Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 116 of 128
Found at i:38588856 original size:44 final size:44
Alignment explanation
Indices: 38588765--38588858 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
38588755 GAAGCACCAG
* * * * ** * *
38588765 TCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGA
1 TCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAA
38588809 TCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAA
1 TCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAA
38588853 TCTTAT
1 TCTTAT
38588859 TTTCCAAGCG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (44 bp):
TCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAGACAGCAAA
Found at i:38589024 original size:100 final size:99
Alignment explanation
Indices: 38588870--38589220 Score: 436
Period size: 100 Copynumber: 3.5 Consensus size: 99
38588860 TTCCAAGCGG
** *
38588870 TGCAGTGGAGCAGATTAAAGCTACAACGGTGAATCCTGCTTCCCCGACATTGCAATTAAAAATAT
1 TGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAATAT
*
38588935 TGAAGTCGCAACGGCGAATCTTACTTCCCTGGCAG
66 TGAAG-CGCAACGGCGAATCTTACTTCCCTGGCAA
* ** * * *
38588970 TGCAGTGGAACAGATTGGAGCTACAACAATGAATCTTGTTTCCCCGACATTGCAATT-AAAATGA
1 TGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAAT-A
***
38589034 TTGAAGCCGCAACGGCGAATCTTACTTTTATGGCAA
65 TTGAAG-CGCAACGGCGAATCTTACTTCCCTGGCAA
* * * * * * *
38589070 TGCAGTAGAGCAGATTGAAA-CTACGATGGCGAATCTTGCTTCTCTGACATTGCAATTAAAAAGA
1 TGCAGTGGAGCAGATT-AAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAATA
*
38589134 TTGAAGCTGCAACGGCGAATCTTACTTCCCTAGCAA
65 TTGAAGC-GCAACGGCGAATCTTACTTCCCTGGCAA
* *
38589170 TGCAGTGGAGCAGATTAAAGTTACGACGACGAATCTTGCTTCCCCGACATT
1 TGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATT
38589221 ACATCGGATT
Statistics
Matches: 211, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
99 9 0.04
100 197 0.93
101 5 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (99 bp):
TGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCCGACATTGCAATTAAAAATAT
TGAAGCGCAACGGCGAATCTTACTTCCCTGGCAA
Found at i:38589185 original size:50 final size:50
Alignment explanation
Indices: 38588870--38589213 Score: 179
Period size: 50 Copynumber: 6.9 Consensus size: 50
38588860 TTCCAAGCGG
* * * * * * * *
38588870 TGCAGTGGAGCAGATTAAAGCTACAACGGTGAATCCTGCTTCCCCGACAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAA
* ** * * * *
38588920 TGCAATTAAAAATATTGAAG-TCGCAACGGCGAATCTTACTTCCCTGGCAG
1 TGCAGTGGAACAGATTGAAGCT-ACAACGGCGAATCTTACTTCCCTGGCAA
* *** ** * * *
38588970 TGCAGTGGAACAGATTGGAGCTACAACAATGAATCTTGTTTCCCCGACAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAA
* * * ** ***
38589020 TGCAAT-TAAAATGATTGAAGCCGCAACGGCGAATCTTACTTTTATGGCAA
1 TGCAGTGGAACA-GATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAA
* * * * * * * * *
38589070 TGCAGTAGAGCAGATTGAAACTACGATGGCGAATCTTGCTTCTCTGACAT
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAA
* ** * * *
38589120 TGCAATTAAAAAGATTGAAGCTGCAACGGCGAATCTTACTTCCCTAGCAA
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAA
* * * * * *
38589170 TGCAGTGGAGCAGATTAAAGTTACGACGACGAATCTTGCTTCCC
1 TGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCC
38589214 CGACATTACA
Statistics
Matches: 205, Mismatches: 85, Indels: 8
0.69 0.29 0.03
Matches are distributed among these distances:
49 4 0.02
50 198 0.97
51 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCAA
Found at i:38590950 original size:31 final size:32
Alignment explanation
Indices: 38590894--38590956 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
38590884 AGATAATTTT
38590894 AAAGAGTTTTATTAGGATTTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTTCAATTACTCTTG
38590926 AAAGAGTTTTATTAGGA-TTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTTCAATTACTCTTG
38590957 TAATTTGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (32 bp):
AAAGAGTTTTATTAGGATTTCAATTACTCTTG
Found at i:38594279 original size:14 final size:15
Alignment explanation
Indices: 38594254--38594282 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38594244 TTGATGAAAA
38594254 ATTTAGTTTTTGTTT
1 ATTTAGTTTTTGTTT
38594269 ATTTA-TTTTTGTTT
1 ATTTAGTTTTTGTTT
38594283 GTCAAGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
ATTTAGTTTTTGTTT
Found at i:38607856 original size:4 final size:4
Alignment explanation
Indices: 38607849--38607899 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
38607839 CACACACATG
* *
38607849 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACG TACG TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
38607897 TAC
1 TAC
38607900 GTACGTACGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.45, C:0.25, G:0.04, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:38608227 original size:24 final size:24
Alignment explanation
Indices: 38608195--38608243 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
38608185 ATATAGACAC
38608195 TAGAAAAATTAACAGAAGTTTTAA
1 TAGAAAAATTAACAGAAGTTTTAA
*
38608219 TAGAAAAATTAACATAAGTTTTAA
1 TAGAAAAATTAACAGAAGTTTTAA
38608243 T
1 T
38608244 CTTCTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (24 bp):
TAGAAAAATTAACAGAAGTTTTAA
Found at i:38613212 original size:38 final size:38
Alignment explanation
Indices: 38613170--38613287 Score: 91
Period size: 38 Copynumber: 3.1 Consensus size: 38
38613160 TGTGTAGATT
38613170 TAACTCGGACGGGGTTACTAGACACTATTGTTTATGAA
1 TAACTCGGACGGGGTTACTAGACACTATTGTTTATGAA
** * * * *** * *
38613208 TAACTTAGAC-GAG-CAATTTTCA-T-TTGTTGTGTAGATT
1 TAACTCGGACGGGGTTACTAGACACTATTGTT-TAT-GA-A
38613245 TAACTCGGACGGGGTTACTAGACACTATTGTTTATGAA
1 TAACTCGGACGGGGTTACTAGACACTATTGTTTATGAA
38613283 TAACT
1 TAACT
38613288 TAGACGAGCA
Statistics
Matches: 53, Mismatches: 20, Indels: 14
0.61 0.23 0.16
Matches are distributed among these distances:
34 5 0.09
35 3 0.06
36 6 0.11
37 10 0.19
38 15 0.28
39 6 0.11
40 3 0.06
41 5 0.09
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (38 bp):
TAACTCGGACGGGGTTACTAGACACTATTGTTTATGAA
Found at i:38613258 original size:75 final size:75
Alignment explanation
Indices: 38613135--38613398 Score: 501
Period size: 75 Copynumber: 3.5 Consensus size: 75
38613125 ATATATATAT
38613135 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAACTCGGACGGGGTTACTAGACACTATTG
1 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAACTCGGACGGGGTTACTAGACACTATTG
38613200 TTTATGAATA
66 TTTATGAATA
38613210 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAACTCGGACGGGGTTACTAGACACTATTG
1 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAACTCGGACGGGGTTACTAGACACTATTG
38613275 TTTATGAATA
66 TTTATGAATA
*
38613285 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGGTTTAACTCGGACGGGGTTACTAGACACTATTG
1 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAACTCGGACGGGGTTACTAGACACTATTG
38613350 TTTATGAATA
66 TTTATGAATA
* *
38613360 GCTTAGACGAGCAATTTTCATTTGTTGTGTAGGTTTAAC
1 ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAAC
38613399 CCAAATGGGT
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 187 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (75 bp):
ACTTAGACGAGCAATTTTCATTTGTTGTGTAGATTTAACTCGGACGGGGTTACTAGACACTATTG
TTTATGAATA
Found at i:38615440 original size:2 final size:2
Alignment explanation
Indices: 38615433--38615458 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38615423 CTCAAATTGG
38615433 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
38615459 TGTAACACCA
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:38616874 original size:27 final size:27
Alignment explanation
Indices: 38616816--38616875 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
38616806 CCGTGGACAG
* * * * *
38616816 CGACCGGCAGTCGCCACGGTGGTCTGG
1 CGACCGACAGTCGCCACGATGGACCGA
*
38616843 TGACCGACAGTCGCCACGATGGACCGA
1 CGACCGACAGTCGCCACGATGGACCGA
38616870 CGACCG
1 CGACCG
38616876 GGGTTCGGTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12
Consensus pattern (27 bp):
CGACCGACAGTCGCCACGATGGACCGA
Found at i:38617475 original size:20 final size:20
Alignment explanation
Indices: 38617452--38617515 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
38617442 TTTAAATAGA
38617452 TTATTCTT-TTTTTGTGTATT
1 TTATTCTTATTTTTGT-TATT
* *
38617472 TTATTTTTATTTTTGTTTTT
1 TTATTCTTATTTTTGTTATT
* *
38617492 TTATTTTTATTTTT-TTGTT
1 TTATTCTTATTTTTGTTATT
38617511 TTATT
1 TTATT
38617516 ATTTCTATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.22
20 24 0.60
21 7 0.17
ACGTcount: A:0.11, C:0.02, G:0.06, T:0.81
Consensus pattern (20 bp):
TTATTCTTATTTTTGTTATT
Found at i:38617482 original size:26 final size:26
Alignment explanation
Indices: 38617452--38617505 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
38617442 TTTAAATAGA
38617452 TTATTCTTT-TTTTGTGTA-TTTTATTT
1 TTATT-TTTGTTTT-TGTATTTTTATTT
*
38617478 TTATTTTTGTTTTTTTATTTTTATTT
1 TTATTTTTGTTTTTGTATTTTTATTT
38617504 TT
1 TT
38617506 TTGTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.11, C:0.02, G:0.06, T:0.81
Consensus pattern (26 bp):
TTATTTTTGTTTTTGTATTTTTATTT
Found at i:38617492 original size:14 final size:14
Alignment explanation
Indices: 38617475--38617512 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
38617465 GTGTATTTTA
*
38617475 TTTTTATTTTTGTT
1 TTTTTATTTTTATT
38617489 TTTTTATTTTTATT
1 TTTTTATTTTTATT
*
38617503 TTTTTGTTTT
1 TTTTTATTTT
38617513 ATTATTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.00, G:0.05, T:0.87
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:38617506 original size:22 final size:22
Alignment explanation
Indices: 38617458--38617524 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
38617448 TAGATTATTC
*
38617458 TTTTTTTGTGTATTTTATTTTTA
1 TTTTTTTGT-TTTTTTATTTTTA
38617481 --TTTTTGTTTTTTTATTTTTA
1 TTTTTTTGTTTTTTTATTTTTA
* *
38617501 TTTTTTTGTTTTATTATTTCTA
1 TTTTTTTGTTTTTTTATTTTTA
38617523 TT
1 TT
38617525 GATTATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.31
21 7 0.18
22 20 0.51
ACGTcount: A:0.12, C:0.01, G:0.06, T:0.81
Consensus pattern (22 bp):
TTTTTTTGTTTTTTTATTTTTA
Found at i:38620548 original size:46 final size:46
Alignment explanation
Indices: 38620483--38620615 Score: 187
Period size: 46 Copynumber: 2.9 Consensus size: 46
38620473 AAAGTGTGGG
* *
38620483 ACGTAGGTATGGTAATTCAGTAAAGAAAACCATACTGAGTTGTGGA
1 ACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAA
* *
38620529 ATGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAA
1 ACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAA
* * *
38620575 ACGTAGGTATAGTATTTCAATAACA-AAAATCATACTGAGTT
1 ACGTAGGTATGGTATTTCAGTAA-AGAAAACCATACTGAGTT
38620616 ATAGCATTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 76 0.99
47 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (46 bp):
ACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAA
Found at i:38622949 original size:10 final size:10
Alignment explanation
Indices: 38622932--38622961 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
38622922 TATTTTTAAA
38622932 AAAATTAATT
1 AAAATTAATT
*
38622942 ATAATTAATT
1 AAAATTAATT
38622952 AAAATTAATT
1 AAAATTAATT
38622962 TGAGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AAAATTAATT
Found at i:38638015 original size:24 final size:24
Alignment explanation
Indices: 38637999--38638052 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
38637989 AATCAAAGTC
38637999 AAATATATTATTTTAATAAATACT
1 AAATATATTATTTTAATAAATACT
** * *
38638023 AAATATATTATACTCATAAATATT
1 AAATATATTATTTTAATAAATACT
38638047 AAATAT
1 AAATAT
38638053 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATATTATTTTAATAAATACT
Found at i:38640523 original size:20 final size:20
Alignment explanation
Indices: 38640498--38640536 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38640488 GGTTCATTCT
38640498 AAATA-TATTTATCAATTTTA
1 AAATATTATTTAT-AATTTTA
*
38640518 AAATATTTTTTATAATTTT
1 AAATATTATTTATAATTTT
38640537 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATATTATTTATAATTTTA
Found at i:38658857 original size:3 final size:3
Alignment explanation
Indices: 38658836--38658872 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
38658826 TCTGTGATGT
* *
38658836 TGC TGC GGC TGC GGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
38658873 CCCACCACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.32, G:0.38, T:0.30
Consensus pattern (3 bp):
TGC
Found at i:38658967 original size:15 final size:15
Alignment explanation
Indices: 38658943--38659015 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 15
38658933 TTTCGCGGCA
*
38658943 GCTGCGGTTGTGGCT
1 GCTGCTGTTGTGGCT
38658958 GCTGCTGTTGT---T
1 GCTGCTGTTGTGGCT
*
38658970 GCT-C--TTGTTGCT
1 GCTGCTGTTGTGGCT
*
38658982 GCTGCTCTTGTGGCT
1 GCTGCTGTTGTGGCT
* *
38658997 GCTGCTGCTGTTGCT
1 GCTGCTGTTGTGGCT
38659012 GCTG
1 GCTG
38659016 GGCGTTGTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
9 4 0.09
11 1 0.02
12 8 0.17
13 1 0.02
15 33 0.70
ACGTcount: A:0.00, C:0.23, G:0.36, T:0.41
Consensus pattern (15 bp):
GCTGCTGTTGTGGCT
Found at i:38659005 original size:24 final size:24
Alignment explanation
Indices: 38658955--38659011 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
38658945 TGCGGTTGTG
* * *
38658955 GCTGCTGCTGTTGTTGCTCTTGTT
1 GCTGCTGCTCTTGTGGCTCTTGCT
38658979 GCTGCTGCTCTTGTGGCTGC-TGCT
1 GCTGCTGCTCTTGTGGCT-CTTGCT
*
38659003 GCTGTTGCT
1 GCTGCTGCT
38659012 GCTGGGCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.00, C:0.25, G:0.32, T:0.44
Consensus pattern (24 bp):
GCTGCTGCTCTTGTGGCTCTTGCT
Found at i:38661294 original size:19 final size:19
Alignment explanation
Indices: 38661262--38661299 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
38661252 ATTAAAGTTT
38661262 TATTTTAATTTATT-TGTA
1 TATTTTAATTTATTATGTA
38661280 TATTTTAATTTTATTATGTA
1 TATTTTAA-TTTATTATGTA
38661300 CACTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTTTAATTTATTATGTA
Found at i:38667124 original size:21 final size:20
Alignment explanation
Indices: 38667090--38667135 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
38667080 CTAAAATGTG
* *
38667090 AATTTGATTGAATTGAATATA
1 AATTTCATTAAATTGAAT-TA
*
38667111 AATTTCATTAAATTGAGTTA
1 AATTTCATTAAATTGAATTA
38667131 AATTT
1 AATTT
38667136 ACCCATATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (20 bp):
AATTTCATTAAATTGAATTA
Found at i:38674998 original size:14 final size:15
Alignment explanation
Indices: 38674979--38675011 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38674969 AGGTATGCTT
*
38674979 CTTTTTT-CTTTTTC
1 CTTTTTTACTTTCTC
38674993 CTTTTTTACTTTCTC
1 CTTTTTTACTTTCTC
38675008 CTTT
1 CTTT
38675012 AGAGGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTTTTACTTTCTC
Found at i:38676242 original size:72 final size:72
Alignment explanation
Indices: 38676151--38676327 Score: 266
Period size: 72 Copynumber: 2.5 Consensus size: 72
38676141 AACTAGTTTT
* * *
38676151 TATCAATTGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTGTACTTATTTATGTGTAAT
1 TATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATGTATAAT
*
38676216 CTAGTTG
66 CTAATTG
* * *
38676223 TATCAATAGTTGCTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTATAAT
1 TATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATGTATAAT
*
38676288 CTAATTT
66 CTAATTG
*
38676295 TATCAATAGTAGTTTATGTTTGA-TTTTGGATAT
1 TATCAATAGTTGTTTATGTTTGATTTTTGGATAT
38676328 AAAATTTGTT
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 10 0.11
72 84 0.89
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (72 bp):
TATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATATTCTACTTATTTATGTATAAT
CTAATTG
Found at i:38679846 original size:1 final size:1
Alignment explanation
Indices: 38679840--38679884 Score: 81
Period size: 1 Copynumber: 45.0 Consensus size: 1
38679830 AATAAGAGAC
*
38679840 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38679885 GACAATACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:38680582 original size:82 final size:83
Alignment explanation
Indices: 38680425--38680582 Score: 239
Period size: 82 Copynumber: 1.9 Consensus size: 83
38680415 ATCCGGCCGT
* *
38680425 CATTCCAATAATGATTAATTAAACAAGTAAAAAATAACAAAAATTAAACAACTTATAAATTAGTT
1 CATTCCAACAATGATTAAATAAACAAGTAAAAAATAACAAAAATTAAACAACTTATAAATTAGTT
*
38680490 CAATATTCATTCAATCGC
66 CAATAATCATTCAATCGC
* * *
38680508 CATTCGAACAATGATTAAATAAACAAGTAAAAAGTAA-AAAATTTAAACAACTTATAAATT-GAT
1 CATTCCAACAATGATTAAATAAACAAGTAAAAAATAACAAAAATTAAACAACTTATAAATTAG-T
38680571 TCAATAATCATT
65 TCAATAATCATT
38680583 TTTTCTTCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 1 0.01
82 34 0.50
83 33 0.49
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.30
Consensus pattern (83 bp):
CATTCCAACAATGATTAAATAAACAAGTAAAAAATAACAAAAATTAAACAACTTATAAATTAGTT
CAATAATCATTCAATCGC
Found at i:38682176 original size:23 final size:23
Alignment explanation
Indices: 38682145--38682192 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
38682135 TTTAGATAAC
38682145 TTACCGTCAATTCATCATTTACA
1 TTACCGTCAATTCATCATTTACA
* *
38682168 TTACTGTCAATTCATCCTTTACA
1 TTACCGTCAATTCATCATTTACA
38682191 TT
1 TT
38682193 TTTCTTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.04, T:0.44
Consensus pattern (23 bp):
TTACCGTCAATTCATCATTTACA
Found at i:38682236 original size:23 final size:24
Alignment explanation
Indices: 38682200--38682248 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
38682190 ATTTTTCTTC
38682200 TTACATTTTTCGTCAATTCATCCT
1 TTACATTTTTCGTCAATTCATCCT
38682224 TTACA-TTTTCGTCAATTCATCCT
1 TTACATTTTTCGTCAATTCATCCT
38682247 TT
1 TT
38682249 CCCAATAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.51
Consensus pattern (24 bp):
TTACATTTTTCGTCAATTCATCCT
Found at i:38685088 original size:6 final size:6
Alignment explanation
Indices: 38685077--38685101 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38685067 TTCTTCAACT
38685077 AAGCCC AAGCCC AAGCCC AAGCCC A
1 AAGCCC AAGCCC AAGCCC AAGCCC A
38685102 TATCCAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGCCC
Found at i:38688363 original size:29 final size:31
Alignment explanation
Indices: 38688298--38688365 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
38688288 AATATCAAAA
38688298 TTATACATGAACTTTGATCTAATGTGCAATG
1 TTATACATGAACTTTGATCTAATGTGCAATG
** * *
38688329 CCATACATGAACTTTGAT-T-TTGTGCAATT
1 TTATACATGAACTTTGATCTAATGTGCAATG
38688358 TTATACAT
1 TTATACAT
38688366 AAAGTTTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 14 0.45
30 1 0.03
31 16 0.52
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (31 bp):
TTATACATGAACTTTGATCTAATGTGCAATG
Found at i:38693184 original size:9 final size:9
Alignment explanation
Indices: 38693172--38693228 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
38693162 TTAACCCATT
38693172 TAAAAATTA
1 TAAAAATTA
38693181 TAAAACATTCA
1 TAAAA-ATT-A
38693192 -AAAAATTA
1 TAAAAATTA
*
38693200 -AATAA-TA
1 TAAAAATTA
*
38693207 TAAAAAATA
1 TAAAAATTA
38693216 TAAAAATTA
1 TAAAAATTA
38693225 -AAAA
1 TAAAA
38693229 GAAGCATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
7 2 0.05
8 13 0.32
9 18 0.44
10 7 0.17
11 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (9 bp):
TAAAAATTA
Found at i:38693211 original size:17 final size:16
Alignment explanation
Indices: 38693179--38693228 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
38693169 ATTTAAAAAT
38693179 TATAAAACATTCAAAAAA
1 TATAAAA-ATT-AAAAAA
38693197 T-TAAATAATATAAAAAA
1 TATAAA-AAT-TAAAAAA
38693214 TATAAAAATTAAAAA
1 TATAAAAATTAAAAA
38693229 GAAGCATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.21
17 16 0.55
18 7 0.24
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
TATAAAAATTAAAAAA
Found at i:38696945 original size:53 final size:53
Alignment explanation
Indices: 38696885--38696995 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
38696875 AAATTTAAGA
38696885 AAAATAATTTTAATAGTGTTAACAATTAAAAATGAACTAAATTTCAATTTTAC
1 AAAATAATTTTAATAGTGTTAACAATTAAAAATGAACTAAATTTCAATTTTAC
38696938 AAAATAATTTTAATAGTGTTAACAATTAAAAATGAACTAAATTTCAATTTTAC
1 AAAATAATTTTAATAGTGTTAACAATTAAAAATGAACTAAATTTCAATTTTAC
38696991 AAAAT
1 AAAAT
38696996 GTACAAGGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.37
Consensus pattern (53 bp):
AAAATAATTTTAATAGTGTTAACAATTAAAAATGAACTAAATTTCAATTTTAC
Found at i:38699419 original size:45 final size:45
Alignment explanation
Indices: 38699355--38699444 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
38699345 TTACCCCATC
38699355 ACTTAATTTATTACTTAAATAATGACCTCTCAGCTCTCTTCCTTT
1 ACTTAATTTATTACTTAAATAATGACCTCTCAGCTCTCTTCCTTT
38699400 ACTTAATTTATTACTTAAATAATGACCTCTCAGCTCTCTTCCTTT
1 ACTTAATTTATTACTTAAATAATGACCTCTCAGCTCTCTTCCTTT
38699445 TTTTATGTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.44
Consensus pattern (45 bp):
ACTTAATTTATTACTTAAATAATGACCTCTCAGCTCTCTTCCTTT
Found at i:38705431 original size:144 final size:145
Alignment explanation
Indices: 38705249--38705536 Score: 569
Period size: 144 Copynumber: 2.0 Consensus size: 145
38705239 AATTATTTGT
38705249 AAATGTTTATATTTTAATAATTTAAATTATATAAATAAATTCCATTATATTTTTTTATGTTATTT
1 AAATGTTTATATTTTAATAATTTAAATTATATAAATAAATTCCATTATATTTTTTTATGTTATTT
38705314 CTTGTTTAGATTATATATTAATTAGTTTTACGTTTGTGTAAACTTTACTTATATTAAACTATTGT
66 CTTGTTTAGATTATATATTAATTAGTTTTACGTTTGTGTAAACTTTACTTATATTAAACTATTGT
38705379 AAGTTTATATTTTAG
131 AAGTTTATATTTTAG
38705394 AAATGTTTA-ATTTTAATAATTTAAATTATATAAATAAATTCCATTATATTTTTTTATGTTATTT
1 AAATGTTTATATTTTAATAATTTAAATTATATAAATAAATTCCATTATATTTTTTTATGTTATTT
38705458 CTTGTTTAGATTATATATTAATTAGTTTTACGTTTGTGTAAACTTTACTTATATTAAACTATTGT
66 CTTGTTTAGATTATATATTAATTAGTTTTACGTTTGTGTAAACTTTACTTATATTAAACTATTGT
38705523 AAGTTTATATTTTA
131 AAGTTTATATTTTA
38705537 ATCACTCAAC
Statistics
Matches: 143, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
144 134 0.94
145 9 0.06
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (145 bp):
AAATGTTTATATTTTAATAATTTAAATTATATAAATAAATTCCATTATATTTTTTTATGTTATTT
CTTGTTTAGATTATATATTAATTAGTTTTACGTTTGTGTAAACTTTACTTATATTAAACTATTGT
AAGTTTATATTTTAG
Found at i:38709382 original size:31 final size:31
Alignment explanation
Indices: 38709347--38709442 Score: 79
Period size: 31 Copynumber: 3.2 Consensus size: 31
38709337 CTCAAAGTTA
*
38709347 TACATCAACTATGGTTTTATATGTAATTGTT
1 TACATCAACTATGGTTTTATATGTAATTATT
* * * * * *
38709378 TACATGAA-TTTTGATTT-GATCTAATTATT
1 TACATCAACTATGGTTTTATATGTAATTATT
* * * *
38709407 AACATCAACTATGGTTTAATATGCAATTTTT
1 TACATCAACTATGGTTTTATATGTAATTATT
38709438 TACAT
1 TACAT
38709443 GAATTTTGAT
Statistics
Matches: 45, Mismatches: 18, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
29 15 0.33
30 11 0.24
31 19 0.42
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (31 bp):
TACATCAACTATGGTTTTATATGTAATTATT
Found at i:38709403 original size:29 final size:29
Alignment explanation
Indices: 38709370--38709466 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
38709360 GTTTTATATG
* *
38709370 TAATTGTTTACATGAATTTTGATTTGATC
1 TAATTATTTACATGAATTTTGATTTAATC
* * * * * *
38709399 TAATTATTAACATCAACTATGGTTTAATA
1 TAATTATTTACATGAATTTTGATTTAATC
* *
38709428 TGCAATTTTTTACATGAATTTTGATTTTATC
1 T--AATTATTTACATGAATTTTGATTTAATC
38709459 TAATTATT
1 TAATTATT
38709467 GATATAATAT
Statistics
Matches: 49, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
29 28 0.57
31 21 0.43
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (29 bp):
TAATTATTTACATGAATTTTGATTTAATC
Found at i:38709421 original size:60 final size:60
Alignment explanation
Indices: 38709348--38709466 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
38709338 TCAAAGTTAT
* *
38709348 ACATCAACTATGGTTTTATATGTAATTGTTTACATGAATTTTGATTTGATCTAATTATTA
1 ACATCAACTATGGTTTAATATGCAATTGTTTACATGAATTTTGATTTGATCTAATTATTA
* *
38709408 ACATCAACTATGGTTTAATATGCAATTTTTTACATGAATTTTGATTTTATCTAATTATT
1 ACATCAACTATGGTTTAATATGCAATTGTTTACATGAATTTTGATTTGATCTAATTATT
38709467 GATATAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.49
Consensus pattern (60 bp):
ACATCAACTATGGTTTAATATGCAATTGTTTACATGAATTTTGATTTGATCTAATTATTA
Found at i:38711054 original size:29 final size:29
Alignment explanation
Indices: 38711003--38711064 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
38710993 TATGCAAAAT
38711003 AAAAATTCTTTAAAACTCAAAAAA-TTTA
1 AAAAATTCTTTAAAACTCAAAAAAGTTTA
* *
38711031 AAAAGATTCTTTAAAAGT-ATAAAAAGTTTT
1 AAAA-ATTCTTTAAAACTCA-AAAAAGTTTA
38711061 AAAA
1 AAAA
38711065 TTTAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 17 0.59
30 7 0.24
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAAATTCTTTAAAACTCAAAAAAGTTTA
Found at i:38713170 original size:34 final size:34
Alignment explanation
Indices: 38713118--38713266 Score: 147
Period size: 34 Copynumber: 4.4 Consensus size: 34
38713108 ACATGCACAT
* * *
38713118 ATCAATACGGTAGCAATTAATATGCTTGTAACAG
1 ATCAATACAGTAGCAATTAATATGCTTATAACAA
* * *
38713152 ATCAGTACAGTAGTAATTAATATGCTTATAACAG
1 ATCAATACAGTAGCAATTAATATGCTTATAACAA
* * *
38713186 ATCAATA-TGATAGCAATTTATATGCTTACAACAA
1 ATCAATACAG-TAGCAATTAATATGCTTATAACAA
** * *
38713220 ATCAATATGGTAGCAATTCATATGCTTCTAACAA
1 ATCAATACAGTAGCAATTAATATGCTTATAACAA
* *
38713254 ATCATTAAAGTAG
1 ATCAATACAGTAG
38713267 TAAAAGACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
33 1 0.01
34 94 0.98
35 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (34 bp):
ATCAATACAGTAGCAATTAATATGCTTATAACAA
Found at i:38713211 original size:68 final size:68
Alignment explanation
Indices: 38713118--38713257 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 68
38713108 ACATGCACAT
* ** * * *
38713118 ATCAATACGGTAGCAATTAATATGCTTGTAACAGATCAGTACAGTAGTAATTAATATGCTTATAA
1 ATCAATACGATAGCAATTAATATGCTTACAACAAATCAATACAGTAGCAATTAATATGCTTATAA
*
38713183 CAG
66 CAA
* * ** * *
38713186 ATCAATATGATAGCAATTTATATGCTTACAACAAATCAATATGGTAGCAATTCATATGCTTCTAA
1 ATCAATACGATAGCAATTAATATGCTTACAACAAATCAATACAGTAGCAATTAATATGCTTATAA
38713251 CAA
66 CAA
38713254 ATCA
1 ATCA
38713258 TTAAAGTAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (68 bp):
ATCAATACGATAGCAATTAATATGCTTACAACAAATCAATACAGTAGCAATTAATATGCTTATAA
CAA
Found at i:38718318 original size:17 final size:19
Alignment explanation
Indices: 38718296--38718334 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
38718286 CGAAATCAAC
*
38718296 AAAATA-AT-TATATTTTA
1 AAAATAGATATATATTCTA
38718313 AAAATAGATATATATTCTA
1 AAAATAGATATATATTCTA
38718332 AAA
1 AAA
38718335 TTAAATGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATAGATATATATTCTA
Found at i:38720575 original size:25 final size:25
Alignment explanation
Indices: 38720539--38720614 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
38720529 GACACACCAT
*
38720539 AGCTTGCATGAGCTTCCCGATATTC
1 AGCTCGCATGAGCTTCCCGATATTC
* * * *
38720564 AGCTCGCTTGAGCTTTCCGTTATAC
1 AGCTCGCATGAGCTTCCCGATATTC
* *
38720589 AGCTTGCATGAGCTTCTCGATATTC
1 AGCTCGCATGAGCTTCCCGATATTC
38720614 A
1 A
38720615 ACTCTGAGGA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCCCGATATTC
Found at i:38720627 original size:50 final size:49
Alignment explanation
Indices: 38720539--38720638 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 49
38720529 GACACACCAT
* **
38720539 AGCTTGCATGAGCTTCCCGATATTCAGCTCGCTTGAGCTTTCCGTTATAC
1 AGCTTGCATGAGCTTCCCGATATTCAACTCGCAGGAGCTTTCCGTT-TAC
*
38720589 AGCTTGCATGAGCTTCTCGATATTCAACTCTG-AGGAGCTTTCCGTTTAC
1 AGCTTGCATGAGCTTCCCGATATTCAACTC-GCAGGAGCTTTCCGTTTAC
38720638 A
1 A
38720639 ACTCATATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
49 4 0.09
50 40 0.89
51 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (49 bp):
AGCTTGCATGAGCTTCCCGATATTCAACTCGCAGGAGCTTTCCGTTTAC
Found at i:38727003 original size:24 final size:22
Alignment explanation
Indices: 38726976--38727020 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
38726966 ATTTAATTTT
38726976 TATATTATATAAATATTAAAAAAA
1 TATATTATA-AAAT-TTAAAAAAA
*
38727000 TATATTATAGAATTTAAAAAA
1 TATATTATAAAATTTAAAAAA
38727021 TAAGTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TATATTATAAAATTTAAAAAAA
Found at i:38727142 original size:131 final size:132
Alignment explanation
Indices: 38726994--38727256 Score: 519
Period size: 131 Copynumber: 2.0 Consensus size: 132
38726984 ATAAATATTA
38726994 AAAAAATATATTATAGAATTTAAAAAATAAGTCAAAGTTCAAATTCCATTCATTTTTAAATAATT
1 AAAAAATATATTATAGAATTTAAAAAATAAGTCAAAGTTCAAATTCCATTCATTTTTAAATAATT
38727059 TAAATCATTATTATCTAAGAGATAATGTAACATTTAATCATTAAAATTTTGACCTGTAGATCGGG
66 TAAATCATTATTATCTAAGAGATAATGTAACATTTAATCATTAAAATTTTGACCTGTAGATCGGG
38727124 TG
131 TG
38727126 AAAAAATATA-TATAGAATTTAAAAAATAAGTCAAAGTTCAAATTCCATTCATTTTTAAATAATT
1 AAAAAATATATTATAGAATTTAAAAAATAAGTCAAAGTTCAAATTCCATTCATTTTTAAATAATT
38727190 TAAATCATTATTATCTAAGAGATAATGTAACATTTAATCATTAAAATTTTGACCTGTAGATCGGG
66 TAAATCATTATTATCTAAGAGATAATGTAACATTTAATCATTAAAATTTTGACCTGTAGATCGGG
38727255 TG
131 TG
38727257 TTTATTTTTT
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 121 0.92
132 10 0.08
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (132 bp):
AAAAAATATATTATAGAATTTAAAAAATAAGTCAAAGTTCAAATTCCATTCATTTTTAAATAATT
TAAATCATTATTATCTAAGAGATAATGTAACATTTAATCATTAAAATTTTGACCTGTAGATCGGG
TG
Found at i:38739997 original size:16 final size:16
Alignment explanation
Indices: 38739959--38739999 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
38739949 ATTTTTAAAC
* *
38739959 TTAAAACTAATTGTTA
1 TTAAAATTAATTATTA
38739975 TTAAAATTAATTATTA
1 TTAAAATTAATTATTA
38739991 TTAAAATTA
1 TTAAAATTA
38740000 TATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAAAATTAATTATTA
Found at i:38741865 original size:21 final size:21
Alignment explanation
Indices: 38741835--38741882 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
38741825 TTTGATTTGA
38741835 TAAGA-TAACACATTATCTCT
1 TAAGAGTAACACATTATCTCT
38741855 TAAGAGTAACACATTATCTCT
1 TAAGAGTAACACATTATCTCT
38741876 TAAGAGT
1 TAAGAGT
38741883 TTTTTTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAGAGTAACACATTATCTCT
Found at i:38748878 original size:41 final size:41
Alignment explanation
Indices: 38748833--38748956 Score: 248
Period size: 41 Copynumber: 3.0 Consensus size: 41
38748823 CTTTTGAGAG
38748833 TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
1 TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
38748874 TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
1 TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
38748915 TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
1 TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
38748956 T
1 T
38748957 TGTTTCATGG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.61
Consensus pattern (41 bp):
TATGCTTTTTTTAGATTTTTCACATTGTTTTTTCCTCTCCT
Found at i:38757124 original size:22 final size:21
Alignment explanation
Indices: 38757086--38757129 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
38757076 GTGAAACAAA
* *
38757086 TATGTAAATATATATAAAGTT
1 TATGTAAAAATAAATAAAGTT
*
38757107 TATGTTAAAAATAAATAAGGTT
1 TATG-TAAAAATAAATAAAGTT
38757129 T
1 T
38757130 TAGTTGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
TATGTAAAAATAAATAAAGTT
Found at i:38758048 original size:10 final size:9
Alignment explanation
Indices: 38758019--38758080 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 9
38758009 ATTTCTAATT
38758019 TTTTTAATAA
1 TTTTT-ATAA
*
38758029 TTTATATAA
1 TTTTTATAA
38758038 TTTTCTATAA
1 TTTT-TATAA
38758048 TTTTT-TAACA
1 TTTTTAT-A-A
38758058 TTTTTATAA
1 TTTTTATAA
38758067 TATTTTAATAA
1 T-TTTT-ATAA
38758078 TTT
1 TTT
38758081 CTAAAAGCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 1 0.02
9 11 0.25
10 26 0.59
11 6 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38758065 original size:19 final size:20
Alignment explanation
Indices: 38758037--38758074 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38758027 AATTTATATA
*
38758037 ATTTTCTATAATTTTTTAAC
1 ATTTTCTATAATATTTTAAC
38758057 ATTTT-TATAATATTTTAA
1 ATTTTCTATAATATTTTAA
38758075 TAATTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTCTATAATATTTTAAC
Found at i:38760745 original size:20 final size:19
Alignment explanation
Indices: 38760720--38760766 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
38760710 CTAATTCTTG
*
38760720 ATTAAAGATGAATTAAATTA
1 ATTAAACATG-ATTAAATTA
*
38760740 ATTAAAACATGATTAACTTA
1 ATT-AAACATGATTAAATTA
38760760 ATTAAAC
1 ATTAAAC
38760767 CAAGTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (19 bp):
ATTAAACATGATTAAATTA
Found at i:38762813 original size:56 final size:56
Alignment explanation
Indices: 38762727--38762836 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
38762717 GAGCAAGATC
38762727 ACACTACCCTTTAGCTCTTTTTGGTATAAATAGCAAACTTTAATTAGGATATAAAT
1 ACACTACCCTTTAGCTCTTTTTGGTATAAATAGCAAACTTTAATTAGGATATAAAT
38762783 ACACTACCCTTTAGCTCTTTTTGGTATAAATAGCAAACTTTAATTAGGATATAA
1 ACACTACCCTTTAGCTCTTTTTGGTATAAATAGCAAACTTTAATTAGGATATAA
38762837 TGACATGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (56 bp):
ACACTACCCTTTAGCTCTTTTTGGTATAAATAGCAAACTTTAATTAGGATATAAAT
Found at i:38767790 original size:271 final size:271
Alignment explanation
Indices: 38767491--38768156 Score: 1125
Period size: 271 Copynumber: 2.5 Consensus size: 271
38767481 GATATGATTT
*
38767491 GCTCTACTGCAACTTTAGAGATATGAGATCTGTTATGGTAGATTTAATCTGTTCCACTGCAACTT
1 GCTCTACTGCAACTTTAGAGAGATGAGATCTGTTATGGTAGATTTAATCTGTTCCACTGCAACTT
* *
38767556 CAGGGAAATAATATTTGCTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATCCATCA
66 CAGGGAAATAAGATTTGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATCCATCA
* * * *
38767621 TTTTAATCCGCTCCACTGCAACTTTAGGGAGGTAGGATTCGTAACTTCAATCTGCTCTACTACAA
131 TTTTAATCCGCTCCACTGCAACTTCAAGGAGGTAGGATTAGTAACTTCAATCTGCTCCACTACAA
*
38767686 CTTCAGGGAGATAAGACTTGTATCTTCAACTTGCCCCACTGCAACTTCATAGGGATAAGGTTTAC
196 CTTCAGGGAGATAAGACTTGTATCTTCAACTTGCCCCACTGCAACTTCATAGGGATAAGGGTTAC
*
38767751 TATTTCAACCT
261 TATTTCAACCG
* * *
38767762 GTTCTACTGCAACTTTAGAGAGATGAGATCTGTTATGGTAGATTTAATTTGTTCCATTGCAACTT
1 GCTCTACTGCAACTTTAGAGAGATGAGATCTGTTATGGTAGATTTAATCTGTTCCACTGCAACTT
*
38767827 CAAGGAAATAAGATTTGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATCCATCA
66 CAGGGAAATAAGATTTGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATCCATCA
* *
38767892 TTTTAATCCGCTCCACTGTAACTTCAAGGAGGTAGGATTAGTAACTTCAATCTGCTCCACTGCAA
131 TTTTAATCCGCTCCACTGCAACTTCAAGGAGGTAGGATTAGTAACTTCAATCTGCTCCACTACAA
* * *
38767957 CTTCAGGGAGATAAGACTTGTATCTTCAACTTGCCCTACTGCAACTTCATGGGGATAAGGGTTGC
196 CTTCAGGGAGATAAGACTTGTATCTTCAACTTGCCCCACTGCAACTTCATAGGGATAAGGGTTAC
38768022 TATTTCAACCG
261 TATTTCAACCG
* *
38768033 GCTCTACTGCAACTTTAGAGAGATGAGATATGTTATGGTAGATTTAATCTGTTCCACTACAACTT
1 GCTCTACTGCAACTTTAGAGAGATGAGATCTGTTATGGTAGATTTAATCTGTTCCACTGCAACTT
* * *
38768098 CAGGGAAACAAGATTTGCGATCTTTAATCTACTCCACTACAACTTCAGGGAGATAGGAT
66 CAGGGAAATAAGATTTGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGAT
38768157 TTGTGGTGAT
Statistics
Matches: 368, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
271 368 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (271 bp):
GCTCTACTGCAACTTTAGAGAGATGAGATCTGTTATGGTAGATTTAATCTGTTCCACTGCAACTT
CAGGGAAATAAGATTTGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATCCATCA
TTTTAATCCGCTCCACTGCAACTTCAAGGAGGTAGGATTAGTAACTTCAATCTGCTCCACTACAA
CTTCAGGGAGATAAGACTTGTATCTTCAACTTGCCCCACTGCAACTTCATAGGGATAAGGGTTAC
TATTTCAACCG
Found at i:38767984 original size:44 final size:44
Alignment explanation
Indices: 38767340--38768160 Score: 378
Period size: 44 Copynumber: 18.2 Consensus size: 44
38767330 ACTTCAAAGG
* *
38767340 TAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGA
1 TAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* * * *
38767385 TAAGAATTGTATCTTCAA-CTTCCCCTACTGCAACTTCATAGG-GA
1 TAAGATTTGTATCTTCAATCTGCTCC-ACTGCAACTTCA-GGGAGA
* * ** *
38767429 TAAGGTTTGCTAT-TTCAACCTGCTGTACTGCAACTTCAGAGAGA
1 TAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* * * * * * *
38767473 TAA-AGTTTG-AT-AT-GATTTGCTCTACTGCAACTTTAGAGATA
1 TAAGA-TTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* ** * * *
38767514 TGAGATCTGTTATGGTAGATTTAATCTGTTCCACTGCAACTTCAGGGAAA
1 TAAGA----TT-T-GTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* *
38767564 TAATATTTGCTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
1 TAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* *** * * * *
38767609 TAGGATCCATCAT-TTTAATCCGCTCCACTGCAACTTTAGGGAGG
1 TAAGATTTGT-ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* * * * *
38767653 TAGGATTCGTAACTTCAATCTGCTCTACTACAACTTCAGGGAGA
1 TAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* * *
38767697 TAAGACTTGTATCTTCAA-CTTGCCCCACTGCAACTTCATAGG-GA
1 TAAGATTTGTATCTTCAATC-TGCTCCACTGCAACTTCA-GGGAGA
* * * * * * *
38767741 TAAGGTTTACTAT-TTCAACCTGTTCTACTGCAACTTTAGAGAGA
1 TAAGATTT-GTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* ** * * * * * *
38767785 TGAGATCTGTTATGGTAGATTTAATTTGTTCCATTGCAACTTCAAGGAAA
1 TAAGA----TT-T-GTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* *
38767835 TAAGATTTGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGA
1 TAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* *** * * * * *
38767880 TAGGATCCATCAT-TTTAATCCGCTCCACTGTAACTTCAAGGAGG
1 TAAGATTTGT-ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* * *
38767924 TAGGATTAGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGA
1 TAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
*
38767968 TAAGACTTGTATCTTCAA-CTTGC-CCTACTGCAACTTCATGGG-GA
1 TAAGATTTGTATCTTCAATC-TGCTCC-ACTGCAACTTCA-GGGAGA
** * * * * *
38768012 TAAGGGTTGCTAT-TTCAACCGGCTCTACTGCAACTTTAGAGAGA
1 TAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* ** * * * *
38768056 TGAGATATGTTATGGTAGATTTAATCTGTTCCACTACAACTTCAGGGAAA
1 T-A-AGA--TT-T-GTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* * * * *
38768106 CAAGATTTGCGATCTTTAATCTACTCCACTACAACTTCAGGGAGA
1 TAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
*
38768151 TAGGATTTGT
1 TAAGATTTGT
38768161 GGTGATTCGA
Statistics
Matches: 584, Mismatches: 145, Indels: 95
0.71 0.18 0.12
Matches are distributed among these distances:
41 24 0.04
42 4 0.01
43 15 0.03
44 300 0.51
45 145 0.25
46 8 0.01
47 1 0.00
48 6 0.01
49 8 0.01
50 73 0.12
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
TAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
Found at i:38769111 original size:104 final size:104
Alignment explanation
Indices: 38768925--38769118 Score: 273
Period size: 104 Copynumber: 1.9 Consensus size: 104
38768915 AAAAAACTTT
* * * * *
38768925 TGAAAAAGATTGTCACAATGGACAAGATGAGATTTTATGGAGAACAAAGCTCGAGATGAATGAGT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATGGAGAACAAAGCTCGAGATGAATAAAT
38768990 TAATAAGGATAGAAAATTTTGCTAATATACGAAATGAGA
66 TAATAAGGATAGAAAATTTTGCTAATATACGAAATGAGA
* * ** *
38769029 TGAAAAAGATTATTATAATGGACAAAATGAAATTTTATTTAGAGCAAAGCTCGAGATGAATAAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATGGAGAACAAAGCTCGAGATGAATAAAT
*
38769094 TAATCAGGATA-ACAAATTTTGCTAA
66 TAATAAGGATAGA-AAATTTTGCTAA
38769119 GATTAAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 1 0.01
104 77 0.99
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (104 bp):
TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATGGAGAACAAAGCTCGAGATGAATAAAT
TAATAAGGATAGAAAATTTTGCTAATATACGAAATGAGA
Found at i:38793349 original size:17 final size:17
Alignment explanation
Indices: 38793307--38793340 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38793297 CTTTTCTTCT
*
38793307 CCAACTTTATCTATTAG
1 CCAACTTTGTCTATTAG
38793324 CCAACTTTGTCTATTAG
1 CCAACTTTGTCTATTAG
38793341 TTAACTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (17 bp):
CCAACTTTGTCTATTAG
Found at i:38795912 original size:41 final size:40
Alignment explanation
Indices: 38795866--38795957 Score: 94
Period size: 41 Copynumber: 2.3 Consensus size: 40
38795856 AGTTTTAGTT
*
38795866 AATAATAATATCCAAAATATTATATTAATTTTAAAAAACAC
1 AATAATAATATCCAAAATATTATATTAATATT-AAAAACAC
* ** * * * *
38795907 AATAATATTATTTAAAGTATTATTTTAATATTAATATCAC
1 AATAATAATATCCAAAATATTATATTAATATTAAAAACAC
*
38795947 AATAATCATAT
1 AATAATAATAT
38795958 GGCTGAGATA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
40 15 0.37
41 26 0.63
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (40 bp):
AATAATAATATCCAAAATATTATATTAATATTAAAAACAC
Found at i:38796542 original size:25 final size:27
Alignment explanation
Indices: 38796514--38796563 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
38796504 ATATTTTTCT
38796514 ATGATGAAACAT-T-TATTATTAAATA
1 ATGATGAAACATATATATTATTAAATA
*
38796539 ATGATGAAATATATATATTATTAAA
1 ATGATGAAACATATATATTATTAAA
38796564 ATAGTAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (27 bp):
ATGATGAAACATATATATTATTAAATA
Found at i:38805894 original size:26 final size:26
Alignment explanation
Indices: 38805856--38805924 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
38805846 CTCGTTATAT
* *
38805856 GGCTCTTCATGAGCTTCTTGATTAAA
1 GGCTCTTCGTGAGCTTCTTGATCAAA
* *
38805882 GGCTCTTCGTGAGCTTCCTGATCAAT
1 GGCTCTTCGTGAGCTTCTTGATCAAA
*
38805908 GGCTCTCCG-GAGCTTCT
1 GGCTCTTCGTGAGCTTCT
38805925 CGATATGGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCTTGATCAAA
Found at i:38808029 original size:25 final size:25
Alignment explanation
Indices: 38807995--38808081 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
38807985 CACACATGTA
38807995 AACGGGAAGCTCTTTCGAGCCATAT
1 AACGGGAAGCTCTTTCGAGCCATAT
*
38808020 AACGGGAAGCTCATGT-GAGCCATGA-
1 AACGGGAAGCTC-TTTCGAGCCAT-AT
* * * **
38808045 AATGGGAAGCTCATTCTAGCTGTAT
1 AACGGGAAGCTCTTTCGAGCCATAT
*
38808070 AACAGGAAGCTC
1 AACGGGAAGCTC
38808082 ATAAGAGGCG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
24 2 0.04
25 44 0.90
26 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (25 bp):
AACGGGAAGCTCTTTCGAGCCATAT
Found at i:38808189 original size:50 final size:50
Alignment explanation
Indices: 38808117--38808214 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
38808107 AGCGAGCCAA
* * *
38808117 TATCGAGAAGCTCCGGAGAGCC-ATTAATCAGGAAA-CTCACAAGAGCCAGT
1 TATCGAGAAGCTCCGAAAAGCCAATT-ATC-GAAAAGCTCACAAGAGCCAGT
* * *
38808167 TATCGCGAAGCTCTGAAAAGCCAATTATCGAAAAGCTCATAAGAGCCA
1 TATCGAGAAGCTCCGAAAAGCCAATTATCGAAAAGCTCACAAGAGCCA
38808215 TAAACGGGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
49 4 0.10
50 33 0.82
51 3 0.08
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (50 bp):
TATCGAGAAGCTCCGAAAAGCCAATTATCGAAAAGCTCACAAGAGCCAGT
Found at i:38808213 original size:25 final size:25
Alignment explanation
Indices: 38808110--38808214 Score: 65
Period size: 25 Copynumber: 4.2 Consensus size: 25
38808100 AAGTTCAAGC
* ***
38808110 GAGCCAA-TATCGAGAAGCTCCGGA
1 GAGCCAATTATCGAAAAGCTCATAA
* *
38808134 GAGCC-ATTAATCAGGAAA-CTCACAA
1 GAGCCAATT-ATC-GAAAAGCTCATAA
* **
38808159 GAGCCAGTTATCGCGAAGCTC-TGAA
1 GAGCCAATTATCGAAAAGCTCAT-AA
*
38808184 AAGCCAATTATCGAAAAGCTCATAA
1 GAGCCAATTATCGAAAAGCTCATAA
38808209 GAGCCA
1 GAGCCA
38808215 TAAACGGGAA
Statistics
Matches: 60, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
23 1 0.02
24 9 0.15
25 44 0.73
26 6 0.10
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (25 bp):
GAGCCAATTATCGAAAAGCTCATAA
Found at i:38808252 original size:25 final size:24
Alignment explanation
Indices: 38808207--38808278 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 24
38808197 AAAAGCTCAT
38808207 AAGAGCCATA-AACGGGAAGCTCGC
1 AAGAGCCATATAACGGGAAGCTC-C
* *
38808231 AAGAACCATATAACGGGTAGCTCC
1 AAGAGCCATATAACGGGAAGCTCC
* *
38808255 ACAGAGCCATATATCGGGATGCTC
1 A-AGAGCCATATAACGGGAAGCTC
38808279 ATAAGAGCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 11 0.28
25 29 0.73
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (24 bp):
AAGAGCCATATAACGGGAAGCTCC
Found at i:38808285 original size:25 final size:25
Alignment explanation
Indices: 38808201--38808286 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 25
38808191 TTATCGAAAA
*
38808201 GCTCATAAGAGCCATA-AACGGGAA
1 GCTCATAAGAGCCATATAACGGGAT
** *
38808225 GCTCGCAAGAACCATATAACGGG-T
1 GCTCATAAGAGCCATATAACGGGAT
* *
38808249 AGCTCCA-CAGAGCCATATATCGGGAT
1 -GCT-CATAAGAGCCATATAACGGGAT
38808275 GCTCATAAGAGC
1 GCTCATAAGAGC
38808287 TACGGTGTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
24 15 0.31
25 31 0.65
26 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (25 bp):
GCTCATAAGAGCCATATAACGGGAT
Found at i:38809996 original size:25 final size:25
Alignment explanation
Indices: 38809949--38810038 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
38809939 TACAGCCCGG
* * *
38809949 ATGAGCTTCCTGTTACATGGCTCAT
1 ATGAGCTTCCCGTTATATAGCTCAT
*
38809974 ATGAGCTTCCCGTTATATAGCTCGAG
1 ATGAGCTTCCCGTTATATAGCTC-AT
* * *
38810000 AGAGAGCTTCCCATT-TATGTGCTCAT
1 A-TGAGCTTCCCGTTATAT-AGCTCAT
38810026 ATGAGCATTCCCG
1 ATGAGC-TTCCCG
38810039 AATATGAATG
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
25 24 0.47
26 12 0.24
27 15 0.29
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATAGCTCAT
Found at i:38811370 original size:361 final size:361
Alignment explanation
Indices: 38810706--38811427 Score: 1444
Period size: 361 Copynumber: 2.0 Consensus size: 361
38810696 TTGAATGATG
38810706 GATAATTTTTAAACATATTGATAGTTGGTTTGAAATTGGTAAATTAGGTACAAATGAGTTTATAT
1 GATAATTTTTAAACATATTGATAGTTGGTTTGAAATTGGTAAATTAGGTACAAATGAGTTTATAT
38810771 ATGCATATGGTCAAGTTGGTAAGTAAAGATTCTTGAATGGATTTGGTAAGATGTTAAGTATAAAA
66 ATGCATATGGTCAAGTTGGTAAGTAAAGATTCTTGAATGGATTTGGTAAGATGTTAAGTATAAAA
38810836 CTTGATTTTGGTTGGATTTGAATGTCTTGTATTGGCTTGAAAGCATATTTAAGTGTTTATGTAGG
131 CTTGATTTTGGTTGGATTTGAATGTCTTGTATTGGCTTGAAAGCATATTTAAGTGTTTATGTAGG
38810901 TGGAAGGAAAATTTGGGTAAGAAATATGGCTTGGAAATGACCTTATTTTGTCCACACGGGCAGGG
196 TGGAAGGAAAATTTGGGTAAGAAATATGGCTTGGAAATGACCTTATTTTGTCCACACGGGCAGGG
38810966 ACACGGGCATGTGTCTCAGCCATATGTGACACACAGCCTAGCATATGGGCATGTGTTTCAGCCGT
261 ACACGGGCATGTGTCTCAGCCATATGTGACACACAGCCTAGCATATGGGCATGTGTTTCAGCCGT
38811031 GTGTCCCCTGCATCTTTAAAATTCAAAACAGAATGC
326 GTGTCCCCTGCATCTTTAAAATTCAAAACAGAATGC
38811067 GATAATTTTTAAACATATTGATAGTTGGTTTGAAATTGGTAAATTAGGTACAAATGAGTTTATAT
1 GATAATTTTTAAACATATTGATAGTTGGTTTGAAATTGGTAAATTAGGTACAAATGAGTTTATAT
38811132 ATGCATATGGTCAAGTTGGTAAGTAAAGATTCTTGAATGGATTTGGTAAGATGTTAAGTATAAAA
66 ATGCATATGGTCAAGTTGGTAAGTAAAGATTCTTGAATGGATTTGGTAAGATGTTAAGTATAAAA
38811197 CTTGATTTTGGTTGGATTTGAATGTCTTGTATTGGCTTGAAAGCATATTTAAGTGTTTATGTAGG
131 CTTGATTTTGGTTGGATTTGAATGTCTTGTATTGGCTTGAAAGCATATTTAAGTGTTTATGTAGG
38811262 TGGAAGGAAAATTTGGGTAAGAAATATGGCTTGGAAATGACCTTATTTTGTCCACACGGGCAGGG
196 TGGAAGGAAAATTTGGGTAAGAAATATGGCTTGGAAATGACCTTATTTTGTCCACACGGGCAGGG
38811327 ACACGGGCATGTGTCTCAGCCATATGTGACACACAGCCTAGCATATGGGCATGTGTTTCAGCCGT
261 ACACGGGCATGTGTCTCAGCCATATGTGACACACAGCCTAGCATATGGGCATGTGTTTCAGCCGT
38811392 GTGTCCCCTGCATCTTTAAAATTCAAAACAGAATGC
326 GTGTCCCCTGCATCTTTAAAATTCAAAACAGAATGC
38811428 TCAGAATTTT
Statistics
Matches: 361, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
361 361 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (361 bp):
GATAATTTTTAAACATATTGATAGTTGGTTTGAAATTGGTAAATTAGGTACAAATGAGTTTATAT
ATGCATATGGTCAAGTTGGTAAGTAAAGATTCTTGAATGGATTTGGTAAGATGTTAAGTATAAAA
CTTGATTTTGGTTGGATTTGAATGTCTTGTATTGGCTTGAAAGCATATTTAAGTGTTTATGTAGG
TGGAAGGAAAATTTGGGTAAGAAATATGGCTTGGAAATGACCTTATTTTGTCCACACGGGCAGGG
ACACGGGCATGTGTCTCAGCCATATGTGACACACAGCCTAGCATATGGGCATGTGTTTCAGCCGT
GTGTCCCCTGCATCTTTAAAATTCAAAACAGAATGC
Found at i:38821709 original size:56 final size:56
Alignment explanation
Indices: 38821618--38821730 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
38821608 CAAATACCAA
* *
38821618 GGAGTTGAATTATACTTCTGATATTTTGACTGACTTGATGAAAGGTTTTCCTATTG
1 GGAGGTGAATTATACCTCTGATATTTTGACTGACTTGATGAAAGGTTTTCCTATTG
*
38821674 GGAGGTGAATTATACCTCTGATATTTTGGCTGACTTGATGAAAGGTTTTCCTATTG
1 GGAGGTGAATTATACCTCTGATATTTTGACTGACTTGATGAAAGGTTTTCCTATTG
38821730 G
1 G
38821731 TGCTCGAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (56 bp):
GGAGGTGAATTATACCTCTGATATTTTGACTGACTTGATGAAAGGTTTTCCTATTG
Found at i:38831306 original size:43 final size:43
Alignment explanation
Indices: 38831230--38831365 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
38831220 TATAGACGAT
* * *
38831230 GCCGCTAAAGACCATGACCTTTAACGGCGCTTTTCTCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCACTTTTGTCACAAAC
* * *
38831273 GCCGTTAAAGACCATGATCTTTAGTGGCACTTTTGTCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCACTTTTGTCACAAAC
*
38831316 GCCGCTAAAGACCATGACCTTTAGCGGCTCTTTTGTCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCACTTTTGTCACAAAC
38831359 GCCGCTA
1 GCCGCTA
38831366 TAAATCAAAC
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGACCATGACCTTTAGCGGCACTTTTGTCACAAAC
Found at i:38832630 original size:5 final size:5
Alignment explanation
Indices: 38832620--38832646 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
38832610 CTTTCTTGCC
38832620 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
38832647 AAACAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:38836466 original size:37 final size:37
Alignment explanation
Indices: 38836416--38836512 Score: 169
Period size: 37 Copynumber: 2.6 Consensus size: 37
38836406 NNNNAAAAGC
*
38836416 ATTTTAAAATTAAAAAATTAAAAAAGTATTTTAAAAT
1 ATTTTAAAATTAAAAAATTAAAAAAGTATTTCAAAAT
*
38836453 ATTTTAAAATTAAAAAATAAAAAAAGTATTTCAAAAT
1 ATTTTAAAATTAAAAAATTAAAAAAGTATTTCAAAAT
38836490 ATTTTAAAATTAAAAAA-TAAAAA
1 ATTTTAAAATTAAAAAATTAAAAA
38836513 TATTTATTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 5 0.09
37 52 0.91
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (37 bp):
ATTTTAAAATTAAAAAATTAAAAAAGTATTTCAAAAT
Found at i:38836826 original size:7 final size:7
Alignment explanation
Indices: 38836814--38836845 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38836804 CTCTTAATCT
38836814 CTAACCC
1 CTAACCC
38836821 CTAACCC
1 CTAACCC
*
38836828 CTAACAC
1 CTAACCC
38836835 CTAACCC
1 CTAACCC
38836842 CTAA
1 CTAA
38836846 ATCACAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:38836884 original size:14 final size:15
Alignment explanation
Indices: 38836865--38836897 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
38836855 CTTAAACCAA
38836865 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
38836879 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
38836894 AATC
1 AATC
38836898 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:38837353 original size:41 final size:41
Alignment explanation
Indices: 38837291--38837507 Score: 251
Period size: 41 Copynumber: 5.3 Consensus size: 41
38837281 TTTTGTGGCG
* * * *
38837291 CTTTATCAAAAACGCCGCTAAAGCCCCGAGCATTAACGGCT
1 CTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCA
* * * *
38837332 CTTTTTCAAAAACACAGCTAAAGCTCTGAGCATTAGCGGTGA
1 CTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGG-CA
* *
38837374 -TTTTTTAAAAACGCCGCTAAAAG-CCTGAGCATTAGTGGCA
1 CTTTTTCAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCA
* * *
38837414 CTTTTTCAAAAACGCCGCTAAAGCTCTGAACATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCA
*
38837455 CTTTTTCAAAAACGTCGCTAAAAG-CCTGAGCATTAGCGGCA
1 CTTTTTCAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCA
*
38837496 CTTTTTTAAAAA
1 CTTTTTCAAAAA
38837508 TGTTGCGAAA
Statistics
Matches: 147, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
40 5 0.03
41 134 0.91
42 8 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
CTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCA
Found at i:38837435 original size:82 final size:82
Alignment explanation
Indices: 38837287--38837507 Score: 300
Period size: 82 Copynumber: 2.7 Consensus size: 82
38837277 ATGTTTTTGT
* * * * *
38837287 GGCGCTTTATCAAAAACGCCGCT-AAAGCCCCGAGCATTAACGGCTCTTTTTCAAAAACACAGCT
1 GGCGATTTTTCAAAAACGCCGCTAAAAG-CCTGAGCATTAGCGGCACTTTTTCAAAAACACAGCT
*
38837351 AAAGCTCTGAGCATTAGC
65 AAAGCTCTGAACATTAGC
* * * * *
38837369 GGTGATTTTTTAAAAACGCCGCTAAAAGCCTGAGCATTAGTGGCACTTTTTCAAAAACGCCGCTA
1 GGCGATTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCACTTTTTCAAAAACACAGCTA
38837434 AAGCTCTGAACATTAGC
66 AAGCTCTGAACATTAGC
* * *
38837451 GGCGCTTTTTCAAAAACGTCGCTAAAAGCCTGAGCATTAGCGGCACTTTTTTAAAAA
1 GGCGATTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCACTTTTTCAAAAA
38837508 TGTTGCGAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
82 117 0.97
83 4 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (82 bp):
GGCGATTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCACTTTTTCAAAAACACAGCTA
AAGCTCTGAACATTAGC
Found at i:38837504 original size:123 final size:123
Alignment explanation
Indices: 38837285--38837507 Score: 317
Period size: 123 Copynumber: 1.8 Consensus size: 123
38837275 AAATGTTTTT
* * *
38837285 GTGGCGCTTTATCAAAAACGCCGCTAAAGCCCCGAGCATTAACGGCTCTTTTTCAAAAACACAGC
1 GTGGCACTTTATCAAAAACGCCGCTAAAGCCCCGAACATTAACGGCGCTTTTTCAAAAACACAGC
*
38837350 TAAAGCTCTGAGCATTAGCGGTGATTTTTTAAAAACGCCGCTAAAAGCCTGAGCATTA
66 TAAAGCTCTGAGCATTAGCGGTCATTTTTTAAAAACGCCGCTAAAAGCCTGAGCATTA
* * * * *
38837408 GTGGCACTTTTTCAAAAACGCCGCTAAAGCTCTGAACATTAGCGGCGCTTTTTCAAAAACGTC-G
1 GTGGCACTTTATCAAAAACGCCGCTAAAGCCCCGAACATTAACGGCGCTTTTTCAAAAAC-ACAG
38837472 CTAAAAGC-CTGAGCATTAGCGG-CACTTTTTTAAAAA
65 CT-AAAGCTCTGAGCATTAGCGGTCA-TTTTTTAAAAA
38837508 TGTTGCGAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
122 1 0.01
123 81 0.92
124 6 0.07
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (123 bp):
GTGGCACTTTATCAAAAACGCCGCTAAAGCCCCGAACATTAACGGCGCTTTTTCAAAAACACAGC
TAAAGCTCTGAGCATTAGCGGTCATTTTTTAAAAACGCCGCTAAAAGCCTGAGCATTA
Found at i:38848819 original size:18 final size:18
Alignment explanation
Indices: 38848796--38848850 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
38848786 ATCATGTTGA
38848796 TCATTTTCAAAACATTAT
1 TCATTTTCAAAACATTAT
* * *
38848814 TCATTTACAAATCGTTAT
1 TCATTTTCAAAACATTAT
*
38848832 TCAATTTCAAAACATTAT
1 TCATTTTCAAAACATTAT
38848850 T
1 T
38848851 TATTGCGGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (18 bp):
TCATTTTCAAAACATTAT
Found at i:38856600 original size:9 final size:9
Alignment explanation
Indices: 38856583--38856619 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38856573 TGAGTTTTCG
38856583 AATTCGAAT
1 AATTCGAAT
*
38856592 AACTCGAAT
1 AATTCGAAT
38856601 AATTCGAAT
1 AATTCGAAT
38856610 AATTCGAAT
1 AATTCGAAT
38856619 A
1 A
38856620 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38856696 original size:21 final size:21
Alignment explanation
Indices: 38856655--38856697 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
38856645 ACCCCAAACT
* *
38856655 CTTAAACCTTTTTACTTTTCC
1 CTTAAAACTTTTTACTCTTCC
38856676 CTTAAAAC-TTTTACTCCTTCC
1 CTTAAAACTTTTTACT-CTTCC
38856697 C
1 C
38856698 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.47
Consensus pattern (21 bp):
CTTAAAACTTTTTACTCTTCC
Found at i:38856702 original size:30 final size:31
Alignment explanation
Indices: 38856668--38856728 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
38856658 AAACCTTTTT
* *
38856668 ACTTTTCCCTTAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCTAAAACTTTTACTCCTCTCCC
38856698 ACTTTCCCCCTAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCTAAAACTTTTACTCCTCTCCC
38856729 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.41, G:0.00, T:0.39
Consensus pattern (31 bp):
ACTTTCCCCCTAAAACTTTTACTCCTCTCCC
Found at i:38856853 original size:14 final size:15
Alignment explanation
Indices: 38856824--38856854 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38856814 AATTTTTATT
38856824 CCCTCCCACTTTTCC
1 CCCTCCCACTTTTCC
38856839 CCCTCCCAC-TTTCC
1 CCCTCCCACTTTTCC
38856853 CC
1 CC
38856855 TAAAACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.06, C:0.65, G:0.00, T:0.29
Consensus pattern (15 bp):
CCCTCCCACTTTTCC
Found at i:38858233 original size:40 final size:40
Alignment explanation
Indices: 38858178--38858280 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 40
38858168 TCAGATGAGT
* * *
38858178 CATACCTACTGAATCTACTGAAACATATGCGA-TTTTGATC
1 CATACCTACTGAATCTACTGAAACATATGC-ACTCTTAAGC
* *
38858218 CATACCTACTGAATCTACTAAAACGTATGCACTCTTAAGC
1 CATACCTACTGAATCTACTGAAACATATGCACTCTTAAGC
* *
38858258 CATACCTACTGAATTTATTGAAA
1 CATACCTACTGAATCTACTGAAA
38858281 AGAATGCTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
39 1 0.02
40 53 0.98
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (40 bp):
CATACCTACTGAATCTACTGAAACATATGCACTCTTAAGC
Found at i:38864288 original size:21 final size:20
Alignment explanation
Indices: 38864264--38864302 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
38864254 AGACATTATC
38864264 ATCTAAAAAAACATAAAAAAA
1 ATCTAAAAAAA-ATAAAAAAA
**
38864285 ATCTTTAAAAAATAAAAA
1 ATCTAAAAAAAATAAAAA
38864303 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
ATCTAAAAAAAATAAAAAAA
Found at i:38864303 original size:17 final size:17
Alignment explanation
Indices: 38864281--38864313 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38864271 AAAACATAAA
38864281 AAAAATCTT-TAAAAAAT
1 AAAAAT-TTATAAAAAAT
38864298 AAAAATTTATAAAAAA
1 AAAAATTTATAAAAAA
38864314 AATTACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATTTATAAAAAAT
Found at i:38864323 original size:21 final size:19
Alignment explanation
Indices: 38864291--38864342 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
38864281 AAAAATCTTT
*
38864291 AAAAAATAAAAATTTATAA
1 AAAAAATAAAAACTTATAA
*
38864310 AAAAAATTACAAAACTTATTA
1 AAAAAA-TA-AAAACTTATAA
*
38864331 AAAATATAAAAA
1 AAAAAATAAAAA
38864343 AATGTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 4 0.14
21 14 0.50
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAATAAAAACTTATAA
Found at i:38864344 original size:49 final size:48
Alignment explanation
Indices: 38864291--38864391 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 48
38864281 AAAAATCTTT
* * *
38864291 AAAAAAT-AAAAATTTA-TAAAAAAAATTACAAAACTTATTAAAAATATA
1 AAAAAATGAAAAA-TTACAAAAAAAAATGACAAAACTTACTAAAAAT-TA
* * *
38864339 AAAAAATGTAAAATTACAAAAAAAAATGATAAAATTTACTAAAAATTA
1 AAAAAATGAAAAATTACAAAAAAAAATGACAAAACTTACTAAAAATTA
38864387 AAAAA
1 AAAAA
38864392 TAGAAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 17 0.38
49 28 0.62
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (48 bp):
AAAAAATGAAAAATTACAAAAAAAAATGACAAAACTTACTAAAAATTA
Found at i:38864362 original size:21 final size:22
Alignment explanation
Indices: 38864338--38864383 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
38864328 TTAAAAATAT
38864338 AAAAAAATG-TAAAA-TTACAA
1 AAAAAAATGATAAAATTTACAA
*
38864358 AAAAAAATGATAAAATTTACTA
1 AAAAAAATGATAAAATTTACAA
38864380 AAAA
1 AAAA
38864384 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 9 0.39
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAAAATGATAAAATTTACAA
Found at i:38864994 original size:9 final size:9
Alignment explanation
Indices: 38864982--38865055 Score: 53
Period size: 9 Copynumber: 8.1 Consensus size: 9
38864972 AATATTTCAA
38864982 ATAATTTTT
1 ATAATTTTT
* *
38864991 ATAACTTCTA
1 ATAA-TTTTT
38865001 ATAA-TTTT
1 ATAATTTTT
*
38865009 A-AAATTTT
1 ATAATTTTT
*
38865017 ATAGTTTTT
1 ATAATTTTT
*
38865026 AAATAGTTTTT
1 --ATAATTTTT
*
38865037 ATTATTTTT
1 ATAATTTTT
38865046 ATAATTTTT
1 ATAATTTTT
38865055 A
1 A
38865056 AAAAAGTCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
7 2 0.04
8 8 0.16
9 25 0.49
10 7 0.14
11 9 0.18
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
ATAATTTTT
Found at i:38865052 original size:45 final size:43
Alignment explanation
Indices: 38864949--38865058 Score: 112
Period size: 46 Copynumber: 2.4 Consensus size: 43
38864939 AAAATATAAC
*
38864949 TATTTTTACTATTTTTAAAATTTAATATTTCAAATAATTTTTAT
1 TATTTTTA-TAATTTTAAAATTTAATATTTCAAATAATTTTTAT
* * * * * *
38864993 AACTTCTAATAATTTTAAAATTTTATAGTTTTTAAATAGTTTTTAT
1 TA-TTTTTATAATTTTAAAATTTAATA--TTTCAAATAATTTTTAT
38865039 TATTTTTATAATTTTTAAAA
1 TATTTTTATAA-TTTTAAAA
38865059 AAGTCTAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
44 17 0.33
45 11 0.21
46 24 0.46
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (43 bp):
TATTTTTATAATTTTAAAATTTAATATTTCAAATAATTTTTAT
Found at i:38872341 original size:29 final size:29
Alignment explanation
Indices: 38872310--38872364 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
38872300 AAAGCCTTTT
38872310 TTTTTAA-AATTTACCGAAATGGGCCACA
1 TTTTTAATAATTTACCGAAATGGGCCACA
* *
38872338 TTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTAATAATTTACCGAAATGGGCCA
38872365 TTTCCGCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTTTAATAATTTACCGAAATGGGCCACA
Found at i:38877455 original size:22 final size:22
Alignment explanation
Indices: 38877393--38877458 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
38877383 CGCACCAGTA
* *
38877393 TATGAGAGCCCTTTATCGAACG
1 TATGAGAGCCCTTTATGGGACG
* * * ** *
38877415 TTTGAGTGCCCCTCGTGGGATG
1 TATGAGAGCCCTTTATGGGACG
38877437 TATGAGAGCCCTTTATGGGACG
1 TATGAGAGCCCTTTATGGGACG
38877459 AATGGAAGAC
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (22 bp):
TATGAGAGCCCTTTATGGGACG
Found at i:38877537 original size:27 final size:28
Alignment explanation
Indices: 38877502--38877592 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 28
38877492 ACTATTTGAT
* *
38877502 ATGTAGAAGTCCGTTAGGACCATC-TAA
1 ATGTGGAAGTCCGTTAGGACTATCGTAA
* * * *
38877529 ATGTGGAAGTCCGTCAGGAATGTCTTAA
1 ATGTGGAAGTCCGTTAGGACTATCGTAA
* *
38877557 ATGGGGAAGTTCGTTAGGACTATCGTAA
1 ATGTGGAAGTCCGTTAGGACTATCGTAA
*
38877585 AAGTGGAA
1 ATGTGGAA
38877593 ATTTGTCAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 19 0.38
28 31 0.62
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (28 bp):
ATGTGGAAGTCCGTTAGGACTATCGTAA
Found at i:38880920 original size:31 final size:31
Alignment explanation
Indices: 38880854--38880920 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
38880844 ACAATTTGCT
* *
38880854 CACTGAACTATTCAAAAATTTTCATTTAAGT
1 CACTGAACTATTCAAAAATTTTCATTCAAGC
* * * *
38880885 CACTGAATTATTCACAAGTTTTTATTCAAGC
1 CACTGAACTATTCAAAAATTTTCATTCAAGC
38880916 CACTG
1 CACTG
38880921 GATTGATAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.37
Consensus pattern (31 bp):
CACTGAACTATTCAAAAATTTTCATTCAAGC
Found at i:38886483 original size:42 final size:42
Alignment explanation
Indices: 38886419--38886615 Score: 250
Period size: 42 Copynumber: 4.7 Consensus size: 42
38886409 TCATGTTTAC
* * * * * *
38886419 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
38886461 TTTCCGTTCAGCTCTTTTGAGCTTCTTTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
**
38886503 TTTTTGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* * * *
38886545 TTTTCGTTAAGCTCTTATGAGCTTTTGTTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
38886587 TTTCTGTTCAGCTCTCATGAGCTTCTGTT
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTT
38886616 CAGCTTTCGG
Statistics
Matches: 134, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 134 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:38886519 original size:21 final size:21
Alignment explanation
Indices: 38886428--38886620 Score: 127
Period size: 21 Copynumber: 9.2 Consensus size: 21
38886418 CTTTCCGTTT
* * *
38886428 AGCTCTCACGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * *
38886449 AACTCATATGAGTTTCCGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * *
38886470 AGCTCTTTTGAGCTTCTTTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * * *
38886491 AACCCTTATGGGTTTTTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
38886512 AGCTCTTATGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * * *
38886533 AACCCTTATG-GGTTTTCGTTA
1 AGCTCTTATGAGCTTCT-GTTC
*
38886554 AGCTCTTATGAGCTTTTGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * * *
38886575 AACCCTTATGGGTTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
38886596 AGCTCTCATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
38886617 AGCT
1 AGCT
38886621 TTCGGGCTTC
Statistics
Matches: 123, Mismatches: 47, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
20 4 0.03
21 114 0.93
22 5 0.04
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:38888352 original size:25 final size:24
Alignment explanation
Indices: 38888316--38888368 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
38888306 ACATACCGCA
*
38888316 GCTCTTTATGAGCGTCTTGATATAG
1 GCTCTTTATGAGCGTCCTGATAT-G
* *
38888341 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTGATATG
38888365 GCTC
1 GCTC
38888369 GCTTGAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTGATATG
Found at i:38888733 original size:42 final size:42
Alignment explanation
Indices: 38888669--38888865 Score: 250
Period size: 42 Copynumber: 4.7 Consensus size: 42
38888659 TCATGTTTAC
* * * * * *
38888669 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
38888711 TTTCCGTTCAGCTCTTTTGAGCTTCTTTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
**
38888753 TTTTTGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* * * *
38888795 TTTTCGTTAAGCTCTTATGAGCTTTTGTTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
* *
38888837 TTTCTGTTCAGCTCTCATGAGCTTCTGTT
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTT
38888866 CAGCTTTCGG
Statistics
Matches: 134, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 134 1.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTATGAGCTTCTGTTTAACCCTTATGGG
Found at i:38888769 original size:21 final size:21
Alignment explanation
Indices: 38888678--38888870 Score: 127
Period size: 21 Copynumber: 9.2 Consensus size: 21
38888668 CTTTCCGTTT
* * *
38888678 AGCTCTCACGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * *
38888699 AACTCATATGAGTTTCCGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * *
38888720 AGCTCTTTTGAGCTTCTTTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * * *
38888741 AACCCTTATGGGTTTTTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
38888762 AGCTCTTATGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* * * * *
38888783 AACCCTTATG-GGTTTTCGTTA
1 AGCTCTTATGAGCTTCT-GTTC
*
38888804 AGCTCTTATGAGCTTTTGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * * *
38888825 AACCCTTATGGGTTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
38888846 AGCTCTCATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
38888867 AGCT
1 AGCT
38888871 TTCGGGCTTC
Statistics
Matches: 123, Mismatches: 47, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
20 4 0.03
21 114 0.93
22 5 0.04
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:38890602 original size:25 final size:24
Alignment explanation
Indices: 38890566--38890618 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
38890556 ACATACCGCA
*
38890566 GCTCTTTATGAGCGTCTTGATATAG
1 GCTCTTTATGAGCGTCCTGATAT-G
* *
38890591 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTGATATG
38890615 GCTC
1 GCTC
38890619 GCTTGAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTGATATG
Found at i:38892620 original size:13 final size:13
Alignment explanation
Indices: 38892602--38892626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38892592 GCGTGTAGTC
38892602 TGGCCATGTGACT
1 TGGCCATGTGACT
38892615 TGGCCATGTGAC
1 TGGCCATGTGAC
38892627 CCTTGCACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (13 bp):
TGGCCATGTGACT
Found at i:38893292 original size:22 final size:23
Alignment explanation
Indices: 38893266--38893308 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
38893256 TATGACTTTA
38893266 GTTTTTAATCCTAATA-TTTTGT
1 GTTTTTAATCCTAATAGTTTTGT
*
38893288 GTTTTTAATCGTAATAGTTTT
1 GTTTTTAATCCTAATAGTTTT
38893309 TAATCATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.58
Consensus pattern (23 bp):
GTTTTTAATCCTAATAGTTTTGT
Found at i:38895430 original size:30 final size:32
Alignment explanation
Indices: 38895369--38895430 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
38895359 ATTTCATGTA
* *
38895369 TTTTTATTTTCAGAAATTTAGTTTCTCTAGTT
1 TTTTTATTTTCAGAAATTTAGTATCTATAGTT
38895401 TTTTTA-TTTCA-AAATTTAG-ATCTAATAGTT
1 TTTTTATTTTCAGAAATTTAGTATCT-ATAGTT
38895431 AATACCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 3 0.11
30 13 0.48
31 5 0.19
32 6 0.22
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.56
Consensus pattern (32 bp):
TTTTTATTTTCAGAAATTTAGTATCTATAGTT
Found at i:38895614 original size:15 final size:14
Alignment explanation
Indices: 38895575--38895618 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38895565 TTAACAATTG
*
38895575 AAATAAAAATTTAA
1 AAATAAAAAATTAA
* *
38895589 AATTTAAAAATTAA
1 AAATAAAAAATTAA
38895603 AAATAAAGAAATTAA
1 AAATAAA-AAATTAA
38895618 A
1 A
38895619 TTCTTGAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATAAAAAATTAA
Found at i:38897278 original size:3 final size:3
Alignment explanation
Indices: 38897258--38897296 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
38897248 TTTGTAAATA
38897258 AAT ATAT AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A
38897297 GAAGATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38900253 original size:17 final size:17
Alignment explanation
Indices: 38900231--38900265 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38900221 TTATTTAAAT
38900231 CAATAATATAATTCCAA
1 CAATAATATAATTCCAA
* *
38900248 CAATAATTTATTTCCAA
1 CAATAATATAATTCCAA
38900265 C
1 C
38900266 CATAGAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (17 bp):
CAATAATATAATTCCAA
Found at i:38903637 original size:18 final size:19
Alignment explanation
Indices: 38903614--38903649 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
38903604 GTATTTTATT
38903614 ATAAAACTTAAA-GTTAAA
1 ATAAAACTTAAATGTTAAA
38903632 ATAAAACTTAAATGTTAA
1 ATAAAACTTAAATGTTAA
38903650 GTATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
ATAAAACTTAAATGTTAAA
Found at i:38903714 original size:4 final size:4
Alignment explanation
Indices: 38903697--38903772 Score: 73
Period size: 4 Copynumber: 18.5 Consensus size: 4
38903687 TAAGTAAAAA
* * * * *
38903697 AAAG AAAT AGAG AAAG AAAG AGAG AAAG AAACG AAAA AAAG AAGG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG
38903746 AAAGG AAAG AAA- AAGAG AAAG AAAG AA
1 AAA-G AAAG AAAG AA-AG AAAG AAAG AA
38903773 GAAGAAAAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
3 2 0.03
4 46 0.79
5 10 0.17
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:38903747 original size:25 final size:25
Alignment explanation
Indices: 38903709--38903772 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
38903699 AGAAATAGAG
*
38903709 AAAGAAAGAGAGAAA-GAAACGAAAA
1 AAAGAAAGAAAGAAAGGAAA-GAAAA
*
38903734 AAAGAAGGAAAGAAAGGAAAGAAAA
1 AAAGAAAGAAAGAAAGGAAAGAAAA
*
38903759 AGAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
38903773 GAAGAAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 30 0.88
26 4 0.12
ACGTcount: A:0.72, C:0.02, G:0.27, T:0.00
Consensus pattern (25 bp):
AAAGAAAGAAAGAAAGGAAAGAAAA
Found at i:38903770 original size:21 final size:21
Alignment explanation
Indices: 38903708--38903780 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
38903698 AAGAAATAGA
* *
38903708 GAAAGAAAGAGAGAAAGAAAC
1 GAAAGAAAAAGAGAAAGAAAG
*
38903729 GAAAAAAAGAAG-GAAAGAAAG
1 GAAAGAAA-AAGAGAAAGAAAG
38903750 GAAAGAAAAAGAGAAAGAAAG
1 GAAAGAAAAAGAGAAAGAAAG
*
38903771 AAGAAGAAAA
1 GA-AAGAAAA
38903781 GTTAGGGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.07
21 32 0.73
22 9 0.20
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAGAAAAAGAGAAAGAAAG
Found at i:38904691 original size:41 final size:41
Alignment explanation
Indices: 38904622--38904752 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
38904612 TTCTTCAACT
*
38904622 TTAAGTCGATGAGACACTGGGTGTCAATTTATTACTTCGAA
1 TTAAGCCGATGAGACACTGGGTGTCAATTTATTACTTCGAA
** * * * *
38904663 TTAATTCGATGAGGCACTAGGTGCCAA--T-TTACTTCG-G
1 TTAAGCCGATGAGACACTGGGTGTCAATTTATTACTTCGAA
* *
38904700 TTTAGCCGATGAGACACTGGGTGTCAATTTATTACTTTGAA
1 TTAAGCCGATGAGACACTGGGTGTCAATTTATTACTTCGAA
*
38904741 TT-ATCCGATGAG
1 TTAAGCCGATGAG
38904753 GTATTGGGTA
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 21 0.29
38 8 0.11
39 2 0.03
40 16 0.22
41 25 0.35
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (41 bp):
TTAAGCCGATGAGACACTGGGTGTCAATTTATTACTTCGAA
Found at i:38904761 original size:40 final size:40
Alignment explanation
Indices: 38904628--38904753 Score: 141
Period size: 37 Copynumber: 3.2 Consensus size: 40
38904618 AACTTTAAGT
* *
38904628 CGATGAGACACTGGGTGTCAATTTATTACTTCGAATTAATT
1 CGATGAGGCACTGGGTGTCAATTTATTACTTCGAATT-ATC
* * ** *
38904669 CGATGAGGCACTAGGTGCCAA--T-TTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGTCAATTTATTACTTCGAATTATC
* *
38904706 CGATGAGACACTGGGTGTCAATTTATTACTTTGAATTATC
1 CGATGAGGCACTGGGTGTCAATTTATTACTTCGAATTATC
38904746 CGATGAGG
1 CGATGAGG
38904754 TATTGGGTAC
Statistics
Matches: 67, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
37 19 0.28
38 10 0.15
39 2 0.03
40 18 0.27
41 18 0.27
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
CGATGAGGCACTGGGTGTCAATTTATTACTTCGAATTATC
Found at i:38904952 original size:21 final size:22
Alignment explanation
Indices: 38904927--38904969 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
38904917 AGCTATTTGT
*
38904927 ATAGCAAGT-ATGAGATTTGAA
1 ATAGCAAGTGATGAGAATTGAA
38904948 ATAGCAAGTGATGAGAATTGAA
1 ATAGCAAGTGATGAGAATTGAA
38904970 TATGTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (22 bp):
ATAGCAAGTGATGAGAATTGAA
Found at i:38906936 original size:30 final size:31
Alignment explanation
Indices: 38906878--38906942 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
38906868 GAAAACCGTA
* *
38906878 AAGTTCAAGCCCCAATGTGAGAATAATTACC
1 AAGTTCAAGCCCCAATATGAGAACAATTACC
*
38906909 AAGTTCAAGCCCCAA-ATGAGAACAATTATC
1 AAGTTCAAGCCCCAATATGAGAACAATTACC
38906939 AAGT
1 AAGT
38906943 CTAGGGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (31 bp):
AAGTTCAAGCCCCAATATGAGAACAATTACC
Found at i:38913891 original size:20 final size:20
Alignment explanation
Indices: 38913856--38913901 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38913846 TATCTCTCAA
*
38913856 CAAAAA-ATTCTAAAAATTT
1 CAAAAATATTCTAAAAAATT
38913875 CAAAAATATT-TATAAAAATT
1 CAAAAATATTCTA-AAAAATT
38913895 CAAAAAT
1 CAAAAAT
38913902 TTATACTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (20 bp):
CAAAAATATTCTAAAAAATT
Found at i:38918239 original size:13 final size:13
Alignment explanation
Indices: 38918197--38918239 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
38918187 AAATACTTAA
*
38918197 ATTTTTCAAAAGC
1 ATTTCTCAAAAGC
* *
38918210 ACTTCTCAAAAAC
1 ATTTCTCAAAAGC
*
38918223 ATTTCTCAAAAGT
1 ATTTCTCAAAAGC
38918236 ATTT
1 ATTT
38918240 TTTCACAGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (13 bp):
ATTTCTCAAAAGC
Found at i:38918250 original size:39 final size:40
Alignment explanation
Indices: 38918198--38918273 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
38918188 AATACTTAAA
38918198 TTTTTCAAAAGCACTTCTCAAAAACATTTCTCAAAAGTAT
1 TTTTTCAAAAGCACTTCTCAAAAACATTTCTCAAAAGTAT
* * * * *
38918238 TTTTTC-ACAGCACTTTTTAAAAATATTTTTCAAAAG
1 TTTTTCAAAAGCACTTCTCAAAAACATTTCTCAAAAG
38918274 CAATAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 25 0.81
40 6 0.19
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.39
Consensus pattern (40 bp):
TTTTTCAAAAGCACTTCTCAAAAACATTTCTCAAAAGTAT
Found at i:38920289 original size:52 final size:52
Alignment explanation
Indices: 38920164--38920338 Score: 228
Period size: 52 Copynumber: 3.3 Consensus size: 52
38920154 CACTGATTGA
* *
38920164 ATGAGTCATTGT-CTGCTTGTAAATTATTGTCCTTTACTTTTATAAAAGTTTG
1 ATGAGTCATTGTCCT-CTTGTAAATTATTGTACTTTACTTTTATTAAAGTTTG
* * *
38920216 TATGAGTCATCGCCCTCTTGTAAATTATTGTACTTTAC-TTTATTAAAGTATG
1 -ATGAGTCATTGTCCTCTTGTAAATTATTGTACTTTACTTTTATTAAAGTTTG
* * *
38920268 AGTGAGTCATTGTCCTTTTGTAAATTATTGAACTTTACTTTTAATAAAGTTTG
1 A-TGAGTCATTGTCCTCTTGTAAATTATTGTACTTTACTTTTATTAAAGTTTG
*
38920321 ATGAGTCATAGTCCTCTT
1 ATGAGTCATTGTCCTCTT
38920339 ATGTATGATT
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
51 1 0.01
52 59 0.56
53 44 0.42
54 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (52 bp):
ATGAGTCATTGTCCTCTTGTAAATTATTGTACTTTACTTTTATTAAAGTTTG
Done.