Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 21 of 30
Found at i:3362021 original size:20 final size:20
Alignment explanation
Indices: 3361996--3362046 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
3361986 ACAAGCAATA
*
3361996 TATCGATACAAT-TCATCATG
1 TATCGATACAATGT-ACCATG
3362016 TATCGATACAATGTACCATG
1 TATCGATACAATGTACCATG
3362036 TATCGATACAA
1 TATCGATACAA
3362047 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (20 bp):
TATCGATACAATGTACCATG
Found at i:3362137 original size:32 final size:33
Alignment explanation
Indices: 3362096--3362158 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
3362086 ACAATTGTCC
*
3362096 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
3362128 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
3362159 CTTCTGGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:3362712 original size:16 final size:16
Alignment explanation
Indices: 3362693--3362725 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3362683 TAGAAAATGA
3362693 TAAATGCTTAAAAAAT
1 TAAATGCTTAAAAAAT
3362709 TAAATGCTTAAAAAAT
1 TAAATGCTTAAAAAAT
3362725 T
1 T
3362726 TCTCCCCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAATGCTTAAAAAAT
Found at i:3364685 original size:13 final size:13
Alignment explanation
Indices: 3364667--3364693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3364657 ATAGTAACCC
3364667 ATGTATCGATACA
1 ATGTATCGATACA
3364680 ATGTATCGATACA
1 ATGTATCGATACA
3364693 A
1 A
3364694 GGAATGTTGT
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:3370957 original size:19 final size:19
Alignment explanation
Indices: 3370909--3370964 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3370899 CTACCAGTTT
**
3370909 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
3370929 CATTTATCGATACAATGAA
1 CATGTATCGATACAATGAA
3370948 CATGTATCGATACAATG
1 CATGTATCGATACAATG
3370965 TATCAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:3371330 original size:20 final size:21
Alignment explanation
Indices: 3371304--3371357 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3371294 TGATATGGTC
*
3371304 TTGTATCAATACATTCACTTA
1 TTGTATCAATACATTCACTAA
* *
3371325 -TGTATCGATAAATTCACTAA
1 TTGTATCAATACATTCACTAA
*
3371345 TTGTATTAATACA
1 TTGTATCAATACA
3371358 AATTGTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (21 bp):
TTGTATCAATACATTCACTAA
Found at i:3371927 original size:52 final size:52
Alignment explanation
Indices: 3371841--3371979 Score: 167
Period size: 51 Copynumber: 2.7 Consensus size: 52
3371831 ATTTGCCTGC
* * * * *
3371841 ATGTACCAATACATTG-AAGAATGTATAGACACATTTGGGTCAAAAACTCAAA
1 ATGTATCAATACAATGAAAGAATGTATCGATACATTTGGGTC-AAAACCCAAA
* * *
3371893 ATGTATCGATATAAT-AAAGAATGTATCGATACATTTGGGTCAAAACCCAGA
1 ATGTATCAATACAATGAAAGAATGTATCGATACATTTGGGTCAAAACCCAAA
*
3371944 ATGTATTAATACAATGAAA-AATGTATCGATACATTT
1 ATGTATCAATACAATGAAAGAATGTATCGATACATTT
3371980 TCATTTGAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
51 37 0.50
52 37 0.50
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCAATACAATGAAAGAATGTATCGATACATTTGGGTCAAAACCCAAA
Found at i:3372509 original size:21 final size:21
Alignment explanation
Indices: 3372485--3372525 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3372475 GACATACACT
3372485 TTAAAATTAACATCAAGATTC
1 TTAAAATTAACATCAAGATTC
*
3372506 TTAAAATTGACATCAAGATT
1 TTAAAATTAACATCAAGATT
3372526 TTGGTGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (21 bp):
TTAAAATTAACATCAAGATTC
Found at i:3372555 original size:24 final size:24
Alignment explanation
Indices: 3372535--3372581 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3372525 TTTGGTGTTG
3372535 CACTAAATGCTCAAAAAGGTGCTT
1 CACTAAATGCTCAAAAAGGTGCTT
* * *
3372559 CACTAGATGCTTAAAGAGGTGCT
1 CACTAAATGCTCAAAAAGGTGCT
3372582 AGGGGTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (24 bp):
CACTAAATGCTCAAAAAGGTGCTT
Found at i:3374364 original size:18 final size:18
Alignment explanation
Indices: 3374341--3374380 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3374331 TGTGACATCT
*
3374341 AATAGAAGACCTAATATG
1 AATAGAAGACCTAATATA
3374359 AATAGAAGACCTAATATA
1 AATAGAAGACCTAATATA
3374377 AATA
1 AATA
3374381 TCTAAAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (18 bp):
AATAGAAGACCTAATATA
Found at i:3376234 original size:22 final size:21
Alignment explanation
Indices: 3376192--3376234 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3376182 ATCCAACTAT
*
3376192 TAAACCTAATTGACTTAAACC
1 TAAACCTAAATGACTTAAACC
*
3376213 TAAACCTAAAATGACTTGAACC
1 TAAACCT-AAATGACTTAAACC
3376235 CAATTTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (21 bp):
TAAACCTAAATGACTTAAACC
Found at i:3376363 original size:16 final size:16
Alignment explanation
Indices: 3376325--3376379 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
3376315 TGACCCGAAT
*
3376325 CCAAAATGACCTGAAC
1 CCAAAATAACCTGAAC
***
3376341 TTGAAATAACCTGAAC
1 CCAAAATAACCTGAAC
*
3376357 CCAAAATAATCTGAAC
1 CCAAAATAACCTGAAC
3376373 CCAAAAT
1 CCAAAAT
3376380 GATCTGAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.47, C:0.25, G:0.09, T:0.18
Consensus pattern (16 bp):
CCAAAATAACCTGAAC
Found at i:3376384 original size:16 final size:16
Alignment explanation
Indices: 3376344--3376387 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
3376334 CCTGAACTTG
*
3376344 AAATAACCTGAACCCA
1 AAATAATCTGAACCCA
3376360 AAATAATCTGAACCCA
1 AAATAATCTGAACCCA
*
3376376 AAATGATCTGAA
1 AAATAATCTGAA
3376388 TCTGAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.09, T:0.18
Consensus pattern (16 bp):
AAATAATCTGAACCCA
Found at i:3376440 original size:15 final size:15
Alignment explanation
Indices: 3376420--3376452 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3376410 TTTAAACCCA
3376420 AAATGACCTAACTCG
1 AAATGACCTAACTCG
*
3376435 AAATGATCTAACTCG
1 AAATGACCTAACTCG
3376450 AAA
1 AAA
3376453 CCAACCTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (15 bp):
AAATGACCTAACTCG
Found at i:3383184 original size:157 final size:159
Alignment explanation
Indices: 3382962--3383431 Score: 531
Period size: 165 Copynumber: 2.9 Consensus size: 159
3382952 CTTTCATGGT
* *
3382962 AACAAACAGAATTGGCTGTCAACTAATCTAGCATAACTTTCATACAAGCTATATGTTCATGTTAC
1 AACAAACAGAATTGGCTCTCAACTAATCTAGCATAACTTTCATACAAGCTA-ATGTTCATATTAC
* *
3383027 TAATACCATCTTTCCAAAAATATCACACATGAAATTTCATAAATAGACCCAAGACAAATGGACAC
65 TAATACTATCTTTCCAAAAATATCACATATGAAATTTCATAAATAGACCCAAGACAAATGGACAC
*
3383092 AACACAAA-AATCATTAT-T-GAAA-A-TCA
130 AACACAAACAA-CATTATATACAAATACTCA
* * *
3383118 AACAAACCGAATTGGCTCTCAACTAATCTAGCAATAACCTTCATACAATCTAAATGTTCATATTA
1 AACAAACAGAATTGGCTCTCAACTAATCTAGC-ATAACTTTCATACAAGCT-AATGTTCATATTA
* * * * * *
3383183 CTATTACTATATTTCCAAAAATATTAAACATATGGAATTTCATAAATAGATCCAAGAC-AATGGT
64 CTAATACTATCTTTCCAAAAATA-T-CACATATGAAATTTCATAAATAGACCCAAGACAAATGGA
3383247 CACAACACAAACAACATTATCGAAGTACAAATTTACTCA
127 CACAACACAAACAACATTAT---A-TACAAA--TACTCA
* * * * *
3383286 AACAAACAGAATTGGCTCTCAACTAATCCACCATAACTTTCATTCAGGCT-ATATTCATATTACT
1 AACAAACAGAATTGGCTCTCAACTAATCTAGCATAACTTTCATACAAGCTAATGTTCATATTACT
* * * *
3383350 AATACTATCTTTTCAAAACTACCACGCATATGAAATTTCATAAATAGACCCAAAACAAATGGACA
66 AATACTATCTTTCCAAAAATATCA--CATATGAAATTTCATAAATAGACCCAAGACAAATGGACA
** *
3383415 CAATGCAAACACCATTA
129 CAACACAAACAACATTA
3383432 GCAAAGTACA
Statistics
Matches: 261, Mismatches: 35, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
156 30 0.11
157 47 0.18
158 24 0.09
159 30 0.11
163 2 0.01
164 3 0.01
165 57 0.22
166 21 0.08
167 15 0.06
168 32 0.12
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.27
Consensus pattern (159 bp):
AACAAACAGAATTGGCTCTCAACTAATCTAGCATAACTTTCATACAAGCTAATGTTCATATTACT
AATACTATCTTTCCAAAAATATCACATATGAAATTTCATAAATAGACCCAAGACAAATGGACACA
ACACAAACAACATTATATACAAATACTCA
Found at i:3386430 original size:19 final size:19
Alignment explanation
Indices: 3386406--3386445 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3386396 AAACATGCAA
3386406 AAAATAATTAAAATAAA-AT
1 AAAATAA-TAAAATAAACAT
*
3386425 AAAATAATAATATAAACAT
1 AAAATAATAAAATAAACAT
3386444 AA
1 AA
3386446 CACAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATAATAAAATAAACAT
Found at i:3386470 original size:16 final size:18
Alignment explanation
Indices: 3386449--3386483 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
3386439 AACATAACAC
3386449 AAATATA-CAAA-TATAT
1 AAATATATCAAAGTATAT
3386465 AAATATATCAAAGTATAT
1 AAATATATCAAAGTATAT
3386483 A
1 A
3386484 TAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATATATCAAAGTATAT
Found at i:3387513 original size:14 final size:14
Alignment explanation
Indices: 3387496--3387522 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3387486 ATTAAGAGAG
3387496 AAAAAGTTAAAAAA
1 AAAAAGTTAAAAAA
3387510 AAAAAGTTAAAAA
1 AAAAAGTTAAAAA
3387523 GAGTTTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAGTTAAAAAA
Found at i:3387527 original size:24 final size:23
Alignment explanation
Indices: 3387451--3387527 Score: 55
Period size: 24 Copynumber: 3.1 Consensus size: 23
3387441 AAGAAAATGG
*
3387451 GTTAAAAAAAAAGAATTTTAAAAAAA
1 GTTAAAAAAAAA-AA-GTT-AAAAAA
* ** **
3387477 TTTAAAAAAATTAAGAGAGAAAAA
1 GTTAAAAAAAAAAAGTTA-AAAAA
3387501 GTTAAAAAAAAAAAGTTAAAAAGA
1 GTTAAAAAAAAAAAGTTAAAAA-A
3387525 GTT
1 GTT
3387528 TTTGAGAATT
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
23 5 0.13
24 22 0.58
25 2 0.05
26 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (23 bp):
GTTAAAAAAAAAAAGTTAAAAAA
Found at i:3387934 original size:15 final size:15
Alignment explanation
Indices: 3387914--3388003 Score: 76
Period size: 15 Copynumber: 5.9 Consensus size: 15
3387904 TCATGTAGTT
3387914 AATTTATTTTCTTGC
1 AATTTATTTTCTTGC
*
3387929 AATTTATTTTCTTAC
1 AATTTATTTTCTTGC
*
3387944 AATTT-TTTAATTTATGC
1 AATTTATTT--TCT-TGC
*
3387961 AATTTATTTTCTTGT
1 AATTTATTTTCTTGC
* **
3387976 AATTTAAATTT-AAGC
1 AATTT-ATTTTCTTGC
3387991 AATTTATTTTCTT
1 AATTTATTTTCTT
3388004 AAAATTTAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
14 7 0.12
15 32 0.56
16 8 0.14
17 7 0.12
18 3 0.05
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (15 bp):
AATTTATTTTCTTGC
Found at i:3387993 original size:30 final size:30
Alignment explanation
Indices: 3387927--3388012 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
3387917 TTATTTTCTT
* * *
3387927 GCAATTTATTTTCTTACAATTTTTTAATTTAT
1 GCAATTTATTTTCTTA-AA-ATTTAAATTTAA
**
3387959 GCAATTTATTTTCTTGTAATTTAAATTTAA
1 GCAATTTATTTTCTTAAAATTTAAATTTAA
3387989 GCAATTTATTTTCTTAAAATTTAA
1 GCAATTTATTTTCTTAAAATTTAA
3388013 CTTTGTGCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 31 0.66
31 1 0.02
32 15 0.32
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.55
Consensus pattern (30 bp):
GCAATTTATTTTCTTAAAATTTAAATTTAA
Found at i:3388023 original size:30 final size:29
Alignment explanation
Indices: 3387926--3388024 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 29
3387916 TTTATTTTCT
*
3387926 TGCAATTTATTTTCTTACAATTTTTTAATTTA
1 TGCAATTTATTTTCTTA-AA--ATTTAATTTA
**
3387958 TGCAATTTATTTTCTTGTAATTTAAATTTA
1 TGCAATTTATTTTCTTAAAATTT-AATTTA
* *
3387988 AGCAATTTATTTTCTTAAAATTTAACTTTG
1 TGCAATTTATTTTCTTAAAATTTAA-TTTA
3388018 TGCAATT
1 TGCAATT
3388025 AAATTTAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
29 5 0.09
30 35 0.61
31 1 0.02
32 16 0.28
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (29 bp):
TGCAATTTATTTTCTTAAAATTTAATTTA
Found at i:3388241 original size:2 final size:2
Alignment explanation
Indices: 3388195--3388222 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3388185 ATTCATACGT
3388195 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3388223 CCTATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3391523 original size:13 final size:13
Alignment explanation
Indices: 3391505--3391534 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3391495 ACAAGTCATC
*
3391505 ATGTATCGATATA
1 ATGTATCGATACA
3391518 ATGTATCGATACA
1 ATGTATCGATACA
3391531 ATGT
1 ATGT
3391535 GCCACGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3391544 original size:33 final size:32
Alignment explanation
Indices: 3391484--3391548 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
3391474 CGTTTGGGAC
*
3391484 AATGTATCGATACAAGTCATCATGTATCGATAT
1 AATGTATCGATACAAGTCA-CACGTATCGATAT
3391517 AATGTATCGATACAATGTGC-CACGTATCGATA
1 AATGTATCGATACAA-GT-CACACGTATCGATA
3391549 CAAACAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.90
34 2 0.07
35 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (32 bp):
AATGTATCGATACAAGTCACACGTATCGATAT
Found at i:3391625 original size:19 final size:20
Alignment explanation
Indices: 3391580--3391635 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
3391570 CTACTAGTTT
* *
3391580 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGATA
*
3391600 TATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
3391619 CATGTATCGATACAATG
1 CATGTATCGATACAATG
3391636 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:3391638 original size:13 final size:13
Alignment explanation
Indices: 3391620--3391646 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3391610 TACAATGAAC
3391620 ATGTATCGATACA
1 ATGTATCGATACA
3391633 ATGTATCGATACA
1 ATGTATCGATACA
3391646 A
1 A
3391647 AGCATAATGT
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:3393044 original size:165 final size:162
Alignment explanation
Indices: 3392858--3393461 Score: 626
Period size: 165 Copynumber: 3.7 Consensus size: 162
3392848 TTTTTCAAGG
* *
3392858 GGATTTTT-TTAGTGTTTAATTTTTAAAATTTATCAAATATTATTATTTATTTCATATTAATTCA
1 GGATTTTTCTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATTTCATATTAATTCA
3392922 ATTTTTAAAAATTCATTCATTT-CATGAATTTTGAATTTTTTCCTTGAAATGCCTTTTTTTTCAA
66 ATTTTTAAAAATTCATTCATTTCCATGAATTTTGAATTTTTTCCTTGAAAT-CC--TTTTTTCAA
3392986 AATACGATGTTTTCTACTCCGTGAATTTTTTGAGA
128 AATACGATGTTTTCTACTCCGTGAATTTTTTGAGA
* *
3393021 GGATTTTTTTTTAGTATTTAATTTTTAAAAGCTATCAAATATTATTATTTATTTCATATTAATTC
1 GGA-TTTTTCTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATTTCATATTAATTC
*
3393086 AATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTTGTTTTCCTTGAAATATCC-TTTTT
65 AATTTTTAAAAATTCATTCATTTCCATGAATTTTGAA--TT-TTTTCCTTG-AA-ATCCTTTTTT
* *
3393150 CCAAATACGGTGTTTTCTACTCCGTGAATTTTTTTGA-A
125 CAAAATACGATGTTTTCTACTCCGTGAA-TTTTTTGAGA
* * * *
3393188 GGGATTTTTCTTGGTTTTTAATTTTTAAAAGTTATAAAATATTATTATATATTTCATATTAATTC
1 -GGATTTTTCTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATTTCATATTAATTC
* * * * *
3393253 AGTTTTCT-AAAATTCATTCATTTCCATGAATTTTGATTTTTTTTCTTTGAAATCCCCTTTATCC
65 AATTTT-TAAAAATTCATTCATTTCCATGAATTTTGA-ATTTTTTCCTTGAAAT--CCTTTTTTC
* *
3393317 GAAAAGT-CGA-G-TTTCTACTCTGTAAATTTTTTCG-GA
126 -AAAA-TACGATGTTTTCTACTCCGTGAATTTTTT-GAGA
* ** *
3393353 GGAATTTTTCTTA--ATTTAAAATTTTTAAAA-TTCAT-ATAATATT-TTCATTGAACTCCTATT
1 GG-ATTTTTCTTAGTATTT--AATTTTTAAAAGTT-ATCA-AATATTATT-ATTTATTTCATATT
* * * * *
3393413 AATTCAATTTTGAAAATTTTTAATTTATTT-CATTAATTTTGAATTTTTT
60 AATTCAATTTTTAAAA--ATTCATTCATTTCCATGAATTTTGAATTTTTT
3393462 TGTATATATT
Statistics
Matches: 377, Mismatches: 36, Indels: 54
0.81 0.08 0.12
Matches are distributed among these distances:
163 8 0.02
164 20 0.05
165 155 0.41
166 31 0.08
167 134 0.36
168 14 0.04
169 9 0.02
170 4 0.01
171 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (162 bp):
GGATTTTTCTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATTTCATATTAATTCA
ATTTTTAAAAATTCATTCATTTCCATGAATTTTGAATTTTTTCCTTGAAATCCTTTTTTCAAAAT
ACGATGTTTTCTACTCCGTGAATTTTTTGAGA
Found at i:3393233 original size:167 final size:165
Alignment explanation
Indices: 3392844--3393305 Score: 659
Period size: 167 Copynumber: 2.8 Consensus size: 165
3392834 TCAACTCTAA
* * *
3392844 AATTTTTTTCAAGGGGATTTTTTTAGTGTTTAATTTTTAAAATTTATCAAATATTATTATTTATT
1 AATTTTTTTGAA-GGGATTTTTTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATT
*
3392909 TCATATTAATTCAATTTTTAAAAATTCATTCATTT-CATGAATTTTGAA--TTTTTTCCTTGAAA
65 TCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTTTTTTCCTTGAAA
3392971 TGCCTTTTTTTTCAAAATACGATGTTTTCTACTCCGTG
130 TGCC--TTTTTTCAAAATACGATGTTTTCTACTCCGTG
*
3393009 AA-TTTTTTG-AGAGGATTTTTTTTTAGTATTTAATTTTTAAAAGCTATCAAATATTATTATTTA
1 AATTTTTTTGAAG-GGA--TTTTTTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTA
3393072 TTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTTGTTTTCCTTG
63 TTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTT-TTTTCCTTG
* * *
3393137 AAATATCC-TTTTTCCAAATACGGTGTTTTCTACTCCGTG
127 AAAT-GCCTTTTTTCAAAATACGATGTTTTCTACTCCGTG
* * * *
3393176 AATTTTTTTGAAGGGATTTTTCTTGGTTTTTAATTTTTAAAAGTTATAAAATATTATTATATATT
1 AATTTTTTTGAAGGGATTTTT-TTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATT
* * *
3393241 TCATATTAATTCAGTTTTCTAAAATTCATTCATTTCCATGAATTTTG-ATTTTTTTTCTTTGAAA
65 TCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTTTTTTCCTTGAAA
3393305 T
130 T
3393306 CCCCTTTATC
Statistics
Matches: 270, Mismatches: 16, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
162 1 0.00
163 4 0.01
164 6 0.02
165 93 0.34
166 23 0.09
167 114 0.42
168 12 0.04
169 15 0.06
170 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (165 bp):
AATTTTTTTGAAGGGATTTTTTTAGTATTTAATTTTTAAAAGTTATCAAATATTATTATTTATTT
CATATTAATTCAATTTTCAAAAATTCATTCATTTCCATGAATTTTGAATTTTTTTTCCTTGAAAT
GCCTTTTTTCAAAATACGATGTTTTCTACTCCGTG
Found at i:3393419 original size:332 final size:330
Alignment explanation
Indices: 3392844--3393459 Score: 768
Period size: 332 Copynumber: 1.9 Consensus size: 330
3392834 TCAACTCTAA
* * *
3392844 AATTTTTTTCAAGGGGATTTTTTTAGTGTTTAATTTTTAAAATTTATCAAATATTATTATTTATT
1 AATTTTTTTCAAGGGGATTTTTTTAGTGTTTAATTTTTAAAAGTTATAAAATATTATTATATATT
3392909 TCATATTAATTCAATTTTTAAAAATTCATTCATTTCATGAATTTTGAATTTTTTCCTTGAAATGC
66 TCATATTAATTCAATTTTTAAAAATTCATTCATTTCATGAATTTTGAATTTTTTCCTTGAAATGC
** * * * * *
3392974 CTTTTTTTTCAAAATACGATGTTTTCTACTCCGTGAATTTTTTGAGAGGATTTTTTTTTAGTATT
131 CCCTTTATCCAAAATACGATGTTTTCTACTCCGTAAATTTTTTGAGAGGAATTTTTCTTAG-ATT
* ** *
3393039 TAATTTTTAAAAGCTATCAAATATTATTATTTATTTCATATTAATTCAATTTTCAAAA-ATTCAT
195 TAATTTTTAAAAGCTAT-AAATATTATTATTGAACTCATATTAATTCAATTTTCAAAATATTAAT
3393103 TCATTTCCATGAATTTTGAATTTTGTTTTCCTTGAAATATCCTTTTTCCAAATACGGTGTTTTCT
259 TCATTT-CATGAATTTTGAATTTTGTTTTCCTTGAAATATCCTTTTTCCAAATACGGTGTTTTCT
3393168 ACTCCGTG
323 ACTCCGTG
* * *
3393176 AATTTTTTTGAA-GGGATTTTTCTTGGTTTTTAATTTTTAAAAGTTATAAAATATTATTATATAT
1 AATTTTTTTCAAGGGGATTTTT-TTAGTGTTTAATTTTTAAAAGTTATAAAATATTATTATATAT
* * *
3393240 TTCATATTAATTCAGTTTTCT-AAAATTCATTCATTTCCATGAATTTTGATTTTTTTTCTTTGAA
65 TTCATATTAATTCAATTTT-TAAAAATTCATTCATTT-CATGAATTTTGA-ATTTTTTCCTTGAA
*
3393304 AT-CCCCTTTATCCGAAAAGT-CGA-G-TTTCTACTCTGTAAATTTTTTCG-GAGGAATTTTTCT
127 ATGCCCCTTTATCC-AAAA-TACGATGTTTTCTACTCCGTAAATTTTTT-GAGAGGAATTTTTCT
* * *
3393364 TA-ATTTAAAATTTTTAAAA-TTCATATAATATT-TTCATTGAACTCCTATTAATTCAATTTTGA
189 TAGATTT--AATTTTTAAAAGCT-ATA-AATATTATT-ATTGAACTCATATTAATTCAATTTTCA
* * *
3393426 AAATTTTTAATTTATTTCATTAATTTTGAATTTT
249 AAA-TATTAATTCATTTCATGAATTTTGAATTTT
3393460 TTTGTATATA
Statistics
Matches: 243, Mismatches: 27, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
330 4 0.02
331 13 0.05
332 157 0.65
333 38 0.16
334 30 0.12
335 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (330 bp):
AATTTTTTTCAAGGGGATTTTTTTAGTGTTTAATTTTTAAAAGTTATAAAATATTATTATATATT
TCATATTAATTCAATTTTTAAAAATTCATTCATTTCATGAATTTTGAATTTTTTCCTTGAAATGC
CCCTTTATCCAAAATACGATGTTTTCTACTCCGTAAATTTTTTGAGAGGAATTTTTCTTAGATTT
AATTTTTAAAAGCTATAAATATTATTATTGAACTCATATTAATTCAATTTTCAAAATATTAATTC
ATTTCATGAATTTTGAATTTTGTTTTCCTTGAAATATCCTTTTTCCAAATACGGTGTTTTCTACT
CCGTG
Found at i:3393538 original size:2 final size:2
Alignment explanation
Indices: 3393531--3393630 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
3393521 CCCAATCAGT
3393531 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3393573 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3393615 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
3393631 GGAGCAATTC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3394052 original size:32 final size:32
Alignment explanation
Indices: 3394010--3394083 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
3394000 AGTTCAGCAC
*
3394010 AAAAAA-AAAAAGGAG-AGAAAAGAGAGAAAGA
1 AAAAAAGAAAAAAGAGAAGAAAAGAGAGAAA-A
* * *
3394041 AAAAAAGAAAAAATAGAAGAAAATATAGAAAA
1 AAAAAAGAAAAAAGAGAAGAAAAGAGAGAAAA
*
3394073 AAAATAGAAAA
1 AAAAAAGAAAA
3394084 GCTAGGCTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 6 0.17
32 18 0.50
33 12 0.33
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (32 bp):
AAAAAAGAAAAAAGAGAAGAAAAGAGAGAAAA
Found at i:3394058 original size:21 final size:21
Alignment explanation
Indices: 3394025--3394074 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3394015 AAAAAAGGAG
*
3394025 AGAAAAGAGAGAAAGAAAA-AA
1 AGAAAAAAGAG-AAGAAAATAA
* *
3394046 AGAAAAAATAGAAGAAAATAT
1 AGAAAAAAGAGAAGAAAATAA
3394067 AGAAAAAA
1 AGAAAAAA
3394075 AATAGAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (21 bp):
AGAAAAAAGAGAAGAAAATAA
Found at i:3394060 original size:12 final size:12
Alignment explanation
Indices: 3394045--3394081 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3394035 GAAAGAAAAA
3394045 AAGAAAAAATAG
1 AAGAAAAAATAG
*
3394057 AAGAAAATATAG
1 AAGAAAAAATAG
3394069 AA-AAAAAATAG
1 AAGAAAAAATAG
3394080 AA
1 AA
3394082 AAGCTAGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (12 bp):
AAGAAAAAATAG
Found at i:3395148 original size:129 final size:129
Alignment explanation
Indices: 3395014--3395260 Score: 372
Period size: 129 Copynumber: 1.9 Consensus size: 129
3395004 TTGTTAATTA
* * * * *
3395014 AAATAAACATTAATTGTTTTTTAA-TCTTTTATATTCTTATGGGTATCTGT-AGGAGTATAAAAG
1 AAATAAACATCAATT-ATTTTCAAGTCTTTTACATTCTTATGGGTATCCGTAAGG-GTATAAAAG
*
3395077 ATTTCAAAAACTTTTTGTATCTTTTCGGGTATCCATTAAGGTACGAAATGATTTTTTTCAAAGCA
64 ATTTCAAAAACTTTTCGTATCTTTTCGGGTATCCATTAAGGTACGAAATGATTTTTTTCAAAGCA
3395142 C
129 C
*
3395143 AAATAAATATCAATTATTTTCAAGTCTTTTACATTCTTATGGGTATCCGTAAGGGTATAAAAGAT
1 AAATAAACATCAATTATTTTCAAGTCTTTTACATTCTTATGGGTATCCGTAAGGGTATAAAAGAT
* * *
3395208 TTTAAAAACTTTTCGTATCTTTTTGGGTATCTATTAAGGTACGAAATGATTTT
66 TTCAAAAACTTTTCGTATCTTTTCGGGTATCCATTAAGGTACGAAATGATTTT
3395261 AGAGATAATT
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
128 6 0.06
129 97 0.92
130 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.43
Consensus pattern (129 bp):
AAATAAACATCAATTATTTTCAAGTCTTTTACATTCTTATGGGTATCCGTAAGGGTATAAAAGAT
TTCAAAAACTTTTCGTATCTTTTCGGGTATCCATTAAGGTACGAAATGATTTTTTTCAAAGCAC
Found at i:3402231 original size:28 final size:29
Alignment explanation
Indices: 3402149--3402725 Score: 620
Period size: 28 Copynumber: 19.9 Consensus size: 29
3402139 AAAAAAAAAT
*
3402149 GTGCCACTAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
*
3402180 GCTGCCACCGACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* * * *
3402212 GTGCCATTAAC-TGTTGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402239 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
3402267 GAGCCAATGACTTGTGGGCTTCGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
3402296 -TGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
3402324 ATGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402352 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402381 -TGTCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
3402409 GTTGCCACTGACTTGTGGGCTTTGAAAAGAA
1 G-TGCCACTGACTTGTGGGCTTTGAAAAG-A
* ** * * *
3402440 TTGCCACCAACTCGTGAGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402468 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402497 -TGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
**
3402525 GTTGCCACCAACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* * *
3402557 GTGCCACTAACTTGTGGTCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402585 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
3402614 -TGCCACTGACTTGTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
3402642 GTTGCCACCGACCCATGTGCGCTTTGAAATG-
1 G-TGCCACTGA--CTTGTGGGCTTTGAAAAGA
* * *
3402673 GTGCCACTAACTTATGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
3402701 GTGCCACTGACTTGTGGGCTTTGAA
1 GTGCCACTGACTTGTGGGCTTTGAA
3402726 GAGATGAACG
Statistics
Matches: 461, Mismatches: 64, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.03
28 247 0.54
29 49 0.11
30 69 0.15
31 21 0.05
32 59 0.13
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:3402492 original size:116 final size:114
Alignment explanation
Indices: 3402163--3402725 Score: 794
Period size: 116 Copynumber: 4.9 Consensus size: 114
3402153 CACTAACTTG
* *
3402163 TGTGGGCTTTGAAAAGAGCTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCATTAAC-TGTT
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACT--TGTGGGCTTTGAAAAGAGTGCCACTAACTTG-T
*
3402227 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGA-GCCAATGACT
63 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGACT
* * * * *
3402279 TGTGGGCTTCG-AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGT-GG
*
3402342 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGTCACTGACT
65 CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
3402392 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAATTGCCACCAACTCGTGA
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAG-AGTGCCACTAACTTGTG-
*
3402457 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
64 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
3402508 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTG
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACT--TGTGGGCTTTGAAAAGAGTGCCACTAACTTGTG
3402573 GTCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
64 G-CTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
3402625 TGTAGGCTTTGAAAAGAGTTGCCACCGACCCATGTGCGCTTTGAAATG-GTGCCACTAACTTATG
1 TGTGGGCTTTGAAAAGAGTTGCCACCGA--CTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGT-
3402689 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
63 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
3402726 GAGATGAACG
Statistics
Matches: 406, Mismatches: 28, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
112 29 0.07
113 58 0.14
114 15 0.04
115 33 0.08
116 149 0.37
117 105 0.26
118 16 0.04
119 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (114 bp):
TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGC
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:3402611 original size:233 final size:226
Alignment explanation
Indices: 3402163--3402725 Score: 797
Period size: 233 Copynumber: 2.4 Consensus size: 226
3402153 CACTAACTTG
* *
3402163 TGTGGGCTTTGAAAAGAGCTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCATTAACTGTTG
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACT--TGTGGGCTTTGAAAAGAGTGCCACTAACTG-TG
*
3402228 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGAGCCAATGACTTGTGGGCTTCGAAA
63 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGAGCCAATAACTTGTGGGCTTCGAAA
** *
3402293 GGATGCCACTGACTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
128 GGATGCCACCAACTTGTGGGCTTTGAAAAGAATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCA
*
3402358 CTGACTTGTGGGCTTTGAAAGGATGTCACTGACT
193 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
3402392 TGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGAATTGCCACCAACTCGTGA
1 TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAG-AGTGCCACTAACT-GTG-
* *
3402457 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTAACTTGTGGGCTTTGAA
63 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGA-GCCAATAACTTGTGGGCTTCG-A
* * *
3402521 AAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGTCTTTGAAAGGG
126 AAG-GATGCCACCAACT--TGTGGGCTTTGAAAAGAATGCCACTAACTTGTGGGCTTTGAAAGGG
3402586 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
188 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
3402625 TGTAGGCTTTGAAAAGAGTTGCCACCGACCCATGTGCGCTTTGAAATG-GTGCCACTAACTTATG
1 TGTGGGCTTTGAAAAGAGTTGCCACCGA--CTTGTGGGCTTTGAAAAGAGTGCCACTAAC-TGT-
3402689 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
62 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
3402726 GAGATGAACG
Statistics
Matches: 299, Mismatches: 23, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
227 16 0.05
228 15 0.05
229 84 0.28
230 4 0.01
231 10 0.03
233 153 0.51
234 2 0.01
235 15 0.05
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (226 bp):
TGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTGTGGCT
TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGAGCCAATAACTTGTGGGCTTCGAAAGGA
TGCCACCAACTTGTGGGCTTTGAAAAGAATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTG
ACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:3403973 original size:1 final size:1
Alignment explanation
Indices: 3403969--3404026 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
3403959 TTTTCCTTGG
* * * * * *
3403969 TTTTTTATTTTTTTTATTTTTTTTGTTTTTTTTTTATTTTTTATTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3404027 GGTATGAAGG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (1 bp):
T
Found at i:3403986 original size:28 final size:26
Alignment explanation
Indices: 3403947--3404020 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 26
3403937 CCTTTCTATT
3403947 TTTTTTGTTATTTTTTCCTTGGTTTTTTA
1 TTTTTT-TTATTTTTT--TTGGTTTTTTA
* *
3403976 TTTTTTTTATTTTTTTTGTTTTTTTT
1 TTTTTTTTATTTTTTTTGGTTTTTTA
3404002 TTATTTTTTATTTTGTTTT
1 TT-TTTTTTATTTT-TTTT
3404021 TTTTTTGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 11 0.27
27 11 0.27
28 13 0.32
29 6 0.15
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.84
Consensus pattern (26 bp):
TTTTTTTTATTTTTTTTGGTTTTTTA
Found at i:3403987 original size:40 final size:36
Alignment explanation
Indices: 3403943--3404026 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 36
3403933 GACCCCTTTC
* *
3403943 TATTTTTTTTGTTATTTTTTCCTTGGTTTTTTATTTTTTT
1 TATTTTTTTTGTT-TTTTTT--TT-ATTTTTTATTTTGTT
3403983 TATTTTTTTTGTTTTTTTTTTATTTTTTATTTTGTT
1 TATTTTTTTTGTTTTTTTTTTATTTTTTATTTTGTT
3404019 T-TTTTTTT
1 TATTTTTTT
3404027 GGTATGAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 7 0.17
36 14 0.33
37 2 0.05
39 6 0.14
40 13 0.31
ACGTcount: A:0.07, C:0.02, G:0.06, T:0.85
Consensus pattern (36 bp):
TATTTTTTTTGTTTTTTTTTTATTTTTTATTTTGTT
Found at i:3403989 original size:29 final size:29
Alignment explanation
Indices: 3403947--3404015 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 29
3403937 CCTTTCTATT
3403947 TTTTTTGTTATTTTTTCCTTGGTTTTTTA
1 TTTTTTGTTATTTTTTCCTTGGTTTTTTA
*
3403976 TTTTTT-TTATTTTTT--TT-GTTTTTTT
1 TTTTTTGTTATTTTTTCCTTGGTTTTTTA
*
3404001 TTTATTTTTTATTTT
1 TTT-TTTGTTATTTT
3404016 GTTTTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 10 0.27
26 5 0.14
27 7 0.19
28 9 0.24
29 6 0.16
ACGTcount: A:0.07, C:0.03, G:0.06, T:0.84
Consensus pattern (29 bp):
TTTTTTGTTATTTTTTCCTTGGTTTTTTA
Found at i:3403997 original size:23 final size:23
Alignment explanation
Indices: 3403945--3404026 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
3403935 CCCCTTTCTA
** *
3403945 TTTTTTTTGTTATTTTTTCCTTGG
1 TTTTTTTT-TTATTTTTTATTTTG
* *
3403969 TTTTTTATTTTTTTTATTTTTTTTG
1 TTTTTT-TTTTATTT-TTTATTTTG
3403994 TTTTTTTTTTATTTTTTATTTTG
1 TTTTTTTTTTATTTTTTATTTTG
3404017 TTTTTTTTTT
1 TTTTTTTTTT
3404027 GGTATGAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
23 18 0.36
24 18 0.36
25 14 0.28
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.85
Consensus pattern (23 bp):
TTTTTTTTTTATTTTTTATTTTG
Found at i:3404024 original size:27 final size:26
Alignment explanation
Indices: 3403947--3404026 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
3403937 CCTTTCTATT
*
3403947 TTTTTTGTTATTTTTTCCTTGGTTTTTTA
1 TTTTTT-TTATTTTTT--TTGTTTTTTTA
*
3403976 TTTTTTTTATTTTTTTTGTTTTTTTT
1 TTTTTTTTATTTTTTTTGTTTTTTTA
*
3404002 TTATTTTTTATTTTGTTT-TTTTTTT
1 TT-TTTTTTATTTTTTTTGTTTTTTT
3404027 GGTATGAAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
26 18 0.38
27 14 0.30
28 9 0.19
29 6 0.13
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.85
Consensus pattern (26 bp):
TTTTTTTTATTTTTTTTGTTTTTTTA
Found at i:3407143 original size:13 final size:13
Alignment explanation
Indices: 3407125--3407152 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3407115 CATTATTCAA
3407125 TGTATCGATACAT
1 TGTATCGATACAT
3407138 TGTATCGATACAT
1 TGTATCGATACAT
3407151 TG
1 TG
3407153 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:3407149 original size:33 final size:33
Alignment explanation
Indices: 3407105--3407170 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3407095 GCCAAGGAAA
3407105 TGTATCAATACATT-ATTCAATGTATCGATACAT
1 TGTATCAATACATTGA-TCAATGTATCGATACAT
* **
3407138 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCAATACATTGATCAATGTATCGATACAT
3407171 GCAGGCAAAT
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:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATTGATCAATGTATCGATACAT
Found at i:3407419 original size:21 final size:21
Alignment explanation
Indices: 3407395--3407442 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3407385 AGCATTTATA
3407395 GCATTTTGAACTATGCTTCAT
1 GCATTTTGAACTATGCTTCAT
3407416 GCATTTTGAACTATGCTTCAT
1 GCATTTTGAACTATGCTTCAT
3407437 GCATTT
1 GCATTT
3407443 ATAGCATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.44
Consensus pattern (21 bp):
GCATTTTGAACTATGCTTCAT
Found at i:3416485 original size:21 final size:22
Alignment explanation
Indices: 3416436--3416485 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3416426 ACAGTAATAG
* * *
3416436 TAAGATTAGGTATTATAACAGT
1 TAAGATTAGATACTATAACAGA
3416458 TAA-ATTAGATACTATAACA-A
1 TAAGATTAGATACTATAACAGA
3416478 TAAGATTA
1 TAAGATTA
3416486 AATTCAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (22 bp):
TAAGATTAGATACTATAACAGA
Found at i:3416825 original size:25 final size:24
Alignment explanation
Indices: 3416784--3416836 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3416774 AAATATTGAA
*
3416784 AAAATAAAAATAAG-AAATATTTTT
1 AAAATAAAAACAAGAAAAT-TTTTT
*
3416808 AAAATAAAAACATGGAAAATTTTTT
1 AAAATAAAAACA-AGAAAATTTTTT
3416833 AAAA
1 AAAA
3416837 ATATTAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.44
25 10 0.40
26 4 0.16
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (24 bp):
AAAATAAAAACAAGAAAATTTTTT
Found at i:3416829 original size:24 final size:25
Alignment explanation
Indices: 3416784--3416836 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3416774 AAATATTGAA
*
3416784 AAAATAAAAATAAGAAATA-TTTTT
1 AAAATAAAAACAAGAAATATTTTTT
*
3416808 AAAATAAAAACATGGAAA-ATTTTTT
1 AAAATAAAAACA-AGAAATATTTTTT
3416833 AAAA
1 AAAA
3416837 ATATTAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAATAAAAACAAGAAATATTTTTT
Found at i:3419975 original size:2 final size:2
Alignment explanation
Indices: 3419968--3419999 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3419958 CTTATGTCTC
3419968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3420000 GTATGTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3420162 original size:2 final size:2
Alignment explanation
Indices: 3420155--3420181 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3420145 TATTTTGTTA
3420155 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3420182 AATTTTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3421887 original size:11 final size:11
Alignment explanation
Indices: 3421871--3421895 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3421861 TAATAATTCA
3421871 TATATTGATAT
1 TATATTGATAT
3421882 TATATTGATAT
1 TATATTGATAT
3421893 TAT
1 TAT
3421896 TTTATATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATTGATAT
Found at i:3421953 original size:24 final size:26
Alignment explanation
Indices: 3421915--3422030 Score: 79
Period size: 24 Copynumber: 4.6 Consensus size: 26
3421905 CATTTCCTAC
3421915 ATATAATTTATATATATT-AT-ATTT
1 ATATAATTTATATATATTAATAATTT
3421939 ATATAAATTTA-ATATATTAATAATTT
1 ATAT-AATTTATATATATTAATAATTT
* *
3421965 ATATTATATTAT-T-T-TTAATATATTC
1 ATATAAT-TTATATATATTAATA-ATTT
* *
3421990 ATAT-GTTTATATCATATTTATATATTT
1 ATATAATTTATAT-ATATTAATA-ATTT
3422017 ATCAT-A-TTATATAT
1 AT-ATAATTTATATAT
3422031 TCTATTCATC
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
23 4 0.05
24 19 0.25
25 18 0.24
26 15 0.20
27 17 0.23
28 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATAATTTATATATATTAATAATTT
Found at i:3422007 original size:33 final size:32
Alignment explanation
Indices: 3421946--3422007 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3421936 TTTATATAAA
*
3421946 TTTAATATATTAATAATTTATATTATATTATT
1 TTTAATATATTAATAATTTATATCATATTATT
* *
3421978 TTTAATATATTCATATGTTTATATCATATT
1 TTTAATATATTAATA-ATTTATATCATATT
3422008 TATATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTAATATATTAATAATTTATATCATATTATT
Found at i:3422028 original size:16 final size:17
Alignment explanation
Indices: 3421999--3422031 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3421989 CATATGTTTA
3421999 TATCATATTTATATATT
1 TATCATATTTATATATT
3422016 TATCATA-TTATATATT
1 TATCATATTTATATATT
3422032 CTATTCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATCATATTTATATATT
Found at i:3424296 original size:19 final size:21
Alignment explanation
Indices: 3424258--3424296 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3424248 AATTATATAA
*
3424258 TATATATTAATTATATTTTTT
1 TATATATTAAGTATATTTTTT
3424279 TATATATTAAGTA-ATTTT
1 TATATATTAAGTATATTTT
3424297 ATCATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TATATATTAAGTATATTTTTT
Found at i:3424308 original size:21 final size:21
Alignment explanation
Indices: 3424247--3424309 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
3424237 ATCCATTTTA
* *
3424247 TAATTATATAATATATATTAAT
1 TAATTTTATAATATA-ATTAAG
* *
3424269 TATATTTTTTTATAT-ATTAAG
1 TA-ATTTTATAATATAATTAAG
*
3424290 TAATTTTATCATATAATTAA
1 TAATTTTATAATATAATTAA
3424310 AGAATACATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.30
21 12 0.36
22 2 0.06
23 9 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATTTTATAATATAATTAAG
Found at i:3425794 original size:19 final size:20
Alignment explanation
Indices: 3425770--3425807 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3425760 AAAATAAGGC
3425770 TGATATAAA-ATAAAAAATA
1 TGATATAAATATAAAAAATA
*
3425789 TGATATAAATATAATAAAT
1 TGATATAAATATAAAAAAT
3425808 TTAATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TGATATAAATATAAAAAATA
Found at i:3425843 original size:17 final size:17
Alignment explanation
Indices: 3425815--3425855 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
3425805 AATTTAATAA
*
3425815 ACTAATATATATATAAAG
1 ACTAA-ATATATAGAAAG
3425833 ACTAAATATATAGAAAG
1 ACTAAATATATAGAAAG
3425850 ACTAAA
1 ACTAAA
3425856 GTAGAATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (17 bp):
ACTAAATATATAGAAAG
Found at i:3431479 original size:142 final size:142
Alignment explanation
Indices: 3431210--3431483 Score: 422
Period size: 142 Copynumber: 1.9 Consensus size: 142
3431200 GAAAAAAAAT
* *
3431210 GAACTTCCAATAATTTACTATCTCACAACAATCAATCCACCAAATTTCTGATCATATCCGAATAA
1 GAACTCCCAATAATTTACTATCTCACAACAATCAATCCACCAAATTTCTGATCATATCCAAATAA
* * * *
3431275 AAGAAAATACCTTGAACGTTGTCGGGTCTTTGGGAAGAAGCAGAAGAATCCATGGATTGAACTGA
66 AAGAAAATACCTTGAACGTTGTCGCGTCTCTGGGAAGAAGCAGAAGAACCCATGGATCGAACTGA
3431340 GATGCGAACAAA
131 GATGCGAACAAA
** ** *
3431352 GAACTCCCAATAATTTACTATCTTGCAACAATCAATTTACCAAATTTCTGGTCATATCCAAATAA
1 GAACTCCCAATAATTTACTATCTCACAACAATCAATCCACCAAATTTCTGATCATATCCAAATAA
* * *
3431417 AAGAAAATACCTTGAACGTTGTTGCGTCTCTGGGACGAAGCAGAAGAACCCATTGATCGAACTGA
66 AAGAAAATACCTTGAACGTTGTCGCGTCTCTGGGAAGAAGCAGAAGAACCCATGGATCGAACTGA
3431482 GA
131 GA
3431484 AGAGAGCTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
142 118 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (142 bp):
GAACTCCCAATAATTTACTATCTCACAACAATCAATCCACCAAATTTCTGATCATATCCAAATAA
AAGAAAATACCTTGAACGTTGTCGCGTCTCTGGGAAGAAGCAGAAGAACCCATGGATCGAACTGA
GATGCGAACAAA
Found at i:3435900 original size:13 final size:13
Alignment explanation
Indices: 3435882--3435906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3435872 CATTATGCTT
3435882 TGTATCGATACAA
1 TGTATCGATACAA
3435895 TGTATCGATACA
1 TGTATCGATACA
3435907 TGTTCACTGT
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:3435943 original size:20 final size:19
Alignment explanation
Indices: 3435891--3435947 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
3435881 TTGTATCGAT
*
3435891 ACAATGTATCGATACATGT
1 ACAATGTATCGATACATGG
* * *
3435910 TCACTGTATTGATACATGG
1 ACAATGTATCGATACATGG
3435929 ACAATTGTATCGATACATG
1 ACAA-TGTATCGATACATG
3435948 AGACTGGCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (19 bp):
ACAATGTATCGATACATGG
Found at i:3442176 original size:13 final size:13
Alignment explanation
Indices: 3442158--3442186 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3442148 ACAACATTCC
3442158 TTGTATCGATACA
1 TTGTATCGATACA
3442171 TTGTATCGATACA
1 TTGTATCGATACA
3442184 TTG
1 TTG
3442187 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3442327 original size:24 final size:22
Alignment explanation
Indices: 3442300--3442344 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3442290 TCATCAAATT
*
3442300 TTCAACAAATTTTCACTTTTTCAC
1 TTCAA-AAACTTTCA-TTTTTCAC
*
3442324 TTCAAATACTTTCATTTTTCA
1 TTCAAAAACTTTCATTTTTCA
3442345 TCAAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (22 bp):
TTCAAAAACTTTCATTTTTCAC
Found at i:3444091 original size:29 final size:30
Alignment explanation
Indices: 3444035--3444091 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3444025 AAATTTTTTA
3444035 TTTGATTAAGGGGGAGAATTTTATAAATGC
1 TTTGATTAAGGGGGAGAATTTTATAAATGC
3444065 TTTGATTAAGGGGGAGAATTTT-TAAAT
1 TTTGATTAAGGGGGAGAATTTTATAAAT
3444092 TCTTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (30 bp):
TTTGATTAAGGGGGAGAATTTTATAAATGC
Found at i:3444809 original size:13 final size:13
Alignment explanation
Indices: 3444791--3444837 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
3444781 TGGGACAATA
3444791 TATCGATACATTG
1 TATCGATACATTG
3444804 TATCGATACA-TG
1 TATCGATACATTG
3444816 -AT-GA-A-ATTG
1 TATCGATACATTG
3444825 TATCGATACATTG
1 TATCGATACATTG
3444838 CTTGTAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.14
11 4 0.14
12 3 0.10
13 14 0.48
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:3444810 original size:33 final size:34
Alignment explanation
Indices: 3444768--3444837 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
3444758 CTATCACTAT
3444768 TTGTATCGATACATG-GGACAA-TATATCGATACA
1 TTGTATCGATACATGAGGA-AATTATATCGATACA
* *
3444801 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGAGGAAATTATATCGATACA
3444835 TTG
1 TTG
3444838 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (34 bp):
TTGTATCGATACATGAGGAAATTATATCGATACA
Found at i:3447517 original size:13 final size:13
Alignment explanation
Indices: 3447499--3447524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3447489 GATAAAGTGT
3447499 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
3447512 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
3447525 AAATTTATCC
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:3447560 original size:21 final size:21
Alignment explanation
Indices: 3447536--3447592 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3447526 AATTTATCCA
3447536 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3447557 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3447578 AATGTATCGATACAT
1 AATGTATCGATACAT
3447593 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3447672 original size:19 final size:19
Alignment explanation
Indices: 3447648--3447715 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3447638 AATTCAACAA
3447648 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3447667 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3447682 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3447699 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3447716 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3447687 original size:13 final size:13
Alignment explanation
Indices: 3447669--3447693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3447659 ACATAAGTTT
3447669 TGTATCGATACAA
1 TGTATCGATACAA
3447682 TGTATCGATACA
1 TGTATCGATACA
3447694 TAAGTATTGT
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:3447691 original size:32 final size:32
Alignment explanation
Indices: 3447650--3447712 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3447640 TTCAACAATT
*
3447650 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3447682 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3447713 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3447773 original size:13 final size:13
Alignment explanation
Indices: 3447755--3447780 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3447745 CATTTTTCTG
3447755 TGTATCGATACAT
1 TGTATCGATACAT
3447768 TGTATCGATACAT
1 TGTATCGATACAT
3447781 GGATCTTTGT
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:3447777 original size:33 final size:33
Alignment explanation
Indices: 3447735--3447801 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3447725 GCCAAGGAAA
***
3447735 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3447768 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3447801 T
1 T
3447802 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3450284 original size:27 final size:27
Alignment explanation
Indices: 3450254--3450329 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
3450244 TTTCTTCACA
3450254 ATCGGGGATACTCCAACCCCGTTGA-TC
1 ATCGGGGATACTCCAACCCCGTT-ATTC
3450281 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTA-TTC
*
3450309 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
3450330 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 1 0.02
27 24 0.53
28 20 0.44
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTATTC
Found at i:3450387 original size:51 final size:51
Alignment explanation
Indices: 3450312--3450535 Score: 214
Period size: 52 Copynumber: 4.4 Consensus size: 51
3450302 TTATTTCTGA
* * * *
3450312 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACTAATTTTTCATAATC
* * * * * *
3450363 GGGGATATTCCAATCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACTAATTTTT-CATAATC
* * * * * *
3450415 GGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACTAATTTTTC-ATAATC
* * * * * ** *
3450467 GAGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCGCATAATT
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACTAATTTTTCATAATC
3450518 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3450536 TTATTTTCGA
Statistics
Matches: 137, Mismatches: 34, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
51 57 0.42
52 80 0.58
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAACACTAATTTTTCATAATC
Found at i:3450427 original size:52 final size:51
Alignment explanation
Indices: 3450312--3450535 Score: 188
Period size: 51 Copynumber: 4.4 Consensus size: 51
3450302 TTATTTCTGA
* * * * *
3450312 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT-CATAATC
1 GGGGATACTCCAACCCCGGCTTTA-TTCTAAAACACTAATTTTTCCATAATC
* * * *
3450363 GGGGATATTCCAATCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGCTTTATT-CTAAAACACTAATTTTTCCATAATC
* * * * *
3450415 GGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGCTTTATTCT-AAAACACTAATTTTTCC-ATAATC
* ** *
3450467 GAGGATACTCCAACCCCGGCTTTATTCCCAAA-A-T-ATTGATTTCGCATAATT
1 GGGGATACTCCAACCCCGGCTTTATTCTAAAACACTAATT--TTTC-CATAATC
3450518 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3450536 TTATTTTCGA
Statistics
Matches: 140, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 3 0.02
51 68 0.49
52 67 0.48
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTCTAAAACACTAATTTTTCCATAATC
Found at i:3452219 original size:21 final size:21
Alignment explanation
Indices: 3452195--3452269 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
3452185 TTCTACAATT
3452195 TGTATCGATACAACAAGTGAA
1 TGTATCGATACAACAAGTGAA
3452216 TGTATCGATAC--CTAAGTGAA
1 TGTATCGATACAAC-AAGTGAA
* * **
3452236 TGTATCAATACATC-TTTGAAA
1 TGTATCGATACAACAAGTG-AA
3452257 TGTATCGATACAA
1 TGTATCGATACAA
3452270 GACCATGTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 1 0.02
20 19 0.42
21 24 0.53
22 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAACAAGTGAA
Found at i:3452234 original size:20 final size:20
Alignment explanation
Indices: 3452195--3452247 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3452185 TTCTACAATT
3452195 TGTATCGATACAACAAGTGAA
1 TGTATCGATAC-ACAAGTGAA
3452216 TGTATCGATAC-CTAAGTGAA
1 TGTATCGATACAC-AAGTGAA
*
3452236 TGTATCAATACA
1 TGTATCGATACA
3452248 TCTTTGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 17 0.59
21 11 0.38
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
TGTATCGATACACAAGTGAA
Found at i:3452388 original size:50 final size:50
Alignment explanation
Indices: 3452304--3452421 Score: 148
Period size: 52 Copynumber: 2.3 Consensus size: 50
3452294 TTCTGAAAAG
* ** *
3452304 AAAATATATCGATACATTTTTATTGTATTGATACATTCTGAG-TTTGATC
1 AAAATGTATCGATACATTTTTATTGTATCAATACATTCTGAGTTTTGACC
* * *
3452353 TAAATGTATTGATACATTTTTCATTGTATCAATACATTCTGGGTTTTTGACC
1 AAAATGTATCGATACATTTTT-ATTGTATCAATACATTCTGAG-TTTTGACC
3452405 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
3452422 ATATCCAGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
49 18 0.32
50 18 0.32
52 21 0.37
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (50 bp):
AAAATGTATCGATACATTTTTATTGTATCAATACATTCTGAGTTTTGACC
Found at i:3456417 original size:2 final size:2
Alignment explanation
Indices: 3456410--3456457 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
3456400 TTTGACCAAA
* * * *
3456410 AT AT AT AT A- AT GT GT AT AT AT AT AT AT AT AT AT AG AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3456451 AT AT AT A
1 AT AT AT A
3456458 AAGAATCTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3458065 original size:21 final size:20
Alignment explanation
Indices: 3458040--3458105 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
3458030 TATATCTATG
3458040 TATAACAATTTACGTATATTA
1 TATAACAATTT-CGTATATTA
* *
3458061 TATAACAAACTTCATATATATA
1 TATAAC-AATTTCGTATAT-TA
3458083 TATAA-ATATTTCGTAT-TTA
1 TATAACA-ATTTCGTATATTA
3458102 TATA
1 TATA
3458106 CTCTTAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.16
20 2 0.05
21 19 0.50
22 11 0.29
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (20 bp):
TATAACAATTTCGTATATTA
Found at i:3463682 original size:20 final size:21
Alignment explanation
Indices: 3463642--3463683 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3463632 TTCTACAATT
*
3463642 TGTATAGATACAATAAGTGAA
1 TGTATAGATACAATAAATGAA
*
3463663 TGTATCGATAC-ATAAATGAA
1 TGTATAGATACAATAAATGAA
3463683 T
1 T
3463684 ATATTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (21 bp):
TGTATAGATACAATAAATGAA
Found at i:3463836 original size:52 final size:52
Alignment explanation
Indices: 3463751--3463890 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 52
3463741 TCTGAAAAGA
** *
3463751 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTTGGTTTTTGA-CT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCAGGGTTTTAGACCT
* * *
3463802 CAAATGTATCAATACATTCTTCATTATATTGATACATTCAGGGTTTTAGACCT
1 -AAATGTATCGATACATTCTTCATTGTATCGATACATTCAGGGTTTTAGACCT
* *
3463855 AAATGTATTGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTCTTCATTGTATCGATACAT
3463891 GCAGACAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
52 74 0.97
53 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCAGGGTTTTAGACCT
Found at i:3465926 original size:15 final size:15
Alignment explanation
Indices: 3465906--3465934 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3465896 CGTGATGTTG
3465906 TCCCCTATTTTTCGA
1 TCCCCTATTTTTCGA
3465921 TCCCCTATTTTTCG
1 TCCCCTATTTTTCG
3465935 GTCATGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.34, G:0.07, T:0.48
Consensus pattern (15 bp):
TCCCCTATTTTTCGA
Found at i:3467534 original size:20 final size:20
Alignment explanation
Indices: 3467481--3467534 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3467471 AATTAACTAG
* *
3467481 ATATATCGATGCACTGAAAA
1 ATATATCGATACATTGAAAA
3467501 ATATATCGATACATTGAAAA
1 ATATATCGATACATTGAAAA
*
3467521 ATGTATCGATACAT
1 ATATATCGATACAT
3467535 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
ATATATCGATACATTGAAAA
Found at i:3467573 original size:19 final size:20
Alignment explanation
Indices: 3467549--3467605 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
3467539 GTAAAAACAC
3467549 AAAATGTATCGATATATT-A
1 AAAATGTATCGATATATTCA
*
3467568 AAAATGTATCGATACATTCA
1 AAAATGTATCGATATATTCA
* * *
3467588 CACACGTATCGATATATT
1 AAAATGTATCGATATATT
3467606 TACTATTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (20 bp):
AAAATGTATCGATATATTCA
Found at i:3471346 original size:23 final size:23
Alignment explanation
Indices: 3471292--3471346 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3471282 ATTTTTTAAT
*
3471292 ATAATTTTTAAAAATTATAAAAT
1 ATAATTTTTAAAAATTATAAAAA
* * *
3471315 TTAAATTTTATCAAA-TATAAAAA
1 ATAATTTTTA-AAAATTATAAAAA
3471338 ATAATTTTT
1 ATAATTTTT
3471347 TAAATTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAATTTTTAAAAATTATAAAAA
Found at i:3472332 original size:17 final size:18
Alignment explanation
Indices: 3472312--3472345 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3472302 TATATACTAA
*
3472312 TATTAAATAT-TAAATAT
1 TATTAAAAATATAAATAT
3472329 TATTAAAAATATAAATA
1 TATTAAAAATATAAATA
3472346 AAAATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATTAAAAATATAAATAT
Found at i:3472712 original size:6 final size:6
Alignment explanation
Indices: 3472701--3472726 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3472691 TTCAACCCCA
3472701 AAAACC AAAACC AAAACC AAAACC AA
1 AAAACC AAAACC AAAACC AAAACC AA
3472727 CCACTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:3483314 original size:13 final size:14
Alignment explanation
Indices: 3483296--3483324 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3483286 TATTATTAAT
3483296 TTAAAATAA-ATTA
1 TTAAAATAATATTA
3483309 TTAAAATAATATTA
1 TTAAAATAATATTA
3483323 TT
1 TT
3483325 TTGAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAATAATATTA
Found at i:3483879 original size:174 final size:172
Alignment explanation
Indices: 3483530--3483917 Score: 433
Period size: 174 Copynumber: 2.2 Consensus size: 172
3483520 ATTATTCACT
*
3483530 AAATATTTACAAATATTAAAATTATGTAAAACAAATTTTTTATGCTTAAAACTGTAAATTTTAAT
1 AAAT-TTTA-AAATA-TAAAATTATGTAAAACAAATTTTTTATGCTTAAAACTATAAATTTTAAT
* * * *
3483595 ACAAAAATGTTAATATATATTTTTCTTTGAGACTTATTATTTCGTAAGTTTTTAACCCAATAAAT
63 ACAAAAACGTCAATATATATTTTTCTTTGAGACTTACTATTTCATAAG-TTTTAACCCAATAAAT
* * **
3483660 GCATTTTATAGTTAAAATATCTAAAATAATCTGGTAAATATTTAAA
127 ACATTTTATAGTCAAAATATCTAAAATAATCTAATAAATATTTAAA
* * ** *
3483706 AAATTTTAAAATCTAAAATTATATAAAACGGATTTTTTACT-CTTAAAAAACTATCATATTTTAA
1 AAATTTTAAAATATAAAATTATGTAAAACAAATTTTTTA-TGCTT--AAAACTAT-AAATTTTAA
* * * * * *
3483770 TACGAAAACGTCAATTTATATTTTTCTTTGAGATTTACTGTTTCATAA-TTTTAACTCGATAAAT
62 TACAAAAACGTCAATATATATTTTTCTTTGAGACTTACTATTTCATAAGTTTTAACCCAATAAAT
* * * *
3483834 ACATTTTATTA-TCCAGATATTTAAAATTATAC-AATAAATATTTAAA
127 ACATTTTA-TAGTCAAAATATCTAAAATAAT-CTAATAAATATTTAAA
*
3483880 AAATTTTAAAATATAAAATTATGTAAAATAAATTTTTT
1 AAATTTTAAAATATAAAATTATGTAAAACAAATTTTTT
3483918 GACGGGAGAA
Statistics
Matches: 177, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
173 26 0.15
174 85 0.48
175 14 0.08
176 52 0.29
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (172 bp):
AAATTTTAAAATATAAAATTATGTAAAACAAATTTTTTATGCTTAAAACTATAAATTTTAATACA
AAAACGTCAATATATATTTTTCTTTGAGACTTACTATTTCATAAGTTTTAACCCAATAAATACAT
TTTATAGTCAAAATATCTAAAATAATCTAATAAATATTTAAA
Found at i:3484529 original size:169 final size:172
Alignment explanation
Indices: 3484146--3484580 Score: 514
Period size: 169 Copynumber: 2.6 Consensus size: 172
3484136 ATTAAAATAC
* * * **
3484146 AATTTTTCAAGCA-AAAAAAATCATTTTATATAATTTTAGAGTTTAAAAAGTTTTAAATATTTA-
1 AATTTTTTAAGCATAAAAAATTCATTTTATATAATTTTAGATTTTAAAATTTTTTAAATATTTAC
* * * *
3484209 TCAAATAATTTTAAATAATTTAATAATAAAATACTTTTGACGAGTTAAAAATTACAAAATAATAA
66 T-AAATAATTTTAAATATTTTAATAATAAAATACATTTGACAAATTAAAAATTACAAAATAATAA
* *
3484274 GTTTAAAAAAACATAAATTAACACTTTCATATTAAAATATGAT
130 GTTTAAAAAAACATAAATTAACACTTTCATATTAAAAAATGAA
* * *
3484317 AATTTCTTAAGTATAAAAAATTTATTTTA-ACTAATTTTAGATTTTAAAATTTTTTAAATATTTA
1 AATTTTTTAAGCATAAAAAATTCATTTTATA-TAATTTTAGATTTTAAAATTTTTTAAATATTTA
* **
3484381 CTAAATAATTTTAGATATTTTAA-AATAAAATA-ATTT-ACTAAATTAAAAAATTATGAAATAAT
65 CTAAATAATTTTAAATATTTTAATAATAAAATACATTTGAC-AAATT-AAAAATTACAAAATAAT
** * * *
3484443 AAG-TT-AAAAAATGTATATTAACATTTTCTTATTAAAAAACT-AA
128 AAGTTTAAAAAAACATAAATTAACACTTTCATATTAAAAAA-TGAA
* *
3484486 AATTTTTTAAACATAAAAAATTCATTTTATATAATTTTAGATTTT-AATTTTTTTAAATATTTAC
1 AATTTTTTAAGCATAAAAAATTCATTTTATATAATTTTAGATTTTAAAATTTTTTAAATATTTAC
*
3484550 T-AATAAATTTTATATATTTTAATAATAAAAT
66 TAAAT-AATTTTAAATATTTTAATAATAAAAT
3484581 GTGTTTACTG
Statistics
Matches: 227, Mismatches: 28, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
167 3 0.01
168 35 0.15
169 78 0.34
170 10 0.04
171 38 0.17
172 62 0.27
173 1 0.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (172 bp):
AATTTTTTAAGCATAAAAAATTCATTTTATATAATTTTAGATTTTAAAATTTTTTAAATATTTAC
TAAATAATTTTAAATATTTTAATAATAAAATACATTTGACAAATTAAAAATTACAAAATAATAAG
TTTAAAAAAACATAAATTAACACTTTCATATTAAAAAATGAA
Found at i:3484566 original size:21 final size:22
Alignment explanation
Indices: 3484536--3484578 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3484526 ATTTTAATTT
*
3484536 TTTTAAATA-TTTACTAATAAA
1 TTTTAAATATTTTAATAATAAA
*
3484557 TTTTATATATTTTAATAATAAA
1 TTTTAAATATTTTAATAATAAA
3484579 ATGTGTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAATATTTTAATAATAAA
Found at i:3484572 original size:19 final size:20
Alignment explanation
Indices: 3484536--3484574 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3484526 ATTTTAATTT
3484536 TTTTAAATATTTACTAATAAA
1 TTTTAAATATTTA-TAATAAA
*
3484557 TTTTATATATTT-TAATAA
1 TTTTAAATATTTATAATAA
3484575 TAAAATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAATATTTATAATAAA
Found at i:3488934 original size:21 final size:21
Alignment explanation
Indices: 3488901--3488944 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3488891 AAAATATAAA
* * *
3488901 TATTTTTATTTTATTAAATTT
1 TATTTGTAATTTATCAAATTT
*
3488922 TATTTGTAATTTATCAATTTT
1 TATTTGTAATTTATCAAATTT
3488943 TA
1 TA
3488945 AATATTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTGTAATTTATCAAATTT
Found at i:3490098 original size:16 final size:16
Alignment explanation
Indices: 3490079--3490110 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3490069 TTAGGTTCGA
*
3490079 GTTATTTCGGGTTTGG
1 GTTATTTCAGGTTTGG
3490095 GTTATTTCAGGTTTGG
1 GTTATTTCAGGTTTGG
3490111 ATCATTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
GTTATTTCAGGTTTGG
Found at i:3490117 original size:16 final size:16
Alignment explanation
Indices: 3490098--3490145 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
3490088 GGTTTGGGTT
* *
3490098 ATTTCAGGTTTGGATC
1 ATTTCAGATTCGGATC
*
3490114 ATTTC-GATTCGGGTC
1 ATTTCAGATTCGGATC
3490129 ATTTCAGATTCGGATC
1 ATTTCAGATTCGGATC
3490145 A
1 A
3490146 ATCAGATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (16 bp):
ATTTCAGATTCGGATC
Found at i:3490132 original size:15 final size:16
Alignment explanation
Indices: 3490093--3490141 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3490083 TTTCGGGTTT
* * *
3490093 GGGTTATTTCAGGTTT
1 GGGTCATTTCAGATTC
*
3490109 GGATCATTTC-GATTC
1 GGGTCATTTCAGATTC
3490124 GGGTCATTTCAGATTC
1 GGGTCATTTCAGATTC
3490140 GG
1 GG
3490142 ATCAATCAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (16 bp):
GGGTCATTTCAGATTC
Found at i:3491023 original size:16 final size:16
Alignment explanation
Indices: 3491004--3491052 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3490994 TTCAGGTTTT
3491004 GATCATTTTAAGTTCA
1 GATCATTTTAAGTTCA
**
3491020 GATCATTTTGGGTTCA
1 GATCATTTTAAGTTCA
*
3491036 GA-CTATTTTATGTTCA
1 GATC-ATTTTAAGTTCA
3491052 G
1 G
3491053 GCCATTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (16 bp):
GATCATTTTAAGTTCA
Found at i:3493256 original size:20 final size:20
Alignment explanation
Indices: 3493231--3493271 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3493221 GAAATATGAC
*
3493231 CTTTCAAATATGTAAAAAAA
1 CTTTCAAATATATAAAAAAA
3493251 CTTTCAAATATATAAAAAAA
1 CTTTCAAATATATAAAAAAA
3493271 C
1 C
3493272 ATAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (20 bp):
CTTTCAAATATATAAAAAAA
Found at i:3497833 original size:52 final size:52
Alignment explanation
Indices: 3497734--3497841 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
3497724 ATGCATTTGA
* * * * *
3497734 AATTCTAGCCGTTGGGCTCAATGTATCGATATAATTCATAATTTATCGATAT
1 AATTATAGCCGTTGGACTCAATGTATCGATATAATTCACAATGTATCGATAC
* * *
3497786 AATTATAGCCGTTGGACTTAATGTATCGATATAATTTACCATGTATCGATAC
1 AATTATAGCCGTTGGACTCAATGTATCGATATAATTCACAATGTATCGATAC
3497838 AATT
1 AATT
3497842 CACTTAGGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (52 bp):
AATTATAGCCGTTGGACTCAATGTATCGATATAATTCACAATGTATCGATAC
Found at i:3497949 original size:33 final size:32
Alignment explanation
Indices: 3497889--3497952 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
3497879 CATTTTATGG
*
3497889 TGTATCGATACAAAGAACATGTATCGATACAA
1 TGTATCGATACAAACAACATGTATCGATACAA
* *
3497921 TGTATTGATACTAAACAATATGTATCGATACA
1 TGTATCGATAC-AAACAACATGTATCGATACA
3497953 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAACAACATGTATCGATACAA
Found at i:3498619 original size:30 final size:30
Alignment explanation
Indices: 3498580--3498637 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3498570 TAATAAATTT
* *
3498580 TTTTTTATTTCTCCCCTTATTGTGTGAAGA
1 TTTTCTATTTCTCCCCCTATTGTGTGAAGA
3498610 TTTTCTATTTCTCCCCCTATTGTGTGAA
1 TTTTCTATTTCTCCCCCTATTGTGTGAA
3498638 TTTTACTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.12, T:0.52
Consensus pattern (30 bp):
TTTTCTATTTCTCCCCCTATTGTGTGAAGA
Found at i:3503718 original size:20 final size:20
Alignment explanation
Indices: 3503693--3503743 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
3503683 GTTAGAAGCA
*
3503693 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
3503713 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
3503733 ATGTATCGATA
1 ATGTATCGATA
3503744 TAAACAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:3503800 original size:20 final size:20
Alignment explanation
Indices: 3503775--3503834 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
3503765 CTGCCAGTTT
3503775 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
*
3503795 CATGTATCGATACAATGAT-
1 CATGTATCGATACAATTATC
3503814 CATGTATCGATACAATGTATC
1 CATGTATCGATACAAT-TATC
3503835 GATACAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:3503819 original size:19 final size:19
Alignment explanation
Indices: 3503774--3503830 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
3503764 ACTGCCAGTT
*
3503774 TCATGTATCGATACAATTA
1 TCATGTATCGATACAATGA
3503793 TCCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
3503813 TCATGTATCGATACAATG
1 TCATGTATCGATACAATG
3503831 TATCGATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:3503833 original size:13 final size:13
Alignment explanation
Indices: 3503815--3503846 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3503805 TACAATGATC
3503815 ATGTATCGATACA
1 ATGTATCGATACA
3503828 ATGTATCGATACA
1 ATGTATCGATACA
*
3503841 AAGTAT
1 ATGTAT
3503847 AATGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3505031 original size:15 final size:14
Alignment explanation
Indices: 3505011--3505088 Score: 86
Period size: 15 Copynumber: 5.4 Consensus size: 14
3505001 GATTTGTTTG
3505011 AAAAAATCATAAAAT
1 AAAAAATCA-AAAAT
*
3505026 AAAAAATTAAAAAT
1 AAAAAATCAAAAAT
* *
3505040 CAAGAAATTAAAAAT
1 -AAAAAATCAAAAAT
*
3505055 AAAATAATCAATAA-
1 AAAA-AATCAAAAAT
3505069 AAAAAATCAAAAAT
1 AAAAAATCAAAAAT
3505083 AAAAAA
1 AAAAAA
3505089 AATTCTTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
13 8 0.15
14 18 0.33
15 28 0.52
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.18
Consensus pattern (14 bp):
AAAAAATCAAAAAT
Found at i:3505037 original size:22 final size:21
Alignment explanation
Indices: 3505011--3505088 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
3505001 GATTTGTTTG
3505011 AAAAAATCATAAAATAAAAAAT
1 AAAAAATCA-AAAATAAAAAAT
* *
3505033 TAAAAATCAAGAAATTAAAAAT
1 AAAAAATCAA-AAATAAAAAAT
*
3505055 AAAATAATCAATAA-AAAAAAT
1 AAAA-AATCAAAAATAAAAAAT
* *
3505076 CAAAAATAAAAAA
1 AAAAAATCAAAAA
3505089 AATTCTTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.15
21 10 0.22
22 23 0.50
23 6 0.13
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.18
Consensus pattern (21 bp):
AAAAAATCAAAAATAAAAAAT
Found at i:3505080 original size:7 final size:7
Alignment explanation
Indices: 3505012--3505087 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
3505002 ATTTGTTTGA
3505012 AAAAATC
1 AAAAATC
*
3505019 ATAAAATA
1 A-AAAATC
*
3505027 AAAAATT
1 AAAAATC
3505034 AAAAATC
1 AAAAATC
*
3505041 AAGAAATT
1 AA-AAATC
*
3505049 AAAAATA
1 AAAAATC
3505056 AAATAATC
1 AAA-AATC
3505064 AATAAA--
1 AA-AAATC
3505070 AAAAATC
1 AAAAATC
3505077 AAAAAT-
1 AAAAATC
3505083 AAAAA
1 AAAAA
3505088 AAATTCTTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
5 3 0.05
6 7 0.12
7 27 0.47
8 19 0.33
9 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.01, T:0.18
Consensus pattern (7 bp):
AAAAATC
Found at i:3505160 original size:17 final size:17
Alignment explanation
Indices: 3505140--3505236 Score: 97
Period size: 17 Copynumber: 5.4 Consensus size: 17
3505130 TGATGAATGA
3505140 ATGAAAGTTGTGAAAGC
1 ATGAAAGTTGTGAAAGC
*
3505157 ATGAAA-TAAAGATGCAAAGC
1 ATGAAAGT--TG-TG-AAAGC
3505177 ATGAAAGTTGTGAAAGC
1 ATGAAAGTTGTGAAAGC
*
3505194 ATGAAATGATGATGCAAAGC
1 ATGAAA-GTTG-TG-AAAGC
*
3505214 ATGAAGGTTGTGAAAGC
1 ATGAAAGTTGTGAAAGC
3505231 ATGAAA
1 ATGAAA
3505237 TGATGATGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 27 0.41
18 8 0.12
19 8 0.12
20 21 0.32
21 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.21
Consensus pattern (17 bp):
ATGAAAGTTGTGAAAGC
Found at i:3505177 original size:20 final size:19
Alignment explanation
Indices: 3505152--3505253 Score: 99
Period size: 20 Copynumber: 5.4 Consensus size: 19
3505142 GAAAGTTGTG
*
3505152 AAAGCATGAAATAAAGATGC
1 AAAGCATGAAAT-ATGATGC
3505172 AAAGCATGAAAGT-TG-TG-
1 AAAGCATGAAA-TATGATGC
3505189 AAAGCATGAAATGATGATGC
1 AAAGCATGAAAT-ATGATGC
*
3505209 AAAGCATGAAGGT-TG-TG-
1 AAAGCATGAA-ATATGATGC
3505226 AAAGCATGAAATGATGATGC
1 AAAGCATGAAAT-ATGATGC
3505246 AAAGCATG
1 AAAGCATG
3505254 TAACGCGAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
16 2 0.03
17 21 0.30
18 8 0.12
19 7 0.10
20 29 0.42
21 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (19 bp):
AAAGCATGAAATATGATGC
Found at i:3505181 original size:37 final size:37
Alignment explanation
Indices: 3505140--3505253 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 37
3505130 TGATGAATGA
* *
3505140 ATGAAAGTTGTGAAAGCATGAAATAAAGATGCAAAGC
1 ATGAAAGTTGTGAAAGCATGAAATGATGATGCAAAGC
3505177 ATGAAAGTTGTGAAAGCATGAAATGATGATGCAAAGC
1 ATGAAAGTTGTGAAAGCATGAAATGATGATGCAAAGC
*
3505214 ATGAAGGTTGTGAAAGCATGAAATGATGATGCAAAGC
1 ATGAAAGTTGTGAAAGCATGAAATGATGATGCAAAGC
3505251 ATG
1 ATG
3505254 TAACGCGAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.44, C:0.08, G:0.27, T:0.21
Consensus pattern (37 bp):
ATGAAAGTTGTGAAAGCATGAAATGATGATGCAAAGC
Found at i:3516213 original size:13 final size:13
Alignment explanation
Indices: 3516195--3516223 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3516185 CAATTCTTCA
3516195 TGTATCGATACAT
1 TGTATCGATACAT
3516208 TGTATCGATACAT
1 TGTATCGATACAT
3516221 TGT
1 TGT
3516224 GCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3517286 original size:28 final size:28
Alignment explanation
Indices: 3517254--3517323 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
3517244 GTCGGTTAAG
3517254 ACGAGAGTGAAGTGCTCATCCATGCACT
1 ACGAGAGTGAAGTGCTCATCCATGCACT
* **
3517282 ACGAGAGTGAAGTGCTCATTCATGTGCT
1 ACGAGAGTGAAGTGCTCATCCATGCACT
* *
3517310 GCGAAAGTGAAGTG
1 ACGAGAGTGAAGTG
3517324 ATCAACTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.23
Consensus pattern (28 bp):
ACGAGAGTGAAGTGCTCATCCATGCACT
Found at i:3525049 original size:19 final size:20
Alignment explanation
Indices: 3525005--3525058 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
3524995 CTGCCAGTTT
* **
3525005 CATGTATCGATACATTTGTT
1 CATGTATCGATACATATGAA
3525025 CATGTATCGATACA-ATGAA
1 CATGTATCGATACATATGAA
*
3525044 CATGTATTGATACAT
1 CATGTATCGATACAT
3525059 TATATCGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
CATGTATCGATACATATGAA
Found at i:3525070 original size:32 final size:33
Alignment explanation
Indices: 3525029--3525091 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
3525019 TTTGTTCATG
*
3525029 TATCGATACAATG-A-ACATGTATTGATACATTA
1 TATCGATACAAAGCATA-ATGTATTGATACATTA
3525061 TATCGATACAAAGCATAATGTATTGATACAT
1 TATCGATACAAAGCATAATGTATTGATACAT
3525092 CTGAAAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.43
33 15 0.54
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (33 bp):
TATCGATACAAAGCATAATGTATTGATACATTA
Found at i:3529696 original size:42 final size:42
Alignment explanation
Indices: 3529646--3530426 Score: 421
Period size: 42 Copynumber: 18.6 Consensus size: 42
3529636 CCCTTCAGTC
** *
3529646 TGCCTGTCGGCTTTGACCCTAAAGACTACCTTATCTAAAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* * * * *
3529688 TGTCTGTCGGCTTTGACCCTGGAAACTTTCCTT-CCTTCAA-TT
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TGCCTTATC-TAAAGTT
** * ** ** *
3529730 TGCCTGTCAACTTTGACCCTAGAGACTTTCTTATCCTTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTAT-CTAAAGTT
* *
3529773 TGCCTGTCGGCTTTGACCTTGGAGACTGCCTTATCTCAAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* * ** * *
3529815 TGCCTGTTGGCTTTGAACCTGGAGACT-TTTCTACCCT-CAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCT-TA-TCTAAAGTT
** * * * *
3529857 TGTTTGTCCGCTTTGA-CCTTGAGATTGCCTCATCTAAAGTCT
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGT-T
* * * * ** *
3529899 T-CCTATCGACTTTGACCTTGGAGACTTTCC-TATCCTTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TGCCTTAT-CTAAAGTT
* ** * * *
3529941 TGCCTGTCGGCTTTGACCTTCAAGATTGCCTAATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* * **
3529983 TGCCTGTCGGCTTTGACCTTGGAGACTTTCC-TATCCTTCAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TGCCTTAT-CTAAAGTT
* *
3530026 TGCCTGTTGGCTTTGACCCTGAAGACTGCCTTATCTAAAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* * ** * * *
3530068 TGCCTGTCAGCTTTGACCTTGGAGACT-TTTCTACCCT-CAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCT-TA-TCTAAAGTT
* * ** * * *
3530110 TGCCTGTTGGCTTTGACCTTGGAGACT-TTTCTACCCT-TAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCT-TA-TCTAAAGTT
* * * * *
3530152 TGCCTGTTGGCTTTAACCTTGGAGACTACCTTATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* *** * *
3530194 TGCCTGTCAGCTTTGACCCTGGAGACTTTTTTACCCT-CAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTA-TCTAAAGTT
* * *
3530236 TGCCTGTCGGCTTTGACCCTAGAGACTGCCTAATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* * * * *
3530278 TGCCTGTCGACTTTGACCCTGAAGACTGTCTCATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* * * ** *
3530320 TG-C--T-GGCTTTGACCTTGGAGACTTTCCTT-CCTTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TGCCTTATCTAAAGTT
* * * * *
3530358 TGCTTGTCAGCTTTGACCCTGGAGACTGCCTCATTTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
* *
3530400 TGTCC-ATCGGCTTTGACCTTGGAGACT
1 TG-CCTGTCGGCTTTGACCCTGGAGACT
3530427 TTTTCACCCT
Statistics
Matches: 565, Mismatches: 143, Indels: 62
0.73 0.19 0.08
Matches are distributed among these distances:
38 23 0.04
39 4 0.01
40 2 0.00
41 38 0.07
42 389 0.69
43 109 0.19
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (42 bp):
TGCCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGTT
Done.