Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 179 of 190
Found at i:52344450 original size:3 final size:3
Alignment explanation
Indices: 52344442--52344486 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
52344432 ATGTATAAGT
52344442 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52344487 CAGAAGGGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:52345605 original size:20 final size:20
Alignment explanation
Indices: 52345580--52345617 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52345570 AATGCTTCGA
52345580 TCTACTCCACTGTAATGTTG
1 TCTACTCCACTGTAATGTTG
52345600 TCTACTCCACTGTAATGT
1 TCTACTCCACTGTAATGT
52345618 CGAGGAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.39
Consensus pattern (20 bp):
TCTACTCCACTGTAATGTTG
Found at i:52346025 original size:132 final size:132
Alignment explanation
Indices: 52345784--52346286 Score: 803
Period size: 132 Copynumber: 3.8 Consensus size: 132
52345774 TTCAGAGAGA
* * *
52345784 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACATGGAGGTAAAAT-TCACCATCTCTGAT
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGAT
* * *
52345848 CTGCTCCACTACTGCTTGGGGAGTCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGG
65 CTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGG
52345913 AAG
130 AAG
*
52345916 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCTGCCATCTTTGATC
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATC
* * ** *
52345981 TGCTCCACTACTGCTTAGGGAGGCAATATCTGAAATCTTCAATCTATTCCGTTGCTGCCCAGGAA
66 TGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGA
52346046 AG
131 AG
* *
52346048 TAGAATTACTAGCTTCAATGTACTCCACTGTAACCATAGGGAGGTAAAATCTGCCATCTTTGATC
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATC
* *
52346113 TGC-CCTACTACTGTTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGG
66 TGCTCC-ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGG
52346177 AAG
130 AAG
* *
52346180 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCATCGATC
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATC
*
52346245 TGCTCCGCTACTGCTTAGGGAGACAAGATCTGAAATCTTCAA
66 TGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAA
52346287 CCTGCTCCAC
Statistics
Matches: 342, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
131 2 0.01
132 337 0.99
133 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATC
TGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGA
AG
Found at i:52354235 original size:2 final size:2
Alignment explanation
Indices: 52354228--52354252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52354218 TGTCAGTAAT
52354228 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 T
52354253 TTAAAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52355459 original size:22 final size:22
Alignment explanation
Indices: 52355426--52355486 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
52355416 GCCCGGCCCG
* *
52355426 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
52355449 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
52355471 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
52355487 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:52355499 original size:16 final size:16
Alignment explanation
Indices: 52355462--52355501 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
52355452 TTAATAAAAT
* *
52355462 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
52355478 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
52355494 TAAAATTA
1 TAAAATTA
52355502 TTAAATTATT
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:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:52355586 original size:9 final size:9
Alignment explanation
Indices: 52355574--52355601 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52355564 TTTATCAAAT
52355574 TATTAATTG
1 TATTAATTG
52355583 TATTAATTG
1 TATTAATTG
52355592 TATTAATTG
1 TATTAATTG
52355601 T
1 T
52355602 TGTAACAAAA
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:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:52355598 original size:68 final size:66
Alignment explanation
Indices: 52355494--52355632 Score: 215
Period size: 68 Copynumber: 2.1 Consensus size: 66
52355484 TAATTGTTAG
* *
52355494 TAAAATTATTAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTAATTA
1 TAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTAATTA
52355559 A
66 A
* *
52355560 TAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGAT
1 TAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAACAAAATCTAACATTTAAT
*
52355625 TAG
64 TAA
52355628 TAAAA
1 TAAAA
52355633 CAAACTTGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 21 0.32
68 44 0.68
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (66 bp):
TAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACATTTAATTA
A
Found at i:52355738 original size:22 final size:24
Alignment explanation
Indices: 52355698--52355741 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52355688 AAATAAACTT
52355698 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
52355722 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
52355742 AATATTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:52357274 original size:29 final size:31
Alignment explanation
Indices: 52357231--52357289 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
52357221 TAAAATATTT
* *
52357231 AATTATAAAAGTTAAAATTTGAAAATAAAAA
1 AATTATAAAAGTTAAAAATTAAAAATAAAAA
52357262 AATTA-AAAA-TTAAAAATTAAAAATAAAA
1 AATTATAAAAGTTAAAAATTAAAAATAAAA
52357290 TTACAATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 4 0.15
31 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (31 bp):
AATTATAAAAGTTAAAAATTAAAAATAAAAA
Found at i:52357284 original size:8 final size:7
Alignment explanation
Indices: 52357231--52357289 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
52357221 TAAAATATTT
52357231 AATTATAA
1 AATTA-AA
52357239 AAGTTAAA
1 AA-TTAAA
* *
52357247 ATTTGAA
1 AATTAAA
*
52357254 AATAAAAA
1 AAT-TAAA
52357262 AATTAAA
1 AATTAAA
52357269 AATTAAA
1 AATTAAA
52357276 AATTAAA
1 AATTAAA
52357283 AA-TAAA
1 AATTAAA
52357289 A
1 A
52357290 TTACAATAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 5 0.12
7 25 0.58
8 10 0.23
9 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (7 bp):
AATTAAA
Found at i:52365445 original size:2 final size:2
Alignment explanation
Indices: 52365438--52365474 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
52365428 TTTTATACTT
52365438 TA TA TA 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 TA TA TA T
52365475 CATGCTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52376332 original size:16 final size:16
Alignment explanation
Indices: 52376311--52376345 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52376301 ATTTGCTATA
* *
52376311 ACACCTCTATTCCATT
1 ACACCTCTAATCCAAT
52376327 ACACCTCTAATCCAAT
1 ACACCTCTAATCCAAT
52376343 ACA
1 ACA
52376346 GCGAACCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACCTCTAATCCAAT
Found at i:52381368 original size:2 final size:2
Alignment explanation
Indices: 52381361--52381388 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52381351 AAATAAAAGA
52381361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52381389 GAAAATTGAA
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):
AT
Found at i:52384380 original size:29 final size:29
Alignment explanation
Indices: 52384347--52384406 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
52384337 AATAATGACT
52384347 TTGCCATCTGAGGTGAGACATTGATAACC
1 TTGCCATCTGAGGTGAGACATTGATAACC
*
52384376 TTGCCATTTGAGGTGAGACATTGATAACC
1 TTGCCATCTGAGGTGAGACATTGATAACC
52384405 TT
1 TT
52384407 TATGTTGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (29 bp):
TTGCCATCTGAGGTGAGACATTGATAACC
Found at i:52387365 original size:50 final size:50
Alignment explanation
Indices: 52387306--52387470 Score: 251
Period size: 50 Copynumber: 3.3 Consensus size: 50
52387296 TATCCCGGAT
* ** * * *
52387306 ATGGTCTTACATGAGAGTTATCATATCGGTGCCCACGCCATGTGCTAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTGCTAGAC
52387356 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTGCTAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTGCTAGAC
* *
52387406 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG-CATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTGCTAGAC
52387455 ATGGTCTTACATGGGA
1 ATGGTCTTACATGGGA
52387471 TCTCATTCCC
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 26 0.24
50 81 0.76
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTGCTAGAC
Found at i:52394888 original size:362 final size:362
Alignment explanation
Indices: 52394161--52394887 Score: 1283
Period size: 362 Copynumber: 2.0 Consensus size: 362
52394151 TCCCTAAATC
*
52394161 TTTAATTTCATAAAAATTCACTTTACAAAAGTTGTTTATCTATCAAAAACCTTTCATTTTCTACC
1 TTTAATTTCATAAAAAATCACTTTACAAAAGTTGTTTATCTATCAAAAACCTTTCATTTTCTACC
52394226 ATAAAACTTCATAATTCATCTATGTTCATCCATGGTAAAACCCTATTACCTTGATAACTTTGCAA
66 ATAAAACTTCATAATTCATCTATGTTCATCCATGGTAAAACCCTATTACCTTGATAACTTTGCAA
* *
52394291 ATTAATCTCTGAGATAGCTAGATTAAGTTATTACGATATCGGAAATGTAAAAATCATTAAAAACG
131 ATTAATCTCCGAGATAGCTAGATTAAGTTATTACGATATCGAAAATGTAAAAATCATTAAAAACG
52394356 GGGAAAAAATACTTACCTAATAAAGCAAAATAAGTTGGCTTGAGCTTAGGCTTCCATGGCTAGGG
196 GGGAAAAAATACTTACCTAATAAAGCAAAATAAGTTGGCTTGAGCTTAGGCTTCCATGGCTAGGG
* * * *
52394421 CTTCCATGCTTTTATTTGGCAAAGTTGATATAAATGATTATATTTTTAGTATTTTGTCATTTATA
261 CTTCCATGCTTTTACTTGGCAAAGATGATATAAATGATTATATTTTCAGTATTTTATCATTTATA
*
52394486 ATCTTTTATTATTTTACTTTCCAATTTAGTCCTTTTT
326 ATCATTTATTATTTTACTTTCCAATTTAGTCCTTTTT
*
52394523 TTTAATTTCATAAAAAATCACTTTACAAAAGTTGTTTATCTATCAACAACCTTTCATTTTCTACC
1 TTTAATTTCATAAAAAATCACTTTACAAAAGTTGTTTATCTATCAAAAACCTTTCATTTTCTACC
*
52394588 ATAAAACTTTATAATTCATCTATGTTCATCCATGGTAAAACCCTATTACCTTGATAACTTTGCAA
66 ATAAAACTTCATAATTCATCTATGTTCATCCATGGTAAAACCCTATTACCTTGATAACTTTGCAA
* *
52394653 ATTAATCTCCGAGATAGCTAGATTAGGTTATTACGATCTCGAAAATGTAAAAATCATTAAAAACG
131 ATTAATCTCCGAGATAGCTAGATTAAGTTATTACGATATCGAAAATGTAAAAATCATTAAAAACG
* *
52394718 GGGAAAAAATACTTACCTAATCAAGCAAAATAAGTTGGCTTGAGCTTAGGTTTCCATGGCTAGGG
196 GGGAAAAAATACTTACCTAATAAAGCAAAATAAGTTGGCTTGAGCTTAGGCTTCCATGGCTAGGG
* * *
52394783 TTTCCATGCTTTTAACTTGGGAAAGATGATATAAATGATTATATTTTCAGTATTTTATCCTTTAT
261 CTTCCATGCTTTT-ACTTGGCAAAGATGATATAAATGATTATATTTTCAGTATTTTATCATTTAT
*
52394848 CATCATTTATTATTTTACTTTCCAATTTAGTCCTTTTT
325 AATCATTTATTATTTTACTTTCCAATTTAGTCCTTTTT
52394886 TT
1 TT
52394888 ATTTTATTTT
Statistics
Matches: 346, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
362 263 0.76
363 83 0.24
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (362 bp):
TTTAATTTCATAAAAAATCACTTTACAAAAGTTGTTTATCTATCAAAAACCTTTCATTTTCTACC
ATAAAACTTCATAATTCATCTATGTTCATCCATGGTAAAACCCTATTACCTTGATAACTTTGCAA
ATTAATCTCCGAGATAGCTAGATTAAGTTATTACGATATCGAAAATGTAAAAATCATTAAAAACG
GGGAAAAAATACTTACCTAATAAAGCAAAATAAGTTGGCTTGAGCTTAGGCTTCCATGGCTAGGG
CTTCCATGCTTTTACTTGGCAAAGATGATATAAATGATTATATTTTCAGTATTTTATCATTTATA
ATCATTTATTATTTTACTTTCCAATTTAGTCCTTTTT
Found at i:52398606 original size:109 final size:108
Alignment explanation
Indices: 52398417--52398670 Score: 375
Period size: 109 Copynumber: 2.4 Consensus size: 108
52398407 TTATTTCCAT
* * * *
52398417 TTTTCTTGTTCGACCAAATAGCCAAATAACCTTTTAAAAATTTTAAAATAAGGCAATGTTTTGCG
1 TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGACAATGTTTTGCG
**
52398482 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGCTTTCGA
66 TTTGGAAATTCGAGAAAACGAACCCTAATGTGCTGGCTTTCGA
*
52398525 TTTTACTCGTTCGACCAAATAGCCAAATATCCTTTTAGAAATTTCAAAATAAGACAATGTTTTGC
1 TTTT-CTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGACAATGTTTTGC
* * * *
52398590 GTTTGGAAATTCGAGAAAATGAACCCTAATGTGTTGGGTTTTGA
65 GTTTGGAAATTCGAGAAAACGAACCCTAATGTGCTGGCTTTCGA
* *
52398634 -TTTCTCGTTGGACCAAATAGCCAAATATCCTCTTAAA
1 TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAA
52398671 TCTTAATCCA
Statistics
Matches: 131, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
107 31 0.24
108 7 0.05
109 93 0.71
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (108 bp):
TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGACAATGTTTTGCG
TTTGGAAATTCGAGAAAACGAACCCTAATGTGCTGGCTTTCGA
Found at i:52399088 original size:22 final size:22
Alignment explanation
Indices: 52399063--52399215 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
52399053 CCATGAGTGG
*
52399063 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
52399085 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
52399107 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
52399129 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
52399151 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
52399173 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
52399195 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
52399216 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:52401095 original size:18 final size:17
Alignment explanation
Indices: 52401062--52401100 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52401052 TTGTATAAAT
52401062 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52401080 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
52401097 TGTG
1 TGTG
52401101 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52401218 original size:8 final size:8
Alignment explanation
Indices: 52401205--52401233 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52401195 CACTAGAGAC
52401205 CAGTGTTA
1 CAGTGTTA
52401213 CAGTGTTA
1 CAGTGTTA
52401221 CAGTGTTA
1 CAGTGTTA
52401229 CAGTG
1 CAGTG
52401234 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:52401347 original size:23 final size:23
Alignment explanation
Indices: 52401320--52401395 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
52401310 AGCGTTATTG
52401320 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52401343 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52401366 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52401389 ATCAGTG
1 ATCAGTG
52401396 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:52407467 original size:18 final size:17
Alignment explanation
Indices: 52407434--52407472 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
52407424 TTGTATAAAT
52407434 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
52407452 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
52407469 TGTG
1 TGTG
52407473 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:52407590 original size:8 final size:8
Alignment explanation
Indices: 52407577--52407604 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
52407567 CACTAGAGAC
52407577 CAGTGTTA
1 CAGTGTTA
52407585 CAGTGTTA
1 CAGTGTTA
52407593 CAGTGTTA
1 CAGTGTTA
52407601 CAGT
1 CAGT
52407605 AAGTCCCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (8 bp):
CAGTGTTA
Found at i:52407719 original size:23 final size:23
Alignment explanation
Indices: 52407692--52407767 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
52407682 AGTGTTATTG
52407692 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
52407715 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52407738 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
52407761 ATCAGTG
1 ATCAGTG
52407768 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:52414721 original size:106 final size:106
Alignment explanation
Indices: 52414536--52414741 Score: 412
Period size: 106 Copynumber: 1.9 Consensus size: 106
52414526 AGTGATTTTC
52414536 AAAACATACTAATTGTTTTAAGCCTAGAGACAGTGAAAACTTTTTGTGAAATGGGCATATGTTTG
1 AAAACATACTAATTGTTTTAAGCCTAGAGACAGTGAAAACTTTTTGTGAAATGGGCATATGTTTG
52414601 AACATTGTGATTTCAATGAAATATATCTTCGCAATATTGAA
66 AACATTGTGATTTCAATGAAATATATCTTCGCAATATTGAA
52414642 AAAACATACTAATTGTTTTAAGCCTAGAGACAGTGAAAACTTTTTGTGAAATGGGCATATGTTTG
1 AAAACATACTAATTGTTTTAAGCCTAGAGACAGTGAAAACTTTTTGTGAAATGGGCATATGTTTG
52414707 AACATTGTGATTTCAATGAAATATATCTTCGCAAT
66 AACATTGTGATTTCAATGAAATATATCTTCGCAAT
52414742 TTTTTTGAGC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (106 bp):
AAAACATACTAATTGTTTTAAGCCTAGAGACAGTGAAAACTTTTTGTGAAATGGGCATATGTTTG
AACATTGTGATTTCAATGAAATATATCTTCGCAATATTGAA
Found at i:52415159 original size:12 final size:12
Alignment explanation
Indices: 52415142--52415166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52415132 CATAGCTAAA
52415142 GAAGCAAAACAT
1 GAAGCAAAACAT
52415154 GAAGCAAAACAT
1 GAAGCAAAACAT
52415166 G
1 G
52415167 CATACCAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.20, T:0.08
Consensus pattern (12 bp):
GAAGCAAAACAT
Found at i:52419580 original size:49 final size:49
Alignment explanation
Indices: 52419500--52419877 Score: 231
Period size: 49 Copynumber: 7.7 Consensus size: 49
52419490 GCAGTGGAAC
* * * * * * *
52419500 AGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTATAATTAAA
1 AGATTGAGGCCACAACGGCGAATCTTACTTCCCCGACATTGTAGTTAAA
* * * * * *
52419549 AGATTGAGGCCACAACGGCAAATCTTACTTCCCTGGCAGTGCT-GTGGAAC
1 AGATTGAGGCCACAACGGCGAATCTTACTTCCCCGACATTG-TAGT-TAAA
* * * * * *
52419599 AGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACGTTGCAGTTAAA
1 AGATTGAGGCCACAACGGCGAATCTTACTTCCCCGACATTGTAGTTAAA
* * * **** * * *
52419648 AGATTAAGGCCACAACGGCGAATCTTATTTCCCTGGTGGTGCAGTGGAAC
1 AGATTGAGGCCACAACGGCGAATCTTACTTCCCCGACATTGTAGT-TAAA
* * * * * * *
52419698 ACATTGAAGCTACAATGACGCATCTTGCTTCCCCGACATTGTAGTTAAA
1 AGATTGAGGCCACAACGGCGAATCTTACTTCCCCGACATTGTAGTTAAA
* ** * * *
52419747 AGATTGAGGCCACAACGGCGAATCTTACTTCCCTAGA-GGTGCAGTGGAAC
1 AGATTGAGGCCACAACGGCGAATCTTACTTCCC-CGACATTGTAGT-TAAA
* * ** * *
52419797 AGATTGAAGCTACAATAGC-AAGTCTTGCTTCCCCGACATTGTAATTAAA
1 AGATTGAGGCCACAACGGCGAA-TCTTACTTCCCCGACATTGTAGTTAAA
**
52419846 AGATTGAGGCCACAACGGTAAATCTTACTTCC
1 AGATTGAGGCCACAACGGCGAATCTTACTTCC
52419878 TTGGCGGTGC
Statistics
Matches: 235, Mismatches: 85, Indels: 18
0.70 0.25 0.05
Matches are distributed among these distances:
49 131 0.56
50 104 0.44
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (49 bp):
AGATTGAGGCCACAACGGCGAATCTTACTTCCCCGACATTGTAGTTAAA
Found at i:52419651 original size:99 final size:99
Alignment explanation
Indices: 52419480--52419979 Score: 687
Period size: 99 Copynumber: 5.0 Consensus size: 99
52419470 TTTCCCATGC
* *
52419480 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTATAAT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGTAAT
*
52419545 TAAAAGATTGAGGCCACAACGGCAAATCTTACTT
66 TAAAAGATTGAGGCCACAACGGCGAATCTTACTT
* * * * *
52419579 CCCTGGCAGTGCTGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACGTTGCAGT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGTAAT
* *
52419644 TAAAAGATTAAGGCCACAACGGCGAATCTTATTT
66 TAAAAGATTGAGGCCACAACGGCGAATCTTACTT
* * * * *
52419678 CCCTGGTGGTGCAGTGGAACACATTGAAGCTACAATGACGCATCTTGCTTCCCCGACATTGTAGT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGTAAT
52419743 TAAAAGATTGAGGCCACAACGGCGAATCTTACTT
66 TAAAAGATTGAGGCCACAACGGCGAATCTTACTT
* * *
52419777 CCCTAGAGGTGCAGTGGAACAGATTGAAGCTACAATAGC-AAGTCTTGCTTCCCCGACATTGTAA
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAA-TCTTGCTTCCCCGACATTGTAA
**
52419841 TTAAAAGATTGAGGCCACAACGGTAAATCTTACTT
65 TTAAAAGATTGAGGCCACAACGGCGAATCTTACTT
* * * * * * *
52419876 CCTTGGCGGTGCAGTGGAACAAATTGGAGCTACAACGACAAATCTTGCTTCCCCGACATTGCAAT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGTAAT
* * * **
52419941 TAAATAGATTAAAGCTACAACAACGAATCTTACTT
66 TAAA-AGATTGAGGCCACAACGGCGAATCTTACTT
52419976 CCCT
1 CCCT
52419980 TTCCCTGGTG
Statistics
Matches: 352, Mismatches: 46, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
98 1 0.00
99 323 0.92
100 28 0.08
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (99 bp):
CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGTAAT
TAAAAGATTGAGGCCACAACGGCGAATCTTACTT
Found at i:52419957 original size:50 final size:49
Alignment explanation
Indices: 52419500--52419978 Score: 282
Period size: 50 Copynumber: 9.7 Consensus size: 49
52419490 GCAGTGGAAC
* * * ** *
52419500 AGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTATAATTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAA
* * * * * * * * *
52419549 AGATTGAGGCCACAACGGCAAATCTTACTTCCCTGGCAGTGCTGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGT-TAAA
* * *
52419599 AGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACGTTGCAGTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAA
* * * **** * *
52419648 AGATT-AAGGCCACAACGGCGAATCTTATTTCCCTGGTGGTGCAGTGGAAC
1 AGATTGAA-GCTACAACGGCGAATCTTACTTCCCCGACATTGCAGT-TAAA
* * * * * *
52419698 ACATTGAAGCTACAATGACGCATCTTGCTTCCCCGACATTGTAGTTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAA
* * * ** * *
52419747 AGATTGAGGCCACAACGGCGAATCTTACTTCCCTAGA-GGTGCAGTGGAAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCC-CGACATTGCAGT-TAAA
** * * *
52419797 AGATTGAAGCTACAATAGC-AAGTCTTGCTTCCCCGACATTGTAATTAAA
1 AGATTGAAGCTACAACGGCGAA-TCTTACTTCCCCGACATTGCAGTTAAA
* * ** ** * ** *
52419846 AGATTGAGGCCACAACGGTAAATCTTACTTCCTTGGCGGTGCAGTGGAACA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGT-TAA-A
* * * * *
52419897 A-ATTGGAGCTACAACGACAAATCTTGCTTCCCCGACATTGCAATTAAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAA
* **
52419945 TAGATTAAAGCTACAACAACGAATCTTACTTCCC
1 -AGATTGAAGCTACAACGGCGAATCTTACTTCCC
52419979 TTTCCCTGGT
Statistics
Matches: 308, Mismatches: 109, Indels: 25
0.70 0.25 0.06
Matches are distributed among these distances:
48 3 0.01
49 139 0.45
50 162 0.53
51 4 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (49 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACATTGCAGTTAAA
Found at i:52421538 original size:30 final size:28
Alignment explanation
Indices: 52421463--52421538 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
52421453 TAACTATTGT
*
52421463 TATATACATAAGTACATTTTCATAATATA
1 TATATACATAAGTA-TTTTTCATAATATA
* *
52421492 TATGTACATATA-TATTTTTTATAACTTATA
1 TATATACATA-AGTATTTTTCATAA--TATA
*
52421522 TATATACATACGTATTT
1 TATATACATAAGTATTT
52421539 ATATATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 8 0.21
29 11 0.29
30 19 0.50
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (28 bp):
TATATACATAAGTATTTTTCATAATATA
Found at i:52421791 original size:6 final size:6
Alignment explanation
Indices: 52421782--52421853 Score: 71
Period size: 6 Copynumber: 12.5 Consensus size: 6
52421772 ATATACATAG
* *
52421782 ATTTTT ATTTTT ATTTTT A---TT ATTTTT ATTTTT ACTTTT ACTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
* *
52421827 ACTTTT ACTTTT ATTTTT -TTATTT ATT
1 ATTTTT ATTTTT ATTTTT ATT-TTT ATT
52421854 CTCATTATTG
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
3 3 0.05
5 2 0.03
6 52 0.88
7 2 0.03
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:52421806 original size:15 final size:15
Alignment explanation
Indices: 52421786--52421815 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52421776 ACATAGATTT
52421786 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
52421801 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
52421816 CTTTTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:52422269 original size:109 final size:108
Alignment explanation
Indices: 52422078--52422392 Score: 490
Period size: 109 Copynumber: 2.9 Consensus size: 108
52422068 TAAAAAAAAA
* * * *
52422078 TCAAAGTAAGGCAATGTTTTGCGGTTGGAAATTCGAGAAAACGTGCCCTAATGCGCTGGGTTTTG
1 TCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCG
*
52422143 ATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTCA-AACTT
66 A-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT-AGAAATT
*
52422187 TCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCTCTAATGTGCTGGGTTTCG
1 TCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCG
52422252 ATTTTACTCGTTCGACCAAATAGCCAAATATCCTTTTAGAAATT
66 ATTTT-CTCGTTCGACCAAATAGCCAAATATCCTTTTAGAAATT
* * *
52422296 TCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAATGTACCCTAATGTGCTGGGTTTCG
1 TCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCG
* *
52422361 A-TTTCTTGTTGGACCAAATAGCCAAATATCCT
66 ATTTTCTCGTTCGACCAAATAGCCAAATATCCT
52422393 CTTAAATCTT
Statistics
Matches: 192, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
107 26 0.14
108 8 0.04
109 158 0.82
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (108 bp):
TCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCG
ATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAGAAATT
Found at i:52424088 original size:9 final size:8
Alignment explanation
Indices: 52424054--52424089 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
52424044 AAGAAAATGA
*
52424054 ATAAAATT
1 ATAAAAAT
52424062 ATAAAAAT
1 ATAAAAAT
52424070 ATAAAAAT
1 ATAAAAAT
52424078 ATAAAAGAT
1 ATAAAA-AT
52424087 ATA
1 ATA
52424090 TATATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 21 0.81
9 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (8 bp):
ATAAAAAT
Found at i:52426169 original size:31 final size:31
Alignment explanation
Indices: 52426131--52426201 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
52426121 GCTATTTTTA
* *
52426131 ATCTGCTTTGCTGCAAACTATGGTGTCTTTG
1 ATCTGCTTCGCTGCAAACTATGGTGTCTTCG
52426162 ATCTGCTTCGCTGCAAACTATGGTGTCTTCG
1 ATCTGCTTCGCTGCAAACTATGGTGTCTTCG
52426193 ATCTGCTTC
1 ATCTGCTTC
52426202 ATTGTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.39
Consensus pattern (31 bp):
ATCTGCTTCGCTGCAAACTATGGTGTCTTCG
Found at i:52426426 original size:133 final size:133
Alignment explanation
Indices: 52426239--52426801 Score: 571
Period size: 133 Copynumber: 4.2 Consensus size: 133
52426229 CTATCTTCTG
* * * *
52426239 TCTGCTTCGCTGTCAATACAGGAAGGCAAGGCTGGTGTCTTCGATTTGTTTCGCTATCAGTACAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAG
* * * *
52426304 GAAGGCAAGATTTTCTATCTTCAGTCTGCTCCGTTGTCAGTACAGGAAGGTAAGGCTAGTGTCTT
66 GAAGGCAAGATTTTCTATCTTCAGTCTGCTCCGCTGTTAGTACAGGAAGGAAAGGCTGGTGTCTT
52426369 CGA
131 CGA
* * *
52426372 TCTGTTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGTGCAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAG
* * * * * * *
52426437 GAATGTAAGATTTGT-TATCTTCAATCTTCTCTGCTGTTAGTATAGGAAGGGAAGGCTGGTGTCT
66 GAAGGCAAGATTT-TCTATCTTCAGTCTGCTCCGCTGTTAGTACAGGAAGGAAAGGCTGGTGTCT
52426501 TCGA
130 TCGA
* * * * * * * *
52426505 TCTACTTCACTGTCAGTACGGGAAGGCAAGATCTGTTATCTTC-AGTCTG-TTCCACTGTCATTA
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTCGA-TCTGCTT-CGCTGTCAGTA
* * ** ** * * * ** *
52426568 TAGGAAGGGAAG-GCTAGTGTCTTC-GATTTGCTTCGCTGTTAGTACAGGAAGGCAAAATCTGCT
63 CAGGAAGGCAAGATTTTCTATCTTCAG-TCTGCTCCGCTGTTAGTACAGGAAGG-AAAGGCTGGT
*
52426631 ATCTTC-A
126 GTCTTCGA
* *
52426638 GTCTGCTTCGCTGTCAGTACAGGAAGGCAAGGTTGGTGTCTTCGATCTGCTTCGTTGTCAGTACA
1 -TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACA
* * * * * *
52426703 TGAAGGCAAGATATGCTATCTTCAGTCTACTCCACTGTTAGTACAGGAAGGCAAGGCTGGTGTCT
65 GGAAGGCAAGATTTTCTATCTTCAGTCTGCTCCGCTGTTAGTACAGGAAGGAAAGGCTGGTGTCT
52426768 TCGA
130 TCGA
* **
52426772 TCTGCTTTGCTGTCAGTGTAGGAAGGCAAG
1 TCTGCTTCGCTGTCAGTACAGGAAGGCAAG
52426802 ATTTGCTATC
Statistics
Matches: 341, Mismatches: 76, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
133 239 0.70
134 101 0.30
135 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (133 bp):
TCTGCTTCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAG
GAAGGCAAGATTTTCTATCTTCAGTCTGCTCCGCTGTTAGTACAGGAAGGAAAGGCTGGTGTCTT
CGA
Found at i:52426458 original size:89 final size:88
Alignment explanation
Indices: 52426204--52426815 Score: 561
Period size: 89 Copynumber: 6.9 Consensus size: 88
52426194 TCTGCTTCAT
* * * * *
52426204 TGTCAATACAGGAAGGCAAGATCTGCTATCTTCTG-TCTGCTTCGCTGTCAATACAGGAAGGCAA
1 TGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTC-GATCTGCTTCGCTGTCAGTACAGGAAGGCAA
* * * *
52426268 G-GCTGGTGTCTTCGATTTGTTTCGC
64 GATCTGCTATCTTC-ATCTGTTTCGC
* ** ** * * * *
52426293 TATCAGTACAGGAAGGCAAGATTTTCTATCTTC-AGTCTGCTCCGTTGTCAGTACAGGAAGGTAA
1 TGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAA
* *
52426357 G-GCTAG-TGTCTTCGATCTGTTTCGC
64 GATCT-GCTATCTTC-ATCTGTTTCGC
* * * *
52426382 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGTGCAGGAATGTAAGA
1 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
* * *
52426447 TTTGTTATCTTCAATCT-TCTCTGC
66 TCTGCTATCTTC-ATCTGTTTC-GC
* * * * * *
52426471 TGTTAGTATAGGAAGGGAAGGCTGGTGTCTTCGATCTACTTCACTGTCAGTACGGGAAGGCAAGA
1 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
* * *
52426536 TCTGTTATCTTCAGTCTGTTCCAC
66 TCTGCTATCTTCA-TCTGTTTCGC
* * * * * * *
52426560 TGTCATTATAGGAAGGGAAGGCTAGTGTCTTCGATTTGCTTCGCTGTTAGTACAGGAAGGCAAAA
1 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
*
52426625 TCTGCTATCTTCAGTCTGCTTCGC
66 TCTGCTATCTTCA-TCTGTTTCGC
* * *
52426649 TGTCAGTACAGGAAGGCAAGGTTGGTGTCTTCGATCTGCTTCGTTGTCAGTACATGAAGGCAAGA
1 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
* ** * *
52426714 TATGCTATCTTCAGTCTACTCCAC
66 TCTGCTATCTTCA-TCTGTTTCGC
* * **
52426738 TGTTAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTTGCTGTCAGTGTAGGAAGGCAAGA
1 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
*
52426803 TTTGCTATCTTCA
66 TCTGCTATCTTCA
52426816 ATGATCTGTT
Statistics
Matches: 440, Mismatches: 74, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
88 37 0.08
89 400 0.91
90 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (88 bp):
TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
TCTGCTATCTTCATCTGTTTCGC
Found at i:52426575 original size:222 final size:223
Alignment explanation
Indices: 52426182--52426757 Score: 606
Period size: 222 Copynumber: 2.6 Consensus size: 223
52426172 CTGCAAACTA
* ** * **
52426182 TGGTGTCTTCGATCTGCTTCATTGTCAATACAGGAAGGCAAGATCTGCTATCTTCTGTCTGCTTC
1 TGGTGTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTTC
* ** *
52426247 GCTGTCAATACAGGAAGGCAAGGCTGGTGTCTTCGATTTGTTTCGCTATCAGTACAGGAAGGCAA
66 GCTGTCAATACAGGAAGGCAAGGCTGGTGTCTTCGATCTACTTCACTATCAGTACAGGAAGGCAA
* ** * *
52426312 GATTTTCTATCTTCAGTCTGCTCCGTTGTCAGTACAGGAAGGTAAGGCTAGTGTCTTCGATCTGT
131 GATTGTCTATCTTCAGTCTGCTCCACTGTCAGTACAGGAAGGGAAGGCTAGTGTCTTCGATCTGC
*
52426377 TTCGCTGTCAGTACAGGAAGGC-AAGGC
196 TTCGCTGTCAGTACAGGAAGGCAAAAGC
* * * * * *
52426404 TGGTGTCTTTGATCTGCTTCGCTGTCAGTGCAGGAATGTAAGATTTGTTATCTTCAATCTTC-TC
1 TGGTGTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTTC
* * * * * *
52426468 TGCTGTTAGTATAGGAAGGGAAGGCTGGTGTCTTCGATCTACTTCACTGTCAGTACGGGAAGGCA
66 -GCTGTCAATACAGGAAGGCAAGGCTGGTGTCTTCGATCTACTTCACTATCAGTACAGGAAGGCA
* * * *
52426533 AGATCTGT-TATCTTCAGTCTGTTCCACTGTCATTATAGGAAGGGAAGGCTAGTGTCTTCGATTT
130 AGAT-TGTCTATCTTCAGTCTGCTCCACTGTCAGTACAGGAAGGGAAGGCTAGTGTCTTCGATCT
* *
52426597 GCTTCGCTGTTAGTACAGGAAGGCAAAATC
194 GCTTCGCTGTCAGTACAGGAAGGCAAAAGC
* * * * * * *
52426627 TGCTATC-TTCAGTCTGCTTCGCTGTCAGTACAGGAAGGCAAGGT-TGGTGTCTTCGATCTGCTT
1 TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTT
* * * ** * * * * *
52426690 CGTTGTCAGTACATGAAGGCAAGATATGCTATCTTC-AGTCTACTCCACTGTTAGTACAGGAAGG
65 CGCTGTCAATACAGGAAGGCAAG-GCTGGTGTCTTCGA-TCTACTTCACTATCAGTACAGGAAGG
52426754 CAAG
128 CAAG
52426758 GCTGGTGTCT
Statistics
Matches: 290, Mismatches: 57, Indels: 13
0.81 0.16 0.04
Matches are distributed among these distances:
221 2 0.01
222 213 0.73
223 75 0.26
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (223 bp):
TGGTGTCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTTC
GCTGTCAATACAGGAAGGCAAGGCTGGTGTCTTCGATCTACTTCACTATCAGTACAGGAAGGCAA
GATTGTCTATCTTCAGTCTGCTCCACTGTCAGTACAGGAAGGGAAGGCTAGTGTCTTCGATCTGC
TTCGCTGTCAGTACAGGAAGGCAAAAGC
Found at i:52426796 original size:311 final size:311
Alignment explanation
Indices: 52426182--52426797 Score: 770
Period size: 311 Copynumber: 2.0 Consensus size: 311
52426172 CTGCAAACTA
* * *
52426182 TGGTGTCTTCGATCTGCTTCATTGTCAATACAGGAAGGCAAGATCTGCTATCTTCTGTCTGCTTC
1 TGGTGTCTTCGATCTACTTCACTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTC
* * *
52426247 GCTGTCAATACAGGAAGGCAAGGCTGGTGTCTTCGATTTGTTTCGCTATCAGTACAGGAAGGCAA
66 ACTGTCAATACAGGAAGGCAAGGCTAGTGTCTTCGATTTGCTTCGCTATCAGTACAGGAAGGCAA
* * * * * *
52426312 GATTTTCTATCTTCAGTCTGCTCCGTTGTCAGTACAGGAAGGTAAGGCTAGTGTCTTCGATCTGT
131 AATCTGCTATCTTCAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGCTAGTGTCTTCGATCTGC
* * * * * * * * *
52426377 TTCGCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCAGTGCAGGAATG
196 TTCGCTGTCAGTACAGGAAGGCAAGGATGCTATCTTAGATCTACTCCACTGTCAGTACAGGAAGG
* ** * * *
52426442 TAAGATTTGTTATCTTCAATCTTCTCTGCTGTTAGTATAGGAAGGGAAGGC
261 CAAGAGCTGGTATCTTCAATCTGCTCTGCTGTCAGTATAGGAAGGGAAGGC
* * *
52426493 TGGTGTCTTCGATCTACTTCACTGTCAGTACGGGAAGGCAAGATCTGTTATCTTCAGTCTG-TTC
1 TGGTGTCTTCGATCTACTTCACTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTT-
* * * * *
52426557 CACTGTCATTATAGGAAGGGAAGGCTAGTGTCTTCGATTTGCTTCGCTGTTAGTACAGGAAGGCA
65 CACTGTCAATACAGGAAGGCAAGGCTAGTGTCTTCGATTTGCTTCGCTATCAGTACAGGAAGGCA
* * *
52426622 AAATCTGCTATCTTCAGTCTGCTTCGCTGTCAGTACAGGAAGGCAAGGTTGGTGTCTTCGATCTG
130 AAATCTGCTATCTTCAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGCTAGTGTCTTCGATCTG
* * * *
52426687 CTTCGTTGTCAGTACATGAAGGCAAGATATGCTATCTTCAG-TCTACTCCACTGTTAGTACAGGA
195 CTTCGCTGTCAGTACAGGAAGGCAAG-GATGCTATCTT-AGATCTACTCCACTGTCAGTACAGGA
* * * *
52426751 AGGCAAG-GCTGGTGTCTTCGATCTGCTTTGCTGTCAGTGTAGGAAGG
258 AGGCAAGAGCTGGTATCTTCAATCTGCTCTGCTGTCAGTATAGGAAGG
52426798 CAAGATTTGC
Statistics
Matches: 256, Mismatches: 46, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
310 2 0.01
311 223 0.87
312 30 0.12
313 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (311 bp):
TGGTGTCTTCGATCTACTTCACTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTC
ACTGTCAATACAGGAAGGCAAGGCTAGTGTCTTCGATTTGCTTCGCTATCAGTACAGGAAGGCAA
AATCTGCTATCTTCAGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGCTAGTGTCTTCGATCTGC
TTCGCTGTCAGTACAGGAAGGCAAGGATGCTATCTTAGATCTACTCCACTGTCAGTACAGGAAGG
CAAGAGCTGGTATCTTCAATCTGCTCTGCTGTCAGTATAGGAAGGGAAGGC
Found at i:52436323 original size:10 final size:10
Alignment explanation
Indices: 52436308--52436344 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
52436298 GGTGCTGCTG
52436308 GAAAAAGAGA
1 GAAAAAGAGA
52436318 GAAAAAGAGA
1 GAAAAAGAGA
*
52436328 GAAAGAGAAGA
1 GAAAAAG-AGA
52436339 GAAAAA
1 GAAAAA
52436345 AAAGGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAAGAGA
Found at i:52436565 original size:42 final size:40
Alignment explanation
Indices: 52436507--52436641 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 40
52436497 TAGATGTTAC
*
52436507 TTAGTATTATTGTTAGTAAAAAACTAGTATTATTATTATGG
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATTATTATGG
** * * *
52436548 TTAGTTATTATTTTTAGTAAAACCCTA-ATTATCATTTTTAG
1 TTAG-TATTATTTTTAGTAAAAAACTATATTATTA-TTATGG
* * *
52436589 TTAGTATTATTTTGAGTATAAAACTATTATTATTGTTATTGTG
1 TTAGTATTATTTTTAGTAAAAAACTA-TATTATTATTA-TG-G
52436632 TTAGTTATTA
1 TTAG-TATTA
52436642 GGGTTAGTGG
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
40 24 0.33
41 14 0.19
42 25 0.34
43 5 0.07
44 5 0.07
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (40 bp):
TTAGTATTATTTTTAGTAAAAAACTATATTATTATTATGG
Found at i:52436597 original size:40 final size:40
Alignment explanation
Indices: 52436507--52436614 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 40
52436497 TAGATGTTAC
* * *
52436507 TTAGTATTATTGTTAGTAAAAAACTAGTATTATTATTATGG
1 TTAGTATTATTTTTAGTAAAAAACTAG-ATTATCATTATAG
** *
52436548 TTAGTTATTATTTTTAGTAAAACCCTA-ATTATCATTTTTAG
1 TTAG-TATTATTTTTAGTAAAAAACTAGATTATCA-TTATAG
* *
52436589 TTAGTATTATTTTGAGTATAAAACTA
1 TTAGTATTATTTTTAGTAAAAAACTA
52436615 TTATTATTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 24 0.44
41 12 0.22
42 19 0.35
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (40 bp):
TTAGTATTATTTTTAGTAAAAAACTAGATTATCATTATAG
Found at i:52442290 original size:160 final size:153
Alignment explanation
Indices: 52441799--52442478 Score: 640
Period size: 160 Copynumber: 4.3 Consensus size: 153
52441789 TTTGAATCAA
* * *
52441799 TACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATGTAGTGTAAAAAAAAACT
1 TACATTATGTTTGAAATTTATTAATTTAGTCTGTTTTTTAAATAAATTTA--GT--AAAAAAA-T
* * *
52441864 CTTATTCCTGCCCTTTGCTCGTATTATTTTCT-CGAATTTTATTACTTTTAATGAAATTATATTA
61 CTTATTCCTGCCCTTTGCTCGTATTATTTTCTCCAAATTTTATTAC-TTTAA--AAAATATATAA
*
52441928 TTTTCGT-ATTTTATTATTTTATATTATTTCAG
123 TTTT--TAATTTTATTATTTTACATTATTTCAG
* * * * *
52441960 TACATTTTGTTTGAAATATT-TGTAATCATTATTTCTGAATTTTTAAA-AAATTTAGTAAAAGAC
1 TACATTATGTTTGAAAT-TTAT-TAAT--TTA-GTCTG-TTTTTTAAATAAATTTAGTAAAAAAA
* * **
52442023 TCTTACTT-CGGCCCTTTGTTCGTATT-TTTTCTCCGCATTTTATTACTTTAAAAAATATCATAA
60 TCTTA-TTCCTGCCCTTTGCTCGTATTATTTTCTCCAAATTTTATTACTTTAAAAAATAT-ATAA
*
52442086 TTTTTAATTTTATAATTTTACATTATTTCAG
123 TTTTTAATTTTATTATTTTACATTATTTCAG
* * * *
52442117 TGCATGATGTTTGAAATTTATTAATTTAGTATGTTTTTTAAATTAATTTAGTGTAAAAAAAATCA
1 TACATTATGTTTGAAATTTATTAATTTAGTCTGTTTTTTAAATAAATTTA--GT-AAAAAAATC-
*
52442182 TTATTCCTGCCCTTTGCTCGTATTATTTTC-CCAAATTTTATTACTTTCAATAAAAATATATTAT
62 TTATTCCTGCCCTTTGCTCGTATTATTTTCTCCAAATTTTATTACTTT--A-AAAAATATATAAT
* *
52442246 TTTTGTATTTTATTATTTTATATTATTTCAG
124 TTTT-AATTTTATTATTTTACATTATTTCAG
* * * * *
52442277 TACATTTTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTTAAA-AAATTTAGTAAAACAC
1 TACATTATGTTTG-AA-A-TT-TATTAATTTA-GTCTG-TTTTTTAAATAAATTTAGTAAAAAAA
* * * * * * *
52442340 TCTTATTTCAGCCATTTGTTCGTATTTTTTTCTCCACATTTTATTACTTTAAAAAATACCATAAT
60 TCTTATTCCTGCCCTTTGCTCGTATTATTTTCTCCAAATTTTATTACTTTAAAAAATA-TATAAT
* *
52442405 TTTTAATTTTATTATTTTACATTATTTTAC
124 TTTTAATTTTATTATTTTACATTATTTCAG
* *
52442435 TACATTATATTTGAAATTTATTAATTTAGTGTGTTTTTTAAATA
1 TACATTATGTTTGAAATTTATTAATTTAGTCTGTTTTTTAAATA
52442479 TACATTTTTT
Statistics
Matches: 429, Mismatches: 58, Indels: 71
0.77 0.10 0.13
Matches are distributed among these distances:
152 8 0.02
153 17 0.04
154 13 0.03
155 7 0.02
156 17 0.04
157 80 0.19
158 52 0.12
159 29 0.07
160 99 0.23
161 49 0.11
162 9 0.02
163 7 0.02
164 18 0.04
165 16 0.04
166 8 0.02
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (153 bp):
TACATTATGTTTGAAATTTATTAATTTAGTCTGTTTTTTAAATAAATTTAGTAAAAAAATCTTAT
TCCTGCCCTTTGCTCGTATTATTTTCTCCAAATTTTATTACTTTAAAAAATATATAATTTTTAAT
TTTATTATTTTACATTATTTCAG
Found at i:52442415 original size:318 final size:318
Alignment explanation
Indices: 52441799--52442477 Score: 1119
Period size: 317 Copynumber: 2.1 Consensus size: 318
52441789 TTTGAATCAA
*
52441799 TACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATGTAGTGTAAAAAAAAACT
1 TACATGATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATGTAGTGTAAAAAAAAACT
* * * * *
52441864 CTTATTCCTGCCCTTTGCTCGTATTATTTTCTCGAATTTTATTACTTTTAATGAAATTATATTAT
66 CTTATTCCTGCCCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTAT
*
52441929 TTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTAATCATTATTT
131 TTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTAATAATTATTT
* * * *
52441994 CTGAATTTTTAAAAAATTTAGTAAAAGACTCTTACTTCGGCCCTTTGTTCGTATTTTTTCTCCGC
196 CTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCAGCCATTTGTTCGTATTTTTTCTCCAC
* *
52442059 ATTTTATTACTTTAAAAAATATCATAATTTTTAATTTTATAATTTTACATTATTTCAG
261 ATTTTATTACTTTAAAAAATACCATAATTTTTAATTTTATAATTTTACATTATTTCAC
* * *
52442117 TGCATGATGTTTGAAATTTATTAATTTAGTATGTTTTTTAAATTAATTTAGTGT-AAAAAAAA-T
1 TACATGATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATGTAGTGTAAAAAAAAACT
52442180 CATTATTCCTGCCCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTA
66 C-TTATTCCTGCCCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTA
* *
52442245 TTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATT
130 TTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTAATAATTATT
*
52442310 TCTGAATTTTTAAAAAATTTAGTAAAACACTCTTATTTCAGCCATTTGTTCGTATTTTTTTCTCC
195 TCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCAGCCATTTGTTCGTA-TTTTTTCTCC
* *
52442375 ACATTTTATTACTTTAAAAAATACCATAATTTTTAATTTTATTATTTTACATTATTTTAC
259 ACATTTTATTACTTTAAAAAATACCATAATTTTTAATTTTATAATTTTACATTATTTCAC
* *
52442435 TACATTATATTTGAAATTTATTAATTTAGTGTGTTTTTTAAAT
1 TACATGATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAAT
52442478 ATACATTTTT
Statistics
Matches: 334, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
316 2 0.01
317 178 0.53
318 154 0.46
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (318 bp):
TACATGATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATGTAGTGTAAAAAAAAACT
CTTATTCCTGCCCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTAT
TTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTAATAATTATTT
CTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCAGCCATTTGTTCGTATTTTTTCTCCAC
ATTTTATTACTTTAAAAAATACCATAATTTTTAATTTTATAATTTTACATTATTTCAC
Found at i:52442822 original size:13 final size:13
Alignment explanation
Indices: 52442804--52442889 Score: 53
Period size: 13 Copynumber: 7.0 Consensus size: 13
52442794 ACAAAAATTA
52442804 CTTTTCCTTCTTT
1 CTTTTCCTTCTTT
*
52442817 CTTTTCCTTGC-CT
1 CTTTTCCTT-CTTT
52442830 CTTCTT-CTTCTTT
1 CTT-TTCCTTCTTT
**
52442843 CTTTTTTTTCTTCT
1 CTTTTCCTTCTT-T
*
52442857 CCTTTCC-T-TTT
1 CTTTTCCTTCTTT
52442868 C-TTTCC-T-TTT
1 CTTTTCCTTCTTT
52442878 C-TTTCCTTCTTT
1 CTTTTCCTTCTTT
52442890 TTCTTTCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
10 15 0.25
11 3 0.05
12 8 0.13
13 26 0.43
14 8 0.13
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.67
Consensus pattern (13 bp):
CTTTTCCTTCTTT
Found at i:52442866 original size:5 final size:5
Alignment explanation
Indices: 52442856--52442965 Score: 57
Period size: 5 Copynumber: 22.4 Consensus size: 5
52442846 TTTTTTCTTC
* * * * * *
52442856 TCCTT TCCTT TTCTT TCCTT TTCTT TCC-T TCTTT TTCTT TCTTTT TTCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC-CTT TCCTT
* * * * * *
52442906 CCCATT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT CCCTC TCCTT TCCTT
1 TCC-TT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
*
52442955 TTCTT T-CTT TC
1 TCCTT TCCTT TC
52442966 TTCTTCTTTC
Statistics
Matches: 75, Mismatches: 24, Indels: 12
0.68 0.22 0.11
Matches are distributed among these distances:
4 13 0.17
5 55 0.73
6 7 0.09
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (5 bp):
TCCTT
Found at i:52442871 original size:10 final size:10
Alignment explanation
Indices: 52442837--52442961 Score: 75
Period size: 10 Copynumber: 12.7 Consensus size: 10
52442827 CCTCTTCTTC
52442837 TTCTTT-CTT
1 TTCTTTCCTT
*
52442846 TT-TTTTCTT
1 TTCTTTCCTT
*
52442855 CTCCTTTCCTT
1 -TTCTTTCCTT
52442866 TTCTTTCCTT
1 TTCTTTCCTT
52442876 TTCTTTCCTT
1 TTCTTTCCTT
52442886 CTT-TTT-CTT
1 -TTCTTTCCTT
* *
52442895 TCTTTTTTCTT
1 T-TCTTTCCTT
**
52442906 CCCATTTCCTT
1 TTC-TTTCCTT
52442917 TTCTTTCCTT
1 TTCTTTCCTT
52442927 CTT-TTT-C-T
1 -TTCTTTCCTT
* *
52442935 TTCTTCCCTC
1 TTCTTTCCTT
*
52442945 TCCTTTCCTT
1 TTCTTTCCTT
52442955 TTCTTTC
1 TTCTTTC
52442962 TTTCTTCTTC
Statistics
Matches: 89, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
7 2 0.02
8 7 0.08
9 11 0.12
10 49 0.55
11 20 0.22
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTTCCTT
Found at i:52442879 original size:35 final size:35
Alignment explanation
Indices: 52442814--52442881 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
52442804 CTTTTCCTTC
* *
52442814 TTTCTTTTCCTTGCCTCTTCTTCTTCTTTCTTTTT
1 TTTCTTCTCCTTGCCTCTTCTTCCTCTTTCTTTTT
* *
52442849 TTTCTTCTCCTTTCCTTTTCTTTCCT-TTTCTTT
1 TTTCTTCTCCTTGCCTCTTC-TTCCTCTTTCTTT
52442882 CCTTCTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.69
Consensus pattern (35 bp):
TTTCTTCTCCTTGCCTCTTCTTCCTCTTTCTTTTT
Found at i:52442904 original size:51 final size:52
Alignment explanation
Indices: 52442830--52442940 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 52
52442820 TTCCTTGCCT
52442830 CTTCTTCTTCTTTCTTTTTTTTCTTCTCC-TTTCCTTTTCTTTCCTT-TTCTTTC
1 CTTCTTCTTCTTTC-TTTTTTTCTTC-CCATTTCCTTTTCTTTCCTTCTT-TTTC
*
52442883 CTTCTTTTTCTTTC-TTTTTTCTTCCCATTTCCTTTTCTTTCCTTCTTTTTC
1 CTTCTTCTTCTTTCTTTTTTTCTTCCCATTTCCTTTTCTTTCCTTCTTTTTC
*
52442934 TTTCTTC
1 CTTCTTC
52442941 CCTCTCCTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
50 2 0.04
51 36 0.68
52 2 0.04
53 13 0.25
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (52 bp):
CTTCTTCTTCTTTCTTTTTTTCTTCCCATTTCCTTTTCTTTCCTTCTTTTTC
Found at i:52442914 original size:41 final size:38
Alignment explanation
Indices: 52442879--52442975 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
52442869 TTTCCTTTTC
***
52442879 TTTCCTTCTTTTTCTTTCTTTTTTCTTCCCATTTCCTTTTC
1 TTTCCTTCTTTTTCTTTCTTCCCTC-T-CC-TTTCCTTTTC
52442920 TTTCCTTCTTTTTCTTTCTTCCCTCTCCTTTCCTTTTC
1 TTTCCTTCTTTTTCTTTCTTCCCTCTCCTTTCCTTTTC
* *
52442958 TTTCTTTCTTCTTCTTTC
1 TTTCCTTCTTTTTCTTTC
52442976 CCTCTCCTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
38 26 0.51
39 2 0.04
40 1 0.02
41 22 0.43
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (38 bp):
TTTCCTTCTTTTTCTTTCTTCCCTCTCCTTTCCTTTTC
Found at i:52442972 original size:10 final size:10
Alignment explanation
Indices: 52442831--52442975 Score: 72
Period size: 10 Copynumber: 14.3 Consensus size: 10
52442821 TCCTTGCCTC
52442831 TTCTTCTTCT
1 TTCTTCTTCT
*
52442841 TTCTT-TTTT
1 TTCTTCTTCT
*
52442850 TTCTTCTCCT
1 TTCTTCTTCT
52442860 TTCCTT-TTCT
1 TT-CTTCTTCT
52442870 TTCCTT-TTCT
1 TT-CTTCTTCT
52442880 TTCCTTCTT-T
1 TT-CTTCTTCT
*
52442890 TTCTTTCTTTT
1 TTC-TTCTTCT
*
52442901 TTCTTC-CCAT
1 TTCTTCTTC-T
52442911 TTCCTT-TTCT
1 TT-CTTCTTCT
52442921 TTCCTTCTT-T
1 TT-CTTCTTCT
*
52442931 TTCTTTCTTCC
1 TTC-TTCTTCT
* * *
52442942 CTCTCCTTTCC
1 TTCTTC-TTCT
52442953 TT-TTCTTTCT
1 TTCTTC-TTCT
52442963 TTCTTCTTCT
1 TTCTTCTTCT
52442973 TTC
1 TTC
52442976 CCTCTCCTTC
Statistics
Matches: 109, Mismatches: 13, Indels: 26
0.74 0.09 0.18
Matches are distributed among these distances:
9 10 0.09
10 74 0.68
11 25 0.23
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:52446103 original size:64 final size:64
Alignment explanation
Indices: 52445996--52446124 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
52445986 GCCGGAGAGC
**
52445996 CATATAACAGGACGCTCACAAAGAGCTGCAGTATGTCTTCAACACATGCAAGACCACTACCGAT
1 CATATAACAGGACGCTCACAAAGAGCTGCAGTATGTCCGCAACACATGCAAGACCACTACCGAT
* * * *
52446060 CATATAACAGGACGCTCACAAAGAGTTGCGGTATGTCCGCAACACATGCAGGATCACTACCGAT
1 CATATAACAGGACGCTCACAAAGAGCTGCAGTATGTCCGCAACACATGCAAGACCACTACCGAT
52446124 C
1 C
52446125 GAGATACTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (64 bp):
CATATAACAGGACGCTCACAAAGAGCTGCAGTATGTCCGCAACACATGCAAGACCACTACCGAT
Found at i:52448363 original size:41 final size:43
Alignment explanation
Indices: 52448244--52448376 Score: 148
Period size: 45 Copynumber: 3.0 Consensus size: 43
52448234 ACTATTTTCG
*
52448244 ATATGTGTTTTCGTGTAAGACCAC-GTCTGGGACGATGGCATCGAT
1 ATATGTG-ATTCGTGTAAGACC-CTGTCTGGGAC-ATGGCATCGAT
* *
52448289 ATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCG-T
1 ATATGTGATT-CGTGTAAGACCCTGTCTGGGACA-TGGCATCGAT
*
52448333 AT-T-TGATTCGTGTAAGACCCTGTCCGGGACAGTGGCATCGAT
1 ATATGTGATTCGTGTAAGACCCTGTCTGGGACA-TGGCATCGAT
52448375 AT
1 AT
52448377 GAGATAGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
41 28 0.36
42 8 0.10
43 1 0.01
44 6 0.08
45 34 0.44
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
ATATGTGATTCGTGTAAGACCCTGTCTGGGACATGGCATCGAT
Found at i:52448759 original size:2 final size:2
Alignment explanation
Indices: 52448752--52448790 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
52448742 GACACTTTGA
52448752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52448791 ATAAATTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52452927 original size:5 final size:5
Alignment explanation
Indices: 52452917--52452995 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
52452907 TAAAAAATAT
* *
52452917 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
52452963 -A-TA TATTA TATTA TATTA TATATA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT
52452996 ATCAAAAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
3 4 0.06
4 4 0.06
5 32 0.51
6 22 0.35
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:52452969 original size:19 final size:19
Alignment explanation
Indices: 52452945--52452997 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
52452935 ATTATGTTTT
52452945 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
52452964 TATATTATATTATATTATA
1 TATATTATATTATATTATA
52452983 TATA-TATATATATAT
1 TATATTATAT-TATAT
52452998 CAAAAGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:52452984 original size:2 final size:2
Alignment explanation
Indices: 52452945--52452997 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
52452935 ATTATGTTTT
52452945 TA TA T- TA TA T- TA T- TA T- TA -A TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52452979 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
52452998 CAAAAGAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 8 0.19
2 35 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:52454556 original size:45 final size:45
Alignment explanation
Indices: 52454491--52454595 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
52454481 ATGTGCCGAC
* * * *
52454491 TACTGTTACTGTTACTGATTC-GATACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAATACTAT
*
52454536 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTAT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTAT
52454581 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
52454596 TGCTACCGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 53 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTAT
Found at i:52454949 original size:13 final size:15
Alignment explanation
Indices: 52454921--52454949 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52454911 CATTGTTGAG
52454921 AAATGAGAAATAAAA
1 AAATGAGAAATAAAA
52454936 AAATGA-AAATAAAA
1 AAATGAGAAATAAAA
52454950 TGATTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (15 bp):
AAATGAGAAATAAAA
Found at i:52462347 original size:21 final size:22
Alignment explanation
Indices: 52462316--52462356 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
52462306 GAGAAAGGGT
52462316 GAAAAGTAAAAAGTTTTGGGGG
1 GAAAAGTAAAAAGTTTTGGGGG
52462338 GAAAA-TAAAAAGTTTTGGG
1 GAAAAGTAAAAAGTTTTGGG
52462357 AAATAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (22 bp):
GAAAAGTAAAAAGTTTTGGGGG
Found at i:52462375 original size:18 final size:17
Alignment explanation
Indices: 52462340--52462382 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
52462330 TTTGGGGGGA
*
52462340 AAATAAAAAGTTTTGGG
1 AAATAAAAAGTTTAGGG
52462357 AAATAAAAAGTTTGAGGG
1 AAATAAAAAGTTT-AGGG
52462375 AAAGTAAA
1 AAA-TAAA
52462383 TAAAGGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.57
18 6 0.26
19 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (17 bp):
AAATAAAAAGTTTAGGG
Found at i:52475947 original size:9 final size:9
Alignment explanation
Indices: 52475930--52475985 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
52475920 AGTGCTACCC
52475930 CCACCACCA
1 CCACCACCA
*
52475939 CCCCCACCA
1 CCACCACCA
*
52475948 CCACCTCCA
1 CCACCACCA
* *
52475957 CCTCCACCT
1 CCACCACCA
*
52475966 CCACCACCG
1 CCACCACCA
*
52475975 CCACCGCCA
1 CCACCACCA
52475984 CC
1 CC
52475986 TCCTCCACCG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.21, C:0.70, G:0.04, T:0.05
Consensus pattern (9 bp):
CCACCACCA
Found at i:52475950 original size:15 final size:15
Alignment explanation
Indices: 52475926--52475985 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
52475916 CAGGAGTGCT
52475926 ACCCCCACCACCACC
1 ACCCCCACCACCACC
*
52475941 -CCCACCACCACCTCC
1 ACCC-CCACCACCACC
* *
52475956 ACCTCCACCTCCACC
1 ACCCCCACCACCACC
* *
52475971 ACCGCCACCGCCACC
1 ACCCCCACCACCACC
52475986 TCCTCCACCG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 3 0.08
15 32 0.86
16 2 0.05
ACGTcount: A:0.22, C:0.70, G:0.03, T:0.05
Consensus pattern (15 bp):
ACCCCCACCACCACC
Found at i:52475969 original size:21 final size:21
Alignment explanation
Indices: 52475945--52476013 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
52475935 ACCACCCCCA
*
52475945 CCACCACCTCCACCTCCACCT
1 CCACCACCGCCACCTCCACCT
*
52475966 CCACCACCGCCACCGCCACCT
1 CCACCACCGCCACCTCCACCT
* * *
52475987 CCTCCACCGCCGCCTCCGCCT
1 CCACCACCGCCACCTCCACCT
52476008 CCACCA
1 CCACCA
52476014 GAAGGTGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.16, C:0.67, G:0.07, T:0.10
Consensus pattern (21 bp):
CCACCACCGCCACCTCCACCT
Found at i:52475984 original size:12 final size:12
Alignment explanation
Indices: 52475930--52475994 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
52475920 AGTGCTACCC
*
52475930 CCACCACCACCC
1 CCACCACCACCT
52475942 CCACCACCACCT
1 CCACCACCACCT
*
52475954 CCACCTCCACCT
1 CCACCACCACCT
* *
52475966 CCACCACCGCCA
1 CCACCACCACCT
* *
52475978 CCGCCACCTCCT
1 CCACCACCACCT
52475990 CCACC
1 CCACC
52475995 GCCGCCTCCG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.20, C:0.69, G:0.03, T:0.08
Consensus pattern (12 bp):
CCACCACCACCT
Found at i:52475993 original size:15 final size:15
Alignment explanation
Indices: 52475957--52476003 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
52475947 ACCACCTCCA
* *
52475957 CCTCCACCTCCACCA
1 CCTCCACCGCCACCT
*
52475972 CCGCCACCGCCACCT
1 CCTCCACCGCCACCT
*
52475987 CCTCCACCGCCGCCT
1 CCTCCACCGCCACCT
52476002 CC
1 CC
52476004 GCCTCCACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.13, C:0.68, G:0.09, T:0.11
Consensus pattern (15 bp):
CCTCCACCGCCACCT
Found at i:52476007 original size:6 final size:6
Alignment explanation
Indices: 52475930--52476012 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
52475920 AGTGCTACCC
* * * * * *
52475930 CCACCA CCACCC CCACCA CCACCT CCACCT CCACCT CCACCA CCGCCA
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* * * * * *
52475978 CCGCCA CCTCCT CCACCG CCGCCT CCGCCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
52476013 AGAAGGTGGG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.17, C:0.69, G:0.06, T:0.08
Consensus pattern (6 bp):
CCACCT
Found at i:52476080 original size:16 final size:16
Alignment explanation
Indices: 52476041--52476080 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
52476031 AGAAGGTGGT
52476041 GGGTTT-GTAACAGGA
1 GGGTTTGGTAACAGGA
*
52476056 GGG-TTGGTAACGGGA
1 GGGTTTGGTAACAGGA
52476071 GGGTTTGGTA
1 GGGTTTGGTA
52476081 TTGGTGGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 14 0.64
16 6 0.27
ACGTcount: A:0.20, C:0.05, G:0.47, T:0.28
Consensus pattern (16 bp):
GGGTTTGGTAACAGGA
Found at i:52480089 original size:2 final size:2
Alignment explanation
Indices: 52480082--52480110 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
52480072 CACCAATAAT
52480082 CA CA CA CA CA CA CA CA CA CA CA CA C- CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
52480111 TTCTGATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:52491801 original size:30 final size:30
Alignment explanation
Indices: 52491762--52491820 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52491752 GGAGGTGGGA
*
52491762 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTA-GGGAAAAG
*
52491793 TGGG-AGGGAGTAAAAATTTTAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAA
52491821 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAG
Found at i:52498031 original size:12 final size:12
Alignment explanation
Indices: 52498014--52498048 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
52498004 TTGTTCATTT
*
52498014 ATTCATCAAGTC
1 ATTCATTAAGTC
52498026 ATTCATTAAGTC
1 ATTCATTAAGTC
52498038 ATTCATTAAGT
1 ATTCATTAAGT
52498049 GTTTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (12 bp):
ATTCATTAAGTC
Found at i:52498065 original size:29 final size:29
Alignment explanation
Indices: 52498027--52498107 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 29
52498017 CATCAAGTCA
* *
52498027 TTCATTAAGTCATTCATTAAGTGTTTTTT
1 TTCATCAAGTCATTCATCAAGTGTTTTTT
*
52498056 TTCATCAAGTCTTTCATCAAGTG---TTT
1 TTCATCAAGTCATTCATCAAGTGTTTTTT
* *
52498082 TTCATCAAGTTATTAATCAAGT-TTTT
1 TTCATCAAGTCATTCATCAAGTGTTTT
52498108 AATTACCAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
26 22 0.51
28 1 0.02
29 20 0.47
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.51
Consensus pattern (29 bp):
TTCATCAAGTCATTCATCAAGTGTTTTTT
Found at i:52498086 original size:14 final size:14
Alignment explanation
Indices: 52498053--52498091 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52498043 TTAAGTGTTT
52498053 TTTTTCATCAA--G
1 TTTTTCATCAAGTG
*
52498065 TCTTTCATCAAGTG
1 TTTTTCATCAAGTG
52498079 TTTTTCATCAAGT
1 TTTTTCATCAAGT
52498092 TATTAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (14 bp):
TTTTTCATCAAGTG
Found at i:52498183 original size:12 final size:11
Alignment explanation
Indices: 52498054--52498106 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 11
52498044 TAAGTGTTTT
52498054 TTTTCATCAAG
1 TTTTCATCAAG
52498065 TCTTTCATCAAGTG
1 T-TTTCATCAA--G
52498079 TTTTTCATCAAG
1 -TTTTCATCAAG
*
52498091 TTATTAATCAAG
1 TT-TTCATCAAG
52498103 TTTT
1 TTTT
52498107 TAATTACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 5 0.14
12 20 0.56
14 10 0.28
15 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (11 bp):
TTTTCATCAAG
Found at i:52502241 original size:14 final size:14
Alignment explanation
Indices: 52502196--52502243 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
52502186 TCTGCTTAAC
52502196 GAATAATGTTAAAA
1 GAATAATGTTAAAA
*
52502210 GTAA-AATGCTT-AAC
1 G-AATAATG-TTAAAA
52502224 GAATAATGTTAAAA
1 GAATAATGTTAAAA
52502238 GAATAA
1 GAATAA
52502244 AAAATGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.14
14 20 0.71
15 4 0.14
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (14 bp):
GAATAATGTTAAAA
Found at i:52511480 original size:41 final size:41
Alignment explanation
Indices: 52511419--52511509 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
52511409 TATATCTTAT
*
52511419 GTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGATATAAACCTAGCAGGCTAAGTGCCG
*
52511460 GTGATCTGAATCAGGATATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGATATAAACCTAGCAGGCTAAGTGCCG
52511501 GTGAATCTG
1 GTG-ATCTG
52511510 TTAAATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 42 0.89
42 5 0.11
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (41 bp):
GTGATCTGAATCAGGATATAAACCTAGCAGGCTAAGTGCCG
Found at i:52537603 original size:22 final size:22
Alignment explanation
Indices: 52537575--52537626 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
52537565 GCACTAATGG
*
52537575 ACAGAGAGAAC-TAAAGTGCTAT
1 ACAGAGAGAACAT-AAGTGCTAA
* *
52537597 ACAGAGAGCACATATGTGCTAA
1 ACAGAGAGAACATAAGTGCTAA
52537619 ACAGAGAG
1 ACAGAGAG
52537627 CAGTGACGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.15
Consensus pattern (22 bp):
ACAGAGAGAACATAAGTGCTAA
Found at i:52537637 original size:22 final size:22
Alignment explanation
Indices: 52537590--52537665 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
52537580 GAGAACTAAA
* *
52537590 GTGCTATACAGAGAGCACATAT
1 GTGCTAAACAGAGAGCACATAC
*
52537612 GTGCTAAACAGAGAGCA-GTGAC
1 GTGCTAAACAGAGAGCACAT-AC
52537634 GTGCTAGTAATCAGAGAGCACCA-AC
1 GTGCTA--AA-CAGAGAGCA-CATAC
52537659 GTGCTAA
1 GTGCTAA
52537666 TAATCAGAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
21 1 0.02
22 23 0.52
23 1 0.02
24 2 0.05
25 17 0.39
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACATAC
Found at i:52544101 original size:23 final size:23
Alignment explanation
Indices: 52544074--52544118 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52544064 GTAATTTTTA
52544074 TATATTATTTTA-AAATTTATAAT
1 TATA-TATTTTAGAAATTTATAAT
*
52544097 TATATATTTTAGAATTTTATAA
1 TATATATTTTAGAAATTTATAA
52544119 AAAAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATATTTTAGAAATTTATAAT
Found at i:52544306 original size:8 final size:8
Alignment explanation
Indices: 52544293--52544343 Score: 56
Period size: 8 Copynumber: 6.9 Consensus size: 8
52544283 TAAAAGTATT
52544293 TTTTAATA
1 TTTTAATA
52544301 TTTTAATA
1 TTTTAATA
*
52544309 -TTTCATA
1 TTTTAATA
*
52544316 TTATAAT-
1 TTTTAATA
52544323 TTTT--TA
1 TTTTAATA
52544329 TTTTAATA
1 TTTTAATA
52544337 TTTTAAT
1 TTTTAAT
52544344 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
5 1 0.03
6 4 0.11
7 9 0.26
8 21 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTAATA
Found at i:52544322 original size:15 final size:14
Alignment explanation
Indices: 52544298--52544348 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
52544288 GTATTTTTTA
52544298 ATATTTTAATATTT
1 ATATTTTAATATTT
*
52544312 CATATTATAAT-TTT
1 -ATATTTTAATATTT
*
52544326 TTATTTTAATATTT
1 ATATTTTAATATTT
52544340 -TAATTTTAA
1 AT-ATTTTAA
52544349 ATAAACTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 9 0.29
14 13 0.42
15 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTTAATATTT
Found at i:52544324 original size:21 final size:22
Alignment explanation
Indices: 52544300--52544348 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
52544290 ATTTTTTAAT
*
52544300 ATTTTAATA-TTTCATATTATA
1 ATTTTAATATTTTAATATTATA
* *
52544321 ATTTT-TTATTTTAATATTTTA
1 ATTTTAATATTTTAATATTATA
52544342 ATTTTAA
1 ATTTTAA
52544349 ATAAACTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTAATATTTTAATATTATA
Found at i:52548379 original size:6 final size:6
Alignment explanation
Indices: 52548368--52548402 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
52548358 ACAATATTTT
*
52548368 TTAAAA TTAAAA TTAAAA TGAAAA TTAAATA TTAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAA-A TTAA
52548403 TTTAATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (6 bp):
TTAAAA
Found at i:52556757 original size:3 final size:3
Alignment explanation
Indices: 52556749--52556815 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
52556739 ATTAATCTTG
52556749 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52556797 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
52556816 TACTCATTAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52556981 original size:38 final size:36
Alignment explanation
Indices: 52556910--52556987 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 36
52556900 ATAGATTTTT
* *
52556910 TTTTATTAATTTTATTTATTTTCGTTATTATTATTG
1 TTTTATTAATTTTATTTATTTTCGTTATCATTATTA
52556946 TTTTATTTAATATTTATTTATTTAT-GTGT-TCATTATTA
1 TTTTA-TTAAT-TTTATTTATTT-TCGT-TATCATTATTA
52556984 TTTT
1 TTTT
52556988 GAAAAACGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
36 5 0.14
37 5 0.14
38 24 0.67
39 2 0.06
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (36 bp):
TTTTATTAATTTTATTTATTTTCGTTATCATTATTA
Found at i:52562156 original size:43 final size:43
Alignment explanation
Indices: 52562050--52562247 Score: 274
Period size: 42 Copynumber: 4.6 Consensus size: 43
52562040 ACGTCGCTAA
* *
52562050 CTTTTGCGGCGCTTACAGAAAAAAATGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGCTTA-AGAAAAAAACGCCGCTAAAGAACATGTT
*
52562094 CTTTAGCGGCGCTT-AGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGAACATGTT
* * *
52562136 CTTTAGCGGCGCTT-GGGAAAAAACGCCGCTAAAGAACATGAT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGAACATGTT
* * *
52562178 CTTTAGCGGCGCTTAAGAAGAAAACGCCGCTAAATATCATGTT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGAACATGTT
* *
52562221 CTTTAGCGGCGCTTAGGAAGAAAACGC
1 CTTTAGCGGCGCTTAAGAAAAAAACGC
52562248 TGTTTACATA
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 78 0.56
43 48 0.35
44 13 0.09
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGAACATGTT
Found at i:52562222 original size:85 final size:84
Alignment explanation
Indices: 52562050--52562247 Score: 297
Period size: 85 Copynumber: 2.3 Consensus size: 84
52562040 ACGTCGCTAA
* * * *
52562050 CTTTTGCGGCGCTTACAGAAAAAAATGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAA
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAGAAAAA
52562115 AACGCCGCTAAAGATCATGTT
64 AACGCCGCTAAAGATCATGTT
* *
52562136 CTTTAGCGGCGCTTGGGAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAAGAAGAAA
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT-AGAAAAAA
*
52562201 ACGCCGCTAAATATCATGTT
65 ACGCCGCTAAAGATCATGTT
52562221 CTTTAGCGGCGCTTAGGAAGAAAACGC
1 CTTTAGCGGCGCTTAGGAA-AAAACGC
52562248 TGTTTACATA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
84 38 0.37
85 44 0.43
86 20 0.20
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (84 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTAGAAAAAAA
CGCCGCTAAAGATCATGTT
Found at i:52562444 original size:4 final size:4
Alignment explanation
Indices: 52562435--52562460 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
52562425 TCTCACATCT
52562435 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
52562461 GTATCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:52562470 original size:16 final size:16
Alignment explanation
Indices: 52562431--52562486 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
52562421 TAAATCTCAC
52562431 ATCTTTTATTTATT-T
1 ATCTTTTATTTATTGT
*
52562446 ATTTATTTATTTATTGT
1 ATCT-TTTATTTATTGT
*
52562463 ATCTTTTATTAATTGT
1 ATCTTTTATTTATTGT
52562479 ATCTTTTA
1 ATCTTTTA
52562487 ATTACTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.08
16 29 0.81
17 4 0.11
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (16 bp):
ATCTTTTATTTATTGT
Found at i:52563027 original size:22 final size:23
Alignment explanation
Indices: 52562989--52563031 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
52562979 CCCGTCAATT
52562989 AACCATTAAACATCAAACCACCA
1 AACCATTAAACATCAAACCACCA
52563012 AACCA-TAAA-ATCCAAACCAC
1 AACCATTAAACAT-CAAACCAC
52563032 AATATATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 12 0.63
23 5 0.26
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (23 bp):
AACCATTAAACATCAAACCACCA
Found at i:52563925 original size:114 final size:112
Alignment explanation
Indices: 52563569--52563925 Score: 285
Period size: 114 Copynumber: 3.1 Consensus size: 112
52563559 TATGTGAAGC
* * * * * *
52563569 CGAAACGATGCGTTTTGGTCAAATTTTTTGCGGCGCTTAAGAAGAAGCGCCACTAAAAGCTGATC
1 CGAAACGATGCGTTTTGTTCAAA-ATTTTGCGGCGATTGAGGA-AAGCGCCACTAAAAGCTGATA
* *
52563634 TATAGCGGCGTTTAT-GGGTAAGCGCCACTAAAGGCGCTGTAGCTCAAGA
64 TATAGCGGCGTTT-TCAGGTAAGCGCCACTAAAGGCGCTATAGCTCAAGA
* * * * * * * **
52563683 CGAAACGTTGAGTTTCGGTTTAAAATTTTTCGGCGTTTGTTAGTTAAA-CGCCACTATTTA--TG
1 CGAAACGATGCGTTT-TGTTCAAAATTTTGCGGCGATTG--AG-GAAAGCGCCACTA-AAAGCTG
** * * * **
52563745 GGATATAGCGGCGTTTTCTGGTAAGCGCCACTAATGCCTTTATA-CGTCAA-A
61 ATATATAGCGGCGTTTTCAGGTAAGCGCCACTAAAGGCGCTATAGC-TCAAGA
* * *
52563796 CCCAAACGATACGTTTTGTTCAAAATATTTGCGGCGATTGAGGAATAGCGCCACGAAAAGCTGAT
1 -CGAAACGATGCGTTTTGTTCAAAAT-TTTGCGGCGATTGAGGAA-AGCGCCACTAAAAGCTGAT
* **
52563861 ATATAGCGGCGTTTTCAGCTAAGCGCCGTTAAAGGCGCTATAGCTCAAGA
63 ATATAGCGGCGTTTTCAGGTAAGCGCCACTAAAGGCGCTATAGCTCAAGA
*
52563911 CGAAACGTTGCGTTT
1 CGAAACGATGCGTTT
52563926 CGGTTTCAAA
Statistics
Matches: 182, Mismatches: 46, Indels: 30
0.71 0.18 0.12
Matches are distributed among these distances:
111 2 0.01
112 4 0.02
113 18 0.10
114 137 0.75
115 15 0.08
116 5 0.03
117 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (112 bp):
CGAAACGATGCGTTTTGTTCAAAATTTTGCGGCGATTGAGGAAAGCGCCACTAAAAGCTGATATA
TAGCGGCGTTTTCAGGTAAGCGCCACTAAAGGCGCTATAGCTCAAGA
Found at i:52563982 original size:228 final size:228
Alignment explanation
Indices: 52563571--52563989 Score: 542
Period size: 228 Copynumber: 1.8 Consensus size: 228
52563561 TGTGAAGCCG
* * * * * *
52563571 AAACGATGCGTTTTGGTCAAATTTTTTGCGGCGCTTAAGAAGAAGCGCCACTAAAAGCTGATCTA
1 AAACGATACGTTTTGGTCAAAATATTTGCGGCGATTAAGAAGAAGCGCCACGAAAAGCTGATATA
* * *
52563636 TAGCGGCGTTTATGGGTAAGCGCCACTAAAGGCGCTGTAGCTCAAGACGAAACGTTGAGTTTCGG
66 TAGCGGCGTTTATAGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGAGTTTCGG
* * * *
52563701 TTTAAAATTTTTCGGCGTTTGTTAGTTAAACGCCACTATTTATGGGATATAGCGGCGTTTTCTGG
131 TTTAAAATGTTTCGGCATTTGTTAGTTAAACGCCACTATATACGGGATATAGCGGCGTTTTCTGG
52563766 TAAGCGCCACTAATGCCTTTATACGTCAAACCC
196 TAAGCGCCACTAATGCCTTTATACGTCAAACCC
* * *
52563799 AAACGATACGTTTTGTTCAAAATATTTGCGGCGATTGAGGAA-TAGCGCCACGAAAAGCTGATAT
1 AAACGATACGTTTTGGTCAAAATATTTGCGGCGATT-AAGAAGAAGCGCCACGAAAAGCTGATAT
** *
52563863 ATAGCGGCGTTT-TCAGCTAAGCGCCGTTAAAGGCGCTATAGCTCAAGACGAAACGTTGCGTTTC
65 ATAGCGGCGTTTAT-AGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGAGTTTC
* ** * *
52563927 GGTTTCAAAA-GTTTCGGCATTT-TTCGTTTACGCGCCGCTA-ATAGCGGGCTATAGCGGCGTTT
129 GGTTT-AAAATGTTTCGGCATTTGTTAG-TTAAACGCCACTATATA-CGGGATATAGCGGCGTTT
52563989 T
191 T
52563990 ACACAAGCGC
Statistics
Matches: 162, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
227 6 0.04
228 148 0.91
229 8 0.05
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (228 bp):
AAACGATACGTTTTGGTCAAAATATTTGCGGCGATTAAGAAGAAGCGCCACGAAAAGCTGATATA
TAGCGGCGTTTATAGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGAGTTTCGG
TTTAAAATGTTTCGGCATTTGTTAGTTAAACGCCACTATATACGGGATATAGCGGCGTTTTCTGG
TAAGCGCCACTAATGCCTTTATACGTCAAACCC
Found at i:52566796 original size:16 final size:18
Alignment explanation
Indices: 52566758--52566798 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
52566748 TTTGGGTTAC
52566758 ATAATATATTAGACCTAT
1 ATAATATATTAGACCTAT
* *
52566776 TTAATATATT-GAGCT-T
1 ATAATATATTAGACCTAT
52566792 ATAATAT
1 ATAATAT
52566799 TTTATTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (18 bp):
ATAATATATTAGACCTAT
Found at i:52566809 original size:14 final size:16
Alignment explanation
Indices: 52566792--52566823 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52566782 TATTGAGCTT
52566792 ATAAT-ATTTT-ATTA
1 ATAATAATTTTAATTA
52566806 ATAATAATTTTAATTA
1 ATAATAATTTTAATTA
52566822 AT
1 AT
52566824 TGATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATAATTTTAATTA
Found at i:52569762 original size:29 final size:30
Alignment explanation
Indices: 52569719--52569776 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
52569709 ATCTTAAAAC
*
52569719 TATATAATATAATATGTAA-AATTTAATTT
1 TATATAATATAATATATAATAATTTAATTT
*
52569748 TATATAAT-TACATATATAATATTTTAATT
1 TATATAATATA-ATATATAATAATTTAATT
52569777 AGACTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.60
30 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TATATAATATAATATATAATAATTTAATTT
Found at i:52569953 original size:31 final size:30
Alignment explanation
Indices: 52569875--52569954 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
52569865 AATTAAATTA
* *
52569875 AAATTAATGTTTTATACATATAATTAAAGT
1 AAATTAAAGTTTTATACATATAATTAAAGG
* * * **
52569905 AAAATAAAATATTTATACGTATAATTACTGG
1 AAATTAAAGT-TTTATACATATAATTAAAGG
52569936 AAATTAAAGTTTATATACA
1 AAATTAAAGTTT-TATACA
52569955 CACTGAACCA
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
30 9 0.24
31 29 0.76
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (30 bp):
AAATTAAAGTTTTATACATATAATTAAAGG
Found at i:52575270 original size:20 final size:19
Alignment explanation
Indices: 52575210--52575270 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
52575200 ATCAACAAAT
* *
52575210 AATTTAAAAATTATAAAAC
1 AATTCAAAAATTATAAAAA
* *
52575229 TATTCAAAAA-AATAAGAAAA
1 AATTCAAAAATTAT-A-AAAA
52575249 AATTCAAAAATTATAAAGAA
1 AATTCAAAAATTATAAA-AA
52575269 AA
1 AA
52575271 ATAACATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 17 0.53
21 2 0.06
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
AATTCAAAAATTATAAAAA
Found at i:52575410 original size:31 final size:31
Alignment explanation
Indices: 52575354--52575425 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
52575344 GTTTTTAAAA
* *
52575354 AAATTCAACTCTTTTTAAAAGATTGATAGTC
1 AAATTCAACTCTTTTTAAAACATTGAGAGTC
*
52575385 AAATTCGACT-TTTTTCAAAACATTGAGAGTC
1 AAATTCAACTCTTTTT-AAAACATTGAGAGTC
*
52575416 AAATTTAACT
1 AAATTCAACT
52575426 TGAAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 5 0.14
31 30 0.86
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (31 bp):
AAATTCAACTCTTTTTAAAACATTGAGAGTC
Found at i:52575531 original size:18 final size:18
Alignment explanation
Indices: 52575508--52575542 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52575498 AAATGTAATT
52575508 TATCAAATAAACTTTAAG
1 TATCAAATAAACTTTAAG
* *
52575526 TATCAAGTAATCTTTAA
1 TATCAAATAAACTTTAA
52575543 CCAAGAGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (18 bp):
TATCAAATAAACTTTAAG
Found at i:52575822 original size:19 final size:21
Alignment explanation
Indices: 52575789--52575830 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
52575779 ACCAATGACA
*
52575789 TTATCATTAAGAGTTT-TTTT
1 TTATCATTAACAGTTTCTTTT
52575809 TTAT-ATTAACAGTTTCTTTT
1 TTATCATTAACAGTTTCTTTT
52575829 TT
1 TT
52575831 TAAGTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (21 bp):
TTATCATTAACAGTTTCTTTT
Found at i:52584171 original size:14 final size:14
Alignment explanation
Indices: 52584136--52584182 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
52584126 TGTTCTTGCG
52584136 TTTTTA-TTTACTTT
1 TTTTTATTTTA-TTT
* *
52584150 CTTCTATTTTATTT
1 TTTTTATTTTATTT
52584164 TTTTTATTTTTATTT
1 TTTTTA-TTTTATTT
52584179 TTTT
1 TTTT
52584183 GTTTATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTATTT
Found at i:52584930 original size:3 final size:3
Alignment explanation
Indices: 52584922--52584997 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
52584912 TTTAGCAACT
52584922 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52584970 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52584998 AATCACATAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:52588623 original size:21 final size:21
Alignment explanation
Indices: 52588575--52588637 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
52588565 ATTAAAGTTC
52588575 ATTTATTTGTATTCTTTTTATGT
1 ATTTATTTGTATT-TTTTTAT-T
52588598 A--TATTTGTATTTTTTTATT
1 ATTTATTTGTATTTTTTTATT
* *
52588617 ATTTATTTATA-TATTTTATT
1 ATTTATTTGTATTTTTTTATT
52588637 A
1 A
52588638 CAAATTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 2 0.06
20 16 0.44
21 17 0.47
23 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.70
Consensus pattern (21 bp):
ATTTATTTGTATTTTTTTATT
Found at i:52590061 original size:14 final size:14
Alignment explanation
Indices: 52590042--52590069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52590032 TCCCTTCCTT
52590042 CCTTCTACCTTCTG
1 CCTTCTACCTTCTG
52590056 CCTTCTACCTTCTG
1 CCTTCTACCTTCTG
52590070 TCGATTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.43, G:0.07, T:0.43
Consensus pattern (14 bp):
CCTTCTACCTTCTG
Found at i:52590780 original size:17 final size:16
Alignment explanation
Indices: 52590760--52590791 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
52590750 CCGTTTTCAT
52590760 TTTCTTTTACTTTTATA
1 TTTCTTTT-CTTTTATA
52590777 TTTCTTTTCTTTTAT
1 TTTCTTTTCTTTTAT
52590792 TCATTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCTTTTCTTTTATA
Found at i:52593659 original size:18 final size:17
Alignment explanation
Indices: 52593637--52593770 Score: 93
Period size: 18 Copynumber: 8.0 Consensus size: 17
52593627 AATACTAAAA
52593637 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
52593654 ATTTTTGTTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
52593670 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
* * *
52593684 GTTTTAATTATATTTTAT
1 ATTTT-ATTAAATTATAT
* *
52593702 AATATTA-TATATTATA-
1 -ATTTTATTAAATTATAT
*
52593718 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
52593736 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
52593753 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
52593771 TTAATAATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
13 2 0.02
14 5 0.06
15 9 0.10
16 11 0.12
17 21 0.23
18 39 0.43
19 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:52593708 original size:15 final size:15
Alignment explanation
Indices: 52593690--52593719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52593680 AATTGTTTTA
*
52593690 ATTATATTTTATAAT
1 ATTATATATTATAAT
52593705 ATTATATATTATAAT
1 ATTATATATTATAAT
52593720 TTTAGTAAAT
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:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATATTATAAT
Found at i:52593990 original size:44 final size:45
Alignment explanation
Indices: 52593927--52594017 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 45
52593917 CTATTACACC
* *
52593927 TCCATTCCATTCAACCAAACACA-AGA-TTACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATTTACTATTACACCTCTAT
* *
52593971 TCCATTACATTCAACCAAACAATTGATTTGCTATTACACCTCTAT
1 TCCATTACATTCAACCAAACAATAGATTTACTATTACACCTCTAT
52594016 TC
1 TC
52594018 TAATACAGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.54
45 18 0.44
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATTTACTATTACACCTCTAT
Found at i:52608050 original size:11 final size:11
Alignment explanation
Indices: 52608036--52608078 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
52608026 ATTTTTTAAA
52608036 TTTTAAAATAT
1 TTTTAAAATAT
52608047 TTTTAAAATACTT
1 TTTTAAAATA--T
* *
52608060 TTTTTAAATTT
1 TTTTAAAATAT
52608071 TTTTAAAA
1 TTTTAAAA
52608079 AATTGGTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 18 0.67
13 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:52608540 original size:8 final size:9
Alignment explanation
Indices: 52608517--52608553 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
52608507 TTGGGTAATT
52608517 TTCGGGTAA
1 TTCGGGTAA
52608526 TTCGGGTAA
1 TTCGGGTAA
52608535 -TCGGGTAA
1 TTCGGGTAA
52608543 TTCGGGTAA
1 TTCGGGTAA
52608552 TT
1 TT
52608554 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.22, C:0.11, G:0.32, T:0.35
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:52608540 original size:17 final size:17
Alignment explanation
Indices: 52608518--52608552 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52608508 TGGGTAATTT
52608518 TCGGGTAATTCGGGTAA
1 TCGGGTAATTCGGGTAA
52608535 TCGGGTAATTCGGGTAA
1 TCGGGTAATTCGGGTAA
52608552 T
1 T
52608553 TTTTAACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.31
Consensus pattern (17 bp):
TCGGGTAATTCGGGTAA
Found at i:52612605 original size:29 final size:28
Alignment explanation
Indices: 52612572--52612634 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
52612562 GACAGAATAT
* *
52612572 AAGTTAAGTAACAACTAGGTACTAAAAAA
1 AAGTTAAGTAACAACTAAGTA-AAAAAAA
* *
52612601 AAGTTTAGGTATCAACTAAGTAAAAAAAA
1 AAG-TTAAGTAACAACTAAGTAAAAAAAA
52612630 AAGTT
1 AAGTT
52612635 CAGGTACCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.07
29 12 0.41
30 15 0.52
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (28 bp):
AAGTTAAGTAACAACTAAGTAAAAAAAA
Found at i:52612639 original size:29 final size:29
Alignment explanation
Indices: 52612595--52612651 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
52612585 ACTAGGTACT
* *
52612595 AAAAAAAAGTTTAGGTATCAACTAAGTAA
1 AAAAAAAAGTTCAGGTACCAACTAAGTAA
*
52612624 AAAAAAAAGTTCAGGTACCAATTAAGTA
1 AAAAAAAAGTTCAGGTACCAACTAAGTA
52612652 CTTTTAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (29 bp):
AAAAAAAAGTTCAGGTACCAACTAAGTAA
Found at i:52626068 original size:27 final size:28
Alignment explanation
Indices: 52626030--52626106 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
52626020 CCAGCCCGAC
*
52626030 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
52626057 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
52626084 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
52626107 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:52640069 original size:25 final size:25
Alignment explanation
Indices: 52640037--52640088 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
52640027 ATACGTTCTG
52640037 TGTGCATTTGTCACGAGTTTTAATC
1 TGTGCATTTGTCACGAGTTTTAATC
52640062 TGTGCATTTGTCACGAGTTTTAATC
1 TGTGCATTTGTCACGAGTTTTAATC
52640087 TG
1 TG
52640089 CAGATTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (25 bp):
TGTGCATTTGTCACGAGTTTTAATC
Found at i:52640423 original size:30 final size:30
Alignment explanation
Indices: 52640368--52640446 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
52640358 GTTGATGTGA
*
52640368 AGAGCTTAATTAATTTTCT--TTATTTTAGG
1 AGAGCTTAATTGATTTT-TAATTATTTTAGG
*
52640397 AGGGCTTAATTGATTTTTAATTATTTTAGG
1 AGAGCTTAATTGATTTTTAATTATTTTAGG
52640427 AGAGCTTAATTGATTTTTAA
1 AGAGCTTAATTGATTTTTAA
52640447 GGATTATATG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.02
29 15 0.33
30 29 0.64
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.49
Consensus pattern (30 bp):
AGAGCTTAATTGATTTTTAATTATTTTAGG
Found at i:52640752 original size:30 final size:30
Alignment explanation
Indices: 52640706--52640779 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
52640696 AAATAATGAT
* *
52640706 AAAA-AATTAGAAATGATAGAAAATTATATA
1 AAAATAATTA-AAATGATAAAAAAATATATA
*
52640736 AAAATAATTAAAATGATAAAAAAATCTATA
1 AAAATAATTAAAATGATAAAAAAATATATA
*
52640766 AAAATTAATAAAAA
1 AAAA-TAATTAAAA
52640780 GTTATAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 25 0.66
31 13 0.34
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (30 bp):
AAAATAATTAAAATGATAAAAAAATATATA
Found at i:52644615 original size:22 final size:22
Alignment explanation
Indices: 52644587--52644629 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
52644577 TAAAAATAGA
52644587 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
52644609 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
52644630 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:52644824 original size:24 final size:24
Alignment explanation
Indices: 52644774--52644825 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
52644764 AATCAAAATC
* * *
52644774 AAATATGTTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
52644798 AAATATATTATACTCATAAATATT
1 AAATATATTATACTAATAAATACT
52644822 AAAT
1 AAAT
52644826 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Done.