Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 283 of 438
Found at i:88576187 original size:54 final size:54
Alignment explanation
Indices: 88576101--88576222 Score: 174
Period size: 54 Copynumber: 2.3 Consensus size: 54
88576091 ATATATATAT
* *
88576101 ATATATCTGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCAC
1 ATATATCTGTTCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCAC
* * * * *
88576155 ATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTTCTGGTGACTTTGTCAC
1 ATATATCTGTTCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCAC
88576209 AT-TATCTGTTCTGG
1 ATATATCTGTTCTGG
88576223 CAACCATGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 12 0.20
54 49 0.80
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (54 bp):
ATATATCTGTTCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCAC
Found at i:88576372 original size:6 final size:6
Alignment explanation
Indices: 88576341--88576419 Score: 81
Period size: 6 Copynumber: 12.8 Consensus size: 6
88576331 TTGCATTCAC
* *
88576341 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
88576390 ATTCTG ATTCTG -TCACCTG ATTCTG ATTCT
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCT
88576420 AGTTTTGATG
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
5 3 0.05
6 50 0.82
7 6 0.10
8 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:88576443 original size:43 final size:43
Alignment explanation
Indices: 88576345--88576445 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
88576335 ATTCACATTC
* * **
88576345 TGATTTTGATTCTGTTACCTGATACTGATTCTGATTCTGATTC
1 TGATTCTGATTCTGTCACCTGATACTGATTCTGATTCTGATGA
* *
88576388 TGATTCTGATTCTGTCACCTGATTCTGATTCT-AGTTTTGATGA
1 TGATTCTGATTCTGTCACCTGATACTGATTCTGA-TTCTGATGA
* *
88576431 TGTTTCTTATTCTGT
1 TGATTCTGATTCTGT
88576446 AATGGGTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 48 0.98
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (43 bp):
TGATTCTGATTCTGTCACCTGATACTGATTCTGATTCTGATGA
Found at i:88578916 original size:46 final size:46
Alignment explanation
Indices: 88578848--88578984 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
88578838 TATATATACA
* ** * *
88578848 CATCTCATACATACCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
88578894 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
88578940 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
88578985 ATACATGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:88579018 original size:47 final size:47
Alignment explanation
Indices: 88578958--88579102 Score: 213
Period size: 47 Copynumber: 3.1 Consensus size: 47
88578948 ACACATTTCG
* **
88578958 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACATATACGCATGTTCACATTCATCA
88579005 CATTGGCCATTCGGCCTTATCGCACAT-T-CGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTA-C-CACATATACGCATGTTCACATTCATCA
* *
88579052 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTACCACATATACGCATGTTCACATTCATCA
88579099 CATT
1 CATT
88579103 AAAATCCTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
45 4 0.04
46 1 0.01
47 77 0.87
48 2 0.02
49 5 0.06
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTACCACATATACGCATGTTCACATTCATCA
Found at i:88579031 original size:24 final size:23
Alignment explanation
Indices: 88579003--88579078 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 23
88578993 TCACATTCAT
88579003 CACATTGGCCATTCGGCCTTATC
1 CACATTGGCCATTCGGCCTTATC
* * *
88579026 GCACATTCG-CATGTTC-ACATTCAT-
1 -CACATTGGCCA--TTCGGCCTT-ATC
88579050 CACATTGGCCATTCGGCCTTATC
1 CACATTGGCCATTCGGCCTTATC
88579073 ACACAT
1 -CACAT
88579079 ACGCATGTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 5 0.13
23 12 0.31
24 17 0.44
25 5 0.13
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.30
Consensus pattern (23 bp):
CACATTGGCCATTCGGCCTTATC
Found at i:88579055 original size:23 final size:23
Alignment explanation
Indices: 88579027--88579102 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
88579017 GGCCTTATCG
88579027 CACATTCGCATGTTCACATTCAT
1 CACATTCGCATGTTCACATTCAT
* * *
88579050 CACATTGGCCA--TTCGGCCTT-AT
1 CACATTCG-CATGTTC-ACATTCAT
*
88579072 CACACATACGCATGTTCACATTCAT
1 --CACATTCGCATGTTCACATTCAT
88579097 CACATT
1 CACATT
88579103 AAAATCCTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 5 0.13
23 17 0.45
24 11 0.29
25 5 0.13
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (23 bp):
CACATTCGCATGTTCACATTCAT
Found at i:88579075 original size:22 final size:22
Alignment explanation
Indices: 88579001--88579075 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
88578991 GTTCACATTC
88579001 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
88579023 ATCGCACATTCG-CATGTTC-ACATT
1 AT--CACATTGGCCA--TTCGGCCTT
88579047 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
88579070 ATCACA
1 ATCACA
88579076 CATACGCATG
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 11 0.28
23 12 0.30
24 12 0.30
25 5 0.12
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:88583310 original size:40 final size:40
Alignment explanation
Indices: 88583265--88583394 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
88583255 CGGAATACAA
88583265 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* * *
88583305 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
88583345 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
88583385 CCGGATATAA
1 CCGGATATAA
88583395 TTTCCAGCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 3 0.04
40 75 0.96
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:88591350 original size:81 final size:81
Alignment explanation
Indices: 88591232--88591651 Score: 535
Period size: 81 Copynumber: 5.2 Consensus size: 81
88591222 TTAGTTTACG
* * **
88591232 AAAA-TACCAAAATACCCTTTGTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTA-CTA
1 AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATC-A
* * * *
88591295 GAATACCCTTGGTTTAT
65 AAATACCCCTAGTTTGT
* *
88591312 AAAATCACCAAAATACCCCTGGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAA
1 AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAA
88591377 AATACCCCTAGTTTGT
66 AATACCCCTAGTTTGT
* * *
88591393 AAAATTACCAAAATACCCTTGGTTTGTAAAATCACCAAAATACCCCTGGTTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAA
*
88591458 AATACCCCTGGTTTGT
66 AATACCCCTAGTTTGT
* *
88591474 AAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAA
1 AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAA
88591539 AATACCCCTAGTTTGT
66 AATACCCCTAGTTTGT
* * ** ** **
88591555 AAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAAT--CCCTCGACTTGTAAAATTATTG
1 AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCT-GGTTTGTAAAATTATCA
* *
88591618 AAATA-CCCTCGACTTGT
65 AAATACCCCTAG-TTTGT
*
88591635 AAAATTACCAAAGTACC
1 AAAATTACCAAAATACC
88591652 ATTGATTTAT
Statistics
Matches: 303, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
79 9 0.03
80 42 0.14
81 251 0.83
82 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAA
AATACCCCTAGTTTGT
Found at i:88591595 original size:27 final size:27
Alignment explanation
Indices: 88591232--88591589 Score: 529
Period size: 27 Copynumber: 13.3 Consensus size: 27
88591222 TTAGTTTACG
* * **
88591232 AAAA-TACCAAAATACCCTTTGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
88591258 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * * *
88591285 AAAATTACTAGAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
88591312 AAAATCACCAAAATACCCCTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
88591339 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
88591366 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
88591393 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
88591420 AAAATCACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
88591447 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
88591474 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
88591501 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
88591528 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
88591555 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
88591582 GAAATTAC
1 AAAATTAC
88591590 TGAAATCCCT
Statistics
Matches: 299, Mismatches: 32, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
26 4 0.01
27 295 0.99
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:88591634 original size:27 final size:26
Alignment explanation
Indices: 88591258--88591651 Score: 286
Period size: 27 Copynumber: 14.7 Consensus size: 26
88591248 CTTTGTTTAC
**
88591258 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCC-GACTTGT
* * * ** *
88591285 AAAATTACTAGAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCC-CGACTTGT
* ** *
88591312 AAAATCACCAAAATACCCCTGGTTTAT
1 AAAATTACCAAAATACCCC-GACTTGT
**
88591339 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCC-GACTTGT
* * *
88591366 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCGA-CTTGT
* **
88591393 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCC-CGACTTGT
* **
88591420 AAAATCACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCC-GACTTGT
**
88591447 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCC-GACTTGT
* * *
88591474 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCGA-CTTGT
**
88591501 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCC-GACTTGT
* * *
88591528 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCGA-CTTGT
*
88591555 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCC-GACTTGT
* **
88591582 GAAATTACTGAAAT-CCCTCGACTTGT
1 AAAATTACCAAAATACCC-CGACTTGT
***
88591608 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCC-CGACTTGT
*
88591635 AAAATTACCAAAGTACC
1 AAAATTACCAAAATACC
88591652 ATTGATTTAT
Statistics
Matches: 315, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.07
27 293 0.93
28 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (26 bp):
AAAATTACCAAAATACCCCGACTTGT
Found at i:88591721 original size:27 final size:27
Alignment explanation
Indices: 88591698--88591986 Score: 389
Period size: 27 Copynumber: 10.7 Consensus size: 27
88591688 CAAAATTATT
*
88591698 GAAATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * *
88591725 AAAATACCCTTGTAGGGTAGAAATATC
1 GAAATACCCCTGTAGGGTAGAATTACC
88591752 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
88591779 GAAATACCCTTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
88591806 GAAATACCCCTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
88591833 GAAATACCCCTATAAGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
88591860 AAAATGCCCGTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
88591887 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
88591914 GAAATACCCCCGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
88591941 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
88591968 GAGATACCCTTGTGGGGTA
1 GAAATACCCCTGTAGGGTA
88591987 AAATAACCAT
Statistics
Matches: 227, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 227 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:88592004 original size:81 final size:81
Alignment explanation
Indices: 88591691--88591991 Score: 451
Period size: 81 Copynumber: 3.7 Consensus size: 81
88591681 CGATTTTCAA
* * * *
88591691 AATTATTGAAATACCCCTGTAGGGTAGAATTATCAAAATACCCTTGTAGGGTAGAAATATCGAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAA
88591756 TACCCCTGTAGGGTAG
66 TACCCCTGTAGGGTAG
* * * *
88591772 AATTACCGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACCGAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAA
* *
88591837 TACCCCTATAAGGTAG
66 TACCCCTGTAGGGTAG
* * *
88591853 AATTACTAAAATGCCCGTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAA
*
88591918 TACCCCCGTAGGGTAG
66 TACCCCTGTAGGGTAG
* *
88591934 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTGTGGGGTA-AAATA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATA
88591992 ACCATTTTAC
Statistics
Matches: 196, Mismatches: 24, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
80 5 0.03
81 191 0.97
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (81 bp):
AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAA
TACCCCTGTAGGGTAG
Found at i:88592263 original size:2 final size:2
Alignment explanation
Indices: 88592256--88592283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
88592246 GCTTCGCCAC
88592256 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
88592284 CTGTCCTGGT
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:88592319 original size:27 final size:26
Alignment explanation
Indices: 88592281--88592399 Score: 125
Period size: 27 Copynumber: 4.5 Consensus size: 26
88592271 TATATATATA
*
88592281 TATCTG-TCCTGGTGGCTATGCCACAAT
1 TATCTGAT-CTGGTGGCTCTGCCAC-AT
88592308 TATCTGATCTGGTGGCTCTGCCACAT
1 TATCTGATCTGGTGGCTCTGCCACAT
*
88592334 ATATCTGTTCTGGTGGCTCTGCCACGAT
1 -TATCTGATCTGGTGGCTCTGCCAC-AT
* * *
88592362 TATCT-ATTCTGGTGACTTTGTCACAT
1 TATCTGA-TCTGGTGGCTCTGCCACAT
*
88592388 TATCTGTTCTGG
1 TATCTGATCTGG
88592400 CAACCATGCT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.17
27 63 0.79
28 3 0.04
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.39
Consensus pattern (26 bp):
TATCTGATCTGGTGGCTCTGCCACAT
Found at i:88592347 original size:54 final size:54
Alignment explanation
Indices: 88592278--88592399 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
88592268 ATATATATAT
* *
88592278 ATATATCTGTCCTGGTGGCTATGCCACAATTATCTGA-TCTGGTGGCTCTGCCAC
1 ATATATCTGTTCTGGTGGCTATGCCACAATTATCT-ATTCTGGTGACTCTGCCAC
* * * *
88592332 ATATATCTGTTCTGGTGGCTCTGCCACGATTATCTATTCTGGTGACTTTGTCAC
1 ATATATCTGTTCTGGTGGCTATGCCACAATTATCTATTCTGGTGACTCTGCCAC
88592386 AT-TATCTGTTCTGG
1 ATATATCTGTTCTGG
88592400 CAACCATGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
53 13 0.21
54 48 0.79
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (54 bp):
ATATATCTGTTCTGGTGGCTATGCCACAATTATCTATTCTGGTGACTCTGCCAC
Found at i:88592549 original size:6 final size:6
Alignment explanation
Indices: 88592518--88592596 Score: 72
Period size: 6 Copynumber: 12.8 Consensus size: 6
88592508 TTGCATTCAC
* *
88592518 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
88592567 -TCACCTG ATTTTG ATTCTG ATTCTG ATTCT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCT
88592597 AGTTTTGATG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 3 0.05
6 48 0.81
7 6 0.10
8 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:88592549 original size:25 final size:25
Alignment explanation
Indices: 88592521--88592591 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
88592511 CATTCACATT
88592521 CTGATTTTGATTCTG-TTACCTGAT-A-
1 CTGATTTTGATTCTGATT--CTG-TCAC
*
88592546 CTGATTCTGATTCTGATTCTGTCAC
1 CTGATTTTGATTCTGATTCTGTCAC
88592571 CTGATTTTGATTCTGATTCTG
1 CTGATTTTGATTCTGATTCTG
88592592 ATTCTAGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.02
24 4 0.10
25 34 0.83
26 2 0.05
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (25 bp):
CTGATTTTGATTCTGATTCTGTCAC
Found at i:88592553 original size:31 final size:31
Alignment explanation
Indices: 88592518--88592596 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
88592508 TTGCATTCAC
* *
88592518 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
**
88592549 ATTCTGATTCTGATTCTGTCACCTGATTTTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
88592580 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
88592597 AGTTTTGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:88596909 original size:15 final size:15
Alignment explanation
Indices: 88596889--88596918 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88596879 AACCTATGAG
88596889 TATTTGCACAATTTC
1 TATTTGCACAATTTC
*
88596904 TATTTGTACAATTTC
1 TATTTGCACAATTTC
88596919 AATCCATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (15 bp):
TATTTGCACAATTTC
Found at i:88597235 original size:30 final size:29
Alignment explanation
Indices: 88597192--88597255 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
88597182 CAAGTAGCCG
*
88597192 AAGCTAGTTAAATCGCACACTTAGTACCA
1 AAGCTAGTTAAATCGCACACTTAATACCA
88597221 AAGCTAGTTTAAATCGCACACTTAATACCA
1 AAGCTAG-TTAAATCGCACACTTAATACCA
88597251 AAGCT
1 AAGCT
88597256 TTCGATTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (29 bp):
AAGCTAGTTAAATCGCACACTTAATACCA
Found at i:88601935 original size:40 final size:40
Alignment explanation
Indices: 88601773--88601928 Score: 226
Period size: 40 Copynumber: 3.9 Consensus size: 40
88601763 TATTCGGATG
88601773 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
88601813 A-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
88601853 A-AATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT
1 ATAA-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
88601893 ATAACCGGGCTATGTCCCAAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
88601929 AGCTATATCC
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 101 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:88604397 original size:22 final size:22
Alignment explanation
Indices: 88604370--88604414 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
88604360 GAGTTGAACA
88604370 AATTATTTAATTCTATTCTTAC
1 AATTATTTAATTCTATTCTTAC
88604392 AATTATTTAATTCTATTCTTAC
1 AATTATTTAATTCTATTCTTAC
88604414 A
1 A
88604415 TTTTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTATTTAATTCTATTCTTAC
Found at i:88611305 original size:2 final size:2
Alignment explanation
Indices: 88611298--88611323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
88611288 CGGTTCTTGC
88611298 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
88611324 GTTTGCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88612068 original size:40 final size:40
Alignment explanation
Indices: 88612012--88612111 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
88612002 GAATGATACC
* * * *
88612012 CGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATATA
1 CGGGCTAAGACCCGAAGGCATTCATACGAGTTG-TTATATA
* * *
88612052 TGGGCTAAGACCCGAAGGCATTCGTACGAGTTGTTATATC
1 CGGGCTAAGACCCGAAGGCATTCATACGAGTTGTTATATA
88612092 CGGGCTAAGACCCGAAGGCA
1 CGGGCTAAGACCCGAAGGCA
88612112 ATTGTGCAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 49 0.96
41 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCATTCATACGAGTTGTTATATA
Found at i:88612133 original size:40 final size:40
Alignment explanation
Indices: 88612053--88612158 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
88612043 GATTATATAT
* * *** *
88612053 GGGCTAAGACCCGAAGGC-ATTCGTACGAGTTGTTATATCC
1 GGGCTAAGACCCGAAGGCAATT-GTGCAAGTTACCAAATCC
88612093 GGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAATCC
1 GGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAATCC
*
88612133 GGGTTAAGACCCGAAGGCAATTGTGC
1 GGGCTAAGACCCGAAGGCAATTGTGC
88612159 TTGTGTTATA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 55 0.95
41 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (40 bp):
GGGCTAAGACCCGAAGGCAATTGTGCAAGTTACCAAATCC
Found at i:88620056 original size:40 final size:40
Alignment explanation
Indices: 88620001--88620204 Score: 205
Period size: 40 Copynumber: 5.1 Consensus size: 40
88619991 TGAATGATAC
* * * *
88620001 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
*
88620041 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGATTATAT
* * ** *
88620081 CCGGGCTAAGACCCGAAGGTAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
* * ** *
88620121 CCGGGTTAAGACCCGAAGGCAATTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
* ** *
88620161 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
88620201 CCGG
1 CCGG
88620205 TTAAATCCCG
Statistics
Matches: 141, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 3 0.02
40 133 0.94
41 5 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGATTATAT
Found at i:88620203 original size:80 final size:80
Alignment explanation
Indices: 88620001--88620218 Score: 235
Period size: 80 Copynumber: 2.7 Consensus size: 80
88619991 TGAATGATAC
* * * *
88620001 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCATTCG
* *** *
88620066 TGCGAGTTGTTATAT
66 TGCAAGTTACCAAAT
* * * ** *
88620081 CCGGGCTAAGACCCGAAGGTAATTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGACCCGAAGGC-ATTC
88620145 GTGCAAGTTACCAAAT
65 GTGCAAGTTACCAAAT
* * *
88620161 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGTTAA-ATCCCGAAGG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGA-CCCGAAGG
88620219 TACGTGATTC
Statistics
Matches: 112, Mismatches: 24, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
78 1 0.01
79 14 0.12
80 94 0.84
81 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATATCCGGGTTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAAT
Found at i:88624664 original size:27 final size:27
Alignment explanation
Indices: 88624629--88624719 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
88624619 AAAATTACCC
*
88624629 AATATCCTCGATTTGTAAAATTATCGA
1 AATACCCTCGATTTGTAAAATTATCGA
* *
88624656 AATACCCTC-AGTTTGCAAAATTATTGA
1 AATACCCTCGA-TTTGTAAAATTATCGA
**
88624683 AATACCCTCGACATGTAAAATTATC-A
1 AATACCCTCGATTTGTAAAATTATCGA
88624709 AAGTA-CCTCGA
1 AA-TACCCTCGA
88624720 ATTACAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
26 10 0.19
27 43 0.80
28 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AATACCCTCGATTTGTAAAATTATCGA
Found at i:88624742 original size:27 final size:27
Alignment explanation
Indices: 88624714--88625013 Score: 336
Period size: 27 Copynumber: 11.1 Consensus size: 27
88624704 TATCAAAGTA
* *
88624714 CCTCGAATTACAAAAATTACTATTTTAC
1 CCTCGATTTAC-AAAATTACTGTTTTAC
* *
88624742 CCTCGATTTACAGAATTACTATTTTAC
1 CCTCGATTTACAAAATTACTGTTTTAC
* * *
88624769 CCTCGATTTATAGAATTATTGTTTTAC
1 CCTCGATTTACAAAATTACTGTTTTAC
* *
88624796 CCTCGATTTATAGAATTA-TCGTTTTA-
1 CCTCGATTTACAAAATTACT-GTTTTAC
* * *
88624822 CCTCGAATTACAAAAATTATTATTTTAC
1 CCTCGATTTAC-AAAATTACTGTTTTAC
*
88624850 CCTCGATTTACAGAATTACTGTTTTAC
1 CCTCGATTTACAAAATTACTGTTTTAC
* * *
88624877 CCTCGATTTATAAAATTGGC-ATTTTAC
1 CCTCGATTTACAAAATT-ACTGTTTTAC
* *
88624904 CCTCGATTTACAAAATTACCGTTTGAC
1 CCTCGATTTACAAAATTACTGTTTTAC
88624931 CCTCGATTTACAAAATTACTGTTTTAC
1 CCTCGATTTACAAAATTACTGTTTTAC
* *
88624958 CCTCGATTTACAGAATTACCGTTTTAC
1 CCTCGATTTACAAAATTACTGTTTTAC
* **
88624985 CCTCGGTTTACAAAATTACCATTTTAC
1 CCTCGATTTACAAAATTACTGTTTTAC
88625012 CC
1 CC
88625014 CTAGGGTGTT
Statistics
Matches: 238, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
26 11 0.05
27 205 0.86
28 22 0.09
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
CCTCGATTTACAAAATTACTGTTTTAC
Found at i:88624787 original size:108 final size:108
Alignment explanation
Indices: 88624672--88625002 Score: 330
Period size: 108 Copynumber: 3.1 Consensus size: 108
88624662 CTCAGTTTGC
*
88624672 AAAATTATTGAAATACCCTCGACATGTAAAATTATCAAAGTACCTCGAATTACAAAAATTACTAT
1 AAAATTATTGAAATACCCTCGACATATAAAATTATCAAAGTACCTCGAATTACAAAAATTACTAT
88624737 TTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTAT
66 TTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTAT
* *** ** * **** *
88624780 AGAATTATTGTTTTACCCTCGATTTATAGAATTATCGTTTTACCTCGAATTACAAAAATTATTAT
1 AAAATTATTGAAATACCCTCGACATATAAAATTATCAAAGTACCTCGAATTACAAAAATTACTAT
*
88624845 TTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTAT
66 TTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTAT
* ** * **** *
88624888 AAAATTGGCATT---TTACCCTCGATTTACAAAATTA-CCGTTTGACCCTCGATTTAC-AAAATT
1 AAAATT---ATTGAAATACCCTCGACATATAAAATTATCAAAGT-A-CCTCGAATTACAAAAATT
* ** * *
88624948 ACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGGTTTAC
61 ACTATTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTAT
88624996 AAAATTA
1 AAAATTA
88625003 CCATTTTACC
Statistics
Matches: 193, Mismatches: 25, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
105 1 0.01
107 4 0.02
108 175 0.91
109 10 0.05
111 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (108 bp):
AAAATTATTGAAATACCCTCGACATATAAAATTATCAAAGTACCTCGAATTACAAAAATTACTAT
TTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTAT
Found at i:88624813 original size:81 final size:81
Alignment explanation
Indices: 88624728--88625013 Score: 371
Period size: 81 Copynumber: 3.5 Consensus size: 81
88624718 GAATTACAAA
* * * *
88624728 AATTACTATTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTATAGAATTATTGTTT
1 AATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACTGTTT
88624793 TACCCTCGATTTATAG
66 TACCCTCGATTTATAG
* * **
88624809 AATTA-TCGTTTTA-CCTCGAATTACAAAAATTATTATTTTACCCTCGATTTACAGAATTACTGT
1 AATTACT-ATTTTACCCTCGATTTAC-AAAATTACCATTTTACCCTCGATTTACAGAATTACTGT
*
88624872 TTTACCCTCGATTTATAA
64 TTTACCCTCGATTTATAG
* * * *
88624890 AATTGGC-ATTTTACCCTCGATTTACAAAATTACCGTTTGACCCTCGATTTACAAAATTACTGTT
1 AATT-ACTATTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACTGTT
*
88624954 TTACCCTCGATTTACAG
65 TTACCCTCGATTTATAG
** *
88624971 AATTACCGTTTTACCCTCGGTTTACAAAATTACCATTTTACCC
1 AATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACCC
88625014 CTAGGGTGTT
Statistics
Matches: 177, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
80 12 0.07
81 155 0.88
82 10 0.06
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (81 bp):
AATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAGAATTACTGTTT
TACCCTCGATTTATAG
Found at i:88625008 original size:108 final size:108
Alignment explanation
Indices: 88624713--88625013 Score: 433
Period size: 108 Copynumber: 2.8 Consensus size: 108
88624703 TTATCAAAGT
*
88624713 ACCTCGAATTACAAAAATTACTATTTTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTT
1 ACCTCGAATTACAAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTT
* *** * * * *
88624778 ATAGAATTATTGTTTTACCCTCGATTTATAGAATTATCGTTTT
66 ATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTG
*
88624821 ACCTCGAATTACAAAAATTATTATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTT
1 ACCTCGAATTACAAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTT
**
88624886 ATAAAATTGGCATTTTACCCTCGATTTACAAAATTACCGTTTG
66 ATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTG
* * * *
88624929 ACCCTCGATTTAC-AAAATTACTGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGGTT
1 A-CCTCGAATTACAAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATT
*
88624993 TACAAAATTACCATTTTACCC
65 TATAAAATTACCATTTTACCC
88625014 CTAGGGTGTT
Statistics
Matches: 173, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
108 163 0.94
109 10 0.06
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (108 bp):
ACCTCGAATTACAAAAATTACTATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTT
ATAAAATTACCATTTTACCCTCGATTTACAAAATTACCGTTTG
Found at i:88625369 original size:26 final size:27
Alignment explanation
Indices: 88625340--88625399 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
88625330 TTACATATAT
*
88625340 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
88625366 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
88625393 ATATCTG
1 ATATCTG
88625400 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:88625549 original size:25 final size:25
Alignment explanation
Indices: 88625521--88625607 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 25
88625511 CATTCACATT
88625521 CTGATTTTAATTCTGTTACCTGATA
1 CTGATTTTAATTCTGTTACCTGATA
* * *
88625546 CTGATTCTGATTCTAATTCTGTCACCTAATT
1 CTGA---T--TT-TAATTCTGTTACCTGATA
* *
88625577 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTTTAATTCTGTTACCTGATA
88625602 CTGATT
1 CTGATT
88625608 CTGATTCTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
25 24 0.50
26 1 0.02
28 2 0.04
30 2 0.04
31 19 0.40
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (25 bp):
CTGATTTTAATTCTGTTACCTGATA
Found at i:88625553 original size:31 final size:31
Alignment explanation
Indices: 88625518--88625653 Score: 149
Period size: 31 Copynumber: 4.6 Consensus size: 31
88625508 TTGCATTCAC
* *
88625518 ATTCTGATTTTAATTCTGTTACCTGATACTG
1 ATTCTGATTCTAATTCTGTCACCTGATACTG
88625549 ATTCTGATTCTAATTCTGTCACC---TA---
1 ATTCTGATTCTAATTCTGTCACCTGATACTG
* *
88625574 ATTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTAATTCTGTCACCTGATACTG
* *
88625605 ATTCTGATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTAATTCTGTCACCTGATACTG
* * *
88625636 ATCCTGATTATGATTCTG
1 ATTCTGATTCTAATTCTG
88625654 ATTCTGTAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
25 21 0.24
28 4 0.05
31 63 0.72
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTCTGATTCTAATTCTGTCACCTGATACTG
Found at i:88625555 original size:6 final size:6
Alignment explanation
Indices: 88625518--88625659 Score: 76
Period size: 6 Copynumber: 23.0 Consensus size: 6
88625508 TTGCATTCAC
* * * *
88625518 ATTCTG ATTTTA ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
88625567 -TCACCTA ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * * *
88625617 ATTCTG -TCACCTA ATTCTG ATCCTG ATTATG ATTCTG ATTCTG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
88625660 TAATGGGCTA
Statistics
Matches: 100, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
5 6 0.06
6 80 0.80
7 10 0.10
8 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (6 bp):
ATTCTG
Found at i:88625604 original size:56 final size:56
Alignment explanation
Indices: 88625518--88625644 Score: 227
Period size: 56 Copynumber: 2.3 Consensus size: 56
88625508 TTGCATTCAC
* *
88625518 ATTCTGATTTTAATTCTGTTACCTGATACTGATTCTGATTCTAATTCTGTCACCTA
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTAATTCTGTCACCTA
88625574 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTAATTCTGTCACCTA
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTAATTCTGTCACCTA
*
88625630 ATTCTGATCCTGATT
1 ATTCTGATTCTGATT
88625645 ATGATTCTGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (56 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTAATTCTGTCACCTA
Found at i:88625633 original size:25 final size:25
Alignment explanation
Indices: 88625549--88625637 Score: 106
Period size: 25 Copynumber: 3.3 Consensus size: 25
88625539 CCTGATACTG
88625549 ATTCTGATTCTAATTCTGTCACCTA
1 ATTCTGATTCTAATTCTGTCACCTA
* *
88625574 ATTCTGATTCTGATTCTGTTACCTGATA
1 ATTCTGATTCTAATTCTGTCACC---TA
88625602 CTGATTCTGATTCTAATTCTGTCACCTA
1 ---ATTCTGATTCTAATTCTGTCACCTA
88625630 ATTCTGAT
1 ATTCTGAT
88625638 CCTGATTATG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
25 29 0.54
28 4 0.07
31 21 0.39
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (25 bp):
ATTCTGATTCTAATTCTGTCACCTA
Found at i:88631140 original size:25 final size:25
Alignment explanation
Indices: 88631111--88631275 Score: 267
Period size: 25 Copynumber: 6.6 Consensus size: 25
88631101 TGATAAATCA
*
88631111 CTCTTAATAATTCCGGTTAAATTTG
1 CTCTTAATATTTCCGGTTAAATTTG
*
88631136 CTCTTAATATTTCCGGTAAAATTTG
1 CTCTTAATATTTCCGGTTAAATTTG
*
88631161 CTCTTAATAATTCCGGTTAAATTTG
1 CTCTTAATATTTCCGGTTAAATTTG
*
88631186 CTCTTAATATTTCCGGTAAAATTTG
1 CTCTTAATATTTCCGGTTAAATTTG
*
88631211 CTCTTAATAATTCCGGTTAAATTTG
1 CTCTTAATATTTCCGGTTAAATTTG
88631236 CTCTTAATATTTCCGGTTAAATTTG
1 CTCTTAATATTTCCGGTTAAATTTG
* *
88631261 CCCTTATTATTTCCG
1 CTCTTAATATTTCCG
88631276 AATAAGTTAC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 129 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (25 bp):
CTCTTAATATTTCCGGTTAAATTTG
Found at i:88631186 original size:50 final size:50
Alignment explanation
Indices: 88631111--88631275 Score: 294
Period size: 50 Copynumber: 3.3 Consensus size: 50
88631101 TGATAAATCA
88631111 CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAAAATTTG
1 CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAAAATTTG
88631161 CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAAAATTTG
1 CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAAAATTTG
*
88631211 CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTTAAATTTG
1 CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAAAATTTG
* * *
88631261 CCCTTATTATTTCCG
1 CTCTTAATAATTCCG
88631276 AATAAGTTAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (50 bp):
CTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAAAATTTG
Found at i:88633141 original size:25 final size:25
Alignment explanation
Indices: 88633111--88633325 Score: 274
Period size: 25 Copynumber: 8.6 Consensus size: 25
88633101 TTGATAAATC
*
88633111 GCTCTTAATAATTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
* *
88633136 TCTCTTAATATTTCCGGTAAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
*
88633161 GCTCTTAATAATTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
*
88633186 GCTCTT-A-ATTT-CAGTAATAAATTT
1 GCTCTTAATATTTCCGGT--TAAATTT
* ** *
88633210 TCTCTTAATATTTTTGGTAAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
*
88633235 GCTCTTAATAATTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
*
88633260 GCTCTTCATATTTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
88633285 GCTCTTAATATTTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
* *
88633310 GCCCTTATTATTTCCG
1 GCTCTTAATATTTCCG
88633326 AATAAGTTAC
Statistics
Matches: 163, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.02
23 3 0.02
24 13 0.08
25 138 0.85
26 4 0.02
27 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (25 bp):
GCTCTTAATATTTCCGGTTAAATTT
Found at i:88633229 original size:74 final size:75
Alignment explanation
Indices: 88633111--88633325 Score: 292
Period size: 74 Copynumber: 2.9 Consensus size: 75
88633101 TTGATAAATC
* * *
88633111 GCTCTTAATAATTCCGGTTAAATTTTCTCTTAATATTTCCGGTAAAATTTGCTCTTAATAATTCC
1 GCTCTTCATATTTCCAGTTAAATTTTCTCTTAATATTTCCGGTAAAATTTGCTCTTAATAATTCC
88633176 GGTTAAATTT
66 GGTTAAATTT
**
88633186 GCTCTT-A-ATTT-CAGTAATAAATTTTCTCTTAATATTTTTGGTAAAATTTGCTCTTAATAATT
1 GCTCTTCATATTTCCAGT--TAAATTTTCTCTTAATATTTCCGGTAAAATTTGCTCTTAATAATT
88633248 CCGGTTAAATTT
64 CCGGTTAAATTT
* * * * * *
88633260 GCTCTTCATATTTCCGGTTAAATTTGCTCTTAATATTTCCGGTTAAATTTGCCCTTATTATTTCC
1 GCTCTTCATATTTCCAGTTAAATTTTCTCTTAATATTTCCGGTAAAATTTGCTCTTAATAATTCC
88633325 G
66 G
88633326 AATAAGTTAC
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
72 3 0.02
73 3 0.02
74 62 0.50
75 48 0.39
76 4 0.03
77 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (75 bp):
GCTCTTCATATTTCCAGTTAAATTTTCTCTTAATATTTCCGGTAAAATTTGCTCTTAATAATTCC
GGTTAAATTT
Found at i:88633283 original size:99 final size:99
Alignment explanation
Indices: 88633112--88633293 Score: 283
Period size: 99 Copynumber: 1.8 Consensus size: 99
88633102 TGATAAATCG
* * *
88633112 CTCTTAATAATTCCGGTTAAATTTTCTCTTAATATTTCCGGTAAAATTTGCTCTTAATAATTCCG
1 CTCTTAATAATTCCGGTAAAATTTGCTCTTAATAATTCCGGTAAAATTTGCTCTTAATAATTCCG
88633177 GTTAAATTTGCTCTTAATTTCAGTAATAAATTTT
66 GTTAAATTTGCTCTTAATTTCAGTAATAAATTTT
* ** * * *
88633211 CTCTTAATATTTTTGGTAAAATTTGCTCTTAATAATTCCGGTTAAATTTGCTCTTCATATTTCCG
1 CTCTTAATAATTCCGGTAAAATTTGCTCTTAATAATTCCGGTAAAATTTGCTCTTAATAATTCCG
88633276 GTTAAATTTGCTCTTAAT
66 GTTAAATTTGCTCTTAAT
88633294 ATTTCCGGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 74 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.47
Consensus pattern (99 bp):
CTCTTAATAATTCCGGTAAAATTTGCTCTTAATAATTCCGGTAAAATTTGCTCTTAATAATTCCG
GTTAAATTTGCTCTTAATTTCAGTAATAAATTTT
Found at i:88635189 original size:25 final size:25
Alignment explanation
Indices: 88635160--88635277 Score: 182
Period size: 25 Copynumber: 4.6 Consensus size: 25
88635150 TTGATAAATC
*
88635160 GCTCTTAATAATTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
88635185 GCTCTTAATATTTCCGGTAATAAATTT
1 GCTCTTAATATTTCCGGT--TAAATTT
*
88635212 TCTCTTAATATTTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
88635237 GCTCTTAATATTTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTT
* *
88635262 GCCCTTATTATTTCCG
1 GCTCTTAATATTTCCG
88635278 AATAAGTTAC
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
25 62 0.72
27 24 0.28
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (25 bp):
GCTCTTAATATTTCCGGTTAAATTT
Found at i:88635230 original size:52 final size:50
Alignment explanation
Indices: 88635160--88635277 Score: 182
Period size: 52 Copynumber: 2.3 Consensus size: 50
88635150 TTGATAAATC
*
88635160 GCTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCCGGTAATAAATTT
1 GCTCTTAATATTTCCGGTTAAATTTGCTCTTAATATTTCCGGT--TAAATTT
*
88635212 TCTCTTAATATTTCCGGTTAAATTTGCTCTTAATATTTCCGGTTAAATTT
1 GCTCTTAATATTTCCGGTTAAATTTGCTCTTAATATTTCCGGTTAAATTT
* *
88635262 GCCCTTATTATTTCCG
1 GCTCTTAATATTTCCG
88635278 AATAAGTTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 20 0.33
52 41 0.67
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (50 bp):
GCTCTTAATATTTCCGGTTAAATTTGCTCTTAATATTTCCGGTTAAATTT
Found at i:88636168 original size:45 final size:45
Alignment explanation
Indices: 88636104--88636369 Score: 396
Period size: 45 Copynumber: 6.0 Consensus size: 45
88636094 ATATCGTACA
* *
88636104 ATACTATTCGAGTCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
88636149 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
* *
88636194 ATACTATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAT
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
* * * *
88636239 ATACTATTCGGGCCTATGACCCTAGTAGGCTATAATGCCGGTGAG
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
* *
88636284 ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAA
1 ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
*
88636329 ATGA-TA-TCGGG-CTTTGAGCCTAGCAGGCGA-AATGCCGGTGA
1 AT-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
88636370 ATGAATTCAG
Statistics
Matches: 203, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
42 11 0.05
43 17 0.08
44 5 0.02
45 169 0.83
46 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (45 bp):
ATACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAT
Found at i:88636392 original size:41 final size:41
Alignment explanation
Indices: 88636304--88636410 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
88636294 GGCCTTCGAG
* * * *
88636304 CCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTTGAG
1 CCTAGCAGGCGA-AATGCCGGTG-AATGATATCAGGCTTTAAA
88636347 CCTAGCAGGCGAAATGCCGGTGAATGA-ATTCAGG-TTTAAAA
1 CCTAGCAGGCGAAATGCCGGTGAATGATA-TCAGGCTTT-AAA
88636388 CCTAGCAGGCTG-AATGCCGGTGA
1 CCTAGCAGGC-GAAATGCCGGTGA
88636411 TTTGATAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
40 4 0.07
41 31 0.54
42 11 0.19
43 11 0.19
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCGAAATGCCGGTGAATGATATCAGGCTTTAAA
Found at i:88638897 original size:29 final size:28
Alignment explanation
Indices: 88638809--88638910 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
88638799 TACTCAATCA
* *
88638809 CGCACACTTAGTGCCACGT-GATTCAAGCC
1 CGCACACTTAGTG-C-CGTACATTCAAGCT
* * * *
88638838 CGCACACATAGTGCCATATAGTCCCAA-CT
1 CGCACACTTAGTGCCGTACA-T-TCAAGCT
88638867 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCGTACATT-CAAGCT
*
88638896 CGCACACTCAGTGCC
1 CGCACACTTAGTGCC
88638911 AATCTCGTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 47 0.81
30 3 0.05
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCGTACATTCAAGCT
Found at i:88653288 original size:50 final size:49
Alignment explanation
Indices: 88653217--88653394 Score: 248
Period size: 50 Copynumber: 3.6 Consensus size: 49
88653207 GCTTGATAAA
*
88653217 TTGCTCTTAATAATTCCGGTTAAAATTGCTCTTAATATTTCCGATAAAAT
1 TTGCTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTT-CGATAAAAT
* **
88653267 TTGCTCTTAATAATTCTGGTTAAATTTGCTCTTAATATTTTTAGTAAAAT
1 TTGCTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCGA-TAAAAT
* *
88653317 TTGCTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTTCGGTTAAAT
1 TTGCTCTTAATAATTCCGGTTAAATTTGCTCTTAATA-TTTCGATAAAAT
* * *
88653367 TTGCTCTTAATATTTTCAGTTAAATTTG
1 TTGCTCTTAATAATTCCGGTTAAATTTG
88653395 GCCTTATTGT
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 110 0.96
51 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.48
Consensus pattern (49 bp):
TTGCTCTTAATAATTCCGGTTAAATTTGCTCTTAATATTTCGATAAAAT
Found at i:88653379 original size:25 final size:25
Alignment explanation
Indices: 88653213--88653394 Score: 224
Period size: 25 Copynumber: 7.3 Consensus size: 25
88653203 TAAAGCTTGA
* *
88653213 TAAA-TTGCTCTTAATAATTCCGGT
1 TAAATTTGCTCTTAATATTTTCGGT
* * *
88653237 TAAAATTGCTCTTAATATTTCCGAT
1 TAAATTTGCTCTTAATATTTTCGGT
* *
88653262 AAAATTTGCTCTTAATA-ATTCTGGT
1 TAAATTTGCTCTTAATATTTTC-GGT
**
88653287 TAAATTTGCTCTTAATATTTTTAGT
1 TAAATTTGCTCTTAATATTTTCGGT
* * *
88653312 AAAATTTGCTCTTAATAATTCCGGT
1 TAAATTTGCTCTTAATATTTTCGGT
88653337 TAAATTTGCTCTTAATATTTTCGGT
1 TAAATTTGCTCTTAATATTTTCGGT
*
88653362 TAAATTTGCTCTTAATATTTTCAGT
1 TAAATTTGCTCTTAATATTTTCGGT
88653387 TAAATTTG
1 TAAATTTG
88653395 GCCTTATTGT
Statistics
Matches: 135, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
24 6 0.04
25 127 0.94
26 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (25 bp):
TAAATTTGCTCTTAATATTTTCGGT
Found at i:88653409 original size:75 final size:75
Alignment explanation
Indices: 88653213--88653394 Score: 251
Period size: 75 Copynumber: 2.4 Consensus size: 75
88653203 TAAAGCTTGA
* * * *
88653213 TAAA-TTGCTCTTAATAATTCCGGTTAAAATTGCTCTTAATATTTCCGATAAAATTTGCTCTTAA
1 TAAATTTGCTCTTAATATTTTCAGTTAAATTTGCTCTTAATATTTCCGATAAAATTTGCTCTTAA
88653277 TAATTCTGGT
66 TAATTCTGGT
* * * * *
88653287 TAAATTTGCTCTTAATATTTTTAGTAAAATTTGCTCTTAATAATTCCGGTTAAATTTGCTCTTAA
1 TAAATTTGCTCTTAATATTTTCAGTTAAATTTGCTCTTAATATTTCCGATAAAATTTGCTCTTAA
*
88653352 T-ATTTTCGGT
66 TAATTCT-GGT
88653362 TAAATTTGCTCTTAATATTTTCAGTTAAATTTG
1 TAAATTTGCTCTTAATATTTTCAGTTAAATTTG
88653395 GCCTTATTGT
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 8 0.09
75 86 0.91
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (75 bp):
TAAATTTGCTCTTAATATTTTCAGTTAAATTTGCTCTTAATATTTCCGATAAAATTTGCTCTTAA
TAATTCTGGT
Found at i:88654296 original size:45 final size:45
Alignment explanation
Indices: 88654232--88654496 Score: 403
Period size: 45 Copynumber: 6.0 Consensus size: 45
88654222 TATCGTACAG
88654232 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
**
88654277 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTAGTGATA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
*
88654322 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGGTGATA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
*
88654367 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
* * *
88654412 TACTATTCGAGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
* * *
88654457 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCAGTGA
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
88654497 ATAAATTCGG
Statistics
Matches: 208, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
42 10 0.05
43 18 0.09
44 4 0.02
45 175 0.84
46 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGATA
Found at i:88655840 original size:16 final size:15
Alignment explanation
Indices: 88655816--88655845 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
88655806 AACTATTTTA
88655816 TTACAAATTTCACTC
1 TTACAAATTTCACTC
88655831 TTACATAATTTCACT
1 TTACA-AATTTCACT
88655846 TACTTCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:88662315 original size:4 final size:4
Alignment explanation
Indices: 88662294--88662326 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
88662284 TTATGGTTTT
*
88662294 TTAA TT-A TTAA GTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
88662327 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:88662475 original size:17 final size:17
Alignment explanation
Indices: 88662453--88662485 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
88662443 TAGAATTGGG
88662453 TTGAGAAAATTATTTAA
1 TTGAGAAAATTATTTAA
*
88662470 TTGAGAAATTTATTTA
1 TTGAGAAAATTATTTA
88662486 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTGAGAAAATTATTTAA
Found at i:88665741 original size:20 final size:22
Alignment explanation
Indices: 88665718--88665759 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
88665708 TAATAACTTT
88665718 AATAATTTT-TAAT-TTTAAAA
1 AATAATTTTATAATATTTAAAA
88665738 AATAATTTTATAATATTTAAAA
1 AATAATTTTATAATATTTAAAA
88665760 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTATAATATTTAAAA
Found at i:88665741 original size:29 final size:30
Alignment explanation
Indices: 88665709--88665775 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
88665699 ATAACTTTTT
*
88665709 AATAACTTTAATAAT-TTT-TAATTTTAAAA
1 AATAA-TTTAATAATATTTAAAATTTTAAAA
*
88665738 AATAATTTTATAATATTTAAAATTTTAAAA
1 AATAATTTAATAATATTTAAAATTTTAAAA
88665768 AATTAATT
1 AA-TAATT
88665776 AAATGCTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 8 0.24
29 8 0.24
30 12 0.36
31 5 0.15
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AATAATTTAATAATATTTAAAATTTTAAAA
Found at i:88669612 original size:11 final size:11
Alignment explanation
Indices: 88669576--88669631 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
88669566 CATGGTATGT
88669576 ATGATATGCAC
1 ATGATATGCAC
* *
88669587 ATGACATG--T
1 ATGATATGCAC
88669596 ATGATATGCAC
1 ATGATATGCAC
*
88669607 ATGATATG--T
1 ATGATATGCAC
88669616 ATGATATGCAC
1 ATGATATGCAC
88669627 ATGAT
1 ATGAT
88669632 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:88669631 original size:20 final size:20
Alignment explanation
Indices: 88669565--88669631 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
88669555 GATTTGATAA
*
88669565 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
88669585 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
88669605 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
88669625 ACATGAT
1 ACATGAT
88669632 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:88669736 original size:24 final size:23
Alignment explanation
Indices: 88669680--88669831 Score: 223
Period size: 24 Copynumber: 6.4 Consensus size: 23
88669670 GAGAAAGTGA
88669680 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
88669703 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
88669726 CAAAAGTGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
88669750 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
88669774 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
88669798 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
88669822 AAAAGAGGCT
1 AAAAG-GGCT
88669832 AGGCCTCCTG
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
23 43 0.36
24 72 0.61
25 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:88669749 original size:47 final size:46
Alignment explanation
Indices: 88669680--88669831 Score: 223
Period size: 47 Copynumber: 3.2 Consensus size: 46
88669670 GAGAAAGTGA
88669680 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
88669726 CAAAAGTGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
* *
88669774 TAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTA-T
88669822 AAAAGAGGCT
1 AAAAG-GGCT
88669832 AGGCCTCCTG
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
47 63 0.67
48 27 0.29
49 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:88669796 original size:71 final size:71
Alignment explanation
Indices: 88669680--88669831 Score: 259
Period size: 71 Copynumber: 2.1 Consensus size: 71
88669670 GAGAAAGTGA
*
88669680 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGTGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
88669745 GTTATC
66 GTTATC
* *
88669751 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
*
88669816 GTTATT
66 GTTATC
88669822 AAAAGAGGCT
1 AAAAG-GGCT
88669832 AGGCCTCCTG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 72 0.95
72 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:88670073 original size:31 final size:31
Alignment explanation
Indices: 88670038--88670098 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
88670028 CGTTTACAGT
88670038 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
**
88670069 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
88670099 AAATATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:88672244 original size:27 final size:27
Alignment explanation
Indices: 88672226--88672293 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
88672216 ATAGTGAGTC
88672226 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* *
88672253 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
88672281 AGCACACTTAGTG
1 CGCACACTTAGTG
88672294 ATGTACAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:88686929 original size:40 final size:39
Alignment explanation
Indices: 88686881--88687051 Score: 229
Period size: 39 Copynumber: 4.3 Consensus size: 39
88686871 ACGACTAGCT
*
88686881 CAAATGCCTTCGGGAC-AAACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAA-CCCGGATT-TAGTAACTCGCA
* *
88686921 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAACCCGGATTTAGTAACTCGCA
*
88686961 CAAATGCCTTCGGGCTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
*
88687000 CAAATGCCTTCGGGCTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
* *
88687039 CGAACGCCTTCGG
1 CAAATGCCTTCGG
88687052 ATCTTAGTCC
Statistics
Matches: 122, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 73 0.60
40 45 0.37
41 4 0.03
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAACCCGGATTTAGTAACTCGCA
Found at i:88686995 original size:39 final size:40
Alignment explanation
Indices: 88686881--88687104 Score: 235
Period size: 40 Copynumber: 5.7 Consensus size: 40
88686871 ACGACTAGCT
*
88686881 CAAATGCCTTCGGGAC-AAACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAA-CCCGGATT-TAGTAACTCGCA
* *
88686921 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
88686961 CAAATGCCTTCGGG-CTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
88687000 CAAATGCCTTCGGG-CTTAACCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * ** * * * **
88687039 CGAACGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAACA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
88687080 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
88687105 CATCATTCAA
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 71 0.44
40 75 0.47
41 13 0.08
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:88695067 original size:38 final size:40
Alignment explanation
Indices: 88694947--88695116 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
88694937 ACGACTAGCT
* * *
88694947 CAAATGCCTTCGGGAC-AAACCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCAGATT-TAGTAACTCGCA
* * *
88694987 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
*
88695027 CAAATGCCTTCGGG-CTTAACCC-GATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
*
88695065 CAAATGCCTTCGGG-CTTAACCCAGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
* *
88695104 CGAACGCCTTCGG
1 CAAATGCCTTCGG
88695117 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
38 36 0.30
39 35 0.29
40 40 0.33
41 9 0.08
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
Found at i:88698077 original size:25 final size:25
Alignment explanation
Indices: 88698048--88698095 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
88698038 TTATAATATG
* * *
88698048 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
88698073 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
88698096 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:88698179 original size:11 final size:11
Alignment explanation
Indices: 88698143--88698198 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
88698133 CATGGTATGT
88698143 ATGATATGCAC
1 ATGATATGCAC
* *
88698154 ATGACATG--T
1 ATGATATGCAC
88698163 ATGATATGCAC
1 ATGATATGCAC
*
88698174 ATGATATG--T
1 ATGATATGCAC
88698183 ATGATATGCAC
1 ATGATATGCAC
88698194 ATGAT
1 ATGAT
88698199 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:88698198 original size:20 final size:20
Alignment explanation
Indices: 88698132--88698198 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
88698122 ATTTTGATAA
*
88698132 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
88698152 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
88698172 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
88698192 ACATGAT
1 ACATGAT
88698199 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:88698303 original size:24 final size:23
Alignment explanation
Indices: 88698247--88698398 Score: 205
Period size: 24 Copynumber: 6.4 Consensus size: 23
88698237 GAGGAAGTGA
*
88698247 AAAAGGGCTTATGCGCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
88698270 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
88698293 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
88698317 CAAAAGGGCTTATGCCCTAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
* *
88698341 TAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
88698365 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
88698389 AAAAGAGGCT
1 AAAAG-GGCT
88698399 AGGCCTCCTG
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 42 0.36
24 72 0.61
25 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:88698316 original size:47 final size:46
Alignment explanation
Indices: 88698247--88698398 Score: 205
Period size: 47 Copynumber: 3.2 Consensus size: 46
88698237 GAGGAAGTGA
*
88698247 AAAAGGGCTTATGCGCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
88698293 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCTAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
* * *
88698341 TAAAGGGCTTATGCCCTAGTTATTAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTA-T
88698389 AAAAGAGGCT
1 AAAAG-GGCT
88698399 AGGCCTCCTG
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
47 62 0.67
48 26 0.28
49 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:88698363 original size:71 final size:71
Alignment explanation
Indices: 88698247--88698398 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 71
88698237 GAGGAAGTGA
88698247 AAAAGGGCTTATGCGCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCGCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
88698312 GTTATC
66 GTTATC
* * *
88698318 AAAAGGGCTTATGC-CCTAGTTATTAAAGGGCTTATGCCCTAGTTATTAAAAGGGCTTTTGCCCC
1 AAAAGGGCTTATGCGCC-AGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
*
88698382 AGTTATT
65 AGTTATC
88698389 AAAAGAGGCT
1 AAAAG-GGCT
88698399 AGGCCTCCTG
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
70 2 0.03
71 69 0.92
72 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (71 bp):
AAAAGGGCTTATGCGCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:88698640 original size:31 final size:31
Alignment explanation
Indices: 88698605--88698665 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
88698595 CGTTTACAGT
88698605 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
**
88698636 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
88698666 AAATATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:88704493 original size:15 final size:15
Alignment explanation
Indices: 88704454--88704524 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
88704444 GTATCTTGGG
* *
88704454 TTTCTTTATCCTAGA
1 TTTCTTTATTCTGGA
*
88704469 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
88704484 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
88704499 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
88704514 TTTCTTTATTC
1 TTTCTTTATTC
88704525 AGTTTTCTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 2 0.04
15 42 0.91
16 2 0.04
ACGTcount: A:0.13, C:0.18, G:0.11, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:88704514 original size:30 final size:30
Alignment explanation
Indices: 88704445--88704524 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
88704435 CATAGTATCG
* * *
88704445 TATCTTGGGTTTCTTTATCCTAGATCTCTT
1 TATCTTGGATTTCTTTATTCTAGATCTCTC
* * *
88704475 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTAGATCTCTC
88704505 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
88704525 AGTTTTCTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTAGATCTCTC
Found at i:88707383 original size:40 final size:40
Alignment explanation
Indices: 88707328--88707537 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
88707318 AACATTGGAA
88707328 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88707368 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88707408 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
88707448 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
88707487 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
88707528 CTATATCCGG
1 ATATATCCGG
88707538 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:88715520 original size:40 final size:40
Alignment explanation
Indices: 88715465--88715673 Score: 296
Period size: 40 Copynumber: 5.2 Consensus size: 40
88715455 AACATTGGAA
88715465 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88715505 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
88715545 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
88715585 ATATATCCGGGCTAAGA-CCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
88715623 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
88715664 CTATATCCGG
1 ATATATCCGG
88715674 TTAAATCCCG
Statistics
Matches: 149, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
38 2 0.01
39 28 0.19
40 119 0.80
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:88715598 original size:80 final size:78
Alignment explanation
Indices: 88715465--88715673 Score: 292
Period size: 79 Copynumber: 2.6 Consensus size: 78
88715455 AACATTGGAA
88715465 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGA-CCGAAGG
* *
88715530 CATTCGTGCGAGTTG
65 CATTCGTGCAAG-TC
88715545 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCGAAGGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCGAAGGC
* *
88715610 CTTTGTGCAAGTC
66 ATTCGTGCAAGTC
* * * * * * *
88715623 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCGCTATATCCGG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGG
88715674 TTAAATCCCG
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
78 2 0.02
79 58 0.50
80 57 0.49
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (78 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCGAAGGC
ATTCGTGCAAGTC
Found at i:88717385 original size:50 final size:50
Alignment explanation
Indices: 88717326--88717420 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
88717316 TAATTTAGAG
*
88717326 ATAAAATAATCATTCAATA-TTATCACT-TAATTAATTTAATTTAATGTGTA
1 ATAAAATAAT-ATTCAATATTTATC-CTATAATTAATTTAAATTAATGTGTA
* * * *
88717376 ATAATATAATATTTATTATTTATCTTATAATTAATTTAAATTAAT
1 ATAAAATAATATTCAATATTTATCCTATAATTAATTTAAATTAAT
88717421 TTCATTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
49 7 0.18
50 31 0.82
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (50 bp):
ATAAAATAATATTCAATATTTATCCTATAATTAATTTAAATTAATGTGTA
Found at i:88721985 original size:40 final size:40
Alignment explanation
Indices: 88721877--88722086 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
88721867 CGGGATTTAA
* * * * *
88721877 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
88721917 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
88721957 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
88721997 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
88722037 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
88722077 CCGGATATAT
1 CCGGATATAT
88722087 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:88730073 original size:71 final size:71
Alignment explanation
Indices: 88729989--88730152 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
88729979 CGATTTGTCT
88729989 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
88730054 CTTTCA
66 CTTTCA
88730060 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
88730125 CTTTCA
66 CTTTCA
88730131 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
88730153 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:88737638 original size:70 final size:71
Alignment explanation
Indices: 88737553--88737715 Score: 319
Period size: 70 Copynumber: 2.3 Consensus size: 71
88737543 CGATTTGTCT
88737553 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA-
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
88737617 CTTTCA
66 CTTTCA
88737623 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
88737688 CTTTCA
66 CTTTCA
88737694 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
88737716 GATACATCTC
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 64 0.70
71 28 0.30
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:88737753 original size:71 final size:69
Alignment explanation
Indices: 88737553--88737749 Score: 265
Period size: 70 Copynumber: 2.8 Consensus size: 69
88737543 CGATTTGTCT
* * *
88737553 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAC
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAC
88737618 TTTCA
65 TTTCA
* * *
88737623 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTA-
88737688 CTTTCA
64 CTTTCA
* *
88737694 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
88737750 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 65 0.54
71 31 0.26
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (69 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTACT
TTCA
Found at i:88746455 original size:40 final size:40
Alignment explanation
Indices: 88746400--88746591 Score: 314
Period size: 40 Copynumber: 4.8 Consensus size: 40
88746390 CGGATGATAA
88746400 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
88746440 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
88746480 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* *
88746520 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
* *
88746560 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
88746592 AGCTATATCC
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:88753338 original size:31 final size:32
Alignment explanation
Indices: 88753278--88753339 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
88753268 CATGGTCAAA
* *
88753278 TATAACCGAACATAAGCAAAATGATCAAGCCT
1 TATAACCGAACATAAGCAAAATAAACAAGCCT
*
88753310 TATAACCGAACTTAA-CAAAATAAACAAGCC
1 TATAACCGAACATAAGCAAAATAAACAAGCC
88753340 ATTTTCGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.18
Consensus pattern (32 bp):
TATAACCGAACATAAGCAAAATAAACAAGCCT
Found at i:88754058 original size:56 final size:56
Alignment explanation
Indices: 88753991--88754367 Score: 576
Period size: 56 Copynumber: 6.7 Consensus size: 56
88753981 TCTTACATGT
** ***
88753991 AATCACATATCGATGCCAGTGTCCCAAACAG-GGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAAC-GTGGTCTTACTCGCACACATATATCAG
* * *
88754047 AATCACATATCGATGCCAATGTATTAAACGTGGTCTTACTCGCACATATATATTAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
* *
88754103 AATCACATATCGATGCCAACGTTTTAAACGTGGTCTTACTCACACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
* * *
88754159 AAGCACATATCGATGCCAACGTTTTAAACGTGGTCTTACTCACACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
* *
88754215 AAGCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAA
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
* * *
88754271 AATCACATATCGATGCCAACGTATTAAACATGGTTTTACTTGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
88754327 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTC
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTC
88754368 ATGATCACAA
Statistics
Matches: 297, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
55 1 0.00
56 296 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
Found at i:88754396 original size:2 final size:2
Alignment explanation
Indices: 88754389--88754415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88754379 TCGAAGCCTC
88754389 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 A
88754416 CATCCATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88760150 original size:46 final size:46
Alignment explanation
Indices: 88760092--88760311 Score: 186
Period size: 46 Copynumber: 4.7 Consensus size: 46
88760082 GGGTTATTAT
* *
88760092 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGA-GATGA
* *
88760138 GAGCCAGTGTAAGACCATGTCTGGGAAATGGCATCGGC-ATCGAGATGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTA-CGAGATGA
* * ** *
88760186 GTGCTAGTGTAAGACATGTCCAGGACATGCATCGACCT-CGAGATGCA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATC-AGCTACGAGATG-A
* *
88760233 -AGCCAAG-GTAAGACATGT-TAGGGACATGCATCGGCT-TGAGAT-A
1 GAGCC-AGTGTAAGACATGTCT-GGGACATGCATCAGCTACGAGATGA
88760276 TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
1 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
88760312 GGTACCTTAC
Statistics
Matches: 141, Mismatches: 18, Indels: 29
0.75 0.10 0.15
Matches are distributed among these distances:
43 1 0.01
44 2 0.01
45 17 0.12
46 61 0.43
47 35 0.25
48 24 0.17
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGATGA
Found at i:88761510 original size:21 final size:22
Alignment explanation
Indices: 88761449--88761511 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
88761439 GTCAAATTAT
* *
88761449 CACACGGGCATGTTACCCCTTC
1 CACACGGGCGTGTTGCCCCTTC
88761471 CACACGGGCGTGTTGCCCCTTC
1 CACACGGGCGTGTTGCCCCTTC
*
88761493 CACATGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
88761512 GTGTCAAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 7 0.18
22 31 0.82
ACGTcount: A:0.13, C:0.40, G:0.25, T:0.22
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTTC
Found at i:88766412 original size:22 final size:22
Alignment explanation
Indices: 88766337--88766412 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
88766327 ACATGCATAT
*
88766337 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCTGAATGGCCA
* *
88766359 ATGTGATGAATG-TGAGCAT-GCATA
1 ATGTGAT-AAGGCTGA--ATGGC-CA
88766383 TATGTGATAAGGCTGAATGGCCA
1 -ATGTGATAAGGCTGAATGGCCA
88766406 ATGTGAT
1 ATGTGAT
88766413 GAATGTGAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
24 8 0.19
25 10 0.24
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCTGAATGGCCA
Found at i:88766480 original size:47 final size:47
Alignment explanation
Indices: 88766312--88766477 Score: 278
Period size: 47 Copynumber: 3.5 Consensus size: 47
88766302 TTAGGATTTT
88766312 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
88766359 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
88766406 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
88766453 ATGTGGTGAATATGAACATGCATAT
1 ATGTGATGAATGTGAACATGCATAT
88766478 GTGGTAAAGC
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 112 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:88766754 original size:35 final size:37
Alignment explanation
Indices: 88766656--88766762 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
88766646 GGAAATATAT
*
88766656 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
88766693 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
88766730 TCC-GGTAAGA-CCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
88766763 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 21 0.31
36 7 0.10
37 39 0.58
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:88768354 original size:40 final size:40
Alignment explanation
Indices: 88768031--88768342 Score: 462
Period size: 40 Copynumber: 7.8 Consensus size: 40
88768021 GAGAATTGAG
*
88768031 AGTGATATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
88768071 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
88768111 AGTGATATATTCGGGCTAAGTCCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
88768151 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCC
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
88768191 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
88768231 AGTGATGTATCCGAGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* **
88768271 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
88768311 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
88768343 ATCATGCTGG
Statistics
Matches: 247, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 247 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:88768559 original size:25 final size:25
Alignment explanation
Indices: 88768518--88768569 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
88768508 TGTGTAATAA
88768518 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
88768543 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
88768568 TG
1 TG
88768570 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:88772587 original size:47 final size:47
Alignment explanation
Indices: 88772484--88772674 Score: 273
Period size: 47 Copynumber: 4.1 Consensus size: 47
88772474 TTAGGATTTT
88772484 ATGTGATGAATGTGAACATGCATATATGTGATAA-GCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
88772530 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
88772577 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATCGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
88772624 ATGTGGTGAATATGAACATGC--ATATGTGGTAAAGCCGAATGG-CA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
88772668 AGTGTGA
1 A-TGTGA
88772675 AATATGTAGG
Statistics
Matches: 132, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
44 3 0.02
45 21 0.16
46 33 0.25
47 75 0.57
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:88772590 original size:93 final size:91
Alignment explanation
Indices: 88772484--88772674 Score: 267
Period size: 93 Copynumber: 2.1 Consensus size: 91
88772474 TTAGGATTTT
* * *
88772484 ATGTGATGAATGTGAACATGCATATATGTGATAA-GCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATCGCCAATGTGATGAATATGAACA
*
88772548 TGCATATATGTGATAAGGCCGAATGGCCA
66 TGC--ATATGTGATAAAGCCGAATGG-CA
* * *
88772577 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATCGCCAATGTGGTGAATATGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATCGCCAATGTGATGAATATGAACA
*
88772642 TGCATATGTGGTAAAGCCGAATGGCA
66 TGCATATGTGATAAAGCCGAATGGCA
88772668 AGTGTGA
1 A-TGTGA
88772675 AATATGTAGG
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
91 3 0.03
92 24 0.27
93 32 0.36
94 29 0.33
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (91 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATCGCCAATGTGATGAATATGAACA
TGCATATGTGATAAAGCCGAATGGCA
Found at i:88772937 original size:37 final size:37
Alignment explanation
Indices: 88772829--88772937 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
88772819 AGAAATATAT
* *
88772829 TCCGGGTAAGACCGGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
88772866 TCCGGGTAAGACCCGATGACTACATGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
88772903 TCCGGGTAAGGCCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
88772938 CGTTTGAGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:88784037 original size:53 final size:53
Alignment explanation
Indices: 88783962--88784066 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
88783952 ATAAACTACG
* * * *
88783962 ATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGCATAACAATGGTGAGTTC
1 ATAAGGCAAAGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAGTTC
* * **
88784015 ATAAGGCAAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 ATAAGGCAAAGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAGTT
88784067 TAAAAAGGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (53 bp):
ATAAGGCAAAGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAGTTC
Found at i:88784086 original size:53 final size:53
Alignment explanation
Indices: 88783865--88784087 Score: 125
Period size: 53 Copynumber: 4.2 Consensus size: 53
88783855 ATTAGAGTTT
* * *
88783865 AAGGATACCAAGTAAGACCATGCCAAGACAT-----TGGTAAGTTTTACAAGGG
1 AAGGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAG-TTAAAAAGGC
* * * ** ** * * ** *
88783914 AAGGAAATCATGTAAGACCATGTTAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAGTTA--AAAAGGC
* * * * * * *
88783969 AAAGATCCCATGTAAGACCATGCCAAGGCATAACAATGGTGAGTTCATAAGGC
1 AAGGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAGTTAAAAAGGC
* **
88784022 AAGGATACCAAGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTAAAAAGG-
1 AAGGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAG-TTAAAAAGGC
* *
88784075 AAGTATTCCAAGT
1 AAGGATACCAAGT
88784088 GGTTCAACGG
Statistics
Matches: 128, Mismatches: 38, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
49 26 0.20
53 54 0.42
54 12 0.09
55 36 0.28
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCAAGTAAGACCATGCCAAGACATAACAATGGTAAGTTAAAAAGGC
Found at i:88789010 original size:52 final size:52
Alignment explanation
Indices: 88788948--88789049 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
88788938 AAGATTGAGC
88788948 ATGGATAATGATAATATAATTCAGCTAGTTTAATCAATTTGCTTATATTAGA
1 ATGGATAATGATAATATAATTCAGCTAGTTTAATCAATTTGCTTATATTAGA
* *
88789000 ATGGATAATGATAATATAATTCGGCTAGTTTAATTAATTTGCTTATATTA
1 ATGGATAATGATAATATAATTCAGCTAGTTTAATCAATTTGCTTATATTA
88789050 CTAAGTTGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (52 bp):
ATGGATAATGATAATATAATTCAGCTAGTTTAATCAATTTGCTTATATTAGA
Found at i:88790472 original size:61 final size:61
Alignment explanation
Indices: 88790377--88790499 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
88790367 TATGTCTGCT
88790377 CAGAAATGTTTGAGAAAAGGATATAAAGCTTATCTTGCTTTTGTGTTGAATACTAAAGATC
1 CAGAAATGTTTGAGAAAAGGATATAAAGCTTATCTTGCTTTTGTGTTGAATACTAAAGATC
88790438 CAGAAATGTTTGAGAAAAGGATATAAAGCTTATCTTGCTTTTGTGTTGAATACTAAAGATC
1 CAGAAATGTTTGAGAAAAGGATATAAAGCTTATCTTGCTTTTGTGTTGAATACTAAAGATC
88790499 C
1 C
88790500 TGAGTTGAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (61 bp):
CAGAAATGTTTGAGAAAAGGATATAAAGCTTATCTTGCTTTTGTGTTGAATACTAAAGATC
Found at i:88793729 original size:46 final size:46
Alignment explanation
Indices: 88793671--88793838 Score: 164
Period size: 46 Copynumber: 3.6 Consensus size: 46
88793661 TCTCGTAGCT
* *
88793671 GATGCATGTCCCAGACATGTCTTACACTGACTTACGTTTCGAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTGACTTACGTATCGAGGCC
* * * *
88793717 GATGCATGTCCCAGACATGTCTTACACTAGCAC-T-CGTCTCAATGCC
1 GATGCATGTCCCAAACATGTCTTACACT-G-ACTTACGTATCGAGGCC
* * * *
88793763 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAC-AAT-GTGGCT
1 GATG-CATGTCCCAAACAT-GTCTTACACTGACT-T-ACGTATCGAGGCC
88793811 GATGCATGTCCCAAACATGTCTTACACT
1 GATGCATGTCCCAAACATGTCTTACACT
88793839 AGCCCACACA
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
46 52 0.50
47 30 0.29
48 19 0.18
49 1 0.01
50 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAAACATGTCTTACACTGACTTACGTATCGAGGCC
Found at i:88793849 original size:46 final size:43
Alignment explanation
Indices: 88793714--88793849 Score: 146
Period size: 47 Copynumber: 3.0 Consensus size: 43
88793704 ACGTTTCGAG
* *
88793714 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGC-C-C-TCACAAT
* *
88793760 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCACAATGT
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCCCTCACAA--T
* *
88793807 GGCTGATGCATGTCCCAAACATGTCTTACACTAGCCCACACAA
1 -GCCGATGCATGTCCCAAACATGTCTTACACTAGCCCTCACAA
88793850 GTGACCCAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
45 5 0.06
46 26 0.34
47 28 0.36
48 18 0.23
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (43 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCCCTCACAAT
Found at i:88794220 original size:30 final size:30
Alignment explanation
Indices: 88794184--88794240 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
88794174 ATTTCATATC
* *
88794184 TTTGATAAAATGACCATTTTGCCCCTAAAT
1 TTTGATAAAATAACCATTTTACCCCTAAAT
88794214 TTTGATAAAATAACCATTTTACCCCTA
1 TTTGATAAAATAACCATTTTACCCCTA
88794241 GGCCCGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTGATAAAATAACCATTTTACCCCTAAAT
Found at i:88795257 original size:42 final size:42
Alignment explanation
Indices: 88795167--88795278 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 42
88795157 AAAGATCGTA
* * *
88795167 CAATGCCACATCCCAGACGTGGTGTTACATGTAATCAAATAT
1 CAATGCCACATCCCAGACGTGGTCTTACACGAAATCAAATAT
*
88795209 CAATGCCACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT
1 CAATGCCAC-ATCCCAGAC-GTGGTCTTACACGAAATCAAATAT
* * *
88795252 -GATGCCAACGTCCCTGACGTGGTCTTA
1 CAATGCC-ACATCCCAGACGTGGTCTTA
88795279 TACGTAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.02
42 29 0.48
43 29 0.48
44 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
CAATGCCACATCCCAGACGTGGTCTTACACGAAATCAAATAT
Found at i:88797410 original size:15 final size:15
Alignment explanation
Indices: 88797392--88797445 Score: 99
Period size: 15 Copynumber: 3.6 Consensus size: 15
88797382 TTTCGCAAAA
88797392 AACGCCACTGTAGAT
1 AACGCCACTGTAGAT
88797407 AACGCCACTGTAGAT
1 AACGCCACTGTAGAT
*
88797422 AACGCCACTATAGAT
1 AACGCCACTGTAGAT
88797437 AACGCCACT
1 AACGCCACT
88797446 AAAGCTTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.19
Consensus pattern (15 bp):
AACGCCACTGTAGAT
Found at i:88797785 original size:26 final size:25
Alignment explanation
Indices: 88797727--88797785 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
88797717 TTAAATATTA
88797727 AAATA-AAAATAAAAATTTAGAATC
1 AAATATAAAATAAAAATTTAGAATC
*
88797751 AAA-ACTAAAATAAATAATATTAG-ATT
1 AAATA-TAAAATAAA-AAT-TTAGAATC
88797777 AAATATAAA
1 AAATATAAA
88797786 GATATCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 8 0.28
26 12 0.41
27 5 0.17
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (25 bp):
AAATATAAAATAAAAATTTAGAATC
Found at i:88801241 original size:19 final size:19
Alignment explanation
Indices: 88801202--88801241 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
88801192 CTTATTCTAC
*
88801202 ATTTAATTTTTTTTATGAA
1 ATTTAATTTTTTTCATGAA
88801221 ATTTAATATTTTTTCAT-AA
1 ATTTAAT-TTTTTTCATGAA
88801240 AT
1 AT
88801242 CAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTAATTTTTTTCATGAA
Found at i:88803386 original size:8 final size:8
Alignment explanation
Indices: 88803375--88803427 Score: 97
Period size: 8 Copynumber: 6.6 Consensus size: 8
88803365 AATATTAAAA
88803375 TTTTAAGT
1 TTTTAAGT
88803383 TTTTAAGT
1 TTTTAAGT
*
88803391 TTTAAAGT
1 TTTTAAGT
88803399 TTTTAAGT
1 TTTTAAGT
88803407 TTTTAAGT
1 TTTTAAGT
88803415 TTTTAAGT
1 TTTTAAGT
88803423 TTTTA
1 TTTTA
88803428 TTTTTCAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.62
Consensus pattern (8 bp):
TTTTAAGT
Found at i:88803439 original size:7 final size:7
Alignment explanation
Indices: 88803429--88803460 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
88803419 AAGTTTTTAT
88803429 TTTTCAA
1 TTTTCAA
88803436 TTTTCAA
1 TTTTCAA
88803443 TTTTCAA
1 TTTTCAA
88803450 TTTTCAA
1 TTTTCAA
88803457 TTTT
1 TTTT
88803461 TTGAAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCAA
Found at i:88804064 original size:14 final size:14
Alignment explanation
Indices: 88804046--88804112 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
88804036 TCCTAAAAAT
88804046 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
88804060 CAAACACC-AAACC-
1 TAAAC-CCTAAACCA
**
88804073 TAAAAACTCAAACCA
1 TAAACCCT-AAACCA
*
88804088 TAAACCCTAAATCA
1 TAAACCCTAAACCA
*
88804102 TAAACCATAAA
1 TAAACCCTAAA
88804113 ACTTACATCC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
12 1 0.02
13 3 0.07
14 29 0.71
15 8 0.20
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.13
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:88804126 original size:21 final size:21
Alignment explanation
Indices: 88804082--88804133 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
88804072 CTAAAAACTC
*
88804082 AAACCATAAACCCTAAATCAT
1 AAACCATAAAACCTAAATCAT
* * *
88804103 AAACCATAAAACTTACATCCT
1 AAACCATAAAACCTAAATCAT
*
88804124 AAACCCTAAA
1 AAACCATAAA
88804134 TATATATTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
AAACCATAAAACCTAAATCAT
Found at i:88804533 original size:40 final size:41
Alignment explanation
Indices: 88804497--88804576 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 41
88804487 GACGTTTTTT
88804497 AAAAAGCGCCGCTAATGCTCGATCTTTAGC-GGCGTTTTCA
1 AAAAAGCGCCGCTAATGCTCGATCTTTAGCGGGCGTTTTCA
*
88804537 AAAAAGTGCCGCTAATGCTCGATCTTTAGCGGGCGTTTTC
1 AAAAAGCGCCGCTAATGCTCGATCTTTAGCGGGCGTTTTC
88804577 TTACTAGCGC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 29 0.76
41 9 0.24
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (41 bp):
AAAAAGCGCCGCTAATGCTCGATCTTTAGCGGGCGTTTTCA
Found at i:88806333 original size:19 final size:19
Alignment explanation
Indices: 88806309--88806347 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
88806299 AGAGGGCAGC
88806309 AAAGTAGTTTAAGGATTAG
1 AAAGTAGTTTAAGGATTAG
88806328 AAAGTAGTTTAAGGATTAG
1 AAAGTAGTTTAAGGATTAG
88806347 A
1 A
88806348 CTTGATTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAGTAGTTTAAGGATTAG
Found at i:88813155 original size:46 final size:46
Alignment explanation
Indices: 88813088--88813261 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
88813078 TGTAACCCGC
*
88813088 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
88813134 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
88813184 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
88813226 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
88813262 ATGCCCAAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 1 0.01
44 3 0.03
45 28 0.25
46 35 0.32
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:88813254 original size:92 final size:93
Alignment explanation
Indices: 88813096--88813266 Score: 308
Period size: 92 Copynumber: 1.8 Consensus size: 93
88813086 GCCCATAAGT
* *
88813096 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
88813161 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
88813189 GAACTCGGACTCAACTCAACGAGTTCGGAC-ATCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
88813253 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
88813267 CAAATATCCC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 47 0.63
93 28 0.37
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGATCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:88815680 original size:29 final size:29
Alignment explanation
Indices: 88815641--88815728 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
88815631 CAAAGATAAC
*
88815641 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
88815670 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
88815699 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
88815729 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Done.