Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 49 of 226
Found at i:20280033 original size:2 final size:2
Alignment explanation
Indices: 20280026--20280061 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20280016 TACATATGCG
20280026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20280062 AGTATAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20280073 original size:3 final size:3
Alignment explanation
Indices: 20280065--20280149 Score: 75
Period size: 3 Copynumber: 27.3 Consensus size: 3
20280055 ATATATAAGT
* * *
20280065 ATA ATA ATA TTA ATA TGTA AT- ATA ATA ATAA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
*
20280111 ATA CAGTA ATA ATA ACA ATA ATA ATA ATTA AT- ATA ATA A
1 ATA -A-TA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA A
20280150 AATTAATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.76
4 10 0.15
5 2 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:20280146 original size:12 final size:11
Alignment explanation
Indices: 20280035--20280149 Score: 60
Period size: 14 Copynumber: 9.8 Consensus size: 11
20280025 GTATATATAT
20280035 ATATATATATATA
1 ATATA-ATA-ATA
20280048 TATATATATATATA
1 -ATATA-ATA-ATA
20280062 AGTATAATAAT-
1 A-TATAATAATA
*
20280073 AT-TAATATGTA
1 ATATAATA-ATA
20280084 ATATAATAATA
1 ATATAATAATA
*
20280095 A-ATAATACT-
1 ATATAATAATA
20280104 A-ATAATAATA
1 ATATAATAATA
*
20280114 CAGTAATAATAACA
1 -A-T-ATAATAATA
20280128 ATAATAATAATTA
1 AT-ATAATAA-TA
20280141 ATATAATAA
1 ATATAATAA
20280150 AATTAATGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
9 13 0.15
10 9 0.11
11 7 0.08
12 23 0.27
13 8 0.09
14 25 0.29
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (11 bp):
ATATAATAATA
Found at i:20280155 original size:14 final size:15
Alignment explanation
Indices: 20280128--20280165 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
20280118 AATAATAACA
20280128 ATAATAATAATTAAT-
1 ATAATAA-AATTAATG
20280143 ATAATAAAATTAATG
1 ATAATAAAATTAATG
20280158 AT-ATAAAA
1 ATAATAAAA
20280166 GAAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATAATAAAATTAATG
Found at i:20280719 original size:21 final size:21
Alignment explanation
Indices: 20280686--20280737 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
20280676 TATTTTTTAC
*
20280686 AAAAAAAACAACAG-AAAAATG
1 AAAAAAAA-AACAGTAAAAAGG
20280707 AAAACAAAAAACAGTAAAAAGG
1 AAAA-AAAAAACAGTAAAAAGG
20280729 AAAAAAAAA
1 AAAAAAAAA
20280738 TGGAGAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.79, C:0.08, G:0.10, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAACAGTAAAAAGG
Found at i:20284160 original size:50 final size:50
Alignment explanation
Indices: 20284104--20284223 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
20284094 ATTAGGGGAT
* * *
20284104 GAGATCCCATGTAAGACCATGTCTAG-GATATGGCGTTGGCACCGAGATGA
1 GAGATCCCATGTAAGACCATGTCT-GCGACATGGCATGGGCACCGAGATGA
*** *
20284154 GAGATCCCCCATAAGACCATGTCTGCGACATGGCATGGGCACCGATATGA
1 GAGATCCCATGTAAGACCATGTCTGCGACATGGCATGGGCACCGAGATGA
*
20284204 GA-ACTCCTATGTAAGACCAT
1 GAGA-TCCCATGTAAGACCAT
20284224 ATTTGGGATA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 2 0.04
50 55 0.96
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (50 bp):
GAGATCCCATGTAAGACCATGTCTGCGACATGGCATGGGCACCGAGATGA
Found at i:20290521 original size:15 final size:15
Alignment explanation
Indices: 20290488--20290530 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20290478 GTTAAAAATA
20290488 TAAAATATAAAATTC
1 TAAAATATAAAATTC
* * *
20290503 TAAAATATATATTTT
1 TAAAATATAAAATTC
20290518 TAAAA-ATAAAATT
1 TAAAATATAAAATT
20290531 ATTATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATATAAAATTC
Found at i:20290700 original size:19 final size:17
Alignment explanation
Indices: 20290668--20290702 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
20290658 TGATTTTCTT
20290668 TTTTAAATTTATAATTA
1 TTTTAAATTTATAATTA
20290685 TTTTAGAATTTAATAATT
1 TTTTA-AATTT-ATAATT
20290703 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTAAATTTATAATTA
Found at i:20290886 original size:21 final size:21
Alignment explanation
Indices: 20290831--20290886 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
20290821 ACATGGATGG
* *
20290831 TCAACAATGGTCCACGGTCGA
1 TCAACAATGGTCAACAGTCGA
* * *
20290852 TCAAC-GTCGATCAACAGTCTA
1 TCAACAAT-GGTCAACAGTCGA
20290873 TCAACAATGGTCAA
1 TCAACAATGGTCAA
20290887 TGTCGGTCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (21 bp):
TCAACAATGGTCAACAGTCGA
Found at i:20291676 original size:28 final size:27
Alignment explanation
Indices: 20291630--20291706 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
20291620 AAAAATTTTA
*
20291630 TATTTATATTTTTTGAATTTTTAATAAT
1 TATTTATATTTTAT-AATTTTTAATAAT
* *
20291658 TATTTATATTTTAATAATTTCTATTAAT
1 TATTTATATTTT-ATAATTTTTAATAAT
*
20291686 T-TTGTA-ATTTTATGATTTTTA
1 TATT-TATATTTTATAATTTTTA
20291707 GAAATATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 8 0.19
27 7 0.17
28 26 0.62
29 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (27 bp):
TATTTATATTTTATAATTTTTAATAAT
Found at i:20291751 original size:20 final size:20
Alignment explanation
Indices: 20291700--20291751 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
20291690 TAATTTTATG
*
20291700 ATTTTTAGA-AATATTTAAT
1 ATTTTTAAATAATATTTAAT
* * **
20291719 AATATTATTTAATATTTAAT
1 ATTTTTAAATAATATTTAAT
20291739 ATTTTTAAATAAT
1 ATTTTTAAATAAT
20291752 TGCTAATAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTTAAATAATATTTAAT
Found at i:20291902 original size:20 final size:21
Alignment explanation
Indices: 20291869--20291908 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20291859 TAAAATAAAA
*
20291869 TTTTAGAATATTTTATTAATT
1 TTTTAAAATATTTTATTAATT
*
20291890 TTTTAAAAT-TTTTGTTAAT
1 TTTTAAAATATTTTATTAAT
20291909 GTGACATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTAAAATATTTTATTAATT
Found at i:20298060 original size:22 final size:22
Alignment explanation
Indices: 20298032--20298073 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20298022 TATATTAAAC
*
20298032 CATGTATTTATTTGATTGATGA
1 CATGTATTTATTTAATTGATGA
20298054 CATGTATTTATTTAATTGAT
1 CATGTATTTATTTAATTGAT
20298074 ATGTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (22 bp):
CATGTATTTATTTAATTGATGA
Found at i:20303659 original size:2 final size:2
Alignment explanation
Indices: 20303652--20303808 Score: 314
Period size: 2 Copynumber: 78.5 Consensus size: 2
20303642 ATCCAAAGTC
20303652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20303694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20303736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20303778 AT 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 AT A
20303809 ACTCATATTT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 155 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20303883 original size:2 final size:2
Alignment explanation
Indices: 20303876--20303903 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20303866 ATATTTACAC
20303876 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
20303904 TACTCATCAG
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:20303945 original size:2 final size:2
Alignment explanation
Indices: 20303938--20303981 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
20303928 TGCACCCATA
20303938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20303980 AT
1 AT
20303982 CAACCACCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20304155 original size:41 final size:41
Alignment explanation
Indices: 20304110--20304211 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
20304100 ACTGGCAATT
* * *
20304110 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCAGAAACATTTCACCGGCATCA
*
20304151 AGCCTGCTAGACGTATAGTCAGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCAGAAACATTTCACCGGCATCA
20304192 AGCCTGCTAGACGTAAAGTC
1 AGCCTGCTAGACGTAAAGTC
20304212 TGAATTATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCAGAAACATTTCACCGGCATCA
Found at i:20315000 original size:20 final size:20
Alignment explanation
Indices: 20314963--20315002 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20314953 AATATGGGTA
* *
20314963 AATTATATAGATAGTCATTT
1 AATTATATAAAAAGTCATTT
*
20314983 AATTATATAAAAATTCATTT
1 AATTATATAAAAAGTCATTT
20315003 TAGGCACTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
AATTATATAAAAAGTCATTT
Found at i:20324328 original size:11 final size:11
Alignment explanation
Indices: 20324312--20324336 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20324302 TTACTTTATG
20324312 AATGCCAGAGA
1 AATGCCAGAGA
20324323 AATGCCAGAGA
1 AATGCCAGAGA
20324334 AAT
1 AAT
20324337 TTTCCACGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.24, T:0.12
Consensus pattern (11 bp):
AATGCCAGAGA
Found at i:20327655 original size:22 final size:22
Alignment explanation
Indices: 20327638--20327701 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
20327628 TATTAAATAT
20327638 ATATATTTTTATTTTTAATCAA
1 ATATATTTTTATTTTTAATCAA
20327660 ATATATTTTTATTTTTAATCAA
1 ATATATTTTTATTTTTAATCAA
*
20327682 ATATATTTTTTGTTTTTAAT
1 ATATA-TTTTTATTTTTAAT
20327702 TTAGATTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
22 27 0.68
23 13 0.32
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATATTTTTATTTTTAATCAA
Found at i:20331464 original size:10 final size:10
Alignment explanation
Indices: 20331451--20331479 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
20331441 TTTCTGCTTG
20331451 TTTATTTTAT
1 TTTATTTTAT
20331461 TTTATTTTA-
1 TTTATTTTAT
20331470 TTTATTTTAT
1 TTTATTTTAT
20331480 CTTTTACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:20331475 original size:4 final size:5
Alignment explanation
Indices: 20331451--20331479 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
20331441 TTTCTGCTTG
20331451 TTTAT TTTAT TTTAT TTTA- TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
20331480 CTTTTACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:20333881 original size:49 final size:49
Alignment explanation
Indices: 20333805--20333948 Score: 207
Period size: 49 Copynumber: 2.9 Consensus size: 49
20333795 ATGTGAACAT
* * *
20333805 GTGATTATGCGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
20333855 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
20333904 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
20333949 AGAAAACGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
49 82 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:20337210 original size:46 final size:45
Alignment explanation
Indices: 20337143--20337560 Score: 527
Period size: 46 Copynumber: 9.6 Consensus size: 45
20337133 TTTGAGTACT
*
20337143 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
20337189 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
20337235 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
20337281 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
20337317 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
20337363 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
20337399 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACTCTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
20337445 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACCCTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
20337491 TCTGATAAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
20337536 TCTGATC-AG-G-GACAAGTGATAAGTG
1 TCTGATCAAGTGAGA-AAGTGATAAGTG
20337561 ATCATATGTA
Statistics
Matches: 335, Mismatches: 16, Indels: 45
0.85 0.04 0.11
Matches are distributed among these distances:
36 58 0.17
37 2 0.01
38 1 0.00
39 2 0.01
40 5 0.01
41 1 0.00
42 7 0.02
43 15 0.04
44 3 0.01
45 20 0.06
46 221 0.66
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:20337312 original size:36 final size:36
Alignment explanation
Indices: 20337271--20337425 Score: 184
Period size: 36 Copynumber: 4.0 Consensus size: 36
20337261 GGTAGCATTA
20337271 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
20337307 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
20337352 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
20337389 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
20337425 G
1 G
20337426 GTAGCCTTAG
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 65 0.63
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.29
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:20337318 original size:82 final size:81
Alignment explanation
Indices: 20337225--20337560 Score: 460
Period size: 82 Copynumber: 4.0 Consensus size: 81
20337215 GGTAGCATTA
*
20337225 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAA
20337290 GTGAAAAAGTGATAAGT
65 GTGAAAAAGTGATAAGT
*
20337307 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAA
20337372 GTGAAAAAGTGATAAGT
65 GTGAAAAAGTGATAAGT
* *
20337389 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACTCTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAA
*
20337454 GTGAGAAAGTGATAAGTGGT
65 GTGAAAAAGTGATAA---GT
* *
20337474 AGCCTTAGCTACCCTTATCTGATAAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCT
1 -G-C-TA-C-A--CTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCT
* *
20337539 GATC-AG-GGACAAGTGATAAGT
59 GATCAAGTGAAAAAGTGATAAGT
20337560 G
1 G
20337561 ATCATATGTA
Statistics
Matches: 229, Mismatches: 14, Indels: 19
0.87 0.05 0.07
Matches are distributed among these distances:
82 153 0.67
83 1 0.00
85 3 0.01
86 3 0.01
87 1 0.00
88 2 0.01
89 10 0.04
90 3 0.01
91 19 0.08
92 34 0.15
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (81 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAG
TGAAAAAGTGATAAGT
Found at i:20337335 original size:128 final size:126
Alignment explanation
Indices: 20337179--20337560 Score: 478
Period size: 128 Copynumber: 3.0 Consensus size: 126
20337169 GGTAGCATTA
20337179 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
20337244 GTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
66 GTGAAAAAGTGATAAGTGGTAGC--TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
20337307 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
*
20337372 GTGAAAAAGTGATAA---GT-GCTA--T--ACTTATCTGATCAAGTGACAAAGTGATAAGTGGT
66 GTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAA---GT
* *
20337428 AGCCTTAGCTACTCTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACCCTTATC
1 -G-C-TA-C-A--CTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATC
* * * *
20337493 TGATAAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AG-GGACAAGTGAT
59 TGATCAAGTGAAAAAGTGATAAGTGGTAG-CTAGCTACACTTATCTGATCAAGTGAAAAAGTGAT
20337556 AAGT
123 AAGT
20337560 G
1 G
20337561 ATCATATGTA
Statistics
Matches: 221, Mismatches: 14, Indels: 35
0.82 0.05 0.13
Matches are distributed among these distances:
118 28 0.13
120 1 0.00
121 2 0.01
122 3 0.01
123 1 0.00
124 4 0.02
125 3 0.01
126 1 0.00
128 144 0.65
131 3 0.01
132 3 0.01
133 3 0.01
135 11 0.05
136 2 0.01
137 12 0.05
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (126 bp):
GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAA
GTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:20340412 original size:29 final size:29
Alignment explanation
Indices: 20340344--20340443 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
20340334 ATTATCATTG
* * * *
20340344 CACTATGACCCTTAAACTTTTTGAAATTT
1 CACTTTGACCCCTAAACTTTTTAAAATTA
* *
20340373 CACTTTAACCCCTCAACTTTTTAAAATTA
1 CACTTTGACCCCTAAACTTTTTAAAATTA
* *
20340402 CATTTTGACCCC-AAAATTTTCTCAAAATTA
1 CACTTTGACCCCTAAACTTTT-T-AAAATTA
*
20340432 CACTTTGGCCCC
1 CACTTTGACCCC
20340444 AGAAGTTTTG
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
28 6 0.11
29 34 0.60
30 17 0.30
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (29 bp):
CACTTTGACCCCTAAACTTTTTAAAATTA
Found at i:20340918 original size:3 final size:3
Alignment explanation
Indices: 20340912--20341024 Score: 90
Period size: 3 Copynumber: 37.0 Consensus size: 3
20340902 GGGGCTGAAC
* * * *
20340912 GAA GAA GAA -AG GAA AAA GAA GAA GAA AAA AAA GAAA GAA -AA -AA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA
*
20340955 GAA GAA GAA GAAA GAA AAA G-A GAAA GAAA GAA GGAA GAA GAA GAA GAA
1 GAA GAA GAA G-AA GAA GAA GAA G-AA G-AA GAA -GAA GAA GAA GAA GAA
*
20341003 GAA GAA GAA GAAA GAA AAA GAA
1 GAA GAA GAA G-AA GAA GAA GAA
20341025 AAAAGAAAGA
Statistics
Matches: 92, Mismatches: 10, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
2 7 0.08
3 67 0.73
4 18 0.20
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20340945 original size:26 final size:25
Alignment explanation
Indices: 20340916--20341041 Score: 109
Period size: 26 Copynumber: 5.0 Consensus size: 25
20340906 CTGAACGAAG
20340916 AAGAAAGGAAAAAGAAGAAGAAAAAA
1 AAGAAA-GAAAAAGAAGAAGAAAAAA
*
20340942 AAGAAAGAAAAAAGAAGAAGAAGAAAG
1 AAGAAAG-AAAAAGAAGAAGAA-AAAA
* * *
20340969 AA-AAAGAGAAAGAAAGAAGGAAGAAG
1 AAGAAAGAAAAAG-AAGAA-GAAAAAA
*
20340995 AAG-AAGAAGAAGAAGAAGAAAGAAA
1 AAGAAAGAAAAAGAAGAAGAAA-AAA
*
20341020 AAGAAA-AAAGA-AAG-AGAAAAAA
1 AAGAAAGAAAAAGAAGAAGAAAAAA
20341042 GGAAAAAGGA
Statistics
Matches: 84, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.04
23 5 0.06
24 6 0.07
25 19 0.23
26 43 0.51
27 8 0.10
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (25 bp):
AAGAAAGAAAAAGAAGAAGAAAAAA
Found at i:20341017 original size:42 final size:42
Alignment explanation
Indices: 20340912--20341034 Score: 149
Period size: 42 Copynumber: 2.8 Consensus size: 42
20340902 GGGGCTGAAC
* *
20340912 GAAGAAGAAAGGAAAAAGAAGAAGAAAAAAAAGAAAGAAAAAAGAA
1 GAAGAAGAAA-GAAAAAGAA-AA-AGAAAAAAGAAAG-AAGAAGAA
* * *
20340958 GAAGAAGAAAGAAAAAGAGAAAGAAAGAAGGAAGAAGAAGAA
1 GAAGAAGAAAGAAAAAGAAAAAGAAAAAAGAAAGAAGAAGAA
20341000 GAAGAAG-AAGAAGAAAGAAAAAGAAAAAAGAAAGA
1 GAAGAAGAAAGAA-AAAGAAAAAGAAAAAAGAAAGA
20341035 GAAAAAAGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 5 0.07
42 33 0.49
43 10 0.15
44 2 0.03
45 8 0.12
46 10 0.15
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (42 bp):
GAAGAAGAAAGAAAAAGAAAAAGAAAAAAGAAAGAAGAAGAA
Found at i:20341025 original size:6 final size:6
Alignment explanation
Indices: 20340913--20341055 Score: 92
Period size: 6 Copynumber: 22.3 Consensus size: 6
20340903 GGGCTGAACG
* * *
20340913 AAGAAGA AAGGAAA AAGAAG AAGAAA AAAAAGA AAGAAAA AAGAAG AAGAAGA
1 AAGAA-A AA-GAAA AAGAAA AAGAAA AAGAA-A AAG-AAA AAGAAA AAGAA-A
* * * * *
20340966 AAGAAA AAGAGA AAG--A AAGAAGG AAGAAG AAGAAG AAGAAG AAGAAGA
1 AAGAAA AAGAAA AAGAAA AAGAA-A AAGAAA AAGAAA AAGAAA AAGAA-A
*
20341014 AAGAAA AAGAAAA AAGAAA GAGAAAA AAGGAAA AAGGAAA AA
1 AAGAAA AAG-AAA AAGAAA AAG-AAA AA-GAAA AA-GAAA AA
20341056 AATATTTTAT
Statistics
Matches: 114, Mismatches: 11, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.04
6 55 0.48
7 49 0.43
8 6 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:20341487 original size:5 final size:5
Alignment explanation
Indices: 20341477--20341520 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
20341467 TTTAAGTATT
20341477 TTTTA TTTTA TATTTA TGTTT- TTTTAA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA T-TTTA T-TTTA TTTT-A TTTTA TTTTA TTTTA TT
20341521 CGTTAAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
4 3 0.09
5 20 0.57
6 12 0.34
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:20341501 original size:16 final size:17
Alignment explanation
Indices: 20341477--20341519 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
20341467 TTTAAGTATT
20341477 TTTTATTTTATA-TTTA
1 TTTTATTTTATATTTTA
20341493 TGTTT-TTTTA-ATTTTA
1 T-TTTATTTTATATTTTA
20341509 TTTTATTTTAT
1 TTTTATTTTAT
20341520 TCGTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.17
16 16 0.70
17 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATATTTTA
Found at i:20341501 original size:21 final size:21
Alignment explanation
Indices: 20341466--20341514 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
20341456 TATTGCATAT
*
20341466 TTTTAAGTATTTTTT-ATTTTA
1 TTTTATGT-TTTTTTAATTTTA
20341487 TATTTATGTTTTTTTAATTTTA
1 T-TTTATGTTTTTTTAATTTTA
20341509 TTTTAT
1 TTTTAT
20341515 TTTATTCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTATGTTTTTTTAATTTTA
Found at i:20341852 original size:15 final size:15
Alignment explanation
Indices: 20341825--20341857 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
20341815 AAAGAAAGAA
20341825 AAATTTTGTG-TTTC
1 AAATTTTGTGTTTTC
20341839 AAATTTTCGTGTTTTC
1 AAATTTT-GTGTTTTC
20341855 AAA
1 AAA
20341858 AATTACTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (15 bp):
AAATTTTGTGTTTTC
Found at i:20341961 original size:21 final size:21
Alignment explanation
Indices: 20341899--20341962 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
20341889 TCGCATTTTC
* *
20341899 AAAAGTCT-TCGTGTTTCAAA
1 AAAAATCTCTCGTATTTCAAA
* * * *
20341919 AAAAATTTCGCGTTTTTAAAA
1 AAAAATCTCTCGTATTTCAAA
20341940 AAAAATCTCTCGTATTTCAAA
1 AAAAATCTCTCGTATTTCAAA
20341961 AA
1 AA
20341963 TTGTCGCGTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.34
Consensus pattern (21 bp):
AAAAATCTCTCGTATTTCAAA
Found at i:20341980 original size:19 final size:18
Alignment explanation
Indices: 20341917--20342104 Score: 66
Period size: 18 Copynumber: 10.4 Consensus size: 18
20341907 TCGTGTTTCA
20341917 AAAAAAATTTCGCGTTTTT
1 AAAAAAATTTCGCG-TTTT
* *
20341936 AAAAAAAAATCTCTCGTATTT
1 --AAAAAAATTTCGCGT-TTT
*
20341957 -CAAAAATTGTCGCGTTTT
1 AAAAAAATT-TCGCGTTTT
**
20341975 AAAAAAATTTCTTGTTTT
1 AAAAAAATTTCGCGTTTT
* * * *
20341993 -CAATAA-TTCTCTTGTTT
1 AAAAAAATTTCGCGT-TTT
* * * *
20342010 CACAAATTTTCGTGTTTT
1 AAAAAAATTTCGCGTTTT
* *
20342028 -AAAAATTTTCGTGTTTT
1 AAAAAAATTTCGCGTTTT
* *
20342045 CAAAAAATTTACCCTGTTTT
1 AAAAAAATTT-CGC-GTTTT
* * *
20342065 -CAAAAA-TTCTCGTGTT
1 AAAAAAATTTCGCGTTTT
*
20342081 -AAAAAATTTCGTGTTTT
1 AAAAAAATTTCGCGTTTT
20342098 AAAAAAA
1 AAAAAAA
20342105 AATCGTGTTT
Statistics
Matches: 126, Mismatches: 30, Indels: 25
0.70 0.17 0.14
Matches are distributed among these distances:
16 14 0.11
17 32 0.25
18 37 0.29
19 22 0.17
20 6 0.05
21 15 0.12
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (18 bp):
AAAAAAATTTCGCGTTTT
Found at i:20342084 original size:53 final size:53
Alignment explanation
Indices: 20342007--20342161 Score: 161
Period size: 53 Copynumber: 2.9 Consensus size: 53
20341997 AATTCTCTTG
* * **
20342007 TTTCACAAATTTTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTTACCCTGT
1 TTTCAAAAATTATCGTG-TTTAAAAATTTTCGTGTTTTCAAAAAA-AAACCCTGT
* * * *
20342062 TTTCAAAAATTCTCGTG-TTAAAAAATTTCGTGTTTT-AAAAAAAAATCGTGT
1 TTTCAAAAATTATCGTGTTTAAAAATTTTCGTGTTTTCAAAAAAAAACCCTGT
* * *
20342113 TTTCAAAAAAGTTATTGTGTTTCAAAATTCTCGTGTTTTCAAAAAAAAA
1 TTTC-AAAAA-TTATCGTGTTTAAAAATTTTCGTGTTTTCAAAAAAAAA
20342162 ATCTCGAGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
51 9 0.11
52 11 0.13
53 24 0.29
54 16 0.19
55 24 0.29
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (53 bp):
TTTCAAAAATTATCGTGTTTAAAAATTTTCGTGTTTTCAAAAAAAAACCCTGT
Found at i:20342092 original size:15 final size:16
Alignment explanation
Indices: 20342066--20342095 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20342056 CCCTGTTTTC
20342066 AAAAATTCTCGTGTTA
1 AAAAATTCTCGTGTTA
20342082 AAAAATT-TCGTGTT
1 AAAAATTCTCGTGTT
20342096 TTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (16 bp):
AAAAATTCTCGTGTTA
Found at i:20342099 original size:17 final size:17
Alignment explanation
Indices: 20341958--20342158 Score: 122
Period size: 18 Copynumber: 11.3 Consensus size: 17
20341948 CTCGTATTTC
*
20341958 AAAAATTGTCGCGTTTTAA
1 AAAAATT-TCGTGTTTT-A
* *
20341977 AAAAATTTCTTGTTTTC
1 AAAAATTTCGTGTTTTA
* * *
20341994 AATAATTCTCTTGTTTCA
1 AAAAATT-TCGTGTTTTA
* *
20342012 CAAATTTTCGTGTTTTA
1 AAAAATTTCGTGTTTTA
*
20342029 AAAATTTTCGTGTTTTCA
1 AAAAATTTCGTGTTTT-A
* *
20342047 AAAAATTTACCCTGTTTTC
1 AAAAATTT--CGTGTTTTA
20342066 AAAAATTCTCGTG--TTA
1 AAAAATT-TCGTGTTTTA
20342082 AAAAATTTCGTGTTTTAA
1 AAAAATTTCGTGTTTT-A
**
20342100 AAAAAAATCGTGTTTTCA
1 AAAAATTTCGTGTTTT-A
*
20342118 AAAAAGTTATTGTG-TTT-
1 AAAAA-TT-TCGTGTTTTA
*
20342135 CAAAATTCTCGTGTTTTCA
1 AAAAATT-TCGTGTTTT-A
20342154 AAAAA
1 AAAAA
20342159 AAAATCTCGA
Statistics
Matches: 142, Mismatches: 27, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
15 5 0.04
16 15 0.11
17 38 0.27
18 51 0.36
19 21 0.15
20 12 0.08
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTA
Found at i:20342157 original size:18 final size:18
Alignment explanation
Indices: 20341940--20342157 Score: 141
Period size: 17 Copynumber: 12.3 Consensus size: 18
20341930 GTTTTTAAAA
*
20341940 AAAAATCTCTCGT-ATTTC
1 AAAAAT-TCTCGTGTTTTC
* * *
20341958 AAAAATTGTCGCGTTTTAA
1 AAAAATTCTCGTGTTTT-C
*
20341977 AAAAATT-TCTTGTTTTC
1 AAAAATTCTCGTGTTTTC
* *
20341994 AATAATTCTCTTG-TTTC
1 AAAAATTCTCGTGTTTTC
* *
20342011 ACAAATTTTCGTGTTTT-
1 AAAAATTCTCGTGTTTTC
*
20342028 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
*
20342046 AAAAAATT-TACCCTGTTTTC
1 -AAAAATTCT--CGTGTTTTC
*
20342066 AAAAATTCTCGTG--TTA
1 AAAAATTCTCGTGTTTTC
*
20342082 AAAAATT-TCGTGTTTTA
1 AAAAATTCTCGTGTTTTC
***
20342099 AAAAAAAATCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
* *
20342117 AAAAAAGTTATTGTG-TTTC
1 -AAAAA-TTCTCGTGTTTTC
20342136 -AAAATTCTCGTGTTTTC
1 AAAAATTCTCGTGTTTTC
20342153 AAAAA
1 AAAAA
20342158 AAAAATCTCG
Statistics
Matches: 160, Mismatches: 24, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.03
16 15 0.09
17 55 0.34
18 41 0.26
19 30 0.19
20 14 0.09
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (18 bp):
AAAAATTCTCGTGTTTTC
Found at i:20343592 original size:7 final size:7
Alignment explanation
Indices: 20343582--20343606 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20343572 TTTACTTTTC
20343582 TATTATT
1 TATTATT
20343589 TATTATT
1 TATTATT
20343596 TATTATT
1 TATTATT
20343603 TATT
1 TATT
20343607 TCATAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTATT
Found at i:20347004 original size:43 final size:43
Alignment explanation
Indices: 20346943--20347029 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
20346933 GGGGTGGTAC
20346943 GGTATGCAAGTCAAGAAAACTTTGCAGTTTGTAAGCTTTAACA
1 GGTATGCAAGTCAAGAAAACTTTGCAGTTTGTAAGCTTTAACA
20346986 GGTATGCAAGTCAAGAAAACTTTGCAGTTTGTAAGCTTTAACA
1 GGTATGCAAGTCAAGAAAACTTTGCAGTTTGTAAGCTTTAACA
20347029 G
1 G
20347030 CCAACAGAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (43 bp):
GGTATGCAAGTCAAGAAAACTTTGCAGTTTGTAAGCTTTAACA
Found at i:20358133 original size:27 final size:27
Alignment explanation
Indices: 20358089--20358142 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20358079 TAGTATGAAG
* *
20358089 TATTTTTAAATTTAAAAAAATAAAAAA
1 TATTTTTAAAATTAAAAAAAGAAAAAA
*
20358116 TATTTTTAAAAATT-AAAATAGAAAAAA
1 TATTTTT-AAAATTAAAAAAAGAAAAAA
20358143 ATAGAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
TATTTTTAAAATTAAAAAAAGAAAAAA
Found at i:20363718 original size:9 final size:9
Alignment explanation
Indices: 20363702--20363752 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
20363692 GAGTTAAACG
20363702 AATCGAGTT
1 AATCGAGTT
*
20363711 ATTCGAGTT
1 AATCGAGTT
20363720 AATCGAGTT
1 AATCGAGTT
20363729 AATCGAGTT
1 AATCGAGTT
20363738 AATCGAGTT
1 AATCGAGTT
*
20363747 ATTCGA
1 AATCGA
20363753 ATCAACTCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (9 bp):
AATCGAGTT
Found at i:20363725 original size:18 final size:18
Alignment explanation
Indices: 20363702--20363752 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
20363692 GAGTTAAACG
20363702 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
*
20363720 AATCGAGTTAATCGAGTT
1 AATCGAGTTATTCGAGTT
20363738 AATCGAGTTATTCGA
1 AATCGAGTTATTCGA
20363753 ATCAACTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:20374368 original size:18 final size:18
Alignment explanation
Indices: 20374314--20374378 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 18
20374304 TTAATTTTTA
20374314 TGAAT-TTTTTATTGAATTT
1 TGAATATTTTTA-T-AATTT
* * *
20374333 TG-ATTTTTTTGTACTTT
1 TGAATATTTTTATAATTT
20374350 TGAATATTTTTATAATTTT
1 TGAATATTTTTATAA-TTT
20374369 TGAATCATTT
1 TGAAT-ATTT
20374379 GTTTACGGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.16
18 12 0.32
19 15 0.41
20 4 0.11
ACGTcount: A:0.25, C:0.03, G:0.09, T:0.63
Consensus pattern (18 bp):
TGAATATTTTTATAATTT
Found at i:20381557 original size:20 final size:20
Alignment explanation
Indices: 20381532--20381571 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20381522 GATTGGTTCG
20381532 CTGTATTAGATTAGAGGTGT
1 CTGTATTAGATTAGAGGTGT
20381552 CTGTATTAGATTAGAGGTGT
1 CTGTATTAGATTAGAGGTGT
20381572 ATTGGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.40
Consensus pattern (20 bp):
CTGTATTAGATTAGAGGTGT
Found at i:20381574 original size:16 final size:16
Alignment explanation
Indices: 20381533--20381604 Score: 81
Period size: 16 Copynumber: 4.2 Consensus size: 16
20381523 ATTGGTTCGC
20381533 TGTATTAGATTAGAGGTG
1 TGTATTAGATTAGA-G-G
20381551 TCTGTATTAGATTAGAGG
1 --TGTATTAGATTAGAGG
*
20381569 TGTATTGGATTAGAGG
1 TGTATTAGATTAGAGG
* *
20381585 TGTAATAGAATAGAGG
1 TGTATTAGATTAGAGG
20381601 TGTA
1 TGTA
20381605 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
16 32 0.67
18 1 0.02
19 1 0.02
20 14 0.29
ACGTcount: A:0.31, C:0.01, G:0.32, T:0.36
Consensus pattern (16 bp):
TGTATTAGATTAGAGG
Found at i:20381848 original size:25 final size:25
Alignment explanation
Indices: 20381816--20381870 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
20381806 TAATTTAATC
*
20381816 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
20381840 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
20381865 ATATAT
1 ATATAT
20381871 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:20383098 original size:36 final size:37
Alignment explanation
Indices: 20383054--20383139 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 37
20383044 AAGAAACGGG
* *
20383054 GGGAGCAAATCGGCAGAAAAGAAAAGAAAATAAAC-T
1 GGGAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAA
*
20383090 GGGAGCAAATCGGCAGAAAAGAAAAGCAAAGAAACAA
1 GGGAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAA
*
20383127 GGAAGCAAATCGG
1 GGGAGCAAATCGG
20383140 ATGAAGGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 33 0.73
37 12 0.27
ACGTcount: A:0.53, C:0.13, G:0.28, T:0.06
Consensus pattern (37 bp):
GGGAGCAAATCGGCAGAAAAGAAAAGAAAAGAAACAA
Found at i:20385044 original size:20 final size:21
Alignment explanation
Indices: 20385014--20385058 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
20385004 TTTCTTCTTT
*
20385014 TTTTGTTATATAAATTTTTTA
1 TTTTGTTATATAAATTTTCTA
*
20385035 TTTT-TTATATTAATTTTCTA
1 TTTTGTTATATAAATTTTCTA
20385055 TTTT
1 TTTT
20385059 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTGTTATATAAATTTTCTA
Found at i:20397193 original size:16 final size:15
Alignment explanation
Indices: 20397172--20397221 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 15
20397162 AAAGATTGTT
20397172 AAAACTCTTATAAAAG
1 AAAACTCTTA-AAAAG
*
20397188 AAAACTC--AAAGAG
1 AAAACTCTTAAAAAG
*
20397201 -AAATTCTTAAAAAG
1 AAAACTCTTAAAAAG
20397215 AAAACTC
1 AAAACTC
20397222 AAAAATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 6 0.22
15 5 0.19
16 7 0.26
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (15 bp):
AAAACTCTTAAAAAG
Found at i:20401371 original size:15 final size:15
Alignment explanation
Indices: 20401339--20401386 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
20401329 AAATTTTATA
*
20401339 ACTTAAA-TTT-AGT
1 ACTTAAATTTTCAAT
20401352 ACTTAAATTTTCAAT
1 ACTTAAATTTTCAAT
* *
20401367 ACTTAATTTTTCAAC
1 ACTTAAATTTTCAAT
20401382 ACTTA
1 ACTTA
20401387 CTTTTTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 7 0.23
14 3 0.10
15 20 0.67
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.46
Consensus pattern (15 bp):
ACTTAAATTTTCAAT
Found at i:20401391 original size:15 final size:15
Alignment explanation
Indices: 20401352--20401392 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20401342 TAAATTTAGT
* *
20401352 ACTTAAATTTTCAAT
1 ACTTAATTTTTCAAC
20401367 ACTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
*
20401382 ACTTACTTTTT
1 ACTTAATTTTT
20401393 TGGCACCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:20403336 original size:18 final size:17
Alignment explanation
Indices: 20403313--20403380 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
20403303 AGTTTGACAA
20403313 AATACATCTCACCATATT
1 AATACAT-TCACCATATT
* *
20403331 AATACAAATCACCAAATT
1 AATAC-ATTCACCATATT
* *
20403349 AACACAGTTCACCATAAT
1 AATACA-TTCACCATATT
*
20403367 AATATAATTCACCA
1 AATA-CATTCACCA
20403381 AGTTAACATG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 1 0.03
18 36 0.92
19 2 0.05
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.26
Consensus pattern (17 bp):
AATACATTCACCATATT
Found at i:20406862 original size:22 final size:22
Alignment explanation
Indices: 20406834--20406876 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20406824 TTTATTGTTC
20406834 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
20406856 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
20406877 TAGCCATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:20410845 original size:42 final size:42
Alignment explanation
Indices: 20410786--20410869 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
20410776 AATTTAACTA
20410786 AACCTAAATGTACTCCTAGGTTAATGTATCAACTTTTCCTAT
1 AACCTAAATGTACTCCTAGGTTAATGTATCAACTTTTCCTAT
20410828 AACCTAAATGTACTCCTAGGTTAATGTATCAACTTTTCCTAT
1 AACCTAAATGTACTCCTAGGTTAATGTATCAACTTTTCCTAT
20410870 TCCTTGTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (42 bp):
AACCTAAATGTACTCCTAGGTTAATGTATCAACTTTTCCTAT
Found at i:20412280 original size:26 final size:26
Alignment explanation
Indices: 20412250--20412325 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
20412240 GCCAACACAC
20412250 CAATATCGCAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* ** *
20412276 TAATATCATAGCAAAGCTGCCAATAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* * *
20412302 CAGTAACGCATCAAAGCTGCCAGT
1 CAATATCGCAGCAAAGCTGCCAGT
20412326 GACAGTATAT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTGCCAGTAA
Found at i:20412538 original size:27 final size:28
Alignment explanation
Indices: 20412508--20412642 Score: 136
Period size: 27 Copynumber: 5.0 Consensus size: 28
20412498 GGGTACAACA
*
20412508 GTCATTTTACCCAATAG-GGGTATTTCG
1 GTCATTTTACCCAATCGAGGGTATTTCG
* * *
20412535 GTCATTTTA-CCATTCGAAGGTATTTTG
1 GTCATTTTACCCAATCGAGGGTATTTCG
* *
20412562 GTCATTTTACCCTAT-GGGGGTATTTCG
1 GTCATTTTACCCAATCGAGGGTATTTCG
* *
20412589 GTAATTTTACCC-TTCGAGGGTATTTCG
1 GTCATTTTACCCAATCGAGGGTATTTCG
* *
20412616 GTAATTTTTACCC-TTCGAGGGTATTTC
1 GTCA-TTTTACCCAATCGAGGGTATTTC
20412643 AGTACTTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.07
27 61 0.66
28 25 0.27
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (28 bp):
GTCATTTTACCCAATCGAGGGTATTTCG
Found at i:20412590 original size:54 final size:54
Alignment explanation
Indices: 20412508--20412651 Score: 173
Period size: 54 Copynumber: 2.6 Consensus size: 54
20412498 GGGTACAACA
* * * *
20412508 GTCATTTTACCCAATAGGGGTATTTCGGTCATTTTACCATTCGAAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCGGTAATTTTACCATTCGAAGGTATTTCG
* *
20412562 GTCATTTTACCCTATGGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGGTAATTTTACCATTCGAAGGTATTTCG
* * * *
20412616 GTAATTTTTACCCT-TCGAGGGTATTTCAGTACTTTT
1 GTCA-TTTTACCCTAT-GGGGGTATTTCGGTAATTTT
20412652 TTAGCCCAAG
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
54 52 0.67
55 26 0.33
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTATGGGGGTATTTCGGTAATTTTACCATTCGAAGGTATTTCG
Found at i:20412633 original size:28 final size:27
Alignment explanation
Indices: 20412525--20412651 Score: 157
Period size: 27 Copynumber: 4.7 Consensus size: 27
20412515 TACCCAATAG
* *
20412525 GGGTATTTCGGTCATTTTACCATTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
* * * *
20412552 AGGTATTTTGGTCATTTTACCCTAT-GG
1 GGGTATTTCGGTAATTTTACCCT-TCGA
20412579 GGGTATTTCGGTAATTTTACCCTTCGA
1 GGGTATTTCGGTAATTTTACCCTTCGA
20412606 GGGTATTTCGGTAATTTTTACCCTTCGA
1 GGGTATTTCGGTAA-TTTTACCCTTCGA
* *
20412634 GGGTATTTCAGTACTTTT
1 GGGTATTTCGGTAATTTT
20412652 TTAGCCCAAG
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 60 0.69
28 26 0.30
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACCCTTCGA
Found at i:20416562 original size:13 final size:14
Alignment explanation
Indices: 20416541--20416574 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
20416531 ACAATTGTGT
*
20416541 AATTGTAATTTAA-
1 AATTATAATTTAAG
20416554 AATTATAATTTAAG
1 AATTATAATTTAAG
20416568 AATTATA
1 AATTATA
20416575 TATAATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
AATTATAATTTAAG
Found at i:20417606 original size:12 final size:12
Alignment explanation
Indices: 20417586--20417645 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
20417576 GTTTTTTAGT
20417586 TTAT-TTTATTA
1 TTATATTTATTA
* *
20417597 ATATAGTTATTA
1 TTATATTTATTA
*
20417609 TTATTTTTATTA
1 TTATATTTATTA
20417621 TTACTA-TTATTA
1 TTA-TATTTATTA
20417633 TTATATTTATTA
1 TTATATTTATTA
20417645 T
1 T
20417646 ACTTACATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 5 0.12
12 34 0.85
13 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATATTTATTA
Found at i:20417618 original size:6 final size:6
Alignment explanation
Indices: 20417586--20417645 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
20417576 GTTTTTTAGT
* * *
20417586 TTATT- TTATTA ATA-TA GTTATTA TTATTT TTATTA TTACTA TTATTA
1 TTATTA TTATTA TTATTA -TTATTA TTATTA TTATTA TTATTA TTATTA
20417633 TTA-TA TTTATTA T
1 TTATTA -TTATTA T
20417646 ACTTACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
5 9 0.20
6 31 0.70
7 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (6 bp):
TTATTA
Found at i:20417619 original size:24 final size:24
Alignment explanation
Indices: 20417589--20417648 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
20417579 TTTTAGTTTA
20417589 TTTTATTAATA-TAGTTATTATTAT
1 TTTTATTAATACTA-TTATTATTAT
*
20417613 TTTTATTATTACTATTATTATTAT
1 TTTTATTAATACTATTATTATTAT
*
20417637 ATTTATT-ATACT
1 TTTTATTAATACT
20417649 TACATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.12
24 26 0.81
25 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATTAATACTATTATTATTAT
Found at i:20417620 original size:9 final size:9
Alignment explanation
Indices: 20417586--20417645 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
20417576 GTTTTTTAGT
20417586 TTATT-TTA
1 TTATTATTA
*
20417594 TTAATA-TA
1 TTATTATTA
20417602 GTTATTATTA
1 -TTATTATTA
*
20417612 TTTTTATTA
1 TTATTATTA
*
20417621 TTACTATTA
1 TTATTATTA
20417630 TTATTA-TA
1 TTATTATTA
20417638 TTTATTAT
1 -TTATTAT
20417646 ACTTACATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 8 0.20
9 31 0.76
10 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTATTATTA
Found at i:20417765 original size:2 final size:2
Alignment explanation
Indices: 20417758--20417797 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
20417748 TACCATATTT
*
20417758 TA TA TA TA TA TA TA GTT TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
20417798 CATTCATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:20417778 original size:17 final size:16
Alignment explanation
Indices: 20417752--20417797 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
20417742 TTTTATTACC
20417752 ATAT-TTTATATATAT
1 ATATATTTATATATAT
20417767 ATATAGTTTATATATAT
1 ATATA-TTTATATATAT
20417784 ATATATATTATATA
1 ATATAT-TTATATA
20417798 CATTCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.14
16 1 0.04
17 23 0.82
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATATATTTATATATAT
Found at i:20417836 original size:25 final size:26
Alignment explanation
Indices: 20417808--20417867 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
20417798 CATTCATATT
20417808 TTTTATAATT-ATTTATGTTT-T-CATG
1 TTTTATAATTCA--TATGTTTATACATG
*
20417833 TTTTATAATTCATATGTTTATACATT
1 TTTTATAATTCATATGTTTATACATG
20417859 TTTTATAAT
1 TTTTATAAT
20417868 ATGTACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 7 0.23
25 11 0.35
26 13 0.42
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (26 bp):
TTTTATAATTCATATGTTTATACATG
Found at i:20417836 original size:26 final size:26
Alignment explanation
Indices: 20417805--20417867 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
20417795 ATACATTCAT
20417805 ATTTTTTATAATT-ATTTATGTTT-T-C
1 ATTTTTTATAATTCA--TATGTTTATAC
*
20417830 ATGTTTTATAATTCATATGTTTATAC
1 ATTTTTTATAATTCATATGTTTATAC
20417856 ATTTTTTATAAT
1 ATTTTTTATAAT
20417868 ATGTACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 7 0.21
25 13 0.39
26 13 0.39
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (26 bp):
ATTTTTTATAATTCATATGTTTATAC
Found at i:20427798 original size:23 final size:25
Alignment explanation
Indices: 20427746--20427799 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
20427736 ATATTAACAA
* *
20427746 CTAAATTTCACAATATTTCATGTTG
1 CTAAATATCAAAATATTTCATGTTG
20427771 -T-AATATCAAAATATTT-A-GTTG
1 CTAAATATCAAAATATTTCATGTTG
20427792 CTAAATAT
1 CTAAATAT
20427800 AATCTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.16
22 2 0.08
23 18 0.72
24 1 0.04
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (25 bp):
CTAAATATCAAAATATTTCATGTTG
Found at i:20434212 original size:20 final size:18
Alignment explanation
Indices: 20434181--20434237 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 18
20434171 GCATAATTTT
*
20434181 AAATTTTAAAAATTTAAA
1 AAATTATAAAAATTTAAA
*
20434199 ATAATATATAAAAATTGAAA
1 A-AAT-TATAAAAATTTAAA
*
20434219 AAATTAAAAAATATTTAAA
1 AAATTATAAAA-ATTTAAA
20434238 TTTCAAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 7 0.22
19 12 0.38
20 13 0.41
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATTATAAAAATTTAAA
Found at i:20434444 original size:19 final size:20
Alignment explanation
Indices: 20434422--20434463 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20434412 TAAATTTTAG
20434422 TTTTATA-A-TTTATATGTTT
1 TTTTATAGATTTTATAT-TTT
*
20434441 TTTTCTAGATTTTATATTTT
1 TTTTATAGATTTTATATTTT
20434461 TTT
1 TTT
20434464 CTGAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTATAGATTTTATATTTT
Found at i:20434461 original size:20 final size:21
Alignment explanation
Indices: 20434430--20434501 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 21
20434420 AGTTTTATAA
*
20434430 TTTATATGTTTTTTTCTAGA-
1 TTTATATATTTTTTTCTAGAT
20434450 TTT-TATATTTTTTTCT-GAATT
1 TTTATATATTTTTTTCTAG-A-T
*
20434471 TTTATATATTTATTTCT--AT
1 TTTATATATTTTTTTCTAGAT
20434490 TTT-TATATTTTT
1 TTTATATATTTTT
20434502 AATGTGTCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 9 0.20
19 17 0.38
20 4 0.09
21 3 0.07
22 12 0.27
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTATATATTTTTTTCTAGAT
Found at i:20434502 original size:20 final size:19
Alignment explanation
Indices: 20434430--20434501 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
20434420 AGTTTTATAA
*
20434430 TTTATATGTTTTTTTCTAGAT
1 TTTATAT-TTTTTTTCTA-TT
20434451 TTTATA-TTTTTTTCTGAATT
1 TTTATATTTTTTTTCT--ATT
*
20434471 TTTATATATTTATTTCTATT
1 TTTATAT-TTTTTTTCTATT
20434491 TTTATATTTTT
1 TTTATATTTTT
20434502 AATGTGTCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 12 0.27
20 17 0.39
21 7 0.16
22 8 0.18
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTATATTTTTTTTCTATT
Found at i:20436219 original size:6 final size:6
Alignment explanation
Indices: 20436210--20436280 Score: 81
Period size: 6 Copynumber: 11.8 Consensus size: 6
20436200 GAAAGTAAAA
* * *
20436210 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAC GTGT-T CGTGTAC GTGTAC
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT -GTGTAT GTGTAT
* *
20436258 GTGTGT GTGTGT GTGTAT GTGTA
1 GTGTAT GTGTAT GTGTAT GTGTA
20436281 ATAATATGTG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.13, C:0.06, G:0.37, T:0.45
Consensus pattern (6 bp):
GTGTAT
Found at i:20436632 original size:30 final size:31
Alignment explanation
Indices: 20436596--20436659 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
20436586 ATGATTCATC
*
20436596 ATTGGAAA-ATTAAATAA-AGAAA-ATGACTAA
1 ATTGGAAAGATGAAATAATA-AAAGATGA-TAA
20436626 ATTGGAAAGATGAAATAATAAAAGATGATAA
1 ATTGGAAAGATGAAATAATAAAAGATGATAA
20436657 ATT
1 ATT
20436660 AATTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 8 0.27
31 17 0.57
32 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.25
Consensus pattern (31 bp):
ATTGGAAAGATGAAATAATAAAAGATGATAA
Found at i:20437685 original size:25 final size:28
Alignment explanation
Indices: 20437657--20437717 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
20437647 CTTATGAGTG
*
20437657 TCTCGATATATA-GCTC-TTC-GGAGCT
1 TCTCGATATAAAGGCTCTTTCAGGAGCT
*
20437682 TCTCGAT-TAAAGGCTCTTTCATGAGCT
1 TCTCGATATAAAGGCTCTTTCAGGAGCT
20437709 TCTCGATAT
1 TCTCGATAT
20437718 TGGCTCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.10
25 11 0.37
26 3 0.10
27 12 0.40
28 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (28 bp):
TCTCGATATAAAGGCTCTTTCAGGAGCT
Found at i:20442482 original size:16 final size:16
Alignment explanation
Indices: 20442450--20442488 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20442440 TTAATTTGGT
*
20442450 ATATTAT-ATAATTTA
1 ATATTATAATAATATA
*
20442465 ATTTTATAATAATATA
1 ATATTATAATAATATA
20442481 ATATTATA
1 ATATTATA
20442489 TAAACATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTATAATAATATA
Found at i:20448907 original size:43 final size:43
Alignment explanation
Indices: 20448859--20448942 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
20448849 ACACTAGGGT
*
20448859 AGGACTTTCATTCATTTTCAGACTGTATGCGCCTGATTTTTTG
1 AGGACTTCCATTCATTTTCAGACTGTATGCGCCTGATTTTTTG
20448902 AGGACTTCCATTCATTTTCAGACTGTATGCGCCTGATTTTT
1 AGGACTTCCATTCATTTTCAGACTGTATGCGCCTGATTTTT
20448943 ACTGTTAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (43 bp):
AGGACTTCCATTCATTTTCAGACTGTATGCGCCTGATTTTTTG
Found at i:20450985 original size:2 final size:2
Alignment explanation
Indices: 20450978--20451003 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20450968 CCATATTCAT
20450978 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20451004 AACCTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20451913 original size:3 final size:3
Alignment explanation
Indices: 20451905--20451935 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20451895 GAGAGAATAT
20451905 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
20451936 CAGCAGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:20452457 original size:2 final size:2
Alignment explanation
Indices: 20452450--20452476 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20452440 TCCAGTTGTC
20452450 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 T
20452477 TAAAGGTCTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20459871 original size:2 final size:2
Alignment explanation
Indices: 20459866--20459891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20459856 ATTCTAAAAA
20459866 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
20459892 TCTAATCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20461377 original size:29 final size:28
Alignment explanation
Indices: 20461307--20461382 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
20461297 TTAATGGCTT
20461307 AATGACTAAAATATTACAACATGATAAAATA
1 AATGACTAAAATA-T--AACATGATAAAATA
**
20461338 AATGACTAAAATATAACATTTTAAACATA
1 AATGACTAAAATATAACATGATAAA-ATA
20461367 AATGACTAAAATATAA
1 AATGACTAAAATATAA
20461383 GTTGAGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 9 0.21
29 19 0.45
30 1 0.02
31 13 0.31
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (28 bp):
AATGACTAAAATATAACATGATAAAATA
Found at i:20463173 original size:23 final size:23
Alignment explanation
Indices: 20463147--20463202 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
20463137 AATTGGTAGT
20463147 TTCTAGGCTTTGATTGTTCTGTC
1 TTCTAGGCTTTGATTGTTCTGTC
20463170 TTCTAGGCTTTGATTGTTCTGTC
1 TTCTAGGCTTTGATTGTTCTGTC
20463193 TTCT-GGCTTT
1 TTCTAGGCTTT
20463203 TCAGCTGCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.07, C:0.18, G:0.21, T:0.54
Consensus pattern (23 bp):
TTCTAGGCTTTGATTGTTCTGTC
Found at i:20465959 original size:19 final size:19
Alignment explanation
Indices: 20465922--20465960 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20465912 TTCCCGTACG
* * *
20465922 TCTCTCTTTTTTTTTTTAA
1 TCTCTCTTTTATGTCTTAA
20465941 TCTCTCTTTTATGTCTTAA
1 TCTCTCTTTTATGTCTTAA
20465960 T
1 T
20465961 AACCCCCCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.67
Consensus pattern (19 bp):
TCTCTCTTTTATGTCTTAA
Found at i:20469168 original size:6 final size:6
Alignment explanation
Indices: 20469157--20469209 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
20469147 TGCTTAGTTG
20469157 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
20469205 GTATA
1 GTATA
20469210 CGTGTGTGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
GTATAT
Found at i:20470810 original size:40 final size:40
Alignment explanation
Indices: 20470733--20470810 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
20470723 TCAAATTTCG
* *
20470733 TCTCAATTTCCTTCCAGATTTCTTTCAATTTCATATTTAA
1 TCTCAATTTCCTTCCAAATTTCTTTCAAATTCATATTTAA
** *
20470773 TCTCAATTTCCTTTTAAATTTCTCTT-AAATTCCTATTT
1 TCTCAATTTCCTTCCAAATTTCT-TTCAAATTCATATTT
20470811 TTAAATAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.01, T:0.53
Consensus pattern (40 bp):
TCTCAATTTCCTTCCAAATTTCTTTCAAATTCATATTTAA
Found at i:20471736 original size:19 final size:19
Alignment explanation
Indices: 20471712--20471760 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
20471702 GCACGGTTAT
*
20471712 AATAAAAAACATCATTCCA
1 AATAAACAACATCATTCCA
20471731 AATAAACAACATCATTCCA
1 AATAAACAACATCATTCCA
20471750 AATAAACAACA
1 AATAAACAACA
20471761 AAAATAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.18
Consensus pattern (19 bp):
AATAAACAACATCATTCCA
Found at i:20474533 original size:96 final size:93
Alignment explanation
Indices: 20474302--20474662 Score: 439
Period size: 90 Copynumber: 4.1 Consensus size: 93
20474292 TTGGATCACT
*
20474302 CATAAATTAAACAAAAAAAAGTATGTTAAACTACATTTTAAACTTTAAAGTTAGTTAATTGAAGC
1 CATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAAGC
* *
20474367 CTAAATTAATAT--TA-TTGTAAAATAG
66 CTAAATTAATATAATAGTAGTACAATAG
* *
20474392 CATAAATTAAACAAAAAAAAGTCTGTTAAGCTATC-GTTTAAACTTTAAAGTTAGTTAATTGAAG
1 CATAAATTAAACAAAAAAAAGTATGTTAAACTA-CAGTTTAAACTTTAAAGTTAGTTAATTGAAG
*
20474456 CCTAAATTAATATAATAGTACAAGTACAACAG
65 CCTAAATTAATATAATAGT---AGTACAATAG
*
20474488 CATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAATTAATTGAAGC
1 CATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAAGC
20474553 CTAAATTAATATAATAGT-G--CAATAG
66 CTAAATTAATATAATAGTAGTACAATAG
20474578 CATAAATT-------AAAAA--A----AAA--ACAGTTTAAACTTTAAAGTTAGTTAATTGAAGC
1 CATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAAGC
*
20474628 CTAAATTAATAT-A-A-TAGTACAACAG
66 CTAAATTAATATAATAGTAGTACAATAG
20474653 CATAAATTAA
1 CATAAATTAA
20474663 TTAATTGAAG
Statistics
Matches: 246, Mismatches: 12, Indels: 39
0.83 0.04 0.13
Matches are distributed among these distances:
72 1 0.00
73 2 0.01
74 1 0.00
75 57 0.23
77 3 0.01
81 1 0.00
83 5 0.02
90 85 0.35
91 1 0.00
92 3 0.01
93 1 0.00
95 1 0.00
96 85 0.35
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (93 bp):
CATAAATTAAACAAAAAAAAGTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAATTGAAGC
CTAAATTAATATAATAGTAGTACAATAG
Found at i:20474608 original size:75 final size:75
Alignment explanation
Indices: 20474520--20474662 Score: 259
Period size: 75 Copynumber: 1.9 Consensus size: 75
20474510 ATGTTAAACT
* *
20474520 ACAGTTTAAACTTTAAAGTTAATTAATTGAAGCCTAAATTAATATAATAGTGCAATAGCATAAAT
1 ACAGTTTAAACTTTAAAGTTAATTAATTGAAGCCTAAATTAATATAATAGTACAACAGCATAAAT
20474585 TAAAAAAAAA
66 TAAAAAAAAA
*
20474595 ACAGTTTAAACTTTAAAGTTAGTTAATTGAAGCCTAAATTAATATAATAGTACAACAGCATAAAT
1 ACAGTTTAAACTTTAAAGTTAATTAATTGAAGCCTAAATTAATATAATAGTACAACAGCATAAAT
20474660 TAA
66 TAA
20474663 TTAATTGAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (75 bp):
ACAGTTTAAACTTTAAAGTTAATTAATTGAAGCCTAAATTAATATAATAGTACAACAGCATAAAT
TAAAAAAAAA
Found at i:20474983 original size:17 final size:17
Alignment explanation
Indices: 20474961--20475012 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
20474951 TTTTCTCTAT
*
20474961 TAATATTACGTTATTAC
1 TAATATTACATTATTAC
* *
20474978 TAATATTATATTATTAT
1 TAATATTACATTATTAC
20474995 TAATATTACATTATTAC
1 TAATATTACATTATTAC
20475012 T
1 T
20475013 TTGGGAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (17 bp):
TAATATTACATTATTAC
Found at i:20475432 original size:19 final size:19
Alignment explanation
Indices: 20475408--20475469 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
20475398 GGAGAAGGAA
20475408 AATAGAGCGAAAATCATTC
1 AATAGAGCGAAAATCATTC
* *
20475427 AATAGAGCGAAACA-AATGC
1 AATAGAGCGAAA-ATCATTC
*
20475446 AAATAGAGCTAAAATCATTC
1 -AATAGAGCGAAAATCATTC
20475466 AATA
1 AATA
20475470 ATTCAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (19 bp):
AATAGAGCGAAAATCATTC
Found at i:20484280 original size:29 final size:30
Alignment explanation
Indices: 20484215--20484280 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
20484205 AATAGCCTAT
*
20484215 ATATTTATATTTTTTAAAAGATTAAATTAA
1 ATATTTATATTTTTTAAAAGATTAAAATAA
* *
20484245 ATATTTATA-TTTTTAGAAGGTTAAAATACA
1 ATATTTATATTTTTTAAAAGATTAAAATA-A
20484275 AT-TTTA
1 ATATTTA
20484281 CTTACTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (30 bp):
ATATTTATATTTTTTAAAAGATTAAAATAA
Found at i:20488474 original size:2 final size:2
Alignment explanation
Indices: 20488467--20488494 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20488457 CTATGTCTAT
20488467 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
20488495 TATATTGCTT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:20496329 original size:21 final size:19
Alignment explanation
Indices: 20496283--20496330 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
20496273 TTTTAACTAG
20496283 TCTATAATTTTTTTTATTT
1 TCTATAATTTTTTTTATTT
*
20496302 TAATATAATTTTTTTATAATTT
1 T-CTATAATTTTTTT-T-ATTT
20496324 TCTATAA
1 TCTATAA
20496331 ACAGAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 6 0.25
22 5 0.21
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTATAATTTTTTTTATTT
Found at i:20501725 original size:18 final size:19
Alignment explanation
Indices: 20501702--20501737 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20501692 TTAGACTGAA
20501702 AATTG-AAAAAAAAGTATC
1 AATTGAAAAAAAAAGTATC
20501720 AATTGAAAAAAAAAGTAT
1 AATTGAAAAAAAAAGTAT
20501738 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.22
Consensus pattern (19 bp):
AATTGAAAAAAAAAGTATC
Found at i:20505380 original size:17 final size:18
Alignment explanation
Indices: 20505347--20505399 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
20505337 CGTTAAAGAT
*
20505347 TAATTACTTATTTAAAATA
1 TAATTATTTA-TTAAAATA
*
20505366 TTATT-TTTATTAAAA-A
1 TAATTATTTATTAAAATA
*
20505382 TAATTATTTATTTAAATA
1 TAATTATTTATTAAAATA
20505400 AAAAAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 5 0.18
17 15 0.54
18 4 0.14
19 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAAATA
Found at i:20505396 original size:18 final size:18
Alignment explanation
Indices: 20505347--20505397 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
20505337 CGTTAAAGAT
*
20505347 TAATTACTTATTT-AAAA
1 TAATTATTTATTTAAAAA
*
20505364 T-ATTATTTTTATTAAAAA
1 TAATTATTTAT-TTAAAAA
20505382 TAATTATTTATTTAAA
1 TAATTATTTATTTAAA
20505398 TAAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.25
17 3 0.11
18 10 0.36
19 8 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTTAAAAA
Found at i:20512506 original size:15 final size:16
Alignment explanation
Indices: 20512486--20512519 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
20512476 CATTTTCAAT
*
20512486 ATTAAAATAAAC-CCC
1 ATTAAAACAAACTCCC
20512501 ATTAAAACAAACTCCC
1 ATTAAAACAAACTCCC
20512517 ATT
1 ATT
20512520 TTCCATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
ATTAAAACAAACTCCC
Found at i:20516598 original size:3 final size:3
Alignment explanation
Indices: 20516590--20516662 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
20516580 TAAAACAATT
**
20516590 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20516638 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
20516663 GATGATGATG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20516667 original size:3 final size:3
Alignment explanation
Indices: 20516661--20516726 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
20516651 AATAATAATA
20516661 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
20516709 ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG
20516727 GTGGTATTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:20518545 original size:3 final size:3
Alignment explanation
Indices: 20518539--20518565 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20518529 TTATTAATAC
20518539 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
20518566 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:20522904 original size:17 final size:18
Alignment explanation
Indices: 20522870--20522915 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
20522860 CCGTTATGTC
20522870 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
20522885 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
20522902 CGCGACCGCGACCG
1 CGCGACCGCGACCG
20522916 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:20531996 original size:17 final size:17
Alignment explanation
Indices: 20531976--20532037 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
20531966 TTTCTTAAAA
*
20531976 TTTTGTATCTCGTAATT
1 TTTTGTATCTCATAATT
*
20531993 TTTTGTATTTCATAATT
1 TTTTGTATCTCATAATT
*
20532010 ATTTGTAATTTCTCATAATT
1 TTTTGT-A--TCTCATAATT
*
20532030 TTTAGTAT
1 TTTTGTAT
20532038 GATATGCTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 21 0.58
18 1 0.03
19 1 0.03
20 13 0.36
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (17 bp):
TTTTGTATCTCATAATT
Found at i:20532233 original size:20 final size:18
Alignment explanation
Indices: 20532200--20532241 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
20532190 TAATTTTTAT
20532200 TTCCTCATAATTTTTGGTA
1 TTCCTCAT-ATTTTTGGTA
*
20532219 CTTCCTTATATTTTTGGTA
1 -TTCCTCATATTTTTGGTA
20532238 TTCC
1 TTCC
20532242 CTAAGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 10 0.48
20 7 0.33
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.55
Consensus pattern (18 bp):
TTCCTCATATTTTTGGTA
Found at i:20540646 original size:42 final size:42
Alignment explanation
Indices: 20540537--20540694 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 42
20540527 AGCTCGTACA
* * * * * *
20540537 ATGCCAACGTACCAAACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATA-CG
* * * *
20540580 ATACCACTGTCCTAGACA-GAGTCTTACACGAAATCATATACG
1 ATGCCAATGTCCCAGACATG-GTCTTACACGAAATCAAATACG
* *
20540622 ATGCTAATGTCCCAGACATGGTCTTAGACGTAAATCTCAAATA-G
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AAA--TCAAATACG
* * *
20540666 ATGCCAACGTCCCAAACGTGGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
20540695 AAGATCACAT
Statistics
Matches: 89, Mismatches: 21, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
42 26 0.29
43 32 0.36
44 25 0.28
45 6 0.07
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATACG
Found at i:20544949 original size:26 final size:27
Alignment explanation
Indices: 20544913--20544965 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20544903 TGTAGTTAGC
20544913 AGATACATGG-AAATCCCGATAAAAAA
1 AGATACATGGAAAATCCCGATAAAAAA
* * *
20544939 AGATATATGGAAAATCTCGGTAAAAAA
1 AGATACATGGAAAATCCCGATAAAAAA
20544966 CATTGGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (27 bp):
AGATACATGGAAAATCCCGATAAAAAA
Found at i:20545584 original size:29 final size:29
Alignment explanation
Indices: 20545542--20545598 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
20545532 TTATGGAAAA
* * *
20545542 GATGGAGAACTTGTTCGTTGAGAGTTCAC
1 GATGAAGAACTTGTTCATTGAGAATTCAC
20545571 GATGAAGAACTTGTTCATTGAGAATTCA
1 GATGAAGAACTTGTTCATTGAGAATTCA
20545599 TGTCAAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (29 bp):
GATGAAGAACTTGTTCATTGAGAATTCAC
Found at i:20553748 original size:20 final size:20
Alignment explanation
Indices: 20553723--20553761 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20553713 TAAATTTTAA
*
20553723 ATATAAAATATTCATCAATT
1 ATATAAAATATTCAACAATT
*
20553743 ATATAAAATTTTCAACAAT
1 ATATAAAATATTCAACAAT
20553762 AAACTCTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAAATATTCAACAATT
Found at i:20557084 original size:29 final size:29
Alignment explanation
Indices: 20557042--20557101 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
20557032 TATTGTTGCG
20557042 AGTTTTCAACCACCTTCGAACACCCATTT
1 AGTTTTCAACCACCTTCGAACACCCATTT
20557071 AGTTTTCAACCACCTTCGAACACCCATTT
1 AGTTTTCAACCACCTTCGAACACCCATTT
20557100 AG
1 AG
20557102 ACATACTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.08, T:0.30
Consensus pattern (29 bp):
AGTTTTCAACCACCTTCGAACACCCATTT
Found at i:20560826 original size:2 final size:2
Alignment explanation
Indices: 20560819--20560871 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
20560809 NNNNNNNNNN
20560819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20560861 AT AT AT GAT AT
1 AT AT AT -AT AT
20560872 GCGTACATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20562080 original size:12 final size:13
Alignment explanation
Indices: 20562043--20562080 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
20562033 ACAAAAAAGA
20562043 TTAAATTCATTTAT
1 TTAAATT-ATTTAT
20562057 TTAAATTA-TTAT
1 TTAAATTATTTAT
20562069 TT-AATTATTTAT
1 TTAAATTATTTAT
20562081 AATTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 10 0.43
13 1 0.04
14 7 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAAATTATTTAT
Found at i:20566737 original size:25 final size:25
Alignment explanation
Indices: 20566703--20566754 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
20566693 GATCGAGATG
20566703 ATAGAAAGAGCACTTCAAGTTATGC
1 ATAGAAAGAGCACTTCAAGTTATGC
*
20566728 ATAGAAAGAGTACTTCAAGTTATGC
1 ATAGAAAGAGCACTTCAAGTTATGC
20566753 AT
1 AT
20566755 TTATGCTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (25 bp):
ATAGAAAGAGCACTTCAAGTTATGC
Found at i:20568525 original size:18 final size:18
Alignment explanation
Indices: 20568484--20568518 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20568474 TTTAGTTACT
20568484 TGTT-TGTTGGTTTTCAA
1 TGTTCTGTTGGTTTTCAA
20568501 TGTTCTGTTGGCTTTTCA
1 TGTTCTGTTGG-TTTTCA
20568519 TTTTCTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (18 bp):
TGTTCTGTTGGTTTTCAA
Found at i:20569148 original size:18 final size:18
Alignment explanation
Indices: 20569113--20569147 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20569103 TACAAACTTG
*
20569113 AACTTTTTTTTAGTTTTT
1 AACTTTTTTTAAGTTTTT
20569131 AACTTTTTTTAA-TTTTT
1 AACTTTTTTTAAGTTTTT
20569148 TTTATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (18 bp):
AACTTTTTTTAAGTTTTT
Found at i:20573521 original size:16 final size:16
Alignment explanation
Indices: 20573492--20573532 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
20573482 TCAAATTCAA
*
20573492 AACTTAAATTTAGTTC
1 AACTTAAATATAGTTC
*
20573508 AACTTCAATATAGTTC
1 AACTTAAATATAGTTC
20573524 AACTTAAAT
1 AACTTAAAT
20573533 TCAAAACTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (16 bp):
AACTTAAATATAGTTC
Done.