Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold193
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: 886014
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 71246 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:246256 original size:21 final size:22
Alignment explanation
Indices: 246230--246272 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
246220 TCCAAAATTT
246230 ATTGCG-TTTTTGGCACGAATG
1 ATTGCGTTTTTTGGCACGAATG
*
246251 ATTGCGTTTTTTTGCACGAATG
1 ATTGCGTTTTTTGGCACGAATG
246273 TAGCAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (22 bp):
ATTGCGTTTTTTGGCACGAATG
Found at i:248489 original size:15 final size:16
Alignment explanation
Indices: 248469--248503 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
248459 TTCAAATTTA
*
248469 TAAATACTCTCAAT-T
1 TAAATACTATCAATAT
248484 TAAATACTATCAATAT
1 TAAATACTATCAATAT
248500 TAAA
1 TAAA
248504 ATCGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATACTATCAATAT
Found at i:262925 original size:46 final size:46
Alignment explanation
Indices: 262860--262955 Score: 174
Period size: 46 Copynumber: 2.1 Consensus size: 46
262850 TTGAATAATC
262860 AACTAACCACCTTAACAATACAACTCTTATTGTTTAACATTCACCT
1 AACTAACCACCTTAACAATACAACTCTTATTGTTTAACATTCACCT
* *
262906 AACTAACCACCTTAACAATACAATTGTTATTGTTTAACATTCACCT
1 AACTAACCACCTTAACAATACAACTCTTATTGTTTAACATTCACCT
262952 AACT
1 AACT
262956 TCTCAACAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (46 bp):
AACTAACCACCTTAACAATACAACTCTTATTGTTTAACATTCACCT
Found at i:271871 original size:11 final size:12
Alignment explanation
Indices: 271842--271873 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
271832 CACTTGTTAA
271842 CAAT-ACTTTCT
1 CAATCACTTTCT
271853 CAATCACTTTCT
1 CAATCACTTTCT
271865 CAA-CACTTT
1 CAATCACTTT
271874 TAATGCACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (12 bp):
CAATCACTTTCT
Found at i:275830 original size:20 final size:20
Alignment explanation
Indices: 275788--275830 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
275778 CTTTTTTTCA
* *
275788 AATCCTAATTTTCACCGCTT
1 AATCCTAATTTTCACCACCT
275808 AATCCTAATTTTCACCACCT
1 AATCCTAATTTTCACCACCT
275828 AAT
1 AAT
275831 TTTAGACCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.37
Consensus pattern (20 bp):
AATCCTAATTTTCACCACCT
Found at i:300397 original size:18 final size:18
Alignment explanation
Indices: 300354--300402 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
300344 CATAAATTAA
*
300354 TTGAAAA-ATACATTATGT
1 TTGAAAATATA-ATTATAT
300372 TT-AAAATATAATTATAT
1 TTGAAAATATAATTATAT
300389 TTGAAAATATAATT
1 TTGAAAATATAATT
300403 TACAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (18 bp):
TTGAAAATATAATTATAT
Found at i:300561 original size:80 final size:81
Alignment explanation
Indices: 300459--300622 Score: 321
Period size: 80 Copynumber: 2.0 Consensus size: 81
300449 ATTTTATTTA
300459 TTTTAAATTGAAATTAATGAATGTAAATTTAAAGATAACAAAATAAATAGAATCATAATTAATAA
1 TTTTAAATTGAAATTAATGAATGTAAATTTAAAGATAACAAAATAAATAGAATCATAATTAATAA
300524 TGGACAAAATCGTGAT
66 TGGACAAAATCGTGAT
300540 TTTTAAATTG-AATTAATGAATGTAAATTTAAAGATAACAAAATAAATAGAATCATAATTAATAA
1 TTTTAAATTGAAATTAATGAATGTAAATTTAAAGATAACAAAATAAATAGAATCATAATTAATAA
300604 TGGACAAAATCGTGAT
66 TGGACAAAATCGTGAT
300620 TTT
1 TTT
300623 ACTTAAAATT
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 73 0.88
81 10 0.12
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.34
Consensus pattern (81 bp):
TTTTAAATTGAAATTAATGAATGTAAATTTAAAGATAACAAAATAAATAGAATCATAATTAATAA
TGGACAAAATCGTGAT
Found at i:307555 original size:24 final size:24
Alignment explanation
Indices: 307503--307555 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
307493 TAATCAAAGT
* *
307503 CAAATATATTATGCTAATAAATGC
1 CAAATATATTATACTAATAAATAC
* *
307527 TAAATATATTATACTCATAAATAC
1 CAAATATATTATACTAATAAATAC
307551 CAAAT
1 CAAAT
307556 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (24 bp):
CAAATATATTATACTAATAAATAC
Found at i:315143 original size:34 final size:34
Alignment explanation
Indices: 315100--315167 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
315090 CTTGATCTGA
315100 ACCAAGTGATATCATTATCTGCACTGAATTAGCT
1 ACCAAGTGATATCATTATCTGCACTGAATTAGCT
315134 ACCAAGTGATATCATTATCTGCACTGAATTAGCT
1 ACCAAGTGATATCATTATCTGCACTGAATTAGCT
315168 TTACGCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (34 bp):
ACCAAGTGATATCATTATCTGCACTGAATTAGCT
Found at i:326687 original size:11 final size:12
Alignment explanation
Indices: 326664--326692 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
326654 TAATTTAAGT
326664 ATAAAAGATAAA
1 ATAAAAGATAAA
326676 ATAAAA-ATAAA
1 ATAAAAGATAAA
326687 ATAAAA
1 ATAAAA
326693 CATTTCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
ATAAAAGATAAA
Found at i:327947 original size:33 final size:33
Alignment explanation
Indices: 327902--327967 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
327892 AAAAATAGTC
327902 TGGGCCTGAGCCCTAAT-CAGTAACAGTACAGTG
1 TGGGCCTGAGCCC-AATACAGTAACAGTACAGTG
* *
327935 TGGGCCTTAGCCCAATACAGTATCAGTACAGTG
1 TGGGCCTGAGCCCAATACAGTAACAGTACAGTG
327968 CAATAATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (33 bp):
TGGGCCTGAGCCCAATACAGTAACAGTACAGTG
Found at i:328093 original size:26 final size:25
Alignment explanation
Indices: 328064--328117 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
328054 AACACACCAA
*
328064 TATCGCAGCAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCCAGT-ACAG
328090 TATCGCAGCAAAGCTGCCAGTACAG
1 TATCGCAGCAAAGCTGCCAGTACAG
328115 TAT
1 TAT
328118 ACTTCCTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (25 bp):
TATCGCAGCAAAGCTGCCAGTACAG
Found at i:340296 original size:15 final size:15
Alignment explanation
Indices: 340276--340308 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
340266 CAAAATCCAT
340276 TTCATCATC-TCCTTC
1 TTCATCATCATCC-TC
340291 TTCATCATCATCCTC
1 TTCATCATCATCCTC
340306 TTC
1 TTC
340309 CTCCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.45
Consensus pattern (15 bp):
TTCATCATCATCCTC
Found at i:349125 original size:37 final size:37
Alignment explanation
Indices: 349079--349205 Score: 184
Period size: 37 Copynumber: 3.4 Consensus size: 37
349069 TAGCTCTTCG
*
349079 GAGCGCTTGGCGTGTTATCGGTTGGATTAACTCTTAT
1 GAGCACTTGGCGTGTTATCGGTTGGATTAACTCTTAT
*
349116 GAGCACTTGGCGTGTTATCGGTTGGATTAGA-TCTTAC
1 GAGCACTTGGCGTGTTATCGGTTGGATTA-ACTCTTAT
* *
349153 GAGAACTTGGCGTGTTATCGGTTGGATTATCTCTTAT
1 GAGCACTTGGCGTGTTATCGGTTGGATTAACTCTTAT
* *
349190 GAGCATTTGGCTTGTT
1 GAGCACTTGGCGTGTT
349206 TCAGCTGGAT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
37 79 0.99
38 1 0.01
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.39
Consensus pattern (37 bp):
GAGCACTTGGCGTGTTATCGGTTGGATTAACTCTTAT
Found at i:359557 original size:11 final size:11
Alignment explanation
Indices: 359543--359576 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
359533 TGAAATTGTA
359543 TGTGAATTAGT
1 TGTGAATTAGT
359554 TGTGAATTAAGT
1 TGTGAATT-AGT
359566 T-TGAATTAGT
1 TGTGAATTAGT
359576 T
1 T
359577 ATATGCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 14 0.64
12 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (11 bp):
TGTGAATTAGT
Found at i:361733 original size:19 final size:19
Alignment explanation
Indices: 361709--361756 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
361699 AATACGAAGG
361709 ACTAAAGTGGCAATTAACC
1 ACTAAAGTGGCAATTAACC
361728 ACTAAAGTGGCAATTAACC
1 ACTAAAGTGGCAATTAACC
361747 ACTAAAGTGG
1 ACTAAAGTGG
361757 TTAGTGCCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (19 bp):
ACTAAAGTGGCAATTAACC
Found at i:361914 original size:3 final size:3
Alignment explanation
Indices: 361906--361972 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
361896 NNNNNNNNNN
361906 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
361954 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
361973 AGAAAGAAAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:363974 original size:9 final size:9
Alignment explanation
Indices: 363942--363982 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
363932 ATTAAATTTA
363942 ATTGATGAT
1 ATTGATGAT
*
363951 GAGTGATGA-
1 -ATTGATGAT
363960 ATTGATGAT
1 ATTGATGAT
363969 ATTGATGAT
1 ATTGATGAT
363978 ATTGA
1 ATTGA
363983 GATCGATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 14 0.50
10 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (9 bp):
ATTGATGAT
Found at i:364363 original size:155 final size:154
Alignment explanation
Indices: 364081--364492 Score: 497
Period size: 155 Copynumber: 2.7 Consensus size: 154
364071 TCGATGAGAG
* * * * * * * *
364081 CTGGGCACAAATTAGTTACTTCGGATGTTCCAATGAGGCACTGGGTGCCTAATGGTGACTTCGAC
1 CTGGGTACAAACTAATTACTTCGGACGTTCCGATGAGGCACTGGATGTC-AATGGTTACTTCGAC
* * * * * **
364146 TATGTGTCGATGAGTGCTGGGA-ACAATTTTTACATCAGACGTTTCGATGAGTGTTGGGCACAAC
65 TATGTGTCGATGAGTGAT-GGACACAATTTTTACTTCGGAAGTTCCGATGAGTACTGGGCACAAC
* *
364210 ATTTACTTCGGTTATACCAATAAACA
129 ATTTACTCCAGTTATACCAATAAACA
364236 CTGGGTACAAACTAATTACTTCGGACGTTCCGATGAGGCACTGGATGTCAAATGGTTACTTCGAC
1 CTGGGTACAAACTAATTACTTCGGACGTTCCGATGAGGCACTGGATGTC-AATGGTTACTTCGAC
*
364301 TACGTGTCGATGAGTGATGGACACAATTTTTACTTCGGAAGTTCCGATGAGTACTGGGCACAACA
65 TATGTGTCGATGAGTGATGGACACAATTTTTACTTCGGAAGTTCCGATGAGTACTGGGCACAACA
* * *
364366 TTTACTCCAGTTATACCAATGAGCC
130 TTTACTCCAGTTATACCAATAAACA
* * * *
364391 CGGGGTGCAAACTAATTACTTC-GAGCGTTCTGATGAGGCACTGGATGTCAATGGTTACTTTGAC
1 CTGGGTACAAACTAATTACTTCGGA-CGTTCCGATGAGGCACTGGATGTCAATGGTTACTTCGAC
* * * *
364455 TATGTTTTGAAGAGT-ACTGGGCACAATTTTTACTTCGG
65 TATGTGTCGATGAGTGA-TGGACACAATTTTTACTTCGG
364493 TCATACCAAT
Statistics
Matches: 223, Mismatches: 31, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
153 1 0.00
154 50 0.22
155 172 0.77
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (154 bp):
CTGGGTACAAACTAATTACTTCGGACGTTCCGATGAGGCACTGGATGTCAATGGTTACTTCGACT
ATGTGTCGATGAGTGATGGACACAATTTTTACTTCGGAAGTTCCGATGAGTACTGGGCACAACAT
TTACTCCAGTTATACCAATAAACA
Found at i:367014 original size:228 final size:229
Alignment explanation
Indices: 366699--367155 Score: 907
Period size: 228 Copynumber: 2.0 Consensus size: 229
366689 TTATTAACTG
366699 CTATTATTATATTAAGATGATTTAAAACGCGGAAGCATTTGAAAACTCTAATGTTTAAAGTCTGT
1 CTATTATTATATTAAGATGATTTAAAACGCGGAAGCATTTGAAAACTCTAATGTTTAAAGTCTGT
366764 GCCTTTGAAAACCGTAATTATTTTGAAAATTCATTTTCACCTAACTAGCAATATAAAATATGTAA
66 GCCTTTGAAAACCGTAATTATTTTGAAAATTCATTTTCACCTAACTAGCAATATAAAATATGTAA
366829 GCAAAGCCCAATTAAAGATAAAAACCCAAATTAAAGGCCTTATTACAAAAACAAAACCCAACAAA
131 GCAAAGCCCAATTAAAGATAAAAACCCAAATTAAAGGCCTTATTACAAAAACAAAACCCAACAAA
366894 TTAATAAAATTAAAAAAAACAAATGTAAACTTCA
196 TTAATAAAATTAAAAAAAACAAATGTAAACTTCA
366928 CTATTATTAT-TTAAGATGATTTAAAACGCGGAAGCATTTGAAAACTCTAATGTTTAAAGTCTGT
1 CTATTATTATATTAAGATGATTTAAAACGCGGAAGCATTTGAAAACTCTAATGTTTAAAGTCTGT
366992 GCCTTTGAAAACCGTAATTATTTTGAAAATTCATTTTCACCTAACTAGCAATATAAAATATGTAA
66 GCCTTTGAAAACCGTAATTATTTTGAAAATTCATTTTCACCTAACTAGCAATATAAAATATGTAA
367057 GCAAAGCCCAATTAAAGATAAAAACCCAAATTAAAGGCCTTATTACAAAAACAAAACCCAACAAA
131 GCAAAGCCCAATTAAAGATAAAAACCCAAATTAAAGGCCTTATTACAAAAACAAAACCCAACAAA
367122 TTAATAAAATTAAAAAAAACAAATGTAAACTTCA
196 TTAATAAAATTAAAAAAAACAAATGTAAACTTCA
367156 GCAGTAGTTG
Statistics
Matches: 228, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
228 218 0.96
229 10 0.04
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (229 bp):
CTATTATTATATTAAGATGATTTAAAACGCGGAAGCATTTGAAAACTCTAATGTTTAAAGTCTGT
GCCTTTGAAAACCGTAATTATTTTGAAAATTCATTTTCACCTAACTAGCAATATAAAATATGTAA
GCAAAGCCCAATTAAAGATAAAAACCCAAATTAAAGGCCTTATTACAAAAACAAAACCCAACAAA
TTAATAAAATTAAAAAAAACAAATGTAAACTTCA
Found at i:367775 original size:27 final size:27
Alignment explanation
Indices: 367753--368149 Score: 448
Period size: 27 Copynumber: 14.7 Consensus size: 27
367743 AGGGGTATAA
*
367753 CAGTTATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * * * * * *
367780 TAGAAAATTTATCATTTGGGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* *
367807 CGGTAATTTTACCCTTTGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
367834 CAATAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * *
367861 CGGTAATTTTACACTTCGAGGGCATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
367888 C-GATAA-TTTACCCTTCGGGGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
*
367914 CAGTAATTTTACCCTTCAAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
367941 C-GATAATTTTACCCTTCGAGGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
*
367968 CAGTAATTTTACCCTTTGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
367995 C-GATAATTTTACCCTTCGAAGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
* *
368022 C-GACAATTTTACCTTTCGAGGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
* *
368049 CGGCAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* *
368076 C-GATAATTTTACCGTTCAAGGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
* *
368103 TAATAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
368130 C-GATAATTTTACCCATCGAG
1 CAG-TAATTTTACCCTTCGAG
368150 TCGCAAGTTG
Statistics
Matches: 315, Mismatches: 45, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
26 25 0.08
27 288 0.91
28 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (27 bp):
CAGTAATTTTACCCTTCGAGGGTATTT
Found at i:367888 original size:81 final size:81
Alignment explanation
Indices: 367758--368149 Score: 495
Period size: 81 Copynumber: 4.9 Consensus size: 81
367748 TATAACAGTT
* * * *
367758 ATTTTACCCTTCGAGGGTATTTTAGA-AAATTTATCA-TTTGGGGGTATTTCGGTAATTTTACCC
1 ATTTTACCCTTCGAGGGTA-TTTCGATAATTTTA-CACTTCGAGGGTATTTCGGTAATTTTACCC
*
367821 TTTGAGGGTATTTCAATA
64 TTCGAGGGTATTTCAATA
* * *
367839 ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACACTTCGAGGGCATTTCGATAA-TTTACCCTT
1 ATTTTACCCTTCGAGGGTATTTCGATAATTTTACACTTCGAGGGTATTTCGGTAATTTTACCCTT
* *
367903 CGGGGGTATTTCAGTA
66 CGAGGGTATTTCAATA
* * *
367919 ATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCTT
1 ATTTTACCCTTCGAGGGTATTTCGATAATTTTACACTTCGAGGGTATTTCGGTAATTTTACCCTT
* *
367984 TGAGGGTATTTCGATA
66 CGAGGGTATTTCAATA
* * *
368000 ATTTTACCCTTCGAAGGTATTTCGACAATTTTAC-CTTTCGAGGGTATTTCGGCAATTTTACCCT
1 ATTTTACCCTTCGAGGGTATTTCGATAATTTTACAC-TTCGAGGGTATTTCGGTAATTTTACCCT
*
368064 TCGAGGGTATTTCGATA
65 TCGAGGGTATTTCAATA
* * ** * * *
368081 ATTTTACCGTTCAAGGGTATTTTAATAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCAT
1 ATTTTACCCTTCGAGGGTATTTCGATAATTTTACACTTCGAGGGTATTTCGGTAATTTTACCCTT
368146 CGAG
66 CGAG
368150 TCGCAAGTTG
Statistics
Matches: 271, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
80 78 0.29
81 192 0.71
82 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (81 bp):
ATTTTACCCTTCGAGGGTATTTCGATAATTTTACACTTCGAGGGTATTTCGGTAATTTTACCCTT
CGAGGGTATTTCAATA
Found at i:369088 original size:17 final size:19
Alignment explanation
Indices: 369052--369091 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
369042 AATTGGCAAC
*
369052 AAGAGAAGAAGAAACCGAA
1 AAGAGAAGAAGAAACAGAA
369071 AAGA-AAGAAGAAA-AGAA
1 AAGAGAAGAAGAAACAGAA
369088 AAGA
1 AAGA
369092 TGAGGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.70, C:0.05, G:0.25, T:0.00
Consensus pattern (19 bp):
AAGAGAAGAAGAAACAGAA
Found at i:383326 original size:8 final size:7
Alignment explanation
Indices: 383307--383352 Score: 60
Period size: 6 Copynumber: 6.6 Consensus size: 7
383297 ATTTCAAAAA
383307 AAAAGATG
1 AAAA-ATG
383315 AAAAATG
1 AAAAATG
383322 AAAAAATG
1 -AAAAATG
383330 -AAAATG
1 AAAAATG
383336 AAAAATG
1 AAAAATG
383343 -AAAATG
1 AAAAATG
383349 AAAA
1 AAAA
383353 GTAATGACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.34
7 12 0.34
8 11 0.31
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:383341 original size:13 final size:13
Alignment explanation
Indices: 383316--383352 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
383306 AAAAAGATGA
383316 AAAATGAAAAAATG
1 AAAATG-AAAAATG
383330 AAAATGAAAAATG
1 AAAATGAAAAATG
383343 AAAATGAAAA
1 AAAATGAAAA
383353 GTAATGACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:384651 original size:43 final size:43
Alignment explanation
Indices: 384598--384718 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 43
384588 AAAATTACAG
* * *
384598 ATCTTGTCTCCCTAAGCA-ATAGTGGAGCAGATTGAAGC-CAGCA
1 ATCTTATCTCCCTAAG-ATACAGCGGAGCAGATTGAAGCTCA-CA
* *
384641 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTCATA
1 ATCTTATCTCCCTAAGA-TACAGCGGAGCAGATTGAAGCTCACA
* * * *
384685 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
1 ATCTTATCTCCCTAAGA-TACAGCGGAGCAGATT
384719 AAAATAAAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 1 0.01
43 14 0.21
44 50 0.75
45 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (43 bp):
ATCTTATCTCCCTAAGATACAGCGGAGCAGATTGAAGCTCACA
Found at i:384676 original size:44 final size:44
Alignment explanation
Indices: 384621--384855 Score: 154
Period size: 44 Copynumber: 5.1 Consensus size: 44
384611 AAGCAATAGT
*
384621 GGAGCAGATTGAAGCCAGCAATCTTATCTCCCTGAGATTACAGC
1 GGAGCAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGC
* *
384665 GGAGCAGATTGAAGCTCA-TAATCCTATCTCCCTGAGATTACAGT
1 GGAGCAGATTGAAGC-CAGTAATCTTATCTCCCTGAGATTACAGC
* * *** * * *
384709 GGAGCGGATTAAAATAAAG-GATCTTATCTCTCTGA-AGTTACAGTAAA
1 GGAGCAGATT-GAAGCCAGTAATCTTATCTCCCTGAGA-TTACAG---C
* * *
384756 GTAGATCGCATCAGATCGAAGCTAGAAATCTTATCTCCCTGAGATTACAGC
1 G--GA--G---CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGC
* * * *
384807 GGAGCAGAATTGAAGCTA-TAATCCTATCTCCCAGAGATTACAGT
1 GGAGCAG-ATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGC
384851 GGAGC
1 GGAGC
384856 GAATTAAAAT
Statistics
Matches: 148, Mismatches: 26, Indels: 34
0.71 0.12 0.16
Matches are distributed among these distances:
43 1 0.01
44 97 0.66
45 13 0.09
47 2 0.01
49 4 0.03
51 2 0.01
53 4 0.03
54 24 0.16
55 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (44 bp):
GGAGCAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGC
Found at i:384879 original size:44 final size:44
Alignment explanation
Indices: 384781--384880 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
384771 TCGAAGCTAG
* **
384781 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGAATTGAAGCTA
1 AAATCTTATCTCCCAGAGATTACAGCGGAGCAGAATTGAAAATA
* * *
384825 TAATCCTATCTCCCAGAGATTACAGTGGAGC-GAATT-AAAATA
1 AAATCTTATCTCCCAGAGATTACAGCGGAGCAGAATTGAAAATA
384867 AAGGATCTTATCTC
1 AA--ATCTTATCTC
384881 TCTGAAGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 5 0.11
43 5 0.11
44 36 0.78
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (44 bp):
AAATCTTATCTCCCAGAGATTACAGCGGAGCAGAATTGAAAATA
Found at i:384881 original size:142 final size:142
Alignment explanation
Indices: 384625--384911 Score: 504
Period size: 142 Copynumber: 2.0 Consensus size: 142
384615 AATAGTGGAG
* *
384625 CAGATTGAAGCCAGCAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTCATAATCCT
1 CAGATCGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTCATAATCCT
* *
384690 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAA
66 ATCTCCCAGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAA
384755 AGTAGATCGCAT
131 AGTAGATCGCAT
*
384767 CAGATCGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGAATTGAAGCT-ATAATCC
1 CAGATCGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAG-ATTGAAGCTCATAATCC
384831 TATCTCCCAGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
65 TATCTCCCAGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
*
384896 GAGTAGATCGCAT
130 AAGTAGATCGCAT
384909 CAG
1 CAG
384912 GTCTTATCTC
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
142 129 0.93
143 9 0.07
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (142 bp):
CAGATCGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTCATAATCCT
ATCTCCCAGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAA
AGTAGATCGCAT
Found at i:385133 original size:50 final size:50
Alignment explanation
Indices: 385079--385542 Score: 377
Period size: 50 Copynumber: 9.3 Consensus size: 50
385069 GTCGTGGAAT
* *
385079 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* *** ** *
385129 AGATTAAAGCTACAACA-TGGAATCTTACTT-CAAAAGCGGTGCAG-CAGAACA
1 AGATTAAAGCCACAACAGT-GAATCTTACTTCCCCGA-CATTGCAGTTA-AA-A
* *
385180 A-ATTAAAGCCACATC-GATGAATCTTACTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACAACAG-TGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** **
385229 ATATTAAAGCTACAACAGCGAATCTTACCTCCCC-AGCGA-TGCAGTGGAGC
1 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGA-C-ATTGCAGTTAAAA
* * * * *
385279 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGATATTGCAGTTCAAA
1 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * * ** *
385329 AGATTAAAGCTACAATAGCGAATCTTACCTCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGAC-ATTGCAGTTAAAA
* * * *
385379 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
1 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * * * **
385429 AGATTAAAGCTACAACAGCGAATCTTACATTCCCAGGCAGTACAGTGAAGC
1 AGATTAAAGCCACAACAGTGAATCTTAC-TTCCCCGACATTGCAGTTAAAA
385480 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
385530 AGATTAAAGCCAC
1 AGATTAAAGCCAC
385543 GATGGCGAAT
Statistics
Matches: 312, Mismatches: 85, Indels: 34
0.72 0.20 0.08
Matches are distributed among these distances:
49 9 0.03
50 254 0.81
51 49 0.16
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:385202 original size:100 final size:100
Alignment explanation
Indices: 385029--385557 Score: 661
Period size: 100 Copynumber: 5.3 Consensus size: 100
385019 CCGACATTGC
* * * * *** *
385029 AGATTAAAGCCACAGCAGCGAATCCTACTTCCTTGGCGATGTC-GTGGAATAGATTAAAGCCACA
1 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATG-CAGTGGAACAGATTAAAGCCACA
* *
385093 ACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
65 TCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* ** * ** *
385129 AGATTAAAGCTACAACATG-GAATCTTACTTCAAAAGCGGTGCAGCAGAACAAATTAAAGCCACA
1 AGATTAAAGCTACAACA-GCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACA
* *
385193 TCGATGAATCTTACTTCCCCGACATTGCAGTTCAAA
65 TCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* * *
385229 ATATTAAAGCTACAACAGCGAATCTTACCTCCCCAGCGATGCAGTGGAGCAGATTAAAGCCACAT
1 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACAT
*
385294 CGGTGAATCTTGCTTCCCCGATATTGCAGTTCAAA
66 CGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* *
385329 AGATTAAAGCTACAATAGCGAATCTTACCTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACAT
1 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACAT
385394 CGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
66 CGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* * *
385429 AGATTAAAGCTACAACAGCGAATCTTACATTCCCAGGC-AGTACAGT-GAAGCAGATTAAAGCCA
1 AGATTAAAGCTACAACAGCGAATCTTAC-CTCCCAAGCGA-TGCAGTGGAA-CAGATTAAAGCCA
* * * *
385492 CAACAGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
63 CATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
* * **
385530 AGATTAAAGCCACGATGGCGAATCTTAC
1 AGATTAAAGCTACAACAGCGAATCTTAC
385558 TTTCTAGAAG
Statistics
Matches: 377, Mismatches: 46, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
99 2 0.01
100 290 0.77
101 85 0.23
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (100 bp):
AGATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACAT
CGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAA
Found at i:385310 original size:200 final size:199
Alignment explanation
Indices: 384983--385557 Score: 729
Period size: 200 Copynumber: 2.9 Consensus size: 199
384973 CGGTGTAGTG
*
384983 GAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAG-------ATTAAAGCCA
1 GAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAAAATTAAAGCTA
* * * *** **
385041 CAGCAGCGAATCCTACTTCCTTGGCGATGTC-GTGGAATAGATTAAAGCCACAACGGTGAATCTT
66 CAACAGCGAATCTTACATCCCCAGCGATG-CAGTGGAGCAGATTAAAGCCACAACGGTGAATCTT
* *
385105 GCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACATG-GAATCTTACTTCAAAAGCGGT
130 GCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACA-GCGAATCTTACCTCAAAAGCGAT
385169 GCAGCA
194 GCAGCA
* * *
385175 GAACAAATTAAAGCCACATCGATGAATCTTACTTCCCCGACATTGCAGTTCAAAATATTAAAGCT
1 GAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAAA-ATTAAAGCT
* *
385240 ACAACAGCGAATCTTACCTCCCCAGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTT
65 ACAACAGCGAATCTTACATCCCCAGCGATGCAGTGGAGCAGATTAAAGCCACAACGGTGAATCTT
* * * ** *
385305 GCTTCCCCGATATTGCAGTTCAAAAGATTAAAGCTACAATAGCGAATCTTACCTCCCAGGCGATG
130 GCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACCTCAAAAGCGATG
**
385370 CAGTG
195 CAGCA
385375 GAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCT
1 GAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAAA-ATTAAAGCT
* * * *
385440 ACAACAGCGAATCTTACATTCCCAG-GCAGTACAGTGAAGCAGATTAAAGCCACAACAGTGAATC
65 ACAACAGCGAATCTTACATCCCCAGCG-A-TGCAGTGGAGCAGATTAAAGCCACAACGGTGAATC
* * * **
385504 TTACTTCCCCGACATTGCAGTTAAAAAGATTAAAGCCACGATGGCGAATCTTAC
128 TTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC
385558 TTTCTAGAAG
Statistics
Matches: 332, Mismatches: 39, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
192 45 0.14
199 3 0.01
200 205 0.62
201 79 0.24
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (199 bp):
GAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAAAATTAAAGCTA
CAACAGCGAATCTTACATCCCCAGCGATGCAGTGGAGCAGATTAAAGCCACAACGGTGAATCTTG
CTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACCTCAAAAGCGATGC
AGCA
Found at i:390336 original size:17 final size:17
Alignment explanation
Indices: 390314--390347 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
390304 AATAGTCAAT
390314 GGAGGCATTTTGAAGTC
1 GGAGGCATTTTGAAGTC
390331 GGAGGCATTTTGAAGTC
1 GGAGGCATTTTGAAGTC
390348 TATCCTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (17 bp):
GGAGGCATTTTGAAGTC
Found at i:392889 original size:7 final size:7
Alignment explanation
Indices: 392877--392901 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
392867 TATTAAAATA
392877 TTAAAAG
1 TTAAAAG
392884 TTAAAAG
1 TTAAAAG
392891 TTAAAAG
1 TTAAAAG
392898 TTAA
1 TTAA
392902 GTATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (7 bp):
TTAAAAG
Found at i:392958 original size:17 final size:17
Alignment explanation
Indices: 392936--392971 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
392926 ATAATTAAAT
392936 AAAAGAAAAAGAATAGA
1 AAAAGAAAAAGAATAGA
* *
392953 AAAAGAAAGAGCATAGA
1 AAAAGAAAAAGAATAGA
392970 AA
1 AA
392972 CGAAAACAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAAGAATAGA
Found at i:392970 original size:22 final size:20
Alignment explanation
Indices: 392943--393003 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
392933 AATAAAAGAA
392943 AAAGAATAGAAAAAGAAAGAGC
1 AAAGAA-AGAAAAAGAAAG-GC
* * *
392965 ATAGAAACGAAAACAGGAAGGG
1 AAAGAAA-GAAAA-AGAAAGGC
392987 AAAGAAAGAAAAAGAAA
1 AAAGAAAGAAAAAGAAA
393004 AAGAAAGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.12
21 6 0.19
22 17 0.53
23 5 0.16
ACGTcount: A:0.67, C:0.05, G:0.25, T:0.03
Consensus pattern (20 bp):
AAAGAAAGAAAAAGAAAGGC
Found at i:393875 original size:41 final size:38
Alignment explanation
Indices: 393828--393940 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 38
393818 TTCGACTTTG
*
393828 AGTCGATGAGATACTGGGTGTCAATTTACTACTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAA-TTA-TACTTCGG-TTA
* * * * *
393869 ATTCGATAAGGCACTGGGTGCCAATT-TACTTCGGTTT
1 AGTCGATGAGACACTGGGTGTCAATTATACTTCGGTTA
*
393906 AGTCGATGAGACACTAGGTGTCAAATTATTACTTC
1 AGTCGATGAGACACTGGGTGTC-AATTA-TACTTC
393941 AAATTATCCG
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
37 19 0.33
38 12 0.21
40 8 0.14
41 19 0.33
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (38 bp):
AGTCGATGAGACACTGGGTGTCAATTATACTTCGGTTA
Found at i:394725 original size:13 final size:13
Alignment explanation
Indices: 394707--394734 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
394697 TGAATGATAT
394707 TTTGATGATATAA
1 TTTGATGATATAA
394720 TTTGATGATATAA
1 TTTGATGATATAA
394733 TT
1 TT
394735 GTGGTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TTTGATGATATAA
Found at i:405583 original size:10 final size:10
Alignment explanation
Indices: 405567--405605 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
405557 AACAAATACT
405567 TATTTTC-TC
1 TATTTTCTTC
405576 TCATTTTCTTC
1 T-ATTTTCTTC
405587 TATTTTCTTC
1 TATTTTCTTC
405597 TATTTTCTT
1 TATTTTCTT
405606 TCTTTGATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 1 0.04
10 24 0.86
11 3 0.11
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTTCTTC
Found at i:406028 original size:23 final size:23
Alignment explanation
Indices: 406000--406047 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
405990 TTAGGGTTTA
406000 TTTTAGGTTTTGAAT-TTGGGCTT
1 TTTTAGGTTTTGAATCTTGGG-TT
* *
406023 TTTTAGTTTTTGCATCTTGGGTT
1 TTTTAGGTTTTGAATCTTGGGTT
406046 TT
1 TT
406048 AAATGGGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.10, C:0.06, G:0.23, T:0.60
Consensus pattern (23 bp):
TTTTAGGTTTTGAATCTTGGGTT
Found at i:408596 original size:18 final size:18
Alignment explanation
Indices: 408573--408610 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
408563 TGTTAGGTGC
*
408573 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
408591 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
408609 GT
1 GT
408611 TTCATTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:409125 original size:62 final size:61
Alignment explanation
Indices: 409003--409125 Score: 133
Period size: 62 Copynumber: 2.0 Consensus size: 61
408993 TATATTTGTA
* ****
409003 TAAACTATTTTTATATTGTTTTCATTTAATAAAATAAAAGTTGCTTTGAATATTTTAATAG
1 TAAACTATTTTTATATTGTTTTCATTTAACAAAATAAAAGTTGCTTTGAATAAGGCAATAG
* * *
409064 TAAATTATTTTTATATT-TTGTCTTATTTAACAAAATAGAAGTT-CTTTTGAATAAGGCAATAG
1 TAAACTATTTTTATATTGTT-T-TCATTTAACAAAATAAAAGTTGC-TTTGAATAAGGCAATAG
409126 GAATAATGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
60 2 0.04
61 18 0.35
62 31 0.61
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (61 bp):
TAAACTATTTTTATATTGTTTTCATTTAACAAAATAAAAGTTGCTTTGAATAAGGCAATAG
Found at i:412297 original size:126 final size:126
Alignment explanation
Indices: 412062--412581 Score: 758
Period size: 126 Copynumber: 4.1 Consensus size: 126
412052 TGGCAAACAA
* * *
412062 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTACTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
* * *
412127 TTG-TTCGAAGCATTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTT-GAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
* * * * *
412188 GAACTACTGTAGAAAAATAGCGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
* * * *
412253 CTGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACTGTATTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
* * *
412314 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTT-AATAATTTTACTGACAGTGCTTA
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
*
412378 CTGCTTGAAGCGTTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
* * *
412439 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTACATT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
* * * *
412504 TTGCTTGAAGCGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTA-
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC-AG
*
412565 AAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
412582 AAAAACAAAA
Statistics
Matches: 356, Mismatches: 35, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
125 116 0.33
126 237 0.67
127 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAG
Found at i:412511 original size:251 final size:252
Alignment explanation
Indices: 412059--412581 Score: 802
Period size: 251 Copynumber: 2.1 Consensus size: 252
412049 TAATGGCAAA
*
412059 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTACTAACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAATAATTTTACTAACAGTGC
* *
412124 ATCTTGTTCGAAGCATTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCAGG
66 ATCTTGTTCGAAGCATTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGG
* * * * *
412189 AACTACTGTAGAAAAATAGCGTCCACGTGGGAGTTTTTTTCAGTAATTTTGCTGACAGTGCATCC
131 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTACATCC
* * * *
412254 TGCTTGAAGCGTTTTTGACACTATTTTTTTAGAACTGTATTCTCAAAATTATTTTTT
196 TGCTTGAAGCGTTTTTGACACTATCTTTTCAGAACCGTATTCTCAAAATTAATTTTT
* * *
412311 CAAGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTT-AATAATTTTACTGACAGTGC
1 CAAGAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAATAATTTTACTAACAGTGC
* *
412375 TTAC-TGCTT-GAAGCGTTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCA
66 AT-CTTG-TTCGAAGCATTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCA
412438 GGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTACAT
129 GGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTACAT
** * *
412503 TTTGCTTGAAGCGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTT
194 CCTGCTTGAAGCGTTTTTGACACTATCTTTTCAGAACCGTATTCTCAAAATTAATTTTT
412562 CTAA-AACTACTGTAGAAAAA
1 C-AAGAACTACTGTAGAAAAA
412582 AAAAACAAAA
Statistics
Matches: 247, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
251 200 0.81
252 47 0.19
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (252 bp):
CAAGAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAATAATTTTACTAACAGTGC
ATCTTGTTCGAAGCATTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGG
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATAATTTTGCTAACAGTACATCC
TGCTTGAAGCGTTTTTGACACTATCTTTTCAGAACCGTATTCTCAAAATTAATTTTT
Found at i:412717 original size:34 final size:34
Alignment explanation
Indices: 412634--412738 Score: 126
Period size: 34 Copynumber: 3.1 Consensus size: 34
412624 CTTAACCTAA
*
412634 ATTTAAAAAAACTAAACTCTAATTTAATT-ATTT
1 ATTTAAAAAAACTAAACCCTAATTTAATTAATTT
*
412667 -TTAAAAAAAATTCTAAACCCTAATTTAATTAATTT
1 ATTTAAAAAAA--CTAAACCCTAATTTAATTAATTT
* * *
412702 ATTTAAAACACCTAAAACCTAATTTAATTAA-TT
1 ATTTAAAAAAACTAAACCCTAATTTAATTAATTT
412735 ATTT
1 ATTT
412739 TTTTAAAACT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
32 9 0.15
33 6 0.10
34 36 0.58
35 4 0.06
36 7 0.11
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (34 bp):
ATTTAAAAAAACTAAACCCTAATTTAATTAATTT
Found at i:412787 original size:28 final size:27
Alignment explanation
Indices: 412729--412787 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
412719 CCTAATTTAA
*
412729 TTAATTATTTTTTTAAAACTCTAAAAT
1 TTAATTATTTTTTTAAAACTCTAAAAC
* *
412756 TTAATT-TATTTTTTAAAATTCTTAAACC
1 TTAATTAT-TTTTTTAAAACTC-TAAAAC
412784 TTAA
1 TTAA
412788 ATAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.67
28 8 0.30
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATTATTTTTTTAAAACTCTAAAAC
Found at i:436823 original size:2 final size:2
Alignment explanation
Indices: 436816--436840 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
436806 AGCCTTTTTG
436816 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
436841 GAGGGGGGAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:444034 original size:63 final size:63
Alignment explanation
Indices: 443905--444026 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
443895 GACCCTACAT
* *
443905 GGCCGTGTAACTCACTATTTTGGAATTAGAATCACACAAGTCAACGACACGGGCGTGTGCCCA
1 GGCCGTGTAACTCACTATTTTGGAATTAGAATCACACAAGCCAACGACACGGGCATGTGCCCA
* * * **
443968 GGCCGTGTAACTCATTGTTTTGGAATTAGAGTCACACGGGCCAGA-GACACGGGCATGTG
1 GGCCGTGTAACTCACTATTTTGGAATTAGAATCACACAAGCCA-ACGACACGGGCATGTG
444027 TCTAGGCCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 50 0.98
64 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (63 bp):
GGCCGTGTAACTCACTATTTTGGAATTAGAATCACACAAGCCAACGACACGGGCATGTGCCCA
Found at i:456272 original size:32 final size:32
Alignment explanation
Indices: 456236--456302 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
456226 ACGCCACATC
456236 ATCCTTTTCTACCCCCACTT-CT-AAACTCCCAA
1 ATCC-TTTCT-CCCCCACTTCCTCAAACTCCCAA
*
456268 ATCCTTTCTCCCCCACTTCCTCAATCTCCCAA
1 ATCCTTTCTCCCCCACTTCCTCAAACTCCCAA
456300 ATC
1 ATC
456303 GACAATCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 9 0.28
31 7 0.22
32 16 0.50
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.31
Consensus pattern (32 bp):
ATCCTTTCTCCCCCACTTCCTCAAACTCCCAA
Found at i:468341 original size:18 final size:18
Alignment explanation
Indices: 468315--468354 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
468305 CTCAAGTCTG
*
468315 TTCTGATTCAGGCTCCTA
1 TTCTAATTCAGGCTCCTA
*
468333 TTCTAATTCAGGGTCCTA
1 TTCTAATTCAGGCTCCTA
468351 TTCT
1 TTCT
468355 GATACAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (18 bp):
TTCTAATTCAGGCTCCTA
Found at i:476004 original size:28 final size:28
Alignment explanation
Indices: 475964--476022 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
475954 AAGCCCACTG
* *
475964 TTTTTTCTTCTCAACTCACAATTTTGTTT
1 TTTTTTCTCCTCAACTCACAAATTT-TTT
475993 TTTTTTC-CCTCAACTCACAAATTTTTT
1 TTTTTTCTCCTCAACTCACAAATTTTTT
476020 TTT
1 TTT
476023 CACTTTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.19, C:0.22, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTTTCTCCTCAACTCACAAATTTTTT
Found at i:479110 original size:15 final size:16
Alignment explanation
Indices: 479085--479117 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
479075 ATAAGTTGTG
479085 TATATTAAAACAAAAT
1 TATATTAAAACAAAAT
*
479101 TATA-TAAAACAATAT
1 TATATTAAAACAAAAT
479116 TA
1 TA
479118 AAATAAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TATATTAAAACAAAAT
Found at i:484163 original size:13 final size:13
Alignment explanation
Indices: 484145--484169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
484135 AATAAAAAAA
484145 ATAATTAATATTC
1 ATAATTAATATTC
484158 ATAATTAATATT
1 ATAATTAATATT
484170 TTAAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAATTAATATTC
Found at i:487759 original size:1 final size:1
Alignment explanation
Indices: 487709--487739 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
487699 CATTCATACC
*
487709 TTTTTTTTTTTTTTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
487740 AGATCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:488455 original size:388 final size:388
Alignment explanation
Indices: 487739--488498 Score: 1520
Period size: 388 Copynumber: 2.0 Consensus size: 388
487729 TTCTTTTTTT
487739 TAGATCAAAATAAATTTTTTTATATCATCATCCACGCCCTTAGTTTGGGGCCTAATTAAGGTTTT
1 TAGATCAAAATAAATTTTTTTATATCATCATCCACGCCCTTAGTTTGGGGCCTAATTAAGGTTTT
487804 ATTTTAAAATTTAATCTTGTCTCATTTGCTTTTTACCCTTTTGTGGCAGATGGGTTAGGCCTGAG
66 ATTTTAAAATTTAATCTTGTCTCATTTGCTTTTTACCCTTTTGTGGCAGATGGGTTAGGCCTGAG
487869 GTCAATAATGGCTTATCCTTGTTTACCAACGGCTTGTTTATTGCTACCATCTGCAACTAGCAACG
131 GTCAATAATGGCTTATCCTTGTTTACCAACGGCTTGTTTATTGCTACCATCTGCAACTAGCAACG
487934 AATGTAGTCAGAAGTGAATTTGGAAGCTTTTCAATTTCTTGATATTTTGGTTTTTGGATGAGGAA
196 AATGTAGTCAGAAGTGAATTTGGAAGCTTTTCAATTTCTTGATATTTTGGTTTTTGGATGAGGAA
487999 AGCTCAAGTGCGCCTGGAATCTATACTTTTCTTTTGATTTTTTTTTTTAAATTCTAAGATTTGTA
261 AGCTCAAGTGCGCCTGGAATCTATACTTTTCTTTTGATTTTTTTTTTTAAATTCTAAGATTTGTA
488064 TTTTATTTTCATTTTCATTTGTAAAACGTCGTCGTACTTATTTATATTTTGTTTCCTATCTTC
326 TTTTATTTTCATTTTCATTTGTAAAACGTCGTCGTACTTATTTATATTTTGTTTCCTATCTTC
488127 TAGATCAAAATAAATTTTTTTATATCATCATCCACGCCCTTAGTTTGGGGCCTAATTAAGGTTTT
1 TAGATCAAAATAAATTTTTTTATATCATCATCCACGCCCTTAGTTTGGGGCCTAATTAAGGTTTT
488192 ATTTTAAAATTTAATCTTGTCTCATTTGCTTTTTACCCTTTTGTGGCAGATGGGTTAGGCCTGAG
66 ATTTTAAAATTTAATCTTGTCTCATTTGCTTTTTACCCTTTTGTGGCAGATGGGTTAGGCCTGAG
488257 GTCAATAATGGCTTATCCTTGTTTACCAACGGCTTGTTTATTGCTACCATCTGCAACTAGCAACG
131 GTCAATAATGGCTTATCCTTGTTTACCAACGGCTTGTTTATTGCTACCATCTGCAACTAGCAACG
488322 AATGTAGTCAGAAGTGAATTTGGAAGCTTTTCAATTTCTTGATATTTTGGTTTTTGGATGAGGAA
196 AATGTAGTCAGAAGTGAATTTGGAAGCTTTTCAATTTCTTGATATTTTGGTTTTTGGATGAGGAA
488387 AGCTCAAGTGCGCCTGGAATCTATACTTTTCTTTTGATTTTTTTTTTTAAATTCTAAGATTTGTA
261 AGCTCAAGTGCGCCTGGAATCTATACTTTTCTTTTGATTTTTTTTTTTAAATTCTAAGATTTGTA
488452 TTTTATTTTCATTTTCATTTGTAAAACGTCGTCGTACTTATTTATAT
326 TTTTATTTTCATTTTCATTTGTAAAACGTCGTCGTACTTATTTATAT
488499 GATTAGTATT
Statistics
Matches: 372, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
388 372 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.44
Consensus pattern (388 bp):
TAGATCAAAATAAATTTTTTTATATCATCATCCACGCCCTTAGTTTGGGGCCTAATTAAGGTTTT
ATTTTAAAATTTAATCTTGTCTCATTTGCTTTTTACCCTTTTGTGGCAGATGGGTTAGGCCTGAG
GTCAATAATGGCTTATCCTTGTTTACCAACGGCTTGTTTATTGCTACCATCTGCAACTAGCAACG
AATGTAGTCAGAAGTGAATTTGGAAGCTTTTCAATTTCTTGATATTTTGGTTTTTGGATGAGGAA
AGCTCAAGTGCGCCTGGAATCTATACTTTTCTTTTGATTTTTTTTTTTAAATTCTAAGATTTGTA
TTTTATTTTCATTTTCATTTGTAAAACGTCGTCGTACTTATTTATATTTTGTTTCCTATCTTC
Found at i:489215 original size:29 final size:30
Alignment explanation
Indices: 489126--489215 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 30
489116 ACCAGCATTT
* *
489126 AAATAATTTTTAAACACTAAAAAAATT-TTACA
1 AAATTATTTTTAAA-ATTAAAAAAATTATT--A
* *
489158 AAATTATTTTTAAAAATT--AAAGATCATTA
1 AAATTATTTTT-AAAATTAAAAAAATTATTA
489187 AAATTA-TTTTAAAATTAAAAAAATTATTA
1 AAATTATTTTTAAAATTAAAAAAATTATTA
489216 TTAATGTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
27 6 0.12
28 4 0.08
29 16 0.33
30 5 0.10
31 2 0.04
32 12 0.25
33 3 0.06
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATTATTTTTAAAATTAAAAAAATTATTA
Found at i:491758 original size:21 final size:20
Alignment explanation
Indices: 491712--491750 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
491702 TATAAAAATT
491712 TTAAAAAATATATTAAAAAC
1 TTAAAAAATATATTAAAAAC
* *
491732 TTAAAAATTATTTTAAAAA
1 TTAAAAAATATATTAAAAA
491751 GTATAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAAAATATATTAAAAAC
Found at i:492499 original size:15 final size:15
Alignment explanation
Indices: 492479--492509 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
492469 TGGAAGCATG
492479 AAGAAATATTTTCAT
1 AAGAAATATTTTCAT
492494 AAGAAATATTTTCAT
1 AAGAAATATTTTCAT
492509 A
1 A
492510 CTCTCTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
AAGAAATATTTTCAT
Found at i:501035 original size:18 final size:16
Alignment explanation
Indices: 501005--501048 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
500995 CGTAAGAAAG
501005 AAAAGAAAAAAAAGAGC
1 AAAA-AAAAAAAAGAGC
*
501022 AAGAAAAAATAAAAGAGT
1 AA-AAAAAA-AAAAGAGC
501040 AAAAAAAAA
1 AAAAAAAAA
501049 CACCTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 12 0.50
18 11 0.46
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (16 bp):
AAAAAAAAAAAAGAGC
Found at i:502239 original size:12 final size:13
Alignment explanation
Indices: 502211--502244 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
502201 ATCACTCTGT
502211 AAATATTTATAAA
1 AAATATTTATAAA
502224 AAATATTTAT-AA
1 AAATATTTATAAA
502236 AAATATTTA
1 AAATATTTA
502245 CGGCTCGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATTTATAAA
Found at i:515206 original size:54 final size:54
Alignment explanation
Indices: 515104--515209 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
515094 CGTGTGACCC
* * * *
515104 AAGTCAGTGAGTTACTCGGGTAGAGACACGGGCTGGGACATGATTGTGTGTCTT
1 AAGTCAGTGAGTTACTCGGGTAGAGACACGAGCTAGGACACGACTGTGTGTCTT
* *
515158 AAGTTAGTGAGTTACAT-GGGTAGAGACACGAGCTAGGACACGGCTGTGTGTC
1 AAGTCAGTGAGTTAC-TCGGGTAGAGACACGAGCTAGGACACGACTGTGTGTC
515210 CTAACTTCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 44 0.98
55 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (54 bp):
AAGTCAGTGAGTTACTCGGGTAGAGACACGAGCTAGGACACGACTGTGTGTCTT
Found at i:518076 original size:16 final size:17
Alignment explanation
Indices: 518054--518099 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
518044 TAAAAATATT
518054 TATATTATATTATTTTA
1 TATATTATATTATTTTA
*
518071 -ATATTA-ATAATTTTA
1 TATATTATATTATTTTA
518086 TATATT-TATTATTT
1 TATATTATATTATTT
518100 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTATATTATTTTA
Found at i:518105 original size:14 final size:15
Alignment explanation
Indices: 518052--518106 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
518042 TTTAAAAATA
518052 TTTA-TATTATATTAT
1 TTTATTATT-TATTAT
* * *
518067 TTTAATATTAATAAT
1 TTTATTATTTATTAT
518082 TTTATATATTTATTA-
1 TTTAT-TATTTATTAT
518097 TTTATTATTT
1 TTTATTATTT
518107 TTTTATATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 5 0.15
15 17 0.52
16 11 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATTATTTATTAT
Found at i:519205 original size:7 final size:7
Alignment explanation
Indices: 519159--519203 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
519149 CATGCTTTTC
519159 AAATGGT
1 AAATGGT
519166 AAATGGT
1 AAATGGT
519173 AAATGGT
1 AAATGGT
519180 AAATGGT
1 AAATGGT
519187 AAATGGT
1 AAATGGT
*
519194 AAAAGGT
1 AAATGGT
519201 AAA
1 AAA
519204 AGAAAGTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (7 bp):
AAATGGT
Found at i:528218 original size:54 final size:53
Alignment explanation
Indices: 528150--528321 Score: 188
Period size: 54 Copynumber: 3.2 Consensus size: 53
528140 TACCCTCGAT
*
528150 GGGTAAAATGATCGAAATACCCACGATGGGTAAAATGACTGAAATGCCCCCGTA
1 GGGTAAAATGATCGAAATACCC-CGATGGGTAAAATGACTGAAATGCCCCCATA
* * *
528204 GGGTAAAATGATCGAAATACCCCCGCA-GGGTAGAATG-CCGAAATACCCCCATA
1 GGGTAAAATGATCGAAATA-CCCCG-ATGGGTAAAATGACTGAAATGCCCCCATA
* * * * * *
528257 GGATAAAATGA-CTGTAATGCCCCTATAGGGTAAAATGACTGTAATGCCCCTATA
1 GGGTAAAATGATC-GAAATACCCCGAT-GGGTAAAATGACTGAAATGCCCCCATA
528311 GGGTAAAATGA
1 GGGTAAAATGA
528322 CCATAATGCC
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
51 1 0.01
52 5 0.05
53 36 0.37
54 52 0.53
55 4 0.04
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (53 bp):
GGGTAAAATGATCGAAATACCCCGATGGGTAAAATGACTGAAATGCCCCCATA
Found at i:528264 original size:80 final size:81
Alignment explanation
Indices: 528135--528294 Score: 209
Period size: 80 Copynumber: 2.0 Consensus size: 81
528125 ATATCTGGAC
* * * *
528135 CGAAATACCCTCGATGGGTAAAATGATCGAAATACCCACGATGGGTAAAATGACTGAAATGCCCC
1 CGAAATACCCCCGATGGGTAAAATGACCGAAATACCCACCATGGATAAAATGACTGAAATGCCCC
*
528200 CGTAGGGTAAAATGAT
66 CATAGGGTAAAATGAT
* *
528216 CGAAATACCCCCGCA-GGGTAGAATG-CCGAAATACCC-CCATAGGATAAAATGACTGTAATGCC
1 CGAAATACCCCCG-ATGGGTAAAATGACCGAAATACCCACCAT-GGATAAAATGACTGAAATGCC
*
528278 CCTATAGGGTAAAATGA
64 CCCATAGGGTAAAATGA
528295 CTGTAATGCC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.04
80 44 0.64
81 21 0.30
82 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (81 bp):
CGAAATACCCCCGATGGGTAAAATGACCGAAATACCCACCATGGATAAAATGACTGAAATGCCCC
CATAGGGTAAAATGAT
Found at i:528279 original size:27 final size:27
Alignment explanation
Indices: 528150--528322 Score: 165
Period size: 27 Copynumber: 6.4 Consensus size: 27
528140 TACCCTCGAT
* *
528150 GGGTAAAATGA-TCGAAATACCCACGAT-
1 GGGTAAAATGACT-GAAATGCCC-CCATA
*
528177 GGGTAAAATGACTGAAATGCCCCCGTA
1 GGGTAAAATGACTGAAATGCCCCCATA
* **
528204 GGGTAAAATGA-TCGAAATACCCCCGCA
1 GGGTAAAATGACT-GAAATGCCCCCATA
* * *
528231 GGGTAGAATG-CCGAAATACCCCCATA
1 GGGTAAAATGACTGAAATGCCCCCATA
* * *
528257 GGATAAAATGACTGTAATGCCCCTATA
1 GGGTAAAATGACTGAAATGCCCCCATA
* *
528284 GGGTAAAATGACTGTAATGCCCCTATA
1 GGGTAAAATGACTGAAATGCCCCCATA
528311 GGGTAAAATGAC
1 GGGTAAAATGAC
528323 CATAATGCCC
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
26 23 0.18
27 101 0.81
28 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (27 bp):
GGGTAAAATGACTGAAATGCCCCCATA
Found at i:528314 original size:80 final size:80
Alignment explanation
Indices: 528150--528320 Score: 193
Period size: 80 Copynumber: 2.1 Consensus size: 80
528140 TACCCTCGAT
* * * *
528150 GGGTAAAATGATCGAAATACCCACGATGGGTAAAATGACTGAAATGCCCCCGTAGGGTAAAATGA
1 GGGTAAAATG-CCGAAATACCCACCATGGATAAAATGACTGAAATGCCCCCATAGGGTAAAATGA
*
528215 TCGAAATACCCCCGCA
65 TCGAAATACCCCCACA
* * *
528231 GGGTAGAATGCCGAAATACCC-CCATAGGATAAAATGACTGTAATGCCCCTATAGGGTAAAATGA
1 GGGTAAAATGCCGAAATACCCACCAT-GGATAAAATGACTGAAATGCCCCCATAGGGTAAAATGA
* * * *
528295 -CTGTAATGCCCCTATA
65 TC-GAAATACCCCCACA
528311 GGGTAAAATG
1 GGGTAAAATG
528321 ACCATAATGC
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
79 4 0.05
80 62 0.83
81 9 0.12
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (80 bp):
GGGTAAAATGCCGAAATACCCACCATGGATAAAATGACTGAAATGCCCCCATAGGGTAAAATGAT
CGAAATACCCCCACA
Found at i:528322 original size:54 final size:54
Alignment explanation
Indices: 528177--528332 Score: 163
Period size: 53 Copynumber: 2.9 Consensus size: 54
528167 TACCCACGAT
* * * *
528177 GGGTAAAATGACTGAAATGCCCCCGTAGGGTAAAATGA-TCGAAATACCCCCGCA
1 GGGTAAAATGACTGAAATGCCCCCATAGGGTAAAATGACT-GTAATGCCCCCACA
* * * * * *
528231 GGGTAGAATG-CCGAAATACCCCCATAGGATAAAATGACTGTAATGCCCCTATA
1 GGGTAAAATGACTGAAATGCCCCCATAGGGTAAAATGACTGTAATGCCCCCACA
* * **
528284 GGGTAAAATGACTGTAATGCCCCTATAGGGTAAAATGACCATAATGCCC
1 GGGTAAAATGACTGAAATGCCCCCATAGGGTAAAATGACTGTAATGCCC
528333 TGGTGGGTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
53 41 0.50
54 41 0.50
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (54 bp):
GGGTAAAATGACTGAAATGCCCCCATAGGGTAAAATGACTGTAATGCCCCCACA
Found at i:528343 original size:26 final size:27
Alignment explanation
Indices: 528249--528332 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
528239 TGCCGAAATA
* * **
528249 CCCCCATAGGATAAAATGACTGTAATG
1 CCCCTATAGGGTAAAATGACCATAATG
**
528276 CCCCTATAGGGTAAAATGACTGTAATG
1 CCCCTATAGGGTAAAATGACCATAATG
528303 CCCCTATAGGGTAAAATGACCATAATG
1 CCCCTATAGGGTAAAATGACCATAATG
528330 CCC
1 CCC
528333 TGGTGGGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (27 bp):
CCCCTATAGGGTAAAATGACCATAATG
Found at i:528425 original size:24 final size:24
Alignment explanation
Indices: 528392--528450 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
528382 TCTGTGGTTA
528392 AATGACTGATTTGTTTGTG-TTTGG
1 AATGACTGATTTGTTTGTGATTT-G
*
528416 TATGACTGATTTGTTTGTGATTTG
1 AATGACTGATTTGTTTGTGATTTG
528440 AATGACTGATT
1 AATGACTGATT
528451 CTGAGCATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTTTGTGATTTG
Found at i:528562 original size:27 final size:27
Alignment explanation
Indices: 528519--528578 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
528509 GGAAGTATTG
*
528519 TACTGGTGGCTCTGCCACA-ATCACTGT
1 TACTGGTGGCTCTGCCACATAT-ACTAT
*
528546 TACTGGTGG-TTTGGCCACATATACTAT
1 TACTGGTGGCTCT-GCCACATATACTAT
528573 TACTGG
1 TACTGG
528579 CAGCTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.07
27 25 0.86
28 2 0.07
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACATATACTAT
Found at i:528663 original size:32 final size:32
Alignment explanation
Indices: 528622--528829 Score: 193
Period size: 32 Copynumber: 6.5 Consensus size: 32
528612 GCTGCGATGC
* **
528622 TACTGATGGCTTTGTGCGGATCATAGAACCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* *
528654 TACTGATGGCTTTGTGCCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * * * * *
528686 TGCCGATGGCTGTGTGTCGATCATTTCACTGT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* * ***
528718 TACTGATGG-TTGTATGCCAATCATATCACTAC
1 TACTGATGGCTT-TGTGCCGATCATATCACCGT
* * *
528750 TACTGATGGCTTTGTGCCGGTCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
* ** *
528782 TACTGATGGCTGTGTGCCGATCATATCATTGC
1 TACTGATGGCTTTGTGCCGATCATATCACCGT
528814 TACTGATGGCTTTGTG
1 TACTGATGGCTTTGTG
528830 TCAATCACTT
Statistics
Matches: 139, Mismatches: 35, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
31 1 0.01
32 136 0.98
33 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATCACCGT
Found at i:528758 original size:64 final size:63
Alignment explanation
Indices: 528690--528859 Score: 189
Period size: 64 Copynumber: 2.7 Consensus size: 63
528680 TATCGTTGCC
*
528690 GATGGCTGTGTGTCGATCATTTCACTGTTACTGATGGTTGTATGCCAATCATATCACTACTACT
1 GATGGCTTTGTGTCGATCATTT-ACTGTTACTGATGGTTGTATGCCAATCATATCACTACTACT
* * ** * * * * *
528754 GATGGCTTTGTGCCGGTCATATTACCATTACTGATGGCTGTGTGCCGATCATATCATTGCTACT
1 GATGGCTTTGTGTCGATCAT-TTACTGTTACTGATGGTTGTATGCCAATCATATCACTACTACT
* *
528818 GATGGCTTTGTGTCAATCACTTTACTG-TACTTATGGCTTGTA
1 GATGGCTTTGTGTCGATCA-TTTACTGTTACTGATGG-TTGTA
528860 ACCATTCTGT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
63 8 0.09
64 74 0.87
65 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (63 bp):
GATGGCTTTGTGTCGATCATTTACTGTTACTGATGGTTGTATGCCAATCATATCACTACTACT
Found at i:528835 original size:96 final size:95
Alignment explanation
Indices: 528619--528836 Score: 249
Period size: 96 Copynumber: 2.3 Consensus size: 95
528609 TTTGCTGCGA
* ** *
528619 TGCTACTGATGGCTTTGTGCGGATCATAGAACCGTTACTGATGGCTTTGTGCCGATCATATTATC
1 TGCTACTGATGGCTTTGTGC-AATCATAGAACCACTACTGATGGCTTTGTGCCGATCATATTACC
* * * *
528684 GTTGCCGATGGCTGTGTGTCGATCATTTCAC
65 ATTACCGATGGCTGTGTGCCGATCATATCAC
* * ** * *
528715 TGTTACTGATGG-TTGTATGCCAATCATATCACTACTACTGATGGCTTTGTGCCGGTCATATTAC
1 TGCTACTGATGGCTT-TGTG-CAATCATAGAACCACTACTGATGGCTTTGTGCCGATCATATTAC
* *
528779 CATTACTGATGGCTGTGTGCCGATCATATCAT
64 CATTACCGATGGCTGTGTGCCGATCATATCAC
528811 TGCTACTGATGGCTTTGTGTCAATCA
1 TGCTACTGATGGCTTTGTG-CAATCA
528837 CTTTACTGTA
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
95 2 0.02
96 95 0.95
97 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (95 bp):
TGCTACTGATGGCTTTGTGCAATCATAGAACCACTACTGATGGCTTTGTGCCGATCATATTACCA
TTACCGATGGCTGTGTGCCGATCATATCAC
Found at i:528935 original size:26 final size:26
Alignment explanation
Indices: 528906--528958 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
528896 GGCTCTTAGC
* *
528906 CATTCTGACTACTGGCAGCTCTGCTG
1 CATTATGACTACTGGCAGCTATGCTG
*
528932 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGGCAGCTATGCTG
528958 C
1 C
528959 GATATTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (26 bp):
CATTATGACTACTGGCAGCTATGCTG
Found at i:538220 original size:42 final size:42
Alignment explanation
Indices: 538173--538440 Score: 403
Period size: 42 Copynumber: 6.4 Consensus size: 42
538163 AAACAAAAAA
* * *
538173 GCCGCTAAAGATCGTGTTCTTTAGCGGCGTTTTTTAT-TAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-TCTAAGC
* *
538215 GCCGCTAAAGAACATGGTTTTTAGCGGTGTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
* *
538257 GCCTCTAAAGAACATGGTCTTTAGCGGCGTTTCTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
*
538299 GCCGCTAAAGAACATGGTCTTTAGCAGCGTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
* *
538341 GCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAGT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
** *
538383 GCCGCTAAAGAACATTATCTTTAGCGGCGTTTTTTTCTAAGT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
538425 GCCGCTAAAGAACATG
1 GCCGCTAAAGAACATG
538441 TTAAATTTTT
Statistics
Matches: 206, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 1 0.00
42 205 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (42 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
Found at i:538745 original size:21 final size:21
Alignment explanation
Indices: 538721--538767 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
538711 TTTTGCTCTG
* *
538721 CTCTGCTTCTCTCGTTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
538742 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCAGC
538763 CTCTG
1 CTCTG
538768 TTTTAAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.43, G:0.19, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:542314 original size:15 final size:15
Alignment explanation
Indices: 542294--542325 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
542284 GTGATAACAG
542294 TAAATTAGTACCAAA
1 TAAATTAGTACCAAA
542309 TAAATTAGTACCAAA
1 TAAATTAGTACCAAA
542324 TA
1 TA
542326 CTTCAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (15 bp):
TAAATTAGTACCAAA
Found at i:543945 original size:147 final size:147
Alignment explanation
Indices: 543637--544027 Score: 407
Period size: 146 Copynumber: 2.7 Consensus size: 147
543627 TTATAAATAT
* * * *
543637 GCGCCACTAACTATAAATCAAAACGAAGCCGTTTCATCAACAAATAGCTCACGCCTGTGGCGTTT
1 GCGCCACTAACTATAAATCAAAACGAAGTCGTTTCATCAACAATTAACTCAAGCCTGTGGCGTTT
** * *** *
543702 TTGAATAAACGCCACTAAT-A-ATACAGCAAAACGGTCTCGTATCAATAAATGTTAAAACATTTT
66 TCAAAAAAACGCCACTAATAACATACA-CAAAACGGTAGAGTATCAATAAATGTTAAAACAATTT
*
543765 TGTGGCGTTTGAACCAAA
130 TGCGGCGTTTGAACCAAA
* * * * * *
543783 GCGCCACTAAATATAAATCAAAAC-ACAGTCGCTTCATCAACATTTACCTCAAACCCGTGGCGTT
1 GCGCCACTAACTATAAATCAAAACGA-AGTCGTTTCATCAACAATTAACTCAAGCCTGTGGCGTT
* ** * * *
543847 TCCAAAAAAACGCCACTAATAACATTTACAAAACGGTAGAGTTTCTATAAATGTTAGAACAATTT
65 TTCAAAAAAACGCCACTAATAACATACACAAAACGGTAGAGTATCAATAAATGTTAAAACAATTT
**
543912 TGCGGCGTTTTG-AGTAAA
130 TGCGGCG-TTTGAACCAAA
* * *
543930 GCGCCACTAACTATAAGCTC-AAACGAAGTCGTTTCA-CAACAGTTAACTCAAGCCTGAGGCGTT
1 GCGCCACTAACTATAA-ATCAAAACGAAGTCGTTTCATCAACAATTAACTCAAGCCTGTGGCGTT
* * * *
543993 TTCATAAAAACGCCACAAATACCATAGACAAAACG
65 TTCAAAAAAACGCCACTAATAACATACACAAAACG
544028 ACAACATTTC
Statistics
Matches: 200, Mismatches: 39, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
145 1 0.00
146 120 0.60
147 69 0.34
148 10 0.05
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (147 bp):
GCGCCACTAACTATAAATCAAAACGAAGTCGTTTCATCAACAATTAACTCAAGCCTGTGGCGTTT
TCAAAAAAACGCCACTAATAACATACACAAAACGGTAGAGTATCAATAAATGTTAAAACAATTTT
GCGGCGTTTGAACCAAA
Found at i:544990 original size:20 final size:20
Alignment explanation
Indices: 544962--545002 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
544952 ATTAATTAAT
*
544962 CAAAACCCTAAATCCTAACC
1 CAAAACCCTAAACCCTAACC
* *
544982 CAAATCCCTAACCCCTAACC
1 CAAAACCCTAAACCCTAACC
545002 C
1 C
545003 TTAAACCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.46, G:0.00, T:0.15
Consensus pattern (20 bp):
CAAAACCCTAAACCCTAACC
Found at i:545558 original size:114 final size:113
Alignment explanation
Indices: 545366--546109 Score: 819
Period size: 114 Copynumber: 6.5 Consensus size: 113
545356 CCACGAATTG
* * * * * *
545366 TCAGAAAACGGTGTCGTTGGGCTTAGTTTTTGTTGCGGCGCATCTT-CA-AAAACGCCACCAAAC
1 TCAGAAAACGGCGTCGTTGGGCTTTGGTTTT-TTGTGGCGC-T-TTCCAGAAAACGCCGCTAAA-
* * * * * * *
545429 CACTTTA-CATTAGCGGTGC-TTACTTAAAAACACCACTAAA-CACCCAAAAAGC
62 GACCTGAGCATTAGCGGCGCTTTAC-TAAAAACGCCGCTAAATC-CCC-GAAAGC
*
545481 TCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTGTGGCGCTTTCCAGAAAACGCCGCTAAAAACC
1 TCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTGTGGCGCTTTCCAGAAAACGCCGCTAAAGACC
* *
545546 TG-GACATTAGCGGCCCTTTACTAAAAGCGCCGCTAAATCCCCGAAAGC
66 TGAG-CATTAGCGGCGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* * * *
545594 TCAGAAAACGGTGCCGTTGGGCTTTCGTTTTTTTGTGGCGC-TTCCTCGAAAACGCCGCTAAAGA
1 TCAGAAAACGGCGTCGTTGGGCTTT-GGTTTTTTGTGGCGCTTTCC-AGAAAACGCCGCTAAAGA
* * * *
545658 CCTGAACATTAGCGGCACTTTACTAAAAGCGCCACTAAATCCCCGAAAGC
64 CCTGAGCATTAGCGGCGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* *
545708 TCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTTGTAGCGCTTCCTCA-AAAACGCCGCTAAAGA
1 TCAGAAAACGGCGTCGTTGGGCTTTGG-TTTTTTGTGGCGCTTTC-CAGAAAACGCCGCTAAAGA
* * * *
545772 CCTGAGCATTAGCGTCGCTTTACCAAAAACGCCGCTGAATCCTCGAAAGC
64 CCTGAGCATTAGCGGCGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* *
545822 TCAAAAAACGGCGTCGTTGGGCTTTGGTTTTTTTTGTGGCGCTTCCTCA-AAAACGCCGCTAAAG
1 TCAGAAAACGGCGTCGTTGGGCTTTGG--TTTTTTGTGGCGCTTTC-CAGAAAACGCCGCTAAAG
* *
545886 ACCTGAGCATTAGCGGTGCTTTA-TCAAAAACGCCGCTAAATCCCCTAAAGC
63 ACCTGAGCATTAGCGGCGCTTTACT-AAAAACGCCGCTAAATCCCCGAAAGC
* * *
545937 TCAGAAAACGGCGTCGTTTGGCTTTGGTTTTTTTGTGGCAC-TTCCTCGAAAACGCCGCTAAAGA
1 TCAGAAAACGGCGTCGTTGGGCTTTGG-TTTTTTGTGGCGCTTTCC-AGAAAACGCCGCTAAAGA
* *
546001 CCTGAGCATTAGCGGCGCTTTATTAAAAAAGCCGCTAAATCCCCGAAAGC
64 CCTGAGCATTAGCGGCGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* * * * * ** *
546051 TCAGAAAACGACGTCATTGGGCTTAGG-TATTTGCGGCGCTTTCTGGATAACGCCGCTAA
1 TCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTGTGGCGCTTTCCAGAAAACGCCGCTAA
546110 TGCTTTTTTT
Statistics
Matches: 548, Mismatches: 63, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
112 25 0.05
113 44 0.08
114 338 0.62
115 140 0.26
116 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (113 bp):
TCAGAAAACGGCGTCGTTGGGCTTTGGTTTTTTGTGGCGCTTTCCAGAAAACGCCGCTAAAGACC
TGAGCATTAGCGGCGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
Found at i:545944 original size:229 final size:228
Alignment explanation
Indices: 545366--546074 Score: 921
Period size: 229 Copynumber: 3.1 Consensus size: 228
545356 CCACGAATTG
* * * * * * * *
545366 TCAGAAAACGGTGTCGTTGGGC-TTAGTTTTTGTTGCGGCGCATCTTCAAAAACGCCACCAAACC
1 TCAGAAAACGGCGTCGTTGGGCTTTAGTTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAA-G
* * * *
545430 ACTTTACATTAGCGGTGC-TTACTTAAAAACACCACTAAA-CACCCAAAAAGCTCAGAAAACGGC
65 ACCTGACATTAGCGGTGCTTTA-TCAAAAACGCCACTAAATC-CCC-AAAAGCTCAGAAAACGGC
* *
545493 GTCGTTGGGCTTTGG-TTTTTTGTGGCGCTTTC-CAGAAAACGCCGCTAAAAACCTG-GACATTA
127 GTCGTTGGGCTTTGGTTTTTTTGTGGCGCTTCCTCA-AAAACGCCGCTAAAGACCTGAG-CATTA
* *
545555 GCGGCCCTTTACTAAAAGCGCCGCTAAATCCCCGAAAGC
190 GCGGCGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* * * *
545594 TCAGAAAACGGTGCCGTTGGGCTTTCG-TTTTTTTGTGGCGCTTCCTCGAAAACGCCGCTAAAGA
1 TCAGAAAACGGCGTCGTTGGGCTTTAGTTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGA
** * *
545658 CCTGAACATTAGCGGCACTTTA-CTAAAAGCGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGT
66 CCTG-ACATTAGCGGTGCTTTATC-AAAAACGCCACTAAATCCCCAAAAGCTCAGAAAACGGCGT
* *
545722 CGTTGGGCTTTGGTTTTTTTGTAGCGCTTCCTCAAAAACGCCGCTAAAGACCTGAGCATTAGCGT
129 CGTTGGGCTTTGGTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGACCTGAGCATTAGCGG
* * *
545787 CGCTTTACCAAAAACGCCGCTGAATCCTCGAAAGC
194 CGCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* *
545822 TCAAAAAACGGCGTCGTTGGGCTTTGGTTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGA
1 TCAGAAAACGGCGTCGTTGGGCTTTAGTTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGA
* *
545887 CCTGAGCATTAGCGGTGCTTTATCAAAAACGCCGCTAAATCCCCTAAAGCTCAGAAAACGGCGTC
66 CCTGA-CATTAGCGGTGCTTTATCAAAAACGCCACTAAATCCCCAAAAGCTCAGAAAACGGCGTC
* * *
545952 GTTTGGCTTTGGTTTTTTTGTGGCACTTCCTCGAAAACGCCGCTAAAGACCTGAGCATTAGCGGC
130 GTTGGGCTTTGGTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGACCTGAGCATTAGCGGC
* *
546017 GCTTTATTAAAAAAGCCGCTAAATCCCCGAAAGC
195 GCTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
* *
546051 TCAGAAAACGACGTCATTGGGCTT
1 TCAGAAAACGGCGTCGTTGGGCTT
546075 AGGTATTTGC
Statistics
Matches: 420, Mismatches: 50, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
227 35 0.08
228 172 0.41
229 212 0.50
230 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (228 bp):
TCAGAAAACGGCGTCGTTGGGCTTTAGTTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGA
CCTGACATTAGCGGTGCTTTATCAAAAACGCCACTAAATCCCCAAAAGCTCAGAAAACGGCGTCG
TTGGGCTTTGGTTTTTTTGTGGCGCTTCCTCAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCG
CTTTACTAAAAACGCCGCTAAATCCCCGAAAGC
Found at i:547029 original size:5 final size:5
Alignment explanation
Indices: 547019--547049 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
547009 CATAAACTCC
*
547019 TAATT TAATT TAATT TAATT CAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT TAATT T
547050 CATATTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TAATT
Found at i:547688 original size:19 final size:18
Alignment explanation
Indices: 547644--547689 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
547634 GAGTTAAACG
* * *
547644 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCGAATC
547662 AATCGAATTATTCGAATC
1 AATCGAATTATTCGAATC
547680 AACTCGAATT
1 AA-TCGAATT
547690 TTTTTTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
AATCGAATTATTCGAATC
Found at i:553565 original size:9 final size:10
Alignment explanation
Indices: 553544--553576 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
553534 TTTTGAGCAA
553544 TTTAAATTTT
1 TTTAAATTTT
*
553554 TTTATATTTT
1 TTTAAATTTT
553564 TTTAAATTTT
1 TTTAAATTTT
553574 TTT
1 TTT
553577 CATTCTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTAAATTTT
Found at i:559146 original size:25 final size:25
Alignment explanation
Indices: 559112--559162 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
559102 TTTTTCGAAG
559112 TAAGATCCTAGCATAAAAAATATCA
1 TAAGATCCTAGCATAAAAAATATCA
559137 TAAGATCCTAGCATAAAAAATATCA
1 TAAGATCCTAGCATAAAAAATATCA
559162 T
1 T
559163 CTTAGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (25 bp):
TAAGATCCTAGCATAAAAAATATCA
Found at i:561175 original size:31 final size:30
Alignment explanation
Indices: 561133--561198 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
561123 ACTGTAAAAT
*
561133 AGTCATTGAATTATTCAAAAGTTTTTATTTA
1 AGTCATAGAATTATTCAAAAGTTTTT-TTTA
*
561164 AGTCATAGAATTATTCTAAAGTTTTTTTTA
1 AGTCATAGAATTATTCAAAAGTTTTTTTTA
*
561194 TGTCA
1 AGTCA
561199 CAAGGGGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (30 bp):
AGTCATAGAATTATTCAAAAGTTTTTTTTA
Found at i:562669 original size:21 final size:22
Alignment explanation
Indices: 562636--562683 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
562626 GACTAAAACG
*
562636 TAAAATTTCAACCAT-AAATAAC
1 TAAAATGTCAACC-TGAAATAAC
*
562658 TAAAATGT-AACCTGAAGTAAC
1 TAAAATGTCAACCTGAAATAAC
562679 TAAAA
1 TAAAA
562684 ATGATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (22 bp):
TAAAATGTCAACCTGAAATAAC
Found at i:563934 original size:201 final size:193
Alignment explanation
Indices: 563589--563984 Score: 702
Period size: 201 Copynumber: 2.0 Consensus size: 193
563579 GTTAATATAC
563589 AACATAAAACAAATACTTTAATATGAATTATATATGTATATGTATCTACAAAATATGTATATACA
1 AACATAAAACAAATACTTTAATATGAATTATATATGTATATGTATCTACAAAATATGTATATACA
563654 TATAAGTACAATATATAAATAAAATTGAAAATATGTGTATGCATATATTAAAACACATATATGTA
66 TATAAGTACAATATATAAATAAAATTGAAAATATGTGTATGCATATATTAAAACACATATATGTA
563719 AGTATACATATAAAAAAGAAAAAGAAAAGGAATGAAATATATAAAACAAAAAAAACTTATAATAA
131 AGTATACATATAAAAAAG---AAG---AGGAATGAAATATATAAAAC--AAAAAACTTATAATAA
563784 TCTCTA
188 TCTCTA
563790 AACATAAAACAAATACTTTAATATGAATTATATATGTATATGTATCTACAAAATATGTATATACA
1 AACATAAAACAAATACTTTAATATGAATTATATATGTATATGTATCTACAAAATATGTATATACA
* *
563855 TATAAGTACAATATATAAGTAAATTTGAAAATATGTGTATGCATATATTAAAACACATATATGTA
66 TATAAGTACAATATATAAATAAAATTGAAAATATGTGTATGCATATATTAAAACACATATATGTA
563920 AGTATACATATAAAAAAGAAGAGGAATGAAATATATAAAACAAAAAACTTATAATAATCTCTA
131 AGTATACATATAAAAAAGAAGAGGAATGAAATATATAAAACAAAAAACTTATAATAATCTCTA
563983 AA
1 AA
563985 AAAATATGTA
Statistics
Matches: 193, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
193 24 0.12
195 20 0.10
198 3 0.02
201 146 0.76
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (193 bp):
AACATAAAACAAATACTTTAATATGAATTATATATGTATATGTATCTACAAAATATGTATATACA
TATAAGTACAATATATAAATAAAATTGAAAATATGTGTATGCATATATTAAAACACATATATGTA
AGTATACATATAAAAAAGAAGAGGAATGAAATATATAAAACAAAAAACTTATAATAATCTCTA
Found at i:564227 original size:3 final size:3
Alignment explanation
Indices: 564219--564266 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
564209 CGTACGTGGA
* * *
564219 AAT AAT AAT TAT AAT ATT AAT AAT AAAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
564265 AA
1 AA
564267 AAAAGAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:564254 original size:22 final size:22
Alignment explanation
Indices: 564222--564267 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
564212 ACGTGGAAAT
* *
564222 AATAATTATAATATTAATAATA
1 AATAATAATAATAATAATAATA
*
564244 AATAATAATAATAATAATGATA
1 AATAATAATAATAATAATAATA
564266 AA
1 AA
564268 AAAGAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AATAATAATAATAATAATAATA
Found at i:564266 original size:25 final size:25
Alignment explanation
Indices: 564218--564266 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
564208 ACGTACGTGG
* *
564218 AAATAATAATTATAATATTAATAAT
1 AAATAATAATAATAATAATAATAAT
*
564243 AAATAATAATAATAATAATGATAA
1 AAATAATAATAATAATAATAATAA
564267 AAAAGAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATAATAATAATAATAATAATAAT
Found at i:565503 original size:30 final size:30
Alignment explanation
Indices: 565450--565507 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
565440 TATTTAAGTA
565450 AAATAAAATACATAAAAATAATAAAAGAAG
1 AAATAAAATACATAAAAATAATAAAAGAAG
565480 AAATATAAATACA-AACAAA-AATAAAAGA
1 AAATA-AAATACATAA-AAATAATAAAAGA
565508 TTAATGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (30 bp):
AAATAAAATACATAAAAATAATAAAAGAAG
Found at i:565895 original size:591 final size:589
Alignment explanation
Indices: 564576--566340 Score: 3259
Period size: 591 Copynumber: 3.0 Consensus size: 589
564566 GCCAGAACGC
* *
564576 GCGGACACTGTTTGCGGGTCGGGTCAACGCGCAGATCTGGCCCCTTTAAACGGCGCCGTTTTGTT
1 GCGGACCCTGTTTGCGGGTCGGGTCAACGCGCGGATCTGGCCCCTTTAAACGGCGCCGTTTTGTT
564641 TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATT-AAAAAATCATTTTGTTTCACGTTTT
66 TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATTAAAAAAATCATTTTGTTTCACGTTTT
* * *
564705 TGAAACGTTTGCTCTACTAGGGCTTTTCTTAACCCTTTTTTGCGCCGTCGTTCATTCGTCCCTTC
131 TGAAACGTTTGCTCTGCTAGGGCTTTTCTTAACCCTTTTTTGGGCCGTCGTTCATCCGTCCCTTC
*
564770 ACCAAAACTCCAATTGCGACGGAGATGGTGGTGGCACGGCGGCTTCGACGAAAGGTAAGCTTTGC
196 ACCAAAACTCCGATTGCGACGGAGATGGTGGTGGCACGGCGGCTTCGACGAAAGGTAAGCTTTGC
* *
564835 CTCATTCTCTTCTTTTTTATTTAAGTAAAATAAAATATATAAAAATAATAAAAGAAGAAATATAA
261 CTCCTTCTCTTCTTTTTTATTTAAGTAAAATAAAATAAATAAAAATAATAAAAGAAGAAATATAA
564900 ATACAAACAAAAATAAAAGATCGATGAACACTACAAAAGATAGGCCTTTTATAGTTTTTCTTTGT
326 ATACAAACAAAAATAAAAGATCGATGAACACTACAAAAGATAGGCCTTTTATAGTTTTTCTTTGT
564965 ATTCTTGTCTCC-TTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACCTT
391 ATTCTTGTCTCCTTTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACCTT
* * *
565029 TTCCATTTTTTTTTGTTGTTTTACACTATTTGGACTCTTTGAATCTGTTTTGTAGGAGAACATGG
456 TTCCCTTTTTTTTTTTTGTTTTACACTATTTGGACTCTTTGAATCCGTTTTGTAGGAGAACATGG
* * *
565094 GAGTACGGCGCGCATGGAGGAGGTCGGTTCCGAGACATGCGATGACTGGGGTTTTTCTGGAAGCT
521 GAGTACGGCGCGCATGGAGGAGGCCGGTTCCGAGACGTGCGATGACTGGGGTCTTTCTGGAAGCT
565159 GTTT
586 GTTT
* *
565163 GCGGACCCTGTTTGCGGGTCGGGTCAACGCACGGATCTGGCCCCTTTAAACGGCGTCGTTTTGTT
1 GCGGACCCTGTTTGCGGGTCGGGTCAACGCGCGGATCTGGCCCCTTTAAACGGCGCCGTTTTGTT
565228 TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATTAAAAAAATCATTTTGTTTCACGTTTT
66 TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATTAAAAAAATCATTTTGTTTCACGTTTT
565293 TGAAACGTTTGCTCTGCTAGGGCTTTTCTTAACCCTTTTTTGGGCCGTCGTTCATCCGTCCCTTC
131 TGAAACGTTTGCTCTGCTAGGGCTTTTCTTAACCCTTTTTTGGGCCGTCGTTCATCCGTCCCTTC
*
565358 ACCAAAACTCCGATTGCGACGGAGATGGTGGTGGCACGACGGCTTCGACGAAAGGTAAGCTTTGC
196 ACCAAAACTCCGATTGCGACGGAGATGGTGGTGGCACGGCGGCTTCGACGAAAGGTAAGCTTTGC
*
565423 CTCCTTCTCTTCTTTTTTATTTAAGTAAAATAAAATACATAAAAATAATAAAAGAAGAAATATAA
261 CTCCTTCTCTTCTTTTTTATTTAAGTAAAATAAAATAAATAAAAATAATAAAAGAAGAAATATAA
** *
565488 ATACAAACAAAAATAAAAGATTAATGAACACTACAAAAGTTAGGCCTTTTATAGTTTTTCTTTGT
326 ATACAAACAAAAATAAAAGATCGATGAACACTACAAAAGATAGGCCTTTTATAGTTTTTCTTTGT
565553 ATTCTTGTCTCCTTTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACCTT
391 ATTCTTGTCTCCTTTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACCTT
565618 TTCCCTTTTTTTTTTTTTTGTTTTACACTATTTGGACTCTTTGAATCCGTTTTGTAGGAGAACAT
456 TTCCC--TTTTTTTTTTTTGTTTTACACTATTTGGACTCTTTGAATCCGTTTTGTAGGAGAACAT
565683 GGGAGTACGGCGCGCATGGAGGAGGCCGGTTCCGAGACGTGCGATGACTGGGGTCTTTCTGGAAG
519 GGGAGTACGGCGCGCATGGAGGAGGCCGGTTCCGAGACGTGCGATGACTGGGGTCTTTCTGGAAG
565748 CTGTTT
584 CTGTTT
*
565754 GCGGACCCTATTTGCGGGTCGGGTCAACGCGCGGATCTGGCCCCTTTAAACGGCGCCGTTTTGTT
1 GCGGACCCTGTTTGCGGGTCGGGTCAACGCGCGGATCTGGCCCCTTTAAACGGCGCCGTTTTGTT
565819 TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATTAAAAAAATCATTTTGTTTCACGTTTT
66 TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATTAAAAAAATCATTTTGTTTCACGTTTT
565884 TGAAACGTTTGCTCTGCTAGGGCTTTTCTTAACCCTTTTTTGGGCCGTCGTTCATCCGTCCCTTC
131 TGAAACGTTTGCTCTGCTAGGGCTTTTCTTAACCCTTTTTTGGGCCGTCGTTCATCCGTCCCTTC
565949 ACCAAAACTCCGATTGCGACGGAGATGGTGGTGGCACGGCGGCTTCGACGAAAGGTAAGCTTTGC
196 ACCAAAACTCCGATTGCGACGGAGATGGTGGTGGCACGGCGGCTTCGACGAAAGGTAAGCTTTGC
*
566014 TTCCTTCTCTTCTTTTTTATTTAAGTAAAATAAAATAAATAAAAATAATAAAAGAAGAAATATAA
261 CTCCTTCTCTTCTTTTTTATTTAAGTAAAATAAAATAAATAAAAATAATAAAAGAAGAAATATAA
566079 ATACAAACAAAAATAAAAGATCGATGAACACTACAAAAGATAGGCCTTTTATAGTTTTTCTTTGT
326 ATACAAACAAAAATAAAAGATCGATGAACACTACAAAAGATAGGCCTTTTATAGTTTTTCTTTGT
*
566144 ATTCTTGTCTCCTTTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACATT
391 ATTCTTGTCTCCTTTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACCTT
*
566209 TTCCC--CTTTTTTTTTGTTTTACACTATTTGGACTCTTTGAATCCGTTTTGTAGGAGAACATGG
456 TTCCCTTTTTTTTTTTTGTTTTACACTATTTGGACTCTTTGAATCCGTTTTGTAGGAGAACATGG
566272 GAGTACGGCGCGCATGGAGGAGGCCGGTTCCGAGACGTGCGATGACTGGGGTCTTTCTGGAAGCT
521 GAGTACGGCGCGCATGGAGGAGGCCGGTTCCGAGACGTGCGATGACTGGGGTCTTTCTGGAAGCT
566337 GTTT
586 GTTT
566341 TAGTTTTAGG
Statistics
Matches: 1143, Mismatches: 31, Indels: 8
0.97 0.03 0.01
Matches are distributed among these distances:
587 226 0.20
588 287 0.25
589 56 0.05
591 574 0.50
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (589 bp):
GCGGACCCTGTTTGCGGGTCGGGTCAACGCGCGGATCTGGCCCCTTTAAACGGCGCCGTTTTGTT
TATGTGTTAAATTAAACACAAAAATAACAAAAAAGGATTAAAAAAATCATTTTGTTTCACGTTTT
TGAAACGTTTGCTCTGCTAGGGCTTTTCTTAACCCTTTTTTGGGCCGTCGTTCATCCGTCCCTTC
ACCAAAACTCCGATTGCGACGGAGATGGTGGTGGCACGGCGGCTTCGACGAAAGGTAAGCTTTGC
CTCCTTCTCTTCTTTTTTATTTAAGTAAAATAAAATAAATAAAAATAATAAAAGAAGAAATATAA
ATACAAACAAAAATAAAAGATCGATGAACACTACAAAAGATAGGCCTTTTATAGTTTTTCTTTGT
ATTCTTGTCTCCTTTTTTTTACAATACAAAACATAGGCCTTTTATAGCCCGAATAGAACAACCTT
TTCCCTTTTTTTTTTTTGTTTTACACTATTTGGACTCTTTGAATCCGTTTTGTAGGAGAACATGG
GAGTACGGCGCGCATGGAGGAGGCCGGTTCCGAGACGTGCGATGACTGGGGTCTTTCTGGAAGCT
GTTT
Found at i:573706 original size:4 final size:4
Alignment explanation
Indices: 573697--573754 Score: 98
Period size: 4 Copynumber: 14.5 Consensus size: 4
573687 ACATTCCTCT
* *
573697 ATAC ATAC ATAC ATAC ATAC ATAA ATAC ATAC ATGC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
573745 ATAC ATAC AT
1 ATAC ATAC AT
573755 TAATATATGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:579437 original size:29 final size:29
Alignment explanation
Indices: 579404--579469 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
579394 GTCAAATGGC
* *
579404 CGTGTGGTTGGCCGTGTGCACCACACGGT
1 CGTGTGGTTGGCAGTGTGCACCACACGGG
579433 CGTGTGGTTGGCAGTGTGCACCACACGGG
1 CGTGTGGTTGGCAGTGTGCACCACACGGG
579462 CGTGTGGT
1 CGTGTGGT
579470 CAGCCATGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.11, C:0.24, G:0.41, T:0.24
Consensus pattern (29 bp):
CGTGTGGTTGGCAGTGTGCACCACACGGG
Found at i:579479 original size:29 final size:28
Alignment explanation
Indices: 579404--579480 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
579394 GTCAAATGGC
* * *
579404 CGTGTGGTTGGCCGTGTGCACCACACGGT
1 CGTGTGG-TAGCCATGTGCACCACACGGG
* *
579433 CGTGTGGTTGGCAGTGTGCACCACACGGG
1 CGTGTGGTAGCCA-TGTGCACCACACGGG
579462 CGTGTGGTCAGCCATGTGC
1 CGTGTGGT-AGCCATGTGC
579481 CAAGGTGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.08
29 34 0.85
30 3 0.08
ACGTcount: A:0.12, C:0.26, G:0.39, T:0.23
Consensus pattern (28 bp):
CGTGTGGTAGCCATGTGCACCACACGGG
Found at i:579493 original size:24 final size:24
Alignment explanation
Indices: 579463--579508 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
579453 CCACACGGGC
579463 GTGTGGTC-AGCCATGTGCCAAGGT
1 GTGTGGTCGA-CCATGTGCCAAGGT
*
579487 GTGTGGTCGACCGTGTGCCAAG
1 GTGTGGTCGACCATGTGCCAAG
579509 CCGTGTACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.15, C:0.22, G:0.39, T:0.24
Consensus pattern (24 bp):
GTGTGGTCGACCATGTGCCAAGGT
Found at i:579514 original size:24 final size:24
Alignment explanation
Indices: 579462--579514 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
579452 ACCACACGGG
*
579462 CGTGTGGTCAGCCATGTGCCAAGG
1 CGTGTGGTCAGCCATGTGCCAAGC
* *
579486 TGTGTGGTC-GACCGTGTGCCAAGC
1 CGTGTGGTCAG-CCATGTGCCAAGC
579510 CGTGT
1 CGTGT
579515 ACGATTGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.13, C:0.25, G:0.38, T:0.25
Consensus pattern (24 bp):
CGTGTGGTCAGCCATGTGCCAAGC
Found at i:579580 original size:22 final size:22
Alignment explanation
Indices: 579532--579580 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
579522 CATGAGCAAT
579532 TGTG-GTAGGTCGTGTAGGACA
1 TGTGAGTAGGTCGTGTAGGACA
* *
579553 TATGAGTAGGTCAG-GTAGGCCA
1 TGTGAGTAGGTC-GTGTAGGACA
579575 TGTGAG
1 TGTGAG
579581 CCCATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.13
22 19 0.83
23 1 0.04
ACGTcount: A:0.22, C:0.10, G:0.41, T:0.27
Consensus pattern (22 bp):
TGTGAGTAGGTCGTGTAGGACA
Found at i:581360 original size:41 final size:39
Alignment explanation
Indices: 581315--581418 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 39
581305 TTAAAGGCTA
* * *
581315 ATATAACACGTCGGAACAAAGCCTGCTAGGCACGGAGCTTG
1 ATATAACAC--CGGCACAAAGCCTGCTAGGCACGAAGCCTG
* *
581356 ATATAATACACCGGCATAAAGCTTGCTAGGCACGAAGCCTG
1 ATAT-A-ACACCGGCACAAAGCCTGCTAGGCACGAAGCCTG
*
581397 A-ATATCACCGGCACAAAGCCTG
1 ATATAACACCGGCACAAAGCCTG
581419 AATATTATCG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
38 15 0.28
39 1 0.02
40 2 0.04
41 30 0.57
42 1 0.02
43 4 0.08
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (39 bp):
ATATAACACCGGCACAAAGCCTGCTAGGCACGAAGCCTG
Found at i:581415 original size:38 final size:41
Alignment explanation
Indices: 581330--581418 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
581320 ACACGTCGGA
* *
581330 ACAAAGCCTGCTAGGCACGGAGCTTGATATAATACACCGGC
1 ACAAAGCCTGCTAGGCACGAAGCCTGATATAATACACCGGC
* *
581371 ATAAAGCTTGCTAGGCACGAAGCCTGA-AT-AT-CACCGGC
1 ACAAAGCCTGCTAGGCACGAAGCCTGATATAATACACCGGC
581409 ACAAAGCCTG
1 ACAAAGCCTG
581419 AATATTATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 15 0.36
39 2 0.05
40 2 0.05
41 23 0.55
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.17
Consensus pattern (41 bp):
ACAAAGCCTGCTAGGCACGAAGCCTGATATAATACACCGGC
Found at i:582299 original size:32 final size:34
Alignment explanation
Indices: 582239--582310 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 34
582229 GCCATGGCCT
582239 GCCCGAAATATGAGAGGATTTGGGTAAAAATAT-AG
1 GCCCGAAATAT-AGAGGATTTGGGTAAAAA-ATGAG
582274 GCCCGAAATAT-G-GGA-TTGGGCTAAAAAATGAG
1 GCCCGAAATATAGAGGATTTGGG-TAAAAAATGAG
582306 GCCCG
1 GCCCG
582311 TTTAGAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
31 7 0.20
32 16 0.46
33 1 0.03
35 11 0.31
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (34 bp):
GCCCGAAATATAGAGGATTTGGGTAAAAAATGAG
Found at i:584320 original size:34 final size:34
Alignment explanation
Indices: 584282--584397 Score: 162
Period size: 34 Copynumber: 3.4 Consensus size: 34
584272 TTTGATATGG
584282 TATGACATTCTGATATGATATATGTTTAT-GAAA
1 TATGACATTCTGATATGATATATGTTTATGGAAA
* * *
584315 CTATGACATTCTGATTTGGTATATGTTTCTGGAAA
1 -TATGACATTCTGATATGATATATGTTTATGGAAA
* *
584350 TATGACATTCTGATATGATATATGTTTCTGGTAA
1 TATGACATTCTGATATGATATATGTTTATGGAAA
*
584384 TGTGACATTCTGAT
1 TATGACATTCTGAT
584398 CTGAGATTCG
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
34 70 0.95
35 4 0.05
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (34 bp):
TATGACATTCTGATATGATATATGTTTATGGAAA
Found at i:585759 original size:2 final size:2
Alignment explanation
Indices: 585752--585778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
585742 TTCAATTTGA
585752 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
585779 ATTTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:586987 original size:97 final size:95
Alignment explanation
Indices: 586792--587078 Score: 405
Period size: 97 Copynumber: 3.0 Consensus size: 95
586782 AACAACTAGT
* * *
586792 TTTATTTGATTTTTCCTTAAAAA-CTCTAAATACTAAACCCCAATCTAATTTTTTCAAAATTTAT
1 TTTATTTGATTTTTCCTTAAAAACCT-TAAACACTAAACCCTAATCTAATTTTTTTAAAATTTAT
*
586856 AATTAATTTACTCAAGTAACCTTAAACCCTAA
65 AATTAATTTACTCAAGTAACC-TAAACCCGAA
586888 TTTATTTGATTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTTAAAAATTTAT
1 TTTATTTGATTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTT-AAAATTTAT
586953 AATTAATTTACTCAAGTAATCCTAAACCCGAA
65 AATTAATTTACTCAAGTAA-CCTAAACCCGAA
* * * * *
586985 TTTATTTAATTTTTTCCTTAAAAACCATAAACTCTAAACTCTAATCTAATTTTTTTTAAATTTAT
1 TTTATTTGA-TTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTAT
* * *
587050 AATTAATTTAATTAAGAAACCCTAAACCC
65 AATTAATTTACTCAAGTAA-CCTAAACCC
587079 TAAACCCTTA
Statistics
Matches: 174, Mismatches: 13, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
96 49 0.28
97 80 0.46
98 45 0.26
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (95 bp):
TTTATTTGATTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTTAAAATTTATA
ATTAATTTACTCAAGTAACCTAAACCCGAA
Found at i:587242 original size:19 final size:19
Alignment explanation
Indices: 587218--587255 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
587208 CACTTTGTCC
* *
587218 ACGTGGACAGAAGGCGCTT
1 ACGTGGACACAAAGCGCTT
587237 ACGTGGACACAAAGCGCTT
1 ACGTGGACACAAAGCGCTT
587256 CCTCAAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.32, T:0.16
Consensus pattern (19 bp):
ACGTGGACACAAAGCGCTT
Found at i:587339 original size:43 final size:43
Alignment explanation
Indices: 587237--587355 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
587227 GAAGGCGCTT
* *
587237 ACGTGGACACAAAGCGCTTCCTCAAGGAAGC---ATTTTCTGTCC
1 ACGTGGACA-AAA-CGCTTCCTTAAGGAAGCGTTTTTTTCTGTCC
* ** *
587279 ACGTGGACAAAGCGCTTCCTTGGGGAAGCGTTTTTTTTTGTCC
1 ACGTGGACAAAACGCTTCCTTAAGGAAGCGTTTTTTTCTGTCC
*
587322 ACGTGGACAAAATGCTTCCTTAAGGAAGCGTTTT
1 ACGTGGACAAAACGCTTCCTTAAGGAAGCGTTTT
587356 CCTGCTTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
40 14 0.22
41 2 0.03
42 9 0.14
43 39 0.61
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (43 bp):
ACGTGGACAAAACGCTTCCTTAAGGAAGCGTTTTTTTCTGTCC
Found at i:589183 original size:34 final size:34
Alignment explanation
Indices: 589145--589213 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
589135 GCTCCCAATA
589145 CACATAGGGTTCACACAACATAGGGTTCACATGT
1 CACATAGGGTTCACACAACATAGGGTTCACATGT
* * * * *
589179 CACATGGGGTTCGCATAGCATAGGGTTCGCATGT
1 CACATAGGGTTCACACAACATAGGGTTCACATGT
589213 C
1 C
589214 TTATGGGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (34 bp):
CACATAGGGTTCACACAACATAGGGTTCACATGT
Found at i:591468 original size:17 final size:18
Alignment explanation
Indices: 591442--591475 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
591432 AAATTTGAGA
591442 ATAAAAAAATAA-AAATT
1 ATAAAAAAATAAGAAATT
*
591459 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
591476 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATT
Found at i:597549 original size:29 final size:29
Alignment explanation
Indices: 597516--597617 Score: 78
Period size: 29 Copynumber: 3.5 Consensus size: 29
597506 TGATATCCAC
597516 CACCGACACATAGTACCTGATAAATATAA
1 CACCGACACATAGTACCTGATAAATATAA
* * ** * * *
597545 CACCGGCATAGGGTGCCTGATAATTGTAA
1 CACCGACACATAGTACCTGATAAATATAA
* * * * * *
597574 CACCAATAGAAAGTACTTGATAACTATAA
1 CACCGACACATAGTACCTGATAAATATAA
597603 TCACCGACACATAGT
1 -CACCGACACATAGT
597618 GCCTAATTAA
Statistics
Matches: 51, Mismatches: 21, Indels: 1
0.70 0.29 0.01
Matches are distributed among these distances:
29 41 0.80
30 10 0.20
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (29 bp):
CACCGACACATAGTACCTGATAAATATAA
Found at i:601880 original size:163 final size:164
Alignment explanation
Indices: 601611--601937 Score: 647
Period size: 163 Copynumber: 2.0 Consensus size: 164
601601 TATTAATATA
601611 ATTATTATAAATATTGTTTAAAACCTTAATCCAATTTTTCAAAGCATAGCGCAGGCATGTTATAG
1 ATTATTATAAATATTGTTTAAAACCTTAATCCAATTTTTCAAAGCATAGCGCAGGCATGTTATAG
601676 TTTTAACTAAAAGAATTCTTTAGAATTCCATAGACAAAAAAATAAAAATTAGGGATAATATTATA
66 TTTTAACTAAAAGAATTCTTTAGAATTCCATAGACAAAAAAATAAAAATTAGGGATAATATTATA
601741 TTTGGTATATTTACTTTTATAGAATGTTTAATGT
131 TTTGGTATATTTACTTTTATAGAATGTTTAATGT
601775 ATTATTAT-AATATTGTTTAAAACCTTAATCCAATTTTTCAAAGCATAGCGCAGGCATGTTATAG
1 ATTATTATAAATATTGTTTAAAACCTTAATCCAATTTTTCAAAGCATAGCGCAGGCATGTTATAG
601839 TTTTAACTAAAAGAATTCTTTAGAATTCCATAGACAAAAAAATAAAAATTAGGGATAATATTATA
66 TTTTAACTAAAAGAATTCTTTAGAATTCCATAGACAAAAAAATAAAAATTAGGGATAATATTATA
601904 TTTGGTATATTTACTTTTATAGAATGTTTAATGT
131 TTTGGTATATTTACTTTTATAGAATGTTTAATGT
601938 GATATTTGTA
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 155 0.95
164 8 0.05
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (164 bp):
ATTATTATAAATATTGTTTAAAACCTTAATCCAATTTTTCAAAGCATAGCGCAGGCATGTTATAG
TTTTAACTAAAAGAATTCTTTAGAATTCCATAGACAAAAAAATAAAAATTAGGGATAATATTATA
TTTGGTATATTTACTTTTATAGAATGTTTAATGT
Found at i:607254 original size:20 final size:20
Alignment explanation
Indices: 607229--607272 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
607219 TTAGGTTTAG
607229 TTTTTTT-TTTTAATTT-AAA
1 TTTTTTTGTTTT-ATTTAAAA
607248 TTTTTTTGTTTTATTTAAAA
1 TTTTTTTGTTTTATTTAAAA
607268 TTTTT
1 TTTTT
607273 ACATAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTTTGTTTTATTTAAAA
Found at i:608541 original size:313 final size:310
Alignment explanation
Indices: 607972--608552 Score: 885
Period size: 313 Copynumber: 1.9 Consensus size: 310
607962 CGTGTATGTG
* * *
607972 TGTGGAAATCATGTATTTAGAATACAAATTTGTGTTTAAAAATAACATACAATAAATAATAAAAT
1 TGTGGAAATCATATATTTAGAACACAAATTTGTATTTAAAAATAACATACAATAAATAATAAAAT
* * *
608037 GTATGATTTGAAACTAATTAATAATAACACATGAAATATGTATAATATTAAAATAAAAAATAGCT
66 GTATGATTTGAAACTAATTAACAATAACACATGAAATATGTACAATATTAAAATAAAAAATAGAT
* * * * *
608102 TAAGTTGTCAGTAAAACGAAATTTAAACACTTGAATACATCAAATTAAGATCACTAAATGAATAC
131 TAAATTGTAAGTAAAACAAAATGTAAACACATGAATACATCAAATTAAGATCACTAAATGAATAC
* * * * * * *
608167 AATTATTTATCAATGTGTTGTCATCAATTCTAAGTTGGTGTCGAGTTTATTTATGACACCATCTC
196 AATTATGTATCAAGGTGTTGTCATCAATCCTAAGTTGGTGTCGAGTTAAGTTATAACACCATATC
*
608232 AATTAACAATATTATTAATATATACTAAAACTCTATCACAATCGTATGCA
261 AATAAACAATATTATTAATATATACTAAAACTCTATCACAATCGTATGCA
608282 TGTGGAAATCATATATTTAGAACACAAATTTGTATTTAAAAATAACATACAATAAATAATAAAAT
1 TGTGGAAATCATATATTTAGAACACAAATTTGTATTTAAAAATAACATACAATAAATAATAAAAT
*
608347 GTATGATTTGAAACTAATTAACAATAACAGCACATGAAATATGTACGATATTAAAATAAAAAATA
66 GTATGATTTGAAACTAATTAACAAT-A-A-CACATGAAATATGTACAATATTAAAATAAAAAATA
* * *
608412 GATTAAATTGTAAGTAAAATAAAATGTAAACACATGAATACATCATATTATGATCACTAAATGAA
128 GATTAAATTGTAAGTAAAACAAAATGTAAACACATGAATACATCAAATTAAGATCACTAAATGAA
* * *
608477 TACAATTGTGTATCAAGGTG-TGATCATCAATCCTAAGTTGGTGTTGAGTTAAGTTGTAACACCA
193 TACAATTATGTATCAAGGTGTTG-TCATCAATCCTAAGTTGGTGTCGAGTTAAGTTATAACACCA
608541 TATCAATAAACA
257 TATCAATAAACA
608553 TCATTGTAAT
Statistics
Matches: 241, Mismatches: 26, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
310 86 0.36
311 1 0.00
312 3 0.01
313 151 0.63
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (310 bp):
TGTGGAAATCATATATTTAGAACACAAATTTGTATTTAAAAATAACATACAATAAATAATAAAAT
GTATGATTTGAAACTAATTAACAATAACACATGAAATATGTACAATATTAAAATAAAAAATAGAT
TAAATTGTAAGTAAAACAAAATGTAAACACATGAATACATCAAATTAAGATCACTAAATGAATAC
AATTATGTATCAAGGTGTTGTCATCAATCCTAAGTTGGTGTCGAGTTAAGTTATAACACCATATC
AATAAACAATATTATTAATATATACTAAAACTCTATCACAATCGTATGCA
Found at i:608976 original size:18 final size:18
Alignment explanation
Indices: 608942--608976 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
608932 AGTTGATTTG
* *
608942 TTATTTTATTGTTTTTAT
1 TTATTTTATTCTATTTAT
608960 TTATTTTATTCTATTTA
1 TTATTTTATTCTATTTA
608977 AAAATAATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTATTTTATTCTATTTAT
Found at i:610818 original size:2 final size:2
Alignment explanation
Indices: 610811--610853 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
610801 AACATTATTA
* *
610811 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
610853 A
1 A
610854 CACACAATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:611389 original size:293 final size:293
Alignment explanation
Indices: 610870--611430 Score: 683
Period size: 293 Copynumber: 1.9 Consensus size: 293
610860 ATTGACGAAG
*
610870 GTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTATCTAAGTG
1 GTAATAAAGTGTACATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTATCTAAGTG
* *
610935 GAAAATTAAAAGTGTTACTAATGTAATTGGTTTCGGTTCAAATTCTACCATACACATTTTTTATT
66 GAAAATTAAAAGTGTTACTAATCTAATTGGTGTCGGTTCAAATTCTACCATACACATTTTTTATT
*
611000 ACTTTTTTTAAATAAAAAAACTAAAATACTCTTGAACAATATATCTTATTTTAATTACAGAAGGA
131 AC-TTTTTTAAATAAAAAAACTAAAATACTCTCGAACAATATATCTTATTTTAATTACAGAAGGA
* * ** ** * * * *
611065 TATTTTTATAATTTTTCTAATTGAGTTGGTGACTTGGTTGAGGGTGACACCAACTC-ATTAGGAG
195 CAATTTTATAATTTTTCTAAGCGAGTTGGTGACCCGGTTGAAGGAGACACCAACTCAATCAAGAG
611129 CTTAAATAATAATATAGATATACAATTGATAGAT
260 CTTAAATAATAATATAGATATACAATTGATAGAT
*
611163 GTAATAAAGTGTACATAATAAAATTAAAATGTATAAAAATATTAAAATCAAACTTTAGT-TAAGT
1 GTAATAAAGTGTACATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTA-TCTAAGT
* ** * ****
611227 GGTAAATTAAGGGTTTTACTAATCTAATTGGTGT-GAGTTCAAATAT-TATCACATGTGTA-TTT
65 GGAAAATTAAAAGTGTTACTAATCTAATTGGTGTCG-GTTCAAAT-TCTA-C-CATACACATTTT
* * * * *
611289 TTGTTA-TTTTTTAATATAAAAAGATTAAAGTAAC-CTCGAATAATATAAT-TTATTTTAATTAC
126 TTATTACTTTTTTAA-ATAAAAAAACTAAAAT-ACTCTCGAACAATAT-ATCTTATTTTAATTAC
* *
611351 -GAAAGGGCAATTTTATAATTTTT-TAAGCGAGTTTGGTGACCCGGTTGAAGGAGATACCAACTC
188 AG-AAGGACAATTTTATAATTTTTCTAAGCGAG-TTGGTGACCCGGTTGAAGGAGACACCAACTC
611414 AATCAAGAGCTTAAATA
251 AATCAAGAGCTTAAATA
611431 TTAGTATATA
Statistics
Matches: 227, Mismatches: 30, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
292 16 0.07
293 178 0.78
294 29 0.13
295 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (293 bp):
GTAATAAAGTGTACATAATAAAATTAAAATGTATAAAAATATTAAAATAAAACTTTATCTAAGTG
GAAAATTAAAAGTGTTACTAATCTAATTGGTGTCGGTTCAAATTCTACCATACACATTTTTTATT
ACTTTTTTAAATAAAAAAACTAAAATACTCTCGAACAATATATCTTATTTTAATTACAGAAGGAC
AATTTTATAATTTTTCTAAGCGAGTTGGTGACCCGGTTGAAGGAGACACCAACTCAATCAAGAGC
TTAAATAATAATATAGATATACAATTGATAGAT
Found at i:614514 original size:15 final size:15
Alignment explanation
Indices: 614494--614523 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
614484 GTTTTAGGGT
*
614494 TTTTAGGTTTTTAAA
1 TTTTAGGGTTTTAAA
614509 TTTTAGGGTTTTAAA
1 TTTTAGGGTTTTAAA
614524 GAAAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTTAGGGTTTTAAA
Found at i:614700 original size:7 final size:7
Alignment explanation
Indices: 614692--614724 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
614682 AATAGATTAG
*
614692 GGTTTAG
1 GGTTTAA
614699 GGTTTAA
1 GGTTTAA
614706 GGTTTAA
1 GGTTTAA
614713 GGTTTAA
1 GGTTTAA
614720 GGTTT
1 GGTTT
614725 TTAAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
GGTTTAA
Done.