 Consensus size: 38
3513236 ATAATAGAGT
*
3513246 TTTTGAAAA-TATTTTTGAAAA-AT-TATAATATATAG
1 TTTTGAAAATTATTTTTGAAAATATATATATTATATAG
** * * *
3513281 TTTTGAAAACGATTTTCGAAAAAATATTTATTATATAG
1 TTTTGAAAATTATTTTTGAAAATATATATATTATATAG
*
3513319 TTTTGAAAATTATTTTTGAAAATATATATATTATATGG
1 TTTTGAAAATTATTTTTGAAAATATATATATTATATAG
* *
3513357 TTTTGAAAATTCTTTTTGAATATATATATATATATATA
1 TTTTGAAAATTATTTTTGAAAATATATATAT-TATATA
3513395 TATATATATT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
35 9 0.09
36 10 0.10
37 2 0.02
38 71 0.73
39 5 0.05
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.48
Consensus pattern (38 bp):
TTTTGAAAATTATTTTTGAAAATATATATATTATATAG
Found at i:3513383 original size:2 final size:2
Alignment explanation
Indices: 3513376--3513403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3513366 TTCTTTTTGA
3513376 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
3513404 TAGTTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3513399 original size:50 final size:49
Alignment explanation
Indices: 3513340--3513443 Score: 156
Period size: 50 Copynumber: 2.1 Consensus size: 49
3513330 ATTTTTGAAA
* * *
3513340 ATATATATAT-TATATGGTTTTGAAAATTCTTTTTGAATATATATATATAT
1 ATATATATATATAT-TAGTTTTGAAAATTATTTTTGAAAATATATATAT-T
3513390 ATATATATATATATTAGTTTTGAAAATTATTTTTGAAAATATATATATT
1 ATATATATATATATTAGTTTTGAAAATTATTTTTGAAAATATATATATT
3513439 ATATA
1 ATATA
3513444 GTTTTGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
49 6 0.12
50 41 0.82
51 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (49 bp):
ATATATATATATATTAGTTTTGAAAATTATTTTTGAAAATATATATATT
Found at i:3513434 original size:34 final size:36
Alignment explanation
Indices: 3513390--3513595 Score: 201
Period size: 41 Copynumber: 5.5 Consensus size: 36
3513380 ATATATATAT
*
3513390 ATATATATATATATTAGTTTTGAAAATTATTTTTGAAA
1 ATATATATATATA-TAGTTTTGAAAATGATTTTTG-AA
*
3513428 ATATATATATTATATAGTTTTGAAAATGATTTTTAATATA
1 ATATATATA-TATATAGTTTTGAAAATGATTTTT--GA-A
3513468 TATATATATATATTATAGTTTTGAAAATGATTTTTG-A
1 -ATATATATATA-TATAGTTTTGAAAATGATTTTTGAA
*
3513505 ATATATATATATATA-TTTTGAAAA-CA-TTTTGAAAA
1 ATATATATATATATAGTTTTGAAAATGATTTTTG--AA
*
3513540 CATATATATAATATATAGTTTTTGAAAA-CA-TTTTGAA
1 -ATATATAT-ATATATAG-TTTTGAAAATGATTTTTGAA
3513577 A-ATATATAATATATAGTTT
1 ATATATAT-ATATATAGTTT
3513596 AAAAAAACAT
Statistics
Matches: 151, Mismatches: 4, Indels: 30
0.82 0.02 0.16
Matches are distributed among these distances:
32 5 0.03
33 1 0.01
34 12 0.08
35 20 0.13
36 20 0.13
37 10 0.07
38 28 0.19
39 21 0.14
40 3 0.02
41 31 0.21
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (36 bp):
ATATATATATATATAGTTTTGAAAATGATTTTTGAA
Found at i:3513434 original size:38 final size:39
Alignment explanation
Indices: 3513388--3513631 Score: 246
Period size: 39 Copynumber: 6.4 Consensus size: 39
3513378 ATATATATAT
*
3513388 ATATATATATATATATTAGTTTTGAAAATTATTTTTGAAA
1 ATATATATATATATA-TAGTTTTGAAAATCATTTTTGAAA
*
3513428 ATATATATAT-TATATAGTTTTGAAAATGATTTTT-AATA
1 ATATATATATATATATAGTTTTGAAAATCATTTTTGAA-A
*
3513466 TATATATATATATATTATAGTTTTGAAAATGATTTTTG---
1 -ATATATATATATA-TATAGTTTTGAAAATCATTTTTGAAA
3513504 A-ATATATATATATATA-TTTTGAAAA-CA-TTTTGAAA
1 ATATATATATATATATAGTTTTGAAAATCATTTTTGAAA
*
3513539 ACATATATATAATATATAGTTTTTGAAAA-CA-TTTTG-AA
1 ATATATATAT-ATATATAG-TTTTGAAAATCATTTTTGAAA
** * *
3513577 A-ATATATA-ATATATAGTTTAAAAAAACATTTTGGAAA
1 ATATATATATATATATAGTTTTGAAAATCATTTTTGAAA
*
3513614 ATAAATATAATATATATA
1 ATATATAT-ATATATATA
3513632 TATTTTTAAA
Statistics
Matches: 180, Mismatches: 6, Indels: 36
0.81 0.03 0.16
Matches are distributed among these distances:
32 5 0.03
33 1 0.01
34 16 0.09
35 15 0.08
36 23 0.13
37 20 0.11
38 28 0.16
39 31 0.17
40 19 0.11
41 22 0.12
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (39 bp):
ATATATATATATATATAGTTTTGAAAATCATTTTTGAAA
Found at i:3513467 original size:26 final size:25
Alignment explanation
Indices: 3513420--3513469 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3513410 TGAAAATTAT
*
3513420 TTTTGAAAATATATATATTATATAG
1 TTTTGAAAATATATATAATATATAG
* *
3513445 TTTTGAAAATGATTTTTAATATATA
1 TTTTGAAAAT-ATATATAATATATA
3513470 TATATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (25 bp):
TTTTGAAAATATATATAATATATAG
Found at i:3513580 original size:28 final size:28
Alignment explanation
Indices: 3513531--3513584 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3513521 TTTGAAAACA
*
3513531 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATAAAATATATAGT
*
3513559 TTTTGAAAACAT-TTTGAAAATATATA
1 TTTTGAAAACATATAT-AAAATATATA
3513585 ATATATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATATATAAAATATATAGT
Found at i:3513582 original size:35 final size:34
Alignment explanation
Indices: 3513469--3513629 Score: 155
Period size: 35 Copynumber: 4.4 Consensus size: 34
3513459 TTTAATATAT
* *
3513469 ATATATATATATTATAGTTTTGAAAATGATTTTTGAAT
1 ATATATA-ATA-TATAGTTTTGAAAA-CA-TTTTGAAA
3513507 ATATAT-ATATATA-TTTTGAAAACATTTTGAAAACA
1 ATATATAATATATAGTTTTGAAAACATTTTG--AA-A
3513542 TATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 -ATATATAATATATAG-TTTTGAAAACATTTTGAAA
**
3513578 ATATATAATATATAGTTTAAAAAAACATTTTGGAAA
1 ATATATAATATATAGTTT-TGAAAACATTTT-GAAA
3513614 ATAAATATAATATATA
1 AT--ATATAATATATA
3513630 TATATTTTTA
Statistics
Matches: 108, Mismatches: 4, Indels: 22
0.81 0.03 0.16
Matches are distributed among these distances:
32 5 0.05
33 1 0.01
34 14 0.13
35 29 0.27
36 16 0.15
37 9 0.08
38 18 0.17
39 16 0.15
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.42
Consensus pattern (34 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:3514922 original size:18 final size:17
Alignment explanation
Indices: 3514878--3514922 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3514868 TTTAGTATGT
* *
3514878 TTTTATTTTTTTATTTG
1 TTTTATTTTTTTACTTC
*
3514895 TTTTAATTTTTTACTTC
1 TTTTATTTTTTTACTTC
3514912 TTATTATTTTT
1 TT-TTATTTTT
3514923 AATTACTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTTTACTTC
Done.