Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 153 of 221
Found at i:46401351 original size:87 final size:91
Alignment explanation
Indices: 46401066--46401444 Score: 550
Period size: 95 Copynumber: 4.0 Consensus size: 91
46401056 AAGATCTGCA
* * *
46401066 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTTAATGTACTCTACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCA-GGAG--AGAG-TATCGGCTTCAATGTACTCCACTG
*
46401131 TAGTCACATGGAGGTAAAATCTGCCATCTTTG
62 TAGT--CAGGGAGGTAAAATCTGCCATCTTTG
*
46401163 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCA-GGAG--AGAG-TATCGGCTTCAATGTACTCCACTG
46401228 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
62 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
46401258 ATCTTCAATCTATTCCACTGCCAAATGCA-G-G-GAG-ATCGGCTTCAATGTACTCCACTGTAGT
1 ATCTTCAATCTATTCCACTGCCAAATGCAGGAGAGAGTATCGGCTTCAATGTACTCCACTGTAGT
46401319 CAGGGAGGTAAAATCTGCCATCTTTG
66 CAGGGAGGTAAAATCTGCCATCTTTG
46401345 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATGCA-GGAG--AGAG-TATCGGCTTCAATGTACTCCACTG
46401410 TAGTCAGGGAGGTAAAATCTGCCATCTTTTG
62 TAGTCAGGGAGGTAAAATCTGCCATC-TTTG
46401441 ATCT
1 ATCT
46401445 GCTTCGCTGC
Statistics
Matches: 269, Mismatches: 4, Indels: 19
0.92 0.01 0.07
Matches are distributed among these distances:
87 82 0.30
89 4 0.01
90 1 0.00
92 1 0.00
93 4 0.01
95 102 0.38
96 8 0.03
97 67 0.25
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (91 bp):
ATCTTCAATCTATTCCACTGCCAAATGCAGGAGAGAGTATCGGCTTCAATGTACTCCACTGTAGT
CAGGGAGGTAAAATCTGCCATCTTTG
Found at i:46404262 original size:62 final size:62
Alignment explanation
Indices: 46404158--46404341 Score: 305
Period size: 62 Copynumber: 3.0 Consensus size: 62
46404148 CTAAACTCGA
* * *
46404158 CGTACTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTGATGCATGAACG
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGCATGAACG
* * *
46404220 TGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATAAAATGTTATGTTAATGCATGAACG
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGCATGAACG
*
46404282 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGAATGAA
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGCATGAA
46404342 GAGATACGTG
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 112 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (62 bp):
CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGCATGAACG
Found at i:46406608 original size:3 final size:3
Alignment explanation
Indices: 46406600--46406668 Score: 54
Period size: 3 Copynumber: 24.0 Consensus size: 3
46406590 AAAATGAGGA
* * * * *
46406600 AAT AAT AAT AAT AAT AGT AGT AGT AAT AAT AAT AGT -GT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
46406646 AGT AAT AAT AAT ATT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
46406669 TAATTTAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 6 0.11
3 49 0.89
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:46406646 original size:13 final size:15
Alignment explanation
Indices: 46406608--46406658 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
46406598 GAAATAATAA
*
46406608 TAATAATAGTAGTAG
1 TAATAATAATAGTAG
46406623 TAATAATAATAGT-G
1 TAATAATAATAGTAG
*
46406637 TAAT-ATAATAGTAA
1 TAATAATAATAGTAG
46406651 TAATAATA
1 TAATAATA
46406659 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 8 0.25
14 9 0.28
15 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
TAATAATAATAGTAG
Found at i:46408017 original size:34 final size:35
Alignment explanation
Indices: 46407978--46408074 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 35
46407968 AAAGGCATGG
* * * * *
46407978 TGGTGGTAGACGGTATGGGGGTGTGTGA-TGGTGC
1 TGGTGGTAGACAGCATGGGAGAGTGGGAGTGGTGC
*
46408012 TGGTGGCAGACAGCATGGGAGAGTGGGAGTGGTGC
1 TGGTGGTAGACAGCATGGGAGAGTGGGAGTGGTGC
46408047 TGGTGGTAGACAGCATGGGAGAGTGGGA
1 TGGTGGTAGACAGCATGGGAGAGTGGGA
46408075 AGAGGCAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 22 0.40
35 33 0.60
ACGTcount: A:0.19, C:0.08, G:0.52, T:0.22
Consensus pattern (35 bp):
TGGTGGTAGACAGCATGGGAGAGTGGGAGTGGTGC
Found at i:46425300 original size:16 final size:18
Alignment explanation
Indices: 46425281--46425314 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46425271 ATAAATGTAA
46425281 AATTAAC-C-AAATTTAT
1 AATTAACACTAAATTTAT
46425297 AATTAACACTAAATTTAT
1 AATTAACACTAAATTTAT
46425315 TCTATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAACACTAAATTTAT
Found at i:46432365 original size:13 final size:13
Alignment explanation
Indices: 46432347--46432371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46432337 GTTTGACGTA
46432347 TAATCTATCTGTG
1 TAATCTATCTGTG
46432360 TAATCTATCTGT
1 TAATCTATCTGT
46432372 ATTTGGTATT
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
TAATCTATCTGTG
Found at i:46433212 original size:23 final size:22
Alignment explanation
Indices: 46433185--46433248 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
46433175 CATGTCTCAC
46433185 TAAAATTCACATATGTTAAAATA
1 TAAAATTCA-ATATGTTAAAATA
* *
46433208 TAAAATTCATTTTGTTAAAATA
1 TAAAATTCAATATGTTAAAATA
* *
46433230 TAAAATTCATTTTGTTAAA
1 TAAAATTCAATATGTTAAA
46433249 CCGTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 30 0.77
23 9 0.23
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAAATTCAATATGTTAAAATA
Found at i:46433226 original size:22 final size:22
Alignment explanation
Indices: 46433198--46433248 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
46433188 AATTCACATA
46433198 TGTTAAAATATAAAATTCATTT
1 TGTTAAAATATAAAATTCATTT
46433220 TGTTAAAATATAAAATTCATTT
1 TGTTAAAATATAAAATTCATTT
46433242 TGTTAAA
1 TGTTAAA
46433249 CCGTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
TGTTAAAATATAAAATTCATTT
Found at i:46433698 original size:50 final size:50
Alignment explanation
Indices: 46433583--46433825 Score: 360
Period size: 50 Copynumber: 4.8 Consensus size: 50
46433573 GATCATAACA
* ** *
46433583 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * **
46433634 TGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
46433684 TACCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
46433734 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
46433784 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46433826 TTACCCAAAT
Statistics
Matches: 173, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 141 0.82
51 32 0.18
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:46434196 original size:29 final size:30
Alignment explanation
Indices: 46434159--46434218 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
46434149 GCCCTCGAAT
*
46434159 CTAACTTTTT-CAAAATTACGA-TTTTGCCC
1 CTAAATTTTTGCAAAATTAC-ATTTTTGCCC
*
46434188 CTAAATTTTTGCATAATTACATTTTTGCCC
1 CTAAATTTTTGCAAAATTACATTTTTGCCC
46434218 C
1 C
46434219 AAGGCCCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (30 bp):
CTAAATTTTTGCAAAATTACATTTTTGCCC
Found at i:46435456 original size:16 final size:16
Alignment explanation
Indices: 46435435--46435466 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46435425 ATAGACAAAG
46435435 AACTGCTATGTGCTTT
1 AACTGCTATGTGCTTT
46435451 AACTGCTATGTGCTTT
1 AACTGCTATGTGCTTT
46435467 TTGTAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
AACTGCTATGTGCTTT
Found at i:46439604 original size:50 final size:50
Alignment explanation
Indices: 46439489--46439677 Score: 288
Period size: 50 Copynumber: 3.8 Consensus size: 50
46439479 GATCATAACA
* ** *
46439489 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
46439540 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
46439590 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
46439640 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAC
46439678 TTCTTTACCC
Statistics
Matches: 125, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 92 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:46440054 original size:30 final size:30
Alignment explanation
Indices: 46440019--46440076 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
46440009 CCTCGACTCT
*
46440019 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTACAATTTTGCCCCTA
* *
46440049 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTGCAAAATTACAATTTTGCCCC
46440077 AAGGCCCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCCTA
Found at i:46444715 original size:13 final size:13
Alignment explanation
Indices: 46444697--46444722 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46444687 TGAATTACTA
46444697 TGTATAAAAATTT
1 TGTATAAAAATTT
46444710 TGTATAAAAATTT
1 TGTATAAAAATTT
46444723 GATCGTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TGTATAAAAATTT
Found at i:46445903 original size:23 final size:23
Alignment explanation
Indices: 46445875--46445921 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
46445865 TGGAGTATAA
* *
46445875 AATTTTT-ATATTTTTATATGTAT
1 AATTTTTGA-ATTTATACATGTAT
46445898 AATTTTTGAATTTATACATGTAT
1 AATTTTTGAATTTATACATGTAT
46445921 A
1 A
46445922 TGCAAGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (23 bp):
AATTTTTGAATTTATACATGTAT
Found at i:46446556 original size:42 final size:42
Alignment explanation
Indices: 46446495--46446721 Score: 246
Period size: 42 Copynumber: 5.5 Consensus size: 42
46446485 CAGTGCCTAT
* *
46446495 CAGGTTTATTGCCGGTGAAATAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAATAATATCAGACTTTACGTCTAG
* * *
46446537 CAGGCTTAATGCCAGTGAAATAATTTCAGACTTTACATCTAG
1 CAGGCTTAATGCCGGTGAAATAATATCAGACTTTACGTCTAG
* *
46446579 CAGGCTTAATGCCGGTGAAACAATATTAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAATAATATCAGACTTTACGTCTAG
* * * * *
46446621 CAGGCTTAATGCCGGTGAAA-CATTTCAGACTATATGTCTGG
1 CAGGCTTAATGCCGGTGAAATAATATCAGACTTTACGTCTAG
* * * * *
46446662 CAGGC-TAAGTGCCGGTGTACTGA-ATCAGGCTTTAAGTCTAG
1 CAGGCTTAA-TGCCGGTGAAATAATATCAGACTTTACGTCTAG
*
46446703 CAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCGGTGAA
46446722 TCTGTTTAAA
Statistics
Matches: 157, Mismatches: 26, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
40 3 0.02
41 59 0.38
42 95 0.61
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAATAATATCAGACTTTACGTCTAG
Found at i:46450255 original size:15 final size:15
Alignment explanation
Indices: 46450235--46450263 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46450225 AAATTAATTG
46450235 AGAATTCTCATTTAA
1 AGAATTCTCATTTAA
46450250 AGAATTCTCATTTA
1 AGAATTCTCATTTA
46450264 TTGCTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
AGAATTCTCATTTAA
Found at i:46454550 original size:19 final size:19
Alignment explanation
Indices: 46454500--46454549 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
46454490 TGTTTTCAAT
46454500 TATTTTAAAAAATAAAAAC
1 TATTTTAAAAAATAAAAAC
46454519 TATTTTAAAAAATAGAAAA-
1 TATTTTAAAAAATA-AAAAC
46454538 TACTTTTAAAAA
1 TA-TTTTAAAAA
46454550 TCAAATAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (19 bp):
TATTTTAAAAAATAAAAAC
Found at i:46459731 original size:14 final size:14
Alignment explanation
Indices: 46459712--46459751 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
46459702 TTGATTGCCA
46459712 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
46459726 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
46459740 GGAAAATGTTTT
1 GTAAAATGTTTT
46459752 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:46459760 original size:20 final size:20
Alignment explanation
Indices: 46459735--46459774 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46459725 CGTAAAATGA
*
46459735 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
46459755 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
46459775 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:46459764 original size:34 final size:35
Alignment explanation
Indices: 46459720--46459786 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
46459710 CAGTAAAATG
*
46459720 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
46459754 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
46459787 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:46459790 original size:14 final size:15
Alignment explanation
Indices: 46459714--46459790 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
46459704 GATTGCCAGT
* *
46459714 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
46459728 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
46459742 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
46459762 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
46459777 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
46459791 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:46460179 original size:18 final size:18
Alignment explanation
Indices: 46460158--46460196 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
46460148 GTTATATCTT
46460158 TAATTAAATTATTATCCA
1 TAATTAAATTATTATCCA
46460176 TAATTAAATTATTATCCA
1 TAATTAAATTATTATCCA
46460194 TAA
1 TAA
46460197 AGTTGGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAAATTATTATCCA
Found at i:46460850 original size:13 final size:13
Alignment explanation
Indices: 46460832--46460856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46460822 AAGGTAAGAC
46460832 AGATACTTAAAAT
1 AGATACTTAAAAT
46460845 AGATACTTAAAA
1 AGATACTTAAAA
46460857 ACATGAACCA
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:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AGATACTTAAAAT
Found at i:46461131 original size:14 final size:13
Alignment explanation
Indices: 46461102--46461128 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46461092 AGAAGGTAAG
46461102 ACAGATACTTAAA
1 ACAGATACTTAAA
46461115 ACAGATACTTAAA
1 ACAGATACTTAAA
46461128 A
1 A
46461129 ACATGAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ACAGATACTTAAA
Found at i:46461387 original size:271 final size:272
Alignment explanation
Indices: 46460723--46461400 Score: 1223
Period size: 272 Copynumber: 2.5 Consensus size: 272
46460713 AATGCAAGTT
* *
46460723 TCATTTACCAGCTTTTCTTTCACTTCTCACAACCAGTCAATGATCCTCACCTTGGCCTGCTTTGG
1 TCATTTACCAGCTTTTCTTTCACTTTTCACAACCAGTCAAAGATCCTCACCTTGGCCTGCTTTGG
*
46460788 GAGGGAAGGCTTGAAAGATATGAAATGGCAGCAGAAGGTAAGACAGATACTTAAAATAGATACTT
66 GAGGGAAGGCTTGAAAGATATGAAATGGCAGCAGAAGGTAAGACAGATACTTAAAACAGATACTT
46460853 AAAAACATGAACCACAAATTCCTATATATGTAGCTGTGAAACAAATATTCAACTACTCTGGAGAA
131 AAAAACATGAACCACAAATTCCTATATATGTAGCTGTGAAACAAATATTCAACTACTCTGGAGAA
46460918 CAAAGGAAAAGCAGATACTTAAAAACATGAACCACAAACCCTGCTTACGTAATGCTAGACTTAAA
196 CAAAGGAAAAGCAGATACTTAAAAACATGAACCACAAACCCTGCTTACGTAATGCTAGACTTAAA
46460983 GCATAACAAGAA
261 GCATAACAAGAA
* *
46460995 TAATTTACCAACTTTTCTTTCACTTTTCACAACCAGTCAAAGATCCTCACCTTGGCCTGCTTTGG
1 TCATTTACCAGCTTTTCTTTCACTTTTCACAACCAGTCAAAGATCCTCACCTTGGCCTGCTTTGG
46461060 GAGGGAAGGCTTGAAAGATATGAAATGGCAGCAGAAGGTAAGACAGATACTTAAAACAGATACTT
66 GAGGGAAGGCTTGAAAGATATGAAATGGCAGCAGAAGGTAAGACAGATACTTAAAACAGATACTT
46461125 AAAAACATGAACCACAAATTCCTATATATGTAGCTGTGAAACAAATATTCAACTACTCTGGAGAA
131 AAAAACATGAACCACAAATTCCTATATATGTAGCTGTGAAACAAATATTCAACTACTCTGGAGAA
* *
46461190 CAAAGGTAAAGCAGATACTT-AAAACATGAACCACAAACCCTGCTTACGTGATGCTAGACTTAAA
196 CAAAGGAAAAGCAGATACTTAAAAACATGAACCACAAACCCTGCTTACGTAATGCTAGACTTAAA
46461254 GCATAACAAGAA
261 GCATAACAAGAA
*
46461266 TCATTTACCAGCTTTTCTTTCACTTTTCACAACCAGTCAAAGATCCTTACCTTGGCCTGCTTTGG
1 TCATTTACCAGCTTTTCTTTCACTTTTCACAACCAGTCAAAGATCCTCACCTTGGCCTGCTTTGG
* * * *
46461331 GAGAGAAGGCTTGAAAGATATGAAATGGCTGCAGAAGGTAAAACATATACTTAAAACAGAATCAC
66 GAGGGAAGGCTTGAAAGATATGAAATGGCAGCAGAAGGTAAGACAGATACTTAAAACAG-AT-AC
46461396 TTAAA
129 TTAAA
46461401 CCAAAAAAAA
Statistics
Matches: 390, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
271 172 0.44
272 211 0.54
273 7 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (272 bp):
TCATTTACCAGCTTTTCTTTCACTTTTCACAACCAGTCAAAGATCCTCACCTTGGCCTGCTTTGG
GAGGGAAGGCTTGAAAGATATGAAATGGCAGCAGAAGGTAAGACAGATACTTAAAACAGATACTT
AAAAACATGAACCACAAATTCCTATATATGTAGCTGTGAAACAAATATTCAACTACTCTGGAGAA
CAAAGGAAAAGCAGATACTTAAAAACATGAACCACAAACCCTGCTTACGTAATGCTAGACTTAAA
GCATAACAAGAA
Found at i:46466983 original size:30 final size:30
Alignment explanation
Indices: 46466939--46466996 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46466929 TTCAAACTGC
*
46466939 ACACACACAAACAAACGCACATACACACGG
1 ACACACACAAACAAACGCACACACACACGG
* * *
46466969 ACACATACATACAAACGCAGACACACAC
1 ACACACACAAACAAACGCACACACACAC
46466997 ACACCGACGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.50, C:0.36, G:0.09, T:0.05
Consensus pattern (30 bp):
ACACACACAAACAAACGCACACACACACGG
Found at i:46466999 original size:34 final size:34
Alignment explanation
Indices: 46466956--46467022 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
46466946 CAAACAAACG
* *
46466956 CACATACACACGGACACATACATACAAACGCAGA
1 CACACACACACCGACACATACATACAAACGCAGA
* *
46466990 CACACACACACCGACGCATACATACAAATGCAG
1 CACACACACACCGACACATACATACAAACGCAG
46467023 GCAAAGGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.45, C:0.34, G:0.12, T:0.09
Consensus pattern (34 bp):
CACACACACACCGACACATACATACAAACGCAGA
Found at i:46469757 original size:12 final size:11
Alignment explanation
Indices: 46469742--46469778 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
46469732 TGATTTTCGA
46469742 TTTTCTTTTTT
1 TTTTCTTTTTT
46469753 CTTTTCTTTTTT
1 -TTTTCTTTTTT
46469765 TTTTCTTTTCTT
1 TTTTCTTTT-TT
46469777 TT
1 TT
46469779 GGCTATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:46469768 original size:16 final size:17
Alignment explanation
Indices: 46469742--46469778 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
46469732 TGATTTTCGA
46469742 TTTTCTTTTTTCTTTTC
1 TTTTCTTTTTTCTTTTC
46469759 TTTT-TTTTTTCTTTTC
1 TTTTCTTTTTTCTTTTC
46469775 TTTT
1 TTTT
46469779 GGCTATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTC
Found at i:46471205 original size:9 final size:9
Alignment explanation
Indices: 46471180--46471213 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
46471170 TTCAAAACAA
46471180 ATAAATTATT
1 ATAAATT-TT
46471190 AATAAATTTT
1 -ATAAATTTT
46471200 ATAAATTTT
1 ATAAATTTT
46471209 ATAAA
1 ATAAA
46471214 ATTCAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 2 0.09
11 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATAAATTTT
Found at i:46471656 original size:15 final size:15
Alignment explanation
Indices: 46471632--46471678 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
46471622 ATTCTCCGTT
46471632 CAACGGTAACTATTC
1 CAACGGTAACTATTC
* * *
46471647 CAACGATAACTTTTT
1 CAACGGTAACTATTC
46471662 CAACGGTAACTATTC
1 CAACGGTAACTATTC
46471677 CA
1 CA
46471679 CCTTCAAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (15 bp):
CAACGGTAACTATTC
Found at i:46471789 original size:7 final size:7
Alignment explanation
Indices: 46471776--46471827 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
46471766 CTGATTTTAT
46471776 ATTTTCA
1 ATTTTCA
*
46471783 ATCTTCA
1 ATTTTCA
*
46471790 ATTTTTA
1 ATTTTCA
46471797 ATTTTCA
1 ATTTTCA
*
46471804 ATTTTTA
1 ATTTTCA
46471811 A-TTTCA
1 ATTTTCA
*
46471817 ATTTTTA
1 ATTTTCA
46471824 ATTT
1 ATTT
46471828 CAGATATTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTCA
Found at i:46471791 original size:28 final size:28
Alignment explanation
Indices: 46471736--46471846 Score: 86
Period size: 28 Copynumber: 4.0 Consensus size: 28
46471726 CTTCCTAAAT
* * **
46471736 TTTC-AATATTCAATCTTCAATCCCCAA
1 TTTCTAATTTTCAATTTTCAATCTTCAA
*
46471763 TTTCTGATTTT-ATATTTTCAATCTTCAA
1 TTTCTAATTTTCA-ATTTTCAATCTTCAA
* *
46471791 TTTTTAATTTTCAATTTTTAAT-TTCAA
1 TTTCTAATTTTCAATTTTCAATCTTCAA
* * *
46471818 TTTTTAA-TTTCAGATATTCAATCCTCAA
1 TTTCTAATTTTCA-ATTTTCAATCTTCAA
46471846 T
1 T
46471847 CATTTTTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
26 5 0.07
27 24 0.35
28 38 0.56
29 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTCTAATTTTCAATTTTCAATCTTCAA
Found at i:46471793 original size:21 final size:21
Alignment explanation
Indices: 46471770--46471814 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46471760 CAATTTCTGA
46471770 TTTTATATTTTCAATCTTCAAT
1 TTTTA-ATTTTCAATCTTCAAT
* *
46471792 TTTTAATTTTCAATTTTTAAT
1 TTTTAATTTTCAATCTTCAAT
46471813 TT
1 TT
46471815 CAATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAATTTTCAATCTTCAAT
Found at i:46471815 original size:13 final size:13
Alignment explanation
Indices: 46471776--46471829 Score: 81
Period size: 14 Copynumber: 4.0 Consensus size: 13
46471766 CTGATTTTAT
*
46471776 ATTTTCAATCTTCA
1 ATTTTTAAT-TTCA
46471790 ATTTTTAATTTTCA
1 ATTTTTAA-TTTCA
46471804 ATTTTTAATTTCA
1 ATTTTTAATTTCA
46471817 ATTTTTAATTTCA
1 ATTTTTAATTTCA
46471830 GATATTCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
13 18 0.47
14 19 0.50
15 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTAATTTCA
Found at i:46474350 original size:18 final size:18
Alignment explanation
Indices: 46474314--46474351 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46474304 GTAAATTTAC
*
46474314 AATTCGAATAACTAGAAT
1 AATTCGAATAACTAAAAT
*
46474332 AATTCGAATAATTAAAAT
1 AATTCGAATAACTAAAAT
46474350 AA
1 AA
46474352 CAAATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (18 bp):
AATTCGAATAACTAAAAT
Found at i:46476604 original size:25 final size:26
Alignment explanation
Indices: 46476576--46476627 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
46476566 CACTTCTTAT
46476576 AAAA-TATT-TATCATTTCAAA-AATTA
1 AAAATTATTATAT-ATTT-AAATAATTA
46476601 AAAATTATTATATATTTAAATAATTA
1 AAAATTATTATATATTTAAATAATTA
46476627 A
1 A
46476628 TTGATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 14 0.58
27 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAATTATTATATATTTAAATAATTA
Found at i:46482487 original size:51 final size:51
Alignment explanation
Indices: 46482432--46482648 Score: 380
Period size: 51 Copynumber: 4.3 Consensus size: 51
46482422 GATCACATTT
* * *
46482432 ATCACTTGTCACTTGTCCCTGATTAGATAAGTGTAGCTAAAGCTACCACAC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
*
46482483 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
46482534 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
* *
46482585 ATCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
46482636 ATCACTTGTCACT
1 ATCACTTGTCACT
46482649 GATCAGAAGT
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 159 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTC
Found at i:46488061 original size:74 final size:74
Alignment explanation
Indices: 46487983--46488157 Score: 260
Period size: 74 Copynumber: 2.4 Consensus size: 74
46487973 GCACCTAGCA
* * * * *
46487983 CTAGTCAGATAAATCGACAAATAAATAGTGAGCCCAGCTCTAGTTGGATATACCAACGATATTTG
1 CTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACACCAACGATATTTG
*
46488048 CGCCTAACG
66 CGCCCAACG
*
46488057 CTAGTCGGATAAGCCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACACCAACGATATTTG
1 CTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACACCAACGATATTTG
* **
46488122 TGCCCAGTG
66 CGCCCAACG
46488131 CTAGTCGGATAAACCGACGAATAAATA
1 CTAGTCGGATAAACCGACGAATAAATA
46488158 ATTATTTATT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 90 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (74 bp):
CTAGTCGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTCGATACACCAACGATATTTG
CGCCCAACG
Found at i:46496260 original size:26 final size:27
Alignment explanation
Indices: 46496204--46496254 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
46496194 ATGCTTCAAG
46496204 ATTTTGATATAATAATATTTCAAATGA
1 ATTTTGATATAATAATATTTCAAATGA
*
46496231 ATTTT-ATAT-ATTATATTTTCAAAT
1 ATTTTGATATAATAATA-TTTCAAAT
46496255 TCATTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ATTTTGATATAATAATATTTCAAATGA
Found at i:46506965 original size:24 final size:26
Alignment explanation
Indices: 46506918--46506966 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
46506908 ACACATTTAT
46506918 TTTCTTATTTATTTTCATTCTTTTCA
1 TTTCTTATTTATTTTCATTCTTTTCA
46506944 TTTCTT-TTT-TTTTCACTT-TTTTC
1 TTTCTTATTTATTTTCA-TTCTTTTC
46506967 CTAGTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 5 0.23
26 6 0.27
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTCTTATTTATTTTCATTCTTTTCA
Found at i:46508149 original size:20 final size:19
Alignment explanation
Indices: 46508112--46508150 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
46508102 AATTTTTAGA
* *
46508112 ATTTTTTATAAAATAAATT
1 ATTTTATATAAAACAAATT
46508131 ATTTTATATAAAAACAAATT
1 ATTTTATAT-AAAACAAATT
46508151 CATTACCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTATATAAAACAAATT
Found at i:46510300 original size:151 final size:151
Alignment explanation
Indices: 46510026--46510327 Score: 586
Period size: 151 Copynumber: 2.0 Consensus size: 151
46510016 TGCGTAAACA
46510026 AATCATTGGTGTTATATAGTTTTGTTTGCACAATTTTTCACAGTGTCAAGCCGTAATGGCCACTG
1 AATCATTGGTGTTATATAGTTTTGTTTGCACAATTTTTCACAGTGTCAAGCCGTAATGGCCACTG
46510091 CCATCAAACACTTCCATTACAGTTTTCATATTAAGCAAACAAGCAATTTAAGGTAACAACATATT
66 CCATCAAACACTTCCATTACAGTTTTCATATTAAGCAAACAAGCAATTTAAGGTAACAACATATT
46510156 GATTTATTAACAAGCTTTGCG
131 GATTTATTAACAAGCTTTGCG
*
46510177 AATCATTGGTGTTATTTAGTTTTGTTTGCACAATTTTTCACAGTGTCAAGCCGTAATGGCCACTG
1 AATCATTGGTGTTATATAGTTTTGTTTGCACAATTTTTCACAGTGTCAAGCCGTAATGGCCACTG
46510242 CCATCAAACACTTCCATTACAGTTTTCATATTAAGCAAACAAGCAATTTAAGGTAACAACATATT
66 CCATCAAACACTTCCATTACAGTTTTCATATTAAGCAAACAAGCAATTTAAGGTAACAACATATT
*
46510307 GATTTATTAACAAGTTTTGCG
131 GATTTATTAACAAGCTTTGCG
46510328 TTGAAGGCTT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (151 bp):
AATCATTGGTGTTATATAGTTTTGTTTGCACAATTTTTCACAGTGTCAAGCCGTAATGGCCACTG
CCATCAAACACTTCCATTACAGTTTTCATATTAAGCAAACAAGCAATTTAAGGTAACAACATATT
GATTTATTAACAAGCTTTGCG
Found at i:46517003 original size:21 final size:21
Alignment explanation
Indices: 46516963--46517008 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
46516953 ACGATCTAAG
*
46516963 CACATAGGCGTGTGGAGTAGT
1 CACATAGGCGTGTGGAGTAGC
46516984 CACATAGGCGTGT-GAGGTAGC
1 CACATAGGCGTGTGGA-GTAGC
46517005 CACA
1 CACA
46517009 CTGCCATGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.26, C:0.20, G:0.35, T:0.20
Consensus pattern (21 bp):
CACATAGGCGTGTGGAGTAGC
Found at i:46536863 original size:16 final size:16
Alignment explanation
Indices: 46536842--46536890 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
46536832 TAAAACATAA
46536842 TTAAAATTTATAAAAT
1 TTAAAATTTATAAAAT
*
46536858 TTAAAATGTTCAAAAAAT
1 TTAAAAT-TT-ATAAAAT
* *
46536876 TAAAAATTAATAAAA
1 TTAAAATTTATAAAA
46536891 ACCATTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TTAAAATTTATAAAAT
Found at i:46536878 original size:17 final size:16
Alignment explanation
Indices: 46536840--46536891 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
46536830 TTTAAAACAT
46536840 AATTAAAATTTATAAA
1 AATTAAAATTTATAAA
*
46536856 ATTTAAAATGTTCA-AAA
1 AATTAAAAT-TT-ATAAA
*
46536873 AATTAAAAATTAATAAA
1 AATT-AAAATTTATAAA
46536890 AA
1 AA
46536892 CCATTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 9 0.31
17 14 0.48
18 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTAAAATTTATAAA
Found at i:46537110 original size:22 final size:23
Alignment explanation
Indices: 46537085--46537129 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
46537075 AGTCTATATA
46537085 AAAATAAATAAA-TAAATTTTAG
1 AAAATAAATAAATTAAATTTTAG
46537107 AAAATAAATAAATTTAAATTTTA
1 AAAATAAATAAA-TTAAATTTTA
46537130 TTAATCGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATAAATAAATTAAATTTTAG
Found at i:46544060 original size:66 final size:67
Alignment explanation
Indices: 46543978--46544172 Score: 189
Period size: 66 Copynumber: 2.9 Consensus size: 67
46543968 CATGACTTAA
* * * *
46543978 GAAGGTCATGAACTTTGAAAAGTT-GTGTTTGAA-AAGGTAAGGCACTTTAAGAAGTACGTGATT
1 GAAGGTCACGAACTTTGAAAAGTTAGTGCTT-AAGAAGGTAAGGCACTCTAAGAAGTACGTGACT
46544041 TGG
65 TGG
* * * *
46544044 GAAGGTTACGAACTTTGAAAAGTTAAGTGCTTAAGAAGGTGAGGTACTCTAAGAAGTATGTGACT
1 GAAGGTCACGAACTTTGAAAAGTT-AGTGCTTAAGAAGGTAAGGCACTCTAAGAAGTACGTGACT
46544109 TGG
65 TGG
* ** * * * * * * *
46544112 GAA-GACACGTGCTTTGAAAACTCAATGCTTAAGAAGGCAAGGTACTTTAAGAAGTATGTGA
1 GAAGGTCACGAACTTTGAAAAGTTAGTGCTTAAGAAGGTAAGGCACTCTAAGAAGTACGTGA
46544173 TCTGGAAAGG
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
66 56 0.52
67 16 0.15
68 36 0.33
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.28
Consensus pattern (67 bp):
GAAGGTCACGAACTTTGAAAAGTTAGTGCTTAAGAAGGTAAGGCACTCTAAGAAGTACGTGACTT
GG
Found at i:46546103 original size:108 final size:108
Alignment explanation
Indices: 46545803--46546106 Score: 337
Period size: 108 Copynumber: 2.8 Consensus size: 108
46545793 AAGTTCAAAG
* ** * * ** * *
46545803 ATACCTTAAGAGATATGTGACCT-AAAATGGTCAAAAGCTTTGGAAAGCTTGACACTTGAGAATG
1 ATACCTTAAAAGATATGTGACCTGAAAA-GACCAAAAGCTTTCGAAAACTCAACACTTCAGAAGG
** * **
46545867 TAAGGTGTATCTTAAATGATACAAGGTGTATCTTAAGAGATGCA
65 CGAGGTGTATCTTAAAAGATATGAGGTGTATCTTAAGAGATGCA
* * *
46545911 ATACCTTAAACGATATGTGACCTGAAAAGACCAAAAGCTTTCGAAAACTCAACCCTTGAGAAGGC
1 ATACCTTAAAAGATATGTGACCTGAAAAGACCAAAAGCTTTCGAAAACTCAACACTTCAGAAGGC
46545976 GAGGTGTATCTTAAAAGATATGAGGTGTATCTTAAGAGA-GACA
66 GAGGTGTATCTTAAAAGATATGAGGTGTATCTTAAGAGATG-CA
* * * *
46546019 ATACCTTAAAAGGTATGTGACTTGAAAA-AGCTAACAGCTTTC-AAAAGCTCAACACTTCAGAAG
1 ATACCTTAAAAGATATGTGACCTGAAAAGA-CCAAAAGCTTTCGAAAA-CTCAACACTTCAGAAG
* *
46546082 GCGAGGTGTATCTTGAGAGATATGA
64 GCGAGGTGTATCTTAAAAGATATGA
46546107 TACCTTAAGA
Statistics
Matches: 168, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
107 6 0.04
108 158 0.94
109 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (108 bp):
ATACCTTAAAAGATATGTGACCTGAAAAGACCAAAAGCTTTCGAAAACTCAACACTTCAGAAGGC
GAGGTGTATCTTAAAAGATATGAGGTGTATCTTAAGAGATGCA
Found at i:46546170 original size:87 final size:87
Alignment explanation
Indices: 46545997--46546328 Score: 256
Period size: 87 Copynumber: 3.8 Consensus size: 87
46545987 TAAAAGATAT
* ** * * * *
46545997 GAGGTGTATCTTAAGAGAGACAATACCTTAAAAGGTATGTGACTTGAAAAAGCTAACAGCTTTCA
1 GAGGTGTATCTTAAGAGATATGATACCTTAAAAGGTACGTGACCTGAAAAAGCTAAAAGCTTTAA
* *
46546062 AAAGCTCAACACTTCAGAAGGC
66 AAAGCTCAACACGTCAAAAGGC
* * *
46546084 GAGGTGTATCTTGAGAGATATGATACCTTAAGAGGTACGTGACCTGAAAAGGCTAAAAGCTTTAA
1 GAGGTGTATCTTAAGAGATATGATACCTTAAAAGGTACGTGACCTGAAAAAGCTAAAAGCTTTAA
* * *
46546149 AAAGCTTAACGCGTGAAAAGGC
66 AAAGCTCAACACGTCAAAAGGC
* * * * * * * * * * *
46546171 AATGTGTATCTTAAAAGATATGATACCTTAATAGGCATGTGTCAT-AAAAAGGTCAAGAGCTTTG
1 GAGGTGTATCTTAAGAGATATGATACCTTAAAAGGTACGTGACCTGAAAAAGCT-AAAAGCTTTA
* * * *
46546235 AAAAGCTCGACGCTTGAAAAGGC
65 AAAAGCTCAACACGTCAAAAGGC
* * * * * * * * * *
46546258 AATGTATATATTAAAAGATACGATACC-TAAAAAGCACGTGACCTGAAAATG-TCAAGAGCTTTA
1 GAGGTGTATCTTAAGAGATATGATACCTTAAAAGGTACGTGACCTGAAAAAGCT-AAAAGCTTTA
*
46546321 AAAGGCTC
65 AAAAGCTC
46546329 GATGCTTGAG
Statistics
Matches: 201, Mismatches: 42, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
86 36 0.18
87 165 0.82
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (87 bp):
GAGGTGTATCTTAAGAGATATGATACCTTAAAAGGTACGTGACCTGAAAAAGCTAAAAGCTTTAA
AAAGCTCAACACGTCAAAAGGC
Found at i:46548794 original size:104 final size:103
Alignment explanation
Indices: 46548677--46549002 Score: 444
Period size: 103 Copynumber: 3.2 Consensus size: 103
46548667 ACCCAGTACG
* * * * * *
46548677 AAAAGAAGGAAAAAAAAAATTTTGGGTGCTAGCCTGTCAATGGTCGGCACCCAGTACAGTATTTT
1 AAAAAAAGTAAAAAAAAAA-TTT-GGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAATTT
46548742 TTTTTTACTTTTTT-GTGTCAGTATCAGGTATCAGTATAC
64 TTTTTTACTTTTTTCGTGTCAGTATCAGGTATCAGTATAC
* *
46548781 -AAAAAAGTAAAAAAAAAA-TTGGTACTGGCCTGTCAATGGCCGGCACCTAGCACAGTAAAATTT
1 AAAAAAAGTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT--AATTT
*
46548844 TTTTTTACTTTTTTCGTGTCAATATCAGGTATCAGTATAC
64 TTTTTTACTTTTTTCGTGTCAGTATCAGGTATCAGTATAC
* * * * *
46548884 GAAAAAAGT-AAAAAAAAATTTGTTGCTGGTCTGTCAATGGCCGACACCCAGCACAGTAAATTTT
1 AAAAAAAGTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAATTTTT
*
46548948 TTTTACTTTTTTTCGTGTCAGTATCAGGTATCAATATAC
66 TTTTAC-TTTTTTCGTGTCAGTATCAGGTATCAGTATAC
46548987 AAAAAAAGTAAAAAAA
1 AAAAAAAGTAAAAAAA
46549003 TTTTTATATC
Statistics
Matches: 197, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
100 31 0.16
101 2 0.01
102 30 0.15
103 87 0.44
104 47 0.24
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (103 bp):
AAAAAAAGTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAATTTTT
TTTTACTTTTTTCGTGTCAGTATCAGGTATCAGTATAC
Found at i:46549289 original size:19 final size:18
Alignment explanation
Indices: 46549265--46549307 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
46549255 TCCATTAAAT
46549265 AAATATTAAAAAAAGAAAA
1 AAATATTAAAAAAA-AAAA
* *
46549284 AAATA-TAAAAATAAAAG
1 AAATATTAAAAAAAAAAA
46549301 AAATATT
1 AAATATT
46549308 TACATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATATTAAAAAAAAAAA
Found at i:46549349 original size:13 final size:13
Alignment explanation
Indices: 46549331--46549355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46549321 TTAAGAAAGT
46549331 AAAAATTAAAATA
1 AAAAATTAAAATA
46549344 AAAAATTAAAAT
1 AAAAATTAAAAT
46549356 TGTCGTGATC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:46549861 original size:110 final size:108
Alignment explanation
Indices: 46549731--46550075 Score: 538
Period size: 110 Copynumber: 3.2 Consensus size: 108
46549721 TGATGACACG
* *
46549731 AATTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTAACAAGAAAAAAAGTAAAAAAAAA
1 AATTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAA
* *
46549796 ATTTACTGTGCTGGGTGCCGGCGATTGACAGGCCAGCACCCAAA
66 TTTTACTGTGCTGGGTGCCGGCCATTGACAGGCCAGCACCC-AA
46549840 AATTTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAA
1 AA-TTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAA
46549905 ATTTTACTGTGCTGGGTGCCGGCCATTGACAGGCCAGCA-CCAA
65 ATTTTACTGTGCTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
* **
46549948 AATTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACG-AAAAAAGTAAAATAATT
1 AATTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAA
* * * *
46550012 TTTTACTATACTGGGTGCCGGCCATTAACAGGCCAGC-CCCCA
66 TTTTACTGTGCTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
46550054 AA--TTTTTTTTACTTTTTTCGTA
1 AATTTTTTTTTTACTTTTTTCGTA
46550076 CCCTGGTGCC
Statistics
Matches: 223, Mismatches: 11, Indels: 9
0.92 0.05 0.04
Matches are distributed among these distances:
104 20 0.09
106 53 0.24
107 45 0.20
108 4 0.02
109 4 0.02
110 97 0.43
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (108 bp):
AATTTTTTTTTTACTTTTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAA
TTTTACTGTGCTGGGTGCCGGCCATTGACAGGCCAGCACCCAA
Found at i:46551394 original size:15 final size:15
Alignment explanation
Indices: 46551374--46551402 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46551364 ATTTTTACAC
46551374 TATTATTATTATAAT
1 TATTATTATTATAAT
46551389 TATTATTATTATAA
1 TATTATTATTATAA
46551403 CCATGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTATTATAAT
Found at i:46551499 original size:12 final size:12
Alignment explanation
Indices: 46551482--46551511 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46551472 ATTTTCTTTA
*
46551482 TATATATATATT
1 TATATATACATT
46551494 TATATATACATT
1 TATATATACATT
46551506 TATATA
1 TATATA
46551512 CATACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATATACATT
Found at i:46551511 original size:14 final size:14
Alignment explanation
Indices: 46551478--46551518 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
46551468 TTACATTTTC
*
46551478 TTTATATATATATA
1 TTTATATATATACA
46551492 -TT-TATATATACA
1 TTTATATATATACA
*
46551504 TTTATATACATACA
1 TTTATATATATACA
46551518 T
1 T
46551519 ATTTTTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 9 0.39
13 4 0.17
14 10 0.43
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTATATATATACA
Found at i:46551918 original size:15 final size:15
Alignment explanation
Indices: 46551878--46551920 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
46551868 ACATTAGTTG
*
46551878 ATTTGTTTTTTTTTT
1 ATTTGTTTTTATTTT
46551893 ATTT-TTCTTTATTTT
1 ATTTGTT-TTTATTTT
*
46551908 ATTTGATTTTATT
1 ATTTGTTTTTATT
46551921 GTTTATTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 21 0.88
16 1 0.04
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (15 bp):
ATTTGTTTTTATTTT
Found at i:46558401 original size:50 final size:50
Alignment explanation
Indices: 46558343--46558724 Score: 278
Period size: 50 Copynumber: 7.6 Consensus size: 50
46558333 ACAGTAGAAT
*
46558343 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
* * * ** *** ** * * ** *
46558393 AGATTGAAGCTACGACAGCGGATCTGGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
46558443 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
** * * ** * * ** *
46558493 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
* * * * * *
46558543 AGATTGACGCCACAACGGCTGATCTTACTTCCCTAGCGGTGCAGTGGAAT
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
* * ** ** ** ** *
46558593 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAACATTGTAGTTAAAT
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
* * ** *
46558643 AGATTGAAGCCACAATGGCGAATCTTACCTCCCTGGTGGTGTAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
* * * * *
46558693 AAATTGAAGTCACAACGGTGAATCTTGTTTCC
1 AGATTGAAGCCACAACGGCGGATCTTATTTCC
46558725 TCGACATTAC
Statistics
Matches: 240, Mismatches: 92, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
50 240 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
Found at i:46558458 original size:100 final size:100
Alignment explanation
Indices: 46558343--46558701 Score: 547
Period size: 100 Copynumber: 3.6 Consensus size: 100
46558333 ACAGTAGAAT
46558343 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
46558408 CAGCGGATCTGGTTTCCCCAACATTGCAATTAAAA
66 CGGCGGATCTGGTTTCCCCAACATTGCAATTAAAA
* * *
46558443 AGATTGAAGCCACAACGGCGGATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCCACAA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
46558508 CGGCGGATCTGGTTTCCCCGACATTGCAATTAAAA
66 CGGCGGATCTGGTTTCCCCAACATTGCAATTAAAA
* * * * *
46558543 AGATTGACGCCACAACGGCTGATCTTACTTCCCTAGCGGTGCAGTGGAATAGATTGAAGCTACGA
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
* * * *
46558608 CGGCGGATCTGGTTTCCCTAACATTGTAGTTAAAT
66 CGGCGGATCTGGTTTCCCCAACATTGCAATTAAAA
* * * * *
46558643 AGATTGAAGCCACAATGGCGAATCTTACCTCCCTGGTGGTGTAGTGGAACAAATTGAAG
1 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAG
46558702 TCACAACGGT
Statistics
Matches: 231, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 231 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (100 bp):
AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
CGGCGGATCTGGTTTCCCCAACATTGCAATTAAAA
Found at i:46558919 original size:45 final size:45
Alignment explanation
Indices: 46558842--46558932 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 45
46558832 TTGCATGCAG
* * ** * *
46558842 TCTTATCTCCCTGAGGTTGTAGCGGAGTAGACTGA-AGATAGCAAA
1 TCTTATCTCCCTAAAGTTACAGCGGAGCAGACT-ACAAATAGCAAA
*
46558887 TCTTATCTCCCTAAAGTTACAGTGGAGCAGACTACAAATAGCAAA
1 TCTTATCTCCCTAAAGTTACAGCGGAGCAGACTACAAATAGCAAA
46558932 T
1 T
46558933 TTTGTTCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTAAAGTTACAGCGGAGCAGACTACAAATAGCAAA
Found at i:46560396 original size:32 final size:31
Alignment explanation
Indices: 46560359--46560425 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
46560349 TACATTTGAA
* * *
46560359 ATATACGTACATATTGTTTTTATAGTTTATAT
1 ATATACGTACATATTCTTTCTATA-TATATAT
* *
46560391 ATATACTTACATTTTCTTTCTATATATATAT
1 ATATACGTACATATTCTTTCTATATATATAT
46560422 ATAT
1 ATAT
46560426 TTTTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (31 bp):
ATATACGTACATATTCTTTCTATATATATAT
Found at i:46560434 original size:16 final size:16
Alignment explanation
Indices: 46560413--46560471 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
46560403 TTTCTTTCTA
*
46560413 TATATATATATATTTT
1 TATACATATATATTTT
* *
46560429 TAT--ATATACATTTG
1 TATACATATATATTTT
*
46560443 TATACATACATATTTT
1 TATACATATATATTTT
*
46560459 TACACATATATAT
1 TATACATATATAT
46560472 ATCTTCATGG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 12 0.35
16 22 0.65
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (16 bp):
TATACATATATATTTT
Found at i:46560469 original size:14 final size:14
Alignment explanation
Indices: 46560418--46560469 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
46560408 TTCTATATAT
*
46560418 ATATATATTTTTAT
1 ATATATATTTTTAC
*
46560432 ATATACATTTGTATAC
1 ATATATATTT-T-TAC
*
46560448 ATACATATTTTTAC
1 ATATATATTTTTAC
*
46560462 ACATATAT
1 ATATATAT
46560470 ATATCTTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 18 0.60
15 2 0.07
16 10 0.33
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (14 bp):
ATATATATTTTTAC
Found at i:46567926 original size:44 final size:44
Alignment explanation
Indices: 46567700--46568122 Score: 214
Period size: 44 Copynumber: 9.6 Consensus size: 44
46567690 AAGATGGCGA
** *
46567700 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA-G
* * *
46567744 AT-TCTATCTCCCTGAAGTCGTAGTGGAGCAGATTAAAATAACAG
1 ATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *
46567788 ATTTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAG
* * * * * **
46567833 -CCTTAT-TCTCCTGAATTTGTAGT-GAGGCAGACTGAAGATGGC-G
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCACAG
**
46567876 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAG
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * *** *
46567921 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT--CGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * **
46567961 GTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAA--AGC-G
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCA-CAG
* *
46568005 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCATACTCAAGAAATCA-AG
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-TA-AAATCACAG
* * * * * *
46568052 -TCTTATCCCCCTGAAATTGCAGTGGGGCAGACT-AAATAAACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-CACAG
* * * *
46568095 ATCTCATCTCTCTAAAGTTGTAGTGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
46568123 TGGATTAGAA
Statistics
Matches: 282, Mismatches: 68, Indels: 58
0.69 0.17 0.14
Matches are distributed among these distances:
40 22 0.08
41 11 0.04
42 4 0.01
43 13 0.05
44 134 0.48
45 85 0.30
46 10 0.04
47 2 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
Found at i:46568012 original size:45 final size:45
Alignment explanation
Indices: 46567701--46568083 Score: 197
Period size: 45 Copynumber: 8.7 Consensus size: 45
46567691 AGATGGCGAA
*** * * *
46567701 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TAAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAG-AAAGCAAG
* * ** *
46567746 TC-TATCTCCCTGAAGTCGTAGTGGAGCAGA-TTAA-AATAAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAA-AGCAAG
* * * *
46567788 ATTTTATCTCCCTGAAGTTGCAATGGAGCAGA-CTAAGTAAGCAAG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAG
* * * ** **
46567833 CCTTAT-TCTCCTGAATTTGTAGT-GAGGCAGACTGAAGATGGCGAA-
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACCCAAGAAAGC-AAG
** ** *
46567878 TCTTATCTCCCTGAAGTTGCAGTGGAGTGGA--TTA-AAATCACAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCA-AG
* * * * * **
46567921 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TC--G-CATCGGG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAG
* *
46567962 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAG
* * *
46568007 TCTTATCTCCCTGAAGTTGCAGTGGAGCATACTCAAGAAATCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAG
* * *
46568052 TCTTATCCCCCTGAAATTGCAGTGGGGCAGAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
46568084 TAAATAAACA
Statistics
Matches: 259, Mismatches: 57, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
40 20 0.08
41 10 0.04
42 9 0.03
43 14 0.05
44 98 0.38
45 102 0.39
46 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAAG
Found at i:46568027 original size:129 final size:132
Alignment explanation
Indices: 46567748--46568035 Score: 327
Period size: 129 Copynumber: 2.2 Consensus size: 132
46567738 CCAATAATTC
* * *
46567748 TATCTCCCTGAAGTCGTAGTGGAGCAGATTAAAATAACAGATTTTATCTCCCTGAAGTTGCAATG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCCTGAAGTTGCAA-G
* ** **
46567813 GAGCAGACTAAGTAAGCAAGCCTTATTCTCCTGAATTTGTAGTGAGGCAGACTGAAGATGGCGAA
65 GAGCAGACTAAGTAAGCAAGCCTTATTCTCCTGAAGTTGTAGTGAGGCAGACCCAAGAAAGCGAA
46567878 TCT
130 TCT
** * *
46567881 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC-AGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCCTGAAGTTGCAAG-
* * * ** *
46567945 GAGCAGA-T-CG-CATCGGGTCTTA-TCTCCCTGAAGTTGTAGTG-GAGCAGACCCAAGAAAGCG
65 GAGCAGACTAAGTAAGCAAGCCTTATTCT-CCTGAAGTTGTAGTGAG-GCAGACCCAAGAAAGCG
*
46568005 AGTCT
128 AATCT
46568010 TATCTCCCTGAAGTTGCAGTGGAGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCA
46568036 TACTCAAGAA
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
128 4 0.03
129 62 0.47
130 1 0.01
131 2 0.02
132 8 0.06
133 54 0.41
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (132 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCCTGAAGTTGCAAGG
AGCAGACTAAGTAAGCAAGCCTTATTCTCCTGAAGTTGTAGTGAGGCAGACCCAAGAAAGCGAAT
CT
Found at i:46568106 original size:174 final size:173
Alignment explanation
Indices: 46567791--46568114 Score: 368
Period size: 174 Copynumber: 1.9 Consensus size: 173
46567781 ATAACAGATT
* * * *
46567791 TTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGCCTTATTCTCCTGAATTTGTAGT
1 TTATCTCCCTGAAGTTGCAATGGAGCAGACCAAGAAAGCAAGCCTTATTCTCCTGAAGTTGCAGT
* ** * * ** * * *
46567856 GAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAG
66 GAGGCAGACTCAAGAAAGCGAATCTTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAATAACAA
* *
46567921 ATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGGGTC
131 ATCTCATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCGGGTC
* * * *
46567964 TTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAGTCTTA-TCTCCCTGAAGTTGCA
1 TTATCTCCCTGAAGTTGCAATGGAGCAGA-CCAAGAAAGCAAGCCTTATTCT-CCTGAAGTTGCA
* * *
46568028 GTG-GAGCATACTCAAGAAATC-AAGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACT-AAATA
64 GTGAG-GCAGACTCAAGAAAGCGAA-TCTTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAAT-
46568090 AACAAATCTCATCTCTCTAAAGTTG
126 AACAAATCTCATCTCTCTAAAGTTG
46568115 TAGTGGAGTG
Statistics
Matches: 123, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
173 37 0.30
174 86 0.70
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (173 bp):
TTATCTCCCTGAAGTTGCAATGGAGCAGACCAAGAAAGCAAGCCTTATTCTCCTGAAGTTGCAGT
GAGGCAGACTCAAGAAAGCGAATCTTATCCCCCTGAAATTGCAGTGGAGCAGACTAAAATAACAA
ATCTCATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCGGGTC
Found at i:46568658 original size:19 final size:19
Alignment explanation
Indices: 46568634--46568725 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
46568624 AATTTTCAAG
*
46568634 GATATGCAATCTTGGATAT
1 GATATGCAATCTTAGATAT
*
46568653 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46568672 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
46568691 AATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
46568710 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
46568726 AGATGTGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:46568679 original size:38 final size:38
Alignment explanation
Indices: 46568634--46568725 Score: 166
Period size: 38 Copynumber: 2.4 Consensus size: 38
46568624 AATTTTCAAG
* *
46568634 GATATGCAATCTTGGATATGATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATATAATATGTAATCTTAGATAT
46568672 GATATGCAATCTTAGATATAATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATATAATATGTAATCTTAGATAT
46568710 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
46568726 AGATGTGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATAATATGTAATCTTAGATAT
Found at i:46573054 original size:20 final size:20
Alignment explanation
Indices: 46573029--46573067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46573019 TAATATTTTC
*
46573029 AATAAAAAATCATAAAAATT
1 AATAAAAAATAATAAAAATT
*
46573049 AATAAAATATAATAAAAAT
1 AATAAAAAATAATAAAAAT
46573068 ATATTGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAAAAATAATAAAAATT
Found at i:46573068 original size:11 final size:11
Alignment explanation
Indices: 46573029--46573070 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
46573019 TAATATTTTC
46573029 AATAAAAA-AT
1 AATAAAAATAT
*
46573039 CATAAAAAT-T
1 AATAAAAATAT
46573049 AAT-AAAATAT
1 AATAAAAATAT
46573059 AATAAAAATAT
1 AATAAAAATAT
46573070 A
1 A
46573071 TTGAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 5 0.19
10 14 0.52
11 8 0.30
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAAATAT
Found at i:46573319 original size:19 final size:20
Alignment explanation
Indices: 46573276--46573330 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
46573266 TTTTAATTCT
46573276 ATAAAAACTTA-AAAAAACTA
1 ATAAAAA-TTATAAAAAACTA
46573296 ATAAACAA-TATAAAAAA-TA
1 ATAAA-AATTATAAAAAACTA
*
46573315 TTAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
46573331 TCATTTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.06
19 16 0.52
20 11 0.35
21 2 0.06
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAAAATTATAAAAAACTA
Found at i:46573980 original size:20 final size:20
Alignment explanation
Indices: 46573911--46573982 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
46573901 TTTTTATTTT
*
46573911 TTTTAT-AATTTATTAGAA-
1 TTTTATAAATTTATTATAAG
* *
46573929 -TTTAAAAATAT-TTATAAGG
1 TTTTATAAATTTATTATAA-G
* *
46573948 TTTTATTATTTTATTATAAG
1 TTTTATAAATTTATTATAAG
46573968 TTTTATAAATTTATT
1 TTTTATAAATTTATT
46573983 TAAAAATAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
17 9 0.22
18 4 0.10
20 21 0.52
21 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTTATAAATTTATTATAAG
Found at i:46575814 original size:11 final size:11
Alignment explanation
Indices: 46575768--46575833 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
46575758 AAATAAAAGG
46575768 AAAAGAAAGAA
1 AAAAGAAAGAA
** * *
46575779 AGGACAAACAA
1 AAAAGAAAGAA
* * *
46575790 AACAGAAGGGA
1 AAAAGAAAGAA
46575801 AAAAGAAAGAA
1 AAAAGAAAGAA
*
46575812 AAAGGAAAGAA
1 AAAAGAAAGAA
46575823 AAAGAGAAAGA
1 AAA-AGAAAGA
46575834 CCAAAGCTAG
Statistics
Matches: 39, Mismatches: 15, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
11 33 0.85
12 6 0.15
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:46577468 original size:67 final size:67
Alignment explanation
Indices: 46577360--46577491 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
46577350 TTTTCAATTC
46577360 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
46577425 CA
66 CA
* * *
46577427 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTATCAGTCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
46577492 TAATTAAACT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:46577709 original size:57 final size:59
Alignment explanation
Indices: 46577637--46577751 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 59
46577627 GTTAAATCTA
46577637 TTTTCCACATATTCTTCGGGAGGGCTATATC-A-A-GATCACCCGTCCGGGCTAGAGCT
1 TTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGCTAGAGCT
46577693 TTTTCACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTAGA
1 TTTTC-CACATATTCTTCGGGAGGGCTATATC--GATAGGATCACCCGTCCGGGCTAGA
46577752 TCCTTTTTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
56 5 0.09
57 26 0.49
60 1 0.02
61 1 0.02
62 20 0.38
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (59 bp):
TTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGCTAGAGCT
Found at i:46580884 original size:13 final size:13
Alignment explanation
Indices: 46580866--46580890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46580856 ATGATTTTTT
46580866 GATAATATAAATA
1 GATAATATAAATA
46580879 GATAATATAAAT
1 GATAATATAAAT
46580891 GTGGTACCAA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
GATAATATAAATA
Found at i:46591724 original size:17 final size:16
Alignment explanation
Indices: 46591698--46591736 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
46591688 ATTTCATATC
*
46591698 ATATATTAATATTTTA
1 ATATAATAATATTTTA
46591714 ATTATAATAATATTTTA
1 A-TATAATAATATTTTA
46591731 ATATAA
1 ATATAA
46591737 GGTCTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATAATATTTTA
Found at i:46592152 original size:44 final size:45
Alignment explanation
Indices: 46592101--46592190 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
46592091 AGATTTTCTT
*
46592101 ATTCTACAGTTTAGTCCTAAACCTTG-TTTTTTATAGATTTGCAA
1 ATTCTACAGTTTAGTCCTAAACCTCGTTTTTTTATAGATTTGCAA
46592145 ATTCTACAGTTTAGTCCTAAACCTCGTTTTTTTATAGATTTGCAA
1 ATTCTACAGTTTAGTCCTAAACCTCGTTTTTTTATAGATTTGCAA
46592190 A
1 A
46592191 CTAGTCCCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 25 0.57
45 19 0.43
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (45 bp):
ATTCTACAGTTTAGTCCTAAACCTCGTTTTTTTATAGATTTGCAA
Found at i:46599431 original size:70 final size:70
Alignment explanation
Indices: 46599313--46599457 Score: 281
Period size: 70 Copynumber: 2.1 Consensus size: 70
46599303 ACTTAGTTGA
*
46599313 TTTGAAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
1 TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
46599378 AAATC
66 AAATC
46599383 TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
1 TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
46599448 AAATC
66 AAATC
46599453 TTTGT
1 TTTGT
46599458 GTTATTCAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (70 bp):
TTTGTAAGCTTAGAGAAACTATAATATAGGCCCATATCTACTTTGTTAGTGGGGTTGCTATTAGT
AAATC
Found at i:46606580 original size:3 final size:3
Alignment explanation
Indices: 46606572--46606627 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
46606562 CTCTGGAGCT
* *
46606572 TCA TCA TCA TCA TCG TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
46606620 TCA TCA TC
1 TCA TCA TC
46606628 TAAGTTCTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:46613260 original size:13 final size:13
Alignment explanation
Indices: 46613233--46613269 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
46613223 TTATTTTTTA
46613233 AATT-TAAAT-TT
1 AATTATAAATATT
46613244 AATTATAAATATT
1 AATTATAAATATT
*
46613257 AATTAAAAATATT
1 AATTATAAATATT
46613270 TTTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 4 0.17
12 5 0.22
13 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTATAAATATT
Found at i:46613573 original size:14 final size:15
Alignment explanation
Indices: 46613554--46613587 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
46613544 AATTTATGTC
46613554 ATATAAAAATT-ATA
1 ATATAAAAATTAATA
46613568 ATATAAAAATTAATA
1 ATATAAAAATTAATA
46613583 ATATA
1 ATATA
46613588 TGTGATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAAATTAATA
Found at i:46615786 original size:168 final size:161
Alignment explanation
Indices: 46615503--46615806 Score: 423
Period size: 168 Copynumber: 1.8 Consensus size: 161
46615493 GGCATTTTTG
* * *
46615503 TTAGTCAGACCATTAGTTAAAATGTTATCTATTTTAAAAAAAAGATTAACCCATAAATTGGTACT
1 TTAGTCAAACCATTAGTTAAAATATTATCTATTTTAAAAAAAAGATTAACCCATAAATTGGTACC
* * * *
46615568 TAAATTATGTCATTTTTTCATTTTGGTATCTAAATATTTTTTTGGTCACAAGTATTACCTAAACT
66 TAAACTATGTCATTTTTTCATTTTGGTATCTAAACATTTTTTTGGTCACAAGTAGTACATAAACT
46615633 ATTTTTTTTCCAAGTTCATGATATATCTTCA
131 ATTTTTTTTCCAAGTTCATGATATATCTTCA
*
46615664 TTAGTCAAACCATTAGTTAAAGTATTAAGTCTATTTTTTTAAAAAAAATGGATTAACCCATAAAT
1 TTAGTCAAACCATTAGTTAAAATATT-A-TCTA---TTTTAAAAAAAA--GATTAACCCATAAAT
* *
46615729 TGGTACCTAAACTATGTTATTTTTCTCATTTTGGTA-CTTAAACATTTTTTT-GTCACAAGTGGT
59 TGGTACCTAAACTATGTCATTTTT-TCATTTTGGTATC-TAAACATTTTTTTGGTCACAAGTAGT
46615792 ACATAAACTATTTTT
122 ACATAAACTATTTTT
46615807 CTCCAAGCTG
Statistics
Matches: 124, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
161 23 0.19
162 1 0.01
163 4 0.03
166 12 0.10
168 61 0.49
169 23 0.19
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (161 bp):
TTAGTCAAACCATTAGTTAAAATATTATCTATTTTAAAAAAAAGATTAACCCATAAATTGGTACC
TAAACTATGTCATTTTTTCATTTTGGTATCTAAACATTTTTTTGGTCACAAGTAGTACATAAACT
ATTTTTTTTCCAAGTTCATGATATATCTTCA
Found at i:46615818 original size:27 final size:28
Alignment explanation
Indices: 46615760--46615818 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
46615750 TTTCTCATTT
* * *
46615760 TGGTACTTAAACATTTTTTTGTCACAAG
1 TGGTACATAAACATATTTTTCTCACAAG
46615788 TGGTACATAAAC-TATTTTTCTC-CAAG
1 TGGTACATAAACATATTTTTCTCACAAG
46615814 CTGGT
1 -TGGT
46615819 GCCTCTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 12 0.44
28 11 0.41
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (28 bp):
TGGTACATAAACATATTTTTCTCACAAG
Found at i:46615963 original size:16 final size:18
Alignment explanation
Indices: 46615942--46615979 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
46615932 TATATATTCT
46615942 TAAAAAATA-TT-AAAAA
1 TAAAAAATATTTAAAAAA
46615958 TAAAAAATATTTAAAAAA
1 TAAAAAATATTTAAAAAA
46615976 TAAA
1 TAAA
46615980 GAAAACTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATATTTAAAAAA
Found at i:46635001 original size:12 final size:12
Alignment explanation
Indices: 46634980--46635009 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46634970 GCAAATGGAT
*
46634980 CATTTCCATTTC
1 CATTTTCATTTC
46634992 CATTTTCATTTC
1 CATTTTCATTTC
46635004 CATTTT
1 CATTTT
46635010 GGAAGCCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (12 bp):
CATTTTCATTTC
Found at i:46656793 original size:41 final size:41
Alignment explanation
Indices: 46656702--46656846 Score: 175
Period size: 41 Copynumber: 3.6 Consensus size: 41
46656692 AGGCTAAGCG
* **** *
46656702 CCTAGCAGGCTAAATGCCGGTGA-ATTTTTCAGACTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
* * *
46656742 TCTAGCAGGCTAAGTGCCGGTGATCGGAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
* * *
46656783 CCTAGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
46656824 CCTAGCAGGCTAAGTGCCGGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
46656847 ATATGTTAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 21 0.24
41 67 0.76
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
Found at i:46660943 original size:32 final size:32
Alignment explanation
Indices: 46660907--46660971 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
46660897 TGGGGAATTC
46660907 TTTGCTTCTGTTCTTTCATGGAGGACCAGTGT
1 TTTGCTTCTGTTCTTTCATGGAGGACCAGTGT
*
46660939 TTTGCTTTTGTTCTTTCATGGAGGACCAGTGT
1 TTTGCTTCTGTTCTTTCATGGAGGACCAGTGT
46660971 T
1 T
46660972 CTTTCATGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.25, T:0.46
Consensus pattern (32 bp):
TTTGCTTCTGTTCTTTCATGGAGGACCAGTGT
Found at i:46660973 original size:21 final size:21
Alignment explanation
Indices: 46660947--46660987 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
46660937 GTTTTGCTTT
46660947 TGTTCTTTCATGGAGGACCAG
1 TGTTCTTTCATGGAGGACCAG
46660968 TGTTCTTTCATGGAGGACCA
1 TGTTCTTTCATGGAGGACCA
46660988 AACTTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (21 bp):
TGTTCTTTCATGGAGGACCAG
Found at i:46662521 original size:20 final size:20
Alignment explanation
Indices: 46662496--46662533 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46662486 TATTTTCCAA
46662496 TAAATCATTTTACAGAAAAG
1 TAAATCATTTTACAGAAAAG
*
46662516 TAAATCATTTTCCAGAAA
1 TAAATCATTTTACAGAAA
46662534 TCATTTTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (20 bp):
TAAATCATTTTACAGAAAAG
Found at i:46662538 original size:34 final size:33
Alignment explanation
Indices: 46662483--46662547 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
46662473 AAACACCAAA
*
46662483 AAATATTTTCCAATAAATCATTTTACAGAAAAGT
1 AAATATTTTCCAAGAAATCATTTTAC-GAAAAGT
46662517 AAATCATTTTCC-AGAAATCATTTTACGAAAA
1 AAAT-ATTTTCCAAGAAATCATTTTACGAAAA
46662548 ATATTTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 17 0.59
35 7 0.24
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (33 bp):
AAATATTTTCCAAGAAATCATTTTACGAAAAGT
Found at i:46663480 original size:9 final size:9
Alignment explanation
Indices: 46663466--46663516 Score: 77
Period size: 9 Copynumber: 5.8 Consensus size: 9
46663456 GTAATTTTCA
46663466 GGTAATTCG
1 GGTAATTCG
46663475 GGTAATTCG
1 GGTAATTCG
*
46663484 GTTAATTCG
1 GGTAATTCG
*
46663493 GTTAA-TCG
1 GGTAATTCG
46663501 GGTAATTCG
1 GGTAATTCG
46663510 GGTAATT
1 GGTAATT
46663517 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
8 7 0.18
9 32 0.82
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (9 bp):
GGTAATTCG
Found at i:46663506 original size:17 final size:17
Alignment explanation
Indices: 46663466--46663515 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
46663456 GTAATTTTCA
46663466 GGTAATTCGGGTAATTCG
1 GGTAATTCGGGTAA-TCG
* *
46663484 GTTAATTCGGTTAATCG
1 GGTAATTCGGGTAATCG
46663501 GGTAATTCGGGTAAT
1 GGTAATTCGGGTAAT
46663516 TTTTAACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.24, C:0.10, G:0.30, T:0.36
Consensus pattern (17 bp):
GGTAATTCGGGTAATCG
Found at i:46664258 original size:21 final size:22
Alignment explanation
Indices: 46664209--46664249 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46664199 ATTTAATTTT
46664209 AAAAAATATAATAATTAAATCG
1 AAAAAATATAATAATTAAATCG
*
46664231 AAAAAAT-TAATAGTTAAAT
1 AAAAAATATAATAATTAAAT
46664250 GATCAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAAAATATAATAATTAAATCG
Found at i:46665223 original size:228 final size:229
Alignment explanation
Indices: 46664956--46665372 Score: 558
Period size: 228 Copynumber: 1.8 Consensus size: 229
46664946 ATGCCGGAAC
*
46664956 TTTTGAAACTGAAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTAGCCGA-AA
1 TTTTGAAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTAGCC-ATAA
* * *
46665020 ACGCCGCTATATATTAGCTTTTCA-TGGCGCTGT-TCCTGAATCGCCGCAAATATTTTGAACAAA
65 ACGCCGCTATATATCAGCTTTT-AGTGGCGCT-TCTCCTGAAGCGCCGCAAAAATTTTGAACAAA
** * * *
46665083 ATGCATCG-TTCGAGTTTGACGTATAAAGGCATTAGTGGCGCTTACCT-GCAAACGCCGCTATAT
128 ACACATCGTTTCG-GCTTCACGTATAAAGGCATTAGCGGCGCTTACCTAG-AAACGCCGCTATAT
46665146 CCCATAAATAGCGGCGTTTAACTAAAAAACGCCGAAAAA
191 CCCATAAATAGCGGCGTTTAACTAAAAAACGCCGAAAAA
* * *
46665185 TTTT-AAACCGAAGCGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCGCTTATCCATAAA
1 TTTTGAAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTAGCCATAAA
* * * *
46665249 CGCCGTTATATATCAGCTTTTAGTGGCGCTTCTGCTTAAGCGCCGCAAAAATTTTGACCAAAACA
66 CGCCGCTATATATCAGCTTTTAGTGGCGCTTCTCCTGAAGCGCCGCAAAAATTTTGAACAAAACA
* ** **
46665314 CATCGTTTCGGCTTCACGTATAGATTCATTAGCGGCGCTTATTTAGAAACGCCGCTATA
131 CATCGTTTCGGCTTCACGTATAAAGGCATTAGCGGCGCTTACCTAGAAACGCCGCTATA
46665373 GAGTAACTTT
Statistics
Matches: 162, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
227 3 0.02
228 150 0.93
229 9 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (229 bp):
TTTTGAAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTAGCCATAAA
CGCCGCTATATATCAGCTTTTAGTGGCGCTTCTCCTGAAGCGCCGCAAAAATTTTGAACAAAACA
CATCGTTTCGGCTTCACGTATAAAGGCATTAGCGGCGCTTACCTAGAAACGCCGCTATATCCCAT
AAATAGCGGCGTTTAACTAAAAAACGCCGAAAAA
Found at i:46665725 original size:13 final size:14
Alignment explanation
Indices: 46665707--46665747 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
46665697 TTTCCAAAGA
46665707 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
46665720 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
46665734 TACGGTTTA-GACT
1 TATGGTTTAGGACT
46665747 T
1 T
46665748 TAGGGGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:46665927 original size:7 final size:7
Alignment explanation
Indices: 46665915--46665985 Score: 63
Period size: 7 Copynumber: 10.1 Consensus size: 7
46665905 TTAATTGACA
46665915 GGTTTAG
1 GGTTTAG
*
46665922 GGTTTAA
1 GGTTTAG
* *
46665929 GTTTTAC
1 GGTTTAG
*
46665936 GATTT-G
1 GGTTTAG
*
46665942 GGATTTGG
1 GG-TTTAG
46665950 GGTTTAG
1 GGTTTAG
46665957 GGTTTAG
1 GGTTTAG
*
46665964 GGTTTAT
1 GGTTTAG
*
46665971 AGTTTAG
1 GGTTTAG
46665978 GGTTTAG
1 GGTTTAG
46665985 G
1 G
46665986 ATCTACGATT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
6 1 0.02
7 47 0.92
8 3 0.06
ACGTcount: A:0.17, C:0.01, G:0.37, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:46666161 original size:15 final size:16
Alignment explanation
Indices: 46666129--46666167 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
46666119 GATATTCTAG
46666129 ATTAATATAAATGAAA
1 ATTAATATAAATGAAA
46666145 A-TAATATAAAT-ATAA
1 ATTAATATAAATGA-AA
46666160 ATTAATAT
1 ATTAATAT
46666168 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATATAAATGAAA
Found at i:46666871 original size:17 final size:19
Alignment explanation
Indices: 46666851--46666893 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
46666841 CTGTCATCTC
46666851 CCCCAAATCCCTAA-A-TT
1 CCCCAAATCCCTAACAGTT
*
46666868 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAACAGTT
46666887 CCCCAAA
1 CCCCAAA
46666894 CCCGACGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (19 bp):
CCCCAAATCCCTAACAGTT
Found at i:46667249 original size:6 final size:6
Alignment explanation
Indices: 46667238--46667346 Score: 218
Period size: 6 Copynumber: 18.2 Consensus size: 6
46667228 CGTTGAAATT
46667238 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
46667286 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
46667334 TATGTA TATGTA T
1 TATGTA TATGTA T
46667347 TAAAACTAAA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 103 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:46669547 original size:20 final size:20
Alignment explanation
Indices: 46669519--46669686 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
46669509 TGGAAATAAC
*
46669519 ATAAAATTAAGATAACTTAT
1 ATAATATTAAGATAACTTAT
*
46669539 ATAATATTAAGATTACTTAT
1 ATAATATTAAGATAACTTAT
* * *
46669559 ATAGTATTAAGACAAAATT-T
1 ATAATATTAAGA-TAACTTAT
* *
46669579 CT-A-ATT-ACATAACTTAT
1 ATAATATTAAGATAACTTAT
46669596 ATAAATATTAAGATAACTTAT
1 AT-AATATTAAGATAACTTAT
*
46669617 ATAATATTAAGATAAAATT-T
1 ATAATATTAAGAT-AACTTAT
* * *
46669637 CT-A-ATT-ACATAACTTCT
1 ATAATATTAAGATAACTTAT
* *
46669654 ATAATATTAATATAAGTTAT
1 ATAATATTAAGATAACTTAT
* *
46669674 ATTATTTTAAGAT
1 ATAATATTAAGAT
46669687 TAAATTTGGA
Statistics
Matches: 113, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
16 8 0.07
17 9 0.08
18 7 0.06
19 5 0.04
20 65 0.58
21 19 0.17
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
ATAATATTAAGATAACTTAT
Found at i:46669692 original size:57 final size:57
Alignment explanation
Indices: 46669530--46669720 Score: 258
Period size: 57 Copynumber: 3.3 Consensus size: 57
46669520 TAAAATTAAG
* *
46669530 ATAACTTATATAATATTAAGATTACTTATA-TAGTATTAAGACAAAATTTCTAATTAC
1 ATAACTTATATAATATTAAGATAACTTATATTA-TATTAAGATAAAATTTCTAATTAC
*
46669587 ATAACTTATATAAATATTAAGATAACTTATATAATATTAAGATAAAATTTCTAATTAC
1 ATAACTTATAT-AATATTAAGATAACTTATATTATATTAAGATAAAATTTCTAATTAC
* * * * * **
46669645 ATAACTTCTATAATATTAATATAAGTTATATTATTTTAAGATTAAATTTGGAATTAC
1 ATAACTTATATAATATTAAGATAACTTATATTATATTAAGATAAAATTTCTAATTAC
*
46669702 ATAAATTATATAATATTAA
1 ATAACTTATATAATATTAA
46669721 ATTGTAATTT
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
57 67 0.56
58 51 0.43
59 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (57 bp):
ATAACTTATATAATATTAAGATAACTTATATTATATTAAGATAAAATTTCTAATTAC
Found at i:46669802 original size:37 final size:35
Alignment explanation
Indices: 46669760--46669866 Score: 118
Period size: 37 Copynumber: 3.1 Consensus size: 35
46669750 TATATTTTAG
*
46669760 ATAACTTATACAATATTAAGATAAAATTTCGAATTAC
1 ATAACTTATATAATATTAAGAT-AAATTTC-AATTAC
46669797 ATAACTTATATAATATT-A-AT---TTCTC-ATTAC
1 ATAACTTATATAATATTAAGATAAATT-TCAATTAC
46669827 ATAACTTATATAATATTAAGATACAATTTCTAATTAC
1 ATAACTTATATAATATTAAGATA-AATTTC-AATTAC
46669864 ATA
1 ATA
46669867 TCAATTTCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
30 22 0.37
31 3 0.05
32 4 0.07
35 4 0.07
36 3 0.05
37 24 0.40
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (35 bp):
ATAACTTATATAATATTAAGATAAATTTCAATTAC
Found at i:46670768 original size:21 final size:21
Alignment explanation
Indices: 46670738--46670784 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
46670728 CTACAACTTA
*
46670738 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAAAGGCGGCAGCGAGAG
*
46670759 AAGCAAAGGCTGCAGCGAGAG
1 AAGCAAAGGCGGCAGCGAGAG
46670780 AAGCA
1 AAGCA
46670785 GTGAGAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.40, T:0.02
Consensus pattern (21 bp):
AAGCAAAGGCGGCAGCGAGAG
Found at i:46671318 original size:43 final size:44
Alignment explanation
Indices: 46671184--46671354 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 44
46671174 GGCATTTTTC
* *
46671184 ATAAAAGCGCCGCTAAA-ACTCATGTTCTCTAGCAGCGTTTGTG
1 ATAAAAGCGCCGCTAAAGACTCATGTTCTTTAGCGGCGTTTGTG
* * * *
46671227 A-AGAAAGCGCCGCTAAATAACTTTACT-TTTTTTA-CGGCGTTTGAG
1 ATA-AAAGCGCCGCTAAA-GAC-TCA-TGTTCTTTAGCGGCGTTTGTG
46671272 ATAAAAGCGCCGCTAAAGA-TCATGTTCTTTAGCGGCGTTTGTG
1 ATAAAAGCGCCGCTAAAGACTCATGTTCTTTAGCGGCGTTTGTG
* *
46671315 ATAAAAGCGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTT
1 ATAAAAGCGCCGCTAAAGACTCATGTTCTTTAGCGGCGTTT
46671355 TTTCTGTAAG
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 9 0.08
43 63 0.58
44 1 0.01
45 26 0.24
46 8 0.07
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
ATAAAAGCGCCGCTAAAGACTCATGTTCTTTAGCGGCGTTTGTG
Found at i:46675966 original size:21 final size:18
Alignment explanation
Indices: 46675921--46675967 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
46675911 TATGTATAAA
46675921 ATATATATATATAAACAT
1 ATATATATATATAAACAT
46675939 ACGTATACTATATATAAAACA-
1 A--TATA-TATATAT-AAACAT
46675960 ATATATAT
1 ATATATAT
46675968 TACATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 4 0.16
19 4 0.16
20 4 0.16
21 8 0.32
22 5 0.20
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (18 bp):
ATATATATATATAAACAT
Found at i:46676014 original size:7 final size:6
Alignment explanation
Indices: 46675993--46676024 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
46675983 CATGTGCATG
46675993 AAAATA AAAATA AAAATA AAAATA AATAATA A
1 AAAATA AAAATA AAAATA AAAATA AA-AATA A
46676025 TGATACAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:46676264 original size:23 final size:23
Alignment explanation
Indices: 46676238--46676282 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
46676228 AAGAAATTTG
*
46676238 AAATCAACAATACACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
46676261 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
46676283 CAAAATAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.18, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:46676488 original size:22 final size:21
Alignment explanation
Indices: 46676453--46676510 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
46676443 AAAGGGTATC
* * *
46676453 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
46676474 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
46676497 TGCATATCATATCT
1 TACAAATCATATCT
46676511 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:46676526 original size:21 final size:19
Alignment explanation
Indices: 46676489--46676563 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
46676479 AATCATATCT
46676489 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
46676508 TCTAAGATTGCATATATCAAA
1 TCTAAGATTGC--ATATCATA
*
46676529 TCTAAGATTGCGTATCATA
1 TCTAAGATTGCATATCATA
*
46676548 TCTAAGATTACATATC
1 TCTAAGATTGCATATC
46676564 CTTGAAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 31 0.63
21 18 0.37
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:46679527 original size:16 final size:18
Alignment explanation
Indices: 46679500--46679532 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46679490 TAAAATAAGG
46679500 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
46679517 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
46679533 TGATGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:46682867 original size:18 final size:18
Alignment explanation
Indices: 46682846--46683285 Score: 110
Period size: 17 Copynumber: 24.6 Consensus size: 18
46682836 CGAAAGTTTT
* *
46682846 TTTTTTAAAATACGAGAA
1 TTTTTGAAAACACGAGAA
46682864 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
46682882 --TTTGTAAACACGA-ATA
1 TTTTTGAAAACACGAGA-A
* *
46682898 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
46682915 TTTTTGGAAAAAAACGA-AA
1 TTTTT-G-AAAACACGAGAA
* * *
46682934 TTTTCTTAAAACACGACATTTT
1 TTTT-TGAAAACACGAGA---A
*
46682956 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAGAA
* * *
46682973 TTTTT-AAAACAAGACATT
1 TTTTTGAAAACACGAGA-A
46682991 TTTTTG-AAACA--A-AA
1 TTTTTGAAAACACGAGAA
*
46683005 TTTTTTCTTAAAA-A--A-AA
1 --TTTT-TGAAAACACGAGAA
* *
46683022 ATTTT--AAATACGAGAA
1 TTTTTGAAAACACGAGAA
*
46683038 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
46683055 TTTTT-AAAACACGGAAATA
1 TTTTTGAAAACAC-GAGA-A
*
46683074 TTTTTTTTTAAAACACGA-AA
1 ---TTTTTGAAAACACGAGAA
* *
46683094 TTTTTTTTTTGAAAACAAGAAAA
1 -----TTTTTGAAAACACGAGAA
*
46683117 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAGAA
46683134 -TTTTGAAAACACGA-AGA
1 TTTTTGAAAACACGAGA-A
*
46683151 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAGAA
*
46683168 TTTTT-AAAAGCACGAGGA
1 TTTTTGAAAA-CACGAGAA
* *
46683186 TTATTGAAAGCACGA-AGA
1 TTTTTGAAAACACGAGA-A
* * *
46683204 TTTAT-AAAAAACGACAA
1 TTTTTGAAAACACGAGAA
*
46683221 TTTTTG-AAATACGAGAAA
1 TTTTTGAAAACACGAG-AA
* * *
46683239 TTTTT-TAAACGCGAAAA
1 TTTTTGAAAACACGAGAA
** *
46683256 TTTTTTTCAAACACGAAAA
1 -TTTTTGAAAACACGAGAA
*
46683275 CTTTTGAAAAC
1 TTTTTGAAAAC
46683286 GCGAAAATTC
Statistics
Matches: 325, Mismatches: 50, Indels: 94
0.69 0.11 0.20
Matches are distributed among these distances:
12 3 0.01
13 1 0.00
14 1 0.00
15 6 0.02
16 30 0.09
17 104 0.32
18 104 0.32
19 21 0.06
20 17 0.05
21 2 0.01
22 27 0.08
23 9 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:46682885 original size:16 final size:16
Alignment explanation
Indices: 46682852--46682917 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
46682842 TTTTTTTTTT
*
46682852 AAAATACGAGAATTTTTG
1 AAAACACGAGAA--TTTG
46682870 AAAACACGAGAATTTG
1 AAAACACGAGAATTTG
* *
46682886 TAAACACGA-ATATTTT
1 AAAACACGAGA-ATTTG
*
46682902 AGAAACACGAAAATTT
1 A-AAACACGAGAATTT
46682918 TTGGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.39
17 12 0.29
18 12 0.29
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAACACGAGAATTTG
Found at i:46683007 original size:16 final size:18
Alignment explanation
Indices: 46682973--46683010 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
46682963 AACACGGGAA
46682973 TTTTTAAAACAAGACATT
1 TTTTTAAAACAAGACATT
*
46682991 TTTTTGAAACAA-A-ATT
1 TTTTTAAAACAAGACATT
46683007 TTTT
1 TTTT
46683011 CTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTTTAAAACAAGACATT
Found at i:46683056 original size:17 final size:17
Alignment explanation
Indices: 46683018--46683294 Score: 142
Period size: 17 Copynumber: 15.4 Consensus size: 17
46683008 TTTCTTAAAA
* *
46683018 AAAAATTTT-AAATACG
1 AAAATTTTTAAAACACG
*
46683034 AGAATTTTTAAAACACG
1 AAAATTTTTAAAACACG
46683051 AAAATTTTTAAAACACGG
1 AAAATTTTTAAAACAC-G
46683069 AAATATTTTTTTTTAAAACACG
1 AAA-A----TTTTTAAAACACG
* *
46683091 AAATTTTTTTTTTGAAAACAAG
1 AAA----ATTTTT-AAAACACG
* *
46683113 AAAATTTTTGAAACACT
1 AAAATTTTTAAAACACG
* *
46683130 AGAATTTTGAAAACACG
1 AAAATTTTTAAAACACG
* * *
46683147 AAGATTTTTGAAACATG
1 AAAATTTTTAAAACACG
*
46683164 AGAATTTTTAAAAGCACG
1 AAAATTTTTAAAA-CACG
** * *
46683182 AGGATTATTGAAAGCACG
1 AAAATT-TTTAAAACACG
* * *
46683200 AAGATTTATAAAAAACG
1 AAAATTTTTAAAACACG
* * *
46683217 ACAATTTTTGAAATACG
1 AAAATTTTTAAAACACG
* *
46683234 AGAAATTTTTTAAACGCG
1 A-AAATTTTTAAAACACG
*
46683252 AAAATTTTTTTCAAACACG
1 AAAA--TTTTTAAAACACG
* *
46683271 AAAACTTTTGAAAACGCG
1 AAAA-TTTTTAAAACACG
46683289 AAAATT
1 AAAATT
46683295 CGAAAATTTC
Statistics
Matches: 199, Mismatches: 46, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.04
17 86 0.43
18 53 0.27
19 21 0.11
21 5 0.03
22 14 0.07
23 12 0.06
25 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAATTTTTAAAACACG
Found at i:46683093 original size:22 final size:22
Alignment explanation
Indices: 46683055--46683121 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 22
46683045 AACACGAAAA
46683055 TTTTTAAAACACGGAAATATTTT
1 TTTTTAAAACAC-GAAATATTTT
46683078 TTTTTAAAACACGAAAT-TTTT
1 TTTTTAAAACACGAAATATTTT
*
46683099 TTTTTGAAAACAAGAAA-ATTTT
1 TTTTT-AAAACACGAAATATTTT
46683121 T
1 T
46683122 GAAACACTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
21 9 0.22
22 20 0.49
23 12 0.29
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTTAAAACACGAAATATTTT
Done.