Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, whole genome shotgun sequence
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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 6 of 117
Found at i:1507505 original size:3 final size:3
Alignment explanation
Indices: 1507493--1507642 Score: 87
Period size: 3 Copynumber: 55.0 Consensus size: 3
1507483 AAAGAAAATT
1507493 ATA A-A ATA ATA AT- ATA ATA AT- ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
1507537 CT- ATA ATA ATA CTA ATA ATA A-G ATG CT- ATA AT- ATA AT- ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
1507580 AT- ATA GTA ATA ACA ATA ATA CTA AT- ATA AT- ATA AT- ATA AT- ATC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1507623 ATA AT- ATC ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA
1507643 CAATAACAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
2 27 0.24
3 87 0.76
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1507541 original size:8 final size:8
Alignment explanation
Indices: 1507493--1507642 Score: 104
Period size: 8 Copynumber: 17.4 Consensus size: 8
1507483 AAAGAAAATT
*
1507493 ATAAAATA
1 ATAATATA
1507501 ATAATATA
1 ATAATATA
1507509 ATAATATA
1 ATAATATA
1507517 ATAATAATA
1 ATAAT-ATA
1507526 ATAATATA
1 ATAATATA
*
1507534 ATACTATA
1 ATAATATA
1507542 ATAATACTA
1 ATAATA-TA
1507551 ATAATA-A
1 ATAATATA
**
1507558 GATGCTATAA
1 -ATAATAT-A
*
1507568 TATAATATG
1 -ATAATATA
1507577 ATAATATA
1 ATAATATA
* *
1507585 GTAATAACA
1 ATAAT-ATA
1507594 ATAATACTAA
1 ATAATA-T-A
1507604 TATAATATAA
1 -ATAATAT-A
*
1507614 TATAATATC
1 -ATAATATA
*
1507623 ATAATATC
1 ATAATATA
1507631 ATAATATTA
1 ATAATA-TA
1507640 ATA
1 ATA
1507643 CAATAACAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 19
0.77 0.11 0.13
Matches are distributed among these distances:
7 1 0.01
8 65 0.56
9 26 0.22
10 18 0.16
11 6 0.05
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (8 bp):
ATAATATA
Found at i:1507581 original size:46 final size:44
Alignment explanation
Indices: 1507492--1507636 Score: 125
Period size: 46 Copynumber: 3.2 Consensus size: 44
1507482 GAAAGAAAAT
* * *
1507492 TATAAAATAATAAT-ATAATAATAT-A-ATAATAATAATAATATAA
1 TATATAATAACAATAATAATAAGATAATATAAT-ATAAT-ATATAA
* * **
1507535 TACTATAATAATACTAATAATAAGATGCTATAATATAATATGATAA
1 TA-TATAATAACAATAATAATAAGATAATATAATATAATAT-ATAA
* *
1507581 TATAGTAATAACAATAATACTAATATAATATAATATAATATCATAA
1 TATA-TAATAACAATAATAATAAGATAATATAATATAATAT-ATAA
1507627 TATCATAATA
1 TAT-ATAATA
1507637 TTAATACAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
43 2 0.02
44 10 0.12
45 13 0.15
46 53 0.63
47 6 0.07
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (44 bp):
TATATAATAACAATAATAATAAGATAATATAATATAATATATAA
Found at i:1513629 original size:15 final size:15
Alignment explanation
Indices: 1513609--1513639 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1513599 ATTTAAGCCT
1513609 TGATCATATTTGTAA
1 TGATCATATTTGTAA
*
1513624 TGATCATGTTTGTAA
1 TGATCATATTTGTAA
1513639 T
1 T
1513640 TTATCAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.48
Consensus pattern (15 bp):
TGATCATATTTGTAA
Found at i:1514206 original size:44 final size:44
Alignment explanation
Indices: 1514158--1514246 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
1514148 AATTACTCAG
1514158 TAAAAATA-AATAATAAA-AACAAGCAAAATA-AAATAAAAAAAACT
1 TAAAAATATAA-AATAAATAA-AAGCAAAATAGAAA-AAAAAAAACT
**
1514202 TAAAAATATAAAATAAATAAAATTAAAATAGAAAAAAAAAAACT
1 TAAAAATATAAAATAAATAAAAGCAAAATAGAAAAAAAAAAACT
1514246 T
1 T
1514247 GCGATCAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
44 33 0.82
45 7 0.17
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (44 bp):
TAAAAATATAAAATAAATAAAAGCAAAATAGAAAAAAAAAAACT
Found at i:1514212 original size:24 final size:22
Alignment explanation
Indices: 1514185--1514243 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
1514175 AACAAGCAAA
1514185 ATAAAATAAAAAAAACTTAAAAAT
1 ATAAAATAAAAAAAA-TT-AAAAT
*
1514209 ATAAAATAAATAAAATTAAAAT
1 ATAAAATAAAAAAAATTAAAAT
*
1514231 AGAAAA-AAAAAAA
1 ATAAAATAAAAAAA
1514244 CTTGCGATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 10 0.31
23 2 0.06
24 14 0.44
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
ATAAAATAAAAAAAATTAAAAT
Found at i:1515046 original size:5 final size:5
Alignment explanation
Indices: 1515019--1515151 Score: 54
Period size: 5 Copynumber: 24.8 Consensus size: 5
1515009 AGAAAGGAAA
* * * * **
1515019 AATAT AAAAT AAAAT AATAT AATAT AATACT -A-CT AATAAT AAGAT GCTAT
1 AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AAT-AT AATAT AATAT
* *
1515069 AATAT AATAGGAT AATAT AGTAAT AACAAT AATACT AATAT AATAT AATAT
1 AATAT AAT---AT AATAT AAT-AT AA-TAT AATA-T AATAT AATAT AATAT
* * *
1515120 AAAAT GATAAT ATTAT AATATT AATATT AATA
1 AATAT AAT-AT AATAT AATA-T AATA-T AATA
1515152 ACAAAATAAT
Statistics
Matches: 96, Mismatches: 20, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
3 1 0.01
4 1 0.01
5 59 0.61
6 30 0.31
8 5 0.05
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:1515058 original size:3 final size:3
Alignment explanation
Indices: 1515022--1515174 Score: 55
Period size: 3 Copynumber: 55.0 Consensus size: 3
1515012 AAGGAAAAAT
* * * *
1515022 ATA A-A ATA A-A ATA AT- ATA AT- ATA ATA CTA CTA ATA ATA A-G ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
1515065 CT- ATA AT- ATA ATA GGATA AT- ATA GTA ATA ACA ATA ATA CTA AT-
1 ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
1515108 ATA AT- ATA AT- ATA A-A ATG ATA AT- ATT ATA ATA TTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
1515152 ACA A-A ATA ATA ACA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
1515175 GACTTGATTG
Statistics
Matches: 111, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
2 26 0.23
3 82 0.74
5 3 0.03
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1515786 original size:27 final size:26
Alignment explanation
Indices: 1515724--1515801 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
1515714 TTAGTTTGAG
* **
1515724 AAAATTTTTTTATTTTTATTTTTAAA
1 AAAATATTTTTATTTTTATTTTTTTA
*
1515750 AAAATATTTTTATTTTTATTTTTTTT
1 AAAATATTTTTATTTTTATTTTTTTA
* *
1515776 TAAATGGTTTTT-TTTTCTATTTTTTT
1 AAAAT-ATTTTTATTTT-TATTTTTTT
1515802 GTTTTTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 30 0.68
27 14 0.32
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.71
Consensus pattern (26 bp):
AAAATATTTTTATTTTTATTTTTTTA
Found at i:1532750 original size:80 final size:80
Alignment explanation
Indices: 1532617--1532776 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
1532607 CCCATTGGTT
*
1532617 GGGATTGTTCTTTTCCGATGTTCAATTTCAAGGATGTTCTAATTCACTTGTATAATGGAACATGG
1 GGGATTGTTCTTTTCCGATGTTCAATTTCAAGGATGATCTAATTCACTTGTATAATGGAACATGG
1532682 AGGTGAATTGTATCA
66 AGGTGAATTGTATCA
*
1532697 GGGATTGTTCTTTTCCGATGTTCAGTTTCAAGGATGATCTAATTCACTTGTATAATGGAACATGG
1 GGGATTGTTCTTTTCCGATGTTCAATTTCAAGGATGATCTAATTCACTTGTATAATGGAACATGG
*
1532762 ATGTGAATTGTATCA
66 AGGTGAATTGTATCA
1532777 AGGGTTACTG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (80 bp):
GGGATTGTTCTTTTCCGATGTTCAATTTCAAGGATGATCTAATTCACTTGTATAATGGAACATGG
AGGTGAATTGTATCA
Found at i:1535578 original size:24 final size:23
Alignment explanation
Indices: 1535540--1535600 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
1535530 TTACGTTCAT
1535540 TTACATGGTGCTTTTTCAGTTAAA
1 TTAC-TGGTGCTTTTTCAGTTAAA
1535564 TTACTGGTGCTTTTTCAGTTAAA
1 TTACTGGTGCTTTTTCAGTTAAA
* *
1535587 TTTCTAGTGCTTTT
1 TTACTGGTGCTTTT
1535601 GAGTTGATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 31 0.89
24 4 0.11
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (23 bp):
TTACTGGTGCTTTTTCAGTTAAA
Found at i:1550005 original size:31 final size:30
Alignment explanation
Indices: 1549946--1550005 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1549936 TATATTTTAA
* *
1549946 AATTTACTTATTAATGAAGTGATTTCATTT
1 AATTTACTTATTAATGAAGTAATATCATTT
1549976 AATTTATCTTATTAAT-AAGATAATATCATT
1 AATTTA-CTTATTAATGAAG-TAATATCATT
1550006 CGATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (30 bp):
AATTTACTTATTAATGAAGTAATATCATTT
Found at i:1555711 original size:18 final size:17
Alignment explanation
Indices: 1555679--1555725 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1555669 ATAATAAATA
*
1555679 TTCTTTTTCATTTTATT
1 TTCTTTTTCATTTTAAT
*
1555696 TTCTTTGTTTATTTTAAT
1 TTCTTT-TTCATTTTAAT
1555714 TTCGTTTTTCAT
1 TTC-TTTTTCAT
1555726 GCACTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (17 bp):
TTCTTTTTCATTTTAAT
Found at i:1560051 original size:45 final size:44
Alignment explanation
Indices: 1560002--1560095 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
1559992 AATTTGTAAA
* * *
1560002 TTTTTCATCATTTGAGCCTATTT-AGAATTTTTTTTATTTCTAATT
1 TTTTTCACCATTTGAGCCTATTTAAAAATTATTTTTATTTCT--TT
**
1560047 TTTTTCACCATTTGAGTGTATTTAAAAATTATTTTTATTTCTTT
1 TTTTTCACCATTTGAGCCTATTTAAAAATTATTTTTATTTCTTT
1560091 TTTTT
1 TTTTT
1560096 AAAAGAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 7 0.16
45 20 0.47
46 16 0.37
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.62
Consensus pattern (44 bp):
TTTTTCACCATTTGAGCCTATTTAAAAATTATTTTTATTTCTTT
Found at i:1560214 original size:26 final size:24
Alignment explanation
Indices: 1560185--1560236 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
1560175 TTTCACATAA
1560185 AAATTTATTAGAAAATCT-ATCATGTG
1 AAATTT-TT-GAAAATCTCATCA-GTG
*
1560211 AAATTTTTGAGAATCTCATCAGTG
1 AAATTTTTGAAAATCTCATCAGTG
1560235 AA
1 AA
1560237 TAATTGTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 12 0.50
25 6 0.25
26 6 0.25
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (24 bp):
AAATTTTTGAAAATCTCATCAGTG
Found at i:1560404 original size:25 final size:27
Alignment explanation
Indices: 1560358--1560413 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
1560348 TCACCTAGAG
* *
1560358 ATTTCTTAAGAATTTTACCATTTGA-A
1 ATTTCTTAAGAATTTCACCATTGGATA
*
1560384 ATTTC-TAAGAATTTCATCATTGGATA
1 ATTTCTTAAGAATTTCACCATTGGATA
1560410 ATTT
1 ATTT
1560414 GTATTTACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (27 bp):
ATTTCTTAAGAATTTCACCATTGGATA
Found at i:1560590 original size:26 final size:25
Alignment explanation
Indices: 1560534--1560590 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1560524 TTTTTACCTA
*
1560534 GAAATTTTATAGAAATTTACTATTT
1 GAAATTTTATAGAAATTTACTATTG
* *
1560559 GAAATTTT-TATAAATTTCATTATTG
1 GAAATTTTATAGAAATTT-ACTATTG
1560584 GATAATT
1 GA-AATT
1560591 AATATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.30
25 15 0.56
26 4 0.15
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (25 bp):
GAAATTTTATAGAAATTTACTATTG
Found at i:1560713 original size:27 final size:27
Alignment explanation
Indices: 1560683--1560740 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1560673 TAAACACATA
*
1560683 AAAAAATAAAAAAAAAACCAAAAACAC
1 AAAAAATAAAAAAAAAACCAAAAAAAC
** * *
1560710 AAAAAATACTAAAAATACTAAAAAAAC
1 AAAAAATAAAAAAAAAACCAAAAAAAC
1560737 AAAA
1 AAAA
1560741 CGGCTCGGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (27 bp):
AAAAAATAAAAAAAAAACCAAAAAAAC
Found at i:1561426 original size:9 final size:8
Alignment explanation
Indices: 1561412--1561450 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
1561402 ATTCAACCAC
1561412 TTTTTTTCA
1 TTTTTTT-A
1561421 TTTTTTTA
1 TTTTTTTA
1561429 TTTTTATTA
1 TTTTT-TTA
1561438 -TTTTTTA
1 TTTTTTTA
1561445 TTTTTT
1 TTTTTT
1561451 AATTACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.11
8 15 0.54
9 10 0.36
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1561990 original size:15 final size:16
Alignment explanation
Indices: 1561954--1561990 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1561944 AAGGTTAATA
1561954 AATGGGTTATGATTTG
1 AATGGGTTATGATTTG
1561970 AATGGGTT-TGGATTT-
1 AATGGGTTAT-GATTTG
1561985 AATGGG
1 AATGGG
1561991 CTTTAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (16 bp):
AATGGGTTATGATTTG
Found at i:1566278 original size:21 final size:24
Alignment explanation
Indices: 1566238--1566284 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
1566228 ACTTTAAATT
*
1566238 TAAAATTTTTATATATTATTTTAA
1 TAAAATTTTTATATATTATTTAAA
1566262 TAAAA-TTTTA-ATA-TATTTAAA
1 TAAAATTTTTATATATTATTTAAA
1566283 TA
1 TA
1566285 GATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 3 0.14
23 5 0.23
24 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAAATTTTTATATATTATTTAAA
Found at i:1569178 original size:2 final size:2
Alignment explanation
Indices: 1569171--1569198 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1569161 ATCTAATCTC
1569171 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
1569199 CATTTCTTAG
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):
AT
Found at i:1576735 original size:115 final size:115
Alignment explanation
Indices: 1576529--1576756 Score: 420
Period size: 115 Copynumber: 2.0 Consensus size: 115
1576519 AGCATAAACA
*
1576529 GTTATATGTTTCATCAATCTTGCTAAAAATAGATTATCTAATTGAAGATGACACATGGTACAAAG
1 GTTATATGTTTCATCAATCTTGCCAAAAATAGATTATCTAATTGAAGATGACACATGGTACAAAG
*
1576594 CAACATGTAAAAGGTTAAATTTCTACCTGATTATGTAACACTCTTAATTC
66 CAACATGTAAAAGGTTAAATTGCTACCTGATTATGTAACACTCTTAATTC
* *
1576644 GTTATATGTTTCATCAATCTTGCCAACAATAGATTATCTAATTGAAGATGACACATGGTACACAG
1 GTTATATGTTTCATCAATCTTGCCAAAAATAGATTATCTAATTGAAGATGACACATGGTACAAAG
1576709 CAACATGTAAAAGGTTAAATTGCTACCTGATTATGTAACACTCTTAAT
66 CAACATGTAAAAGGTTAAATTGCTACCTGATTATGTAACACTCTTAAT
1576757 CCTAAACAGA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 109 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (115 bp):
GTTATATGTTTCATCAATCTTGCCAAAAATAGATTATCTAATTGAAGATGACACATGGTACAAAG
CAACATGTAAAAGGTTAAATTGCTACCTGATTATGTAACACTCTTAATTC
Found at i:1584102 original size:29 final size:28
Alignment explanation
Indices: 1584022--1584104 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
1584012 CGTTTGTTGT
*
1584022 TTAAAAAGATTTTAAATAATTTTT-TAT-
1 TTAAAAATATTTTAAATAATTTTTAT-TG
* * * *
1584049 TTAAAAATTTTGTTTAAGACGTTTTTATTG
1 TTAAAAATATT-TTAAATA-ATTTTTATTG
1584079 TCTAAAAATATTTTAAATAATTTTTA
1 T-TAAAAATATTTTAAATAATTTTTA
1584105 AAAAACTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
27 9 0.21
28 5 0.12
29 12 0.29
30 7 0.17
31 9 0.21
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (28 bp):
TTAAAAATATTTTAAATAATTTTTATTG
Found at i:1584484 original size:27 final size:26
Alignment explanation
Indices: 1584427--1584485 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1584417 TAACCTAATT
*
1584427 TAATTTTTTATAAAAAATTATTCAAA
1 TAATTTTTAATAAAAAATTATTCAAA
* *
1584453 AAATTTTCTAATAAAAAATGTCTT-AAA
1 TAATTTT-TAATAAAAAAT-TATTCAAA
1584480 TAATTT
1 TAATTT
1584486 CAAAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 6 0.22
27 18 0.67
28 3 0.11
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTTTTAATAAAAAATTATTCAAA
Found at i:1584619 original size:62 final size:62
Alignment explanation
Indices: 1584482--1584612 Score: 151
Period size: 62 Copynumber: 2.1 Consensus size: 62
1584472 GTCTTAAATA
* * *
1584482 ATTTCAAAAAATGA-AAGGAAATTTTTAAAGATATTTTTGACAAAAAATATATTGAATAATTT
1 ATTTAAAAAAATTAGAA-GAAATTTTTAAAGATATTTTTGAAAAAAAATATATTGAATAATTT
* * *
1584544 CTTTAAAAAAATTAGAAGAAATTATTT-AAGATGTTTTTGATAAAAAAAT-TTTTGAATAACTTT
1 ATTTAAAAAAATTAGAAGAAATT-TTTAAAGATATTTTTGA-AAAAAAATATATTGAATAA-TTT
1584607 ATTTAA
1 ATTTAA
1584613 TTAATTAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
62 38 0.66
63 20 0.34
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (62 bp):
ATTTAAAAAAATTAGAAGAAATTTTTAAAGATATTTTTGAAAAAAAATATATTGAATAATTT
Found at i:1584920 original size:26 final size:27
Alignment explanation
Indices: 1584884--1584940 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
1584874 CCGGGTAGTG
1584884 CAATGACATAATTGCCCCTAC-TTGTA
1 CAATGACATAATTGCCCCTACATTGTA
*
1584910 CAATGACATAATTGCCCCTACATTTTA
1 CAATGACATAATTGCCCCTACATTGTA
1584937 CAAT
1 CAAT
1584941 TGTGCGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (27 bp):
CAATGACATAATTGCCCCTACATTGTA
Found at i:1585030 original size:2 final size:2
Alignment explanation
Indices: 1585014--1585059 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1585004 TTCCTTCCTT
*
1585014 TC TC T- TC TG TC TC TC TC TC TC TC TC TC TC -C 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
1585054 TC TC TC
1 TC TC TC
1585060 CTTTCTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1585046 original size:17 final size:17
Alignment explanation
Indices: 1585009--1585061 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
1584999 CTCAGTTCCT
* *
1585009 TCCTTTCTCT-TCTGTC
1 TCCTCTCTCTCTCTCTC
1585025 T-CTCTCTCTCTCTCTC
1 TCCTCTCTCTCTCTCTC
1585041 TCCTCTCTCTCTCTCTC
1 TCCTCTCTCTCTCTCTC
1585058 TCCT
1 TCCT
1585062 TTCTATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 7 0.21
16 7 0.21
17 19 0.58
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (17 bp):
TCCTCTCTCTCTCTCTC
Found at i:1587115 original size:2 final size:2
Alignment explanation
Indices: 1587108--1587136 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1587098 GGTATTGTAA
1587108 AT 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 AT A
1587137 AAATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1591743 original size:13 final size:13
Alignment explanation
Indices: 1591725--1591764 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
1591715 ACGGCATAGA
1591725 TTTTTTTTTTCTTT
1 TTTTTTTTTTC-TT
1591739 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
*
1591752 TCTTTTTTTTCTT
1 TTTTTTTTTTCTT
1591765 AGAAACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:1591744 original size:14 final size:15
Alignment explanation
Indices: 1591725--1591761 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
1591715 ACGGCATAGA
1591725 TTTTTTTTTTCTTT-
1 TTTTTTTTTTCTTTC
1591739 TTTTTTTTTTCTTTC
1 TTTTTTTTTTCTTTC
1591754 TTTTTTTT
1 TTTTTTTT
1591762 CTTAGAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (15 bp):
TTTTTTTTTTCTTTC
Found at i:1591748 original size:18 final size:18
Alignment explanation
Indices: 1591725--1591761 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1591715 ACGGCATAGA
1591725 TTTTTTT-TTTCTTTTTT
1 TTTTTTTCTTTCTTTTTT
1591742 TTTTTTTCTTTCTTTTTT
1 TTTTTTTCTTTCTTTTTT
1591760 TT
1 TT
1591762 CTTAGAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (18 bp):
TTTTTTTCTTTCTTTTTT
Found at i:1592753 original size:18 final size:19
Alignment explanation
Indices: 1592730--1592797 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 19
1592720 AACAATTTAT
1592730 ATATTA-ATATTATATAAA
1 ATATTATATATTATATAAA
*
1592748 ATATTA-ATAATTGATATATTA
1 ATATTATAT-ATT-ATATA-AA
* *
1592769 ATATCATATTTTATATAAA
1 ATATTATATATTATATAAA
1592788 A-ATTATATAT
1 ATATTATATAT
1592798 CATAATTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 15 0.38
19 5 0.12
20 10 0.25
21 8 0.20
22 2 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (19 bp):
ATATTATATATTATATAAA
Found at i:1592797 original size:20 final size:20
Alignment explanation
Indices: 1592739--1592797 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
1592729 TATATTAATA
*
1592739 TTATATAAAATATTA-ATAAT
1 TTATATAAAA-ATTATATATT
* **
1592759 TGATATATTAA-TATCATATT
1 TTATATAAAAATTAT-ATATT
1592779 TTATATAAAAATTATATAT
1 TTATATAAAAATTATATAT
1592798 CATAATTCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.07
19 1 0.03
20 23 0.79
21 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TTATATAAAAATTATATATT
Found at i:1593400 original size:17 final size:17
Alignment explanation
Indices: 1593367--1593400 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1593357 AAATATGAAA
**
1593367 TATATTTTTAATTTTAT
1 TATATTTTTAAAATTAT
1593384 TATATTTTTAAAATTAT
1 TATATTTTTAAAATTAT
1593401 AAATTTCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTTTAAAATTAT
Found at i:1598226 original size:30 final size:30
Alignment explanation
Indices: 1598174--1598231 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1598164 AGATTTTAAT
*
1598174 TTGTATCAAAATAAACACTTAACTTAAAAC
1 TTGTATCAAAATAAACACTTAACATAAAAC
* **
1598204 TTGTATCAAAATAAGCTTTTAACATAAA
1 TTGTATCAAAATAAACACTTAACATAAA
1598232 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (30 bp):
TTGTATCAAAATAAACACTTAACATAAAAC
Found at i:1599521 original size:24 final size:25
Alignment explanation
Indices: 1599501--1599556 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
1599491 TTTTTATTAA
*
1599501 AATTTTTTT-AATTATAATTATAAT
1 AATTTTTTTAAATCATAATTATAAT
1599525 AATTTTTTTAAATCATAATTATAAT
1 AATTTTTTTAAATCATAATTATAAT
1599550 AATTTTT
1 AATTTTT
1599557 ATTATTACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTTTTTAAATCATAATTATAAT
Found at i:1600531 original size:2 final size:2
Alignment explanation
Indices: 1600524--1600548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1600514 TTTTATCTTC
1600524 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 A
1600549 ACTGAATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1601883 original size:14 final size:14
Alignment explanation
Indices: 1601853--1601900 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1601843 TTACTACTTA
* *
1601853 TATACATATACAAG
1 TATACATATATATG
1601867 TATACATATATATG
1 TATACATATATATG
* * *
1601881 TATATATGTATATA
1 TATACATATATATG
1601895 TATACA
1 TATACA
1601901 CACACACACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (14 bp):
TATACATATATATG
Found at i:1612706 original size:17 final size:17
Alignment explanation
Indices: 1612684--1612733 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1612674 ACTTTCATAC
1612684 CATTTCATTCTATGCAT
1 CATTTCATTCTATGCAT
1612701 CATTTC---C-AT--AT
1 CATTTCATTCTATGCAT
1612712 CATTTCATTCTATGCAT
1 CATTTCATTCTATGCAT
1612729 CATTT
1 CATTT
1612734 TCATGCTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
11 8 0.30
13 2 0.07
14 2 0.07
15 2 0.07
17 13 0.48
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (17 bp):
CATTTCATTCTATGCAT
Found at i:1612710 original size:28 final size:27
Alignment explanation
Indices: 1612668--1612733 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 27
1612658 TATATGCATC
1612668 TGCATCACTTTCATACCATTTCATTCTA
1 TGCATCA-TTTCATACCATTTCATTCTA
*
1612696 TGCATCATTTCCATATCATTTCATTCTA
1 TGCATCATTT-CATACCATTTCATTCTA
1612724 TGCATCATTT
1 TGCATCATTT
1612734 TCATGCTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 3 0.08
28 33 0.92
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (27 bp):
TGCATCATTTCATACCATTTCATTCTA
Found at i:1615145 original size:13 final size:13
Alignment explanation
Indices: 1615127--1615154 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1615117 GAGAAATGAA
1615127 TGCCACAGATAAG
1 TGCCACAGATAAG
1615140 TGCCACAGATAAG
1 TGCCACAGATAAG
1615153 TG
1 TG
1615155 GGGCAAAGCA
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:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (13 bp):
TGCCACAGATAAG
Found at i:1615517 original size:19 final size:19
Alignment explanation
Indices: 1615493--1615552 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1615483 GTGAAGAGAA
1615493 AAAAAAAGAAAAAAATGAG
1 AAAAAAAGAAAAAAATGAG
*
1615512 AAAAAAATG-AAAGAATGA-
1 AAAAAAA-GAAAAAAATGAG
* *
1615530 AAAAAGATGAAAATAA-GAG
1 AAAAA-AAGAAAAAAATGAG
1615549 AAAA
1 AAAA
1615553 GAAATACTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 8 0.24
19 25 0.74
20 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (19 bp):
AAAAAAAGAAAAAAATGAG
Found at i:1615519 original size:11 final size:11
Alignment explanation
Indices: 1615488--1615521 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1615478 AATGGGTGAA
1615488 GAGAAAAAAA-
1 GAGAAAAAAAT
*
1615498 AAGAAAAAAAT
1 GAGAAAAAAAT
1615509 GAGAAAAAAAT
1 GAGAAAAAAAT
1615520 GA
1 GA
1615522 AAGAATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (11 bp):
GAGAAAAAAAT
Found at i:1616879 original size:46 final size:46
Alignment explanation
Indices: 1616807--1616919 Score: 163
Period size: 46 Copynumber: 2.5 Consensus size: 46
1616797 AAGTTTTGAG
* * *
1616807 TTTCAAATGAGAATATTTGAGTCTTAAAAAAGAATCATTAAGACAT
1 TTTCAAATGAGAATCTTTGAGCCTTAAAAAAGAATCATTAAAACAT
* *
1616853 TTTCAAATGAGAATCTTTGAGCCTTAAATAAGAATCTTTAAAACAT
1 TTTCAAATGAGAATCTTTGAGCCTTAAAAAAGAATCATTAAAACAT
* *
1616899 TTTCAAATAAGAAGCTTTGAG
1 TTTCAAATGAGAATCTTTGAG
1616920 TTTCAAATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (46 bp):
TTTCAAATGAGAATCTTTGAGCCTTAAAAAAGAATCATTAAAACAT
Found at i:1616925 original size:21 final size:21
Alignment explanation
Indices: 1616899--1616941 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1616889 TTTAAAACAT
1616899 TTTCAAATAAGAAGCTTTGAG
1 TTTCAAATAAGAAGCTTTGAG
* *
1616920 TTTCAAATGAGAATCTTTGAG
1 TTTCAAATAAGAAGCTTTGAG
1616941 T
1 T
1616942 ATCTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (21 bp):
TTTCAAATAAGAAGCTTTGAG
Found at i:1616933 original size:46 final size:46
Alignment explanation
Indices: 1616807--1616937 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 46
1616797 AAGTTTTGAG
* ** * * * *
1616807 TTTCAAATGAGAATATTTGAGTCTTAAAAAAGAATCATTAAGACAT
1 TTTCAAATAAGAAGCTTTGAGCCTTAAATAAGAATCTTTAAAACAT
* *
1616853 TTTCAAATGAGAATCTTTGAGCCTTAAATAAGAATCTTTAAAACAT
1 TTTCAAATAAGAAGCTTTGAGCCTTAAATAAGAATCTTTAAAACAT
* *
1616899 TTTCAAATAAGAAGCTTTGAG-TTTCAAATGAGAATCTTT
1 TTTCAAATAAGAAGCTTTGAGCCTT-AAATAAGAATCTTT
1616938 GAGTATCTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
45 2 0.03
46 73 0.97
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (46 bp):
TTTCAAATAAGAAGCTTTGAGCCTTAAATAAGAATCTTTAAAACAT
Found at i:1616955 original size:31 final size:31
Alignment explanation
Indices: 1616913--1616971 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1616903 AAATAAGAAG
* *
1616913 CTTTGAGTTTCAAATGAGAATCTTTGAGTAT
1 CTTTGAATTTCAAATAAGAATCTTTGAGTAT
1616944 CTTTGAATTTCAAATAAGAATCTTTGAG
1 CTTTGAATTTCAAATAAGAATCTTTGAG
1616972 GTGTGACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (31 bp):
CTTTGAATTTCAAATAAGAATCTTTGAGTAT
Found at i:1617035 original size:30 final size:30
Alignment explanation
Indices: 1617001--1617059 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1616991 TCGAATACGA
**
1617001 ATCTTCAAACTCAAATGAAAATCTTTGAAG
1 ATCTTCAAACTCAAAAAAAAATCTTTGAAG
1617031 ATCTTCAAACTCAAAAAAAAATCTTTGAA
1 ATCTTCAAACTCAAAAAAAAATCTTTGAA
1617060 TAAGAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (30 bp):
ATCTTCAAACTCAAAAAAAAATCTTTGAAG
Found at i:1617160 original size:31 final size:31
Alignment explanation
Indices: 1617117--1617183 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1617107 CGAATTCAAA
*
1617117 TGAGAATCTTTAAAACTCAAATAAGAATCTT
1 TGAGGATCTTTAAAACTCAAATAAGAATCTT
* * *
1617148 TGAGGATCTTTAAATCTTAAATGAGAATCTT
1 TGAGGATCTTTAAAACTCAAATAAGAATCTT
1617179 TGAGG
1 TGAGG
1617184 TGTGAAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
TGAGGATCTTTAAAACTCAAATAAGAATCTT
Found at i:1617233 original size:58 final size:58
Alignment explanation
Indices: 1617153--1617303 Score: 185
Period size: 66 Copynumber: 2.4 Consensus size: 58
1617143 ATCTTTGAGG
*
1617153 ATCTTTAAATCTTAAATGAGAATCTTTGAGGTGTGAAACTTAAAATTTATCGAATGTGA
1 ATCTTCAAA-CTTAAATGAGAATCTTTGAGGTGTGAAACTTAAAATTTATCGAATGTGA
*
1617212 CTCTTCAAACTTAAATGAGAATCTTTGAATCTCTGAGGTGTGAAACTTAAAATTTATCGAATGTG
1 ATCTTCAAACTTAAATGAGAATC------T-T-TGAGGTGTGAAACTTAAAATTTATCGAATGTG
1617277 A
58 A
* *
1617278 ATCTTCGAACTTAAATAAGAATCTTT
1 ATCTTCAAACTTAAATGAGAATCTTT
1617304 AAAAATTTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
58 15 0.19
59 8 0.10
60 1 0.01
64 1 0.01
65 1 0.01
66 53 0.67
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (58 bp):
ATCTTCAAACTTAAATGAGAATCTTTGAGGTGTGAAACTTAAAATTTATCGAATGTGA
Found at i:1617249 original size:66 final size:66
Alignment explanation
Indices: 1617172--1617303 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
1617162 TCTTAAATGA
* * *
1617172 GAATCTTTGAGGTGTGAAACTTAAAATTTATCGAATGTGACTCTTCAAACTTAAATGAGAATCTT
1 GAATCTCTGAGGTGTGAAACTTAAAATTTATCGAATGTGAATCTTCAAACTTAAATAAGAATCTT
1617237 T
66 T
*
1617238 GAATCTCTGAGGTGTGAAACTTAAAATTTATCGAATGTGAATCTTCGAACTTAAATAAGAATCTT
1 GAATCTCTGAGGTGTGAAACTTAAAATTTATCGAATGTGAATCTTCAAACTTAAATAAGAATCTT
1617303 T
66 T
1617304 AAAAATTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (66 bp):
GAATCTCTGAGGTGTGAAACTTAAAATTTATCGAATGTGAATCTTCAAACTTAAATAAGAATCTT
T
Found at i:1617320 original size:277 final size:277
Alignment explanation
Indices: 1616961--1617580 Score: 911
Period size: 277 Copynumber: 2.2 Consensus size: 277
1616951 TTTCAAATAA
* *
1616961 GAATCTTTGAGGTGTGACACCTAAAATTTATCGAATACGAATCTTCAAACTCAAATGAA-AATCT
1 GAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATATGAATCTTCAAACTCAAAT-AAGAATCT
* * * *
1617025 TTGAAGATCTTCAAACTCAAAAAAAAATCTTTGAATAAGAATCTTTAAGGTGTGAAACCCAAATT
65 TTAAAAATCTTCAAACTCAAAAAAAAATCTTTAAATAAGAATCTTTAAGATGTGAAACCCAAATT
*
1617090 TATCAAATGTCAATCTTCGAATTCAAATGAGAATCTTTAAAACTCAAATAAGAATCTTTGAGGAT
130 TATCAAATGTCAATCTTCGAATTCAAATGAGAATCTTTAAAACTCAAATAAGAATCTTTAAGGAT
* * * * * *
1617155 CTTTAAATCTTAAATGAGAATCTTTGAGGTGTGAAACTTAAAATTTATCGAATGTGACTCTTCAA
195 CTTTAAATCTCAAATGAGAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATATTCAA
1617220 ACTTAAATGAGAATCTTT
260 ACTTAAATGAGAATCTTT
* * * * *
1617238 GAATCTCTGAGGTGTGAAACTTAAAATTTATCGAATGTGAATCTTCGAACTTAAATAAGAATCTT
1 GAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATATGAATCTTCAAACTCAAATAAGAATCTT
* * * * *
1617303 TAAAAATTTTTAAACTCAAAAGAAAATCTTTAAATGAGAATCTTTAAGATGTGAAACCTAAATTT
66 TAAAAATCTTCAAACTCAAAAAAAAATCTTTAAATAAGAATCTTTAAGATGTGAAACCCAAATTT
* * * *
1617368 ATCGAATGTGAATCTTCGAATTCAAATGAGAATCTTTGAAACTCAAATGAGAATCTTTAAGGATC
131 ATCAAATGTCAATCTTCGAATTCAAATGAGAATCTTTAAAACTCAAATAAGAATCTTTAAGGATC
**
1617433 TTTAAATCTCAAATGAGAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATATTTGAA
196 TTTAAATCTCAAATGAGAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATATTCAAA
1617498 CTTAAATGAGAATCTTT
261 CTTAAATGAGAATCTTT
* * * *
1617515 GAATCTTTGAGGTGTGAAACCAAAAATTTAT-TATATATGAATCTTTAAACTCAAATGAGAATCT
1 GAATCTTTGAGGTGTGAAACCTAAAATTTATCGA-ATATGAATCTTCAAACTCAAATAAGAATCT
1617579 TT
65 TT
1617581 GAATGAGAAT
Statistics
Matches: 303, Mismatches: 38, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
276 3 0.01
277 300 0.99
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (277 bp):
GAATCTTTGAGGTGTGAAACCTAAAATTTATCGAATATGAATCTTCAAACTCAAATAAGAATCTT
TAAAAATCTTCAAACTCAAAAAAAAATCTTTAAATAAGAATCTTTAAGATGTGAAACCCAAATTT
ATCAAATGTCAATCTTCGAATTCAAATGAGAATCTTTAAAACTCAAATAAGAATCTTTAAGGATC
TTTAAATCTCAAATGAGAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATATTCAAA
CTTAAATGAGAATCTTT
Found at i:1617415 original size:21 final size:20
Alignment explanation
Indices: 1617372--1617425 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
1617362 AAATTTATCG
* * *
1617372 AATGTGAATCTTCGAATTCA
1 AATGAGAATCTTTGAACTCA
1617392 AATGAGAATCTTTGAAACTCA
1 AATGAGAATCTTTG-AACTCA
1617413 AATGAGAATCTTT
1 AATGAGAATCTTT
1617426 AAGGATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGAGAATCTTTGAACTCA
Found at i:1617523 original size:66 final size:66
Alignment explanation
Indices: 1617449--1617656 Score: 247
Period size: 66 Copynumber: 3.1 Consensus size: 66
1617439 TCTCAAATGA
* *
1617449 GAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATATTTGAACTTAAATGAGAATCTT
1 GAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATCTTTGAACTCAAATGAGAATCTT
1617514 T
66 T
* * * * * *
1617515 GAATCTTTGAGGTGTGAAACCAAAAATTTATTATATATGAATCTTTAAACTCAAATGAGAATCTT
1 GAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATCTTTGAACTCAAATGAGAATC-T
1617580 TGAAT
65 T---T
* * *
1617585 GAGAATCTTT-AAGGTATGAAACCTAAAATTTGTCTAATGTGAATCTTTGAACTCAAATGAGAAT
1 --GAATCTTTGAA-GTGTGAAACCTAAAATTTATCAAATGTGAATCTTTGAACTCAAATGAGAAT
1617649 CTTT
63 CTTT
1617653 GAAT
1 GAAT
1617657 TTCAAATGAG
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
66 59 0.50
67 2 0.02
68 1 0.01
70 1 0.01
71 3 0.03
72 52 0.44
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (66 bp):
GAATCTTTGAAGTGTGAAACCTAAAATTTATCAAATGTGAATCTTTGAACTCAAATGAGAATCTT
T
Found at i:1617587 original size:14 final size:14
Alignment explanation
Indices: 1617568--1617594 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1617558 TTTAAACTCA
1617568 AATGAGAATCTTTG
1 AATGAGAATCTTTG
1617582 AATGAGAATCTTT
1 AATGAGAATCTTT
1617595 AAGGTATGAA
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:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (14 bp):
AATGAGAATCTTTG
Found at i:1617628 original size:72 final size:72
Alignment explanation
Indices: 1617515--1617656 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
1617505 GAGAATCTTT
* *
1617515 GAATCTTTGAGGTGTGAAACCAAAAATTTATTATATATGAATCTTTAAACTCAAATGAGAATCTT
1 GAATCTTTAAGGTATGAAACCAAAAATTTATTATATATGAATCTTTAAACTCAAATGAGAATCTT
1617580 TGAATGA
66 TGAATGA
* * * *
1617587 GAATCTTTAAGGTATGAAACCTAAAATTTGTCTA-ATGTGAATCTTTGAACTCAAATGAGAATCT
1 GAATCTTTAAGGTATGAAACCAAAAATTTAT-TATATATGAATCTTTAAACTCAAATGAGAATCT
1617651 TTGAAT
65 TTGAAT
1617657 TTCAAATGAG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 61 0.97
73 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (72 bp):
GAATCTTTAAGGTATGAAACCAAAAATTTATTATATATGAATCTTTAAACTCAAATGAGAATCTT
TGAATGA
Found at i:1617648 original size:20 final size:21
Alignment explanation
Indices: 1617620--1617675 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1617610 AAATTTGTCT
*
1617620 AATGTGAATCTTTGAA-CTCA
1 AATGAGAATCTTTGAATCTCA
*
1617640 AATGAGAATCTTTGAATTTCA
1 AATGAGAATCTTTGAATCTCA
1617661 AATGAGAATCTTTGA
1 AATGAGAATCTTTGA
1617676 GGTGTGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
AATGAGAATCTTTGAATCTCA
Found at i:1617725 original size:79 final size:79
Alignment explanation
Indices: 1617582--1617734 Score: 198
Period size: 79 Copynumber: 1.9 Consensus size: 79
1617572 AGAATCTTTG
* *
1617582 AATGAGAATCTTTAAGGTATGAAACCTAAAATTTGTCTAATGTGAATCTTTGAACTCAAATGAGA
1 AATGAGAATCTTTAAGGTATGAAACCTAAAATTTGTCAAATGTGAACCTTTGAACTCAAATGAGA
*
1617647 ATCTTTGAATTTCA
66 AGCTTTGAATTTCA
* * * * ** * * *
1617661 AATGAGAATCTTTGAGGTGTGAATCCTAAGATTTGTCAAATGTGTGCCTTTGGACTCGATTGAGA
1 AATGAGAATCTTTAAGGTATGAAACCTAAAATTTGTCAAATGTGAACCTTTGAACTCAAATGAGA
1617726 AGCTTTGAA
66 AGCTTTGAA
1617735 CTTTTGGATG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (79 bp):
AATGAGAATCTTTAAGGTATGAAACCTAAAATTTGTCAAATGTGAACCTTTGAACTCAAATGAGA
AGCTTTGAATTTCA
Found at i:1618070 original size:41 final size:41
Alignment explanation
Indices: 1618006--1618184 Score: 150
Period size: 41 Copynumber: 4.4 Consensus size: 41
1617996 GATTATCGAT
* * * * *
1618006 GAGTCTTTTACTTTTTTAGAGTTGTGGTACCTCTGTTTATAA
1 GAGTATTTTA-TTTTTAAAAGTTGTGGTACCTCTATTTAGAA
* *
1618048 GAGTATTTTATTTTTTAAAGTTGTGGTGCCTCTATTTAGAA
1 GAGTATTTTATTTTTAAAAGTTGTGGTACCTCTATTTAGAA
** * * * *
1618089 GAACAATTTATTTTTAAAAGTTGTAGTACCTCT-GTTAGAG
1 GAGTATTTTATTTTTAAAAGTTGTGGTACCTCTATTTAGAA
* *
1618129 GAGCT-TTTTATTTTTCAAAAGTTATGGTGCCTCTATTTA-AA
1 GAG-TATTTTATTTTT-AAAAGTTGTGGTACCTCTATTTAGAA
*
1618170 GAAGCA-TTTATTTTT
1 G-AGTATTTTATTTTT
1618185 CTTAAAGTCG
Statistics
Matches: 110, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
40 16 0.15
41 80 0.73
42 14 0.13
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (41 bp):
GAGTATTTTATTTTTAAAAGTTGTGGTACCTCTATTTAGAA
Found at i:1618182 original size:81 final size:82
Alignment explanation
Indices: 1618025--1618184 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
1618015 ACTTTTTTAG
* * * *
1618025 AGTTGTGGTACCTCTGTTTATAAGAGTATTTTATTTTTTAAAGTTGTGGTGCCTCTATTTAGAAG
1 AGTTGTAGTACCTCTGTTTAGAAGAGTATTTTATTTTTAAAAGTTATGGTGCCTCTATTTAGAAG
1618090 AACAATTTATTTTTAAA
66 AACAATTTATTTTTAAA
*
1618107 AGTTGTAGTACCTCTG-TTAGAGGAGCT-TTTTATTTTTCAAAAGTTATGGTGCCTCTATTTA-A
1 AGTTGTAGTACCTCTGTTTAGAAGAG-TATTTTATTTTT-AAAAGTTATGGTGCCTCTATTTAGA
1618169 AGAAGC-ATTTATTTTT
64 AGAA-CAATTTATTTTT
1618185 CTTAAAGTCG
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
81 32 0.46
82 38 0.54
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (82 bp):
AGTTGTAGTACCTCTGTTTAGAAGAGTATTTTATTTTTAAAAGTTATGGTGCCTCTATTTAGAAG
AACAATTTATTTTTAAA
Found at i:1618386 original size:19 final size:19
Alignment explanation
Indices: 1618362--1618398 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1618352 TTTTTGTAAA
1618362 AATAAAAAGAGAAAAAATT
1 AATAAAAAGAGAAAAAATT
1618381 AATAAAAAGAGAAAAAAT
1 AATAAAAAGAGAAAAAAT
1618399 GGGAAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.14
Consensus pattern (19 bp):
AATAAAAAGAGAAAAAATT
Found at i:1618405 original size:18 final size:18
Alignment explanation
Indices: 1618365--1618417 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1618355 TTGTAAAAAT
*
1618365 AAAAAGAGAAAAAATTAAT
1 AAAAAGAGAAAAAA-TAAG
**
1618384 AAAAAGAGAAAAAATGGG
1 AAAAAGAGAAAAAATAAG
**
1618402 AAAACTAGAAAAAATA
1 AAAAAGAGAAAAAATA
1618418 GGGGTTGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (18 bp):
AAAAAGAGAAAAAATAAG
Found at i:1628312 original size:187 final size:186
Alignment explanation
Indices: 1627888--1629565 Score: 1622
Period size: 187 Copynumber: 9.0 Consensus size: 186
1627878 GAACGGATAG
* * * * * * *
1627888 TGAAGGCATTTCTTGAGACCAAATGCCTTCAATAATTTCTTCTTAAAATTTTTAGAATTATTAAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTT-GGATTATTAAA
* ** * * * * *
1627953 AGCATCTTTTAGTGAAAAATGACTTCAATATTCCACAACTTAAAATTTT-AAATAG-TTAGTTG-
65 GGCATCTTCCAATGAAAAATGCCTTCAATATTTCACAAC-TCAAATTTTGAGAT-GCTTAG-TGA
* * ** * * *
1628015 AGGTGTTTATTCAATAA-AAACACCTTTAGTAATT-CTTTCTAATTTATGTGCATAATTAT
127 AGGTGTTTATTCTAGAATAAATGCCTTCACTAATTGC-TTCTAATTTACGTGCATAATTAT
** ** * *
1628074 TGAAGGTGTTTTTGAAGAACAAATGCCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGG-ATTATTAAA
* * *
1628139 GGCGTCTTCCAATGAAAAACGCCTTCAATATTTCACAACTCAAAATTTGAGATGCTTAGTGAAGG
65 GGCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGAGATGCTTAGTGAAGG
* * * *
1628204 TGTTTTTTCTAGAATAAATGCCTTTACTAATTGCTTCTAATTTATGTGCATAAATAT
130 TGTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
* *
1628261 TGAAAGCATTTTTTTAGAACAAACGACTTTAATAATTTTTTCTTAAAATTTTTGAGATTATTAAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTG-GATTATTAAA
* * * * * ** * *
1628326 GGTATTTTTCAGTGAAAAATGCCTTCAATAGTAAACAACTTAAATTTTGAGACT-ATTAGTGAAG
65 GGCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGAGA-TGCTTAGTGAAG
* * * * * * *
1628390 GCGTTTATTCTAGAAAAAAATACATTCACTAATTTCTTCTAATTTGCGTGTATAATTAT
129 GTGTTTATTCTAG-AATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
* * * *
1628449 TAAAGGCGTTTTTTTAGAACAAACGCCTTTAATAA-ATTTTCTTTAAAATTTTTGGCATTATTCA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTC-TTAAAATTTTTGG-ATTATTAA
* * * * * **
1628513 AGGCGTCTTTCAGTGGAAAAA-ACCTTTAATA-TTCTACAACTCAAATTTTGAGACACTTAGTGA
64 AGGCATCTTCCAAT-GAAAAATGCCTTCAATATTTC-ACAACTCAAATTTTGAGATGCTTAGTGA
* * *
1628576 ATGTGTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACATGCATAAATATT
127 AGGTGTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTA-T
* * * * * *
1628637 TG-AGGTATTTTTTTAGAATAAATGCCTTCAATAATTTTTTTTTAAAATTTTTAGAATTATTAAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTT-GGATTATTAAA
* * * * *
1628701 GGTATCTTCTAATAAAAAATGCCTTCAATATTCCACAACTCAAATTTTG-GATTAG-TTAATGAA
65 GGCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGAGA-T-GCTTAGTGAA
* * * * * * *
1628764 GGTGTTTTATTCTAGAAAAAACGTCTTCACTAATT-CTTTGTAGTTTACTTGTATAATTAT
128 GGTG-TTTATTCTAGAATAAATGCCTTCACTAATTGC-TTCTAATTTACGTGCATAATTAT
* * * * * *
1628824 TAAAGGTATTTTTTGAAAACAAACACCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGG-ATTATTAAA
* * * * * * * *
1628889 GGTATCTTCCAGTGAAAAACGCTTTCAATATTTCATAACTCAAATTTTGATACGCTTAGTGAATG
65 GGCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGAGATGCTTAGTGAAGG
* * * * *
1628954 CGTTTATTCTAAAATAAATGCCTTCACTAATTGCTTCTAATTTACTTGTATAAATAT
130 TGTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
* * *
1629011 TGAAGGCA--TTTTGAGAACAAATGCCTTTAATAATTTTTTCTTAAAATTTTTGGGATTATTGAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTT-GGATTATTAAA
* * *
1629074 GGCGTCTTCCAATGGAAAATGCCTTTAATATTTCACAACTCAAATTTT-ACGATGCTTAGTGAAG
65 GGCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGA-GATGCTTAGTGAAG
* * **
1629138 GCGTTTATTCTAGAA-AAATACCTTCACTAATTTATTCTAATTTACGTGCATAATTAT
129 GTGTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
* *
1629195 TGAAGGTATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTCTTAGGATTATTAAA
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATT-TTTGGATTATTAAA
* * * *
1629260 AG-AGTCTT-TAAGTGAAAAATGCCTTCAATA-TTCTACAACTCAAAATTTGAAACT-CTTAGTG
65 GGCA-TCTTCCAA-TGAAAAATGCCTTCAATATTTC-ACAACTCAAATTTTGAGA-TGCTTAGTG
* ** * * *
1629321 AACGCATTTATTCTAGAATAAATGCCTTCACTAATTCCATCTAATTTACGTTCATAATTAT
126 AAGGTGTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
* * * * *
1629382 TGAAGGCATCTTTTGAGAACAAACGCTTTTAATAA--TTCTCTTAAATTTTTTGGATTATTAAAG
1 TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGGATTATTAAAG
* * ** * * * * *
1629445 GCACCTTTCAATGAAAAACACTTTTAATATTTTAGAACTCAAATTTTGAGACGCTTAGTGAAGGT
66 GCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGAGATGCTTAGTGAAGGT
* * * * * **
1629510 ATTTATTCCA-AAAAAATGCATTCACTAATTCCTTCTAATTTACGTATATAATTAT
131 GTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
1629565 T
1 T
1629566 AAACACAATT
Statistics
Matches: 1237, Mismatches: 212, Indels: 89
0.80 0.14 0.06
Matches are distributed among these distances:
183 41 0.03
184 109 0.09
185 144 0.12
186 222 0.18
187 411 0.33
188 303 0.24
189 7 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (186 bp):
TGAAGGCATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGGATTATTAAAG
GCATCTTCCAATGAAAAATGCCTTCAATATTTCACAACTCAAATTTTGAGATGCTTAGTGAAGGT
GTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAATTAT
Found at i:1628610 original size:375 final size:375
Alignment explanation
Indices: 1627888--1629568 Score: 1786
Period size: 375 Copynumber: 4.5 Consensus size: 375
1627878 GAACGGATAG
* * * * *
1627888 TGAAGGCATTTCTTGAGACCAAATGCCTTCAATAATTTCTTCTTAAAATTTTT-AGAATTATTAA
1 TGAAGGCATTTTTTGAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGAG-ATTATTAA
* * * * *
1627952 AAGCATCTTTT-AGTGAAAAATGACTTCAATATTCCACAACTTAAAATTTT-A-AATAGTTAGTT
65 AGGCAT-TTTTCAATGAAAAATGCCTTCAATATTCCACAAC-TCAAATTTTGAGACTA-TTAG-T
* * * * * * *
1628014 G-AGGTGTTTATTC-A-ATAAAAACACCTTTAGTAA-TTCTTTCTAATTTATGTGCATAATTATT
126 GAAGGTGTTTATTCTAGAAAAAAATACATTCACTAATTTC-TTCTAATTTACGTGTATAATTATT
* * ** *
1628075 GAAGGTGTTTTTGAAGAACAAATGCCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAAG
190 AAAGGTATTTTTTTAGAACAAACGCCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAAG
* * * * *
1628140 GCGTCTTCCAATGAAAAACGCCTTCAATATTTCACAACTCAAAATTTGAGATGCTTAGTGAAGGT
255 GCGTCTTCCAGTGAAAAACACCTTCAATATTTCACAACTCAAAATTTGAGACGCTTAGTGAATGC
* * *
1628205 GTTTTTTCTAGAATAAATGCCTTTACTAATTGCTTCTAATTTATGTGCATAAATAT
320 GTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAAATAT
* * *
1628261 TGAAAGCATTTTTTTAGAACAAACGACTTTAATAATTTTTTCTTAAAATTTTTGAGATTATTAAA
1 TGAAGGCATTTTTTGAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGAGATTATTAAA
* * * ** *
1628326 GGTATTTTTCAGTGAAAAATGCCTTCAATAGTAAACAACTTAAATTTTGAGACTATTAGTGAAGG
66 GGCATTTTTCAATGAAAAATGCCTTCAATATTCCACAACTCAAATTTTGAGACTATTAGTGAAGG
* * *
1628391 CGTTTATTCTAGAAAAAAATACATTCACTAATTTCTTCTAATTTGCGTGTATAATTATTAAAGGC
131 TGTTTATTCTAGAAAAAAATACATTCACTAATTTCTTCTAATTTACGTGTATAATTATTAAAGGT
* * * *
1628456 GTTTTTTTAGAACAAACGCCTTTAATAA-ATTTTCTTTAAAATTTTTGGCATTATTCAAGGCGTC
196 ATTTTTTTAGAACAAACGCCTTCAATAATTTTTTC-TTAAAATTTTTGGCATTATTAAAGGCGTC
* * * * *
1628520 TTTCAGTGGAAAAA-ACCTTTAATA-TTCTACAACTCAAATTTTGAGACACTTAGTGAATGTGTT
260 TTCCAGT-GAAAAACACCTTCAATATTTC-ACAACTCAAAATTTGAGACGCTTAGTGAATGCGTT
*
1628583 TATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACATGCATAAATATT
323 TATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAAATA-T
* * * * * *
1628637 TG-AGGTATTTTTTTAGAATAAATGCCTTCAATAATTTTTTTTTAAAATTTTT-AGAATTATTAA
1 TGAAGGCATTTTTTGAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGAG-ATTATTAA
* * * * *
1628700 AGGTA-TCTTCTAATAAAAAATGCCTTCAATATTCCACAACTCAAATTTTG-GATTAGTTAATGA
65 AGGCATTTTTC-AATGAAAAATGCCTTCAATATTCCACAACTCAAATTTTGAGACTA-TTAGTGA
* * * *
1628763 AGGTGTTTTATTCTAGAAAAAACGT-C-TTCACTAA-TTCTTTGTAGTTTACTTGTATAATTATT
128 AGGTG-TTTATTCTAGAAAAAA-ATACATTCACTAATTTC-TTCTAATTTACGTGTATAATTATT
* * *
1628825 AAAGGTATTTTTTGAAAACAAACACCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAAG
190 AAAGGTATTTTTTTAGAACAAACGCCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAAG
** * * * * *
1628890 GTATCTTCCAGTGAAAAACGCTTTCAATATTTCATAACTCAAATTTTGATACGCTTAGTGAATGC
255 GCGTCTTCCAGTGAAAAACACCTTCAATATTTCACAACTCAAAATTTGAGACGCTTAGTGAATGC
* * *
1628955 GTTTATTCTAAAATAAATGCCTTCACTAATTGCTTCTAATTTACTTGTATAAATAT
320 GTTTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAAATAT
* * *
1629011 TGAAGGCA--TTTTGAGAACAAATGCCTTTAATAATTTTTTCTTAAAATTTTTGGGATTATTGAA
1 TGAAGGCATTTTTTGAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGAGATTATTAAA
* * * * * * *
1629074 GGCGTCTTCCAATGGAAAATGCCTTTAATATTTCACAACTCAAATTTT-ACGA-TGCTTAGTGAA
66 GGCATTTTTCAATGAAAAATGCCTTCAATATTCCACAACTCAAATTTTGA-GACT-ATTAGTGAA
* * * * *
1629137 GGCGTTTATTCTAG--AAAAATACCTTCACTAATTTATTCTAATTTACGTGCATAATTATTGAAG
129 GGTGTTTATTCTAGAAAAAAATACATTCACTAATTTCTTCTAATTTACGTGTATAATTATTAAAG
* * * *
1629200 GTATTTTTTTAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTCTTAGG-ATTATTAAAAGAG
194 GTATTTTTTTAGAACAAACGCCTTCAATAATTTTTTCTTAAAATT-TTTGGCATTATTAAAGGCG
** ** * * * *
1629264 TCTTTAAGTGAAAAATGCCTTCAATA-TTCTACAACTCAAAATTTGAAACTCTTAGTGAACGCAT
258 TCTTCCAGTGAAAAACACCTTCAATATTTC-ACAACTCAAAATTTGAGACGCTTAGTGAATGCGT
* * * *
1629328 TTATTCTAGAATAAATGCCTTCACTAATTCCATCTAATTTACGTTCATAATTAT
322 TTATTCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAAATAT
* * * *
1629382 TGAAGGCATCTTTTGAGAACAAACGCTTTTAATAA--TTCTCTTAAATTTTTTG-GATTATTAAA
1 TGAAGGCATTTTTTGAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGAGATTATTAAA
** ** * * ** * **
1629444 GGCACCTTTCAATGAAAAACACTTTTAATATTTTAGAACTCAAATTTTGAGACGCTTAGTGAAGG
66 GGCATTTTTCAATGAAAAATGCCTTCAATATTCCACAACTCAAATTTTGAGACTATTAGTGAAGG
* * * * *
1629509 TATTTATTC--CAAAAAAATGCATTCACTAATTCCTTCTAATTTACGTATATAATTATTAAA
131 TGTTTATTCTAGAAAAAAATACATTCACTAATTTCTTCTAATTTACGTGTATAATTATTAAA
1629569 CACAATTGTC
Statistics
Matches: 1106, Mismatches: 164, Indels: 79
0.82 0.12 0.06
Matches are distributed among these distances:
369 1 0.00
370 117 0.11
371 203 0.18
372 30 0.03
373 215 0.19
374 41 0.04
375 461 0.42
376 37 0.03
377 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (375 bp):
TGAAGGCATTTTTTGAGAACAAACGCCTTTAATAATTTTTTCTTAAAATTTTTGAGATTATTAAA
GGCATTTTTCAATGAAAAATGCCTTCAATATTCCACAACTCAAATTTTGAGACTATTAGTGAAGG
TGTTTATTCTAGAAAAAAATACATTCACTAATTTCTTCTAATTTACGTGTATAATTATTAAAGGT
ATTTTTTTAGAACAAACGCCTTCAATAATTTTTTCTTAAAATTTTTGGCATTATTAAAGGCGTCT
TCCAGTGAAAAACACCTTCAATATTTCACAACTCAAAATTTGAGACGCTTAGTGAATGCGTTTAT
TCTAGAATAAATGCCTTCACTAATTGCTTCTAATTTACGTGCATAAATAT
Found at i:1640155 original size:60 final size:60
Alignment explanation
Indices: 1640072--1640189 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 60
1640062 ATTGAAAGTG
*
1640072 TCTATTATTAACAAACACTTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGGCA
1 TCTATTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGGCA
* *
1640132 TCTATTATTAACAAACACCTTCAGTAATGGATTGCTAAGTTTAAAGGTATATTGAAGG
1 TCTATTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGG
1640190 TATTTTTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (60 bp):
TCTATTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGGCA
Found at i:1646759 original size:18 final size:20
Alignment explanation
Indices: 1646718--1646759 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1646708 TATGCAAATT
* *
1646718 AATAGTTATTGTTATGTTTT
1 AATAGTTATTGATATGTTTC
1646738 AATAGTT-TTGATA-GTTTC
1 AATAGTTATTGATATGTTTC
1646756 AATA
1 AATA
1646760 CATAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.52
Consensus pattern (20 bp):
AATAGTTATTGATATGTTTC
Found at i:1652995 original size:17 final size:17
Alignment explanation
Indices: 1652973--1653007 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1652963 TCTTCTTATT
*
1652973 CTTATTCTAAGCTCTTC
1 CTTATTCTAAACTCTTC
1652990 CTTATTCTAAACTCTTC
1 CTTATTCTAAACTCTTC
1653007 C
1 C
1653008 CCACCATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.31, G:0.03, T:0.46
Consensus pattern (17 bp):
CTTATTCTAAACTCTTC
Found at i:1654716 original size:24 final size:24
Alignment explanation
Indices: 1654682--1654736 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1654672 AGTCAAGTTT
* *
1654682 AATAAT-TTAAAATATAATGTAAA
1 AATAATATTAAAATAAAATATAAA
*
1654705 TATAATATTAAAATAAAATATAAA
1 AATAATATTAAAATAAAATATAAA
1654729 AATAATAT
1 AATAATAT
1654737 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAATATTAAAATAAAATATAAA
Found at i:1654756 original size:24 final size:26
Alignment explanation
Indices: 1654726--1654788 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
1654716 AATAAAATAT
1654726 AAAAATAATATATTTTA-AAATTTT-
1 AAAAATAATATATTTTATAAATTTTA
* *
1654750 AATAATAAT-TA-TATATAAATTTTA
1 AAAAATAATATATTTTATAAATTTTA
1654774 AAAAATAA-ATATTTT
1 AAAAATAATATATTTT
1654789 TGTGTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
22 3 0.10
23 9 0.29
24 17 0.55
25 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAAATAATATATTTTATAAATTTTA
Found at i:1654840 original size:14 final size:14
Alignment explanation
Indices: 1654821--1654848 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1654811 TTTATATAAA
1654821 ATAAATTTTAATAT
1 ATAAATTTTAATAT
1654835 ATAAATTTTAATAT
1 ATAAATTTTAATAT
1654849 TTTATGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAAATTTTAATAT
Found at i:1661231 original size:3 final size:3
Alignment explanation
Indices: 1661223--1661248 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1661213 CATCTTTATG
1661223 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1661249 TTTACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1664179 original size:314 final size:314
Alignment explanation
Indices: 1663610--1664238 Score: 1240
Period size: 314 Copynumber: 2.0 Consensus size: 314
1663600 CAAATACAAG
1663610 AATAAAGCAGGCATCAGCATTTGTGTAGTTATAACAAACAATTAACAAAACACATGCCTAGAAAT
1 AATAAAGCAGGCATCAGCATTTGTGTAGTTATAACAAACAATTAACAAAACACATGCCTAGAAAT
1663675 TCTATAGCATCAAAAGGTAAAACCAAGCCAGTACGTGACAGAAAATAGAACCATTTTCAAATTGT
66 TCTATAGCATCAAAAGGTAAAACCAAGCCAGTACGTGACAGAAAATAGAACCATTTTCAAATTGT
1663740 CATTAACTCATTATGATAATTGTCTTCATAAAAAACTTGTAATCCAATGTCTAAAGATTTCATAG
131 CATTAACTCATTATGATAATTGTCTTCATAAAAAACTTGTAATCCAATGTCTAAAGATTTCATAG
1663805 TAAGAAAATAAAACAAGCTAGTACATGACAGAAAATTGAATCATTGTCAAATTGTCATTCTGATA
196 TAAGAAAATAAAACAAGCTAGTACATGACAGAAAATTGAATCATTGTCAAATTGTCATTCTGATA
*
1663870 ATTGTCTTTGTAAAAAAACTTGAAATTCAATATCATAGTAAGAAAATAAACCAA
261 ATTGTCTTTGTAAAAAAACTTGAAATTAAATATCATAGTAAGAAAATAAACCAA
1663924 AATAAAGCAGGCATCAGCATTTGTGTAGTTATAACAAACAATTAACAAAACACATGCCTAGAAAT
1 AATAAAGCAGGCATCAGCATTTGTGTAGTTATAACAAACAATTAACAAAACACATGCCTAGAAAT
1663989 TCTATAGCATCAAAAGGTAAAACCAAGCCAGTACGTGACAGAAAATAGAACCATTTTCAAATTGT
66 TCTATAGCATCAAAAGGTAAAACCAAGCCAGTACGTGACAGAAAATAGAACCATTTTCAAATTGT
*
1664054 CATTAACTCATTATGATAATTGTCTTCATAAAAAACTTGTAATCCAATGTCTACAGATTTCATAG
131 CATTAACTCATTATGATAATTGTCTTCATAAAAAACTTGTAATCCAATGTCTAAAGATTTCATAG
1664119 TAAGAAAATAAAACAAGCTAGTACATGACAGAAAATTGAATCATTGTCAAATTGTCATTCTGATA
196 TAAGAAAATAAAACAAGCTAGTACATGACAGAAAATTGAATCATTGTCAAATTGTCATTCTGATA
1664184 ATTGTCTTTGTAAAAAAACTTGAAATTAAATATCATAGTAAGAAAATAAACCAA
261 ATTGTCTTTGTAAAAAAACTTGAAATTAAATATCATAGTAAGAAAATAAACCAA
1664238 A
1 A
1664239 CCTATAAACA
Statistics
Matches: 313, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 313 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (314 bp):
AATAAAGCAGGCATCAGCATTTGTGTAGTTATAACAAACAATTAACAAAACACATGCCTAGAAAT
TCTATAGCATCAAAAGGTAAAACCAAGCCAGTACGTGACAGAAAATAGAACCATTTTCAAATTGT
CATTAACTCATTATGATAATTGTCTTCATAAAAAACTTGTAATCCAATGTCTAAAGATTTCATAG
TAAGAAAATAAAACAAGCTAGTACATGACAGAAAATTGAATCATTGTCAAATTGTCATTCTGATA
ATTGTCTTTGTAAAAAAACTTGAAATTAAATATCATAGTAAGAAAATAAACCAA
Found at i:1665623 original size:12 final size:12
Alignment explanation
Indices: 1665606--1665630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1665596 GGGTGGGCGG
1665606 CCCGATGCCGAC
1 CCCGATGCCGAC
1665618 CCCGATGCCGAC
1 CCCGATGCCGAC
1665630 C
1 C
1665631 ATTTCTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.52, G:0.24, T:0.08
Consensus pattern (12 bp):
CCCGATGCCGAC
Found at i:1666245 original size:3 final size:3
Alignment explanation
Indices: 1666231--1666282 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
1666221 TATTTTCAAG
* * * * * *
1666231 ATA ATA ACA ATA ATA ATA ATA ATA ACA ATA ACA ACA ACA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1666279 ATA A
1 ATA A
1666283 AAACTTACAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (3 bp):
ATA
Found at i:1666245 original size:9 final size:9
Alignment explanation
Indices: 1666231--1666282 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
1666221 TATTTTCAAG
1666231 ATAATAACA
1 ATAATAACA
*
1666240 ATAATAATA
1 ATAATAACA
1666249 ATAATAACA
1 ATAATAACA
*
1666258 ATAACAACA
1 ATAATAACA
* * *
1666267 ACAACAATA
1 ATAATAACA
1666276 ATAATAA
1 ATAATAA
1666283 AAACTTACAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAATAACA
Found at i:1666297 original size:27 final size:27
Alignment explanation
Indices: 1666231--1666285 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1666221 TATTTTCAAG
* * * *
1666231 ATAATAACAATAATAATAATAATAACA
1 ATAACAACAACAACAATAATAATAAAA
1666258 ATAACAACAACAACAATAATAATAAAA
1 ATAACAACAACAACAATAATAATAAAA
1666285 A
1 A
1666286 CTTACACAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (27 bp):
ATAACAACAACAACAATAATAATAAAA
Found at i:1666484 original size:16 final size:16
Alignment explanation
Indices: 1666465--1666499 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1666455 TATACTGTCG
*
1666465 TCACAATATTATATCT
1 TCACAATATAATATCT
*
1666481 TCACAATATAATGTCT
1 TCACAATATAATATCT
1666497 TCA
1 TCA
1666500 AATGAACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (16 bp):
TCACAATATAATATCT
Found at i:1666590 original size:22 final size:22
Alignment explanation
Indices: 1666548--1666590 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1666538 CACAAAAAGA
*
1666548 ATAATTACATAATAAACAAATT
1 ATAATTACATAATAAAAAAATT
1666570 ATAATTA-ATAATAAGAAAAAT
1 ATAATTACATAATAA-AAAAAT
1666591 AGTAGAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAATTACATAATAAAAAAATT
Found at i:1666754 original size:125 final size:125
Alignment explanation
Indices: 1666619--1666868 Score: 500
Period size: 125 Copynumber: 2.0 Consensus size: 125
1666609 AAAAAAAAAG
1666619 ATTGTGATATTATTACAATGATCAATAACTTTAAATTTTTAACATTAGCATCAACATGAATTTTA
1 ATTGTGATATTATTACAATGATCAATAACTTTAAATTTTTAACATTAGCATCAACATGAATTTTA
1666684 TCTTGTCAATTACCTTATAATCAAAGCAAAAAAATATAGACAGTGTCTTGTAAATTACCC
66 TCTTGTCAATTACCTTATAATCAAAGCAAAAAAATATAGACAGTGTCTTGTAAATTACCC
1666744 ATTGTGATATTATTACAATGATCAATAACTTTAAATTTTTAACATTAGCATCAACATGAATTTTA
1 ATTGTGATATTATTACAATGATCAATAACTTTAAATTTTTAACATTAGCATCAACATGAATTTTA
1666809 TCTTGTCAATTACCTTATAATCAAAGCAAAAAAATATAGACAGTGTCTTGTAAATTACCC
66 TCTTGTCAATTACCTTATAATCAAAGCAAAAAAATATAGACAGTGTCTTGTAAATTACCC
1666869 TAACATGAGT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (125 bp):
ATTGTGATATTATTACAATGATCAATAACTTTAAATTTTTAACATTAGCATCAACATGAATTTTA
TCTTGTCAATTACCTTATAATCAAAGCAAAAAAATATAGACAGTGTCTTGTAAATTACCC
Found at i:1669867 original size:12 final size:12
Alignment explanation
Indices: 1669845--1669875 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1669835 AACTTCTTTT
1669845 ATAATAAAATAAA
1 ATAA-AAAATAAA
1669858 ATAAAAAATAAA
1 ATAAAAAATAAA
1669870 ATAAAA
1 ATAAAA
1669876 TTCTAGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:1670560 original size:34 final size:34
Alignment explanation
Indices: 1670522--1670641 Score: 107
Period size: 34 Copynumber: 3.5 Consensus size: 34
1670512 ATAAAGGCAT
* *
1670522 TTACTATGCAGAAAGGTAGCACACAGTAACCTGC
1 TTACTATGCAGAAAGGCAGCACACAGTAACCTGA
** * ** *
1670556 TTACTATATAGAAATGCAGCATGCAGTAACTTGA
1 TTACTATGCAGAAAGGCAGCACACAGTAACCTGA
* * **
1670590 TTACTATGTAGAAAAGCAGCACACAACAACCT-A
1 TTACTATGCAGAAAGGCAGCACACAGTAACCTGA
*
1670623 TTTACTATGCAAAAAGGCA
1 -TTACTATGCAGAAAGGCA
1670642 ACATGTGATA
Statistics
Matches: 67, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
33 1 0.01
34 66 0.99
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (34 bp):
TTACTATGCAGAAAGGCAGCACACAGTAACCTGA
Found at i:1678569 original size:20 final size:21
Alignment explanation
Indices: 1678540--1678602 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1678530 AAAAATTAAA
1678540 AAAATCATAAAAAATAATTTT
1 AAAATCATAAAAAATAATTTT
*
1678561 AAAAT-ATAAAAAAAAAGTTTT
1 AAAATCATAAAAAATAA-TTTT
* *
1678582 -AGATGATAACAAAATAATTTT
1 AAAATCATAA-AAAATAATTTT
1678603 GGGGCATCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 13 0.36
21 17 0.47
22 6 0.17
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAATCATAAAAAATAATTTT
Found at i:1679265 original size:15 final size:16
Alignment explanation
Indices: 1679245--1679282 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1679235 AAGTTGGAAA
*
1679245 GTTAATTTGATTT-TT
1 GTTAATTTCATTTATT
1679260 GTTAATTTCATTTATT
1 GTTAATTTCATTTATT
1679276 G-TAATTT
1 GTTAATTT
1679283 AAAATTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (16 bp):
GTTAATTTCATTTATT
Found at i:1682860 original size:21 final size:21
Alignment explanation
Indices: 1682819--1682861 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1682809 AAATTAAAAA
*
1682819 AAAATCATAAAAAATAATTTT
1 AAAATCATAAAAAAGAATTTT
*
1682840 AAAAT-ATGAAAAAAGAGTTTT
1 AAAATCAT-AAAAAAGAATTTT
1682861 A
1 A
1682862 GATGATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAATCATAAAAAAGAATTTT
Found at i:1695893 original size:357 final size:357
Alignment explanation
Indices: 1695188--1696759 Score: 1800
Period size: 357 Copynumber: 4.5 Consensus size: 357
1695178 TTTAACATGG
* * * *
1695188 TTATTGAAGGTGTATATCCAAAAAAGATACCTTTTATAATTTCTATCATAGTTTGTATATAATTA
1 TTATTGAAGGCGTATATCCAAGAAAGATACCTTTAATAATTTCTATCATAGTTTGTAGATAATTA
* * * *
1695253 ATGAATG-TGGTTGCAGAAAATAATACCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTAGT
66 CTGAA-GATGGTTGCAGATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATT
* * *
1695317 AAAGGCGTCTTTTATTATGACACGCCTTCAATATATCACGATGGTTATAGAATGCGTTTATTCAA
130 AAAGGCGTCTTTTATTATGACACGCCTTCAATATACCACGATGGTAATAGAAGGCGTTTATT-AA
* * * * * * *
1695382 AAATGTGCCTTCAATATACTTTTAAACTTAGTAATCTATTACTGAAGGCCTTCGTTAATAATAGA
194 AAAAGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACAAA
* * * ** ** *
1695447 CGCCTTCAAAATTTGTTCATTAAAAATTTTGGAAATTATTAAAGAAATCTTCTACTATAAAATAC
259 CGCCTTCAAAATTTTTTCACTAAATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAATAC
* *
1695512 CTTCTATATACCGTCATA-AAAATTCTAACACTG
324 CTTCTATATACCGTCACACAAAATTCTAACACTA
* * *
1695545 TTATTGAAGGCATATATCCAAGAAAGATACCTTTAATAATTTCTATTATAGTTTATAGATAATTA
1 TTATTGAAGGCGTATATCCAAGAAAGATACCTTTAATAATTTCTATCATAGTTTGTAGATAATTA
* * *
1695610 CTGAAGACGGTTACATATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTA
66 CTGAAGATGGTTGCAGATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTA
* * *
1695675 AAGGCGTCTTTTATTATGACATGCCTTCAATATACCACGATAGTAAT-GAAAGGTGTTTATTAAA
131 AAGGCGTCTTTTATTATGACACGCCTTCAATATACCACGATGGTAATAG-AAGGCGTTTATTAAA
* * *
1695739 AAAGTACCTTCAATATACCTTTAAACTTAGTAATCCATTATTGAAGGCGTTTGTTAATAACAAAA
195 AAAGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACAAAC
* * *
1695804 GCCTTCAAAATTTTTTCACTAAATATTTTGAGAATTATTAAAGACTTCTTCTACTGTAAAATACC
260 GCCTTCAAAATTTTTTCACTAAATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAATACC
* **
1695869 TTATATATACCACCACACAAAATTCTAACACTA
325 TTCTATATACCGTCACACAAAATTCTAACACTA
* *
1695902 TTATTGAAGGCATATATCC----AAG-T-CC-----T-A--TC-A-C--AGTTTGTCGATAATTA
1 TTATTGAAGGCGTATATCCAAGAAAGATACCTTTAATAATTTCTATCATAGTTTGTAGATAATTA
* * *** * * * * * ***** *
1695949 TTTAAGGCAGTTACAGATAATAAGGTCTTTAATAATTTTCCTAAAATTTTTTTTTTGGATTATTA
66 CTGAAGATGGTTGCAGATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTA
* * * * ** *
1696014 AATGCGTCTTTTATTATGACACACTTTCAATATATCACGATGGTTCTAGAAGGAGTTTATTAAAA
131 AAGGCGTCTTTTATTATGACACGCCTTCAATATACCACGATGGTAATAGAAGGCGTTTATTAAAA
* * *
1696079 AATGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAAGCTTTTGTTAATAACAAAC
196 AA-GTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACAAAC
* * * *
1696144 GCCTTCAAAATTTTCTCACTAAATATTTTAAAAATTATTAAAGGCGTCTTCTACTGTAAAATGCT
260 GCCTTCAAAATTTTTTCACTAAATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAATACC
* *
1696209 TTCTATATACCGTCACA-AAAATTTTAACATTA
325 TTCTATATACCGTCACACAAAATTCTAACACTA
* * *
1696241 TTATTAAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTTCTATCATAGTTTGTAGGTAATTA
1 TTATTGAAGGCGTATATCCAAGAAAGATACCTTTAATAATTTCTATCATAGTTTGTAGATAATTA
* * ***
1696306 CT-AA-ATGTAGTTGTAGATAATAATGCCTTCAATAATTTT-TTTAAAAATTTTTTTTCGAATTA
66 CTGAAGATG--GTTGCAGATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTT-GAATTA
* * * *
1696368 TTAAAGGCATCTTTTATTATGACACGCCTTTAATATACTACGATGGTAATTA-AAGGCATTTATT
128 TTAAAGGCGTCTTTTATTATGACACGCCTTCAATATACCACGATGGTAA-TAGAAGGCGTTTATT
* * *
1696432 AAAAAAGATGCATTCAATATACTTTTAAACTTAGTAATCCATTACTGAAGGCGTTTATTAATAAC
192 AAAAAAG-TGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAAC
* * **
1696497 AGACGCTTTCAAAAAATTTTCACTAAATATTTTAAAAATTATTAAA-AGCGTCTTCTACTGTAAA
256 AAACGCCTTCAAAATTTTTTCACTAAATATTTTAAAAATTATTAAAGA-CGTCTTCTACTGTAAA
1696561 ATACCTTCTATATACCGTCACAC-AAATTCTAACACTA
320 ATACCTTCTATATACCGTCACACAAAATTCTAACACTA
* * * * * * *
1696598 TTTTTAAAGGCGTATATCCAAGAAAGATGCATTTAATAATTCCTATAATAGTTTGTATATAATTA
1 TTATTGAAGGCGTATATCCAAGAAAGATACCTTTAATAATTTCTATCATAGTTTGTAGATAATTA
* * ** *
1696663 CTGAACATGGTTGCAGATAACAACACCTTCAATAA-TTTC-TCAAAAAAAATTTTCTCGAATTAT
66 CTGAAGATGGTTGCAGATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTT-T-GAATTAT
* * *
1696726 TAAAGACGTCTTTTATTATAAAACGCCTTCAATA
129 TAAAGGCGTCTTTTATTATGACACGCCTTCAATA
1696760 ATTTGTTATA
Statistics
Matches: 1029, Mismatches: 152, Indels: 68
0.82 0.12 0.05
Matches are distributed among these distances:
339 150 0.15
340 129 0.13
342 1 0.00
343 5 0.00
344 1 0.00
345 3 0.00
346 1 0.00
350 1 0.00
351 3 0.00
352 1 0.00
353 5 0.00
354 1 0.00
355 1 0.00
356 158 0.15
357 562 0.55
358 4 0.00
359 3 0.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (357 bp):
TTATTGAAGGCGTATATCCAAGAAAGATACCTTTAATAATTTCTATCATAGTTTGTAGATAATTA
CTGAAGATGGTTGCAGATAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTA
AAGGCGTCTTTTATTATGACACGCCTTCAATATACCACGATGGTAATAGAAGGCGTTTATTAAAA
AAGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACAAACG
CCTTCAAAATTTTTTCACTAAATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAATACCT
TCTATATACCGTCACACAAAATTCTAACACTA
Found at i:1696590 original size:696 final size:695
Alignment explanation
Indices: 1695304--1696619 Score: 1886
Period size: 696 Copynumber: 1.9 Consensus size: 695
1695294 TAAAAAAAAA
*
1695304 TTTTTGAATTAGTAAAGGCGTCTTTTATTATGACACGCCTTCAATATATCACGATGGTTATAGAA
1 TTTTTGAATTAGTAAAGGCGTCTTTTATTATGACACACCTTCAATATATCACGATGGTTATAGAA
* * * * * * *
1695369 TGCGTTTATTCAAAAATGTGCCTTCAATATACTTTTAAACTTAGTAATCTATTACTGAAGGCCTT
66 GGAGTTTATTAAAAAATGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAAGCCTT
* * * **
1695434 CGTTAATAATAGACGCCTTCAAAATTTGTTCATTAAAAATTTTGGAAATTATTAAAGAAATCTTC
131 CGTTAATAACAAACGCCTTCAAAATTTGTTCACTAAAAATTTTAAAAATTATTAAAGAAATCTTC
* * *
1695499 TACTATAAAATACCTTCTATATACCGTCATAAAAATTCTAACACTGTTATTGAAGGCATATATCC
196 TACTATAAAATACCTTCTATATACCGTCACAAAAATTCTAACACTATTATTAAAGGCATATATCC
* * *
1695564 AAGAAAGATACCTTTAATAATTTCTATTATAGTTTATAGATAATTACTGAAGACGGTTACATATA
261 AAGAAAGATACCTTTAATAATTTCTATCATAGTTTATAGATAATTACTAAAGAC-GTTACAGATA
*
1695629 ATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTAAAGGCGTCTTTTATTATGA
325 ATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTAAAGGCATCTTTTATTATGA
* ** *
1695694 CATGCCTTCAATATACCACGATAGTAATGAAAGGTGTTTATTAAAAAAGTACCTTCAATATACCT
390 CACGCCTTCAATATACCACGATAGTAATGAAAGGCATTTATTAAAAAAGTACATTCAATATACCT
* * **
1695759 TTAAACTTAGTAATCCATTATTGAAGGCGTTTGTTAATAACAAAAGCCTTCAAAATTTTTTCACT
455 TTAAACTTAGTAATCCATTACTGAAGGCGTTTATTAATAACAAAAGCCTTCAAAAAATTTTCACT
* * *
1695824 AAATATTTTGAGAATTATTAAAGACTTCTTCTACTGTAAAATACCTTATATATACCACCACACAA
520 AAATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAATACCTTATATATACCACCACACAA
*
1695889 AATTCTAACACTATTATTGAAGGCATATATCCAAGTCCTATCACAGTTTGTCGATAATTATTTAA
585 AATTCTAACACTATTATTAAAGGCATATATCCAAGTCCTATCACAGTTTGTCGATAATTATTTAA
1695954 GGCAGTTACAGATAATAAGGTCTTTAATAATTTTCCTAAAATTTTT
650 GGCAGTTACAGATAATAAGGTCTTTAATAATTTTCCTAAAATTTTT
* * * * *
1696000 TTTTTGGATTATTAAATGCGTCTTTTATTATGACACACTTTCAATATATCACGATGGTTCTAGAA
1 TTTTTGAATTAGTAAAGGCGTCTTTTATTATGACACACCTTCAATATATCACGATGGTTATAGAA
*
1696065 GGAGTTTATTAAAAAATGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAAGCTTT
66 GGAGTTTATTAAAAAATGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAAGCCTT
* * ***
1696130 TGTTAATAACAAACGCCTTCAAAATTT-TCTCACTAAATATTTTAAAAATTATTAAAGGCGTCTT
131 CGTTAATAACAAACGCCTTCAAAATTTGT-TCACTAAAAATTTTAAAAATTATTAAAGAAATCTT
* * * * * *
1696194 CTACTGTAAAATGCTTTCTATATACCGTCACAAAAATTTTAACATTATTATTAAAGGCGTATATC
195 CTACTATAAAATACCTTCTATATACCGTCACAAAAATTCTAACACTATTATTAAAGGCATATATC
* * * **
1696259 CAAGAAAGATGCCTTTAATAATTTCTATCATAGTTTGTAGGTAATTACTAAATGTA-GTTGTAGA
260 CAAGAAAGATACCTTTAATAATTTCTATCATAGTTTATAGATAATTACTAAA-G-ACGTTACAGA
* ***
1696323 TAATAATGCCTTCAATAATTTT-TTTAAAAATTTTTTTTCGAATTATTAAAGGCATCTTTTATTA
323 TAATAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTT-GAATTATTAAAGGCATCTTTTATTA
* * * * *
1696387 TGACACGCCTTTAATATACTACGATGGTAATTAAAGGCATTTATTAAAAAAGATGCATTCAATAT
387 TGACACGCCTTCAATATACCACGATAGTAATGAAAGGCATTTATTAAAAAAG-TACATTCAATAT
* * * *
1696452 ACTTTTAAACTTAGTAATCCATTACTGAAGGCGTTTATTAATAACAGACGCTTTCAAAAAATTTT
451 ACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTATTAATAACAAAAGCCTTCAAAAAATTTT
* **
1696517 CACTAAATATTTTAAAAATTATTAAA-AGCGTCTTCTACTGTAAAATACCTTCTATATACCGTCA
516 CACTAAATATTTTAAAAATTATTAAAGA-CGTCTTCTACTGTAAAATACCTTATATATACCACCA
* *
1696581 CAC-AAATTCTAACACTATTTTTAAAGGCGTATATCCAAG
580 CACAAAATTCTAACACTATTATTAAAGGCATATATCCAAG
1696620 AAAGATGCAT
Statistics
Matches: 542, Mismatches: 72, Indels: 12
0.87 0.12 0.02
Matches are distributed among these distances:
695 13 0.02
696 401 0.74
697 127 0.23
698 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (695 bp):
TTTTTGAATTAGTAAAGGCGTCTTTTATTATGACACACCTTCAATATATCACGATGGTTATAGAA
GGAGTTTATTAAAAAATGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAAGCCTT
CGTTAATAACAAACGCCTTCAAAATTTGTTCACTAAAAATTTTAAAAATTATTAAAGAAATCTTC
TACTATAAAATACCTTCTATATACCGTCACAAAAATTCTAACACTATTATTAAAGGCATATATCC
AAGAAAGATACCTTTAATAATTTCTATCATAGTTTATAGATAATTACTAAAGACGTTACAGATAA
TAATGCCTTCAATAATTTTCTTAAAAAAAAATTTTTGAATTATTAAAGGCATCTTTTATTATGAC
ACGCCTTCAATATACCACGATAGTAATGAAAGGCATTTATTAAAAAAGTACATTCAATATACCTT
TAAACTTAGTAATCCATTACTGAAGGCGTTTATTAATAACAAAAGCCTTCAAAAAATTTTCACTA
AATATTTTAAAAATTATTAAAGACGTCTTCTACTGTAAAATACCTTATATATACCACCACACAAA
ATTCTAACACTATTATTAAAGGCATATATCCAAGTCCTATCACAGTTTGTCGATAATTATTTAAG
GCAGTTACAGATAATAAGGTCTTTAATAATTTTCCTAAAATTTTT
Found at i:1700820 original size:35 final size:36
Alignment explanation
Indices: 1700781--1700848 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1700771 TATATAAACT
*
1700781 AAATA-TTTTTTGGGCATAAATATACAACTGACAGC
1 AAATATTTTTTTGGGCATAAACATACAACTGACAGC
* *
1700816 AAATATTTTTTTGGGTATAAACCTACAACTGAC
1 AAATATTTTTTTGGGCATAAACATACAACTGAC
1700849 TTCACATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (36 bp):
AAATATTTTTTTGGGCATAAACATACAACTGACAGC
Found at i:1702256 original size:20 final size:18
Alignment explanation
Indices: 1702228--1702277 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1702218 TTTTAATAAC
1702228 AAAAAAATTAAAAAATCAT
1 AAAAAAATTAAAAAAT-AT
**
1702247 AAAAATAATTTTAAAATAT
1 AAAAA-AATTAAAAAATAT
1702266 AAAAAAA-TAAAA
1 AAAAAAATTAAAA
1702278 GTTTTAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 3 0.12
18 2 0.08
19 12 0.46
20 9 0.35
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAAATTAAAAAATAT
Found at i:1702406 original size:2 final size:2
Alignment explanation
Indices: 1702401--1702427 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1702391 CATACTATTA
1702401 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
1702428 GACACACACA
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:1704160 original size:21 final size:21
Alignment explanation
Indices: 1704122--1704161 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1704112 AAATCCTTTA
* * *
1704122 TTTTTATTTTTTATTTTATTT
1 TTTTTAATTTCTAATTTATTT
1704143 TTTTTAATTTCTAATTTAT
1 TTTTTAATTTCTAATTTAT
1704162 CCTTAAAGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTAATTTCTAATTTATTT
Found at i:1715904 original size:83 final size:83
Alignment explanation
Indices: 1715765--1715919 Score: 274
Period size: 83 Copynumber: 1.9 Consensus size: 83
1715755 ATATATACCT
* * *
1715765 TTTCCCTACATGTTTTTTCCTTTTGCTTTTCTTAGTTATAAATCTATCCAAGGGTTCAACGTGTA
1 TTTCCCTACATGTTTTTCCCTTTTGCTTTTCATAGTTATAAATCTATCCAAGGGTTCAACATGTA
1715830 CTCCTCCATCCCATAGCG
66 CTCCTCCATCCCATAGCG
*
1715848 TTTCCCTACATGTTTTTCCCTTTTGCTTTTCATAGTTATGAATCTATCCAAGGGTTCAACATGTA
1 TTTCCCTACATGTTTTTCCCTTTTGCTTTTCATAGTTATAAATCTATCCAAGGGTTCAACATGTA
1715913 CTCCTCC
66 CTCCTCC
1715920 TGTTTGTCTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.43
Consensus pattern (83 bp):
TTTCCCTACATGTTTTTCCCTTTTGCTTTTCATAGTTATAAATCTATCCAAGGGTTCAACATGTA
CTCCTCCATCCCATAGCG
Found at i:1723406 original size:46 final size:46
Alignment explanation
Indices: 1723339--1723429 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
1723329 TTTAAGATTG
* *
1723339 TGCTAGAGAGTGTGGTCAGTTACCAACAATCTATTAGTTCTATCCA
1 TGCTAGAGAGTGCGGTCAGTTACCAACAATCCATTAGTTCTATCCA
1723385 TGCTAGAGAGTGCGGTCAGTTACCAACAATCCATTAGTTCTATCC
1 TGCTAGAGAGTGCGGTCAGTTACCAACAATCCATTAGTTCTATCC
1723430 TTATTTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (46 bp):
TGCTAGAGAGTGCGGTCAGTTACCAACAATCCATTAGTTCTATCCA
Found at i:1727069 original size:65 final size:65
Alignment explanation
Indices: 1726958--1727093 Score: 218
Period size: 65 Copynumber: 2.1 Consensus size: 65
1726948 CAGGTATAAG
* * * *
1726958 GGGACACCTCAATGGTTAGAGCTTGAGATTTTCACTTGGAAGCCTCAAGTTCAAATCTTGTGTAT
1 GGGAGACCTCAATGGTTAGAACTTGAGATTTTCACTTGGAAGCCTCAAGTTCAAATCTCGGGTAT
* *
1727023 GGGAGACCTCTATGGTTAGAACTTGAGATTTTCACTTGGAATCCTCAAGTTCAAATCTCGGGTAT
1 GGGAGACCTCAATGGTTAGAACTTGAGATTTTCACTTGGAAGCCTCAAGTTCAAATCTCGGGTAT
1727088 GGGAGA
1 GGGAGA
1727094 GAGCTACCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (65 bp):
GGGAGACCTCAATGGTTAGAACTTGAGATTTTCACTTGGAAGCCTCAAGTTCAAATCTCGGGTAT
Found at i:1731785 original size:22 final size:22
Alignment explanation
Indices: 1731760--1731801 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1731750 TTGTCTATCC
* *
1731760 TAATTTTAGGGATAAAAATACT
1 TAATTCTAGAGATAAAAATACT
*
1731782 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATAAAAATA
1731802 TAAATATACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATAAAAATACT
Found at i:1735484 original size:23 final size:25
Alignment explanation
Indices: 1735427--1735485 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1735417 AAAAGTTTCG
* * *
1735427 GCAATGAAGGCCTAAACAGGATTCG
1 GCAATGAAGGCCTAAACAGAAGTCA
*
1735452 GGAATGAAGGCCTAAA-A-AAGTCA
1 GCAATGAAGGCCTAAACAGAAGTCA
1735475 GCAATGAAGGC
1 GCAATGAAGGC
1735486 TGAAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 13 0.45
24 1 0.03
25 15 0.52
ACGTcount: A:0.41, C:0.17, G:0.29, T:0.14
Consensus pattern (25 bp):
GCAATGAAGGCCTAAACAGAAGTCA
Found at i:1751075 original size:21 final size:20
Alignment explanation
Indices: 1751042--1751080 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1751032 GATTGATTAC
1751042 AAATAATGATATATAATATAT
1 AAATAATGATATA-AATATAT
**
1751063 AAATAATTTTATAAATAT
1 AAATAATGATATAAATAT
1751081 TATTTTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATAATGATATAAATATAT
Found at i:1751134 original size:29 final size:31
Alignment explanation
Indices: 1751110--1751169 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1751100 ATAATTTAAG
1751110 TATTATATTAAA-ATTTT-TTAAAATTAAAA
1 TATTATATTAAATATTTTATTAAAATTAAAA
*
1751139 TATTATATTAAATATTTTATTATAATTAAAA
1 TATTATATTAAATATTTTATTAAAATTAAAA
1751170 AATCATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 5 0.18
31 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TATTATATTAAATATTTTATTAAAATTAAAA
Found at i:1751184 original size:31 final size:30
Alignment explanation
Indices: 1751114--1751185 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
1751104 TTTAAGTATT
* *
1751114 ATATTAAA-ATTTTTTAAAATTAAAATATT
1 ATATTAAATATTTTTTAAAATTAAAAAATC
*
1751143 ATATTAAATATTTTATTATAATTAAAAAATC
1 ATATTAAATATTTT-TTAAAATTAAAAAATC
1751174 AT-TTATAATATT
1 ATATTA-AATATT
1751186 AATCCACTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 8 0.22
30 8 0.22
31 21 0.57
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATTAAATATTTTTTAAAATTAAAAAATC
Found at i:1752244 original size:21 final size:20
Alignment explanation
Indices: 1752190--1752245 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1752180 TTAATTCTAT
*
1752190 TTTAAGATTATTTATATTTG
1 TTTAAGTTTATTTATATTTG
*
1752210 TTTAAGTTTATTTATATTTT
1 TTTAAGTTTATTTATATTTG
*
1752230 TTTAAGGTTTGTTTAT
1 TTTAA-GTTTATTTAT
1752246 TTAAATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 23 0.72
21 9 0.28
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (20 bp):
TTTAAGTTTATTTATATTTG
Found at i:1752245 original size:25 final size:24
Alignment explanation
Indices: 1752215--1752274 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
1752205 ATTTGTTTAA
*
1752215 GTTTATTTATATTTTTTTAAGGTT-T
1 GTTTATTTATATTTATTT-A-GTTAT
*
1752240 GTTTATTTAAATTTATTTAGTTAT
1 GTTTATTTATATTTATTTAGTTAT
1752264 GATTTATTTAT
1 G-TTTATTTAT
1752275 TATTCATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 3 0.10
25 24 0.80
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (24 bp):
GTTTATTTATATTTATTTAGTTAT
Found at i:1755646 original size:2 final size:2
Alignment explanation
Indices: 1755641--1755669 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1755631 TAAGTGTGTG
1755641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1755670 TAAAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1763892 original size:18 final size:19
Alignment explanation
Indices: 1763869--1763910 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1763859 GTATTCATAA
1763869 AAATT-AAAATCAATT-AAT
1 AAATTAAAAAT-AATTCAAT
1763887 AAATTAAAAATAATTCAAT
1 AAATTAAAAATAATTCAAT
1763906 AAATT
1 AAATT
1763911 CAATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTAAAAATAATTCAAT
Found at i:1764175 original size:18 final size:18
Alignment explanation
Indices: 1764127--1764181 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1764117 CCTAATCCGA
1764127 ATAAACTATATATAATTA-
1 ATAAA-TATATATAATTAT
1764145 A-AAATAT-TATAATTAT
1 ATAAATATATATAATTAT
*
1764161 ATAAATATATATAATTTT
1 ATAAATATATATAATTAT
1764179 ATA
1 ATA
1764182 TTTTTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 9 0.27
18 12 0.36
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATATATATAATTAT
Found at i:1764190 original size:21 final size:21
Alignment explanation
Indices: 1764166--1764209 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1764156 ATTATATAAA
1764166 TATATATAAT-TTTATATTTTT
1 TATATATAATATTT-TATTTTT
* *
1764187 TATATTTTATATTTTATTTTT
1 TATATATAATATTTTATTTTT
1764208 TA
1 TA
1764210 AAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TATATATAATATTTTATTTTT
Found at i:1768768 original size:68 final size:68
Alignment explanation
Indices: 1768651--1768783 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 68
1768641 ATTTGTGCAA
1768651 AAATCTGGGTGCACATATTACAAAATTACTTCAACCCTCTGACAGAATAGATTTATCG-TCTAAA
1 AAATCTGGGTGCACATATTACAAAATTACTTCAACCCTCTGACAGAATAGATTTAT-GTTCTAAA
1768715 GAAG
65 GAAG
* * *
1768719 AAATCTGGGTGCA-AGTATTACAAAGTTACTTTAACCCTCCT-A-TGAAATAGATTTATGTTCTA
1 AAATCTGGGTGCACA-TATTACAAAATTACTTCAACCCT-CTGACAG-AATAGATTTATGTTCTA
1768781 AAG
63 AAG
1768784 TAAGCATTAC
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
67 3 0.05
68 53 0.91
69 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (68 bp):
AAATCTGGGTGCACATATTACAAAATTACTTCAACCCTCTGACAGAATAGATTTATGTTCTAAAG
AAG
Found at i:1780628 original size:13 final size:12
Alignment explanation
Indices: 1780610--1780645 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
1780600 TGCTTAGTTT
1780610 TCTTGTTATTTGG
1 TCTTG-TATTTGG
1780623 TCTTGTATATTGG
1 TCTTGTAT-TTGG
1780636 TCTTGTATTT
1 TCTTGTATTT
1780646 TTTAAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.61
Consensus pattern (12 bp):
TCTTGTATTTGG
Found at i:1782883 original size:161 final size:150
Alignment explanation
Indices: 1782481--1782918 Score: 424
Period size: 148 Copynumber: 2.9 Consensus size: 150
1782471 GCAATTAGCC
** * *
1782481 AAAAGAAAAGGAATTTACT---AGCCTGTACCCAAGAGAAGATCCTTTCAGCAGCCAACAAAATT
1 AAAAGAAAA-GAATTTACTCGAAGCCTCCACCCAAGAGTAGATCCTTTCAGCAGCCAACAAAATC
* * *
1782543 GATTCCCTTAGAAACCTAAAAATCCGATTGAGCCCTATACCAGACAGGCCCATGTGAACTGAAAA
65 GATTCCCTTAGGAACCCAAAAATCCGATTGAGCCCTATACCAGAGAGGCCCATGTGAACTGAAAA
* * *
1782608 AG---ATTTTTGTAATTGTCA
130 AGTTCATTATTATAATTGGCA
* * ** *
1782626 AAAAGAAAAGAATTTATTCGAAGCCTGCACTAAAGAGTAGATCTTTTCAGCAGCCAACAAAAATC
1 AAAAGAAAAGAATTTACTCGAAGCCTCCACCCAAGAGTAGATCCTTTCAGCAGCCAAC-AAAATC
* * *
1782691 GAATCCCTTATGAACCCAAAAATCTGATTGAGCCCTATACCAGAGAGGCCCATGTGAACTGAAAA
65 GATTCCCTTAGGAACCCAAAAATCCGATTGAGCCCTATACCAGAGAGGCCCATGTGAACTG-AAA
1782756 AAGTTCAATCTACATTATAATTGGCA
129 AAGTTC-AT-T--ATTATAATTGGCA
* * * * * *
1782782 AAAAGAAAGGAATTTACTCGTAGCCTATACCCAAACCCAAGAGTAGATCCCTTCACCAGCTAGCA
1 AAAAGAAAAGAATTTACTCGAAGCC--T--CC--ACCCAAGAGTAGATCCTTTCAGCAGCCAACA
* * **
1782847 AAATCGATTCTCTTAGGAACCCAAAAATCCGATTGAG-TCTCAGGCCAGAGAGAG-CCATGTGAA
60 AAATCGATTCCCTTAGGAACCCAAAAATCCGATTGAGCCCT-ATACCAGAGAG-GCCCATGTGAA
*
1782910 CTGCAAAAG
123 CTGAAAAAG
1782919 GTTCTTGAAC
Statistics
Matches: 238, Mismatches: 35, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
144 8 0.03
145 9 0.04
147 32 0.13
148 60 0.25
149 6 0.03
153 2 0.01
154 1 0.00
156 32 0.13
158 1 0.00
160 8 0.03
161 55 0.23
162 24 0.10
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (150 bp):
AAAAGAAAAGAATTTACTCGAAGCCTCCACCCAAGAGTAGATCCTTTCAGCAGCCAACAAAATCG
ATTCCCTTAGGAACCCAAAAATCCGATTGAGCCCTATACCAGAGAGGCCCATGTGAACTGAAAAA
GTTCATTATTATAATTGGCA
Found at i:1789068 original size:2 final size:2
Alignment explanation
Indices: 1789063--1789100 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
1789053 TATTTTTTGT
*
1789063 TA TA TA TA TA TA TA TA TA TA TGA T- TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
1789101 ATGTATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1797450 original size:20 final size:23
Alignment explanation
Indices: 1797419--1797461 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1797409 AAGCTTAGTT
1797419 AATATATTTTTAT-TATA-ATAA
1 AATATATTTTTATGTATATATAA
1797440 AATAT-TTTTTATGTATATATAA
1 AATATATTTTTATGTATATATAA
1797462 GATTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATATATTTTTATGTATATATAA
Found at i:1797466 original size:20 final size:20
Alignment explanation
Indices: 1797425--1797472 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1797415 AGTTAATATA
*
1797425 TTTTTATTATAATAAAATAT
1 TTTTTATTATAATAAAAGAT
*
1797445 TTTTTATGTAT-ATATAAGAT
1 TTTTTAT-TATAATAAAAGAT
*
1797465 TTTATATT
1 TTTTTATT
1797473 TATGCACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTTATTATAATAAAAGAT
Found at i:1802486 original size:31 final size:31
Alignment explanation
Indices: 1802451--1802509 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1802441 TAACTTACTA
* * *
1802451 ATTAATGACGTATTATTATTTGATTTATCTT
1 ATTAATGAAGTATTATTATCTAATTTATCTT
*
1802482 ATTAATGAATTATTATTATCTAATTTAT
1 ATTAATGAAGTATTATTATCTAATTTAT
1802510 TGATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (31 bp):
ATTAATGAAGTATTATTATCTAATTTATCTT
Found at i:1809017 original size:355 final size:355
Alignment explanation
Indices: 1808108--1809164 Score: 1408
Period size: 357 Copynumber: 3.0 Consensus size: 355
1808098 TTTTTTTGAG
* * *
1808108 AAATTATTGAAGGCATTGTTATCTACAACCACTTTCACTAATTATCTATAAACTGTGATAAAAAT
1 AAATTATTGAAGGCATTGTTATATACAACCACCTTCACTAATTATCTACAAACTGTGAT-AAAAT
* ** * * *
1808173 TATTAAATGCATCTTTCTTGGATATTTGCCTTCACTAACCGTGTTAAAATTTGTGTGACGGTATA
65 TATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTGTGTGACAGTATA
* * * *
1808238 TAAAAAGTATTTTACAGTAGAAGACGCCTTTAATAATTACTAAAATTTTTAGTGAAAAAATTTTG
130 TAGAAAGTATTTTACAGTAGAAGACGCTTTTAATGATTCCTAAAATTTTTAGTGAAAAAATTTTG
* * *
1808303 AAGGCTTCTGTTATTAACAAACA-CCTTCAGTAATGGATTACTAAGTTTAAAGATATATTAAAAG
195 AAGGCTTCTGTTATTAACAAA-AGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGG
* * * *
1808367 TGCATTTTCGAATAAACGC-TTTCTATAACCATCGTGGTATATTAAAAGTGTGTCACAATAAAAG
259 CGC-TTTTCGAATAAACGCTTTTC-ATAACCATCGTGATATATTGAAAGTGTTTCACAATAAAAG
*
1808431 ACGCCTTTAATAGTCTGAAAAAAAAATTTTAAGA
322 ACGCCTTTAATAATCTGAAAAAAAAATTTTAAGA
* * ** * * * *
1808465 AAATTTTTGAAGGCATTGTTATATGCAACCGTCTTTATTAATTATATACAAACTGTTATAAGAAT
1 AAATTATTGAAGGCATTGTTATATACAACCACCTTCACTAATTATCTACAAACTGTGATAA-AAT
* ** *
1808530 TATTAAAGGCGTCTTTCTTGGATATACATCTTTAATAACCATGTTAAAATTTGTGTGACAGTATA
65 TATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTGTGTGACAGTATA
* * *
1808595 TAGAACGTATTTTACAGTAGAAGACGCTTTTAATGATTCTTAAAATTTTTAGTGAAAAAAATTTG
130 TAGAAAGTATTTTACAGTAGAAGACGCTTTTAATGATTCCTAAAATTTTTAGTGAAAAAATTTTG
* *
1808660 AAGGCATCTGTTATTAACAAAAGCCTTCAGTAATAGATTACTAAGTTTAAAGGTATATTGAAGGC
195 AAGGCTTCTGTTATTAACAAAAGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGC
* *
1808725 GTCTTTTCAAATAAACGCTTTTCATAACCATCGTGATATATTGAAAGTGTTTCATAATAAAAGAC
260 G-CTTTTCGAATAAACGCTTTTCATAACCATCGTGATATATTGAAAGTGTTTCACAATAAAAGAC
*
1808790 GCCTCTAATAATCTGAAAAAAAAATTTT-A-A
324 GCCTTTAATAATCTGAAAAAAAAATTTTAAGA
* * * *
1808820 AAATTATTGAAGACATTGTTATTTATAACCACCTTCACTAATTATCTACAAAGTGTGATAGAAAT
1 AAATTATTGAAGGCATTGTTATATACAACCACCTTCACTAATTATCTACAAACTGTGATA-AAAT
* * *
1808885 TATTAAAGGCATCTTTCTTAGATATACGCCTTCAATAACTATGTTAAAATTTGTGTTACAGTATA
65 TATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTGTGTGACAGTATA
* * * *
1808950 TAGAATGTATTTTACAGTAGAAGATGCTTTTAATGATTCCCAAAATTTTTAGTGAGAAAATTTTG
130 TAGAAAGTATTTTACAGTAGAAGACGCTTTTAATGATTCCTAAAATTTTTAGTGAAAAAATTTTG
* * *
1809015 AAGACTTCTGTTATTAACAAATGCCTTCAATAATGGATTACTAAGTTTAAAGGTATATTGAAGGC
195 AAGGCTTCTGTTATTAACAAAAGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGC
* * * * * * *
1809080 ACCTTTTTGAAT-AA-GCATCTTCCATAACTATCATGATATATTGAAGGCGTTTCACAATAAAAG
260 -GCTTTTCGAATAAACGC-T-TTTCATAACCATCGTGATATATTGAAAGTGTTTCACAATAAAAG
1809143 ACGCCTTTAATAAT-TCGAAAAA
322 ACGCCTTTAATAATCT-GAAAAA
1809165 CTTTTGTTAA
Statistics
Matches: 610, Mismatches: 81, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
353 2 0.00
354 4 0.01
355 294 0.48
356 5 0.01
357 300 0.49
358 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (355 bp):
AAATTATTGAAGGCATTGTTATATACAACCACCTTCACTAATTATCTACAAACTGTGATAAAATT
ATTAAAGGCATCTTTCTTGGATATACGCCTTCAATAACCATGTTAAAATTTGTGTGACAGTATAT
AGAAAGTATTTTACAGTAGAAGACGCTTTTAATGATTCCTAAAATTTTTAGTGAAAAAATTTTGA
AGGCTTCTGTTATTAACAAAAGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCG
CTTTTCGAATAAACGCTTTTCATAACCATCGTGATATATTGAAAGTGTTTCACAATAAAAGACGC
CTTTAATAATCTGAAAAAAAAATTTTAAGA
Found at i:1812444 original size:38 final size:38
Alignment explanation
Indices: 1812402--1812474 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
1812392 TATGACTAAT
1812402 GTCTTATTGTCGCAACAAATACTATCTGAAAGGTTAAA
1 GTCTTATTGTCGCAACAAATACTATCTGAAAGGTTAAA
1812440 GTCTTATTGTCGCAACAAATACTATCTGAAAGGTT
1 GTCTTATTGTCGCAACAAATACTATCTGAAAGGTT
1812475 CGATTGCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (38 bp):
GTCTTATTGTCGCAACAAATACTATCTGAAAGGTTAAA
Found at i:1823204 original size:58 final size:58
Alignment explanation
Indices: 1823114--1823230 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1823104 CCTTAATTGG
1823114 AGGTAACCCTACGAAGACTATTTTGACCTACACTAATTTATTAAATAATTAAAATATT
1 AGGTAACCCTACGAAGACTATTTTGACCTACACTAATTTATTAAATAATTAAAATATT
1823172 AGGTAACCCTACGAAGACTATTTTGACCTACACTAATTTATTAAATAATTAAAATATT
1 AGGTAACCCTACGAAGACTATTTTGACCTACACTAATTTATTAAATAATTAAAATATT
1823230 A
1 A
1823231 ATTCTTCTCT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (58 bp):
AGGTAACCCTACGAAGACTATTTTGACCTACACTAATTTATTAAATAATTAAAATATT
Found at i:1835248 original size:17 final size:17
Alignment explanation
Indices: 1835228--1835270 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1835218 ACTTTTCCTC
**
1835228 AAAAATTGATTTTTTTG
1 AAAAATTGATTTTTAAG
*
1835245 -AAAATTTATTTTTAAG
1 AAAAATTGATTTTTAAG
1835261 AAAAATTGAT
1 AAAAATTGAT
1835271 ACTTTCAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (17 bp):
AAAAATTGATTTTTAAG
Found at i:1835299 original size:118 final size:119
Alignment explanation
Indices: 1835143--1835362 Score: 347
Period size: 119 Copynumber: 1.9 Consensus size: 119
1835133 TTTGTGCAAA
* *
1835143 AAAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTTG-AAACTTT-AATTTCGAGAAAAA
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAATA-TTTTTTGAAAACTTTGAATTTCAAGAAAAA
*
1835206 TTGATACTTTCAACTTTTCCTCAAAAAT-TGATTTTTTTGAAAATTTATTTTTAAG
65 TTGATACTTTCAACTTTTCCCCAAAAATAT-ATTTTTTTGAAAATTTATTTTTAAG
* *
1835261 AAAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGAAAAAT
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGAAAACTTTGAATTTCAAGAAAAAT
*
1835326 TGATATTTTCAACTTTTCCCCAAAAATATATTTTTTT
66 TGATACTTTCAACTTTTCCCCAAAAATATATTTTTTT
1835363 ATTTTTATTT
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
117 7 0.08
118 39 0.42
119 46 0.49
120 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (119 bp):
AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGAAAACTTTGAATTTCAAGAAAAAT
TGATACTTTCAACTTTTCCCCAAAAATATATTTTTTTGAAAATTTATTTTTAAG
Found at i:1835329 original size:59 final size:59
Alignment explanation
Indices: 1835143--1835361 Score: 300
Period size: 60 Copynumber: 3.7 Consensus size: 59
1835133 TTTGTGCAAA
* * * *
1835143 AAAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTTG-AAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAACTTTATTTTCAAG
* *
1835201 AAAAATTGATACTTTCAACTTTTCCTCAAAAATTGATTTTTTTGAAAA-TTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAA-T-ATTTTTTTGAAAACTTTATTTTCAAG
**
1835261 AAAAATTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTGAAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAACTTT-ATTTTCAAG
*
1835320 AAAAATTGATATTTTCAACTTTTCCCCAAAAATATATTTTTT
1 AAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTT
1835362 TATTTTTATT
Statistics
Matches: 141, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
57 11 0.08
58 33 0.23
59 41 0.29
60 47 0.33
61 9 0.06
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (59 bp):
AAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAACTTTATTTTCAAG
Found at i:1835427 original size:11 final size:11
Alignment explanation
Indices: 1835411--1835547 Score: 54
Period size: 11 Copynumber: 12.0 Consensus size: 11
1835401 AAGTGAAGAT
1835411 AAATAAATAAA
1 AAATAAATAAA
1835422 AAAT-AA-AAA
1 AAATAAATAAA
*
1835431 AAATAAA-GAA
1 AAATAAATAAA
*
1835441 AAGTAAA-ACAA
1 AAATAAATA-AA
1835452 AAATAAA-AATA
1 AAATAAATAA-A
1835463 AAATAAAGATAAA
1 AAAT-AA-ATAAA
*
1835476 AGAAT-ATTAAA
1 A-AATAAATAAA
*
1835487 TAAACCTAATCTAAA
1 -AAA--TAA-ATAAA
*
1835502 AATTAAA-AAA
1 AAATAAATAAA
* *
1835512 ATTAAAAAAAAAA
1 A--AATAAATAAA
1835525 AAATAAATAAA
1 AAATAAATAAA
1835536 CAAATAAATAAA
1 -AAATAAATAAA
1835548 TTCAAAAAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 31
0.70 0.09 0.22
Matches are distributed among these distances:
9 7 0.07
10 17 0.17
11 32 0.33
12 22 0.22
13 8 0.08
14 8 0.08
15 4 0.04
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.18
Consensus pattern (11 bp):
AAATAAATAAA
Done.