Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 111 of 433
Found at i:33905134 original size:6 final size:6
Alignment explanation
Indices: 33905123--33905182 Score: 93
Period size: 6 Copynumber: 9.8 Consensus size: 6
33905113 GGTTTTCTCC
* *
33905123 AAATGG AAATGG AAATGG AAATGG AAATGG AAACGG AAATGG AAATGA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
33905171 AAATGAG AAATG
1 AAATG-G AAATG
33905183 ATTTATTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
6 44 0.90
7 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:33907146 original size:27 final size:25
Alignment explanation
Indices: 33907093--33907141 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
33907083 TCACACGGCC
33907093 GTGTCACATGCCCGTGTGCTAGGCT
1 GTGTCACATGCCCGTGTGCTAGGCT
* *
33907118 GTGTCACATGCTCGTGTGTTAGGC
1 GTGTCACATGCCCGTGTGCTAGGC
33907142 CCTGTAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (25 bp):
GTGTCACATGCCCGTGTGCTAGGCT
Found at i:33909100 original size:14 final size:14
Alignment explanation
Indices: 33909081--33909136 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
33909071 TATTCGGTCT
33909081 TATGAATATGTGTA
1 TATGAATATGTGTA
* *
33909095 TATGAATCTCT-TA
1 TATGAATATGTGTA
33909108 T-T-AATATGTGTA
1 TATGAATATGTGTA
* *
33909120 TATGAATTTATGTA
1 TATGAATATGTGTA
33909134 TAT
1 TAT
33909137 TAGATCATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
11 5 0.15
12 4 0.12
13 4 0.12
14 20 0.61
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (14 bp):
TATGAATATGTGTA
Found at i:33909113 original size:25 final size:25
Alignment explanation
Indices: 33909078--33909126 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
33909068 ATATATTCGG
33909078 TCTTATGAATATGTGTATATGAATC
1 TCTTATGAATATGTGTATATGAATC
*
33909103 TCTTATTAATATGTGTATATGAAT
1 TCTTATGAATATGTGTATATGAAT
33909127 TTATGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (25 bp):
TCTTATGAATATGTGTATATGAATC
Found at i:33921400 original size:42 final size:41
Alignment explanation
Indices: 33921300--33921456 Score: 154
Period size: 43 Copynumber: 3.7 Consensus size: 41
33921290 CAATGCTAAC
* * *
33921300 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACA
1 GTCCCAGACATGGTCTTACACGAAATCAAATA-CGATGCCA-A
*
33921343 GTCCCAGACAGGGTCTTACACGAAATCAAATACGATGCCAA
1 GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCCAA
*
33921384 TGTCCCAAACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAA
1 -GTCCCAGACATGGTCTTACACG-AAA--TCAAATACGATGCCAA
* * * * *
33921428 CTTCCCAGACGTAGTATTACACAAAATCA
1 -GTCCCAGACATGGTCTTACACGAAATCA
33921457 CATATCGAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.04
42 28 0.29
43 34 0.35
44 25 0.26
45 6 0.06
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCCAA
Found at i:33923881 original size:19 final size:20
Alignment explanation
Indices: 33923827--33923882 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
33923817 ATTGGGCCTT
33923827 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
*
33923847 GCCCAT-TTCAATACAGTT-G
1 GCCCATATT-AACACAGTTGG
33923866 GCCCATAATTAA-ACAGT
1 GCCCAT-ATTAACACAGT
33923883 CTCATATGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 14 0.44
20 16 0.50
21 2 0.06
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:33928173 original size:60 final size:60
Alignment explanation
Indices: 33928085--33928221 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
33928075 TAGAGTTAAT
* * *
33928085 TGGGCCTTAACCCATATCAATATTAATCTGGGCCATAGCCC-CTTACAATATC-AGAGTATAC
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAA-ATCGAGA-TATAC
* * * *
33928146 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCGAGATATAC
*
33928206 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
33928222 TAACATAGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
60 51 0.77
61 15 0.23
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAATCGAGATATAC
Found at i:33930597 original size:3 final size:3
Alignment explanation
Indices: 33930589--33930643 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
33930579 AAACATACGA
33930589 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33930637 AAT AAT A
1 AAT AAT A
33930644 TCCAAAATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:33932018 original size:36 final size:36
Alignment explanation
Indices: 33931959--33932050 Score: 123
Period size: 36 Copynumber: 2.5 Consensus size: 36
33931949 ATTTTTAACA
* *
33931959 ATTATATTTT-ATACAATAAAATATTTATTATATTT
1 ATTATTTTTTAATATAATAAAATATTTATTATATTT
33931994 ATTATTTTTTAATATAATAAAATATTTATTATATTT
1 ATTATTTTTTAATATAATAAAATATTTATTATATTT
33932030 ATGATAGTGTTTTTAATATAA
1 AT--TA-T-TTTTTAATATAA
33932051 ATACTTTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
35 9 0.18
36 26 0.52
38 2 0.04
39 1 0.02
40 12 0.24
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
ATTATTTTTTAATATAATAAAATATTTATTATATTT
Found at i:33932027 original size:19 final size:19
Alignment explanation
Indices: 33931967--33932027 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
33931957 CAATTATATT
*
33931967 TTATACAATAAAATATTTA
1 TTATATAATAAAATATTTA
* * *
33931986 TTATAT--T-TATTATTTT
1 TTATATAATAAAATATTTA
33932002 TTAATATAATAAAATATTTA
1 TT-ATATAATAAAATATTTA
33932022 TTATAT
1 TTATAT
33932028 TTATGATAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
16 8 0.26
17 5 0.16
19 10 0.32
20 8 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATAATAAAATATTTA
Found at i:33938057 original size:31 final size:31
Alignment explanation
Indices: 33938016--33938079 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
33938006 CCTTTTCATA
*
33938016 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
** *
33938047 TTTCAAATTTCATATTACTGGGCTGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
33938078 TT
1 TT
33938080 ATGGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:33938315 original size:25 final size:23
Alignment explanation
Indices: 33938272--33938537 Score: 318
Period size: 25 Copynumber: 11.0 Consensus size: 23
33938262 TGCTTTATCA
*
33938272 TATAACTGGAGGCCT-AGCCTCTTT
1 TATAACTGG-GGCATAAGCC-CTTT
*
33938296 TAGTAACTGGGGCAAAAGCCCTTT
1 TA-TAACTGGGGCATAAGCCCTTT
33938320 TATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
*
33938343 ATCACAACTGGGGCATAAGCCCTTCAT
1 -T-ATAACTGGGGCATAAGCCCTT--T
* **
33938370 CATAACTAAGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
33938393 ATCATAACTGGGGCATAAGCCCTTT
1 -T-ATAACTGGGGCATAAGCCCTTT
*
33938418 AATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
33938441 ATCATAACTGGGGCATAAGCCCTTT
1 -T-ATAACTGGGGCATAAGCCCTTT
*
33938466 ATCATAACTGGGGTATAAGCCCTTT
1 -T-ATAACTGGGGCATAAGCCCTTT
*
33938491 AATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
*
33938514 AATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
33938537 T
1 T
33938538 GCACTTCCTC
Statistics
Matches: 215, Mismatches: 17, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
23 87 0.40
24 12 0.06
25 115 0.53
27 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (23 bp):
TATAACTGGGGCATAAGCCCTTT
Found at i:33938352 original size:48 final size:48
Alignment explanation
Indices: 33938299--33938536 Score: 363
Period size: 48 Copynumber: 4.9 Consensus size: 48
33938289 CCTCTTTTAG
* *
33938299 TAACTGGGGCAAAAGCCCTTTTATAACTGGGGCATAAGCCCTTTATCA
1 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTATCA
* * **
33938347 CAACTGGGGCATAAGCCCTTCATCATAACTAAGGCATAAGCCCTTTATCA
1 TAACTGGGGCATAAGCCCTT--TAATAACTGGGGCATAAGCCCTTTATCA
33938397 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTATCA
1 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTATCA
*
33938445 TAACTGGGGCATAAGCCCTTTATCATAACTGGGGTATAAGCCCTTTA--A
1 TAACTGGGGCATAAGCCCTTTA--ATAACTGGGGCATAAGCCCTTTATCA
33938493 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTT
1 TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTT
33938537 TGCACTTCCT
Statistics
Matches: 175, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
46 21 0.12
48 88 0.50
50 66 0.38
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (48 bp):
TAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTATCA
Found at i:33938388 original size:73 final size:72
Alignment explanation
Indices: 33938299--33938536 Score: 365
Period size: 73 Copynumber: 3.3 Consensus size: 72
33938289 CCTCTTTTAG
* *
33938299 TAACTGGGGCAAAAGCCCTTT-T-ATAACTGGGGCATAAGCCCTTTATCACAACTGGGGCATAAG
1 TAACTGGGGCATAAGCCCTTTATCATAACTGGGGCATAAGCCCTTTA--ATAACTGGGGCATAAG
33938362 CCCTTCATCA
64 CCCTT-ATCA
**
33938372 TAACTAAGGCATAAGCCCTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 TAACTGGGGCATAAGCCCTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
33938437 CTTTATCA
66 C-TTATCA
*
33938445 TAACTGGGGCATAAGCCCTTTATCATAACTGGGGTATAAGCCCTTTAATAACTGGGGCATAAGCC
1 TAACTGGGGCATAAGCCCTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
*
33938510 CTT-TAA
66 CTTATCA
33938516 TAACTGGGGCATAAGCCCTTT
1 TAACTGGGGCATAAGCCCTTT
33938537 TGCACTTCCT
Statistics
Matches: 154, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
71 23 0.15
72 2 0.01
73 103 0.67
74 3 0.02
75 23 0.15
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (72 bp):
TAACTGGGGCATAAGCCCTTTATCATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
CTTATCA
Found at i:33938609 original size:9 final size:9
Alignment explanation
Indices: 33938595--33938651 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
33938585 ATCTCATGTG
33938595 CATATCATA
1 CATATCATA
*
33938604 CATATCATGTG
1 CATATCA--TA
33938615 CATATCATA
1 CATATCATA
* *
33938624 CATGTCATGTG
1 CATATCA--TA
33938635 CATATCATA
1 CATATCATA
33938644 CATATCAT
1 CATATCAT
33938652 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:33938611 original size:20 final size:20
Alignment explanation
Indices: 33938583--33938653 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
33938573 GCATTTATGA
*
33938583 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
33938603 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
33938623 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
33938643 ACATATCATGT
1 ACATATCATGT
33938654 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:33938618 original size:11 final size:11
Alignment explanation
Indices: 33938588--33938642 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
33938578 TATGAACATC
33938588 TCATGTGCATA
1 TCATGTGCATA
*
33938599 TCA--TACATA
1 TCATGTGCATA
33938608 TCATGTGCATA
1 TCATGTGCATA
* *
33938619 TCA--TACATG
1 TCATGTGCATA
33938628 TCATGTGCATA
1 TCATGTGCATA
33938639 TCAT
1 TCAT
33938643 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:33939956 original size:27 final size:27
Alignment explanation
Indices: 33939865--33939947 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
33939855 GGGCATATTT
*
33939865 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCATACAGGGGCT-TTACG
*
33939892 GTCACTTTACCTTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
*
33939919 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTTACG
33939946 GT
1 GT
33939948 TTTTTTACCT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
27 51 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTTACG
Found at i:33940040 original size:27 final size:27
Alignment explanation
Indices: 33940010--33940265 Score: 131
Period size: 27 Copynumber: 9.4 Consensus size: 27
33940000 GTAAATCTAC
*
33940010 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
33940037 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * * *
33940065 AAAGTCAAGGGTATTT-TGTAACTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
* * ** *
33940092 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * *
33940119 AAATTGAGGGTATTTCGGTAATTTCAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
33940146 AAACCAAGGGTATTT-TGATAATTTTAC
1 AAACCAAGGGTATTTCAG-TAATTTTAT
* * ** *
33940173 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *
33940200 AAACTAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* * *** * *
33940227 AAATCGAGGGTAAAACAGTAATTCTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
*
33940254 AAATCAAGGGTA
1 AAACCAAGGGTA
33940266 AAATAGTAAT
Statistics
Matches: 182, Mismatches: 40, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
26 12 0.07
27 148 0.81
28 12 0.07
29 10 0.05
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:33940161 original size:54 final size:54
Alignment explanation
Indices: 33940099--33940238 Score: 183
Period size: 54 Copynumber: 2.6 Consensus size: 54
33940089 TGTAAATCAG
33940099 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * * * *
33940153 GGGTATTTTGATAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
* ** *
33940207 GGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
33940239 AAACAGTAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.01
54 71 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:33940238 original size:81 final size:80
Alignment explanation
Indices: 33940070--33940223 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 80
33940060 TTTAGAAAGT
* * *
33940070 CAAGGGTATTTTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTC
1 CAAGGGTATTTTGTAACTTTGTAAAACAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTC
*
33940135 GGTAATTTCACAAAC
66 AGTAATTTCACAAAC
33940150 CAAGGGTATTTTGATAA-TTT-TACAAACTAGGGGTATTTTGGTAATTTTACAAACTAAGGGTAT
1 CAAGGGTATTTTG-TAACTTTGTA-AAAC-AGGGGTATTTTGGTAATTTTACAAACTAAGGGTAT
*
33940213 TTTAGTAATTT
63 TTCAGTAATTT
33940224 TGTAAATCGA
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
79 2 0.03
80 19 0.29
81 45 0.68
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (80 bp):
CAAGGGTATTTTGTAACTTTGTAAAACAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTC
AGTAATTTCACAAAC
Found at i:33940266 original size:27 final size:27
Alignment explanation
Indices: 33940217--33940427 Score: 271
Period size: 27 Copynumber: 7.8 Consensus size: 27
33940207 GGGTATTTTA
* *
33940217 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
33940244 GTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
33940271 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
33940298 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
33940325 GTAATTATGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
33940352 ATAATTATGTAAATC-AGGGGTAAAACG
1 GTAATTCTGTAAATCGA-GGGTAAAACG
* * * *
33940379 GTAATTATGTAAATTGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
33940406 GTAATTCTGTAAATCAAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
33940428 CTTTGGTAAT
Statistics
Matches: 162, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 161 0.99
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:33940463 original size:27 final size:27
Alignment explanation
Indices: 33940433--33940521 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
33940423 GGGTACTTTG
* *
33940433 GTAATTTTACAAGTCGAAGGTGTTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
33940460 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
33940487 GTATTTTTACAAA-CTAAGGGTATTTCG
1 GTAATTTTACAAATCGAA-GGTATTTCA
33940514 GTAATTTT
1 GTAATTTT
33940522 TGTAAACTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.04
27 51 0.96
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:33940529 original size:28 final size:27
Alignment explanation
Indices: 33940455--33940531 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
33940445 GTCGAAGGTG
* *
33940455 TTTCAGTAATTTTACAAA-TCGAGGGTA
1 TTTCAGTATTTTTACAAACT-AAGGGTA
33940482 TTTCAGTATTTTTACAAACTAAGGGTA
1 TTTCAGTATTTTTACAAACTAAGGGTA
* **
33940509 TTTCGGTAATTTTTGTAAACTAA
1 TTTCAGT-ATTTTTACAAACTAA
33940532 AGTATTCTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 29 0.67
28 14 0.33
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (27 bp):
TTTCAGTATTTTTACAAACTAAGGGTA
Found at i:33951341 original size:53 final size:54
Alignment explanation
Indices: 33951159--33951365 Score: 227
Period size: 53 Copynumber: 3.8 Consensus size: 54
33951149 ATTAGGGTTT
* * * * *
33951159 AATGATACCAAGTAAAACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGC
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
* * * * * * * *
33951213 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTCTATAAGGC
* * * *
33951268 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC-ATAAGGC
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
* *
33951321 AATGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
33951366 TAAAAAGCAA
Statistics
Matches: 124, Mismatches: 28, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
53 46 0.37
54 35 0.28
55 43 0.35
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (54 bp):
AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
Found at i:33952456 original size:2 final size:2
Alignment explanation
Indices: 33952449--33952479 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33952439 ACATTAATTA
33952449 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
33952480 AGAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33953042 original size:7 final size:7
Alignment explanation
Indices: 33953026--33953132 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
33953016 AATAAATGAA
*
33953026 ATAATTT
1 ATAATAT
33953033 ATAATAT
1 ATAATAT
33953040 ATAATAT
1 ATAATAT
*
33953047 A-AAAAT
1 ATAATAT
* *
33953053 GTAAGTTT
1 ATAA-TAT
*
33953061 TTAA-A-
1 ATAATAT
*
33953066 ATAATGT
1 ATAATAT
33953073 ATAATAT
1 ATAATAT
*
33953080 A-AATAA
1 ATAATAT
33953086 ATAAATAT
1 AT-AATAT
33953094 ATAAGATAT
1 AT-A-ATAT
33953103 ATAAGT-T
1 ATAA-TAT
33953110 A-AA-AT
1 ATAATAT
33953115 ATAATAT
1 ATAATAT
33953122 ATAATA-
1 ATAATAT
33953128 ATAAT
1 ATAAT
33953133 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:33953096 original size:21 final size:21
Alignment explanation
Indices: 33953064--33953128 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
33953054 TAAGTTTTTA
*
33953064 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
33953084 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
33953105 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
33953127 AA
1 AA
33953129 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:33953097 original size:28 final size:29
Alignment explanation
Indices: 33953066--33953126 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
33953056 AGTTTTTAAA
33953066 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
33953094 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
33953122 ATAAT
1 ATAAT
33953127 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:33953167 original size:12 final size:13
Alignment explanation
Indices: 33953148--33953178 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
33953138 AATTTTGAAA
33953148 ATATAAATAATAT
1 ATATAAATAATAT
33953161 A-ATAAATAATAT
1 ATATAAATAATAT
33953173 ATATAA
1 ATATAA
33953179 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:33953176 original size:16 final size:15
Alignment explanation
Indices: 33953153--33953183 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
33953143 TGAAAATATA
33953153 AATAATATAATAAAT
1 AATAATATAATAAAT
33953168 AATATATATAATAAAT
1 AATA-ATATAATAAAT
33953184 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:33953512 original size:19 final size:19
Alignment explanation
Indices: 33953488--33953524 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33953478 AATCATATCT
*
33953488 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
33953507 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
33953525 TGAAGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:33953532 original size:17 final size:19
Alignment explanation
Indices: 33953491--33953532 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
33953481 CATATCTTCT
* *
33953491 AAGATTGTATATCATATCT
1 AAGATTGCATATCATATCG
33953510 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
33953527 AAGATT
1 AAGATT
33953533 ATATTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 14 0.67
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:33954308 original size:83 final size:83
Alignment explanation
Indices: 33953901--33954332 Score: 728
Period size: 82 Copynumber: 5.2 Consensus size: 83
33953891 TTCGATTTGT
* * * *
33953901 AAGGATGTCAAATCATCTTGAGTCTGTTTGAGAACATTTGAGAATCATATCTGCAAGGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
*
33953966 CTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* * * *
33953984 AAGGATGCCTAAACCATCTTGAGTCAGTTTGAGAACATTTGAGAATCATGTCTGCAAGGTCCTCG
1 AAGGATGCC-AAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCG
33954049 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
33954068 AAGGATG-CAAACCATC--GAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
33954130 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
33954148 AAGGATGCCAAACCATCTTGA-TCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
33954212 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
*
33954230 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTACAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
*
33954295 TTTATTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
33954313 AAGGATGCCAAACCATCTTG
1 AAGGATGCCAAACCATCTTG
33954333 GATCTGCTTC
Statistics
Matches: 333, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
80 67 0.20
81 9 0.03
82 90 0.27
83 90 0.27
84 77 0.23
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:33954467 original size:119 final size:119
Alignment explanation
Indices: 33954256--33954846 Score: 1010
Period size: 119 Copynumber: 5.0 Consensus size: 119
33954246 CTTGAGTCTG
* * * * * * * *
33954256 TTTGAGAACATTTGAGAGTCATATCTACAATGTCCTCGATTTATTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
33954321 CAAACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
* *
33954375 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
33954440 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGTTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
33954494 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAG
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT-G
*
33954559 -CAAATCAT-TT-GTTCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
65 CCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
33954611 TTTGAGAACGTCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
33954676 CAAATCATCTTGGAT-TGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
33954729 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
33954794 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
33954847 CTTGATCTAT
Statistics
Matches: 447, Mismatches: 20, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
116 1 0.00
117 110 0.25
118 120 0.27
119 216 0.48
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:33954671 original size:236 final size:237
Alignment explanation
Indices: 33954256--33954846 Score: 1008
Period size: 236 Copynumber: 2.5 Consensus size: 237
33954246 CTTGAGTCTG
* * * * * * * *
33954256 TTTGAGAACATTTGAGAGTCATATCTACAATGTCCTCGATTTATTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
33954321 CAAACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
* *
33954386 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCAAATCATCTT
131 CTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
*
33954451 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGTTATA
196 GGAT-TGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
33954494 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAG
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT-G
*
33954559 -CAAATCAT-TT-GTTCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACG
65 CCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACG
*
33954621 TCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCT
130 TCTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCT
*
33954686 TGGATTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
195 TGGATTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
33954729 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
33954794 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
33954847 CTTGATCTAT
Statistics
Matches: 333, Mismatches: 16, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
234 1 0.00
235 107 0.32
236 120 0.36
237 42 0.13
238 62 0.19
239 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (237 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
CTAAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
GGATTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:33955902 original size:20 final size:21
Alignment explanation
Indices: 33955879--33955941 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
33955869 TCACCTTGGC
33955879 CTCTCCATTTTTTCT-TTTTT
1 CTCTCCATTTTTTCTCTTTTT
**
33955899 CTCTTTATTTTTTCTCTTTTT
1 CTCTCCATTTTTTCTCTTTTT
* **
33955920 CTTTTCTTTTTTTTCTCTTTTT
1 C-TCTCCATTTTTTCTCTTTTT
33955942 TTTTTGAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 13 0.36
21 6 0.17
22 17 0.47
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (21 bp):
CTCTCCATTTTTTCTCTTTTT
Found at i:33955911 original size:13 final size:12
Alignment explanation
Indices: 33955893--33955945 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
33955883 CCATTTTTTC
33955893 TTTTTTCTCTTT
1 TTTTTTCTCTTT
33955905 ATTTTTTCTCTTT
1 -TTTTTTCTCTTT
*
33955918 TTCTTT-TC-TT
1 TTTTTTCTCTTT
33955928 TTTTTTCTCTTT
1 TTTTTTCTCTTT
33955940 TTTTTT
1 TTTTTT
33955946 TGAAATAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 7 0.19
11 4 0.11
12 13 0.36
13 12 0.33
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:33955927 original size:11 final size:10
Alignment explanation
Indices: 33955886--33955945 Score: 59
Period size: 11 Copynumber: 5.6 Consensus size: 10
33955876 GGCCTCTCCA
33955886 TTTTTTCTTT
1 TTTTTTCTTT
33955896 TTTCTCTT-TATT
1 TTT-T-TTCT-TT
*
33955908 TTTTCTCTTT
1 TTTTTTCTTT
33955918 TTCTTTTCTTT
1 TT-TTTTCTTT
33955929 TTTTTCTCTTT
1 TTTTT-TCTTT
33955940 TTTTTT
1 TTTTTT
33955946 TGAAATAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 12 0.29
11 23 0.55
12 7 0.17
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:33955944 original size:20 final size:22
Alignment explanation
Indices: 33955886--33955944 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
33955876 GGCCTCTCCA
*
33955886 TTTTT-TCTTTTTTCTCTTTAT
1 TTTTTCTCTTTTTTTTCTTTAT
33955907 TTTTTCTCTTTTTCTTT-TCTT-T
1 TTTTTCTCTTTTT-TTTCT-TTAT
33955929 TTTTTCTCTTTTTTTT
1 TTTTTCTCTTTTTTTT
33955945 TTGAAATAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 8 0.24
22 22 0.65
23 4 0.12
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTCTCTTTTTTTTCTTTAT
Found at i:33955946 original size:13 final size:13
Alignment explanation
Indices: 33955888--33955946 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
33955878 CCTCTCCATT
33955888 TTTTCTTTTTTCTC
1 TTTT-TTTTTTCTC
*
33955902 TTTATTTTTTCTC
1 TTTTTTTTTTCTC
*
33955915 -TTTTTCTTT-TC
1 TTTTTTTTTTCTC
33955926 --TTTTTTTTCTC
1 TTTTTTTTTTCTC
33955937 TTTTTTTTTT
1 TTTTTTTTTT
33955947 GAAATAGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 7 0.18
11 4 0.11
12 7 0.18
13 17 0.45
14 3 0.08
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTCTC
Found at i:33962219 original size:53 final size:54
Alignment explanation
Indices: 33962037--33962243 Score: 227
Period size: 53 Copynumber: 3.8 Consensus size: 54
33962027 ATTAGGGTTT
* * * *
33962037 AATGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGC
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
* * * * * * * *
33962091 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTCTATAAGGC
* * * *
33962146 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC-ATAAGGC
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
* * *
33962199 AATGATACCACGTAAGACCATGTCAAGACATGACAATGGTAAGTT
1 AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
33962244 TAAAAAGCAA
Statistics
Matches: 124, Mismatches: 28, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
53 45 0.36
54 36 0.29
55 43 0.35
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (54 bp):
AATGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGC
Found at i:33963548 original size:12 final size:13
Alignment explanation
Indices: 33963531--33963563 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
33963521 AAACAAATAC
33963531 AATAATATATAA-
1 AATAATATATAAT
33963543 AATAATA-ATAAT
1 AATAATATATAAT
33963555 AATAATATA
1 AATAATATA
33963564 GTAACATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 14 0.74
13 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:33963912 original size:7 final size:7
Alignment explanation
Indices: 33963896--33964002 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
33963886 AATAAATGAA
*
33963896 ATAATTT
1 ATAATAT
33963903 ATAATAT
1 ATAATAT
33963910 ATAATAT
1 ATAATAT
*
33963917 A-AAAAT
1 ATAATAT
* *
33963923 GTAAGTTT
1 ATAA-TAT
*
33963931 TTAA-A-
1 ATAATAT
*
33963936 ATAATGT
1 ATAATAT
33963943 ATAATAT
1 ATAATAT
*
33963950 A-AATAA
1 ATAATAT
33963956 ATAAATAT
1 AT-AATAT
33963964 ATAAGATAT
1 AT-A-ATAT
33963973 ATAAGT-T
1 ATAA-TAT
33963980 A-AA-AT
1 ATAATAT
33963985 ATAATAT
1 ATAATAT
33963992 ATAATA-
1 ATAATAT
33963998 ATAAT
1 ATAAT
33964003 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:33963966 original size:21 final size:21
Alignment explanation
Indices: 33963934--33963998 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
33963924 TAAGTTTTTA
*
33963934 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
33963954 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
33963975 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
33963997 AA
1 AA
33963999 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:33963967 original size:28 final size:29
Alignment explanation
Indices: 33963936--33963996 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
33963926 AGTTTTTAAA
33963936 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
33963964 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
33963992 ATAAT
1 ATAAT
33963997 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:33964037 original size:12 final size:13
Alignment explanation
Indices: 33964018--33964048 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
33964008 AATTTTGAAA
33964018 ATATAAATAATAT
1 ATATAAATAATAT
33964031 A-ATAAATAATAT
1 ATATAAATAATAT
33964043 ATATAA
1 ATATAA
33964049 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:33964046 original size:16 final size:15
Alignment explanation
Indices: 33964023--33964053 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
33964013 TGAAAATATA
33964023 AATAATATAATAAAT
1 AATAATATAATAAAT
33964038 AATATATATAATAAAT
1 AATA-ATATAATAAAT
33964054 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:33964398 original size:18 final size:18
Alignment explanation
Indices: 33964358--33964429 Score: 92
Period size: 19 Copynumber: 3.9 Consensus size: 18
33964348 AATCATATCT
*
33964358 TCTAAGATTGTATATCATA
1 TCTAAGATTGCA-ATCATA
*
33964377 TCTAAGATTGCAATCTTA
1 TCTAAGATTGCAATCATA
*
33964395 TCTAAGATTG-TATCATA
1 TCTAAGATTGCAATCATA
33964412 TCTAAGATTGCATATCAT
1 TCTAAGATTGCA-ATCAT
33964430 TGAAGATTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 15 0.33
18 15 0.33
19 16 0.35
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:33967864 original size:27 final size:28
Alignment explanation
Indices: 33967834--33967934 Score: 111
Period size: 27 Copynumber: 3.7 Consensus size: 28
33967824 TTTAGTTTAC
33967834 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
33967861 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
33967888 TAAATTTACCGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
33967915 TAAAATTACC-AAAGTACCCT
1 TAAAATTACCGAAA-TACCCT
33967935 CAATTTACAG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
26 7 0.11
27 52 0.84
28 3 0.05
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:33967933 original size:54 final size:54
Alignment explanation
Indices: 33967834--33967940 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
33967824 TTTAGTTTAC
* * *
33967834 TAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCTCAATTTG
* * *
33967888 TAAATTTACCGAAATA-CCTTCGACTTGTAAAATTAC-CAAAGTACCCTCAATTT
1 TAAAATTACCGAAATACCCTTAG-CTTGTAAAAATACTCAAA-TACCCTCAATTT
33967941 ACAGAATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 8 0.18
54 37 0.82
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCTCAATTTG
Found at i:33967951 original size:54 final size:53
Alignment explanation
Indices: 33967836--33967952 Score: 121
Period size: 54 Copynumber: 2.2 Consensus size: 53
33967826 TAGTTTACTA
* * * **
33967836 AAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTGT
1 AAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCTCAATTTAC
* *
33967889 AAATTTACCGAAATA-CCTTCGACTTGTAAAATTAC-CAAAGTACCCTCAATTTAC
1 AAA-TTACCGAAATACCCTTAG-CTTGTAAAAATACTCAAA-TACCCTCAATTTAC
33967943 AGAATTACCG
1 A-AATTACCG
33967953 TTTTACCCCT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
53 11 0.21
54 40 0.75
55 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (53 bp):
AAATTACCGAAATACCCTTAGCTTGTAAAAATACTCAAATACCCTCAATTTAC
Found at i:33968223 original size:27 final size:27
Alignment explanation
Indices: 33967929--33968222 Score: 319
Period size: 27 Copynumber: 10.9 Consensus size: 27
33967919 ATTACCAAAG
* *
33967929 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
33967956 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACTGTTT
*
33967983 TACCC-CTGATTTACATAATTA-TCGTTT
1 TACCCTC-GATTTACAGAATTACT-GTTT
* *
33968010 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
33968037 TACCCTCGATTTACTA-AATTACTGTTT
1 TACCCTCGATTTAC-AGAATTACTGTTT
* *
33968064 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
33968091 TACCCTTGATTTACAGAATTACTTTTTT
1 TACCCTCGATTTACAGAATTAC-TGTTT
*
33968119 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* * * *
33968146 TACCGTCGATTTATAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
33968173 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
33968200 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
33968223 AAAATACCCT
Statistics
Matches: 234, Mismatches: 24, Indels: 18
0.85 0.09 0.07
Matches are distributed among these distances:
26 3 0.01
27 205 0.88
28 26 0.11
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:33968230 original size:27 final size:27
Alignment explanation
Indices: 33968119--33968420 Score: 123
Period size: 27 Copynumber: 11.1 Consensus size: 27
33968109 TTACTTTTTT
**
33968119 TACCCTCGATTTACAAAATTATCGT--TT
1 TACCCTCGATTTACAAAATTA-C-TAAAA
* * ***
33968146 TACCGTCGATTTATAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAA
* * ***
33968173 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTAAAA
33968200 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * ** *
33968227 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
33968254 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACTAAAA
* ** *** **
33968281 TACCCTTGGCTTGTGAAATTACCGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
33968308 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
*
33968335 TACCC-CTGATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
*
33968362 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTCGA-TTTAC--AAAATTACTA-AAA
* * * *
33968391 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
33968418 TAC
1 TAC
33968421 TTTTGGTTTG
Statistics
Matches: 222, Mismatches: 40, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
25 1 0.00
26 3 0.01
27 192 0.86
28 7 0.03
29 19 0.09
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:33968247 original size:136 final size:136
Alignment explanation
Indices: 33967980--33968248 Score: 326
Period size: 136 Copynumber: 2.0 Consensus size: 136
33967970 ATAATTACCG
* * *
33967980 TTTTACCCCTGATTTACATAATTATCGTTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCG
1 TTTTACCCCTGATTTACAAAATTATCGTTTTACCCTCGACTTACAAAATTACCATTTTACCCTCG
* * * * **** *
33968045 ATTTACTAAATTACTGTTTTACCCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAAT
66 ATTTACTAAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAAAAT
33968110 TACTTT
131 TACTTT
* * * * *
33968116 TTTTA-CCCTCGATTTACAAAATTATCGTTTTACCGTCGATTTATAAAATTACTATTTTACCCTT
1 TTTTACCCCT-GATTTACAAAATTATCGTTTTACCCTCGACTTACAAAATTACCATTTTACCCTC
* **
33968180 GATTTAC-AGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAA
65 GATTTACTA-AATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAAA
33968244 ATTAC
129 ATTAC
33968249 CAAAATACCC
Statistics
Matches: 111, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
135 5 0.05
136 106 0.95
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (136 bp):
TTTTACCCCTGATTTACAAAATTATCGTTTTACCCTCGACTTACAAAATTACCATTTTACCCTCG
ATTTACTAAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTTACAAAAT
TACTTT
Found at i:33968258 original size:54 final size:54
Alignment explanation
Indices: 33968200--33968339 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
33968190 ATTACTATTT
* ** * *
33968200 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTTGGCTTGTAAAATTACCAAAA
* * *
33968254 TACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGCTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACCCTTGGCTTGTAAAATTACCAAAA
33968308 TACCCTCAATTTGTAAAATTACCAAAATACCC
1 TACCCTCAATTTGTAAAATTACCAAAATACCC
33968340 CTGATTTACA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 73 0.97
55 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTTGGCTTGTAAAATTACCAAAA
Found at i:33968362 original size:54 final size:52
Alignment explanation
Indices: 33968200--33968367 Score: 151
Period size: 54 Copynumber: 3.1 Consensus size: 52
33968190 ATTACTATTT
* ** * * *
33968200 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCA-AAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTT-GATT-TCAAATTA-CAGAAA
* * * *
33968254 TACCC-CTAGTTTGTAAAATTACCAAAATACCCTTGGCTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAATACCCTT-GATT-TCAAATTACAGAAA
*
33968308 TACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTT-CAAA-TTACAGAAA
33968362 TACCCT
1 TACCCT
33968368 TGACTTTCTA
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
52 1 0.01
53 8 0.08
54 86 0.90
55 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (52 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTCAAATTACAGAAA
Found at i:33968426 original size:27 final size:27
Alignment explanation
Indices: 33968378--33968429 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
33968368 TGACTTTCTA
33968378 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
**
33968405 AAAATTACT-GAAATACTTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
33968430 GTAGATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:33968513 original size:27 final size:27
Alignment explanation
Indices: 33968483--33968574 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
33968473 ACCCTTATTA
*
33968483 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
33968510 GGTAAAGTGACCGTAAAGCCCTTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
33968537 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
33968564 GGTAAAATGAC
1 GGTAAAATGAC
33968575 GAATATGCCC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:33969763 original size:25 final size:25
Alignment explanation
Indices: 33969734--33969781 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33969724 TTATACCATG
* * *
33969734 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
33969759 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
33969782 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:33969884 original size:20 final size:20
Alignment explanation
Indices: 33969825--33969884 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
33969815 TAAATATGGC
* *
33969825 ATGTATGAGATGCACATGAC
1 ATGTATGATATGCACATGAT
33969845 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAT
33969865 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAT
33969885 GTAATCATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAT
Found at i:33969961 original size:24 final size:24
Alignment explanation
Indices: 33969934--33970100 Score: 257
Period size: 24 Copynumber: 7.0 Consensus size: 24
33969924 GAGGAAGTGA
33969934 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33969958 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33969982 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33970006 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
33970029 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
33970053 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
33970077 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
33970101 ATGATAAAGC
Statistics
Matches: 135, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.17
24 101 0.75
25 11 0.08
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:33970051 original size:71 final size:71
Alignment explanation
Indices: 33969934--33970101 Score: 257
Period size: 71 Copynumber: 2.3 Consensus size: 71
33969924 GAGGAAGTGA
33969934 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
33969999 AGTTATC
65 AGTTATC
** *
33970006 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
*
33970071 GTTATT
66 GTTATC
*
33970077 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
33970102 TGATAAAGCA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
71 54 0.61
72 35 0.39
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:33970327 original size:31 final size:31
Alignment explanation
Indices: 33970292--33970386 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
33970282 CGTTTACAGT
33970292 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
33970323 AAAGGCATCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
33970354 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
33970385 AA
1 AA
33970387 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:33972074 original size:2 final size:2
Alignment explanation
Indices: 33972062--33972094 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
33972052 CAAGTTAACC
*
33972062 TA TA AA 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 TA TA T
33972095 CCAATTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33972567 original size:18 final size:19
Alignment explanation
Indices: 33972528--33972572 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
33972518 AGTTATTTAC
*
33972528 TTCCAGAATGATATTAAAT
1 TTCCAAAATGATATTAAAT
*
33972547 TTCCAAAATGTTATT-AAT
1 TTCCAAAATGATATTAAAT
33972565 TTCCAAAA
1 TTCCAAAA
33972573 CATCACTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (19 bp):
TTCCAAAATGATATTAAAT
Found at i:33974922 original size:41 final size:42
Alignment explanation
Indices: 33974864--33974984 Score: 129
Period size: 41 Copynumber: 2.9 Consensus size: 42
33974854 GTGCCATCAT
* * *
33974864 ATATTGATGCCATTGTCCTAGACAGGGTCTTACACGAACCAA
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAACCAA
* * * *
33974906 ATA-CGATGCCAATGTCCCAGACATGGTCTTACATGTAATCAC
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACG-AACCAA
* *
33974948 ATATCGATGCCAACGTCCCAGA-TGTGGTCTTACACGA
1 ATATCGATGCCAATGTCCCAGACAG-GGTCTTACACGA
33974985 GAACATATAT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
41 27 0.42
42 11 0.17
43 27 0.42
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAACCAA
Found at i:33974977 original size:84 final size:84
Alignment explanation
Indices: 33974822--33974984 Score: 193
Period size: 84 Copynumber: 1.9 Consensus size: 84
33974812 CACACATATC
* * * * * ** *
33974822 ATACAATGCCAACGTCCCAAACGTGGTCTTACGTGCCATCATATATTGATGCCATTGTCCTAGAC
1 ATACAATGCCAACGTCCCAAACATGGTCTTACATGCAATCACATATCGATGCCAACGTCCCAGAC
33974887 AGGGTCTTACACGAACCAA
66 AGGGTCTTACACGAACCAA
* * * *
33974906 ATACGATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCGATGCCAACGTCCCAGA-
1 ATACAATGCCAACGTCCCAAACATGGTCTTACATGCAATCACATATCGATGCCAACGTCCCAGAC
*
33974970 TGTGGTCTTACACGA
66 AG-GGTCTTACACGA
33974985 GAACATATAT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
83 1 0.02
84 64 0.98
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (84 bp):
ATACAATGCCAACGTCCCAAACATGGTCTTACATGCAATCACATATCGATGCCAACGTCCCAGAC
AGGGTCTTACACGAACCAA
Found at i:33974995 original size:43 final size:42
Alignment explanation
Indices: 33974827--33974995 Score: 144
Period size: 43 Copynumber: 4.0 Consensus size: 42
33974817 ATATCATACA
* ** * *
33974827 ATGCCAACGTCCCAAACGTGGTCTTACGTGCCATCATATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AATCATATATCG
** * * *
33974870 ATGCCATTGTCCTAGACAG-GGTCTTACACGAACCAAATA-CG
1 ATGCCAACGTCCCAGAC-GTGGTCTTACACGAATCATATATCG
* * * *
33974911 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AATCATATATCG
* *
33974954 ATGCCAACGTCCCAGATGTGGTCTTACACGAGAACATATATC
1 ATGCCAACGTCCCAGACGTGGTCTTACACGA-ATCATATATC
33974996 AGAAATCCTA
Statistics
Matches: 99, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
41 26 0.26
42 14 0.14
43 58 0.59
44 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAATCATATATCG
Found at i:33977690 original size:22 final size:22
Alignment explanation
Indices: 33977665--33977706 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33977655 ACTTCTCACT
33977665 CCTTAAT-TTCCTCACCAAAATC
1 CCTTAATCTT-CTCACCAAAATC
*
33977687 CCTTAATCTTCTCCCCAAAA
1 CCTTAATCTTCTCACCAAAA
33977707 CTATCCACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (22 bp):
CCTTAATCTTCTCACCAAAATC
Found at i:33981853 original size:28 final size:28
Alignment explanation
Indices: 33981784--33981885 Score: 114
Period size: 30 Copynumber: 3.5 Consensus size: 28
33981774 GACAAGATTG
* * * *
33981784 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
33981814 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
33981842 GCACTAAGTGTGCGAGGTTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
33981872 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
33981886 GATTCACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
28 25 0.39
29 2 0.03
30 37 0.58
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:33989776 original size:28 final size:28
Alignment explanation
Indices: 33989707--33989807 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
33989697 GACAAGATTG
* * * *
33989707 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
33989737 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
33989765 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
33989794 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
33989808 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:33993177 original size:46 final size:46
Alignment explanation
Indices: 33993127--33993302 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
33993117 TGGTTGAGCA
33993127 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
33993173 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
33993218 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
33993266 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
33993303 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:33993283 original size:93 final size:93
Alignment explanation
Indices: 33993124--33993294 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
33993114 GGATGGTTGA
* *
33993124 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
33993189 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
33993217 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
33993282 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
33993295 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:33995274 original size:9 final size:9
Alignment explanation
Indices: 33995262--33995338 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
33995252 TTTGATAAAC
33995262 ATGATATGT
1 ATGATATGT
*
33995271 ATGATATGCAC
1 ATGATATG--T
33995282 ATGATATGT
1 ATGATATGT
*
33995291 ATGATATGCAC
1 ATGATATG--T
*
33995302 ATGACATGT
1 ATGATATGT
*
33995311 ATGATATGCAC
1 ATGATATG--T
33995322 ATGATATGT
1 ATGATATGT
33995331 ATGATATG
1 ATGATATG
33995339 CACACGAGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:33995287 original size:11 final size:11
Alignment explanation
Indices: 33995271--33995342 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
33995261 CATGATATGT
33995271 ATGATATGCAC
1 ATGATATGCAC
*
33995282 ATGATATG--T
1 ATGATATGCAC
33995291 ATGATATGCAC
1 ATGATATGCAC
* *
33995302 ATGACATG--T
1 ATGATATGCAC
33995311 ATGATATGCAC
1 ATGATATGCAC
*
33995322 ATGATATG--T
1 ATGATATGCAC
33995331 ATGATATGCAC
1 ATGATATGCAC
33995342 A
1 A
33995343 CGAGATGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:33995350 original size:20 final size:20
Alignment explanation
Indices: 33995260--33995342 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
33995250 ATTTTGATAA
33995260 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
33995280 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
33995300 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
33995320 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
33995340 ACA
1 ACA
33995343 CGAGATGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:33995453 original size:24 final size:24
Alignment explanation
Indices: 33995397--33995538 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
33995387 GAGGAAGTGA
33995397 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
33995420 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
33995444 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
33995468 AAAAGGGCTTACGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
33995492 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
33995515 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
33995539 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
23 43 0.39
24 55 0.50
25 11 0.10
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:33995519 original size:47 final size:48
Alignment explanation
Indices: 33995397--33995538 Score: 218
Period size: 47 Copynumber: 3.0 Consensus size: 48
33995387 GAGGAAGTGA
*
33995397 AAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATC
*
33995444 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATC
*
33995492 -AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAAG-GGCTTACGCC-CCAGTTAT
33995539 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 55 0.62
48 33 0.38
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTACGCCCCAGTTATC
Found at i:33995770 original size:31 final size:31
Alignment explanation
Indices: 33995732--33995795 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
33995722 CGTTTACCGT
* *
33995732 AAAGGCTTTGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
33995763 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
33995794 AA
1 AA
33995796 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:33997575 original size:25 final size:25
Alignment explanation
Indices: 33997519--33997575 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
33997509 TTTTAGGTGT
* *
33997519 TTTCAGTATAGTCTATCTATAGTAG
1 TTTCAGTATAGTCTACCTATAGAAG
**
33997544 TCACAGTATA-TACTACCTATAGAAG
1 TTTCAGTATAGT-CTACCTATAGAAG
33997569 TTTCAGT
1 TTTCAGT
33997576 CAAAAACATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (25 bp):
TTTCAGTATAGTCTACCTATAGAAG
Found at i:33999919 original size:22 final size:22
Alignment explanation
Indices: 33999894--33999937 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
33999884 ACTCTTCACT
33999894 CCTTAAT-TTCCTCACCAAAATC
1 CCTTAATCTT-CTCACCAAAATC
*
33999916 CCTTAATCTTCTCCCCAAAATC
1 CCTTAATCTTCTCACCAAAATC
33999938 GTCTACCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.32
Consensus pattern (22 bp):
CCTTAATCTTCTCACCAAAATC
Found at i:34009110 original size:24 final size:23
Alignment explanation
Indices: 34009083--34009138 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
34009073 TTTTCTTCTA
* *
34009083 AATTTTTATTTTATTTAATTATTT
1 AATTTTTAATTTATTGAATTA-TT
*
34009107 AATTTTCCAATTTATTGAATTATT
1 AATTTT-TAATTTATTGAATTATT
*
34009131 AATATTTA
1 AATTTTTA
34009139 GCTATTAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 13 0.50
25 12 0.46
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
AATTTTTAATTTATTGAATTATT
Found at i:34010973 original size:19 final size:17
Alignment explanation
Indices: 34010938--34010976 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
34010928 AAATGCTCGT
*
34010938 GAAAAAAAAAAGTAAAA
1 GAAAAAAAAAAGCAAAA
34010955 GAAAAGAAAAAGAGCAAAA
1 GAAAA-AAAAA-AGCAAAA
34010974 GAA
1 GAA
34010977 GAGCATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (17 bp):
GAAAAAAAAAAGCAAAA
Found at i:34015793 original size:48 final size:48
Alignment explanation
Indices: 34015714--34015808 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
34015704 AATTATATGG
* *
34015714 TGGTCTATCCACGATGTGCTTTGTGCCCGTTCATCGATATCTATGTGA
1 TGGTCTATCCACGATGTGCTATGTGACCGTTCATCGATATCTATGTGA
* * *
34015762 TGGTTTATCCACGATGTGCTATGTGATCGTTCATCGGTATCTATGTG
1 TGGTCTATCCACGATGTGCTATGTGACCGTTCATCGATATCTATGTG
34015809 GTGGCTTGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (48 bp):
TGGTCTATCCACGATGTGCTATGTGACCGTTCATCGATATCTATGTGA
Found at i:34015821 original size:48 final size:48
Alignment explanation
Indices: 34015719--34015821 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 48
34015709 TATGGTGGTC
* * *
34015719 TATCCACGATGTGCTTTGTGCCCGTTCATCGATATCTATGTGATGGTT
1 TATCCACGATGTGCTATGTGACCGTTCATCGATATCTATGTGATGGCT
* * *
34015767 TATCCACGATGTGCTATGTGATCGTTCATCGGTATCTATGTGGTGGCT
1 TATCCACGATGTGCTATGTGACCGTTCATCGATATCTATGTGATGGCT
*
34015815 TGTCCAC
1 TATCCAC
34015822 AAACTGATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (48 bp):
TATCCACGATGTGCTATGTGACCGTTCATCGATATCTATGTGATGGCT
Found at i:34016804 original size:10 final size:10
Alignment explanation
Indices: 34016789--34016813 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34016779 ATGGATTGTA
34016789 AAACTATAGG
1 AAACTATAGG
34016799 AAACTATAGG
1 AAACTATAGG
34016809 AAACT
1 AAACT
34016814 TTTGATTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (10 bp):
AAACTATAGG
Found at i:34031097 original size:46 final size:46
Alignment explanation
Indices: 34031030--34031211 Score: 258
Period size: 46 Copynumber: 4.0 Consensus size: 46
34031020 AGTGTGCTCT
*
34031030 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
34031076 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
34031122 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
34031168 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
34031212 TCATGTCAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 123 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:34037773 original size:43 final size:43
Alignment explanation
Indices: 34037702--34037815 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
34037692 GGAATTAAGA
* **
34037702 AATCTGAGCTCGTTGAGCGGTCTGAGTTCGTGATATATGTGAG
1 AATCTGAACTCGTTGAGCGGTCCAAGTTCGTGATATATGTGAG
* * *
34037745 AATCTGAACTTGTTGAGTGGTCCAAGTTCGTGATCTATGTG-G
1 AATCTGAACTCGTTGAGCGGTCCAAGTTCGTGATATATGTGAG
* * * * *
34037787 CATCCGAGCTCGTTGAGAGGTCCGAGTTC
1 AATCTGAACTCGTTGAGCGGTCCAAGTTC
34037816 ATTATGGACG
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 24 0.41
43 35 0.59
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.32
Consensus pattern (43 bp):
AATCTGAACTCGTTGAGCGGTCCAAGTTCGTGATATATGTGAG
Found at i:34049147 original size:48 final size:48
Alignment explanation
Indices: 34048924--34049200 Score: 252
Period size: 48 Copynumber: 5.8 Consensus size: 48
34048914 AACATAAGGT
* * * *
34048924 ATAC-TGCCGATGCCATGTCCCAAACATGGTCTTATACTGGCTCATCC
1 ATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCC
* * *
34048971 ATCAAGT--CGATGCCATGTCCCAGACATGGTCTTACACTGAC-TATCG
1 AT-ACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCC
* *
34049017 ATACCGAGGCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCTC-TCAC
1 ATA-CG-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CACATC-C
* ** * * *
34049067 ATATCTGTGCCGATGCCATCTCTTAGAGATGGTCTTACACTGACACCTCT
1 ATA-C-GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCC
*
34049117 ATACGTGCCGATGCCATGTCTCAGACATGGTCTTACACTGACACAT-C
1 ATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCC
*
34049164 -T-CGTAGCCGATG-CATGTCCTAGACAT-GTCTTACACTG
1 ATACGT-GCCGATGCCATGTCCCAGACATGGTCTTACACTG
34049201 GCTTACATCT
Statistics
Matches: 192, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
44 11 0.06
45 16 0.08
46 14 0.07
47 33 0.17
48 40 0.21
49 36 0.19
50 38 0.20
51 4 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
ATACGTGCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCC
Found at i:34049236 original size:46 final size:44
Alignment explanation
Indices: 34048978--34049240 Score: 169
Period size: 46 Copynumber: 5.5 Consensus size: 44
34048968 TCCATCAAGT
*
34048978 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCGATAC-CG-AGGC
1 CGATG-CATGTCTCAGACAT-GTCTTACACTGAC-A-C-AT-CTCGTA-GC
* * *
34049027 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTGT-GC
1 CGATG-CATGTCTCAGACAT-GTCTTACACT-G---ACACATCTC-GTAGC
* * * *
34049077 CGATGCCATCTCTTAGAGATGGTCTTACACTGACACCTCTATACGT-GC
1 CGATG-CATGTCTCAGACAT-GTCTTACACTGACACATC--T-CGTAGC
34049125 CGATGCCATGTCTCAGACATGGTCTTACACTGACACATCTCGTAGC
1 CGATG-CATGTCTCAGACAT-GTCTTACACTGACACATCTCGTAGC
*
34049171 CGATGCATGTC-CTAGACATGTCTTACACTGGCTTACATCTCG-AGGC
1 CGATGCATGTCTC-AGACATGTCTTACACTGAC--ACATCTCGTA-GC
*
34049217 CGATGCATGTCTCAAACATGTCTT
1 CGATGCATGTCTCAGACATGTCTT
34049241 GTACTAGCTC
Statistics
Matches: 183, Mismatches: 15, Indels: 35
0.79 0.06 0.15
Matches are distributed among these distances:
44 13 0.07
45 16 0.09
46 43 0.23
47 1 0.01
48 40 0.22
49 33 0.18
50 33 0.18
51 2 0.01
52 1 0.01
53 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (44 bp):
CGATGCATGTCTCAGACATGTCTTACACTGACACATCTCGTAGC
Found at i:34054804 original size:11 final size:11
Alignment explanation
Indices: 34054772--34054815 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
34054762 ATCTTCTCTA
34054772 TTTGG-TCCTT
1 TTTGGCTCCTT
*
34054782 TTTGTC-CCTT
1 TTTGGCTCCTT
*
34054792 TTTGGCTCGTT
1 TTTGGCTCCTT
34054803 TTTGGCTCCTT
1 TTTGGCTCCTT
34054814 TT
1 TT
34054816 GACTCTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.00, C:0.23, G:0.18, T:0.59
Consensus pattern (11 bp):
TTTGGCTCCTT
Found at i:34055119 original size:49 final size:49
Alignment explanation
Indices: 34055062--34055229 Score: 189
Period size: 49 Copynumber: 3.4 Consensus size: 49
34055052 TATTGTGTGT
*
34055062 CAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGC
* * * *
34055111 CAGTGTAAGACCTGCCTGGGACATGGCATCGGCCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGC
* * * * **
34055160 CAATGTAAGACCTGTCTGGGACACGGCATCGACTTC-A-ATATGCTAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGC
*
34055207 CAGTGTAAGACCATGTCTAGGAC
1 CAGTGTAAGACC-TGTCTGGGAC
34055230 CATGTCAGCA
Statistics
Matches: 102, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
47 18 0.18
48 11 0.11
49 73 0.72
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGC
Found at i:34060569 original size:26 final size:27
Alignment explanation
Indices: 34060463--34060735 Score: 228
Period size: 27 Copynumber: 9.8 Consensus size: 27
34060453 ATTACCAAAG
* * *
34060463 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
34060490 TACCCTCGATTTATAGAAGTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
34060517 TACCCTTGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
34060544 TACCCTTGATTTACA-AATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
34060570 TACCC-CGATTTACATAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
34060596 TACCC-CGTTTTACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCG-ATT----T--AC--A--GAATTACCATTT
* *
34060633 TACCCTCGATTTACAAAATTATCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * * *
34060660 TATCGTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
34060687 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
34060714 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
34060736 AGAAATACCC
Statistics
Matches: 203, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
25 8 0.04
26 33 0.16
27 135 0.67
29 1 0.00
31 3 0.01
33 3 0.01
35 1 0.00
37 17 0.08
38 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:34060626 original size:37 final size:37
Alignment explanation
Indices: 34060567--34060646 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
34060557 CAAATTACCA
* *
34060567 TTTTACCCCGATTTACATAATTACCATTTTACCC-CG
1 TTTTACCCCGACTTACAGAATTACCATTTTACCCTCG
*
34060603 TTTTACCCTCGACTTACAGAATTACCGTTTTACCCTCG
1 TTTTACCC-CGACTTACAGAATTACCATTTTACCCTCG
*
34060641 ATTTAC
1 TTTTAC
34060647 AAAATTATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 8 0.21
37 23 0.61
38 7 0.18
ACGTcount: A:0.24, C:0.30, G:0.07, T:0.39
Consensus pattern (37 bp):
TTTTACCCCGACTTACAGAATTACCATTTTACCCTCG
Found at i:34060744 original size:27 final size:28
Alignment explanation
Indices: 34060714--34060937 Score: 112
Period size: 27 Copynumber: 8.2 Consensus size: 28
34060704 ATTACTATTT
34060714 TACCCTCGATTTACAAAATTA-CAGAAA
1 TACCCTCGATTTACAAAATTACCAGAAA
* **
34060741 TACCCTCAATTTGTAAAATTACCA-AAA
1 TACCCTCGATTTACAAAATTACCAGAAA
* **
34060768 TACCC-CTAGTTTGTAAAATTACCA-AAA
1 TACCCTCGA-TTTACAAAATTACCAGAAA
* *** *
34060795 TACCACT-GGTTTGTGAAATTATC-GAAA
1 TACC-CTCGATTTACAAAATTACCAGAAA
* **
34060822 TACCCTCAATTTTTAAAATTACCA-AAA
1 TACCCTCGATTTACAAAATTACCAGAAA
* *
34060849 TACCC-CTGATTTACAAAGTTA-TAGAAA
1 TACCCTC-GATTTACAAAATTACCAGAAA
* *
34060876 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTCGA-TTTAC--AAAATTACCAGAAA
* * * *
34060905 TACCATTGGTTTACAAAATTA-CTGAAA
1 TACCCTCGATTTACAAAATTACCAGAAA
34060932 TACCCT
1 TACCCT
34060938 TGGTTTGTAG
Statistics
Matches: 158, Mismatches: 25, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
26 6 0.04
27 123 0.78
28 9 0.06
29 20 0.13
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (28 bp):
TACCCTCGATTTACAAAATTACCAGAAA
Found at i:34060772 original size:81 final size:82
Alignment explanation
Indices: 34060606--34060863 Score: 204
Period size: 81 Copynumber: 3.2 Consensus size: 82
34060596 TACCCCGTTT
* * * *** * * *
34060606 TACCCTCGACTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTATCA-TTTTATCGTCGAT
1 TACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTATCAGAAATACCCTCAAT
* * ***
34060670 TTATAGAATTACTATTT
66 TTATAAAATTACCAAAA
*
34060687 TACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTA-CAGAAATACCCTCAAT
1 TACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTATCAGAAATACCCTCAAT
*
34060751 TTGTAAAATTACCAAAA
66 TTATAAAATTACCAAAA
* * *** * ***
34060768 TACCCCTAGTTTGTA-A-AATTACCAAAATACCACT-GGTTTGTGAAATTATC-GAAATACCCTC
1 TA-CCCTTGATT-TACAGAATTACCATTTTACC-CTCGATTTACAAAATTATCAGAAATACCCTC
*
34060829 AATTTTTAAAATTACCAAAA
63 AATTTATAAAATTACCAAAA
*
34060849 TACCCCTGATTTACA
1 TACCCTTGATTTACA
34060864 AAGTTATAGA
Statistics
Matches: 141, Mismatches: 30, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
79 2 0.01
80 9 0.06
81 117 0.83
82 11 0.08
83 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (82 bp):
TACCCTTGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTATCAGAAATACCCTCAAT
TTATAAAATTACCAAAA
Found at i:34060808 original size:54 final size:54
Alignment explanation
Indices: 34060750--34060852 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
34060740 ATACCCTCAA
*
34060750 TTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGG
1 TTTGTAAAATTACCAAAATACCCTC-AATTTGTAAAATTACCAAAATACCACTGG
* * * *
34060804 TTTGTGAAATTATCGAAATACCCTCAATTTTTAAAATTACCAAAATACC
1 TTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACC
34060853 CCTGATTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 42 0.98
55 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCACTGG
Found at i:34061027 original size:27 final size:27
Alignment explanation
Indices: 34060996--34061088 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
34060986 TACCCCTATT
*
34060996 AGGTAAAAAGACCGTAAAGCCCCTGTA
1 AGGTAAAATGACCGTAAAGCCCCTGTA
* * *
34061023 GGGTAAAGTGACCGTAAAGCTCCTGTA
1 AGGTAAAATGACCGTAAAGCCCCTGTA
*
34061050 AGGTAAAGTGACCGTAATA-CCCCTGTA
1 AGGTAAAATGACCGTAA-AGCCCCTGTA
*
34061077 TGGTAAAATGAC
1 AGGTAAAATGAC
34061089 GAATATGCCC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 56 0.98
28 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (27 bp):
AGGTAAAATGACCGTAAAGCCCCTGTA
Found at i:34062403 original size:20 final size:20
Alignment explanation
Indices: 34062333--34062395 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
34062323 ATTTTGATAA
*
34062333 ACATGATATGTATGATATGC
1 ACATGACATGTATGATATGC
34062353 ACATGACATGTATGATATGC
1 ACATGACATGTATGATATGC
34062373 ACATGACATGTATGATATGC
1 ACATGACATGTATGATATGC
34062393 ACA
1 ACA
34062396 CGAGATGTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (20 bp):
ACATGACATGTATGATATGC
Found at i:34062507 original size:24 final size:23
Alignment explanation
Indices: 34062451--34062641 Score: 258
Period size: 24 Copynumber: 8.0 Consensus size: 23
34062441 GAGGAAGTGA
34062451 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
34062474 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
34062497 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
34062521 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
34062545 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
34062569 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
34062592 AGAAAGGACTTTTGCCCCAGTTATT
1 A-AAAGGGCTTATGCCCCAGTTA-T
*
34062617 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
34062641 A
1 A
34062642 TGATAAAGCA
Statistics
Matches: 152, Mismatches: 11, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
23 43 0.28
24 98 0.64
25 11 0.07
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:34062520 original size:47 final size:47
Alignment explanation
Indices: 34062451--34062619 Score: 277
Period size: 47 Copynumber: 3.6 Consensus size: 47
34062441 GAGGAAGTGA
34062451 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
*
34062498 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATC
*
34062546 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
* *
34062592 AGAAAGGACTTTTGCCCCAGTTATTAAA
1 A-AAAGGGCTTATGCCCCAGTTATTAAA
34062620 AGAGGCTAGG
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.01
47 68 0.60
48 45 0.39
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
Found at i:34062574 original size:71 final size:70
Alignment explanation
Indices: 34062451--34062640 Score: 258
Period size: 71 Copynumber: 2.7 Consensus size: 70
34062441 GAGGAAGTGA
* *
34062451 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTATGCCCCA
34062516 GTTAT
66 GTTAT
*
34062521 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTAT-TAAAGGGCTTATGCCC
1 -AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTATGCCC
34062585 CAGTTAT
64 CAGTTAT
* * *
34062592 AGAAAGGACTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 A-AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTACGCC-CCAGTTAT
34062641 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
70 1 0.01
71 74 0.69
72 33 0.31
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (70 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTAT
Found at i:34062869 original size:31 final size:31
Alignment explanation
Indices: 34062834--34062897 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
34062824 CGTTTACCGT
*
34062834 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* **
34062865 AAAGGCTTCGGCCTAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
34062896 AA
1 AA
34062898 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:34069951 original size:64 final size:64
Alignment explanation
Indices: 34069871--34070054 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
34069861 AGACATTATG
* *
34069871 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGTGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
** * * * *
34069935 ATGTAGCTAGGTCGCATGCATGGCT-CCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
34069999 TAA
62 TAA
* * * * *
34070002 AT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
34070055 CGAACTCTAT
Statistics
Matches: 96, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 22 0.23
65 4 0.04
66 18 0.19
67 32 0.33
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:34075259 original size:10 final size:10
Alignment explanation
Indices: 34075244--34075272 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
34075234 CGTTCCTTTC
34075244 GCTCTCCTAT
1 GCTCTCCTAT
34075254 GCTCTCCTAT
1 GCTCTCCTAT
34075264 GCTCTCCTA
1 GCTCTCCTA
34075273 AGCATAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.41, G:0.10, T:0.38
Consensus pattern (10 bp):
GCTCTCCTAT
Found at i:34079978 original size:19 final size:20
Alignment explanation
Indices: 34079938--34079978 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
34079928 TTGCACAAGT
*
34079938 TGTGAAATAGGTAATAAATG
1 TGTGAAATAGGTAAGAAATG
*
34079958 TGTGAAATA-GTAAGAATTG
1 TGTGAAATAGGTAAGAAATG
34079977 TG
1 TG
34079979 GCCTACTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (20 bp):
TGTGAAATAGGTAAGAAATG
Found at i:34083885 original size:18 final size:18
Alignment explanation
Indices: 34083862--34083898 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
34083852 TCTTGGTCCC
34083862 AAAACCATTATTCCGACT
1 AAAACCATTATTCCGACT
34083880 AAAACCATTATTCCGACT
1 AAAACCATTATTCCGACT
34083898 A
1 A
34083899 GGCCCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAACCATTATTCCGACT
Found at i:34089872 original size:39 final size:39
Alignment explanation
Indices: 34089698--34089856 Score: 219
Period size: 39 Copynumber: 4.1 Consensus size: 39
34089688 TGTGAATATA
* *
34089698 TATATGCGAGAATTATATCCGGACTACAGGTCCGTAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * *
34089737 TATAAGCGAGAATTATATCCGGACTTCAAGTCCACAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * * *
34089776 TATATGTGAGAATTATATCAGGACTTTATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* *
34089815 TATATGCGAGAATTATATCCGGACTTTAGGTCCGTAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
34089854 TAT
1 TAT
34089857 GTGCTGGACA
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 105 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:34092059 original size:6 final size:6
Alignment explanation
Indices: 34092048--34092157 Score: 202
Period size: 6 Copynumber: 18.3 Consensus size: 6
34092038 ACATGTGATA
34092048 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
34092096 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG AATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
*
34092144 AATGTG TATGTG TA
1 TATGTG TATGTG TA
34092158 CATGTATGTT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 100 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (6 bp):
TATGTG
Found at i:34096501 original size:22 final size:22
Alignment explanation
Indices: 34096433--34096501 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
34096423 CCTAAAAACT
34096433 TAAAATATCCTAAGAAATAAAA
1 TAAAATATCCTAAGAAATAAAA
* **
34096455 TAAAGTA----AAGTAAA-AACT
1 TAAAATATCCTAAG-AAATAAAA
34096473 TAAAATATCCTAAGAAATAAAA
1 TAAAATATCCTAAGAAATAAAA
34096495 TAAAATA
1 TAAAATA
34096502 AAGTAAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 11 0.31
19 3 0.09
21 3 0.09
22 18 0.51
ACGTcount: A:0.64, C:0.07, G:0.06, T:0.23
Consensus pattern (22 bp):
TAAAATATCCTAAGAAATAAAA
Found at i:34096509 original size:45 final size:40
Alignment explanation
Indices: 34096425--34096508 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
34096415 ATTCTAAGCC
34096425 TAAAAACTTAAAATATCCTAAGAAATAAAATAAAGTAAAG
1 TAAAAACTTAAAATATCCTAAGAAATAAAATAAAGTAAAG
*
34096465 TAAAAACTTAAAATATCCTAAGAAATAAAATAAAATAAAG
1 TAAAAACTTAAAATATCCTAAGAAATAAAATAAAGTAAAG
34096505 TAAA
1 TAAA
34096509 GAAAATATCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.64, C:0.07, G:0.06, T:0.23
Consensus pattern (40 bp):
TAAAAACTTAAAATATCCTAAGAAATAAAATAAAGTAAAG
Found at i:34101036 original size:13 final size:13
Alignment explanation
Indices: 34101018--34101042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34101008 GGGATTATTA
34101018 TAGTCTTAGATGC
1 TAGTCTTAGATGC
34101031 TAGTCTTAGATG
1 TAGTCTTAGATG
34101043 TCCAACCGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
TAGTCTTAGATGC
Found at i:34101833 original size:44 final size:43
Alignment explanation
Indices: 34101772--34101860 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 43
34101762 TAATAAGTAA
* *
34101772 GTAAATGGCTGGCGACACGGTCGTGTGATCCTATTTTTGAATT
1 GTAAAAGGCTGGCGACACAGTCGTGTGATCCTATTTTTGAATT
* * ** *
34101815 GTAAAAGGCCTGGTGACACAGTCGTTTGATTTTATTTTTGCATT
1 GTAAAAGG-CTGGCGACACAGTCGTGTGATCCTATTTTTGAATT
34101859 GT
1 GT
34101861 GCATGTTCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 7 0.18
44 31 0.82
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (43 bp):
GTAAAAGGCTGGCGACACAGTCGTGTGATCCTATTTTTGAATT
Found at i:34102725 original size:15 final size:16
Alignment explanation
Indices: 34102696--34102725 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34102686 CAAGCATACT
34102696 TTAACACATTATCAAA
1 TTAACACATTATCAAA
34102712 TTAACACA-TATCAA
1 TTAACACATTATCAA
34102726 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:34104305 original size:12 final size:12
Alignment explanation
Indices: 34104288--34104317 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34104278 ATTGGGACGG
34104288 TAGCTTATTATT
1 TAGCTTATTATT
*
34104300 TAGCTTATTGTT
1 TAGCTTATTATT
34104312 TAGCTT
1 TAGCTT
34104318 TACCGTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (12 bp):
TAGCTTATTATT
Found at i:34123701 original size:22 final size:23
Alignment explanation
Indices: 34123673--34123718 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
34123663 TGACGGTATT
34123673 TGAAAATTCTAT-GGATGCGTGC
1 TGAAAATTCTATAGGATGCGTGC
34123695 TGAAAATTCTATAGGATGCGTGC
1 TGAAAATTCTATAGGATGCGTGC
34123718 T
1 T
34123719 TGGCCAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (23 bp):
TGAAAATTCTATAGGATGCGTGC
Found at i:34126882 original size:44 final size:43
Alignment explanation
Indices: 34126788--34126884 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 43
34126778 ATGAGCTTTA
* *
34126788 ACCCTCTAAGCAGTAGAGTAACTAGCTAAATTTACAGACCTTG
1 ACCCCCTAAGCAGTAGAGTAACTAGCTAAAATTACAGACCTTG
* * *
34126831 ACCCCCTAAGCAGTAGGGTAA-TGGGCTGAAAATTACAGATCTTG
1 ACCCCCTAAGCAGTAGAGTAACT-AGCT-AAAATTACAGACCTTG
* *
34126875 TCTCCCTAAG
1 ACCCCCTAAG
34126885 GTCGCAGTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 22 0.49
44 22 0.49
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (43 bp):
ACCCCCTAAGCAGTAGAGTAACTAGCTAAAATTACAGACCTTG
Found at i:34127488 original size:25 final size:26
Alignment explanation
Indices: 34127459--34127510 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
34127449 TCCACTAAAG
34127459 ACCCAAACACCCCAAA-ACAACCCAA
1 ACCCAAACACCCCAAATACAACCCAA
** *
34127484 ACCCACGCAGCCCAAATACAACCCAA
1 ACCCAAACACCCCAAATACAACCCAA
34127510 A
1 A
34127511 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.48, C:0.46, G:0.04, T:0.02
Consensus pattern (26 bp):
ACCCAAACACCCCAAATACAACCCAA
Found at i:34128946 original size:2 final size:2
Alignment explanation
Indices: 34128939--34128964 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34128929 TTATCTTTTA
34128939 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
34128965 GTATCGTATC
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
Done.