Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_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: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 13
Found at i:478834 original size:83 final size:83
Alignment explanation
Indices: 478686--479413 Score: 1341
Period size: 83 Copynumber: 8.8 Consensus size: 83
478676 GGTTTCATAT
* *
478686 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCT-TCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCT-CAA
* *
478750 ATTCAATAACTGGTTTTAC
65 ATTCAATGATTGGTTTTAC
*
478769 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAGCACATTCATCTCTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
478834 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* * *
478852 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
478917 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
*
478935 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479000 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
479018 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479083 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
479101 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479166 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
479184 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479249 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* *
479267 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479332 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
479350 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAA
479414 GCTAATGTTT
Statistics
Matches: 628, Mismatches: 16, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
83 627 1.00
84 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
TTCAATGATTGGTTTTAC
Found at i:478960 original size:166 final size:166
Alignment explanation
Indices: 478593--479413 Score: 1367
Period size: 166 Copynumber: 4.9 Consensus size: 166
478583 GGTTTTATAT
* * * *
478593 CAAACCAAATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTAGCACATTCCTCT-TCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCT-CAA
* *
478657 ATTCAATAACTGGTTCTGTGGTTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
65 ATTC---AA-T-G--AT-TGGTTT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
* * * *
478722 AGATGCTATTAGCACATTCCTCT-TCCAAATTCAATAACTGGTTTTAC
120 AGATGCTATGAGCACATTCATCTCT-CAAATTCAATGATTGGTTTTAC
*
478769 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAGCACATTCATCTCTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
* *
478834 TTCAATGATTGGTTTTACCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGA
66 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
478899 GCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
131 GCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
*
478935 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479000 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
479065 GCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
131 GCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
479101 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479166 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
479231 GCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
131 GCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
* *
479267 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479332 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
479397 GCACATTCATCTCTCAA
131 GCACATTCATCTCTCAA
479414 GCTAATGTTT
Statistics
Matches: 622, Mismatches: 21, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
166 548 0.88
167 1 0.00
168 6 0.01
169 1 0.00
171 1 0.00
172 1 0.00
173 2 0.00
176 61 0.10
177 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (166 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
Found at i:479041 original size:249 final size:249
Alignment explanation
Indices: 478593--479413 Score: 1374
Period size: 249 Copynumber: 3.3 Consensus size: 249
478583 GGTTTTATAT
* * *
478593 CAAACCAAATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTAGCACATTCCTCT-TCCAA
1 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCT-CAA
* *
478657 ATTCAATAACTGGTTCTGTGGTTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
65 ATTC---AA-T-G--AT-TGGTTT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
* * * * *
478722 AGATGCTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTTTACCAAACCAGATCAGATAAC
120 AGATGCTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAAC
*
478787 TCAAAGAACACTTCCAGAAGATACTATGAGCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
185 TCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
* *
478852 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
478917 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
478982 GCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
479047 TTCCAGAAGATGCTATGAGCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
*
479101 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
1 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
479166 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
479231 GCACATTCATCTCTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
131 GCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
* *
479296 TTCCAGAAAATGCTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTTTAC
196 TTCCAGAAGATGCTATGAGCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
*
479350 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAA
1 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAA
479414 GCTAATGTTT
Statistics
Matches: 543, Mismatches: 18, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
249 469 0.86
251 6 0.01
252 1 0.00
254 1 0.00
255 1 0.00
256 2 0.00
259 62 0.11
260 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (249 bp):
CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTCTCAAA
TTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATGAGCACATTCATCTCTCAAATTCAATGATTGGTTTTAC
Found at i:480562 original size:10 final size:10
Alignment explanation
Indices: 480549--480605 Score: 66
Period size: 9 Copynumber: 5.9 Consensus size: 10
480539 TTGACCCCCC
480549 TTTTTCTTCT
1 TTTTTCTTCT
480559 TTTTTC-TCT
1 TTTTTCTTCT
*
480568 TTTTTTTTC-
1 TTTTTCTTCT
480577 TTTTTC-TCT
1 TTTTTCTTCT
*
480586 TTTTTTTTCT
1 TTTTTCTTCT
480596 TTTTCTCTTC
1 TTTT-TCTTC
480606 AAGCATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 2 0.05
9 18 0.46
10 15 0.38
11 4 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:480569 original size:18 final size:18
Alignment explanation
Indices: 480549--480604 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
480539 TTGACCCCCC
*
480549 TTTTTCTTCTTTTTTCTCT
1 TTTTTTTTC-TTTTTCTCT
480568 TTTTTTTTCTTTTTCTCT
1 TTTTTTTTCTTTTTCTCT
480586 TTTTTTTTCTTTTTCTCT
1 TTTTTTTTCTTTTTCTCT
480604 T
1 T
480605 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 28 0.78
19 8 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTTCTTTTTCTCT
Found at i:487950 original size:15 final size:15
Alignment explanation
Indices: 487927--487958 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
487917 TGAAATGAAT
487927 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
487942 AATGCATGTATGCAA
1 AATGAATGTATGCAA
487957 AA
1 AA
487959 AGGTATTGAT
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:492946 original size:18 final size:19
Alignment explanation
Indices: 492925--492960 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
492915 GGTTTGTTGG
492925 GTTGTTGTT-CTCTGTTTT
1 GTTGTTGTTGCTCTGTTTT
*
492943 GTTGTTTTTGCTCTGTTT
1 GTTGTTGTTGCTCTGTTT
492961 CTGTCTCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (19 bp):
GTTGTTGTTGCTCTGTTTT
Found at i:493408 original size:3 final size:3
Alignment explanation
Indices: 493390--493438 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
493380 TGTAATATTA
* * * *
493390 AAT AAT ATAT ATT AAT AAT AAT AAT CAT TAT AAT TAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
493436 AAT
1 AAT
493439 TATTATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:493431 original size:9 final size:9
Alignment explanation
Indices: 493382--493445 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
493372 TTGGGTTTTG
493382 TAAT-ATTA
1 TAATAATTA
493390 -AATAATATA
1 TAATAAT-TA
* *
493399 TATTAATAA
1 TAATAATTA
*
493408 TAATAATCA
1 TAATAATTA
*
493417 TTATAATTA
1 TAATAATTA
*
493426 TAATAATAA
1 TAATAATTA
*
493435 TAATTATTA
1 TAATAATTA
493444 TA
1 TA
493446 TAAATAACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
7 3 0.07
8 2 0.05
9 33 0.77
10 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATAATTA
Found at i:493451 original size:21 final size:21
Alignment explanation
Indices: 493390--493452 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 21
493380 TGTAATATTA
*
493390 AATAA-TA-TATATTAATAAT
1 AATAATTATTATATAAATAAT
*
493409 AATAATCATTATAATTATAATAAT
1 AATAATTATTAT-A-TA-AATAAT
493433 AATAATTATTATATAAATAA
1 AATAATTATTATATAAATAA
493453 CATTAAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 8 0.22
22 3 0.08
23 2 0.06
24 17 0.47
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATTATTATATAAATAAT
Found at i:495928 original size:20 final size:20
Alignment explanation
Indices: 495905--496032 Score: 184
Period size: 20 Copynumber: 6.3 Consensus size: 20
495895 AATTTGTAAA
495905 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
495925 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
495945 TCGCAACACAGAATTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
495965 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
495985 TTGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
496005 TCGCAACATATAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
496026 TCGCAAC
1 TCGCAAC
496033 TGTATTTCAA
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
20 86 0.87
21 13 0.13
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:496065 original size:20 final size:19
Alignment explanation
Indices: 495999--496071 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
495989 AACACAAAAG
*
495999 TCAAATTCGCAACATATAATT
1 TCAAATTCGCAAC-TGT-ATT
496020 TCAAATTCGCAACTGTATT
1 TCAAATTCGCAACTGTATT
496039 TCAAATTCGCAACTCG-ATTT
1 TCAAATTCGCAACT-GTA-TT
*
496059 TCGAATTCGCAAC
1 TCAAATTCGCAAC
496072 ACGAATTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.38
20 17 0.35
21 13 0.27
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTGTATT
Found at i:496088 original size:19 final size:19
Alignment explanation
Indices: 496064--496110 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
496054 GATTTTCGAA
496064 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
496083 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
496101 TTCGCAACAC
1 TTCGCAACAC
496111 ATATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:498834 original size:20 final size:20
Alignment explanation
Indices: 498809--498851 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
498799 TCTAAGAGCC
*
498809 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
498829 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
498849 CAT
1 CAT
498852 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:506476 original size:355 final size:355
Alignment explanation
Indices: 505815--506520 Score: 1358
Period size: 355 Copynumber: 2.0 Consensus size: 355
505805 TTTGACGAGC
505815 AAATTACTGGGGAGAAACGATTACTTGATCTAAATGAAATAGAAGAGTTTCGAGTGCAAGCATAT
1 AAATTACTGGGGAGAAACGATTACTTGATCTAAATGAAATAGAAGAGTTTCGAGTGCAAGCATAT
505880 GAAAATGCCAAGCTCTACAAGGAAAAAACCAAAAAGTGGCACAACAGAATGCTTTTGCCACGGTA
66 GAAAATGCCAAGCTCTACAAGGAAAAAACCAAAAAGTGGCACAACAGAATGCTTTTGCCACGGTA
505945 ATTTCATATGGGTCAGAAAGTACTGTTGTTCAATTCTAGGCTCAAGCTCTTCCCAGGCAAATTAA
131 ATTTCATATGGGTCAGAAAGTACTGTTGTTCAATTCTAGGCTCAAGCTCTTCCCAGGCAAATTAA
*
506010 AGTCACGCTGGTCTGGACCATTTGAAGTTCACCATGTTTACCCTTATGGTGCTGTTGATATCAAG
196 AGTCACGCTGGTCTGGACCATTTGAAGTTCACCATGTTTACCCTTATAGTGCTGTTGATATCAAG
*
506075 AACCTGGATGATGGATCCATCTTTAAAGTCAATGGCCAGCGCCTAAAGGCTTATCAAGGAGTCCC
261 AACCTGGACGATGGATCCATCTTTAAAGTCAATGGCCAGCGCCTAAAGGCTTATCAAGGAGTCCC
506140 ACCTGCACGTGACAAGTCGGCGTTGCGCCT
326 ACCTGCACGTGACAAGTCGGCGTTGCGCCT
*
506170 AAATTGCTGGGGAGAAACGATTACTTGATCTAAATGAAATAGAAGAGTTTCGAGTGCAAGCATAT
1 AAATTACTGGGGAGAAACGATTACTTGATCTAAATGAAATAGAAGAGTTTCGAGTGCAAGCATAT
*
506235 GAAAATGCCAAGCTCTACAAGGAAAAAACCAAAAAGTGGCACGACAGAATGCTTTTGCCACGGTA
66 GAAAATGCCAAGCTCTACAAGGAAAAAACCAAAAAGTGGCACAACAGAATGCTTTTGCCACGGTA
506300 ATTTCATATGGGTCAGAAAGTACTGTTGTTCAATTCTAGGCTCAAGCTCTTCCCAGGCAAATTAA
131 ATTTCATATGGGTCAGAAAGTACTGTTGTTCAATTCTAGGCTCAAGCTCTTCCCAGGCAAATTAA
506365 AGTCACGCTGGTCTGGACCATTTGAAGTTCACCATGTTTACCCTTATAGTGCTGTTGATATCAAG
196 AGTCACGCTGGTCTGGACCATTTGAAGTTCACCATGTTTACCCTTATAGTGCTGTTGATATCAAG
* *
506430 AACCTGGACGATGGATCCATCTTTAAAGTCAATGGCCAGTGCCTAAAGGCTTATCAAGGAGTCTC
261 AACCTGGACGATGGATCCATCTTTAAAGTCAATGGCCAGCGCCTAAAGGCTTATCAAGGAGTCCC
506495 ACCTGCACGTGACAAGTCGGCGTTGC
326 ACCTGCACGTGACAAGTCGGCGTTGC
506521 TCTTGCAAGA
Statistics
Matches: 345, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
355 345 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (355 bp):
AAATTACTGGGGAGAAACGATTACTTGATCTAAATGAAATAGAAGAGTTTCGAGTGCAAGCATAT
GAAAATGCCAAGCTCTACAAGGAAAAAACCAAAAAGTGGCACAACAGAATGCTTTTGCCACGGTA
ATTTCATATGGGTCAGAAAGTACTGTTGTTCAATTCTAGGCTCAAGCTCTTCCCAGGCAAATTAA
AGTCACGCTGGTCTGGACCATTTGAAGTTCACCATGTTTACCCTTATAGTGCTGTTGATATCAAG
AACCTGGACGATGGATCCATCTTTAAAGTCAATGGCCAGCGCCTAAAGGCTTATCAAGGAGTCCC
ACCTGCACGTGACAAGTCGGCGTTGCGCCT
Found at i:506898 original size:13 final size:13
Alignment explanation
Indices: 506877--506911 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
506867 CCCACTTACT
506877 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
506890 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
506903 TTTCACTTT
1 TTTCACTTT
506912 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:509500 original size:20 final size:20
Alignment explanation
Indices: 509475--509517 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
509465 TCTAAGAGCC
*
509475 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
509495 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
509515 CAT
1 CAT
509518 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:510819 original size:6 final size:6
Alignment explanation
Indices: 510808--510842 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
510798 AACCAAAAGG
* *
510808 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
510843 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:510832 original size:18 final size:18
Alignment explanation
Indices: 510809--510849 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
510799 ACCAAAAGGA
*
510809 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
510827 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
510845 AATCA
1 AATCA
510850 CAACCGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:511129 original size:20 final size:20
Alignment explanation
Indices: 511104--511181 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
511094 GCGATTGTTA
*
511104 CGAAAGTTAAATTCGCAACG
1 CGAAAGTCAAATTCGCAACG
*
511124 CGAAAGTCAAATTCACAACG
1 CGAAAGTCAAATTCGCAACG
*
511144 TGAAAGTCAAATTCGCAACG
1 CGAAAGTCAAATTCGCAACG
* *
511164 CGAAAATCAAAATCGCAA
1 CGAAAGTCAAATTCGCAA
511182 ACTGAAAATC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAACG
Found at i:511223 original size:20 final size:20
Alignment explanation
Indices: 511198--511280 Score: 94
Period size: 20 Copynumber: 4.2 Consensus size: 20
511188 AATCGTAACA
511198 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* * **
511218 CGAATTTAATTTTAACGTTG
1 CGAATTTGACTTTCGCGTTG
* **
511238 CGAATTTGACTATCGCAATG
1 CGAATTTGACTTTCGCGTTG
*
511258 CGAATTTGACTTTGGCGTTG
1 CGAATTTGACTTTCGCGTTG
511278 CGA
1 CGA
511281 TTGCGAATTT
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:511343 original size:20 final size:20
Alignment explanation
Indices: 511318--511361 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
511308 AATTGCAATG
*
511318 CGAATTTGACTTTCGCGTTA
1 CGAATTTAACTTTCGCGTTA
*
511338 CGAATTTAACTTTCGCGTTG
1 CGAATTTAACTTTCGCGTTA
511358 CGAA
1 CGAA
511362 AGTGTACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
CGAATTTAACTTTCGCGTTA
Found at i:512962 original size:21 final size:21
Alignment explanation
Indices: 512938--513032 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
512928 GCGGGACCTA
* *
512938 TTGAATGATGACAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* *
512959 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* * *
512980 TTCAATGATGAGAGGAGCCTC
1 TTGAACGATGAGAGGGGCCTC
*
513001 TTGAACGAT-AGGAGGCGCCTC
1 TTGAACGATGA-GAGGGGCCTC
513022 TTGAACGATGA
1 TTGAACGATGA
513033 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (21 bp):
TTGAACGATGAGAGGGGCCTC
Found at i:512987 original size:42 final size:42
Alignment explanation
Indices: 512914--513032 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
512904 GTGAATCGGG
* * * * *
512914 CTCTTGAACGGCGGGCGGGACCTATTGAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGACAGGAGC
* *
512956 CTCTTGAACGGTGGGAGGGGCCTCTTCAATGATGAGAGGAGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGACAGGAGC
* * * *
512998 CTCTTGAACGATAGGAGGCGCCTCTTGAACGATGA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGA
513033 TAGGTGCATC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGACAGGAGC
Found at i:513195 original size:12 final size:12
Alignment explanation
Indices: 513176--513222 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
513166 AGGCCGCTGA
513176 AAATAAATTAAT
1 AAATAAATTAAT
* *
513188 ACATAAATCAAT
1 AAATAAATTAAT
*
513200 AAATAAATAAAT
1 AAATAAATTAAT
513212 AAATAAGATTA
1 AAATAA-ATTA
513223 TTTGCATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 26 0.90
13 3 0.10
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:513206 original size:4 final size:4
Alignment explanation
Indices: 513176--513217 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
513166 AGGCCGCTGA
* * *
513176 AAAT AAAT TAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
513218 GATTATTTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:515200 original size:21 final size:21
Alignment explanation
Indices: 515176--515222 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
515166 TTAAATTCGG
515176 AACGCGAAAA-ATGAAAATCGC
1 AACGCGAAAATA-GAAAATCGC
* *
515197 AACGCGAAACTAGAAAATCTC
1 AACGCGAAAATAGAAAATCGC
515218 AACGC
1 AACGC
515223 AAATATCGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (21 bp):
AACGCGAAAATAGAAAATCGC
Found at i:515280 original size:20 final size:20
Alignment explanation
Indices: 515255--515297 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
515245 AATTGTGTTA
515255 CGATTTTCATTTTCGCGTTG
1 CGATTTTCATTTTCGCGTTG
*
515275 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGCGTTG
515295 CGA
1 CGA
515298 ATTTAAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.49
Consensus pattern (20 bp):
CGATTTTCATTTTCGCGTTG
Found at i:515308 original size:20 final size:20
Alignment explanation
Indices: 515265--515308 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
515255 CGATTTTCAT
* * *
515265 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
515285 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
515305 TTTC
1 TTTC
515309 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:515848 original size:20 final size:20
Alignment explanation
Indices: 515823--515948 Score: 198
Period size: 20 Copynumber: 6.3 Consensus size: 20
515813 TAAACGCTCT
*
515823 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTTTGTG
*
515843 TTGCGAATTTGACTTTTGTA
1 TTGCGAATTTGACTTTTGTG
515863 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
515883 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
*
515903 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
* * *
515923 TTGCAAATTTGACTTATGTA
1 TTGCGAATTTGACTTTTGTG
515943 TTGCGA
1 TTGCGA
515949 TTTACAAATT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:515966 original size:60 final size:60
Alignment explanation
Indices: 515823--515968 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 60
515813 TAAACGCTCT
* * * * * *
515823 TTGCGAATTTGAC-TTATGTGTTGCGAATTTGACTTTTGTATTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACATT-CGCGTTGCGAATTTGACTTCTGTATTGCAAATTTGACTTATGTA
* * * *
515883 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCAAATTTGACTTATGTA
1 TTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCTGTATTGCAAATTTGACTTATGTA
515943 TTGCG-ATTT-ACAAATTCGCGTTGCGA
1 TTGCGAATTTGAC--ATTCGCGTTGCGA
515969 TTTACATAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.03
59 4 0.05
60 67 0.89
61 2 0.03
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (60 bp):
TTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCTGTATTGCAAATTTGACTTATGTA
Found at i:515968 original size:20 final size:20
Alignment explanation
Indices: 515943--515985 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
515933 GACTTATGTA
515943 TTGCGATTTACA-AATTCGCG
1 TTGCGATTTACATAA-TCGCG
515963 TTGCGATTTACATAATCGCG
1 TTGCGATTTACATAATCGCG
515983 TTG
1 TTG
515986 TGAATTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACATAATCGCG
Found at i:521780 original size:95 final size:95
Alignment explanation
Indices: 521617--521809 Score: 386
Period size: 95 Copynumber: 2.0 Consensus size: 95
521607 AGAATTTGCC
521617 GATATGCCTCATCTCGGTGACTATGAATATTACTCATCAATAAATAATGGTGAGTTATATTTAGG
1 GATATGCCTCATCTCGGTGACTATGAATATTACTCATCAATAAATAATGGTGAGTTATATTTAGG
521682 CATGGAGTTTTCAAGCAAAGAAGAAGCGGT
66 CATGGAGTTTTCAAGCAAAGAAGAAGCGGT
521712 GATATGCCTCATCTCGGTGACTATGAATATTACTCATCAATAAATAATGGTGAGTTATATTTAGG
1 GATATGCCTCATCTCGGTGACTATGAATATTACTCATCAATAAATAATGGTGAGTTATATTTAGG
521777 CATGGAGTTTTCAAGCAAAGAAGAAGCGGT
66 CATGGAGTTTTCAAGCAAAGAAGAAGCGGT
521807 GAT
1 GAT
521810 GGCTATAAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 98 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (95 bp):
GATATGCCTCATCTCGGTGACTATGAATATTACTCATCAATAAATAATGGTGAGTTATATTTAGG
CATGGAGTTTTCAAGCAAAGAAGAAGCGGT
Found at i:525845 original size:29 final size:29
Alignment explanation
Indices: 525800--525878 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
525790 TACTACTACG
525800 GGTGTTAGATCGAGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTGACC
*
525829 GGTGTTAGATCGGGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTGACC
*
525858 GGTGTTAGATCGATAAATATA
1 GGTGTTAGATCGAGAAATATA
525879 CCGATCACCG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAATCTGACC
Found at i:548017 original size:3 final size:3
Alignment explanation
Indices: 548009--548054 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
547999 TTTTACCCAC
*
548009 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
548055 AATATATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:548081 original size:14 final size:15
Alignment explanation
Indices: 548053--548087 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
548043 TTATTATTAT
548053 TAAATATATATTAAA
1 TAAATATATATTAAA
*
548068 TAAATCTATA-TAAA
1 TAAATATATATTAAA
548082 TAAATA
1 TAAATA
548088 ATTACAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:548652 original size:14 final size:14
Alignment explanation
Indices: 548629--548659 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
548619 AGAAACAAAA
548629 AAAAAAGAAGAAGG
1 AAAAAAGAAGAAGG
*
548643 AAAAAGGAAGAAGG
1 AAAAAAGAAGAAGG
548657 AAA
1 AAA
548660 GACTTACCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAGAAGG
Found at i:549523 original size:13 final size:13
Alignment explanation
Indices: 549507--549552 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
549497 ATATAATAAA
549507 TAAATATTTATTT
1 TAAATATTTATTT
*
549520 TAAATAAATTATTT
1 TAAAT-ATTTATTT
549534 T-AATATTTATTT
1 TAAATATTTATTT
*
549546 TTAATAT
1 TAAATAT
549553 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:550226 original size:22 final size:22
Alignment explanation
Indices: 550184--550226 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
550174 TTCATATATT
*
550184 TAATTTTTAATTCTTTCTTTTC
1 TAATTTTTAATTCTTTATTTTC
*
550206 TAATTTTTTATT-TATTATTTT
1 TAATTTTTAATTCT-TTATTTT
550227 TATAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TAATTTTTAATTCTTTATTTTC
Found at i:560880 original size:7 final size:7
Alignment explanation
Indices: 560868--560966 Score: 94
Period size: 7 Copynumber: 13.9 Consensus size: 7
560858 ATTATGCTTG
560868 AAGAAAA
1 AAGAAAA
560875 AAGAAAA
1 AAGAAAA
*
560882 AAGAAAG
1 AAGAAAA
*
560889 AA-AAGA
1 AAGAAAA
560895 AAGAAAA
1 AAGAAAA
*
560902 TAGAAAA
1 AAGAAAA
560909 AAGAAAGA
1 AAGAAA-A
560917 ATAGAAAA
1 A-AGAAAA
560925 AAGAAAAAA
1 AAG--AAAA
560934 AAGAAAA
1 AAGAAAA
**
560941 AAGAGGA
1 AAGAAAA
*
560948 AA-AAAG
1 AAGAAAA
560954 AAGAAAA
1 AAGAAAA
560961 AAGAAA
1 AAGAAA
560967 GGGGGTCATG
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
6 7 0.09
7 51 0.69
8 4 0.05
9 12 0.16
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
AAGAAAA
Found at i:560892 original size:9 final size:8
Alignment explanation
Indices: 560871--560966 Score: 79
Period size: 9 Copynumber: 11.2 Consensus size: 8
560861 ATGCTTGAAG
560871 AAAAAAG-
1 AAAAAAGA
560878 AAAAAAGA
1 AAAAAAGA
560886 AAGAAAAGA
1 AA-AAAAGA
*
560895 AAGAAAATA
1 AA-AAAAGA
560904 GAAAAAAGA
1 -AAAAAAGA
*
560913 AAGAATAG-
1 AA-AAAAGA
560921 AAAAAAGAA
1 AAAAAAG-A
560930 AAAAAAGA
1 AAAAAAGA
*
560938 AAAAAGAGG
1 AAAAA-AGA
560947 AAAAAAGAA
1 AAAAAAG-A
560956 GAAAAAAGA
1 -AAAAAAGA
560965 AA
1 AA
560967 GGGGGTCATG
Statistics
Matches: 74, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
7 11 0.15
8 16 0.22
9 38 0.51
10 9 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:560894 original size:16 final size:16
Alignment explanation
Indices: 560868--560966 Score: 89
Period size: 16 Copynumber: 6.1 Consensus size: 16
560858 ATTATGCTTG
560868 AAGAAAAAAG-AA-AA
1 AAGAAAAAAGAAAGAA
560882 AAGAAAGAAAAGAAAGAAA
1 AAG-AA-AAAAGAAAG-AA
560901 ATAGAAAAAAGAAAGAA
1 A-AGAAAAAAGAAAGAA
* *
560918 TAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAGAA
560934 AAGAAAAAAGAGGAA-AA
1 AAGAAAAAAGA--AAGAA
*
560951 AAGAAGAAA-AAAGAA
1 AAGAAAAAAGAAAGAA
560966 A
1 A
560967 GGGGGTCATG
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
14 5 0.07
15 5 0.07
16 30 0.42
17 14 0.19
18 11 0.15
19 5 0.07
20 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAGAAAAAAGAAAGAA
Found at i:560900 original size:27 final size:26
Alignment explanation
Indices: 560871--560967 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 26
560861 ATGCTTGAAG
560871 AAAAAAGAAAAAAGAAAGAAAAGAAA
1 AAAAAAGAAAAAAGAAAGAAAAGAAA
* *
560897 GAAAATAGAAAAAAGAAAGAATAGAAA
1 -AAAAAAGAAAAAAGAAAGAAAAGAAA
*
560924 AAAGAA-AAAAAAGAAA-AAAGAGGAAA
1 AAAAAAGAAAAAAGAAAGAAA-A-GAAA
*
560950 AAAGAAGAAAAAAGAAAG
1 AAAAAAGAAAAAAGAAAG
560968 GGGGTCATGG
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
24 2 0.03
25 11 0.18
26 14 0.23
27 34 0.56
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (26 bp):
AAAAAAGAAAAAAGAAAGAAAAGAAA
Found at i:561302 original size:16 final size:16
Alignment explanation
Indices: 561276--561320 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
561266 TTTGAATACA
*
561276 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
561293 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
561308 ATTCAATTTATTT
1 ATTCAATTTATTT
561321 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:562239 original size:83 final size:83
Alignment explanation
Indices: 562100--562492 Score: 700
Period size: 83 Copynumber: 4.7 Consensus size: 83
562090 CATTAACTGA
*
562100 AAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
*
562163 GAACCAATCATTGAATTTAG
64 GAACCAATCATTGAATTTGG
* *
562183 AAGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
562248 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
562266 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
562331 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
562349 AAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
562414 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTGG
*
562432 AAGATGAATGTGCTCATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
562493 TAGGAAATAC
Statistics
Matches: 301, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
83 296 0.98
84 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTGG
Found at i:563653 original size:116 final size:113
Alignment explanation
Indices: 563224--563867 Score: 918
Period size: 114 Copynumber: 5.6 Consensus size: 113
563214 ATTCAAATCT
* *
563224 ATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * * *
563289 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TTCTGAATTG
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCT-TGAATTC
* * *
563337 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
563402 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
* * *
563451 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-ATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
563516 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
* * *
563565 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
563629 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
* * *
563681 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGATCATCATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
563745 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
** * *
563797 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCATTTGATGGATCATCATTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
563861 AGAAGAA
65 AGAAGAA
563868 TTTATTCAAT
Statistics
Matches: 503, Mismatches: 20, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
112 3 0.01
113 45 0.09
114 231 0.46
115 2 0.00
116 203 0.40
117 17 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
ATCATTTGATGGATCATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
Found at i:564012 original size:3 final size:3
Alignment explanation
Indices: 564004--564067 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
563994 TTTTACCCAC
* *
564004 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
564052 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
564068 AATATATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:564094 original size:14 final size:15
Alignment explanation
Indices: 564066--564100 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
564056 TTATTATTAT
564066 TAAATATATATTAAA
1 TAAATATATATTAAA
*
564081 TAAATCTATA-TAAA
1 TAAATATATATTAAA
564095 TAAATA
1 TAAATA
564101 ATTACAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:564575 original size:18 final size:18
Alignment explanation
Indices: 564552--564587 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
564542 GATACAGAAC
564552 CAGAGAAAGAAAAAAAAA
1 CAGAGAAAGAAAAAAAAA
564570 CAGAGAAAGAAAAAAAAA
1 CAGAGAAAGAAAAAAAAA
564588 AGCAACTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.78, C:0.06, G:0.17, T:0.00
Consensus pattern (18 bp):
CAGAGAAAGAAAAAAAAA
Found at i:571109 original size:42 final size:42
Alignment explanation
Indices: 571058--571298 Score: 120
Period size: 42 Copynumber: 5.8 Consensus size: 42
571048 CAAATTATAC
*
571058 TTTAGCGGCGTTTTTCCAACAAACGCCGTAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTCCAACAAACGCCGTAATAGAGTAGTAA
** * * * * *
571100 TTTAGCGGCGTTTATAGCTA-AAACGACGGAATAGATTTGT--
1 TTTAGCGGCGTTT-TTCCAACAAACGCCGTAATAGAGTAGTAA
* ** *
571140 TTACAATGGCGTGTTTT-CAATAAACGCCGTAATAGAGTAGTAA
1 TT-TAGCGGCGT-TTTTCCAACAAACGCCGTAATAGAGTAGTAA
* * ** * * * *
571183 TTTAGCGGTGTTTGTATAA-AAACGTCGTAACAGGGTTGT--
1 TTTAGCGGCGTTTTTCCAACAAACGCCGTAATAGAGTAGTAA
* * * * * *
571222 TTATAGTGGCATTTATCCAACAAACGACGCT-ATAGAGAATTAA
1 TT-TAGCGGCGTTTTTCCAACAAACGCCG-TAATAGAGTAGTAA
* * *
571265 TTTAGCGGCGTTTATCAAACAAACGCTGTAATAG
1 TTTAGCGGCGTTTTTCCAACAAACGCCGTAATAG
571299 GTTGATTTAT
Statistics
Matches: 143, Mismatches: 43, Indels: 26
0.67 0.20 0.12
Matches are distributed among these distances:
39 2 0.01
40 15 0.10
41 55 0.38
42 64 0.45
43 7 0.05
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTCCAACAAACGCCGTAATAGAGTAGTAA
Found at i:572383 original size:19 final size:18
Alignment explanation
Indices: 572359--572396 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
572349 TTCGACTCTC
*
572359 AGTGCATCGGTGCACTAAA
1 AGTGCATCGATGCA-TAAA
572378 AGTGCATCGATGCATAAA
1 AGTGCATCGATGCATAAA
572396 A
1 A
572397 TGTATTCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (18 bp):
AGTGCATCGATGCATAAA
Found at i:572430 original size:64 final size:63
Alignment explanation
Indices: 572359--572480 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 63
572349 TTCGACTCTC
* *
572359 AGTGCATCGGTGCACT-AAAAGTGCATCGATGCATAAAATGTATTCGATGTTTTGAAAAAGCCTG
1 AGTGCATCGATGCA-TGAAAAGTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAAGCCTG
** *
572423 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAA
1 AGTGCATCGATGCATGAAAAGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAA
572481 TTAATTGGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 10 0.19
64 42 0.81
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATGAAAAGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAAAGCCTG
Found at i:572492 original size:64 final size:64
Alignment explanation
Indices: 572379--572503 Score: 182
Period size: 64 Copynumber: 2.0 Consensus size: 64
572369 TGCACTAAAA
* **
572379 GTGCATCGATGCATAAAATGTATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAAACTGAGTGCATCGATGCATGGTAT
*
572443 GTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATTAATTG-GTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAA--AACTGAGTGCATCGATGCATGG
572504 ATTGGTGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
63 9 0.16
64 44 0.80
65 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAAACTGAGTGCATCGATGCATGGTAT
Found at i:578236 original size:24 final size:22
Alignment explanation
Indices: 578209--578266 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
578199 ATGCACAGGT
*
578209 AGTGCATCGATGCACACATTAAGG
1 AGTGCATCGATGCACAC-TGAA-G
*
578233 AGTGCATCGAT--ACACTGCAG
1 AGTGCATCGATGCACACTGAAG
578253 AGTGCATCGATGCA
1 AGTGCATCGATGCA
578267 TACCCTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 5 0.17
24 11 0.37
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (22 bp):
AGTGCATCGATGCACACTGAAG
Found at i:578611 original size:31 final size:30
Alignment explanation
Indices: 578573--578643 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
578563 ATTATATGAA
578573 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTATGG-AAATGAAATGT
*
578604 TTATGTGATAAAGGTATGGAAATGATATGT
1 TTATGTGATAAAGGTATGGAAATGAAATGT
* *
578634 CTATGCGATA
1 TTATGTGATA
578644 TAAATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
TTATGTGATAAAGGTATGGAAATGAAATGT
Found at i:579126 original size:3 final size:3
Alignment explanation
Indices: 579118--579143 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
579108 AGTTCCTGGC
579118 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
579144 CACTGCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:585573 original size:30 final size:31
Alignment explanation
Indices: 585519--585589 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
585509 ATTATATGAA
585519 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTATGGAAAATGAAATGT
*
585550 TTATGTGATAAAGGTAT-GAAAATGATATGT
1 TTATGTGATAAAGGTATGGAAAATGAAATGT
* *
585580 CTATGCGATA
1 TTATGTGATA
585590 TAAATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (31 bp):
TTATGTGATAAAGGTATGGAAAATGAAATGT
Found at i:585835 original size:25 final size:24
Alignment explanation
Indices: 585783--585858 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
585773 TATATAGTCA
* *
585783 TTCGGGACAAATTCTACGCGGTC-T
1 TTCGGGACAAATTCTACGC-GACAC
585807 TTCGGGACAAATTTCTACGCGACAC
1 TTCGGGACAAA-TTCTACGCGACAC
*
585832 TTCGGTG-CAAAACTCTACGCGACAC
1 TTCGG-GAC-AAATTCTACGCGACAC
585857 TT
1 TT
585859 TGGTGCAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
24 13 0.29
25 28 0.62
26 4 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (24 bp):
TTCGGGACAAATTCTACGCGACAC
Found at i:588303 original size:22 final size:21
Alignment explanation
Indices: 588261--588300 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
588251 GAGTTTATTT
*
588261 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
588282 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
588301 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:590788 original size:22 final size:22
Alignment explanation
Indices: 590760--590808 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
590750 GTGTTTTTCT
590760 GCTTTCGAATACAAAAATAATA
1 GCTTTCGAATACAAAAATAATA
** *
590782 GCTTTCGAATATGATAATAATA
1 GCTTTCGAATACAAAAATAATA
590804 GCTTT
1 GCTTT
590809 TCAAAATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
GCTTTCGAATACAAAAATAATA
Found at i:591697 original size:77 final size:73
Alignment explanation
Indices: 591563--591705 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 73
591553 AAGTGAACAA
* *
591563 TATGGTCAAGACTTTGTATGCATAACTTTAATGTTTCCAAATTTTAATGTATTTTGTTGTTAAGT
1 TATGGTCAAGACTTTGTATGCATAACTTTAATGTTTACAAATTATAATGTATTTTGTTGTTAAGT
591628 ATTAATTT
66 ATTAATTT
* *
591636 TATGGTGAAGACTGTT-TATGCATAACTTTAATTAATGTTTATAAATTATAATGTATTTTGTTGT
1 TATGGTCAAGACT-TTGTATGCATAAC--T--TTAATGTTTACAAATTATAATGTATTTTGTTGT
591700 TAAGTA
61 TAAGTA
591706 GTTTTATGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
73 22 0.36
74 2 0.03
75 1 0.02
77 36 0.59
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (73 bp):
TATGGTCAAGACTTTGTATGCATAACTTTAATGTTTACAAATTATAATGTATTTTGTTGTTAAGT
ATTAATTT
Found at i:594755 original size:28 final size:26
Alignment explanation
Indices: 594723--594799 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 26
594713 CATAGGATGC
594723 ATGAAGTGTTGTTTTTAAGAGACAAATA
1 ATGAAGTGTTG-TTTTAAGAGACAAA-A
*
594751 ATGAAGTGTTGTTTTAAGAGGC--AA
1 ATGAAGTGTTGTTTTAAGAGACAAAA
*
594775 ATGAAGTATTGTTTTAAGAGACAAA
1 ATGAAGTGTTGTTTTAAGAGACAAA
594800 CTTATTATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 21 0.48
25 1 0.02
26 1 0.02
27 10 0.23
28 11 0.25
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (26 bp):
ATGAAGTGTTGTTTTAAGAGACAAAA
Found at i:594970 original size:18 final size:18
Alignment explanation
Indices: 594947--594981 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
594937 TTAGAAATAA
*
594947 ATGTGAACTTAAATTATT
1 ATGTGAAATTAAATTATT
594965 ATGTGAAATTAAATTAT
1 ATGTGAAATTAAATTAT
594982 GCTTGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
ATGTGAAATTAAATTATT
Found at i:600855 original size:20 final size:20
Alignment explanation
Indices: 600810--600867 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
600800 GCACTGAATA
*
600810 TTTGTCCCGAATGACCAC--
1 TTTGTCCCGAAGGACCACTG
*
600828 TATGTCCCGAAGGACCACTG
1 TTTGTCCCGAAGGACCACTG
600848 TTTGTCCCGAAGGACCACTG
1 TTTGTCCCGAAGGACCACTG
600868 ATAATCCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 16 0.46
20 19 0.54
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (20 bp):
TTTGTCCCGAAGGACCACTG
Found at i:601453 original size:12 final size:11
Alignment explanation
Indices: 601438--601498 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
601428 AAATAGTAAG
601438 TAAAAAAATATA
1 TAAAAAAATA-A
*
601450 TAAAAAAAGAA
1 TAAAAAAATAA
601461 -AAAGAAAATAAA
1 TAAA-AAAAT-AA
601473 TAAAAAAATAA
1 TAAAAAAATAA
601484 -ACAAAATAATAA
1 TA-AAAA-AATAA
601496 TAA
1 TAA
601499 CAAAGTACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 4 0.10
11 11 0.27
12 22 0.54
13 4 0.10
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:601477 original size:21 final size:21
Alignment explanation
Indices: 601438--601492 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
601428 AAATAGTAAG
*
601438 TAAA-AAAATATATAAAAAAAGA
1 TAAACAAAATAAAT-AAAAAA-A
* *
601460 AAAAGAAAATAAATAAAAAAA
1 TAAACAAAATAAATAAAAAAA
601481 TAAACAAAATAA
1 TAAACAAAATAA
601493 TAATAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.39
22 9 0.32
23 8 0.29
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.15
Consensus pattern (21 bp):
TAAACAAAATAAATAAAAAAA
Found at i:601497 original size:23 final size:21
Alignment explanation
Indices: 601439--601498 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 21
601429 AATAGTAAGT
601439 AAAAAAATATATAAAAAAAGAA
1 AAAAAAATA-ATAAAAAAAGAA
*
601461 AAAGAAAATAAATAAAAAAATAA
1 AAA-AAAAT-AATAAAAAAAGAA
601484 ACAAAATAATAATAA
1 A-AAAA-AATAATAA
601499 CAAAGTACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 3 0.09
23 24 0.73
24 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (21 bp):
AAAAAAATAATAAAAAAAGAA
Found at i:601843 original size:2 final size:2
Alignment explanation
Indices: 601796--601824 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
601786 CTTGTGTAGA
601796 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 A
601825 ATAGTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:602017 original size:2 final size:2
Alignment explanation
Indices: 602010--602072 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
602000 GAACATATGC
602010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
602052 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
602073 CAAAATAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:602108 original size:12 final size:11
Alignment explanation
Indices: 602080--602120 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
602070 ATACAAAATA
* *
602080 AATAATATAAA
1 AATAATACAAG
602091 AATAATACAAG
1 AATAATACAAG
602102 TAATAATACAAG
1 -AATAATACAAG
602114 AATAATA
1 AATAATA
602121 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:602180 original size:61 final size:63
Alignment explanation
Indices: 602114--602249 Score: 142
Period size: 61 Copynumber: 2.2 Consensus size: 63
602104 ATAATACAAG
602114 AATAATAAAAAGAAAG-AGAAAGTAAAA-AAAATAATAATAAT-AAAAT-ATAA-AAATATACAT
1 AATAATAAAAA-AAAGTAG-AA-TAAAAGAAAAT-ATAATAATAAAAATAATAATAAATATA-AT
602174 A-T
61 AGT
* * *
602176 -ATAATATAAATAAGTAGAATAAAAGGAAAATATAATAGTAAAAATAATAATAAATATAATAGT
1 AATAATAAAAAAAAGTAGAATAAAA-GAAAATATAATAATAAAAATAATAATAAATATAATAGT
602239 AATAATAAAAA
1 AATAATAAAAA
602250 TGCAAAGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
59 5 0.08
60 12 0.19
61 21 0.34
62 7 0.11
63 8 0.13
64 9 0.15
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (63 bp):
AATAATAAAAAAAAGTAGAATAAAAGAAAATATAATAATAAAAATAATAATAAATATAATAGT
Found at i:602224 original size:12 final size:12
Alignment explanation
Indices: 602202--602246 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
602192 GAATAAAAGG
602202 AAAATATAATAGT
1 AAAA-ATAATAGT
*
602215 AAAAATAATAAT
1 AAAAATAATAGT
*
602227 AAATATAATAGT
1 AAAAATAATAGT
*
602239 AATAATAA
1 AAAAATAA
602247 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:602633 original size:15 final size:15
Alignment explanation
Indices: 602613--602642 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
602603 AAAGAAAACA
602613 CGATTAACAACGCAT
1 CGATTAACAACGCAT
602628 CGATTAACAACGCAT
1 CGATTAACAACGCAT
602643 GCAAGTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
CGATTAACAACGCAT
Found at i:602876 original size:37 final size:37
Alignment explanation
Indices: 602835--602939 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
602825 GTGCTTATGG
* * *
602835 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
602872 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
602909 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
602940 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:603988 original size:106 final size:106
Alignment explanation
Indices: 603670--605138 Score: 2064
Period size: 106 Copynumber: 14.0 Consensus size: 106
603660 GCATTGTTCC
* * ** ** *
603670 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAAAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
603734 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
603776 CAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
603835 TCAGCCGG-CCTTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
603877 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTTGCTCTGAAGTTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
603941 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
603982 GAGTCCAATATCCTACACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
604047 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
604088 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
604153 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
604194 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGATTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
604259 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
604300 GAGTCCAATATCCTTCACTGTGAAGTTGAAA-----T-T---A---GGAAATTGTTTGCTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
604353 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
604394 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
604459 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
604500 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
604565 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
604606 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
604671 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
604712 GAGTCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
604777 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
604818 GAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGAAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
604883 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTATGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
604924 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
604989 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
605030 GAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGGCTCCGAAATTGGAAAATT-ATTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
605094 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
605135 GAGT
1 GAGT
605139 GGCACGATAT
Statistics
Matches: 1232, Mismatches: 108, Indels: 47
0.89 0.08 0.03
Matches are distributed among these distances:
94 83 0.07
97 1 0.00
99 1 0.00
100 77 0.06
101 6 0.00
102 3 0.00
103 1 0.00
104 3 0.00
105 57 0.05
106 999 0.81
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:605651 original size:16 final size:16
Alignment explanation
Indices: 605614--605657 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
605604 TTTTATCCCT
*
605614 TTTTC-TTTTTGATTT
1 TTTTCTTTTTTGATTC
*
605629 TTGTTCTTTTTTGCTTC
1 TT-TTCTTTTTTGATTC
605646 TTTTCTTTTTTG
1 TTTTCTTTTTTG
605658 TTTTTGCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 13 0.52
17 10 0.40
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTGATTC
Found at i:610318 original size:23 final size:23
Alignment explanation
Indices: 610292--610339 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
610282 ATATATATAT
610292 ATATAAAATAAA-TAAAAAATTAA
1 ATAT-AAATAAATTAAAAAATTAA
* *
610315 ATATATATAAATTAATAAATTAA
1 ATATAAATAAATTAAAAAATTAA
610338 AT
1 AT
610340 GACGAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAAATAAATTAAAAAATTAA
Found at i:610612 original size:2 final size:2
Alignment explanation
Indices: 610562--610596 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
610552 CTTGTGTAGA
610562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
610597 GTAAAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:610838 original size:12 final size:11
Alignment explanation
Indices: 610811--610850 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
610801 ATAACAAAAT
*
610811 AATAATATAA-
1 AATAATACAAG
610821 AATAATACAAG
1 AATAATACAAG
610832 TAATAATACAAG
1 -AATAATACAAG
610844 AATAATA
1 AATAATA
610851 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (11 bp):
AATAATACAAG
Found at i:611580 original size:37 final size:37
Alignment explanation
Indices: 611539--611643 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
611529 GTTCTTGTGG
* * *
611539 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
611576 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
611613 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
611644 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:616578 original size:18 final size:18
Alignment explanation
Indices: 616555--616625 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
616545 TGAATATTTT
*
616555 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATA
*
616573 TCCCGAAGGACTACTGATTA
1 TCCCGAAGGACCACT-A-TA
* *
616593 TTCCGAAGAACCACTATA
1 TCCCGAAGGACCACTATA
* *
616611 TCTCGAAGGAACACT
1 TCCCGAAGGACCACT
616626 GATAATCCCT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
18 27 0.64
19 2 0.05
20 13 0.31
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:619188 original size:103 final size:103
Alignment explanation
Indices: 619009--619223 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
618999 GTCGAGGGTC
*
619009 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
619074 TTGATCCCTAGTATATTTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
619112 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
619177 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
619215 TATGTGGTC
1 TATGTGGTC
619224 CTTATGGATA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:619310 original size:23 final size:23
Alignment explanation
Indices: 619242--619300 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
619232 TATTATTATA
619242 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
619265 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
619288 TGGCACTTCGGTG
1 TGGCACTACGGTG
619301 TATTTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:621437 original size:64 final size:62
Alignment explanation
Indices: 621328--621464 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 62
621318 CCTTTAACAT
*
621328 GTGCATCGATGCACTTCCCATGCATCGATACACCAATCATCTTCGATGTTTTCAT-TTTAAGGA
1 GTGCATCGATGCACTTCCCATGCATCGATACACCAATCA-CTTCGATGTTTT-ATCTTTAAAGA
* * * *
621391 GGTGCATCGATGCAC-TCCTTATGCATCGATGCACTAATTGCA-TTCGATGTTTTTTCTTTAAAG
1 -GTGCATCGATGCACTTCC-CATGCATCGATACACCAA-T-CACTTCGATGTTTTATCTTTAAAG
621454 A
62 A
621455 GTGCATCGAT
1 GTGCATCGAT
621465 ACACATTGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
63 14 0.22
64 47 0.73
65 1 0.02
66 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (62 bp):
GTGCATCGATGCACTTCCCATGCATCGATACACCAATCACTTCGATGTTTTATCTTTAAAGA
Found at i:623261 original size:44 final size:44
Alignment explanation
Indices: 623183--623318 Score: 175
Period size: 44 Copynumber: 3.1 Consensus size: 44
623173 CTTTTTTAAC
* *
623183 AAACGTCGCTATATATCA-ACCTTTAACGGCGTTTGTATTCTAA
1 AAACGTCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
* *
623226 AAACGTCGCTATATACCAGACCTTTAGTGGCGTTTGTATTATAA
1 AAACGTCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
* * * * * *
623270 AAATGCCGCTATATGCCAGACCTTTAGCGGCGTTTATATACTGA
1 AAACGTCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
623314 AAACG
1 AAACG
623319 CCACTAAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 17 0.22
44 62 0.78
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
AAACGTCGCTATATACCAGACCTTTAGCGGCGTTTGTATTCTAA
Found at i:625146 original size:156 final size:157
Alignment explanation
Indices: 624913--625228 Score: 514
Period size: 160 Copynumber: 2.0 Consensus size: 157
624903 GGATATATAG
624913 GTGTATATTGCAGACATCCCGTTACTGTGTGTGTATATATATTGGTGTATCCAAGGATGGACCAA
1 GTGTATATTGCAGACATCCCGTTACTGTGTGTGTATATATATTGGTGTATCCAAGGATGGACCAA
* *
624978 ATGGGCGAAC-G-G-A-CTCTAAAAATTTCAAATCATTATATATTTCAGATATTTTCTTTTATAT
66 ATGGGCGAACGGAGCACCCCTAAAAA-TTCAAATCATCATATATTTCAGATATTTTCTTTTATAT
625039 CTCTGGTGTATCTATATATATTTAACTT
130 CTCTGGTGTATCTATATATATTTAACTT
*
625067 GTGTATATTGCAGACATCCGGTTACTGTGTGTGTATATATATATTGGTGTATCCAAGGATGGACC
1 GTGTATATTGCAGACATCCCGTTACTGTGTGTG--TATATATATTGGTGTATCCAAGGATGGACC
* * *
625132 GAATGGGCGGACGGAGCAGCCCCTAAAAATTCAAATCATCATATATTTCAGATATTTTCTTTTGT
64 AAATGGGCGAACGGAGCA-CCCCTAAAAATTCAAATCATCATATATTTCAGATATTTTCTTTTAT
625197 ATCTCTGGTGTATCTATATATATTTAACTT
128 ATCTCTGGTGTATCTATATATATTTAACTT
625227 GT
1 GT
625229 TAACATGAAG
Statistics
Matches: 149, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
154 32 0.21
156 40 0.27
157 1 0.01
158 1 0.01
159 1 0.01
160 66 0.44
161 8 0.05
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (157 bp):
GTGTATATTGCAGACATCCCGTTACTGTGTGTGTATATATATTGGTGTATCCAAGGATGGACCAA
ATGGGCGAACGGAGCACCCCTAAAAATTCAAATCATCATATATTTCAGATATTTTCTTTTATATC
TCTGGTGTATCTATATATATTTAACTT
Found at i:625581 original size:2 final size:2
Alignment explanation
Indices: 625574--625611 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
625564 GAAAGAACTT
625574 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
625612 GAAAACATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:627948 original size:36 final size:37
Alignment explanation
Indices: 627896--627977 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 37
627886 TGGTAACCAA
627896 CTTTGAAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
627933 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
627970 -GTTGAAAA
1 CTTTGAAAA
627978 TGATAATGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:632536 original size:36 final size:37
Alignment explanation
Indices: 632483--632565 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
632473 TGGTAACCAA
*
632483 CTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTT-AAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
632520 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
* *
632557 GTTGAAAAA
1 CTTTAAAAA
632566 TGATAATGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 7 0.17
37 34 0.83
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (37 bp):
CTTTAAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:632566 original size:36 final size:36
Alignment explanation
Indices: 632456--632567 Score: 108
Period size: 37 Copynumber: 3.2 Consensus size: 36
632446 TGAAAGTATT
**
632456 AAAATGGTTTTC-AAGTTTGGTAACCAACTTT-G--AA
1 AAAATGGTTTTCAAAGTTTGGTAA--ATGTTTCGTTAA
*
632490 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
* * *
632526 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
632562 AAAATG
1 AAAATG
632568 ATAATGTGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.06
34 12 0.18
35 12 0.18
36 15 0.23
37 23 0.35
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
Found at i:640160 original size:11 final size:11
Alignment explanation
Indices: 640144--640168 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
640134 TATATAAACA
640144 AATAAAAATAC
1 AATAAAAATAC
640155 AATAAAAATAC
1 AATAAAAATAC
640166 AAT
1 AAT
640169 TGGAGCTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (11 bp):
AATAAAAATAC
Found at i:641517 original size:14 final size:14
Alignment explanation
Indices: 641498--641571 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
641488 TTGGGCTTTG
*
641498 TAATATTTAATAAA
1 TAATATATAATAAA
641512 TAATATATAATAATTA
1 TAATATATAATAA--A
641528 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
641543 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
641558 TAATA-ATAATAAA
1 TAATATATAATAAA
641571 T
1 T
641572 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:641524 original size:3 final size:3
Alignment explanation
Indices: 641505--641569 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
641495 TTGTAATATT
* *
641505 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
641552 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
641570 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:641574 original size:18 final size:18
Alignment explanation
Indices: 641540--641575 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
641530 ATAATAATAC
*
641540 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
641558 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
641576 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:641823 original size:76 final size:76
Alignment explanation
Indices: 641697--643250 Score: 2713
Period size: 76 Copynumber: 20.5 Consensus size: 76
641687 GATGGAAATG
*
641697 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
641761 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
641773 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
641838 CCCGAAGGCTT
66 CCCGAAGGCTT
*
641849 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
641913 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
641925 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
641990 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
642001 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642066 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
642077 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642142 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
642153 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642218 CCCGAAGGCTT
66 CCCGAAGGCTT
642229 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
642293 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* * *
642305 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642370 CCCGAAGGCTT
66 CCCGAAGGCTT
*
642381 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642446 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
642457 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642522 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
642533 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642597 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
642608 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642673 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
642684 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642749 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
642760 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642825 CCCGAAGGCTT
66 CCCGAAGGCTT
642836 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGC
642900 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
642912 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
642977 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
642988 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
643053 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
643064 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
643129 CCCGAAGGCTT
66 CCCGAAGGCTT
*
643140 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
643205 CCCGAAGGCTT
66 CCCGAAGGCTT
643216 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
643251 TGGGAAATAG
Statistics
Matches: 1405, Mismatches: 65, Indels: 16
0.95 0.04 0.01
Matches are distributed among these distances:
75 73 0.05
76 1329 0.95
77 3 0.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:643942 original size:22 final size:22
Alignment explanation
Indices: 643914--643968 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
643904 CATAAAATTT
* **
643914 TCATCTTTGGAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCCA
*
643936 TCATCTTTAAAAAGAGAATCCA
1 TCATCTTTGAAAAGAGAATCCA
643958 TCATCTTTGAA
1 TCATCTTTGAA
643969 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCCA
Found at i:648661 original size:20 final size:20
Alignment explanation
Indices: 648632--648672 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
648622 CATTAAAGAT
*
648632 TTTTTTTAAAAAAAAAACAA
1 TTTTTGTAAAAAAAAAACAA
* *
648652 TTTTTGTAAATAAAAACCAA
1 TTTTTGTAAAAAAAAAACAA
648672 T
1 T
648673 CTTGGAAGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (20 bp):
TTTTTGTAAAAAAAAAACAA
Found at i:655856 original size:14 final size:14
Alignment explanation
Indices: 655837--655910 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
655827 TTGGGCTTTG
*
655837 TAATATTTAATAAA
1 TAATATATAATAAA
655851 TAATATATAATAATTA
1 TAATATATAATAA--A
655867 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
655882 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
655897 TAATA-ATAATAAA
1 TAATATATAATAAA
655910 T
1 T
655911 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:655863 original size:3 final size:3
Alignment explanation
Indices: 655844--655908 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
655834 TTGTAATATT
* *
655844 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
655891 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
655909 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:655913 original size:18 final size:18
Alignment explanation
Indices: 655879--655914 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
655869 ATAATAATAC
*
655879 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
655897 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
655915 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:657028 original size:29 final size:29
Alignment explanation
Indices: 656924--657020 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 29
656914 TAAACGCTAA
* * *
656924 AAAAATGATCGTAAACATTGTTAGGCACT
1 AAAAATGACCGAAAATATTGTTAGGCACT
* *
656953 AAATAATGACCGAAAATATTATTAGGCATT
1 AAA-AATGACCGAAAATATTGTTAGGCACT
* * *
656983 AAAAAATAACCAAAAATATTGTTAGGCGCT
1 -AAAAATGACCGAAAATATTGTTAGGCACT
657013 AAAAATGA
1 AAAAATGA
657021 GTGAAAATGT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
29 10 0.18
30 42 0.76
31 3 0.05
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (29 bp):
AAAAATGACCGAAAATATTGTTAGGCACT
Found at i:657055 original size:20 final size:21
Alignment explanation
Indices: 657032--657073 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
657022 TGAAAATGTT
*
657032 AAAAAAAT-ATGTTTTAAATA
1 AAAAAAATAATATTTTAAATA
*
657052 AAAATAATAATATTTTAAATA
1 AAAAAAATAATATTTTAAATA
657073 A
1 A
657074 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAAAATAATATTTTAAATA
Found at i:657483 original size:17 final size:17
Alignment explanation
Indices: 657461--657499 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
657451 TGAATCAAAT
657461 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
657478 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
657495 -AATTA
1 TAATTA
657500 ATTGTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:657670 original size:23 final size:23
Alignment explanation
Indices: 657644--657688 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
657634 AACGGTTAAA
*
657644 GAAAA-AAAAAGTTCGATTAATTT
1 GAAAATAAAAA-TTCGATCAATTT
*
657667 GAAAATAATAATTCGATCAATT
1 GAAAATAAAAATTCGATCAATT
657689 CAGCCACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (23 bp):
GAAAATAAAAATTCGATCAATTT
Found at i:658343 original size:22 final size:23
Alignment explanation
Indices: 658268--658342 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
658258 ATAAATTATT
658268 TAAAATAAATCAATCTATAC-AA
1 TAAAATAAATCAATCTATACTAA
**
658290 CTACAATAATAAATCAATCTATA-TTT
1 -T--AA-AATAAATCAATCTATACTAA
658316 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATACTAA
658339 TAAA
1 TAAA
658343 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAATAAATCAATCTATACTAA
Found at i:658353 original size:32 final size:32
Alignment explanation
Indices: 658314--658415 Score: 118
Period size: 32 Copynumber: 3.5 Consensus size: 32
658304 CAATCTATAT
658314 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
658346 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
658368 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTA
658400 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
658416 TCATACAACT
Statistics
Matches: 59, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
22 16 0.27
23 1 0.02
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 1 0.02
32 33 0.56
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:658361 original size:54 final size:54
Alignment explanation
Indices: 658297--658528 Score: 215
Period size: 54 Copynumber: 4.2 Consensus size: 54
658287 CAACTACAAT
658297 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
*
658351 AATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAA
* * ** ** * * *
658405 AATAAATCAATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCAT
1 AATAAATCAA-TC-TA-TATTTTAA-AATAAATCAAT-C-TATACT--AATAAAT-TATTTAA
* * *
658468 ACT-AAT-AA-AT-TA-TTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
658517 AATAAATCAATC
1 AATAAATCAATC
658529 GATACTAATA
Statistics
Matches: 140, Mismatches: 24, Indels: 30
0.72 0.12 0.15
Matches are distributed among these distances:
49 6 0.04
50 10 0.07
51 2 0.01
52 3 0.02
53 2 0.01
54 72 0.51
55 5 0.04
56 2 0.01
57 4 0.03
58 12 0.09
60 3 0.02
61 3 0.02
62 10 0.07
63 6 0.04
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
Found at i:658371 original size:134 final size:133
Alignment explanation
Indices: 658204--658650 Score: 526
Period size: 134 Copynumber: 3.2 Consensus size: 133
658194 ACAACTACAA
* * *
658204 TAATAAATTA-TT-AAATAAATTAATCTATTTTTTAAAATAAATCAATATATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TATACTAATAAATTAT
658267 TTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAA-TC
65 TTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATTC
658331 TATAC
130 -ATAC
658336 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATT-ATACTAATAAATTAT
*
658401 TTAAAATAAATCAAT-TCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATT
65 TTAAAATAAATCAATCT-ATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATT
658465 CATAC
129 CATAC
*
658470 TAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCGATACT
1 TAATAAATTATTTAAAATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAAT-TATACT
* *** * * *
658535 AATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACTAATAAATTAT
55 AATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-CT-AT--A-T-T
* *
658599 TTAAAATAAATCACTTCATAT
113 TTAAAATAAATCAATTCATAC
*
658620 TAATAAATTATTTAAAATAAGTCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
658651 CAACTACAAT
Statistics
Matches: 275, Mismatches: 16, Indels: 38
0.84 0.05 0.12
Matches are distributed among these distances:
132 10 0.04
133 4 0.01
134 136 0.49
135 2 0.01
138 1 0.00
140 2 0.01
142 2 0.01
143 6 0.02
144 60 0.22
145 1 0.00
146 3 0.01
148 1 0.00
149 1 0.00
150 46 0.17
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (133 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTATACTAATAAATTATT
TAAAATAAATCAATCTATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATTCA
TAC
Found at i:658372 original size:22 final size:22
Alignment explanation
Indices: 658346--658388 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
658336 TAATAAATTA
658346 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
658368 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
658389 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:658394 original size:18 final size:18
Alignment explanation
Indices: 658372--658423 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
658362 CCATATTTTA
658372 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
* *
658390 TAATAAAT-TATT--TA-
1 AAATAAATCAATTCATAC
658404 AAATAAATCAATTCATAC
1 AAATAAATCAATTCATAC
658422 AA
1 AA
658424 CTACAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
17 5 0.19
18 9 0.35
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATCAATTCATAC
Found at i:658397 original size:22 final size:22
Alignment explanation
Indices: 658348--658396 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
658338 ATAAATTATT
**
658348 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
658370 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
658393 TAAA
1 TAAA
658397 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:658474 original size:18 final size:18
Alignment explanation
Indices: 658453--658541 Score: 54
Period size: 18 Copynumber: 5.4 Consensus size: 18
658443 CATATTTTAA
658453 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
658471 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
658485 AATAAATCAA-TCGATACT
1 AATAAATCAATTC-ATACT
* *
658503 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
658517 AATAAATCAA-TCGATACT
1 AATAAATCAATTC-ATACT
658535 AATAAAT
1 AATAAAT
658542 TATTTAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 22
0.63 0.10 0.27
Matches are distributed among these distances:
14 16 0.31
15 6 0.12
17 8 0.15
18 22 0.42
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:658477 original size:22 final size:23
Alignment explanation
Indices: 658402--658476 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
658392 ATAAATTATT
658402 TAAAATAAATCAATTCATAC-AA
1 TAAAATAAATCAATTCATACTAA
* **
658424 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATTCATACTAA
658450 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATACTAA
658473 TAAA
1 TAAA
658477 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAATAAATCAATTCATACTAA
Found at i:658487 original size:32 final size:32
Alignment explanation
Indices: 658448--658651 Score: 261
Period size: 32 Copynumber: 6.7 Consensus size: 32
658438 CAATCCATAT
658448 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
658480 TTTAAAATAAATCAA-TCGATACTAATAAATTA
1 TTTAAAATAAATCAATTC-ATACTAATAAATTA
658512 TTTAAAATAAATCAA-TCGATACTAATAAATTA
1 TTTAAAATAAATCAATTC-ATACTAATAAATTA
658544 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
658566 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
* *
658598 TTTAAAATAAATCACTTCATATTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
* *
658630 TTTAAAATAAGTCAATCCATAC
1 TTTAAAATAAATCAATTCATAC
658652 AACTACAATA
Statistics
Matches: 153, Mismatches: 8, Indels: 22
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.10
23 2 0.01
24 1 0.01
26 3 0.02
28 3 0.02
30 1 0.01
31 3 0.02
32 125 0.82
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:658536 original size:198 final size:195
Alignment explanation
Indices: 658314--658753 Score: 604
Period size: 198 Copynumber: 2.2 Consensus size: 195
658304 CAATCTATAT
658314 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* *
658379 TCAATTCATACTAATAAATTATTTAAAATAAATCAATTCATA-CAACTACA-A-T-AATAAATCA
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATCAA-TAAATATTAAATAAATCA
*** * *
658440 ATCCATA-TTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCGATACT
130 ATCCATACAACTAAAAT-AAT-AAATCAAT-CT-AT--A-T-TTTAAAATAAATCAATCCATACT
658503 AATAAATTA
187 AATAAATTA
*
658512 TTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * *
658577 TCAATCCATACTAATAAATTATTTAAAATAAATCACTTCATATTAATAAATTATTTAAAATAAGT
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATCAATAAA-TA-TT-AAATAAAT
* *
658642 CAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATTAATCCATACTAATAAA
128 CAATCCATACAACTAAAATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAA
658707 TTA
193 TTA
*
658710 TCTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
658754 TATTTAAAAA
Statistics
Matches: 218, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
198 179 0.82
199 3 0.01
200 2 0.01
202 3 0.01
203 6 0.03
204 20 0.09
205 5 0.02
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (195 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATCAATAAATATTAAATAAATCAA
TCCATACAACTAAAATAATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:658570 original size:22 final size:22
Alignment explanation
Indices: 658544--658586 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
658534 TAATAAATTA
658544 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
658566 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
658587 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:658572 original size:54 final size:53
Alignment explanation
Indices: 658431--658788 Score: 272
Period size: 54 Copynumber: 6.5 Consensus size: 53
658421 CAACTACAAT
658431 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAA-TCATACTAATAAATTATTTAA
658485 AATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAATC-ATACTAATAAATTATTTAA
658549 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAA
* * * * * *
658603 AATAAATCACTTCATATTAATAAATTATTTAAAAT-AAGTCA-A-TCCATACAACTA--CAA
1 AATAAATCAATCCATATT-TTAAA--A--T-AAATCAA-TCATACT-AATA-AATTATTTAA
* * *
658660 TAATAAATCAATCTATATTTTAAAATAAATTAATCCATACTAATAAATTATCTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAA
** * * *
658715 AATAAATCAAT-C-TATACT--AATAAAT-TAT-TTA-AAATAAATTATTTAAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATTATTT-AA
*
658762 AATAAATCAATCCATATTTTATAATAA
1 AATAAATCAATCCATATTTTAAAATAA
658789 TTTATTTTAA
Statistics
Matches: 249, Mismatches: 22, Indels: 69
0.73 0.06 0.20
Matches are distributed among these distances:
46 11 0.04
47 15 0.06
48 1 0.00
49 6 0.02
50 7 0.03
51 5 0.02
52 9 0.04
53 9 0.04
54 78 0.31
55 10 0.04
56 1 0.00
57 8 0.03
58 22 0.09
59 9 0.04
60 8 0.03
62 1 0.00
63 3 0.01
64 46 0.18
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (53 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCATACTAATAAATTATTTAA
Found at i:658595 original size:22 final size:22
Alignment explanation
Indices: 658546--658594 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
658536 ATAAATTATT
**
658546 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
658568 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
658591 TAAA
1 TAAA
658595 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:658704 original size:18 final size:18
Alignment explanation
Indices: 658683--658741 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
658673 TATATTTTAA
658683 AATAAATTAATCCATACT
1 AATAAATTAATCCATACT
*
658701 AATAAATT-AT-C-TA-A
1 AATAAATTAATCCATACT
* *
658715 AATAAATCAATCTATACT
1 AATAAATTAATCCATACT
658733 AATAAATTA
1 AATAAATTA
658742 TTTAAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
14 7 0.22
15 4 0.12
16 1 0.03
17 4 0.12
18 16 0.50
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAATTAATCCATACT
Found at i:658718 original size:112 final size:112
Alignment explanation
Indices: 658368--658753 Score: 571
Period size: 112 Copynumber: 3.4 Consensus size: 112
658358 CAATCCATAT
*
658368 TTTAAAATAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATA
1 TTTAAAATAAATCAA-TCGATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
*
658432 ATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA
65 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
* *
658480 TTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCGATACTAA-TAAATTA
1 TTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA--A
658544 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
63 --T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
* * *
658598 TTTAAAATAAATCACTTC-ATATTAATAAATTATTTAAAATAAGTCAATCCATACAACTACAATA
1 TTTAAAATAAATCA-ATCGATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
* *
658662 ATAAATCAATCTATATTTTAAAATAAATTAATCCATACTAATAAATTA
65 ATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
* *
658710 TCTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAAT
658754 TATTTAAAAA
Statistics
Matches: 248, Mismatches: 15, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
111 4 0.02
112 136 0.55
113 2 0.01
114 2 0.01
116 2 0.01
117 2 0.01
118 98 0.40
119 2 0.01
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (112 bp):
TTTAAAATAAATCAATCGATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
Done.