Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 96 of 433
Found at i:29189860 original size:30 final size:30
Alignment explanation
Indices: 29189824--29189882 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
29189814 ATTTCACAAC
29189824 AACTTGATTCCATCAATTATTTTCAACTTT
1 AACTTGATTCCATCAATTATTTTCAACTTT
29189854 AACTTGATTCCATCAATTATTTTCAACTT
1 AACTTGATTCCATCAATTATTTTCAACTT
29189883 ACTTTTACCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (30 bp):
AACTTGATTCCATCAATTATTTTCAACTTT
Found at i:29192333 original size:43 final size:44
Alignment explanation
Indices: 29192192--29192344 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 44
29192182 TGTTCTCGTA
* * *
29192192 TAAGACCATGTCTGGGA-CGTTGGCATCGATATGAGATTACGTG
1 TAAGACCACGTCTGGGATAGTTGGCATCGATATGTGATTACGTG
* * * * * * *
29192235 TAATACTATGTATGGGACA-TCGGCATCG-TATTTGATT-CGTG
1 TAAGACCACGTCTGGGATAGTTGGCATCGATATGTGATTACGTG
* *
29192276 TAAGACC-CTATCTGGGATAG-TGGCATCGATATGTGATTACATG
1 TAAGACCAC-GTCTGGGATAGTTGGCATCGATATGTGATTACGTG
29192319 TAAGACCACGTCTGGGAT-GTTGGCAT
1 TAAGACCACGTCTGGGATAGTTGGCAT
29192345 TGTACAATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
41 23 0.27
42 16 0.19
43 46 0.53
44 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (44 bp):
TAAGACCACGTCTGGGATAGTTGGCATCGATATGTGATTACGTG
Found at i:29196393 original size:40 final size:40
Alignment explanation
Indices: 29196266--29196395 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
29196256 ATGCTGGAAA
* * *
29196266 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * *
29196306 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
29196346 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
29196386 TTATATCCGG
1 TTATATCCGG
29196396 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:29204331 original size:40 final size:39
Alignment explanation
Indices: 29204286--29204396 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 39
29204276 CTGGAAATTA
* *
29204286 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-AGTCG-TAC
*
29204327 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAGTCGTTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCAGTCGTAC
*
29204365 TATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCA
29204397 CGTGGTTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.03
39 34 0.54
40 27 0.43
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTCGTAC
Found at i:29204380 original size:39 final size:38
Alignment explanation
Indices: 29204286--29204411 Score: 155
Period size: 40 Copynumber: 3.2 Consensus size: 38
29204276 CTGGAAATTA
* *
29204286 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAC
1 TATCCGGGCTAAGACCCGAAGGC-ATTGTGC-AGTGG-TTC
*
29204327 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTCGTTC
1 TATCCGGGCTAAGACCCGAAGGCATT-GTGCAGTGGTTC
*
29204365 TATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCA-TTGTGCA-GTGGTTC
29204405 TATCCGG
1 TATCCGG
29204412 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
38 2 0.03
39 35 0.46
40 39 0.51
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (38 bp):
TATCCGGGCTAAGACCCGAAGGCATTGTGCAGTGGTTC
Found at i:29212733 original size:30 final size:30
Alignment explanation
Indices: 29212678--29212837 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
29212668 ATAGTGAATC
29212678 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
29212707 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
29212737 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
29212766 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
29212794 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
29212824 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29212838 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:29212770 original size:59 final size:57
Alignment explanation
Indices: 29212678--29212837 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
29212668 ATAGTGAATC
*
29212678 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
29212737 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
29212794 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
29212838 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:29227604 original size:43 final size:43
Alignment explanation
Indices: 29227448--29227595 Score: 187
Period size: 43 Copynumber: 3.5 Consensus size: 43
29227438 TATGTGTTCT
* *
29227448 CGTGTAAGACCACGTCTTGGACATTGGTATCGATATGAT-ATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATG-TGATTA
* *
29227491 CGTGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTA
* *
29227532 CGTGTAAGACC-CTGTCTGAGACAGTGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATGTGATTA
*
29227575 CATGTAAGACCACGTCTGGGA
1 CGTGTAAGACCACGTCTGGGA
29227596 TGTCGGCATT
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
41 29 0.32
42 14 0.16
43 46 0.51
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTA
Found at i:29227604 original size:84 final size:84
Alignment explanation
Indices: 29227447--29227604 Score: 205
Period size: 84 Copynumber: 1.9 Consensus size: 84
29227437 ATATGTGTTC
* * * *
29227447 TCGTGTAAGACCACGTCTTGGACATTGGTATCGATATGATATTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACGTCTTGGACAGTGGCATCGATATGATATTACATGTAAGACCACGTCTGGGA
*
29227512 CATTGGCATCGTATTTGAT
66 CATCGGCATCGTATTTGAT
29227531 TCGTGTAAGACC-CTGTC-TGAGACAGTGGCATCGATATG-TGATTACATGTAAGACCACGTCTG
1 TCGTGTAAGACCAC-GTCTTG-GACAGTGGCATCGATATGAT-ATTACATGTAAGACCACGTCTG
**
29227593 GGATGTCGGCAT
63 GGACATCGGCAT
29227605 TGTACGATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 4 0.06
84 60 0.94
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTTGGACAGTGGCATCGATATGATATTACATGTAAGACCACGTCTGGGA
CATCGGCATCGTATTTGAT
Found at i:29228886 original size:2 final size:2
Alignment explanation
Indices: 29228879--29228932 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
29228869 TTTGGCTATA
29228879 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29228921 TG TG TG TG TG TG
1 TG TG TG TG TG TG
29228933 ACTAACCGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29230631 original size:15 final size:16
Alignment explanation
Indices: 29230604--29230633 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29230594 ATAGTACGAG
29230604 ATATGAGAATGTATAT
1 ATATGAGAATGTATAT
29230620 ATATGA-AATGTATA
1 ATATGAGAATGTATA
29230634 ATCTTTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (16 bp):
ATATGAGAATGTATAT
Found at i:29235399 original size:29 final size:29
Alignment explanation
Indices: 29235341--29235427 Score: 140
Period size: 29 Copynumber: 3.0 Consensus size: 29
29235331 ATACCTGTAC
29235341 ATGGCTCATTAGGCCC-AATCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
29235369 ATGGCTCATTAGGCCCAAATCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
* * *
29235398 ATGGCCCGTTAGGCCCAATTCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
29235427 A
1 A
29235428 GTCATGCTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 16 0.29
29 39 0.71
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (29 bp):
ATGGCTCATTAGGCCCAAATCACATTTAT
Found at i:29235661 original size:8 final size:8
Alignment explanation
Indices: 29235648--29235683 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
29235638 ACTTTTAGCT
29235648 TTTCAGCA
1 TTTCAGCA
*
29235656 TTTCAGCT
1 TTTCAGCA
*
29235664 TTTCGGCA
1 TTTCAGCA
29235672 TTTCAGCA
1 TTTCAGCA
29235680 TTTC
1 TTTC
29235684 GGCTTTTGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (8 bp):
TTTCAGCA
Found at i:29235665 original size:16 final size:16
Alignment explanation
Indices: 29235644--29235683 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29235634 TCAAACTTTT
29235644 AGCTTTTCAGCATTTC
1 AGCTTTTCAGCATTTC
*
29235660 AGCTTTTCGGCATTTC
1 AGCTTTTCAGCATTTC
*
29235676 AGCATTTC
1 AGCTTTTC
29235684 GGCTTTTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.42
Consensus pattern (16 bp):
AGCTTTTCAGCATTTC
Found at i:29239391 original size:29 final size:29
Alignment explanation
Indices: 29239336--29239419 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
29239326 CCTGTATGCA
*
29239336 GCCCACTAGGCCC-AATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATTTATATG
29239364 GCCCATTAGGCCCAAATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATTTATATG
* *
29239393 GCCCATCAGGCCCAATTCACATTTATA
1 GCCCATTAGGCCCAAATCACATTTATA
29239420 GTCATGATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 12 0.23
29 40 0.77
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTTATATG
Found at i:29239660 original size:8 final size:8
Alignment explanation
Indices: 29239647--29239684 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
29239637 GCTTTTCAGT
29239647 ATTTCGGC
1 ATTTCGGC
*
29239655 TTTTCGGC
1 ATTTCGGC
*
29239663 ATTTTGGC
1 ATTTCGGC
29239671 ATTTCGGC
1 ATTTCGGC
29239679 ATTTCG
1 ATTTCG
29239685 AGTTTTGTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.45
Consensus pattern (8 bp):
ATTTCGGC
Found at i:29239666 original size:16 final size:16
Alignment explanation
Indices: 29239632--29239684 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
29239622 GTAGTCAAAC
* * *
29239632 TTTCAGCTTTTCAGTA
1 TTTCGGCTTTTCGGCA
29239648 TTTCGGCTTTTCGGCA
1 TTTCGGCTTTTCGGCA
* *
29239664 TTTTGGCATTTCGGCA
1 TTTCGGCTTTTCGGCA
29239680 TTTCG
1 TTTCG
29239685 AGTTTTGTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (16 bp):
TTTCGGCTTTTCGGCA
Found at i:29246743 original size:60 final size:61
Alignment explanation
Indices: 29246679--29246805 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 61
29246669 GATCTTAAAT
* * * * * * *
29246679 TAAAAAATTCAATAAATTTAGCTC-TTAATATTTACAAAATTTGT-CATTTAGTTTTAATTC
1 TAAAAAATTCAATAAATTTAAC-CATCAACATTTACAAAATTTATAAATTTAATTCTAATTC
*
29246739 TAAAAATTTCAATAAATTTAACCATCAACATTTACAAAATTTATAAATTTAATTCTAATTC
1 TAAAAAATTCAATAAATTTAACCATCAACATTTACAAAATTTATAAATTTAATTCTAATTC
29246800 TAAAAA
1 TAAAAA
29246806 TTTTAAAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.02
60 37 0.65
61 19 0.33
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (61 bp):
TAAAAAATTCAATAAATTTAACCATCAACATTTACAAAATTTATAAATTTAATTCTAATTC
Found at i:29250346 original size:39 final size:39
Alignment explanation
Indices: 29250297--29250519 Score: 265
Period size: 39 Copynumber: 5.7 Consensus size: 39
29250287 TCGAATGATG
* * *
29250297 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAATGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
29250336 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
29250375 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
29250414 TCCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 T-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
* * *
29250454 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGCTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* *
29250494 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
29250520 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
39 92 0.56
40 72 0.44
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:29250473 original size:79 final size:78
Alignment explanation
Indices: 29250297--29250517 Score: 259
Period size: 79 Copynumber: 2.8 Consensus size: 78
29250287 TCGAATGATG
* * * * * *
29250297 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAATGACTATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCTAAGACCCGAAGGCATTG
29250361 GTGCGAGTTACTAA
65 GTGCGAGTTACTAA
*
29250375 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATCCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT-CCGGGCTAAGACCCGAAGGCATT
29250438 GGTGCGAGTTACTAAA
64 GGTGCGAGTTACT-AA
* * * * * *
29250454 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGCTACTATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCTAAGACCCGAAGGCATT
29250518 TGAACGAGTA
Statistics
Matches: 123, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 44 0.36
79 66 0.54
80 13 0.11
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATCCGGGCTAAGACCCGAAGGCATTGG
TGCGAGTTACTAA
Found at i:29250541 original size:79 final size:76
Alignment explanation
Indices: 29250349--29250552 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 76
29250339 GGACTAAGAT
* * *
29250349 CCGAAGGCATTTGTGCGAGTTACTAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATCCGG-TTAAG-TCCGAAGGCATTTGTACGAGCTACTAA
*
29250414 TCCCGGGCTAAGC
64 TACCGGGCTAAGC
*
29250427 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGCTACT-
1 CCGAAGGCATTTGTGCGAGTTACT-AATCC-GGTTAAGT-CCGAAGGCATTTGTACGAGCTACTA
*
29250491 ATAACCGGGCTATGTC
63 AT-ACCGGGCTAAG-C
** *
29250507 CCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGTGCGAGTTA-CTA-ATCCGGTT-AAGTCCGAAGG
29250553 TACGTGATTC
Statistics
Matches: 108, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
78 26 0.24
79 54 0.50
80 28 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (76 bp):
CCGAAGGCATTTGTGCGAGTTACTAATCCGGTTAAGTCCGAAGGCATTTGTACGAGCTACTAATA
CCGGGCTAAGC
Found at i:29262231 original size:39 final size:39
Alignment explanation
Indices: 29262141--29262363 Score: 265
Period size: 40 Copynumber: 5.6 Consensus size: 39
29262131 TCGAATGATG
* * *
29262141 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
29262181 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
29262221 T-CGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29262259 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29262298 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
29262339 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
29262364 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 26 0.16
39 55 0.34
40 73 0.45
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29266976 original size:15 final size:15
Alignment explanation
Indices: 29266958--29266988 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29266948 GTTTATTTCT
29266958 TTAGAATCTTGATTC
1 TTAGAATCTTGATTC
29266973 TTAGAATCTTGATTC
1 TTAGAATCTTGATTC
29266988 T
1 T
29266989 AGTCATATTT
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:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (15 bp):
TTAGAATCTTGATTC
Found at i:29269595 original size:21 final size:22
Alignment explanation
Indices: 29269571--29269611 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
29269561 ATGGTATATA
29269571 AAAATGTACA-AGTA-ATATAAT
1 AAAAT-TACATAGTATATATAAT
29269592 AAAATTACATAGTATATATA
1 AAAATTACATAGTATATATA
29269612 TACGTTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
AAAATTACATAGTATATATAAT
Found at i:29270172 original size:11 final size:11
Alignment explanation
Indices: 29270158--29270225 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
29270148 TATTAAAAGC
29270158 ATATACATAAT
1 ATATACATAAT
*
29270169 ATATATATAAT
1 ATATACATAAT
* *
29270180 ATACAAAACAAAAT
1 AT---ATACATAAT
*
29270194 ATACACATAAT
1 ATATACATAAT
29270205 ATATTA-A-AAT
1 ATA-TACATAAT
29270215 ATATACATAAT
1 ATATACATAAT
29270226 GTACATAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
9 2 0.05
10 7 0.16
11 26 0.59
12 1 0.02
14 8 0.18
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATACATAAT
Found at i:29270213 original size:21 final size:22
Alignment explanation
Indices: 29270189--29270240 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
29270179 TATACAAAAC
*
29270189 AAAATATACACATAATATA-TT
1 AAAATATACACATAATATACAT
* *
29270210 AAAATATATACATAATGTACAT
1 AAAATATACACATAATATACAT
29270232 AAAATATAC
1 AAAATATAC
29270241 GTATATACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATATACACATAATATACAT
Found at i:29272126 original size:45 final size:44
Alignment explanation
Indices: 29272069--29272220 Score: 139
Period size: 44 Copynumber: 3.5 Consensus size: 44
29272059 TAAATTCAGC
*
29272069 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCTTTTACCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTC-TTTACATTCGAT
* * * * ** * *
29272114 CTGTTTCCCTACTACTTAGGGAG-ATAA-GATCTGCA-ATTTGGT
1 CTGTTACCCTACTGCTTAGGG-GTTTAAGGCTCTTTACATTCGAT
* * * *
29272156 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCATTGCATTCGAT
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCTTTACATTCGAT
*
29272200 CTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGG
29272221 TAATAAGATC
Statistics
Matches: 81, Mismatches: 22, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
41 1 0.01
42 26 0.32
43 3 0.04
44 28 0.35
45 22 0.27
46 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGCTCTTTACATTCGAT
Found at i:29272172 original size:87 final size:87
Alignment explanation
Indices: 29272035--29272234 Score: 269
Period size: 86 Copynumber: 2.3 Consensus size: 87
29272025 TCTGCTCTAG
* *
29272035 TACTGCTTAGGGAGGTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCT
1 TACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGAC-
** *
29272100 CTTTTACCTTCGATCTGTTTCCC
65 CCATTACATTCGATCTGTTTCCC
* * ** *
29272123 TACTACTTAGGGAGATAAGATCTG-CAATTTGGTCTGTTACCCTACTGCTTAGGGGTTTAAGACC
1 TACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGACC
*
29272187 CATTGCATTCGATCTGTTTCCC
66 CATTACATTCGATCTGTTTCCC
29272209 TACTGCTTAGGGTA-ATAAGATCTGTA
1 TACTGCTTAGGG-AGATAAGATCTGTA
29272235 GATCTTCAGT
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
86 40 0.41
87 35 0.36
88 22 0.23
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (87 bp):
TACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGACC
CATTACATTCGATCTGTTTCCC
Found at i:29272604 original size:129 final size:130
Alignment explanation
Indices: 29272413--29272655 Score: 316
Period size: 129 Copynumber: 1.9 Consensus size: 130
29272403 AAAGCTCGAC
* **
29272413 CTGTTTCCCTACTACTTAGGGGGTTAAGATCTTGTAAATTTAGCCCGTTACCCTACTGCTTAGGG
1 CTGTTTCCCTACTACTTAGGGGGATAAGATCTTGTAAATTTAGCCCGTTACCCTACCACTTAGGG
* * * *
29272478 AG-ATGAGG-CTTGTGAATTTGGCTTGTTACCCTACTGCTTAGGGGGTTAAGCCTATCATCTTTG
66 -GTATAAGGTC-TGTAAATTTGGCTTATTACCCTACTGCTTAGGGAGTTAAGCCTATCATCTTTG
29272541 AT
129 AT
* * *
29272543 CTGTTTCCCTACTGCTT-GGGGTGAT-AGAATC-TGTATATTTAGCCTGTTACCCTACCACTTAG
1 CTGTTTCCCTACTACTTAGGGG-GATAAG-ATCTTGTAAATTTAGCCCGTTACCCTACCACTTAG
*
29272605 GGGTTTAAGGTCTGTAAATTTGGCTTATTACCCTACTGCTTAGGGAGTTAA
64 GGGTATAAGGTCTGTAAATTTGGCTTATTACCCTACTGCTTAGGGAGTTAA
29272656 AGCTTGTAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
128 1 0.01
129 75 0.77
130 22 0.22
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (130 bp):
CTGTTTCCCTACTACTTAGGGGGATAAGATCTTGTAAATTTAGCCCGTTACCCTACCACTTAGGG
GTATAAGGTCTGTAAATTTGGCTTATTACCCTACTGCTTAGGGAGTTAAGCCTATCATCTTTGAT
Found at i:29272664 original size:43 final size:43
Alignment explanation
Indices: 29272414--29272667 Score: 165
Period size: 43 Copynumber: 5.9 Consensus size: 43
29272404 AAGCTCGACC
* * * * * *
29272414 TGTTTCCCTACTACTTAGGGGGTTAAGATCTTGTAAATTTAGCC
1 TGTTACCCTACTGCTTAGGGAGTTAA-AGCTTGTAAATTTGGCT
* * * * *
29272458 CGTTACCCTACTGCTTAGGGAGATGAGGCTTGTGAATTTGGCT
1 TGTTACCCTACTGCTTAGGGAGTTAAAGCTTGTAAATTTGGCT
* * * * * *
29272501 TGTTACCCTACTGCTTAGGGGGTT-AAGCCTAT-CATCTTTGAT
1 TGTTACCCTACTGCTTAGGGAGTTAAAGCTTGTAAAT-TTGGCT
* * * * * * * *
29272543 CTGTTTCCCTACTGCTTGGGGTGATAGAATC-TGTATATTTAGCC
1 -TGTTACCCTACTGCTTAGGGAGTTA-AAGCTTGTAAATTTGGCT
** * *
29272587 TGTTACCCTACCACTTAGGG-GTTTAAGGTCTGTAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGAGTTAAAGCT-TGTAAATTTGGCT
*
29272630 TATTACCCTACTGCTTAGGGAGTTAAAGCTTGTAAATT
1 TGTTACCCTACTGCTTAGGGAGTTAAAGCTTGTAAATT
29272668 CATCGGTTCT
Statistics
Matches: 156, Mismatches: 46, Indels: 17
0.71 0.21 0.08
Matches are distributed among these distances:
41 4 0.03
42 11 0.07
43 104 0.67
44 32 0.21
45 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (43 bp):
TGTTACCCTACTGCTTAGGGAGTTAAAGCTTGTAAATTTGGCT
Found at i:29280715 original size:9 final size:9
Alignment explanation
Indices: 29280701--29280728 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29280691 ATGCTGACGT
29280701 ATGAATGCA
1 ATGAATGCA
29280710 ATGAATGCA
1 ATGAATGCA
29280719 ATGAATGCA
1 ATGAATGCA
29280728 A
1 A
29280729 AAAAACGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.21
Consensus pattern (9 bp):
ATGAATGCA
Found at i:29284504 original size:40 final size:40
Alignment explanation
Indices: 29284305--29284509 Score: 181
Period size: 40 Copynumber: 5.2 Consensus size: 40
29284295 TGAATGATAC
* * * *
29284305 CCGGGCTAAGTCCCGAA-GCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
29284344 -CGGGCTAAGTCCCGAA-GCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* *
29284382 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * ** *
29284422 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTATAT
* * *
29284462 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
29284502 CC-GGCTAA
1 CCGGGCTAA
29284510 ATTCCGAAGA
Statistics
Matches: 139, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 37 0.27
39 23 0.17
40 75 0.54
41 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:29292567 original size:40 final size:40
Alignment explanation
Indices: 29292366--29292572 Score: 199
Period size: 40 Copynumber: 5.2 Consensus size: 40
29292356 TGAATGATAC
* * * *
29292366 CCGGGCTAAGTCCCGAA-GCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
29292405 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* *
29292445 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TCATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * ** *
29292485 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTATAT
* * *
29292525 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
29292565 CC-GGCTAA
1 CCGGGCTAA
29292573 ATTCGAAGAA
Statistics
Matches: 142, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
39 25 0.18
40 113 0.80
41 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:29296611 original size:21 final size:21
Alignment explanation
Indices: 29296577--29296617 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29296567 TATACAAAAC
* *
29296577 AAAATATACGCATAATATATT
1 AAAATATACACATAAAATATT
*
29296598 AAAATATATACATAAAATAT
1 AAAATATACACATAAAATAT
29296618 ACGTATATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATATACACATAAAATATT
Found at i:29296796 original size:2 final size:2
Alignment explanation
Indices: 29296789--29296820 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
29296779 ACTACATAAC
*
29296789 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29296821 TAAGCAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29298293 original size:44 final size:44
Alignment explanation
Indices: 29298244--29298327 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
29298234 GTAAACCAAT
*
29298244 TACACTCCCTAAATATGATATCATAGGATGAATGTAGAGCTAGC
1 TACACTCCCTAAATATGATATCATAGGATGAACGTAGAGCTAGC
*
29298288 TACACTCCTTAAATATGATATCATAGGATGAACGTAGAGC
1 TACACTCCCTAAATATGATATCATAGGATGAACGTAGAGC
29298328 CAATAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (44 bp):
TACACTCCCTAAATATGATATCATAGGATGAACGTAGAGCTAGC
Found at i:29298620 original size:12 final size:12
Alignment explanation
Indices: 29298605--29298639 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
29298595 TTCATATAAT
29298605 AATTTTATTAAG
1 AATTTTATTAAG
29298617 AATTTTATTAAG
1 AATTTTATTAAG
29298629 AATTTTATTAA
1 AATTTTATTAA
29298640 ATTATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (12 bp):
AATTTTATTAAG
Found at i:29298913 original size:16 final size:16
Alignment explanation
Indices: 29298892--29298930 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29298882 TGAATTACTG
29298892 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
* *
29298908 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCA
29298924 ATTACAG
1 ATTACAG
29298931 TGAACCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:29299537 original size:9 final size:9
Alignment explanation
Indices: 29299514--29299696 Score: 61
Period size: 10 Copynumber: 19.6 Consensus size: 9
29299504 CTGCTTTTAT
29299514 TAAAAATTA
1 TAAAAATTA
*
29299523 GAAAAAATTA
1 -TAAAAATTA
*
29299533 TAAAAA-AA
1 TAAAAATTA
*
29299541 TTAAAATCTA
1 TAAAAAT-TA
*
29299551 TAAATATTA
1 TAAAAATTA
**
29299560 TTAAATTTTAA
1 -TAAAAATT-A
29299571 TAAAAATT-
1 TAAAAATTA
* *
29299579 CAAATA-T-
1 TAAAAATTA
29299586 TAAAAATTA
1 TAAAAATTA
*
29299595 TGAAAAAAATA
1 T--AAAAATTA
*
29299606 TAAAAATCA
1 TAAAAATTA
*
29299615 TAAAAAATA
1 TAAAAATTA
* *
29299624 TAAAAAAGTG
1 T-AAAAATTA
**
29299634 TACAATTTTA
1 TA-AAAATTA
*
29299644 TAAAAATCA
1 TAAAAATTA
29299653 TAAAACAATTA
1 T-AAA-AATTA
29299664 T-AAAATATA
1 TAAAAAT-TA
*
29299673 TAGAAATATA
1 TAAAAAT-TA
*
29299683 AAAAAATTA
1 TAAAAATTA
29299692 TAAAA
1 TAAAA
29299697 TTTTATAAAG
Statistics
Matches: 126, Mismatches: 33, Indels: 29
0.67 0.18 0.15
Matches are distributed among these distances:
7 5 0.04
8 14 0.11
9 39 0.31
10 54 0.43
11 14 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:29299595 original size:35 final size:35
Alignment explanation
Indices: 29299527--29299595 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
29299517 AAATTAGAAA
* *
29299527 AAATTATAAAAAAATTAAAATCTATAAATATTATT
1 AAATTATAAAAAAATTAAAATATATAAAAATTATT
* *
29299562 AAATTTTAATAAAAATTCAAATAT-TAAAAATTAT
1 AAATTATAA-AAAAATTAAAATATATAAAAATTAT
29299596 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (35 bp):
AAATTATAAAAAAATTAAAATATATAAAAATTATT
Found at i:29299687 original size:38 final size:37
Alignment explanation
Indices: 29299601--29299696 Score: 88
Period size: 39 Copynumber: 2.5 Consensus size: 37
29299591 ATTATGAAAA
*
29299601 AAATAT-AAAAATCATAAAAAATATAAAAAAGTGTAC
1 AAATATAAAAAATCATAAAAAATATAAAAAAGTATAC
* * * *
29299637 AATTTTATAAAAATCATAAAACAATTATAAAATA-TATAG
1 AAATATA-AAAAATCATAAAA-AA-TATAAAAAAGTATAC
*
29299676 AAATATAAAAAAATTATAAAA
1 AAATAT-AAAAAATCATAAAA
29299697 TTTTATAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
36 4 0.09
38 13 0.28
39 21 0.45
40 9 0.19
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (37 bp):
AAATATAAAAAATCATAAAAAATATAAAAAAGTATAC
Found at i:29299697 original size:28 final size:29
Alignment explanation
Indices: 29299580--29299697 Score: 95
Period size: 28 Copynumber: 4.1 Consensus size: 29
29299570 ATAAAAATTC
*
29299580 AAATAT-TAAAAATTATGAAAAAAA-TATA
1 AAATATATAAAAATCAT-AAAAAAATTATA
* *
29299608 AAA-ATCATAAAAAAT-ATAAAAAAGTGTA-C
1 AAATAT-AT-AAAAATCATAAAAAAAT-TATA
* * *
29299637 AATTTTATAAAAATCATAAAACAATTATA
1 AAATATATAAAAATCATAAAAAAATTATA
*
29299666 AAATATATAGAAAT-ATAAAAAAATTATA
1 AAATATATAAAAATCATAAAAAAATTATA
29299694 AAAT
1 AAAT
29299698 TTTATAAAGT
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
27 2 0.03
28 34 0.48
29 26 0.37
30 9 0.13
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (29 bp):
AAATATATAAAAATCATAAAAAAATTATA
Found at i:29299703 original size:29 final size:28
Alignment explanation
Indices: 29299618--29299725 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 28
29299608 AAAATCATAA
* * *
29299618 AAAATAT-AAAAAAGTGTACAATTTTAT
1 AAAATATAAAAAAATTATAAAATTTTAT
* *
29299645 AAAAATCATAAAACAATTATAAAA-TATAT
1 -AAAAT-ATAAAAAAATTATAAAATTTTAT
29299674 AGAAATATAAAAAAATTATAAAATTTTAT
1 A-AAATATAAAAAAATTATAAAATTTTAT
* * *
29299703 AAAGTTGTAAGAAAATTATAAAA
1 AAA-ATATAAAAAAATTATAAAA
29299726 AATGTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
28 24 0.37
29 31 0.48
30 10 0.15
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (28 bp):
AAAATATAAAAAAATTATAAAATTTTAT
Found at i:29300245 original size:91 final size:88
Alignment explanation
Indices: 29300070--29300285 Score: 303
Period size: 90 Copynumber: 2.4 Consensus size: 88
29300060 TTTAAATAAG
* * *
29300070 AGCAGGAGCTTAATTG-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCTTTTGAAAGTTCAA
1 AGCAGG-GCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATACTTTTGAAAGTTCAA
29300134 GTACTCAATTAAGTGAAAAAAAAAAA
65 GTACTCAATTAAGTG--AAAAAAAAA
* *
29300160 AGCAGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATACATTTTGAAAGTTCAA
1 AGCAGGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATAC-TTTTGAAAGTTCAA
* * *
29300225 GTGCTCAATTGAGTGCAAAAAAAA
65 GTACTCAATTAAGTGAAAAAAAAA
29300249 AG--GGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGC
1 AGCAGGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGC
29300286 TATTTACACC
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
87 33 0.29
89 19 0.17
90 36 0.31
91 27 0.23
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (88 bp):
AGCAGGGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATACTTTTGAAAGTTCAAG
TACTCAATTAAGTGAAAAAAAAA
Found at i:29300281 original size:87 final size:88
Alignment explanation
Indices: 29300077--29300285 Score: 298
Period size: 87 Copynumber: 2.4 Consensus size: 88
29300067 AAGAGCAGGA
* * *
29300077 GCTTAATTG-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCTTTTGAAAGTTCAAGTACTCA
1 GCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATACTTTTGAAAGTTCAAGTACTCA
29300141 ATTAAGTGAAAAAAAAAAAAGCAGG
66 ATTAAGTG-AAAAAAAAAAAG-AGG
* * *
29300166 GCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATACATTTTGAAAGTTCAAGTGCTC
1 GCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATAC-TTTTGAAAGTTCAAGTACTC
* *
29300231 AATTGAGTG-CAAAAAAAAAG-GG
65 AATTAAGTGAAAAAAAAAAAGAGG
29300253 GCTTAATTGCTTTTTTTGAAAAAATTTGAGGGC
1 GCTTAATTGCTTTTTTTGAAAAAATTTGAGGGC
29300286 TATTTACACC
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
87 33 0.30
89 19 0.17
90 30 0.28
91 27 0.25
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (88 bp):
GCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATACTTTTGAAAGTTCAAGTACTCA
ATTAAGTGAAAAAAAAAAAGAGG
Found at i:29308347 original size:37 final size:37
Alignment explanation
Indices: 29308282--29308366 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
29308272 CTTAGTGCCA
* *
29308282 TGGCGTGTTATCGAATGGATTAGCTCTTACAAGCATT
1 TGGCGTGTTTTCGAATGGATTAGATCTTACAAGCATT
* * * **
29308319 TGGCATGTTTTCGATTGGATTATATCTTATGAGCATT
1 TGGCGTGTTTTCGAATGGATTAGATCTTACAAGCATT
29308356 TGGCGTGTTTT
1 TGGCGTGTTTT
29308367 TAGTTGGATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (37 bp):
TGGCGTGTTTTCGAATGGATTAGATCTTACAAGCATT
Found at i:29313802 original size:26 final size:26
Alignment explanation
Indices: 29313773--29313823 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
29313763 AATATTTCTT
*
29313773 TTTTCTTTCCAGTGATAAGTTTTTCA
1 TTTTCTTTCCAATGATAAGTTTTTCA
29313799 TTTTCTTTCCAATGATAAGTTTTTC
1 TTTTCTTTCCAATGATAAGTTTTTC
29313824 TTACGCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.10, T:0.55
Consensus pattern (26 bp):
TTTTCTTTCCAATGATAAGTTTTTCA
Found at i:29314533 original size:20 final size:19
Alignment explanation
Indices: 29314504--29314591 Score: 81
Period size: 19 Copynumber: 4.6 Consensus size: 19
29314494 TTAAAAATTC
*
29314504 ATTA-AAAATTAGAAAAAA
1 ATTATAAAATTAGTAAAAA
29314522 ATTATAACAATT-GTAAAAA
1 ATTATAA-AATTAGTAAAAA
* *
29314541 ATATATAAAAATTTGTAAAAT
1 AT-TAT-AAAATTAGTAAAAA
* * *
29314562 TTTATAAAAATAGCAAAAA
1 ATTATAAAATTAGTAAAAA
29314581 ATTATAAAATT
1 ATTATAAAATT
29314592 TTATAAAGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.07
19 29 0.52
20 14 0.25
21 9 0.16
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTATAAAATTAGTAAAAA
Found at i:29314540 original size:21 final size:21
Alignment explanation
Indices: 29314506--29314560 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
29314496 AAAAATTCAT
* *
29314506 TAAAAATTAG-AAAAAAATTA
1 TAAAAATTTGTAAAAAAAATA
* *
29314526 TAACAA-TTGTAAAAAATATA
1 TAAAAATTTGTAAAAAAAATA
29314546 TAAAAATTTGTAAAA
1 TAAAAATTTGTAAAA
29314561 TTTTATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.07
20 18 0.64
21 8 0.29
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAAAATTTGTAAAAAAAATA
Found at i:29314589 original size:10 final size:10
Alignment explanation
Indices: 29314496--29314636 Score: 53
Period size: 10 Copynumber: 14.2 Consensus size: 10
29314486 TCAAAATATT
*
29314496 AAAAATTCATT
1 AAAAATT-ATA
*
29314507 AAAAATTAGAA
1 AAAAATTA-TA
29314518 AAAAATTAT-
1 AAAAATTATA
* *
29314527 AACAATTGTA
1 AAAAATTATA
29314537 AAAAATATATA
1 AAAAAT-TATA
* *
29314548 AAAATTTGTA
1 AAAAATTATA
**
29314558 AAATTTTAT-
1 AAAAATTATA
*
29314567 AAAAA-TAGCA
1 AAAAATTA-TA
29314577 AAAAATTAT-
1 AAAAATTATA
*
29314586 -AAAATTTTA
1 AAAAATTATA
* * *
29314595 TAAAGTCATA
1 AAAAATTATA
29314605 AGAAAATTATA
1 A-AAAATTATA
*
29314616 TAAAA-TATA
1 AAAAATTATA
29314625 AAGAAA-TATA
1 AA-AAATTATA
29314635 AA
1 AA
29314637 TTTCGTAAAA
Statistics
Matches: 96, Mismatches: 24, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
8 9 0.09
9 15 0.16
10 40 0.42
11 32 0.33
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:29314592 original size:29 final size:29
Alignment explanation
Indices: 29314464--29314598 Score: 109
Period size: 29 Copynumber: 4.6 Consensus size: 29
29314454 AACTATAAAT
* * *
29314464 ATTATTAAATTTTAATAAAAAT-TCAAAAT
1 ATTATAAAATTTT-ATAAAAATAGCAAAAA
* *
29314493 ATTA-AAAATTCATTA-AAAATTAGAAAAAA
1 ATTATAAAATT--TTATAAAAATAGCAAAAA
* *
29314522 ATTATAACAATTGTA-AAAAATA-TATAAAA
1 ATTATAA-AATTTTATAAAAATAGCA-AAAA
*
29314551 ATTTGTAAAATTTTATAAAAATAGCAAAAA
1 A-TTATAAAATTTTATAAAAATAGCAAAAA
29314581 ATTATAAAATTTTATAAA
1 ATTATAAAATTTTATAAA
29314599 GTCATAAGAA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
28 11 0.13
29 48 0.56
30 21 0.25
31 5 0.06
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (29 bp):
ATTATAAAATTTTATAAAAATAGCAAAAA
Found at i:29314628 original size:21 final size:21
Alignment explanation
Indices: 29314586--29314630 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29314576 AAAAAATTAT
* *
29314586 AAAATTTTATAAAGTCATAAG
1 AAAATTATATAAAATCATAAG
29314607 AAAATTATATAAAAT-ATAAAG
1 AAAATTATATAAAATCAT-AAG
29314628 AAA
1 AAA
29314631 TATAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAATTATATAAAATCATAAG
Found at i:29314908 original size:18 final size:17
Alignment explanation
Indices: 29314861--29314916 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 17
29314851 TTTTTAATTT
29314861 TTTA-TATTTTATTAAAA
1 TTTATTATTTT-TTAAAA
*
29314878 TTTAATAATTTTTCTAAAA
1 TTT-ATTATTTTT-TAAAA
*
29314897 TTTATTATTTTTTATAA
1 TTTATTATTTTTTAAAA
29314914 TTT
1 TTT
29314917 TTTCTAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.30
18 10 0.30
19 13 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATTATTTTTTAAAA
Found at i:29315109 original size:89 final size:88
Alignment explanation
Indices: 29314935--29315136 Score: 203
Period size: 89 Copynumber: 2.3 Consensus size: 88
29314925 TTTTAATAAG
* * *
29314935 AGCAGGGGCTTAATTACTTTTTTGGAAAATTTTAAGGGTCTTTTTAATATATTTTGAAAGTTCAA
1 AGCAGGGGCTTAATTACTTTTTTGGAAAAGTTTAAGGCTCTTTTTAATATATTTTGAAAATTCAA
*
29315000 GTACCTAATTGAGTGAAAAAAAA
66 GTACCTAATTAAGTGAAAAAAAA
* * * *
29315023 AGCAGGGGCTTAATTGCCTTTTTT-GAAGAAGTTTGAGGACT-TTTTTGATGTATTTTGAAAATT
1 AGCAGGGGCTTAATT-ACTTTTTTGGAA-AAGTTTAAGG-CTCTTTTTAATATATTTTGAAAATT
* * *
29315086 GAAGTA-TTCAATTAAGTACAAAAAAAAA
63 CAAGTACCT-AATTAAGT--GAAAAAAAA
* **
29315114 AGAAGAAGCTTAATTACTTTTTT
1 AGCAGGGGCTTAATTACTTTTTT
29315137 TTTAAATTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
88 19 0.20
89 46 0.49
90 8 0.09
91 20 0.22
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (88 bp):
AGCAGGGGCTTAATTACTTTTTTGGAAAAGTTTAAGGCTCTTTTTAATATATTTTGAAAATTCAA
GTACCTAATTAAGTGAAAAAAAA
Found at i:29315174 original size:1 final size:1
Alignment explanation
Indices: 29315170--29315203 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
29315160 ACCCTTAAGT
29315170 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29315204 CCTATTATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29316844 original size:53 final size:54
Alignment explanation
Indices: 29316764--29316970 Score: 220
Period size: 53 Copynumber: 3.8 Consensus size: 54
29316754 TTCCTTTTTA
* *
29316764 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
29316817 AACTCGCCATTGTCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * *
29316871 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGAT-TACCTTGCCTTGTAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTAT-CCTTGCCTTATAG
* * *
29316926 AACTTACCAATGTCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29316971 AAACACTAAT
Statistics
Matches: 122, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
53 45 0.37
54 37 0.30
55 40 0.33
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:29323930 original size:55 final size:54
Alignment explanation
Indices: 29323775--29323981 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 54
29323765 TTCCTTTTTA
* * ** *
29323775 AACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATCCTTTCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
29323828 AACTCACCATTGCCATGCCTTGGCATGGTTTTACATGGGATCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
29323882 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * *
29323937 AACTTACCAATGCGATGCCTTGGCATGGTCTTACTTGGCATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29323982 AAACCCTAAT
Statistics
Matches: 120, Mismatches: 32, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 43 0.36
54 36 0.30
55 41 0.34
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:29337326 original size:15 final size:15
Alignment explanation
Indices: 29337306--29337341 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
29337296 TGTCATAACC
29337306 ACAACATGACATATG
1 ACAACATGACATATG
29337321 ACAACATGACATATG
1 ACAACATGACATATG
29337336 ACAACA
1 ACAACA
29337342 AATTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.17
Consensus pattern (15 bp):
ACAACATGACATATG
Found at i:29337380 original size:26 final size:27
Alignment explanation
Indices: 29337347--29337404 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
29337337 CAACAAATTT
29337347 ATAAAAAT-AAAAATTATT-AAATTTTA
1 ATAAAAATAAAAAATT-TTAAAATTTTA
29337373 ATAAAAATAAAAAATTTTAAAATTTTA
1 ATAAAAATAAAAAATTTTAAAATTTTA
29337400 A-AAAA
1 ATAAAA
29337405 TCGTAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAAAAATAAAAAATTTTAAAATTTTA
Found at i:29337487 original size:10 final size:10
Alignment explanation
Indices: 29337472--29337497 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29337462 GTAACAAAAT
29337472 TATAAAGAAA
1 TATAAAGAAA
29337482 TATAAAGAAA
1 TATAAAGAAA
29337492 TATAAA
1 TATAAA
29337498 ATTCATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
TATAAAGAAA
Found at i:29344593 original size:33 final size:33
Alignment explanation
Indices: 29344551--29344618 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
29344541 CTCAAAGTTT
29344551 ATTCGTTGGATTGGCATAGACATTCCAACTCTA
1 ATTCGTTGGATTGGCATAGACATTCCAACTCTA
29344584 ATTCGTTGGATTGGCATAGACATTCCAACTCTA
1 ATTCGTTGGATTGGCATAGACATTCCAACTCTA
29344617 AT
1 AT
29344619 AAGTGACACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (33 bp):
ATTCGTTGGATTGGCATAGACATTCCAACTCTA
Found at i:29346128 original size:2 final size:2
Alignment explanation
Indices: 29346087--29346117 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29346077 GGATTGAATT
29346087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29346118 TATGAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29346678 original size:12 final size:12
Alignment explanation
Indices: 29346661--29346694 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
29346651 CCGGCCCGCC
29346661 TATATTAATTTT
1 TATATTAATTTT
29346673 TATATT-ATTTT
1 TATATTAATTTT
29346684 TATA-TAATTTT
1 TATATTAATTTT
29346695 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:29346859 original size:30 final size:30
Alignment explanation
Indices: 29346811--29346892 Score: 141
Period size: 30 Copynumber: 2.8 Consensus size: 30
29346801 CAAATGCATC
29346811 TAAAATAATAAC-AAATTAACAAATATCTT
1 TAAAATAATAACAAAATTAACAAATATCTT
29346840 TAAAAT-ATAAACAAAATTAACAAATATCTT
1 TAAAATAAT-AACAAAATTAACAAATATCTT
29346870 TAAAATAATAACAAAATTAACAA
1 TAAAATAATAACAAAATTAACAA
29346893 TAAAATAAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.04
29 9 0.18
30 37 0.74
31 2 0.04
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (30 bp):
TAAAATAATAACAAAATTAACAAATATCTT
Found at i:29348306 original size:56 final size:56
Alignment explanation
Indices: 29348220--29348333 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
29348210 CAAAGCTTAA
*
29348220 AATGAGCTTTAAGATACAAAGGGGTTGGACTTGAGAATGAAAAATGACCAAATTAT
1 AATGAGCTTTAAGATACAAAGGGGTTGGACTTGAGAACGAAAAATGACCAAATTAT
29348276 AATGAGCTTTAAGATACAAAGGGGTTGGACTTGAGAACGAAAAATGACCAAATTAT
1 AATGAGCTTTAAGATACAAAGGGGTTGGACTTGAGAACGAAAAATGACCAAATTAT
29348332 AA
1 AA
29348334 ACTTTTCAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (56 bp):
AATGAGCTTTAAGATACAAAGGGGTTGGACTTGAGAACGAAAAATGACCAAATTAT
Found at i:29348422 original size:21 final size:21
Alignment explanation
Indices: 29348356--29348410 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
29348346 TTGAACAAAG
29348356 TATCGATATTTTTGTAATAAA
1 TATCGATATTTTTGTAATAAA
29348377 TATCGATATTTTTGTAATAAA
1 TATCGATATTTTTGTAATAAA
29348398 TATCGATATTTTT
1 TATCGATATTTTT
29348411 TTATTCGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (21 bp):
TATCGATATTTTTGTAATAAA
Found at i:29350182 original size:21 final size:20
Alignment explanation
Indices: 29350137--29350204 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
29350127 TGTCTAGGTC
*
29350137 GTGTGGAGGCTTACACACCC-
1 GTGTGAAGGC-TACACACCCT
*
29350157 ATGTGAAGGCTACACACACCT
1 GTGTGAAGGCTACACAC-CCT
* **
29350178 GTGTGGAGGGGACACACGCCT
1 GTGTGAAGGCTACACAC-CCT
29350199 GTGTGA
1 GTGTGA
29350205 GTAGCCCGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 7 0.18
20 10 0.26
21 21 0.55
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.19
Consensus pattern (20 bp):
GTGTGAAGGCTACACACCCT
Found at i:29357242 original size:3 final size:3
Alignment explanation
Indices: 29357230--29357260 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29357220 CATCAGGGAC
29357230 CAT C-T CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
29357261 AAGAACTCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:29359376 original size:3 final size:3
Alignment explanation
Indices: 29359368--29359409 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
29359358 AAACTCAATC
29359368 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29359410 TTTTTATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29359747 original size:10 final size:10
Alignment explanation
Indices: 29359728--29359792 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
29359718 TAAAAAATAT
29359728 TAAAAA-TCA
1 TAAAAATTCA
*
29359737 TATAAATTCA
1 TAAAAATTCA
29359747 TAAAAATT-A
1 TAAAAATTCA
*
29359756 TAAAAAAT-A
1 TAAAAATTCA
*
29359765 TAATAAATT-T
1 TAA-AAATTCA
29359775 TAACAAATT-A
1 TAA-AAATTCA
29359785 TAAAAATT
1 TAAAAATT
29359793 ACAAAACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
9 22 0.47
10 25 0.53
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
TAAAAATTCA
Found at i:29359761 original size:29 final size:28
Alignment explanation
Indices: 29359717--29359790 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
29359707 ATTTATAAAA
* *
29359717 ATAAAAAATATTAAAAATCAT-ATAAATT
1 ATAAAAATTATAAAAAAT-ATAATAAATT
29359745 CATAAAAATTATAAAAAATATAATAAATT
1 -ATAAAAATTATAAAAAATATAATAAATT
*
29359774 TTAACAAATTATAAAAA
1 ATAA-AAATTATAAAAA
29359791 TTACAAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
ATAAAAATTATAAAAAATATAATAAATT
Found at i:29359791 original size:9 final size:9
Alignment explanation
Indices: 29359709--29359901 Score: 86
Period size: 9 Copynumber: 20.0 Consensus size: 9
29359699 CATAAAATAT
29359709 TTATAAAAA
1 TTATAAAAA
29359718 -TA-AAAAA
1 TTATAAAAA
29359725 -TATTAAAAA
1 TTA-TAAAAA
* *
29359734 TCATATAAA
1 TTATAAAAA
29359743 TTCATAAAAA
1 TT-ATAAAAA
29359753 TTATAAAAA
1 TTATAAAAA
*
29359762 ATATAATAAA
1 TTATAA-AAA
*
29359772 TTTTAACAAA
1 TTATAA-AAA
29359782 TTATAAAAA
1 TTATAAAAA
* *
29359791 TTACAAAAC
1 TTATAAAAA
* *
29359800 TAACAAAACA
1 TTATAAAA-A
* **
29359810 TATTTATAATT
1 T-TATA-AAAA
29359821 TTATAAAAA
1 TTATAAAAA
**
29359830 TATATTAAACTT
1 T-TA-TAAA-AA
29359842 TTATAAAAA
1 TTATAAAAA
*
29359851 TTATTAAAA
1 TTATAAAAA
*
29359860 TTCATATAAAC
1 TT-ATA-AAAA
29359871 TTATAAAAAA
1 TTAT-AAAAA
29359881 TATATAAAAAAA
1 T-TAT--AAAAA
29359893 TTATAAAAA
1 TTATAAAAA
29359902 CTTCAACTAG
Statistics
Matches: 139, Mismatches: 29, Indels: 32
0.69 0.14 0.16
Matches are distributed among these distances:
7 7 0.05
8 2 0.01
9 58 0.42
10 42 0.30
11 20 0.14
12 10 0.07
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:29359834 original size:22 final size:22
Alignment explanation
Indices: 29359804--29359855 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
29359794 CAAAACTAAC
*
29359804 AAAACATATTTATAA-TTTTATA
1 AAAATATATTTA-AACTTTTATA
29359826 AAAATATA-TTAAACTTTTATA
1 AAAATATATTTAAACTTTTATA
29359847 AAAAT-TATT
1 AAAATATATT
29359856 AAAATTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATATATTTAAACTTTTATA
Found at i:29359843 original size:21 final size:20
Alignment explanation
Indices: 29359819--29359858 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
29359809 ATATTTATAA
29359819 TTTTATAAAAATATATTAAAC
1 TTTTATAAAAAT-TATTAAAC
29359840 TTTTATAAAAATTATTAAA
1 TTTTATAAAAATTATTAAA
29359859 ATTCATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTATAAAAATTATTAAAC
Found at i:29359867 original size:21 final size:20
Alignment explanation
Indices: 29359746--29359890 Score: 72
Period size: 20 Copynumber: 7.3 Consensus size: 20
29359736 ATATAAATTC
*
29359746 ATAAAAATTA-TAAAA-AAT
1 ATAAAAATTATTAAAATTAT
*
29359764 ATAATAAATT-TTAACAAAT-T
1 ATAA-AAATTATTAA-AATTAT
* *
29359784 ATAAAAATTA-CAAAACTA-
1 ATAAAAATTATTAAAATTAT
* * *
29359802 ACAAAACA-TATTTATAATTTT
1 ATAAAA-ATTA-TTAAAATTAT
* *
29359823 ATAAAAATATATTAAACTTTT
1 ATAAAAAT-TATTAAAATTAT
29359844 ATAAAAATTATTAAAATTCAT
1 ATAAAAATTATTAAAATT-AT
* * *
29359865 AT-AAACTTATAAAAAATAT
1 ATAAAAATTATTAAAATTAT
29359884 ATAAAAA
1 ATAAAAA
29359891 AATTATAAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
18 14 0.15
19 20 0.21
20 36 0.38
21 24 0.25
22 2 0.02
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAAATTATTAAAATTAT
Found at i:29359900 original size:10 final size:10
Alignment explanation
Indices: 29359842--29359901 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
29359832 TATTAAACTT
29359842 TTAT-AAAAA
1 TTATAAAAAA
*
29359851 TTAT-TAAAA
1 TTATAAAAAA
* *
29359860 TTCATATAAAC
1 TT-ATAAAAAA
29359871 TTATAAAAAA
1 TTATAAAAAA
29359881 TATATAAAAAAA
1 T-TAT-AAAAAA
29359893 TTATAAAAA
1 TTATAAAAA
29359902 CTTCAACTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
9 10 0.23
10 14 0.33
11 12 0.28
12 7 0.16
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:29360333 original size:20 final size:20
Alignment explanation
Indices: 29360305--29360356 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
29360295 TTATAAGTTT
29360305 ATATATTTTTAATTTTATTTA-
1 ATAT-TTTTTAATTTT-TTTAC
29360326 ATATTTTTTATATTTTTTTAC
1 ATATTTTTTA-ATTTTTTTAC
29360347 A-ATTTTTTAA
1 ATATTTTTTAA
29360357 GAGTTCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
20 18 0.62
21 10 0.34
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTTTTTAATTTTTTTAC
Found at i:29360334 original size:21 final size:22
Alignment explanation
Indices: 29360305--29360354 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
29360295 TTATAAGTTT
*
29360305 ATATATTTTTA-ATTTTATTTA-
1 ATATTTTTTTATATTTT-TTTAC
29360326 ATA-TTTTTTATATTTTTTTAC
1 ATATTTTTTTATATTTTTTTAC
29360347 A-ATTTTTT
1 ATATTTTTT
29360355 AAGAGTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATTTTTTTATATTTTTTTAC
Found at i:29360340 original size:9 final size:9
Alignment explanation
Indices: 29360285--29360459 Score: 59
Period size: 9 Copynumber: 18.3 Consensus size: 9
29360275 TTTATGGTTA
*
29360285 TTTATAATT
1 TTTATATTT
*
29360294 TTTATAAGTT
1 TTTAT-ATTT
*
29360304 TATATATTT
1 TTTATATTT
*
29360313 TTAAT-TTT
1 TTTATATTT
29360321 ATTTAATATTT
1 -TTT-ATATTT
29360332 TTTATATTTT
1 TTTATA-TTT
*
29360342 TTTACAATTT
1 TTTA-TATTT
* *
29360352 TTTAAGAGTT
1 TTT-ATATTT
* *
29360362 CTAATATGTT
1 TTTATAT-TT
*
29360372 TTT-TTTTAT
1 TTTATATT-T
* *
29360381 TTTAAATAT
1 TTTATATTT
*
29360390 TTTATGA-AT
1 TTTAT-ATTT
*
29360399 TTTATAACTT
1 TTTAT-ATTT
29360409 TTTATTAATTT
1 TTTA-T-ATTT
* *
29360420 ATTAGATTT
1 TTTATATTT
29360429 TTTATATTT
1 TTTATATTT
*
29360438 TTGATATTT
1 TTTATATTT
29360447 TTTATAGTTT
1 TTTATA-TTT
29360457 TTT
1 TTT
29360460 TATGAATTTT
Statistics
Matches: 123, Mismatches: 29, Indels: 27
0.69 0.16 0.15
Matches are distributed among these distances:
8 4 0.03
9 61 0.50
10 45 0.37
11 13 0.11
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (9 bp):
TTTATATTT
Found at i:29360469 original size:11 final size:10
Alignment explanation
Indices: 29360398--29360470 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 10
29360388 ATTTTATGAA
*
29360398 TTTTATAACT
1 TTTTATAATT
29360408 TTTTATTAATT
1 TTTTA-TAATT
* *
29360419 TATTA-GATT
1 TTTTATAATT
29360428 TTTTAT-ATT
1 TTTTATAATT
*
29360437 TTTGAT-ATT
1 TTTTATAATT
*
29360446 TTTTATAGTTT
1 TTTTATA-ATT
29360457 TTTTATGAATT
1 TTTTAT-AATT
29360468 TTT
1 TTT
29360471 ATTTTTAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
9 23 0.46
10 5 0.10
11 21 0.42
12 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:29360476 original size:29 final size:29
Alignment explanation
Indices: 29360398--29360476 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
29360388 ATTTTATGAA
**
29360398 TTTTATAACTTTTTATTAATTTATTAGATT
1 TTTTATAA-TTTTTATTTTTTTATTAGATT
*
29360428 TTTTAT-ATTTTTGATATTTTTTA-TAGTTT
1 TTTTATAATTTTT-AT-TTTTTTATTAGATT
29360457 TTTTATGAATTTTTATTTTT
1 TTTTAT-AATTTTTATTTTT
29360477 AATGTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
28 5 0.12
29 18 0.43
30 13 0.31
31 6 0.14
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTATAATTTTTATTTTTTTATTAGATT
Found at i:29360528 original size:22 final size:23
Alignment explanation
Indices: 29360498--29360541 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
29360488 ACTTTTATAT
29360498 TTTTGATAAATTTTTTGATATCC
1 TTTTGATAAATTTTTTGATATCC
* *
29360521 TTTT-ATAATTTTTTTTATATC
1 TTTTGATAAATTTTTTGATATC
29360542 TATTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTTGATAAATTTTTTGATATCC
Found at i:29360547 original size:21 final size:21
Alignment explanation
Indices: 29360490--29360554 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
29360480 GTTTAATAAC
*
29360490 TTTTATAT-TTTTGATAAATTT
1 TTTTATATCTTTT-ATAATTTT
*
29360511 TTTGATATCCTTTTATAATTTT
1 TTTTATAT-CTTTTATAATTTT
* *
29360533 TTTTATATCTATTATTATTTT
1 TTTTATATCTTTTATAATTTT
29360554 T
1 T
29360555 ATAATTAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 19 0.51
22 14 0.38
23 4 0.11
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTATATCTTTTATAATTTT
Found at i:29360631 original size:13 final size:12
Alignment explanation
Indices: 29360598--29360634 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
29360588 TTACAAGGGT
29360598 GAATTTAATTGA
1 GAATTTAATTGA
29360610 GAATTTAATTGA
1 GAATTTAATTGA
*
29360622 GAGGTTTAATTGA
1 GA-ATTTAATTGA
29360635 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (12 bp):
GAATTTAATTGA
Found at i:29361154 original size:2 final size:2
Alignment explanation
Indices: 29361149--29361173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29361139 ATTACACACA
29361149 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
29361174 TTATAATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29366857 original size:48 final size:48
Alignment explanation
Indices: 29366791--29366887 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
29366781 GTATGACTAA
29366791 ATTGGTATATATAAGCCTCAATAACACATCGTTGAAGGAAAAAAAATT
1 ATTGGTATATATAAGCCTCAATAACACATCGTTGAAGGAAAAAAAATT
29366839 ATTGGTATATATAAGCCTCAATAACACATCGTTGAAGGAAAAAAAATT
1 ATTGGTATATATAAGCCTCAATAACACATCGTTGAAGGAAAAAAAATT
29366887 A
1 A
29366888 CTTACACTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (48 bp):
ATTGGTATATATAAGCCTCAATAACACATCGTTGAAGGAAAAAAAATT
Found at i:29367569 original size:28 final size:30
Alignment explanation
Indices: 29367538--29367600 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
29367528 ATGTGAAATC
*
29367538 AAGAAAATTA-AAGGGACATTTTTAA-AGA
1 AAGAAAATTATAACGGACATTTTTAATAGA
29367566 AAG--AATTATAACGGACATTTTTAATAGA
1 AAGAAAATTATAACGGACATTTTTAATAGA
*
29367594 AATAAAA
1 AAGAAAA
29367601 AAACGGAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 5 0.17
27 14 0.48
28 8 0.28
30 2 0.07
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (30 bp):
AAGAAAATTATAACGGACATTTTTAATAGA
Found at i:29367583 original size:27 final size:27
Alignment explanation
Indices: 29367543--29367595 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
29367533 AAATCAAGAA
*
29367543 AATTAAAGGGACATTTTTAA-AGAAAG
1 AATTAAACGGACATTTTTAATAGAAAG
29367569 AATTATAACGGACATTTTTAATAGAAA
1 AATTA-AACGGACATTTTTAATAGAAA
29367596 TAAAAAAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 14 0.58
28 5 0.21
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (27 bp):
AATTAAACGGACATTTTTAATAGAAAG
Found at i:29367605 original size:27 final size:27
Alignment explanation
Indices: 29367551--29367607 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
29367541 AAAATTAAAG
* *
29367551 GGACATTTTTAAAGAAAGAATTATAAC
1 GGACATTTTTAAAGAAAGAATAAAAAC
*
29367578 GGACATTTTTAATAGAAATAA-AAAAAC
1 GGACATTTTTAA-AGAAAGAATAAAAAC
29367605 GGA
1 GGA
29367608 GGACCAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (27 bp):
GGACATTTTTAAAGAAAGAATAAAAAC
Found at i:29368034 original size:9 final size:9
Alignment explanation
Indices: 29368010--29368043 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
29368000 ATATAATAAT
*
29368010 TAATTATATT
1 TAATT-TATG
29368020 TAATTTATG
1 TAATTTATG
29368029 TAATTTATG
1 TAATTTATG
29368038 TAATTT
1 TAATTT
29368044 TTTTAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (9 bp):
TAATTTATG
Found at i:29372073 original size:3 final size:3
Alignment explanation
Indices: 29372067--29372092 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29372057 TATTATTATT
29372067 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
29372093 TCCATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:29372292 original size:5 final size:5
Alignment explanation
Indices: 29372278--29372310 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
29372268 TGCATAGTAT
29372278 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TT
29372311 GATTTATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:29385732 original size:43 final size:43
Alignment explanation
Indices: 29385682--29385788 Score: 162
Period size: 43 Copynumber: 2.5 Consensus size: 43
29385672 GTTTATTTAA
*
29385682 AAAAACGCTGCTAAAAGTCATGATCTTTAGCGGCGC-TTTCTCC
1 AAAAACGCCGCTAAAAGTCATGATCTTTAGCGGCGCTTTTC-CC
* * *
29385725 ACAAACGCCGCTAAAAGCCATGTTCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAAGTCATGATCTTTAGCGGCGCTTTTCCC
29385768 AAAAACGCCGCTAAAAGTCAT
1 AAAAACGCCGCTAAAAGTCAT
29385789 AAAATTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 53 0.93
44 4 0.07
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAAGTCATGATCTTTAGCGGCGCTTTTCCC
Found at i:29385976 original size:19 final size:19
Alignment explanation
Indices: 29385931--29385977 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
29385921 ATCAAATTAA
*
29385931 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
29385950 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
29385969 AATAAAAAT
1 AATAAAAAT
29385978 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:29386001 original size:31 final size:32
Alignment explanation
Indices: 29385921--29386001 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 32
29385911 AAAATTCATT
29385921 ATCAAAT-TAAAATAAA-AATAAAAATATAGA
1 ATCAAATATAAAATAAATAATAAAAATATAGA
29385951 ATCAAA-ACTAAAATAAATAATAAAAAT-TAG-
1 ATCAAATA-TAAAATAAATAATAAAAATATAGA
*
29385981 ATTAAATATAAATATAAATAA
1 ATCAAATATAAA-ATAAATAA
29386002 AATATAGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
30 15 0.33
31 21 0.47
32 9 0.20
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (32 bp):
ATCAAATATAAAATAAATAATAAAAATATAGA
Found at i:29386768 original size:15 final size:15
Alignment explanation
Indices: 29386748--29386776 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29386738 AAAAGAATAT
29386748 TAGCAACAAATTATG
1 TAGCAACAAATTATG
29386763 TAGCAACAAATTAT
1 TAGCAACAAATTAT
29386777 AAATTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (15 bp):
TAGCAACAAATTATG
Found at i:29391791 original size:14 final size:14
Alignment explanation
Indices: 29391752--29391840 Score: 115
Period size: 14 Copynumber: 6.1 Consensus size: 14
29391742 ATATTAAATA
29391752 TTAAATATTTAAGTATT
1 TTAAAT-TTTAA-T-TT
*
29391769 TTATATTTTAATTT
1 TTAAATTTTAATTT
*
29391783 TTAATTTTTAATTT
1 TTAAATTTTAATTT
*
29391797 TTAATTTTTAATTT
1 TTAAATTTTAATTT
*
29391811 TTAAATTTTAAATT
1 TTAAATTTTAATTT
29391825 TTAAATTTTAATTT
1 TTAAATTTTAATTT
29391839 TT
1 TT
29391841 TTTGAAGATT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
14 55 0.83
15 1 0.02
16 5 0.08
17 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (14 bp):
TTAAATTTTAATTT
Found at i:29391840 original size:7 final size:7
Alignment explanation
Indices: 29391774--29391840 Score: 107
Period size: 7 Copynumber: 9.6 Consensus size: 7
29391764 GTATTTTATA
29391774 TTTTAAT
1 TTTTAAT
29391781 TTTTAAT
1 TTTTAAT
29391788 TTTTAAT
1 TTTTAAT
29391795 TTTTAAT
1 TTTTAAT
29391802 TTTTAAT
1 TTTTAAT
*
29391809 TTTTAAA
1 TTTTAAT
*
29391816 TTTTAAA
1 TTTTAAT
*
29391823 TTTTAAA
1 TTTTAAT
29391830 TTTTAAT
1 TTTTAAT
29391837 TTTT
1 TTTT
29391841 TTTGAAGATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:29391860 original size:9 final size:8
Alignment explanation
Indices: 29391752--29391867 Score: 79
Period size: 7 Copynumber: 14.9 Consensus size: 8
29391742 ATATTAAATA
*
29391752 TTAAATAT
1 TTAAATTT
*
29391760 TTAAGTATT
1 TTAAAT-TT
*
29391769 TTATA-TT
1 TTAAATTT
29391776 TT-AATTT
1 TTAAATTT
29391783 TT-AATTT
1 TTAAATTT
29391790 TT-AATTT
1 TTAAATTT
29391797 TT-AATTT
1 TTAAATTT
29391804 TT-AATTT
1 TTAAATTT
29391811 TTAAA-TT
1 TTAAATTT
29391818 TTAAA-TT
1 TTAAATTT
29391825 TTAAA-TT
1 TTAAATTT
*
29391832 TTAATTTTTT
1 TTAA--ATTT
29391842 TTGAAGATTT
1 TT-AA-ATTT
29391852 TTATAATTT
1 TTA-AATTT
29391861 TTAAATT
1 TTAAATT
29391868 ATCGTATAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
6 1 0.01
7 56 0.61
8 11 0.12
9 12 0.13
10 10 0.11
11 2 0.02
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TTAAATTT
Found at i:29392205 original size:37 final size:37
Alignment explanation
Indices: 29392152--29392282 Score: 199
Period size: 37 Copynumber: 3.5 Consensus size: 37
29392142 CTATGCAGCA
*
29392152 GATGCACAGGGCGAAGGCGATGGAGGAGATGGGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
* * *
29392189 GATGCACGAGGTGAAGGCAATGGAGGAGATGGGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
* * *
29392226 AATGCACGGGGCGAAGGCGATGGAGGGGATGGGTTGT
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
29392263 GATGCACGGGGCGAAGGCGA
1 GATGCACGGGGCGAAGGCGA
29392283 CAAACGAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.24, C:0.13, G:0.49, T:0.14
Consensus pattern (37 bp):
GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
Found at i:29392613 original size:24 final size:25
Alignment explanation
Indices: 29392586--29392633 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
29392576 TATCAATTTT
29392586 TTTAAATCT-AATA-TTTTAAATATG
1 TTTAAAT-TAAATATTTTTAAATATG
*
29392610 TTTAGATTAAATATTTTTAAATAT
1 TTTAAATTAAATATTTTTAAATAT
29392634 AAAAGCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 10 0.48
25 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTAAATTAAATATTTTTAAATATG
Found at i:29392752 original size:18 final size:16
Alignment explanation
Indices: 29392729--29392770 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
29392719 TTTCTCTTAA
29392729 ATAATTTAAACTATATT
1 ATAATTTAAA-TATATT
*
29392746 CATAATTTTAATATATT
1 -ATAATTTAAATATATT
29392763 A-AATTTAA
1 ATAATTTAA
29392771 TATTATCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 1 0.05
17 6 0.27
18 9 0.41
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATTTAAATATATT
Found at i:29392881 original size:7 final size:7
Alignment explanation
Indices: 29392835--29392902 Score: 66
Period size: 7 Copynumber: 9.7 Consensus size: 7
29392825 ACTAATTAAT
29392835 CTAAACC
1 CTAAACC
*
29392842 CTAACCC
1 CTAAACC
29392849 CT-AACC
1 CTAAACC
*
29392855 CTTAACC
1 CTAAACC
*
29392862 CTTAACC
1 CTAAACC
29392869 CTTAAACC
1 C-TAAACC
29392877 CTAAACC
1 CTAAACC
* *
29392884 ATAAAAC
1 CTAAACC
*
29392891 ATAAACC
1 CTAAACC
29392898 CTAAA
1 CTAAA
29392903 TTTCTACCCC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.10
7 41 0.79
8 6 0.12
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:29393228 original size:15 final size:15
Alignment explanation
Indices: 29393205--29393239 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29393195 CTACTCATGG
* *
29393205 CCATTAAACCTTAAA
1 CCATAAAACCCTAAA
29393220 CCATAAAACCCTAAA
1 CCATAAAACCCTAAA
29393235 CCATA
1 CCATA
29393240 GACCTTAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (15 bp):
CCATAAAACCCTAAA
Found at i:29393493 original size:46 final size:46
Alignment explanation
Indices: 29393369--29393499 Score: 181
Period size: 47 Copynumber: 2.8 Consensus size: 46
29393359 TCAACATCCA
*
29393369 TATGATGTTTTTTGGGGTTTAGGGTTTTAAGGGTTATAGATTAATGTT
1 TATGAT-TTTTTT-GGGTTTAGGGTTTTAGGGGTTATAGATTAATGTT
* * * * *
29393417 TAGGGTTTTTTAGGGTTTAAGGATTTTAGGGGTTATAGATTAGTGTT
1 TATGATTTTTTTGGGTTT-AGGGTTTTAGGGGTTATAGATTAATGTT
29393464 TATGATTTTTTTGGGTTTAGGGTTTTAGGGGTTATA
1 TATGATTTTTTTGGGTTTAGGGTTTTAGGGGTTATA
29393500 TGGCTTTTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
46 23 0.32
47 45 0.62
48 4 0.06
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.50
Consensus pattern (46 bp):
TATGATTTTTTTGGGTTTAGGGTTTTAGGGGTTATAGATTAATGTT
Found at i:29396495 original size:6 final size:6
Alignment explanation
Indices: 29396486--29396524 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
29396476 AATAAAATTG
* * *
29396486 AAATAA AAATAG AAATAA AAAGAA AAAGAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
29396525 GATAAGAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (6 bp):
AAATAA
Found at i:29403699 original size:25 final size:25
Alignment explanation
Indices: 29403664--29403711 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
29403654 CTAAAAGAGC
*
29403664 TCATGGGCTCTGTTGGCACCTTAGT
1 TCATGGACTCTGTTGGCACCTTAGT
29403689 TCATGGACTCTGTTGGCACCTTA
1 TCATGGACTCTGTTGGCACCTTA
29403712 CTCATCACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (25 bp):
TCATGGACTCTGTTGGCACCTTAGT
Found at i:29406235 original size:56 final size:56
Alignment explanation
Indices: 29406167--29406276 Score: 168
Period size: 56 Copynumber: 2.0 Consensus size: 56
29406157 TGAGACAAAA
* *
29406167 TTGATGAGATTTTATTTATTTCTTTCTTTAGGA-TGGAGTCAATCCTTGATTATAAT
1 TTGATGAGATTTTATTTATTACTTTCTTTAAGATTGG-GTCAATCCTTGATTATAAT
* *
29406223 TTGATGAGATTTTCTTTCTTACTTTCTTTAAGATTGGGTCAATCCTTGATTATA
1 TTGATGAGATTTTATTTATTACTTTCTTTAAGATTGGGTCAATCCTTGATTATA
29406277 GGGATTCTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 46 0.94
57 3 0.06
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (56 bp):
TTGATGAGATTTTATTTATTACTTTCTTTAAGATTGGGTCAATCCTTGATTATAAT
Found at i:29406608 original size:20 final size:20
Alignment explanation
Indices: 29406564--29406608 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29406554 AATAAAACTT
* * *
29406564 TAAAAATTTTAAAGTTTATA
1 TAAAAATATTAAAGATAATA
*
29406584 AAAAAATATTAAAGATAATA
1 TAAAAATATTAAAGATAATA
29406604 TAAAA
1 TAAAA
29406609 TTACAAAATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAATATTAAAGATAATA
Found at i:29417779 original size:40 final size:40
Alignment explanation
Indices: 29417683--29417900 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
29417673 TGGATGATAA
*
29417683 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* * *
29417724 CCGGGCTAAGACCCGAAGGCATTTGTGTGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29417764 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29417804 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
29417844 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
29417883 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29417901 TACTTGGCTT
Statistics
Matches: 158, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
38 15 0.09
39 16 0.10
40 101 0.64
41 23 0.15
42 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:29420648 original size:33 final size:33
Alignment explanation
Indices: 29420604--29420672 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
29420594 CCATGGGTGA
*
29420604 ATTGTCGTAAGATAAATGATTTAATTACTACAT
1 ATTGTCATAAGATAAATGATTTAATTACTACAT
29420637 ATTGTCATAAGATAAATGATTTAATTACTACAT
1 ATTGTCATAAGATAAATGATTTAATTACTACAT
29420670 ATT
1 ATT
29420673 AGTAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (33 bp):
ATTGTCATAAGATAAATGATTTAATTACTACAT
Found at i:29421308 original size:18 final size:17
Alignment explanation
Indices: 29421280--29421313 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
29421270 ATTGTGTTGA
29421280 GAAAATAATTTAATTAG
1 GAAAATAATTTAATTAG
29421297 GAAAATTAATTTAATTA
1 GAAAA-TAATTTAATTA
29421314 ATTAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
GAAAATAATTTAATTAG
Found at i:29421931 original size:16 final size:15
Alignment explanation
Indices: 29421906--29421953 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
29421896 CTATTTTAAG
29421906 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
29421921 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
29421938 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
29421953 T
1 T
29421954 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:29429204 original size:22 final size:22
Alignment explanation
Indices: 29429179--29429226 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
29429169 CTCCACACCT
*
29429179 GACCTTGCGCCGCGCCACCGTC
1 GACCTTGCGCCGCGCCACCGAC
** *
29429201 GACCTTGTTCTGCGCCACCGAC
1 GACCTTGCGCCGCGCCACCGAC
29429223 GACC
1 GACC
29429227 ACGCGCCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.12, C:0.46, G:0.25, T:0.17
Consensus pattern (22 bp):
GACCTTGCGCCGCGCCACCGAC
Found at i:29432238 original size:16 final size:15
Alignment explanation
Indices: 29432213--29432260 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
29432203 CTATTTTAAG
29432213 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
29432228 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
29432245 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
29432260 T
1 T
29432261 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:29435884 original size:23 final size:23
Alignment explanation
Indices: 29435857--29435965 Score: 121
Period size: 23 Copynumber: 4.7 Consensus size: 23
29435847 AGTGCCATTA
29435857 TGGTGTGTTTGGGTGGATTATTC
1 TGGTGTGTTTGGGTGGATTATTC
* ** * *
29435880 TGGTGTGGTTGGGAAGAATATTT
1 TGGTGTGTTTGGGTGGATTATTC
* *
29435903 TGGTGTGTTTGGATGGATCATTC
1 TGGTGTGTTTGGGTGGATTATTC
*
29435926 TGGTGTGTTT-GGTGGAATAATTC
1 TGGTGTGTTTGGGTGG-ATTATTC
*
29435949 TGGTGTGTTTGGTTGGA
1 TGGTGTGTTTGGGTGGA
29435966 ATTTGTGTAT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
22 4 0.06
23 61 0.88
24 4 0.06
ACGTcount: A:0.14, C:0.04, G:0.39, T:0.44
Consensus pattern (23 bp):
TGGTGTGTTTGGGTGGATTATTC
Found at i:29435926 original size:46 final size:46
Alignment explanation
Indices: 29435857--29435965 Score: 141
Period size: 46 Copynumber: 2.4 Consensus size: 46
29435847 AGTGCCATTA
* * *
29435857 TGGTGTGTTTGGGTGGATTATTCTGGTGTGGTTGG-GAAGAAT-ATTT
1 TGGTGTGTTTGGATGGATCATTCTGGTGTGGTTGGTG--GAATAATTC
*
29435903 TGGTGTGTTTGGATGGATCATTCTGGTGTGTTTGGTGGAATAATTC
1 TGGTGTGTTTGGATGGATCATTCTGGTGTGGTTGGTGGAATAATTC
*
29435949 TGGTGTGTTTGGTTGGA
1 TGGTGTGTTTGGATGGA
29435966 ATTTGTGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 4 0.07
46 51 0.91
47 1 0.02
ACGTcount: A:0.14, C:0.04, G:0.39, T:0.44
Consensus pattern (46 bp):
TGGTGTGTTTGGATGGATCATTCTGGTGTGGTTGGTGGAATAATTC
Found at i:29440254 original size:16 final size:16
Alignment explanation
Indices: 29440227--29440259 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29440217 AGCCCAGCTA
29440227 GAAGATGAAAAGTTGAT
1 GAAGATGAAAAG-TGAT
29440244 GAAGA-GAAAAGTGAT
1 GAAGATGAAAAGTGAT
29440259 G
1 G
29440260 GTATGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.18
Consensus pattern (16 bp):
GAAGATGAAAAGTGAT
Found at i:29442336 original size:23 final size:23
Alignment explanation
Indices: 29442310--29442400 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
29442300 ATACACGAAT
* *
29442310 TCCAACCAAACACACTAGAATGA
1 TCCACCCAAACACACCAGAATGA
* * *
29442333 TCCATCCAAACACACTAAAAT-A
1 TCCACCCAAACACACCAGAATGA
* *
29442355 TTCCTCCCAAACACACCAGAATAA
1 -TCCACCCAAACACACCAGAATGA
*
29442379 TCCACCCAAACTCACCAGAATG
1 TCCACCCAAACACACCAGAATG
29442401 GCACTAAGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.02
23 55 0.96
24 1 0.02
ACGTcount: A:0.44, C:0.35, G:0.05, T:0.15
Consensus pattern (23 bp):
TCCACCCAAACACACCAGAATGA
Found at i:29443444 original size:25 final size:25
Alignment explanation
Indices: 29443400--29443447 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29443390 CTCTATTTCT
* *
29443400 TTTTATGCTTTGTTTCCTTTATTCC
1 TTTTATGCTTTATTTACTTTATTCC
*
29443425 TTTTATGTTTTATTTACTTTATT
1 TTTTATGCTTTATTTACTTTATT
29443448 AGTTTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTTATGCTTTATTTACTTTATTCC
Done.