Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002648.1 Hibiscus syriacus cultivar Beakdansim tig00005411_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: 636717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:396660 original size:27 final size:26
Alignment explanation
Indices: 396630--396691 Score: 99
Period size: 27 Copynumber: 2.4 Consensus size: 26
396620 ATTAGAACAA
396630 AAAGAGAAAAAAAAAAGAGAAAAAAGC
1 AAAGAGAAAAAAAAAAGAGAAAAAA-C
*
396657 AAAGAGAAAATAAAAAGAGAAAAAAC
1 AAAGAGAAAAAAAAAAGAGAAAAAAC
396683 AAAG-GAAAA
1 AAAGAGAAAA
396692 TTGAAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 5 0.15
26 5 0.15
27 24 0.71
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAGAGAAAAAAAAAAGAGAAAAAAC
Found at i:396874 original size:69 final size:69
Alignment explanation
Indices: 396763--396900 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
396753 GATTCAAACT
*
396763 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
396828 TCAA
66 TCAA
* * *
396832 ATGAGATTGATCAAGTATAATTATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
396897 TCAA
66 TCAA
396901 GAGAGAGACA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:397848 original size:31 final size:30
Alignment explanation
Indices: 397813--397927 Score: 108
Period size: 31 Copynumber: 3.7 Consensus size: 30
397803 GGAACAATGA
397813 GGCATCTTTGAAGATTCAACATCAATGTTGG
1 GGCATCTTTG-AGATTCAACATCAATGTTGG
* * *
397844 GGCATTTTTTAGATTTAACA-CAAATGTTGG
1 GGCATCTTTGAGATTCAACATC-AATGTTGG
* * * *
397874 GGTATTTTTTGAGATTCAACATCGATATTGGG
1 GGCA-TCTTTGAGATTCAACATCAATGTT-GG
397906 GGCATCTTTG-GAATTCAACATC
1 GGCATCTTTGAG-ATTCAACATC
397928 CTGATAAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.01
30 21 0.30
31 41 0.59
32 6 0.09
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (30 bp):
GGCATCTTTGAGATTCAACATCAATGTTGG
Found at i:397858 original size:30 final size:31
Alignment explanation
Indices: 397819--397927 Score: 116
Period size: 30 Copynumber: 3.5 Consensus size: 31
397809 ATGAGGCATC
397819 TTTGAAGATTCAACATCAATGTTGGGGCATTT
1 TTTG-AGATTCAACATCAATGTTGGGGCATTT
* *
397851 TTT-AGATTTAACA-CAAATGTTGGGGTATTT
1 TTTGAGATTCAACATC-AATGTTGGGGCATTT
* * *
397881 TTTGAGATTCAACATCGATATTGGGGGCATCT
1 TTTGAGATTCAACATCAATGTT-GGGGCATTT
*
397913 TTGGA-ATTCAACATC
1 TTTGAGATTCAACATC
397928 CTGATAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
29 1 0.02
30 26 0.40
31 23 0.35
32 15 0.23
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (31 bp):
TTTGAGATTCAACATCAATGTTGGGGCATTT
Found at i:398615 original size:106 final size:106
Alignment explanation
Indices: 398491--398813 Score: 441
Period size: 106 Copynumber: 3.0 Consensus size: 106
398481 ATATTGTGAC
* * * **
398491 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGATGATTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
398556 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
* *
398597 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTACC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
398662 AATTTCGGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
* * *
398703 ACTCGAGACAACACAAGCTCAACTTCACAACGAA-GGAGCGGCTGGCTGTCAACAAACAATTTCT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGGCTGGTTGTCAACAAACAATTTCC
* ** * * * *
398767 TAGCTCCAGAGCCAATTTTAAGTTCACGGCGAAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
398809 ACTCG
1 ACTCG
398814 GAACAATACA
Statistics
Matches: 190, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
105 3 0.02
106 187 0.98
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
Found at i:398960 original size:88 final size:90
Alignment explanation
Indices: 398856--399033 Score: 333
Period size: 88 Copynumber: 2.0 Consensus size: 90
398846 CGACAAAGGA
398856 ATCCAATTCCAAGGCTCAACTTCACAACGAA-GGGTCATCCACGGTTTCAACTTCACGACG-AGG
1 ATCCAATTCCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGG
398919 GAATCGTGCTCACCATTGTCTCTCT
66 GAATCGTGCTCACCATTGTCTCTCT
*
398944 ATCCAATTCCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGGTTTCAACTTTACGACGAAGG
1 ATCCAATTCCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGG
399009 GAATCGTGCTCACCATTGTCTCTCT
66 GAATCGTGCTCACCATTGTCTCTCT
399034 TGAGACAGTT
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
88 31 0.36
89 28 0.32
90 28 0.32
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (90 bp):
ATCCAATTCCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGGTTTCAACTTCACGACGAAGG
GAATCGTGCTCACCATTGTCTCTCT
Found at i:399291 original size:86 final size:89
Alignment explanation
Indices: 399129--399325 Score: 310
Period size: 86 Copynumber: 2.2 Consensus size: 89
399119 TTTTGGAACT
*
399129 AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATGAATTTAATCTCG
1 AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATAAATTTAATCTCG
399194 ATTGAGATAGTTTCCCTTGAAACA
66 ATTGAGATAGTTTCCCTTGAAACA
* * *
399218 AAATTTTGTCTCCCTTGA-A-ACATAAACATTGAAAATATTTCTC-TGAAATAAATTTTATCTCG
1 AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATAAATTTAATCTCG
* * *
399280 CTTGGGGTAGTTTCCCTTGAAACA
66 ATTGAGATAGTTTCCCTTGAAACA
399304 AAATTTTGTCTCCCTTGAGACA
1 AAATTTTGTCTCCCTTGAGACA
399326 GTTTCTCTTG
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
86 56 0.57
87 23 0.23
88 2 0.02
89 18 0.18
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (89 bp):
AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATAAATTTAATCTCG
ATTGAGATAGTTTCCCTTGAAACA
Found at i:399310 original size:37 final size:37
Alignment explanation
Indices: 399267--399442 Score: 111
Period size: 37 Copynumber: 5.0 Consensus size: 37
399257 TCTCTGAAAT
* * **
399267 AAATTTTATCTCGCTTGGGGTAGTTTCCCTTGAAACA
1 AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
* *
399304 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
* * * * *
399341 TAA----A----CATTGA-AAAGATTTCCTTTGAAA-T
1 AAATTTTATCTCCCTTGAGACAG-TTTCCCTTGAAACA
* * ** *
399369 TAATTTTGTCTATCTTGAGATAGTTTCCCTTGAAACA
1 AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
* *
399406 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
399443 TAAACCTTGA
Statistics
Matches: 104, Mismatches: 24, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
28 6 0.06
29 15 0.14
36 15 0.14
37 68 0.65
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (37 bp):
AAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA
Found at i:399406 original size:102 final size:102
Alignment explanation
Indices: 399231--399469 Score: 365
Period size: 102 Copynumber: 2.4 Consensus size: 102
399221 TTTTGTCTCC
* * * * *
399231 CTTGAAACATAAACATTGAAAATATTT-CTCTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAAGATTTCCTTTGAAATAAATTTTATCTAGCTTGAGATAGTTTCC
399295 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* * *
399332 CTTGAAACATAAACATTGAAAAGATTTCCTTTGAAATTAATTTTGTCTATCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAAGATTTCCTTTGAAATAAATTTTATCTAGCTTGAGATAGTTTCC
399397 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
66 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
399434 CTTGAAACATAAACCTTGAAAACG-TTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAA-GATTTCCTTTGAAA
399470 CACAAAATAT
Statistics
Matches: 126, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 26 0.21
102 99 0.79
103 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAAGATTTCCTTTGAAATAAATTTTATCTAGCTTGAGATAGTTTCC
CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:399718 original size:36 final size:35
Alignment explanation
Indices: 399623--399732 Score: 127
Period size: 36 Copynumber: 3.1 Consensus size: 35
399613 CTTTTCCTTG
* *
399623 AACAAATTTCGT-CTCCTTGAGACAGTCTCTTTT-A
1 AACAAATTTTGTCCT-CTTGAGACAGTTTCTTTTGA
*
399657 GAACTAAGTTTTGT-CTCTTGAGACAGTTTCTTTTGA
1 -AAC-AAATTTTGTCCTCTTGAGACAGTTTCTTTTGA
*
399693 AACAAATTTTGTCCCTCTTGAGACAGTTTCTCTTGA
1 AACAAATTTTGT-CCTCTTGAGACAGTTTCTTTTGA
399729 AACA
1 AACA
399733 CAAAAAAACC
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.12
35 23 0.35
36 35 0.53
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (35 bp):
AACAAATTTTGTCCTCTTGAGACAGTTTCTTTTGA
Found at i:400745 original size:13 final size:13
Alignment explanation
Indices: 400729--400756 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
400719 TTGTCTCTAT
400729 ATTAAAAATTAAA
1 ATTAAAAATTAAA
400742 ATTAAAAATTAAA
1 ATTAAAAATTAAA
400755 AT
1 AT
400757 ATATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAAAAATTAAA
Found at i:401141 original size:44 final size:44
Alignment explanation
Indices: 401045--401142 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
401035 TAAAAATATT
*
401045 TAAATAAAGCAATAAAAATACAATTTGAACAAATATTTAAAGCAG
1 TAAAT-AAGCAATAAAAATACAATTAGAACAAATATTTAAAGCAG
* *
401090 TAAAAATAA-CAAT-AAAATACAATTAGAATGATATATTTAAAAGCAG
1 T--AAATAAGCAATAAAAATACAATTAGAA-CAAATATTT-AAAGCAG
401136 TAAATAA
1 TAAATAA
401143 ATGAACACCT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
44 20 0.43
45 12 0.26
46 10 0.22
47 4 0.09
ACGTcount: A:0.59, C:0.07, G:0.08, T:0.26
Consensus pattern (44 bp):
TAAATAAGCAATAAAAATACAATTAGAACAAATATTTAAAGCAG
Found at i:402477 original size:3 final size:3
Alignment explanation
Indices: 402469--402591 Score: 156
Period size: 3 Copynumber: 41.0 Consensus size: 3
402459 TATATATATT
* *
402469 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * *
402517 TAT TTA TAA TAA TAA TAA TAA TAA TAA TTT TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
402565 TAA TAA TTA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
402592 ATAAATCAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:403015 original size:113 final size:113
Alignment explanation
Indices: 402829--403692 Score: 1192
Period size: 113 Copynumber: 7.7 Consensus size: 113
402819 CAGAGTCATT
* **
402829 CAAAAGGTTGAATAAGCTCTTCT-ATTTATGAACTTC--C-T-CTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCA-TTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * *
402889 ATTATGAACTTTCTCTGTAAAAGTTGATCCATCGAGTGATGGATTTGAG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
402938 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTC
*
403002 ATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGTGATGGATTTGAG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
*
403051 CAAAA-ATCTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCT
1 CAAAAGGT-TGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCT
*
403114 CATTATGAACTTTCTCTAGAAAAGTTGATCTATCAAGTGATGGATTTGAG
64 CATTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
* *
403164 CAAAA-ATCTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTT
1 CAAAAGGT-TGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
**** * * *
403228 ATTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
*
403277 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
**** * * *
403342 TTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
* *
403390 CAAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCATCCTTCGTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGAT---GAGTTCTTC
* * * * * * * *
403455 TCATTATGAACTCTAC-CTGGCAATGTTAATCCATCATA-TGATGAATTTAAA
63 TCATTATGAACT-TTCTCTGGAAAAGTTGATCTATCA-AGTGATGGATTTGAG
403506 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * * *
403571 TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
*
403619 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
403684 TTATGAACT
66 TTATGAACT
403693 CGAACTGGAA
Statistics
Matches: 694, Mismatches: 45, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
109 31 0.04
110 1 0.00
111 1 0.00
112 8 0.01
113 551 0.79
114 4 0.01
116 97 0.14
117 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAG
Found at i:403619 original size:342 final size:339
Alignment explanation
Indices: 402829--403728 Score: 1266
Period size: 342 Copynumber: 2.7 Consensus size: 339
402819 CAGAGTCATT
* **
402829 CAAAAGGTTGAATAAGCTCTTCT-ATTTATGAACTTC--C-T-CTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCA-TTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * * *
402889 ATTATGAACTTTCTCTGTAAAAGTTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 ATTATGAACTTCCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
* ****
402954 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
130 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTCGAACT
* * *
403018 AGAAAAGTTGATCTATCAAGTGATGGATTTGAGCAAAAATCTGAACAAATTCTTCTCATTATGAA
194 GGAAAAGCTAATCTATCAAGTGATGGATTTGAGCAAAAATCTGAACAAATTCTTCTCATTATGAA
* * * *
403083 CTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGTTGATCTATC
259 CTTCTTCATCCTTCTGTCGATGAGTTCTTCTCATTATGAACTTACTCTAGAAAAGTTAATCCATC
* * *
403148 AAGTGATGGATTTGAG
324 AAGTGATGAATTTAAA
* *
403164 CAAAA-ATCTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTT
1 CAAAAGGT-TGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
** * * *
403228 ATTATGAAC-TCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAA
65 ATTATGAACTTC-CTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
403292 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT
129 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT
* * *
403357 GGAAAAGCTAATCTATCAAGTGATAGATTTGAGCAAAAGGT-TGAACAAATTCTTTTCATTATGA
194 GGAAAAGCTAATCTATCAAGTGATGGATTTGAGCAAAA-ATCTGAACAAATTCTTCTCATTATGA
* * *
403421 ACTTCTTCATCCTTC-GTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTAA
258 ACTTCTTCATCCTTCTGTC-GAT---GAGTTCTTCTCATTATGAACT-TACTCTAGAAAAGTTAA
403484 TCCATCATA-TGATGAATTTAAA
318 TCCATCA-AGTGATGAATTTAAA
403506 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
403571 TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
403636 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * *
403701 AAAATCTAATCCATCAAGTAATGGATTT
196 AAAAGCTAATCTATCAAGTGATGGATTT
403729 AAATATTTTC
Statistics
Matches: 501, Mismatches: 47, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
334 1 0.00
335 28 0.06
336 1 0.00
337 1 0.00
338 7 0.01
339 204 0.41
340 1 0.00
342 252 0.50
343 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (339 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AAAAGCTAATCTATCAAGTGATGGATTTGAGCAAAAATCTGAACAAATTCTTCTCATTATGAACT
TCTTCATCCTTCTGTCGATGAGTTCTTCTCATTATGAACTTACTCTAGAAAAGTTAATCCATCAA
GTGATGAATTTAAA
Found at i:404621 original size:83 final size:83
Alignment explanation
Indices: 404440--405243 Score: 1303
Period size: 83 Copynumber: 9.7 Consensus size: 83
404430 GTAGTTCCTA
* * *
404440 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTCATCCTCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATCTTCC
*
404505 CAATTCAATGATTGGTTCTG
64 AAATTCAATGATTGGTTCTG
*
404525 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
404589 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
404608 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
404672 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * * *
404691 TCC-AACCAGATCAGATAACTCATAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
*
404755 AATTCAATAATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
404774 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCACATTCATCTTCCA
404838 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
404857 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
404922 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
404940 CCAAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAGCACATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
*
405005 ATTCAATAATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
405023 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCG-GCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCACATTCATCTTCCA
405087 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * *
405106 CCAAACCATATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATCAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
405171 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
405189 CCAAACCAAATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
405244 GCATTTATTC
Statistics
Matches: 685, Mismatches: 28, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
82 3 0.00
83 633 0.92
84 5 0.01
85 42 0.06
86 2 0.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:405952 original size:16 final size:18
Alignment explanation
Indices: 405915--405958 Score: 65
Period size: 16 Copynumber: 2.5 Consensus size: 18
405905 AATAAAATAG
405915 TAAATTGAATCTTCGAAAA
1 TAAATTGAATCTTC-AAAA
405934 TAAATTGAATC-TC-AAA
1 TAAATTGAATCTTCAAAA
405950 TAAATTGAA
1 TAAATTGAA
405959 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.48
18 2 0.08
19 11 0.44
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (18 bp):
TAAATTGAATCTTCAAAA
Found at i:405966 original size:16 final size:16
Alignment explanation
Indices: 405915--405967 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
405905 AATAAAATAG
405915 TAAATTGAATCTTCGAAAA
1 TAAATTGAA-CTT-G-AAA
*
405934 TAAATTGAA-TCTCAAA
1 TAAATTGAACT-TGAAA
405950 TAAATTGAACTTGAAA
1 TAAATTGAACTTGAAA
405966 TA
1 TA
405968 GATAGAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 18 0.60
17 2 0.07
18 1 0.03
19 9 0.30
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (16 bp):
TAAATTGAACTTGAAA
Found at i:406296 original size:8 final size:8
Alignment explanation
Indices: 406285--406362 Score: 90
Period size: 8 Copynumber: 9.6 Consensus size: 8
406275 ACCTTGACCC
406285 CTTTTTTT
1 CTTTTTTT
406293 CTTTTTTT
1 CTTTTTTT
406301 -TTCTTTTT
1 CTT-TTTTT
406309 C-TTTTTT
1 CTTTTTTT
406316 CTTTTTTT
1 CTTTTTTT
406324 CTTTTTCTCT
1 CTTTTT-T-T
406334 CTCTTTTTT
1 CT-TTTTTT
*
406343 CTTCTTTT
1 CTTTTTTT
406351 C-TTTTTT
1 CTTTTTTT
406358 CTTTT
1 CTTTT
406363 CTTCAAGCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
7 14 0.23
8 35 0.57
9 4 0.07
10 4 0.07
11 4 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
CTTTTTTT
Found at i:406299 original size:7 final size:7
Alignment explanation
Indices: 406287--406362 Score: 75
Period size: 7 Copynumber: 10.6 Consensus size: 7
406277 CTTGACCCCT
406287 TTTTTTC
1 TTTTTTC
*
406294 TTTTTTTT
1 -TTTTTTC
406302 TCTTTTTC
1 T-TTTTTC
406310 TTTTTTC
1 TTTTTTC
406317 TTTTTT-
1 TTTTTTC
406323 TCTTTTTC
1 T-TTTTTC
* *
406331 -TCTCTC
1 TTTTTTC
406337 TTTTTTC
1 TTTTTTC
406344 TTCTTTTC
1 TT-TTTTC
406352 TTTTTTC
1 TTTTTTC
406359 TTTT
1 TTTT
406363 CTTCAAGCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
6 5 0.09
7 33 0.58
8 19 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:406307 original size:6 final size:6
Alignment explanation
Indices: 406288--406362 Score: 55
Period size: 6 Copynumber: 11.7 Consensus size: 6
406278 TTGACCCCTT
* *
406288 TTTTTC -TTTT- TTTTTC TTTTTC TTTTTTC TTTTTTTC TTTTTC TCTCTC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC --TTTTTC TTTTTC TTTTTC
406337 TTTTTTC TTCTTTTC TTTTTTC TTTT
1 -TTTTTC -T-TTTTC -TTTTTC TTTT
406363 CTTCAAGCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.14
6 20 0.34
7 17 0.29
8 14 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:406338 original size:27 final size:24
Alignment explanation
Indices: 406287--406357 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 24
406277 CTTGACCCCT
*
406287 TTTTTTCTTTTTTT-TTCTTTTTC
1 TTTTTTCTTTTTTTCTTTTTTTTC
406310 TTTTTTCTTTTTTTCTTTTTCTCTCTC
1 TTTTTTCTTTTTTTCTTTTT-T-T-TC
*
406337 TTTTTTCTTCTTTTCTTTTTT
1 TTTTTTCTTTTTTTCTTTTTT
406358 CTTTTCTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 14 0.33
24 4 0.10
25 1 0.02
26 2 0.05
27 21 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTTCTTTTTTTCTTTTTTTTC
Found at i:406358 original size:15 final size:15
Alignment explanation
Indices: 406289--406360 Score: 87
Period size: 15 Copynumber: 4.9 Consensus size: 15
406279 TGACCCCTTT
*
406289 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTCTTC
*
406304 TTTTTCTTTTTTCTTT
1 -TTTTCTTTTTTCTTC
406320 TTTTC-TTTTTC-TC
1 TTTTCTTTTTTCTTC
*
406333 -TCTCTTTTTTCTTC
1 TTTTCTTTTTTCTTC
406347 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
406361 TTCTTCAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
12 3 0.06
13 7 0.15
14 8 0.17
15 17 0.35
16 13 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTCTTC
Found at i:406365 original size:27 final size:29
Alignment explanation
Indices: 406297--406365 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 29
406287 TTTTTTCTTT
*
406297 TTTTTTCTTTTTCTTTTTTCTT-TTTTTC
1 TTTTTTCTTCTTCTTTTTTCTTCTTTTTC
406325 -TTTTTC-TCTCTCTTTTTTCTTC-TTTTC
1 TTTTTTCTTCT-TCTTTTTTCTTCTTTTTC
406352 TTTTTTCTT-TTCTT
1 TTTTTTCTTCTTCTT
406366 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 2 0.06
27 26 0.72
28 7 0.19
29 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (29 bp):
TTTTTTCTTCTTCTTTTTTCTTCTTTTTC
Found at i:413703 original size:15 final size:15
Alignment explanation
Indices: 413680--413711 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
413670 TGGAATGAAT
413680 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
413695 AATGCATGTATGCAA
1 AATGAATGTATGCAA
413710 AA
1 AA
413712 AAGGTATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:417020 original size:24 final size:23
Alignment explanation
Indices: 416993--417057 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
416983 ATGAAATATT
*
416993 AATAATATATATAAATACTATAAA
1 AATAATATATATAAATA-TAAAAA
* *
417017 AATAATATGTATATATATAAAAA
1 AATAATATATATAAATATAAAAA
* *
417040 AATTATAAAT-TAAATATA
1 AATAATATATATAAATATA
417058 TGAAATTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 7 0.21
23 12 0.35
24 15 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AATAATATATATAAATATAAAAA
Found at i:417849 original size:50 final size:51
Alignment explanation
Indices: 417779--417890 Score: 190
Period size: 50 Copynumber: 2.2 Consensus size: 51
417769 TAAAAATATT
417779 TAAATAAAGCAATAAAAATACAATTAGAACGATATATTTAAAAGCAGTAAAA
1 TAAATAAA-CAATAAAAATACAATTAGAACGATATATTTAAAAGCAGTAAAA
*
417831 TAAAT-AACAATAAAAATACAATTAGAATGATATATTTAAAAGCAGTAAAA
1 TAAATAAACAATAAAAATACAATTAGAACGATATATTTAAAAGCAGTAAAA
*
417881 TAAATGAACA
1 TAAATAAACA
417891 CCTTTAAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
50 47 0.81
51 6 0.10
52 5 0.09
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (51 bp):
TAAATAAACAATAAAAATACAATTAGAACGATATATTTAAAAGCAGTAAAA
Found at i:417870 original size:26 final size:26
Alignment explanation
Indices: 417791--417871 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
417781 AATAAAGCAA
*
417791 TAAAAATACAATTAGAACGATATATT
1 TAAAAATACAATTAGAATGATATATT
* * *
417817 TAAAAGCAGTA-AAATA-AAT-A-ACA-A
1 TAAAA--A-TACAATTAGAATGATATATT
417841 TAAAAATACAATTAGAATGATATATT
1 TAAAAATACAATTAGAATGATATATT
417867 TAAAA
1 TAAAA
417872 GCAGTAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 16
0.63 0.11 0.25
Matches are distributed among these distances:
21 2 0.05
22 5 0.12
23 3 0.08
24 6 0.15
25 4 0.10
26 11 0.28
27 2 0.05
28 5 0.12
29 2 0.05
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.27
Consensus pattern (26 bp):
TAAAAATACAATTAGAATGATATATT
Found at i:418676 original size:15 final size:14
Alignment explanation
Indices: 418652--418693 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
418642 TGACAGTAGG
*
418652 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
418667 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
418681 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
418694 GCTGTGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:418684 original size:20 final size:20
Alignment explanation
Indices: 418652--418693 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
418642 TGACAGTAGG
*
418652 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
418672 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
418692 TT
1 TT
418694 GCTGTGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:419245 original size:3 final size:3
Alignment explanation
Indices: 419237--419360 Score: 167
Period size: 3 Copynumber: 41.3 Consensus size: 3
419227 ATATATATAT
* *
419237 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTT ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
419285 ATA TTT ATA ATA ATA ATA ATA ATA ATA TTT ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
419333 ATA ATA ATT ATA GTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
419361 ATAAATCAAA
Statistics
Matches: 103, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:419923 original size:2 final size:2
Alignment explanation
Indices: 419918--420024 Score: 57
Period size: 2 Copynumber: 55.5 Consensus size: 2
419908 TTTTTTAGAT
* * *
419918 TA TA TA TA TA TA TA TA TA TA TA T- TA TT TT TT TA T- TA TCA GT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA
* * * * * *
419959 TT TA T- TA -A TT TA TA TA TA TA TA TA TT TA CTA T- TT TT TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
419999 TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
420025 TATTTTTACT
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
1 7 0.08
2 74 0.87
3 3 0.04
4 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (2 bp):
TA
Found at i:419998 original size:7 final size:7
Alignment explanation
Indices: 419959--420075 Score: 57
Period size: 8 Copynumber: 16.4 Consensus size: 7
419949 TATTATCAGT
419959 TTTATTAA
1 TTTATT-A
419967 TTTATATA
1 TTTAT-TA
*
419975 TATATATA
1 TTTAT-TA
*
419983 TTTACTA
1 TTTATTA
*
419990 TTTTTTA
1 TTTATTA
419997 TTTATTA
1 TTTATTA
*
420004 TATATATA
1 TTTAT-TA
*
420012 TATATATA
1 TTTAT-TA
*
420020 TATATTA
1 TTTATTA
420027 TTT-TTA
1 TTTATTA
*
420033 CTTTTTTA
1 -TTTATTA
420041 -TTATTA
1 TTTATTA
420047 -TT-TTA
1 TTTATTA
420052 TTTATT-
1 TTTATTA
420058 TGTT-TTA
1 T-TTATTA
420065 TTTATATA
1 TTTAT-TA
420073 TTT
1 TTT
420076 TTTCTTCTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
5 3 0.03
6 17 0.19
7 30 0.33
8 39 0.43
9 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:420010 original size:37 final size:38
Alignment explanation
Indices: 419959--420031 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
419949 TATTATCAGT
* *
419959 TTTATTAATTTATATATATATATATTTACTATTTTTTA
1 TTTATTAATATATATATATATATATATACTATTTTTTA
*
419997 TTTATT-ATATATATATATATATATATATTATTTTT
1 TTTATTAATATATATATATATATATATACTATTTTT
420032 ACTTTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 26 0.81
38 6 0.19
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (38 bp):
TTTATTAATATATATATATATATATATACTATTTTTTA
Found at i:420045 original size:43 final size:42
Alignment explanation
Indices: 419894--420047 Score: 151
Period size: 43 Copynumber: 3.6 Consensus size: 42
419884 TTTACTTTAG
419894 TATATATTTTTATTTTTT--TTAGATTATATATATATATATATA
1 TATATATTTTTATTTTTTAGTT--ATTATATATATATATATATA
* *
419936 TATATTATTTTT-TTATTATCAGTT-TTAT-TA-ATTTATATATA
1 TATA-TATTTTTATT-TT-TTAGTTATTATATATATATATATATA
* *
419977 TATATATTTACTATTTTTTATTTATTATATATATATATATATA
1 TATATATTT-TTATTTTTTAGTTATTATATATATATATATATA
420020 TATATTATTTTTACTTTTTTA-TTATTAT
1 TATA-TATTTTTA-TTTTTTAGTTATTAT
420048 TTTATTTATT
Statistics
Matches: 93, Mismatches: 7, Indels: 23
0.76 0.06 0.19
Matches are distributed among these distances:
40 9 0.10
41 21 0.23
42 12 0.13
43 36 0.39
44 13 0.14
46 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (42 bp):
TATATATTTTTATTTTTTAGTTATTATATATATATATATATA
Found at i:420078 original size:47 final size:49
Alignment explanation
Indices: 419993--420115 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
419983 TTTACTATTT
* * *
419993 TTTA-TTTATTATATATATATATATATATATATTATTTTTACTT-TTTTAT-
1 TTTATTTTATTATATTTAT-TTTATTTATATATTATTTTT-CTTCTTTT-TC
*
420042 TATTATTTTATT-TATTTGTTTTATTTATATA-T-TTTTTCTTCTTTTTC
1 T-TTATTTTATTATATTTATTTTATTTATATATTATTTTTCTTCTTTTTC
*
420089 TTTATTTTTTTATATTTATTTTATTTA
1 TTTATTTTATTATATTTATTTTATTTA
420116 CTACTTTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
46 13 0.21
47 24 0.38
48 1 0.02
49 11 0.17
50 8 0.13
51 6 0.10
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (49 bp):
TTTATTTTATTATATTTATTTTATTTATATATTATTTTTCTTCTTTTTC
Found at i:420096 original size:10 final size:9
Alignment explanation
Indices: 420044--420114 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
420034 TTTTTTATTA
*
420044 TTATTTTAT
1 TTATTTTTT
*
420053 TTATTTGTT
1 TTATTTTTT
*
420062 TTA-TTTAT
1 TTATTTTTT
*
420070 ATATTTTTT
1 TTATTTTTT
*
420079 CTTCTTTTTCT
1 -TTATTTTT-T
420090 TTATTTTTT
1 TTATTTTTT
*
420099 TATATTTATT
1 T-TATTTTTT
420109 TTATTT
1 TTATTT
420115 ACTACTTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
8 5 0.10
9 21 0.44
10 21 0.44
11 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (9 bp):
TTATTTTTT
Found at i:420128 original size:37 final size:37
Alignment explanation
Indices: 420052--420128 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
420042 TATTATTTTA
* *
420052 TTTATTTGTTTTATTTATATATTTTTTCTTCTTTTTC
1 TTTATTTGTTTTATTTATATATTTTTTCTACTTTATC
420089 TTTATTT-TTTTATATT-TAT-TTTATTTACTACTTTATC
1 TTTATTTGTTTTAT-TTATATATTT-TTT-CTACTTTATC
420126 TTT
1 TTT
420129 GCTTTCTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 3 0.09
36 12 0.34
37 20 0.57
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (37 bp):
TTTATTTGTTTTATTTATATATTTTTTCTACTTTATC
Found at i:431343 original size:21 final size:22
Alignment explanation
Indices: 431314--431353 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
431304 CATGTCTTTT
431314 TTTTCTTTTTC-TTTCGAACAA
1 TTTTCTTTTTCTTTTCGAACAA
431335 TTTT-TTTTTCTTTTCGAAC
1 TTTTCTTTTTCTTTTCGAAC
431354 TGCTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTTCTTTTTCTTTTCGAACAA
Found at i:442351 original size:33 final size:32
Alignment explanation
Indices: 442314--442384 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
442304 GACGCCGAAA
442314 TTAACCCAAAACAAAAGCAACCTGAACCAAATT
1 TTAACCCAAAACAAAAGCAACCTGAACCAAA-T
* ** *
442347 TTAACCCGATCCAAAAGCAACCTGAACCGAAT
1 TTAACCCAAAACAAAAGCAACCTGAACCAAAT
442379 TTAACC
1 TTAACC
442385 TGACCCGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.45, C:0.30, G:0.08, T:0.17
Consensus pattern (32 bp):
TTAACCCAAAACAAAAGCAACCTGAACCAAAT
Found at i:443432 original size:41 final size:41
Alignment explanation
Indices: 443386--443484 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
443376 TCAAGAAAAA
* * * *
443386 AAACGCGGCTATATACTAGTATTTTAGTGGCATTTTTGAAC
1 AAACGCCGCTAAAGACTAGTATTTTAGTGGCATTTTTAAAC
* * *
443427 AAACGCCGCTAAAGACTTGTGTTTTAGTGGCGTTTTTAAAC
1 AAACGCCGCTAAAGACTAGTATTTTAGTGGCATTTTTAAAC
*
443468 AAATGCCGCTAAAGACT
1 AAACGCCGCTAAAGACT
443485 TGTACATTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTAGTATTTTAGTGGCATTTTTAAAC
Found at i:443485 original size:41 final size:41
Alignment explanation
Indices: 443404--443519 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
443394 CTATATACTA
* *
443404 GTATTTTAGTGGCATTTTTGAACAAACGCCGCTAAAGACTT
1 GTATTTTAGTGGCATTTTTAAACAAATGCCGCTAAAGACTT
* *
443445 GTGTTTTAGTGGCGTTTTTAAACAAATGCCGCTAAAGACTT
1 GTATTTTAGTGGCATTTTTAAACAAATGCCGCTAAAGACTT
** **
443486 GTACATTAGTGGTTTTTTTATAAACAAATGCCGC
1 GTATTTTAGTGG-CATTTT-TAAACAAATGCCGC
443520 AAGTTTTGCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 46 0.72
42 4 0.06
43 14 0.22
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (41 bp):
GTATTTTAGTGGCATTTTTAAACAAATGCCGCTAAAGACTT
Found at i:445463 original size:25 final size:25
Alignment explanation
Indices: 445434--445486 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
445424 AGCTCAATTT
*
445434 CATAACTGAATTTCATAGAGTTAAA
1 CATAACTCAATTTCATAGAGTTAAA
445459 CATAACTCAATTTCATAGAGTTAAA
1 CATAACTCAATTTCATAGAGTTAAA
445484 CAT
1 CAT
445487 TACCATCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (25 bp):
CATAACTCAATTTCATAGAGTTAAA
Found at i:446342 original size:40 final size:40
Alignment explanation
Indices: 446292--446383 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
446282 AATAGACAAA
* * * * * *
446292 TAGCAACGTTTTAGAAAATGTCACTAAAGATCATAACCTT
1 TAGCGACGTTTGAAAAAATGACACTAAAAAGCATAACCTT
* *
446332 TAGTGACGTTTGAAAAAATGACACTAAAAAGCGTAACCTT
1 TAGCGACGTTTGAAAAAATGACACTAAAAAGCATAACCTT
446372 TAGCGACGTTTG
1 TAGCGACGTTTG
446384 TTTCAAAGGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (40 bp):
TAGCGACGTTTGAAAAAATGACACTAAAAAGCATAACCTT
Found at i:450494 original size:6 final size:6
Alignment explanation
Indices: 450465--450513 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
450455 TAAATATATT
*
450465 AAATGAA AAATAGA AAAT-A AAATAA AAATAA AAATAA AAGTTAA AAATA
1 AAAT-AA AAATA-A AAATAA AAATAA AAATAA AAATAA AA-ATAA AAATA
450514 TAAGAAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
5 5 0.14
6 18 0.49
7 14 0.38
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:451693 original size:12 final size:13
Alignment explanation
Indices: 451676--451710 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
451666 TTTTTGCATC
451676 ATTATTATTTAT-
1 ATTATTATTTATA
451688 ATTATTATTTATA
1 ATTATTATTTATA
451701 ATTATATATT
1 ATTAT-TATT
451711 ATTTTACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 5 0.24
14 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTATTTATA
Found at i:451948 original size:26 final size:26
Alignment explanation
Indices: 451908--452020 Score: 138
Period size: 26 Copynumber: 4.3 Consensus size: 26
451898 TTCCAGAACA
* *
451908 AGCCACCACCACTTGGACCACTCAAT
1 AGCCACCACCGCTTGGACCACTCAAC
*
451934 AGCCACTACCGCTTGGACCACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
*
451960 AGCCACCACCGCTTTGACCACTCAAC
1 AGCCACCACCGCTTGGACCACTCAAC
* * *
451986 AACCACCGCCGGC-TAGACCACTCAAC
1 AGCCACCACC-GCTTGGACCACTCAAC
*
452012 AACCACCAC
1 AGCCACCAC
452021 TGCTGCCAAC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 75 0.97
27 2 0.03
ACGTcount: A:0.30, C:0.45, G:0.12, T:0.12
Consensus pattern (26 bp):
AGCCACCACCGCTTGGACCACTCAAC
Found at i:456416 original size:32 final size:30
Alignment explanation
Indices: 456370--456484 Score: 104
Period size: 32 Copynumber: 3.7 Consensus size: 30
456360 ACCTAAACCA
**
456370 AAAATCAACCGATCCGATATTGATCCGACCC
1 AAAATCAATTGATCCGATATTGA-CCGACCC
* *
456401 AAAATCTAATTGATCCTATATTAACCCGACCC
1 AAAATC-AATTGATCCGATATTGA-CCGACCC
*** * *
456433 AAAATCACCCGACCCGATATTGACCTGAACCG
1 AAAATCAATTGATCCGATATTGACC-G-ACCC
456465 AAAATCAATTGATCCGATAT
1 AAAATCAATTGATCCGATAT
456485 ATTGAACCGA
Statistics
Matches: 65, Mismatches: 16, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
30 2 0.03
31 18 0.28
32 45 0.69
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (30 bp):
AAAATCAATTGATCCGATATTGACCGACCC
Found at i:465878 original size:19 final size:21
Alignment explanation
Indices: 465840--465878 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
465830 AGAGGGTAAG
465840 ATAAGAAGGCGTGAGAGAGAA
1 ATAAGAAGGCGTGAGAGAGAA
*
465861 ATAA-AAGG-GTGAGGGAGA
1 ATAAGAAGGCGTGAGAGAGA
465879 GAAAGAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.41, T:0.10
Consensus pattern (21 bp):
ATAAGAAGGCGTGAGAGAGAA
Found at i:467062 original size:32 final size:31
Alignment explanation
Indices: 467036--467097 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
467026 ATATTTCAAT
467036 TTCATCCCCCAAACTATGACCTATATTCTAAC
1 TTCAT-CCCCAAACTATGACCTATATTCTAAC
* *
467068 TTGATCCTCAAACTATGACCT-TCATTCTAA
1 TTCATCCCCAAACTATGACCTAT-ATTCTAA
467098 ATTTGTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 1 0.04
31 22 0.81
32 4 0.15
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.34
Consensus pattern (31 bp):
TTCATCCCCAAACTATGACCTATATTCTAAC
Found at i:473559 original size:23 final size:23
Alignment explanation
Indices: 473533--473601 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
473523 CACCACAGCT
*
473533 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * **
473556 CGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGAAGTGCCA
* *
473579 CATAGAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
473602 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:474921 original size:64 final size:63
Alignment explanation
Indices: 474817--474938 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 63
474807 CTTATTACCC
* *
474817 ATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGATGCATCGATGCACTCCTT
1 ATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGAG-TGCATCGATGCACTCCTT
** * *
474881 ATGCATCGATGTACCAATTACATTCGATG-TTTCTTCTTTAAAGAGTGCATCGATGCAC
1 ATGCATCGATACACAAATTACATTCGATGTTTTCAT-TTTAAAGAGTGCATCGATGCAC
474939 ATTCAATGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 18 0.35
64 33 0.65
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (63 bp):
ATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGAGTGCATCGATGCACTCCTT
Found at i:476778 original size:19 final size:20
Alignment explanation
Indices: 476742--476779 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
476732 AAACCATTCA
476742 GGGGGGAATCGGTATCCCTT
1 GGGGGGAATCGGTATCCCTT
476762 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
476780 CTGAGCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.21, G:0.42, T:0.24
Consensus pattern (20 bp):
GGGGGGAATCGGTATCCCTT
Found at i:477143 original size:44 final size:44
Alignment explanation
Indices: 477093--477180 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
477083 AATTACTCCC
477093 CCTTACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACT
1 CCTTACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACT
477137 CCTTACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACT
1 CCTTACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACT
477181 TAAAACACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.30, G:0.00, T:0.39
Consensus pattern (44 bp):
CCTTACTTTAACACTTCTCCCATTTATCATTTTAAAAACACACT
Found at i:477868 original size:12 final size:12
Alignment explanation
Indices: 477851--477879 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
477841 GATCTTCGTC
477851 AGCTTCGGGTGA
1 AGCTTCGGGTGA
477863 AGCTTCGGGTGA
1 AGCTTCGGGTGA
477875 AGCTT
1 AGCTT
477880 GTGAAGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (12 bp):
AGCTTCGGGTGA
Found at i:479481 original size:20 final size:20
Alignment explanation
Indices: 479452--479489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
479442 CCCCTTCAAA
*
479452 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
479472 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
479490 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:483310 original size:22 final size:21
Alignment explanation
Indices: 483268--483307 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
483258 TGAGTTGTTT
*
483268 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
483289 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
483308 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:486712 original size:18 final size:18
Alignment explanation
Indices: 486684--486729 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
486674 AGTTGTTGTT
486684 AATTA-TTGTCCTATTAA
1 AATTATTTGTCCTATTAA
486701 AATTATTTGTCCTATTAA
1 AATTATTTGTCCTATTAA
486719 AATTATTTGTC
1 AATTATTTGTC
486730 TTAGTAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (18 bp):
AATTATTTGTCCTATTAA
Found at i:490609 original size:196 final size:198
Alignment explanation
Indices: 490275--490670 Score: 760
Period size: 196 Copynumber: 2.0 Consensus size: 198
490265 AGGTATTTTT
490275 CATTTCATTTTTCAATTCCTAGCATGTTGTGTATCGTTGGCGTTTCGAAATCAATAAAAAATAGA
1 CATTTCATTTTTCAATTCCTAGCATGTTGTGTATCGTTGGCGTTTCGAAATCAATAAAAAATAGA
490340 TATGGATTGGATATTTACCTGTGTTGTGCGAACTCAGATGGAGTCGTGTTGACTCCATTTCATTT
66 TATGGATTGGATATTTACCTGTGTTGTGCGAACTCAGATGGAGTCGTGTTGACTCCATTTCATTT
490405 CCATTCTGATTTCATTGTAGGAAAAGAAGAGTTGAG-AGTAAAT-AATATTTTTAATCAAAACAG
131 CCATTCTGATTTCATTGTAGGAAAAGAAGAGTTGAGTAGTAAATAAATATTTTTAATCAAAACAG
490468 TAG
196 TAG
490471 CATTTCATTTTTCAATTCCTAGCATGTTGTGTATCGTTGGCGTTTCGAAATCAATAAAAAATAGA
1 CATTTCATTTTTCAATTCCTAGCATGTTGTGTATCGTTGGCGTTTCGAAATCAATAAAAAATAGA
490536 TATGGATTGGATATTTACCTGTGTTGTGCGAACTCAGATGGAGTCGTGTTGACTCCATTTCATTT
66 TATGGATTGGATATTTACCTGTGTTGTGCGAACTCAGATGGAGTCGTGTTGACTCCATTTCATTT
490601 CCATTCTGATTTCATTGTAGGAAAAGAAGAGTTGAGATTAGTAAATAAATATTTTTAATCAAAAC
131 CCATTCTGATTTCATTGTAGGAAAAGAAGAGTTGAG--TAGTAAATAAATATTTTTAATCAAAAC
490666 AGTAG
194 AGTAG
490671 AAGGAAAAGA
Statistics
Matches: 196, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
196 166 0.85
199 7 0.04
200 23 0.12
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (198 bp):
CATTTCATTTTTCAATTCCTAGCATGTTGTGTATCGTTGGCGTTTCGAAATCAATAAAAAATAGA
TATGGATTGGATATTTACCTGTGTTGTGCGAACTCAGATGGAGTCGTGTTGACTCCATTTCATTT
CCATTCTGATTTCATTGTAGGAAAAGAAGAGTTGAGTAGTAAATAAATATTTTTAATCAAAACAG
TAG
Found at i:493420 original size:20 final size:21
Alignment explanation
Indices: 493376--493433 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
493366 TGCATGGTAG
493376 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
493400 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
*
493420 TGCACCGATGCACT
1 TGCATCGATGCACT
493434 TCAATGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:494306 original size:27 final size:27
Alignment explanation
Indices: 494232--494306 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
494222 GTCTTTCGGG
*
494232 ATATAGTGGTCCTTCGGGATATATATGTT
1 ATAT-GTGGTCCTTCGGGA-CTATATGTT
*
494261 ATATGTGGTCCTTCGGGACTATGTGTT
1 ATATGTGGTCCTTCGGGACTATATGTT
494288 ATATGTGGTCCTTCGGGAC
1 ATATGTGGTCCTTCGGGAC
494307 ATCTACGTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 26 0.59
28 14 0.32
29 4 0.09
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.39
Consensus pattern (27 bp):
ATATGTGGTCCTTCGGGACTATATGTT
Found at i:497549 original size:20 final size:21
Alignment explanation
Indices: 497505--497562 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
497495 TGCATGGTAG
497505 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
497529 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
*
497549 TGCACCGATGCACT
1 TGCATCGATGCACT
497563 TCAATGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:498433 original size:28 final size:28
Alignment explanation
Indices: 498393--498465 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
498383 TCGGGACATA
498393 GTGGTCCTTCGGGACATATGTGTTATAT
1 GTGGTCCTTCGGGACATATGTGTTATAT
498421 GTGGTCCTTCGGGACATATGTGTTATAT
1 GTGGTCCTTCGGGACATATGTGTTATAT
* *
498449 GTTGTCCTTCAGGACAT
1 GTGGTCCTTCGGGACAT
498466 CTACGTGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38
Consensus pattern (28 bp):
GTGGTCCTTCGGGACATATGTGTTATAT
Found at i:500069 original size:21 final size:21
Alignment explanation
Indices: 500043--500116 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
500033 CCCTACCAAG
500043 GACGAGAAGACTATTCATAAA
1 GACGAGAAGACTATTCATAAA
*
500064 GACGAGAAGACTACTCATAAA
1 GACGAGAAGACTATTCATAAA
*
500085 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACTATTCATAAA
500106 GAC-ATGAAGAC
1 GACGA-GAAGAC
500117 CACTTCGCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (21 bp):
GACGAGAAGACTATTCATAAA
Found at i:500376 original size:6 final size:6
Alignment explanation
Indices: 500365--500394 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
500355 TAACACTTCA
*
500365 TGCATT TGCATT TGCTTT TGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT
500395 ATTATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (6 bp):
TGCATT
Found at i:500421 original size:20 final size:20
Alignment explanation
Indices: 500380--500417 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
500370 TTGCATTTGC
*
500380 TTTTGCATTTGCATTATTAT
1 TTTTGCATTAGCATTATTAT
500400 TTTTGCATTAGCA-TATTA
1 TTTTGCATTAGCATTATTA
500418 ATTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTGCATTAGCATTATTAT
Found at i:502205 original size:6 final size:6
Alignment explanation
Indices: 502185--502220 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
502175 CCTTTTGTAA
502185 TTGCAT TTAGCAT TTGCAT TTGCAT TTGCA- TTGCAT
1 TTGCAT TT-GCAT TTGCAT TTGCAT TTGCAT TTGCAT
502221 ATATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (6 bp):
TTGCAT
Found at i:504334 original size:2 final size:2
Alignment explanation
Indices: 504327--504365 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
504317 ATACCCAACA
504327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
504366 TATGTGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:506496 original size:36 final size:37
Alignment explanation
Indices: 506402--506554 Score: 193
Period size: 37 Copynumber: 4.1 Consensus size: 37
506392 ATGAGATTGG
*
506402 AGCAAAGTTAATCTTAAGCCTTCACCGAAA-AGGAGTGA
1 AGCAAA-TCAATCTTAAGCCTTCACC-AAAGAGGAGTGA
506440 AGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
* * * *
506477 AGCAAA-CCATCTTAAGCCTTCACCAAAAAAGAGAGA
1 AGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
* * *
506513 AGCAAATCAATTTGTAAGCCTTCACCGAAGAGTAGTGA
1 AGCAAATCAATCT-TAAGCCTTCACCAAAGAGGAGTGA
506551 AGCA
1 AGCA
506555 CCACCTTGAG
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
36 35 0.35
37 36 0.36
38 29 0.29
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (37 bp):
AGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
Found at i:506498 original size:73 final size:72
Alignment explanation
Indices: 506412--506571 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 72
506402 AGCAAAGTTA
* * *
506412 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCT-TAAGCCTTCACCAAAGAGGAGTG
1 ATCTTAAGCCTTCACCAAAAAAGAGAGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
506476 AAGCAAACC
66 AAGC--ACC
* * *
506485 ATCTTAAGCCTTCACCAAAAAAGAGAGAAGCAAATCAATTTGTAAGCCTTCACCGAAGAGTAGTG
1 ATCTTAAGCCTTCACCAAAAAAGAGAGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
506550 AAGCACC
66 AAGCACC
* *
506557 ACCTTGAGCCTTCAC
1 ATCTTAAGCCTTCAC
506572 AGAAGAATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 16 0.21
73 37 0.47
74 25 0.32
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (72 bp):
ATCTTAAGCCTTCACCAAAAAAGAGAGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
AAGCACC
Found at i:507396 original size:427 final size:428
Alignment explanation
Indices: 506592--507774 Score: 1811
Period size: 427 Copynumber: 2.8 Consensus size: 428
506582 TGAAGCAAAC
*
506592 CCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
506657 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGAATGATGTTTTCACATGAATTTGGAAA
66 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
506722 TAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAA-TGAAGAATGCGATTTTTAAAATTTCA
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACT-AAGAATGCGATTTTCAAAA-TTCA
* * *
506786 CAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCA
194 CAATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
* * * * *
506851 TCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATG
259 TTTATAAGCCTTTAAAGAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAATG
*
506916 TTTTCACATGAATTTAAAAATGAAAACATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGA
324 TTTTCACATGAATTTAAAAATGAAAACATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGA
506981 ATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
389 ATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
* *
507021 CCATCAGTAAGTATTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * * * *
507086 GATGATAAGTCATTCGGGCCATCCATAAAACATTCGGGTAGGATGTTTTTACATGAATTTGAAAA
66 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
507151 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAA-TCACA
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTCACA
507215 ATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
196 ATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
* * *
507280 TATAAGCCTTTAAATAAATATGATAAGTCCTTCGTGCCATCCATAAAACCTTCGGGTAGAATGTT
261 TATAAGCCTTTAAAGAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTT
* *
507345 TTCACATGAATTTGAAAATGAAAA-ATTGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAA
326 TTCACATGAATTTAAAAATGAAAACA-TGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAA
507409 TGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
390 TGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
*
507448 CCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
507513 GATAATAAGTCCTTTGGGCCATCCATAAGACCTAT-GGGTAGGATGTTTTCACATGAATTTGAAA
66 GATGATAAGTCCTTTGGGCCATCCATAAGACCT-TCGGGTAGGATGTTTTCACATGAATTTGAAA
* * * *
507577 ATG-AAAATGATGTTTGAAGATGATGAAATTTTTGGAAACTAAGAATGCGATTTCCAAAATTTCA
130 ATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAA-TTCA
* **
507641 C-ACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATATTTAAATCCTTCGGGTC
194 CAATTTA-TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTC
* * * * ** * * * * * * * *
507705 ATTTGTGAGTCTCTCGAGCAAGATGATAAATCCTTTGGGTCATCCATAAGATCTTCGGGCAGGAT
258 ATTTATAAGCCTTTAAAGAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAAT
507770 GTTTT
323 GTTTT
507775 TCACCAAGAT
Statistics
Matches: 687, Mismatches: 61, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
426 53 0.08
427 347 0.51
428 113 0.16
429 173 0.25
430 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (428 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTCACA
ATTTATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATT
TATAAGCCTTTAAAGAAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGAATGTT
TTCACATGAATTTAAAAATGAAAACATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAAT
GCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
Found at i:507604 original size:213 final size:214
Alignment explanation
Indices: 506592--507774 Score: 1820
Period size: 215 Copynumber: 5.5 Consensus size: 214
506582 TGAAGCAAAC
*
506592 CCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * * * *
506657 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGAATGATGTTTTCACATGAATTTGGAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
506722 TAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAA-TGAAGAATGCGATTTTTAAAATTTCA
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACT-AAGAATGCGATTTTCAAAATTTCA
*
506786 CAATTTATAAGTCTTTCGGG
195 CAATTTATAAGTCCTTCGGG
*
506806 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
506871 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTAAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
506936 TGAAAACATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCA
131 TGAAAA-ATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCA
507001 CAATTTATAAGTCCTTCGGG
195 CAATTTATAAGTCCTTCGGG
* *
507021 CCATCAGTAAGTATTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
507086 GATGATAAGTCATTCGGGCCATCCATAAAACATTCGGGTAGGATGTTTTTACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
507151 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAA--TCAC
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
507214 AATTTATAAGTCCTTCGGG
196 AATTTATAAGTCCTTCGGG
* * * * **
507233 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTATAAGCCTTTAAATAAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
507298 TATGATAAGTCCTTCGTGCCATCCATAAAACCTTCGGGTAGAATGTTTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
507363 TGAAAAATTGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCA
131 TGAAAAA-TGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCA
507428 CAATTTATAAGTCCTTCGGG
195 CAATTTATAAGTCCTTCGGG
*
507448 CCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
507513 GATAATAAGTCCTTTGGGCCATCCATAAGACCTAT-GGGTAGGATGTTTTCACATGAATTTGAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCT-TCGGGTAGGATGTTTTCACATGAATTTGAAA
* * * *
507577 ATG-AAAATGATGTTTGAAGATGATGAAATTTTTGGAAACTAAGAATGCGATTTCCAAAATTTCA
130 ATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCA
*
507641 C-ACTTAGTAAGTCCTTCGGG
195 CAATTTA-TAAGTCCTTCGGG
* ** * * * * *
507661 CCATCAATAAGTCTTTCGAGCATGATATTTAAATCCTTCGGGTCATTTGTGAGTCTCTCGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * * * * *
507726 GATGATAAATCCTTTGGGTCATCCATAAGATCTTCGGGCAGGATGTTTT
66 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTT
507775 TCACCAAGAT
Statistics
Matches: 896, Mismatches: 65, Indels: 17
0.92 0.07 0.02
Matches are distributed among these distances:
212 151 0.17
213 217 0.24
214 182 0.20
215 345 0.39
216 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (214 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
AATTTATAAGTCCTTCGGG
Found at i:511619 original size:20 final size:19
Alignment explanation
Indices: 511571--511902 Score: 201
Period size: 20 Copynumber: 16.6 Consensus size: 19
511561 ACCCAGTTTC
511571 CAAATTCGCAACGCGAA-T
1 CAAATTCGCAACGCGAAGT
* * *
511589 ATATAAATCGCAACACAGAAGT
1 -CA-AATTCGCAACGC-GAAGT
*
511611 CAAATTCGCAACGCAATAGT
1 CAAATTCGCAACGCGA-AGT
*
511631 CAAATTCACAACGCGATAGT
1 CAAATTCGCAACGCGA-AGT
* *
511651 CAAATTTGCAACACGATAGT
1 CAAATTCGCAACGCGA-AGT
*
511671 CAAATTCGCAACACTGAAGT
1 CAAATTCGCAACGC-GAAGT
511691 CAAATTCGCAACGCGAA-T
1 CAAATTCGCAACGCGAAGT
*
511709 CTGTAAA-TCACAACGCGAATTTGT
1 C---AAATTCGCAACGCGAA---GT
511733 -AAA-TCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAA---GT
* **
511753 -AAA-TCGTAAAACAGAAGT
1 CAAATTCGCAACGC-GAAGT
* * *
511771 CAAATTCGTAACACAGAAAT
1 CAAATTCGCAACGC-GAAGT
511791 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-AGT
* *
511811 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACGC-GAA-GT
* * * *
511832 CAAATTCGTAACACAAAACT
1 CAAATTCGCAACGC-GAAGT
511852 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-AGT
*
511872 CAAATTCACAACGCGAAAGT
1 CAAATTCGCAACGCG-AAGT
511892 CAAATTCGCAA
1 CAAATTCGCAA
511903 AGCGCGTTTA
Statistics
Matches: 257, Mismatches: 36, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
18 4 0.02
19 11 0.04
20 209 0.81
21 31 0.12
22 1 0.00
24 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACGCGAAGT
Found at i:514574 original size:21 final size:21
Alignment explanation
Indices: 514550--514606 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
514540 TCAGGAGGCT
*
514550 CCTCTCATCGTTTAAGAGACC
1 CCTCTCATCGTTCAAGAGACC
* * *
514571 CCTCCCACCGTTCAAGAGGCC
1 CCTCTCATCGTTCAAGAGACC
* *
514592 TCTATCATCGTTCAA
1 CCTCTCATCGTTCAA
514607 TGGGTCCCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (21 bp):
CCTCTCATCGTTCAAGAGACC
Found at i:514624 original size:21 final size:20
Alignment explanation
Indices: 514570--514630 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
514560 TTTAAGAGAC
514570 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** *
514590 CCTCTATCATCGTTCAATG-GG
1 CC-CTCCCACCGTTCAA-GAGG
514611 TCCCTCCCACCGTTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
514631 CCCGATTCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 3 0.10
21 25 0.81
22 3 0.10
ACGTcount: A:0.20, C:0.39, G:0.18, T:0.23
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:516117 original size:66 final size:65
Alignment explanation
Indices: 515958--516133 Score: 239
Period size: 66 Copynumber: 2.6 Consensus size: 65
515948 TGGGGTACAC
515958 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
516022 GAATTA
60 GAATTA
* * *
516028 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTTATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
516092 A
65 A
*
516093 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTTATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
516134 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
64 17 0.17
65 18 0.18
66 39 0.39
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:516213 original size:20 final size:20
Alignment explanation
Indices: 516187--516234 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
516177 GTTGAAGGTA
516187 CAAATTCGCAACGCAAAAGGT
1 CAAATTCGCAACGCAAAA-GT
*
516208 -AAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCAAAAGT
516227 CAAATTCG
1 CAAATTCG
516235 TGTTGTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCAAAAGT
Found at i:518845 original size:24 final size:24
Alignment explanation
Indices: 518794--518845 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
518784 ATCCGAGTAT
** *
518794 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
* *
518818 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
518842 TGAC
1 TGAC
518846 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:519609 original size:16 final size:16
Alignment explanation
Indices: 519586--519626 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
519576 GAAATCATTG
*
519586 AAAAAATTATATAGAA
1 AAAAAATTATATAAAA
* *
519602 ATAAAATTATGTAAAA
1 AAAAAATTATATAAAA
519618 AAAAAATTA
1 AAAAAATTA
519627 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAAAATTATATAAAA
Found at i:519848 original size:21 final size:20
Alignment explanation
Indices: 519782--519955 Score: 117
Period size: 20 Copynumber: 8.7 Consensus size: 20
519772 AACTAAAACC
*
519782 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
* *
519801 TGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTTGAAATTCG
*
519821 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
*
519842 TGTTGCGAATTTGACTATT-G
1 TGTTGCGAATTTGA-AATTCG
* *
519862 CGTTGCGAATTTG-ACTATCG
1 TGTTGCGAATTTGAAAT-TCG
* * ** *
519882 CGTTGCAAATTTGACTTTTG
1 TGTTGCGAATTTGAAATTCG
519902 TGTTGCG-ATTT-ACAGATTCG
1 TGTTGCGAATTTGA-A-ATTCG
* *
519922 CGTTGCGAATTTG-ATTATCG
1 TGTTGCGAATTTGAAAT-TCG
*
519942 CGTTGCGAATTTGA
1 TGTTGCGAATTTGA
519956 CTTATATGTT
Statistics
Matches: 121, Mismatches: 22, Indels: 22
0.73 0.13 0.13
Matches are distributed among these distances:
18 2 0.02
19 16 0.13
20 81 0.67
21 19 0.16
22 3 0.02
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:519848 original size:41 final size:40
Alignment explanation
Indices: 519783--519875 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
519773 ACTAAAACCT
*
519783 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGTGTTGCGAATTCGAAAATCGA
* ** * *
519822 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGAAATTC-GTGTTGCGAATTCGAAAATCGA
519863 GTTGCGAATTTGA
1 GTTGCGAATTTGA
519876 CTATCGCGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 10 0.22
40 6 0.13
41 30 0.65
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:519868 original size:20 final size:20
Alignment explanation
Indices: 519843--519990 Score: 144
Period size: 20 Copynumber: 7.4 Consensus size: 20
519833 GAAATTCAGT
519843 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTATTGC
*
519863 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATTGC
* * *
519883 GTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACTATTGC
*
519903 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TATT-GC
* *
519923 GTTGCGAATTTGATTATCGC
1 GTTGCGAATTTGACTATTGC
519943 GTTGCGAATTTGACTTATAT--
1 GTTGCGAATTTGAC-TAT-TGC
*
519963 GTTGCGAATTTGACT-TCTGG
1 GTTGCGAATTTGACTAT-TGC
519983 GTTGCGAA
1 GTTGCGAA
519991 ATTGGAGATC
Statistics
Matches: 105, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
18 4 0.04
19 7 0.07
20 84 0.80
21 9 0.09
22 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGACTATTGC
Found at i:519896 original size:40 final size:41
Alignment explanation
Indices: 519822--520014 Score: 150
Period size: 40 Copynumber: 4.8 Consensus size: 41
519812 CGAAAATCGA
*
519822 GTTGCGAATTTGA-A-ATTCAGTGTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACAGA-TC-GCGTTGCGAATTTGACTATTGC
* * * *
519863 GTTGCGAATTTGAC-TATCGCGTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACAGATCGCGTTGCGAATTTGACTATTGC
* *
519903 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGATTATCGC
1 GTTGCGAATTTGACAGA-TCGCGTTGCGAATTTGACTATTGC
** ** *
519943 GTTGCGAATTTGACTTAT-ATGTTGCGAATTTGACT-TCTGG
1 GTTGCGAATTTGACAGATCGCGTTGCGAATTTGACTAT-TGC
* * * *
519983 GTTGCGAAATTG-GAGATCGCGATGCAAATTTG
1 GTTGCGAATTTGACAGATCGCGTTGCGAATTTG
520015 TTGGTCATTT
Statistics
Matches: 119, Mismatches: 25, Indels: 17
0.74 0.16 0.11
Matches are distributed among these distances:
38 2 0.02
39 8 0.07
40 85 0.71
41 20 0.17
42 4 0.03
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.38
Consensus pattern (41 bp):
GTTGCGAATTTGACAGATCGCGTTGCGAATTTGACTATTGC
Found at i:519987 original size:60 final size:60
Alignment explanation
Indices: 519802--520014 Score: 202
Period size: 60 Copynumber: 3.5 Consensus size: 60
519792 TTAAATTCGT
* * * *
519802 GTTGCGAATTCGAAAATCGAGTTGCGAATTTGAAATTCA-GTGTTGCGAATTTGACTAT-TGC
1 GTTGCGAATTTGAATATCGCGTTGCGAATTTG-ACTT-ATGTGTTGCGAATTTGACT-TCTGC
* * *
519863 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTTTGTGTTGCG-ATTT-ACAGATTC-GC
1 GTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGAC---TTCTGC
* * *
519923 GTTGCGAATTTGATTATCGCGTTGCGAATTTGACTTATATGTTGCGAATTTGACTTCTGG
1 GTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACTTCTGC
* * * * *
519983 GTTGCGAAATTGGAGATCGCGATGCAAATTTG
1 GTTGCGAATTTGAATATCGCGTTGCGAATTTG
520015 TTGGTCATTT
Statistics
Matches: 126, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
59 7 0.06
60 83 0.66
61 32 0.25
62 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.37
Consensus pattern (60 bp):
GTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACTTCTGC
Found at i:521382 original size:2 final size:2
Alignment explanation
Indices: 521375--521405 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
521365 ATATAATTTC
521375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
521406 ATCATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:522319 original size:2 final size:2
Alignment explanation
Indices: 522312--522363 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
522302 CAAATATTAT
522312 TA TA TA TA TA TA TA TA TA T- 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
522353 TA TA TA TA TA T
1 TA TA TA TA TA T
522364 TAAATAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:536797 original size:49 final size:49
Alignment explanation
Indices: 536716--536819 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
536706 AGCCTGAACT
* * * * * *
536716 ACATCATCGATTTAAGTGATATGTCACGTGTCACATTATCATTTCGAATG
1 ACAT-ATCAATTTAACTGATATGTCACATGTCACATCATCACTTCCAATG
*
536766 ACATATCAATTTAACTGATATG-CTACATGTCACATCATCACTTCCAGTG
1 ACATATCAATTTAACTGATATGTC-ACATGTCACATCATCACTTCCAATG
536815 ACATA
1 ACATA
536820 ATATGTTCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
48 1 0.02
49 41 0.89
50 4 0.09
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (49 bp):
ACATATCAATTTAACTGATATGTCACATGTCACATCATCACTTCCAATG
Found at i:539846 original size:44 final size:44
Alignment explanation
Indices: 539757--539856 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
539747 AGACCAGTAA
* * *
539757 TCACGTAGGTTATGTCACATAGCTTATATCTTATGTTCATGTAT
1 TCACGTAGATCATGTCACATAGCTTATATCTTATGTTCATATAT
*
539801 TCACGTAGATCATGTCACATAGCTTATATCTTGT-TCTCATATAT
1 TCACGTAGATCATGTCACATAGCTTATATCTTATGT-TCATATAT
*
539845 TCACATAGATCA
1 TCACGTAGATCA
539857 CATAGCACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (44 bp):
TCACGTAGATCATGTCACATAGCTTATATCTTATGTTCATATAT
Found at i:545221 original size:21 final size:22
Alignment explanation
Indices: 545183--545252 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 22
545173 CATCGAAGTG
*
545183 CCACATAGAATATCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
545205 CCACATAG-ATGTCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
* * *
545226 CCGCGTAGAATTGTCTCGAAGGA
1 CCACATAGAA-TGTCCCGAAGGA
545249 CCAC
1 CCAC
545253 GTATAACCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.44
22 9 0.22
23 14 0.34
ACGTcount: A:0.33, C:0.29, G:0.23, T:0.16
Consensus pattern (22 bp):
CCACATAGAATGTCCCGAAGGA
Found at i:545245 original size:23 final size:21
Alignment explanation
Indices: 545195--545255 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
545185 ACATAGAATA
*
545195 TCCCGAAGGACCACATAGATG
1 TCCCGAAGGACCACGTAGATG
*
545216 TCCCGAAGGACCGCGTAGAATTG
1 TCCCGAAGGACCACGTAG-A-TG
*
545239 TCTCGAAGGACCACGTA
1 TCCCGAAGGACCACGTA
545256 TAACCCTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
23 17 0.50
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
TCCCGAAGGACCACGTAGATG
Found at i:545454 original size:44 final size:44
Alignment explanation
Indices: 545365--545464 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
545355 AGACCAGTAA
* * *
545365 TCACGTAGGTTATGTCACATAGCTTATATCTTATGTTCATGTAT
1 TCACGTAGATCATGTCACATAGCTTATATCTTATGTTCATATAT
*
545409 TCACGTAGATCATGTCACATAGCTTATATCTTGT-TCTCATATAT
1 TCACGTAGATCATGTCACATAGCTTATATCTTATGT-TCATATAT
*
545453 TCACATAGATCA
1 TCACGTAGATCA
545465 CATAGCACAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (44 bp):
TCACGTAGATCATGTCACATAGCTTATATCTTATGTTCATATAT
Found at i:556229 original size:12 final size:12
Alignment explanation
Indices: 556174--556230 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
556164 AAAAAGAAAT
*
556174 AATATATTTATA
1 AATATATATATA
*
556186 AAGTATAAATATA
1 AA-TATATATATA
*
556199 AATATAAATATA
1 AATATATATATA
556211 AATATATATATA
1 AATATATATATA
*
556223 TATATATA
1 AATATATA
556231 GAATTATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 30 0.75
13 10 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
AATATATATATA
Found at i:556230 original size:6 final size:6
Alignment explanation
Indices: 556182--556228 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
556172 ATAATATATT
* *
556182 TATAAA GTATAAA TATAAA TATAAA TATAAA TATATA TATATA TATA
1 TATAAA -TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATA
556229 TAGAATTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:556371 original size:30 final size:31
Alignment explanation
Indices: 556299--556373 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
556289 GCTAAATATG
556299 AACAAATATGTATAGTTTTGAAATGAACGTT
1 AACAAATATGTATAGTTTTGAAATGAACGTT
556330 AACAAATATGTATAGTTTTGAAATGAACGTT
1 AACAAATATGTATAGTTTTGAAATGAACGTT
*
556361 AA-ATATATGTATA
1 AACAAATATGTATA
556374 TGTAGATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 10 0.23
31 33 0.77
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (31 bp):
AACAAATATGTATAGTTTTGAAATGAACGTT
Found at i:560800 original size:20 final size:20
Alignment explanation
Indices: 560770--560810 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
560760 AGATCATTTT
560770 TATTTTTTTATT-TTTGAAA
1 TATTTTTTTATTCTTTGAAA
560789 TATTTTTCTTATTCTTTGAAA
1 TATTTTT-TTATTCTTTGAAA
560810 T
1 T
560811 CATGATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTTATTCTTTGAAA
Found at i:564299 original size:3 final size:3
Alignment explanation
Indices: 564291--564364 Score: 78
Period size: 3 Copynumber: 24.0 Consensus size: 3
564281 TAATTCATTT
* * *
564291 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
564339 ATA TTA -TA TATA TATA TTA TTTA TTA
1 TTA TTA TTA T-TA T-TA TTA -TTA TTA
564365 AATATTACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 48 0.80
4 10 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:565659 original size:21 final size:20
Alignment explanation
Indices: 565613--565700 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 20
565603 GATTATGACT
* *
565613 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTACCTAA
* *
565633 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTACCTAA
* *
565655 ATCGCAATGCGATTACGT-A
1 ATCGCATTGCGATTACCTAA
*
565674 ATCGCATTGCGATTTACGTAA
1 ATCGCATTGCGA-TTACCTAA
565695 ATCGCA
1 ATCGCA
565701 ATGCAAATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.21
20 11 0.19
21 26 0.46
22 8 0.14
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATTACCTAA
Found at i:565678 original size:19 final size:21
Alignment explanation
Indices: 565641--565704 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
565631 AAATTCGCGT
* *
565641 TGCGATTTTCCTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
565662 TGCGA-TTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
565681 TGCGATTTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
565702 TGC
1 TGC
565705 AAATCTGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.32
20 10 0.27
21 15 0.41
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:566610 original size:24 final size:24
Alignment explanation
Indices: 566583--566636 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
566573 GTATTCGAAA
566583 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
566607 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
566631 TTTGAT
1 TTTGAT
566637 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:568165 original size:189 final size:186
Alignment explanation
Indices: 567848--568223 Score: 725
Period size: 189 Copynumber: 2.0 Consensus size: 186
567838 TAGGGAAAAT
567848 CAATTGACAACGCTGTTAGAAGGTGTTTCCCAGATCTTTTCATGGACTTTGTGGTGTTCATTTGT
1 CAATTGACAACGCTGTTAGAAGGTGTTTCCCAGATCTTTTCATGGACTTTGTGGTGTTCATTTGT
567913 ATAGAATCTAAAATCAAGGTCGTTGGTATAAAAAATCACAAATGGACATACTGGAAGGCTGTAAA
66 ATAGAATCTAAAATCAAGGTCGTTGGTATAAAAAATCACAAATGGACATACTGGAAGGCTGTAAA
567978 AGCTTATCGGGAAGTGGATTTTAATAAGCATATAAACTGTTTAAGACGTGTTTTGC
131 AGCTTATCGGGAAGTGGATTTTAATAAGCATATAAACTGTTTAAGACGTGTTTTGC
568034 CAATTGACAACGCTGTTAGAAGGTGTTTCCCAGATTCTTTTCATGGACTTTGTGGTGTTCATTTG
1 CAATTGACAACGCTGTTAGAAGGTGTTTCCCAGA-TCTTTTCATGGACTTTGTGGTGTTCATTTG
568099 TATAGATATCTAAAATCAAGGTCTGTTGGTATAAAAAATCACAAATGGACATACTGGAAGGCTGT
65 TATAGA-ATCTAAAATCAAGGTC-GTTGGTATAAAAAATCACAAATGGACATACTGGAAGGCTGT
568164 AAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAACTGTTTAAGACGTGTTTTGC
128 AAAAGCTTATCGGGAAGTGGATTTTAATAAGCATATAAACTGTTTAAGACGTGTTTTGC
568223 C
1 C
568224 TCAGTGTTCT
Statistics
Matches: 187, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
186 34 0.18
187 36 0.19
188 16 0.09
189 101 0.54
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (186 bp):
CAATTGACAACGCTGTTAGAAGGTGTTTCCCAGATCTTTTCATGGACTTTGTGGTGTTCATTTGT
ATAGAATCTAAAATCAAGGTCGTTGGTATAAAAAATCACAAATGGACATACTGGAAGGCTGTAAA
AGCTTATCGGGAAGTGGATTTTAATAAGCATATAAACTGTTTAAGACGTGTTTTGC
Found at i:569272 original size:20 final size:20
Alignment explanation
Indices: 569247--569314 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
569237 CAATGCGGAA
*
569247 ATCGCAACGC-GAATATGACT
1 ATCGCAACACGGAA-ATGACT
569267 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
*
569287 ATTGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
569307 ATCGCAAC
1 ATCGCAAC
569315 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.93
21 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:569353 original size:19 final size:19
Alignment explanation
Indices: 569329--569366 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
569319 GAATCGCATT
*
569329 TGCGAAATAAAAATTGCAA
1 TGCGAAATAAAAATCGCAA
*
569348 TGCGAAATGAAAATCGCAA
1 TGCGAAATAAAAATCGCAA
569367 CGAGTGAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.18
Consensus pattern (19 bp):
TGCGAAATAAAAATCGCAA
Found at i:569395 original size:53 final size:53
Alignment explanation
Indices: 569298--569408 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 53
569288 TTGCAACACG
** * * * *
569298 GAAATGACTATCGCAACGAGAGAATCGCATTTGCGAAATAAAAATTGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCATGTGCAAAATAAAAATCGCAACGC
* *
569351 GAAATGAAAATCGCAACGAGTGAATCGCAATGTG-AAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGC-ATGTGCAAAATAAAAATCGCAACGC
569404 GAAAT
1 GAAAT
569409 TAGTTTCGCG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 45 0.92
54 4 0.08
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (53 bp):
GAAATGAAAATCGCAACGAGAGAATCGCATGTGCAAAATAAAAATCGCAACGC
Found at i:569437 original size:20 final size:20
Alignment explanation
Indices: 569412--569544 Score: 223
Period size: 20 Copynumber: 6.7 Consensus size: 20
569402 GCGAAATTAG
569412 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
569432 TTTCGCTTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
569452 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
569472 TTTCGCGTTGC-AATTTCAT
1 TTTCGCGTTGCGATTTTCAT
* *
569491 TTTCGCATTGCGGTTTTCAT
1 TTTCGCGTTGCGATTTTCAT
569511 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
569531 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
569545 AGTCTGTTTG
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 17 0.16
20 87 0.84
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:569558 original size:59 final size:59
Alignment explanation
Indices: 569412--569544 Score: 230
Period size: 59 Copynumber: 2.2 Consensus size: 59
569402 GCGAAATTAG
*
569412 TTTCGCGTTGCGATTTTCATTTTCGCTTTGCGATTTTCATTTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGA-TTTCATTTTCGCATTGCGATTTTCATTTTCGCGTTGCGATTTTCAT
* *
569472 TTTCGCGTTGCAATTTCATTTTCGCATTGCGGTTTTCATTTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTCATTTTCGCATTGCGATTTTCATTTTCGCGTTGCGATTTTCAT
569531 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
569545 AGTCTGTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
59 57 0.83
60 12 0.17
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (59 bp):
TTTCGCGTTGCGATTTCATTTTCGCATTGCGATTTTCATTTTCGCGTTGCGATTTTCAT
Found at i:569719 original size:33 final size:32
Alignment explanation
Indices: 569677--569751 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 32
569667 ATTAGTTTCG
569677 CGTTGCGATTTCATTTTCGCATTGCGATTCA-CT
1 CGTTGCGATTTCA-TTTCGCATTGCGATT-ATCT
569710 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGA-TTTCATTTCGCATTGCGATTATCT
569743 CGTTGCGAT
1 CGTTGCGAT
569752 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
32 2 0.05
33 33 0.82
34 5 0.12
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTCATTTCGCATTGCGATTATCT
Found at i:569736 original size:19 final size:18
Alignment explanation
Indices: 569672--569738 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
569662 GCGAAATTAG
*
569672 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTTCA
569690 TTTTCGCATTGCGA-TTCA
1 -TTTCGCATTGCGATTTCA
*
569708 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
569724 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
569739 ATCTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 3 0.08
18 6 0.15
19 18 0.45
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (18 bp):
TTTCGCATTGCGATTTCA
Found at i:569868 original size:14 final size:14
Alignment explanation
Indices: 569849--569885 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
569839 CATCAATTAA
569849 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
569863 ACAAATCATCTTTT
1 ACAAATCAACATTT
569877 ACAAATCAA
1 ACAAATCAA
569886 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:571750 original size:20 final size:20
Alignment explanation
Indices: 571727--571774 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
571717 GAAACTTAAA
571727 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
571747 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
571767 ATCGCAAC
1 ATCGCAAC
571775 AAGAGAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:571843 original size:20 final size:20
Alignment explanation
Indices: 571818--572002 Score: 249
Period size: 20 Copynumber: 9.6 Consensus size: 20
571808 GCGATTCTTT
* **
571818 CATTGCGATAATCAAATTCG
1 CATTGCGATAGTCATTTTCG
571838 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
571858 CATTGTGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
571878 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
571898 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
571918 CA-TGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
571937 CATTGCGAT--TC----TCT
1 CATTGCGATAGTCATTTTCG
*
571951 CATTGCGATAGTCATTTTCA
1 CATTGCGATAGTCATTTTCG
* *
571971 CGTTACGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
571991 CATTGCGATAGT
1 CATTGCGATAGT
572003 AAACTATTCT
Statistics
Matches: 146, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
14 11 0.08
16 2 0.01
18 2 0.01
19 19 0.13
20 112 0.77
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:571924 original size:113 final size:110
Alignment explanation
Indices: 571782--572002 Score: 252
Period size: 113 Copynumber: 2.0 Consensus size: 110
571772 AACAAGAGAA
**
571782 TCGCAATGCGATTTTCATTTCGCATTGCGAT-TC-TTT-CATTGCGATAATCAAATTCGCATTGC
1 TCGCAATGCGATAGTCATTTCGCATTGCGATATCATTTCCATTGCGAT--TC----TCGCATTGC
* **
571844 GATAGTCATTTTCGCATTGTGATAGTCATTTTCGCATTGCGATAGTCATTT
60 GATAGTCATTTTCACATTACGATAGTCATTTTCGCATTGCGATAGTCATTT
* *
571895 TCGCATTGCGATAGTCATTTTCGCA-TGCGATAGTCATTTTCGCATTGCGATTCTCTCATTGCGA
1 TCGCAATGCGATAGTCA-TTTCGCATTGCGATA-TCA-TTTC-CATTGCGATTCTCGCATTGCGA
*
571959 TAGTCATTTTCACGTTACGATAGTCATTTTCGCATTGCGATAGT
62 TAGTCATTTTCACATTACGATAGTCATTTTCGCATTGCGATAGT
572003 AAACTATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
113 70 0.75
114 7 0.08
115 2 0.02
117 5 0.05
119 9 0.10
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (110 bp):
TCGCAATGCGATAGTCATTTCGCATTGCGATATCATTTCCATTGCGATTCTCGCATTGCGATAGT
CATTTTCACATTACGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:574572 original size:20 final size:20
Alignment explanation
Indices: 574549--574605 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
574539 CGATAGTCAG
*
574549 ATTCTCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
574569 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
574589 AATCGCATTGCGATTTA
1 ATTCGCATTGCGATTTA
574606 GGAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:574615 original size:21 final size:20
Alignment explanation
Indices: 574554--574644 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
574544 GTCAGATTCT
* *
574554 CATTGCGATTTACGTATTCG
1 CATTGCGATTTACGAAATCG
*
574574 CATTGCGATTTACGTAATCG
1 CATTGCGATTTACGAAATCG
*
574594 CATTGCGATTTAGGAAAATCG
1 CATTGCGATTTACG-AAATCG
* **
574615 CAATGCGAATTTGGGAAATCG
1 CATTGCG-ATTTACGAAATCG
*
574636 CAATGCGAT
1 CATTGCGAT
574645 AGTCAGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 34 0.53
21 24 0.38
22 6 0.09
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (20 bp):
CATTGCGATTTACGAAATCG
Found at i:574631 original size:22 final size:21
Alignment explanation
Indices: 574571--574643 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
574561 ATTTACGTAT
* * *
574571 TCGCATTGCG-ATTTACGTAA
1 TCGCAATGCGAATTTAGGAAA
*
574591 TCGCATTGCG-ATTTAGGAAAA
1 TCGCAATGCGAATTTAGG-AAA
*
574612 TCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATTTAGGAAA
574633 TCGCAATGCGA
1 TCGCAATGCGA
574644 TAGTCAGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
20 16 0.34
21 25 0.53
22 6 0.13
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGGAAA
Found at i:578292 original size:22 final size:22
Alignment explanation
Indices: 578245--578295 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
578235 TACATCTTCG
* *
578245 AAGATGATAGATTTTCTCTCCG
1 AAGATGATAGATTCTCTCTCCA
* *
578267 AAGATGATAGATTCTCTTTTCA
1 AAGATGATAGATTCTCTCTCCA
578289 AAGATGA
1 AAGATGA
578296 AAGCTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (22 bp):
AAGATGATAGATTCTCTCTCCA
Found at i:579025 original size:46 final size:46
Alignment explanation
Indices: 578953--579377 Score: 703
Period size: 46 Copynumber: 9.3 Consensus size: 46
578943 CTATTTCCTA
* *
578953 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAACAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
578999 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* **
579045 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAATGTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
**
579091 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTATGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
579137 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
579182 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
579227 CATCTATAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
579273 CATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
579319 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
579364 CATCTGTAAGCCCT
1 CATCTGTAAGCCCT
579378 ACAATGCAAG
Statistics
Matches: 355, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
45 109 0.31
46 246 0.69
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
Found at i:579262 original size:182 final size:183
Alignment explanation
Indices: 578953--579377 Score: 735
Period size: 182 Copynumber: 2.3 Consensus size: 183
578943 CTATTTCCTA
*
578953 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAACAACCTTTGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAA-AACCTTCGGGTCATCTGTAAGCCCTTCAGT
* *
579018 GCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAT
65 GCATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAAC
* * *
579083 GTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTATGGT
130 CTTCGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAAACCTTAGGGT
*
579137 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
*
579202 CATGATGTTTTC-AAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCTTGATGTTTTCAAAAACC
66 CATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAACC
*
579266 TTCGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAAACCTTCGGGT
131 TTCGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAAACCTTAGGGT
* *
579319 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCT
579378 ACAATGCAAG
Statistics
Matches: 229, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 154 0.67
183 41 0.18
184 34 0.15
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (183 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAACC
TTCGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAAACCTTAGGGT
Found at i:579556 original size:6 final size:6
Alignment explanation
Indices: 579545--579625 Score: 74
Period size: 6 Copynumber: 13.0 Consensus size: 6
579535 TAGTTCATTT
** * *
579545 TTATTA TTATTA AAATTA TTATTA TTATTA TTATAA ATATTA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
*
579593 TTAATA TTA-TA TATATATA TATATTA TTTATTA
1 TTATTA TTATTA T-TAT-TA T-TATTA -TTATTA
579626 AATATTACAA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
5 3 0.05
6 44 0.71
7 7 0.11
8 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTATTA
Found at i:579565 original size:15 final size:15
Alignment explanation
Indices: 579545--579625 Score: 74
Period size: 15 Copynumber: 5.2 Consensus size: 15
579535 TAGTTCATTT
* **
579545 TTATTATTATTAAAA
1 TTATTAATATTATTA
*
579560 TTATTATTATTATTA
1 TTATTAATATTATTA
*
579575 TTATAAATATTATTA
1 TTATTAATATTATTA
579590 TTATTAATATTA-TA
1 TTATTAATATTATTA
579604 TATATATATATATTATTTA
1 T-TAT-TA-ATATTA-TTA
579623 TTA
1 TTA
579626 AATATTACAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
14 3 0.05
15 40 0.71
16 2 0.04
17 6 0.11
18 2 0.04
19 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTAATATTATTA
Found at i:579571 original size:21 final size:21
Alignment explanation
Indices: 579545--579632 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 21
579535 TAGTTCATTT
579545 TTATTATTATTA-AAATTATTA
1 TTATTATTATTATAAA-TATTA
579566 TTATTATTATTATAAATATTA
1 TTATTATTATTATAAATATTA
* *
579587 TTATTATTAATAT-TATATATA
1 TTATTATTATTATAAATAT-TA
579608 TATATATATTATTTATTAAATATTA
1 T-TAT-TATTA-TTA-TAAATATTA
579633 CAAAGCCCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.07
21 32 0.57
22 6 0.11
23 5 0.09
24 2 0.04
25 3 0.05
26 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTATTATTATAAATATTA
Done.