Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009459.1 Hibiscus syriacus cultivar Beakdansim tig00113721_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: 1147073
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:300074 original size:3 final size:3
Alignment explanation
Indices: 300052--300090 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
300042 CTACAAAAAC
300052 ATT A-T ATT A-T ATT A-T ATT ATT ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
300091 ATTTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.25
3 24 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:300152 original size:27 final size:27
Alignment explanation
Indices: 300114--300169 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
300104 AATTATTTTA
300114 CAGGCCTTGGTATCTTTGAATGTGTGG
1 CAGGCCTTGGTATCTTTGAATGTGTGG
300141 CAGGCCTTGGTATCTTTGAATGTGTGG
1 CAGGCCTTGGTATCTTTGAATGTGTGG
300168 CA
1 CA
300170 ACCCGAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (27 bp):
CAGGCCTTGGTATCTTTGAATGTGTGG
Found at i:301286 original size:2 final size:2
Alignment explanation
Indices: 301279--301306 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
301269 TTCGTCATTC
301279 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
301307 TAAAATCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:312637 original size:34 final size:34
Alignment explanation
Indices: 312594--312664 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
312584 CTATTAACGA
312594 CGTACCACTCCACAATTGCAAAATATAGTAACAG
1 CGTACCACTCCACAATTGCAAAATATAGTAACAG
*
312628 CGTACCACTCCACAATTGCAAAATATAGTAACGG
1 CGTACCACTCCACAATTGCAAAATATAGTAACAG
312662 CGT
1 CGT
312665 CACGACACAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (34 bp):
CGTACCACTCCACAATTGCAAAATATAGTAACAG
Found at i:313550 original size:19 final size:19
Alignment explanation
Indices: 313526--313570 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
313516 GTAAAAATAA
313526 CCTCGTTCTCGGTAGAGTC
1 CCTCGTTCTCGGTAGAGTC
313545 CCTCGTTCTCGGTAGAGTC
1 CCTCGTTCTCGGTAGAGTC
313564 CCTCGTT
1 CCTCGTT
313571 ACTTCGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.09, C:0.33, G:0.24, T:0.33
Consensus pattern (19 bp):
CCTCGTTCTCGGTAGAGTC
Found at i:314239 original size:15 final size:16
Alignment explanation
Indices: 314200--314240 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
314190 CCCTTTTTAA
*
314200 TTTT-ATAAATATTTT
1 TTTTAATAAATATATT
314215 TTTTACATAAA-ATATT
1 TTTTA-ATAAATATATT
314231 TTTTAATAAA
1 TTTTAATAAA
314241 CTCGTCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 5 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAATAAATATATT
Found at i:319575 original size:16 final size:16
Alignment explanation
Indices: 319554--319586 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
319544 TAATAAATAG
319554 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
319570 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
319586 A
1 A
319587 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:319673 original size:16 final size:16
Alignment explanation
Indices: 319652--319710 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
319642 CATTTAATAA
319652 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
319668 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
319684 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
319700 ATAAACGAACA
1 ATAAACGAACA
319711 TAAACGTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:320480 original size:14 final size:14
Alignment explanation
Indices: 320463--320518 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
320453 AATGAACATA
320463 AACGAACATAATCG
1 AACGAACATAATCG
320477 AACGAACAT-A---
1 AACGAACATAATCG
* *
320487 AACAAACATAACCG
1 AACGAACATAATCG
320501 AACGAACATAATCG
1 AACGAACATAATCG
320515 AACG
1 AACG
320519 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:320483 original size:24 final size:24
Alignment explanation
Indices: 320443--320517 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
320433 GATTGAGTTA
*
320443 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
320467 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
320491 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
320515 AAC
1 AAC
320518 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:321161 original size:16 final size:15
Alignment explanation
Indices: 321124--321161 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
321114 AAAATATAAA
*
321124 TAAAAA-ATTAATTT
1 TAAAAATATTAAATT
321138 TAAAAATATTAAATT
1 TAAAAATATTAAATT
321153 TAAATAATA
1 TAAA-AATA
321162 AACAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 11 0.52
16 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAATATTAAATT
Found at i:323124 original size:30 final size:30
Alignment explanation
Indices: 323090--323158 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
323080 TATGTCACTA
* *
323090 ATAACAAATATTGAAGAAA-TTGGACTCTTG
1 ATAACAAATATT-AAAAAATTTGGACCCTTG
*
323120 ATAACAATTATTAAAAAATTTGGACCCTTG
1 ATAACAAATATTAAAAAATTTGGACCCTTG
*
323150 ATAATAAAT
1 ATAACAAAT
323159 GCTAACATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (30 bp):
ATAACAAATATTAAAAAATTTGGACCCTTG
Found at i:324390 original size:2 final size:2
Alignment explanation
Indices: 324383--324407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
324373 TTATTGAAAG
324383 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 A
324408 AAGTATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:327246 original size:53 final size:53
Alignment explanation
Indices: 327131--327249 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 53
327121 TATAATATAG
* * * * * *
327131 TAAAACAATAATTAAAGTAATGATTGAAAATATATTAAAATAATAAAAATTAAGT
1 TAAAAC-ATAACTAAA-CAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
**
327186 TAAAACATAACTAAACAATGATTAAAAATA-AATAAAATAATAAATGTAAAAT
1 TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
*
327238 TATGAACATAAC
1 TA-AAACATAAC
327250 CTGAATCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 19 0.35
53 21 0.39
54 8 0.15
55 6 0.11
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (53 bp):
TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
Found at i:328106 original size:16 final size:16
Alignment explanation
Indices: 328087--328121 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
328077 CTTTTCCTCC
328087 TCTGTTTTTTTTTCGT
1 TCTGTTTTTTTTTCGT
*
328103 TCTGTTTTTTTTTTGT
1 TCTGTTTTTTTTTCGT
328119 TCT
1 TCT
328122 CTGCCGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (16 bp):
TCTGTTTTTTTTTCGT
Found at i:328547 original size:3 final size:3
Alignment explanation
Indices: 328539--328654 Score: 153
Period size: 3 Copynumber: 37.7 Consensus size: 3
328529 TTATTTATTA
*
328539 AAT AAT AAT AAT ATAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* *
328586 AAT AAT AAAT AAT TAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
328632 AAT AAT AAT -TT CAAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AA
328655 ATTTAAATGA
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
2 1 0.01
3 89 0.89
4 10 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:328912 original size:76 final size:76
Alignment explanation
Indices: 328781--329424 Score: 1189
Period size: 76 Copynumber: 8.5 Consensus size: 76
328771 GATGGAAATG
* * *
328781 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
328846 CCTGAAGGCTT
66 CCCGAAGGCTT
*
328857 TTTGGAAACATCATGCACTGAAGGACTTACAGATTACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
328922 CCCGAAGGCTT
66 CCCGAAGGCTT
*
328933 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCGAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
328998 CTCGAAGGCTT
66 CCCGAAGGCTT
*
329009 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
329074 CTCGAAGGCTT
66 CCCGAAGGCTT
329085 TTTGGAAACATCATGCACTGAAGGAACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGG-ACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGC
329150 TCCCGAAGGCTT
65 TCCCGAAGGCTT
329162 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
329227 CCCGAAGGCTT
66 CCCGAAGGCTT
329238 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
329303 CCCGAAGGCTT
66 CCCGAAGGCTT
329314 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
329379 CCCAAAGGCTT
66 CCCGAAGGCTT
329390 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
329425 TGAGAAATAG
Statistics
Matches: 554, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
76 480 0.87
77 74 0.13
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:329356 original size:305 final size:304
Alignment explanation
Indices: 328781--329424 Score: 1189
Period size: 305 Copynumber: 2.1 Consensus size: 304
328771 GATGGAAATG
* * *
328781 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
* *
328846 CCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATTACCCGAAGGATTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
328911 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
* *
328976 GATTTGAAAACATCGAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
196 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
* * *
329041 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTT
261 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCAAAGGCTT
329085 TTTGGAAACATCATGCACTGAAGGAACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGG-ACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGC
329150 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAA
329215 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
329280 GGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACA
195 GGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACA
329345 GATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCAAAGGCTT
260 GATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCAAAGGCTT
329390 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
329425 TGAGAAATAG
Statistics
Matches: 329, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
304 34 0.10
305 295 0.90
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (304 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCAAAGGCTT
Found at i:332643 original size:114 final size:114
Alignment explanation
Indices: 332443--332761 Score: 541
Period size: 114 Copynumber: 2.8 Consensus size: 114
332433 ACAATCATGT
* * * * * *
332443 AATTCACCTTTCAATTCCAATGATTGGTTCTGG-GATTCATACCAAACCAGACCAGATAACTTAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAG-TTCATACCAAACCAGATCAGATAACTCAA
*
332507 AGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
65 AGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCA
*
332557 AATTCATCTTTCAAATCTAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
*
332622 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCA
332671 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
332736 GAACACTTCCAGAAGATGCTATTGAG
66 GAACACTTCCAGAAGATGCTATTGAG
332762 CACATTATTC
Statistics
Matches: 194, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 193 0.99
115 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCA
Found at i:332841 original size:84 final size:84
Alignment explanation
Indices: 332715--332937 Score: 430
Period size: 84 Copynumber: 2.7 Consensus size: 84
332705 GTTCATACCA
332715 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
332780 TCAATGATTGG-TCTTGTCC
66 TCAATGATTGGTTC-TGTCC
332799 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
332864 TCAATGATTGGTTCTGTCC
66 TCAATGATTGGTTCTGTCC
332883 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
332938 ATTTGTTCCA
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
84 136 0.99
85 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
TCAATGATTGGTTCTGTCC
Found at i:340563 original size:53 final size:53
Alignment explanation
Indices: 340448--340566 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 53
340438 TATAATATAG
* * * * * *
340448 TAAAACAATAATTAAAGTAATGATTGAAAATATATTAAAATAATAAAAATTAAGT
1 TAAAAC-ATAACTAAA-CAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
**
340503 TAAAACATAACTAAACAATGATTAAAAATA-AATAAAATAATAAATGTAAAAT
1 TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
*
340555 TATGAACATAAC
1 TA-AAACATAAC
340567 CTGAATCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 19 0.35
53 21 0.39
54 8 0.15
55 6 0.11
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (53 bp):
TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
Found at i:341425 original size:16 final size:16
Alignment explanation
Indices: 341406--341440 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
341396 CTTTTCCTCC
341406 TCTGTTTTTTTTTCGT
1 TCTGTTTTTTTTTCGT
*
341422 TCTGTTTTTTTTTTGT
1 TCTGTTTTTTTTTCGT
341438 TCT
1 TCT
341441 CTGCCGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (16 bp):
TCTGTTTTTTTTTCGT
Found at i:341866 original size:3 final size:3
Alignment explanation
Indices: 341858--341976 Score: 150
Period size: 3 Copynumber: 38.7 Consensus size: 3
341848 TTATTTATTA
*
341858 AAT AAT AAT AAT ATAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * *
341905 AAT AAT AAAT AAT TAT AAT TAT AAT AAT AAT AAT AAT ACT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
341951 AAT AAT AAT AAT -TT CAAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AA
341977 ATTTAAATGA
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 90 0.89
4 10 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:345029 original size:15 final size:15
Alignment explanation
Indices: 345005--345055 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
344995 TATTTAGCTA
*
345005 GGCGGGCGGATGTGG
1 GGCGGGCGGATGCGG
*
345020 GGCGGACGGATGCGG
1 GGCGGGCGGATGCGG
345035 GGCGGGCGGATGCGG
1 GGCGGGCGGATGCGG
345050 GGCGGG
1 GGCGGG
345056 TAATGTCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.18, G:0.67, T:0.08
Consensus pattern (15 bp):
GGCGGGCGGATGCGG
Found at i:347379 original size:34 final size:34
Alignment explanation
Indices: 347336--347420 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
347326 TATGATTGAT
347336 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
347370 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
347404 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
347421 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:347474 original size:22 final size:22
Alignment explanation
Indices: 347449--347505 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
347439 CGTGAGAAAT
347449 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAGAG
347471 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAGAG
*
347493 CACGGGTCCTGCA
1 CACGGGTTCTGCA
347506 GGGCTGCACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.23, G:0.39, T:0.14
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAGAG
Found at i:347539 original size:23 final size:23
Alignment explanation
Indices: 347509--347552 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
347499 TCCTGCAGGG
347509 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
347532 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
347553 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:347559 original size:23 final size:22
Alignment explanation
Indices: 347506--347559 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
347496 GGGTCCTGCA
347506 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
347528 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
347551 GGGCATGCA
1 GGGC-TGCA
347560 ACTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:348297 original size:172 final size:173
Alignment explanation
Indices: 348010--348353 Score: 548
Period size: 172 Copynumber: 2.0 Consensus size: 173
348000 TTGTAAAGTT
* * *
348010 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGACCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
*
348075 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
348138 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
* * * *
348182 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGACCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
348247 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
348312 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTA
131 GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTA
348354 GATAACATGC
Statistics
Matches: 157, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
172 110 0.70
173 46 0.29
174 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (173 bp):
TTAGGGACCGTTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:350075 original size:6 final size:6
Alignment explanation
Indices: 350064--350088 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
350054 CAAGAAGGAC
350064 TGGGAG TGGGAG TGGGAG TGGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG T
350089 TCTTCTCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.64, T:0.20
Consensus pattern (6 bp):
TGGGAG
Found at i:350669 original size:37 final size:37
Alignment explanation
Indices: 350619--351591 Score: 1118
Period size: 37 Copynumber: 26.0 Consensus size: 37
350609 CATTAAAATT
*
350619 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
350656 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATCATTA
1 AAGT-A--ATTA-T---T-ATTAAATCATTAAA--ATTAAATCATTA
* *
350703 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
350740 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
*
350779 AAATAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
*
350818 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATT-A
*
350856 ATCATTAAAGTTAAATTATTAAATCATTAAAATTAAATCATTA
1 A--AGT-AA-TT--ATTATTAAATCATTAAAATTAAATCATTA
350899 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
350936 AAGTAATTATTATTAAATCATT-AAAGT-AATTATT-
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
350970 -ATTAA--ATCATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* *
351006 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
351043 AAGTAATTATTATTAAATCATTAAATCATTAAATCATT-
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* * **
351081 -A--AATCATTA--AAATAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* * * **
351113 AA-TCATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATTATTAAA-TCATTAAAATTAAATCATTA
*
351152 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAATTAAATCATTA
351188 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
351225 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
351262 AAGTAATTATTATTAAATC------ATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
351293 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
351330 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
*
351369 AAATAATTATTATTAAATC------ATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
351400 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTAA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATT-A
* *
351438 ATTATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTA
1 A--AGT-AA-TT--ATTATTAAATCATTAAAATTAAATCATTA
*
351481 AAGTAATTATTATTAAATCACTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
351518 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
351555 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
351592 TTATTAAATC
Statistics
Matches: 821, Mismatches: 53, Indels: 124
0.82 0.05 0.12
Matches are distributed among these distances:
31 83 0.10
32 2 0.00
33 13 0.02
34 4 0.00
35 22 0.03
36 27 0.03
37 375 0.46
38 8 0.01
39 166 0.20
40 13 0.02
41 11 0.01
42 4 0.00
43 5 0.01
44 58 0.07
45 13 0.02
46 1 0.00
47 16 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:351500 original size:23 final size:22
Alignment explanation
Indices: 350630--351468 Score: 243
Period size: 23 Copynumber: 37.3 Consensus size: 22
350620 AGTAATTATT
* **
350630 ATTAAATTATTAAAATTAAATC
1 ATTAAATAATTATCATTAAATC
*
350652 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TAATTATCATTAAATC
*
350675 ATTAAATCATTAAATCATTAAATC
1 ATTAAATAATT--ATCATTAAATC
* *
350699 ATTAAAGTAATTATTATTAAAGC
1 ATTAAA-TAATTATCATTAAATC
*
350722 ATTAAAGTTAA--ATCATTAAAGTA
1 ATTAAA--TAATTATCATTAAA-TC
*
350745 ATT--ATTATTAAATCATTAAATC
1 ATTAAATAATT--ATCATTAAATC
* * * *
350767 ATTAAATCATTA-AAAT-AATT
1 ATTAAATAATTATCATTAAATC
*
350787 ATT-ATTAA--ATCATTAAATC
1 ATTAAATAATTATCATTAAATC
* * * *
350806 ATTAAATCATTA-AAGTAATTATT
1 ATTAAATAATTATCATTAA--ATC
* *
350829 ATTAAATCATTA-AAGTTAAATC
1 ATTAAATAATTATCA-TTAAATC
* * *
350851 ATTAAATCATTA-AAGTTAAATT
1 ATTAAATAATTATCA-TTAAATC
* **
350873 ATTAAATCATTAAAATTAAATC
1 ATTAAATAATTATCATTAAATC
*
350895 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TAATTATCATTAAATC
*
350918 ATT-AA-AATTAAATCATTAAAGTA
1 ATTAAATAATT--ATCATTAAA-TC
* *
350941 ATT--ATTATTAAATCATTAAAGTA
1 ATTAAATAATT--ATCATTAAA-TC
*
350964 ATT--ATTATTAAATCATTAAATC
1 ATTAAATAATT--ATCATTAAATC
* *
350986 ATTAAATCATTAAATCATTAAAGTA
1 ATTAAATAATT--ATCATTAAA-TC
* *
351011 ATTATTATTAAAGCATTA-AAGTTAAATC
1 ATTA--A--ATA--ATTATCA-TTAAATC
*
351039 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TAATTATCATTAAATC
*
351062 ATTAAATCATTAAATCATTAAATC
1 ATTAAATAATT--ATCATTAAATC
*
351086 ATTAAAATAATTATTATTAAATC
1 ATT-AAATAATTATCATTAAATC
* *
351109 ATTAAATCATTAAATCATTAAAGTA
1 ATTAAATAATT--ATCATTAAA-TC
*
351134 ATT--ATTATTAAATCATTAAA--
1 ATTAAATAATT--ATCATTAAATC
* *
351154 GTTAAATCATTAAATCATTAAA--
1 ATTAAATAATT--ATCATTAAATC
* * * *
351176 ATTAAATCATTA-AAGTAATTATT
1 ATTAAATAATTATCATTAA--ATC
* **
351199 ATTAAATCATTAAAATTAAATC
1 ATTAAATAATTATCATTAAATC
*
351221 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TAATTATCATTAAATC
*
351244 ATTAAAGTTAA--ATCATTAAAGTA
1 ATTAAA--TAATTATCATTAAA-TC
*
351267 ATT--ATTATTAAATCATTAAATC
1 ATTAAATAATT--ATCATTAAATC
* *
351289 ATTAAAGTAATTATTATTAAAGC
1 ATTAAA-TAATTATCATTAAATC
*
351312 ATTAAAGTTAA--ATCATTAAAGTA
1 ATTAAA--TAATTATCATTAAA-TC
*
351335 ATT--ATTATTAAATCATTAAATC
1 ATTAAATAATT--ATCATTAAATC
* * * *
351357 ATTAAATCATTA-AAAT-AATT
1 ATTAAATAATTATCATTAAATC
*
351377 ATT-ATTAA--ATCATTAAATC
1 ATTAAATAATTATCATTAAATC
*
351396 ATTAAAGTAATTATTATTAAATC
1 ATTAAA-TAATTATCATTAAATC
*
351419 ATTAAAGTTAA--ATCATTAAATT
1 ATTAAA--TAATTATCATTAAATC
351441 ATTAAAGTTAA--ATCATTAAATC
1 ATTAAA--TAATTATCATTAAATC
351463 ATTAAA
1 ATTAAA
351469 ATTAAATCAT
Statistics
Matches: 647, Mismatches: 94, Indels: 152
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.00
18 4 0.01
19 28 0.04
20 23 0.04
21 15 0.02
22 192 0.30
23 254 0.39
24 86 0.13
25 25 0.04
26 1 0.00
27 1 0.00
28 6 0.01
29 7 0.01
31 3 0.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (22 bp):
ATTAAATAATTATCATTAAATC
Found at i:351622 original size:8 final size:8
Alignment explanation
Indices: 350588--351607 Score: 623
Period size: 8 Copynumber: 135.8 Consensus size: 8
350578 AGTAATTATT
350588 ATTAAATC
1 ATTAAATC
350596 ATTAAA--
1 ATTAAATC
350602 ATTAAATC
1 ATTAAATC
350610 ATTAAA--
1 ATTAAATC
* *
350616 ATTAAGTA
1 ATTAAATC
*
350624 ATT--ATT
1 ATTAAATC
*
350630 ATTAAATT
1 ATTAAATC
350638 ATTAAA--
1 ATTAAATC
350644 ATTAAATC
1 ATTAAATC
*
350652 ATTAAAGTA
1 ATTAAA-TC
*
350661 ATT--ATT
1 ATTAAATC
350667 ATTAAATC
1 ATTAAATC
350675 ATTAAATC
1 ATTAAATC
350683 ATTAAATC
1 ATTAAATC
350691 ATTAAATC
1 ATTAAATC
*
350699 ATTAAAGTA
1 ATTAAA-TC
*
350708 ATT--ATT
1 ATTAAATC
*
350714 ATTAAAGC
1 ATTAAATC
350722 ATTAAA--
1 ATTAAATC
*
350728 GTTAAATC
1 ATTAAATC
*
350736 ATTAAAGTA
1 ATTAAA-TC
*
350745 ATT--ATT
1 ATTAAATC
350751 ATTAAATC
1 ATTAAATC
350759 ATTAAATC
1 ATTAAATC
350767 ATTAAATC
1 ATTAAATC
*
350775 ATTAAAATA
1 ATT-AAATC
*
350784 ATT--ATT
1 ATTAAATC
350790 ATTAAATC
1 ATTAAATC
350798 ATTAAATC
1 ATTAAATC
350806 ATTAAATC
1 ATTAAATC
*
350814 ATTAAAGTA
1 ATTAAA-TC
*
350823 ATT--ATT
1 ATTAAATC
350829 ATTAAATC
1 ATTAAATC
350837 ATTAAA--
1 ATTAAATC
*
350843 GTTAAATC
1 ATTAAATC
350851 ATTAAATC
1 ATTAAATC
350859 ATTAAA--
1 ATTAAATC
* *
350865 GTTAAATT
1 ATTAAATC
350873 ATTAAATC
1 ATTAAATC
350881 ATTAAA--
1 ATTAAATC
350887 ATTAAATC
1 ATTAAATC
*
350895 ATTAAAGTA
1 ATTAAA-TC
*
350904 ATT--ATT
1 ATTAAATC
350910 ATTAAATC
1 ATTAAATC
350918 ATTAAA--
1 ATTAAATC
350924 ATTAAATC
1 ATTAAATC
*
350932 ATTAAAGTA
1 ATTAAA-TC
*
350941 ATT--ATT
1 ATTAAATC
350947 ATTAAATC
1 ATTAAATC
*
350955 ATTAAAGTA
1 ATTAAA-TC
*
350964 ATT--ATT
1 ATTAAATC
350970 ATTAAATC
1 ATTAAATC
350978 ATTAAATC
1 ATTAAATC
350986 ATTAAATC
1 ATTAAATC
350994 ATTAAATC
1 ATTAAATC
*
351002 ATTAAAGTA
1 ATTAAA-TC
*
351011 ATT--ATT
1 ATTAAATC
*
351017 ATTAAAGC
1 ATTAAATC
351025 ATTAAA--
1 ATTAAATC
*
351031 GTTAAATC
1 ATTAAATC
*
351039 ATTAAAGTA
1 ATTAAA-TC
*
351048 ATT--ATT
1 ATTAAATC
351054 ATTAAATC
1 ATTAAATC
351062 ATTAAATC
1 ATTAAATC
351070 ATTAAATC
1 ATTAAATC
351078 ATTAAATC
1 ATTAAATC
*
351086 ATTAAAATA
1 ATT-AAATC
*
351095 ATT--ATT
1 ATTAAATC
351101 ATTAAATC
1 ATTAAATC
351109 ATTAAATC
1 ATTAAATC
351117 ATTAAATC
1 ATTAAATC
*
351125 ATTAAAGTA
1 ATTAAA-TC
*
351134 ATT--ATT
1 ATTAAATC
351140 ATTAAATC
1 ATTAAATC
351148 ATTAAA--
1 ATTAAATC
*
351154 GTTAAATC
1 ATTAAATC
351162 ATTAAATC
1 ATTAAATC
351170 ATTAAA--
1 ATTAAATC
351176 ATTAAATC
1 ATTAAATC
*
351184 ATTAAAGTA
1 ATTAAA-TC
*
351193 ATT--ATT
1 ATTAAATC
351199 ATTAAATC
1 ATTAAATC
351207 ATTAAA--
1 ATTAAATC
351213 ATTAAATC
1 ATTAAATC
*
351221 ATTAAAGTA
1 ATTAAA-TC
*
351230 ATT--ATT
1 ATTAAATC
351236 ATTAAATC
1 ATTAAATC
351244 ATTAAA--
1 ATTAAATC
*
351250 GTTAAATC
1 ATTAAATC
*
351258 ATTAAAGTA
1 ATTAAA-TC
*
351267 ATT--ATT
1 ATTAAATC
351273 ATTAAATC
1 ATTAAATC
351281 ATTAAATC
1 ATTAAATC
*
351289 ATTAAAGTA
1 ATTAAA-TC
*
351298 ATT--ATT
1 ATTAAATC
*
351304 ATTAAAGC
1 ATTAAATC
351312 ATTAAA--
1 ATTAAATC
*
351318 GTTAAATC
1 ATTAAATC
*
351326 ATTAAAGTA
1 ATTAAA-TC
*
351335 ATT--ATT
1 ATTAAATC
351341 ATTAAATC
1 ATTAAATC
351349 ATTAAATC
1 ATTAAATC
351357 ATTAAATC
1 ATTAAATC
*
351365 ATTAAAATA
1 ATT-AAATC
*
351374 ATT--ATT
1 ATTAAATC
351380 ATTAAATC
1 ATTAAATC
351388 ATTAAATC
1 ATTAAATC
*
351396 ATTAAAGTA
1 ATTAAA-TC
*
351405 ATT--ATT
1 ATTAAATC
351411 ATTAAATC
1 ATTAAATC
351419 ATTAAA--
1 ATTAAATC
*
351425 GTTAAATC
1 ATTAAATC
*
351433 ATTAAATT
1 ATTAAATC
351441 ATTAAA--
1 ATTAAATC
*
351447 GTTAAATC
1 ATTAAATC
351455 ATTAAATC
1 ATTAAATC
351463 ATTAAA--
1 ATTAAATC
351469 ATTAAATC
1 ATTAAATC
*
351477 ATTAAAGTA
1 ATTAAA-TC
*
351486 ATT--ATT
1 ATTAAATC
351492 ATTAAATC
1 ATTAAATC
*
351500 ACTAAA--
1 ATTAAATC
351506 ATTAAATC
1 ATTAAATC
*
351514 ATTAAAGTA
1 ATTAAA-TC
*
351523 ATT--ATT
1 ATTAAATC
351529 ATTAAATC
1 ATTAAATC
351537 ATTAAA--
1 ATTAAATC
*
351543 GTTAAATC
1 ATTAAATC
*
351551 ATTAAAGTA
1 ATTAAA-TC
*
351560 ATT--ATT
1 ATTAAATC
351566 ATTAAATC
1 ATTAAATC
351574 ATTAAA--
1 ATTAAATC
* *
351580 GTTAAATA
1 ATTAAATC
*
351588 ATT--ATT
1 ATTAAATC
351594 ATTAAATC
1 ATTAAATC
351602 ATTAAA
1 ATTAAA
351608 GTTAAATAAT
Statistics
Matches: 802, Mismatches: 100, Indels: 220
0.71 0.09 0.20
Matches are distributed among these distances:
6 207 0.26
7 19 0.02
8 479 0.60
9 97 0.12
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (8 bp):
ATTAAATC
Found at i:351642 original size:14 final size:13
Alignment explanation
Indices: 351162--351633 Score: 103
Period size: 14 Copynumber: 35.9 Consensus size: 13
351152 AAGTTAAATC
*
351162 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
351176 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
351189 AGT-AATTATT--
1 ATTAAATAATTAA
*
351199 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
351213 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
351226 AGT-AATTATT--
1 ATTAAATAATTAA
*
351236 ATTAAATCATTAA
1 ATTAAATAATTAA
*
351249 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* *
351263 AGT-AATTATT--
1 ATTAAATAATTAA
*
351273 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
351287 TCATTAAAGTAATTATT
1 --ATTAAA-TAATTA-A
**
351304 ATTAAAGCATTAA
1 ATTAAATAATTAA
*
351317 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* *
351331 AGT-AATTATT--
1 ATTAAATAATTAA
*
351341 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
351355 TCATTAAATCATTAA
1 --ATTAAATAATTAA
* *
351370 AAT-AATTATT--
1 ATTAAATAATTAA
*
351380 ATTAAATCATTAAA
1 ATTAAATAATT-AA
*
351394 TCATTAAAGTAATTATT
1 --ATTAAA-TAATTA-A
*
351411 ATTAAATCATTAA
1 ATTAAATAATTAA
*
351424 AGTTAAATCATTAA
1 A-TTAAATAATTAA
*
351438 ATTATTAA-AGTTAAA
1 ATTA--AATAATT-AA
*
351453 TCATTAAATCATTAAA
1 --ATTAAATAATT-AA
*
351469 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
351482 AGT-AATTATT--
1 ATTAAATAATTAA
* *
351492 ATTAAATCACTAAA
1 ATTAAAT-AATTAA
*
351506 ATTAAATCATTAA
1 ATTAAATAATTAA
* *
351519 AGT-AATTATT--
1 ATTAAATAATTAA
*
351529 ATTAAATCATTAA
1 ATTAAATAATTAA
*
351542 AGTTAAATCATTAA
1 A-TTAAATAATTAA
* *
351556 AGT-AATTATT--
1 ATTAAATAATTAA
*
351566 ATTAAATCATTAA
1 ATTAAATAATTAA
*
351579 AGTTAAATAATTATT
1 A-TTAAATAATTA-A
*
351594 ATTAAATCATTAA
1 ATTAAATAATTAA
351607 AGTTAAATAATTAA
1 A-TTAAATAATTAA
351621 ATTTAAATAATTA
1 A-TTAAATAATTA
351634 TTATTAAATT
Statistics
Matches: 349, Mismatches: 57, Indels: 104
0.68 0.11 0.20
Matches are distributed among these distances:
10 16 0.05
11 45 0.13
12 49 0.14
13 31 0.09
14 145 0.42
15 21 0.06
16 30 0.09
17 12 0.03
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (13 bp):
ATTAAATAATTAA
Found at i:355001 original size:18 final size:18
Alignment explanation
Indices: 354978--355024 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
354968 AAATTATTAG
354978 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
354996 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
355014 TCTCACGCTTC
1 TCTCACGCTTC
355025 GACCACAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:358037 original size:18 final size:18
Alignment explanation
Indices: 358016--358051 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
358006 CATCAATACT
358016 ATGATGAAATTCAATTCC
1 ATGATGAAATTCAATTCC
358034 ATGATGAAATTCAATTCC
1 ATGATGAAATTCAATTCC
358052 CTTATTGGAG
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:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
ATGATGAAATTCAATTCC
Found at i:359222 original size:21 final size:22
Alignment explanation
Indices: 359187--359228 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
359177 GAAAGGAATA
359187 ATCATTAAAACTTA-TAAAATT
1 ATCATTAAAACTTATTAAAATT
**
359208 ATCATTAAATTTTATTAAAAT
1 ATCATTAAAACTTATTAAAAT
359229 CATTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
ATCATTAAAACTTATTAAAATT
Found at i:375706 original size:25 final size:25
Alignment explanation
Indices: 375672--375719 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
375662 ACTTAAGGCT
375672 CAATTGGGATTTAAATAGAAATTTA
1 CAATTGGGATTTAAATAGAAATTTA
*
375697 CAATTGGGATTTACATAGAAATT
1 CAATTGGGATTTAAATAGAAATT
375720 AACAGATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (25 bp):
CAATTGGGATTTAAATAGAAATTTA
Found at i:382865 original size:186 final size:186
Alignment explanation
Indices: 382540--382931 Score: 673
Period size: 186 Copynumber: 2.1 Consensus size: 186
382530 TTTTATAATT
* *
382540 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTAAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
382604 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
382669 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGACTGAG-TCCATATGTTA
131 TTGAATCTTAAATTATTAATTAGATTTTAAATGGTTTGGACTGAGCT-CATATGTTA
* *
382725 TATATAATATATTAAATATTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTAAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
382790 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
382855 TTGGATCTTAAATTATTAATTAGATTTTAAATGGTTTGGGCTGAGCTCATATGTTA
131 TTGAATCTTAAATTATTAATTAGATTTTAAATGGTTTGGACTGAGCTCATATGTTA
382911 TATATAATATATTTAAA-ATTT
1 TATATAATATA-TTAAATATTT
382932 AAAATTTTAT
Statistics
Matches: 196, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
185 7 0.04
186 183 0.93
187 6 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (186 bp):
TATATAATATATTAAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTAGATTTTAAATGGTTTGGACTGAGCTCATATGTTA
Found at i:382956 original size:9 final size:9
Alignment explanation
Indices: 382942--382970 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
382932 AAAATTTTAT
382942 TTCGGTTAA
1 TTCGGTTAA
382951 TTCGGTTAA
1 TTCGGTTAA
382960 TTCGGTTAA
1 TTCGGTTAA
382969 TT
1 TT
382971 AACCGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:386996 original size:20 final size:20
Alignment explanation
Indices: 386967--387004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
386957 TTTCAAGGGT
386967 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
* *
386987 ATGCATCGATGCATCAAT
1 ATGCACCGATGCACCAAT
387005 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:387060 original size:19 final size:20
Alignment explanation
Indices: 387032--387084 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
387022 AATGCATTTT
*
387032 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAAGACC
* *
387051 ATGTATCGATGCACAAGACT
1 ATGCATCGATGCACAAGACC
387071 ATGCATCGATGCAC
1 ATGCATCGATGCAC
387085 TCAGGCCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:387124 original size:45 final size:45
Alignment explanation
Indices: 387070--387176 Score: 178
Period size: 45 Copynumber: 2.4 Consensus size: 45
387060 TGCACAAGAC
387070 TATGCATCGATGCACTCAGGCCTTTTCAAAACATCGAATACATTT
1 TATGCATCGATGCACTCAGGCCTTTTCAAAACATCGAATACATTT
** * *
387115 TATGCATCGATGCACTCAGGTTTTTTTAAAACATCGAATGCATTT
1 TATGCATCGATGCACTCAGGCCTTTTCAAAACATCGAATACATTT
387160 TATGCATCGATGCACTC
1 TATGCATCGATGCACTC
387177 TTAGTGCACC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (45 bp):
TATGCATCGATGCACTCAGGCCTTTTCAAAACATCGAATACATTT
Found at i:396536 original size:28 final size:28
Alignment explanation
Indices: 396496--396562 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
396486 ACAATTGTTG
396496 AAAATGTTGTATTGAAGTTGAGATAGGT
1 AAAATGTTGTATTGAAGTTGAGATAGGT
396524 AAAATGTTGTATTGAAGTTGAGATAGGT
1 AAAATGTTGTATTGAAGTTGAGATAGGT
396552 AAAATGTTGTA
1 AAAATGTTGTA
396563 GCAAAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.36
Consensus pattern (28 bp):
AAAATGTTGTATTGAAGTTGAGATAGGT
Found at i:401363 original size:930 final size:930
Alignment explanation
Indices: 399563--401422 Score: 3405
Period size: 930 Copynumber: 2.0 Consensus size: 930
399553 TTCTTAATCA
399563 TAGTAGGCATACAATTGTGTATAAAATTCAGGAGCAAGTAACCGTGTCCTAAAGTTAGTTCTATC
1 TAGTAGGCATACAATTGTGTATAAAATTCAGGAGCAAGTAACCGTGTCCTAAAGTTAGTTCTATC
*
399628 AACCACAACAATCATTTATTCAATAAATCACAACCTACAGCTTCTCATCATCGGGCATCATCAAA
66 AACCACAACAATCATTTATTCAATAAATCACAACCTACAGCTTCACATCATCGGGCATCATCAAA
* *
399693 TTTTCCATAAACTATTCTAAACCAAACAAATGTTATAACAAATATTTTGTTAAACAAAATACTGA
131 TTTTCCATAAACTATTCTAAACCAAACAAATGTTATAACAAATATTTTGTTAAACAAAACACTAA
*
399758 CGCAAATAATTAAATATAACACCACCTCCCCCAAACTCGAGAGATACAGTGTCCTCAATACATGG
196 CGCAAATAATTAAATATAACACCACCTCCCCCAAACTCGAGAGATACAGTATCCTCAATACATGG
* * *
399823 AAACTAAAATATATGCAATGCAAATGCAACATGTGGAACCTCATTTTGGTGGACATATTATCTTT
261 AAACTAAAATATATACAATACAAATGCAACATGTGAAACCTCATTTTGGTGGACATATTATCTTT
* *
399888 CTGGTCGTATGCTTCACATGCTTCTTGCGAAGGGCTGCAATGGGTTGTTCAGTATCGCATGGTGT
326 CTGGTCGTATGCTTCACATGCTTCTTGCGAAGGGCTGCAATGGGTTATTCAATATCGCATGGTGT
*
399953 TGAAGATGGGTTGTCCTCGATGGCCTCATCATTCTCCTCAGTAGGAGAGTTCCATATTATTCATG
391 TGAAGATGGGTTGTCCTCGATGGCCTCATCATTCTCCTCAGTAGGAGAGTTCAATATTATTCATG
* *
400018 TAGTTCGTTTCAGATGATACTTAGTCCATGGAGTGGTCTTGGGTGGTGCGACAAGTGTAGGATCA
456 TAGTTCGTTTCAGACGATACTTAGTCCATGGAGTGGTATTGGGTGGTGCGACAAGTGTAGGATCA
400083 GGGTTGGTGTTAATATTTTCATCATCGTCACTGTCCACCGTGATAAGTTCTTATTCAGTCGCTTA
521 GGGTTGGTGTTAATATTTTCATCATCGTCACTGTCCACCGTGATAAGTTCTTATTCAGTCGCTTA
*
400148 TGATGTTGGAGTGTGTATGGGAGCTTTGGCTTTGTCTTGCTGCAAAAAAGGTTGATGTGCAGTTG
586 TGATGTTGGAGTGTATATGGGAGCTTTGGCTTTGTCTTGCTGCAAAAAAGGTTGATGTGCAGTTG
*
400213 TTTCAGCACTGACACTATCTTGCATTATGTCCTTTGGAAGGGGTGCAACTTCACTTGGTTGTGGA
651 CTTCAGCACTGACACTATCTTGCATTATGTCCTTTGGAAGGGGTGCAACTTCACTTGGTTGTGGA
*
400278 GGTGTTTTCACTGGCGCAAGTAAGGAGTTCGGGAATAGAAGGAAGTCAGCAGTTACTTACAACAA
716 GGTGTTTTCACTGGCGCAAGTAAAGAGTTCGGGAATAGAAGGAAGTCAGCAGTTACTTACAACAA
*
400343 CATTTCTTGAAAACAGTTGTTTAACACCGAATCCCTCTCCTTGACGTAGGCGAAAAAGGTTCGTA
781 CATTTCTTGAAAACAGTTGTTTAACACCGAATCCCTCTCCTTGACGTAGGCAAAAAAGGTTCGTA
400408 GATTCTTCTTGAGTTCCTCCAGCTCCCCCTCCTGGTTTGTGTTGAGGCCACCGCTGAGGTTAATC
846 GATTCTTCTTGAGTTCCTCCAGCTCCCCCTCCTGGTTTGTGTTGAGGCCACCGCTGAGGTTAATC
400473 ATGTTGTAGCAAAAGTTTTG
911 ATGTTGTAGCAAAAGTTTTG
*
400493 TAGTAGGCATACAATTGTGTATAAAATTCAGGAGCAAGTAACTGTGTCCTAAAGTTAGTTCTATC
1 TAGTAGGCATACAATTGTGTATAAAATTCAGGAGCAAGTAACCGTGTCCTAAAGTTAGTTCTATC
400558 AACCACAACAATCATTTATTCAATAAATCACAACCTACAGCTTCACATCATCGGGCATCATCAAA
66 AACCACAACAATCATTTATTCAATAAATCACAACCTACAGCTTCACATCATCGGGCATCATCAAA
*
400623 TTTTCCATAAACTATTCTAAACCAAACAAATGTTATAACAAATATTTTGTTAAACAAAACGCTAA
131 TTTTCCATAAACTATTCTAAACCAAACAAATGTTATAACAAATATTTTGTTAAACAAAACACTAA
* * * *
400688 TGCAAATGATTAACTATAACACCACCTCCCCCAAACTCGAGAGATGCAGTATCCTCAATACATGG
196 CGCAAATAATTAAATATAACACCACCTCCCCCAAACTCGAGAGATACAGTATCCTCAATACATGG
* *
400753 AAACTAAAATATATACAATACAAATGCAACATGTGAAACCTCATTTTGGTGTACATATTGTCTTT
261 AAACTAAAATATATACAATACAAATGCAACATGTGAAACCTCATTTTGGTGGACATATTATCTTT
*
400818 CTGGTCGTATGCTTCACATGCTTCTTGCGAAGGGTTGCAATGGGTTATTCAATATCGCATGGTGT
326 CTGGTCGTATGCTTCACATGCTTCTTGCGAAGGGCTGCAATGGGTTATTCAATATCGCATGGTGT
*
400883 TGAAGATGGGTTGTCCTCGATGGCCTCATCATTCTCCTCAGTAGGAGAGTTCAATATTATTCCTG
391 TGAAGATGGGTTGTCCTCGATGGCCTCATCATTCTCCTCAGTAGGAGAGTTCAATATTATTCATG
*
400948 TAGTTCGTTTCAGACGATACTTAGTCCATGGAGTGGTATTGGGTGGTGCGATAAGTGTAGGATCA
456 TAGTTCGTTTCAGACGATACTTAGTCCATGGAGTGGTATTGGGTGGTGCGACAAGTGTAGGATCA
* *
401013 GGGTTGGTGTTGATATTTTCATCATCGTCACTGTCTACCGTGATAAGTTCTTATTCAGTCGCTTA
521 GGGTTGGTGTTAATATTTTCATCATCGTCACTGTCCACCGTGATAAGTTCTTATTCAGTCGCTTA
*
401078 TGATGTTGGAGTGTATATGGGAGCTTTGGCTTTGTCTTGTTGCAAAAAAGGTTGATGTGCAGTTG
586 TGATGTTGGAGTGTATATGGGAGCTTTGGCTTTGTCTTGCTGCAAAAAAGGTTGATGTGCAGTTG
* *
401143 CTTCAGCACTGGCACTATGTTGCATTATGTCCTTTGGAAGGGGTGCAACTTCACTTGGTTGTGGA
651 CTTCAGCACTGACACTATCTTGCATTATGTCCTTTGGAAGGGGTGCAACTTCACTTGGTTGTGGA
* *
401208 GGTGTTTTCACTGGCGTAAGTAAAGAGTTCGGGAATAGAGGGAAGTCAGCAGTTACTTACAACAA
716 GGTGTTTTCACTGGCGCAAGTAAAGAGTTCGGGAATAGAAGGAAGTCAGCAGTTACTTACAACAA
*
401273 CATTTCTTGAAAATAGTTGTTTAACACCGAATCCCTCTCCTTGACGTAGGCAAAAAAGGTTCGTA
781 CATTTCTTGAAAACAGTTGTTTAACACCGAATCCCTCTCCTTGACGTAGGCAAAAAAGGTTCGTA
401338 GATTCTTCTTGAGTTCCTCCAGCTCCCCCTCCTGGTTTGTGTTGAGGCCACCGCTGAGGTTAATC
846 GATTCTTCTTGAGTTCCTCCAGCTCCCCCTCCTGGTTTGTGTTGAGGCCACCGCTGAGGTTAATC
401403 ATGTTGTAGCAAAAGTTTTG
911 ATGTTGTAGCAAAAGTTTTG
401423 GCTCATCCTT
Statistics
Matches: 895, Mismatches: 35, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
930 895 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (930 bp):
TAGTAGGCATACAATTGTGTATAAAATTCAGGAGCAAGTAACCGTGTCCTAAAGTTAGTTCTATC
AACCACAACAATCATTTATTCAATAAATCACAACCTACAGCTTCACATCATCGGGCATCATCAAA
TTTTCCATAAACTATTCTAAACCAAACAAATGTTATAACAAATATTTTGTTAAACAAAACACTAA
CGCAAATAATTAAATATAACACCACCTCCCCCAAACTCGAGAGATACAGTATCCTCAATACATGG
AAACTAAAATATATACAATACAAATGCAACATGTGAAACCTCATTTTGGTGGACATATTATCTTT
CTGGTCGTATGCTTCACATGCTTCTTGCGAAGGGCTGCAATGGGTTATTCAATATCGCATGGTGT
TGAAGATGGGTTGTCCTCGATGGCCTCATCATTCTCCTCAGTAGGAGAGTTCAATATTATTCATG
TAGTTCGTTTCAGACGATACTTAGTCCATGGAGTGGTATTGGGTGGTGCGACAAGTGTAGGATCA
GGGTTGGTGTTAATATTTTCATCATCGTCACTGTCCACCGTGATAAGTTCTTATTCAGTCGCTTA
TGATGTTGGAGTGTATATGGGAGCTTTGGCTTTGTCTTGCTGCAAAAAAGGTTGATGTGCAGTTG
CTTCAGCACTGACACTATCTTGCATTATGTCCTTTGGAAGGGGTGCAACTTCACTTGGTTGTGGA
GGTGTTTTCACTGGCGCAAGTAAAGAGTTCGGGAATAGAAGGAAGTCAGCAGTTACTTACAACAA
CATTTCTTGAAAACAGTTGTTTAACACCGAATCCCTCTCCTTGACGTAGGCAAAAAAGGTTCGTA
GATTCTTCTTGAGTTCCTCCAGCTCCCCCTCCTGGTTTGTGTTGAGGCCACCGCTGAGGTTAATC
ATGTTGTAGCAAAAGTTTTG
Found at i:401879 original size:66 final size:66
Alignment explanation
Indices: 401789--401995 Score: 396
Period size: 66 Copynumber: 3.1 Consensus size: 66
401779 ACTCAACCGT
401789 CATCTTGTTAGCGACCGTCACTCCTTACTGTATATGAACCTGTGTGTTCCTTGCCGTAAACCTTC
1 CATCTTGTTAGCGACCGTCACTCCTTACTGTATATGAACCTGTGTGTTCCTTGCCGTAAACCTTC
401854 A
66 A
*
401855 CATCTTGTTAGCGACCGTCACTCCTTACTGTATATGAACCTATGTGTTCCTTGCCGTAAACCTTC
1 CATCTTGTTAGCGACCGTCACTCCTTACTGTATATGAACCTGTGTGTTCCTTGCCGTAAACCTTC
401920 A
66 A
*
401921 CATCTTGTTAGCGACCGTCACTCCTTACTGTATATAAACCTGTGTGTTCCTTGCCGTAAACCTTC
1 CATCTTGTTAGCGACCGTCACTCCTTACTGTATATGAACCTGTGTGTTCCTTGCCGTAAACCTTC
401986 A
66 A
401987 CATCTTGTT
1 CATCTTGTT
401996 GATCGACTTT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 138 1.00
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (66 bp):
CATCTTGTTAGCGACCGTCACTCCTTACTGTATATGAACCTGTGTGTTCCTTGCCGTAAACCTTC
A
Found at i:403615 original size:3 final size:3
Alignment explanation
Indices: 403609--403643 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
403599 CTGCTGCTGC
403609 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
403644 TCCTCCATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:405361 original size:24 final size:23
Alignment explanation
Indices: 405328--405373 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
405318 GGGGATAATT
405328 TAAAATTTTAAAAAATATAAAGG
1 TAAAATTTTAAAAAATATAAAGG
*
405351 TAAAACTTTTAAAAAATTTAAAG
1 TAAAA-TTTTAAAAAATATAAAG
405374 AGTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (23 bp):
TAAAATTTTAAAAAATATAAAGG
Found at i:408285 original size:15 final size:15
Alignment explanation
Indices: 408265--408293 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
408255 ATTTTAGTCC
408265 ATATATATTATATAT
1 ATATATATTATATAT
408280 ATATATATTATATA
1 ATATATATTATATA
408294 GTTTACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATTATATAT
Found at i:408543 original size:17 final size:17
Alignment explanation
Indices: 408498--408554 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
408488 ATATAATATA
*
408498 TATTTGTTTTTATTATTT
1 TATTCGTTTTTATT-TTT
* *
408516 TGTTTCATTTTTATTTTT
1 T-ATTCGTTTTTATTTTT
*
408534 TATTCGTTTTAATTTTT
1 TATTCGTTTTTATTTTT
408551 TATT
1 TATT
408555 TATTTTATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 17 0.53
18 5 0.16
19 10 0.31
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (17 bp):
TATTCGTTTTTATTTTT
Found at i:408560 original size:17 final size:17
Alignment explanation
Indices: 408498--408561 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
408488 ATATAATATA
* *
408498 TATTTGTTTTTATTATTT
1 TATTTATTTTAATT-TTT
* *
408516 TGTTTCATTTTTATTTTT
1 TATTT-ATTTTAATTTTT
**
408534 TATTCGTTTTAATTTTT
1 TATTTATTTTAATTTTT
408551 TATTTATTTTA
1 TATTTATTTTA
408562 TTCTTTCGGC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 19 0.51
18 10 0.27
19 8 0.22
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (17 bp):
TATTTATTTTAATTTTT
Found at i:421853 original size:20 final size:21
Alignment explanation
Indices: 421824--421863 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
421814 TTAATATATC
421824 AAATACATTC-TAAAATTATG
1 AAATACATTCATAAAATTATG
* *
421844 AAATATATTCATAATATTAT
1 AAATACATTCATAAAATTAT
421864 ATTTTAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATACATTCATAAAATTATG
Found at i:424564 original size:7 final size:7
Alignment explanation
Indices: 424552--424581 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
424542 CTCTAACTTA
424552 AAACCCT
1 AAACCCT
424559 AAACCCT
1 AAACCCT
424566 AAACCCT
1 AAACCCT
424573 AAACCCT
1 AAACCCT
424580 AA
1 AA
424582 CCTACTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:431969 original size:31 final size:31
Alignment explanation
Indices: 431931--432058 Score: 213
Period size: 31 Copynumber: 4.1 Consensus size: 31
431921 GAACCTCGGC
431931 AACTGTCCATAGGTCCCGACA-AACCTAGGTA
1 AACTGTCCATAGGTCCCGA-AGAACCTAGGTA
*
431962 AACTGTCCATAGGTCCCGAATAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
431993 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* *
432024 AAATGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
432055 AACT
1 AACT
432059 CTCGACTCTT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
30 1 0.01
31 91 0.99
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:433026 original size:20 final size:22
Alignment explanation
Indices: 433001--433058 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
432991 TTCCCCTTGA
433001 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
433021 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
433044 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
433059 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:433124 original size:64 final size:63
Alignment explanation
Indices: 433046--433186 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
433036 TCTTTAACAT
* * *
433046 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTTGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
433109 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
433173 GTGCATCGATGCAC
1 GTGCATCGATGCAC
433187 ATTCAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 21 0.32
64 45 0.68
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:436151 original size:31 final size:31
Alignment explanation
Indices: 436104--436200 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
436094 CAGAGGTCAC
* * *
436104 AACTGTCTATAAGTCCCGAATAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
436135 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
436166 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
436197 AACT
1 AACT
436201 CTCGACTCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:438794 original size:65 final size:65
Alignment explanation
Indices: 438683--438842 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
438673 AATTAAATTG
* * * *
438683 AACATCGAATGTATTTCATGCATCGATGCA-CATAACATGTACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCATAACATGCACCGATGCACTCAGGATATTT-TG
438746 AA
65 -A
* ** * * *
438748 AACATCGAATACATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATAACATGCACCGATGCACTCAGGATATTTTGA
*
438812 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
438843 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 30 0.37
65 46 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATAACATGCACCGATGCACTCAGGATATTTTGA
Found at i:438842 original size:17 final size:19
Alignment explanation
Indices: 438814--438862 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
438804 TATTTTGAAA
438814 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
438832 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
438851 CACCGATGCACT
1 CATCGATGCACT
438863 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:440795 original size:21 final size:21
Alignment explanation
Indices: 440770--440809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
440760 AAGACTCTAT
440770 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
440791 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
440810 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:446298 original size:21 final size:21
Alignment explanation
Indices: 446256--446299 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
446246 ACTCTGGGAG
* *
446256 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
446277 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
446298 CT
1 CT
446300 CCTCATTCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:447446 original size:56 final size:56
Alignment explanation
Indices: 447393--447511 Score: 143
Period size: 57 Copynumber: 2.1 Consensus size: 56
447383 TTCATGCATC
* *
447393 GATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTT
1 GATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTT
* * * *
447450 GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTT
1 GATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTT
447506 GATGCA
1 GATGCA
447512 TCGGTGCACT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 22 0.41
57 27 0.50
58 5 0.09
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (56 bp):
GATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTT
Found at i:447465 original size:57 final size:56
Alignment explanation
Indices: 447403--447511 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 56
447393 GATGCACATA
* *
447403 CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCACCAG
1 CCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCACCAG
* * *
447460 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCA
447512 TCGGTGCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 22 0.48
57 21 0.46
58 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (56 bp):
CCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCACCAG
Found at i:455054 original size:23 final size:23
Alignment explanation
Indices: 455024--455072 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
455014 TATATACATA
455024 CATAGTCTAGTGCCAATTTAGGC
1 CATAGTCTAGTGCCAATTTAGGC
455047 CATAGTCTAGTGCCAATTTAGGC
1 CATAGTCTAGTGCCAATTTAGGC
455070 CAT
1 CAT
455073 TGTCATTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (23 bp):
CATAGTCTAGTGCCAATTTAGGC
Found at i:457306 original size:16 final size:16
Alignment explanation
Indices: 457285--457318 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
457275 GAGCACAAGT
*
457285 CGAGCAATGAGCTTAA
1 CGAGCAACGAGCTTAA
*
457301 CGAGCAACGAGTTTAA
1 CGAGCAACGAGCTTAA
457317 CG
1 CG
457319 CAACGAGTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (16 bp):
CGAGCAACGAGCTTAA
Found at i:457350 original size:78 final size:79
Alignment explanation
Indices: 457220--457369 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 79
457210 GAGTGACGAG
457220 ACGAGCAACGAGCTTAACGAGCAACAAGTCGAGTTGAGCAACAACTTTTTTTAACGAGCACAAGT
1 ACGAGCAACGAGCTTAAC-AGCAACAAGTCGAGTTGAGCAACAACTTTTTTTAACGAGCACAAGT
457285 CGAGCAATGAGCTTA
65 CGAGCAATGAGCTTA
* * * * *
457300 ACGAGCAACGAGTTTAAC-GCAACGAGTCGAGTTTAGCAACAATTTTTTTTAACGAGCACAAGTT
1 ACGAGCAACGAGCTTAACAGCAACAAGTCGAGTTGAGCAACAACTTTTTTTAACGAGCACAAGTC
457364 GAGCAA
66 GAGCAA
457370 AAATTTAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 48 0.74
80 17 0.26
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (79 bp):
ACGAGCAACGAGCTTAACAGCAACAAGTCGAGTTGAGCAACAACTTTTTTTAACGAGCACAAGTC
GAGCAATGAGCTTA
Found at i:457916 original size:14 final size:17
Alignment explanation
Indices: 457882--457914 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
457872 TCCTCTAAAA
457882 ATTTCAAATTATTATAT
1 ATTTCAAATTATTATAT
457899 ATTTCAAATT-TTATAT
1 ATTTCAAATTATTATAT
457915 TTTGTATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTCAAATTATTATAT
Found at i:464621 original size:60 final size:60
Alignment explanation
Indices: 464554--464754 Score: 249
Period size: 60 Copynumber: 3.4 Consensus size: 60
464544 AAGTCACTCG
* * *
464554 ACTATTAAAAGTTATAAAATGGTCCTCTAACTATATAGAGTAGCTTTATTGAGGCCATCA
1 ACTATTAAAAGTTACAAAATGGTCCTCTAACTATAAAGAGTAGCTTTATTGAGCCCATCA
* * * *
464614 ATTATTAAAAGTTACAAAATGATCCTCTAACTATAAAGAGTAGCTTTGTTGAGCCCCTCA
1 ACTATTAAAAGTTACAAAATGGTCCTCTAACTATAAAGAGTAGCTTTATTGAGCCCATCA
* *** * * * * **
464674 ACTATTAAAAGCTACAAAATGGTCCTCTAACCGGAGATAGTAGCTTTGTTGAGCCCCTTG
1 ACTATTAAAAGTTACAAAATGGTCCTCTAACTATAAAGAGTAGCTTTATTGAGCCCATCA
464734 ACTATTAAAAGTTACAAAATG
1 ACTATTAAAAGTTACAAAATG
464755 ATCACTTGAT
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 123 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (60 bp):
ACTATTAAAAGTTACAAAATGGTCCTCTAACTATAAAGAGTAGCTTTATTGAGCCCATCA
Found at i:470559 original size:21 final size:21
Alignment explanation
Indices: 470526--470565 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
470516 TAAGGATTTT
470526 TATTTTTATATTATTAAAATA
1 TATTTTTATATTATTAAAATA
470547 TATTCTTTA-ATTATTAAAA
1 TATT-TTTATATTATTAAAA
470566 AACATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTTTATATTATTAAAATA
Found at i:471169 original size:21 final size:21
Alignment explanation
Indices: 471143--471185 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
471133 CAAAAACTCG
471143 ACCTCATCTATGGTCATTCAT
1 ACCTCATCTATGGTCATTCAT
471164 ACCTCATCTATGGTCATTCAT
1 ACCTCATCTATGGTCATTCAT
471185 A
1 A
471186 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (21 bp):
ACCTCATCTATGGTCATTCAT
Found at i:475529 original size:20 final size:20
Alignment explanation
Indices: 475506--475579 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
475496 AACATTCCCA
475506 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCTCACTG
475526 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCTCACTG
*
475546 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCTCACTG
475566 GTAATCTTACATTC
1 GTAATCTTACATTC
475580 CGTGAACCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (20 bp):
GTAATCTTACATTCTCACTG
Found at i:477530 original size:4 final size:4
Alignment explanation
Indices: 477521--477546 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
477511 AAAAAACATT
477521 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
477547 AGTAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:487651 original size:26 final size:26
Alignment explanation
Indices: 487621--487694 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 26
487611 AAAAGTCCAA
**
487621 TAAATTTAACAAAATAAAGTAAGTAT
1 TAAATTTAACAAAATAAAGTAAAAAT
*
487647 TAAA-TGAGA-AATAAT-AA-TAAAAAT
1 TAAATTTA-ACAA-AATAAAGTAAAAAT
487671 TACAATTTAACAAAATAAAGTAAA
1 TA-AATTTAACAAAATAAAGTAAA
487695 TACAAATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
24 7 0.19
25 12 0.32
26 14 0.38
27 4 0.11
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (26 bp):
TAAATTTAACAAAATAAAGTAAAAAT
Found at i:488238 original size:18 final size:18
Alignment explanation
Indices: 488215--488254 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
488205 AAAGGCGATG
*
488215 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGCT
488233 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
488251 GCGG
1 GCGG
488255 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:490036 original size:19 final size:20
Alignment explanation
Indices: 489998--490038 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
489988 CTTAAAAAAG
* *
489998 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTAAGAGAAATTT
490018 AGAGAATTTAAGA-AAATTT
1 AGAGAATTTAAGAGAAATTT
490037 AG
1 AG
490039 TGTGATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (20 bp):
AGAGAATTTAAGAGAAATTT
Found at i:490184 original size:32 final size:32
Alignment explanation
Indices: 490147--490210 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
490137 TAAGATATAT
* *
490147 AGGTATAGCGCGCTGTAGGGGCCGCGCAATAC
1 AGGTATAACGCGCTGCAGGGGCCGCGCAATAC
*
490179 AGGTATAACGCGCTGCAGGGGCCGCGCTATAC
1 AGGTATAACGCGCTGCAGGGGCCGCGCAATAC
490211 CCACGTGGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.36, T:0.16
Consensus pattern (32 bp):
AGGTATAACGCGCTGCAGGGGCCGCGCAATAC
Found at i:490246 original size:50 final size:51
Alignment explanation
Indices: 490181--490307 Score: 184
Period size: 51 Copynumber: 2.5 Consensus size: 51
490171 CGCAATACAG
* * * * **
490181 GTATAACGCGCTGCAGGGGCCGCGCTATA-CCCACGTGGCGCCATCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCACC
*
490231 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCACC
490282 GTATAGCGCGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
490308 TTACTGCTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 26 0.38
51 43 0.62
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACATGGCGCCAAATCACC
Found at i:516209 original size:3 final size:3
Alignment explanation
Indices: 516201--516228 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
516191 TTAAGAAAGA
516201 AGG AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG A
516229 TATATAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:517189 original size:14 final size:16
Alignment explanation
Indices: 517170--517201 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
517160 AATCTCCTAC
517170 AAAAAAC-ACA-CACA
1 AAAAAACAACACCACA
517184 AAAAAACAACACCACA
1 AAAAAACAACACCACA
517200 AA
1 AA
517202 GCGAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAACAACACCACA
Found at i:522881 original size:37 final size:37
Alignment explanation
Indices: 522808--522882 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
522798 GTTGAAAAAT
* *
522808 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* * *
522845 ATTTATATAATTTTTTTTACAAAGTTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
522882 A
1 A
522883 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:524875 original size:23 final size:23
Alignment explanation
Indices: 524849--524917 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
524839 CACCAGAGCT
*
524849 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
524872 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
524895 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
524918 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:525104 original size:103 final size:103
Alignment explanation
Indices: 524933--525150 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
524923 TAATGTCCAT
* * *
524933 AAGGACCACATATCATTCCTTAAGAATTATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
524998 GACTTCACACATGTTCCCAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATAAATATATGTCCCG
* *
525036 AAGGACCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
525101 GACTTCACACATGTTCCAAAGAATAAATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATAAATATATGTCCCG
525139 AAGGACCACATA
1 AAGGACCACATA
525151 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATAAATATATGTCCCG
Found at i:532040 original size:64 final size:64
Alignment explanation
Indices: 531928--532148 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 64
531918 TAATGTAGGT
* * ** * * *
531928 ATGCACCGATGCACTACTGATGCATC-AGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGA-TGCACGAATTGCATTCGATGTT-TCATTATTAATGG
531991 G
64 G
* *
531992 ATGCATCGATGCATTACTTATGCATCGATGCACGAATTGCATTAGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
* * **
532056 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAATGGG
* * *
532119 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
532149 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.02
64 126 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:536134 original size:64 final size:64
Alignment explanation
Indices: 536022--536228 Score: 240
Period size: 64 Copynumber: 3.2 Consensus size: 64
536012 TAATGAAGGT
* * * * ** * **
536022 ATGCATCAATACACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTT-TCATTATTAAGGGG
* *
536086 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTTGATGTTTCATTATTAAGGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTTTCATTATTAAGGGG
* **
536150 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGT-TTCATTATTAAGGGG
536213 AGTGCATCGATGCACT
1 A-TGCATCGATGCACT
536229 TCCTGTTATG
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 3 0.02
64 116 0.94
65 5 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGTATTCGATGTTTCATTATTAAGGGG
Found at i:556117 original size:22 final size:21
Alignment explanation
Indices: 556065--556124 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
556055 GATTTCTGGG
556065 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
556086 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
556106 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
556125 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:556202 original size:23 final size:22
Alignment explanation
Indices: 556158--556202 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
556148 AATCTCATAG
*
556158 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
556180 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
556203 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:557678 original size:103 final size:103
Alignment explanation
Indices: 557497--557708 Score: 388
Period size: 103 Copynumber: 2.1 Consensus size: 103
557487 GAGGATCTAC
557497 GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
1 GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
* *
557562 ATCCTTGGCATATGTATATGATTCTTAAGGAATGATAT
66 ATCCCTAGCATATGTATATGATTCTTAAGGAATGATAT
*
557600 GTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
1 GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
*
557665 ATCCCTAGTATATGTATATGATTCTTAAGGAATGATAT
66 ATCCCTAGCATATGTATATGATTCTTAAGGAATGATAT
557703 GTGGTC
1 GTGGTC
557709 ATTATGGACA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (103 bp):
GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
ATCCCTAGCATATGTATATGATTCTTAAGGAATGATAT
Found at i:557761 original size:23 final size:23
Alignment explanation
Indices: 557735--557818 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
557725 TATGGCATTA
557735 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
557758 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* * * * *
557781 TGGTGTAATTCTATGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
557804 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
557819 AGCTGTGGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:560011 original size:21 final size:20
Alignment explanation
Indices: 559962--560006 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
559952 TTACAGGAAT
559962 TTATTTTGTACAATAATCAAA
1 TTATTTTGTACAATAAT-AAA
559983 TTATTTTGTACAATAAT-AA
1 TTATTTTGTACAATAATAAA
560002 TTATT
1 TTATT
560007 GTTTGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.29
21 17 0.71
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (20 bp):
TTATTTTGTACAATAATAAA
Found at i:560638 original size:33 final size:34
Alignment explanation
Indices: 560596--560701 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 34
560586 GTGGTAAGAA
* *
560596 ATTTATTTTTATGTTAGTAT-TTT-T-TAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
560629 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
* * *
560664 A-TTTTTTTAT-TAAAATAATATTTATATAATTATT
1 ATTTTTTTTATAT-TAAT-ATATTTATGTAAATATT
560698 ATTT
1 ATTT
560702 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
32 1 0.02
33 27 0.44
34 21 0.34
35 6 0.10
36 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:560683 original size:36 final size:34
Alignment explanation
Indices: 560628--560706 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
560618 TTTAAATAGT
*
560628 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
560660 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
560694 TATTATTTATTTA
1 TATTATTTTTTTA
560707 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:560868 original size:17 final size:17
Alignment explanation
Indices: 560846--560899 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
560836 AATGTTAATA
560846 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
560863 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
560880 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
560897 TTT
1 TTT
560900 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:561625 original size:33 final size:34
Alignment explanation
Indices: 561566--561662 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
561556 AAATGTTTTT
* *
561566 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
561600 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
561633 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
561663 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:561669 original size:34 final size:32
Alignment explanation
Indices: 561564--561669 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 32
561554 ATAAATGTTT
*
561564 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTT-AAA
* *
561598 TAAAAATAAAAATAATATTATTCAAATTTAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAA
* *
561630 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTC-AAATTTAA-A
561665 TTAAA
1 TTAAA
561670 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (32 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAA
Found at i:569705 original size:3 final size:3
Alignment explanation
Indices: 569697--569727 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
569687 ATCTTTTCTC
*
569697 ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
569728 AAAAAGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:573229 original size:3 final size:3
Alignment explanation
Indices: 573221--573321 Score: 202
Period size: 3 Copynumber: 33.7 Consensus size: 3
573211 TTTTTATCCA
573221 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
573269 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
573317 TAT TA
1 TAT TA
573322 ATTTATATTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:586148 original size:9 final size:9
Alignment explanation
Indices: 586134--586202 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
586124 GCTTGAAGAA
586134 AAAGAAAAG
1 AAAGAAAAG
586143 AAAGAAAAG
1 AAAGAAAAG
*
586152 AAA-AAAGG
1 AAAGAAAAG
*
586160 AAAGAAAAA
1 AAAGAAAAG
*
586169 AATAGAAAAT
1 AA-AGAAAAG
586179 AGAA-AAAAG
1 A-AAGAAAAG
586188 ACAAGAAAAAG
1 A-AAG-AAAAG
586199 AAAG
1 AAAG
586203 GGGGTCAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.14
9 24 0.49
10 11 0.22
11 7 0.14
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:586152 original size:14 final size:13
Alignment explanation
Indices: 586133--586197 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
586123 TGCTTGAAGA
586133 AAAAGAAAAGAAAG
1 AAAAGAAAA-AAAG
586147 AAAAG-AAAAAAG
1 AAAAGAAAAAAAG
*
586159 GAAAGAAAAAAATAG
1 AAAAG-AAAAAA-AG
*
586174 AAAATAGAAAAAAG
1 AAAAGA-AAAAAAG
*
586188 ACAAGAAAAA
1 AAAAGAAAAA
586198 GAAAGGGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 8 0.19
13 7 0.17
14 17 0.40
15 10 0.24
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:586158 original size:21 final size:21
Alignment explanation
Indices: 586132--586201 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
586122 ATGCTTGAAG
586132 AAAAAGAAAAGAAAGAAAAGA
1 AAAAAGAAAAGAAAGAAAAGA
* *
586153 AAAAAGGAAAGAAAAAAATAGA
1 AAAAAGAAAAGAAAGAAA-AGA
* *
586175 AAATAG-AAA-AAAGACAAG-
1 AAAAAGAAAAGAAAGAAAAGA
586193 AAAAAGAAA
1 AAAAAGAAA
586202 GGGGGTCAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 5 0.12
19 4 0.10
20 5 0.12
21 19 0.46
22 8 0.20
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAAGAAAGAAAAGA
Found at i:587412 original size:50 final size:50
Alignment explanation
Indices: 587337--588128 Score: 1512
Period size: 50 Copynumber: 15.8 Consensus size: 50
587327 TGAATTTACC
587337 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587387 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
587437 AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
587487 AATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587537 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587587 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
587637 AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587687 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587737 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
587787 AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587837 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
587887 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
587937 AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
587987 AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
588037 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
588087 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
588129 AGAAGTGTAT
Statistics
Matches: 731, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 731 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:588887 original size:113 final size:112
Alignment explanation
Indices: 588689--589547 Score: 1310
Period size: 113 Copynumber: 7.6 Consensus size: 112
588679 TCAAATCCAC
* *
588689 TTGATGGATCATTCATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCA-TCATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
588754 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAT
65 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
* *
588802 TTGATGGATCATTCATTACCAGATAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCA-TCATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
588867 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAT
65 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
*
588915 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
588980 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAT
65 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
*
589028 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
589093 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCCTGAATTCATCAC
65 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
* **
589141 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
589206 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTTC-TGAATTCATCAC
65 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
* **
589253 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
589318 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATTAT
65 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
* * *
589366 TTGATGGATCAACTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGAAG
1 TTGATGGATCATCATTGCCAGAG-A-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
589430 AAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
61 AAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
** *
589482 TTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAG
1 TTGATGGATCATCATTGCCAG-AG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
589546 AA
64 AA
589548 TTTATTCAAT
Statistics
Matches: 710, Mismatches: 26, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
112 123 0.17
113 466 0.66
114 15 0.02
115 2 0.00
116 84 0.12
117 18 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (112 bp):
TTGATGGATCATCATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
Found at i:589692 original size:3 final size:3
Alignment explanation
Indices: 589684--589727 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
589674 TTTTTATCCA
589684 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
589728 ATTTATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:590247 original size:17 final size:17
Alignment explanation
Indices: 590225--590259 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
590215 ACAGAACCGG
590225 AGAGAAGAA-AAAAAAAC
1 AGAGAA-AAGAAAAAAAC
590242 AGAGAAAAGAAAAAAAC
1 AGAGAAAAGAAAAAAAC
590259 A
1 A
590260 AACTATACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (17 bp):
AGAGAAAAGAAAAAAAC
Found at i:601991 original size:21 final size:21
Alignment explanation
Indices: 601967--602094 Score: 154
Period size: 21 Copynumber: 6.1 Consensus size: 21
601957 AATCGCAATA
601967 CGATAGTCCAAGTTCGCATTG
1 CGATAGTCCAAGTTCGCATTG
* *
601988 CGATAG-CCGACTATCGCATTG
1 CGATAGTCCAAGT-TCGCATTG
* *
602009 CGAT-TTACATA-TTCGCATTG
1 CGATAGTCCA-AGTTCGCATTG
602029 CGATAGTCCAAGTTCGCATTG
1 CGATAGTCCAAGTTCGCATTG
*
602050 CGATAGTCAAAGTTCGCATTG
1 CGATAGTCCAAGTTCGCATTG
* *
602071 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTCCAAGTTCGCATTG
602092 CGA
1 CGA
602095 ATCTGGAAAC
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.18
21 74 0.80
22 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (21 bp):
CGATAGTCCAAGTTCGCATTG
Found at i:602002 original size:62 final size:62
Alignment explanation
Indices: 601934--602055 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
601924 TGCGATTTTG
601934 GACTATCGCAATGCGAATATGTA-A-A-TCGCAATACGATAGTCCAAGTTCGCATTGCGATAGCC
1 GACTATCGCAATGCG-AT-T-TACATATTCGCAATACGATAGTCCAAGTTCGCATTGCGATAGCC
* * *
601996 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 GACTATCGCAATGCGATTTACATATTCGCAATACGATAGTCCAAGTTCGCATTGCGATAG
602056 TCAAAGTTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
59 2 0.04
60 2 0.04
61 3 0.06
62 47 0.87
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (62 bp):
GACTATCGCAATGCGATTTACATATTCGCAATACGATAGTCCAAGTTCGCATTGCGATAGCC
Found at i:613224 original size:18 final size:18
Alignment explanation
Indices: 613198--613232 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
613188 GAAATCACAG
613198 ATGACGTAATGAGTCGAA
1 ATGACGTAATGAGTCGAA
*
613216 ATGATGTAATGAGTCGA
1 ATGACGTAATGAGTCGA
613233 TACAATCTAT
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:0.37, C:0.09, G:0.29, T:0.26
Consensus pattern (18 bp):
ATGACGTAATGAGTCGAA
Found at i:616674 original size:23 final size:20
Alignment explanation
Indices: 616624--616680 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
616614 ATGCAATATG
*
616624 GGTATCGATACCCAAGCTAT
1 GGTATCGATACCCTAGCTAT
616644 -GTATCGATACCCTAGCTAT
1 GGTATCGATACCCTAGCTAT
616663 AGAGGTATCGATACCCTA
1 ---GGTATCGATACCCTA
616681 TGGGGGTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 18 0.56
23 14 0.44
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCCTAGCTAT
Found at i:631160 original size:20 final size:20
Alignment explanation
Indices: 631135--631176 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
631125 ACTAAAACGC
631135 CATACCAGCATTTAATGTAA
1 CATACCAGCATTTAATGTAA
631155 CATACCAGCATTTAATGTAA
1 CATACCAGCATTTAATGTAA
631175 CA
1 CA
631177 CAGGCCCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (20 bp):
CATACCAGCATTTAATGTAA
Found at i:632185 original size:19 final size:20
Alignment explanation
Indices: 632144--632184 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
632134 ATCAAATTGT
*
632144 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGAACAGATTCCCC
632164 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGAACAGATTCCCC
632184 C
1 C
632185 ATGTTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.37, G:0.29, T:0.12
Consensus pattern (20 bp):
CCAGGGGGAACAGATTCCCC
Found at i:633619 original size:3 final size:3
Alignment explanation
Indices: 633593--633641 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
633583 TGAAGAAAGG
* *
633593 GAA G-A GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
633639 GAA
1 GAA
633642 TGAGGACGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:636447 original size:2 final size:2
Alignment explanation
Indices: 636440--636464 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
636430 AATAAAAACT
636440 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
636465 CGAAAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:637795 original size:136 final size:136
Alignment explanation
Indices: 637620--637873 Score: 309
Period size: 137 Copynumber: 1.9 Consensus size: 136
637610 TCTAAAATTT
*
637620 AAGATCTAATATTAAACCTAATAAATTTTAAAAAATTATTCAATCGAATAATT-AAAAT-GAAGC
1 AAGATCTAATATTAAACCTAATAAATTTTAAAAAATTATTCAATCAAATAATTAAAAATGGAA-C
* * * * **
637683 C-CGATCATTGACTGGGATCATTTTGAATATTCCCCTAATTTAA-GGACTAAAATGATATTAAAC
65 CTCGAGCATTGAC-GGGACCATTTTAAACATTCCCCTAAAATAAGGGACTAAAATGATATTAAAC
637746 CTAAAGTG
129 CTAAAGTG
* * * ** *
637754 AAGACTCTAATATTGAACCTTAATAATTTTTATAATTTTATTGAATCAAATAATTAAAAATGGAA
1 AAGA-TCTAATATTAAACC-TAATAAATTTTAAAAAATTATTCAATCAAATAATTAAAAATGGAA
* *
637819 CCTCGAGCATTGGCGGGGCCATTTTAAACATTCCCCTAAAATAAGGGACTAAAAT
64 CCTCGAGCATTGACGGGACCATTTTAAACATTCCCCTAAAATAAGGGACTAAAAT
637874 AAAGAAAACT
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
134 4 0.04
135 13 0.13
136 29 0.29
137 31 0.31
138 22 0.22
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (136 bp):
AAGATCTAATATTAAACCTAATAAATTTTAAAAAATTATTCAATCAAATAATTAAAAATGGAACC
TCGAGCATTGACGGGACCATTTTAAACATTCCCCTAAAATAAGGGACTAAAATGATATTAAACCT
AAAGTG
Found at i:637886 original size:136 final size:134
Alignment explanation
Indices: 637620--637886 Score: 290
Period size: 136 Copynumber: 2.0 Consensus size: 134
637610 TCTAAAATTT
*
637620 AAGATCTAATATTAAACCTAATAAATTTTAAAAAATTATTCAATCGAATAATTAAAATGAAGCCC
1 AAGATCTAATATTAAACCTAATAAATTTTAAAAAATTATTCAATCAAATAATTAAAATGAAGCCC
* * * * ** ** *
637685 GATCATTGACTGGGATCATTTTGAATATTCCCCTAATTTAAGGACTAAAATGATATTAAACCTAA
66 GAGCATTGACTGGGACCATTTTAAACATTCCCCTAAAATAAGGACTAAAATGATAAGAAAACTAA
637750 AGTG
131 AGTG
* * * ** *
637754 AAGACTCTAATATTGAACCTTAATAATTTTTATAATTTTATTGAATCAAATAATTAAAAATGGAA
1 AAGA-TCTAATATTAAACC-TAATAAATTTTAAAAAATTATTCAATCAAATAATT-AAAAT-GAA
* *
637819 -CCTCGAGCATTGGC-GGGGCCATTTTAAACATTCCCCTAAAATAAGGGACTAAAAT-A-AAGAA
62 GCC-CGAGCATTGACTGGGACCATTTTAAACATTCCCCTAAAATAA-GGACTAAAATGATAAGAA
637880 AACTAAA
125 AACTAAA
637887 CTTAAGGTGC
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
134 4 0.04
135 13 0.12
136 38 0.35
137 32 0.29
138 22 0.20
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (134 bp):
AAGATCTAATATTAAACCTAATAAATTTTAAAAAATTATTCAATCAAATAATTAAAATGAAGCCC
GAGCATTGACTGGGACCATTTTAAACATTCCCCTAAAATAAGGACTAAAATGATAAGAAAACTAA
AGTG
Found at i:648630 original size:25 final size:26
Alignment explanation
Indices: 648578--648638 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
648568 ATTTATAATT
*
648578 TTTTATATATATTAACTTTTAAAAATA
1 TTTTAT-TATATTAACTTCTAAAAATA
*
648605 TTTT-TTATATTAACTTACT-AATATA
1 TTTTATTATATTAACTT-CTAAAAATA
648630 TTTTATTAT
1 TTTTATTAT
648639 TAATTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 20 0.67
26 6 0.20
27 4 0.13
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATTATATTAACTTCTAAAAATA
Found at i:650943 original size:29 final size:30
Alignment explanation
Indices: 650908--650970 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
650898 TAAAATTATT
*
650908 TTTTTATTTTTGTTTTAACTTATTAA-ATA
1 TTTTTATTTTTGTCTTAACTTATTAATATA
*
650937 TTTTTATTTTTGTCTTAATTTATTAATATA
1 TTTTTATTTTTGTCTTAACTTATTAATATA
650967 TTTT
1 TTTT
650971 GTTTTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (30 bp):
TTTTTATTTTTGTCTTAACTTATTAATATA
Found at i:650983 original size:29 final size:29
Alignment explanation
Indices: 650908--650984 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
650898 TAAAATTATT
** *
650908 TTTTTATTTTTGTTTTAACTTATTAAATA
1 TTTTTATTTTCATTTTAATTTATTAAATA
** *
650937 TTTTTATTTTTGTCTTAATTTATT-AATA
1 TTTTTATTTTCATTTTAATTTATTAAATA
*
650965 TATTTTGTTTTCATTTTAAT
1 T-TTTTATTTTCATTTTAAT
650985 GTAAAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (29 bp):
TTTTTATTTTCATTTTAATTTATTAAATA
Found at i:651101 original size:33 final size:34
Alignment explanation
Indices: 651058--651142 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
651048 AATATATTTA
651058 AATATTTTACTATTAATTTAATATAAAAATATAT
1 AATATTTTACTATTAATTTAATATAAAAATATAT
* * * * *
651092 -ATATTTTACTCTTATTTTTATTTAAAAATATTT
1 AATATTTTACTATTAATTTAATATAAAAATATAT
651125 AATATTTTACTATTAATT
1 AATATTTTACTATTAATT
651143 AAAAATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 28 0.65
34 15 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (34 bp):
AATATTTTACTATTAATTTAATATAAAAATATAT
Found at i:651421 original size:29 final size:30
Alignment explanation
Indices: 651380--651457 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
651370 ATATTTTTAC
* *
651380 ATTAAAATAAAAACAAAATATATTTAATAA
1 ATTAAAACAAAAACAAAAAATATTTAATAA
* *
651410 ATTAAGACAAAAA-TAAAAATATTTAATAA
1 ATTAAAACAAAAACAAAAAATATTTAATAA
*
651439 GTTAAAACAAAAACAAAAA
1 ATTAAAACAAAAACAAAAA
651458 GATAATTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (30 bp):
ATTAAAACAAAAACAAAAAATATTTAATAA
Found at i:652652 original size:57 final size:57
Alignment explanation
Indices: 652589--652770 Score: 208
Period size: 57 Copynumber: 3.2 Consensus size: 57
652579 TTTGGACCCT
* * * *
652589 TATTTTTTGGGTTTCTTAATAGCAACAACTAATAGATATATTTGATTTCGGGATCTC
1 TATTTTTTGGGCTTCTTAATAGCAACAACTGATAGATATACTCGATTTCGGGATCTC
* *
652646 TATTTTTTGAGCTTCTTAAT-GTCAACAACTGATAGATATACTCGATTTC-GGA-CCC
1 TATTTTTTGGGCTTCTTAATAG-CAACAACTGATAGATATACTCGATTTCGGGATCTC
* * * * * *
652701 TTATTTTTTAGGACTTATTAATAGTAAAAATTGATAGATATACTCGATTTCGGGGTCTC
1 -TATTTTTT-GGGCTTCTTAATAGCAACAACTGATAGATATACTCGATTTCGGGATCTC
652760 TATTTTTTGGG
1 TATTTTTTGGG
652771 TCATACGCCG
Statistics
Matches: 104, Mismatches: 15, Indels: 12
0.79 0.11 0.09
Matches are distributed among these distances:
55 2 0.02
56 12 0.12
57 77 0.74
58 11 0.11
59 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (57 bp):
TATTTTTTGGGCTTCTTAATAGCAACAACTGATAGATATACTCGATTTCGGGATCTC
Found at i:654070 original size:22 final size:20
Alignment explanation
Indices: 654033--654072 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
654023 TTTTTACTCG
*
654033 ATTATTTTAACTTTGAATCT
1 ATTATTTTAAATTTGAATCT
654053 ATTATATTTAAATATTGAAT
1 ATTAT-TTTAAAT-TTGAAT
654073 GTAATACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTATTTTAAATTTGAATCT
Done.