Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 24
Found at i:3636069 original size:44 final size:44
Alignment explanation
Indices: 3635999--3636104 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
3635989 AAGCAAAAAA
* *
3635999 TTAGGGAATAAGTTGGAAAAGTTGGTAATAGCTCCAACATAGTC
1 TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
* *
3636043 TTAGGAAATAAGTTGGAAAGGCTGGTAATAGCTTCAACATAGTC
1 TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
*
3636087 TTAGGCAATAAGTTGGAA
1 TTAGGAAATAAGTTGGAA
3636105 TGCTCTAACA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (44 bp):
TTAGGAAATAAGTTGGAAAAGCTGGTAATAGCTCCAACATAGTC
Found at i:3638455 original size:17 final size:17
Alignment explanation
Indices: 3638433--3638477 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
3638423 GAACCTAGCT
3638433 CCTGAGATACAACACTA
1 CCTGAGATACAACACTA
*
3638450 CCTGAGATACAACACTG
1 CCTGAGATACAACACTA
3638467 CCTGAGATACA
1 CCTGAGATACA
3638478 GAAGATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.18
Consensus pattern (17 bp):
CCTGAGATACAACACTA
Found at i:3650366 original size:13 final size:13
Alignment explanation
Indices: 3650348--3650373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3650338 AAATTTTGAG
3650348 GATCAAAGTAGAA
1 GATCAAAGTAGAA
3650361 GATCAAAGTAGAA
1 GATCAAAGTAGAA
3650374 AATTAGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
GATCAAAGTAGAA
Found at i:3652643 original size:22 final size:24
Alignment explanation
Indices: 3652586--3652643 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
3652576 TATATTTTTA
3652586 ATTATATTTTTTATTTATTTACTAT
1 ATTATATTTTTTATTTA-TTACTAT
* * *
3652611 ATTCCTCTTTTTTATTTA-TATTAT
1 ATT-ATATTTTTTATTTATTACTAT
3652635 ATTAT-TTTT
1 ATTATATTTT
3652644 ATTAAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 4 0.14
23 1 0.04
24 8 0.29
25 3 0.11
26 12 0.43
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (24 bp):
ATTATATTTTTTATTTATTACTAT
Found at i:3652735 original size:18 final size:18
Alignment explanation
Indices: 3652712--3652774 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
3652702 TTACTATGTA
3652712 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* *
3652730 TATATTTTATACGTT-TTA-
1 TATATTTT-TTC-TTAATAT
*
3652748 TATATATTTTCTTAATAT
1 TATATTTTTTCTTAATAT
*
3652766 TCTATTTTT
1 TATATTTTT
3652775 GTTTGTTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
16 2 0.06
17 4 0.12
18 22 0.65
19 4 0.12
20 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:3652965 original size:17 final size:17
Alignment explanation
Indices: 3652943--3652975 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3652933 TGTACACATT
3652943 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
3652960 ATTTTTTTACCTTTTT
1 ATTTTTTTACCTTTTT
3652976 TTTACTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:3653043 original size:18 final size:17
Alignment explanation
Indices: 3653022--3653060 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3653012 GTTTTTTAAC
3653022 ATTTTATTCATTTTGTTT
1 ATTTTATT-ATTTTGTTT
*
3653040 ATTTTTATTATTTTTTTT
1 A-TTTTATTATTTTGTTT
3653058 ATT
1 ATT
3653061 ATTTTTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 2 0.11
18 10 0.53
19 7 0.37
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (17 bp):
ATTTTATTATTTTGTTT
Found at i:3653058 original size:12 final size:12
Alignment explanation
Indices: 3653041--3653067 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3653031 ATTTTGTTTA
3653041 TTTTTATTATTT
1 TTTTTATTATTT
3653053 TTTTTATTATTT
1 TTTTTATTATTT
3653065 TTT
1 TTT
3653068 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTATTT
Found at i:3657466 original size:32 final size:32
Alignment explanation
Indices: 3657386--3657499 Score: 115
Period size: 32 Copynumber: 3.5 Consensus size: 32
3657376 TGAGGGCATC
*
3657386 TTTGAAGATTCAACATCAAATGTTGGGACATTTTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCA--TTT
* *
3657421 TTTTA-ATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
* * *
3657452 TTTGAGATTCAACATCGAATATTGGGGCA-TC
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
*
3657483 TTTGGGAATTCAACATC
1 TTTGAG-ATTCAACATC
3657500 CTGATGTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 13 0.19
32 30 0.44
33 21 0.31
34 1 0.01
35 3 0.04
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:3658201 original size:106 final size:106
Alignment explanation
Indices: 3658077--3658399 Score: 432
Period size: 106 Copynumber: 3.0 Consensus size: 106
3658067 ATATCGTGCC
* *
3658077 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGAACGGCTGGTTGTCAACAAACAATTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCC
* *
3658142 AATTTTAGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
3658183 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCC
* * **
3658248 AATTTCGGAGCCAATTTCATCTTCACATTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
3658289 AATCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAA-TTTCT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-
* * * * * * *
3658353 TAGTTACATAGCCAATTTTAACTTCACGGCGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
3658395 ACTCG
1 ACTCG
3658400 GAACAATATA
Statistics
Matches: 188, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
105 3 0.02
106 185 0.98
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:3658711 original size:36 final size:37
Alignment explanation
Indices: 3658671--3658755 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
3658661 ATTGAAAACA
* *
3658671 TTTCCCTTGAAATGAA-TTTTATCTCGATTGAGATAG
1 TTTCCCTTGAAATGAAGTTTTATCTCCATTGAGACAG
* *
3658707 TTTCCCTTGAAATGAAGTTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATGAAGTTTTATCTCCATTGAGACAG
*
3658744 TTTCTCTTGAAA
1 TTTCCCTTGAAA
3658756 CATAAACATT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 16 0.37
37 27 0.63
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAATGAAGTTTTATCTCCATTGAGACAG
Found at i:3658745 original size:102 final size:102
Alignment explanation
Indices: 3658623--3658867 Score: 409
Period size: 102 Copynumber: 2.4 Consensus size: 102
3658613 TTTTCTTTTG
* *
3658623 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAACATTGAAAACATTTCCCTTGAAATGAAT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAAT
** *
3658688 TTTATCTCGATTGAGATAGTTTCCCTTGAAATGAAGT
66 TTTATCTCGATTGAGATAGTTTCCCTTGAAACAAAAT
3658725 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAAT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAAT
* * *
3658790 TTTATCTCGCTTGGGGTAGTTTCCCTTGAAACAAAAT
66 TTTATCTCGATTGAGATAGTTTCCCTTGAAACAAAAT
*
3658827 TTTGTATCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
3658868 TCCATTGAAA
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 134 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (102 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAAT
TTTATCTCGATTGAGATAGTTTCCCTTGAAACAAAAT
Found at i:3658903 original size:93 final size:93
Alignment explanation
Indices: 3658623--3658957 Score: 400
Period size: 102 Copynumber: 3.4 Consensus size: 93
3658613 TTTTCTTTTG
3658623 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAACATTGAAAACATTTCCCTTGAAATGAAT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTG------AAACA-T--AAACATTTCCCTTGAAATGAAT
* ** *
3658688 TTTATCTCGATTGAGATAGTTTCCCTTGAAATGAAGT
57 TTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAAT
*
3658725 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAAT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTG------AAACA-T--AAACATTTCCCTTGAAATGAAT
* *
3658790 TTTATCTCGCTTGGGGTAGTTTCCCTTGAAACAAAAT
57 TTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAAT
* * * *
3658827 TTTGTATCCCTTGAGACAGTTTCTCTTGAAACATAAACATTTCCATTGAAATGAATTTTGTCTCT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTTCCCTTGAAATGAATTTTATCTCG
3658892 CTTGAGATAGTTTCCCTTGAAACAAAAT
66 CTTGAGATAGTTTCCCTTGAAACAAAAT
*
3658920 TTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAAC
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
3658958 CTTGAAAACG
Statistics
Matches: 216, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
93 89 0.41
95 1 0.00
96 5 0.02
102 121 0.56
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (93 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTTCCCTTGAAATGAATTTTATCTCG
CTTGAGATAGTTTCCCTTGAAACAAAAT
Found at i:3658927 original size:37 final size:37
Alignment explanation
Indices: 3658880--3658952 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
3658870 CATTGAAATG
*
3658880 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
*
3658917 AATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
3658953 TAAACCTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:3659067 original size:37 final size:37
Alignment explanation
Indices: 3659017--3659119 Score: 172
Period size: 36 Copynumber: 2.8 Consensus size: 37
3659007 AAAATAAGTT
*
3659017 TTGAGATAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
3659054 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
3659090 TTGAGACAGTTTCCCTTGAATCAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
3659120 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:3659196 original size:37 final size:36
Alignment explanation
Indices: 3659134--3659250 Score: 155
Period size: 36 Copynumber: 3.2 Consensus size: 36
3659124 TATCTTTTCC
** *
3659134 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
*
3659170 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
3659207 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
3659243 TTGAAACA
1 TTGAAACA
3659251 CAAAAAAACC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 1 0.01
36 39 0.55
37 30 0.42
38 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:3659211 original size:102 final size:102
Alignment explanation
Indices: 3659030--3659216 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
3659020 AGATAGTTTC
* *
3659030 CCTTGAAACAAAATCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
1 CCTTGAAACAAAATCTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
*
3659095 ACAGTTTCCCTTGAATCAAAATCTTTGAATATCTTTT
66 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * *
3659132 CCTTGAAAC-AAAT-TTCATCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTT
1 CCTTGAAACAAAATCTT-ATCTCCCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTT
**
3659194 GAGACAGTTTCTTTTGAAACAAA
63 GAGACAGTTTCCCTTGAAACAAA
3659217 TTTTGTCCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 6 0.08
101 24 0.32
102 44 0.59
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (102 bp):
CCTTGAAACAAAATCTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:3659298 original size:40 final size:39
Alignment explanation
Indices: 3659248--3659324 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
3659238 TTCTCTTGAA
*
3659248 ACACAAAAAAACCCTCGAAATTGTTTCTCTTGAAACACAC
1 ACACAAAAAAAACCTCGAAA-TGTTTCTCTTGAAACACAC
* **
3659288 ACACACAAAAAACCTTTAAATGTTTCTCTTGAAACAC
1 ACACAAAAAAAACCTCGAAATGTTTCTCTTGAAACAC
3659325 CAAACACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 17 0.52
40 16 0.48
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (39 bp):
ACACAAAAAAAACCTCGAAATGTTTCTCTTGAAACACAC
Found at i:3660159 original size:33 final size:31
Alignment explanation
Indices: 3660121--3660189 Score: 120
Period size: 33 Copynumber: 2.2 Consensus size: 31
3660111 GGGTTATATG
3660121 ACAAGGATCTATGAGATCATACAAGAATGTTAT
1 ACAAGGATCTATGAGATCATACAAGAATG--AT
3660154 ACAAGGATCTATGAGATCATACAAGAATGAT
1 ACAAGGATCTATGAGATCATACAAGAATGAT
3660185 ACAAG
1 ACAAG
3660190 AGATGTGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 7 0.19
33 29 0.81
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (31 bp):
ACAAGGATCTATGAGATCATACAAGAATGAT
Found at i:3660177 original size:20 final size:20
Alignment explanation
Indices: 3660121--3660178 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
3660111 GGGTTATATG
3660121 ACAAGGATCTATGAGATCAT
1 ACAAGGATCTATGAGATCAT
*
3660141 ACAA-GA---AT--G-TTAT
1 ACAAGGATCTATGAGATCAT
3660154 ACAAGGATCTATGAGATCAT
1 ACAAGGATCTATGAGATCAT
3660174 ACAAG
1 ACAAG
3660179 AATGATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
13 7 0.24
14 3 0.10
16 2 0.07
17 2 0.07
19 3 0.10
20 12 0.41
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (20 bp):
ACAAGGATCTATGAGATCAT
Found at i:3660453 original size:30 final size:30
Alignment explanation
Indices: 3660410--3660500 Score: 148
Period size: 30 Copynumber: 3.0 Consensus size: 30
3660400 CTCAGTACTG
* *
3660410 TACATGGGATTATAAAAGATATCAAAAGTA
1 TACATGAGCTTATAAAAGATATCAAAAGTA
3660440 TACATGAGCTTATAAAAGATATCAAAAGTA
1 TACATGAGCTTATAAAAGATATCAAAAGTA
3660470 TACAT-AGGCTTATAAAAGATATCAAAAGTA
1 TACATGA-GCTTATAAAAGATATCAAAAGTA
3660500 T
1 T
3660501 TTGAATTATT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 1 0.02
30 57 0.98
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.27
Consensus pattern (30 bp):
TACATGAGCTTATAAAAGATATCAAAAGTA
Found at i:3663485 original size:16 final size:16
Alignment explanation
Indices: 3663464--3663507 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
3663454 AGAAGAAGAA
*
3663464 AGAAGAAAACAACAGT
1 AGAAGAAAAAAACAGT
3663480 AGAAGAAAAAAACAGT
1 AGAAGAAAAAAACAGT
3663496 AGAAGAAAAAAA
1 AGAAGAAAAAAA
3663508 TGAAAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.70, C:0.07, G:0.18, T:0.05
Consensus pattern (16 bp):
AGAAGAAAAAAACAGT
Found at i:3663540 original size:20 final size:19
Alignment explanation
Indices: 3663496--3663544 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
3663486 AAAAAACAGT
3663496 AGAAGAAAAAAATGAAAAAA
1 AGAA-AAAAAAATGAAAAAA
*
3663516 TGAAAAAAAAA-GAAAAGAAA
1 AGAAAAAAAAATG-AAA-AAA
3663536 AGAAAAAAA
1 AGAAAAAAA
3663545 TGAGAGATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.04
19 10 0.40
20 14 0.56
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (19 bp):
AGAAAAAAAAATGAAAAAA
Found at i:3664408 original size:30 final size:29
Alignment explanation
Indices: 3664374--3664447 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
3664364 AATGGATTTA
* * *
3664374 TTTAGTGATCAAATTATAAGATTTTGAAAG
1 TTTAGTGACCAAAGTATAA-ACTTTGAAAG
*
3664404 TTTAGTTACCAAAGTATAAACTTTGAAAAAG
1 TTTAGTGACCAAAGTATAAACTTTG--AAAG
*
3664435 TTTAGGGACCAAA
1 TTTAGTGACCAAA
3664448 ATGTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 5 0.14
30 16 0.44
31 15 0.42
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTAGTGACCAAAGTATAAACTTTGAAAG
Found at i:3666878 original size:30 final size:30
Alignment explanation
Indices: 3666835--3666893 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3666825 CACAGTGTTG
*
3666835 TACATAGGATTATAAAAGATATTAAAAGTA
1 TACATAGGATTATAAAAGATATCAAAAGTA
* *
3666865 TACATGGGCTTATAAAAGATATCAAAAGT
1 TACATAGGATTATAAAAGATATCAAAAGT
3666894 GTTTGCATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (30 bp):
TACATAGGATTATAAAAGATATCAAAAGTA
Found at i:3667169 original size:18 final size:18
Alignment explanation
Indices: 3667114--3667169 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
3667104 ATATTACATA
**
3667114 ATAATGATATTGATGTTG
1 ATAATGATATTGATAATG
* ** *
3667132 AGAATGATAGAGATCATG
1 ATAATGATATTGATAATG
3667150 ATAATGATATTGATAATG
1 ATAATGATATTGATAATG
3667168 AT
1 AT
3667170 GATATATGTG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (18 bp):
ATAATGATATTGATAATG
Found at i:3668337 original size:5 final size:5
Alignment explanation
Indices: 3668319--3668351 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
3668309 GTAAAGAAGA
3668319 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AA
3668352 GGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3668861 original size:17 final size:17
Alignment explanation
Indices: 3668839--3668877 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3668829 TGAATCAAAT
3668839 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3668856 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3668873 -AATTA
1 TAATTA
3668878 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:3672463 original size:25 final size:25
Alignment explanation
Indices: 3672435--3672487 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
3672425 AATTGTTCTA
3672435 GGTGGATTTAAACCAATGTCTAAAG
1 GGTGGATTTAAACCAATGTCTAAAG
3672460 GGTGGATTTAAACCAATGTCTAAAG
1 GGTGGATTTAAACCAATGTCTAAAG
3672485 GGT
1 GGT
3672488 AGAGAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (25 bp):
GGTGGATTTAAACCAATGTCTAAAG
Found at i:3674824 original size:21 final size:21
Alignment explanation
Indices: 3674799--3674838 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3674789 AAGACTTTAT
3674799 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
3674820 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
3674839 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:3679225 original size:14 final size:14
Alignment explanation
Indices: 3679206--3679245 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3679196 TGCATATTAA
3679206 TTTTCAAAACTTAT
1 TTTTCAAAACTTAT
*
3679220 TTTTC-AAACATAAT
1 TTTTCAAAAC-TTAT
3679234 TTTTCAAAACTT
1 TTTTCAAAACTT
3679246 TGCCCATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTCAAAACTTAT
Found at i:3680615 original size:21 final size:21
Alignment explanation
Indices: 3680590--3680637 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3680580 ACATTTTGAA
* *
3680590 TGTTT-TTGGATTGTTTTACTT
1 TGTTTGTTGGA-TGTTTGAATT
3680611 TGTTTGTTGGATGTTTGAATT
1 TGTTTGTTGGATGTTTGAATT
3680632 TGTTTG
1 TGTTTG
3680638 ATATTGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.10, C:0.02, G:0.25, T:0.62
Consensus pattern (21 bp):
TGTTTGTTGGATGTTTGAATT
Found at i:3681272 original size:24 final size:25
Alignment explanation
Indices: 3681245--3681291 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3681235 GGGTAGATTG
3681245 CCCAA-AGGGAACCGATTCCCCCCC
1 CCCAAGAGGGAACCGATTCCCCCCC
* *
3681269 CCCAAGGGGGTACCGATTCCCCC
1 CCCAAGAGGGAACCGATTCCCCC
3681292 TGAATGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (25 bp):
CCCAAGAGGGAACCGATTCCCCCCC
Found at i:3682325 original size:14 final size:14
Alignment explanation
Indices: 3682306--3682332 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3682296 ATTTTAATGG
3682306 AATAATTAAAATAA
1 AATAATTAAAATAA
3682320 AATAATTAAAATA
1 AATAATTAAAATA
3682333 TAATTAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATTAAAATAA
Found at i:3682372 original size:27 final size:27
Alignment explanation
Indices: 3682292--3682375 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
3682282 ATTTCAATTT
* *
3682292 ATATATTTTAATGGAATAATTAAAATA
1 ATATATATTAATGGAATAATTAAAAGA
* * *
3682319 AAATA-ATTAA--AATATAATT-AATG-
1 ATATATATTAATGGA-ATAATTAAAAGA
3682342 -TATATATTAATGGAATAATTAAAAGA
1 ATATATATTAATGGAATAATTAAAAGA
3682368 ATATATAT
1 ATATATAT
3682376 ATATATATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
22 3 0.07
23 5 0.12
24 9 0.21
25 10 0.24
26 4 0.10
27 11 0.26
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (27 bp):
ATATATATTAATGGAATAATTAAAAGA
Found at i:3682464 original size:29 final size:29
Alignment explanation
Indices: 3682427--3682764 Score: 213
Period size: 29 Copynumber: 11.2 Consensus size: 29
3682417 TCTAAAAAAA
* * *
3682427 TTAATATAAGAATAACATATATTTTTATG
1 TTAAGATAAGAATAAAATATATTTTTAAG
* * *
3682456 TTAAGATAATATTAAAATA-ATTATTTAAA
1 TTAAGATAAGAATAAAATATATT-TTTAAG
* * *
3682485 TTAAAATAAGAGTAAAATATA-TTTTAAA
1 TTAAGATAAGAATAAAATATATTTTTAAG
* * * *
3682513 TTAATATAATAAT-AAATATATTTAATAAA
1 TTAAGATAAGAATAAAATATATTT-TTAAG
* *
3682542 TTAAGATAAAAAT-ATATATATTTTTAAAG
1 TTAAGATAAGAATAAAATATATTTTT-AAG
*
3682571 TTAAGTCCCATTAAGATAAAAAAATTATATTTTTAAAAG
1 TTAAG----A-TAAG--AATAAAA-TATATTTTT--AAG
*
3682610 TTAAGATAAAAATAAAATATATTGTTTAAG
1 TTAAGATAAGAATAAAATATATT-TTTAAG
* *
3682640 TTAAGAGAAGACTAAAATAT-TTTTTAAG
1 TTAAGATAAGAATAAAATATATTTTTAAG
* * *
3682668 -TAAAAGTAAGAATAATATATGTTTTTAAG
1 TTAAGA-TAAGAATAAAATATATTTTTAAG
* * *
3682697 TAAAAGATAAAAATAAAATATATTTTTAAA
1 T-TAAGATAAGAATAAAATATATTTTTAAG
* *
3682727 TTAAAATTAA-AATAAATATATTTTTTGTAAG
1 TTAAGA-TAAGAATAAA-ATATATTTT-TAAG
3682758 TTAAGAT
1 TTAAGAT
3682765 GTTAACTTAA
Statistics
Matches: 245, Mismatches: 41, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
27 11 0.04
28 39 0.16
29 86 0.35
30 53 0.22
31 17 0.07
32 9 0.04
33 1 0.00
34 6 0.02
35 1 0.00
36 2 0.01
37 2 0.01
38 9 0.04
39 9 0.04
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.39
Consensus pattern (29 bp):
TTAAGATAAGAATAAAATATATTTTTAAG
Found at i:3682751 original size:28 final size:28
Alignment explanation
Indices: 3682587--3682751 Score: 102
Period size: 30 Copynumber: 5.6 Consensus size: 28
3682577 CCCATTAAGA
*
3682587 TAAAA-AAATTATATTTTTAAAAGTTAAGAT
1 TAAAATAAA-TATATTTTT-AAA-TTAAAAT
* * *
3682617 AAAAATAAAATATATTGTTTAAGTTAAGA-
1 TAAAAT-AAATATATT-TTTAAATTAAAAT
* * * * *
3682646 GAAGACTAAA-ATATTTTTTAAGTAAAAG
1 TAA-AATAAATATATTTTTAAATTAAAAT
* * *
3682674 TAAGAATAATATATGTTTTTAAGTAAAAGAT
1 TAA-AATAA-ATATATTTTTAAATTAAA-AT
*
3682705 AAAAATAAAATATATTTTTAAATTAAAAT
1 TAAAAT-AAATATATTTTTAAATTAAAAT
3682734 TAAAATAAATATATTTTT
1 TAAAATAAATATATTTTT
3682752 TGTAAGTTAA
Statistics
Matches: 105, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
27 8 0.08
28 24 0.23
29 13 0.12
30 41 0.39
31 13 0.12
32 6 0.06
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (28 bp):
TAAAATAAATATATTTTTAAATTAAAAT
Found at i:3684024 original size:19 final size:21
Alignment explanation
Indices: 3683992--3684030 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3683982 TGTAAATTAA
*
3683992 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
3684012 TGTTAGAAT-ATGAAATTTG
1 TGTTAGAATGATGAAATTTG
3684031 ACTATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:3685802 original size:19 final size:18
Alignment explanation
Indices: 3685770--3685807 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3685760 TATGCATTGG
3685770 GCTATGAACTTGAAAATAA
1 GCTATGAACTTG-AAATAA
3685789 GCTATGAA-TATGAAATAA
1 GCTATGAACT-TGAAATAA
3685807 G
1 G
3685808 TTAAGAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.26
Consensus pattern (18 bp):
GCTATGAACTTGAAATAA
Found at i:3685881 original size:6 final size:6
Alignment explanation
Indices: 3685870--3685917 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
3685860 AGTATGGATT
* * *
3685870 ATGAAA ATGAAA TGTGAAA ATGAAT ATGAAA GTGAAA GATGAAA ATGA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA -ATGAAA ATGA
3685918 GATATGAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (6 bp):
ATGAAA
Found at i:3685898 original size:19 final size:19
Alignment explanation
Indices: 3685870--3685917 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
3685860 AGTATGGATT
3685870 ATGAAAATGAAATGTGAAA-
1 ATGAAAATGAAA-GTGAAAG
*
3685889 ATGAATATGAAAGTGAAAG
1 ATGAAAATGAAAGTGAAAG
3685908 ATGAAAATGA
1 ATGAAAATGA
3685918 GATATGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (19 bp):
ATGAAAATGAAAGTGAAAG
Found at i:3685905 original size:25 final size:25
Alignment explanation
Indices: 3685851--3685928 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
3685841 ATGAGTTCTA
* *
3685851 AAATGTGAAAGTATGGATTATGAAAATG
1 AAATGTGAAA--AT-GAATATGAAAGTG
3685879 AAATGTGAAAATGAATATGAAAGTG
1 AAATGTGAAAATGAATATGAAAGTG
3685904 AAA-GATGAAAATGAGATATGAAAGT
1 AAATG-TGAAAATGA-ATATGAAAGT
3685929 TTTATATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 1 0.02
25 23 0.50
26 12 0.26
28 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (25 bp):
AAATGTGAAAATGAATATGAAAGTG
Found at i:3685924 original size:13 final size:13
Alignment explanation
Indices: 3685869--3685926 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
3685859 AAGTATGGAT
3685869 TATGAAAATGAAA
1 TATGAAAATGAAA
*
3685882 TGTGAAAATG-AA
1 TATGAAAATGAAA
*
3685894 TATGAAAGTGAAA
1 TATGAAAATGAAA
* *
3685907 GATGAAAATGAGA
1 TATGAAAATGAAA
3685920 TATGAAA
1 TATGAAA
3685927 GTTTTATATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
12 10 0.27
13 27 0.73
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.22
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:3687270 original size:17 final size:17
Alignment explanation
Indices: 3687248--3687286 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3687238 TGAATCAAAT
3687248 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3687265 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
3687282 -AATTA
1 TAATTA
3687287 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:3689768 original size:37 final size:37
Alignment explanation
Indices: 3689718--3689830 Score: 136
Period size: 37 Copynumber: 3.0 Consensus size: 37
3689708 TATTGTGTAC
*
3689718 TAAAATGACACTAATATAAAATAAAAATTAAAGTTTT
1 TAAAATGATACTAATATAAAATAAAAATTAAAGTTTT
* *
3689755 TAAAATGATACTAATATAAAATAAAAACTAAAATTTT
1 TAAAATGATACTAATATAAAATAAAAATTAAAGTTTT
* * * *
3689792 TAACAATAAAATATTAAAATGAAATAAAAATTAAAGTTT
1 TAA-AAT--GATACTAATATAAAATAAAAATTAAAGTTT
3689831 AGCTATGGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
37 37 0.58
38 3 0.05
40 24 0.38
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (37 bp):
TAAAATGATACTAATATAAAATAAAAATTAAAGTTTT
Found at i:3690261 original size:21 final size:21
Alignment explanation
Indices: 3690219--3690270 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3690209 ATCATGTGAA
3690219 AATATAAAATATTAAATAATT
1 AATATAAAATATTAAATAATT
**
3690240 AATATCAAAATATTGCAT-ATT
1 AATAT-AAAATATTAAATAATT
3690261 AATAATAAAA
1 AAT-ATAAAA
3690271 CAACATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AATATAAAATATTAAATAATT
Found at i:3691677 original size:81 final size:81
Alignment explanation
Indices: 3691500--3691820 Score: 502
Period size: 81 Copynumber: 4.0 Consensus size: 81
3691490 TATAATTTCT
* * ** * * *
3691500 TTATTCTCTTACTCAACAGTGTTTAA-CGTTCGTCTAAATGGTATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
3691564 -TGCACAGTTAGACCA
66 TTGCACAGTTAGGCCA
* *
3691579 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGTCATAATTGACACCTTTCTACCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
3691644 TTGCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
*
3691660 TTATTCTTTTACTCAACGGTACTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
3691725 TTGCACAGTTAGGTCA
66 TTGCACAGTTAGGCCA
*
3691741 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAA
1 TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
3691806 TTGCATAGTTAGGCC
66 TTGCACAGTTAGGCC
3691821 TCAAAGACAC
Statistics
Matches: 222, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
79 22 0.10
80 33 0.15
81 167 0.75
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
TTGCACAGTTAGGCCA
Found at i:3691861 original size:68 final size:68
Alignment explanation
Indices: 3691770--3692025 Score: 426
Period size: 68 Copynumber: 3.8 Consensus size: 68
3691760 TACTTAACCG
* *
3691770 TTCATCTAACTGGCATAATTGACACCTTTCT-TCCA-ATTGCATAGTTAGGCCTCAAAGACACTT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGT-CATA-TGCACAGTTAGGCCTCAAAGACACTT
3691833 AGTCT
64 AGTCT
* *
3691838 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATATGCACAGTTAGGCCTCAAAGATACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
3691903 TCT
66 TCT
3691906 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
3691971 TCT
66 TCT
* *
3691974 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTATGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCT
3692026 TTATTCTTTA
Statistics
Matches: 178, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
68 176 0.99
69 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
TCT
Found at i:3691862 original size:32 final size:32
Alignment explanation
Indices: 3691826--3691998 Score: 104
Period size: 32 Copynumber: 5.2 Consensus size: 32
3691816 AGGCCTCAAA
3691826 GACACTTAGTCTTTCATCTAACTGGCATAAAT
1 GACACTTAGTCTTTCATCTAACTGGCATAAAT
* * * * *
3691858 GACACTT-TTCTGTCATATGCACAGTTAGGCCTCAAA-
1 GACACTTAGTCTTTCATCT--A-A-CT-GGCAT-AAAT
*
3691894 GATACTTAGTCTTTCATCTAACTGGCATAAAT
1 GACACTTAGTCTTTCATCTAACTGGCATAAAT
* * * *
3691926 GACACCTT--TCTGTCATATGCACAGTTAGGCCTCAAA-
1 GACA-CTTAGTCTTTCATCT--A-A-CT-GGCAT-AAAT
3691962 GACACTTAGTCTTTCATCTAACTGGCATAAAT
1 GACACTTAGTCTTTCATCTAACTGGCATAAAT
3691994 GACAC
1 GACAC
3691999 ATTTCTGTCA
Statistics
Matches: 103, Mismatches: 20, Indels: 36
0.65 0.13 0.23
Matches are distributed among these distances:
31 22 0.21
32 23 0.22
33 7 0.07
34 4 0.04
35 7 0.07
36 18 0.17
37 22 0.21
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (32 bp):
GACACTTAGTCTTTCATCTAACTGGCATAAAT
Found at i:3692490 original size:58 final size:59
Alignment explanation
Indices: 3692395--3692567 Score: 235
Period size: 58 Copynumber: 3.0 Consensus size: 59
3692385 TATAAATTCC
*
3692395 ATACGGAAATTCATACACTTAGTATGAATTTCTTATCAT-TTAGCACAC-AAGGTGCCCG
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAA-GTGCCCG
* * *
3692453 ATACAGAAATTCATACACTTAGTCTGAATTTCTTATCATGTTAGCACACGAAGTGCTCT
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCG
* * * * *
3692512 ATACTGAAATTCATACACTTAGTATAAATTTATTAACATCTT-GCACACGAAGTGCC
1 ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCC
3692568 ATTTGGTAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
58 50 0.49
59 50 0.49
60 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.32
Consensus pattern (59 bp):
ATACAGAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGAAGTGCCCG
Found at i:3693008 original size:20 final size:20
Alignment explanation
Indices: 3692979--3693036 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
3692969 GATGTTTCTT
* *
3692979 GGTATTGATACCCTTACCAG
1 GGTATCGATACCCCTACCAG
*
3692999 GGTATCGATACTACCCTACTAG
1 GGTATCGATAC--CCCTACCAG
3693021 GGTATCGATACCCCTA
1 GGTATCGATACCCCTA
3693037 TCGATATCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.45
22 18 0.55
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCCCTACCAG
Found at i:3693024 original size:22 final size:23
Alignment explanation
Indices: 3692987--3693031 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3692977 TTGGTATTGA
3692987 TACCCTTACCAGGGTATCGATAC
1 TACCCTTACCAGGGTATCGATAC
*
3693010 TACCC-TACTAGGGTATCGATAC
1 TACCCTTACCAGGGTATCGATAC
3693032 CCCTATCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (23 bp):
TACCCTTACCAGGGTATCGATAC
Found at i:3696466 original size:68 final size:68
Alignment explanation
Indices: 3696374--3696697 Score: 461
Period size: 68 Copynumber: 4.8 Consensus size: 68
3696364 TACTTAACCG
* * * *
3696374 TTCATTTAACTGGCATAATTGACACTTTTCTGCCA-ATTGCACAGTTAGGCCTCAAAGACACTTA
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATA-TGCACAGTTAGGCCTCAAAGACACTTA
3696438 GTCT
65 GTCT
* * * * *
3696442 TTCATCTAACTGGTATAAACGACACCTTTCTATCATATGCACAGTTAGGACTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
3696507 TCT
66 TCT
* * *
3696510 TTCATCTAACTAGCATAAATGACACATTTATGTCATATGCACAGTTAGGCCTCAAACACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
3696575 TCT
66 TCT
* *
3696578 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCATAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
*
3696643 TGT
66 TCT
* * * *
3696646 TTCATTTAACTGGAATAAATGACACATTTATGTCATATCCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCT
3696698 TTCTTCTTTC
Statistics
Matches: 227, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 226 1.00
69 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
TCT
Found at i:3697623 original size:20 final size:19
Alignment explanation
Indices: 3697598--3697652 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
3697588 GATGTTGTCT
3697598 GGTATCGATACCCTTACCAG
1 GGTATCGATACCC-TACCAG
**
3697618 GGTATCGTTACTACCCTATTAG
1 GGTATCG--A-TACCCTACCAG
3697640 GGTATCGATACCC
1 GGTATCGATACCC
3697653 CCCTATCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 5 0.17
20 8 0.27
22 12 0.40
23 5 0.17
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (19 bp):
GGTATCGATACCCTACCAG
Found at i:3697656 original size:22 final size:22
Alignment explanation
Indices: 3697616--3697658 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3697606 TACCCTTACC
* *
3697616 AGGGTATCGTTACTACCCTATT
1 AGGGTATCGATACCACCCTATT
*
3697638 AGGGTATCGATACCCCCCTAT
1 AGGGTATCGATACCACCCTAT
3697659 CGATATTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (22 bp):
AGGGTATCGATACCACCCTATT
Found at i:3699190 original size:24 final size:24
Alignment explanation
Indices: 3699179--3699290 Score: 147
Period size: 24 Copynumber: 4.7 Consensus size: 24
3699169 ATCAAAACAT
3699179 AATCCAGGTCAAGTATCATATCAA
1 AATCCAGGTCAAGTATCATATCAA
3699203 AATCCAGGTCAAGTATCATATCAA
1 AATCCAGGTCAAGTATCATATCAA
* *
3699227 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCATATCAA
* *
3699251 AATCCAGTTCAAGTATCCA-ATCAG
1 AATCCAGGTCAAGTAT-CATATCAA
*
3699275 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
3699291 TATAATAGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 1 0.01
24 77 0.96
25 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCATATCAA
Found at i:3701748 original size:20 final size:20
Alignment explanation
Indices: 3701723--3701764 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3701713 TCAAAGTTTT
3701723 GGTCAACAATGGTCAACGCC
1 GGTCAACAATGGTCAACGCC
3701743 GGTCAACAATGGTCAACGCC
1 GGTCAACAATGGTCAACGCC
3701763 GG
1 GG
3701765 ATCGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (20 bp):
GGTCAACAATGGTCAACGCC
Found at i:3704320 original size:29 final size:30
Alignment explanation
Indices: 3704236--3704327 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 30
3704226 GGCTAAAATA
*
3704236 TATAACTTTTAAAAATTACAATTTTAGTCC-C
1 TATAACTTTCAAAAATTAC-ATTTTAG-CCAC
* ** * *
3704267 TATAATTTTCAAAGTTTATACTTTAGCCAC
1 TATAACTTTCAAAAATTACATTTTAGCCAC
* *
3704297 TA-AACTTTCAAAACTTACATTTTAGTCAC
1 TATAACTTTCAAAAATTACATTTTAGCCAC
3704326 TA
1 TA
3704328 GACAAAATCT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 25 0.52
30 9 0.19
31 14 0.29
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (30 bp):
TATAACTTTCAAAAATTACATTTTAGCCAC
Found at i:3709854 original size:36 final size:36
Alignment explanation
Indices: 3709681--3709855 Score: 296
Period size: 36 Copynumber: 4.9 Consensus size: 36
3709671 ACGATGCTGG
*
3709681 ACATTGATACACGAATGTACCAAAGCTGGTATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
3709717 ACATTGATACACGAATGTACCAAAGCTGACATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
3709753 ACATTTATACACGAATGTACCAAAGCTGACATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
3709789 ACATTGATACACGAATGTACCAAAGCTGATATAATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
3709825 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
3709856 ATACTCAACT
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 132 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:3712695 original size:243 final size:243
Alignment explanation
Indices: 3712267--3712714 Score: 709
Period size: 243 Copynumber: 1.8 Consensus size: 243
3712257 TTACATGACC
* * *
3712267 GTTGAGTAAAAGATAAATGGTCTAGCTGTGCATTTGGCAGACATGTGTCAATTATGCCAGTTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGA
*
3712332 TGAACTGTTAAAGACTGTTGAGCAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGATGTC
66 TGAACTGTTAAAGACTGTTAAGCAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGATGTC
* * * *
3712397 AAATATACCAGTTAGATGAATGGTTAAAGACCGTTGAGTAAAAAATAAATGGCCTACCTGTGCAT
131 AAATATACCAATTAGATGAACGGTTAAAGACCATTGAGTAAAAAATAAATGGCCTAACTGTGCAT
3712462 TTGGAAGAAAGGTGCCAATTATGTCAGTTAGATGAACGGTTAAAGACT
196 TTGGAAGAAAGGTGCCAATTATGTCAGTTAGATGAACGGTTAAAGACT
3712510 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGA
* * * * * *
3712575 TGAA-TGGTTAAAGACTGTTAAGTAAAAGATAATTGGCCTAGTTGTGCATTTGGCATAAAGGTGT
66 TGAACT-GTTAAAGACTGTTAAGCAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGATGT
** * **
3712639 CAAATATGGCAATTAGATGAACGGTTAAAGGCCATTGAGTAAAAGCTAAATGGCCTAACTGTGCA
130 CAAATATACCAATTAGATGAACGGTTAAAGACCATTGAGTAAAAAATAAATGGCCTAACTGTGCA
3712704 TTTGGAAGAAA
195 TTTGGAAGAAA
3712715 AGGGTCAATC
Statistics
Matches: 185, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
242 1 0.01
243 184 0.99
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (243 bp):
GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGA
TGAACTGTTAAAGACTGTTAAGCAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGATGTC
AAATATACCAATTAGATGAACGGTTAAAGACCATTGAGTAAAAAATAAATGGCCTAACTGTGCAT
TTGGAAGAAAGGTGCCAATTATGTCAGTTAGATGAACGGTTAAAGACT
Found at i:3712769 original size:81 final size:81
Alignment explanation
Indices: 3712267--3712740 Score: 635
Period size: 81 Copynumber: 5.9 Consensus size: 81
3712257 TTACATGACC
* * * *
3712267 GTTGAGTAAAAGATAAATGGTCTAGCTGTGCATTTGGCAGACATGTGTCAATTATGCCAGTTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGA
*
3712332 TGAACTGTTAAAGACT
66 TGAACGGTTAAAGACT
* * * *
3712348 GTTGAGCAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGATGTCAAATATACCAGTTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGA
* *
3712413 TGAATGGTTAAAGACC
66 TGAACGGTTAAAGACT
* * * *
3712429 GTTGAGTAAAAAATAAATGGCCTACCTGTGCATTTGGAAGAAAGGTGCCAATTATGTCAGTTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGA
3712494 TGAACGGTTAAAGACT
66 TGAACGGTTAAAGACT
*
3712510 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGA
*
3712575 TGAATGGTTAAAGACT
66 TGAACGGTTAAAGACT
* * * * * * * *
3712591 GTTAAGTAAAAGATAATTGGCCTAGTTGTGCATTTGGCATAAAGGTGTCAAATATGGCAATTAGA
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGA
* *
3712656 TGAACGGTTAAAGGCC
66 TGAACGGTTAAAGACT
* * * * * *
3712672 ATTGAGTAAAAGCTAAATGGCCTAACTGTGCATTTGGAAGAAAAGG-GTCAATCATACAAGTTAG
1 GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAG-AAAGGTGTCAATTATGCCAGTTAG
3712736 ATGAA
65 ATGAA
3712741 AAGTAAATGC
Statistics
Matches: 341, Mismatches: 51, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
81 336 0.99
82 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (81 bp):
GTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGA
TGAACGGTTAAAGACT
Found at i:3716523 original size:27 final size:24
Alignment explanation
Indices: 3716479--3716527 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
3716469 CTTTTTTATC
3716479 TTTTCCATCTCTATTTTCTCTTTA
1 TTTTCCATCTCTATTTTCTCTTTA
3716503 TTTTCCTATCTTCTCATTTTCTCTT
1 TTTTCC-ATC-TCT-ATTTTCTCTT
3716528 CATCCCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 3 0.14
27 10 0.45
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTCCATCTCTATTTTCTCTTTA
Found at i:3717085 original size:19 final size:19
Alignment explanation
Indices: 3717061--3717133 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
3717051 GAGTTTAGGC
3717061 CAAGAGTATCGATACTTTT
1 CAAGAGTATCGATACTTTT
3717080 CAAGAGTATCGATACTTTACCT
1 CAAGAGTATCGATACTTT---T
* * *
3717102 C-AGAGCATCGATAATTTC
1 CAAGAGTATCGATACTTTT
*
3717120 CAAGAGTATTGATA
1 CAAGAGTATCGATA
3717134 TTACGCACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 1 0.02
19 28 0.62
21 14 0.31
22 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CAAGAGTATCGATACTTTT
Found at i:3717692 original size:18 final size:17
Alignment explanation
Indices: 3717671--3717720 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
3717661 TCAATATAGA
3717671 TAATCAGTAATAACTCAG
1 TAAT-AGTAATAACTCAG
* *
3717689 TAATAGAAATAGAATCAG
1 TAATAGTAATA-ACTCAG
*
3717707 TAATAGTAACAACT
1 TAATAGTAATAACT
3717721 AAAAAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (17 bp):
TAATAGTAATAACTCAG
Found at i:3718140 original size:32 final size:32
Alignment explanation
Indices: 3718094--3718169 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
3718084 CCAATATTAT
*
3718094 ATTCAGATAATGCATACCAAAGTTAATCTTGC
1 ATTCAGATAATGCATACCAAAGTTAATCCTGC
* * * *
3718126 ATTCAGATACTGCATATCAGAGTTAGTCCTGC
1 ATTCAGATAATGCATACCAAAGTTAATCCTGC
*
3718158 ATTCAGACAATG
1 ATTCAGATAATG
3718170 TATAGTAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (32 bp):
ATTCAGATAATGCATACCAAAGTTAATCCTGC
Found at i:3722289 original size:20 final size:20
Alignment explanation
Indices: 3722266--3722304 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3722256 GAAACTTACC
*
3722266 CTAGAGTATCAATACTACAG
1 CTAGAGTACCAATACTACAG
*
3722286 CTAGAGTACCGATACTACA
1 CTAGAGTACCAATACTACA
3722305 CATTCAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CTAGAGTACCAATACTACAG
Found at i:3723256 original size:32 final size:32
Alignment explanation
Indices: 3723220--3723302 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
3723210 AAAACCATTA
* *
3723220 TTGCATTTAAATAATGCATTCCATAGTTAATT
1 TTGCATTCAAATAATGCATTCCAGAGTTAATT
* *
3723252 TTGCATTCAAATAATGCATTCTAGAGTTAATC
1 TTGCATTCAAATAATGCATTCCAGAGTTAATT
* * *
3723284 ATGCATTCAGACAATGCAT
1 TTGCATTCAAATAATGCAT
3723303 AGTACTTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (32 bp):
TTGCATTCAAATAATGCATTCCAGAGTTAATT
Found at i:3725460 original size:15 final size:16
Alignment explanation
Indices: 3725440--3725472 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3725430 CGATTATAAA
3725440 TAAAATAG-CCAAAAT
1 TAAAATAGTCCAAAAT
*
3725455 TAAAATAGTCCTAAAT
1 TAAAATAGTCCAAAAT
3725471 TA
1 TA
3725473 CTATTACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAATAGTCCAAAAT
Found at i:3725990 original size:12 final size:12
Alignment explanation
Indices: 3725960--3725993 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3725950 ACTTTTCTTA
3725960 ACTTTCATATTC
1 ACTTTCATATTC
*
3725972 ACTTTTCATATTT
1 AC-TTTCATATTC
3725985 ACTTTCATA
1 ACTTTCATA
3725994 GCCCACTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:3727725 original size:20 final size:21
Alignment explanation
Indices: 3727700--3727746 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3727690 TCCAAAATAG
3727700 TCAAATTTC-ACATTCTAACA
1 TCAAATTTCAACATTCTAACA
* *
3727720 TCAAA-TTCAATATTCTAACT
1 TCAAATTTCAACATTCTAACA
3727740 TCAAATT
1 TCAAATT
3727747 CTAGCATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 19 0.83
21 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAAATTTCAACATTCTAACA
Found at i:3731965 original size:21 final size:20
Alignment explanation
Indices: 3731933--3731971 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3731923 AATATCCCCA
*
3731933 TAAATTAAAATAACTAAATT
1 TAAATTAAAATAAATAAATT
3731953 TAAATTAAAAATAAATAAA
1 TAAATT-AAAATAAATAAA
3731972 AATAGGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAATTAAAATAAATAAATT
Found at i:3735444 original size:31 final size:30
Alignment explanation
Indices: 3735386--3735454 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
3735376 ATGTAATTAG
* *
3735386 ATGTATATATAAAAAATTTATGATGATTCAA
1 ATGTATATATAAAAAATTAATCATGATTC-A
** *
3735417 ATGTATATATAAAACCTTAATCTTGATTCA
1 ATGTATATATAAAAAATTAATCATGATTCA
3735447 AT-TATATA
1 ATGTATATA
3735455 CATTTAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 6 0.18
30 3 0.09
31 24 0.73
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (30 bp):
ATGTATATATAAAAAATTAATCATGATTCA
Found at i:3740885 original size:2 final size:2
Alignment explanation
Indices: 3740878--3740920 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3740868 AGAAACACAT
3740878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3740920 T
1 T
3740921 CAACATCCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3749143 original size:7 final size:7
Alignment explanation
Indices: 3749123--3749158 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3749113 TTTATCAAAA
3749123 TATATTT
1 TATATTT
3749130 T-TATTT
1 TATATTT
3749136 TATATTT
1 TATATTT
3749143 TATATTT
1 TATATTT
3749150 TATATTT
1 TATATTT
3749157 TA
1 TA
3749159 AGATTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATATTT
Found at i:3750066 original size:16 final size:16
Alignment explanation
Indices: 3750045--3750112 Score: 77
Period size: 16 Copynumber: 4.2 Consensus size: 16
3750035 TTTTATAAAG
3750045 AAAAAATATTTTTATT
1 AAAAAATATTTTTATT
*
3750061 AAAAAAT-TTATTT-TC
1 AAAAAATATT-TTTATT
*
3750076 AATCAAATATTTTTATT
1 AA-AAAATATTTTTATT
3750093 AAAAAATATTTTTTATT
1 AAAAAATA-TTTTTATT
3750110 AAA
1 AAA
3750113 TTTTATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.12
16 22 0.51
17 16 0.37
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAAATATTTTTATT
Found at i:3750453 original size:17 final size:17
Alignment explanation
Indices: 3750431--3750463 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3750421 TTTTATAACT
*
3750431 TTATTTAAATTAATTTA
1 TTATTTAAAATAATTTA
3750448 TTATTTAAAATAATTT
1 TTATTTAAAATAATTT
3750464 TCATCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTTAAAATAATTTA
Found at i:3750739 original size:16 final size:16
Alignment explanation
Indices: 3750720--3750803 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
3750710 TAAATTAAAA
3750720 TTGGGTTATTTTCGGT
1 TTGGGTTATTTTCGGT
* *
3750736 TTGGGTGA-TTTCTGT
1 TTGGGTTATTTTCGGT
* *
3750751 TCGAGTTATTTTCGGT
1 TTGGGTTATTTTCGGT
* ** * *
3750767 TCGAATTAATTTCGAT
1 TTGGGTTATTTTCGGT
*
3750783 TTGGGTTACTTTCGGAT
1 TTGGGTTATTTTCGG-T
3750800 TTGG
1 TTGG
3750804 TTAAATTTGG
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
15 11 0.21
16 36 0.69
17 5 0.10
ACGTcount: A:0.13, C:0.10, G:0.27, T:0.50
Consensus pattern (16 bp):
TTGGGTTATTTTCGGT
Found at i:3750830 original size:16 final size:16
Alignment explanation
Indices: 3750809--3750848 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3750799 TTTGGTTAAA
3750809 TTTGGTTCAAATTGCT
1 TTTGGTTCAAATTGCT
3750825 TTTGGTTCAAATTGCT
1 TTTGGTTCAAATTGCT
*
3750841 TTCGGTTC
1 TTTGGTTC
3750849 GGGTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (16 bp):
TTTGGTTCAAATTGCT
Found at i:3750888 original size:16 final size:16
Alignment explanation
Indices: 3750867--3750922 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
3750857 TTCAGTTCAG
3750867 TCGGTTCGGGTTATTT
1 TCGGTTCGGGTTATTT
* *
3750883 TCGGTTTGGGTTGTTT
1 TCGGTTCGGGTTATTT
**
3750899 TTTGTTCGGGTTATTT
1 TCGGTTCGGGTTATTT
3750915 TCGGTTCG
1 TCGGTTCG
3750923 AATCAAATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.04, C:0.11, G:0.32, T:0.54
Consensus pattern (16 bp):
TCGGTTCGGGTTATTT
Found at i:3757716 original size:42 final size:42
Alignment explanation
Indices: 3757660--3757749 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
3757650 TTCCTCCAAC
* *
3757660 CAAACATTAAAAAATATTTTCTAG-AAAATAAATTACGTAAAA
1 CAAACATAAAAAAATATTTT-TAGAAAAATAAATTACATAAAA
* * *
3757702 CAAACATAAAAAAATATTTTTCGAAAAATGAATTACATGAAA
1 CAAACATAAAAAAATATTTTTAGAAAAATAAATTACATAAAA
3757744 CAAACA
1 CAAACA
3757750 CGAGATTTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.26
Consensus pattern (42 bp):
CAAACATAAAAAAATATTTTTAGAAAAATAAATTACATAAAA
Found at i:3762933 original size:21 final size:21
Alignment explanation
Indices: 3762907--3762953 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3762897 GATTTAGTTT
3762907 GGTCGGCTATCGAATTAATTC
1 GGTCGGCTATCGAATTAATTC
*
3762928 GGTCGGCTATCGAATTAGTTC
1 GGTCGGCTATCGAATTAATTC
3762949 GGTCG
1 GGTCG
3762954 AGGAATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (21 bp):
GGTCGGCTATCGAATTAATTC
Found at i:3763058 original size:14 final size:12
Alignment explanation
Indices: 3763041--3763092 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
3763031 AAATTATTAA
3763041 ATATGAAATATTAT
1 ATAT-AAATA-TAT
*
3763055 ATATATATATAT
1 ATATAAATATAT
*
3763067 ATATATATATAT
1 ATATAAATATAT
*
3763079 ATATAAATACAT
1 ATATAAATATAT
3763091 AT
1 AT
3763093 TTTAAGCTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
12 27 0.77
13 4 0.11
14 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:3763059 original size:2 final size:2
Alignment explanation
Indices: 3763048--3763083 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3763038 TAAATATGAA
3763048 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3763084 AATACATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3763313 original size:20 final size:19
Alignment explanation
Indices: 3763247--3763341 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 19
3763237 AAATAACCAA
* *
3763247 CGAATTCGCAACTCAATTT
1 CGAATTTGCAACACAATTT
**
3763266 CGAATTTGCAACACGAAAGT
1 CGAATTTGCAACAC-AATTT
3763286 C-AATTTTGCAACACAATTT
1 CGAA-TTTGCAACACAATTT
3763305 CCGAATTTGCAACACATAATTT
1 -CGAATTTGCAACAC--AATTT
* *
3763327 GGAATTCGCAACACA
1 CGAATTTGCAACACA
3763342 GAAGTCTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
19 18 0.29
20 25 0.40
21 14 0.23
22 5 0.08
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (19 bp):
CGAATTTGCAACACAATTT
Found at i:3763378 original size:22 final size:21
Alignment explanation
Indices: 3763351--3763420 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
3763341 AGAAGTCTAA
3763351 TTCGCAACTCGAATTTGACAAT
1 TTCGCAACTCGAATTT-ACAAT
* **
3763373 TTCGCAACACGAATTT-CTTT
1 TTCGCAACTCGAATTTACAAT
*
3763393 TTCGCAACTCGATTTTTA-AA-
1 TTCGCAACTCGA-ATTTACAAT
3763413 TTCGCAAC
1 TTCGCAAC
3763421 ACTACTTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 21 0.54
21 3 0.08
22 15 0.38
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (21 bp):
TTCGCAACTCGAATTTACAAT
Found at i:3763382 original size:42 final size:40
Alignment explanation
Indices: 3763322--3763422 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 40
3763312 TGCAACACAT
*
3763322 AATTTGGAATTCGCAACACAGAA-GTCTAATTCGCAACTCG
1 AATTTGAAATTCGCAACAC-GAATGTCTAATTCGCAACTCG
* **
3763362 AATTTGACAATTTCGCAACACGAATTTCTTTTTCGCAACTCG
1 AATTTGA-AA-TTCGCAACACGAATGTCTAATTCGCAACTCG
* *
3763404 ATTTTTAAATTCGCAACAC
1 AATTTGAAATTCGCAACAC
3763423 TACTTTCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
40 16 0.31
41 7 0.13
42 29 0.56
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (40 bp):
AATTTGAAATTCGCAACACGAATGTCTAATTCGCAACTCG
Found at i:3763397 original size:20 final size:20
Alignment explanation
Indices: 3763372--3763500 Score: 73
Period size: 20 Copynumber: 6.5 Consensus size: 20
3763362 AATTTGACAA
3763372 TTTCGCAACACGAATTTCTT
1 TTTCGCAACACGAATTTCTT
*
3763392 TTTCGCAACTCG-ATTT-TT
1 TTTCGCAACACGAATTTCTT
* * *
3763410 AAATTCGCAACACTACTTTCTT
1 --TTTCGCAACACGAATTTCTT
* * * *
3763432 TTTCGCAAAAAGATTTTCTA
1 TTTCGCAACACGAATTTCTT
* ** * * **
3763452 ATTCGCAATGCTAGTTTCAA
1 TTTCGCAACACGAATTTCTT
* *
3763472 TTTCGCAAAACGAATTTCGT
1 TTTCGCAACACGAATTTCTT
3763492 TTTCGCAAC
1 TTTCGCAAC
3763501 TCAACTTTTA
Statistics
Matches: 79, Mismatches: 26, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
18 2 0.03
19 4 0.05
20 68 0.86
21 3 0.04
22 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTCGCAACACGAATTTCTT
Found at i:3763430 original size:40 final size:42
Alignment explanation
Indices: 3763351--3763439 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 42
3763341 AGAAGTCTAA
3763351 TTCGCAACTCGAATTTGACAATTTCGCAACACGAATTTCTTT
1 TTCGCAACTCGAATTTGACAATTTCGCAACACGAATTTCTTT
* * * *
3763393 TTCGCAACTCGATTTTTA-AA-TTCGCAACACTACTTTCTTT
1 TTCGCAACTCGAATTTGACAATTTCGCAACACGAATTTCTTT
3763433 TTCGCAA
1 TTCGCAA
3763440 AAAGATTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 25 0.58
41 2 0.05
42 16 0.37
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (42 bp):
TTCGCAACTCGAATTTGACAATTTCGCAACACGAATTTCTTT
Found at i:3763447 original size:40 final size:40
Alignment explanation
Indices: 3763373--3763459 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
3763363 ATTTGACAAT
***
3763373 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTT-TAAA
1 TTCGCAACACGAATTTCTTTTTCGCAAAAAGATTTTCT-AA
* *
3763413 TTCGCAACACTACTTTCTTTTTCGCAAAAAGATTTTCTAA
1 TTCGCAACACGAATTTCTTTTTCGCAAAAAGATTTTCTAA
3763453 TTCGCAA
1 TTCGCAA
3763460 TGCTAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 40 0.98
41 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (40 bp):
TTCGCAACACGAATTTCTTTTTCGCAAAAAGATTTTCTAA
Found at i:3763515 original size:20 final size:20
Alignment explanation
Indices: 3763492--3763540 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3763482 CGAATTTCGT
3763492 TTTCGCAACTCAACTTTTAA
1 TTTCGCAACTCAACTTTTAA
*
3763512 TTTCGTAACTCAACTTTTAA
1 TTTCGCAACTCAACTTTTAA
3763532 TTTCGCAAC
1 TTTCGCAAC
3763541 ACAAATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (20 bp):
TTTCGCAACTCAACTTTTAA
Found at i:3763657 original size:22 final size:22
Alignment explanation
Indices: 3763640--3763701 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
3763630 TCTCTCCGGT
*
3763640 GACATCAGTCCCCATCTCCGAC
1 GACATCCGTCCCCATCTCCGAC
3763662 GACATCCGTCCCCATCTCCGAC
1 GACATCCGTCCCCATCTCCGAC
3763684 GACATCCGTCCCCATCTC
1 GACATCCGTCCCCATCTC
3763702 TAATCTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.48, G:0.13, T:0.19
Consensus pattern (22 bp):
GACATCCGTCCCCATCTCCGAC
Found at i:3766676 original size:53 final size:53
Alignment explanation
Indices: 3766635--3767196 Score: 928
Period size: 53 Copynumber: 10.5 Consensus size: 53
3766625 TCACTTTCTC
* * **
3766635 TTTCTTTAGGGAGTAGAACTCGAACATTCTTCTTCCTACGGG-CTCGCTCTCTAT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCT-T
* * *
3766689 TTTCTTCAAGGAGTAGAACTCGAACAATCATCTTCCTACGAGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* * *
3766742 TTTCTTCAAGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCACTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
3766795 TTTATTCAGGGAGTAGAACTCAAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
3766848 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
3766902 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACAGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
3766955 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
3767009 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
3767062 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
3767116 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
3767169 TTTCTTCAGGGAGTAGAACTCGAACAAT
1 TTTCTTCAGGGAGTAGAACTCGAACAAT
3767197 CTTCTGTTGC
Statistics
Matches: 481, Mismatches: 23, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
53 280 0.58
54 200 0.42
55 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (53 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
Found at i:3766760 original size:107 final size:107
Alignment explanation
Indices: 3766635--3767196 Score: 952
Period size: 107 Copynumber: 5.3 Consensus size: 107
3766625 TCACTTTCTC
* * ** *
3766635 TTTCTTTAGGGAGT-AGAACTCGAACATTCTTCTTCCTACGGG-CTCGCTCTCTATTTTCTTCAA
1 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCTA-TTTCTTCAG
* *
3766698 GGAGTAGAACTCGAACAATCATCTTCCTACGAGTCCGCTCTCTT
64 GGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* * *
3766742 TTTCTTCAAGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCACTCTCTATTTATTCAGGG
1 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
*
3766806 AGTAGAACTCAAACAATAATCTTCCTACGGGTCCGCTCTCTT
66 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
3766848 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
1 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
*
3766913 AGTAGAACTCGAACAATAATCTTCCTACAGGTCCGCTCTCTT
66 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
3766955 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
1 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
3767020 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
66 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
3767062 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGG
1 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
*
3767127 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
66 AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
3767169 TTTCTTCAGGGAGT-AGAACTCGAACAAT
1 TTTCTTCAGGGAGTAAGAACTCGAACAAT
3767197 CTTCTGTTGC
Statistics
Matches: 434, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
106 75 0.17
107 358 0.82
108 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (107 bp):
TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGG
AGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
Found at i:3766908 original size:160 final size:159
Alignment explanation
Indices: 3766619--3767196 Score: 933
Period size: 160 Copynumber: 3.6 Consensus size: 159
3766609 TCTTCGGCCA
* * * * * **
3766619 ACGGGTTCACTTTCTCTTTCTTTAGGGAGTAGAACTCGAACATTCTTCTTCCTACGGG-CTCGCT
1 ACGGGTCCACTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCT
* * *
3766683 CTCTATTTTCTTCAAGGAGTAGAACTCGAACAATCATCTTCCTACGAGTCCGCTCTCTTTTTCTT
65 CTCTA-TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTT
*
3766748 CAAGGAGTAGAACTCGAACAATAATCTTCCT
129 CAGGGAGTAGAACTCGAACAATAATCTTCCT
* * *
3766779 ACGGGTCCACTCTCTATTTATTCAGGGAGTAGAACTCAAACAATAATCTTCCTACGGGTCCGCTC
1 ACGGGTCCACTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTC
* *
3766844 TCTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTC
66 TCTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTC
3766909 AGGGAGTAGAACTCGAACAATAATCTTCCT
130 AGGGAGTAGAACTCGAACAATAATCTTCCT
* *
3766939 ACAGGTCCGCTCTCTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCT
1 ACGGGTCCACTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCT
3767004 CTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTC
65 CTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTC
3767069 AGGGAGTAAGAACTCGAACAATAATCTTCCT
130 AGGGAGT-AGAACTCGAACAATAATCTTCCT
*
3767100 ACGGGTCCGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTC
1 ACGGGTCCACTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTC
3767165 TCTATTTCTTCAGGGAGTAGAACTCGAACAAT
66 TCTATTTCTTCAGGGAGTAGAACTCGAACAAT
3767197 CTTCTGTTGC
Statistics
Matches: 391, Mismatches: 23, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
159 13 0.03
160 274 0.70
161 104 0.27
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (159 bp):
ACGGGTCCACTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTC
TCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCA
GGGAGTAGAACTCGAACAATAATCTTCCT
Found at i:3768551 original size:9 final size:9
Alignment explanation
Indices: 3768534--3768605 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
3768524 TTTTATTTGT
3768534 TTTTGTTTTA
1 TTTT-TTTTA
3768544 TTTTTTTTCA
1 TTTTTTTT-A
* *
3768554 TTTTCTTCA
1 TTTTTTTTA
* *
3768563 TTTTCTTCA
1 TTTTTTTTA
* *
3768572 TTTTCTTCA
1 TTTTTTTTA
3768581 TTTTTTTTCA
1 TTTTTTTT-A
3768591 TTTTTTTTCA
1 TTTTTTTT-A
3768601 TTTTT
1 TTTTT
3768606 CATTTTTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
9 29 0.52
10 27 0.48
ACGTcount: A:0.10, C:0.12, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3768581 original size:27 final size:26
Alignment explanation
Indices: 3768546--3768625 Score: 101
Period size: 26 Copynumber: 3.0 Consensus size: 26
3768536 TTGTTTTATT
* *
3768546 TTTTTTCATTTTCTTCATTTTCTTCA
1 TTTTTTCATTTTTTTCATTTTTTTCA
3768572 TTTTCTTCATTTTTTTTCATTTTTTTTCA
1 TTTT-TTCA-TTTTTTTCA-TTTTTTTCA
3768601 -TTTTTCATTTTTTTC-TTTTTTTCA
1 TTTTTTCATTTTTTTCATTTTTTTCA
3768625 T
1 T
3768626 CTTCAAGCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
24 9 0.19
26 12 0.25
27 8 0.17
28 11 0.23
29 8 0.17
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTTCATTTTTTTCATTTTTTTCA
Found at i:3768613 original size:9 final size:9
Alignment explanation
Indices: 3768545--3768625 Score: 96
Period size: 9 Copynumber: 9.1 Consensus size: 9
3768535 TTTGTTTTAT
3768545 TTTTTTTCA
1 TTTTTTTCA
*
3768554 TTTTCTTCA
1 TTTTTTTCA
*
3768563 TTTTCTTCA
1 TTTTTTTCA
*
3768572 TTTTCTTCA
1 TTTTTTTCA
3768581 TTTTTTTTCA
1 -TTTTTTTCA
3768591 TTTTTTTTCA
1 -TTTTTTTCA
3768601 --TTTTTCA
1 TTTTTTTCA
3768608 TTTTTTTC-
1 TTTTTTTCA
3768616 TTTTTTTCA
1 TTTTTTTCA
3768625 T
1 T
3768626 CTTCAAGCAA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
7 7 0.11
8 8 0.12
9 33 0.50
10 18 0.27
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:3768614 original size:10 final size:10
Alignment explanation
Indices: 3768533--3768605 Score: 80
Period size: 10 Copynumber: 7.5 Consensus size: 10
3768523 CTTTTATTTG
*
3768533 TTTTTGTTTTA
1 TTTTT-TTTCA
3768544 TTTTTTTTCA
1 TTTTTTTTCA
*
3768554 -TTTTCTTCA
1 TTTTTTTTCA
*
3768563 -TTTTCTTCA
1 TTTTTTTTCA
*
3768572 -TTTTCTTCA
1 TTTTTTTTCA
3768581 TTTTTTTTCA
1 TTTTTTTTCA
3768591 TTTTTTTTCA
1 TTTTTTTTCA
3768601 TTTTT
1 TTTTT
3768606 CATTTTTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
9 26 0.45
10 27 0.47
11 5 0.09
ACGTcount: A:0.10, C:0.12, G:0.01, T:0.77
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:3779527 original size:24 final size:24
Alignment explanation
Indices: 3779500--3779549 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3779490 TTGAAATTTA
3779500 ATCTTGGTCAATACCCAGACTTTG
1 ATCTTGGTCAATACCCAGACTTTG
* *
3779524 ATCTTGGTCAATACTCAGATTTTG
1 ATCTTGGTCAATACCCAGACTTTG
3779548 AT
1 AT
3779550 GATGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCAGACTTTG
Found at i:3779808 original size:9 final size:9
Alignment explanation
Indices: 3779794--3779823 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3779784 TAAAACCCTG
3779794 AAGAAGAAA
1 AAGAAGAAA
*
3779803 AAGAAGAAG
1 AAGAAGAAA
3779812 AAGAAGAAA
1 AAGAAGAAA
3779821 AAG
1 AAG
3779824 TCCCCGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:3781442 original size:21 final size:21
Alignment explanation
Indices: 3781416--3781525 Score: 141
Period size: 21 Copynumber: 5.2 Consensus size: 21
3781406 AATGCCATTT
3781416 TCATCACGTAAAACACCTACC
1 TCATCACGTAAAACACCTACC
*
3781437 TCATCACGTAAAGCACCTACC
1 TCATCACGTAAAACACCTACC
* * *
3781458 TTATCAC-AAAAAGCACCGACC
1 TCATCACGTAAAA-CACCTACC
*
3781479 TCATCACGTAAAACACATACC
1 TCATCACGTAAAACACCTACC
* *
3781500 TCATCACGTAAAGCACCTAAC
1 TCATCACGTAAAACACCTACC
3781521 TCATC
1 TCATC
3781526 CTGTGGAGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
20 3 0.04
21 68 0.91
22 4 0.05
ACGTcount: A:0.38, C:0.35, G:0.07, T:0.19
Consensus pattern (21 bp):
TCATCACGTAAAACACCTACC
Found at i:3781722 original size:42 final size:42
Alignment explanation
Indices: 3781625--3781832 Score: 271
Period size: 42 Copynumber: 5.0 Consensus size: 42
3781615 GTGATGAAAT
* * * *
3781625 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTTGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
* *
3781664 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
* *
3781706 AGGTGATAGATCTCGGTGTCGAAGTGGAGAAT-GGACTTGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGG-CTCGATG
* * *
3781748 AGGTGATGGATCTCGGTGTTGAAGTAGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
*
3781790 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
3781832 A
1 A
3781833 AAAAGTTGGG
Statistics
Matches: 151, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 35 0.23
41 3 0.02
42 112 0.74
43 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.39, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
Found at i:3784633 original size:22 final size:22
Alignment explanation
Indices: 3784606--3784675 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
3784596 AGATGGAGGG
3784606 GTCGTCGGAGATGGGGACGGAT
1 GTCGTCGGAGATGGGGACGGAT
*
3784628 GTCGTCAGAGATGGGGACGGAT
1 GTCGTCGGAGATGGGGACGGAT
*
3784650 GTCGTCGGAGATGGGGATGGAT
1 GTCGTCGGAGATGGGGACGGAT
3784672 GTCG
1 GTCG
3784676 CCAGAGAGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.13, G:0.49, T:0.20
Consensus pattern (22 bp):
GTCGTCGGAGATGGGGACGGAT
Found at i:3784810 original size:20 final size:20
Alignment explanation
Indices: 3784787--3784962 Score: 133
Period size: 20 Copynumber: 8.7 Consensus size: 20
3784777 ACTAAAAGTT
3784787 GAGTTGCGAATTCGAAAATC
1 GAGTTGCGAATTCGAAAATC
** *
3784807 GAGTTGCGAAAACGAAATTC
1 GAGTTGCGAATTCGAAAATC
* *
3784827 GTGTTGCGAATTAGAAAATC
1 GAGTTGCGAATTCGAAAATC
**
3784847 GAGTTGCGAAAACGAAAATC
1 GAGTTGCGAATTCGAAAATC
* **
3784867 GTGTTGCGAATTTAAAAATC
1 GAGTTGCGAATTCGAAAATC
* * *
3784887 GAGTTGCGAA-ACAGAAATTT
1 GAGTTGCGAATTC-GAAAATC
* *
3784907 GTGTTGCGAAAATGT-TAAATAT-
1 GAGTTGCG--AAT-TCGAAA-ATC
* *
3784929 GAGTTGCGAATTCCAAATTC
1 GAGTTGCGAATTCGAAAATC
3784949 GAGTTGCGAATTCG
1 GAGTTGCGAATTCG
3784963 GAAACTGTGT
Statistics
Matches: 117, Mismatches: 31, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.02
20 102 0.87
22 12 0.10
23 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (20 bp):
GAGTTGCGAATTCGAAAATC
Found at i:3784833 original size:40 final size:40
Alignment explanation
Indices: 3784789--3785017 Score: 198
Period size: 40 Copynumber: 5.7 Consensus size: 40
3784779 TAAAAGTTGA
3784789 GTTGCGAATTCGAAAATCGAGTTGCGAAAACGAAATTCGT
1 GTTGCGAATTCGAAAATCGAGTTGCGAAAACGAAATTCGT
* *
3784829 GTTGCGAATTAGAAAATCGAGTTGCGAAAACGAAAATCGT
1 GTTGCGAATTCGAAAATCGAGTTGCGAAAACGAAATTCGT
** *
3784869 GTTGCGAATTTAAAAATCGAGTTGCG-AAACAGAAATTTGT
1 GTTGCGAATTCGAAAATCGAGTTGCGAAAAC-GAAATTCGT
* ** * *
3784909 GTTGCGAAAATGT-TAAATAT-GAGTTGCGAATTCCAAATTCGA
1 GTTGCG--AAT-TCGAAA-ATCGAGTTGCGAAAACGAAATTCGT
* * ** **
3784951 GTTGCGAATTCGGAAA-CTGTGTTGCGAAATTGACTTTCGT
1 GTTGCGAATTCGAAAATC-GAGTTGCGAAAACGAAATTCGT
* * *
3784991 GCTGCGAATTCG-AATTTGAGTTGCGAA
1 GTTGCGAATTCGAAAATCGAGTTGCGAA
3785018 TTCGTTGGTT
Statistics
Matches: 154, Mismatches: 25, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
39 17 0.11
40 106 0.69
42 26 0.17
43 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (40 bp):
GTTGCGAATTCGAAAATCGAGTTGCGAAAACGAAATTCGT
Found at i:3784893 original size:60 final size:60
Alignment explanation
Indices: 3784787--3784960 Score: 170
Period size: 60 Copynumber: 2.9 Consensus size: 60
3784777 ACTAAAAGTT
** ** * *
3784787 GAGTTGCGAATTCGAAAATCGAGTTGCGAAAACGAAATTCGTGTTGCGAATTAGAAAATC
1 GAGTTGCGAAAACGAAAATCGAGTTGCGAATTCAAAATTCGAGTTGCGAATTAGAAAATC
* * * ** * *
3784847 GAGTTGCGAAAACGAAAATCGTGTTGCGAATTTAAAAATCGAGTTGCGAAACAGAAATTT
1 GAGTTGCGAAAACGAAAATCGAGTTGCGAATTCAAAATTCGAGTTGCGAATTAGAAAATC
* * *
3784907 GTGTTGCGAAAATGTTAAATAT-GAGTTGCGAATTCCAAATTCGAGTTGCGAATT
1 GAGTTGCGAAAACG--AAA-ATCGAGTTGCGAATTCAAAATTCGAGTTGCGAATT
3784961 CGGAAACTGT
Statistics
Matches: 90, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
60 59 0.66
62 29 0.32
63 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (60 bp):
GAGTTGCGAAAACGAAAATCGAGTTGCGAATTCAAAATTCGAGTTGCGAATTAGAAAATC
Found at i:3786470 original size:17 final size:17
Alignment explanation
Indices: 3786446--3786483 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
3786436 TTTCAATAAT
3786446 ATATATATATATATTTAAA
1 ATATATATA-AT-TTTAAA
3786465 ATATATATAATTTTAAA
1 ATATATATAATTTTAAA
3786482 AT
1 AT
3786484 TTTAAAGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATAATTTTAAA
Found at i:3787881 original size:24 final size:24
Alignment explanation
Indices: 3787844--3787896 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
3787834 TCGTTATTTC
* *
3787844 CCGCGATAGTTATTTCAGATACTA
1 CCGCGACAGCTATTTCAGATACTA
3787868 CCGCGACAGCTATTTCAGATACTA
1 CCGCGACAGCTATTTCAGATACTA
3787892 CCGCG
1 CCGCG
3787897 CCTCGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (24 bp):
CCGCGACAGCTATTTCAGATACTA
Found at i:3791329 original size:45 final size:45
Alignment explanation
Indices: 3791230--3791358 Score: 136
Period size: 45 Copynumber: 2.9 Consensus size: 45
3791220 ATTGTTTGAT
* * * ** *
3791230 AATGCTCTTGGGACC-CGCCTGTTGGAGCTATGCCCGACCGTGAT
1 AATGTTCTTGGGACCACGCCTATTGGAGCTATGGCCGACCACGAC
* *
3791274 GATGTGCTTGGGACCACGCCTATTGGAGCTATGGCCGACCACGAC
1 AATGTTCTTGGGACCACGCCTATTGGAGCTATGGCCGACCACGAC
* * *
3791319 AATGTTCTT-GGAGCCACGCCTTTTGGAGCAATGGTCGACC
1 AATGTTCTTGGGA-CCACGCCTATTGGAGCTATGGCCGACC
3791359 GTGCCAATGT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
44 15 0.21
45 55 0.79
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (45 bp):
AATGTTCTTGGGACCACGCCTATTGGAGCTATGGCCGACCACGAC
Found at i:3793877 original size:20 final size:20
Alignment explanation
Indices: 3793852--3793931 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
3793842 GGAATGAGAA
3793852 AATATTATAATAATTTAAAT
1 AATATTATAATAATTTAAAT
* *
3793872 AATATTAT--TCATTATAAAAA
1 AATATTATAATAATT-T-AAAT
* * * *
3793892 AATCAATATTATTATTTTAA-
1 AAT-ATTATAATAATTTAAAT
3793912 AATATTATAATAATTTAAAT
1 AATATTATAATAATTTAAAT
3793932 TATACTATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
18 4 0.09
19 13 0.29
20 17 0.38
21 6 0.13
22 1 0.02
23 4 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTATAATAATTTAAAT
Found at i:3793923 original size:24 final size:23
Alignment explanation
Indices: 3793868--3793913 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3793858 ATAATAATTT
3793868 AAATAATATTATTCATTATAAAA
1 AAATAATATTATTCATTATAAAA
*
3793891 AAATCAATATTATT-ATTTTAAAA
1 AAAT-AATATTATTCATTATAAAA
3793914 TATTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATATTATTCATTATAAAA
Found at i:3806496 original size:2 final size:2
Alignment explanation
Indices: 3806489--3806516 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3806479 TTAACAAAAC
3806489 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
3806517 TTGAGGAATA
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:3813772 original size:10 final size:10
Alignment explanation
Indices: 3813752--3813781 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3813742 AAAGTAATTT
3813752 TAATA-TTTA
1 TAATATTTTA
3813761 TAATATTTTA
1 TAATATTTTA
3813771 TAATATTTTA
1 TAATATTTTA
3813781 T
1 T
3813782 GTCATCGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TAATATTTTA
Found at i:3841136 original size:21 final size:20
Alignment explanation
Indices: 3841050--3841207 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
3841040 AAATGACCAA
**
3841050 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3841069 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3841089 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3841109 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3841130 GAAAATCGCAATGCAATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3841151 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3841171 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3841192 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3841208 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3841236 original size:20 final size:20
Alignment explanation
Indices: 3841174--3841403 Score: 214
Period size: 20 Copynumber: 11.5 Consensus size: 20
3841164 CGATTTTCCA
* ** *
3841174 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3841194 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3841214 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3841234 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* **
3841254 AAATCGAAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
3841274 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3841294 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3841314 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * * *
3841334 AAATCGTAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
3841354 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
3841374 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
3841394 AAATCACAAC
1 AAATCGCAAC
3841404 ACTGAAATTT
Statistics
Matches: 172, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 168 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3842125 original size:24 final size:24
Alignment explanation
Indices: 3842086--3842132 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3842076 AAATTTGGTC
3842086 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3842110 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3842133 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3842324 original size:12 final size:12
Alignment explanation
Indices: 3842307--3842331 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3842297 ATATAATCCT
3842307 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3842319 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3842331 G
1 G
3842332 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3844665 original size:33 final size:33
Alignment explanation
Indices: 3844628--3844885 Score: 168
Period size: 33 Copynumber: 7.5 Consensus size: 33
3844618 GCAACGAGAG
3844628 AATCGCAATGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAA
* *
3844661 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAAC-ATGAA
* *
3844695 AATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CCA----ACATGAA
* * * * *
3844733 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
* * * * *
3844766 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
*
3844799 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
* *
3844837 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
3844870 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
3844886 TATAAACGCA
Statistics
Matches: 189, Mismatches: 19, Indels: 34
0.78 0.08 0.14
Matches are distributed among these distances:
31 1 0.01
32 8 0.04
33 90 0.48
34 32 0.17
35 1 0.01
36 1 0.01
37 1 0.01
38 48 0.25
39 6 0.03
40 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAA
Found at i:3844719 original size:19 final size:19
Alignment explanation
Indices: 3844628--3844863 Score: 278
Period size: 19 Copynumber: 13.4 Consensus size: 19
3844618 GCAACGAGAG
3844628 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3844647 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3844661 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3844681 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3844695 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3844714 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3844733 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3844747 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3844766 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3844780 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3844799 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3844818 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3844837 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3844856 AATCGCAA
1 AATCGCAA
3844864 CGAGAGAATC
Statistics
Matches: 186, Mismatches: 10, Indels: 42
0.78 0.04 0.18
Matches are distributed among these distances:
14 42 0.23
15 3 0.02
16 7 0.04
17 5 0.03
18 4 0.02
19 112 0.60
20 13 0.07
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3844741 original size:52 final size:52
Alignment explanation
Indices: 3844656--3844844 Score: 258
Period size: 52 Copynumber: 3.6 Consensus size: 52
3844646 AAATCCCAAC
*
3844656 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATG-AGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3844709 ATGAAAATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
3844761 ATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAA
1 ATGAAAATCGCAATGAGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAA
*
3844813 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGAGAAATGAAAATCGCAA
3844845 TGCGAAATGA
Statistics
Matches: 122, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
50 5 0.04
51 6 0.05
52 82 0.67
53 22 0.18
54 7 0.06
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Done.