Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 88 of 279
Found at i:29091724 original size:20 final size:18
Alignment explanation
Indices: 29091686--29091720 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29091676 TTTAAATTGT
29091686 TGTTTTTATTATTATATG
1 TGTTTTTATTATTATATG
29091704 TGTTTTTATTATTATAT
1 TGTTTTTATTATTATAT
29091721 ATGTATGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (18 bp):
TGTTTTTATTATTATATG
Found at i:29097812 original size:92 final size:94
Alignment explanation
Indices: 29097669--29097853 Score: 230
Period size: 92 Copynumber: 2.0 Consensus size: 94
29097659 TTAGGGTTAT
* * * ** * *
29097669 GTTTCTCAATGGTGACATTGACGATAAGGTTTATGTGGTGCAACTAGAAATGTAACA-CCCTAA-
1 GTTTCTCAATGGTGACATTAACAAGAAGGTTTACATGGTGCAACAAAAAATGTAACACCCCTAAC
*
29097732 CGTATCCATCACCGAAATAGGGTTACGAA
66 CGCATCCATCACCGAAATAGGGTTACGAA
* *
29097761 GTTTCTCAATGGTGACATTAACAAGATGGTTTACATGGTGTAACAAAAAATGTAACACCCCTAAC
1 GTTTCTCAATGGTGACATTAACAAGAAGGTTTACATGGTGCAACAAAAAATGTAACACCCCTAAC
* * *
29097826 TCGCATCCATCGCTGGAATAGGGTTACG
66 -CGCATCCATCACCGAAATAGGGTTACG
29097854 GAGCATTACC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
92 48 0.62
93 6 0.08
95 23 0.30
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (94 bp):
GTTTCTCAATGGTGACATTAACAAGAAGGTTTACATGGTGCAACAAAAAATGTAACACCCCTAAC
CGCATCCATCACCGAAATAGGGTTACGAA
Found at i:29099409 original size:89 final size:88
Alignment explanation
Indices: 29099194--29099447 Score: 257
Period size: 90 Copynumber: 2.9 Consensus size: 88
29099184 TGATGGTTGG
* * * ***
29099194 CACCA-CCCTTTTCCATAATTCGATAGCC-AGAGCTATCCCTTTTCATAATTTTGATAGTCGTCA
1 CACCATCCC-TTTACATAATTCGATAGCCGA-AGCTATCCCTTTTCGT-A-TTAGATAG-CCAAA
* * * *
29099257 -CCATCCCTTTTCATTGTTGATGGTCGT
61 GCCATCACTTTTCATAGTCGATGGTCAT
*
29099284 CACCATCCCTTTACATAATTTGATAGCCGAAGCTATCCCTTTTCAAG-ATTAGATAGCCAAAGCC
1 CACCATCCCTTTACATAATTCGATAGCCGAAGCTATCCCTTTTC--GTATTAGATAGCCAAAGCC
*
29099348 ATCTCTTTTCATAGCTCGATGGTCAT
64 ATCACTTTTCATAG-TCGATGGTCAT
* * * *
29099374 CACCATCCCTTTTCATAA-TCGATAGTCGAAGCTATCCCTTTTCGTATTCGATAGCCAAAGCTAT
1 CACCATCCCTTTACATAATTCGATAGCCGAAGCTATCCCTTTTCGTATTAGATAGCCAAAGCCAT
29099438 CACTTTTCAT
66 CACTTTTCAT
29099448 TCGTTAATGA
Statistics
Matches: 140, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
87 1 0.01
88 28 0.20
89 44 0.31
90 63 0.45
91 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.35
Consensus pattern (88 bp):
CACCATCCCTTTACATAATTCGATAGCCGAAGCTATCCCTTTTCGTATTAGATAGCCAAAGCCAT
CACTTTTCATAGTCGATGGTCAT
Found at i:29099410 original size:29 final size:30
Alignment explanation
Indices: 29099199--29099447 Score: 138
Period size: 29 Copynumber: 8.3 Consensus size: 30
29099189 GTTGGCACCA
* *
29099199 CCCTTTTCCATAATTCGATAG-CCAGAGCTAT
1 CCCTTTT-CATAATTCGATAGTCGA-AGCCAT
* *
29099230 CCCTTTTCATAATTTTGATAGTCGTCA-CCAT
1 CCCTTTTCATAA-TTCGATAGTCG-AAGCCAT
** * *
29099261 CCCTTTTCATTGTT-GATGGTCGTCA-CCAT
1 CCCTTTTCATAATTCGATAGTCG-AAGCCAT
* * * *
29099290 CCCTTTACATAATTTGATAGCCGAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCCAT
* * *
29099320 CCCTTTTCA-AGATTAGATAGCCAAAGCCAT
1 CCCTTTTCATA-ATTCGATAGTCGAAGCCAT
* ** *
29099350 CTCTTTTCATAGCTCGATGGTC-ATCA-CCAT
1 CCCTTTTCATAATTCGATAGTCGA--AGCCAT
*
29099380 CCCTTTTCATAA-TCGATAGTCGAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCCAT
* * * *
29099409 CCCTTTTCGT-ATTCGATAGCCAAAGCTAT
1 CCCTTTTCATAATTCGATAGTCGAAGCCAT
*
29099438 CACTTTTCAT
1 CCCTTTTCAT
29099448 TCGTTAATGA
Statistics
Matches: 173, Mismatches: 33, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
28 2 0.01
29 71 0.41
30 69 0.40
31 29 0.17
32 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (30 bp):
CCCTTTTCATAATTCGATAGTCGAAGCCAT
Found at i:29100439 original size:20 final size:20
Alignment explanation
Indices: 29100406--29100443 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29100396 TGATATGTAT
29100406 ATATGTATTATATAATAATG
1 ATATGTATTATATAATAATG
29100426 ATAT-TATTATTATAATAA
1 ATATGTATTA-TATAATAA
29100444 AAAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
ATATGTATTATATAATAATG
Found at i:29101521 original size:18 final size:18
Alignment explanation
Indices: 29101484--29101521 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29101474 TGGCATGTGA
*
29101484 AATGGAAATGAGATAGTG
1 AATGGAAATGAAATAGTG
29101502 AATGGAAAATGAAATA-TG
1 AATGG-AAATGAAATAGTG
29101520 AA
1 AA
29101522 ATAGGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (18 bp):
AATGGAAATGAAATAGTG
Found at i:29118177 original size:40 final size:40
Alignment explanation
Indices: 29118088--29118351 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
29118078 TTGAATGATG
* *
29118088 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
29118127 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
29118167 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29118206 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29118246 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29118286 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29118327 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29118352 AACGAGGAGC
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 143 0.69
41 10 0.05
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29118369 original size:120 final size:118
Alignment explanation
Indices: 29118088--29118384 Score: 338
Period size: 119 Copynumber: 2.5 Consensus size: 118
29118078 TTGAATGATG
* *
29118088 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* *
29118148 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
29118206 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
29118271 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
29118327 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
29118385 TACGTGATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 64 0.42
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:29132928 original size:32 final size:30
Alignment explanation
Indices: 29132851--29132929 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
29132841 CGTCACCATT
* * * **
29132851 CCTTTACATAGTTTGATAGTCGAAGTTATC
1 CCTTTTCATAGTTCGATAGCCGAAGACATC
29132881 CCTTTTCAT-GATTCGATAGCCGAAGACATCC
1 CCTTTTCATAG-TTCGATAGCCGAAGACAT-C
29132912 ACCTTTTCATAGTTCGAT
1 -CCTTTTCATAGTTCGAT
29132930 GGTCATCACC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 1 0.03
30 22 0.55
31 1 0.03
32 15 0.38
33 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (30 bp):
CCTTTTCATAGTTCGATAGCCGAAGACATC
Found at i:29132960 original size:29 final size:29
Alignment explanation
Indices: 29132913--29132983 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
29132903 AAGACATCCA
* *
29132913 CCTTTTCATAGTTCGATGGTCATCACCATC
1 CCTTTTCATA-ATCTATGGTCATCACCATC
* *
29132943 CTTTTTCATAATCTATGGTCGTCACCATC
1 CCTTTTCATAATCTATGGTCATCACCATC
29132972 CCTTTTCATAAT
1 CCTTTTCATAAT
29132984 TGATAGCTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (29 bp):
CCTTTTCATAATCTATGGTCATCACCATC
Found at i:29132962 original size:121 final size:119
Alignment explanation
Indices: 29132760--29133035 Score: 291
Period size: 121 Copynumber: 2.3 Consensus size: 119
29132750 TCGACACCAC
* * * *
29132760 CCCTTTCCATAATTCGATAGCTGAAGCTATCCCTTTTCATAATTTTAATGGTCATCACCATCTCT
1 CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAAGTTCAATGGTCATCACCATCTCT
** * * * *
29132825 TTTCATTGTTGATGGTCGTCACCATTCCTTTACATAGTTTGATAG-TCGAAGTTAT
66 TTTCATAATTGATGGTCGTCACCATCCCTTTACATA-ATTGATAGCT-AAAGCTAT
* *
29132880 CCCTTTTCATGATTCGATAGCCGAAGAC-ATCCACCTTTTCAT-AGTTCGATGGTCATCACCATC
1 CCCTTTTCATAATTCGATAGCCGAAG-CTAT-C-CCTTTTCATAAGTTCAATGGTCATCACCATC
*
29132943 -CTTTTTCATAATCT-ATGGTCGTCACCATCCCTTTTCATAATTGATAGCTAAAGCTAT
63 TC-TTTTCATAAT-TGATGGTCGTCACCATCCCTTTACATAATTGATAGCTAAAGCTAT
* *
29133000 CCCTTTTCGT-ATTCAATAG-C-AA-CTATCCCTTTTCAT
1 CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCAT
29133036 TCGTTGATGA
Statistics
Matches: 134, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
114 9 0.07
115 2 0.01
116 2 0.01
117 2 0.01
118 1 0.01
119 8 0.06
120 48 0.36
121 52 0.39
122 10 0.07
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (119 bp):
CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAAGTTCAATGGTCATCACCATCTCT
TTTCATAATTGATGGTCGTCACCATCCCTTTACATAATTGATAGCTAAAGCTAT
Found at i:29133001 original size:29 final size:26
Alignment explanation
Indices: 29132969--29133035 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
29132959 GGTCGTCACC
*
29132969 ATCCCTTTTCATAATT-GATAGCTAAAGCT
1 ATCCCTTTTCAT-ATTCAATAGC--AA-CT
*
29132998 ATCCCTTTTCGTATTCAATAGCAACT
1 ATCCCTTTTCATATTCAATAGCAACT
29133024 ATCCCTTTTCAT
1 ATCCCTTTTCAT
29133036 TCGTTGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 13 0.38
27 2 0.06
28 3 0.09
29 16 0.47
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.40
Consensus pattern (26 bp):
ATCCCTTTTCATATTCAATAGCAACT
Found at i:29134811 original size:18 final size:19
Alignment explanation
Indices: 29134774--29134817 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29134764 ATATCAAATA
*
29134774 CTAAAAAATAAAACAAAAC
1 CTAAAAAAAAAAACAAAAC
* *
29134793 C-AAAAAAAAAAAGAGAAC
1 CTAAAAAAAAAAACAAAAC
29134811 CTAAAAA
1 CTAAAAA
29134818 CAGATTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.75, C:0.14, G:0.05, T:0.07
Consensus pattern (19 bp):
CTAAAAAAAAAAACAAAAC
Found at i:29135557 original size:29 final size:26
Alignment explanation
Indices: 29135517--29135569 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
29135507 GAATTTGAGT
*
29135517 AATTAGGGCTAAATTGTAAAGATAATA
1 AATTAGGGCTAAAATGTAAA-ATAATA
29135544 AATTGAGGGACTAAAATGTAAAATAA
1 AATT-AGGG-CTAAAATGTAAAATAA
29135570 ATGAAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.35
29 11 0.48
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (26 bp):
AATTAGGGCTAAAATGTAAAATAATA
Found at i:29136137 original size:43 final size:43
Alignment explanation
Indices: 29136076--29136247 Score: 244
Period size: 43 Copynumber: 4.0 Consensus size: 43
29136066 ATAGGATTTC
* *
29136076 CGATATGTG-TTCTCATGTAAGACCAC-ATCTGGGAC-GTTGGCAT
1 CGATATGTGATT-ACATGTAAGACC-CTGTCTGGGACAG-TGGCAT
29136119 CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
1 CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
*
29136162 CGATATGTGATTACATGTAAGACCCTGTCTAGGACAGTGGCAT
1 CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
*
29136205 CGATATGTGATTACATGTAAGACCAC-GTCTGGGACATTGGCAT
1 CGATATGTGATTACATGTAAGACC-CTGTCTGGGACAGTGGCAT
29136248 TGTATGATAT
Statistics
Matches: 120, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
42 1 0.01
43 115 0.96
44 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
CGATATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGCAT
Found at i:29149505 original size:79 final size:81
Alignment explanation
Indices: 29149369--29149553 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
29149359 TTGAATGATG
*
29149369 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
29149433 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
29149448 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
29149510 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
29149528 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29149554 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:29149567 original size:40 final size:40
Alignment explanation
Indices: 29149370--29149553 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
29149360 TGAATGATGT
* * * *
29149370 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
29149410 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
29149450 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29149488 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29149529 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29149554 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29149575 original size:79 final size:79
Alignment explanation
Indices: 29149422--29149586 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
29149412 GGACTAAGAT
* **
29149422 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
29149487 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
29149501 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
29149564 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
29149580 CCGAAGG
1 CCGAAGG
29149587 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29164301 original size:40 final size:40
Alignment explanation
Indices: 29164218--29164520 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
29164208 TTGAATGCTG
* * * * * *
29164218 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
29164258 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
29164298 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
29164338 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
29164378 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
29164418 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29164458 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
29164497 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
29164521 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:29171503 original size:25 final size:25
Alignment explanation
Indices: 29171433--29171494 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
29171423 GTAATGAGGG
29171433 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
29171457 GATAAGGGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
29171482 GATAAGGGGAGAA
1 GATAAGGGGAGAA
29171495 AATCAAGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.14
25 32 0.86
ACGTcount: A:0.39, C:0.03, G:0.40, T:0.18
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGCT
Found at i:29172586 original size:28 final size:26
Alignment explanation
Indices: 29172555--29172618 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
29172545 AATTACTTGA
* **
29172555 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTA-G-ATGCAAAATTACCATT
*
29172583 ATACCCCTAGGTGCAAAATTACCATT
1 ATACCCCTAGATGCAAAATTACCATT
29172609 ATACCCCTAG
1 ATACCCCTAG
29172619 GGTTACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 9 0.28
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCATT
Found at i:29172764 original size:27 final size:26
Alignment explanation
Indices: 29172726--29172834 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 26
29172716 AAGCGTCCTA
*
29172726 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCAC-ATTATCTGATCTG
*
29172753 GTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACAT-TATCTGATCTG
*
29172780 GTGGCTCTGCCACGATTATCTATATCTG
1 GTGGCTCTGCCAC-ATTATCT-GATCTG
* * * *
29172808 GTGACTCTGTCACATTTTCTGTTCTG
1 GTGGCTCTGCCACATTATCTGATCTG
29172834 G
1 G
29172835 CAGCCATGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 46 0.66
28 17 0.24
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
GTGGCTCTGCCACATTATCTGATCTG
Found at i:29172829 original size:54 final size:54
Alignment explanation
Indices: 29172726--29172834 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 54
29172716 AAGCGTCCTA
*
29172726 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTG
* * * * *
29172780 GTGGCTCTGCCACGATTATCTATATCTGGTGACTCTGTCACAT-TTTCTGTTCTG
1 GTGGCTATGCCACAATTATCT-GATCTGGTGACTCTGCCACATATATCTGTTCTG
29172834 G
1 G
29172835 CAGCCATGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
54 30 0.62
55 18 0.38
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.38
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTG
Found at i:29180161 original size:39 final size:39
Alignment explanation
Indices: 29180117--29180195 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
29180107 TTAAATTAAA
29180117 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
1 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
29180156 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
1 TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
29180195 T
1 T
29180196 TCCTCATCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (39 bp):
TAAAATAAAAATAAAAGTTATTATCATCATTTTCATGTC
Found at i:29181426 original size:61 final size:62
Alignment explanation
Indices: 29181326--29181549 Score: 267
Period size: 61 Copynumber: 3.6 Consensus size: 62
29181316 CACACAGCCA
* * * *
29181326 TGTCCCTGGCCATATGGTTTTATACTATGAATAGTGAGTTTCACAGCCTGGCCACATGCCCG
1 TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTTCACGGCCTGGGCACATGCCCG
* * * * * **
29181388 TGTCCCTGGTCGTGTGG-TTTATACAATGAACAGTGAGTTACATGGCCTGGGCACACT-CTTG
1 TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTTCACGGCCTGGGCACA-TGCCCG
* *
29181449 TGTCCCTGGCCGTATGG-TTTATACAATGAACAGTGA-TTTACACGGCCTGGGCACACGCCCG
1 TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTT-CACGGCCTGGGCACATGCCCG
* *
29181510 TGTCCCTGGCCATGTGGTTTTATATAATGAACAGTGAGTT
1 TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTT
29181550 ACATGGTCGT
Statistics
Matches: 136, Mismatches: 21, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
60 2 0.01
61 99 0.73
62 33 0.24
63 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (62 bp):
TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTTCACGGCCTGGGCACATGCCCG
Found at i:29181526 original size:122 final size:124
Alignment explanation
Indices: 29181326--29181555 Score: 349
Period size: 122 Copynumber: 1.9 Consensus size: 124
29181316 CACACAGCCA
* * *
29181326 TGTCCCTGGCCATATGGTTTTATACTATGAATAGTGAGTTTCACAGCCTGGCCACATGCCCGTGT
1 TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTTCACAGCCTGGCCACACGCCCGTGT
* *
29181391 CCCTGGTCGTGTGG-TTTATACAATGAACAGTGAGTTACATGGCCTGGGCACACTCTTG
66 CCCTGGCCATGTGGTTTTATACAATGAACAGTGAGTTACATGGCCTGGGCACACTCTTG
* * *
29181449 TGTCCCTGGCCGTATGG-TTTATACAATGAACAGTGA-TTTACACGGCCTGGGCACACGCCCGTG
1 TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTT-CACAGCCTGGCCACACGCCCGTG
*
29181512 TCCCTGGCCATGTGGTTTTATATAATGAACAGTGAGTTACATGG
65 TCCCTGGCCATGTGGTTTTATACAATGAACAGTGAGTTACATGG
29181556 TCGTTCATAG
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
121 3 0.03
122 50 0.52
123 43 0.45
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (124 bp):
TGTCCCTGGCCATATGGTTTTATACAATGAACAGTGAGTTTCACAGCCTGGCCACACGCCCGTGT
CCCTGGCCATGTGGTTTTATACAATGAACAGTGAGTTACATGGCCTGGGCACACTCTTG
Found at i:29187027 original size:18 final size:18
Alignment explanation
Indices: 29187004--29187039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29186994 TTTAGCAATA
29187004 TTTTTTATCTCAAAAGTG
1 TTTTTTATCTCAAAAGTG
* *
29187022 TTTTTTGTCTCAGAAGTG
1 TTTTTTATCTCAAAAGTG
29187040 CTTCTAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTTTTATCTCAAAAGTG
Found at i:29190932 original size:20 final size:20
Alignment explanation
Indices: 29190888--29190935 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
29190878 GGAAAAATCC
*
29190888 ATATTTTTATACTTTCTAATA
1 ATATTTTTATAATTTCTAA-A
*
29190909 AT-TTTTCATAATTT-TAAA
1 ATATTTTTATAATTTCTAAA
29190927 ATATTTTTA
1 ATATTTTTA
29190936 CAGTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 10 0.43
21 2 0.09
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTTATAATTTCTAAA
Found at i:29194003 original size:10 final size:10
Alignment explanation
Indices: 29193988--29194037 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
29193978 GATTTTTAGA
29193988 ATTTATTTTT
1 ATTTATTTTT
*
29193998 ATTTATCTTT
1 ATTTATTTTT
*
29194008 ATTTATATTT
1 ATTTATTTTT
* *
29194018 AATTATTTGT
1 ATTTATTTTT
29194028 ATTTATTTTT
1 ATTTATTTTT
29194038 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:29196632 original size:9 final size:9
Alignment explanation
Indices: 29196618--29196646 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
29196608 AAACAAAGAA
29196618 TCCTTACCT
1 TCCTTACCT
29196627 TCCTTACCT
1 TCCTTACCT
29196636 TCCTTACCT
1 TCCTTACCT
29196645 TC
1 TC
29196647 GATCGCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.45, G:0.00, T:0.45
Consensus pattern (9 bp):
TCCTTACCT
Found at i:29196902 original size:30 final size:29
Alignment explanation
Indices: 29196865--29196948 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
29196855 TTCTTTTGTT
*
29196865 TCAATTTCTTTTTCATCTTTTTTTCACTC
1 TCAATTTCTTTTTCATCTTTTTTTCAATC
* *
29196894 TCAAATTTC-TTTTCGTTCTCTTTTTCAATC
1 TC-AATTTCTTTTTC-ATCTTTTTTTCAATC
* *
29196924 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCATCTT-TTTTT
29196949 GATTTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 14 0.32
30 30 0.68
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTTCATCTTTTTTTCAATC
Found at i:29196939 original size:12 final size:12
Alignment explanation
Indices: 29196924--29196955 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29196914 TTTTTCAATC
29196924 TCATTTTCTTTT
1 TCATTTTCTTTT
29196936 TCATTTTCTTTT
1 TCATTTTCTTTT
*
29196948 TGATTTTC
1 TCATTTTC
29196956 AAAGGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:29197053 original size:15 final size:15
Alignment explanation
Indices: 29197019--29197062 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
29197009 TTTGCCTCTC
*
29197019 TTTTCTTTTTATTTCA
1 TTTTCTTTTT-CTTCA
*
29197035 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCA
29197050 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
29197063 TTCTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTCA
Found at i:29197083 original size:21 final size:21
Alignment explanation
Indices: 29197015--29197084 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 21
29197005 GCCTTTTGCC
29197015 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTTATTT-ATTT
*
29197038 TCT-TTTTCTTCTT-TTTCTTT
1 TCTCTTTTCTT-TTATTTATTT
*
29197058 T-TCTTTTCTTTTATTTGTTT
1 TCTCTTTTCTTTTATTTATTT
29197078 TCTCTTT
1 TCTCTTT
29197085 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 18 0.44
21 10 0.24
22 7 0.17
23 3 0.07
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.77
Consensus pattern (21 bp):
TCTCTTTTCTTTTATTTATTT
Found at i:29199336 original size:30 final size:30
Alignment explanation
Indices: 29199302--29199398 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
29199292 TAAACTAAAA
29199302 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
29199332 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
29199362 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
29199392 TGAGCTA
1 TGAGCTA
29199399 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:29228970 original size:19 final size:18
Alignment explanation
Indices: 29228916--29229036 Score: 86
Period size: 20 Copynumber: 6.3 Consensus size: 18
29228906 TTATTAAATT
*
29228916 TTAATAAAAA-ATTCAAATA
1 TTAA-AAAAATATT-AAAAA
*
29228935 TTAAAAAATTATTAAAAA
1 TTAAAAAAATATTAAAAA
29228953 TTAGAAAAAATA-TAAAAA
1 TTA-AAAAAATATTAAAAA
29228971 TCGTAAAAAAATATTAAAAA
1 T--TAAAAAAATATTAAAAA
*
29228991 TTGTAAAAAAAAATTATAAAA
1 -T-TAAAAAAATATTA-AAAA
* *
29229012 TATATAGAAATA-TAAAAA
1 T-TAAAAAAATATTAAAAA
29229030 TATAAAA
1 T-TAAAA
29229037 TTTTATAAAG
Statistics
Matches: 85, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
18 27 0.32
19 24 0.28
20 29 0.34
21 5 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAAATATTAAAAA
Found at i:29228996 original size:20 final size:20
Alignment explanation
Indices: 29228936--29229012 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
29228926 ATTCAAATAT
*
29228936 TAAAAAATTATTAAAAA-T-
1 TAAAAAAATATTAAAAATTG
*
29228954 TAGAAAAAATA-TAAAAATCG
1 TA-AAAAAATATTAAAAATTG
29228974 TAAAAAAATATTAAAAATTG
1 TAAAAAAATATTAAAAATTG
*
29228994 TAAAAAAAAATTATAAAAT
1 TAAAAAAATATTA-AAAAT
29229013 ATATAGAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.16
19 15 0.30
20 22 0.44
21 5 0.10
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (20 bp):
TAAAAAAATATTAAAAATTG
Found at i:29229280 original size:34 final size:34
Alignment explanation
Indices: 29229240--29229307 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
29229230 TCGTTAAATT
* **
29229240 TTTTTTATGATTTTATAAAATTTTATAATTTTTA
1 TTTTTTACGATTTTATAAAAAATTATAATTTTTA
*
29229274 TTTTTTACGATTTTATAAAAAATTCTAATTTTTA
1 TTTTTTACGATTTTATAAAAAATTATAATTTTTA
29229308 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (34 bp):
TTTTTTACGATTTTATAAAAAATTATAATTTTTA
Found at i:29229319 original size:17 final size:17
Alignment explanation
Indices: 29229283--29229323 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29229273 ATTTTTTACG
29229283 ATTTTATAAAAAATTCTA
1 ATTTT-TAAAAAATTCTA
* *
29229301 ATTTTTAATAAATTTTA
1 ATTTTTAAAAAATTCTA
29229318 ATTTTT
1 ATTTTT
29229324 TATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTAAAAAATTCTA
Found at i:29229343 original size:18 final size:18
Alignment explanation
Indices: 29229322--29229363 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
29229312 ATTTTAATTT
*
29229322 TTTATA-TTTTTATTAAAA
1 TTTATAGTTTTT-CTAAAA
29229340 TTTAATAGTTTTTCTAAAA
1 TTT-ATAGTTTTTCTAAAA
29229359 TTTAT
1 TTTAT
29229364 TAATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATAGTTTTTCTAAAA
Found at i:29231440 original size:19 final size:19
Alignment explanation
Indices: 29231399--29231440 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
29231389 AACTGGTAGA
*
29231399 AATAAATATGATTGGCGTT
1 AATAAATATGATTGGCGTG
*
29231418 AATAAATAT-ATTTGGTGTG
1 AATAAATATGA-TTGGCGTG
29231437 AATA
1 AATA
29231441 TAATTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (19 bp):
AATAAATATGATTGGCGTG
Found at i:29234679 original size:17 final size:16
Alignment explanation
Indices: 29234659--29234712 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
29234649 TCATTCCAAT
29234659 TAACAGTTCATACTACA
1 TAACAGTTCATAC-ACA
*
29234676 TAACAGTTTATAACACA
1 TAACAGTTCAT-ACACA
29234693 TAACAGTTCATATCACA
1 TAACAGTTCATA-CACA
29234710 TAA
1 TAA
29234713 TAATTCTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 1 0.03
17 30 0.91
18 2 0.06
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (16 bp):
TAACAGTTCATACACA
Found at i:29235387 original size:18 final size:18
Alignment explanation
Indices: 29235373--29235416 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29235363 CACAGTTTGG
29235373 CAAATTAATACAGTTCGC
1 CAAATTAATACAGTTCGC
* ** *
29235391 CATATTAATACAAATCAC
1 CAAATTAATACAGTTCGC
29235409 CAAATTAA
1 CAAATTAA
29235417 CATAGTTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAATTAATACAGTTCGC
Found at i:29235813 original size:15 final size:15
Alignment explanation
Indices: 29235793--29235823 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29235783 TAATGACAAT
29235793 AACAAATTAAATGAA
1 AACAAATTAAATGAA
29235808 AACAAATTAAATGAA
1 AACAAATTAAATGAA
29235823 A
1 A
29235824 TAGAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AACAAATTAAATGAA
Found at i:29241751 original size:13 final size:14
Alignment explanation
Indices: 29241734--29241774 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
29241724 ATGGGGGTAG
29241734 GATTCTGTATATCT
1 GATTCTGTATATCT
*
29241748 -ATTCTGTTTATCT
1 GATTCTGTATATCT
29241761 GATTCTG-ATATCT
1 GATTCTGTATATCT
29241774 G
1 G
29241775 TATCTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (14 bp):
GATTCTGTATATCT
Found at i:29242556 original size:41 final size:41
Alignment explanation
Indices: 29242507--29242587 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
29242497 TACTTTTAGG
29242507 TCCCCGTAGACTCGTAATAGGGGTTGTAAGAGTTACTTTTT
1 TCCCCGTAGACTCGTAATAGGGGTTGTAAGAGTTACTTTTT
29242548 TCCCCGTAGACTCGTAATAGGGGTTGTAAGAGTTACTTTT
1 TCCCCGTAGACTCGTAATAGGGGTTGTAAGAGTTACTTTT
29242588 ACTCTAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
TCCCCGTAGACTCGTAATAGGGGTTGTAAGAGTTACTTTTT
Found at i:29242827 original size:49 final size:49
Alignment explanation
Indices: 29242750--29242855 Score: 167
Period size: 49 Copynumber: 2.1 Consensus size: 49
29242740 TCTAGAAGGG
* * * *
29242750 ATAAATAGTGATAAGAGTGTAGATAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGAAAGTGGAAGACCAAGTTTAGAAATGC
29242799 ATAAATAGTGATAAGAGTGTAGAAAGTGGAAGACCAAGTTTAGAAATGC
1 ATAAATAGTGATAAGAGTGTAGAAAGTGGAAGACCAAGTTTAGAAATGC
29242848 ATAGAATA
1 ATA-AATA
29242856 ATTTATTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 48 0.92
50 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.25, T:0.25
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGAAAGTGGAAGACCAAGTTTAGAAATGC
Found at i:29243314 original size:33 final size:34
Alignment explanation
Indices: 29243256--29243361 Score: 100
Period size: 32 Copynumber: 3.3 Consensus size: 34
29243246 CGCAAGCATT
* *
29243256 TCAAAACCCATATACATATATATTATATA-A-AA
1 TCAAGACCCATATACATATAAATTATATATATAA
29243288 -CAAGACCCATATATGCATATAAATTATATATATAA
1 TCAAGACCCATATA--CATATAAATTATATATATAA
** *
29243323 TCAAGACCC--ACGCATATATATTATATATATAA
1 TCAAGACCCATATACATATAAATTATATATATAA
29243355 -CAA-ACCC
1 TCAAGACCC
29243362 CACACATATT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.06
31 15 0.23
32 19 0.30
33 14 0.22
34 2 0.03
35 2 0.03
36 8 0.12
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (34 bp):
TCAAGACCCATATACATATAAATTATATATATAA
Found at i:29243346 original size:32 final size:31
Alignment explanation
Indices: 29243302--29243370 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
29243292 ACCCATATAT
29243302 GCATATAAATTATATATATAATCAAGA-CCCAC
1 GCATATAAATTATATATATAA-CAA-ACCCCAC
*
29243334 GCATATATATTATATATATAACAAACCCCAC
1 GCATATAAATTATATATATAACAAACCCCAC
*
29243365 ACATAT
1 GCATAT
29243371 TTTGCATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 13 0.38
32 20 0.59
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.29
Consensus pattern (31 bp):
GCATATAAATTATATATATAACAAACCCCAC
Found at i:29259270 original size:19 final size:19
Alignment explanation
Indices: 29259246--29259287 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
29259236 TGTTACCCTG
29259246 TTTCAACTCAAGAAATTCT
1 TTTCAACTCAAGAAATTCT
29259265 TTTCAACTCAAGAAATTCT
1 TTTCAACTCAAGAAATTCT
29259284 TTTC
1 TTTC
29259288 TTTTCTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTCAACTCAAGAAATTCT
Found at i:29260907 original size:16 final size:16
Alignment explanation
Indices: 29260886--29260920 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29260876 TCTGAATTAC
29260886 CAGTCCAAACTAAATT
1 CAGTCCAAACTAAATT
**
29260902 CAGTCCAGGCTAAATT
1 CAGTCCAAACTAAATT
29260918 CAG
1 CAG
29260921 ACCCTAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (16 bp):
CAGTCCAAACTAAATT
Found at i:29265041 original size:18 final size:18
Alignment explanation
Indices: 29264980--29265043 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
29264970 AATCGGTTAA
* *
29264980 TCAGTAATATTCATTTAT
1 TCAGTAACAGTCATTTAT
* *
29264998 TCAGTATCAGTCGTTTAT
1 TCAGTAACAGTCATTTAT
* *
29265016 TCTGTAACAGTCAATTAT
1 TCAGTAACAGTCATTTAT
29265034 TCAGTAACAG
1 TCAGTAACAG
29265044 ATAGTCTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:29266259 original size:13 final size:13
Alignment explanation
Indices: 29266241--29266271 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
29266231 TTTAATTTTC
29266241 TCTTTTCTTCCTT
1 TCTTTTCTTCCTT
29266254 TCTTTTCTTCCTT
1 TCTTTTCTTCCTT
29266267 TCTTT
1 TCTTT
29266272 CTTTTTCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTCCTT
Found at i:29274017 original size:64 final size:63
Alignment explanation
Indices: 29273910--29274100 Score: 229
Period size: 64 Copynumber: 3.0 Consensus size: 63
29273900 TGTATGCTTT
* * * ** * * *
29273910 GGTTAAATTTCGATAATGCACTAAGTGCCAGAATGACAAGATAGTGCTAAGTGCATATTACTTC
1 GGTTATATTTTGATGATGCACTAAGTGATAGAATGATATGATAGTGTTAA-TGCATATTACTTC
* *
29273974 GGTTATATTTTGATGATGCACTAAGTGTTAGAATGATATGATAGTGTTGAACGCATATTACTTC
1 GGTTATATTTTGATGATGCACTAAGTGATAGAATGATATGATAGTGTT-AATGCATATTACTTC
* * * *
29274038 GGTTATATTCTGATGATGCACTAAGTGATAGAATAATATGATAGCGTTGACTGCATATTACTT
1 GGTTATATTTTGATGATGCACTAAGTGATAGAATGATATGATAGTGTT-AATGCATATTACTT
29274101 TGGACTTTCC
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
64 109 0.98
65 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (63 bp):
GGTTATATTTTGATGATGCACTAAGTGATAGAATGATATGATAGTGTTAATGCATATTACTTC
Found at i:29290987 original size:9 final size:9
Alignment explanation
Indices: 29290973--29291004 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
29290963 AACTTGGTGC
29290973 ATTTTGTTT
1 ATTTTGTTT
29290982 ATTTTGTTT
1 ATTTTGTTT
29290991 ATTTTGTTT
1 ATTTTGTTT
29291000 ATTTT
1 ATTTT
29291005 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:29291085 original size:23 final size:23
Alignment explanation
Indices: 29291055--29291106 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
29291045 TGCAACTTGG
29291055 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
29291078 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
29291101 TTTCAT
1 TTTCAT
29291107 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:29300404 original size:19 final size:19
Alignment explanation
Indices: 29300376--29300430 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
29300366 ATTACAAAAT
*
29300376 AATTTCAAAATAATTTTTAA
1 AATTTCAAAAT-ATTTATAA
29300396 AATTT-AAAATATTTATAA
1 AATTTCAAAATATTTATAA
* *
29300414 AAATTCCAAA-ATTTATA
1 AATTTCAAAATATTTATA
29300431 TTTTGGGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 18 0.58
19 8 0.26
20 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTCAAAATATTTATAA
Found at i:29300414 original size:18 final size:20
Alignment explanation
Indices: 29300376--29300425 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
29300366 ATTACAAAAT
*
29300376 AATTTCAAAATAATTTTTAA
1 AATTTCAAAATAATTTATAA
29300396 AATTT-AAAAT-ATTTATAAA
1 AATTTCAAAATAATTTAT-AA
*
29300415 AATTCCAAAAT
1 AATTTCAAAAT
29300426 TTATATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
20 10 0.38
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTCAAAATAATTTATAA
Found at i:29313962 original size:311 final size:311
Alignment explanation
Indices: 29313399--29314643 Score: 2400
Period size: 311 Copynumber: 4.0 Consensus size: 311
29313389 TTCCTACAAG
* * * * *
29313399 CCTCCAAATATCCAGAATGGATGGCTAACATAGTCTCGGTACCAAAGAAAGATGGCAAAGTACGA
1 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
* * *
29313464 ATGTGCATGAATTATCGTGACCTGAATCGAGCAAGTCTTAAAGATAATTTTCCCTTACCACACAT
66 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
29313529 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
131 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
29313594 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
196 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
29313659 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
261 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
29313710 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
1 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
29313775 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
66 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
29313840 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
131 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
29313905 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
196 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
29313970 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
261 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
29314021 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
1 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
29314086 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
66 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
29314151 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
131 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
29314216 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
196 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
29314281 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
261 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
29314332 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
1 CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
29314397 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
66 ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
29314462 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
131 TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
* *
29314527 ATAATCAGATCAAAATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATATAGGGAACA
196 ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
29314592 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
261 TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
29314643 C
1 C
29314644 AAAGGGCTAT
Statistics
Matches: 924, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
311 924 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (311 bp):
CCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCAGTACTAAAGAAAGACGGCAAAGTACGA
ATGTGCGTGAATTATCATGACCTGAATCGAGCAAGTCCTAAAGATAATTTTCCCTTACCACACAT
TGATACGTTGGTGGATAACACAATAAAACATTCATTGTTTTCCTTCATGGATGGATTCTCGGGGT
ATAATCAGATCAAGATGGCCCCTGAGGATATGGAGAAAACTACCTTCGTAACAATGTAGGGAACA
TTCTATTACAAGGTGATGCCATTTGGGTTAAAGAATACTGGGGCAACATAT
Found at i:29317402 original size:43 final size:43
Alignment explanation
Indices: 29317320--29317402 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
29317310 ATTATGCCTA
* *
29317320 AAAAAAGATCAAGGTGAAAACCCAAAAAGGGCGTCTTGATAAT
1 AAAAAAGATCAAGGTGAAAACCCAAAAAGGGCATATTGATAAT
*
29317363 AAAAAGGATCAAGGTGAAAACCCAAAAAGGGCATATTGAT
1 AAAAAAGATCAAGGTGAAAACCCAAAAAGGGCATATTGAT
29317403 TAACACAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.49, C:0.13, G:0.22, T:0.16
Consensus pattern (43 bp):
AAAAAAGATCAAGGTGAAAACCCAAAAAGGGCATATTGATAAT
Found at i:29318371 original size:73 final size:73
Alignment explanation
Indices: 29318224--29318434 Score: 282
Period size: 73 Copynumber: 2.9 Consensus size: 73
29318214 TTGTTTTTCA
* *
29318224 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTTCGATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTA
* *
29318288 CTGTTTTTC
66 ATG-TCTTC
* * * * *
29318297 AAAAATCAATTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACACGCTGAGGTATTTTCAATT
29318362 AATG-CTTC
65 AATGTCTTC
* *
29318370 AAAAATTAACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACACGCTGAGGTATTTTCAATT
29318435 CCTGTTTTCT
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
73 98 0.82
75 21 0.18
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACACGCTGAGGTATTTTCAATTA
ATGTCTTC
Found at i:29318495 original size:161 final size:161
Alignment explanation
Indices: 29318297--29318682 Score: 460
Period size: 161 Copynumber: 2.4 Consensus size: 161
29318287 TCTGTTTTTC
* *
29318297 AAAAATCAATTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAATT
* *
29318362 AATGC-TTC-AAAAATTAACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACACGCTGAGGT
66 AATGCTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCA-G-CACACGCTGAGGT
*
29318425 ATTTTCAATTCCT-GTTTTCTAA-AAAAAAAGAA
129 ATTTTCAATTCCTATTTTTC-AATAAAAAAAGAA
* * * *
29318457 AAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCGGGGCAC--GCCGATGTATTTTCAAT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAT
** *
29318520 TTCTTCTTTTCAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCACACGCTGAGG
65 TAATGC-TTTC-AAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCACACGCTGAGG
* * * ******
29318585 TATTTTCAATTTCTATTTTTCAATTTATATTTTTC
128 TATTTTCAATTCCTATTTTTCAA-TAAAAAAAGAA
* *
29318620 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCATATGTCGAGGTATTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAA
29318683 AATCTACTTT
Statistics
Matches: 189, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
159 19 0.10
160 5 0.03
161 65 0.34
162 42 0.22
163 44 0.23
164 14 0.07
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (161 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAATT
AATGCTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCACACGCTGAGGTAT
TTTCAATTCCTATTTTTCAATAAAAAAAGAA
Found at i:29318536 original size:86 final size:88
Alignment explanation
Indices: 29318377--29318595 Score: 220
Period size: 75 Copynumber: 2.7 Consensus size: 88
29318367 TTCAAAAATT
* *
29318377 AACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACACGCTGAGGTATTTTCAATTCCTGTTT
1 AACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTCCTCTTT
29318442 TCTAAAAAAAAAGAAAAAAAGTC
66 TCTAAAAAAAAAGAAAAAAAGTC
* ** * *
29318465 AACTCGTATTGCGAGAGGC-GAGTTGAGCCTC-GG-GGCACGCCGATGTATTTTCAATTTCTTCT
1 AACTCATATTGCGAGA-GCTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAA-TTCCTCT
29318527 TTTC-----------AAAAAAA-TC
64 TTTCTAAAAAAAAAGAAAAAAAGTC
* *
29318540 AACTCATATTGCGAGAGATGAGTTGAGCCTCA-G-CACACGCTGAGGTATTTTCAATT
1 AACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATT
29318596 TCTATTTTTC
Statistics
Matches: 114, Mismatches: 13, Indels: 22
0.77 0.09 0.15
Matches are distributed among these distances:
74 3 0.03
75 47 0.41
76 7 0.06
86 17 0.15
87 11 0.10
88 27 0.24
89 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (88 bp):
AACTCATATTGCGAGAGCTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTCCTCTTT
TCTAAAAAAAAAGAAAAAAAGTC
Found at i:29318606 original size:14 final size:14
Alignment explanation
Indices: 29318587--29318621 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
29318577 CGCTGAGGTA
*
29318587 TTTTCAATTTCTAT
1 TTTTCAATTTATAT
29318601 TTTTCAATTTATAT
1 TTTTCAATTTATAT
29318615 TTTTCAA
1 TTTTCAA
29318622 AAATCAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATAT
Found at i:29318619 original size:89 final size:88
Alignment explanation
Indices: 29318512--29318835 Score: 288
Period size: 89 Copynumber: 3.7 Consensus size: 88
29318502 CGCCGATGTA
*
29318512 TTTTCAATTTCT-TCTTTTCAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCAC
1 TTTTCAATTTATAT-TTTTC-AAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCAC
29318576 ACGCTGAGGTATTTTCAATTTCTAT
64 ACGCTGAGGTATTTTCAATTTCTAT
* * *
29318601 TTTTCAATTTATATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAT
1 TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTC-AG-CAC
* ** *
29318665 ATG-TCGAGGTATTTTCAAAATCTAC
64 ACGCT-GAGGTATTTTCAATTTCTAT
* * * * * ** *
29318690 TTTTCAAATTA-A-GTTTCAAAAAAACCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCA
1 TTTTCAATTTATATTTTTC-AAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCACA
* *
29318753 CGTGCTGAGCTATTTTCAATTTCTGT
65 C--GCTGAGGTATTTTCAATTTCTAT
* * * * * *
29318779 TTTT-AATGTT-TGTTTTT-AAAGAGTTAATTCATATTGCGAGAAATGAGTTGAG-CTCAG
1 TTTTCAAT-TTATATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAG
29318836 GATCACATGC
Statistics
Matches: 189, Mismatches: 34, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
87 46 0.24
88 34 0.18
89 104 0.55
90 5 0.03
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (88 bp):
TTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGCACAC
GCTGAGGTATTTTCAATTTCTAT
Found at i:29319006 original size:21 final size:21
Alignment explanation
Indices: 29318960--29319008 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29318950 ACCAGAGCCC
* **
29318960 TGAAGTTACATTGGAGCTGAT
1 TGAAGTTACAGTGGAGCACAT
*
29318981 CGAAGTTACAGTGGAGCACAT
1 TGAAGTTACAGTGGAGCACAT
29319002 TGAAGTT
1 TGAAGTT
29319009 GCAGATCTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
TGAAGTTACAGTGGAGCACAT
Found at i:29319072 original size:44 final size:44
Alignment explanation
Indices: 29319023--29319122 Score: 157
Period size: 44 Copynumber: 2.3 Consensus size: 44
29319013 ATCTTATCTT
29319023 CCTGAAGATACAGCAGAAGAGCAGA-TCACAACAAATTTTATATC
1 CCTGAAGATACAGCAGAAGAGCA-ACTCACAACAAATTTTATATC
* * *
29319067 TCTGAAGATATAGCAGAAGAGCAACTCACAACGAATTTTATATC
1 CCTGAAGATACAGCAGAAGAGCAACTCACAACAAATTTTATATC
29319111 CCTGAAGATACA
1 CCTGAAGATACA
29319123 AGTAGACTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (44 bp):
CCTGAAGATACAGCAGAAGAGCAACTCACAACAAATTTTATATC
Found at i:29320656 original size:23 final size:25
Alignment explanation
Indices: 29320602--29320656 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
29320592 CATATACTAT
*
29320602 TATGTATACATTTTAATGTTATTAG
1 TATGTATACATTTTAATGCTATTAG
* *
29320627 T-TATATACCTTTT-ATGCTATT-G
1 TATGTATACATTTTAATGCTATTAG
29320649 TATGTATA
1 TATGTATA
29320657 TTCTTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.08
23 12 0.48
24 10 0.40
25 1 0.04
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (25 bp):
TATGTATACATTTTAATGCTATTAG
Found at i:29320927 original size:31 final size:32
Alignment explanation
Indices: 29320864--29320927 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
29320854 CCATCTTATG
* * *
29320864 TATATATTTTTAAATACTATATTATATGTATA
1 TATATATTCTTAAATACCATATTATATATATA
* *
29320896 TATATATTCTT-AGTACCATATTATGTATATA
1 TATATATTCTTAAATACCATATTATATATATA
29320927 T
1 T
29320928 TTATTTTTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (32 bp):
TATATATTCTTAAATACCATATTATATATATA
Found at i:29320938 original size:26 final size:28
Alignment explanation
Indices: 29320844--29320932 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
29320834 TCCATGTACA
* *
29320844 TATTTTTATACCATCTTATGTATATATT
1 TATTATTATACCATATTATGTATATATT
* * *
29320872 T-TTA-AATACTATATTATATGTATATATA
1 TATTATTATACCATA-T-TATGTATATATT
*
29320900 TATTCTTAGTACCATATTATGTATATATT
1 TATTATTA-TACCATATTATGTATATATT
29320929 TATT
1 TATT
29320933 TTTACCCCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
26 6 0.13
27 3 0.06
28 13 0.28
29 17 0.36
30 2 0.04
31 6 0.13
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (28 bp):
TATTATTATACCATATTATGTATATATT
Found at i:29329971 original size:40 final size:40
Alignment explanation
Indices: 29329926--29330161 Score: 210
Period size: 40 Copynumber: 5.9 Consensus size: 40
29329916 CGAATACACG
* * * *
29329926 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* ** *
29329966 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
29330006 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
29330046 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * * * *
29330086 GTAACTC-GCACCAATGC-CTTCGGGTCTTAGTCCGGATATGG
1 -TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT-A
* * *
29330127 TCACTTAGCAC-AAAGC-CTTCGGGACTTAGCGCGGA
1 TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGA
29330162 CATCATTCAA
Statistics
Matches: 159, Mismatches: 33, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
40 144 0.91
41 15 0.09
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
Found at i:29330147 original size:120 final size:120
Alignment explanation
Indices: 29329926--29330161 Score: 270
Period size: 120 Copynumber: 2.0 Consensus size: 120
29329916 CGAATACACG
* *
29329926 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGG
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACCAATGCTCTTCGGGG
*
29329991 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 TTTAGCACGGATATATCACTAGCACGAAAGCTCTTCGGAACTTAGCCCGGATACA
* * * *
29330046 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAAC-TC-GCACCAATGC-CTTC-
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGA--CA-TAACACCAGCACCAATGCTCTTCG
* * *
29330107 GGGTCTTAGTC-CGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCGCGGA
63 GGGT-TTAG-CACGGATAT-ATCAC-TAGCACGAAAGCTCTTCGGAACTTAGCCCGGA
29330162 CATCATTCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
119 4 0.04
120 65 0.66
121 18 0.18
122 8 0.08
123 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (120 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACCAATGCTCTTCGGGG
TTTAGCACGGATATATCACTAGCACGAAAGCTCTTCGGAACTTAGCCCGGATACA
Found at i:29330510 original size:29 final size:29
Alignment explanation
Indices: 29330471--29330549 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
29330461 CTTAATAATC
*
29330471 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
29330501 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
29330530 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29330550 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:29330579 original size:43 final size:43
Alignment explanation
Indices: 29330531--29330633 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
29330521 TGCATTTCAA
29330531 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
*
29330574 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
29330617 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
29330634 TGAAAACCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCATGAACACTTATT
Found at i:29332550 original size:37 final size:37
Alignment explanation
Indices: 29332492--29332567 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
29332482 TTACGAAGTT
* * *
29332492 TTACCCGGACATAATCTCCACACGAAGTTATCGGGTC
1 TTACCCGGACAAAATCCCCACACGAAGTCATCGGGTC
*
29332529 TTACCCGGACAAAATCCCCACACGTAGTCATCGGGTC
1 TTACCCGGACAAAATCCCCACACGAAGTCATCGGGTC
29332566 TT
1 TT
29332568 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
TTACCCGGACAAAATCCCCACACGAAGTCATCGGGTC
Found at i:29332760 original size:49 final size:49
Alignment explanation
Indices: 29332686--29333263 Score: 914
Period size: 47 Copynumber: 12.1 Consensus size: 49
29332676 CCCTTCGGGA
* * * * * *
29332686 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
29332733 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29332782 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29332829 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29332878 CGTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29332925 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29332974 CGTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29333021 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29333068 CTTAT--TATATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29333115 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29333162 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29333211 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29333260 CTTA
1 CTTA
29333264 CTATCATTTC
Statistics
Matches: 496, Mismatches: 23, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
47 277 0.56
48 1 0.00
49 218 0.44
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29332850 original size:96 final size:96
Alignment explanation
Indices: 29332686--29333263 Score: 948
Period size: 96 Copynumber: 6.0 Consensus size: 96
29332676 CCCTTCGGGA
* * * * * * * *
29332686 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGACCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
29332751 ACTTCCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
29332782 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
29332847 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
29332878 CGTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
29332943 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
29332974 CGTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
29333037 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
29333068 CTTATTATATATATACACTTTCACATTCATCACATCGGTCATTAGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
*
29333131 ACTTTCACATTCATCACATCGGCCACTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
29333162 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
29333227 ACACTTTCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
29333260 CTTA
1 CTTA
29333264 CTATCATTTC
Statistics
Matches: 458, Mismatches: 20, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
94 134 0.29
96 282 0.62
98 42 0.09
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29337121 original size:40 final size:40
Alignment explanation
Indices: 29337064--29337166 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
29337054 CCAGCATGAT
* * * *
29337064 TGCTCTTCGGGATTTAGCATGGATATATCACTAGCAAGAA
1 TGCTCTTCGGAACTTAGCACGGATACATCACTAGCAAGAA
* * *
29337104 TGCTCTTTGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGAACTTAGCACGGATACATCACTAGCAAGAA
* *
29337144 TGCTCTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGAACTTAGCACGGA
29337167 CATCATTCGA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCACGGATACATCACTAGCAAGAA
Found at i:29337511 original size:29 final size:29
Alignment explanation
Indices: 29337472--29337550 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
29337462 CTTAATAATC
*
29337472 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
29337502 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
* *
29337531 AGCCCGCACACTTACTGCCA
1 AACCCGCACACTTAGTGCCA
29337551 ATCTCACAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 37 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:29337593 original size:43 final size:43
Alignment explanation
Indices: 29337532--29337677 Score: 274
Period size: 43 Copynumber: 3.4 Consensus size: 43
29337522 TGCATTTCAA
* *
29337532 GCCCGCACACTTACTGCCAATCTCACAATCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
29337575 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
29337618 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
29337661 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
29337678 TGAAAACCAA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:29348089 original size:39 final size:39
Alignment explanation
Indices: 29348035--29348114 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
29348025 ACAACCAATA
29348035 CCATTCAATGATGCATCACTATAAATCATGAACTCTTTC
1 CCATTCAATGATGCATCACTATAAATCATGAACTCTTTC
*
29348074 CCATTCAATGATGCATCACTATAAATCATGATCTCTTTC
1 CCATTCAATGATGCATCACTATAAATCATGAACTCTTTC
29348113 CC
1 CC
29348115 CATCTCAGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (39 bp):
CCATTCAATGATGCATCACTATAAATCATGAACTCTTTC
Found at i:29359451 original size:15 final size:16
Alignment explanation
Indices: 29359433--29359463 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29359423 TTTAACTGAG
29359433 TAAAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
29359448 TAAAATAAAAATAAAA
1 TAAAATAAAAATAAAA
29359464 GTTTCAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:29359460 original size:6 final size:5
Alignment explanation
Indices: 29359433--29359463 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
29359423 TTTAACTGAG
29359433 TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
29359464 GTTTCAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:29363488 original size:157 final size:157
Alignment explanation
Indices: 29363237--29363707 Score: 926
Period size: 157 Copynumber: 3.0 Consensus size: 157
29363227 TTTCTTAAGG
29363237 AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
1 AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
*
29363302 ACATAACAATTATTTGAAATAACATAACTTTATTCATACTAGAGTTTAGCATATTTAAAAAAAAA
66 ACATAACAATTATTTGAAATAACAGAACTTTATTCATACTAGAGTTTAGCATATTTAAAAAAAAA
29363367 TCATATTTTTGAACAAAATATAACCTA
131 TCATATTTTTGAACAAAATATAACCTA
29363394 AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
1 AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
29363459 ACATAACAATTATTTGAAATAACAGAACTTTATTCATACTAGAGTTTAGCATATTTAAAAAAAAA
66 ACATAACAATTATTTGAAATAACAGAACTTTATTCATACTAGAGTTTAGCATATTTAAAAAAAAA
29363524 TCATATTTTTGAACAAAATATAACCTA
131 TCATATTTTTGAACAAAATATAACCTA
29363551 AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
1 AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
29363616 ACATAACAATTATTTGAAATAACAGAACTTTATTCATACTAGAGTTTAGCATATTT-AAAAAAAA
66 ACATAACAATTATTTGAAATAACAGAACTTTATTCATACTAGAGTTTAGCATATTTAAAAAAAAA
29363680 TCATATTTTTGAACAAAATATAACCTA
131 TCATATTTTTGAACAAAATATAACCTA
29363707 A
1 A
29363708 TCATAATTAA
Statistics
Matches: 313, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
156 36 0.12
157 277 0.88
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (157 bp):
AACTAAAAGTTTATGATATGATTTACATACTTTTTTAATAGTACATTTATGTCATAATTTAGCTA
ACATAACAATTATTTGAAATAACAGAACTTTATTCATACTAGAGTTTAGCATATTTAAAAAAAAA
TCATATTTTTGAACAAAATATAACCTA
Found at i:29366032 original size:16 final size:15
Alignment explanation
Indices: 29366007--29366040 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29365997 AAAGTTGATA
*
29366007 ATAATTAATATATATT
1 ATAATAAATATA-ATT
29366023 ATAATAAATATAATT
1 ATAATAAATATAATT
29366038 ATA
1 ATA
29366041 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:29366159 original size:30 final size:30
Alignment explanation
Indices: 29366102--29366160 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29366092 TGCCTTTAAA
* *
29366102 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
29366132 AATATTTACAAAAAGAG-CAACCAAATTTT
1 AATATTTACAAAAAGAGAC-ACCAAATTTT
29366161 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:29368119 original size:27 final size:27
Alignment explanation
Indices: 29368089--29368215 Score: 139
Period size: 27 Copynumber: 4.7 Consensus size: 27
29368079 TTGGTTTTAC
* *
29368089 AAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* * *
29368116 AAAATTACTAAAGTACCCTCGGTTTGT
1 AAAATTACCAAAATACCCTCGATTTGT
* * *
29368143 AAAATTACCAAAGTACCCTTGATTTGC
1 AAAATTACCAAAATACCCTCGATTTGT
*
29368170 AAAATTACCAAAATACCCTC-AGTTTGA
1 AAAATTACCAAAATACCCTCGA-TTTGT
* *
29368197 AAAATTATCGAAATACCCT
1 AAAATTACCAAAATACCCT
29368216 TATAAGTTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 86 0.99
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTGT
Found at i:29368228 original size:54 final size:54
Alignment explanation
Indices: 29368114--29368228 Score: 126
Period size: 54 Copynumber: 2.1 Consensus size: 54
29368104 CCCTCGACTT
* * * * **
29368114 GTAAAATTACTAAAGTACCCTCGGTTTGTAAAATTACCAAAGTACCCTTGATTT
1 GTAAAATTACCAAAATACCCTCAGTTTGAAAAATTACCAAAGTACCCTTGATAA
* *
29368168 GCAAAATTACCAAAATACCCTCAGTTTGAAAAATTATCGAAA-TACCCTT-ATAA
1 GTAAAATTACCAAAATACCCTCAGTTTGAAAAATTA-CCAAAGTACCCTTGATAA
29368221 GTTAAAAT
1 G-TAAAAT
29368229 GATCGTTTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
53 3 0.06
54 43 0.86
55 4 0.08
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (54 bp):
GTAAAATTACCAAAATACCCTCAGTTTGAAAAATTACCAAAGTACCCTTGATAA
Found at i:29368708 original size:27 final size:27
Alignment explanation
Indices: 29368670--29368725 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
29368660 TACTAATATG
* *
29368670 GTATTGGGCTAAGGCCCACCTTGTTCT
1 GTATTGGGCTAAAGCCCACATTGTTCT
*
29368697 GTATTGGGCTAAAGTCCACATTGTTCT
1 GTATTGGGCTAAAGCCCACATTGTTCT
29368724 GT
1 GT
29368726 TCTGTTACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (27 bp):
GTATTGGGCTAAAGCCCACATTGTTCT
Found at i:29374310 original size:27 final size:27
Alignment explanation
Indices: 29374272--29374434 Score: 111
Period size: 27 Copynumber: 6.1 Consensus size: 27
29374262 CTGGACCGGC
* *
29374272 AATGACTGAAATAACCTCGAT-GGGTAA
1 AATGATTGAAATAACC-CCATAGGGTAA
*
29374299 AATGATTGAAAT-GCCCCATAGGGTAA
1 AATGATTGAAATAACCCCATAGGGTAA
* * **
29374325 AATGATTGAAATACCCCCGTAGGGTGG
1 AATGATTGAAATAACCCCATAGGGTAA
***
29374352 AAT-ACCAAAAT-ACCCCTATAGGGTAA
1 AATGATTGAAATAACCCC-ATAGGGTAA
* * *
29374378 AATGATCGTAAT-ACCCTTATAGGGTAA
1 AATGATTGAAATAACCC-CATAGGGTAA
* * **
29374405 AATGATCGTAATAACCCTGTAGGGTAA
1 AATGATTGAAATAACCCCATAGGGTAA
29374432 AAT
1 AAT
29374435 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
25 7 0.06
26 34 0.31
27 66 0.59
28 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (27 bp):
AATGATTGAAATAACCCCATAGGGTAA
Found at i:29374329 original size:26 final size:26
Alignment explanation
Indices: 29374293--29374434 Score: 124
Period size: 27 Copynumber: 5.3 Consensus size: 26
29374283 TAACCTCGAT
* *
29374293 GGGTAAAATGATTGAAATGCCCCATA
1 GGGTAAAATGATCGAAATACCCCATA
* *
29374319 GGGTAAAATGATTGAAATACCCCCGTA
1 GGGTAAAATGATCGAAATA-CCCCATA
** * *
29374346 GGGTGGAAT-ACCAAAATACCCCTATA
1 GGGTAAAATGATCGAAATACCCC-ATA
* *
29374372 GGGTAAAATGATCGTAATACCCTTATA
1 GGGTAAAATGATCGAAATACCC-CATA
* **
29374399 GGGTAAAATGATCGTAATAACCCTGTA
1 GGGTAAAATGATCGAAAT-ACCCCATA
29374426 GGGTAAAAT
1 GGGTAAAAT
29374435 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.04
26 33 0.34
27 55 0.57
28 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (26 bp):
GGGTAAAATGATCGAAATACCCCATA
Found at i:29388897 original size:38 final size:38
Alignment explanation
Indices: 29388846--29388921 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
29388836 AATATTTATC
29388846 GAATATCAATTCAAAAGAAAGTAGATAAATCTCCAAGG
1 GAATATCAATTCAAAAGAAAGTAGATAAATCTCCAAGG
29388884 GAATATCAATTCAAAAGAAAGTAGATAAATCTCCAAGG
1 GAATATCAATTCAAAAGAAAGTAGATAAATCTCCAAGG
29388922 CTTTTATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (38 bp):
GAATATCAATTCAAAAGAAAGTAGATAAATCTCCAAGG
Found at i:29394919 original size:21 final size:21
Alignment explanation
Indices: 29394895--29394938 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29394885 GAATCTTTAG
*
29394895 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
29394916 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
29394937 TA
1 TA
29394939 ATTAGGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:29395488 original size:21 final size:23
Alignment explanation
Indices: 29395463--29395515 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
29395453 TGGGTTTAAA
29395463 AATTTTAATTTTAATTGA-A-TT
1 AATTTTAATTTTAATTGAGATTT
* *
29395484 AATTTTAAATTTAGTTGAGATTT
1 AATTTTAATTTTAATTGAGATTT
*
29395507 AATTATAAT
1 AATTTTAAT
29395516 CTAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 16 0.62
22 1 0.04
23 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (23 bp):
AATTTTAATTTTAATTGAGATTT
Found at i:29397584 original size:13 final size:14
Alignment explanation
Indices: 29397566--29397594 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29397556 AAGAGAAGAT
29397566 AATATTT-TATAAA
1 AATATTTATATAAA
29397579 AATATTTATATAAA
1 AATATTTATATAAA
29397593 AA
1 AA
29397595 CATGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTATATAAA
Found at i:29398481 original size:10 final size:10
Alignment explanation
Indices: 29398466--29398492 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29398456 ATACTCACTA
29398466 TCTTTTAGCT
1 TCTTTTAGCT
29398476 TCTTTTAGCT
1 TCTTTTAGCT
29398486 TCTTTTA
1 TCTTTTA
29398493 TCGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.07, T:0.63
Consensus pattern (10 bp):
TCTTTTAGCT
Found at i:29404436 original size:24 final size:24
Alignment explanation
Indices: 29404380--29404436 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
29404370 CCGTGTGTGT
* * *
29404380 GAATCTGAATATGCATTTGTTTCT
1 GAATATGAATATGCATTTGTATCC
* *
29404404 GAATCTGAATATGTATTTGTATCC
1 GAATATGAATATGCATTTGTATCC
*
29404428 GATTATGAA
1 GAATATGAA
29404437 ATACATATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (24 bp):
GAATATGAATATGCATTTGTATCC
Found at i:29408958 original size:19 final size:20
Alignment explanation
Indices: 29408907--29408958 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
29408897 CTAGCAGTTA
*
29408907 CAAATCAAGCAATGAAAATCC
1 CAAAT-AAGCCATGAAAATCC
*
29408928 CAAATAATCCATGAAAAT-C
1 CAAATAAGCCATGAAAATCC
*
29408947 CAAATAGGCCAT
1 CAAATAAGCCAT
29408959 TATTACAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 11 0.41
21 5 0.19
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.17
Consensus pattern (20 bp):
CAAATAAGCCATGAAAATCC
Found at i:29409768 original size:18 final size:17
Alignment explanation
Indices: 29409742--29409775 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29409732 CATGTAATTT
29409742 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
29409760 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
29409776 AGGCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:29412335 original size:21 final size:20
Alignment explanation
Indices: 29412298--29412350 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
29412288 ATCAGCTCAC
*
29412298 TTGAGCTCATTTCAGCTTGT
1 TTGAGCTCATTTCAGCTCGT
* *
29412318 TTGAGCTTGATTTTAGCTCGT
1 TTGAGC-TCATTTCAGCTCGT
* *
29412339 TTCAGCCCATTT
1 TTGAGCTCATTT
29412351 ATTATTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (20 bp):
TTGAGCTCATTTCAGCTCGT
Found at i:29412595 original size:13 final size:13
Alignment explanation
Indices: 29412577--29412601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29412567 TAGTTGTGTT
29412577 TTATTTAATTATG
1 TTATTTAATTATG
29412590 TTATTTAATTAT
1 TTATTTAATTAT
29412602 ATAGGTTCAG
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:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTATTTAATTATG
Found at i:29413702 original size:13 final size:14
Alignment explanation
Indices: 29413686--29413721 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
29413676 CAATCTCATA
29413686 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
29413699 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
29413712 TCTC-ATTTCA
1 TCTCAATTTCA
29413722 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:29413711 original size:18 final size:19
Alignment explanation
Indices: 29413673--29413713 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
29413663 TGGTTCATGT
29413673 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
29413692 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
29413710 TTTC
1 TTTC
29413714 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:29413903 original size:39 final size:38
Alignment explanation
Indices: 29413836--29413970 Score: 92
Period size: 39 Copynumber: 3.4 Consensus size: 38
29413826 ACCAATATGG
* * * *
29413836 CACCCAGTGGCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGTCTCATCGGCTAG-CCGAAGAAATATTTGA
* * *
29413875 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGTCTCATCGG-CTAGCCGAAGAAATATTTGA
* ** * * * *
29413913 TACCCAGTACCTCATAGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGTCTCATCG--GCTAGCCGAAGAAATAT-TTGA
29413954 CACCCAGTGTCTCATCG
1 CACCCAGTGTCTCATCG
29413971 ACTCGAGGTC
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
38 17 0.24
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (38 bp):
CACCCAGTGTCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:29414236 original size:18 final size:19
Alignment explanation
Indices: 29414210--29414248 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29414200 TTTCAATTCA
29414210 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
29414229 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
29414247 AT
1 AT
29414249 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:29415574 original size:5 final size:5
Alignment explanation
Indices: 29415564--29415625 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
29415554 TTACTTATTT
* *
29415564 ATATA ATATA ATATAA TATATA ATATA ATATA CTATA GTATA ATAATA
1 ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA
*
29415612 ATTTA ATAT- ATATA
1 ATATA ATATA ATATA
29415626 TTTTAACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 4 0.08
5 33 0.69
6 7 0.15
7 4 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:29415584 original size:12 final size:12
Alignment explanation
Indices: 29415569--29415623 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
29415559 TATTTATATA
29415569 ATATAATATAAT
1 ATATAATATAAT
29415581 ATATAATATAAT
1 ATATAATATAAT
29415593 ATACTATAGTATAAT
1 ATA-TA-A-TATAAT
*
29415608 A-ATAATTTAAT
1 ATATAATATAAT
29415619 ATATA
1 ATATA
29415624 TATTTTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.16
12 19 0.50
13 4 0.11
14 2 0.05
15 7 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:29415638 original size:26 final size:26
Alignment explanation
Indices: 29415564--29415625 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 26
29415554 TTACTTATTT
* * *
29415564 ATATAATATAATATAATATATAATATA
1 ATATACTATAGTATAACA-ATAATATA
* *
29415591 ATATACTATAGTATAATAATAATTTA
1 ATATACTATAGTATAACAATAATATA
29415617 ATATA-TATA
1 ATATACTATA
29415626 TTTTAACACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 4 0.12
26 12 0.38
27 16 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATACTATAGTATAACAATAATATA
Found at i:29417547 original size:12 final size:12
Alignment explanation
Indices: 29417530--29417559 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
29417520 CGGCTCAATG
29417530 CATTGGCCACCA
1 CATTGGCCACCA
29417542 CATTGGCCACCA
1 CATTGGCCACCA
29417554 CATTGG
1 CATTGG
29417560 TCTTACCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (12 bp):
CATTGGCCACCA
Found at i:29417727 original size:16 final size:17
Alignment explanation
Indices: 29417681--29417734 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
29417671 TGTTCGGATA
29417681 TATATTTATAATTT-TAT
1 TATA-TTATAATTTATAT
* *
29417698 TATATTGTGA-TTATAT
1 TATATTATAATTTATAT
29417714 TATATTAT-ATTTATACT
1 TATATTATAATTTATA-T
29417731 TATA
1 TATA
29417735 ATCTCTCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.10
16 19 0.61
17 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
TATATTATAATTTATAT
Found at i:29424483 original size:134 final size:134
Alignment explanation
Indices: 29424036--29424487 Score: 764
Period size: 134 Copynumber: 3.4 Consensus size: 134
29424026 NNNNNNNNNN
*
29424036 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
1 GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
* * * *
29424101 TACAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTGGTTAGGGAGGTAAAATCTGCCAT
66 TACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCAT
29424166 CTTT
131 CTTT
*
29424170 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
1 GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
*
29424235 TACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCC
66 TACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCC
29424300 ATCTTT
129 ATCTTT
*
29424306 GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTG-ATATCTTCAATCTATTCCACTGCCAG
1 GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGCA-ATCTTCAATCTATTCCACTGCCAA
*
29424370 ATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTTGTCAGGGAGGTAAAATCTGCCA
65 ATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCA
*
29424435 TCTTC
130 TCTTT
29424440 GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTG-ATATCTTCAA
1 GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGCA-ATCTTCAA
29424488 CTAGCTCTGC
Statistics
Matches: 305, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
134 177 0.58
135 1 0.00
136 127 0.42
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (134 bp):
GATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
TACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCAT
CTTT
Found at i:29424581 original size:86 final size:86
Alignment explanation
Indices: 29424435--29424698 Score: 393
Period size: 86 Copynumber: 3.1 Consensus size: 86
29424425 AAATCTGCCA
* * * *
29424435 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGATATCTTCAACTAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTA
29424500 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* * * *
29424522 TCTTCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
*
29424587 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
29424608 TCTTCGATCTGCTTCGCTGTCAATGCACGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
* * *
29424673 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
29424694 TCTTC
1 TCTTC
29424699 AATTTTCACT
Statistics
Matches: 158, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
86 139 0.88
87 19 0.12
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTGCTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:29428868 original size:19 final size:20
Alignment explanation
Indices: 29428844--29428887 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
29428834 CGTGAAAGTC
* *
29428844 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
29428863 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
29428883 -AATGC
1 TAATGC
29428888 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:29433545 original size:23 final size:23
Alignment explanation
Indices: 29433512--29433569 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
29433502 ATTTTATTAT
*
29433512 GAAATAAATAATAATAATA-ATAA
1 GAAATATATAATAATAA-ACATAA
* * *
29433535 TAAATTTATAATCATAAACATAA
1 GAAATATATAATAATAAACATAA
29433558 GAAATATATAAT
1 GAAATATATAAT
29433570 GTAAAACTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (23 bp):
GAAATATATAATAATAAACATAA
Found at i:29433605 original size:18 final size:18
Alignment explanation
Indices: 29433582--29433616 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29433572 AAAACTCTAT
29433582 TTCTAATAAATATTAAAA
1 TTCTAATAAATATTAAAA
*
29433600 TTCTAATATATATTAAA
1 TTCTAATAAATATTAAA
29433617 TTTATTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TTCTAATAAATATTAAAA
Found at i:29437385 original size:5 final size:5
Alignment explanation
Indices: 29437375--29437417 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
29437365 TATCCCTTCT
* * *
29437375 TTTCC TTTCC TTGCC TTTCT TTTCC TTTCC TTGCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTT
29437418 ATAATTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.35, G:0.05, T:0.60
Consensus pattern (5 bp):
TTTCC
Found at i:29437394 original size:20 final size:20
Alignment explanation
Indices: 29437371--29437413 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
29437361 TAACTATCCC
29437371 TTCTTTTCCTTTCCTTGCCT
1 TTCTTTTCCTTTCCTTGCCT
29437391 TTCTTTTCCTTTCCTTGCCT
1 TTCTTTTCCTTTCCTTGCCT
29437411 TTC
1 TTC
29437414 CTTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.05, T:0.60
Consensus pattern (20 bp):
TTCTTTTCCTTTCCTTGCCT
Found at i:29448806 original size:131 final size:129
Alignment explanation
Indices: 29448427--29448869 Score: 415
Period size: 131 Copynumber: 3.4 Consensus size: 129
29448417 CCCAAACGGT
* * * ** * *
29448427 AAATCGAAACCCAGCACGATTGGGCACGATTTATCGAA-TTTCCAAATATGAAACATTGCCTCAT
1 AAAT-GAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCA-
* * * * * * *
29448491 TTTAA----TTTGAGAAAACATGGACGAAAGTTCAAAAGGATATTCTGTATTTTAGTCGAATAGA
64 TTTAATTTTTTTTAAAAAAAATGGACGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAAGAAA
29448552 A
129 A
* * * * * **
29448553 AATTGAAGCCCAGCATGATTGGGCACGA-CTCCCCAAACT-TCCAAGCACGAAATATTGCCTC--
1 AAATGAAACCCAGCACGATTGGGCACGATCT-CTCAAACTCCCCAAATACGAAATATTGCCTCAT
* * * * *
29448614 GT--TTTATTTTAAGAAAACGA-GGATGAAAATTTCAAAAAAGGATATTCCATATTTTAGTCGAA
65 TTAATTTTTTTTAA-AAAA-AATGGACG-AAATTTC--AAAAGGATATTCCGTATTTTAGTCGAA
29448676 CGAAAA
125 -GAAAA
*
29448682 AAATGAAACCCAGCACAATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCATT
1 AAATGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCATT
*
29448747 TAATTTTTTTTTAAAAAAAATGGACGAAATTTCCAAAGGATATTCCGTATTTTAGTCGAATGAAA
66 TAA-TTTTTTTTAAAAAAAATGGACGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAA-GAAA
29448812 A
129 A
* * * *
29448813 GAACGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAACTACGAGATATT
1 AAATGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATT
29448870 TCCTTATGTT
Statistics
Matches: 256, Mismatches: 41, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
122 1 0.00
124 5 0.02
125 51 0.20
126 11 0.04
128 25 0.10
129 34 0.13
130 21 0.08
131 82 0.32
132 1 0.00
133 8 0.03
134 8 0.03
135 9 0.04
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (129 bp):
AAATGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAATACGAAATATTGCCTCATT
TAATTTTTTTTAAAAAAAATGGACGAAATTTCAAAAGGATATTCCGTATTTTAGTCGAAGAAAA
Found at i:29449508 original size:15 final size:16
Alignment explanation
Indices: 29449496--29449525 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29449486 GTATATAAGA
29449496 AAATT-TAAAATAAAC
1 AAATTATAAAATAAAC
29449511 AAATTATAAAATAAA
1 AAATTATAAAATAAA
29449526 ACAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTATAAAATAAAC
Found at i:29450891 original size:89 final size:88
Alignment explanation
Indices: 29450791--29450988 Score: 288
Period size: 89 Copynumber: 2.2 Consensus size: 88
29450781 CCTGCTCCAT
* ** *
29450791 TGCAACTTCAGGGAGATAAGGTTGGTAGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGA
1 TGCAACTTCAGGAAGATAAGACTAGTAGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGA
*
29450856 TCTGTAACTTTTCAGTCTGCTTCC
66 TCTGTAA-TTTTCAGCCTGCTTCC
* * *
29450880 TGCAACTTCAGGAAGATAAGACTAGTAGCTGAGATCTGCTCCATAGCTGATACATGGAGATAAGA
1 TGCAACTTCAGGAAGATAAGACTAGTAGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGA
*
29450945 TTTGTAATTTTCAGCCTGCTTCC
66 TCTGTAATTTTCAGCCTGCTTCC
* *
29450968 TACAACTTCAAGAAGATAAGA
1 TGCAACTTCAGGAAGATAAGA
29450989 TTTGCTATCT
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 34 0.35
89 64 0.65
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (88 bp):
TGCAACTTCAGGAAGATAAGACTAGTAGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGA
TCTGTAATTTTCAGCCTGCTTCC
Done.