Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 82 of 93
Found at i:31516734 original size:17 final size:17
Alignment explanation
Indices: 31516708--31516742 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31516698 GGGAGCACCA
31516708 GTGCTCCCTTCTCTTGG
1 GTGCTCCCTTCTCTTGG
* *
31516725 GTGCTTCCTTTTCTTGG
1 GTGCTCCCTTCTCTTGG
31516742 G
1 G
31516743 GAGTTGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.26, T:0.46
Consensus pattern (17 bp):
GTGCTCCCTTCTCTTGG
Found at i:31519061 original size:26 final size:26
Alignment explanation
Indices: 31519012--31519061 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
31519002 ATGCCAGCAA
* *
31519012 AAGAAAAAGAAAATATATTCTTACAC
1 AAGAAAAACAAAATAAATTCTTACAC
* *
31519038 AAGAAAAACAAATTAAATTTTTAC
1 AAGAAAAACAAAATAAATTCTTAC
31519062 TGTACACCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (26 bp):
AAGAAAAACAAAATAAATTCTTACAC
Found at i:31525034 original size:18 final size:19
Alignment explanation
Indices: 31524999--31525043 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
31524989 ATTACACAGC
*
31524999 AAGAAAAATGCATCGAAGA
1 AAGAAAAATGAATCGAAGA
*
31525018 AAGAAAAATTAAT-GAAGA
1 AAGAAAAATGAATCGAAGA
*
31525036 CAGAAAAA
1 AAGAAAAA
31525044 AGATCAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.07, G:0.18, T:0.11
Consensus pattern (19 bp):
AAGAAAAATGAATCGAAGA
Found at i:31525976 original size:81 final size:82
Alignment explanation
Indices: 31525788--31526009 Score: 227
Period size: 81 Copynumber: 2.7 Consensus size: 82
31525778 AACTAGACTC
** * * * * *
31525788 TTCTTTTTCTTCTGATTTTGGTTTGTAGGAA-TCTGGCTTTGTGCTGTAATTAGGTTTTTCTACC
1 TTCTTTTTCTTCTGGCTGTGGTTTGTA-GAAGTCTGGCTTAGTGCTATAATCAGG--CTTCTACC
*
31525852 TCCTCTGATGACTCTGGCTT
63 TCCTCTGATGACTCTGGATT
* *
31525872 TT-TGTTTACTTCTGGCTGTGGTTTGTAGAAGTCTGGCTTAGTGCTATAATCAGGCTTCT-CTTC
1 TTCT-TTTTCTTCTGGCTGTGGTTTGTAGAAGTCTGGCTTAGTGCTATAATCAGGCTTCTACCTC
**
31525935 CTCTTCTGACTCTGGATT
65 CTCTGATGACTCTGGATT
* * * *
31525953 TTCTTTTTCTTCTGGCTGCGGTTTGTAGAAGTTCT-GTTTAGTGCCATTATCAGGCTT
1 TTCTTTTTCTTCTGGCTGTGGTTTGTAGAAG-TCTGGCTTAGTGCTATAATCAGGCTT
31526010 TTCTGGCTGT
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
81 64 0.55
82 8 0.07
83 4 0.03
84 41 0.35
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (82 bp):
TTCTTTTTCTTCTGGCTGTGGTTTGTAGAAGTCTGGCTTAGTGCTATAATCAGGCTTCTACCTCC
TCTGATGACTCTGGATT
Found at i:31526119 original size:69 final size:69
Alignment explanation
Indices: 31526005--31526196 Score: 321
Period size: 69 Copynumber: 2.8 Consensus size: 69
31525995 GCCATTATCA
* * *
31526005 GGCTTTTCTGGCTGTGGTTGGTAAACTGGTTTTCTGCCATCATCAGGTTTTTCTTCCTTTCCTGA
1 GGCTTTTCTGGCTGTGGTTGGTAAACTGGTTTTCTGCCATAATCAGGCTTTTCTTCCGTTCCTGA
*
31526070 CTCT
66 CACT
31526074 GGCTTTTCTGGCTGTGGTTGGTAAACTGGTTTTCTGCCATAATCAGGCTTTTCTTCCGTTCCTGA
1 GGCTTTTCTGGCTGTGGTTGGTAAACTGGTTTTCTGCCATAATCAGGCTTTTCTTCCGTTCCTGA
31526139 CACT
66 CACT
* * *
31526143 GGCTTTTCTGGCTGTGTTTGGTAAACTGGTTTTCTACCATAGTCAGGCTTTTCT
1 GGCTTTTCTGGCTGTGGTTGGTAAACTGGTTTTCTGCCATAATCAGGCTTTTCT
31526197 GACACTACCG
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 116 1.00
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (69 bp):
GGCTTTTCTGGCTGTGGTTGGTAAACTGGTTTTCTGCCATAATCAGGCTTTTCTTCCGTTCCTGA
CACT
Found at i:31529089 original size:15 final size:16
Alignment explanation
Indices: 31529041--31529118 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 16
31529031 GTGTATTAAG
31529041 ATATATA-T-TATATA
1 ATATATACTATATATA
* * * *
31529055 ATGTATAACTGTAAACA
1 ATATAT-ACTATATATA
*
31529072 ATATATACTGTAT-TA
1 ATATATACTATATATA
*
31529087 ATATTTACTATATATA
1 ATATATACTATATATA
*
31529103 ATTATATAGTATATAT
1 A-TATATACTATATAT
31529119 GTCTATTGTA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
14 5 0.10
15 13 0.27
16 10 0.20
17 21 0.43
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATATACTATATATA
Found at i:31529300 original size:20 final size:20
Alignment explanation
Indices: 31529260--31529300 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31529250 ATATATATAC
* *
31529260 TATATAATAGTATATTGTTA
1 TATACAATAGTAAATTGTTA
*
31529280 TATACAATAGTAAATTTTTA
1 TATACAATAGTAAATTGTTA
31529300 T
1 T
31529301 TAACTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
TATACAATAGTAAATTGTTA
Found at i:31529439 original size:20 final size:19
Alignment explanation
Indices: 31529385--31529441 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
31529375 GTTATATTAC
*
31529385 TATAAG-ATACTAATAATAA
1 TATAAGTATACT-ATAGTAA
*
31529404 TATAAGT-TACTTTAGTAA
1 TATAAGTATACTATAGTAA
31529422 TATAAGCTATACTATAGTAA
1 TATAAG-TATACTATAGTAA
31529442 CATTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.34
19 11 0.34
20 10 0.31
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (19 bp):
TATAAGTATACTATAGTAA
Found at i:31529456 original size:8 final size:8
Alignment explanation
Indices: 31529443--31529556 Score: 51
Period size: 8 Copynumber: 13.8 Consensus size: 8
31529433 CTATAGTAAC
31529443 ATTAATAT
1 ATTAATAT
31529451 ATTAATATAT
1 ATT-A-ATAT
31529461 ATTAATA-
1 ATTAATAT
*
31529468 AGTTACTAT
1 A-TTAATAT
31529477 ATTAA-ATT
1 ATTAATA-T
31529485 ATTAATAT
1 ATTAATAT
31529493 AAGTT-ATACT
1 -A-TTAATA-T
* *
31529503 A-TAGTAAC
1 ATTAAT-AT
31529511 ATTAATAT
1 ATTAATAT
31529519 ATTAATAT
1 ATTAATAT
*
31529527 -TATAGTAT
1 AT-TAATAT
31529535 ATTAATA-
1 ATTAATAT
*
31529542 AGTTACTAT
1 A-TTAATAT
31529551 ATTAAT
1 ATTAAT
31529557 GTAAGTTATA
Statistics
Matches: 80, Mismatches: 10, Indels: 32
0.66 0.08 0.26
Matches are distributed among these distances:
7 5 0.06
8 50 0.62
9 15 0.19
10 10 0.12
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (8 bp):
ATTAATAT
Found at i:31529458 original size:34 final size:33
Alignment explanation
Indices: 31529419--31529571 Score: 113
Period size: 34 Copynumber: 4.5 Consensus size: 33
31529409 GTTACTTTAG
31529419 TAATATAAGCTATACTATAGTAACATTAATATAT
1 TAATATAAG-TATACTATAGTAACATTAATATAT
* *
31529453 TAATAT-A-TATTAATA-AGTTACTATATTAA-ATTAT
1 TAATATAAGTA-TACTATAG-TA--ACATTAATA-TAT
31529487 TAATATAAGTTATACTATAGTAACATTAATATAT
1 TAATATAAG-TATACTATAGTAACATTAATATAT
* * *
31529521 TAATATTATAGTATA-T-TAATAA-GTTACTATAT
1 TAATA-TA-AGTATACTATAGTAACATTAATATAT
*
31529553 TAATGTAAGTTATACTATA
1 TAATATAAG-TATACTATA
31529572 TTACTATAGT
Statistics
Matches: 96, Mismatches: 8, Indels: 31
0.71 0.06 0.23
Matches are distributed among these distances:
30 2 0.02
31 10 0.10
32 19 0.20
33 9 0.09
34 36 0.38
35 8 0.08
36 8 0.08
37 4 0.04
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (33 bp):
TAATATAAGTATACTATAGTAACATTAATATAT
Found at i:31529491 original size:68 final size:72
Alignment explanation
Indices: 31529419--31529555 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 72
31529409 GTTACTTTAG
31529419 TAATATAAGCTATACTATAGTAACATTAATATA-T-TA-ATA-TATATTAATAAGTTACTATATT
1 TAATATAAGCTATACTATAGTAACATTAATATATTATATATAGTATATTAATAAGTTACTATATT
31529480 AAATTAT
66 AAATTAT
*
31529487 TAATATAAGTTATACTATAGTAACATTAATATATTAATATTATAGTATATTAATAAGTTACTATA
1 TAATATAAGCTATACTATAGTAACATTAATATATT-ATA-TATAGTATATTAATAAGTTACTATA
31529552 TTAA
64 TTAA
31529556 TGTAAGTTAT
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
68 32 0.52
69 1 0.02
71 2 0.03
73 3 0.05
74 24 0.39
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (72 bp):
TAATATAAGCTATACTATAGTAACATTAATATATTATATATAGTATATTAATAAGTTACTATATT
AAATTAT
Found at i:31529563 original size:18 final size:18
Alignment explanation
Indices: 31529491--31529574 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 18
31529481 AATTATTAAT
*
31529491 ATAAGTTATACTATAGTA
1 ATAAGTTATACTATATTA
*
31529509 A-CA-TTA-A-TATATTA
1 ATAAGTTATACTATATTA
*
31529523 AT-A-TTATAGTATATTA
1 ATAAGTTATACTATATTA
31529539 ATAAG-T-TACTATATTA
1 ATAAGTTATACTATATTA
31529555 ATGTAAGTTATACTATATTA
1 A--TAAGTTATACTATATTA
31529575 CTATAGTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
14 11 0.20
15 2 0.04
16 22 0.41
17 3 0.06
18 5 0.09
19 1 0.02
20 10 0.19
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (18 bp):
ATAAGTTATACTATATTA
Found at i:31529904 original size:18 final size:20
Alignment explanation
Indices: 31529881--31529926 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31529871 TATTAATAAT
*
31529881 TTAATATAA-CT-TAGTATA
1 TTAATATAAGCTATACTATA
*
31529899 TTAATATAAGTTATACTATA
1 TTAATATAAGCTATACTATA
31529919 TTAATATA
1 TTAATATA
31529927 GTTTATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 1 0.04
20 14 0.58
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (20 bp):
TTAATATAAGCTATACTATA
Found at i:31530166 original size:350 final size:344
Alignment explanation
Indices: 31529539--31530192 Score: 974
Period size: 350 Copynumber: 1.9 Consensus size: 344
31529529 TAGTATATTA
* * * * * *
31529539 ATAAGTTACTATATTAATGTAAGTTATACTATATTACTATAGTTTATTGATCATTTATAAAAAGT
1 ATAACTTACTATATTAATATAAGTTATACTATATTAATATAGTTTATTAATAATTTATAAAAAAT
* * * * *
31529604 ATGTTACTATATTCTATACTCTATAGCATATAGACTATGTATTGTATATTAATAAATATGATATA
66 AAGTTACTATAGTCTATACTCTATAGCATATAAACTATATATTGCATATTAATAAATATGATATA
* * * * *
31529669 CAAAGTTTAATATATTAATAAGTTAATATAATAAGTTATATTCATAACTTAAGGTTTGTGTATAG
131 CAAAGTTAAATATATTAATAACTTAATAAAATAAGTTATATTAATAACTTAAGGTTTGGGTATAG
31529734 TTTTCATTATATTTTGCATTAATTTTATATCAATTTTGTATGGCTATATTTATATAAATATTCAA
196 TTTTCATTATATTTTGCATTAATTTTATATCAATTTTGTATGGCTATATTTATATAAATATTCAA
31529799 TAACATTAATATCTAAATAAAGTGTATTTTATTATTTTTATTTTTTNTAGTTATATTACTAAAGT
261 TAACATTAATATCTAAATAAAGTGTATTTTA-T-TTTTTATTTTTT-TAGTTATATTACTAAAGT
31529864 ACATTAATATTAATAATTTAAT
323 ACATTAATATTAATAATTTAAT
*
31529886 ATAACTTAGTATATTAATATAAGTTATACTATATTAATATAGTTTATTAATAATTTATAAAAAAA
1 ATAACTTACTATATTAATATAAGTTATACTATATTAATATAGTTTATTAATAATTTAT-AAAAAA
* * *
31529951 TAAGTTACTATAGTCTATAGTCTATA-TAGTATAAATTATATATTGCATATTAATAAATAT-ACT
65 TAAGTTACTATAGTCTATACTCTATAGCA-TATAAACTATATATTGCATATTAATAAATATGA-T
* *
31530014 ATATATAG-TAAATATATTAATAACTTAAGATAAAAATAAGTTATATTAATAACTTAA-GTTTAG
128 ATACAAAGTTAAATATATTAATAACTT-A-AT-AAAATAAGTTATATTAATAACTTAAGGTTT-G
31530077 GGTATAGTTTTCATTATATTTTGCATTAATTTTATATCAATTTTGTATGGCTATATTTATATAAA
189 GGTATAGTTTTCATTATATTTTGCATTAATTTTATATCAATTTTGTATGGCTATATTTATATAAA
* *
31530142 TATTCAATAATATTAATGTCTAAATAAAGTGTATTTTATTTTTTATTTTTT
254 TATTCAATAACATTAATATCTAAATAAAGTGTATTTTATTTTTTATTTTTT
31530193 GATGATTAAA
Statistics
Matches: 276, Mismatches: 24, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
347 70 0.25
348 75 0.27
349 7 0.03
350 124 0.45
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (344 bp):
ATAACTTACTATATTAATATAAGTTATACTATATTAATATAGTTTATTAATAATTTATAAAAAAT
AAGTTACTATAGTCTATACTCTATAGCATATAAACTATATATTGCATATTAATAAATATGATATA
CAAAGTTAAATATATTAATAACTTAATAAAATAAGTTATATTAATAACTTAAGGTTTGGGTATAG
TTTTCATTATATTTTGCATTAATTTTATATCAATTTTGTATGGCTATATTTATATAAATATTCAA
TAACATTAATATCTAAATAAAGTGTATTTTATTTTTTATTTTTTTAGTTATATTACTAAAGTACA
TTAATATTAATAATTTAAT
Found at i:31532046 original size:84 final size:82
Alignment explanation
Indices: 31531937--31532129 Score: 203
Period size: 81 Copynumber: 2.3 Consensus size: 82
31531927 AACTAGACTC
* ** * * * * *
31531937 TTCTTTTTCTTCTGATTTTGGTTTGTAGGAA-TCTGGCTTTGTGCTGTAATTAGGTTTTTCTACC
1 TTCTTTTACTTCTGGCTGTGGTTTGTAGGAAGTCTGGCTTAGTGCTATAATCAGG--CTTCT-CC
31532001 TCCTCTGATGACTCTGGCTT
63 TCCTCTGATGACTCTGGCTT
*
31532021 TT-TGTTTACTTCTGGCTGTGGTTTGTA-GAAGTCTGGCTTAGTGCTATAATCAGGCTTCTCTTC
1 TTCT-TTTACTTCTGGCTGTGGTTTGTAGGAAGTCTGGCTTAGTGCTATAATCAGGCTTCTCCTC
** *
31532084 CTCTTCTGACTCTGGGTT
65 CTCTGATGACTCTGGCTT
* *
31532102 TTCTTTTTCTTCTGGCTGCGGTTTGTAG
1 TTCTTTTACTTCTGGCTGTGGTTTGTAG
31532130 TTCTGTTTAG
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
81 41 0.45
82 5 0.05
83 4 0.04
84 41 0.45
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (82 bp):
TTCTTTTACTTCTGGCTGTGGTTTGTAGGAAGTCTGGCTTAGTGCTATAATCAGGCTTCTCCTCC
TCTGATGACTCTGGCTT
Found at i:31532125 original size:81 final size:80
Alignment explanation
Indices: 31531937--31532183 Score: 248
Period size: 78 Copynumber: 3.0 Consensus size: 80
31531927 AACTAGACTC
** * * * * * *
31531937 TTCTTTTTCTTCTGATTTTGGTTTGTAGGAATCTGGCTTTGTGCTGTAATTAGGTTTTTCTACCT
1 TTCTTTTTCTTCTGGCTGTGGTTTGTA-GAATCTGGCTTAGTGCTATAATCAGG--CTTCT-CTT
**
31532002 CCTCTGATGACTCTGGCTT
62 CCTCTTCTGACTCTGGCTT
*
31532021 TT-TGTTTACTTCTGGCTGTGGTTTGTAGAAGTCTGGCTTAGTGCTATAATCAGGCTTCTCTTCC
1 TTCT-TTTTCTTCTGGCTGTGGTTTGTAGAA-TCTGGCTTAGTGCTATAATCAGGCTTCTCTTCC
*
31532085 TCTTCTGACTCTGGGTT
64 TCTTCTGACTCTGGCTT
* * * * * * *
31532102 TTCTTTTTCTTCTGGCTGCGGTTTGTAG-TTCT-GTTTAGTGCCATTATCAGGCTTTTCTTCCTT
1 TTCTTTTTCTTCTGGCTGTGGTTTGTAGAATCTGGCTTAGTGCTATAATCAGGCTTCTCTTCCTC
31532165 TTCTGACTCTGGCTT
66 TTCTGACTCTGGCTT
31532180 TTCT
1 TTCT
31532184 GGCTGTTGTT
Statistics
Matches: 139, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
78 44 0.32
79 3 0.02
81 42 0.30
82 5 0.04
83 4 0.03
84 41 0.29
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.49
Consensus pattern (80 bp):
TTCTTTTTCTTCTGGCTGTGGTTTGTAGAATCTGGCTTAGTGCTATAATCAGGCTTCTCTTCCTC
TTCTGACTCTGGCTT
Found at i:31532213 original size:69 final size:69
Alignment explanation
Indices: 31532140--31532366 Score: 368
Period size: 69 Copynumber: 3.3 Consensus size: 69
31532130 TTCTGTTTAG
* *
31532140 TGCCATTATCAGGCTTTTCTTCCTTTTCTGACTCTGGCTTTTCTGGCTGTTGTTGGTAAACTGGT
1 TGCCATAATCAGGCTTTTCTTCCTTTTCTGACTCTGGTTTTTCTGGCTGTTGTTGGTAAACTGGT
31532205 TTTC
66 TTTC
* *
31532209 TGCCATAATCAGGCTTTTCCT-CTTTTCCTGACTCTGGTTTTTCTGGCTGTGGTTGGTAAACTGG
1 TGCCATAATCAGGCTTTTCTTCCTTTT-CTGACTCTGGTTTTTCTGGCTGTTGTTGGTAAACTGG
31532273 TTTTC
65 TTTTC
* *
31532278 TTCCATAATCAGGCTTTTCTTCCTTTCCTGACTCTGGTTTTTCTGGCTG-TGTTTGGTAAACTGG
1 TGCCATAATCAGGCTTTTCTTCCTTTTCTGACTCTGGTTTTTCTGGCTGTTG-TTGGTAAACTGG
31532342 TTTTC
65 TTTTC
31532347 TGCCATAATCAGGCTTTTCT
1 TGCCATAATCAGGCTTTTCT
31532367 GAGTCTATTG
Statistics
Matches: 146, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
68 6 0.04
69 136 0.93
70 4 0.03
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (69 bp):
TGCCATAATCAGGCTTTTCTTCCTTTTCTGACTCTGGTTTTTCTGGCTGTTGTTGGTAAACTGGT
TTTC
Found at i:31533377 original size:2 final size:2
Alignment explanation
Indices: 31533347--31533402 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
31533337 CTATATTTCT
* * *
31533347 TA TA TA T- TA AA T- TA TA TT TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31533387 TA TA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA
31533403 AACAACATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31540567 original size:16 final size:15
Alignment explanation
Indices: 31540546--31540580 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31540536 AAATTCAGGG
31540546 GAAAAAAATTCCGTTA
1 GAAAAAAA-TCCGTTA
*
31540562 GAAAAAAATCCGTTG
1 GAAAAAAATCCGTTA
31540577 GAAA
1 GAAA
31540581 TGGTGTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.20
Consensus pattern (15 bp):
GAAAAAAATCCGTTA
Found at i:31540617 original size:15 final size:15
Alignment explanation
Indices: 31540597--31540626 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31540587 TCCAACGAAA
31540597 AATTCCGTTGAAAAC
1 AATTCCGTTGAAAAC
*
31540612 AATTCCGTTGGAAAC
1 AATTCCGTTGAAAAC
31540627 TCAGTTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (15 bp):
AATTCCGTTGAAAAC
Found at i:31540670 original size:45 final size:45
Alignment explanation
Indices: 31540549--31540652 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 45
31540539 TTCAGGGGAA
* **
31540549 AAAAATTCCGTTAGAAAA-AAATCCGTTGGAAA-TGGTGTTCCAACG
1 AAAAATTCCGTT-GAAAACAATTCCGTTGGAAACT-CAGTTCCAACG
31540594 AAAAATTCCGTTGAAAACAATTCCGTTGGAAACTCAGTTCCAACG
1 AAAAATTCCGTTGAAAACAATTCCGTTGGAAACTCAGTTCCAACG
*
31540639 GAAAATTCCGTTGA
1 AAAAATTCCGTTGA
31540653 TAATTTTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
44 5 0.09
45 47 0.89
46 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (45 bp):
AAAAATTCCGTTGAAAACAATTCCGTTGGAAACTCAGTTCCAACG
Found at i:31541261 original size:2 final size:2
Alignment explanation
Indices: 31541254--31541281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31541244 TTTAAACATT
31541254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31541282 AAATTGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31541524 original size:30 final size:30
Alignment explanation
Indices: 31541488--31541555 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
31541478 TTGATCTTCA
31541488 TCTTCATCTTCATCTCCTTCCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCATCT
* * *
31541518 TTTTCATCTTCATCTCTTTGCATGTCATCT
1 TCTTCATCTTCATCTCCTTCCATGTCATCT
31541548 TCTTCATC
1 TCTTCATC
31541556 CGCAATCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.50
Consensus pattern (30 bp):
TCTTCATCTTCATCTCCTTCCATGTCATCT
Found at i:31541530 original size:15 final size:16
Alignment explanation
Indices: 31541490--31541547 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 16
31541480 GATCTTCATC
* *
31541490 TTCATCTTCATCTCCT
1 TTCATCGTCATCTCTT
*
31541506 TCCAT-GTCATCT-TT
1 TTCATCGTCATCTCTT
*
31541520 TTCATCTTCATCTCTT
1 TTCATCGTCATCTCTT
*
31541536 TGCAT-GTCATCT
1 TTCATCGTCATCT
31541548 TCTTCATCCG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
14 5 0.15
15 18 0.55
16 10 0.30
ACGTcount: A:0.14, C:0.31, G:0.05, T:0.50
Consensus pattern (16 bp):
TTCATCGTCATCTCTT
Found at i:31547834 original size:157 final size:157
Alignment explanation
Indices: 31547569--31547925 Score: 400
Period size: 157 Copynumber: 2.3 Consensus size: 157
31547559 AGGTAGAGGT
* * * *
31547569 AGAGCTCAA-CAAAAGGACCGACTTTTAGAGAGAGGTGAGAGCGCCGGACGGGAGAGCTGCCGTC
1 AGAGCT-AAGCAAAATGATCGACTTTTAGAGAGA-GTGAGAGCACCGGACGGGAGAGCTACCGTC
* * * * * *
31547633 GGTAAGGGAGAAAGTCGACCGAGAGAAAGGGAAGGAATAAAAAAAA-AA-AAGAAATGAAGGTCG
64 GGTAAGGGAGAAAGCCGACCAAAAGAAAGGGAAGGAAAAAAAAAAAGAAGAAGAAAGGAAGGCCG
* * * *
31547696 CTCAAAAGGAAGAGACGTCGGTGGCATAAG
129 CCCAAAAGGAAGAGACGCCGGCGG-ACAAG
* *
31547726 AGAGCTAAGCAAAATGATCGA-TTGTTAGAGAGACGTGAGAGCACTGGATGGGAGAGCTACCGTC
1 AGAGCTAAGCAAAATGATCGACTT-TTAGAGAGA-GTGAGAGCACCGGACGGGAGAGCTACCGTC
* *
31547790 GGTAAGGGAGAAAGCCGACCAAAAGAGAGGGAA-GAAAAAGAAAAAAGAAGAAGAAAGGAGGGCC
64 GGTAAGGGAGAAAGCCGACCAAAAGAAAGGGAAGGAAAAA-AAAAAAGAAGAAGAAAGGAAGGCC
** * **
31547854 GCCCGGAAGGAAGAGATGCCGGCGGACGGG
128 GCCCAAAAGGAAGAGACGCCGGCGGACAAG
*
31547884 AGAGCTCAGCAAAATGATCGACTTTTAGAGAGAGTTGAGAGC
1 AGAGCTAAGCAAAATGATCGACTTTTAGAGAGAG-TGAGAGC
31547926 GTCGACCGGT
Statistics
Matches: 168, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
156 9 0.05
157 87 0.52
158 40 0.24
159 32 0.19
ACGTcount: A:0.39, C:0.15, G:0.35, T:0.11
Consensus pattern (157 bp):
AGAGCTAAGCAAAATGATCGACTTTTAGAGAGAGTGAGAGCACCGGACGGGAGAGCTACCGTCGG
TAAGGGAGAAAGCCGACCAAAAGAAAGGGAAGGAAAAAAAAAAAGAAGAAGAAAGGAAGGCCGCC
CAAAAGGAAGAGACGCCGGCGGACAAG
Found at i:31548661 original size:18 final size:17
Alignment explanation
Indices: 31548614--31548663 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
31548604 TATATAAAGT
*
31548614 TGTATGTAAACACAT-A
1 TGTATGTAAACATATAA
*
31548630 TGTAT-TAACTCATATACA
1 TGTATGTAA-ACATATA-A
31548648 TGTATGTAAACATATA
1 TGTATGTAAACATATA
31548664 TATTAACTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.11
16 9 0.33
18 12 0.44
19 3 0.11
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (17 bp):
TGTATGTAAACATATAA
Found at i:31548668 original size:32 final size:34
Alignment explanation
Indices: 31548614--31548677 Score: 105
Period size: 32 Copynumber: 1.9 Consensus size: 34
31548604 TATATAAAGT
*
31548614 TGTATGTAAACACATATGTATTAACTCATATACA
1 TGTATGTAAACACATATATATTAACTCATATACA
31548648 TGTATGT-AA-ACATATATATTAACTCATATA
1 TGTATGTAAACACATATATATTAACTCATATA
31548678 AATAAAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 20 0.69
33 2 0.07
34 7 0.24
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (34 bp):
TGTATGTAAACACATATATATTAACTCATATACA
Found at i:31548704 original size:2 final size:2
Alignment explanation
Indices: 31548697--31548754 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
31548687 GTATGAGTAC
* * * * *
31548697 AT AT AT AT AT GT AT GT AA AC AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31548739 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
31548755 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:31555375 original size:23 final size:21
Alignment explanation
Indices: 31555344--31555395 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
31555334 GTTTACTGTT
*
31555344 TATTCAAATTCTGTTGGAAATC
1 TATTCAAA-TCCGTTGGAAATC
*
31555366 TATTGCAAATCCGTTGGAAAGC
1 TATT-CAAATCCGTTGGAAATC
31555388 T-TTCAAAT
1 TATTCAAAT
31555396 TTTTTTGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 2 0.07
22 16 0.59
23 4 0.15
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
TATTCAAATCCGTTGGAAATC
Found at i:31555455 original size:12 final size:12
Alignment explanation
Indices: 31555428--31555467 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
31555418 ACGGAAAATT
31555428 TTTCGTTGAAAAA
1 TTTCGTTG-AAAA
*
31555441 TTTCGTTGGAAA
1 TTTCGTTGAAAA
31555453 TTTCGTTGAAAA
1 TTTCGTTGAAAA
31555465 TTT
1 TTT
31555468 TGGTCCGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (12 bp):
TTTCGTTGAAAA
Found at i:31563960 original size:44 final size:44
Alignment explanation
Indices: 31563849--31563960 Score: 179
Period size: 44 Copynumber: 2.5 Consensus size: 44
31563839 CTATGACATG
* * * *
31563849 ATAAGATTCCATTACAACATTTTATTTTCCACAAAAGCACCATT
1 ATAAGATTCCATTACAACTTTTTTTTTTCCACAAAAACACCAGT
*
31563893 ATAAGATTCCATTACAACTTTTTTTTTTCCACAAAAACACTAGT
1 ATAAGATTCCATTACAACTTTTTTTTTTCCACAAAAACACCAGT
31563937 ATAAGATTCCATTACAACTTTTTT
1 ATAAGATTCCATTACAACTTTTTT
31563961 CTTATTCTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (44 bp):
ATAAGATTCCATTACAACTTTTTTTTTTCCACAAAAACACCAGT
Found at i:31585525 original size:18 final size:17
Alignment explanation
Indices: 31585492--31585532 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
31585482 CATATTCCCT
*
31585492 AAATAAAAATTAATCAA
1 AAATAAAAAATAATCAA
31585509 AAATAATAAAATAATCAA
1 AAATAA-AAAATAATCAA
31585527 ATAATA
1 A-AATA
31585533 CAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 11 0.52
19 4 0.19
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAAATAATCAA
Found at i:31586698 original size:2 final size:2
Alignment explanation
Indices: 31586691--31586738 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
31586681 ATAGATTTAG
*
31586691 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31586732 TA -A TA TA
1 TA TA TA TA
31586739 ANAATGAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:31592403 original size:30 final size:30
Alignment explanation
Indices: 31592367--31592428 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
31592357 ATTTATAGGC
*
31592367 AGAGAATGAAGTGAATGTGACACCAAATCA
1 AGAGAATGAAGTGAACGTGACACCAAATCA
* * *
31592397 AGAGAATGAGGTGAACGTTACACCCAATCA
1 AGAGAATGAAGTGAACGTGACACCAAATCA
31592427 AG
1 AG
31592429 GGAGTTGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (30 bp):
AGAGAATGAAGTGAACGTGACACCAAATCA
Found at i:31595905 original size:22 final size:21
Alignment explanation
Indices: 31595880--31595924 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
31595870 CAAATTATTT
31595880 ATTTAT-TCAATGAAATAAATAA
1 ATTTATGT-AATGAAAT-AATAA
*
31595902 ATTTATGTAATTAAATAATAA
1 ATTTATGTAATGAAATAATAA
31595923 AT
1 AT
31595925 AAGTAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTTATGTAATGAAATAATAA
Found at i:31601449 original size:20 final size:21
Alignment explanation
Indices: 31601426--31601471 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
31601416 AATTTCTATT
31601426 TAAACTTATAATAC-T-AAATA
1 TAAAC-TATAATACATAAAATA
*
31601446 TAAAACTATAATGCATAAAATA
1 T-AAACTATAATACATAAAATA
31601468 TAAA
1 TAAA
31601472 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 8 0.36
21 8 0.36
22 6 0.27
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAACTATAATACATAAAATA
Found at i:31601903 original size:18 final size:18
Alignment explanation
Indices: 31601880--31601919 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
31601870 ACATATGAAC
31601880 AAATAAT-ATAAAAAATAT
1 AAATAATAAT-AAAAATAT
*
31601898 AAATAATAATAATAATAT
1 AAATAATAATAAAAATAT
31601916 AAAT
1 AAAT
31601920 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAATAATAAAAATAT
Found at i:31601919 original size:24 final size:21
Alignment explanation
Indices: 31601880--31601930 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
31601870 ACATATGAAC
31601880 AAATAATATAAAAAATATAAA
1 AAATAATATAAAAAATATAAA
* *
31601901 TAATAATAATAATATAAATTTAAA
1 AAATAAT-ATAA-A-AAATATAAA
31601925 AAATAA
1 AAATAA
31601931 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 6 0.25
22 4 0.17
23 1 0.04
24 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAATATAAAAAATATAAA
Found at i:31620769 original size:20 final size:20
Alignment explanation
Indices: 31620744--31620783 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31620734 TGATGTATTA
31620744 CTGCCTGGTCATATGCCAGG
1 CTGCCTGGTCATATGCCAGG
31620764 CTGCCTGGTCATATGCCAGG
1 CTGCCTGGTCATATGCCAGG
31620784 TGACAGTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (20 bp):
CTGCCTGGTCATATGCCAGG
Found at i:31626510 original size:20 final size:20
Alignment explanation
Indices: 31626485--31626530 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
31626475 TTTAAAGATT
* *
31626485 TTGTCTAATAGTATGAAAGG
1 TTGTCTAATACTATAAAAGG
**
31626505 TTGTCTTTTACTATAAAAGG
1 TTGTCTAATACTATAAAAGG
31626525 TTGTCT
1 TTGTCT
31626531 TTTTATAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGTCTAATACTATAAAAGG
Found at i:31632147 original size:15 final size:15
Alignment explanation
Indices: 31632129--31632158 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31632119 TATTACAACA
*
31632129 GCAGCAGTTGCAGAG
1 GCAGCAGCTGCAGAG
31632144 GCAGCAGCTGCAGAG
1 GCAGCAGCTGCAGAG
31632159 ACCGTTGCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.40, T:0.10
Consensus pattern (15 bp):
GCAGCAGCTGCAGAG
Found at i:31632194 original size:24 final size:24
Alignment explanation
Indices: 31632149--31632198 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
31632139 CAGAGGCAGC
* ***
31632149 AGCTGCAGAGACCGTTGCAGAAGG
1 AGCTACAGAGACCGTCAAAGAAGG
31632173 AGCTACAGAGACCGTCAAAGAAGG
1 AGCTACAGAGACCGTCAAAGAAGG
31632197 AG
1 AG
31632199 AGCCGAGTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.34, T:0.10
Consensus pattern (24 bp):
AGCTACAGAGACCGTCAAAGAAGG
Found at i:31635921 original size:15 final size:15
Alignment explanation
Indices: 31635903--31635934 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31635893 GAAGCGACAA
31635903 CAGTGGAACGGAAAT
1 CAGTGGAACGGAAAT
31635918 CAGTGGAACGGAAAT
1 CAGTGGAACGGAAAT
31635933 CA
1 CA
31635935 AGTCCAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.31, T:0.12
Consensus pattern (15 bp):
CAGTGGAACGGAAAT
Found at i:31643058 original size:33 final size:32
Alignment explanation
Indices: 31643019--31643084 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 32
31643009 GTAACGTTAT
31643019 AATTAAAATAAAATATATAATATAA-AAATTAAA
1 AATTAAAATAAAATA-A-AATATAAGAAATTAAA
31643052 AATTAAAATAAAATAAAATATAAGAAATTAAA
1 AATTAAAATAAAATAAAATATAAGAAATTAAA
31643084 A
1 A
31643085 TTTATATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 7 0.22
32 10 0.31
33 15 0.47
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (32 bp):
AATTAAAATAAAATAAAATATAAGAAATTAAA
Found at i:31648943 original size:2 final size:2
Alignment explanation
Indices: 31648936--31648967 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31648926 ATCCTAGTAA
*
31648936 TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31648968 ATGTACTTGT
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:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31651806 original size:6 final size:6
Alignment explanation
Indices: 31651795--31651820 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31651785 ACGGACAAGG
31651795 GAAGAT GAAGAT GAAGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
31651821 TGGAGAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAGAT
Found at i:31668215 original size:2 final size:2
Alignment explanation
Indices: 31668208--31668232 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31668198 TATCTCCTTT
31668208 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
31668233 TTTCTTTATT
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:31680406 original size:2 final size:2
Alignment explanation
Indices: 31680399--31680510 Score: 131
Period size: 2 Copynumber: 53.5 Consensus size: 2
31680389 AAGTGTGAGG
31680399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NAGT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T A-T
31680444 AGT AGT AGT AGT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T A-T A-T A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31680489 AT AT AT AT -T AT -T AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31680511 AAGCCGAAAT
Statistics
Matches: 104, Mismatches: 0, Indels: 12
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.03
2 82 0.79
3 17 0.16
4 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31696736 original size:15 final size:15
Alignment explanation
Indices: 31696716--31696750 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
31696706 TGGCGGAGGT
31696716 GGTGGCAGTGATGGC
1 GGTGGCAGTGATGGC
*
31696731 GGTGGCGGTGATGGC
1 GGTGGCAGTGATGGC
31696746 GGTGG
1 GGTGG
31696751 AGGAGAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.11, G:0.60, T:0.20
Consensus pattern (15 bp):
GGTGGCAGTGATGGC
Found at i:31719149 original size:27 final size:27
Alignment explanation
Indices: 31719111--31719163 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
31719101 TCTTTTTATG
31719111 GCAACAATTGGTGAGAATTCGAGCAAT
1 GCAACAATTGGTGAGAATTCGAGCAAT
31719138 GCAACAATTGGTGAGAATTCGAGCAA
1 GCAACAATTGGTGAGAATTCGAGCAA
31719164 AACCAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (27 bp):
GCAACAATTGGTGAGAATTCGAGCAAT
Found at i:31723082 original size:25 final size:25
Alignment explanation
Indices: 31723048--31723097 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
31723038 NNNNNNNNNN
31723048 ATTAAAATATT-AGTAATTAAATTAT
1 ATTAAAATATTGA-TAATTAAATTAT
*
31723073 ATTAAAATATTGATATTTAAATTAT
1 ATTAAAATATTGATAATTAAATTAT
31723098 TAATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTAAAATATTGATAATTAAATTAT
Found at i:31723111 original size:21 final size:22
Alignment explanation
Indices: 31723075--31723139 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
31723065 TAAATTATAT
* *
31723075 TAAAATATTGATATTTAAATTA
1 TAAATTATTAATATTTAAATTA
*
31723097 TTAATTATT-ATATTTAATTAATTA
1 TAAATTATTAATATTT-A--AATTA
31723121 TAAATTATTAATATTTAAA
1 TAAATTATTAATATTTAAA
31723140 AATAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.17
22 10 0.28
24 14 0.39
25 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATTATTAATATTTAAATTA
Found at i:31723126 original size:24 final size:25
Alignment explanation
Indices: 31723092--31723138 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
31723082 TTGATATTTA
*
31723092 AATTATTAATTATT-ATATTTAATT
1 AATTATAAATTATTAATATTTAATT
31723116 AATTATAAATTATTAATATTTAA
1 AATTATAAATTATTAATATTTAA
31723139 AAATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTATAAATTATTAATATTTAATT
Found at i:31723144 original size:21 final size:20
Alignment explanation
Indices: 31723075--31723146 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 20
31723065 TAAATTATAT
* *
31723075 TAAAATATTGATATTTAAATTA
1 TAAATTATT-ATATTTAAA-AA
*
31723097 TTAATTATTATATTTAATTAATTA
1 TAAATTATTATATTTAA--AA--A
31723121 TAAATTATTAATATTTAAAAA
1 TAAATTATT-ATATTTAAAAA
31723142 TAAAT
1 TAAAT
31723147 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
21 14 0.34
22 7 0.17
23 3 0.07
24 9 0.22
25 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TAAATTATTATATTTAAAAA
Found at i:31723154 original size:21 final size:20
Alignment explanation
Indices: 31723130--31723177 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
31723120 ATAAATTATT
31723130 AATATTTAAAA-ATAAATAAAA
1 AATATTTAAAATAT-AAT-AAA
* *
31723151 AATAATTAAAGTATAATAAA
1 AATATTTAAAATATAATAAA
31723171 AATATTT
1 AATATTT
31723178 TATCTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 12 0.52
22 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATTTAAAATATAATAAA
Found at i:31731579 original size:27 final size:27
Alignment explanation
Indices: 31731522--31731579 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
31731512 ACCTTTGGTG
*
31731522 TTTTCATGCTTGAAACGACTTTAGACG
1 TTTTCATGCTTGAAACGACTTTAGACA
* *
31731549 TTTTCGTGCTTGAAAC-ACTTTTAGATA
1 TTTTCATGCTTGAAACGAC-TTTAGACA
31731576 TTTT
1 TTTT
31731580 TGCATTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (27 bp):
TTTTCATGCTTGAAACGACTTTAGACA
Found at i:31759548 original size:47 final size:47
Alignment explanation
Indices: 31759479--31759573 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
31759469 TAATCTCTAT
*
31759479 TTATGATTCAATTTCAGGCACACTCAACTCTCAAGCACCATAATTAA
1 TTATGATTCAATTTCAGACACACTCAACTCTCAAGCACCATAATTAA
* *
31759526 TTATGATTCTATTTCAGACACACTCATCTCTCAAGCACCATAATTAA
1 TTATGATTCAATTTCAGACACACTCAACTCTCAAGCACCATAATTAA
31759573 T
1 T
31759574 AATCTAGCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (47 bp):
TTATGATTCAATTTCAGACACACTCAACTCTCAAGCACCATAATTAA
Found at i:31761918 original size:2 final size:2
Alignment explanation
Indices: 31761882--31761906 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31761872 CTGCATCCAC
31761882 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
31761907 TGGAGGGAGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31764123 original size:3 final size:3
Alignment explanation
Indices: 31764115--31764139 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31764105 GGAAAGCTTT
31764115 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
31764140 CAGCAGCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31768761 original size:39 final size:39
Alignment explanation
Indices: 31768647--31768763 Score: 198
Period size: 39 Copynumber: 3.0 Consensus size: 39
31768637 CAGATTCAAC
* * *
31768647 CATATCACTCACACCACAACTGAAGATAATTACAAACAG
1 CATATCTCTCACACAACAACTGAAGATAATTACAAATAG
31768686 CATATCTCTCACACAACAACTGAAGATAATTACAAATAG
1 CATATCTCTCACACAACAACTGAAGATAATTACAAATAG
*
31768725 CATATCTCTCACACTACAACTGAAGATAATTACAAATAG
1 CATATCTCTCACACAACAACTGAAGATAATTACAAATAG
31768764 GACATTCATT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (39 bp):
CATATCTCTCACACAACAACTGAAGATAATTACAAATAG
Found at i:31771711 original size:29 final size:29
Alignment explanation
Indices: 31771653--31771749 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
31771643 AGACATTAAA
* * *
31771653 GTGTAATAA-AATA-TTTTTGAATATGTC
1 GTGTAACAACAATATTTTTTCAATATGAC
*
31771680 GTGTAACAACAATATTTTTTCAACATGAC
1 GTGTAACAACAATATTTTTTCAATATGAC
* *
31771709 GTGTAACAATAATATTTTTTTTCAATATGGC
1 GTGTAACAACAATA--TTTTTTCAATATGAC
31771740 GTGTAACAAC
1 GTGTAACAAC
31771750 CTTTTTAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.14
28 4 0.07
29 24 0.41
31 22 0.38
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTCAATATGAC
Found at i:31771915 original size:24 final size:24
Alignment explanation
Indices: 31771883--31771928 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
31771873 AAGCTAACCA
*
31771883 TAGCTTGTCACATGTTTTTGTATT
1 TAGCTTGTCACATATTTTTGTATT
31771907 TAGCTTGTCACATATTTTTGTA
1 TAGCTTGTCACATATTTTTGTA
31771929 CATAGCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
TAGCTTGTCACATATTTTTGTATT
Found at i:31771928 original size:69 final size:68
Alignment explanation
Indices: 31771845--31772052 Score: 247
Period size: 69 Copynumber: 3.0 Consensus size: 68
31771835 CCATGGTTTA
* * * * *
31771845 TCACAGATTTTTGTACATAGTATGTAACAAGCTAACCATAGCTTGTCACATGTTTTTGTAT-TTA
1 TCACATATTTTTGTACATAGCATGTAACACGCTAACCAT-GCTTGTCACAAGTTTTTGTATATGA
*
31771909 GCTTG
65 -CGTG
*
31771914 TCACATATTTTTGTACATAGCATGTAACACGCTAACTATGACTTGTCACAAGTTTTTGTATATGA
1 TCACATATTTTTGTACATAGCATGTAACACGCTAACCATG-CTTGTCACAAGTTTTTGTATATGA
31771979 CGTG
65 CGTG
* * * * * * *
31771983 TCACATATTTTTTTACATAGCGTGTAACACGTTAATCATGGCTTGTTACAAGTTTTTTTACATGA
1 TCACATATTTTTGTACATAGCATGTAACACGCTAACCAT-GCTTGTCACAAGTTTTTGTATATGA
31772048 CGTG
65 CGTG
31772052 T
1 T
31772053 AACAAACTAA
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
68 1 0.01
69 117 0.97
70 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (68 bp):
TCACATATTTTTGTACATAGCATGTAACACGCTAACCATGCTTGTCACAAGTTTTTGTATATGAC
GTG
Found at i:31771934 original size:24 final size:24
Alignment explanation
Indices: 31771881--31771934 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
31771871 ACAAGCTAAC
*
31771881 CATAGCTTGTCACATGTTTTTGTA
1 CATAGCTTGTCACATATTTTTGTA
**
31771905 TTTAGCTTGTCACATATTTTTGTA
1 CATAGCTTGTCACATATTTTTGTA
31771929 CATAGC
1 CATAGC
31771935 ATGTAACACG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (24 bp):
CATAGCTTGTCACATATTTTTGTA
Found at i:31772027 original size:114 final size:114
Alignment explanation
Indices: 31771910--31772273 Score: 392
Period size: 114 Copynumber: 3.2 Consensus size: 114
31771900 TTGTATTTAG
* * * *
31771910 CTTGTCACATATTTTTGTACATAGCATGTAACACGCTAACTATGACTTGTCACAAGTTTTTGTAT
1 CTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTAT
* * *
31771975 ATGACGTGTCACATATTTTTTTACATAGCGTGTAACACGTTAATCATGG
66 ATGACATGTCACATATTTTTATACATAGCGTGTAACACGTTAATCATGA
* * * *
31772024 CTTGTTACA-AGTTTTTTTACAT-GACGTGTAACAAACTAACCAT-AGTTTGTCACAGGTTTTTG
1 CTTGTCACATA-TTTTTGTACATAG-CGTGTAACAAGCTAACCATGA-CTTGTCACAGGTTTTTG
* * * ** * * *
31772086 TATATGACTTGTCACATATATTTGTACACGGCATGTAACAAGTTAACCATGA
63 TATATGACATGTCACATATTTTTATACATAGCGTGTAACACGTTAATCATGA
* * * * ** *
31772138 CTTGTCACATATTTTTGTACATAGCGTATAACATGCTAACCATGGCTGGTCATTGGTTTTTGTAC
1 CTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTAT
* * * *
31772203 ATGGCATGTCACATATTTTTATACATAGTGTATAACACGCTAATCATGA
66 ATGACATGTCACATATTTTTATACATAGCGTGTAACACGTTAATCATGA
* *
31772252 CTTGTCATAGATTTTTGTACAT
1 CTTGTCACATATTTTTGTACAT
31772274 GACGTGTCAC
Statistics
Matches: 202, Mismatches: 42, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
113 3 0.01
114 197 0.98
115 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (114 bp):
CTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATGACTTGTCACAGGTTTTTGTAT
ATGACATGTCACATATTTTTATACATAGCGTGTAACACGTTAATCATGA
Found at i:31772057 original size:24 final size:24
Alignment explanation
Indices: 31771951--31772057 Score: 62
Period size: 24 Copynumber: 4.6 Consensus size: 24
31771941 CACGCTAACT
* * * *
31771951 ATGACTTGTCACAAGTTTTTGTAT
1 ATGACGTGTAACAAGTTTTTTTAC
*
31771975 ATGACGTGTCACATA-TTTTTTTAC
1 ATGACGTGTAACA-AGTTTTTTTAC
* **
31771999 AT-AGCGTGTAACACG--TTAAT-C
1 ATGA-CGTGTAACAAGTTTTTTTAC
* * *
31772020 ATGGCTTGTTACAAGTTTTTTTAC
1 ATGACGTGTAACAAGTTTTTTTAC
31772044 ATGACGTGTAACAA
1 ATGACGTGTAACAA
31772058 ACTAACCATA
Statistics
Matches: 60, Mismatches: 16, Indels: 14
0.67 0.18 0.16
Matches are distributed among these distances:
21 11 0.18
22 3 0.05
23 4 0.07
24 41 0.68
25 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (24 bp):
ATGACGTGTAACAAGTTTTTTTAC
Found at i:31772083 original size:45 final size:45
Alignment explanation
Indices: 31771981--31772093 Score: 104
Period size: 45 Copynumber: 2.5 Consensus size: 45
31771971 GTATATGACG
*** * *
31771981 TGTCACATA-TTTTTTTACAT-AGCGTGTAACACGTTAATCATGGCT
1 TGTCACA-AGTTTTTTTACATGA-CGTGTAACAAACTAACCATAGCT
* *
31772026 TGTTACAAGTTTTTTTACATGACGTGTAACAAACTAACCATAGTT
1 TGTCACAAGTTTTTTTACATGACGTGTAACAAACTAACCATAGCT
* * *
31772071 TGTCACAGGTTTTTGTATATGAC
1 TGTCACAAGTTTTTTTACATGAC
31772094 TTGTCACATA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
44 1 0.02
45 53 0.96
46 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (45 bp):
TGTCACAAGTTTTTTTACATGACGTGTAACAAACTAACCATAGCT
Found at i:31772170 original size:45 final size:45
Alignment explanation
Indices: 31772089--31772181 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 45
31772079 GTTTTTGTAT
* * *
31772089 ATGACTTGTCACATATATTTGTACACGGCATGTAACAAGTTAACC
1 ATGACTTGTCACATATATTTGTACACAGCATATAACAAGCTAACC
* * * *
31772134 ATGACTTGTCACATATTTTTGTACATAGCGTATAACATGCTAACC
1 ATGACTTGTCACATATATTTGTACACAGCATATAACAAGCTAACC
31772179 ATG
1 ATG
31772182 GCTGGTCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (45 bp):
ATGACTTGTCACATATATTTGTACACAGCATATAACAAGCTAACC
Found at i:31772259 original size:69 final size:69
Alignment explanation
Indices: 31772133--31772355 Score: 284
Period size: 69 Copynumber: 3.2 Consensus size: 69
31772123 ACAAGTTAAC
* * * * *
31772133 CATGACTTGTCACATATTTTTGTACATAGCGTATAACATGCTAACCATGGCTGGTCATTGGTTTT
1 CATGACATGTCACATATTTTTGTACATAGCGTATAACACGCTAATCATGGCTTGTCATAGGTTTT
31772198 TGTA
66 TGTA
* * * * *
31772202 CATGGCATGTCACATATTTTTATACATAGTGTATAACACGCTAATCATGACTTGTCATAGATTTT
1 CATGACATGTCACATATTTTTGTACATAGCGTATAACACGCTAATCATGGCTTGTCATAGGTTTT
31772267 TGTA
66 TGTA
* * * * * *
31772271 CATGACGTGTCACATATTTTTGTATATAGCGTGTAACACGCTAATTATGGCTTGTCGTAAGTTTT
1 CATGACATGTCACATATTTTTGTACATAGCGTATAACACGCTAATCATGGCTTGTCATAGGTTTT
31772336 TGTA
66 TGTA
* *
31772340 CATGACGTGTAACATA
1 CATGACATGTCACATA
31772356 ATAGCGTGTA
Statistics
Matches: 132, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 132 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (69 bp):
CATGACATGTCACATATTTTTGTACATAGCGTATAACACGCTAATCATGGCTTGTCATAGGTTTT
TGTA
Found at i:31772281 original size:24 final size:24
Alignment explanation
Indices: 31772247--31772294 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31772237 ACACGCTAAT
* *
31772247 CATGACTTGTCATAGATTTTTGTA
1 CATGACGTGTCACAGATTTTTGTA
*
31772271 CATGACGTGTCACATATTTTTGTA
1 CATGACGTGTCACAGATTTTTGTA
31772295 TATAGCGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.44
Consensus pattern (24 bp):
CATGACGTGTCACAGATTTTTGTA
Found at i:31776353 original size:6 final size:6
Alignment explanation
Indices: 31776342--31776371 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
31776332 AATAGTATAT
31776342 CCCATC CCCATC CCCATC CCCATC CCCATC
1 CCCATC CCCATC CCCATC CCCATC CCCATC
31776372 GCATCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCATC
Found at i:31778721 original size:39 final size:39
Alignment explanation
Indices: 31778659--31778735 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
31778649 GTAGACTCAT
* *
31778659 ATTAGTGTAAGAATTCATTTTCTTTATGGATAAAGAGTC
1 ATTAATGTAAAAATTCATTTTCTTTATGGATAAAGAGTC
31778698 ATTAATGTAAAAATT-ATTCTTCTTTATGGATAAAGAGT
1 ATTAATGTAAAAATTCATT-TTCTTTATGGATAAAGAGT
31778736 TAGTGCACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 3 0.09
39 32 0.91
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (39 bp):
ATTAATGTAAAAATTCATTTTCTTTATGGATAAAGAGTC
Found at i:31779411 original size:16 final size:17
Alignment explanation
Indices: 31779392--31779423 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31779382 CCTCTTTTCT
31779392 TTTC-TTGTTTTTTTAG
1 TTTCATTGTTTTTTTAG
31779408 TTTCATTGTTTTTTTA
1 TTTCATTGTTTTTTTA
31779424 ATGCCCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTCATTGTTTTTTTAG
Found at i:31790569 original size:15 final size:15
Alignment explanation
Indices: 31790545--31790574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31790535 TATTTGTGGA
31790545 TAATTAATTAATATT
1 TAATTAATTAATATT
*
31790560 TAATTGATTAATATT
1 TAATTAATTAATATT
31790575 ATATATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TAATTAATTAATATT
Found at i:31790653 original size:15 final size:15
Alignment explanation
Indices: 31790635--31790666 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31790625 AATAGGATAA
*
31790635 ATTTAAATTTAATTT
1 ATTTAAATTTAAATT
31790650 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
31790665 AT
1 AT
31790667 CTATCTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAAATTTAAATT
Found at i:31796677 original size:19 final size:19
Alignment explanation
Indices: 31796653--31796691 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31796643 AATTAATATG
* *
31796653 AAATATATATTATTTTAAA
1 AAATATATAATATATTAAA
31796672 AAATATATAATATATTAAA
1 AAATATATAATATATTAAA
31796691 A
1 A
31796692 GTTTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATATAATATATTAAA
Found at i:31806762 original size:19 final size:19
Alignment explanation
Indices: 31806695--31806762 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
31806685 ATTATATATT
*
31806695 ATAAAATTTTAATATT-TAA
1 ATAAAATATTAA-ATTATAA
*
31806714 ATAAAAAATT-AATTA-AA
1 ATAAAATATTAAATTATAA
* **
31806731 ATTATTTATTTAAATTATAA
1 ATAAAATA-TTAAATTATAA
31806751 ATAAAATATTAA
1 ATAAAATATTAA
31806763 CATTTAAACT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 17 0.47
20 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAATATTAAATTATAA
Found at i:31806963 original size:41 final size:43
Alignment explanation
Indices: 31806907--31807015 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 43
31806897 AAAAATTAAT
31806907 TAAAATTATTAATATTTGAAACATAATAAAT-TTAAATTATAAA
1 TAAAA-TATTAATATTTGAAACATAATAAATATTAAATTATAAA
* * *
31806950 T-AAATATTGATATTTGAAA-AT-ATTAATGATTAAATTATGAA
1 TAAAATATTAATATTTGAAACATAATAAAT-ATTAAATTATAAA
31806991 TAAAATATTAATATTT-AAACGATAA
1 TAAAATATTAATATTTGAAAC-ATAA
31807016 ATTATTAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
39 5 0.09
40 2 0.04
41 29 0.52
42 16 0.29
43 3 0.05
44 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (43 bp):
TAAAATATTAATATTTGAAACATAATAAATATTAAATTATAAA
Found at i:31807067 original size:162 final size:158
Alignment explanation
Indices: 31806866--31807169 Score: 384
Period size: 162 Copynumber: 1.9 Consensus size: 158
31806856 AAGTTTTTAA
* *
31806866 TTATATATTATAAAAAAAATATCTAAAATTTAAAAATTAATTAAAATTATTAAT-ATTTGAAACA
1 TTATATATTAAAAAAAAAATATCTAAAATTTAAAAATTAATTAAAATTATAAATAATTT-AAACA
** *
31806930 TAATAA-ATTTAAATTATAAAT-AAATATTGATAT-TTGAAAATATTAATGATTAAATTATGAAT
65 TAATAATATTTAAACCATAAATAAAATATTAATATCTT-AAAATATTAAT-ATTAAA--ATG-AT
31806992 AAAATATTAATATTTAAACGATAAATTATTAATG
125 AAAATATTAATATTTAAACGATAAATTATTAATG
* *
31807026 NTTATATATTACAAAAAAAAATA-CTTTAAATTTAAAAATTAATTAAAATTATAAATAATTTAAT
1 -TTATATATTA-AAAAAAAAATATC-TAAAATTTAAAAATTAATTAAAATTATAAATAATTTAAA
* * * *
31807090 CATAATAATATTTAAACCATACATAAAATATTAATATCTTAAAATGTTAATATTTAAATGATCAA
63 CATAATAATATTTAAACCATAAATAAAATATTAATATCTTAAAATATTAATATTAAAATGATAAA
*
31807155 TTATTAATATTTAAA
128 ATATTAATATTTAAA
31807170 AATATAAATT
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
160 18 0.14
161 14 0.11
162 49 0.39
163 21 0.17
164 21 0.17
165 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (158 bp):
TTATATATTAAAAAAAAAATATCTAAAATTTAAAAATTAATTAAAATTATAAATAATTTAAACAT
AATAATATTTAAACCATAAATAAAATATTAATATCTTAAAATATTAATATTAAAATGATAAAATA
TTAATATTTAAACGATAAATTATTAATG
Found at i:31807088 original size:17 final size:17
Alignment explanation
Indices: 31807042--31807088 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
31807032 TATTACAAAA
* *
31807042 AAAAATACTTTAAATTT
1 AAAAATAATTTAAAATT
31807059 AAAAATTAA-TTAAAATT
1 AAAAA-TAATTTAAAATT
*
31807076 ATAAATAATTTAA
1 AAAAATAATTTAA
31807089 TCATAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 20 0.80
18 2 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATAATTTAAAATT
Found at i:31807134 original size:16 final size:15
Alignment explanation
Indices: 31807113--31807147 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
31807103 AAACCATACA
31807113 TAAAATATTAATATCT
1 TAAAATATTAATAT-T
*
31807129 TAAAATGTTAATATT
1 TAAAATATTAATATT
31807144 TAAA
1 TAAA
31807148 TGATCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:31807161 original size:22 final size:21
Alignment explanation
Indices: 31807136--31807197 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
31807126 TCTTAAAATG
*
31807136 TTAATATTTAAATGATCAATTA
1 TTAATATTTAAAT-ATAAATTA
31807158 TTAATATTTAAAAATATAAATTA
1 TTAATATTT--AAATATAAATTA
*
31807181 TAAATATTTAAA-ATAAA
1 TTAATATTTAAATATAAA
31807198 ATAAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 5 0.14
21 3 0.08
22 9 0.25
23 15 0.42
24 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAATATTTAAATATAAATTA
Found at i:31809817 original size:23 final size:21
Alignment explanation
Indices: 31809752--31809821 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 21
31809742 TTTTAATATT
*
31809752 AAATATTATTTAATTATAATA
1 AAATATTATTAAATTATAATA
* ** *
31809773 AAAGATTTAATTATCTTCTAATTCA
1 AAATA-TT-ATTAAATTATAA-T-A
31809798 AAATATTATTAAATTATAATA
1 AAATATTATTAAATTATAATA
31809819 AAA
1 AAA
31809822 ATATGTTTGT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
21 8 0.22
22 3 0.08
23 17 0.47
24 3 0.08
25 5 0.14
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (21 bp):
AAATATTATTAAATTATAATA
Found at i:31809952 original size:24 final size:25
Alignment explanation
Indices: 31809890--31809952 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
31809880 TATTACTTAA
31809890 AATATTTTTATC-TTTTAACAAAAT
1 AATATTTTTATCATTTTAACAAAAT
* *
31809914 AAAATTCTTTA--ATTTTAATAAAAT
1 AATATT-TTTATCATTTTAACAAAAT
*
31809938 -GTATTTTTATCATTT
1 AATATTTTTATCATTT
31809953 ACCACTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 20 0.65
25 4 0.13
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATTTTTATCATTTTAACAAAAT
Found at i:31812133 original size:25 final size:26
Alignment explanation
Indices: 31812099--31812151 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
31812089 NNNNNNNNNN
31812099 AAATAGAAAATATGATAA-TAAAA-AAT
1 AAATAGAAAATA--ATAATTAAAATAAT
31812125 AAAT-GAAAATAATAATTAAAATAAT
1 AAATAGAAAATAATAATTAAAATAAT
31812150 AA
1 AA
31812152 TAAATGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.16
24 5 0.20
25 12 0.48
26 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (26 bp):
AAATAGAAAATAATAATTAAAATAAT
Found at i:31812229 original size:30 final size:30
Alignment explanation
Indices: 31812173--31812235 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
31812163 AAAATAGATA
* * *
31812173 ATTGCATTAGCATATCATATATATATATAT
1 ATTGCATCAGCATATCATATACATATAAAT
*
31812203 ATTGCATCATGCATATCAT-TGCATATAAAT
1 ATTGCATCA-GCATATCATATACATATAAAT
31812233 ATT
1 ATT
31812236 TTTGTTTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (30 bp):
ATTGCATCAGCATATCATATACATATAAAT
Found at i:31812631 original size:23 final size:23
Alignment explanation
Indices: 31812603--31812658 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
31812593 TCTCACACCA
* *
31812603 TGCATTTCATCTTGTCTCACGTT
1 TGCATTTCATCTTGCCTCACATT
31812626 TGCATTTCATCTTGCCTCACATT
1 TGCATTTCATCTTGCCTCACATT
31812649 TGCATTTCAT
1 TGCATTTCAT
31812659 TTTAGGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.46
Consensus pattern (23 bp):
TGCATTTCATCTTGCCTCACATT
Found at i:31820451 original size:11 final size:10
Alignment explanation
Indices: 31820432--31820465 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31820422 AAATAAATTT
31820432 TTATAATTAA
1 TTATAATTAA
31820442 TTATTAATTAA
1 TTA-TAATTAA
*
31820453 TTATCATTAA
1 TTATAATTAA
31820463 TTA
1 TTA
31820466 AAACATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TTATAATTAA
Found at i:31822562 original size:17 final size:17
Alignment explanation
Indices: 31822542--31822581 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
31822532 ATTTTTAATT
31822542 ATTATTTATTTATATTA
1 ATTATTTATTTATATTA
31822559 ATTATTTATTTATATTA
1 ATTATTTATTTATATTA
31822576 ATTATT
1 ATTATT
31822582 AAATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTATTTATTTATATTA
Found at i:31823149 original size:41 final size:39
Alignment explanation
Indices: 31823070--31823149 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 39
31823060 AATAATTACT
* * *
31823070 TTATTAAATATAACTTTTTAATAGTTGTATTATGAAAGG
1 TTATTAAATATAACTTTTTAATAGCTATATTATAAAAGG
**
31823109 TTATTAAATATATTTTTTATAAATAGCTATATTATAAAAGG
1 TTATTAAATATAACTTTT-T-AATAGCTATATTATAAAAGG
31823150 AAATAACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 16 0.47
40 1 0.03
41 17 0.50
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (39 bp):
TTATTAAATATAACTTTTTAATAGCTATATTATAAAAGG
Found at i:31823165 original size:32 final size:33
Alignment explanation
Indices: 31823124--31823198 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
31823114 AAATATATTT
*
31823124 TTTATAAATAGCTATATTATAAAAGG-AAATAAC
1 TTTA-AAATAGCTATATTATAAAAGGAAAACAAC
* * *
31823157 TTTAAAATAGTTATCTTATGAAAGGAAAACAAC
1 TTTAAAATAGCTATATTATAAAAGGAAAACAAC
*
31823190 TTTTAAATA
1 TTTAAAATA
31823199 ATTATCTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 18 0.50
33 18 0.50
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (33 bp):
TTTAAAATAGCTATATTATAAAAGGAAAACAAC
Found at i:31823198 original size:33 final size:33
Alignment explanation
Indices: 31823128--31823217 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 33
31823118 ATATTTTTTA
* * * *
31823128 TAAATAGCTATATTATAAAAGG-AAATAACTTT
1 TAAATAGTTATCTTATGAAAGGAAAACAACTTT
*
31823160 AAAATAGTTATCTTATGAAAGGAAAACAACTTT
1 TAAATAGTTATCTTATGAAAGGAAAACAACTTT
* *
31823193 TAAATAATTATCTTATGAAAAGAAA
1 TAAATAGTTATCTTATGAAAGGAAA
31823218 TGACTATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 18 0.37
33 31 0.63
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (33 bp):
TAAATAGTTATCTTATGAAAGGAAAACAACTTT
Found at i:31825655 original size:21 final size:21
Alignment explanation
Indices: 31825631--31825670 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31825621 TATATTTTTA
*
31825631 TAATAATAATAATAATATAAT
1 TAATAATAATAAAAATATAAT
* *
31825652 TAATTATATTAAAAATATA
1 TAATAATAATAAAAATATA
31825671 TCAAATTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATAATAATAAAAATATAAT
Found at i:31839712 original size:27 final size:27
Alignment explanation
Indices: 31839660--31839712 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31839650 AACATTAATG
* * *
31839660 ATTAATATTTTAAATTAATAATAAATT
1 ATTAATATTTTAAAATAAAAAAAAATT
31839687 ATTAATATTTTAAAATAAAAAAAAAT
1 ATTAATATTTTAAAATAAAAAAAAAT
31839713 AAAAATAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATTAATATTTTAAAATAAAAAAAAATT
Found at i:31856263 original size:18 final size:18
Alignment explanation
Indices: 31856242--31856279 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31856232 CGGTAGAACA
31856242 CCGCTAGACCAGAGTTCC
1 CCGCTAGACCAGAGTTCC
31856260 CCGCTAGACCAGAGTTCC
1 CCGCTAGACCAGAGTTCC
31856278 CC
1 CC
31856280 ACTCCAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.42, G:0.21, T:0.16
Consensus pattern (18 bp):
CCGCTAGACCAGAGTTCC
Found at i:31857215 original size:2 final size:2
Alignment explanation
Indices: 31857208--31857242 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
31857198 AACCATGAAC
31857208 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31857243 TTCTTTCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:31874462 original size:2 final size:2
Alignment explanation
Indices: 31874455--31874492 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31874445 GGAGAAACAC
31874455 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31874493 CCAAAGGGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31893572 original size:22 final size:22
Alignment explanation
Indices: 31893547--31893606 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
31893537 TGAAAGTTAA
31893547 ATAAATAAATTAAAAATAATTC
1 ATAAATAAATTAAAAATAATTC
* * * *
31893569 ATAAAAAAATAAAAAATTATTT
1 ATAAATAAATTAAAAATAATTC
31893591 AT-AAT-AATTAATAAAT
1 ATAAATAAATTAA-AAAT
31893607 TTTAATAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 20 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATAAATTAAAAATAATTC
Found at i:31911010 original size:50 final size:51
Alignment explanation
Indices: 31910956--31911057 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
31910946 AAATTTGAAT
* * *
31910956 AATATATTTTATATATGCGT-GTATTAATATTTTTATAATATA-TCTCAAAA
1 AATATATTATATATATGCATAGTATTAATATTTTTAAAATATACT-TCAAAA
* * *
31911006 AATATGTTATGTATATGCATATTATTAATATTTTTAAAATATACTTCAAAA
1 AATATATTATATATATGCATAGTATTAATATTTTTAAAATATACTTCAAAA
31911057 A
1 A
31911058 TACTCTCATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 16 0.36
51 27 0.61
52 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (51 bp):
AATATATTATATATATGCATAGTATTAATATTTTTAAAATATACTTCAAAA
Found at i:31912125 original size:29 final size:29
Alignment explanation
Indices: 31912061--31912119 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
31912051 AGAGGAAACT
31912061 TTGCTTTGCCTTTTCCTGTCTTCCATTAG
1 TTGCTTTGCCTTTTCCTGTCTTCCATTAG
31912090 TTGCTTTGCCTTTTCCTGTCTTCCATTAG
1 TTGCTTTGCCTTTTCCTGTCTTCCATTAG
31912119 T
1 T
31912120 GTCTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.07, C:0.27, G:0.14, T:0.53
Consensus pattern (29 bp):
TTGCTTTGCCTTTTCCTGTCTTCCATTAG
Found at i:31915795 original size:2 final size:2
Alignment explanation
Indices: 31915788--31915818 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31915778 TCTCCCAAAT
31915788 TC TC TC 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 TC TC TC T
31915819 TTTTTTTTAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31926318 original size:30 final size:31
Alignment explanation
Indices: 31926282--31926376 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 31
31926272 AATGAATTAT
31926282 AAAAATTTATTTAACTCAAAATAAAA-ATAA
1 AAAAATTTATTTAACTCAAAATAAAATATAA
* * *
31926312 AAAAATTTATTTCACTTAAAATAAAATATAT
1 AAAAATTTATTTAACTCAAAATAAAATATAA
*
31926343 ATAAATTTATTTAACTCAAAATAAAATTATAA
1 AAAAATTTATTTAACTCAAAATAAAA-TATAA
31926375 AA
1 AA
31926377 GTTTGATTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 24 0.44
31 26 0.47
32 5 0.09
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAAATTTATTTAACTCAAAATAAAATATAA
Found at i:31926352 original size:31 final size:31
Alignment explanation
Indices: 31926279--31926376 Score: 146
Period size: 30 Copynumber: 3.2 Consensus size: 31
31926269 AATAATGAAT
31926279 TATAAAAATTTATTTAACTCAAAATAAAA-A
1 TATAAAAATTTATTTAACTCAAAATAAAATA
* * *
31926309 TAAAAAAATTTATTTCACTTAAAATAAAATA
1 TATAAAAATTTATTTAACTCAAAATAAAATA
*
31926340 TATATAAATTTATTTAACTCAAAATAAAAT-
1 TATAAAAATTTATTTAACTCAAAATAAAATA
31926370 TATAAAA
1 TATAAAA
31926377 GTTTGATTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
30 32 0.54
31 27 0.46
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (31 bp):
TATAAAAATTTATTTAACTCAAAATAAAATA
Found at i:31926597 original size:29 final size:30
Alignment explanation
Indices: 31926519--31926597 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
31926509 TAAAAAATTT
*
31926519 AAATAAATTTTTATTATTT-TATTATATTC
1 AAATAAATTTTTATTATTTATATTATAATC
* * *
31926548 AATTAAATTTTTA-TATTTTTATTTTAAATC
1 AAATAAATTTTTATTATTTATATTAT-AATC
* *
31926578 AAATAAACTTTTATTCTTTA
1 AAATAAATTTTTATTATTTA
31926598 AAAATTAACT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.12
29 17 0.43
30 14 0.35
31 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (30 bp):
AAATAAATTTTTATTATTTATATTATAATC
Found at i:31957317 original size:25 final size:25
Alignment explanation
Indices: 31957242--31957318 Score: 104
Period size: 25 Copynumber: 3.1 Consensus size: 25
31957232 TTAATAATTA
*
31957242 ATTAATTATTATTAATTAAAATATT
1 ATTATTTATTATTAATTAAAATATT
* *
31957267 ATT-TATTATT-TTGATTAAAATTTT
1 ATTAT-TTATTATTAATTAAAATATT
31957291 ATTATTTATTATTAATTAAAATATT
1 ATTATTTATTATTAATTAAAATATT
31957316 ATT
1 ATT
31957319 TGTCATTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 20 0.45
25 24 0.55
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
ATTATTTATTATTAATTAAAATATT
Found at i:31997540 original size:12 final size:13
Alignment explanation
Indices: 31997514--31997542 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31997504 CAACCAAATT
31997514 CAAATTCACTTTC
1 CAAATTCACTTTC
31997527 CAAATTCA-TTTC
1 CAAATTCACTTTC
31997539 CAAA
1 CAAA
31997543 CATAGCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (13 bp):
CAAATTCACTTTC
Found at i:31998466 original size:26 final size:23
Alignment explanation
Indices: 31998330--31998755 Score: 168
Period size: 26 Copynumber: 17.6 Consensus size: 23
31998320 TATAATCCTC
*
31998330 AAATATTAATGATTAAATTATAAATA
1 AAATATTAAT-ATTTAA--ATAAATA
*
31998356 AAATATTAATATTTAAAT-AATC
1 AAATATTAATATTTAAATAAATA
* *
31998378 AATTATTAGTATTTTAAATAAATTA
1 AAATATTAATA-TTTAAATAAA-TA
*
31998403 TAAATTATTAATATTTAAA-AATTA
1 -AAA-TATTAATATTTAAATAAATA
31998427 ATAATCATAATAATATTTAACTTATAAATA
1 A-AAT-AT--TAATATTTAA---ATAAATA
*
31998457 AAATATTAATATTT--TTAAATA
1 AAATATTAATATTTAAATAAATA
*
31998478 TTAATGATTAA-A-TT--ATAAATA
1 -AAAT-ATTAATATTTAAATAAATA
* *
31998499 AAATATTAATATTTAAAT-GATC
1 AAATATTAATATTTAAATAAATA
*
31998521 AATTATTAATATTTAAATAAATTA
1 AAATATTAATATTTAAATAAA-TA
* *
31998545 TAAATTATAAATATTTAAA-AATTA
1 -AAA-TATTAATATTTAAATAAATA
*
31998569 ATAATCATAATAACATTTAACTTATAAATA
1 A-AAT-AT--TAATATTTAA---ATAAATA
* *
31998599 AAGTATTAATATTT---T---TT
1 AAATATTAATATTTAAATAAATA
*
31998616 AAA-ATTAATTATTAAAATATAATA
1 AAATATTAA-TATTTAAATA-AATA
* * *
31998640 AAATATTTAATATTTTAAT-TATC
1 AAATA-TTAATATTTAAATAAATA
* *
31998663 AATTATCAATATTTTAAATAAATTA
1 AAATATTAATA-TTTAAATAAA-TA
31998688 TAAATTATTAATATTTAAAAATAAATA
1 -AAA-TATTAATATTT--AAATAAATA
* *
31998715 ATCATAATAATATTTAAATTATAAATA
1 A-AATATTAATATTT-AA--ATAAATA
31998742 AAATATTAATATTT
1 AAATATTAATATTT
31998756 CATAATGTTA
Statistics
Matches: 304, Mismatches: 45, Indels: 102
0.67 0.10 0.23
Matches are distributed among these distances:
16 5 0.02
17 7 0.02
19 5 0.02
20 6 0.02
21 16 0.05
22 40 0.13
23 33 0.11
24 20 0.07
25 24 0.08
26 95 0.31
27 25 0.08
28 11 0.04
29 7 0.02
30 10 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (23 bp):
AAATATTAATATTTAAATAAATA
Found at i:31998501 original size:42 final size:41
Alignment explanation
Indices: 31998443--31998541 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
31998433 ATAATAATAT
* *
31998443 TTAACTTATAAATAAAATATTAATATTTTTAAAT-ATTAATGA
1 TTAAATTATAAATAAAATATTAATA--TTTAAATGATCAATGA
*
31998485 TTAAATTATAAATAAAATATTAATATTTAAATGATCAATTA
1 TTAAATTATAAATAAAATATTAATATTTAAATGATCAATGA
31998526 TTAATATT-TAAATAAA
1 TTAA-ATTATAAATAAA
31998542 TTATAAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 7 0.13
41 18 0.35
42 27 0.52
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (41 bp):
TTAAATTATAAATAAAATATTAATATTTAAATGATCAATGA
Found at i:31998688 original size:20 final size:21
Alignment explanation
Indices: 31998648--31998701 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
31998638 TAAAATATTT
*
31998648 AATATTTTAATTATCAATTATC
1 AATATTTTAA-TATAAATTATC
31998670 AATATTTTAA-ATAAATTAT-
1 AATATTTTAATATAAATTATC
31998689 AA-ATTATTAATAT
1 AATATT-TTAATAT
31998702 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 3 0.10
19 6 0.21
20 10 0.34
22 10 0.34
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATTTTAATATAAATTATC
Found at i:31998851 original size:27 final size:27
Alignment explanation
Indices: 31998656--31998843 Score: 91
Period size: 27 Copynumber: 6.8 Consensus size: 27
31998646 TTAATATTTT
* *
31998656 AATTATCAATTATCAATATTTTAAATA
1 AATTATAAATTATAAATATTTTAAATA
* *
31998683 AATTATAAATTATTAATATTTAAAAATA
1 AATTATAAATTATAAATATTT-TAAATA
* * *
31998711 AATAAT-CATAAT-AATA-TTTAAATTA
1 AATTATAAATTATAAATATTTTAAA-TA
* * * *
31998736 TAA--ATAAAATATTAATATTTCATAATGTT
1 -AATTATAAATTATAAATATTT--TAA-ATA
* **
31998765 AATGATTAAATTATAAATGA-AATATAATA
1 AATTA-TAAATTATAAAT-ATTTTA-AATA
* * *
31998794 TTATTATCAATTATTAATATTTTAAATA
1 -AATTATAAATTATAAATATTTTAAATA
31998822 AATTATAAATTATAAATATTTT
1 AATTATAAATTATAAATATTTT
31998844 TTAAAAATAA
Statistics
Matches: 118, Mismatches: 27, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
24 5 0.04
25 7 0.06
26 10 0.08
27 44 0.37
28 17 0.14
29 19 0.16
30 5 0.04
31 10 0.08
32 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTATAAATTATAAATATTTTAAATA
Found at i:31998982 original size:27 final size:28
Alignment explanation
Indices: 31998949--31999007 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
31998939 TAATATTATT
* *
31998949 TAAATTATCAATTATTAATATTT-AAAA
1 TAAATTATAAATTACTAATATTTAAAAA
31998976 TAAATTATAAATTACTAATATTTAAAAA
1 TAAATTATAAATTACTAATATTTAAAAA
31999004 TAAA
1 TAAA
31999008 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAATTATAAATTACTAATATTTAAAAA
Found at i:31998989 original size:156 final size:152
Alignment explanation
Indices: 31998335--31999183 Score: 989
Period size: 143 Copynumber: 5.7 Consensus size: 152
31998325 TCCTCAAATA
* * *
31998335 TTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAGTATTTTAAATAAA
1 TTAATGATTAAATTATAAATAAAATAATAATATTTAAATTATCAATTATTAATATTTTAAATAAA
* * ** *
31998400 TTATAAATTATTAATATTTAAAAAT-TAATAATCAT-AATAAT-AT-TTAAC--TT-A-TA-AAT
66 TTATAAATTATAAATATTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAATTATAAT
*
31998456 AAAATATTAATATTTT-TAAATA
131 AAAATATTAATATTTTAT-AATG
* *
31998478 TTAATGATTAAATTATAAATAAAATATTAATATTTAAATGATCAATTATTAATA-TTTAAATAAA
1 TTAATGATTAAATTATAAATAAAATAATAATATTTAAATTATCAATTATTAATATTTTAAATAAA
31998542 TTATAAATTATAAATATTT----A-AAAAT-----T-AATAATCATAATAACATTTAACTTATAA
66 TTATAAATTATAAATATTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAA-TTAT-A
* * **
31998596 ATAAAGTATTAATATTTTTTAAAA
129 ATAAAATATTAATATTTTATAATG
* * * * *
31998620 TTAATTATTAAAATAT-AATAAAATATTTAATATTTTAATTATCAATTATCAATATTTTAAATAA
1 TTAATGATTAAATTATAAATAAAATA-ATAATATTTAAATTATCAATTATTAATATTTTAAATAA
* ** *
31998684 ATTATAAATTATTAATATTTAAAAAT-AAATAATCAT-AATAAT-AT-TTAA-A-TT-A-TA-AA
65 ATTATAAATTATAAATATTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAATTATAA
*
31998740 TAAAATATTAATATTTCATAATG
130 TAAAATATTAATATTTTATAATG
*
31998763 TTAATGATTAAATTATAAATGAAAT-ATAATA-TT--ATTATCAATTATTAATATTTTAAATAAA
1 TTAATGATTAAATTATAAATAAAATAATAATATTTAAATTATCAATTATTAATATTTTAAATAAA
31998824 TTATAAATTATAAATATTTTTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAATTTA
66 TTATAAATTATAAATA---TTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAA-TTA
31998889 TAATAAAATATTAATATTTTATAATG
127 TAATAAAATATTAATATTTTATAATG
* * * *
31998915 TTAATCATTAAAGTATAAATAAAATAATATTATTTAAATTATCAATTATTAATATTTAAAATAAA
1 TTAATGATTAAATTATAAATAAAATAATAATATTTAAATTATCAATTATTAATATTTTAAATAAA
*
31998980 TTATAAATTACT-AATATTTAAAAATAAAATAAAATAAAAAATAATCATAATAACATTTACATTA
66 TTATAAATTA-TAAATATTTAAAAATAAAAT-AAA-AATAAATAATCATAATAACATTTA-ATTA
* * *
31999044 TAATATAATCTTAATATTATATAATG
127 TAATAAAATATTAATATTTTATAATG
* *
31999070 CTAATGATTAAATTTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAA
1 TTAATGATTAAA-TTATAAATAAAATAATAATATTTAAATTATCAATTATTAATATTTTAAATAA
31999135 ATTATAAATTATAAATATTTTAAAAATAAAATAAAAATAAATAATCATA
65 ATTATAAATTATAAATA-TTTAAAAATAAAATAAAAATAAATAATCATA
31999184 TGTATAATAA
Statistics
Matches: 613, Mismatches: 45, Indels: 84
0.83 0.06 0.11
Matches are distributed among these distances:
133 7 0.01
134 2 0.00
135 4 0.01
137 2 0.00
138 5 0.01
139 42 0.07
140 2 0.00
141 11 0.02
142 102 0.17
143 123 0.20
144 13 0.02
145 4 0.01
146 3 0.00
147 7 0.01
148 4 0.01
149 2 0.00
150 3 0.00
151 4 0.01
152 53 0.09
153 19 0.03
154 5 0.01
155 73 0.12
156 108 0.18
157 15 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (152 bp):
TTAATGATTAAATTATAAATAAAATAATAATATTTAAATTATCAATTATTAATATTTTAAATAAA
TTATAAATTATAAATATTTAAAAATAAAATAAAAATAAATAATCATAATAACATTTAATTATAAT
AAAATATTAATATTTTATAATG
Found at i:31999014 original size:27 final size:27
Alignment explanation
Indices: 31998949--31999014 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
31998939 TAATATTATT
* * *
31998949 TAAATTATCAATTATTAATATTTAAAA
1 TAAAATATAAATTACTAATATTTAAAA
*
31998976 TAAATTATAAATTACTAATATTTAAAAA
1 TAAAATATAAATTACTAATATTT-AAAA
31999004 TAAAATA-AAAT
1 TAAAATATAAAT
31999015 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAAATATAAATTACTAATATTTAAAA
Found at i:31999022 original size:27 final size:27
Alignment explanation
Indices: 31998965--31999022 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
31998955 ATCAATTATT
* * **
31998965 AATATTTAAAATAAATTATAAATTACT
1 AATATTTAAAATAAAATATAAATAAAA
31998992 AATATTTAAAAATAAAATA-AAATAAAA
1 AATATTT-AAAATAAAATATAAATAAAA
31999019 AATA
1 AATA
31999023 ATCATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
AATATTTAAAATAAAATATAAATAAAA
Found at i:31999135 original size:27 final size:27
Alignment explanation
Indices: 31999105--31999158 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
31999095 TATTAATATT
* *
31999105 TAAATTATCAATTATTAATATTTTAAA
1 TAAATTATAAATTATAAATATTTTAAA
31999132 TAAATTATAAATTATAAATATTTTAAA
1 TAAATTATAAATTATAAATATTTTAAA
31999159 AATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAATTATAAATTATAAATATTTTAAA
Found at i:31999217 original size:156 final size:153
Alignment explanation
Indices: 31998703--31999210 Score: 579
Period size: 156 Copynumber: 3.3 Consensus size: 153
31998693 TATTAATATT
* * * * *
31998703 TAAAAATAAATAATCATAATAATATTTAAAT-TATAAATAAAATATTAATATT-TCATAATGTTA
1 TAAAAATAAATAATCAT-ATTATAATAAAATATAT-TATAATATATTAATATTAT-ATAATGTTA
*
31998766 ATGATTAAATTATAAATGAAATATAATA-TT--ATTATCAATTATTAATATTTTAAATAAATTAT
63 ATGATTAAATTATAAATAAAATATAATATTTAAATTATCAATTATTAATATTTTAAATAAATTAT
31998828 AAATTATAAATATTTTTTAAAAATAAAA
128 AAATTATAAATA--TTTTAAAAATAAAA
* ** * * * *
31998856 TAAAAATAAATAATCATAATA-ACATTTAATTTATAATAAAATATTAATATTTTATAATGTTAAT
1 TAAAAATAAATAATCATATTATA-ATAAAATATATTATAATATATTAATATTATATAATGTTAAT
* * * *
31998920 CATTAAAGTATAAATAAAATAATATTATTTAAATTATCAATTATTAATATTTAAAATAAATTATA
65 GATTAAATTATAAATAAAAT-ATAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATA
31998985 AATTACT-AATA-TTTAAAAATAAAA
129 AATTA-TAAATATTTTAAAAATAAAA
* * * * *
31999009 T-AAAATAAAAAAT-A-ATCATAATAACATTTACATTATAATATAATCTTAATATTATATAATGC
1 TAAAAATAAATAATCATATTATAATAA-A-ATATATTATAATAT-A--TTAATATTATATAATGT
31999071 TAATGATTAAATTTATAAATAAAATATTAATATTTAAATTATCAATTATTAATATTTTAAATAAA
61 TAATGATTAAA-TTATAAATAAAATA-TAATATTTAAATTATCAATTATTAATATTTTAAATAAA
31999136 TTATAAATTATAAATATTTTAAAAATAAAA
124 TTATAAATTATAAATATTTTAAAAATAAAA
* *
31999166 TAAAAATAAATAATCATATGTATAATAAAATATATTTTTATATAT
1 TAAAAATAAATAATCATAT-TATAATAAAATATATTATAATATAT
31999211 ATATATTTTT
Statistics
Matches: 302, Mismatches: 31, Indels: 41
0.81 0.08 0.11
Matches are distributed among these distances:
150 4 0.01
151 4 0.01
152 72 0.24
153 41 0.14
154 2 0.01
155 27 0.09
156 104 0.34
157 15 0.05
158 12 0.04
159 11 0.04
160 3 0.01
161 7 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (153 bp):
TAAAAATAAATAATCATATTATAATAAAATATATTATAATATATTAATATTATATAATGTTAATG
ATTAAATTATAAATAAAATATAATATTTAAATTATCAATTATTAATATTTTAAATAAATTATAAA
TTATAAATATTTTAAAAATAAAA
Found at i:32005956 original size:21 final size:21
Alignment explanation
Indices: 32005912--32005965 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
32005902 TGTTTTAATC
*
32005912 ATAATAATATTTA-AATTATAA
1 ATAA-AATATTAATAATTATAA
32005933 ATAAAATATTAATNAATTAT-A
1 ATAAAATATTAAT-AATTATAA
32005954 ATAAAATATTAA
1 ATAAAATATTAA
32005966 CATTTAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 7 0.23
21 17 0.57
22 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATATTAATAATTATAA
Found at i:32006002 original size:27 final size:28
Alignment explanation
Indices: 32005970--32006028 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
32005960 TATTAACATT
* * *
32005970 TAAATTATTATTTATTAATCTTTTAA-A
1 TAAATTATAAATTATTAATATTTTAAGA
32005997 TAAATTATAAATTATTAATATTTTAAGA
1 TAAATTATAAATTATTAATATTTTAAGA
32006025 TAAA
1 TAAA
32006029 ATAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TAAATTATAAATTATTAATATTTTAAGA
Found at i:32006043 original size:28 final size:27
Alignment explanation
Indices: 32005985--32006043 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
32005975 TATTATTTAT
* * * * *
32005985 TAATCTTTTAAATAAATTATAAATTAT
1 TAATATTTTAAATAAAATAAAAATAAA
32006012 TAATATTTTAAGATAAAATAAAAATAAA
1 TAATATTTTAA-ATAAAATAAAAATAAA
32006040 TAAT
1 TAAT
32006044 TATATATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TAATATTTTAAATAAAATAAAAATAAA
Found at i:32006063 original size:33 final size:33
Alignment explanation
Indices: 32005994--32006064 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
32005984 TTAATCTTTT
* * * *
32005994 AAATAAATTATAAATTATTAATATTTTAAGATA
1 AAATAAATAATAAATAATTAATATTATAAGAAA
*
32006027 AAATAAA-AATAAATAATTATATATTATAATAAA
1 AAATAAATAATAAATAATTA-ATATTATAAGAAA
32006060 AAATA
1 AAATA
32006065 TTTTTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (33 bp):
AAATAAATAATAAATAATTAATATTATAAGAAA
Done.