Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 122 of 204
Found at i:37999332 original size:14 final size:14
Alignment explanation
Indices: 37999313--37999340 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37999303 TGGGTGCAAC
37999313 TTATTACTTTGGAT
1 TTATTACTTTGGAT
37999327 TTATTACTTTGGAT
1 TTATTACTTTGGAT
37999341 ATGTGTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
TTATTACTTTGGAT
Found at i:38006490 original size:6 final size:6
Alignment explanation
Indices: 38006481--38006562 Score: 146
Period size: 6 Copynumber: 13.7 Consensus size: 6
38006471 AAGAAAAAGA
* *
38006481 AAAATC AAAATC AAAGTC AAAATT AAAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
38006529 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
38006563 AAAGAAGAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 72 1.00
ACGTcount: A:0.67, C:0.15, G:0.01, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:38006602 original size:45 final size:46
Alignment explanation
Indices: 38006535--38006628 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 46
38006525 AATCAAAATC
38006535 AAAATCAAAATCAAAATCAAAATCA-AAAAA-AGAAGAAAGAA-GAAA
1 AAAATCAAAATCAAAATCAAAATCAGAAAAATA-AAG-AAGAATGAAA
* * *
38006580 AAAATCAAGATCAAAATGAAAATGAGAAAAATAAAGAAGAATGAAA
1 AAAATCAAAATCAAAATCAAAATCAGAAAAATAAAGAAGAATGAAA
38006626 AAA
1 AAA
38006629 GAGAAATCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 27 0.63
46 15 0.35
47 1 0.02
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.11
Consensus pattern (46 bp):
AAAATCAAAATCAAAATCAAAATCAGAAAAATAAAGAAGAATGAAA
Found at i:38007555 original size:7 final size:7
Alignment explanation
Indices: 38007537--38007578 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
38007527 CTCTAAGTCA
38007537 GAAAATAT
1 GAAAA-AT
38007545 GAAAAAT
1 GAAAAAT
38007552 G-AAAAT
1 GAAAAAT
38007558 G-AAAAT
1 GAAAAAT
*
38007564 GGAAAAT
1 GAAAAAT
38007571 GAAAAAT
1 GAAAAAT
38007578 G
1 G
38007579 GAGAGGCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 12 0.38
7 15 0.47
8 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (7 bp):
GAAAAAT
Found at i:38007561 original size:13 final size:13
Alignment explanation
Indices: 38007543--38007578 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
38007533 GTCAGAAAAT
38007543 ATGAAAAATGAAA
1 ATGAAAAATGAAA
38007556 ATG-AAAATGGAAA
1 ATGAAAAAT-GAAA
38007569 ATGAAAAATG
1 ATGAAAAATG
38007579 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:38008941 original size:86 final size:87
Alignment explanation
Indices: 38008787--38009091 Score: 436
Period size: 86 Copynumber: 3.5 Consensus size: 87
38008777 TAGATCAGTG
* * *
38008787 AAGATAGCAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCTA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
38008852 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* *
38008874 AAGA-AGCAGATCTTACCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAATCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
38008938 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * * *
38008960 AATA-AGCAGATCTTGCCTTCCTACATTAACAGTGGAGCATATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
38009024 TCGGTTGCAGTGGAGCT-GTGA
66 TCGGTTGCAGTGGAGCTGGTTA
* ** ** *
38009045 AAGATAGCAGATCTTGCCCTCCTGTGTCGACAGTGAAGCAGATCGAA
1 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA
38009092 GATTACAAGT
Statistics
Matches: 195, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
85 6 0.03
86 185 0.95
87 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCTGGTTA
Found at i:38008995 original size:44 final size:43
Alignment explanation
Indices: 38008859--38008997 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 43
38008849 CTATCGGTTG
* *
38008859 CAGTGGAGCTGGTTAAAGAAGCAGATCTTACCTTCCTGCATTAA
1 CAGTGGAGCTGGTTAAA-AAGCAGATCTTGCCTTCCTACATTAA
* * * * ** * * *
38008903 CAGCGAAGCAGATCGAAAA-CAAATCCTTGCC-TCC-ATCGGTT-G
1 CAGTGGAGCTGGTTAAAAAGCAGAT-CTTGCCTTCCTA-C-ATTAA
38008945 CAGTGGAGCTGGTTAAATAAGCAGATCTTGCCTTCCTACATTAA
1 CAGTGGAGCTGGTTAAA-AAGCAGATCTTGCCTTCCTACATTAA
38008989 CAGTGGAGC
1 CAGTGGAGC
38008998 ATATCGAAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
42 19 0.28
43 19 0.28
44 28 0.42
45 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (43 bp):
CAGTGGAGCTGGTTAAAAAGCAGATCTTGCCTTCCTACATTAA
Found at i:38009061 original size:43 final size:41
Alignment explanation
Indices: 38008928--38009062 Score: 98
Period size: 43 Copynumber: 3.1 Consensus size: 41
38008918 AAAACAAATC
*
38008928 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAATAAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCT-GTGAAA-AAGCAGAT
* * * * *
38008971 CTTGCCTTCC-TAC-ATTAACAGTGGAGCATATCG-AAAA-CAAAGC
1 CTTGCC-TCCAT-CGGTT-GCAGTGGAGC-TGT-GAAAAAGCAGA-T
38009014 CTTGCCTCCATCGGTTGCAGTGGAGCTGTGAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGTGAAA-A-AGCAGAT
38009057 CTTGCC
1 CTTGCC
38009063 CTCCTGTGTC
Statistics
Matches: 69, Mismatches: 11, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
40 1 0.01
41 4 0.06
42 17 0.25
43 27 0.39
44 19 0.28
45 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (41 bp):
CTTGCCTCCATCGGTTGCAGTGGAGCTGTGAAAAAGCAGAT
Found at i:38009297 original size:44 final size:44
Alignment explanation
Indices: 38009188--38009344 Score: 129
Period size: 44 Copynumber: 3.6 Consensus size: 44
38009178 TATCGGGTCT
* * * *
38009188 TATCTCCCTGAAGTTGAAGCGGAGCAGACTG-AGAAAATAAGTCT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAGATAA-TCC
* * *** * * *
38009232 TATCACCTTGAAGTCACAGTGGGGTAGACTGAAGAAGCA-AATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAG-ATAATCC
* * ***
38009276 TATCTCCCTGAGGTTGTAGTGGAGCAGATTGAATTCGATAATCC
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAGATAATCC
38009320 TATCTCCCTGAAGTTGTAGTGGAGC
1 TATCTCCCTGAAGTTGTAGTGGAGC
38009345 GGATTAAAGT
Statistics
Matches: 87, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
43 1 0.01
44 79 0.91
45 6 0.07
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAGATAATCC
Found at i:38009378 original size:45 final size:44
Alignment explanation
Indices: 38009271--38009393 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
38009261 TGAAGAAGCA
* * * *
38009271 AATCTTATCTCCCTGAGGTTGTAGTGGAGCAGATTGAATTCGAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCAAT
* *
38009315 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGT-AAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCAAT
* * *
38009358 AAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 -A-ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGAT
38009394 CGCATCAAGT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.03
44 36 0.55
45 28 0.42
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCAAT
Found at i:38015652 original size:11 final size:11
Alignment explanation
Indices: 38015636--38015687 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
38015626 TTTTATACTA
38015636 AATAAAATATT
1 AATAAAATATT
*
38015647 AATAAAATAAT
1 AATAAAATATT
*
38015658 AAT-ATATATT
1 AATAAAATATT
*
38015668 ATTAAAATATT
1 AATAAAATATT
*
38015679 AATTAAATA
1 AATAAAATA
38015688 ATATTTATCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
10 7 0.21
11 26 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAAAATATT
Found at i:38015668 original size:21 final size:21
Alignment explanation
Indices: 38015642--38015681 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38015632 ACTAAATAAA
38015642 ATATTAATAAAATAATAATAT
1 ATATTAATAAAATAATAATAT
* *
38015663 ATATTATTAAAATATTAAT
1 ATATTAATAAAATAATAAT
38015682 TAAATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTAATAAAATAATAATAT
Found at i:38018786 original size:46 final size:46
Alignment explanation
Indices: 38018719--38018806 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
38018709 TATTGCAATT
* *
38018719 AGAGTTTTAGTTTTATTTATTTTCTTTATTACATCAGGTTTTGTTA
1 AGAGTTTTAGTTTTACTTATTTTCTCTATTACATCAGGTTTTGTTA
* *
38018765 AGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTT
1 AGAGTTTTAGTTTTACTTATTTTCTCTATTACATCAGGTTTT
38018807 TACTTCCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.59
Consensus pattern (46 bp):
AGAGTTTTAGTTTTACTTATTTTCTCTATTACATCAGGTTTTGTTA
Found at i:38020022 original size:21 final size:21
Alignment explanation
Indices: 38019997--38020039 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
38019987 ACATGAACCA
38019997 AATTT-AATGTTAAGTGTGAAC
1 AATTTCAATGTT-AGTGTGAAC
*
38020018 AATTTCATTGTTAGTGTGAAC
1 AATTTCAATGTTAGTGTGAAC
38020039 A
1 A
38020040 CATCTAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (21 bp):
AATTTCAATGTTAGTGTGAAC
Found at i:38020727 original size:18 final size:20
Alignment explanation
Indices: 38020685--38020728 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38020675 GTTGTTAAGC
*
38020685 ATGATGAATGGAGAGCAACA
1 ATGATTAATGGAGAGCAACA
*
38020705 ATGATTAAT-GAGATCAA-A
1 ATGATTAATGGAGAGCAACA
38020723 ATGATT
1 ATGATT
38020729 GAGAAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (20 bp):
ATGATTAATGGAGAGCAACA
Found at i:38027247 original size:30 final size:30
Alignment explanation
Indices: 38027210--38027317 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
38027200 ATTGAGAAGC
38027210 ATTTTTATATTAATTATATTATGA-AAAAG
1 ATTTTTATATTAATTATATTATGAGAAAAG
* * * * *
38027239 AATGTTTATATTTATTGTATTATGATAAAAT
1 -ATTTTTATATTAATTATATTATGAGAAAAG
* **
38027270 ATTTTTACATTAATTACGTTATGAGAAAATG
1 ATTTTTATATTAATTATATTATGAGAAAA-G
38027301 -TTTTTATATTAATTATA
1 ATTTTTATATTAATTATA
38027318 GGAATAATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
30 57 0.93
31 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (30 bp):
ATTTTTATATTAATTATATTATGAGAAAAG
Found at i:38034627 original size:5 final size:5
Alignment explanation
Indices: 38034617--38034647 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
38034607 TGAGCATTCG
38034617 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
38034648 AATTTTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:38035430 original size:30 final size:31
Alignment explanation
Indices: 38035391--38035450 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
38035381 GGAGGTGGGA
*
38035391 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
38035422 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
38035451 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:38035678 original size:9 final size:9
Alignment explanation
Indices: 38035664--38035700 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38035654 TATAGTTTGA
38035664 TATTCGAAT
1 TATTCGAAT
38035673 TATTCGAAT
1 TATTCGAAT
*
38035682 TATTCGAGT
1 TATTCGAAT
38035691 TATTCGAAT
1 TATTCGAAT
38035700 T
1 T
38035701 CGAAAACTCA
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:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:38036868 original size:29 final size:31
Alignment explanation
Indices: 38036823--38036880 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
38036813 GATGGAGAAG
*
38036823 AAAAAGTATAAACATATTGGGTCATTTATGC
1 AAAAAGTATAAACATATTGAGTCATTTATGC
38036854 AAAAAGTA-AAA-ATATTGAGTCATTTAT
1 AAAAAGTATAAACATATTGAGTCATTTAT
38036881 TAAAAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.58
30 3 0.12
31 8 0.31
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (31 bp):
AAAAAGTATAAACATATTGAGTCATTTATGC
Found at i:38036886 original size:29 final size:31
Alignment explanation
Indices: 38036823--38036887 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
38036813 GATGGAGAAG
* *
38036823 AAAAAGTATAAACATATTGGGTCATTTATGC
1 AAAAAGTATAAACATATTGAGTCATTTATGA
*
38036854 AAAAAGTA-AAA-ATATTGAGTCATTTATTA
1 AAAAAGTATAAACATATTGAGTCATTTATGA
38036883 AAAAA
1 AAAAA
38036888 TAGAAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.65
30 3 0.10
31 8 0.26
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (31 bp):
AAAAAGTATAAACATATTGAGTCATTTATGA
Found at i:38036894 original size:29 final size:29
Alignment explanation
Indices: 38036830--38036894 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
38036820 AAGAAAAAGT
* *
38036830 ATAAACATATTGGGTCATTTATGCAAAAA
1 ATAAAAATATTGAGTCATTTATGCAAAAA
* *
38036859 GTAAAAATATTGAGTCATTTAT-TAAAAA
1 ATAAAAATATTGAGTCATTTATGCAAAAA
38036887 ATAGAAAA
1 ATA-AAAA
38036895 GGAAGTACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (29 bp):
ATAAAAATATTGAGTCATTTATGCAAAAA
Found at i:38037368 original size:9 final size:9
Alignment explanation
Indices: 38037351--38037387 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38037341 TGAGTTTTCG
38037351 AATTCGAAT
1 AATTCGAAT
*
38037360 AACTCGAAT
1 AATTCGAAT
38037369 AATTCGAAT
1 AATTCGAAT
38037378 AATTCGAAT
1 AATTCGAAT
38037387 A
1 A
38037388 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:38041699 original size:3 final size:3
Alignment explanation
Indices: 38041691--38041730 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
38041681 GTGATTGGCT
38041691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38041731 AGCTTCTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38052387 original size:19 final size:19
Alignment explanation
Indices: 38052360--38052402 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
38052350 TGTATTCTAA
* *
38052360 ATATTGTATAAAATCATGT
1 ATATAGTATAAAATCATAT
* *
38052379 ATATAGTATGAAATTATAT
1 ATATAGTATAAAATCATAT
38052398 ATATA
1 ATATA
38052403 TTTAATATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (19 bp):
ATATAGTATAAAATCATAT
Found at i:38064337 original size:27 final size:26
Alignment explanation
Indices: 38064289--38064557 Score: 251
Period size: 26 Copynumber: 10.2 Consensus size: 26
38064279 GATTCTTAGA
38064289 AAAATGACCGAAATACCCCGAAGGGT
1 AAAATGACCGAAATACCCCGAAGGGT
*
38064315 AAAATGATCGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCC-CGAAGGGT
* *
38064342 AAAATGATCGAAATACCCTCGAGGGGT
1 AAAATGACCGAAATACCC-CGAAGGGT
* *
38064369 -AAATGACCAAAATACCCTCGAATGGT
1 AAAATGACCGAAATACCC-CGAAGGGT
** *
38064395 AAAATGATTGAACTACCCCAGAAGGGT
1 AAAATGACCGAAATACCCC-GAAGGGT
38064422 -AAATGACCGAAATACCCC-AGAGGAGT
1 AAAATGACCGAAATACCCCGA-AGG-GT
* * *
38064448 AAAATAACTGAAATAACCCCAAAGGGT
1 AAAATGACCGAAAT-ACCCCGAAGGGT
**
38064475 -AAATGACCGAAATACCTTTGAA-GGT
1 AAAATGACCGAAATACC-CCGAAGGGT
* **
38064500 AAAATAACTTAAATACCCCGAAGGGT
1 AAAATGACCGAAATACCCCGAAGGGT
* * *
38064526 AACATGACCGAAATACCTCTGAAGGGC
1 AAAATGACCGAAATACC-CCGAAGGGT
38064553 AAAAT
1 AAAAT
38064558 AACTGTTATA
Statistics
Matches: 198, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
24 1 0.01
25 12 0.06
26 99 0.50
27 77 0.39
28 8 0.04
29 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (26 bp):
AAAATGACCGAAATACCCCGAAGGGT
Found at i:38064354 original size:53 final size:52
Alignment explanation
Indices: 38064289--38064557 Score: 280
Period size: 53 Copynumber: 5.1 Consensus size: 52
38064279 GATTCTTAGA
* *
38064289 AAAATGACCGAAATACCCCGAAGGGTAAAATGATCGAAATACCCTCGAAGGGT
1 AAAATGAACGAAATACCCCGAAGGGT-AAATGACCGAAATACCCTCGAAGGGT
* * * *
38064342 AAAATGATCGAAATACCCTCGAGGGGTAAATGACCAAAATACCCTCGAATGGT
1 AAAATGAACGAAATACCC-CGAAGGGTAAATGACCGAAATACCCTCGAAGGGT
** *
38064395 AAAATGATTGAACTACCCCAGAAGGGTAAATGACCGAAATACCC-C-AGAGGAGT
1 AAAATGAACGAAATACCCC-GAAGGGTAAATGACCGAAATACCCTCGA-AGG-GT
* * *
38064448 AAAAT-AACTGAAATAACCCCAAAGGGTAAATGACCGAAATACCTTTGAA-GGT
1 AAAATGAAC-GAAAT-ACCCCGAAGGGTAAATGACCGAAATACCCTCGAAGGGT
* *
38064500 AAAAT-AACTTAAATACCCCGAAGGGTAACATGACCGAAATA-CCTCTGAAGGGC
1 AAAATGAAC-GAAATACCCCGAAGGGTAA-ATGACCGAAATACCCTC-GAAGGGT
38064553 AAAAT
1 AAAAT
38064558 AACTGTTATA
Statistics
Matches: 184, Mismatches: 21, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
51 16 0.09
52 35 0.19
53 119 0.65
54 13 0.07
55 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (52 bp):
AAAATGAACGAAATACCCCGAAGGGTAAATGACCGAAATACCCTCGAAGGGT
Found at i:38066701 original size:47 final size:48
Alignment explanation
Indices: 38066629--38066726 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 48
38066619 TACTTTAATT
* *
38066629 TTTTTATATATTACAATCATATATTAGCGT-TAAATTTCATTATGTATTA
1 TTTTTATATATTACAATCATATATTAACATATAAATTT--TTATGTATTA
38066678 TTTTTA-A-ATTACAAT-ATATTATTAACATCATAAATTTTTATGTATTA
1 TTTTTATATATTACAATCATA-TATTAACAT-ATAAATTTTTATGTATTA
38066725 TT
1 TT
38066727 AGATTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 3 0.07
47 27 0.61
48 1 0.02
49 13 0.30
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (48 bp):
TTTTTATATATTACAATCATATATTAACATATAAATTTTTATGTATTA
Found at i:38071332 original size:22 final size:22
Alignment explanation
Indices: 38071304--38071349 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
38071294 TTCAGAGTAA
38071304 AAAAAATGAAAA-GTGAAAAATG
1 AAAAAATGAAAAGGT-AAAAATG
38071326 AAAAAATGAAAAGGTAAAAATG
1 AAAAAATGAAAAGGTAAAAATG
38071348 AA
1 AA
38071350 GAGGCTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (22 bp):
AAAAAATGAAAAGGTAAAAATG
Found at i:38073485 original size:88 final size:88
Alignment explanation
Indices: 38072540--38073482 Score: 1361
Period size: 88 Copynumber: 10.8 Consensus size: 88
38072530 AACAGATCAG
* * * * * *
38072540 TGAATACAGCAGATCTTGCCTTCCTGCATCGACAGGGAAGCAGATCGAAGACACAAGCGTTACCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
*
38072605 CTCTTGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
38072628 TGAAGACAACGGATCTTGCCTTCCTGCATTGACAACGAAGCAAATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* * *
38072693 CTCTCAGTTTTAGTGAAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
38072716 TGAAGACAACAGATCTTGACTTCCTGCATTGACAACGAAGCAGATCGAAGACAGAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
*
38072781 CTCTCGGTTGTAGTGG-GCTAGT
66 CTCTCGGTTGTAGTGGAGCTGGT
38072803 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
*
38072868 CTCTCGGTTGTAGCGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * *
38072891 TGAAGACAACAAATCTTG-CTTCCTACATTGACAGCGAAGCAGATCAAAGACACAAGCCTTACCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* **
38072955 CACTCGGTTGTAGTAAAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
38072978 TGAAGACAGCAGA-CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCGTTACCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
38073042 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * *
38073065 TGAAGACAACAGATCTTGCTTTCCTGCATCGACAGGGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
38073130 CTCTCGGTTGTAGTGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* *
38073153 TAAAGACAACAGATCTTGCCTTCCTGCATTGATAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
*
38073218 CTCTCGGTTGTAGCGGAGCTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* *
38073241 TGAAGACAACAAATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCATTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* * * *
38073306 CTCTTGGTTGTAGCGAAACTGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * * * * *
38073329 TGAAGACAACAGATATTTCCTGCTTGTATTGACAGTGAAGCAGATCGAAAACACAAGCCTTGCCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
* *
38073394 CCCTCGGTTGTAGTGGAGCAGGT
66 CTCTCGGTTGTAGTGGAGCTGGT
* * * * * * *
38073417 TGAGGATAGCAGATGTTGCCTTCCTGCATTGATAGCGAAGCAGATCGAAGATACAAGCCTTACCT
1 TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
38073482 C
66 C
38073483 CCTGGCGGTG
Statistics
Matches: 763, Mismatches: 89, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
86 4 0.01
87 230 0.30
88 529 0.69
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
TGAAGACAACAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCT
CTCTCGGTTGTAGTGGAGCTGGT
Found at i:38074929 original size:5 final size:5
Alignment explanation
Indices: 38074919--38074943 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38074909 ATCCTCTTTG
38074919 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
38074944 AATTAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:38075143 original size:47 final size:48
Alignment explanation
Indices: 38075071--38075168 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 48
38075061 TACTTTAATT
* *
38075071 TTTTTATATATTACAATCATATATTAGCGT-TAAATTTCATTATGTATTA
1 TTTTTATATATTACAATCATATATTAACATATAAATTT--TTATGTATTA
38075120 TTTTTA-A-ATTACAAT-ATATTATTAACATCATAAATTTTTATGTATTA
1 TTTTTATATATTACAATCATA-TATTAACAT-ATAAATTTTTATGTATTA
38075167 TT
1 TT
38075169 AGATTAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 3 0.07
47 27 0.61
48 1 0.02
49 13 0.30
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (48 bp):
TTTTTATATATTACAATCATATATTAACATATAAATTTTTATGTATTA
Found at i:38087152 original size:91 final size:89
Alignment explanation
Indices: 38086978--38087173 Score: 243
Period size: 90 Copynumber: 2.2 Consensus size: 89
38086968 GCAAACATTT
*
38086978 GTGGTTTATCCACAAATTTACTGCAGCTTTTATCTGCAAAGCTATTGTGCATTCACAACCTACTG
1 GTGGTTTATCCACAAATTTACTGCAGATTTTATCTGCAAAGCTATTGTGCATTCACAACCTACTG
*
38087043 GAAGCGTATTAACCTGCAAATACTG
66 GAAGCGTATTAACCTGC-AACACTG
* * * * *
38087068 GTGGTTTATCCACAACTTTTACTAGCATATTTTATTTGCAAA-CTCGTTGTGTATTCACAA-CTA
1 GTGGTTTATCCACAA-ATTTACT-GCAGATTTTATCTGCAAAGCT-ATTGTGCATTCACAACCTA
* * *
38087131 CTGGCAGCGTATTAACTTGCAACACTT
63 CTGGAAGCGTATTAACCTGCAACACTG
*
38087158 GTGGTTCATCCACAAA
1 GTGGTTTATCCACAAA
38087174 CTGGACTGTC
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
90 34 0.37
91 29 0.32
92 28 0.31
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (89 bp):
GTGGTTTATCCACAAATTTACTGCAGATTTTATCTGCAAAGCTATTGTGCATTCACAACCTACTG
GAAGCGTATTAACCTGCAACACTG
Found at i:38096164 original size:44 final size:45
Alignment explanation
Indices: 38096101--38096216 Score: 162
Period size: 44 Copynumber: 2.6 Consensus size: 45
38096091 TATATTACAT
* *
38096101 AGTTTGTTCTAACACATCTCATTTAAAACTAGAAAGTTTGTTC-A
1 AGTTTGTTCCAACACATCTCATTTAAAACTACAAAGTTTGTTCAA
* *
38096145 AGTTTTTTCCAACACATCTCATTTAAAATTACAAAGTTTGTTCAA
1 AGTTTGTTCCAACACATCTCATTTAAAACTACAAAGTTTGTTCAA
* * *
38096190 AATTTGTTCCAATACTTCTCATTTAAA
1 AGTTTGTTCCAACACATCTCATTTAAA
38096217 TTTCAATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 39 0.62
45 24 0.38
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (45 bp):
AGTTTGTTCCAACACATCTCATTTAAAACTACAAAGTTTGTTCAA
Found at i:38099749 original size:13 final size:14
Alignment explanation
Indices: 38099712--38099751 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
38099702 ATGGGAGTAG
38099712 GATTCTGTATATCT
1 GATTCTGTATATCT
*
38099726 G-TTATGTATATCT
1 GATTCTGTATATCT
38099739 GATTCTG-ATATCT
1 GATTCTGTATATCT
38099752 ATATCTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
GATTCTGTATATCT
Found at i:38099758 original size:13 final size:13
Alignment explanation
Indices: 38099712--38099762 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
38099702 ATGGGAGTAG
38099712 GATTCTGTATATCT
1 GATTCTG-ATATCT
*
38099726 G-TTATGTATATCT
1 GATTCTG-ATATCT
38099739 GATTCTGATATCT
1 GATTCTGATATCT
38099752 -ATATCTGATAT
1 GAT-TCTGATAT
38099763 GGACTTAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 2 0.06
13 26 0.79
14 5 0.15
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (13 bp):
GATTCTGATATCT
Found at i:38101393 original size:32 final size:31
Alignment explanation
Indices: 38101348--38101457 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 31
38101338 TTGATCTTTT
38101348 TTAA-CCTTTTTTAAACCCTAAATAAAGCCC
1 TTAATCCTTTTTTAAACCCTAAATAAAGCCC
* * *
38101378 TCTAATCCTTTTTT-AACCCTAGACAAAACACC
1 T-TAATCCTTTTTTAAACCCTAAATAAAGC-CC
* *
38101410 TTAATCCTTTTTTAGACCCT-AATCATAGCCC
1 TTAATCCTTTTTTAAACCCTAAAT-AAAGCCC
38101441 TTTAATCCCTCTTTTTA
1 -TTAAT-CCT-TTTTTA
38101458 TTCAAACACT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
30 1 0.02
31 30 0.47
32 24 0.38
33 3 0.05
34 6 0.09
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (31 bp):
TTAATCCTTTTTTAAACCCTAAATAAAGCCC
Found at i:38101494 original size:32 final size:33
Alignment explanation
Indices: 38101453--38101514 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
38101443 TAATCCCTCT
* *
38101453 TTTTATTCAAACACTAAA-CTCTAACAAAACCC
1 TTTTATTCAAACACCAAATCCCTAACAAAACCC
* *
38101485 TTTTCTTCAAACCCCAAATCCCTAACAAAA
1 TTTTATTCAAACACCAAATCCCTAACAAAA
38101515 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 15 0.60
33 10 0.40
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (33 bp):
TTTTATTCAAACACCAAATCCCTAACAAAACCC
Found at i:38101675 original size:10 final size:11
Alignment explanation
Indices: 38101646--38101679 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
38101636 TTCTTTTTTT
38101646 TCCTTCTCCTTC
1 TCCTTCT-CTTC
38101658 TCCTTCTCTTC
1 TCCTTCTCTTC
38101669 T-CTTCTCTTC
1 TCCTTCTCTTC
38101679 T
1 T
38101680 AAATCTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 5 0.23
12 7 0.32
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (11 bp):
TCCTTCTCTTC
Found at i:38101919 original size:11 final size:11
Alignment explanation
Indices: 38101899--38101932 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
38101889 TTTCTATTTC
*
38101899 TATTTTTTTTG
1 TATTTGTTTTG
38101910 TATTTGTTTTG
1 TATTTGTTTTG
38101921 TATTTGTATTTG
1 TATTTGT-TTTG
38101933 GGTATTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (11 bp):
TATTTGTTTTG
Found at i:38103713 original size:17 final size:16
Alignment explanation
Indices: 38103678--38103727 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
38103668 TTAATTTTTT
*
38103678 TTAAATATTAAATAAAA
1 TTAAAAATT-AATAAAA
38103695 TTCAAAAAGTTAA-AAAA
1 TT-AAAAA-TTAATAAAA
38103712 TTAAAAATTAATAAAA
1 TTAAAAATTAATAAAA
38103728 AGCATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 8 0.28
18 6 0.21
19 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAATAAAA
Found at i:38103728 original size:17 final size:16
Alignment explanation
Indices: 38103678--38103728 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
38103668 TTAATTTTTT
*
38103678 TTAAATATTAAATAAAA
1 TTAAAAATTAAA-AAAA
38103695 TTCAAAAAGTT-AAAAAA
1 TT-AAAAA-TTAAAAAAA
38103712 TTAAAAATTAATAAAAA
1 TTAAAAATTAA-AAAAA
38103729 GCATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 6 0.21
17 13 0.45
18 6 0.21
19 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
TTAAAAATTAAAAAAA
Found at i:38104215 original size:21 final size:22
Alignment explanation
Indices: 38104178--38104220 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
38104168 GAATTTTACT
*
38104178 TAATATTTATATAATTT-TTAA
1 TAATATTTATACAATTTATTAA
38104199 TAATATTT-TACAGATTTATTAA
1 TAATATTTATACA-ATTTATTAA
38104221 AAAATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATATTTATACAATTTATTAA
Found at i:38105462 original size:3 final size:3
Alignment explanation
Indices: 38105454--38105484 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38105444 CTCCATTGAT
38105454 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
38105485 AGGCAACGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:38108480 original size:31 final size:29
Alignment explanation
Indices: 38108414--38108480 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
38108404 ATGGATATGA
*
38108414 TTTTTAACAAAAGGATCAATTTGCTCTTT
1 TTTTTAACAAAAGGATCAATTTGCACTTT
**
38108443 AATTTAACATATAAGGA-CTAATTTGCACTTT
1 TTTTTAACA-A-AAGGATC-AATTTGCACTTT
38108474 TTTTTAA
1 TTTTTAA
38108481 TAAAGGGTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 7 0.23
30 2 0.07
31 21 0.70
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTTTAACAAAAGGATCAATTTGCACTTT
Found at i:38110635 original size:13 final size:13
Alignment explanation
Indices: 38110617--38110668 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
38110607 AGTCATTTTC
38110617 TCAATAAGAAAGA
1 TCAATAAGAAAGA
*
38110630 TCAATAAGAAA-T
1 TCAATAAGAAAGA
38110642 TCCAA-ATA-AAAGA
1 T-CAATA-AGAAAGA
38110655 TCAATAAGAAAGA
1 TCAATAAGAAAGA
38110668 T
1 T
38110669 ATTGTAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (13 bp):
TCAATAAGAAAGA
Found at i:38111105 original size:18 final size:18
Alignment explanation
Indices: 38111061--38111105 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
38111051 CATTCGTTTC
*
38111061 CAAAACATTATTCATTTA
1 CAAAACGTTATTCATTTA
*
38111079 CAAATCGTTATTCAATTT-
1 CAAAACGTTATTC-ATTTA
38111097 CAAAACGTT
1 CAAAACGTT
38111106 TTCTTCTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCATTTA
Found at i:38113949 original size:11 final size:11
Alignment explanation
Indices: 38113935--38113978 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
38113925 AGATAAATAT
38113935 TATTTTATTAA
1 TATTTTATTAA
*
38113946 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
38113959 TATTTTATTAT
1 TATTTTATTAA
38113970 TATTTTATT
1 TATTTTATT
38113979 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:38115792 original size:2 final size:2
Alignment explanation
Indices: 38115787--38115815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38115777 ATATTATATA
38115787 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
38115816 TCTATTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38116038 original size:33 final size:32
Alignment explanation
Indices: 38115994--38116119 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 32
38115984 CAGTGTTTAT
38115994 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* * **
38116026 ATGATAAGACCATAACTGGGTTATGGCATTACAA
1 ATG-TAAGACCATAGCTGGGCTATGGCATT-CTG
* * *
38116060 ATGTAAGACCATGGCAGGG-TCATGGCAATGCATG
1 ATGTAAGACCATAGCTGGGCT-ATGGC-ATTC-TG
* *
38116094 -TGTAAGACCATAGTTGGACTATGGCA
1 ATGTAAGACCATAGCTGGGCTATGGCA
38116120 CAAAAAGAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
32 5 0.07
33 62 0.84
34 7 0.09
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTG
Found at i:38117285 original size:25 final size:25
Alignment explanation
Indices: 38117256--38117311 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
38117246 TTCAAATTCC
*
38117256 AAAAAGTCATTAAGAAAT-ATCAATA
1 AAAAAGTC-TAAAGAAATGATCAATA
* * *
38117281 AAAAATTCTAAATAAATGATCGATA
1 AAAAAGTCTAAAGAAATGATCAATA
38117306 AAAAAG
1 AAAAAG
38117312 ATATCGACTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (25 bp):
AAAAAGTCTAAAGAAATGATCAATA
Found at i:38117673 original size:207 final size:206
Alignment explanation
Indices: 38117111--38117674 Score: 903
Period size: 206 Copynumber: 2.8 Consensus size: 206
38117101 GGGGCGTTAC
* * * *
38117111 AGATATTGACTACACATGTTGAAAAATTATGTTAGAATATGACTAATCAAAGGAAATTGGTGAAT
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
*
38117176 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGTATGTAATGTGTGCTTTG
66 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
* * *
38117241 AAAAATTCAAATTCCAAAAAG-------TCATTAAGAAATATCAATAAAAAATTCTAAATAAATG
131 AAAAATTCAAATTCCAAAAAGTCATTTTTCATTAAGAAAGATCAATAAAAAATTCCAAATAAAAG
*
38117299 ATCGATAAAAA
196 ATCAATAAAAA
* *
38117310 AGATATCGACTCCACATGTTGAGAAATTACGTGAGAATATAACTAATCAAAGGAAATTGGTGAAT
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
38117375 GAAATTG-TTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
66 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
* *
38117439 AAAAATTCAAATTCCAAAAAGTCATTTTCTCATTAAGAAAGATTAATAAGAAATTCCAAATAAAA
131 AAAAATTCAAATTCCAAAAAGTCATTTT-TCATTAAGAAAGATCAATAAAAAATTCCAAATAAAA
*
38117504 GATCAATAAGAA
195 GATCAATAAAAA
* *
38117516 AGATATCGACTCCACATATTGAGAAATTATGTGAGAATATGACTAATCGAAA-GAAATTAGTGAA
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATC-AAAGGAAATTGGTGAA
38117580 TGAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTT
65 TGAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTT
38117645 GAAAAATTCAAATTCCAAAAAGTCATTTTT
130 GAAAAATTCAAATTCCAAAAAGTCATTTTT
38117675 GTACCATTCT
Statistics
Matches: 337, Mismatches: 18, Indels: 13
0.92 0.05 0.04
Matches are distributed among these distances:
198 77 0.23
199 66 0.20
206 106 0.31
207 88 0.26
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (206 bp):
AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
AAAAATTCAAATTCCAAAAAGTCATTTTTCATTAAGAAAGATCAATAAAAAATTCCAAATAAAAG
ATCAATAAAAA
Found at i:38117716 original size:86 final size:85
Alignment explanation
Indices: 38117620--38117780 Score: 200
Period size: 85 Copynumber: 1.9 Consensus size: 85
38117610 ATTATTTTAG
* * * *
38117620 ATGCAATGGATGTAATGTGTGCTTTGA-AAAATTCA-AATTCCAAAAAGTCATTTTTGTACCATT
1 ATGCAATGGATGCAATGTCTACTTT-ATAAAA-T-AGAATTCCAAAAAGACATTTTTGTACCATT
*
38117683 CTATCACCAAAATGTTTCTAGGC
63 CTATCACAAAAATGTTTCTAGGC
* * **
38117706 ATGCAATGGATGCATTGTCTACTTTATAAAATAGAATTCCAAAATGACATTTTTGTACTTTTCTA
1 ATGCAATGGATGCAATGTCTACTTTATAAAATAGAATTCCAAAAAGACATTTTTGTACCATTCTA
38117771 TCACAAAAAT
66 TCACAAAAAT
38117781 ATTCCAAGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.02
85 38 0.59
86 25 0.39
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (85 bp):
ATGCAATGGATGCAATGTCTACTTTATAAAATAGAATTCCAAAAAGACATTTTTGTACCATTCTA
TCACAAAAATGTTTCTAGGC
Found at i:38130430 original size:26 final size:27
Alignment explanation
Indices: 38130376--38130432 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
38130366 AATTTTAAAG
** * *
38130376 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATACAATTTTGATTGTT
38130403 TATTTTTAAAATACAATTTTGA-TGTT
1 TATTTTTAAAATACAATTTTGATTGTT
38130429 TATT
1 TATT
38130433 AAAAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (27 bp):
TATTTTTAAAATACAATTTTGATTGTT
Found at i:38133059 original size:40 final size:40
Alignment explanation
Indices: 38133000--38133140 Score: 212
Period size: 40 Copynumber: 3.5 Consensus size: 40
38132990 AGGCTTGTGC
* *
38133000 CTAGCAGGCTTAATGCCGGTGAAATATTCAAACTACAAGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATAAGT
* *
38133040 CTAGCAGGCTTAATACCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATAAGT
*
38133080 CTAGCAGGCTTAATGCCAGTGAAATATTCAGACTATACA-T
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATA-AGT
*
38133120 CTAGCAGGCTTCATGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
38133141 TACGGAATCA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 91 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATAAGT
Found at i:38134548 original size:12 final size:12
Alignment explanation
Indices: 38134529--38134559 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38134519 TTAGTAAATA
38134529 TCATATATATAT
1 TCATATATATAT
*
38134541 TTATATATATAT
1 TCATATATATAT
38134553 TCATATA
1 TCATATA
38134560 GAACGTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATATATATAT
Found at i:38135822 original size:30 final size:32
Alignment explanation
Indices: 38135759--38135823 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
38135749 ATAAAAATGG
38135759 TGAAAATGGAGAAATGAGAAATCATTTGAAAA
1 TGAAAATGGAGAAATGAGAAATCATTTGAAAA
*
38135791 TGAAAATGGAGAAATG-GAAA-CATTTGGAAA
1 TGAAAATGGAGAAATGAGAAATCATTTGAAAA
38135821 TGA
1 TGA
38135824 TTATGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 12 0.38
31 4 0.12
32 16 0.50
ACGTcount: A:0.51, C:0.03, G:0.25, T:0.22
Consensus pattern (32 bp):
TGAAAATGGAGAAATGAGAAATCATTTGAAAA
Found at i:38135854 original size:57 final size:57
Alignment explanation
Indices: 38135785--38135910 Score: 193
Period size: 57 Copynumber: 2.2 Consensus size: 57
38135775 AGAAATCATT
* *
38135785 TGAAAATGAAAATGGAGAAATGGAAA-CATTTGGAAA-TGATTATGATTTTCTCCAAAA
1 TGAAAATGAAAATAGAGAAAT-GAAATCATTTAGAAATTGA-TATGATTTTCTCCAAAA
38135842 TGAAAATGAAAATAGAGAAATGAAATCATTTAGAAATTGATATGATTTTCTCCAAAA
1 TGAAAATGAAAATAGAGAAATGAAATCATTTAGAAATTGATATGATTTTCTCCAAAA
*
38135899 TGAAAATAAAAA
1 TGAAAATGAAAA
38135911 ATTAAAATGA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 4 0.06
57 57 0.89
58 3 0.05
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (57 bp):
TGAAAATGAAAATAGAGAAATGAAATCATTTAGAAATTGATATGATTTTCTCCAAAA
Found at i:38138563 original size:5 final size:5
Alignment explanation
Indices: 38138555--38138604 Score: 58
Period size: 5 Copynumber: 11.2 Consensus size: 5
38138545 CAATGATAAA
38138555 TAATT TAATT TAATT TAATT TAATT T--TT TAATT T--TT TAATT T--TT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT
38138599 TAATT T
1 TAATT T
38138605 TAATATTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
3 9 0.23
5 30 0.77
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TAATT
Found at i:38138586 original size:8 final size:8
Alignment explanation
Indices: 38138563--38138605 Score: 68
Period size: 8 Copynumber: 5.1 Consensus size: 8
38138553 AATAATTTAA
38138563 TTTAATTT
1 TTTAATTT
38138571 AATTTAATTT
1 --TTTAATTT
38138581 TTTAATTT
1 TTTAATTT
38138589 TTTAATTT
1 TTTAATTT
38138597 TTTAATTT
1 TTTAATTT
38138605 T
1 T
38138606 AATATTGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 25 0.76
10 8 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTAATTT
Found at i:38140934 original size:11 final size:11
Alignment explanation
Indices: 38140916--38140945 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38140906 ACTAGATTAC
38140916 AAATATTTTAA
1 AAATATTTTAA
*
38140927 ATATATTTTAA
1 AAATATTTTAA
38140938 AAATATTT
1 AAATATTT
38140946 GTCCAGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:38143344 original size:18 final size:18
Alignment explanation
Indices: 38143321--38143366 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
38143311 TAAATAGTTT
38143321 GAGTTATTCGAATTAATC
1 GAGTTATTCGAATTAATC
*
38143339 GAGTTATTCAAATTAATC
1 GAGTTATTCGAATTAATC
*
38143357 AAGTTATTCG
1 GAGTTATTCG
38143367 GATCAACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (18 bp):
GAGTTATTCGAATTAATC
Found at i:38143534 original size:70 final size:66
Alignment explanation
Indices: 38143451--38143582 Score: 192
Period size: 70 Copynumber: 1.9 Consensus size: 66
38143441 TCCGAATAAA
* * *
38143451 AAAAGGAAAAACTACATCGTTTTGATAAATGTTTACATTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGAAAAACTACATCATTTTGATAAATGTTTAC-CTAT-T-AAGTTAAAAG-CAAAACCATT
38143516 AAGTC
62 AAGTC
*
38143521 AAAAGGCAAAACTACATCATTTTGATAAATGTTTACCTATTAAGTTAAAAGCAAAACCATTA
1 AAAAGGAAAAACTACATCATTTTGATAAATGTTTACCTATTAAGTTAAAAGCAAAACCATTA
38143583 TATTTTTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
66 11 0.19
67 10 0.17
68 1 0.02
69 2 0.03
70 34 0.59
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (66 bp):
AAAAGGAAAAACTACATCATTTTGATAAATGTTTACCTATTAAGTTAAAAGCAAAACCATTAAGT
C
Found at i:38149038 original size:62 final size:62
Alignment explanation
Indices: 38148972--38149135 Score: 217
Period size: 62 Copynumber: 2.6 Consensus size: 62
38148962 ACGCAGTAAA
* *
38148972 TTACACGGCCTGGGCACACAC-CAGTGTCCCTGGCTGTGTGGTCTTGTACCAAAAATAATGAG
1 TTACACGGCCTAGGCACA-ACGCAGTGTCCCTGGCCGTGTGGTCTTGTACCAAAAATAATGAG
* *
38149034 TTACACGGCCTAGGCA-AACGCATGTGTCCCTGGCCGTGTGGTCTTGTACCACAAATAGTGAG
1 TTACACGGCCTAGGCACAACGCA-GTGTCCCTGGCCGTGTGGTCTTGTACCAAAAATAATGAG
* * *
38149096 TTACACAGCCTAGGCAC-ATGCTCGTGTCCCTGGCCGTGTG
1 TTACACGGCCTAGGCACAACGC-AGTGTCCCTGGCCGTGTG
38149136 AACTCTTCAC
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 86 0.95
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (62 bp):
TTACACGGCCTAGGCACAACGCAGTGTCCCTGGCCGTGTGGTCTTGTACCAAAAATAATGAG
Found at i:38156018 original size:62 final size:62
Alignment explanation
Indices: 38155946--38156088 Score: 171
Period size: 62 Copynumber: 2.3 Consensus size: 62
38155936 TTACATGGCT
* * * *
38155946 TGGGCACACGCTCGTGTCCCTGGCCATGTTGTCTTGTACCACAAACAGTGAGTTACACAGCC
1 TGGGCACACGCTCGTGTCCCTAGCCATATGGTCTTATACCACAAACAGTGAGTTACACAGCC
* * * * * *
38156008 TGGGAACACGCTTGTGTCCCTAGTCGTATGGTCTTATACCACAAATAGTGAGTTACACGGCC
1 TGGGCACACGCTCGTGTCCCTAGCCATATGGTCTTATACCACAAACAGTGAGTTACACAGCC
*
38156070 TAGGCACACG-TACGTGTCC
1 TGGGCACACGCT-CGTGTCC
38156089 TTGGACGTGT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 1 0.01
62 66 0.99
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (62 bp):
TGGGCACACGCTCGTGTCCCTAGCCATATGGTCTTATACCACAAACAGTGAGTTACACAGCC
Found at i:38159203 original size:18 final size:20
Alignment explanation
Indices: 38159174--38159219 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
38159164 TATGATTTAT
38159174 AGGTTGAATTGAA-TACTTG
1 AGGTTGAATTGAAGTACTTG
38159193 AGGTT-AATTGAAGTACTT-
1 AGGTTGAATTGAAGTACTTG
38159211 A-GTTGAATT
1 AGGTTGAATT
38159220 AAATTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 12 0.48
19 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (20 bp):
AGGTTGAATTGAAGTACTTG
Found at i:38160816 original size:54 final size:54
Alignment explanation
Indices: 38160734--38160850 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
38160724 CAATTCAGTG
* * *
38160734 AGTTACACAGTCTAGCACACGGCCTGCGACACGACTGTGTGTCAC-AAATTAGAA
1 AGTTACACGGTCTAGCACACGGCCTGCGACACGACCGTGTGAC-CTAAATTAGAA
* * * * **
38160788 AGTTACACGGTTTGGCACATGGCCTGCGATACGACCGTGTGACCTAAATTAGGG
1 AGTTACACGGTCTAGCACACGGCCTGCGACACGACCGTGTGACCTAAATTAGAA
38160842 AGTTACACG
1 AGTTACACG
38160851 ATTTAAGACA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (54 bp):
AGTTACACGGTCTAGCACACGGCCTGCGACACGACCGTGTGACCTAAATTAGAA
Found at i:38161930 original size:2 final size:2
Alignment explanation
Indices: 38161923--38161981 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
38161913 CGAGTTTAGG
38161923 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
38161965 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
38161982 TTTGTCCATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38162625 original size:9 final size:9
Alignment explanation
Indices: 38162611--38162642 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
38162601 AATAATTATA
38162611 AAAGAAAGG
1 AAAGAAAGG
38162620 AAAGAAAGG
1 AAAGAAAGG
38162629 AAAGGAAAGG
1 AAA-GAAAGG
38162639 AAAG
1 AAAG
38162643 TAGAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:38162631 original size:5 final size:5
Alignment explanation
Indices: 38162614--38162642 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
38162604 AATTATAAAA
38162614 GAAAG GAAA- GAAAG GAAAG GAAAG GAAAG
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG
38162643 TAGAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:38162655 original size:19 final size:18
Alignment explanation
Indices: 38162610--38162657 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
38162600 AAATAATTAT
38162610 AAAAGAAAGGAAAGAAAGG
1 AAAAGAAAGGAAAGAAA-G
*
38162629 AAAGGAAAGGAAAGTAGAA-
1 AAAAGAAAGGAAAG-A-AAG
38162648 AAAAGAAAGG
1 AAAAGAAAGG
38162658 TTAAGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 22 0.88
20 1 0.04
21 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (18 bp):
AAAAGAAAGGAAAGAAAG
Found at i:38162973 original size:3 final size:3
Alignment explanation
Indices: 38162965--38162993 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38162955 TTTTCTCTTA
38162965 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38162994 CCTTATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38167355 original size:21 final size:22
Alignment explanation
Indices: 38167306--38167355 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
38167296 TAAAAATATT
* *
38167306 TATAACATTATTTTTATGAATA
1 TATAATATTATATTTATGAATA
38167328 -AGT-ATATTATATTTAT-AATA
1 TA-TAATATTATATTTATGAATA
38167348 TATAATAT
1 TATAATAT
38167356 ATACACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TATAATATTATATTTATGAATA
Found at i:38168755 original size:33 final size:32
Alignment explanation
Indices: 38168617--38168777 Score: 124
Period size: 33 Copynumber: 4.8 Consensus size: 32
38168607 ACATTCGTAG
*
38168617 TGCCATAACCCAGGTATGGTCTTATCATCAGAA
1 TGCCATAACCCAGCTATGGTCTTA-CATCAGAA
* * * *
38168650 TACCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGCCATAACCCAGCTATGGTCTTACAT-CAGA-A
*** * * * * *
38168684 CTGCCATGGTCCAACCATGGTCTTACGTTCATAG
1 -TGCCATAACCCAGCTATGGTCTTAC-ATCAGAA
* *
38168718 TGCCATAACCAAGTTATGGTCTTATCATCAGAA
1 TGCCATAACCCAGCTATGGTCTTA-CATCAGAA
*
38168751 TGCCATAGCCCAGCTATGGTCTTACAT
1 TGCCATAACCCAGCTATGGTCTTACAT
38168778 ATAAACACTG
Statistics
Matches: 96, Mismatches: 27, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
32 6 0.06
33 65 0.68
34 2 0.02
35 22 0.23
36 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (32 bp):
TGCCATAACCCAGCTATGGTCTTACATCAGAA
Found at i:38171527 original size:8 final size:8
Alignment explanation
Indices: 38171514--38171556 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
38171504 TAAAAATTAT
38171514 AATTAAAA
1 AATTAAAA
38171522 AATTAAAA
1 AATTAAAA
*
38171530 AGTTCAAAA
1 AATT-AAAA
38171539 AA-TAATAA
1 AATTAA-AA
38171547 AATTAAAA
1 AATTAAAA
38171555 AA
1 AA
38171557 ATTACAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 20 0.67
9 8 0.27
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (8 bp):
AATTAAAA
Found at i:38171540 original size:17 final size:18
Alignment explanation
Indices: 38171514--38171560 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
38171504 TAAAAATTAT
38171514 AATT-AAAAAATTAA-AA
1 AATTAAAAAAATTAATAA
* *
38171530 AGTTCAAAAAA-TAATAA
1 AATTAAAAAAATTAATAA
38171547 AATTAAAAAAATTA
1 AATTAAAAAAATTA
38171561 CAATTCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 6 0.24
17 17 0.68
18 2 0.08
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AATTAAAAAAATTAATAA
Found at i:38171565 original size:15 final size:15
Alignment explanation
Indices: 38171505--38171575 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
38171495 TAAATAATCT
*
38171505 AAAAATTATAATT-A
1 AAAAATTAAAATTAA
38171519 AAAAATTAAAAAGTTCAA
1 AAAAATT-AAAA-TT-AA
*
38171537 AAAATAATAAAATTAA
1 AAAA-ATTAAAATTAA
* **
38171553 AAAAATTACAATTCC
1 AAAAATTAAAATTAA
38171568 AAAAATTA
1 AAAAATTA
38171576 TAAAAATGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.15
15 18 0.39
16 8 0.17
17 2 0.04
18 9 0.20
19 2 0.04
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAATTAA
Found at i:38171614 original size:21 final size:20
Alignment explanation
Indices: 38171568--38171632 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
38171558 TTACAATTCC
* *
38171568 AAAAATTATAAAAATGTAAA
1 AAAAATTATAAAATTTTAAA
*
38171588 ACAAAATTATAAAATTTTCCAA
1 A-AAAATTATAAAATTTT-AAA
*
38171610 AAAAATTCTAAAATTTTAGAA
1 AAAAATTATAAAATTTTA-AA
38171631 AA
1 AA
38171633 TAGGAATACA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 33 0.89
22 3 0.08
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAATTTTAAA
Found at i:38171708 original size:3 final size:3
Alignment explanation
Indices: 38171700--38171744 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
38171690 AAAATGTTTT
38171700 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38171745 CCTAAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38173380 original size:26 final size:26
Alignment explanation
Indices: 38173340--38173423 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 26
38173330 TAGATTGTTA
38173340 AAATTCTTTTAAAAGAAAACTCAAGAG
1 AAATTC-TTTAAAAGAAAACTCAAGAG
* *
38173367 AACTTCTTTAAAAGAAAACTCGAGAG
1 AAATTCTTTAAAAGAAAACTCAAGAG
*
38173393 AAATTCTTTAAAAAACAAAACTCAAAGAG
1 AAATTCTTT--AAAAGAAAACTC-AAGAG
38173422 AA
1 AA
38173424 TTTTATTAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 27 0.55
27 5 0.10
28 11 0.22
29 6 0.12
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.23
Consensus pattern (26 bp):
AAATTCTTTAAAAGAAAACTCAAGAG
Found at i:38179786 original size:111 final size:111
Alignment explanation
Indices: 38179564--38179859 Score: 420
Period size: 111 Copynumber: 2.7 Consensus size: 111
38179554 GTTAAACAAG
* * * *
38179564 AAATCGAAACCCAGCACATTAGGACACG-TTCCTTGAATTTCCAAACGCAAAACATTACCTTATT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
**
38179628 TTGAAA--TTTTTGGAAGGATATTTAGCTATTTGGTTGAACGAGAA
66 TTGAAATTTTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAA
* *
38179672 AAATTGAAACCCAGCACATTAGGGCACGTTTTCACGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
38179737 TTGAAATTTTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAA
66 TTGAAATTTTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAA
* * * * **
38179783 AAATCAAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAAAGC-TAATGTTGCCTTATT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* *
38179847 TAGAATTTTTTTT
66 TTGAAATTTTTTT
38179860 TGAAGTATGG
Statistics
Matches: 167, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
108 26 0.16
109 38 0.23
110 23 0.14
111 80 0.48
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (111 bp):
AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTGAAATTTTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAA
Found at i:38179917 original size:20 final size:20
Alignment explanation
Indices: 38179881--38179918 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38179871 GTTAATATAC
*
38179881 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
38179901 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
38179919 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:38180199 original size:17 final size:18
Alignment explanation
Indices: 38180179--38180212 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38180169 TATATGTTTT
38180179 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
38180196 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
38180213 TACATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:38180220 original size:84 final size:88
Alignment explanation
Indices: 38180132--38180301 Score: 233
Period size: 90 Copynumber: 2.0 Consensus size: 88
38180122 ATATATATGT
*
38180132 ATGTATATACATAAAATTATAAAAATAT-G-AAAATA-TATATATG-TTTTAAGGA-TATTAAAT
1 ATGTATATACATAAAATTATAAAAATATGGAAAAATAGTATATATGATTTTAA-AATTATTAAAT
38180192 ATAAAAGGTTATGTAAATATATAC
65 ATAAAAGGTTATGTAAATATATAC
* * *
38180216 ATGTATATATATATAATTATGAAAATATGGAAAAATATGTATATATGTATTTTAAAATTATTAAA
1 ATGTATATACATAAAATTATAAAAATATGGAAAAATA-GTATATATG-ATTTTAAAATTATTAAA
*
38180281 TATAAAAGTTTATGTAAATAT
64 TATAAAAGGTTATGTAAATAT
38180302 GTATATGCAC
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
84 25 0.34
85 1 0.01
86 6 0.08
88 8 0.11
89 1 0.01
90 33 0.45
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.39
Consensus pattern (88 bp):
ATGTATATACATAAAATTATAAAAATATGGAAAAATAGTATATATGATTTTAAAATTATTAAATA
TAAAAGGTTATGTAAATATATAC
Found at i:38181402 original size:12 final size:12
Alignment explanation
Indices: 38181363--38181403 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
38181353 TGCAGGTGCA
*
38181363 GGTGGCAGAGTT
1 GGTGGCTGAGTT
*
38181375 GGTAGCTGAGTT
1 GGTGGCTGAGTT
38181387 GGTGGCTGAGTT
1 GGTGGCTGAGTT
38181399 GGTGG
1 GGTGG
38181404 TGGCAGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.07, G:0.51, T:0.29
Consensus pattern (12 bp):
GGTGGCTGAGTT
Found at i:38182115 original size:98 final size:97
Alignment explanation
Indices: 38181945--38182242 Score: 465
Period size: 98 Copynumber: 3.0 Consensus size: 97
38181935 GGGAGATAAG
* * *
38181945 ATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-TTGTGATTTTAATCCACTCCA
1 ATCTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCTT-T-ATTTTAATCCACTCCA
* * * *
38182009 CTGCAACTTCAGGGAGATAGGATTA-TCGGCTTCA
64 CTGTAACTTCAGAGAGTTAGGATTACT-AGCTTCA
38182043 ATCTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCAC
1 ATCTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATC-TTTATTTTAATCCACTCCAC
38182108 TGTAACTTCAGAGAGTTAGGATTACTAGCTTCA
65 TGTAACTTCAGAGAGTTAGGATTACTAGCTTCA
*
38182141 ATCTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCTACTCCAC
1 ATCTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGAT-CTTTATTTTAATCCACTCCAC
38182206 TGTAACTTCAGAGAGTTAGGATTACTAGCTTCA
65 TGTAACTTCAGAGAGTTAGGATTACTAGCTTCA
38182239 ATCT
1 ATCT
38182243 ACTCCATGGT
Statistics
Matches: 188, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
98 183 0.97
99 3 0.02
100 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (97 bp):
ATCTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCTTTATTTTAATCCACTCCACT
GTAACTTCAGAGAGTTAGGATTACTAGCTTCA
Found at i:38182214 original size:44 final size:44
Alignment explanation
Indices: 38182164--38182703 Score: 254
Period size: 44 Copynumber: 12.4 Consensus size: 44
38182154 TACTCTATTA
* * *
38182164 TAACTTCAGAGAGATAAGATC-CTTTATTTTAATCTACTCCACTG
1 TAACTTCAGAGAGATAAGATCTC-TGACTTTAATCTGCTCCACTG
* * * *
38182208 TAACTTCAGAGAGTTAGGAT-TACT-AGCTTCAATCTACTCCA-TGG
1 TAACTTCAGAGAGATAAGATCT-CTGA-CTTTAATCTGCTCCACT-G
* * *
38182252 TAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTG
1 TAACT-TCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
* * *** * *
38182296 TAACCTCAGGGAGATAAGATCTGAAATTCTTCT-GTCTACTCCACTG
1 TAACTTCAGAGAGATAAGATCTCTGA--CTT-TAATCTGCTCCACTG
* * * * * **
38182342 TAACCTCAGGGATATAAGA-C-CTGA-TTCAATCTACTCTGCTG
1 TAACTTCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
* * * *
38182383 TAACTTCAGAGAGATGAGATC-CTTTATTTTAATCCGCTCCACTG
1 TAACTTCAGAGAGATAAGATCTC-TGACTTTAATCTGCTCCACTG
* ** * **
38182427 TAACTTCAGAGAGATAGGAT-AGTGTCTTGGATCTGCTCCACTG
1 TAACTTCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
* * *
38182470 TAA-TCTCAGGGAGATAAGATCTCTGGCTTGAATCTGCTCCACTG
1 TAACT-TCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
* * * ** *
38182514 TAACCTCAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTG
1 TAACTTCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
* * * **
38182558 CAACTTCAGGAAGAGATATGAT-TACT-TCTTTCGTCTGCTCCACTG
1 TAACTTCA-G-AGAGATAAGATCT-CTGACTTTAATCTGCTCCACTG
* * *** * *
38182603 CAACTTCAG-GAAGATAAGA-CT-GGA-TACGATCTACTCTACTG
1 TAACTTCAGAG-AGATAAGATCTCTGACTTTAATCTGCTCCACTG
* * * * *
38182644 CT-ACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTACTCTG
1 -TAACTTCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
* *
38182688 CAACTTCAGGGAGATA
1 TAACTTCAGAGAGATA
38182704 GGATTATCTG
Statistics
Matches: 377, Mismatches: 87, Indels: 64
0.71 0.16 0.12
Matches are distributed among these distances:
41 53 0.14
42 7 0.02
43 45 0.12
44 202 0.54
45 28 0.07
46 42 0.11
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TAACTTCAGAGAGATAAGATCTCTGACTTTAATCTGCTCCACTG
Found at i:38182403 original size:87 final size:90
Alignment explanation
Indices: 38182240--38182403 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 90
38182230 CTAGCTTCAA
* * *
38182240 TCTACTCCATGGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAG
1 TCTACTCCATGGTAACCTCAGGGAGATAAGATCTCTGGATTCAATCTACTCCACTGTAACCTCAG
*
38182305 GGAGATAAGATCTGAAATTCTTCTG
66 AGAGATAAGATCTGAAATTCTTCTG
* ** *
38182330 TCTACTCCACT-GTAACCTCAGGGATATAAGA-C-CT-GATTCAATCTACTCTGCTGTAACTTCA
1 TCTACTCCA-TGGTAACCTCAGGGAGATAAGATCTCTGGATTCAATCTACTCCACTGTAACCTCA
*
38182391 GAGAGATGAGATC
65 GAGAGATAAGATC
38182404 CTTTATTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
87 33 0.52
88 2 0.03
89 1 0.02
90 27 0.42
91 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (90 bp):
TCTACTCCATGGTAACCTCAGGGAGATAAGATCTCTGGATTCAATCTACTCCACTGTAACCTCAG
AGAGATAAGATCTGAAATTCTTCTG
Found at i:38182693 original size:130 final size:128
Alignment explanation
Indices: 38182323--38182717 Score: 385
Period size: 130 Copynumber: 3.0 Consensus size: 128
38182313 GATCTGAAAT
* * * * *
38182323 TCTTCTGTCTACTCCACTGTAACCTCAGGGATATAAGACCT-GATTCAATCTACTCTGCTGTAAC
1 TCTTC-GTCTGCTCCACTGTAACTTCAGGGAGATAAGACCTGGA-TCGATCTACTCTACTGTAAC
* * *
38182387 TTCAGAGAGATGAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCA-GAGAGATAGGA-TAGT
64 TTCAGAGAGATAAGAT-CTTTATTTTAATCCGCTCCACTGCAACTTCAGGAGAGATAGGATTACT
38182450 G
128 G
* * * * *
38182451 TCTTGGATCTGCTCCACTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTGAATCTGCTCCACTGT
1 TCTTCG-TCTGCTCCACTGTAACT-TCAGGGAGATAAGA-C-CTGGATCG-ATCTACTCTACTGT
* * ** *
38182515 AACCTCAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGAGATATGAT
61 AACTTCAGAGAGATAAGATCT-TTATTTTAATCCGCTCCACTGCAACTTCAGG-AGAGATAGGAT
38182580 TACT-
124 TACTG
* *
38182584 TCTTTCGTCTGCTCCACTGCAACTTCAGGAAGATAAGA-CTGGATACGATCTACTCTACTGCT-A
1 TC-TTCGTCTGCTCCACTGTAACTTCAGGGAGATAAGACCTGGAT-CGATCTACTCTACTG-TAA
* * *
38182647 CTTCAGAGAGATAAGATCTATTACTTTAATCCGCTACTCTGCAACTTCAGG-GAGATAGGATTAT
63 CTTCAGAGAGATAAGATCT-TTATTTTAATCCGCTCCACTGCAACTTCAGGAGAGATAGGATTA-
38182711 CTG
126 CTG
38182714 -CTTC
1 TCTTC
38182718 AATCAGGGAG
Statistics
Matches: 217, Mismatches: 34, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
127 1 0.00
128 45 0.21
129 4 0.02
130 65 0.30
131 56 0.26
132 1 0.00
133 38 0.18
134 7 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (128 bp):
TCTTCGTCTGCTCCACTGTAACTTCAGGGAGATAAGACCTGGATCGATCTACTCTACTGTAACTT
CAGAGAGATAAGATCTTTATTTTAATCCGCTCCACTGCAACTTCAGGAGAGATAGGATTACTG
Found at i:38184406 original size:20 final size:20
Alignment explanation
Indices: 38184370--38184408 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38184360 GCCTCTCCAT
*
38184370 TTTTCATTTTTTATTTTTTA
1 TTTTCATTTTATATTTTTTA
38184390 TTTTCATTTTCAT-TTTTTT
1 TTTTCATTTT-ATATTTTTT
38184409 TTGCTCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCATTTTATATTTTTTA
Found at i:38188898 original size:112 final size:109
Alignment explanation
Indices: 38188647--38188940 Score: 409
Period size: 112 Copynumber: 2.7 Consensus size: 109
38188637 AAAATTCAAG
* * * * *
38188647 AGGATATTTGGCAATATGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGACACGTTCCTT-
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTT--TTC
**
38188709 A--AATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTGGA
64 ACGAATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTAAA
*
38188753 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCAC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
*
38188818 GAATTTCCAAACGCAAAACATTTCCTTATTTTGAAATATTTTTAAAA
66 GAATTTCCAAACGCAAAACATTACCTTATTTTG-AA-ATTTTT-AAA
*
38188865 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
*
38188930 GAATTTTCAAA
66 GAATTTCCAAA
38188941 AGCTAATGTT
Statistics
Matches: 168, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
106 26 0.15
107 1 0.01
108 28 0.17
109 31 0.18
110 2 0.01
111 6 0.04
112 74 0.44
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (109 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
GAATTTCCAAACGCAAAACATTACCTTATTTTGAAATTTTTAAA
Found at i:38189029 original size:20 final size:20
Alignment explanation
Indices: 38188993--38189030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38188983 GTTAATATAC
*
38188993 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
38189013 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
38189031 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:38189299 original size:17 final size:18
Alignment explanation
Indices: 38189279--38189312 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38189269 TATATGTTTT
38189279 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
38189296 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
38189313 TACATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:38189479 original size:29 final size:29
Alignment explanation
Indices: 38189412--38189500 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
38189402 GTATATGCAC
* * *
38189412 GTATATGTATACAAAATGTATATAAAAAT
1 GTATATATATAAAAAATATATATAAAAAT
* **
38189441 -TATAAAATATAAAAAATATATATAAGTAT
1 GTAT-ATATATAAAAAATATATATAAAAAT
*
38189470 GTATATATATAAATAAATAAATTATAAAAAT
1 GTATATATATAAA-AAATATA-TATAAAAAT
38189501 ATGAACGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 3 0.07
29 27 0.59
30 9 0.20
31 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (29 bp):
GTATATATATAAAAAATATATATAAAAAT
Found at i:38190068 original size:30 final size:30
Alignment explanation
Indices: 38190032--38190090 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
38190022 GGCCCATTTT
38190032 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAG
*
38190062 TATTTTAAAAATATTTTAAAATTAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAA
38190091 ATTAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAG
Found at i:38190071 original size:11 final size:10
Alignment explanation
Indices: 38190032--38190083 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
38190022 GGCCCATTTT
38190032 TATTTTAAAA
1 TATTTTAAAA
38190042 -ATTTTAAAA
1 TATTTTAAAA
* **
38190051 AATTAAAAAA
1 TATTTTAAAA
38190061 GTATTTTAAAAA
1 -TATTTT-AAAA
38190073 TATTTTAAAA
1 TATTTTAAAA
38190083 T
1 T
38190084 TAAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.26
10 12 0.35
11 9 0.26
12 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:38190096 original size:39 final size:39
Alignment explanation
Indices: 38190032--38190135 Score: 154
Period size: 39 Copynumber: 2.6 Consensus size: 39
38190022 GGCCCATTTT
* * *
38190032 TATTTTAAAAATTTTAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAGTATGTAAAAAA
38190073 TATTTTAAAATTAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATGTAAAAAA
*
38190112 TATTTTAAAATTAAAAAAAATAAA
1 TATTTTAAAATTAAAAAAATTAAA
38190136 TATATTTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 49 0.83
40 4 0.07
41 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATGTAAAAAA
Found at i:38190965 original size:12 final size:12
Alignment explanation
Indices: 38190934--38190974 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
38190924 TGCAGGTACA
* *
38190934 GGTGGCAGATTT
1 GGTGGCTGAGTT
*
38190946 GGTAGCTGAGTT
1 GGTGGCTGAGTT
38190958 GGTGGCTGAGTT
1 GGTGGCTGAGTT
38190970 GGTGG
1 GGTGG
38190975 TGGCAGAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.49, T:0.32
Consensus pattern (12 bp):
GGTGGCTGAGTT
Found at i:38196435 original size:29 final size:29
Alignment explanation
Indices: 38196402--38196460 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
38196392 ACTACTATGC
38196402 AAGTAGTATCAGCTATCACCACTAATGTA
1 AAGTAGTATCAGCTATCACCACTAATGTA
38196431 AAGTAGTATCAGCTATCACCACTAATGTA
1 AAGTAGTATCAGCTATCACCACTAATGTA
38196460 A
1 A
38196461 CGTAAGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (29 bp):
AAGTAGTATCAGCTATCACCACTAATGTA
Found at i:38196488 original size:29 final size:29
Alignment explanation
Indices: 38196456--38196513 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
38196446 TCACCACTAA
38196456 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
1 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
38196485 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
1 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
38196514 AGTAGAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (29 bp):
TGTAACGTAAGCAAGGTAAGTCTTAGTAC
Found at i:38198787 original size:98 final size:98
Alignment explanation
Indices: 38198616--38198814 Score: 366
Period size: 98 Copynumber: 2.0 Consensus size: 98
38198606 TGTACAGCCC
38198616 TTTAAACTAGAGGCAGCAAAATGATCAAAACCCAAAACCCACTCAAAATAGATCAAACCTAAGTG
1 TTTAAACTAGAGGCAGCAAAATGATCAAAACCCAAAACCCACTCAAAATAGATCAAACCTAAGTG
38198681 TTCAAACTATATTTGACAAAAAAAGGTCACAGGCA
66 TTCAAACTATATTTGACAAAAAAAGGTCA-AGG-A
38198716 TTTAAACTAGAGGCAGC-AAATGATCAAAACCC-AAACCCACTCAAAATAGATCAAACCTAAGTG
1 TTTAAACTAGAGGCAGCAAAATGATCAAAACCCAAAACCCACTCAAAATAGATCAAACCTAAGTG
38198779 TTCAAACTATATTTGACAAAAAAAGGTCAAGGA
66 TTCAAACTATATTTGACAAAAAAAGGTCAAGGA
38198812 TTT
1 TTT
38198815 GAACCCTAAA
Statistics
Matches: 99, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
96 4 0.04
97 3 0.03
98 60 0.61
99 15 0.15
100 17 0.17
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (98 bp):
TTTAAACTAGAGGCAGCAAAATGATCAAAACCCAAAACCCACTCAAAATAGATCAAACCTAAGTG
TTCAAACTATATTTGACAAAAAAAGGTCAAGGA
Found at i:38208920 original size:23 final size:24
Alignment explanation
Indices: 38208881--38208926 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
38208871 AAAAAAAGAA
*
38208881 ACATTTGTATTTCTCAATTCTCAC
1 ACATTTGTATTTCTCAATACTCAC
38208905 ACATTTGT-TTTCTCAATACTCA
1 ACATTTGTATTTCTCAATACTCA
38208927 TATGTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.46
Consensus pattern (24 bp):
ACATTTGTATTTCTCAATACTCAC
Found at i:38209362 original size:21 final size:21
Alignment explanation
Indices: 38209336--38209449 Score: 76
Period size: 21 Copynumber: 5.6 Consensus size: 21
38209326 ATATTTTTGG
38209336 TGAGTTGGGGCAGCTTGTTGA
1 TGAGTTGGGGCAGCTTGTTGA
* *
38209357 TGAGTTGTGGCAGCTTG-TAA
1 TGAGTTGGGGCAGCTTGTTGA
* *
38209377 CTGAGTTAGGGCAGCCTG-T--
1 -TGAGTTGGGGCAGCTTGTTGA
* * *
38209396 TGAGTTGGGGTA-CTCTCTTGC
1 TGAGTTGGGGCAGCT-TGTTGA
* * * *
38209417 TGATTTGGGGTAGCCTGTTGC
1 TGAGTTGGGGCAGCTTGTTGA
38209438 TGAGTTGGGGCA
1 TGAGTTGGGGCA
38209450 ACCACTTGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.01
18 11 0.15
19 1 0.01
20 2 0.03
21 57 0.78
22 1 0.01
ACGTcount: A:0.14, C:0.14, G:0.39, T:0.33
Consensus pattern (21 bp):
TGAGTTGGGGCAGCTTGTTGA
Found at i:38210105 original size:2 final size:2
Alignment explanation
Indices: 38210098--38210131 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38210088 AACCCCACCA
38210098 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
38210132 CTAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:38210205 original size:26 final size:25
Alignment explanation
Indices: 38210158--38210206 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38210148 ACATGCATAT
**
38210158 TATTAAAAAATACTTATTGCATGCA
1 TATTAAAAAATACTTACAGCATGCA
*
38210183 TATTAAAAAATAGTTAACAGCATG
1 TATTAAAAAATACTT-ACAGCATG
38210207 TGACCATCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (25 bp):
TATTAAAAAATACTTACAGCATGCA
Found at i:38210271 original size:136 final size:136
Alignment explanation
Indices: 38210116--38210431 Score: 485
Period size: 136 Copynumber: 2.3 Consensus size: 136
38210106 ACACACACAC
* * *
38210116 ACACACACACACACACCTAAAAAATAGTCACTACATGCATATTATTAAAAAA-TACTTATTGCAT
1 ACACACACACACACACCTAAAAAATAGTCACTACATGCATATTA-CAAAAAATTACTCACTGCAT
* * *
38210180 GCATATTAAAAAATAGTTAACAGCATGTGACCATCCCCACCAACAATTACTGCATGCATATTAAA
65 GCATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAA
38210245 AAAACAGT
130 AAAA-AGT
* * *
38210253 -CACACACACACACTCCTAAATAATAATCACTACATGCATATTACAAAAAATTACTCACTGCATG
1 ACACACACACACACACCTAAAAAATAGTCACTACATGCATATTACAAAAAATTACTCACTGCATG
38210317 CATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAA
66 CATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAA
38210382 AAAAGT
131 AAAAGT
* *
38210388 CACACACACACACACACCTAAAAAA-AGTCACTTCATACATATTA
1 -ACACACACACACACACCTAAAAAATAGTCACTACATGCATATTA
38210432 AATAGTTATA
Statistics
Matches: 162, Mismatches: 14, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
135 9 0.06
136 132 0.81
137 21 0.13
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (136 bp):
ACACACACACACACACCTAAAAAATAGTCACTACATGCATATTACAAAAAATTACTCACTGCATG
CATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAA
AAAAGT
Found at i:38212451 original size:62 final size:62
Alignment explanation
Indices: 38212320--38212457 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 62
38212310 CCATTTCTGT
*
38212320 CAGACAATAACCAATACAAAAATAATTTAATACAAACGCAACCATTTAAGTCATGCACATGG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
* * ** *
38212382 CAAACAATAACCAATACAAAAATAATTTAATACAAACACAATCATTTCTGTCATGCACATTG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
* *
38212444 TAGACAATAGCCAA
1 CAGACAATAACCAA
38212458 ACACTTTAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (62 bp):
CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
Found at i:38212771 original size:16 final size:17
Alignment explanation
Indices: 38212752--38212787 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
38212742 ATAAAAATTG
38212752 AAATAACCCTAAAT-CA
1 AAATAACCCTAAATCCA
38212768 AAATAACCCTAAATCCA
1 AAATAACCCTAAATCCA
38212785 AAA
1 AAA
38212788 AATACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAACCCTAAATCCA
Found at i:38212788 original size:40 final size:39
Alignment explanation
Indices: 38212705--38212781 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
38212695 AATAAAACCC
**
38212705 AAAATTGAAATAACCCTAAATCAAAATCAAAGTCAAAATA
1 AAAATTGAAATAACCCTAAATCAAAAT-AAACCCAAAATA
*
38212745 AAAATTGAAATAACCCTAAATCAAAAT-AACCCTAAAT
1 AAAATTGAAATAACCCTAAATCAAAATAAACCCAAAAT
38212782 CCAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 7 0.21
40 27 0.79
ACGTcount: A:0.58, C:0.17, G:0.04, T:0.21
Consensus pattern (39 bp):
AAAATTGAAATAACCCTAAATCAAAATAAACCCAAAATA
Found at i:38213073 original size:16 final size:17
Alignment explanation
Indices: 38213052--38213083 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38213042 AATCACAATT
38213052 ATTTTTT-CCCAAATCA
1 ATTTTTTCCCCAAATCA
38213068 ATTTTTTCCCCAAATC
1 ATTTTTTCCCCAAATC
38213084 CCCTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTTTCCCCAAATCA
Found at i:38213223 original size:21 final size:21
Alignment explanation
Indices: 38213197--38213237 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38213187 CAACATCGTA
* *
38213197 AGTTAACTTTCCATATCAGCT
1 AGTTAACTTGCCACATCAGCT
38213218 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
38213238 AGTCCCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:38213314 original size:30 final size:30
Alignment explanation
Indices: 38213274--38213339 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
38213264 TATTAATCAA
* *
38213274 TGACTATTTTGTCACTTTT-TATAACGTT-AG
1 TGACTGTTTTGTAACTTTTCTA-AA-GTTGAG
38213304 TGACTGTTTTGTAACTTTTCTAAAGTTGAG
1 TGACTGTTTTGTAACTTTTCTAAAGTTGAG
38213334 TGACTG
1 TGACTG
38213340 AAATGAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.09
30 27 0.84
31 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (30 bp):
TGACTGTTTTGTAACTTTTCTAAAGTTGAG
Found at i:38214015 original size:29 final size:31
Alignment explanation
Indices: 38213983--38214046 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
38213973 TTAATTTTAT
*
38213983 TATTAAATTT-AAA-TAAAATAATGTATTTC
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
* *
38214012 TATT--TTTTAAAAGGAAAATAATGTATTTT
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
38214041 TATTAA
1 TATTAA
38214047 TAACCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.11
28 3 0.11
29 22 0.79
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (31 bp):
TATTAAATTTAAAAGGAAAATAATGTATTTC
Found at i:38216938 original size:22 final size:22
Alignment explanation
Indices: 38216899--38216940 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38216889 AGATCAACAC
38216899 AAATATAATCACATACATATTA
1 AAATATAATCACATACATATTA
*
38216921 AAATATCAATCTCA-ACATAT
1 AAATAT-AATCACATACATAT
38216941 CAATCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAATCACATACATATTA
Found at i:38230160 original size:42 final size:42
Alignment explanation
Indices: 38230107--38230224 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
38230097 TGATATGAGT
* *
38230107 TTCAGATTAACCCTTTTGGGTTTCAGTTTAGCTCTT-TTGAGC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTT-AGC
* ** * * * *
38230149 TTTAGTTTAACCCTAATGGGCTTCAATTTAGCTATTCTTAGC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
* *
38230191 TTCAAATTAACCCTTATGGGTTTCCGTTCAGCTC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTC
38230225 CAATGAGCTT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
42 57 0.97
43 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (42 bp):
TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
Found at i:38230277 original size:42 final size:42
Alignment explanation
Indices: 38230199--38230302 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 42
38230189 GCTTCAAATT
* * * * *
38230199 AACCCTTATGGGTTTCCGTTCAGCTCCAATGAGCTTCCGTTC
1 AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
** * *
38230241 AACCCTTACGGGTTTCTGTTTAGCACTTATGTGCTTCTGTGC
1 AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
* *
38230283 -AGCCTT-CGGGCTTCTGTTTA
1 AACCCTTACGGGTTTCTGTTTA
38230303 CGATGTACTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 13 0.25
41 5 0.10
42 33 0.65
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (42 bp):
AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
Found at i:38241153 original size:19 final size:18
Alignment explanation
Indices: 38241129--38241164 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
38241119 GCAAATGGAT
*
38241129 CATTTCTCATTTTCATTTC
1 CATTTCT-ATTTCCATTTC
38241148 CATTTCTATTTCCATTT
1 CATTTCTATTTCCATTT
38241165 TTTTAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (18 bp):
CATTTCTATTTCCATTTC
Found at i:38241158 original size:12 final size:12
Alignment explanation
Indices: 38241128--38241165 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
38241118 TGCAAATGGA
38241128 TCATTTCTCATTT
1 TCATTTC-CATTT
38241141 TCATTTCCA-TT
1 TCATTTCCATTT
38241152 TCTATTTCCATTT
1 TC-ATTTCCATTT
38241165 T
1 T
38241166 TTTAAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 9 0.39
13 10 0.43
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:38250728 original size:21 final size:22
Alignment explanation
Indices: 38250674--38250728 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
38250664 ATATTCTGAG
38250674 TTGACATTAT-TTCATATGAAAT
1 TTGA-ATTATATTCATATGAAAT
*
38250696 TT-AATTATTATT-ATATGATAT
1 TTGAATTA-TATTCATATGAAAT
38250717 TTGAATTATATT
1 TTGAATTATATT
38250729 TTGAGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGAATTATATTCATATGAAAT
Found at i:38251286 original size:20 final size:20
Alignment explanation
Indices: 38251263--38251301 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38251253 CTTAAATTAA
*
38251263 TTTTCTTTTAAATTTTAAAT
1 TTTTATTTTAAATTTTAAAT
*
38251283 TTTTATTTTATATTTTAAA
1 TTTTATTTTAAATTTTAAA
38251302 ATTATTTTTA
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:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTTTAAATTTTAAAT
Done.