Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 40 of 171
Found at i:17741508 original size:12 final size:12
Alignment explanation
Indices: 17741464--17741509 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
17741454 TATAAATAAT
17741464 TTTTAA-ATTTA
1 TTTTAATATTTA
17741475 TTTTAAT-TTTA
1 TTTTAATATTTA
*
17741486 TTTAAAATATTTA
1 TTT-TAATATTTA
17741499 TTTTAATATTT
1 TTTTAATATTT
17741510 TTAATTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 13 0.43
12 10 0.33
13 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTAATATTTA
Found at i:17741578 original size:13 final size:13
Alignment explanation
Indices: 17741550--17741588 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
17741540 ATTTATTTTT
*
17741550 ATATAAAAATAATA
1 ATATAAAAA-ATTA
17741564 ATATAAAAAATTA
1 ATATAAAAAATTA
17741577 ATATAAATAAAT
1 ATATAAA-AAAT
17741589 CAAATCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAAATTA
Found at i:17760897 original size:17 final size:17
Alignment explanation
Indices: 17760875--17760922 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
17760865 ACAGTAAAAT
17760875 TTAATATTATAACAACA
1 TTAATATTATAACAACA
17760892 TTAATA-TA-AA-AA-A
1 TTAATATTATAACAACA
*
17760905 AT-ATATTATAACAACA
1 TTAATATTATAACAACA
17760921 TT
1 TT
17760923 GTAATAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 9
0.69 0.06 0.25
Matches are distributed among these distances:
12 3 0.12
13 4 0.16
14 4 0.16
15 4 0.16
16 4 0.16
17 6 0.24
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAATATTATAACAACA
Found at i:17761565 original size:29 final size:31
Alignment explanation
Indices: 17761533--17761595 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
17761523 GAAATTTAAA
17761533 ATTTTAAAAGATTAAAT-TAATTTT-TTATT
1 ATTTTAAAAGATTAAATATAATTTTATTATT
** *
17761562 ATTTTTGAAGATTAAGTATAATTTTATTATT
1 ATTTTAAAAGATTAAATATAATTTTATTATT
17761593 ATT
1 ATT
17761596 AATTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.48
30 7 0.24
31 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (31 bp):
ATTTTAAAAGATTAAATATAATTTTATTATT
Found at i:17763485 original size:36 final size:35
Alignment explanation
Indices: 17763414--17763484 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
17763404 GATTGAACTA
*
17763414 AAATTTTTAAATAAAAAATAAAATATTTTAATTTTT
1 AAATTTTTAAATAAAAAAT-AAATATCTTAATTTTT
17763450 AAATTTTTAAATACAAAAACT-AA-ATCTTAATTTTT
1 AAATTTTTAAATA-AAAAA-TAAATATCTTAATTTTT
17763485 TTTTCAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 11 0.34
36 15 0.47
37 5 0.16
38 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (35 bp):
AAATTTTTAAATAAAAAATAAATATCTTAATTTTT
Found at i:17766014 original size:19 final size:18
Alignment explanation
Indices: 17765975--17766012 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17765965 ACGAATTTTG
*
17765975 AATATAAATAATAAAACA
1 AATATAAATAATAAAAAA
17765993 AATATTAAAT-ATAAAAAA
1 AATA-TAAATAATAAAAAA
17766011 AA
1 AA
17766013 ATTATCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AATATAAATAATAAAAAA
Found at i:17767721 original size:21 final size:24
Alignment explanation
Indices: 17767687--17767736 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
17767677 AAATTACTTA
17767687 ATTTTTTTGAT-A-AAGTAATGAAT
1 ATTTTTTT-ATAAGAAGTAATGAAT
17767710 ATTTTTTT-TAAAGAAGTAATGAAT
1 ATTTTTTTAT-AAGAAGTAATGAAT
17767734 ATT
1 ATT
17767737 AATATAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
23 9 0.38
24 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (24 bp):
ATTTTTTTATAAGAAGTAATGAAT
Found at i:17768880 original size:96 final size:95
Alignment explanation
Indices: 17768744--17768937 Score: 289
Period size: 96 Copynumber: 2.0 Consensus size: 95
17768734 CAAAATTAAA
* * *
17768744 TTTTATTTTTTTACGATAAAGAACATGTCATTCTACTATTTTAATAGTTTATATTTTTATAATTT
1 TTTTATTTTTTTACGATAAAGAAAATGTCATTCTACTATTTTAATAGTCTATATCTTTATAATTT
*
17768809 TTAAAAGATTAATTTAAAATTTTATCATTT
66 TTAAAAGATTAATTCAAAATTTTATCATTT
* * * * *
17768839 TTTTATTTTTTTTATGATCAAGAAAATGTTATTTTATTATTTTAATAGTCTATATCTTTATAATT
1 TTTTA-TTTTTTTACGATAAAGAAAATGTCATTCTACTATTTTAATAGTCTATATCTTTATAATT
*
17768904 TTTAAAATATTAATTCAAAATTTTATCATTT
65 TTTAAAAGATTAATTCAAAATTTTATCATTT
17768935 TTT
1 TTT
17768938 AGAAACGAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 5 0.06
96 83 0.94
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (95 bp):
TTTTATTTTTTTACGATAAAGAAAATGTCATTCTACTATTTTAATAGTCTATATCTTTATAATTT
TTAAAAGATTAATTCAAAATTTTATCATTT
Found at i:17769369 original size:2 final size:2
Alignment explanation
Indices: 17769362--17769388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17769352 TTTTATATCG
17769362 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17769389 TGTTAGATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17772348 original size:30 final size:33
Alignment explanation
Indices: 17772300--17772359 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
17772290 TAAAATGAAA
17772300 TTTTAGGCTCTTTAAAAA-TTGG-AAAAAATTT
1 TTTTAGGCTCTTTAAAAATTTGGTAAAAAATTT
*
17772331 TTTTAGG-TCTTTTAAAATTTGGTAAAAAA
1 TTTTAGGCTCTTTAAAAATTTGGTAAAAAA
17772360 AAAAATTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.35
31 11 0.42
32 6 0.23
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.43
Consensus pattern (33 bp):
TTTTAGGCTCTTTAAAAATTTGGTAAAAAATTT
Found at i:17773503 original size:20 final size:20
Alignment explanation
Indices: 17773480--17773517 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17773470 TGAATTAATT
17773480 AAAA-ATTAATAAAATTATCG
1 AAAACATTAA-AAAATTATCG
17773500 AAAACATTAAAAAATTAT
1 AAAACATTAAAAAATTAT
17773518 TAAACATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAACATTAAAAAATTATCG
Found at i:17780468 original size:2 final size:2
Alignment explanation
Indices: 17780463--17780496 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17780453 TCTCTCTCTC
17780463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17780497 AGAAAGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17788843 original size:18 final size:18
Alignment explanation
Indices: 17788799--17788834 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17788789 TTGATAATGT
17788799 TGATGATGAGGCCGATGA
1 TGATGATGAGGCCGATGA
*
17788817 TGATGATGAGGTCGATGA
1 TGATGATGAGGCCGATGA
17788835 GTTGAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.39, T:0.25
Consensus pattern (18 bp):
TGATGATGAGGCCGATGA
Found at i:17788866 original size:3 final size:3
Alignment explanation
Indices: 17788855--17788894 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
17788845 GACGACGACA
* *
17788855 ATG ACG ATG ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
17788895 ATTTCAAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:17788870 original size:12 final size:12
Alignment explanation
Indices: 17788800--17788894 Score: 59
Period size: 12 Copynumber: 7.9 Consensus size: 12
17788790 TGATAATGTT
* *
17788800 GATGATGAGGCC
1 GATGATGATGAC
*
17788812 GATGATGATGAT
1 GATGATGATGAC
*
17788824 GA-GGTCGATGA-
1 GATGAT-GATGAC
*
17788835 GTTGAATGATGAC
1 GATG-ATGATGAC
* **
17788848 GACGACAATGAC
1 GATGATGATGAC
*
17788860 GATGATGATGAT
1 GATGATGATGAC
* *
17788872 GATAATGATGAT
1 GATGATGATGAC
17788884 GATGATGATGA
1 GATGATGATGA
17788895 ATTTCAAGCC
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
11 3 0.05
12 57 0.90
13 3 0.05
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.25
Consensus pattern (12 bp):
GATGATGATGAC
Found at i:17789365 original size:24 final size:24
Alignment explanation
Indices: 17789332--17789377 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17789322 AGAAATAATC
* * *
17789332 TTTCAGTTAAACTTTGTTTATTAT
1 TTTCAATTAAACTCTGCTTATTAT
17789356 TTTCAATTAAACTCTGCTTATT
1 TTTCAATTAAACTCTGCTTATT
17789378 TGTTTGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTCAATTAAACTCTGCTTATTAT
Found at i:17791358 original size:25 final size:25
Alignment explanation
Indices: 17791324--17791371 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17791314 AGAAATAATC
* *
17791324 TTTCAGTTAAACTTTGTTTATTTAT
1 TTTCAATTAAACTCTGTTTATTTAT
17791349 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
17791372 GTTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTCAATTAAACTCTGTTTATTTAT
Found at i:17801991 original size:3 final size:3
Alignment explanation
Indices: 17801983--17802026 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
17801973 CCCACAAGTT
17801983 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17802027 TCCACTACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17806022 original size:13 final size:14
Alignment explanation
Indices: 17805993--17806034 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
17805983 ATTGGTCGAA
* *
17805993 AAAGTCAATG-GTT
1 AAAGTCAACGAGTC
17806006 AAAGTCAACGA-TC
1 AAAGTCAACGAGTC
17806019 AAAGTCAACGAGTC
1 AAAGTCAACGAGTC
17806033 AA
1 AA
17806035 CGGGTCAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (14 bp):
AAAGTCAACGAGTC
Found at i:17811181 original size:3 final size:3
Alignment explanation
Indices: 17811168--17811230 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
17811158 AGGTGCCGGT
* *
17811168 TGA TAA TGA TGA TGA -GA CCGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA TGA
17811213 TGA TGA TGA -GA TCGA TGA
1 TGA TGA TGA TGA T-GA TGA
17811231 GTCGAATGAC
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.35, C:0.05, G:0.32, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:17813764 original size:17 final size:19
Alignment explanation
Indices: 17813744--17813779 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17813734 ATACTAACGG
17813744 TGTTA-AAAAA-ATTGTTA
1 TGTTACAAAAATATTGTTA
17813761 TGTTACAAAAATATTGTTA
1 TGTTACAAAAATATTGTTA
17813780 GTATTAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (19 bp):
TGTTACAAAAATATTGTTA
Found at i:17814175 original size:30 final size:29
Alignment explanation
Indices: 17814139--17814196 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
17814129 CGATCCCCAA
* * *
17814139 AAATTTAAGTACCGATTTAAGAAAAATATC
1 AAATTTAAATACCAAATTAA-AAAAATATC
17814169 AAATTTAAATACCAAATTAAAAAAATAT
1 AAATTTAAATACCAAATTAAAAAAATAT
17814197 ATATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (29 bp):
AAATTTAAATACCAAATTAAAAAAATATC
Found at i:17816153 original size:17 final size:17
Alignment explanation
Indices: 17816131--17816163 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17816121 ACATATCATG
17816131 TAATTTATG-TTTTTTCA
1 TAATTT-TGCTTTTTTCA
17816148 TAATTTTGCTTTTTTC
1 TAATTTTGCTTTTTTC
17816164 TATATCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (17 bp):
TAATTTTGCTTTTTTCA
Found at i:17827967 original size:262 final size:262
Alignment explanation
Indices: 17827502--17828025 Score: 1039
Period size: 262 Copynumber: 2.0 Consensus size: 262
17827492 TAGATGGCTC
17827502 CCCAAATGAAAAAAAGAATAAGCCATCAACTTCTAATAAATTAAAATTTTAGCTTCACACAACTA
1 CCCAAATGAAAAAAAGAATAAGCCATCAACTTCTAATAAATTAAAATTTTAGCTTCACACAACTA
17827567 TCTCTTATCTTCGCACCAACATGAAGTAACCCATCTATTCATCATGTTCTAAGACAATTTTTATT
66 TCTCTTATCTTCGCACCAACATGAAGTAACCCATCTATTCATCATGTTCTAAGACAATTTTTATT
*
17827632 TTGGAAAAAGAAGGAAAGCAAGAGACTTCGTACTAAATATTCTTCCAGACAGTTCATTACAAGGA
131 TTGGAAAAAGAAGGAAAGCAAGAGACCTCGTACTAAATATTCTTCCAGACAGTTCATTACAAGGA
17827697 TTTGCTGATTCTAGAGGTACCAACAGATTTTCAATAGAAGGGGTACACTGACTATTGGACTGTGA
196 TTTGCTGATTCTAGAGGTACCAACAGATTTTCAATAGAAGGGGTACACTGACTATTGGACTGTGA
17827762 AG
261 AG
17827764 CCCAAATGAAAAAAAGAATAAGCCATCAACTTCTAATAAATTAAAATTTTAGCTTCACACAACTA
1 CCCAAATGAAAAAAAGAATAAGCCATCAACTTCTAATAAATTAAAATTTTAGCTTCACACAACTA
17827829 TCTCTTATCTTCGCACCAACATGAAGTAACCCATCTATTCATCATGTTCTAAGACAATTTTTATT
66 TCTCTTATCTTCGCACCAACATGAAGTAACCCATCTATTCATCATGTTCTAAGACAATTTTTATT
17827894 TTGGAAAAAGAAGGAAAGCAAGAGACCTCGTACTAAATATTCTTCCAGACAGTTCATTACAAGGA
131 TTGGAAAAAGAAGGAAAGCAAGAGACCTCGTACTAAATATTCTTCCAGACAGTTCATTACAAGGA
17827959 TTTGCTGATTCTAGAGGTACCAACAGATTTTCAATAGAAGGGGTACACTGACTATTGGACTGTGA
196 TTTGCTGATTCTAGAGGTACCAACAGATTTTCAATAGAAGGGGTACACTGACTATTGGACTGTGA
17828024 AG
261 AG
17828026 AAGCTATACG
Statistics
Matches: 261, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 261 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (262 bp):
CCCAAATGAAAAAAAGAATAAGCCATCAACTTCTAATAAATTAAAATTTTAGCTTCACACAACTA
TCTCTTATCTTCGCACCAACATGAAGTAACCCATCTATTCATCATGTTCTAAGACAATTTTTATT
TTGGAAAAAGAAGGAAAGCAAGAGACCTCGTACTAAATATTCTTCCAGACAGTTCATTACAAGGA
TTTGCTGATTCTAGAGGTACCAACAGATTTTCAATAGAAGGGGTACACTGACTATTGGACTGTGA
AG
Found at i:17832592 original size:29 final size:27
Alignment explanation
Indices: 17832558--17832619 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
17832548 ATATATGAGA
17832558 AATTTTT-AAATTATAA-TTTATATTTAT
1 AATTTTTCAAATTATAACTTT-T-TTTAT
*
17832585 AATCTTTTCAATTTATAACTTTTTTTAT
1 AAT-TTTTCAAATTATAACTTTTTTTAT
17832613 AATTTTT
1 AATTTTT
17832620 AATTATTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 7 0.23
28 12 0.39
29 9 0.29
30 3 0.10
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (27 bp):
AATTTTTCAAATTATAACTTTTTTTAT
Found at i:17837160 original size:298 final size:300
Alignment explanation
Indices: 17836589--17837188 Score: 1141
Period size: 298 Copynumber: 2.0 Consensus size: 300
17836579 ATCACTGCAC
17836589 AAAAGAGATGTAAGCTTCAATAAAGCATCATAGTAAATGACTTACAAATTATGCACCCAAAGATT
1 AAAAGAGATGTAAGCTTCAATAAAGCATCATAGTAAATGACTTACAAATTATGCACCCAAAGATT
* *
17836654 GAACAGTTGCAATCATGAAAGATATAAAAGGGTATGTATAAAGAAACCTATCGTTCAGTTTCAAC
66 GAACAATTGCAATCATGAAAGATATAAAAGGGAATGTATAAAGAAACCTATCGTTCAGTTTCAAC
17836719 TAATGCTGAATGTTTTCAAACCATACCAATATAGTAAAAATCTTTAAACATCTCTATCTCAAAGT
131 TAATGCTGAATGTTTTCAAACCATACCAATATAGTAAAAATCTTTAAACATCTCTATCTCAAAGT
17836784 CTAACCAAGCATATTCAATAGGTTAACTTCAAAAAACACTAAAAACCCACCTCTAAATCCTGTCC
196 CTAACCAAGCATATTCAATAGGTTAACTTCAAAAAACACTAAAAACCCACCTCTAAATCCTGTCC
17836849 CTTTACGTTGCTGGTAAGGCAACTTGCCAACCTCAAGCAA
261 CTTTACGTTGCTGGTAAGGCAACTTGCCAACCTCAAGCAA
17836889 AAAAGAGATGTAAGCTTCAATAAAGCATCATAGTAAATGACTTACAAATTATGCACCCAAAGATT
1 AAAAGAGATGTAAGCTTCAATAAAGCATCATAGTAAATGACTTACAAATTATGCACCCAAAGATT
*
17836954 GAACAATTGCAATCATGAAAGATA-CAAAGGGAATGTATAAAGAAACCTATCGTTCAGTTTCAAC
66 GAACAATTGCAATCATGAAAGATATAAAAGGGAATGTATAAAGAAACCTATCGTTCAGTTTCAAC
17837018 TAATGCTGAATGTTTTCAAACCATACCAATATAGTAAAAATCTTTAAACATCT-TATCTCAAAGT
131 TAATGCTGAATGTTTTCAAACCATACCAATATAGTAAAAATCTTTAAACATCTCTATCTCAAAGT
* *
17837082 CTAACCAAGCATATTCAATGGGTTAACTTCAAAAAACACTAAAAACCCACCTCTAAATCCTGTTC
196 CTAACCAAGCATATTCAATAGGTTAACTTCAAAAAACACTAAAAACCCACCTCTAAATCCTGTCC
17837147 CTTTACGTTGCTGGTAAGGCAACTTGCCAACCTCAAGCAA
261 CTTTACGTTGCTGGTAAGGCAACTTGCCAACCTCAAGCAA
17837187 AA
1 AA
17837189 CAGCAACTTC
Statistics
Matches: 295, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
298 116 0.39
299 91 0.31
300 88 0.30
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (300 bp):
AAAAGAGATGTAAGCTTCAATAAAGCATCATAGTAAATGACTTACAAATTATGCACCCAAAGATT
GAACAATTGCAATCATGAAAGATATAAAAGGGAATGTATAAAGAAACCTATCGTTCAGTTTCAAC
TAATGCTGAATGTTTTCAAACCATACCAATATAGTAAAAATCTTTAAACATCTCTATCTCAAAGT
CTAACCAAGCATATTCAATAGGTTAACTTCAAAAAACACTAAAAACCCACCTCTAAATCCTGTCC
CTTTACGTTGCTGGTAAGGCAACTTGCCAACCTCAAGCAA
Found at i:17839199 original size:3 final size:3
Alignment explanation
Indices: 17839191--17839216 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17839181 TTGCAGAAAG
17839191 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
17839217 GCTCGTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:17842680 original size:14 final size:13
Alignment explanation
Indices: 17842645--17842688 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
17842635 ATGTATCATA
*
17842645 ATTTAAAATAAAT
1 ATTTAAAAAAAAT
*
17842658 ATTTCAAAAAAAT
1 ATTTAAAAAAAAT
*
17842671 ATTGTAAAAAAATT
1 ATT-TAAAAAAAAT
17842685 ATTT
1 ATTT
17842689 TGAGATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATTTAAAAAAAAT
Found at i:17843998 original size:18 final size:18
Alignment explanation
Indices: 17843975--17844017 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17843965 TTTTCAGTTG
17843975 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
17843993 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
17844011 TAATTAA
1 TAATTAA
17844018 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:17845484 original size:18 final size:17
Alignment explanation
Indices: 17845453--17845487 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
17845443 AGTTTAGGGT
17845453 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
17845470 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
17845488 AGATTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:17846188 original size:23 final size:23
Alignment explanation
Indices: 17846160--17846237 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 23
17846150 AAAATTGAAT
17846160 TTCGAGTTAATCGAATTGAGTTA
1 TTCGAGTTAATCGAATTGAGTTA
*
17846183 TTCGAGCTAAATCGAATTGAGTTA
1 TTCGAG-TTAATCGAATTGAGTTA
* * *
17846207 TTCGAGCTAACTCGAA-TAAGTGA
1 TTCGAGTTAA-TCGAATTGAGTTA
17846230 TTCGAGTT
1 TTCGAGTT
17846238 TTGAGTTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.43
24 27 0.57
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.35
Consensus pattern (23 bp):
TTCGAGTTAATCGAATTGAGTTA
Found at i:17846197 original size:24 final size:24
Alignment explanation
Indices: 17846160--17846223 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
17846150 AAAATTGAAT
*
17846160 TTCGAG-TTAATCGAATTGAGTTA
1 TTCGAGCTAAATCGAATTGAGTTA
17846183 TTCGAGCTAAATCGAATTGAGTTA
1 TTCGAGCTAAATCGAATTGAGTTA
*
17846207 TTCGAGCTAACTCGAAT
1 TTCGAGCTAAATCGAAT
17846224 AAGTGATTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 6 0.16
24 32 0.84
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (24 bp):
TTCGAGCTAAATCGAATTGAGTTA
Found at i:17846387 original size:18 final size:19
Alignment explanation
Indices: 17846353--17846395 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17846343 CAAAAATAAA
*
17846353 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
17846372 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
17846390 AAAAAT
1 AAAAAT
17846396 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:17846398 original size:27 final size:27
Alignment explanation
Indices: 17846368--17846429 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
17846358 TCAAAATAAT
17846368 TTTTAAAATTCAAAATATTTATAAAAA
1 TTTTAAAATTCAAAATATTTATAAAAA
* * * * *
17846395 TTTTAAAATTTATATTTTTTATAATAA
1 TTTTAAAATTCAAAATATTTATAAAAA
17846422 TTTTAAAA
1 TTTTAAAA
17846430 AATTCTAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTTAAAATTCAAAATATTTATAAAAA
Found at i:17859709 original size:14 final size:14
Alignment explanation
Indices: 17859692--17859722 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17859682 AGGGTTTAAA
17859692 AAATTTAATTAATT
1 AAATTTAATTAATT
*
17859706 AAATTTATTTAATT
1 AAATTTAATTAATT
17859720 AAA
1 AAA
17859723 AATTATTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:17861391 original size:19 final size:19
Alignment explanation
Indices: 17861363--17861402 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17861353 TGTGTTTGAA
17861363 TTTTAAAATTTTAAAATAT
1 TTTTAAAATTTTAAAATAT
* *
17861382 TTTTATAATTTTAAATTAT
1 TTTTAAAATTTTAAAATAT
17861401 TT
1 TT
17861403 ATTGACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAAATTTTAAAATAT
Found at i:17877697 original size:23 final size:23
Alignment explanation
Indices: 17877669--17877793 Score: 150
Period size: 23 Copynumber: 5.4 Consensus size: 23
17877659 TGCTGGACAA
17877669 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCGAAT
17877691 CCAGTAAGCACACACAGTGCTG-AT
1 -CAGTAAGCACACACAGTGC-GAAT
*
17877715 CAGTAAGCACACATAGTGC-AAT
1 CAGTAAGCACACACAGTGCGAAT
*
17877737 CCAGTAAGCACACACAATGCGAAT
1 -CAGTAAGCACACACAGTGCGAAT
* *
17877761 CAGTAAGCATACACAATGCTGAA-
1 CAGTAAGCACACACAGTGC-GAAT
17877784 CAGTAAGCAC
1 CAGTAAGCAC
17877794 GCTAATGTTC
Statistics
Matches: 91, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.02
23 81 0.89
24 8 0.09
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCGAAT
Found at i:17877721 original size:46 final size:46
Alignment explanation
Indices: 17877669--17877775 Score: 171
Period size: 46 Copynumber: 2.3 Consensus size: 46
17877659 TGCTGGACAA
*
17877669 CAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAGTGCTG-AT
1 CAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAATGC-GAAT
*
17877715 CAGTAAGCACACATAGTGCAATCCAGTAAGCACACACAATGCGAAT
1 CAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAATGCGAAT
*
17877761 CAGTAAGCATACACA
1 CAGTAAGCACACACA
17877776 ATGCTGAACA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
45 1 0.02
46 55 0.98
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.15
Consensus pattern (46 bp):
CAGTAAGCACACACAGTGCAATCCAGTAAGCACACACAATGCGAAT
Found at i:17880501 original size:24 final size:24
Alignment explanation
Indices: 17880464--17880524 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
17880454 GACTAATAAA
* *
17880464 AGTTTGACTCAAACAAATAAACAG
1 AGTTTAACTGAAACAAATAAACAG
* *
17880488 AGTTTAATTGAAACAATTAAACAG
1 AGTTTAACTGAAACAAATAAACAG
17880512 AGTTTAACTGAAA
1 AGTTTAACTGAAA
17880525 GATTATTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAG
Found at i:17882509 original size:24 final size:24
Alignment explanation
Indices: 17882450--17882510 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
17882440 GACTAATAAG
* * *
17882450 AGTTTGACTCAAACAAATAAACAG
1 AGTTTAACTGAAACAAATAAACAA
* *
17882474 AGTTTAATTGAAACAATTAAACAA
1 AGTTTAACTGAAACAAATAAACAA
17882498 AGTTTAACTGAAA
1 AGTTTAACTGAAA
17882511 TATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:17886209 original size:18 final size:19
Alignment explanation
Indices: 17886181--17886231 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
17886171 AAGTCATAAG
17886181 AAAATTATAAAAAT-GTAA
1 AAAATTATAAAAATCGTAA
*
17886199 AGAAA-TATAAAATTCGTAA
1 A-AAATTATAAAAATCGTAA
17886218 AAAATTATAAAAAT
1 AAAATTATAAAAAT
17886232 TATGAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (19 bp):
AAAATTATAAAAATCGTAA
Found at i:17886418 original size:9 final size:9
Alignment explanation
Indices: 17886406--17886479 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 9
17886396 TTTTTGATGC
17886406 TTTTTATAA
1 TTTTTATAA
17886415 TTTTT-TAAA
1 TTTTTAT-AA
*
17886424 TTTTAATAAAA
1 TTTT--TATAA
* *
17886435 TTTTAATAT
1 TTTTTATAA
17886444 TTTTTATTAAA
1 TTTTTA-T-AA
* *
17886455 ATTTAATAA
1 TTTTTATAA
17886464 TTTTTATAA
1 TTTTTATAA
17886473 TTTTTAT
1 TTTTTAT
17886480 TTTTTTATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
8 1 0.02
9 34 0.69
10 2 0.04
11 12 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17886447 original size:20 final size:21
Alignment explanation
Indices: 17886424--17886473 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
17886414 ATTTTTTAAA
17886424 TTTTAATAAAATTTTAAT-ATT
1 TTTTAATAAAA-TTTAATAATT
*
17886445 TTTTATTAAAATTTAATAATT
1 TTTTAATAAAATTTAATAATT
17886466 TTTATAAT
1 TTT-TAAT
17886474 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAATAAAATTTAATAATT
Found at i:17886454 original size:21 final size:20
Alignment explanation
Indices: 17886424--17886470 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
17886414 ATTTTTTAAA
* *
17886424 TTTTAATAAAATTTTAATATT
1 TTTTATTAAAA-TTTAATAAT
17886445 TTTTATTAAAATTTAATAAT
1 TTTTATTAAAATTTAATAAT
17886465 TTTTAT
1 TTTTAT
17886471 AATTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTAAAATTTAATAAT
Found at i:17886460 original size:31 final size:29
Alignment explanation
Indices: 17886406--17886480 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
17886396 TTTTTGATGC
* *
17886406 TTTTTATAA-TTTT-TTAAATTTTAATAAAA
1 TTTTAATAATTTTTATTAAAATTTAAT--AA
*
17886435 TTTTAATATTTTTTATTAAAATTTAATAA
1 TTTTAATAATTTTTATTAAAATTTAATAA
*
17886464 TTTTTATAATTTTTATT
1 TTTTAATAATTTTTATT
17886481 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 24 0.62
30 4 0.10
31 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTAATAATTTTTATTAAAATTTAATAA
Found at i:17890740 original size:11 final size:11
Alignment explanation
Indices: 17890721--17890764 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
17890711 ATATTAAATT
*
17890721 TTAATATTTTA
1 TTAAAATTTTA
17890732 TTAAAATTTTA
1 TTAAAATTTTA
17890743 TTAAAAATTTTA
1 TT-AAAATTTTA
*
17890755 -AAAAATTTTA
1 TTAAAATTTTA
17890765 AAAAGCACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 9 0.30
11 12 0.40
12 9 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAAAATTTTA
Found at i:17890760 original size:10 final size:10
Alignment explanation
Indices: 17890734--17890768 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
17890724 ATATTTTATT
17890734 AAAATTTTATTA
1 AAAATTTTA--A
17890746 AAAATTTTAA
1 AAAATTTTAA
17890756 AAAATTTTAA
1 AAAATTTTAA
17890766 AAA
1 AAA
17890769 GCACCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.61
12 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:17891068 original size:30 final size:29
Alignment explanation
Indices: 17891032--17891093 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
17891022 TTCTTATAAG
*
17891032 TTTTTTTACGATTTTTATAAAATTTTATAT
1 TTTTTTTACAATTTTTATAAAATTTTA-AT
* *
17891062 TTTTTTTACAATTTTTATATATTTTTAAT
1 TTTTTTTACAATTTTTATAAAATTTTAAT
17891091 TTT
1 TTT
17891094 AATAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTTTTACAATTTTTATAAAATTTTAAT
Found at i:17891088 original size:10 final size:10
Alignment explanation
Indices: 17890959--17891137 Score: 65
Period size: 10 Copynumber: 18.1 Consensus size: 10
17890949 TTTACAATTT
17890959 TATATTTCTT-
1 TATATTT-TTA
17890969 TATATTTTTA
1 TATATTTTTA
17890979 TA-ATTATCTTA
1 TATATT-T-TTA
*
17890990 TA-A-CTTTA
1 TATATTTTTA
* *
17890998 TAAAATTTTA
1 TATATTTTTA
* *
17891008 CAT-TTTTTC
1 TATATTTTTA
17891017 TATATTTCTTA
1 TATATTT-TTA
*
17891028 TA-AGTTTTTT
1 TATA-TTTTTA
*
17891038 TACGATTTTTA
1 TA-TATTTTTA
* *
17891049 TAAAATTTTA
1 TATATTTTTA
*
17891059 TAT-TTTTTT
1 TATATTTTTA
*
17891068 TACAATTTTTA
1 TA-TATTTTTA
17891079 TATA-TTTT-
1 TATATTTTTA
*
17891087 TA-ATTTTAA
1 TATATTTTTA
*
17891096 TA-AATTTTA
1 TATATTTTTA
*
17891105 AATATTTTTA
1 TATATTTTTA
17891115 TAATAATTTTTA
1 T-AT-ATTTTTA
*
17891127 TTTATTTTTA
1 TATATTTTTA
17891137 T
1 T
17891138 TTTTATTTTT
Statistics
Matches: 127, Mismatches: 25, Indels: 34
0.68 0.13 0.18
Matches are distributed among these distances:
7 1 0.01
8 10 0.08
9 31 0.24
10 46 0.36
11 30 0.24
12 9 0.07
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (10 bp):
TATATTTTTA
Found at i:17896789 original size:63 final size:58
Alignment explanation
Indices: 17896686--17896808 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 58
17896676 AAGAAAGAGA
17896686 AGCCAAGAGAGGGGGAGAGGGGGGGGGAACTTAACAGAGAATGACCTACAATCAAATG
1 AGCCAAGAGAGGGGGAGAGGGGGGGGGAACTTAACAGAGAATGACCTACAATCAAATG
17896744 AGCCAAGAGAGGGGGGAGAGGGGGGGGGGGGGAACTTAACAGAGAATGACCTACAATCAAATG
1 AGCCAAGAGA-GGGGGAGA----GGGGGGGGGAACTTAACAGAGAATGACCTACAATCAAATG
17896807 AG
1 AG
17896809 ATGTTCTTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
58 10 0.17
59 8 0.13
63 42 0.70
ACGTcount: A:0.37, C:0.13, G:0.41, T:0.10
Consensus pattern (58 bp):
AGCCAAGAGAGGGGGAGAGGGGGGGGGAACTTAACAGAGAATGACCTACAATCAAATG
Found at i:17909444 original size:12 final size:12
Alignment explanation
Indices: 17909427--17909462 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
17909417 ATTTTTATTT
*
17909427 AATATTAATATA
1 AATATTAATACA
17909439 AATATTAATACA
1 AATATTAATACA
17909451 AATATTAATACA
1 AATATTAATACA
17909463 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (12 bp):
AATATTAATACA
Found at i:17929578 original size:20 final size:20
Alignment explanation
Indices: 17929553--17929601 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
17929543 AATTGAATTA
17929553 TTTAGTTAAAACCAAATTTT
1 TTTAGTTAAAACCAAATTTT
*
17929573 TTTAGTTAAAACCAATTTTT
1 TTTAGTTAAAACCAAATTTT
17929593 TTTAGTTAA
1 TTTAGTTAA
17929602 TCCTTCTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (20 bp):
TTTAGTTAAAACCAAATTTT
Found at i:17942950 original size:4 final size:4
Alignment explanation
Indices: 17942941--17942965 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17942931 TGCCTAAACT
17942941 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
17942966 GACTCTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:17943319 original size:21 final size:22
Alignment explanation
Indices: 17943293--17943334 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17943283 TATTATTATT
17943293 ATATAA-AAAT-AAATTTAAAAA
1 ATATAATAAATCAAA-TTAAAAA
17943314 ATATAATAAATCAAATTAAAA
1 ATATAATAAATCAAATTAAAA
17943335 TAAAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
ATATAATAAATCAAATTAAAAA
Found at i:17944578 original size:33 final size:32
Alignment explanation
Indices: 17944510--17944577 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
17944500 AAAAGTTGGT
* *
17944510 AAAACAATTTTTTGAGCTCTTTAAAAGCTGAA
1 AAAACAATTTTTGGAGCTCTTTAAAAACTGAA
* *
17944542 AAAACTAATTTTTGGATC-CTTTAAAAATTGAA
1 AAAAC-AATTTTTGGAGCTCTTTAAAAACTGAA
17944574 AAAA
1 AAAA
17944578 AAAAATGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (32 bp):
AAAACAATTTTTGGAGCTCTTTAAAAACTGAA
Found at i:17944871 original size:98 final size:98
Alignment explanation
Indices: 17944702--17944896 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
17944692 TTTAATCACC
* * * * *
17944702 AAATCAATCAACCAAAACAATACGTCTCTATCGACTAAAGTCTATAATCCTTTTACAAGTTAAGG
1 AAATCAATCAACCAAAACAATACATCTCTATCGACTAAAGCCCAAAATCCTTTTACAAGTTAAGA
*
17944767 GTTAGTTTAACATTACTTTTGAGAAGTGCTTTG
66 GCTAGTTTAACATTACTTTTGAGAAGTGCTTTG
*
17944800 AAATCAATCAACCAAAACAATATATCTCTATCGACTAAAGCCCAAAATCCTTTTACAAGTTAAGA
1 AAATCAATCAACCAAAACAATACATCTCTATCGACTAAAGCCCAAAATCCTTTTACAAGTTAAGA
17944865 GCTAGTTTAACATTACTTTTGAGAAGTGCTTT
66 GCTAGTTTAACATTACTTTTGAGAAGTGCTTT
17944897 TAAAAAGTAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.32
Consensus pattern (98 bp):
AAATCAATCAACCAAAACAATACATCTCTATCGACTAAAGCCCAAAATCCTTTTACAAGTTAAGA
GCTAGTTTAACATTACTTTTGAGAAGTGCTTTG
Found at i:17944904 original size:13 final size:13
Alignment explanation
Indices: 17944888--17944928 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
17944878 TACTTTTGAG
*
17944888 AAGTGCTTTTAAA
1 AAGTGATTTTAAA
17944901 AAGT-ATTTTGAAA
1 AAGTGATTTT-AAA
17944914 AAGTGATTTTAAA
1 AAGTGATTTTAAA
17944927 AA
1 AA
17944929 AATATTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 16 0.64
14 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (13 bp):
AAGTGATTTTAAA
Found at i:17944924 original size:26 final size:28
Alignment explanation
Indices: 17944888--17944942 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
17944878 TACTTTTGAG
* *
17944888 AAGTGCTTTT-AAAAAGTA-TTTTGAAA
1 AAGTGATTTTAAAAAAATATTTTTGAAA
17944914 AAGTGATTTTAAAAAAATATTTTTGAAA
1 AAGTGATTTTAAAAAAATATTTTTGAAA
17944942 A
1 A
17944943 GCTTGGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.36
27 7 0.28
28 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (28 bp):
AAGTGATTTTAAAAAAATATTTTTGAAA
Found at i:17944942 original size:13 final size:14
Alignment explanation
Indices: 17944894--17944942 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
17944884 TGAGAAGTGC
17944894 TTTT-AAAAAGTA-
1 TTTTGAAAAAGTAT
17944906 TTTTGAAAAAGTGA-
1 TTTTGAAAAAGT-AT
* *
17944920 TTTTAAAAAAATAT
1 TTTTGAAAAAGTAT
17944934 TTTTGAAAA
1 TTTTGAAAA
17944943 GCTTGGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 19 0.61
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTTGAAAAAGTAT
Found at i:17946598 original size:9 final size:9
Alignment explanation
Indices: 17946586--17946612 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17946576 CGATGACCTG
17946586 AATGATGAA
1 AATGATGAA
17946595 AATGATGAA
1 AATGATGAA
17946604 AATGATGAA
1 AATGATGAA
17946613 GCAGGCGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
AATGATGAA
Found at i:17949090 original size:18 final size:19
Alignment explanation
Indices: 17949056--17949091 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17949046 AATTATGTTA
*
17949056 TTATATATAATATTTAATT
1 TTATATATAAAATTTAATT
17949075 TTATATA-AAAATTTAAT
1 TTATATATAAAATTTAAT
17949092 AAGTATGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATATAAAATTTAATT
Found at i:17966419 original size:13 final size:13
Alignment explanation
Indices: 17966401--17966428 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17966391 AATATAGGGG
17966401 AAAATGTACCATT
1 AAAATGTACCATT
17966414 AAAATGTACCATT
1 AAAATGTACCATT
17966427 AA
1 AA
17966429 CGAATTTTCA
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:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATGTACCATT
Found at i:17970148 original size:21 final size:20
Alignment explanation
Indices: 17970119--17970157 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
17970109 ACGCCTACGA
17970119 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
17970139 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
17970158 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:17970313 original size:18 final size:15
Alignment explanation
Indices: 17970274--17970308 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
17970264 ATTTGGTTTG
17970274 TTTATTTTATTATTA
1 TTTATTTTATTATTA
17970289 TTTATTTTATTATTA
1 TTTATTTTATTATTA
17970304 TTTAT
1 TTTAT
17970309 CATTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTATTA
Found at i:17970345 original size:13 final size:13
Alignment explanation
Indices: 17970315--17970413 Score: 55
Period size: 11 Copynumber: 8.6 Consensus size: 13
17970305 TTATCATTTA
*
17970315 AATATATATATTT
1 AATATATATAATT
17970328 AATATATATAA--
1 AATATATATAATT
*
17970339 ATTATATA-AATT
1 AATATATATAATT
17970351 AA-A-ATAT-ATT
1 AATATATATAATT
*
17970361 AATA-ATATAGAAT
1 AATATATATA-ATT
17970374 AATATATA-AA-T
1 AATATATATAATT
17970385 -A-ATAT-TAA-T
1 AATATATATAATT
*
17970394 AATATATA-AATA
1 AATATATATAATT
17970406 AATATATA
1 AATATATA
17970414 AAGAAAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
9 7 0.10
10 12 0.17
11 20 0.29
12 10 0.14
13 17 0.25
14 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (13 bp):
AATATATATAATT
Found at i:17970352 original size:23 final size:22
Alignment explanation
Indices: 17970313--17970415 Score: 77
Period size: 23 Copynumber: 4.6 Consensus size: 22
17970303 ATTTATCATT
**
17970313 TAAATATATATATTTAATATATA
1 TAAAT-TATATAAATAATATATA
*
17970336 TAAATTATATAAATTAAAATATA
1 TAAATTATATAAA-TAATATATA
* *
17970359 TTAATAATATAGAAT-A-ATATA
1 TAAATTATATA-AATAATATATA
* *
17970380 TAAATAATATTAATAATATATAAA
1 TAAATTATATAAATAATATAT--A
17970404 TAAA-TATATAAA
1 TAAATTATATAAA
17970416 GAAAATATGC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.05
21 15 0.23
22 11 0.17
23 29 0.45
24 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAATTATATAAATAATATATA
Found at i:17970368 original size:9 final size:9
Alignment explanation
Indices: 17970335--17970398 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
17970325 TTTAATATAT
17970335 ATAA-ATTA
1 ATAATATTA
17970343 TATAA-ATTA
1 -ATAATATTA
*
17970352 AAATATATTA
1 ATA-ATATTA
*
17970362 ATAATATAGA
1 ATAATAT-TA
17970372 ATAATATATAA
1 ATAATAT-T-A
17970383 ATAATATTA
1 ATAATATTA
17970392 ATAATAT
1 ATAATAT
17970399 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
8 2 0.04
9 21 0.45
10 16 0.34
11 8 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAATATTA
Found at i:17970377 original size:21 final size:21
Alignment explanation
Indices: 17970331--17970411 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
17970321 TATATTTAAT
*
17970331 ATATATAAATTATATA-AATTAAA
1 ATATATAAATAATATAGAA-T--A
*
17970354 ATATATTAATAATATAGAATA
1 ATATATAAATAATATAGAATA
*
17970375 ATATATAAATAATAT-TAATA
1 ATATATAAATAATATAGAATA
17970395 ATATATAAATAAATATA
1 ATATATAAAT-AATATA
17970412 TAAAGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
20 14 0.27
21 20 0.39
23 15 0.29
24 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
ATATATAAATAATATAGAATA
Found at i:17970392 original size:30 final size:31
Alignment explanation
Indices: 17970313--17970415 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 31
17970303 ATTTATCATT
17970313 TAAATATAT--ATAT-TTAAT-ATATATAAA
1 TAAATATATAAATATATTAATAATATATAAA
* * *
17970340 TTATATAAATTAAAATATATTAATAATATA-GAA
1 -TAAATATA-T-AAATATATTAATAATATATAAA
17970373 T-AATATATAAATAATATTAATAATATATAAA
1 TAAATATATAAAT-ATATTAATAATATATAAA
17970404 TAAATATATAAA
1 TAAATATATAAA
17970416 GAAAATATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
28 6 0.10
29 5 0.08
30 15 0.25
31 7 0.12
32 15 0.25
33 7 0.12
34 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAATATATAAATATATTAATAATATATAAA
Found at i:17970463 original size:22 final size:22
Alignment explanation
Indices: 17970430--17970479 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
17970420 ATATGCGTTA
17970430 TATATATATATA-TATAACTA-AT
1 TATATATATATACT-TAA-TATAT
17970452 TATATACT-TATACTTAATATAT
1 TATATA-TATATACTTAATATAT
17970474 TATATA
1 TATATA
17970480 AAGTATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATATATATACTTAATATAT
Found at i:17970886 original size:13 final size:13
Alignment explanation
Indices: 17970870--17970894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17970860 GATTTCGTTG
17970870 AAATCAATATAGT
1 AAATCAATATAGT
17970883 AAATCAATATAG
1 AAATCAATATAG
17970895 ATTTATAGTA
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:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATCAATATAGT
Found at i:17978685 original size:83 final size:83
Alignment explanation
Indices: 17978589--17978753 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 83
17978579 CATAATAAGG
17978589 TTTGGGGTTTTTTCATATACCTGCACCTCAACATAATTCTCGCTTATAAATTTATTCA-TCTAAT
1 TTTGGGGTTTTTTCATATACCTGCACCTCAACATAATTCTCGCTTATAAATTTATTCATTC-AAT
17978653 CAGTTACTCTGTTATATTT
65 CAGTTACTCTGTTATATTT
* * *
17978672 TTTGGGGTTTTTTCATATACCTGCACCTTATCATAATTCTCGCTTATAAATTTATTTATTCAATC
1 TTTGGGGTTTTTTCATATACCTGCACCTCAACATAATTCTCGCTTATAAATTTATTCATTCAATC
*
17978737 AGTTACTCTGTTGTATT
66 AGTTACTCTGTTATATT
17978754 CTTTAGAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 75 0.97
84 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.47
Consensus pattern (83 bp):
TTTGGGGTTTTTTCATATACCTGCACCTCAACATAATTCTCGCTTATAAATTTATTCATTCAATC
AGTTACTCTGTTATATTT
Found at i:17984844 original size:59 final size:60
Alignment explanation
Indices: 17984772--17984905 Score: 193
Period size: 60 Copynumber: 2.3 Consensus size: 60
17984762 ATATTTAATA
* * *
17984772 AATTT-AGGTACCAAATTGGGTC-CAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTATC
1 AATTTCAGGTACCAAATTGGATCAAAAAAAAGTTCAGGTACCAAATTAGGAAAAAGTATC
* *
17984830 AATTTCAGGTACCAAATTGGATCAAAAAAAAGTTCAGGTACCGAATTAGGAAAAAGTGTC
1 AATTTCAGGTACCAAATTGGATCAAAAAAAAGTTCAGGTACCAAATTAGGAAAAAGTATC
*
17984890 AA-TTCAGGTACAAAAT
1 AATTTCAGGTACCAAAT
17984906 ATTATATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
58 5 0.07
59 29 0.43
60 34 0.50
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.25
Consensus pattern (60 bp):
AATTTCAGGTACCAAATTGGATCAAAAAAAAGTTCAGGTACCAAATTAGGAAAAAGTATC
Found at i:17984898 original size:30 final size:30
Alignment explanation
Indices: 17984799--17984905 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 30
17984789 GGGTCCAAAA
*
17984799 AAGTTTAGGTACCAAATTAGGAAAAAGTATC
1 AAGTTCAGGTACCAAATTAGGAAAAAGT-TC
* **
17984830 AATTTCAGGTACCAAATT-GGATCAAAA--AA
1 AAGTTCAGGTACCAAATTAGGA--AAAAGTTC
*
17984859 AAGTTCAGGTACCGAATTAGGAAAAAGTGTC
1 AAGTTCAGGTACCAAATTAGGAAAAAGT-TC
*
17984890 AA-TTCAGGTACAAAAT
1 AAGTTCAGGTACCAAAT
17984906 ATTATATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.07
29 16 0.27
30 18 0.30
31 18 0.30
32 4 0.07
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (30 bp):
AAGTTCAGGTACCAAATTAGGAAAAAGTTC
Found at i:17996649 original size:18 final size:17
Alignment explanation
Indices: 17996595--17996649 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
17996585 TCCAACTTAT
17996595 TTTTTTAAATT-TATAA
1 TTTTTTAAATTATATAA
* *
17996611 TGTTTTTAAATTATGTTA
1 T-TTTTTAAATTATATAA
*
17996629 TTTTTATATATTATATAA
1 TTTTT-TAAATTATATAA
17996647 TTT
1 TTT
17996650 ATTAGGCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 1 0.03
17 14 0.45
18 16 0.52
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTTTAAATTATATAA
Found at i:17996748 original size:15 final size:15
Alignment explanation
Indices: 17996728--17996779 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
17996718 TAAAATTTTA
17996728 ATAAATTAAAAATAT
1 ATAAATTAAAAATAT
** *
17996743 ATAAATT-ATTATAC
1 ATAAATTAAAAATAT
17996757 ACTAAATTAAAAATAAT
1 A-TAAATTAAAAAT-AT
17996774 ATAAAT
1 ATAAAT
17996780 AATATAGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
14 5 0.18
15 13 0.46
16 8 0.29
17 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATTAAAAATAT
Found at i:17996798 original size:30 final size:30
Alignment explanation
Indices: 17996729--17996785 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17996719 AAAATTTTAA
*
17996729 TAAATTAAAAATATATAAATTATTATACAC
1 TAAATTAAAAATATATAAATTAATATACAC
17996759 TAAATTAAAAATAATATAAA-TAATATA
1 TAAATTAAAAAT-ATATAAATTAATATA
17996786 GATAGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (30 bp):
TAAATTAAAAATATATAAATTAATATACAC
Found at i:17997271 original size:38 final size:38
Alignment explanation
Indices: 17997228--17997315 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 38
17997218 AACACATTAA
17997228 AAATA-TTTA-TACTAAAAAAACAATACCATAAATATAAT
1 AAATATTTTATTA-TAAAAAAA-AATACCATAAATATAAT
**
17997266 AAATATTTTATTATATTAAAAAATACCATAAATATAAT
1 AAATATTTTATTATAAAAAAAAATACCATAAATATAAT
*
17997304 AAATTTTTTATT
1 AAATATTTTATT
17997316 GTATTAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 33 0.73
39 10 0.22
40 2 0.04
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (38 bp):
AAATATTTTATTATAAAAAAAAATACCATAAATATAAT
Found at i:17997321 original size:38 final size:39
Alignment explanation
Indices: 17997244--17997323 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
17997234 TTATACTAAA
17997244 AAAACAATACCATAAATATAATAAATATTTTATTATATT
1 AAAACAATACCATAAATATAATAAATATTTTATTATATT
* *
17997283 AAAA-AATACCATAAATATAATAAATTTTTTATTGTATT
1 AAAACAATACCATAAATATAATAAATATTTTATTATATT
17997321 AAA
1 AAA
17997324 TATGATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 35 0.90
39 4 0.10
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (39 bp):
AAAACAATACCATAAATATAATAAATATTTTATTATATT
Found at i:18002550 original size:28 final size:28
Alignment explanation
Indices: 18002519--18002624 Score: 83
Period size: 30 Copynumber: 3.7 Consensus size: 28
18002509 TGGATACCCG
*
18002519 AGGGCAAAATGGTAATTTTGATGAAATC
1 AGGGAAAAATGGTAATTTTGATGAAATC
* **
18002547 AGGGTTAAAAAT-GAAATTTTTGA-GAGTTC
1 AGGG--AAAAATGGTAA-TTTTGATGAAATC
* *
18002576 GAGGGTAAAATGGTAATTTTGGTGAAATC
1 -AGGGAAAAATGGTAATTTTGATGAAATC
18002605 AGGGTTAAAAATGG-AATTTT
1 AGGG--AAAAATGGTAATTTT
18002625 TAAGAGTTCG
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
28 18 0.30
29 20 0.33
30 22 0.37
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (28 bp):
AGGGAAAAATGGTAATTTTGATGAAATC
Found at i:18002565 original size:29 final size:29
Alignment explanation
Indices: 18002532--18002624 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
18002522 GCAAAATGGT
18002532 AATTTTGATGAAATCAGGGTTAAAAATGA
1 AATTTTGATGAAATCAGGGTTAAAAATGA
** *
18002561 AATTTTTGA-GAGTTCGAGGG-T-AAAATGGT
1 AA-TTTTGATGAAATC-AGGGTTAAAAAT-GA
* *
18002590 AATTTTGGTGAAATCAGGGTTAAAAATGG
1 AATTTTGATGAAATCAGGGTTAAAAATGA
18002619 AATTTT
1 AATTTT
18002625 TAAGAGTTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
28 14 0.27
29 22 0.43
30 15 0.29
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
AATTTTGATGAAATCAGGGTTAAAAATGA
Found at i:18002568 original size:30 final size:30
Alignment explanation
Indices: 18002534--18002625 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
18002524 AAAATGGTAA
18002534 TTTTGATGAAATCAGGGTTAAAAATGAAAT
1 TTTTGATGAAATCAGGGTTAAAAATGAAAT
** *
18002564 TTTTGA-GAGTTCGAGGG-T-AAAATGGTAA-
1 TTTTGATGAAATC-AGGGTTAAAAAT-GAAAT
* *
18002592 TTTTGGTGAAATCAGGGTTAAAAATGGAAT
1 TTTTGATGAAATCAGGGTTAAAAATGAAAT
18002622 TTTT
1 TTTT
18002626 AAGAGTTCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
28 14 0.29
29 16 0.33
30 19 0.39
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
TTTTGATGAAATCAGGGTTAAAAATGAAAT
Found at i:18002644 original size:30 final size:29
Alignment explanation
Indices: 18002561--18002831 Score: 135
Period size: 29 Copynumber: 9.2 Consensus size: 29
18002551 TTAAAAATGA
* *
18002561 AATTTTTGAGAGTTCGAGGGTAAAATGGT
1 AATTTTTAAGAGTTCGGGGGTAAAATGGT
*** ** * *
18002590 AATTTTGGTGAAATCAGGGTTAAAAATGG-
1 AATTTTTAAGAGTTCGGGGGT-AAAATGGT
18002619 AATTTTTAAGAGTTCGGGGGGTAAAATGGT
1 AATTTTTAAGAGTTC-GGGGGTAAAATGGT
** *
18002649 AATTTTTTGTAA-A-ACCGGGGTTAAAATGG-
1 AA--TTTT-TAAGAGTTCGGGGGTAAAATGGT
* *
18002678 AA-TTTTAGAAAGTTCAGGGGTAAAATGGT
1 AATTTTTA-AGAGTTCGGGGGTAAAATGGT
* ** * *
18002707 AATTTTTAGTGAAATCGGGGTTAAAAATAG-
1 AATTTTTA-AGAGTTCGGGGGT-AAAATGGT
*
18002737 AATTTTTAAGAGTTTGGGGGTAAAATGGT
1 AATTTTTAAGAGTTCGGGGGTAAAATGGT
** ** * *
18002766 AATTTTTGGTGAAATCGAGGTTAAAAATGG-
1 AATTTTT-AAGAGTTCGGGGGT-AAAATGGT
* *
18002796 AATTTTGGAA-AGTTCGGGGGTAAAACGGT
1 AATTTT-TAAGAGTTCGGGGGTAAAATGGT
18002825 AATTTTT
1 AATTTTT
18002832 TGGTAAAATC
Statistics
Matches: 175, Mismatches: 50, Indels: 35
0.67 0.19 0.13
Matches are distributed among these distances:
25 2 0.01
26 4 0.02
27 1 0.01
28 24 0.14
29 63 0.36
30 59 0.34
31 14 0.08
32 5 0.03
33 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
AATTTTTAAGAGTTCGGGGGTAAAATGGT
Found at i:18002675 original size:59 final size:59
Alignment explanation
Indices: 18002524--18002861 Score: 434
Period size: 59 Copynumber: 5.7 Consensus size: 59
18002514 ACCCGAGGGC
* * * * *
18002524 AAAATGGTAA-TTTTGATGAAATCAGGGTTAAAAATGAAATTTTTGAGAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTAAGAGTTCGGGGGT
*
18002582 AAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTAAGAGTTCGGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTAAGAGTTC-GGGGGT
* * * * *
18002641 AAAATGGTAATTTTTTGTAAAACCGGGGTT-AAAATGGAA-TTTTAGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTA-AGAGTTCGGGGGT
* * *
18002699 AAAATGGTAATTTTTAGTGAAATCGGGGTTAAAAATAGAATTTTTAAGAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTAAGAGTTCGGGGGT
* *
18002758 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAA-AGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-TAAGAGTTCGGGGGT
* * *
18002817 AAAACGGTAATTTTTTGGTAAAATCGGGGTTAAAAATGGAGTTTT
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT
18002862 GGAAAGTTTG
Statistics
Matches: 247, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
58 86 0.35
59 108 0.44
60 53 0.21
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTAAGAGTTCGGGGGT
Found at i:18002915 original size:29 final size:29
Alignment explanation
Indices: 18002883--18002947 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
18002873 GGATAAAACA
*
18002883 GTAATTTTC-AGAAGTTTCGGGGTCAAAAT
1 GTAATTTTCTA-AAATTTCGGGGTCAAAAT
* *
18002912 GTAATTTTCTAAAATTTTGGGGTCCAAAT
1 GTAATTTTCTAAAATTTCGGGGTCAAAAT
*
18002941 GGAATTT
1 GTAATTT
18002948 CTGGGCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (29 bp):
GTAATTTTCTAAAATTTCGGGGTCAAAAT
Found at i:18004653 original size:6 final size:6
Alignment explanation
Indices: 18004644--18004747 Score: 87
Period size: 6 Copynumber: 18.0 Consensus size: 6
18004634 TAATATCATT
* *
18004644 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* *
18004691 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -TAAAA TTTAAA ATT-AA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
18004736 TTTAAA CTTAAA
1 TTTAAA TTTAAA
18004748 AAATCAAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 51 0.65
7 1 0.01
8 5 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:18004676 original size:11 final size:11
Alignment explanation
Indices: 18004662--18004713 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
18004652 TAATTAAATT
18004662 TAAATTTAAAA
1 TAAATTTAAAA
18004673 TAAATTT-AAA
1 TAAATTTAAAA
*
18004683 TAAA--TAAATT
1 TAAATTTAAA-A
*
18004693 TAAATTTAAGA
1 TAAATTTAAAA
18004704 TAAATTTAAA
1 TAAATTTAAA
18004714 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
8 1 0.03
9 2 0.06
10 11 0.33
11 16 0.48
12 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:18004678 original size:17 final size:16
Alignment explanation
Indices: 18004644--18004735 Score: 125
Period size: 17 Copynumber: 5.7 Consensus size: 16
18004634 TAATATCATT
*
18004644 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
18004660 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
18004677 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
18004691 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
18004708 TTTAAATTTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
18004725 TTTAAAATTAA
1 TTTAAATTTAA
18004736 TTTAAACTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
14 13 0.19
15 1 0.01
16 14 0.20
17 41 0.59
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:18011302 original size:25 final size:25
Alignment explanation
Indices: 18011237--18011302 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
18011227 TGGTCAAAAA
18011237 ATTTA-TTAT-AAAAA--ATAATAT
1 ATTTATTTATAAAAAATTATAATAT
* **
18011258 ACTTATTT-TAAAAGTGTTATAATAT
1 ATTTATTTATAAAA-AATTATAATAT
18011283 ATTTATTTATAAAAAATTAT
1 ATTTATTTATAAAAAATTAT
18011303 GATCAAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
25 18 0.55
26 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
ATTTATTTATAAAAAATTATAATAT
Found at i:18011518 original size:14 final size:14
Alignment explanation
Indices: 18011473--18011520 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
18011463 ATTGAACAAT
*
18011473 TTATAAAATATTAT-
1 TTATAAAGT-TTATA
18011487 TTATAAAGATTATATA
1 TTATAAAG-TT-TATA
18011503 TTATAAAGTTTATA
1 TTATAAAGTTTATA
18011517 TTAT
1 TTAT
18011521 TTTTTACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 16 0.53
15 6 0.20
16 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (14 bp):
TTATAAAGTTTATA
Found at i:18011788 original size:21 final size:22
Alignment explanation
Indices: 18011753--18011803 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
18011743 TAGTGTAAAA
* *
18011753 ATAAAAAATATGAAATGACTAG
1 ATAAAAAAGATGAAAGGACTAG
18011775 ATAAAAAAGA-GAAAGGACTAG
1 ATAAAAAAGATGAAAGGACTAG
18011796 A-AAAAAAG
1 ATAAAAAAG
18011804 TCAACCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 7 0.26
21 11 0.41
22 9 0.33
ACGTcount: A:0.65, C:0.04, G:0.18, T:0.14
Consensus pattern (22 bp):
ATAAAAAAGATGAAAGGACTAG
Found at i:18014006 original size:15 final size:16
Alignment explanation
Indices: 18013981--18014019 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
18013971 ATATTTAATA
18013981 ATTATATTTTAATTTG
1 ATTATATTTTAATTTG
18013997 ATTA-ATTTTAATTT-
1 ATTATATTTTAATTTG
18014011 -TTATATTTT
1 ATTATATTTT
18014020 TCGATTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 5 0.23
15 10 0.45
16 4 0.18
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTATATTTTAATTTG
Found at i:18022773 original size:20 final size:20
Alignment explanation
Indices: 18022735--18022773 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18022725 ATAGGGAATG
* * *
18022735 TATTAAATTAATCATTTTAT
1 TATTAAATAAATAAATTTAT
18022755 TATTAAATAAATAAATTTA
1 TATTAAATAAATAAATTTA
18022774 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAATAAATAAATTTAT
Found at i:18042237 original size:3 final size:3
Alignment explanation
Indices: 18042229--18042253 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18042219 CCTCCTACAT
18042229 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
18042254 GCCAACCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:18051955 original size:50 final size:50
Alignment explanation
Indices: 18051891--18051990 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
18051881 ACCGAATTAA
18051891 TTATCTGAAATTTGAACACCCTAATTTCAAGCAACCGATGAATTTAAATT
1 TTATCTGAAATTTGAACACCCTAATTTCAAGCAACCGATGAATTTAAATT
18051941 TTATCTGAAATTTGAACACCCTAATTTCAAGCAACCGATGAATTTAAATT
1 TTATCTGAAATTTGAACACCCTAATTTCAAGCAACCGATGAATTTAAATT
18051991 GAAATGTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (50 bp):
TTATCTGAAATTTGAACACCCTAATTTCAAGCAACCGATGAATTTAAATT
Found at i:18053750 original size:2 final size:2
Alignment explanation
Indices: 18053737--18053769 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
18053727 AATAGATTCC
*
18053737 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
18053770 GTTTTCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:18060417 original size:2 final size:2
Alignment explanation
Indices: 18060410--18060445 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18060400 AGAAGAAAAC
18060410 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
18060446 GGAATCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18062254 original size:13 final size:13
Alignment explanation
Indices: 18062238--18062264 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18062228 ACATGTAGTG
18062238 ACAACACAGGTGT
1 ACAACACAGGTGT
18062251 ACAACACAGGTGT
1 ACAACACAGGTGT
18062264 A
1 A
18062265 GTAGGAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (13 bp):
ACAACACAGGTGT
Found at i:18066720 original size:34 final size:34
Alignment explanation
Indices: 18066677--18066743 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
18066667 CCGTAAAGGA
18066677 ATATCATGTTGGAATAGTGGCAACCTAGTTAATT
1 ATATCATGTTGGAATAGTGGCAACCTAGTTAATT
18066711 ATATCATGTTGGAATAGTGGCAACCTAGTTAAT
1 ATATCATGTTGGAATAGTGGCAACCTAGTTAAT
18066744 GCATTGACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (34 bp):
ATATCATGTTGGAATAGTGGCAACCTAGTTAATT
Found at i:18069887 original size:22 final size:24
Alignment explanation
Indices: 18069836--18069896 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
18069826 AGGTGTCAAA
*
18069836 ATTAAATTATAATTTTTATGATAGC
1 ATTAAATTATAATTTTTA-GAAAGC
18069861 A--AAATTATAATTTTTA-AAAG-
1 ATTAAATTATAATTTTTAGAAAGC
*
18069881 ATTAAATTAAAATTTT
1 ATTAAATTATAATTTT
18069897 ATCATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 12 0.38
23 15 0.47
25 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (24 bp):
ATTAAATTATAATTTTTAGAAAGC
Found at i:18069905 original size:30 final size:30
Alignment explanation
Indices: 18069865--18069929 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
18069855 GATAGCAAAA
* *
18069865 TTATAATTTTTAAAAGATTAAATTAAAATT
1 TTATCATTTTTAAAAGATCAAATTAAAATT
** * *
18069895 TTATCATTTTTAGGAGGTCAAATTACAATT
1 TTATCATTTTTAAAAGATCAAATTAAAATT
18069925 TTATC
1 TTATC
18069930 TTTACTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (30 bp):
TTATCATTTTTAAAAGATCAAATTAAAATT
Found at i:18079181 original size:7 final size:7
Alignment explanation
Indices: 18079131--18079362 Score: 79
Period size: 7 Copynumber: 33.6 Consensus size: 7
18079121 AATTTGATAA
18079131 GTTTAGG
1 GTTTAGG
*
18079138 GCTTAGG
1 GTTTAGG
*
18079145 GCTTAGG
1 GTTTAGG
*
18079152 GCTTAGG
1 GTTTAGG
*
18079159 GCTTAGG
1 GTTTAGG
18079166 GTTTAGG
1 GTTTAGG
18079173 GTTTAGG
1 GTTTAGG
* *
18079180 GTCTCAAG
1 GT-TTAGG
*
18079188 TTTTA--
1 GTTTAGG
*
18079193 ATTTAGG
1 GTTTAGG
18079200 GTTTAGG
1 GTTTAGG
*
18079207 GTTTCAAG
1 GTTT-AGG
*
18079215 TTTTA--
1 GTTTAGG
*
18079220 ATTTAGG
1 GTTTAGG
18079227 GTTTAGG
1 GTTTAGG
*
18079234 GTTTCGAG
1 GTTTAG-G
*
18079242 TTTTA--
1 GTTTAGG
* *
18079247 ATTTAAG
1 GTTTAGG
18079254 GTTTAGG
1 GTTTAGG
*
18079261 GTTTCA-A
1 GTTT-AGG
18079268 GTTCTA--
1 GTT-TAGG
* *
18079274 ATTTAAG
1 GTTTAGG
18079281 GTTTAGG
1 GTTTAGG
18079288 GTTTAGG
1 GTTTAGG
*
18079295 GTTTAAGA
1 GTTT-AGG
*
18079303 TTTTAGG
1 GTTTAGG
*
18079310 GTTTAAGA
1 GTTT-AGG
*
18079318 TTTTAGG
1 GTTTAGG
*
18079325 GTTTA-A
1 GTTTAGG
* *
18079331 GATTAAG
1 GTTTAGG
18079338 GTTTAGG
1 GTTTAGG
* *
18079345 ATTTAGT
1 GTTTAGG
*
18079352 GTTTAAG
1 GTTTAGG
18079359 GTTT
1 GTTT
18079363 TATGTTTGAA
Statistics
Matches: 169, Mismatches: 40, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
5 14 0.08
6 6 0.04
7 124 0.73
8 25 0.15
ACGTcount: A:0.22, C:0.04, G:0.30, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:18079201 original size:27 final size:27
Alignment explanation
Indices: 18079167--18079291 Score: 205
Period size: 27 Copynumber: 4.6 Consensus size: 27
18079157 GGGCTTAGGG
*
18079167 TTTAGGGTTTAGGGTCTCAAGTTTTAA
1 TTTAGGGTTTAGGGTTTCAAGTTTTAA
18079194 TTTAGGGTTTAGGGTTTCAAGTTTTAA
1 TTTAGGGTTTAGGGTTTCAAGTTTTAA
*
18079221 TTTAGGGTTTAGGGTTTCGAGTTTTAA
1 TTTAGGGTTTAGGGTTTCAAGTTTTAA
* *
18079248 TTTAAGGTTTAGGGTTTCAAGTTCTAA
1 TTTAGGGTTTAGGGTTTCAAGTTTTAA
*
18079275 TTTAAGGTTTAGGGTTT
1 TTTAGGGTTTAGGGTTT
18079292 AGGGTTTAAG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (27 bp):
TTTAGGGTTTAGGGTTTCAAGTTTTAA
Found at i:18079309 original size:15 final size:15
Alignment explanation
Indices: 18079289--18079364 Score: 95
Period size: 15 Copynumber: 5.3 Consensus size: 15
18079279 AGGTTTAGGG
18079289 TTTAGGGTTTAAGAT
1 TTTAGGGTTTAAGAT
18079304 TTTAGGGTTTAAGAT
1 TTTAGGGTTTAAGAT
18079319 TTTAGGGTTTAAGA-
1 TTTAGGGTTTAAGAT
* *
18079333 -TTAAGGTTTAGGA-
1 TTTAGGGTTTAAGAT
* *
18079346 TTTAGTGTTTAAGGT
1 TTTAGGGTTTAAGAT
18079361 TTTA
1 TTTA
18079365 TGTTTGAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
13 11 0.21
14 9 0.17
15 33 0.62
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (15 bp):
TTTAGGGTTTAAGAT
Found at i:18079396 original size:27 final size:28
Alignment explanation
Indices: 18079366--18079568 Score: 62
Period size: 35 Copynumber: 6.9 Consensus size: 28
18079356 AAGGTTTTAT
18079366 GTTTGA-AGTTCTAATTTAGGGTTTAAG
1 GTTTGATAGTTCTAATTTAGGGTTTAAG
*
18079393 GTTTTAGGACTTTAGGTTCCAATTTAGGGTTTAAG
1 G-TTT--GA---TA-GTTCTAATTTAGGGTTTAAG
*
18079428 GTTTTTGGACTATAGGTTCCAATTTAGGGTTTAAG
1 G--TTT-G---ATA-GTTCTAATTTAGGGTTTAAG
* * *
18079463 GTTTTTG-GACTT-TAATTTAGGATTT-AG
1 G--TTTGATAGTTCTAATTTAGGGTTTAAG
*
18079490 GTTT--TAGGTTCTAGTTTAGGGTTTAAG
1 GTTTGATA-GTTCTAATTTAGGGTTTAAG
* ** * *
18079517 ATTT-AGGGTTTTAATTTAGGATTT-AG
1 GTTTGATAGTTCTAATTTAGGGTTTAAG
* * * *
18079543 GTTTTAGAGTTTTGATTTAGGGTTTA
1 GTTTGATAGTTCTAATTTAGGGTTTA
18079569 GGATTTAGGG
Statistics
Matches: 139, Mismatches: 19, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
24 1 0.01
25 5 0.04
26 16 0.12
27 40 0.29
28 14 0.10
29 2 0.01
30 3 0.02
34 2 0.01
35 51 0.37
36 4 0.03
38 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.26, T:0.47
Consensus pattern (28 bp):
GTTTGATAGTTCTAATTTAGGGTTTAAG
Found at i:18079400 original size:15 final size:15
Alignment explanation
Indices: 18079275--18079400 Score: 82
Period size: 15 Copynumber: 8.4 Consensus size: 15
18079265 CAAGTTCTAA
* *
18079275 TTTAAGGTTT-AGGG
1 TTTAGGGTTTAAGGT
*
18079289 TTTAGGGTTTAAGAT
1 TTTAGGGTTTAAGGT
*
18079304 TTTAGGGTTTAAGAT
1 TTTAGGGTTTAAGGT
18079319 TTTAGGGTTTAA-G-
1 TTTAGGGTTTAAGGT
* * *
18079332 ATTAAGGTTT-AGGA
1 TTTAGGGTTTAAGGT
*
18079346 TTTAGTGTTTAAGGT
1 TTTAGGGTTTAAGGT
* *
18079361 TTTA-TGTTTGAAGTTCT
1 TTTAGGGTTT-AAG--GT
18079378 AATTTAGGGTTTAAGGT
1 --TTTAGGGTTTAAGGT
18079395 TTTAGG
1 TTTAGG
18079401 ACTTTAGGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 19
0.74 0.11 0.16
Matches are distributed among these distances:
12 1 0.01
13 9 0.10
14 21 0.24
15 45 0.51
17 2 0.02
19 7 0.08
20 4 0.04
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.47
Consensus pattern (15 bp):
TTTAGGGTTTAAGGT
Found at i:18079420 original size:20 final size:20
Alignment explanation
Indices: 18079395--18079455 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
18079385 GGTTTAAGGT
18079395 TTTAGGACTTTAGGTTCCAA
1 TTTAGGACTTTAGGTTCCAA
*
18079415 TTTAGG-GTTTAAGGTT----
1 TTTAGGACTTT-AGGTTCCAA
*
18079431 TTT-GGACTATAGGTTCCAA
1 TTTAGGACTTTAGGTTCCAA
18079450 TTTAGG
1 TTTAGG
18079456 GTTTAAGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
19 6 0.19
20 13 0.42
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.43
Consensus pattern (20 bp):
TTTAGGACTTTAGGTTCCAA
Found at i:18079424 original size:35 final size:35
Alignment explanation
Indices: 18079345--18079476 Score: 178
Period size: 35 Copynumber: 3.8 Consensus size: 35
18079335 AAGGTTTAGG
* * * *
18079345 ATTTAGTGTTTAAGGTTTTATG--TTTGAAGTTCTA
1 ATTTAGGGTTTAAGGTTTTAGGACTTT-AGGTTCCA
18079379 ATTTAGGGTTTAAGGTTTTAGGACTTTAGGTTCCA
1 ATTTAGGGTTTAAGGTTTTAGGACTTTAGGTTCCA
* *
18079414 ATTTAGGGTTTAAGGTTTTTGGACTATAGGTTCCA
1 ATTTAGGGTTTAAGGTTTTAGGACTTTAGGTTCCA
*
18079449 ATTTAGGGTTTAAGGTTTTTGGACTTTA
1 ATTTAGGGTTTAAGGTTTTAGGACTTTA
18079477 ATTTAGGATT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
34 20 0.22
35 66 0.74
36 3 0.03
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.47
Consensus pattern (35 bp):
ATTTAGGGTTTAAGGTTTTAGGACTTTAGGTTCCA
Found at i:18079488 original size:35 final size:35
Alignment explanation
Indices: 18079378--18079499 Score: 138
Period size: 35 Copynumber: 3.5 Consensus size: 35
18079368 TTGAAGTTCT
* ** *
18079378 AATTTAGGGTTTAAGGTTTTAGGACTTTAGGTTCC
1 AATTTAGGGTTTAAGGTTTTTGGACTTTAATTTAC
* ** *
18079413 AATTTAGGGTTTAAGGTTTTTGGACTATAGGTTCC
1 AATTTAGGGTTTAAGGTTTTTGGACTTTAATTTAC
*
18079448 AATTTAGGGTTTAAGGTTTTTGGACTTTAATTTAG
1 AATTTAGGGTTTAAGGTTTTTGGACTTTAATTTAC
* *
18079483 GATTTA-GGTTTTAGGTT
1 AATTTAGGGTTTAAGGTT
18079500 CTAGTTTAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
34 10 0.13
35 68 0.87
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46
Consensus pattern (35 bp):
AATTTAGGGTTTAAGGTTTTTGGACTTTAATTTAC
Found at i:18079488 original size:70 final size:69
Alignment explanation
Indices: 18079339--18079499 Score: 175
Period size: 70 Copynumber: 2.3 Consensus size: 69
18079329 AAGATTAAGG
* * *
18079339 TTTAGGATTTAGTGTTTAAGGTTTTATGTTTGAAGTTCTAATTTAGGGTTTAAGGTTTTAGGACT
1 TTTAGGATTTAGGGTTTAAGGTTTTATGTATGAAGTTCCAATTTAGGGTTTAAGGTTTTAGGACT
*
18079404 TTAG
66 TTAA
* *** * *
18079408 GTTCCAATTTAGGGTTTAAGGTTTT-TGGACTAT-AGGTTCCAATTTAGGGTTTAAGGTTTTTGG
1 TTTAGGATTTAGGGTTTAAGGTTTTAT-G--TATGAAGTTCCAATTTAGGGTTTAAGGTTTTAGG
18079471 ACTTTAA
63 ACTTTAA
*
18079478 TTTAGGATTTA-GGTTTTAGGTT
1 TTTAGGATTTAGGGTTTAAGGTT
18079500 CTAGTTTAGG
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
68 1 0.01
69 31 0.42
70 40 0.54
71 2 0.03
ACGTcount: A:0.22, C:0.05, G:0.25, T:0.48
Consensus pattern (69 bp):
TTTAGGATTTAGGGTTTAAGGTTTTATGTATGAAGTTCCAATTTAGGGTTTAAGGTTTTAGGACT
TTAA
Found at i:18079489 original size:7 final size:7
Alignment explanation
Indices: 18079477--18079577 Score: 63
Period size: 7 Copynumber: 15.0 Consensus size: 7
18079467 TTGGACTTTA
18079477 ATTTAGG
1 ATTTAGG
18079484 ATTTAGG
1 ATTTAGG
*
18079491 TTTTAGG
1 ATTTAGG
18079498 -TTCTA-G
1 ATT-TAGG
18079504 -TTTAGG
1 ATTTAGG
* *
18079510 GTTTAAG
1 ATTTAGG
18079517 ATTTAGGG
1 ATTTA-GG
*
18079525 TTTTA--
1 ATTTAGG
18079530 ATTTAGG
1 ATTTAGG
18079537 ATTTAGG
1 ATTTAGG
*
18079544 TTTTA-G
1 ATTTAGG
*
18079550 AGTTT-TG
1 A-TTTAGG
18079557 ATTTAGG
1 ATTTAGG
*
18079564 GTTTAGG
1 ATTTAGG
18079571 ATTTAGG
1 ATTTAGG
18079578 GTTTTAATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
5 6 0.08
6 10 0.14
7 53 0.72
8 5 0.07
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.49
Consensus pattern (7 bp):
ATTTAGG
Found at i:18079497 original size:14 final size:13
Alignment explanation
Indices: 18079473--18079593 Score: 72
Period size: 14 Copynumber: 9.2 Consensus size: 13
18079463 GTTTTTGGAC
*
18079473 TTTA-ATTTAGGA
1 TTTAGATTTAGGT
*
18079485 TTTAGGTTTTAGGT
1 TTTA-GATTTAGGT
*
18079499 TCTAG-TTTAGGGT
1 TTTAGATTTA-GGT
*
18079512 TTAAGATTTAGGGT
1 TTTAGATTTA-GGT
*
18079526 TTTA-ATTTAGGA
1 TTTAGATTTAGGT
*
18079538 TTTAGGTTTTAGAGT
1 TTTA-GATTTAG-GT
*
18079553 TTT-GATTTAGGG
1 TTTAGATTTAGGT
18079565 TTTAGGATTTAGGGT
1 TTTA-GATTTA-GGT
*
18079580 TTTA-ATTTGGGT
1 TTTAGATTTAGGT
18079592 TT
1 TT
18079594 AGGGTTTACG
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
12 23 0.27
13 22 0.26
14 31 0.36
15 10 0.12
ACGTcount: A:0.21, C:0.01, G:0.26, T:0.51
Consensus pattern (13 bp):
TTTAGATTTAGGT
Found at i:18079539 original size:20 final size:20
Alignment explanation
Indices: 18079511--18079600 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
18079501 TAGTTTAGGG
*
18079511 TTTAAGATTTAGGGTTTTAA
1 TTTAGGATTTAGGGTTTTAA
18079531 TTTAGGATTTA-GGTTTTAGA
1 TTTAGGATTTAGGGTTTTA-A
*
18079551 GTTT-TGATTTAGGG------
1 -TTTAGGATTTAGGGTTTTAA
18079565 TTTAGGATTTAGGGTTTTAA
1 TTTAGGATTTAGGGTTTTAA
*
18079585 TTT-GGGTTTAGGGTTT
1 TTTAGGATTTAGGGTTT
18079601 ACGGTTTATG
Statistics
Matches: 56, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 19 0.34
20 20 0.36
21 5 0.09
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (20 bp):
TTTAGGATTTAGGGTTTTAA
Found at i:18079569 original size:27 final size:26
Alignment explanation
Indices: 18079448--18079607 Score: 160
Period size: 27 Copynumber: 6.0 Consensus size: 26
18079438 TATAGGTTCC
* *
18079448 AATTTAGGGTTTAAGGTTTTTGGACTTT
1 AATTTAGGGTTT-AGGTTTTAGG-TTTT
* *
18079476 AATTTAGGATTTAGGTTTTAGGTTCT
1 AATTTAGGGTTTAGGTTTTAGGTTTT
* * *
18079502 AGTTTAGGGTTTAAGATTTAGGGTTTT
1 AATTTAGGGTTTAGGTTTTA-GGTTTT
*
18079529 AATTTAGGATTTAGGTTTTAGAGTTTT
1 AATTTAGGGTTTAGGTTTTAG-GTTTT
* *
18079556 GATTTAGGGTTTAGGATTTAGGGTTTT
1 AATTTAGGGTTTAGGTTTTA-GGTTTT
*
18079583 AATTT-GGGTTTAGGGTTTACGGTTT
1 AATTTAGGGTTTAGGTTTTA-GGTTT
18079608 ATGGTAATGA
Statistics
Matches: 110, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
26 37 0.34
27 61 0.55
28 12 0.11
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (26 bp):
AATTTAGGGTTTAGGTTTTAGGTTTT
Found at i:18079600 original size:7 final size:7
Alignment explanation
Indices: 18079478--18079608 Score: 55
Period size: 7 Copynumber: 19.6 Consensus size: 7
18079468 TGGACTTTAA
*
18079478 TTTAGGA
1 TTTAGGG
*
18079485 TTTAGGT
1 TTTAGGG
18079492 TTTA-GG
1 TTTAGGG
18079498 TTCTA--G
1 TT-TAGGG
18079504 TTTAGGG
1 TTTAGGG
* *
18079511 TTTAAGA
1 TTTAGGG
18079518 TTTAGGG
1 TTTAGGG
*
18079525 TTTTA--A
1 -TTTAGGG
*
18079531 TTTAGGA
1 TTTAGGG
*
18079538 TTTAGGT
1 TTTAGGG
*
18079545 TTTAGAG
1 TTTAGGG
* *
18079552 TTT-TGA
1 TTTAGGG
18079558 TTTAGGG
1 TTTAGGG
*
18079565 TTTAGGA
1 TTTAGGG
18079572 TTTAGGG
1 TTTAGGG
*
18079579 TTTTA--A
1 -TTTAGGG
18079585 TTT-GGG
1 TTTAGGG
18079591 TTTAGGG
1 TTTAGGG
*
18079598 TTTACGG
1 TTTAGGG
18079605 TTTA
1 TTTA
18079609 TGGTAATGAT
Statistics
Matches: 93, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
5 9 0.10
6 12 0.13
7 64 0.69
8 8 0.09
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:18080940 original size:5 final size:5
Alignment explanation
Indices: 18080932--18080965 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
18080922 TAAATTAATA
18080932 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCT
18080966 AGGCAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:18081428 original size:40 final size:41
Alignment explanation
Indices: 18081376--18081454 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
18081366 CAAATTTTTG
*
18081376 GTTCTAGAATCTTCA-TTAGACAATCAAACCTCCAAATTTA
1 GTTCTAGAATCTTCACTTAAACAATCAAACCTCCAAATTTA
18081416 GTTCTA-AGATCTTCACTTAAACAATCAAACCTCCAAATT
1 GTTCTAGA-ATCTTCACTTAAACAATCAAACCTCCAAATT
18081455 AGATAGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 1 0.03
40 13 0.36
41 22 0.61
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (41 bp):
GTTCTAGAATCTTCACTTAAACAATCAAACCTCCAAATTTA
Found at i:18081967 original size:3 final size:3
Alignment explanation
Indices: 18081959--18081987 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18081949 CGACATCATT
18081959 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
18081988 TGTTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:18083189 original size:29 final size:30
Alignment explanation
Indices: 18083136--18083216 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
18083126 AAATTGAATC
* *
18083136 AAATCAAAATATTATGTATAAAATTACACA-
1 AAATCAAAAT-TCATATATAAAATTACACAT
* *
18083166 AAATCAAAATTCATATATATAATTATACATT
1 AAATCAAAATTCATATATAAAATTACACA-T
* *
18083197 AAATCATAGTTCATATATAA
1 AAATCAAAATTCATATATAA
18083217 TTTTGATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.36
30 10 0.24
31 17 0.40
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTCATATATAAAATTACACAT
Found at i:18085730 original size:27 final size:25
Alignment explanation
Indices: 18085680--18085744 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
18085670 ATCCCGACTT
*
18085680 ATAGCTCGTGTGAGCAGGTCCATTTTC
1 ATAGCTCGTGTGAGCAGGTACA--TTC
**
18085707 ATAGCTCGTGTGAGCATTTACATTC
1 ATAGCTCGTGTGAGCAGGTACATTC
*
18085732 ATGGCTCGTGTGA
1 ATAGCTCGTGTGA
18085745 AAATTGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 15 0.44
27 19 0.56
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (25 bp):
ATAGCTCGTGTGAGCAGGTACATTC
Done.