Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold494
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: 556777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:453170 original size:60 final size:61
Alignment explanation
Indices: 453076--453267 Score: 199
Period size: 60 Copynumber: 3.1 Consensus size: 61
453066 ACCTTTTTCT
* * *
453076 TTTTAAAGCCCACAACTCTGTAGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA-CCC
1 TTTT-AAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCC
* *
453138 TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCTACAACTCTGTGGCACCTTGTTC
1 TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC-----C
453203 C
61 C
* * * * * * *
453204 TTTTAAGTCCACAACTCCATGGCA-CCTTGTCTTTTTAAGTTCACGACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCC
453264 TTTT
1 TTTT
453268 TCCTGTAAGT
Statistics
Matches: 110, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
60 37 0.34
61 18 0.16
62 4 0.04
65 26 0.24
66 25 0.23
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (61 bp):
TTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCC
Found at i:453173 original size:33 final size:33
Alignment explanation
Indices: 453041--453298 Score: 271
Period size: 33 Copynumber: 7.9 Consensus size: 33
453031 TCTGTGGCAC
* *
453041 CCTTTTAAGTCCACAATTCCATGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * * *
453074 CTTTTTAAAGCCCACAACTCTGTAGCACTCTTTTT
1 CCTTTT-AAGTCCACAACTCCGTGGCAC-CTTTTT
453109 CCTTTTAAGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
*
453136 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
453169 CCTTTTAAGTCTACAACTCTGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
453202 CCTTTTAAGTCCACAACTCCATGGCACC-TTGT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
453234 CTTTTTAAGTTCACGACTCCGTGGCATCCCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA--CCTTTTT
* *
453269 CC-TGTAAGTCCATAACTCCGTGGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTT
453299 AAGTCCAACA
Statistics
Matches: 185, Mismatches: 29, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
27 26 0.14
28 1 0.01
32 30 0.16
33 59 0.32
34 54 0.29
35 15 0.08
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:453370 original size:49 final size:49
Alignment explanation
Indices: 453295--453762 Score: 374
Period size: 49 Copynumber: 10.0 Consensus size: 49
453285 TCCGTGGCAC
* * *
453295 CTTTAAGTCCAACATCGCTGGCCTTGAATCAACATATTGGCACCTTTAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * * *
453344 CTTTAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGGCACCTTTA-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * *
453392 ----AA-TCTAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * *
453436 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA-C-----
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * *
453479 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * * * *
453528 CATCTTGAGCCCAATATCACTGGCCTTGAATTAGCATATTGGCACC-TTGT
1 C-T-TTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * * * *
453578 CTCTAAGACCAATGTCGATGGCCTTGAATCAACACATTGG---C---A-
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * * *
453620 ---TAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATC-TTGT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * * * *
453665 CTTTAAGACTAATGTCGCTAGGCCTTGAATCAGCACATTGGCACATTCAT
1 CTTTAAGACCAATATCGCT-GGCCTTGAATCAGCATATTGGCACCTTTAT
* * * *
453715 CTTTAAG-CTAGATATCACTGGCCTTGAATCAGCAGATTGGCATCTTTA
1 CTTTAAGACCA-ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
453763 ACATTCCTAA
Statistics
Matches: 329, Mismatches: 64, Indels: 52
0.74 0.14 0.12
Matches are distributed among these distances:
39 31 0.09
42 1 0.00
43 71 0.22
44 3 0.01
45 1 0.00
48 44 0.13
49 122 0.37
50 19 0.06
51 37 0.11
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
Found at i:453446 original size:92 final size:92
Alignment explanation
Indices: 453289--453575 Score: 412
Period size: 92 Copynumber: 3.1 Consensus size: 92
453279 CATAACTCCG
* *
453289 TGGCACCTTTAAGTCCAACATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGACC
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
**
453354 AATGTTGCTAGCCTTGAATCAGCACAT
66 AATGTCACTAGCCTTGAATCAGCACAT
* * *
453381 TGGCACCTTTAAATCTAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTATCTTTAAGACC
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
*
453446 AATGTCACTGGCCTTGAATCAGCACAT
66 AATGTCACTAGCCTTGAATCAGCACAT
* * * *
453473 TGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTGAGC
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-T-TTAAGA
* * * *
453538 CCAATATCACTGGCCTTGAATTAGCATAT
64 CCAATGTCACTAGCCTTGAATCAGCACAT
453567 TGGCACCTT
1 TGGCACCTT
453576 GTCTCTAAGA
Statistics
Matches: 175, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
92 135 0.77
93 1 0.01
94 39 0.22
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACC
AATGTCACTAGCCTTGAATCAGCACAT
Found at i:453481 original size:21 final size:21
Alignment explanation
Indices: 453457--453524 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
453447 ATGTCACTGG
453457 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
453478 CCTTTAAGTCCAATATCGTTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
453500 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
453521 CCTT
1 CCTT
453525 TACCATCTTG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.33
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:453681 original size:87 final size:88
Alignment explanation
Indices: 453535--453707 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 88
453525 TACCATCTTG
*
453535 AGCCCAATATCACTGGCCTTGAATTAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGAT-GG
1 AGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGATAGG
453599 CCTTGAATCAACACATTGGCATA
66 CCTTGAATCAACACATTGGCATA
* * * * * *
453622 AGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTGTCTTTAAGACTAATGTCGCTAGG
1 AGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGATAGG
*
453687 CCTTGAATCAGCACATTGGCA
66 CCTTGAATCAACACATTGGCA
453708 CATTCATCTT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 55 0.71
88 22 0.29
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (88 bp):
AGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGATAGG
CCTTGAATCAACACATTGGCATA
Found at i:459834 original size:95 final size:91
Alignment explanation
Indices: 459639--459817 Score: 232
Period size: 95 Copynumber: 1.9 Consensus size: 91
459629 AAATACTTGC
*
459639 TTTGCATGAATGTTTGAACATGTTATGAATTAAAACACCTAGAATGAATCAATCTTAACTCATAG
1 TTTGCATGAATCTTTGAACATGTTATGAATTAAAACACCTAGAATGAATCAATCTTAACTCATAG
*
459704 TTCATAATGTTTATACTTGAAATACTTA
66 TTCATAATGCTTATACTTG-AATA-TTA
* *
459732 CTTTGCATTAATCTTTGAACATGTCTATGAATTAAAACACCTTGAATGAATCAACCTTGACTTAA
1 -TTTGCATGAATCTTTGAACATGT-TATGAATTAAAACACCTAGAATGAATCAA---T--CTTAA
*
459797 CTTATAGTTCATAATGCTTAT
59 CTCATAGTTCATAATGCTTAT
459818 GTTTGATTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
94 21 0.28
95 28 0.38
98 1 0.01
100 24 0.32
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (91 bp):
TTTGCATGAATCTTTGAACATGTTATGAATTAAAACACCTAGAATGAATCAATCTTAACTCATAG
TTCATAATGCTTATACTTGAATATTA
Found at i:462598 original size:13 final size:13
Alignment explanation
Indices: 462580--462605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
462570 CAATTTTTTG
462580 TGTATCGATACAT
1 TGTATCGATACAT
462593 TGTATCGATACAT
1 TGTATCGATACAT
462606 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:462620 original size:32 final size:33
Alignment explanation
Indices: 462560--462623 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
462550 TACAAGCCAA
** *
462560 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
462593 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
462624 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:464719 original size:21 final size:20
Alignment explanation
Indices: 464690--464732 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
464680 GACTAGTGTG
**
464690 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTTACGACCT
*
464711 GGGAGTGCCGGTTACGACCT
1 GGGACTGCCGGTTACGACCT
464731 GG
1 GG
464733 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.42, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGGTTACGACCT
Found at i:465183 original size:13 final size:13
Alignment explanation
Indices: 465165--465202 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
465155 ATAATCCCTC
465165 TGTATCGATACAG
1 TGTATCGATACAG
*
465178 TGTATCGATACAT
1 TGTATCGATACAG
465191 TGTATCGATACA
1 TGTATCGATACA
465203 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:467306 original size:15 final size:15
Alignment explanation
Indices: 467286--467316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
467276 ATTTCGTTTG
*
467286 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
467301 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
467316 G
1 G
467317 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:469147 original size:21 final size:21
Alignment explanation
Indices: 469118--469162 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
469108 AAGTTTTTAT
*
469118 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
469138 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
469160 TTT
1 TTT
469163 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:471089 original size:32 final size:30
Alignment explanation
Indices: 471053--471111 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
471043 GAAATCAAAT
471053 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
471085 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
471112 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:471410 original size:13 final size:13
Alignment explanation
Indices: 471392--471417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
471382 CAATTTTTTG
471392 TGTATCGATACAT
1 TGTATCGATACAT
471405 TGTATCGATACAT
1 TGTATCGATACAT
471418 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:471432 original size:32 final size:33
Alignment explanation
Indices: 471372--471435 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
471362 TACAAGCCAA
** *
471372 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
471405 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
471436 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:473063 original size:31 final size:30
Alignment explanation
Indices: 473027--473093 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
473017 AAAACTCTCC
* *
473027 ATTATT-TACTTTTTTTTAAGAAATTAAAATT
1 ATTATTGTACATTTATTT-AGAAATT-AAATT
* *
473058 ATTATTGTAGATTTATTTATAAATTAAATT
1 ATTATTGTACATTTATTTAGAAATTAAATT
473088 ATTATT
1 ATTATT
473094 AAAAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 11 0.35
31 12 0.39
32 8 0.26
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (30 bp):
ATTATTGTACATTTATTTAGAAATTAAATT
Found at i:473226 original size:22 final size:24
Alignment explanation
Indices: 473179--473249 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 24
473169 TTATTTTAAT
473179 TAATATTTATAATTTAAATAAAAA
1 TAATATTTATAATTTAAATAAAAA
*
473203 TAATATTT-T-ATTT-ATTAAATAA
1 TAATATTTATAATTTAAATAAA-AA
*
473225 TAAT-TTTAATCAAATTAAATAAAAA
1 TAATATTT-AT-AATTTAAATAAAAA
473250 ATATAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
21 8 0.21
22 10 0.26
23 2 0.05
24 8 0.21
25 5 0.13
26 5 0.13
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATATTTATAATTTAAATAAAAA
Found at i:479241 original size:23 final size:23
Alignment explanation
Indices: 479212--479257 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
479202 TTCAGACCCT
*
479212 CTTGTTGCATAACATATGATTCA
1 CTTGTTGCAAAACATATGATTCA
*
479235 CTTGTTGCAAAACATATGTTTCA
1 CTTGTTGCAAAACATATGATTCA
479258 ACTGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
CTTGTTGCAAAACATATGATTCA
Found at i:483567 original size:2 final size:2
Alignment explanation
Indices: 483560--483586 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
483550 GTTTTTACAT
483560 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
483587 TAGGATCTGC
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:484901 original size:7 final size:7
Alignment explanation
Indices: 484889--484923 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
484879 AAGTATGGAA
484889 CCAATCT
1 CCAATCT
484896 CCAATCT
1 CCAATCT
484903 CCAATCT
1 CCAATCT
484910 CCAATCT
1 CCAATCT
484917 CCAATCT
1 CCAATCT
484924 AAATCAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (7 bp):
CCAATCT
Found at i:491985 original size:16 final size:16
Alignment explanation
Indices: 491964--491994 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
491954 GAAGAATTTG
491964 TTTATAACTTGATAAA
1 TTTATAACTTGATAAA
*
491980 TTTATAAGTTGATAA
1 TTTATAACTTGATAA
491995 TAAAATTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (16 bp):
TTTATAACTTGATAAA
Found at i:492132 original size:13 final size:13
Alignment explanation
Indices: 492114--492141 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
492104 GGGCTGGTCT
492114 CCCTCTTCCATTG
1 CCCTCTTCCATTG
492127 CCCTCTTCCATTG
1 CCCTCTTCCATTG
492140 CC
1 CC
492142 TTACAACTCA
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:0.07, C:0.50, G:0.07, T:0.36
Consensus pattern (13 bp):
CCCTCTTCCATTG
Found at i:492787 original size:20 final size:20
Alignment explanation
Indices: 492762--492866 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
492752 TTTTTACCCA
492762 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
492782 AATGTATCGATACATTCTGTCTTTTACTC
1 AATGTATCGATACA-------TTTT--TC
*
492811 AGATGTATCGATATATTTTTC
1 A-ATGTATCGATACATTTTTC
* *
492832 GATGAATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
492852 AATGTATCGATACAT
1 AATGTATCGATACAT
492867 GTATGAGTTG
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
20 44 0.64
21 2 0.03
23 4 0.06
27 4 0.06
29 3 0.04
30 12 0.17
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:492829 original size:50 final size:50
Alignment explanation
Indices: 492753--492847 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
492743 AAAGTCATAT
*
492753 TTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC
1 TTTTACCCAAATGTATCGATACATTTTTCAATGAATCGATACATTCTGTC
* * * *
492803 TTTTACTCAGATGTATCGATATATTTTTCGATGAATCGATACATT
1 TTTTACCCAAATGTATCGATACATTTTTCAATGAATCGATACATT
492848 TTTCAATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (50 bp):
TTTTACCCAAATGTATCGATACATTTTTCAATGAATCGATACATTCTGTC
Found at i:493279 original size:24 final size:24
Alignment explanation
Indices: 493247--493292 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
493237 AACATAACAG
493247 TTTTTTTTTCCATTAAGAAACAAT
1 TTTTTTTTTCCATTAAGAAACAAT
493271 TTTTTTTTTCCATTAAGAAACA
1 TTTTTTTTTCCATTAAGAAACA
493293 TCATTAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTTTTTTCCATTAAGAAACAAT
Found at i:493328 original size:17 final size:17
Alignment explanation
Indices: 493306--493338 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
493296 TTAAGGTTAC
493306 CGTTTTTAGATGAAAAG
1 CGTTTTTAGATGAAAAG
*
493323 CGTTTTTTGATGAAAA
1 CGTTTTTAGATGAAAA
493339 CAATTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (17 bp):
CGTTTTTAGATGAAAAG
Found at i:496952 original size:13 final size:13
Alignment explanation
Indices: 496934--496959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
496924 TACAGCAAGT
496934 ATGTATCGATACA
1 ATGTATCGATACA
496947 ATGTATCGATACA
1 ATGTATCGATACA
496960 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:499219 original size:21 final size:21
Alignment explanation
Indices: 499186--499230 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
499176 TTGCAAGTTG
*
499186 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
499208 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
499228 AAA
1 AAA
499231 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:501054 original size:15 final size:15
Alignment explanation
Indices: 501034--501064 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
501024 TAAAAATGTC
*
501034 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
501049 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
501064 C
1 C
501065 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:503158 original size:20 final size:20
Alignment explanation
Indices: 503079--503158 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
503069 AATGTCCAAA
*
503079 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
503099 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
503124 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
503144 TTGTATCGATACATT
1 ATGTATCGATACATT
503159 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:503162 original size:13 final size:13
Alignment explanation
Indices: 503144--503182 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
503134 ACATTTTTCT
503144 TTGTATCGATACA
1 TTGTATCGATACA
503157 TTGTATCGATACA
1 TTGTATCGATACA
*
503170 CTGTATCGATACA
1 TTGTATCGATACA
503183 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:503327 original size:21 final size:21
Alignment explanation
Indices: 503303--503349 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
503293 AAATCTTTTG
503303 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
503324 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
503344 CAAAAT
1 CAAAAT
503350 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:503346 original size:20 final size:19
Alignment explanation
Indices: 503305--503347 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
503295 ATCTTTTGCA
503305 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
503325 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
503345 AAA
1 AAA
503348 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:505721 original size:13 final size:13
Alignment explanation
Indices: 505703--505728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
505693 TACAGCAAGT
505703 ATGTATCGATACA
1 ATGTATCGATACA
505716 ATGTATCGATACA
1 ATGTATCGATACA
505729 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:508487 original size:2 final size:2
Alignment explanation
Indices: 508480--508514 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
508470 AAACAAATAC
* *
508480 AT AT AT AT AG AT AT AT AT AT AT AT AT CT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
508515 AACAAAAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:509524 original size:20 final size:20
Alignment explanation
Indices: 509499--509536 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
509489 CAACAGTATG
509499 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
509519 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
509537 GTCTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:513295 original size:13 final size:13
Alignment explanation
Indices: 513277--513315 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
513267 TTAAATTTTT
*
513277 TATATTTTAAATG
1 TATATTTTAAATA
513290 TATATTTTAAA-A
1 TATATTTTAAATA
*
513302 TATAATTTAAATA
1 TATATTTTAAATA
513315 T
1 T
513316 TTTTGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TATATTTTAAATA
Found at i:513497 original size:21 final size:23
Alignment explanation
Indices: 513439--513500 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
513429 CCTATTTAAT
*
513439 AATATTAAAATTTAATATTATATT
1 AATATTAAAATTTAATA-TATATA
513463 AATA--AATAATTTAATA-ATATA
1 AATATTAA-AATTTAATATATATA
513484 AATATTAAAA-TTAATAT
1 AATATTAAAATTTAATAT
513501 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
21 14 0.42
22 4 0.12
23 11 0.33
24 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATATTAAAATTTAATATATATA
Found at i:513523 original size:28 final size:30
Alignment explanation
Indices: 513472--513527 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
513462 TAATAAATAA
*
513472 TTTAATAATATAAATATTAAAATTAATATT
1 TTTAATAATAAAAATATTAAAATTAATATT
513502 TTTAA-AATAAAAATATT-AAATTAATA
1 TTTAATAATAAAAATATTAAAATTAATA
513528 AATTTACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 9 0.36
29 11 0.44
30 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTAATAATAAAAATATTAAAATTAATATT
Found at i:513529 original size:44 final size:44
Alignment explanation
Indices: 513434--513530 Score: 105
Period size: 44 Copynumber: 2.2 Consensus size: 44
513424 TCATTCCTAT
513434 TTAAT-AATATTAAAATTTAATATTATATTAATAAATAATTTAA
1 TTAATAAATATTAAAATTTAATATTATATTAATAAATAATTTAA
*
513477 TAATATAAATATTAAAA-TTAATATT-T-TTAAAATAAA-AATATTAAA
1 TTA-ATAAATATTAAAATTTAATATTATATT--AATAAATAAT-TT-AA
513522 TTAATAAAT
1 TTAATAAAT
513531 TTACTAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
42 2 0.04
43 6 0.13
44 24 0.52
45 14 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (44 bp):
TTAATAAATATTAAAATTTAATATTATATTAATAAATAATTTAA
Found at i:513855 original size:18 final size:17
Alignment explanation
Indices: 513828--513861 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
513818 AAAAGTTTTT
*
513828 AATAAATAAATTTTAAA
1 AATAAATAAAATTTAAA
513845 AATATAATAAAATTTAA
1 AATA-AATAAAATTTAA
513862 TAACTCATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAATAAAATTTAAA
Found at i:515622 original size:13 final size:13
Alignment explanation
Indices: 515604--515628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
515594 CAATTCATCA
515604 TGTATCGATACAT
1 TGTATCGATACAT
515617 TGTATCGATACA
1 TGTATCGATACA
515629 ATGTGCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:515639 original size:33 final size:32
Alignment explanation
Indices: 515584--515648 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
515574 TTTGAAGCAA
515584 TGTATCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTCA-CATGTATCGATACAT
*
515617 TGTATCGATACAATGTGC-CATGTATTGATACA
1 TGTATCGATACAAT-T-CACATGTATCGATACA
515649 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATTCACATGTATCGATACAT
Found at i:515722 original size:19 final size:20
Alignment explanation
Indices: 515678--515730 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
515668 TTGCTAGTTT
**
515678 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
515698 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
515717 CATGTATCGATACA
1 CATGTATCGATACA
515731 TCTAGATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:516665 original size:33 final size:33
Alignment explanation
Indices: 516623--516689 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
516613 AAGTGCACTA
* * *
516623 AAGTGCTCATCCATGCGTTGTGAGAGTGAAGTG
1 AAGTGCTCATCCATGCGCTGCGAAAGTGAAGTG
* *
516656 AAGTGCTCATTCATGTGCTGCGAAAGTGAAGTG
1 AAGTGCTCATCCATGCGCTGCGAAAGTGAAGTG
516689 A
1 A
516690 TCAACTCTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (33 bp):
AAGTGCTCATCCATGCGCTGCGAAAGTGAAGTG
Found at i:518508 original size:13 final size:13
Alignment explanation
Indices: 518490--518514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518480 ATAATGCACA
518490 GTATCGATACATT
1 GTATCGATACATT
518503 GTATCGATACAT
1 GTATCGATACAT
518515 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:524785 original size:13 final size:12
Alignment explanation
Indices: 524767--524815 Score: 64
Period size: 13 Copynumber: 4.0 Consensus size: 12
524757 CAGCATTCTC
524767 TGTATCGATACA
1 TGTATCGATACA
524779 TTGTATCGATACA
1 -TGTATCGATACA
*
524792 -GCATCGATACA
1 TGTATCGATACA
524803 GTGTATCGATACA
1 -TGTATCGATACA
524816 AAGGGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.31
13 22 0.69
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:524802 original size:24 final size:24
Alignment explanation
Indices: 524770--524815 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
524760 CATTCTCTGT
*
524770 ATCGATACATTGTATCGATACAGC
1 ATCGATACAGTGTATCGATACAGC
524794 ATCGATACAGTGTATCGATACA
1 ATCGATACAGTGTATCGATACA
524816 AAGGGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (24 bp):
ATCGATACAGTGTATCGATACAGC
Found at i:527423 original size:13 final size:13
Alignment explanation
Indices: 527405--527443 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
527395 TACACACAAG
527405 ATGTATCGATACA
1 ATGTATCGATACA
527418 ATGTATCGATACA
1 ATGTATCGATACA
527431 ATGTATCGATACA
1 ATGTATCGATACA
527444 TCCCAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:528488 original size:24 final size:24
Alignment explanation
Indices: 528418--528488 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
528408 TTATCACTAT
* *
528418 TCATTACTGTCATCACTATTCACATA
1 TCATTA-T-TCATCACTGTTCATATA
* * * *
528444 TCACTGTTCATCATTGTTCATGTA
1 TCATTATTCATCACTGTTCATATA
528468 TCATTATTCATCACTGTTCAT
1 TCATTATTCATCACTGTTCAT
528489 CTGTATCGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 31 0.86
25 1 0.03
26 4 0.11
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (24 bp):
TCATTATTCATCACTGTTCATATA
Found at i:529632 original size:13 final size:13
Alignment explanation
Indices: 529614--529640 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
529604 ACATTATGCT
529614 TTGTATCGATACA
1 TTGTATCGATACA
529627 TTGTATCGATACA
1 TTGTATCGATACA
529640 T
1 T
529641 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:529726 original size:13 final size:13
Alignment explanation
Indices: 529705--529736 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
529695 CGATACATGG
*
529705 TACAATGTATCGA
1 TACATTGTATCGA
529718 TACATTGTATCGA
1 TACATTGTATCGA
529731 TACATT
1 TACATT
529737 ACTTGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:531971 original size:20 final size:21
Alignment explanation
Indices: 531930--531972 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
531920 TATTAAAAAG
*
531930 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAATGAA
531951 TTAGCTAA-GAAAAGCAA-GAA
1 TTAGCTAATGAAAA-CAATGAA
531971 TT
1 TT
531973 TGCATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAACAATGAA
Found at i:535483 original size:14 final size:13
Alignment explanation
Indices: 535463--535502 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
535453 ATTTGACTGC
535463 ATGTATCGATACA
1 ATGTATCGATACA
*
535476 CTTGTATCGATACA
1 -ATGTATCGATACA
535490 ATGTATCGATACA
1 ATGTATCGATACA
535503 TTTGAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:535496 original size:13 final size:14
Alignment explanation
Indices: 535462--535502 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
535452 AATTTGACTG
535462 CATGTATCGATACA
1 CATGTATCGATACA
*
535476 CTTGTATCGATACA
1 CATGTATCGATACA
535490 -ATGTATCGATACA
1 CATGTATCGATACA
535503 TTTGAGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (14 bp):
CATGTATCGATACA
Found at i:535592 original size:13 final size:13
Alignment explanation
Indices: 535574--535598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
535564 ACAAAACTTA
535574 TGTATCGATACAT
1 TGTATCGATACAT
535587 TGTATCGATACA
1 TGTATCGATACA
535599 AATCGTTGAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:541711 original size:79 final size:79
Alignment explanation
Indices: 541615--541784 Score: 250
Period size: 79 Copynumber: 2.2 Consensus size: 79
541605 ACAACGCGGC
* * * * * *
541615 TGGAGGATCCCTGATTATGGAAAATTGGTGTTCTGGAAATAAAATCGGGGTTGGAGTATCCCTTT
1 TGGAGTATCCCTAATTATAGAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
*
541680 AGAAATAACAAGGT
66 AAAAATAACAAGGT
541694 TGGAGTATCCCTAATTATAGAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCTAATTATAGAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
**
541759 AAAAATAACGGGGT
66 AAAAATAACAAGGT
*
541773 TAGAGTATCCCT
1 TGGAGTATCCCT
541785 GCGAAAATAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (79 bp):
TGGAGTATCCCTAATTATAGAAAATTGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTC
AAAAATAACAAGGT
Found at i:541773 original size:28 final size:29
Alignment explanation
Indices: 541739--541812 Score: 116
Period size: 28 Copynumber: 2.6 Consensus size: 29
541729 AAAATAAAAT
541739 CGGGGTTGGAGTATCCCCT-CAAAAATAA
1 CGGGGTTGGAGTATCCCCTGCAAAAATAA
* *
541767 CGGGGTTAGAGTAT-CCCTGCGAAAATAA
1 CGGGGTTGGAGTATCCCCTGCAAAAATAA
541795 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
541813 GATTGTGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.10
28 34 0.83
29 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCTGCAAAAATAA
Found at i:541940 original size:51 final size:51
Alignment explanation
Indices: 541874--542159 Score: 305
Period size: 51 Copynumber: 5.6 Consensus size: 51
541864 TCGGAAATAA
* * * * *
541874 CGGGGTTGGAGTATCCCCGATTGTGAGAGATCAATATTTTAGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTAGAAATAAAAT
* * *
541925 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTAGAAATAAAAT
* * * * *
541976 CAGAGTTGGAGTATCTCCGATTAT-AGAAAATTGGTGTTTT-GAAAATAAAA-
1 CGGGGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTAG-AAATAAAAT
* * *
542026 CTGGGTTGGAGTATCCCCGATTGTG-GAAAATTGGTG-TTTCGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTAG-AAATAAAAT
* *
542077 CGGAGTTGGAGTATCCCCGATTATG-GAAAATTAGTGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTAGAAATAAAAT
* *
542128 CGGGGTTGGAGTATCCCCGATTATGAAAAATT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATT
542160 GAGAAACTTA
Statistics
Matches: 204, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
49 3 0.01
50 43 0.21
51 154 0.75
52 4 0.02
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTAGAAATAAAAT
Found at i:541942 original size:79 final size:80
Alignment explanation
Indices: 541767--541942 Score: 293
Period size: 79 Copynumber: 2.2 Consensus size: 80
541757 TCAAAAATAA
*
541767 CGGGGTTAGAGTAT-CCCTGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
1 CGGGGTTGGAGTATCCCCTGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
* *
541831 TTTTAGGAATAAAGC
66 TTTTAGAAATAAAAC
* *
541846 CGGGGTTGGAGTATCCCCT-CGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAGATCAATA
1 CGGGGTTGGAGTATCCCCTGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
541910 TTTTAGAAATAAAAC
66 TTTTAGAAATAAAAC
541925 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
541943 GATTGTGAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 87 0.96
80 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCTGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
TTTTAGAAATAAAAC
Found at i:542059 original size:101 final size:102
Alignment explanation
Indices: 541878--542160 Score: 392
Period size: 101 Copynumber: 2.8 Consensus size: 102
541868 AAATAACGGG
* * * * *
541878 GTTGGAGTATCCCCGATTGT-GAGAGATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATAGA-AAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
* *
541942 CGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCAGA
65 CGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCAGA
* * *
541980 GTTGGAGTATCTCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAA-CTGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCC
* *
542043 CGATTGTGGAAAATTGGTGTTTCGAAAATAAAATCGGA
65 CGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCAGA
* *
542081 GTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
*
542146 GATTATGAAAAATTG
66 GATTGTGAAAAATTG
542161 AGAAACTTAA
Statistics
Matches: 159, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
101 92 0.58
102 65 0.41
103 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (102 bp):
GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
GATTGTGAAAAATTGGTGTTTCGAAAATAAAATCAGA
Found at i:544475 original size:20 final size:20
Alignment explanation
Indices: 544450--544562 Score: 142
Period size: 20 Copynumber: 5.7 Consensus size: 20
544440 AAAATGCTTG
*
544450 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
544470 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
544490 AATGTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
544510 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAGA
* *
544530 AATGTATCGATATAAT-AAA
1 AATGTATCGATACAATGAGA
544549 CAATGTATCGATAC
1 -AATGTATCGATAC
544563 GAATTGTGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.05
20 78 0.94
21 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:544512 original size:40 final size:40
Alignment explanation
Indices: 544450--544562 Score: 165
Period size: 40 Copynumber: 2.8 Consensus size: 40
544440 AAAATGCTTG
* * *
544450 AATGTATCGATACATTGTAAAATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAAAATGTATCGATACAATGAGA
*
544490 AATGTATCGATACAATGCAAAATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAAAAATGTATCGATACAATGAGA
*
544530 AATGTATCGATATAAT-AAACAATGTATCGATAC
1 AATGTATCGATACAATGAAA-AATGTATCGATAC
544563 GAATTGTGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
39 2 0.03
40 65 0.97
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (40 bp):
AATGTATCGATACAATGAAAAATGTATCGATACAATGAGA
Found at i:544517 original size:60 final size:60
Alignment explanation
Indices: 544450--544562 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
544440 AAAATGCTTG
* * *
544450 AATGTATCGATACATTGTA-AAATGTATCGATACAATGAGCAATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AGAAATGTATCGATACAATAAACAATGTATCGATACAATGCAA
*
544510 AATGTATCGATACAATGAGAAATGTATCGATATAATAAACAATGTATCGATAC
1 AATGTATCGATACAATGAGAAATGTATCGATACAATAAACAATGTATCGATAC
544563 GAATTGTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (60 bp):
AATGTATCGATACAATGAGAAATGTATCGATACAATAAACAATGTATCGATACAATGCAA
Found at i:545271 original size:19 final size:19
Alignment explanation
Indices: 545247--545309 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
545237 AGTGATACAT
545247 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
545266 TGTATCGGT---ACA--T-
1 TGTATCGATACAACACTTA
545279 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
545298 TGTATCGATACA
1 TGTATCGATACA
545310 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.17
18 1 0.03
19 20 0.56
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:545283 original size:32 final size:32
Alignment explanation
Indices: 545240--545309 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
545230 GCTTTGTAGT
545240 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
545272 GGTACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
545304 GATACA
1 GATACA
545310 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:546261 original size:49 final size:49
Alignment explanation
Indices: 546202--546438 Score: 279
Period size: 49 Copynumber: 4.9 Consensus size: 49
546192 ATGTTAAAGA
*
546202 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * **
546251 TGTCAATATGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT---GAAGG
* *
546303 CGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * *
546352 TGCCAATGTGCTAATTCAAGGCCAACAACATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
*
546395 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA-AAGA
546439 AGATGCCACC
Statistics
Matches: 158, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
43 37 0.23
45 1 0.01
48 1 0.01
49 77 0.49
52 42 0.27
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
Found at i:546310 original size:101 final size:101
Alignment explanation
Indices: 546203--546385 Score: 303
Period size: 101 Copynumber: 1.8 Consensus size: 101
546193 TGTTAAAGAT
* * *
546203 GCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGTCAATATGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAACAATATCGGACTTAAAGATGAAGGTGCCAATATGCTAATTC
* *
546268 AAGGCCAGCGACATTGGTTTTAAAGATGACGAAGGC
66 AAGGCCAACAACATTGGTTTTAAAGATGACGAAGGC
* *
546304 GCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTGCCAATGTGCTAATTC
1 GCCAATATGCTGATTCAAGGCCAACAATATCGGACTTAAAGATGAAGGTGCCAATATGCTAATTC
546369 AAGGCCAACAACATTGG
66 AAGGCCAACAACATTGG
546386 ACTTAAAGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (101 bp):
GCCAATATGCTGATTCAAGGCCAACAATATCGGACTTAAAGATGAAGGTGCCAATATGCTAATTC
AAGGCCAACAACATTGGTTTTAAAGATGACGAAGGC
Found at i:546514 original size:28 final size:28
Alignment explanation
Indices: 546455--546722 Score: 282
Period size: 28 Copynumber: 9.5 Consensus size: 28
546445 CACCAACTTG
* **
546455 TGTGGGCTTTTGAAAGGGTTG-TACCAACT
1 TGTGGGC-TTTGAAA-GGTTGCCACTGACT
* *
546484 TGTGTGCTTTTG-AAGGTTGCCACTGTCT
1 TGTGGGC-TTTGAAAGGTTGCCACTGACT
*
546512 TGTAGGCTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACT
* *
546539 TGTAGGCTTTGAAA-ATGTGCCACTGACT
1 TGTGGGCTTTGAAAGGT-TGCCACTGACT
*
546567 TGTGGGCTTTGAAAAAG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGTTGCCACTGACT
*
546595 TGTGGGCTTTGAAAAAG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGTTGCCACTGACT
546623 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGTTGCCACTGACT
*
546651 TGTAGGCTTCT-AAAGGTTGCCACTGACT
1 TGTGGGCTT-TGAAAGGTTGCCACTGACT
*
546679 TGTGGGCTTTTGAAAAGGGTGCCACTGACT
1 TGTGGGC-TTTG-AAAGGTTGCCACTGACT
546709 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
546723 AGGTGAGGAA
Statistics
Matches: 214, Mismatches: 15, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
27 41 0.19
28 129 0.60
29 21 0.10
30 23 0.11
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGTTGCCACTGACT
Found at i:546647 original size:84 final size:84
Alignment explanation
Indices: 546499--546727 Score: 322
Period size: 84 Copynumber: 2.7 Consensus size: 84
546489 GCTTTTGAAG
* * * *
546499 GTTGCCACTGTCTTGTAGGCTTTG--AAGGTTGCCACTGACTTGTAGGCTTTGAAAATGTGCCAC
1 GTTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAAGGTGCCAC
*
546562 TGACTTGTGGGCTT-TGAAAAA
65 TGACTTGTAGGCTTCT--AAAA
*
546583 G-TGCCACTGACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACT
1 GTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACT
*
546647 GACTTGTAGGCTTCTAAAG
66 GACTTGTAGGCTTCTAAAA
546666 GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTG
1 GTTGCCACTGACTTGTGGGC-TTTGAAAA-GGTGCCACTGACTTGTGGGCTTTGAAAAGGTG
546728 AGGAATGTCT
Statistics
Matches: 131, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
83 24 0.18
84 64 0.49
85 12 0.09
86 31 0.24
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (84 bp):
GTTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACT
GACTTGTAGGCTTCTAAAA
Found at i:548171 original size:1 final size:1
Alignment explanation
Indices: 548167--548234 Score: 64
Period size: 1 Copynumber: 68.0 Consensus size: 1
548157 TTTGTTGTTG
* * * * * * * *
548167 TTTTTTTGTTTATTTTTTTTTGTTTTGTTTTTTTTTCTTTTTTGTTTGTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
548232 TTT
1 TTT
548235 GCGGAGGACG
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.01, C:0.01, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:548173 original size:15 final size:14
Alignment explanation
Indices: 548155--548234 Score: 75
Period size: 14 Copynumber: 6.1 Consensus size: 14
548145 ATTCGGACCC
548155 TTTTTGTTGTTG-TT
1 TTTTTGTT-TTGTTT
548169 TTTTTGTTTAT-TTT
1 TTTTTGTTT-TGTTT
548183 TTTTTGTTTTGTTT
1 TTTTTGTTTTGTTT
*
548197 TTTTT-TCTT-TTT
1 TTTTTGTTTTGTTT
*
548209 TGTTTG-TTTGTTT
1 TTTTTGTTTTGTTT
548222 TTTTT-TTTT-TTT
1 TTTTTGTTTTGTTT
548234 T
1 T
548235 GCGGAGGACG
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
12 13 0.23
13 15 0.27
14 28 0.50
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTGTTT
Found at i:548184 original size:25 final size:23
Alignment explanation
Indices: 548155--548235 Score: 90
Period size: 25 Copynumber: 3.3 Consensus size: 23
548145 ATTCGGACCC
548155 TTTTTGTTGTTGTTTTTTTGTTTAT
1 TTTTTGTTGTTGTTTTTTT-TTT-T
* *
548180 TTTTTTTTGTTTTGTTTTTTTTTCT
1 TTTTTGTTG--TTGTTTTTTTTTTT
548205 TTTTTGTTTGTTTGTTTTTTTTTTT
1 TTTTTG-TTG-TTGTTTTTTTTTTT
548230 TTTTTG
1 TTTTTG
548236 CGGAGGACGC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 34 0.69
26 5 0.10
27 10 0.20
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (23 bp):
TTTTTGTTGTTGTTTTTTTTTTT
Found at i:548185 original size:26 final size:24
Alignment explanation
Indices: 548155--548234 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 24
548145 ATTCGGACCC
548155 TTTTTGTTGTTGTTTTTTTGTTTATT
1 TTTTTGTTGTTGTTTTTTT-TTT-TT
548181 TTTTT-TTGTT-TTGTTTTTTTTTCT
1 TTTTTGTTGTTGTT-TTTTTTTTT-T
548205 TTTTTGTTTGTTTGTTTTTTTTTTTT
1 TTTTTG-TTG-TTGTTTTTTTTTTTT
548231 TTTT
1 TTTT
548235 GCGGAGGACG
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
23 1 0.02
24 11 0.23
25 10 0.21
26 13 0.27
27 11 0.23
28 2 0.04
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (24 bp):
TTTTTGTTGTTGTTTTTTTTTTTT
Found at i:548201 original size:30 final size:29
Alignment explanation
Indices: 548157--548234 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 29
548147 TCGGACCCTT
* *
548157 TTTGTTGTTGTTTTTTTGTTTATTT-TTT-
1 TTTGTT-TTGTTTTTTTTTTTTTTTGTTTG
548185 TTTGTTTTGTTTTTTTTTCTTTTTTGTTTG
1 TTTGTTTTGTTTTTTTTT-TTTTTTGTTTG
548215 TTTGTTTT-TTTTTTTTTTTT
1 TTTGTTTTGTTTTTTTTTTTT
548235 GCGGAGGACG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.24
28 14 0.31
29 12 0.27
30 8 0.18
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.86
Consensus pattern (29 bp):
TTTGTTTTGTTTTTTTTTTTTTTTGTTTG
Found at i:549381 original size:79 final size:78
Alignment explanation
Indices: 549271--549479 Score: 258
Period size: 79 Copynumber: 2.7 Consensus size: 78
549261 TGGAGATAAT
* * * * *
549271 AACGGGGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGAT
1 AACGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT
549336 GA-TTAGAAAAAAA
66 -ATTTAGAAAAAAA
* * * *
549349 AATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAA
1 AA-CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAA
* * *
549414 TATTTTGGGAATAAA
65 TA-TTTAGAAAAAAA
* *
549429 GACGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGAAGTATCCCCGAT
1 AACGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
549480 AAAATAACGA
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
78 3 0.03
79 98 0.89
80 9 0.08
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT
ATTTAGAAAAAAA
Found at i:549622 original size:51 final size:51
Alignment explanation
Indices: 549489--549663 Score: 171
Period size: 52 Copynumber: 3.4 Consensus size: 51
549479 TAAAATAACG
* * * *
549489 AGGTTGGAGTATCCTCGATTGTG-AAAAATTGGTATTTTTGGAAATAAAATC
1 AGGTTGGAGTATCCCCGATTGTGAAAAAATTGGT-GTTTTGAAAATAAAACC
*
549540 GGAGTTGGAGTATCCCCGA-T-T-AAAGGTAAATTGGTGTTTTGAAAATAAAACC
1 AG-GTTGGAGTATCCCCGATTGTGAAA---AAATTGGTGTTTTGAAAATAAAACC
* * *
549592 AGGTTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTT-AGCAATAAAATCG
1 AGGTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTGA-AAATAAAA-CC
*
549644 GGGTTGGAGTATCCCCGATT
1 AGGTTGGAGTATCCCCGATT
549664 ACGAAAAATC
Statistics
Matches: 104, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
50 4 0.04
51 37 0.36
52 51 0.49
53 9 0.09
54 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTGAAAATAAAACC
Found at i:549671 original size:51 final size:51
Alignment explanation
Indices: 549490--549876 Score: 243
Period size: 51 Copynumber: 7.4 Consensus size: 51
549480 AAAATAACGA
* * * *
549490 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAATCGG
* * ** * * **
549542 AGTTGGAGTATCCCCGATTAAAGGTAAATTGGTGTTTTGAAAATAAAA-CCA
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * *
549593 GGTTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATG-AAAAATTAGTGTTTTGGAAATAAAATCGG
* * * * *
549645 GGTTGGAGTATCCCCGATTACGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * ** * *
549696 GGTTGGAGTATCCCC-----TCAAAAATAACG-GGGTTGGAGTATCCCCGATGATTAA-CTG
1 GGTTGGAGTATCCCCGATTATGAAAAATTA-GTGTTTTGGA--A------AT-A-AAATCGG
* *
549751 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG----TTTTGGAAATAAAATCGG
* *
549807 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAATCGG
* *
549858 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
549877 GTGGAGAATT
Statistics
Matches: 257, Mismatches: 51, Indels: 55
0.71 0.14 0.15
Matches are distributed among these distances:
46 12 0.05
48 1 0.00
50 1 0.00
51 111 0.43
52 51 0.20
53 9 0.04
54 2 0.01
55 29 0.11
56 24 0.09
57 2 0.01
60 4 0.02
61 5 0.02
63 1 0.00
65 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:549699 original size:262 final size:265
Alignment explanation
Indices: 549380--549879 Score: 760
Period size: 262 Copynumber: 1.9 Consensus size: 265
549370 TCGAAAATAA
* * *
549380 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGACGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTTTGGAAATAAAGACGGGGTTGGAGTAT
** * *
549445 CCCCTCGGAAGTAACGGGGTTGAAGTATCCCCGATAAAATAAC-GAGGTTGGAGTATCCTCGATT
66 CCCCTCAAAAATAACGGGGTTGAAGTATCCCCGAT-AAATAACTG-GGTTGGAGTATCCCCGATT
*
549509 GTGAA-AAATT-G-G-TATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGTAAA
129 GTGAAGAAATTGGTGTTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAA
* *
549570 TTGGTGTTTTGAAAATAAAACCAG-GTTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGC
193 TTAGTGTTTTGAAAATAAAACCAGAGTTGGAATATCCCCGATTGTGAAAAAATTAGTGTTTTAGC
549634 AATAAAAT
258 AATAAAAT
* *
549642 CGGGGTTGGAGTATCCCCGATTACGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTTTGGAAATAAAGACGGGGTTGGAGTAT
* * *
549707 CCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGATTAACTGGGTTGGAGTATCCCCGATTGT
66 CCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATAAATAACTGGGTTGGAGTATCCCCGATTGT
* *
549772 GAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTA
131 GAAGAAATTGGTGTTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTA
* *
549837 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTG
196 GTGTTTTGAAAATAAAACCAGAGTTGGAATATCCCCGATTGTG
549880 GAGAATTGGA
Statistics
Matches: 213, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
261 28 0.13
262 97 0.46
263 1 0.00
264 26 0.12
265 61 0.29
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (265 bp):
CGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTTTGGAAATAAAGACGGGGTTGGAGTAT
CCCCTCAAAAATAACGGGGTTGAAGTATCCCCGATAAATAACTGGGTTGGAGTATCCCCGATTGT
GAAGAAATTGGTGTTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTA
GTGTTTTGAAAATAAAACCAGAGTTGGAATATCCCCGATTGTGAAAAAATTAGTGTTTTAGCAAT
AAAAT
Found at i:549700 original size:103 final size:103
Alignment explanation
Indices: 549489--549710 Score: 259
Period size: 103 Copynumber: 2.2 Consensus size: 103
549479 TAAAATAACG
* * * *
549489 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 AGGTTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTTAGAAATAAAATCGGAGTTGGAGTATC
** *** *
549554 CCCGATTAAAGGTAAATTGGTGTTTTGAAAATAAAACC
66 CCCGATTAAAGAAAAATCAATATTTTGAAAATAAAACC
* *
549592 AGGTTGGAGTATCCCCGATTGTGAAAAAATTAGT-GTTTTAGCAATAAAATCGGGGTTGGAGTAT
1 AGGTTGGAGTATCCCCGATTGTG-AAAAATTAGTAGTTTTAGAAATAAAATCGGAGTTGGAGTAT
* * * *
549656 CCCCGATT-ACGAAAAATCAATATTTTGGAAATAAAGTCG
65 CCCCGATTAAAGAAAAATCAATATTTTGAAAATAAA-ACC
*
549695 GGGTTGGAGTATCCCC
1 AGGTTGGAGTATCCCC
549711 TCAAAAATAA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
102 19 0.19
103 72 0.72
104 9 0.09
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (103 bp):
AGGTTGGAGTATCCCCGATTGTGAAAAATTAGTAGTTTTAGAAATAAAATCGGAGTTGGAGTATC
CCCGATTAAAGAAAAATCAATATTTTGAAAATAAAACC
Found at i:549756 original size:27 final size:27
Alignment explanation
Indices: 549693--549768 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
549683 GAAATAAAGT
* *
549693 CGGGGTTGGAGTATCCCCTCAAAAATAA
1 CGGGGTTGGAGTATCCCC-GATAAATAA
* *
549721 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATAAATAA
*
549748 CTGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
549769 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:552252 original size:13 final size:13
Alignment explanation
Indices: 552234--552259 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
552224 ACATTGATCC
552234 ATGTATCGATACA
1 ATGTATCGATACA
552247 ATGTATCGATACA
1 ATGTATCGATACA
552260 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:552880 original size:119 final size:116
Alignment explanation
Indices: 552672--552883 Score: 261
Period size: 119 Copynumber: 1.8 Consensus size: 116
552662 GGGTGTCCAC
* * * *
552672 TTTTCAAGGACAAAGGAAAAGAGAATGAAATAGGTCTTGCTCCTTGAAGACCAAGGAAGAGAAGA
1 TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
552737 AAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCA
66 AAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCA
* *
552788 TTTTCCAAGGACAAAGGAAAAAGGGAAATGAAATACGTCCTGCT-CTCTGAGGACAAAAGAA-AG
1 TTTT-CAAGGACAAAGG-AAAAGAG-AATGAAATACGTCCTGCTCCT-TGAAGACAAAAGAAGAG
* *
552851 AGGAAAA-TAAAGTGTATCCTGC-TCTTTGAGGAC
62 AAGAAAAGGAAAGTG--TCCTGCTTC-TTGAGGAC
552884 TAAAAAGTGC
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
116 4 0.05
117 18 0.22
118 18 0.22
119 41 0.51
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (116 bp):
TTTTCAAGGACAAAGGAAAAGAGAATGAAATACGTCCTGCTCCTTGAAGACAAAAGAAGAGAAGA
AAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCA
Found at i:553054 original size:26 final size:26
Alignment explanation
Indices: 553025--553112 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
553015 GTGGGCTTTA
553025 AAAGGTGTCCTGCTCTTTGGGGATTG
1 AAAGGTGTCCTGCTCTTTGGGGATTG
** * *
553051 AAAGGTG-CCACCAACTTGTGTGGGCTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGG-ATTG
* * *
553080 AAAGGGGTCCTGCTCTTTAGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGATTG
553106 AAAGGTG
1 AAAGGTG
553113 CCACCAACTT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 5 0.11
28 4 0.09
29 12 0.27
30 3 0.07
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.28
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGATTG
Found at i:553236 original size:59 final size:59
Alignment explanation
Indices: 552867--553760 Score: 1079
Period size: 55 Copynumber: 15.3 Consensus size: 59
552857 ATAAAGTGTA
* * *
552867 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
552922 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** *
552977 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
553032 TCCTGCTCTTTGGGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
553087 TCCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGA-GGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * *
553148 TCATGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAAAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
553207 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAAATGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT---AAAAGAAAAGGCG
* * *
553269 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
553328 TCCCGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
**
553387 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
553447 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
553506 T-TTCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCT-GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
553567 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GG-G
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
553622 TCCTGCTCTTTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
553682 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
553743 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
553761 AAAAAGCGGA
Statistics
Matches: 747, Mismatches: 57, Indels: 64
0.86 0.07 0.07
Matches are distributed among these distances:
53 1 0.00
54 3 0.00
55 231 0.31
56 3 0.00
57 1 0.00
59 193 0.26
60 156 0.21
61 96 0.13
62 63 0.08
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:553251 original size:119 final size:118
Alignment explanation
Indices: 552871--553760 Score: 1062
Period size: 119 Copynumber: 7.6 Consensus size: 118
552861 AGTGTATCCT
** * * *
552871 GCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----GAAAGGCGTCCTGCTCTT
1 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCCTGCTCTT
* *
552932 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCT
66 TGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
** *
552981 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAG----GTGTCCTGCTCTT
1 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCCTGCTCTT
* * * *
553042 TGGGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGGGTCCT
66 TGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* * *
553091 GCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCATGCT
1 GCTCTTTGA-GGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAGCGTCCTGCT
* *
553155 CTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAAAAAAGGCGTCCC
63 CTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
553211 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAAATGCGTCCCGC
1 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT---AAAAGAAAA-GCGTCCTGC
* *
553275 TCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGTGTCCC
62 TCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
* *
553332 GCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCT
1 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-GCGTCCTGCTCT
**
553396 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
65 TTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
*
553451 GCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-TTCGCTC
1 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-GCGTCCT-GCTC
** * *
553514 TTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCT
64 TTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGTCCC
*
553571 GCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG----GGGTCCTGCTCT
1 GCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCCTGCTCT
* * *
553631 TTGGGGACGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTCCC
65 TTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
** *
553686 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTC
1 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAA-GCGTCCTGCTC
553751 TTTGAGGACT
64 TTTGAGGACT
553761 AAAAAGCGGA
Statistics
Matches: 688, Mismatches: 56, Indels: 61
0.85 0.07 0.08
Matches are distributed among these distances:
108 1 0.00
109 1 0.00
110 132 0.19
111 5 0.01
114 5 0.01
115 79 0.11
116 61 0.09
117 1 0.00
118 28 0.04
119 169 0.25
120 50 0.07
121 153 0.22
122 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (118 bp):
GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCCTGCTCTT
TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
Found at i:554750 original size:1 final size:1
Alignment explanation
Indices: 554746--554803 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
554736 TTTTCTCTCC
* * * * * **
554746 TTTTTCTTTGTTTTGTTTCTTTTTTTTTTTCTTTTTTTTTTTTTTGCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
554804 GAAGAGAAGG
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:554766 original size:13 final size:11
Alignment explanation
Indices: 554727--554803 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
554717 CTTAAGCAGG
*
554727 TTCTTTTTCTT
1 TTCTTTTTTTT
* **
554738 TTCTCTCCTTT
1 TTCTTTTTTTT
554749 TTCTTTGTTTTGT
1 TTCTTT-TTTT-T
554762 TTCTTTTTTTTT
1 TTC-TTTTTTTT
554774 TTCTTTTTTTT
1 TTCTTTTTTTT
554785 TT-TTTTGCTTTT
1 TTCTTTT--TTTT
554797 TT-TTTTT
1 TTCTTTTT
554804 GAAGAGAAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 5 0.09
11 22 0.41
12 16 0.30
13 8 0.15
14 3 0.06
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:554776 original size:12 final size:13
Alignment explanation
Indices: 554746--554804 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
554736 TTTTCTCTCC
554746 TTTTTCTTTGTTT
1 TTTTTCTTTGTTT
*
554759 TGTTTCTTT-TTT
1 TTTTTCTTTGTTT
554771 TTTTTCTTT-TTT
1 TTTTTCTTTGTTT
554783 TTTTT-TTTGCTTT
1 TTTTTCTTTG-TTT
554796 TTTTT-TTTG
1 TTTTTCTTTG
554805 AAGAGAAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
11 3 0.07
12 19 0.45
13 20 0.48
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTGTTT
Found at i:554784 original size:16 final size:16
Alignment explanation
Indices: 554746--554803 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
554736 TTTTCTCTCC
* * *
554746 TTTTTCTTTGTTTTGT
1 TTTTTTTTTTTTTTCT
*
554762 TTCTTTTTTTTTTTCT
1 TTTTTTTTTTTTTTCT
*
554778 TTTTTTTTTTTTTGCT
1 TTTTTTTTTTTTTTCT
554794 TTTTTTTTTT
1 TTTTTTTTTT
554804 GAAGAGAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTTTTCT
Found at i:554796 original size:9 final size:8
Alignment explanation
Indices: 554746--554803 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 8
554736 TTTTCTCTCC
554746 TTTTTCTT
1 TTTTTCTT
*
554754 TGTTTTGTT
1 T-TTTTCTT
554763 TCTTTT-TT
1 T-TTTTCTT
554771 TTTTTCTT
1 TTTTTCTT
554779 TTTTT-TT
1 TTTTTCTT
554786 TTTTTGCTT
1 TTTTT-CTT
554795 TTTTT-TT
1 TTTTTCTT
554802 TT
1 TT
554804 GAAGAGAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 15 0.34
8 11 0.25
9 18 0.41
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:554804 original size:13 final size:12
Alignment explanation
Indices: 554746--554800 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
554736 TTTTCTCTCC
554746 TTTTTCTTTGTTT
1 TTTTTCTTT-TTT
*
554759 TGTTTCTTTTTT
1 TTTTTCTTTTTT
554771 TTTTTCTTTTTT
1 TTTTTCTTTTTT
554783 TTTTT-TTTGCTTT
1 TTTTTCTTT--TTT
554796 TTTTT
1 TTTTT
554801 TTTGAAGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 3 0.08
12 19 0.50
13 16 0.42
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.87
Consensus pattern (12 bp):
TTTTTCTTTTTT
Done.