Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold30
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: 2650045
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.30
Warning! 144233 characters in sequence are not A, C, G, or T
File 17 of 17
Found at i:2568465 original size:13 final size:13
Alignment explanation
Indices: 2568447--2568471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2568437 CAAAAAAATA
2568447 TGTATCGATACAT
1 TGTATCGATACAT
2568460 TGTATCGATACA
1 TGTATCGATACA
2568472 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2569393 original size:13 final size:13
Alignment explanation
Indices: 2569375--2569402 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2569365 ATACAAAGAT
2569375 CAATGTATCGATA
1 CAATGTATCGATA
2569388 CAATGTATCGATA
1 CAATGTATCGATA
2569401 CA
1 CA
2569403 TTGAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2569401 original size:33 final size:33
Alignment explanation
Indices: 2569357--2569422 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2569347 AAATTCCTAG
*
2569357 ATGTATTGATACAAAGA-TCAATGTATCGATACA
1 ATGTATCGATACAAAGAGT-AATGTATCGATACA
**
2569390 ATGTATCGATACATTGAGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
2569423 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:2572404 original size:20 final size:21
Alignment explanation
Indices: 2572365--2572406 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2572355 ATAGCCCATG
2572365 TTCATGAATTTTGAGCTATGT
1 TTCATGAATTTTGAGCTATGT
* *
2572386 TTCATGCATTTTTAG-TATGT
1 TTCATGAATTTTGAGCTATGT
2572406 T
1 T
2572407 CAACACCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (21 bp):
TTCATGAATTTTGAGCTATGT
Found at i:2575077 original size:19 final size:21
Alignment explanation
Indices: 2575032--2575085 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
2575022 ATTCAACAAT
2575032 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
2575053 TTGTATCGATACATA-AGT-G
1 TTGTATCGATACAAACAGTAA
2575072 TTGTATCGATACAA
1 TTGTATCGATACAA
2575086 TGTATCGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:2575154 original size:13 final size:13
Alignment explanation
Indices: 2575136--2575163 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2575126 CATTATTCAA
2575136 TGTATCGATACAT
1 TGTATCGATACAT
2575149 TGTATCGATACAT
1 TGTATCGATACAT
2575162 TG
1 TG
2575164 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2575158 original size:33 final size:33
Alignment explanation
Indices: 2575116--2575181 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2575106 GCCAAGGAAA
2575116 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
2575149 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
2575182 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:2575484 original size:22 final size:22
Alignment explanation
Indices: 2575454--2575508 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2575444 CCAACCACCC
*
2575454 TATCTTCTACCATAGGCAATGA
1 TATCATCTACCATAGGCAATGA
2575476 TATCATCTACCATAGGCAATGA
1 TATCATCTACCATAGGCAATGA
2575498 TATCATCTACC
1 TATCATCTACC
2575509 TCAGCCAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (22 bp):
TATCATCTACCATAGGCAATGA
Found at i:2579488 original size:18 final size:17
Alignment explanation
Indices: 2579446--2579488 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2579436 AACACCTAAG
*
2579446 ATTTTTCTTTTTATTTA
1 ATTTTTATTTTTATTTA
*
2579463 TTTATTTATTTTTATTCTA
1 ATT-TTTATTTTTATT-TA
2579482 ATTTTTA
1 ATTTTTA
2579489 ATTCCTGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 15 0.71
19 4 0.19
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTTATTTTTATTTA
Found at i:2579971 original size:60 final size:60
Alignment explanation
Indices: 2579895--2580015 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
2579885 CAATTGGAAT
* *
2579895 TTTACATGATTTAATTTTTAATAAAATTTTATCACGTATAAAATTTTAATTGAGTCCTCG
1 TTTAAATGATTTAATTTTTAATAAAATTTTATCACGTATAAAATTTTAATTGAGTCATCG
* *
2579955 TTTAAATGATTTAATTTTTAATGAAATTTTATCATGTATAAAATTTTAATTGAGTCATCG
1 TTTAAATGATTTAATTTTTAATAAAATTTTATCACGTATAAAATTTTAATTGAGTCATCG
2580015 T
1 T
2580016 GTACACACAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (60 bp):
TTTAAATGATTTAATTTTTAATAAAATTTTATCACGTATAAAATTTTAATTGAGTCATCG
Found at i:2583004 original size:20 final size:20
Alignment explanation
Indices: 2582958--2583010 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2582948 ATTGATACAA
* *
2582958 TGTATCGATACAT-GTTCAT
1 TGTATCGATACATGGATAAT
*
2582977 TCTATCGATACATGGATAAT
1 TGTATCGATACATGGATAAT
2582997 TGTATCGATACATG
1 TGTATCGATACATG
2583011 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGATAAT
Found at i:2583078 original size:13 final size:13
Alignment explanation
Indices: 2583060--2583084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2583050 CATGGTAGAT
2583060 TATATCGATACAA
1 TATATCGATACAA
2583073 TATATCGATACA
1 TATATCGATACA
2583085 TGATGAATTG
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TATATCGATACAA
Found at i:2583084 original size:33 final size:33
Alignment explanation
Indices: 2583042--2583104 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2583032 CCACTGTTTG
*
2583042 TATCGATACATGGT-AGATTATATCGATACAATA
1 TATCGATACATGATGA-ATTATATCGATACAATA
*
2583075 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGATGAATTATATCGATACA
2583105 TTGCTTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (33 bp):
TATCGATACATGATGAATTATATCGATACAATA
Found at i:2584027 original size:34 final size:35
Alignment explanation
Indices: 2583989--2584055 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2583979 CCTTACAACA
2583989 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCGAAGGCTAAGATAG-AACCTCTCTCT
2584023 CTATCTTTTTCGAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCGAAGGCTAAGATAGAACCTCTC
2584056 AATCACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCGAAGGCTAAGATAGAACCTCTCTCT
Found at i:2584532 original size:13 final size:13
Alignment explanation
Indices: 2584514--2584539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2584504 ACAATTTTTG
2584514 TGTATCGATACAT
1 TGTATCGATACAT
2584527 TGTATCGATACAT
1 TGTATCGATACAT
2584540 ACTTTCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2584536 original size:32 final size:32
Alignment explanation
Indices: 2584495--2584557 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2584485 TACAAGCCAA
* *
2584495 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
2584527 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
2584558 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:2584604 original size:21 final size:21
Alignment explanation
Indices: 2584578--2584653 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2584568 CTGCCAAGAA
*
2584578 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2584599 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2584619 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2584640 ATGTATCGATACAT
1 ATGTATCGATACAT
2584654 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2584624 original size:20 final size:20
Alignment explanation
Indices: 2584599--2584671 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2584589 CATCTTTTTT
2584599 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2584619 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2584640 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2584660 ATGTATCGATAC
1 ATGTATCGATAC
2584672 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2584635 original size:41 final size:41
Alignment explanation
Indices: 2584578--2584671 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2584568 CTGCCAAGAA
*
2584578 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2584619 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2584660 ATGTATCGATAC
1 ATGTATCGATAC
2584672 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2586306 original size:13 final size:13
Alignment explanation
Indices: 2586288--2586312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2586278 ACTGAAGCAA
2586288 TGTATCGATACAT
1 TGTATCGATACAT
2586301 TGTATCGATACA
1 TGTATCGATACA
2586313 ATCTAGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2588003 original size:84 final size:83
Alignment explanation
Indices: 2587849--2588016 Score: 196
Period size: 84 Copynumber: 2.0 Consensus size: 83
2587839 ATTTTCCACT
* * * * *
2587849 TGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAACT
1 TGCAACTCATTTATATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAACT
2587914 CATTGATTTACTTTCATTC
66 CATTGATTTACTTTC-TTC
* * * *
2587933 TGCAACTCTTTTATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTACA
1 TGCAACTCATTTATATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTAAA
* *
2587996 CTTATTGATTTATTTTCTTC
64 CTCATTGATTTACTTTCTTC
2588016 T
1 T
2588017 TTGAGTTTAG
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
82 6 0.08
83 9 0.13
84 56 0.79
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (83 bp):
TGCAACTCATTTATATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAACT
CATTGATTTACTTTCTTC
Found at i:2589573 original size:34 final size:35
Alignment explanation
Indices: 2589535--2589601 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2589525 CCTTACAACA
2589535 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCGAAGGCTAAGATAG-AACCTCTCTCT
2589569 CTATCTTTTTCGAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCGAAGGCTAAGATAGAACCTCTC
2589602 AATCACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCGAAGGCTAAGATAGAACCTCTCTCT
Found at i:2590078 original size:13 final size:13
Alignment explanation
Indices: 2590060--2590085 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2590050 ACAATTTTTG
2590060 TGTATCGATACAT
1 TGTATCGATACAT
2590073 TGTATCGATACAT
1 TGTATCGATACAT
2590086 ACTTTCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2590082 original size:32 final size:32
Alignment explanation
Indices: 2590041--2590103 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2590031 TACAAGCCAA
* *
2590041 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
2590073 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
2590104 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:2590150 original size:21 final size:21
Alignment explanation
Indices: 2590124--2590199 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2590114 CTGCCAAGAA
*
2590124 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2590145 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2590165 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2590186 ATGTATCGATACAT
1 ATGTATCGATACAT
2590200 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2590170 original size:20 final size:20
Alignment explanation
Indices: 2590145--2590217 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2590135 CATCTTTTTT
2590145 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2590165 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2590186 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2590206 ATGTATCGATAC
1 ATGTATCGATAC
2590218 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2590181 original size:41 final size:41
Alignment explanation
Indices: 2590124--2590217 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2590114 CTGCCAAGAA
*
2590124 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2590165 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2590206 ATGTATCGATAC
1 ATGTATCGATAC
2590218 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2591470 original size:3 final size:3
Alignment explanation
Indices: 2591448--2591481 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2591438 AACCATCAAA
* *
2591448 GAT GAT GAA GAT GAT AAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
2591482 GTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:2596009 original size:13 final size:13
Alignment explanation
Indices: 2595991--2596017 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2595981 GAAAACCCAG
2595991 ATGTATCGATACA
1 ATGTATCGATACA
2596004 ATGTATCGATACA
1 ATGTATCGATACA
2596017 A
1 A
2596018 GGGTTACTAT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2598512 original size:13 final size:13
Alignment explanation
Indices: 2598494--2598518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2598484 CATTATGCTT
2598494 TGTATCGATACAA
1 TGTATCGATACAA
2598507 TGTATCGATACA
1 TGTATCGATACA
2598519 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2598515 original size:33 final size:32
Alignment explanation
Indices: 2598473--2598537 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
2598463 ACACACCCAG
*
2598473 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
2598506 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
2598538 TGAAACTGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:2598607 original size:13 final size:13
Alignment explanation
Indices: 2598589--2598613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2598579 CATGACACAT
2598589 TGTATCGATACAA
1 TGTATCGATACAA
2598602 TGTATCGATACA
1 TGTATCGATACA
2598614 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2600516 original size:79 final size:79
Alignment explanation
Indices: 2600416--2600771 Score: 403
Period size: 79 Copynumber: 4.5 Consensus size: 79
2600406 ATTCATGTTT
* * * * * *
2600416 TTATTTCCGAGGGGATACTCCAACCCTGGTTTTATTTCCAAAATACCAATTTTTCACAATCGGGG
1 TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGG
2600481 ATACTCTC-ACCCCA
66 ATACTC-CAACCCCA
* * *
2600495 TTATTTTCGAAGGGATACTCCAACCTCGATTTTATTTCCAAAACATCAATTTTTCACAATCGGGG
1 TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGG
*
2600560 ATACTCCAACCCCG
66 ATACTCCAACCCCA
* * ** * * *
2600574 TTATTTCCGAA-GGATACTCTAACCCCGATTTTATTTTTAAAATACCGATTTTCCACAATTGGGG
1 TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGG
*
2600638 ATACTCCAACCCTA
66 ATACTCCAACCCCA
* * * * * * *
2600652 TTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAGAACACCGATTTTCCATAATTGAGG
1 TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGG
* *
2600717 ATACTCCAGCCTCA
66 ATACTCCAACCCCA
* * *
2600731 TTATTTTTGAAAGGATACTCCAACCCC-ATCTTTATCTCCAA
1 TTATTTTCGAAGGGATACTCCAACCCCGAT-TTTATTTCCAA
2600772 GATATTAAAT
Statistics
Matches: 237, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
78 68 0.29
79 169 0.71
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (79 bp):
TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGG
ATACTCCAACCCCA
Found at i:2600719 original size:157 final size:157
Alignment explanation
Indices: 2600416--2600771 Score: 428
Period size: 157 Copynumber: 2.3 Consensus size: 157
2600406 ATTCATGTTT
* * * *
2600416 TTATTTCCGAGGGGATACTCCAACCCTGGTTTTATTTCCAAAATACCAATTTTTCACAATCGGGG
1 TTATTTCCGA-AGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTCCACAATCGGGG
* *
2600481 ATACTCTCACCCCATTATTTTCGAAGGGATACTCCAACCTCGATTTTATTTCCAAAACATCAATT
65 ATACTCTCACCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATT
* * *
2600546 TTTCACAATCGGGGATACTCCAACCCCG
130 TTCCACAATCGAGGATACTCCAACCCCA
* ** * *
2600574 TTATTTCCGAAGGATACTCTAACCCCGATTTTATTTTTAAAATACCGATTTTCCACAATTGGGGA
1 TTATTTCCGAAGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTCCACAATCGGGGA
* * * * *
2600639 TACTC-CAACCCTATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTCAGAACACCGATT
66 TACTCTC-ACCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATT
* * * *
2600703 TTCCATAATTGAGGATACTCCAGCCTCA
130 TTCCACAATCGAGGATACTCCAACCCCA
** *
2600731 TTATTTTTGAAAGGATACTCCAACCCC-ATCTTTATCTCCAA
1 TTATTTCCG-AAGGATACTCCAACCCCGAT-TTTATTTCCAA
2600772 GATATTAAAT
Statistics
Matches: 166, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
156 1 0.01
157 131 0.79
158 34 0.20
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (157 bp):
TTATTTCCGAAGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTCCACAATCGGGGA
TACTCTCACCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTT
TCCACAATCGAGGATACTCCAACCCCA
Found at i:2609748 original size:13 final size:13
Alignment explanation
Indices: 2609730--2609754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2609720 CATAAAGTGT
2609730 TGTATCGATACAA
1 TGTATCGATACAA
2609743 TGTATCGATACA
1 TGTATCGATACA
2609755 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2609752 original size:33 final size:33
Alignment explanation
Indices: 2609710--2609776 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2609700 TTCAACGATT
2609710 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2609743 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2609776 T
1 T
2609777 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2609835 original size:13 final size:13
Alignment explanation
Indices: 2609817--2609841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2609807 ATTACTCAAA
2609817 TGTATCGATACAT
1 TGTATCGATACAT
2609830 TGTATCGATACA
1 TGTATCGATACA
2609842 CCGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2609906 original size:52 final size:52
Alignment explanation
Indices: 2609850--2609969 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
2609840 CACCGATCTT
* *
2609850 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
*
2609902 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
2609954 TGTATCGATACATGCA
1 TGTATCGATACATGCA
2609970 AGTAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:2616918 original size:7 final size:7
Alignment explanation
Indices: 2616906--2616954 Score: 66
Period size: 7 Copynumber: 7.1 Consensus size: 7
2616896 AAAAGTAAAC
2616906 ACAAAAA
1 ACAAAAA
2616913 ACAAAAA
1 ACAAAAA
2616920 A-AACAAA
1 ACAA-AAA
2616927 A-AAAAA
1 ACAAAAA
2616933 ACAAAAA
1 ACAAAAA
*
2616940 ACAACAA
1 ACAAAAA
2616947 ACAAAAA
1 ACAAAAA
2616954 A
1 A
2616955 AAAGTGCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:2616929 original size:18 final size:17
Alignment explanation
Indices: 2616902--2616956 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
2616892 AGTCAAAAGT
2616902 AAACACAAAAAACAAAAA
1 AAACA-AAAAAACAAAAA
*
2616920 AAACAAAAAAAAAACAAA
1 AAACAAAAAAACAA-AAA
*
2616938 AAAC-AACAAACAAAAA
1 AAACAAAAAAACAAAAA
2616954 AAA
1 AAA
2616957 AGTGCAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 6 0.18
17 15 0.45
18 12 0.36
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAACAAAAAAACAAAAA
Found at i:2616954 original size:27 final size:27
Alignment explanation
Indices: 2616906--2616957 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
2616896 AAAAGTAAAC
2616906 ACAAAAAACAAAAAAAACAAAAAAAAA
1 ACAAAAAACAAAAAAAACAAAAAAAAA
*
2616933 ACAAAAAAC--AACAAACAAAAAAAAA
1 ACAAAAAACAAAAAAAACAAAAAAAAA
2616958 GTGCAAAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.62
27 9 0.38
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (27 bp):
ACAAAAAACAAAAAAAACAAAAAAAAA
Found at i:2616957 original size:18 final size:18
Alignment explanation
Indices: 2616902--2616957 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2616892 AGTCAAAAGT
2616902 AAAC-ACAAAAAACAAAAA
1 AAACAACAAAAAA-AAAAA
2616920 AAACAA-AAAAAAAACAAA
1 AAACAACAAAAAAAA-AAA
2616938 AAACAACAAACAAAAAAAA
1 AAACAACAAA-AAAAAAAA
2616957 A
1 A
2616958 GTGCAAAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.06
18 19 0.56
19 8 0.24
20 5 0.15
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
AAACAACAAAAAAAAAAA
Found at i:2617218 original size:17 final size:18
Alignment explanation
Indices: 2617196--2617239 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2617186 GTTCTTTTCC
*
2617196 AAAAAAGAAACA-AAACA
1 AAAAAAGAAACAGAAAAA
**
2617213 AAAAAAGATGCAGAAAAA
1 AAAAAAGAAACAGAAAAA
2617231 AAAAAAGAA
1 AAAAAAGAA
2617240 CAACCCCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAACAGAAAAA
Found at i:2618224 original size:34 final size:34
Alignment explanation
Indices: 2618178--2618629 Score: 481
Period size: 34 Copynumber: 13.5 Consensus size: 34
2618168 CTTCAAATAC
*
2618178 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* *
2618212 CTTTTTACAGCCCACAACTCTGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
*
2618247 CCTTGTTAAAGCCCACAACTCCGTGGCACC---TT
1 -CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
2618279 CTTTTCAAAGCCCACAACTCCGTGGCACC-----
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* * *
2618308 C-TTTT-AAGTCCACGACTACGTGGCA-CTCTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCT-TTTT
* *
2618340 C-CTTTAAAGCCCACAACTACGTGGCA-CTCTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCT-TTTT
* *
2618373 CCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
* *
2618407 CCTTCT-AAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
2618440 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
*
2618475 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 --CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
2618511 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
2618545 C-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
* * * *
2618579 CCATTTT-AAGTCCACAACTCTGTGGCATCTTTTT
1 -CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
2618613 -TTCTTCTAAAGCCCACA
1 CTT-TT-TAAAGCCCACA
2618630 CAAGTCGGTG
Statistics
Matches: 367, Mismatches: 29, Indels: 43
0.84 0.07 0.10
Matches are distributed among these distances:
26 1 0.00
27 17 0.05
28 3 0.01
29 1 0.00
31 27 0.07
32 7 0.02
33 82 0.22
34 126 0.34
35 42 0.11
36 35 0.10
37 26 0.07
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (34 bp):
CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:2618305 original size:67 final size:65
Alignment explanation
Indices: 2618177--2618615 Score: 409
Period size: 67 Copynumber: 6.6 Consensus size: 65
2618167 TCTTCAAATA
* * *
2618177 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTACAGCCCACAACTCTGTGGCACTC
1 CCTTTT-AAAGCCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCAC-C
2618242 TTTTT
61 TTTTT
2618247 CCTTGTTAAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCA-C----
1 CCTT-TTAAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
2618307 -
65 T
* * * * *
2618307 CCTTTT-AAGTCCACGACTACGTGGCACTCTT-TTCCTTTAAAGCCCACAACTACGTGGCA-CTC
1 CCTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--TTCAAAGCCCACAACTCCGTGGCACCT-
2618369 TTTT
62 TTTT
* * *
2618373 CCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTT
1 CCTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--TTCAAAGCCCACAACTCCGTGGCACCTT
2618437 TTT
63 TTT
* *
2618440 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAAGCCCACAACTCCGTGGCAC-C---TT--CTTTTCAAAGCCCACAACTCCGTGGCAC
2618505 CTTTTT
60 CTTTTT
2618511 -CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTC
1 CCTTTT-AAAGCCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCAC-C
2618574 TTTTT
61 TTTTT
* * * *
2618579 CCATTTT-AAGTCCACAACTCTGTGGCATCTTTTTTTC
1 CC-TTTTAAAGCCCACAACTCCGTGGCACCTTCTTTTC
2618616 TTCTAAAGCC
Statistics
Matches: 320, Mismatches: 26, Indels: 50
0.81 0.07 0.13
Matches are distributed among these distances:
58 20 0.06
59 5 0.02
60 27 0.08
65 7 0.02
66 27 0.08
67 81 0.25
68 54 0.17
69 1 0.00
70 41 0.13
71 55 0.17
73 2 0.01
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.33
Consensus pattern (65 bp):
CCTTTTAAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:2618642 original size:105 final size:101
Alignment explanation
Indices: 2618185--2618629 Score: 483
Period size: 105 Copynumber: 4.4 Consensus size: 101
2618175 TACCTTTTCA
* *
2618185 AAGCCCACAACTCCGTGGCACCTTTTTCTT-TT-TACAGCCCACAACTCTGTGGCACTCTTTTTC
1 AAGCCCACAACTCCGTGGCA-CTTTTT-TTCTTCTAAAGCCCACAACTCCGTGGCAC-CTTTTT-
* **
2618248 CTTGTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--TTCA
62 CTT-TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * * *
2618286 AAGCCCACAACTCCGTGGCAC------CCTT-TTAAGTCCACGACTACGTGGCA-CTCTTTTCCT
1 AAGCCCACAACTCCGTGGCACTTTTTTTCTTCTAAAGCCCACAACTCCGTGGCACCT-TTTTCTT
* *
2618343 TTAAAGCCCACAACTACGTGGCACTC-TTTTCCTTCT
65 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
2618379 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAGCCCACAACTCCGTGGCACT-TTTTTTCTTCTAAAGCCCACAACTCCGTGGCACCTTTTTC-T
*
2618443 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
64 TTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTT
2618482 CAAAGCCCACAACTCCGTGGCACCTTTTTCTT-TTC-AAAGCCCACAACTCCGTGGCACCTTTTT
1 --AAGCCCACAACTCCGTGGCA-CTTTTT-TTCTTCTAAAGCCCACAACTCCGTGGCACCTTTTT
2618545 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCATTTT
62 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC-TTTT
* *
2618586 AAGTCCACAACTCTGTGGCATCTTTTTTTCTTCTAAAGCCCACA
1 AAGCCCACAACTCCGTGGCA-CTTTTTTTCTTCTAAAGCCCACA
2618630 CAAGTCGGTG
Statistics
Matches: 296, Mismatches: 23, Indels: 48
0.81 0.06 0.13
Matches are distributed among these distances:
91 26 0.09
92 5 0.02
93 28 0.09
94 18 0.06
100 27 0.09
101 50 0.17
102 31 0.10
103 17 0.06
104 36 0.12
105 55 0.19
106 3 0.01
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (101 bp):
AAGCCCACAACTCCGTGGCACTTTTTTTCTTCTAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
TAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:2618655 original size:33 final size:33
Alignment explanation
Indices: 2618613--2618678 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2618603 GCATCTTTTT
2618613 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
2618646 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
2618679 CTTTTAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.21
Consensus pattern (33 bp):
TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:2618738 original size:49 final size:49
Alignment explanation
Indices: 2618681--2619236 Score: 767
Period size: 49 Copynumber: 11.7 Consensus size: 49
2618671 TGGCAACCCT
*
2618681 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
2618730 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
2618779 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C--CA--
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
2618823 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
2618871 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
2618920 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
2618968 CTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCA-C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
2619015 TTTTATGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C--CA--
1 -TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
2619060 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
2619108 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
2619151 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATC
*
2619203 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
2619237 GTTGACATCC
Statistics
Matches: 462, Mismatches: 23, Indels: 41
0.88 0.04 0.08
Matches are distributed among these distances:
43 113 0.24
44 2 0.00
45 1 0.00
46 8 0.02
47 2 0.00
48 89 0.19
49 214 0.46
50 1 0.00
52 32 0.07
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:2618869 original size:92 final size:93
Alignment explanation
Indices: 2618681--2619236 Score: 702
Period size: 92 Copynumber: 5.9 Consensus size: 93
2618671 TGGCAACCCT
2618681 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCA--TTTAAGTCCAATGTAG
*
2618746 CTGGCCTTGACTCAGCACATTGGCACCTTCATC
63 CTGGCCTTGAATCAGCACATTGGCA-C-TCATC
*
2618779 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-CA-TTAAGTCCAATATAGCTG
1 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCATTTAAGTCCAATGTAGCTG
*
2618841 GCCTTGAATCAGCATATTGGCATCTTCATC
66 GCCTTGAATCAGCACATTGGCA-C-TCATC
2618871 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCA--TTTAAGTCCAATGTAG
2618936 CTGGCCTTGAATCAGCACATTGGCACCTCATC
63 CTGGCCTTGAATCAGCACATTGGCA-CTCATC
* *
2618968 CTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCACTTTTATGTCCAATGTAGC
1 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCA--TTTAAGTCCAATGTAGC
*
2619033 TGGCCTTGACTCAGCACATTGGCAC-CA--
64 TGGCCTTGAATCAGCACATTGGCACTCATC
* * * *
2619060 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CCTCA--TTTAAGTCCAATGTAG
2619124 CTGGCCTTGAATCAGCACATTGGCA--C--C
63 CTGGCCTTGAATCAGCACATTGGCACTCATC
* * * * *
2619151 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC---CT-CA--TTTAAGTCCAATG
2619216 TAGCTGGCCTTGAATCAGCAC
60 TAGCTGGCCTTGAATCAGCAC
2619237 GTTGACATCC
Statistics
Matches: 424, Mismatches: 21, Indels: 29
0.89 0.04 0.06
Matches are distributed among these distances:
91 39 0.09
92 168 0.40
93 1 0.00
94 4 0.01
95 42 0.10
96 42 0.10
97 48 0.11
98 80 0.19
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (93 bp):
TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCATTTAAGTCCAATGTAGCTG
GCCTTGAATCAGCACATTGGCACTCATC
Found at i:2619098 original size:237 final size:232
Alignment explanation
Indices: 2618681--2619236 Score: 909
Period size: 237 Copynumber: 2.4 Consensus size: 232
2618671 TGGCAACCCT
*
2618681 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCCAATGTAG
2618746 CTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGC
65 CTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGC
2618811 ACATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAA
130 ACATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAA
*
2618876 GTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
195 GTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
*
2618920 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCCTTAAGTCCAATGTAGC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
*
2618985 TGGCCTTGACTCAGCACATTGGCACC-TCA-CTTTTATGTCCAATGTAGCTGGCCTTGACTCAGC
66 TGGCCTTGACTCAGCACATTGGCACCTTCATC-TTTAAGTCCAATGTAGCTGGCCTTGACTCAGC
2619048 ACATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAA
130 ACATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAA
2619113 GTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
195 GTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
* * * *
2619151 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC---CT-CATCTTTAAGTCCAATG
*
2619216 TAGCTGGCCTTGAATCAGCAC
62 TAGCTGGCCTTGACTCAGCAC
2619237 GTTGACATCC
Statistics
Matches: 302, Mismatches: 10, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
231 41 0.14
233 1 0.00
234 1 0.00
235 35 0.12
236 1 0.00
237 134 0.44
238 47 0.16
239 42 0.14
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (232 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
TGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCA
CATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAG
TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:2619220 original size:52 final size:54
Alignment explanation
Indices: 2619150--2619538 Score: 243
Period size: 55 Copynumber: 6.8 Consensus size: 54
2619140 ACATTGGCAC
2619150 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
2619202 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
2619257 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-----CA--TTT-TC-TCAT
* *
2619321 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG---CA-TCT-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
2619373 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * * *
2619428 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-----CA---TT-T--TC-TC
2619493 AT
53 AT
*
2619495 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
2619539 TTCATCATCT
Statistics
Matches: 256, Mismatches: 48, Indels: 57
0.71 0.13 0.16
Matches are distributed among these distances:
49 33 0.13
52 42 0.16
53 1 0.00
54 9 0.04
55 75 0.29
58 2 0.01
60 2 0.01
61 1 0.00
62 3 0.01
63 4 0.02
64 6 0.02
66 3 0.01
67 75 0.29
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:2619285 original size:55 final size:55
Alignment explanation
Indices: 2619150--2619533 Score: 273
Period size: 67 Copynumber: 6.7 Consensus size: 55
2619140 ACATTGGCAC
* *
2619150 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2619202 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2619257 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
2619321 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
2619373 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * * *
2619428 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
2619493 AT
54 AT
*
2619495 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
2619534 GCACCTTCAT
Statistics
Matches: 257, Mismatches: 42, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
49 36 0.14
50 1 0.00
52 42 0.16
54 8 0.03
55 64 0.25
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
61 8 0.03
62 6 0.02
63 5 0.02
64 7 0.03
66 4 0.02
67 69 0.27
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:2619440 original size:171 final size:171
Alignment explanation
Indices: 2619150--2619544 Score: 700
Period size: 171 Copynumber: 2.3 Consensus size: 171
2619140 ACATTGGCAC
*
2619150 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
2619215 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
2619280 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2619324 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
2619389 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
*
2619454 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2619495 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
2619545 ATCTCTAAAA
Statistics
Matches: 213, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
171 170 0.80
172 5 0.02
174 38 0.18
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:2620351 original size:13 final size:13
Alignment explanation
Indices: 2620333--2620357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2620323 CATAAAGTGT
2620333 TGTATCGATACAA
1 TGTATCGATACAA
2620346 TGTATCGATACA
1 TGTATCGATACA
2620358 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2620355 original size:33 final size:33
Alignment explanation
Indices: 2620313--2620379 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2620303 TTCAACGATT
2620313 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2620346 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2620379 T
1 T
2620380 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2620438 original size:13 final size:13
Alignment explanation
Indices: 2620420--2620444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2620410 ATTACTCAAA
2620420 TGTATCGATACAT
1 TGTATCGATACAT
2620433 TGTATCGATACA
1 TGTATCGATACA
2620445 CCGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2620509 original size:52 final size:52
Alignment explanation
Indices: 2620453--2620572 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
2620443 CACCGATCTT
* *
2620453 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
*
2620505 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
2620557 TGTATCGATACATGCA
1 TGTATCGATACATGCA
2620573 AGTAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:2627517 original size:6 final size:6
Alignment explanation
Indices: 2627506--2627549 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
2627496 AAAAGTAAAC
*
2627506 ACAAAA ACAAAA A-AACAA AAAAAA ACAAAA ACAACAA ACAAAA A
1 ACAAAA ACAAAA ACAA-AA ACAAAA ACAAAA ACAA-AA ACAAAA A
2627550 AAAGTGCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
5 2 0.06
6 24 0.71
7 8 0.24
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:2627519 original size:8 final size:8
Alignment explanation
Indices: 2627502--2627551 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
2627492 AGTCAAAAGT
*
2627502 AAACACAA
1 AAACAAAA
2627510 AAACAAAA
1 AAACAAAA
2627518 AAACAAAA
1 AAACAAAA
2627526 AAA-AACAA
1 AAACAA-AA
*
2627534 AAAC-AAC
1 AAACAAAA
2627541 AAACAAAA
1 AAACAAAA
2627549 AAA
1 AAA
2627552 AGTGCAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 7 0.19
8 29 0.81
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (8 bp):
AAACAAAA
Found at i:2627544 original size:23 final size:24
Alignment explanation
Indices: 2627506--2627552 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2627496 AAAAGTAAAC
2627506 ACAAAAACAAAAAAACAAAAAAAA
1 ACAAAAACAAAAAAACAAAAAAAA
*
2627530 ACAAAAAC-AACAAACAAAAAAAA
1 ACAAAAACAAAAAAACAAAAAAAA
2627553 GTGCAAAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (24 bp):
ACAAAAACAAAAAAACAAAAAAAA
Found at i:2627813 original size:17 final size:18
Alignment explanation
Indices: 2627791--2627834 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2627781 GTTCTTTTCC
*
2627791 AAAAAAGAAACA-AAACA
1 AAAAAAGAAACAGAAAAA
**
2627808 AAAAAAGATGCAGAAAAA
1 AAAAAAGAAACAGAAAAA
2627826 AAAAAAGAA
1 AAAAAAGAA
2627835 CAACCCCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAACAGAAAAA
Found at i:2628819 original size:34 final size:34
Alignment explanation
Indices: 2628773--2629224 Score: 481
Period size: 34 Copynumber: 13.5 Consensus size: 34
2628763 CTTCAAATAC
*
2628773 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* *
2628807 CTTTTTACAGCCCACAACTCTGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
*
2628842 CCTTGTTAAAGCCCACAACTCCGTGGCACC---TT
1 -CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
2628874 CTTTTCAAAGCCCACAACTCCGTGGCACC-----
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* * *
2628903 C-TTTT-AAGTCCACGACTACGTGGCA-CTCTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCT-TTTT
* *
2628935 C-CTTTAAAGCCCACAACTACGTGGCA-CTCTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCT-TTTT
* *
2628968 CCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
* *
2629002 CCTTCT-AAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
2629035 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
*
2629070 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 --CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
*
2629106 CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
2629140 C-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT
* * * *
2629174 CCATTTT-AAGTCCACAACTCTGTGGCATCTTTTT
1 -CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
2629208 -TTCTTCTAAAGCCCACA
1 CTT-TT-TAAAGCCCACA
2629225 CAAGTCGGTG
Statistics
Matches: 367, Mismatches: 29, Indels: 43
0.84 0.07 0.10
Matches are distributed among these distances:
26 1 0.00
27 17 0.05
28 3 0.01
29 1 0.00
31 27 0.07
32 7 0.02
33 82 0.22
34 126 0.34
35 42 0.11
36 35 0.10
37 26 0.07
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (34 bp):
CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:2628900 original size:67 final size:65
Alignment explanation
Indices: 2628772--2629210 Score: 409
Period size: 67 Copynumber: 6.6 Consensus size: 65
2628762 TCTTCAAATA
* * *
2628772 CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTACAGCCCACAACTCTGTGGCACTC
1 CCTTTT-AAAGCCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCAC-C
2628837 TTTTT
61 TTTTT
2628842 CCTTGTTAAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCA-C----
1 CCTT-TTAAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
2628902 -
65 T
* * * * *
2628902 CCTTTT-AAGTCCACGACTACGTGGCACTCTT-TTCCTTTAAAGCCCACAACTACGTGGCA-CTC
1 CCTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--TTCAAAGCCCACAACTCCGTGGCACCT-
2628964 TTTT
62 TTTT
* * *
2628968 CCTTCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACCTT
1 CCTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--TTCAAAGCCCACAACTCCGTGGCACCTT
2629032 TTT
63 TTT
* *
2629035 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAAGCCCACAACTCCGTGGCAC-C---TT--CTTTTCAAAGCCCACAACTCCGTGGCAC
2629100 CTTTTT
60 CTTTTT
2629106 -CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTC
1 CCTTTT-AAAGCCCACAACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCAC-C
2629169 TTTTT
61 TTTTT
* * * *
2629174 CCATTTT-AAGTCCACAACTCTGTGGCATCTTTTTTTC
1 CC-TTTTAAAGCCCACAACTCCGTGGCACCTTCTTTTC
2629211 TTCTAAAGCC
Statistics
Matches: 320, Mismatches: 26, Indels: 50
0.81 0.07 0.13
Matches are distributed among these distances:
58 20 0.06
59 5 0.02
60 27 0.08
65 7 0.02
66 27 0.08
67 81 0.25
68 54 0.17
69 1 0.00
70 41 0.13
71 55 0.17
73 2 0.01
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.33
Consensus pattern (65 bp):
CCTTTTAAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:2629237 original size:105 final size:101
Alignment explanation
Indices: 2628780--2629224 Score: 483
Period size: 105 Copynumber: 4.4 Consensus size: 101
2628770 TACCTTTTCA
* *
2628780 AAGCCCACAACTCCGTGGCACCTTTTTCTT-TT-TACAGCCCACAACTCTGTGGCACTCTTTTTC
1 AAGCCCACAACTCCGTGGCA-CTTTTT-TTCTTCTAAAGCCCACAACTCCGTGGCAC-CTTTTT-
* **
2628843 CTTGTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--TTCA
62 CTT-TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
* * * * * *
2628881 AAGCCCACAACTCCGTGGCAC------CCTT-TTAAGTCCACGACTACGTGGCA-CTCTTTTCCT
1 AAGCCCACAACTCCGTGGCACTTTTTTTCTTCTAAAGCCCACAACTCCGTGGCACCT-TTTTCTT
* *
2628938 TTAAAGCCCACAACTACGTGGCACTC-TTTTCCTTCT
65 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
2628974 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAGCCCACAACTCCGTGGCACT-TTTTTTCTTCTAAAGCCCACAACTCCGTGGCACCTTTTTC-T
*
2629038 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
64 TTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTT
2629077 CAAAGCCCACAACTCCGTGGCACCTTTTTCTT-TTC-AAAGCCCACAACTCCGTGGCACCTTTTT
1 --AAGCCCACAACTCCGTGGCA-CTTTTT-TTCTTCTAAAGCCCACAACTCCGTGGCACCTTTTT
2629140 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCATTTT
62 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC-TTTT
* *
2629181 AAGTCCACAACTCTGTGGCATCTTTTTTTCTTCTAAAGCCCACA
1 AAGCCCACAACTCCGTGGCA-CTTTTTTTCTTCTAAAGCCCACA
2629225 CAAGTCGGTG
Statistics
Matches: 296, Mismatches: 23, Indels: 48
0.81 0.06 0.13
Matches are distributed among these distances:
91 26 0.09
92 5 0.02
93 28 0.09
94 18 0.06
100 27 0.09
101 50 0.17
102 31 0.10
103 17 0.06
104 36 0.12
105 55 0.19
106 3 0.01
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (101 bp):
AAGCCCACAACTCCGTGGCACTTTTTTTCTTCTAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
TAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:2629250 original size:33 final size:33
Alignment explanation
Indices: 2629208--2629273 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2629198 GCATCTTTTT
2629208 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
2629241 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
2629274 CTTTTAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.21
Consensus pattern (33 bp):
TTCTTCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:2629333 original size:49 final size:48
Alignment explanation
Indices: 2629276--2629823 Score: 692
Period size: 49 Copynumber: 11.7 Consensus size: 48
2629266 TGGCAACCCT
*
2629276 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
2629325 TTTAAGTCCAATGTAGCTGGCC-T---T-AGCACATT-GCACCTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
*
2629367 -TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC-CC-CA--
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* * *
2629410 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTCATC
* *
2629458 TTTAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
2629507 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* *
2629555 CTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCA-C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
*
2629602 TTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-CA--
1 -TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* * *
2629647 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTCATC
2629695 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* * * *
2629738 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACATTTTCCATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC---CT-CATC
*
2629790 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
2629824 GTTGACATCC
Statistics
Matches: 444, Mismatches: 26, Indels: 55
0.85 0.05 0.10
Matches are distributed among these distances:
41 21 0.05
42 6 0.01
43 117 0.26
44 8 0.02
45 6 0.01
46 16 0.04
47 4 0.01
48 91 0.20
49 142 0.32
50 1 0.00
52 32 0.07
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATC
Found at i:2629685 original size:237 final size:228
Alignment explanation
Indices: 2629276--2629823 Score: 834
Period size: 237 Copynumber: 2.4 Consensus size: 228
2629266 TGGCAACCCT
*
2629276 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTTTAAGTCCAATGTAG
2629341 CTGGCC-T--T-AGCACATTGCACCTCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACAT
65 CTGGCCTTGATCAGCACATTGCACCTCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACAT
*
2629402 TGGCCCCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCC
130 TGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCC
* *
2629467 AATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTCATC
195 AATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
*
2629507 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCCTTAAGTCCAATGTAGC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
*
2629572 TGGCCTTGACTCAGCACATTGGCACCTCACTTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 TGGCCTTGA-TCAGCACATT-GCACCTCA-TCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
2629637 ATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
128 ATTGGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
2629702 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
193 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
* * * * *
2629738 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACATTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC---CT-CATCTTTAAGTCCAATG
2629803 TAGCTGGCCTTGAATCAGCAC
62 TAGCTGGCCTTG-ATCAGCAC
2629824 GTTGACATCC
Statistics
Matches: 293, Mismatches: 12, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
230 26 0.09
231 83 0.28
233 1 0.00
234 2 0.01
235 42 0.14
236 9 0.03
237 130 0.44
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (228 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTTTAAGTCCAATGTAGC
TGGCCTTGATCAGCACATTGCACCTCATCTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATT
GGCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCA
ATGTAGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:2629872 original size:55 final size:55
Alignment explanation
Indices: 2629737--2630045 Score: 233
Period size: 55 Copynumber: 5.6 Consensus size: 55
2629727 ACATTGGCAC
* * *
2629737 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-AGCA--CATTTTC-CAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGA-CATCCTTTTTCTCAT
* * * *
2629789 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * * *
2629844 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
2629908 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * *
2629960 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * *
2630015 CTTTAGGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCA
2630046 ACATATTGGC
Statistics
Matches: 203, Mismatches: 32, Indels: 41
0.74 0.12 0.15
Matches are distributed among these distances:
49 36 0.18
50 1 0.00
52 41 0.20
53 1 0.00
54 8 0.04
55 60 0.30
56 1 0.00
57 1 0.00
58 1 0.00
59 1 0.00
61 5 0.02
62 5 0.02
63 2 0.01
64 6 0.03
66 1 0.00
67 33 0.16
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:2630027 original size:171 final size:171
Alignment explanation
Indices: 2629737--2630131 Score: 682
Period size: 171 Copynumber: 2.3 Consensus size: 171
2629727 ACATTGGCAC
* *
2629737 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-GCATCTT-CATCTTTAAGTTCAAT
2629802 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
2629867 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* *
2629911 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
2629976 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
*
2630041 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
* * *
2630082 CTTTAAGTCCAATATTGCTGGCCTTGAATTAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
2630132 ATCTCTAAAA
Statistics
Matches: 211, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
171 169 0.80
172 5 0.02
173 1 0.00
174 36 0.17
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTTTTCTCATCATCAT
Found at i:2630938 original size:13 final size:13
Alignment explanation
Indices: 2630920--2630944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2630910 CATAAAGTGT
2630920 TGTATCGATACAA
1 TGTATCGATACAA
2630933 TGTATCGATACA
1 TGTATCGATACA
2630945 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2630942 original size:33 final size:33
Alignment explanation
Indices: 2630900--2630966 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2630890 TTCAACGATT
2630900 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
2630933 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2630966 T
1 T
2630967 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2631025 original size:13 final size:13
Alignment explanation
Indices: 2631007--2631031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2630997 ATTACTCAAA
2631007 TGTATCGATACAT
1 TGTATCGATACAT
2631020 TGTATCGATACA
1 TGTATCGATACA
2631032 CCGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2631096 original size:52 final size:52
Alignment explanation
Indices: 2631040--2631159 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
2631030 CACCGATCTT
* * *
2631040 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
* *
2631092 TGTATCGATACATGCAGGTAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
2631144 TGTATCGATACATGCA
1 TGTATCGATACATGCA
2631160 AGTAACTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:2635139 original size:16 final size:16
Alignment explanation
Indices: 2635098--2635139 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2635088 ACAAGAAATT
*
2635098 TAAAAATAAACCTAAA
1 TAAAAAAAAACCTAAA
*
2635114 TAATAAAAAACCTAAA
1 TAAAAAAAAACCTAAA
2635130 TAAAAAAAAA
1 TAAAAAAAAA
2635140 AAAACCTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (16 bp):
TAAAAAAAAACCTAAA
Found at i:2636177 original size:13 final size:13
Alignment explanation
Indices: 2636159--2636197 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2636149 TACAGCAAGT
2636159 ATGTATCGATACA
1 ATGTATCGATACA
2636172 ATGTATCGATACA
1 ATGTATCGATACA
2636185 ATGTATCGATACA
1 ATGTATCGATACA
2636198 CAAAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2638703 original size:154 final size:155
Alignment explanation
Indices: 2638365--2638744 Score: 417
Period size: 154 Copynumber: 2.5 Consensus size: 155
2638355 CTAAGTTCAA
* * * *
2638365 AAAAAATTATGAAAATGCCCCTAGGGGATACCTTTGACGTAGAAGTACATGATACCCCTAAAAGA
1 AAAAAATTATGAAAATGACCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAGA
*
2638430 CTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGAGGACT
66 CTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGAGGACC
*
2638495 CGGTGACAACTTAAGACTTGGTTCT
131 CGGTGACAACCTAAGACTTGGTTCT
* * ** * * * * *
2638520 AAAAAATTATGAAAA-CATCCTTAAAGGATACTTTTGATGTCGAAGTGCCCGATACCCCTAAAGG
1 AAAAAATTATGAAAATGA-CCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAG
* * * ** * * *
2638584 AC-T-GAAAGGATTTTAGAATTTGATGAACCTATCCTAAATACCCATCTTT-AGCATAACAGCGG
65 ACTTAAAAAAGATTATAG-ATGGGATGAACCTATCCTAAATACCCACCTTTGA-CATAAAAGAGG
* *
2638646 ACCCGGTGACGACCTAAGAGTTGGTTCT
128 ACCCGGTGACAACCTAAGACTTGGTTCT
* * * * * * *
2638674 AAAAAATTACGAAAATGACCATAGGGGATACTTTCGACGTAAAAGTACTCAATACCTCTAAATGA
1 AAAAAATTATGAAAATGACCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAGA
2638739 CTTAAA
66 CTTAAA
2638745 GATGATAATC
Statistics
Matches: 180, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
153 11 0.06
154 113 0.63
155 55 0.31
156 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (155 bp):
AAAAAATTATGAAAATGACCATAGGGGATACTTTTGACGTAGAAGTACACGATACCCCTAAAAGA
CTTAAAAAAGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGACATAAAAGAGGACC
CGGTGACAACCTAAGACTTGGTTCT
Found at i:2640966 original size:23 final size:23
Alignment explanation
Indices: 2640940--2640985 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2640930 AATTTCAAGG
2640940 AAAAAATTCAAAACTCATGCAAA
1 AAAAAATTCAAAACTCATGCAAA
2640963 AAAAAATTCAAAACTCATGCAAA
1 AAAAAATTCAAAACTCATGCAAA
2640986 TAAATGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (23 bp):
AAAAAATTCAAAACTCATGCAAA
Found at i:2642645 original size:36 final size:34
Alignment explanation
Indices: 2642577--2642645 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 34
2642567 AAAAACAGAA
*
2642577 AAAAATGAAAAAAAAAAAACAAATATGGAATATC
1 AAAAATGAAAAAAAAAAAACAAATATGCAATATC
* *
2642611 AAAAATTAAGAAAAAAGAAAACAAATATTCAATAT
1 AAAAATGAA-AAAAAA-AAAACAAATATGCAATAT
2642646 TATGTTACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 8 0.27
35 6 0.20
36 16 0.53
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (34 bp):
AAAAATGAAAAAAAAAAAACAAATATGCAATATC
Found at i:2647616 original size:20 final size:18
Alignment explanation
Indices: 2647572--2647622 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
2647562 ATATTTAGGG
*
2647572 ATGTATCAATACATTTGT
1 ATGTATCGATACATTTGT
*
2647590 ATGTATCGATACATTTTT
1 ATGTATCGATACATTTGT
2647608 ATGTGTATCGATACA
1 A--TGTATCGATACA
2647623 AAAAGGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.59
20 12 0.41
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (18 bp):
ATGTATCGATACATTTGT
Done.