Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 39 of 128
Found at i:12114280 original size:43 final size:43
Alignment explanation
Indices: 12114227--12114360 Score: 110
Period size: 44 Copynumber: 3.1 Consensus size: 43
12114217 GTCTGCTATT
*
12114227 TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCCGGGGTC
1 TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTGGGGTC
* * * * * * *** *
12114270 TTCAATCTACTTCGCT-GT-CAATACAGGAAGACAAGGTCTGCTATT
1 TTCAACCTACTCCACTACTGC--T-CAGGGAGATAAGG-CTGGGGTC
*
12114315 TTTAACCTACTCCACTACTGCTCAGGGAGATAAGGCTGGGGTC
1 TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTGGGGTC
12114358 TTC
1 TTC
12114361 GATCTACTTC
Statistics
Matches: 62, Mismatches: 23, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
41 1 0.02
42 1 0.02
43 20 0.32
44 22 0.35
45 16 0.26
46 1 0.02
47 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (43 bp):
TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTGGGGTC
Found at i:12114366 original size:265 final size:266
Alignment explanation
Indices: 12113917--12114528 Score: 938
Period size: 265 Copynumber: 2.3 Consensus size: 266
12113907 CTGGTGTTCG
* * * * ** * *
12113917 TCGATCTGCTTCGCTCCCAATACAAGAAGGCAAGATCTAATATTTTCAACCTACTCTACTGCTGC
1 TCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGC
* * * *
12113982 TCAGGGAGATAAGGCTTGCTGTCTTCAATCTACTTCGCTGCCAATACAGGAAGACAAGTTCTGTT
66 TCAGGGAGATAAGGCTCGCGGTCTTCAATCTACTTCGCTGCCAATACAGGAAGACAAGGTCTGCT
* *
12114047 ATTTTCAATATACTCCACTGCTGCCCAGAGAGATAAGGCTGGGGTCTTCGATCTACTTCGCTGCC
131 ATTTTCAACATACTCCACTACTGCCCAGAGAGATAAGGCTGGGGTCTTCGATCTACTTCGCTGCC
* *
12114112 AATACAGGAAGACAATATCTACTATTTTCAACCTACTTCACTGCTGCTCAGGGAGATAAGGCTTG
196 AATACAGGAAGACAAGATCTACTATTTTCAACCTACTTCACTGCTGCTCAAGGAGATAAGGCTTG
12114177 CTATCT
261 CTATCT
*
12114183 TCGATCTACTTCGCTGCCAATACAGGAAGACAAGGTCTGCTATTTTCAACCTACTCCACTACTGC
1 TCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGC
* *
12114248 TCAGGGAGATAAGGC-CGGGGTCTTCAATCTACTTCGCTGTCAATACAGGAAGACAAGGTCTGCT
66 TCAGGGAGATAAGGCTCGCGGTCTTCAATCTACTTCGCTGCCAATACAGGAAGACAAGGTCTGCT
* * * *
12114312 ATTTTTAACCTACTCCACTACTGCTCAGGGAGATAAGGCTGGGGTCTTCGATCTACTTCGCTGCC
131 ATTTTCAACATACTCCACTACTGCCCAGAGAGATAAGGCTGGGGTCTTCGATCTACTTCGCTGCC
* * **
12114377 AATATAGGAAGACAAGATCTGCTATTTTCAACCTACTTCGTTGCTGCTCAAGGAGATAAGGCTTG
196 AATACAGGAAGACAAGATCTACTATTTTCAACCTACTTCACTGCTGCTCAAGGAGATAAGGCTTG
12114442 CTATCT
261 CTATCT
* * *
12114448 TCGGTCTACTTTGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGC
1 TCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGC
*
12114513 TCAGAGAGATAAGGCT
66 TCAGGGAGATAAGGCT
12114529 TTGTGGTTTC
Statistics
Matches: 313, Mismatches: 32, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
265 242 0.77
266 71 0.23
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (266 bp):
TCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTACTGC
TCAGGGAGATAAGGCTCGCGGTCTTCAATCTACTTCGCTGCCAATACAGGAAGACAAGGTCTGCT
ATTTTCAACATACTCCACTACTGCCCAGAGAGATAAGGCTGGGGTCTTCGATCTACTTCGCTGCC
AATACAGGAAGACAAGATCTACTATTTTCAACCTACTTCACTGCTGCTCAAGGAGATAAGGCTTG
CTATCT
Found at i:12114502 original size:45 final size:45
Alignment explanation
Indices: 12114099--12114502 Score: 151
Period size: 45 Copynumber: 9.1 Consensus size: 45
12114089 GGTCTTCGAT
* * *
12114099 CTACTTCGCTGCCAATACAGGAAGACAATATCTACTATTTTCAAC
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
* *** * * * * * * *
12114144 CTACTTCACTGCTGCT-CAGGGAGATAAG-GCTTGCTATCTTCGAT
1 CTACTTCGCTGCCAATATAGGAAGACAAGATC-TGCTATTTTCAAC
* *
12114188 CTACTTCGCTGCCAATACAGGAAGACAAGGTCTGCTATTTTCAAC
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
* * * *** * * * * * *** * *
12114233 CTACTCCACTACTGCT-CAGGGAGATAAG-GCCGGGGTCTTCAAT
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
* * * *
12114276 CTACTTCGCTGTCAATACAGGAAGACAAGGTCTGCTATTTTTAAC
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
* * * *** * * * * *** * * *
12114321 CTACTCCACTACTGCT-CAGGGAGATAAG-GCTGGGGTCTTCGAT
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
12114364 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
* *** * * * ***
12114409 CTACTTCGTTGCTGCTCA-AGG-AGATAAG-GCTTGCTATCTTCGGT
1 CTACTTCGCTGCCAAT-ATAGGAAGACAAGATC-TGCTATTTTCAAC
*
12114453 CTACTTTGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
1 CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
12114498 CTACT
1 CTACT
12114503 CCACTACTGC
Statistics
Matches: 239, Mismatches: 108, Indels: 24
0.64 0.29 0.06
Matches are distributed among these distances:
43 37 0.15
44 98 0.41
45 101 0.42
46 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (45 bp):
CTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAAC
Found at i:12121511 original size:3 final size:3
Alignment explanation
Indices: 12121497--12121541 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
12121487 AAATAAAACC
12121497 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12121542 ATAAATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12123064 original size:14 final size:14
Alignment explanation
Indices: 12123045--12123078 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
12123035 ATTTATTCTA
12123045 AATAAAA-TATAATT
1 AATAAAACTA-AATT
12123059 AATAAAACTAAATT
1 AATAAAACTAAATT
12123073 AATAAA
1 AATAAA
12123079 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAAACTAAATT
Found at i:12129814 original size:29 final size:29
Alignment explanation
Indices: 12129781--12129873 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
12129771 GGTTCACCAT
12129781 AAAGGCTTACTCTTCTAGAGTTTTGCCAC
1 AAAGGCTTACTCTTCTAGAGTTTTGCCAC
* * *
12129810 AAAGG-TTA-TCCTT-TAACAGGTTCGCCAC
1 AAAGGCTTACT-CTTCT-AGAGTTTTGCCAC
*
12129838 AAAGGCTTGC-CTTTCTAGAGTTTTGCCAC
1 AAAGGCTTACTC-TTCTAGAGTTTTGCCAC
12129867 AAAGGCT
1 AAAGGCT
12129874 ATCCTTTCAC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.04
28 22 0.43
29 26 0.51
30 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (29 bp):
AAAGGCTTACTCTTCTAGAGTTTTGCCAC
Found at i:12129831 original size:57 final size:57
Alignment explanation
Indices: 12129722--12129891 Score: 184
Period size: 57 Copynumber: 3.0 Consensus size: 57
12129712 TAAGTACTTG
* * * * * * * *
12129722 CCACAAATGCTTTCCTTTC-AGAGTCTCGCCATAAAGAC-GTCCTTTAAGAGGTTCA
1 CCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCA
* * *
12129777 CCATAAAGGCTTA-CTCTTCTAGAGTTTTGCCACAAAGGTTATCCTTTAACAGGTTCG
1 CCACAAAGGCTTACCT-TTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCA
* * *
12129834 CCACAAAGGCTTGCCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTCACAAGTTCA
1 CCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCA
12129891 C
1 C
12129892 TGTAAATAGA
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
54 2 0.02
55 13 0.14
56 14 0.15
57 63 0.67
58 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (57 bp):
CCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGGTTCA
Found at i:12129879 original size:29 final size:29
Alignment explanation
Indices: 12129793--12129881 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
12129783 AGGCTTACTC
*
12129793 TTCTAGAGTTTTGCCACAAAGGTTATCCT
1 TTCTAGAGTTTTGCCACAAAGGCTATCCT
* * * *
12129822 TT-AACAGGTTCGCCACAAAGGCT-TGCCT
1 TTCTAGAGTTTTGCCACAAAGGCTAT-CCT
12129850 TTCTAGAGTTTTGCCACAAAGGCTATCCT
1 TTCTAGAGTTTTGCCACAAAGGCTATCCT
12129879 TTC
1 TTC
12129882 ACAAGTTCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.02
28 21 0.44
29 25 0.52
30 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (29 bp):
TTCTAGAGTTTTGCCACAAAGGCTATCCT
Found at i:12131806 original size:29 final size:29
Alignment explanation
Indices: 12131699--12131791 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
12131689 CATTCACTAA
*
12131699 AAAGGCTTACCTTTCTAGAGTTTTGCCAC
1 AAAGGCTTACCTTTCCAGAGTTTTGCCAC
* * *
12131728 AAAGG-TTGTCC-TT-AAGTAGGTTTGCCAC
1 AAAGGCTT-ACCTTTCCAG-AGTTTTGCCAC
*
12131756 AAAGGCTTACCTTTCCAGAGTTTTGTCAC
1 AAAGGCTTACCTTTCCAGAGTTTTGCCAC
12131785 AAAGGCT
1 AAAGGCT
12131792 ACCCTTTAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
27 2 0.04
28 21 0.40
29 27 0.52
30 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (29 bp):
AAAGGCTTACCTTTCCAGAGTTTTGCCAC
Found at i:12131817 original size:57 final size:57
Alignment explanation
Indices: 12131695--12131827 Score: 167
Period size: 57 Copynumber: 2.3 Consensus size: 57
12131685 GTTACATTCA
* * ** * * *
12131695 CTAAAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTTAAGTAGGTTTG
1 CTAAAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGCTACCCTTAAGCAAGTTCG
* * * *
12131752 CCACAAAGGCTTACCTTTCCAGAGTTTTGTCACAAAGGCTACCCTTTAGCAAGTTCG
1 CTAAAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGCTACCCTTAAGCAAGTTCG
12131809 CTAAAAAGGCTTACCTTTC
1 CTAAAAAGGCTTACCTTTC
12131828 TTGGTGATTT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (57 bp):
CTAAAAAGGCTTACCTTTCCAGAGTTTTGCCACAAAGGCTACCCTTAAGCAAGTTCG
Found at i:12138309 original size:26 final size:27
Alignment explanation
Indices: 12138255--12138319 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
12138245 TAATTTTACT
* * * *
12138255 CTAGTTAAATTTTGACGATTTTACTCC
1 CTAGTAAAATTTTAACAATTTTACACC
12138282 CT-GATAAAATTTTAACAATTTTA-ACC
1 CTAG-TAAAATTTTAACAATTTTACACC
12138308 CTAGTAAAATTT
1 CTAGTAAAATTT
12138320 CGAGAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 13 0.41
27 19 0.59
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (27 bp):
CTAGTAAAATTTTAACAATTTTACACC
Found at i:12141906 original size:127 final size:127
Alignment explanation
Indices: 12141680--12141925 Score: 420
Period size: 127 Copynumber: 1.9 Consensus size: 127
12141670 CTCATTTCTA
* * *
12141680 GTTATACTAAGTACATGTTTAGGTTTGTCTATTAATGCAAGTTGTCTTTCCATACTACGATCTGA
1 GTTATACTAAGGACATGTTTAGGTTTGTCTACTAATGCAAGTTGTCTTTCCATACTACGATCTAA
*
12141745 CCTCGTAATACCACTTAGTACTAGTTAAACATTTAGACAACAAATAAACAACATTTTCTTTG
66 CCACGTAATACCACTTAGTACTAGTTAAACATTTAGACAACAAATAAACAACATTTTCTTTG
*
12141807 GTTATACTAAGGACATGTTTAGGTTTGTCTACTAATGTAAGTTGTCTTTCCATACTACGATCTAA
1 GTTATACTAAGGACATGTTTAGGTTTGTCTACTAATGCAAGTTGTCTTTCCATACTACGATCTAA
* * *
12141872 CCACGTAATACCACTTAGTATTAGTTAAACATTTAGACAACCAATAAGCAACAT
66 CCACGTAATACCACTTAGTACTAGTTAAACATTTAGACAACAAATAAACAACAT
12141926 GTTCCTCCAT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 111 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (127 bp):
GTTATACTAAGGACATGTTTAGGTTTGTCTACTAATGCAAGTTGTCTTTCCATACTACGATCTAA
CCACGTAATACCACTTAGTACTAGTTAAACATTTAGACAACAAATAAACAACATTTTCTTTG
Found at i:12144943 original size:15 final size:15
Alignment explanation
Indices: 12144923--12144962 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
12144913 ATCAATTCAA
12144923 TTCATCATTCCTTTT
1 TTCATCATTCCTTTT
12144938 TTCATCATTCCTTTT
1 TTCATCATTCCTTTT
12144953 TTCATCATTC
1 TTCATCATTC
12144963 TACACTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCATCATTCCTTTT
Found at i:12151238 original size:43 final size:43
Alignment explanation
Indices: 12151170--12151258 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
12151160 GTACACAAGA
* * * ** *
12151170 TCTAGGGGTTTTTCGGCTCTTGTTCCTTTTTGATTAAAAGGTC
1 TCTAAGGGTTTTTCGACTCTCGTTCCTTTAGGATTAAAAGATC
12151213 TCTAAGGGTTTTTCGACTCTCGTTCCTTTAGGATTAAAAGATC
1 TCTAAGGGTTTTTCGACTCTCGTTCCTTTAGGATTAAAAGATC
12151256 TCT
1 TCT
12151259 TAGTCATCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (43 bp):
TCTAAGGGTTTTTCGACTCTCGTTCCTTTAGGATTAAAAGATC
Found at i:12158962 original size:42 final size:42
Alignment explanation
Indices: 12158899--12158981 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
12158889 GAAAGATGTG
*
12158899 TTTGGCAAGATGATTGCGAGATGGTATGATCAATTTATGGGT
1 TTTGGCAAGATGATTGAGAGATGGTATGATCAATTTATGGGT
12158941 TTTGGCAAGATGATTGAGAGATGGTATGATCAATTTATGGG
1 TTTGGCAAGATGATTGAGAGATGGTATGATCAATTTATGGG
12158982 AACTGCTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.35
Consensus pattern (42 bp):
TTTGGCAAGATGATTGAGAGATGGTATGATCAATTTATGGGT
Found at i:12164114 original size:15 final size:16
Alignment explanation
Indices: 12164086--12164115 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12164076 CAACCATGCT
12164086 TTAACACAATATCAAA
1 TTAACACAATATCAAA
12164102 TTAACAC-ATATCAA
1 TTAACACAATATCAA
12164116 TAAGGCGCCA
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:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAACACAATATCAAA
Found at i:12164184 original size:21 final size:21
Alignment explanation
Indices: 12164160--12164200 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
12164150 AATGTCGTAT
12164160 ACATTC-CAAATACATCAACTA
1 ACATTCACAAAT-CATCAACTA
12164181 ACATTCAGCAAATCATCAAC
1 ACATTCA-CAAATCATCAAC
12164201 CATAAGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.22
Consensus pattern (21 bp):
ACATTCACAAATCATCAACTA
Found at i:12167151 original size:19 final size:19
Alignment explanation
Indices: 12167124--12167163 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
12167114 CACAGGAACG
*
12167124 AAATCCTCGCGGTAAATCT
1 AAATACTCGCGGTAAATCT
12167143 AAATACTCGCGGTAAATCT
1 AAATACTCGCGGTAAATCT
12167162 AA
1 AA
12167164 GGGCAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (19 bp):
AAATACTCGCGGTAAATCT
Found at i:12180753 original size:124 final size:124
Alignment explanation
Indices: 12180540--12180771 Score: 403
Period size: 124 Copynumber: 1.9 Consensus size: 124
12180530 TTCTCTGAGC
*
12180540 AGAATACAAATAGTCATTTATGCGTATGTTTAGTATGATGTCCTTTCATGCATAAGGATGTTTAG
1 AGAATACAAATAGTAATTTATGCGTATGTTTAGTATGATGTCCTTTCATGCATAAGGATGTTTAG
*
12180605 GTCACATAAGACTTTTCGGTTTGTAATGTTCTAAGGCTTAGGAATTTAATTCTCTGGTT
66 GTCACATAAGACTTTTCGGCTTGTAATGTTCTAAGGCTTAGGAATTTAATTCTCTGGTT
12180664 AGAATACAAATAGTAATTTATGCGTATGTTTAGTATGATGT-CTATTCATGCATAAGGATGTTTA
1 AGAATACAAATAGTAATTTATGCGTATGTTTAGTATGATGTCCT-TTCATGCATAAGGATGTTTA
* * *
12180728 GGTCACATAGGACTTTTCGGCTTGTAATGTTTTGAGGCTTAGGA
65 GGTCACATAAGACTTTTCGGCTTGTAATGTTCTAAGGCTTAGGA
12180772 CAGGTATGGA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
123 2 0.02
124 100 0.98
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (124 bp):
AGAATACAAATAGTAATTTATGCGTATGTTTAGTATGATGTCCTTTCATGCATAAGGATGTTTAG
GTCACATAAGACTTTTCGGCTTGTAATGTTCTAAGGCTTAGGAATTTAATTCTCTGGTT
Found at i:12186850 original size:13 final size:13
Alignment explanation
Indices: 12186832--12186859 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12186822 ATAAAATTAG
12186832 AAAGATGATAAAT
1 AAAGATGATAAAT
12186845 AAAGATGATAAAT
1 AAAGATGATAAAT
12186858 AA
1 AA
12186860 TCAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:12188013 original size:24 final size:25
Alignment explanation
Indices: 12187977--12188150 Score: 164
Period size: 24 Copynumber: 7.2 Consensus size: 25
12187967 TGGTATCCGA
12187977 AGCTTCCCGATTAATGGCTCTTCA-G
1 AGCTTCCC-ATTAATGGCTCTTCATG
* * *
12188002 AGCTACCCATTATTGGCTC-GCATG
1 AGCTTCCCATTAATGGCTCTTCATG
*
12188026 AGCTTCCCATTTATGGCTCTT-ATG
1 AGCTTCCCATTAATGGCTCTTCATG
* * * *
12188050 AGCTACCCGTTATTGGCTC-GCATG
1 AGCTTCCCATTAATGGCTCTTCATG
*
12188074 AGCTTCCCATTTATGGCTCTT-ATG
1 AGCTTCCCATTAATGGCTCTTCATG
* * * *
12188098 AGCTACCCGTTATTGGCTC-GCATG
1 AGCTTCCCATTAATGGCTCTTCATG
*
12188122 AGCTTCCCATTTATGGCTCTT-ATG
1 AGCTTCCCATTAATGGCTCTTCATG
12188146 AGCTT
1 AGCTT
12188151 TCTATTATAA
Statistics
Matches: 116, Mismatches: 27, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
23 2 0.02
24 107 0.92
25 7 0.06
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (25 bp):
AGCTTCCCATTAATGGCTCTTCATG
Found at i:12188053 original size:48 final size:48
Alignment explanation
Indices: 12187977--12188149 Score: 303
Period size: 48 Copynumber: 3.6 Consensus size: 48
12187967 TGGTATCCGA
* *
12187977 AGCTTCCCGATTAATGGCTCTTCA-GAGCTACCCATTATTGGCTCGCATG
1 AGCTTCCC-ATTTATGGCTCTT-ATGAGCTACCCGTTATTGGCTCGCATG
12188026 AGCTTCCCATTTATGGCTCTTATGAGCTACCCGTTATTGGCTCGCATG
1 AGCTTCCCATTTATGGCTCTTATGAGCTACCCGTTATTGGCTCGCATG
12188074 AGCTTCCCATTTATGGCTCTTATGAGCTACCCGTTATTGGCTCGCATG
1 AGCTTCCCATTTATGGCTCTTATGAGCTACCCGTTATTGGCTCGCATG
12188122 AGCTTCCCATTTATGGCTCTTATGAGCT
1 AGCTTCCCATTTATGGCTCTTATGAGCT
12188150 TTCTATTATA
Statistics
Matches: 121, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
47 1 0.01
48 112 0.93
49 8 0.07
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (48 bp):
AGCTTCCCATTTATGGCTCTTATGAGCTACCCGTTATTGGCTCGCATG
Found at i:12190431 original size:23 final size:22
Alignment explanation
Indices: 12190388--12190431 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
12190378 TTCTAAGTCG
12190388 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
12190411 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
12190432 TTAGTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:12190540 original size:45 final size:45
Alignment explanation
Indices: 12190476--12190569 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
12190466 AACATGTACT
* * * *
12190476 CGGTGGATTTAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAAACAATGATGTC
*
12190521 CGGTGGAATCAGCACATAGCAACCACCTTACTAAACAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAAACAATGATGTC
12190566 CGGT
1 CGGT
12190570 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAAACAATGATGTC
Found at i:12190780 original size:101 final size:102
Alignment explanation
Indices: 12190572--12190791 Score: 232
Period size: 101 Copynumber: 2.2 Consensus size: 102
12190562 TGTTCGGTTC
* * *
12190572 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCTATACAAGTATTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACAAGTAGTAGCCTGC
* * **
12190637 ACATGGTACTACACACATGATCGAAACTATTCGGTATT
65 ACATAGTACTACACACATGATCCAAACTATTCACTATT
* * * * *
12190675 -CATAGTAGCCTGTACATAGTACTACACTTGCGACC-TATCATTCCGGTACACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACAAGTAGTAGCCTGC
* * *
12190738 ACATAGTACTACACACGTGA-CCATCACT-TTCACTTTT
65 ACATAGTACTACACACATGATCCA-AACTATTCACTATT
* *
12190775 ACATAGTGGCCTACACA
1 ACATAGTAGCCTGCACA
12190792 CGATCTGTGC
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
100 12 0.12
101 52 0.54
102 32 0.33
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (102 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACAAGTAGTAGCCTGCA
CATAGTACTACACACATGATCCAAACTATTCACTATT
Found at i:12204446 original size:312 final size:313
Alignment explanation
Indices: 12203868--12204495 Score: 1249
Period size: 312 Copynumber: 2.0 Consensus size: 313
12203858 AAAATTAAAT
12203868 ATATAAATATTATTTTTTATTTGAGAAGGGTAAATTCATAAATTATCATTACATTACTAAGAGAC
1 ATATAAATATTATTTTTTATTTGAGAAGGGTAAATTCATAAATTATCATTACATTACTAAGAGAC
12203933 TACTTAGTGAGTACCAAATGTGATAATGTAACTTTCTTAAGATTTTGATCAATACCTTCCAATGT
66 TACTTAGTGAGTACCAAATGTGATAATGTAACTTTCTTAAGATTTTGATCAATACCTTCCAATGT
12203998 ATACCAAATGTTATAAAGTAACTTTCTCGACAATCAGATTCCACTGAAATCATAATATGGGAAAG
131 ATACCAAATGTTATAAAGTAACTTTCTCGACAATCAGATTCCACTGAAATCATAATATGGGAAAG
12204063 CACTAAATGCTACCTATATGTTTCTAAAATATTTATATTTCTTCTTTTATAATATATATGATATA
196 CACTAAATGCTACCTATATGTTTCTAAAATATTTATATTTCTTCTTTTATAATATATATGATATA
12204128 TACAATACGTCACATCATCTTGTCAAAAAGTTTATACAAATATAAATATAGAC
261 TACAATACGTCACATCATCTTGTCAAAAAGTTTATACAAATATAAATATAGAC
12204181 ATATAAATATTA-TTTTTATTTGAGAAGGGTAAATTCATAAATTATCATTACATTACTAAGAGAC
1 ATATAAATATTATTTTTTATTTGAGAAGGGTAAATTCATAAATTATCATTACATTACTAAGAGAC
12204245 TACTTAGTGAGTACCAAATGTGATAATGTAACTTTCTTAAGATTTTGATCAATACCTTCCAATGT
66 TACTTAGTGAGTACCAAATGTGATAATGTAACTTTCTTAAGATTTTGATCAATACCTTCCAATGT
12204310 ATACCAAATGTTATAAAGTAACTTTCTCGACAATCAGATTCCACTGAAATCATAATATGGGAAAG
131 ATACCAAATGTTATAAAGTAACTTTCTCGACAATCAGATTCCACTGAAATCATAATATGGGAAAG
12204375 CACTAAATGCTACCTATATGTTTCTAAAATATTTATATTTCTTCTTTTATAATATATATGATATA
196 CACTAAATGCTACCTATATGTTTCTAAAATATTTATATTTCTTCTTTTATAATATATATGATATA
12204440 TACAATACGTCACATCATCTTGTCAAAAAGTTTATACAAATATAAATATAGAC
261 TACAATACGTCACATCATCTTGTCAAAAAGTTTATACAAATATAAATATAGAC
12204493 ATA
1 ATA
12204496 CATATCAAAG
Statistics
Matches: 315, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
312 303 0.96
313 12 0.04
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (313 bp):
ATATAAATATTATTTTTTATTTGAGAAGGGTAAATTCATAAATTATCATTACATTACTAAGAGAC
TACTTAGTGAGTACCAAATGTGATAATGTAACTTTCTTAAGATTTTGATCAATACCTTCCAATGT
ATACCAAATGTTATAAAGTAACTTTCTCGACAATCAGATTCCACTGAAATCATAATATGGGAAAG
CACTAAATGCTACCTATATGTTTCTAAAATATTTATATTTCTTCTTTTATAATATATATGATATA
TACAATACGTCACATCATCTTGTCAAAAAGTTTATACAAATATAAATATAGAC
Found at i:12205352 original size:16 final size:17
Alignment explanation
Indices: 12205331--12205364 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12205321 TACACTATTT
12205331 AAAATA-ATATTTTTTA
1 AAAATATATATTTTTTA
12205347 AAAATATATATTTTTTA
1 AAAATATATATTTTTTA
12205364 A
1 A
12205365 TTTTATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATATATATTTTTTA
Found at i:12211115 original size:23 final size:24
Alignment explanation
Indices: 12211089--12211134 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12211079 GTCCAATCTG
12211089 AAAT-TTTATTTAAAAAAATAAAA
1 AAATATTTATTTAAAAAAATAAAA
* * *
12211112 AAATATTTTTTTATAAAATTAAA
1 AAATATTTATTTAAAAAAATAAA
12211135 GAATCAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATATTTATTTAAAAAAATAAAA
Found at i:12211333 original size:20 final size:19
Alignment explanation
Indices: 12211299--12211337 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
12211289 AAATAGATTT
*
12211299 ATAATTATATTTAAATAAA
1 ATAATAATATTTAAATAAA
12211318 ATAATAATAGTTTAAATAAA
1 ATAATAATA-TTTAAATAAA
12211338 GCAATTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAATAATATTTAAATAAA
Found at i:12221055 original size:4 final size:4
Alignment explanation
Indices: 12221046--12221103 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
12221036 ATCTATATTA
12221046 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
12221094 ATAC ATAC AT
1 ATAC ATAC AT
12221104 CAGTGTCAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:12221386 original size:2 final size:2
Alignment explanation
Indices: 12221379--12221407 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12221369 TTAGTAAAAC
12221379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12221408 TACTAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12222747 original size:12 final size:12
Alignment explanation
Indices: 12222710--12222760 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
12222700 ATTAGAATCT
12222710 TTACTTGCTT-C
1 TTACTTGCTTAC
* *
12222721 TTTACTTACTCAC
1 -TTACTTGCTTAC
*
12222734 TTACTTGTTTAC
1 TTACTTGCTTAC
12222746 TTACTTGCTTAC
1 TTACTTGCTTAC
12222758 TTA
1 TTA
12222761 AATAACTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 31 0.97
13 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:12223076 original size:50 final size:50
Alignment explanation
Indices: 12223008--12223353 Score: 566
Period size: 50 Copynumber: 6.9 Consensus size: 50
12222998 TTTTCTGTAC
* * ** * *
12223008 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * **
12223058 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
12223108 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
12223158 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
12223208 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
12223258 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
12223308 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATC
12223354 ATGAAATAAA
Statistics
Matches: 280, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 280 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:12224954 original size:93 final size:94
Alignment explanation
Indices: 12224831--12225026 Score: 385
Period size: 93 Copynumber: 2.1 Consensus size: 94
12224821 AATTTTTTAA
12224831 ATTTATTTTATTTTTATAAAATTATTAAAAATATATCAAATTATAATTTTATTAATAAAATACTA
1 ATTTATTTTATTTTTATAAAATTATTAAAAATATATCAAATTATAATTTTATTAATAAAATACTA
12224896 ATATATAATAAATTATTATTAATGTAATT
66 ATATATAATAAATTATTATTAATGTAATT
12224925 ATTTATTTTA-TTTTATAAAATTATTAAAAATATATCAAATTATAATTTTATTAATAAAATACTA
1 ATTTATTTTATTTTTATAAAATTATTAAAAATATATCAAATTATAATTTTATTAATAAAATACTA
12224989 ATATATAATAAATTATTATTAATGTAATT
66 ATATATAATAAATTATTATTAATGTAATT
12225018 ATTTATTTT
1 ATTTATTTT
12225027 TTATAATTTA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 92 0.90
94 10 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (94 bp):
ATTTATTTTATTTTTATAAAATTATTAAAAATATATCAAATTATAATTTTATTAATAAAATACTA
ATATATAATAAATTATTATTAATGTAATT
Found at i:12233991 original size:36 final size:37
Alignment explanation
Indices: 12233946--12234028 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
12233936 TAATAAATAT
12233946 CAAACAATTCCTCTTGAT-ATTGGCATTGATGAAGAA
1 CAAACAATTCCTCTTGATAATTGGCATTGATGAAGAA
*
12233982 CAAACAATTCCTCTTGATAATTGGCGTTGATGAAGAA
1 CAAACAATTCCTCTTGATAATTGGCATTGATGAAGAA
12234019 CAAACAATTC
1 CAAACAATTC
12234029 ATTCTTTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 18 0.40
37 27 0.60
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (37 bp):
CAAACAATTCCTCTTGATAATTGGCATTGATGAAGAA
Found at i:12235357 original size:8 final size:8
Alignment explanation
Indices: 12235312--12235365 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
12235302 ATTTTTTTAG
12235312 AAAAATAT
1 AAAAATAT
12235320 AAAAGATAT
1 AAAA-ATAT
**
12235329 AAATTTAT
1 AAAAATAT
*
12235337 TAAAATAT
1 AAAAATAT
*
12235345 TAAAATAT
1 AAAAATAT
*
12235353 AAAAAAAT
1 AAAAATAT
12235361 AAAAA
1 AAAAA
12235366 GCTAAAGATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
8 31 0.82
9 7 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:12235579 original size:24 final size:25
Alignment explanation
Indices: 12235539--12235586 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
12235529 AATAAGAAAT
*
12235539 GAGTTACAAGAAGATGAAATGTGAA
1 GAGTTACAAGAAGATGAAAGGTGAA
*
12235564 GAGTTA-AGGAAGATGAAAGGTGA
1 GAGTTACAAGAAGATGAAAGGTGA
12235587 TAGGTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.19
Consensus pattern (25 bp):
GAGTTACAAGAAGATGAAAGGTGAA
Found at i:12245143 original size:65 final size:65
Alignment explanation
Indices: 12245063--12245192 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
12245053 TCAAAGAGTA
12245063 AGGAAAAAGAATTTTCAATTGCCAAAAACCACAAAAAAGGAAAACCAACGTCAGAATTTTTGAGG
1 AGGAAAAAGAATTTTCAATTGCCAAAAACCACAAAAAAGGAAAACCAACGTCAGAATTTTTGAGG
12245128 AGGAAAAAGAATTTTCAATTGCCAAAAACCACAAAAAAGGAAAACCAACGTCAGAATTTTTGAGG
1 AGGAAAAAGAATTTTCAATTGCCAAAAACCACAAAAAAGGAAAACCAACGTCAGAATTTTTGAGG
12245193 GAGAGAGGGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.18
Consensus pattern (65 bp):
AGGAAAAAGAATTTTCAATTGCCAAAAACCACAAAAAAGGAAAACCAACGTCAGAATTTTTGAGG
Found at i:12245284 original size:17 final size:17
Alignment explanation
Indices: 12245262--12245297 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12245252 ATCTTAACCA
12245262 CCCACTAAC-CATCAAAT
1 CCCACTAACTCA-CAAAT
12245279 CCCACTAACTCACAAAT
1 CCCACTAACTCACAAAT
12245296 CC
1 CC
12245298 TTCAGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.17
Consensus pattern (17 bp):
CCCACTAACTCACAAAT
Found at i:12250770 original size:43 final size:43
Alignment explanation
Indices: 12250705--12250791 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
12250695 TGTTACAAGG
*
12250705 CTCAGACCGTGTGGATAGTCGAAGTAGGGACACACGGTCATGT
1 CTCAGACCGTGTGGATAGTCGAAATAGGGACACACGGTCATGT
* ** * * *
12250748 CTCAGCCCGTGTTTATATTCGAAATAGGGCCACACGGTCGTGT
1 CTCAGACCGTGTGGATAGTCGAAATAGGGACACACGGTCATGT
12250791 C
1 C
12250792 GCAAGCCATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (43 bp):
CTCAGACCGTGTGGATAGTCGAAATAGGGACACACGGTCATGT
Found at i:12252184 original size:20 final size:20
Alignment explanation
Indices: 12252161--12252226 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
12252151 GTATAGACAA
12252161 AGGCACAATTATGCAATCAG
1 AGGCACAATTATGCAATCAG
*
12252181 AGGCACCAA--AGTGCAAACAG
1 AGGCA-CAATTA-TGCAATCAG
* *
12252201 AGGCACAATTGTGTAATCAG
1 AGGCACAATTATGCAATCAG
12252221 AGGCAC
1 AGGCAC
12252227 CGAAGTGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.11
20 31 0.82
21 3 0.08
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.15
Consensus pattern (20 bp):
AGGCACAATTATGCAATCAG
Found at i:12252233 original size:40 final size:40
Alignment explanation
Indices: 12252138--12252236 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
12252128 AGATGCATAA
** *
12252138 CAGAGGCACCGAAGTATAGACAAAGGCACAATTATGCAAT
1 CAGAGGCACCGAAGTGCAAACAAAGGCACAATTATGCAAT
* * * *
12252178 CAGAGGCACCAAAGTGCAAACAGAGGCACAATTGTGTAAT
1 CAGAGGCACCGAAGTGCAAACAAAGGCACAATTATGCAAT
12252218 CAGAGGCACCGAAGTGCAA
1 CAGAGGCACCGAAGTGCAA
12252237 TCTCGTACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.13
Consensus pattern (40 bp):
CAGAGGCACCGAAGTGCAAACAAAGGCACAATTATGCAAT
Found at i:12252238 original size:20 final size:19
Alignment explanation
Indices: 12252172--12252238 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
12252162 GGCACAATTA
12252172 TGCAATCAGAGGCACCAAAG
1 TGCAATCAGAGGCACC-AAG
*
12252192 TGCAAACAGAGGCA-CAATTG
1 TGCAATCAGAGGCACCAA--G
*
12252212 TGTAATCAGAGGCACCGAAG
1 TGCAATCAGAGGCACC-AAG
12252232 TGCAATC
1 TGCAATC
12252239 TCGTACAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 33 0.85
21 1 0.03
22 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (19 bp):
TGCAATCAGAGGCACCAAG
Found at i:12263113 original size:27 final size:27
Alignment explanation
Indices: 12263071--12263123 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
12263061 AATCATTAGG
* *
12263071 GGGTAACTCACTAGAAGAGGAAGATTC
1 GGGTAACTCACCAGAAAAGGAAGATTC
12263098 GGGTAACTCACCAGAAAAGGAAGATT
1 GGGTAACTCACCAGAAAAGGAAGATT
12263124 ATTTGCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17
Consensus pattern (27 bp):
GGGTAACTCACCAGAAAAGGAAGATTC
Found at i:12268962 original size:20 final size:19
Alignment explanation
Indices: 12268935--12268976 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
12268925 CTTTCAAAAT
12268935 TTTCTTACTTT-CATATGCA
1 TTTCTTACTTTCCAT-TGCA
12268954 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
12268974 TTT
1 TTT
12268977 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:12286705 original size:18 final size:18
Alignment explanation
Indices: 12286682--12286716 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12286672 GTTGGGCTAA
12286682 AATGGG-TCGTGTGGTCCC
1 AATGGGCTCGTG-GGTCCC
12286700 AATGGGCTCGTGGGTCC
1 AATGGGCTCGTGGGTCC
12286717 TAGACGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.11, C:0.23, G:0.40, T:0.26
Consensus pattern (18 bp):
AATGGGCTCGTGGGTCCC
Found at i:12297312 original size:12 final size:12
Alignment explanation
Indices: 12297295--12297319 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12297285 TTAGTTATAA
12297295 GGCAATCTTTGT
1 GGCAATCTTTGT
12297307 GGCAATCTTTGT
1 GGCAATCTTTGT
12297319 G
1 G
12297320 AAATGGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (12 bp):
GGCAATCTTTGT
Found at i:12297334 original size:29 final size:29
Alignment explanation
Indices: 12297320--12297482 Score: 218
Period size: 29 Copynumber: 5.6 Consensus size: 29
12297310 AATCTTTGTG
*
12297320 AAATGGAAGCCTTTGGGGTGATCTCTATT
1 AAATGGAAGCCTTTGTGGTGATCTCTATT
* * * *
12297349 AAATTGAAGACTTTGTGGTGATCTTTGTT
1 AAATGGAAGCCTTTGTGGTGATCTCTATT
***
12297378 AAATGGAAGCCTTTGTAACGATCTCTATT
1 AAATGGAAGCCTTTGTGGTGATCTCTATT
**
12297407 AAATGGAAGCCTTTGTAATGATCTCTATT
1 AAATGGAAGCCTTTGTGGTGATCTCTATT
* *
12297436 AAATGGAAGCCTTTATGGTGATCTCTGTT
1 AAATGGAAGCCTTTGTGGTGATCTCTATT
12297465 AAATGGAAGCCTTTGTGG
1 AAATGGAAGCCTTTGTGG
12297483 CAATCACTGT
Statistics
Matches: 116, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 116 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (29 bp):
AAATGGAAGCCTTTGTGGTGATCTCTATT
Found at i:12297492 original size:29 final size:29
Alignment explanation
Indices: 12297301--12297513 Score: 212
Period size: 29 Copynumber: 7.4 Consensus size: 29
12297291 ATAAGGCAAT
* * *
12297301 CTTTGTGGCAATCTTTGTGAAATGGAAGC
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
* * * * *
12297330 CTTTGGGGTGATCTCTATTAAATTGAAGA
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
* *
12297359 CTTTGTGGTGATCTTTGTTAAATGGAAGC
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
** *
12297388 CTTTGTAACGATCTCTATTAAATGGAAGC
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
*** *
12297417 CTTTGTAATGATCTCTATTAAATGGAAGC
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
* *
12297446 CTTTATGGTGATCTCTGTTAAATGGAAGC
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
* * *
12297475 CTTTGTGGCAATCACTGTTAAA-GGATGC
1 CTTTGTGGCGATCTCTGTTAAATGGAAGC
*
12297503 CTTCGTGGCGA
1 CTTTGTGGCGA
12297514 GACTACGAAA
Statistics
Matches: 154, Mismatches: 30, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 14 0.09
29 140 0.91
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (29 bp):
CTTTGTGGCGATCTCTGTTAAATGGAAGC
Found at i:12297496 original size:87 final size:87
Alignment explanation
Indices: 12297301--12297505 Score: 268
Period size: 87 Copynumber: 2.4 Consensus size: 87
12297291 ATAAGGCAAT
* * ** * *
12297301 CTTTGTGGCAATCTTTGTGAAATGGAAGCCTTTGGGGTGATCTCTATTAAATTGAAGACTTTGTG
1 CTTTGTGGCAATCTCTGTTAAATGGAAGCCTTTGGAATGATCTCTATTAAATGGAAGACTTTATG
*
12297366 GTGATCTTTGTTAAATGGAAGC
66 GTGATCTCTGTTAAATGGAAGC
** * * * *
12297388 CTTTGTAACGATCTCTATTAAATGGAAGCCTTTGTAATGATCTCTATTAAATGGAAGCCTTTATG
1 CTTTGTGGCAATCTCTGTTAAATGGAAGCCTTTGGAATGATCTCTATTAAATGGAAGACTTTATG
12297453 GTGATCTCTGTTAAATGGAAGC
66 GTGATCTCTGTTAAATGGAAGC
* *
12297475 CTTTGTGGCAATCACTGTTAAA-GGATGCCTT
1 CTTTGTGGCAATCTCTGTTAAATGGAAGCCTT
12297506 CGTGGCGAGA
Statistics
Matches: 99, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
86 8 0.08
87 91 0.92
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (87 bp):
CTTTGTGGCAATCTCTGTTAAATGGAAGCCTTTGGAATGATCTCTATTAAATGGAAGACTTTATG
GTGATCTCTGTTAAATGGAAGC
Found at i:12301911 original size:22 final size:22
Alignment explanation
Indices: 12301883--12301994 Score: 92
Period size: 22 Copynumber: 5.4 Consensus size: 22
12301873 CCTAGTAGGG
12301883 TTAGTGCCGGTGTTATTCAGGC
1 TTAGTGCCGGTGTTATTCAGGC
* * *
12301905 TTAGTGCTGGTGGTATTCAAGC
1 TTAGTGCCGGTGTTATTCAGGC
* *
12301927 TTAGTGCC-----TA-GCAGGA
1 TTAGTGCCGGTGTTATTCAGGC
* * *
12301943 TTGGTGCCAGTGATATTCAGGC
1 TTAGTGCCGGTGTTATTCAGGC
*
12301965 TTAGTGCCGGTTTTATTCAGGC
1 TTAGTGCCGGTGTTATTCAGGC
*
12301987 TGAGTGCC
1 TTAGTGCC
12301995 TAGTAGGATT
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
16 10 0.14
17 2 0.03
21 2 0.03
22 55 0.80
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.34
Consensus pattern (22 bp):
TTAGTGCCGGTGTTATTCAGGC
Found at i:12302027 original size:60 final size:60
Alignment explanation
Indices: 12301853--12302031 Score: 223
Period size: 60 Copynumber: 3.0 Consensus size: 60
12301843 TACTCAAAGA
* * *
12301853 GGTGTTATTTAGGCTTAGTGCCTAGTAGGGTTAGTGCCGGTGTTATTCAGGCTTAGTGCT
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGATTAGTGCCGGTGTTATTCAGGCTTAGTGCC
* * * * * *
12301913 GGTGGTATTCAAGCTTAGTGCCTAGCAGGATTGGTGCCAGTGATATTCAGGCTTAGTGCC
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGATTAGTGCCGGTGTTATTCAGGCTTAGTGCC
* * * * * *
12301973 GGTTTTATTCAGGCTGAGTGCCTAGTAGGATTAGTACTGGTGTTATCCAAGCTTAGTGC
1 GGTGTTATTCAGGCTTAGTGCCTAGTAGGATTAGTGCCGGTGTTATTCAGGCTTAGTGC
12302032 TTAGCAGGCT
Statistics
Matches: 98, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (60 bp):
GGTGTTATTCAGGCTTAGTGCCTAGTAGGATTAGTGCCGGTGTTATTCAGGCTTAGTGCC
Found at i:12308365 original size:50 final size:50
Alignment explanation
Indices: 12308221--12308504 Score: 268
Period size: 50 Copynumber: 5.6 Consensus size: 50
12308211 CAATCTCGTA
* * * *
12308221 TAAGACCATGTCTGGGACATGGCATCGACATTGATATGTGA-G--CCAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAGAGGTCCCA-TG
* *
12308269 TAAGACCATGTTTGGGACATGGCATTGGCATTATTGAAATTATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGC---ACTG--A-TATGAGAGGTCCCATG
* *
12308325 TAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAGAGGTCCCATG
** * * **
12308375 TAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAGAGGTCCCATG
* * * ** **
12308425 TAAGACTATGTCTGGGACATCGCATGGGCACCAATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAGAGGTCCCATG
* * *
12308475 TAAGACCATATCTGAGATATGGCATTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
12308505 GTACAGGAAA
Statistics
Matches: 198, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
48 26 0.13
50 124 0.63
51 5 0.03
53 4 0.02
54 6 0.03
55 1 0.01
56 29 0.15
57 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACTGATATGAGAGGTCCCATG
Found at i:12308778 original size:16 final size:16
Alignment explanation
Indices: 12308754--12308785 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12308744 ATGAGTTATT
12308754 CAAGCAAGAAAGTAAA
1 CAAGCAAGAAAGTAAA
*
12308770 CAAGTAAGAAAGTAAA
1 CAAGCAAGAAAGTAAA
12308786 TAAAGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.19, T:0.09
Consensus pattern (16 bp):
CAAGCAAGAAAGTAAA
Found at i:12309694 original size:25 final size:25
Alignment explanation
Indices: 12309666--12309713 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12309656 GGAGTTTAGC
12309666 GTGCTCTCTGATTATTAGCACATCG
1 GTGCTCTCTGATTATTAGCACATCG
12309691 GTGCTCTCTGATTATTAGCACAT
1 GTGCTCTCTGATTATTAGCACAT
12309714 TTATGTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCG
Found at i:12325069 original size:49 final size:49
Alignment explanation
Indices: 12324880--12325069 Score: 200
Period size: 49 Copynumber: 3.9 Consensus size: 49
12324870 CTAAACACCA
* * * * * * *
12324880 TTTGTGGACAAGCCACCACTAATTTGTAGATAATCTGCCACTGATAATAC
1 TTTGTGGACAAGCCACCACTGATATGCAAATAAACTGCCACTGA-AACAT
* * ** * * *
12324930 TTTGTGGACAAGCCACCACAGATATGCAGATGTATTACCACAGAAACAT
1 TTTGTGGACAAGCCACCACTGATATGCAAATAAACTGCCACTGAAACAT
* * *
12324979 TTTATGGACAAGCCACCACTGACATGCAAATATACTGCCACTGAAACAT
1 TTTGTGGACAAGCCACCACTGATATGCAAATAAACTGCCACTGAAACAT
* *
12325028 TTTGTGGACAAGCCACCACTGATTTGCAAATAAACTTCCACT
1 TTTGTGGACAAGCCACCACTGATATGCAAATAAACTGCCACT
12325070 TACTTCCTCC
Statistics
Matches: 115, Mismatches: 25, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
49 81 0.70
50 34 0.30
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (49 bp):
TTTGTGGACAAGCCACCACTGATATGCAAATAAACTGCCACTGAAACAT
Found at i:12327106 original size:27 final size:27
Alignment explanation
Indices: 12327064--12327147 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
12327054 TTGATATCTA
* *
12327064 GACCAAAATACACCCATAGGGTAAAAT
1 GACCAAAAAACCCCCATAGGGTAAAAT
* * * *
12327091 GGCTAAAAAACCCCCATTGGATAAAAT
1 GACCAAAAAACCCCCATAGGGTAAAAT
* * * *
12327118 AACCGAAATACCCGCATAGGGTAAAAT
1 GACCAAAAAACCCCCATAGGGTAAAAT
12327145 GAC
1 GAC
12327148 TGTTATACCC
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (27 bp):
GACCAAAAAACCCCCATAGGGTAAAAT
Found at i:12327648 original size:33 final size:35
Alignment explanation
Indices: 12327604--12327675 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
12327594 ACTGCTGGAT
** * *
12327604 TGATATCTATTACTGTTA-TGGGCCAAGGCCCCAC
1 TGATATCTATTACTGAAATTGGGCAAAGGCCCAAC
12327638 TGATA-CTATTACTGAAATTGGGCAAAGGCCCAAC
1 TGATATCTATTACTGAAATTGGGCAAAGGCCCAAC
12327672 TGAT
1 TGAT
12327676 TACTGGCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 10 0.30
34 23 0.70
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (35 bp):
TGATATCTATTACTGAAATTGGGCAAAGGCCCAAC
Found at i:12333969 original size:19 final size:19
Alignment explanation
Indices: 12333929--12333973 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12333919 GAAGTCTAAA
**
12333929 AAAACAGTCCAAAATGTTC
1 AAAACAGTCCAAAATGACC
12333948 AAAACAGTCCAACAAT-ACC
1 AAAACAGTCCAA-AATGACC
12333967 AAAACAG
1 AAAACAG
12333974 AACAAACTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.53, C:0.24, G:0.09, T:0.13
Consensus pattern (19 bp):
AAAACAGTCCAAAATGACC
Found at i:12340233 original size:138 final size:138
Alignment explanation
Indices: 12339985--12340406 Score: 625
Period size: 138 Copynumber: 3.1 Consensus size: 138
12339975 TACAAAAAGG
* * * *
12339985 AATTATATTCTTTCC-AAATGAAAAATAA-TTTCAATGTCTTTTATATTTTGATCAAAATTACTT
1 AATTATATTATTTCCAAAAT-AAAATTAATTTTC-ATGTCTTTTATATTTTGAACAAAATTAATT
* * *
12340048 AATATAACTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATTAAA
64 AATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAA
*
12340113 TTCATAAATT
129 TTCATATATT
* *
12340123 AATTACATTATTTCCAAAATAAAATTAATTTTCATGTCTTTTATATTTTGAACGAAATTAATTAA
1 AATTATATTATTTCCAAAATAAAATTAATTTTCATGTCTTTTATATTTTGAACAAAATTAATTAA
*
12340188 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
12340253 CATATATT
131 CATATATT
* * * * * *
12340261 CATTATATTTTTTTCCAAAA-GAAATTAATTTCCATTTCTTTTATATTTTGACCAAAATTAATTA
1 AATTATA-TTATTTCCAAAATAAAATTAATTTTCATGTCTTTTATATTTTGAACAAAATTAATTA
* *
12340325 ATATAACAGTTTATATTAATAAATTCGTTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
12340390 TCATATATT
130 TCATATATT
12340399 AATTATAT
1 AATTATAT
12340407 CTATGTTCTC
Statistics
Matches: 258, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
137 1 0.00
138 238 0.92
139 19 0.07
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (138 bp):
AATTATATTATTTCCAAAATAAAATTAATTTTCATGTCTTTTATATTTTGAACAAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:12344111 original size:17 final size:17
Alignment explanation
Indices: 12344086--12344118 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12344076 AAAAGCCAAA
*
12344086 GGAGGAAACATAAAAAG
1 GGAGAAAACATAAAAAG
12344103 GGAGAAAACATAAAAA
1 GGAGAAAACATAAAAA
12344119 AATGGGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.06, G:0.24, T:0.06
Consensus pattern (17 bp):
GGAGAAAACATAAAAAG
Found at i:12344816 original size:16 final size:16
Alignment explanation
Indices: 12344795--12344825 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12344785 GACGTAAAAA
*
12344795 TATTTATTTTTTATTT
1 TATTTATTTATTATTT
12344811 TATTTATTTATTATT
1 TATTTATTTATTATT
12344826 ACTTTAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTATTTATTATTT
Found at i:12345920 original size:39 final size:39
Alignment explanation
Indices: 12345872--12346132 Score: 281
Period size: 39 Copynumber: 6.7 Consensus size: 39
12345862 TATCCTGATT
* *
12345872 GCACGTACGTGCCCCTATTGTACTTCGGTACTCCTAATC
1 GCACATACGTGCCCCTGTTGTACTTCGGTACTCCTAATC
* * *
12345911 GCATATACGTGCCCCTGTCGTACTTCGGTACTCCTGATC
1 GCACATACGTGCCCCTGTTGTACTTCGGTACTCCTAATC
* * * *
12345950 GCACATACGTTCCCCTGTTGTACTCCGGT-GTCCCTGATC
1 GCACATACGTGCCCCTGTTGTACTTCGGTACT-CCTAATC
* * **
12345989 CCACATACGTGCCCCTGTAGTACTTCAATACTCCTAATC
1 GCACATACGTGCCCCTGTTGTACTTCGGTACTCCTAATC
** * * * *
12346028 ATACATATGTGCCCCTGTTCTACTTCGGTACCCCTAATT
1 GCACATACGTGCCCCTGTTGTACTTCGGTACTCCTAATC
* * * * * *
12346067 TCACATACGTGCCCTTATTGTACTTTGGTACTCTTGATC
1 GCACATACGTGCCCCTGTTGTACTTCGGTACTCCTAATC
12346106 GCACATACGTGCCCCTGTTGTACTTCG
1 GCACATACGTGCCCCTGTTGTACTTCG
12346133 ATACCTCTGA
Statistics
Matches: 178, Mismatches: 42, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
38 1 0.01
39 176 0.99
40 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.33
Consensus pattern (39 bp):
GCACATACGTGCCCCTGTTGTACTTCGGTACTCCTAATC
Found at i:12346154 original size:39 final size:38
Alignment explanation
Indices: 12345866--12346157 Score: 253
Period size: 39 Copynumber: 7.5 Consensus size: 38
12345856 TAATTATATC
* * *
12345866 CTGATTGCACGTACGTGCCCCTATTGTACTTCGGTACT
1 CTGATCGCACATACGTGCCCCTGTTGTACTTCGGTACT
* * *
12345904 CCTAATCGCATATACGTGCCCCTGTCGTACTTCGGTACT
1 -CTGATCGCACATACGTGCCCCTGTTGTACTTCGGTACT
* * * *
12345943 CCTGATCGCACATACGTTCCCCTGTTGTACTCCGGTGTCC
1 -CTGATCGCACATACGTGCCCCTGTTGTACTTCGGT-ACT
* * **
12345983 CTGATCCCACATACGTGCCCCTGTAGTACTTCAATACT
1 CTGATCGCACATACGTGCCCCTGTTGTACTTCGGTACT
* ** * * *
12346021 CCTAATCATACATATGTGCCCCTGTTCTACTTCGGTACCC
1 -CTGATCGCACATACGTGCCCCTGTTGTACTTCGGTA-CT
* ** * * *
12346061 CTAATTTCACATACGTGCCCTTATTGTACTTTGGTACT
1 CTGATCGCACATACGTGCCCCTGTTGTACTTCGGTACT
*
12346099 CTTGATCGCACATACGTGCCCCTGTTGTACTTCGATACCT
1 C-TGATCGCACATACGTGCCCCTGTTGTACTTCGGTA-CT
*
12346139 CTGA-CTGCACTTACGTGCC
1 CTGATC-GCACATACGTGCC
12346158 TTGTTTACAT
Statistics
Matches: 200, Mismatches: 47, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
38 4 0.02
39 191 0.95
40 5 0.03
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.33
Consensus pattern (38 bp):
CTGATCGCACATACGTGCCCCTGTTGTACTTCGGTACT
Found at i:12346157 original size:117 final size:116
Alignment explanation
Indices: 12345865--12346157 Score: 290
Period size: 117 Copynumber: 2.5 Consensus size: 116
12345855 ATAATTATAT
* * * *
12345865 CCTGATTGCACGTACGTGCCCCTATTGTACTTCGGTACTCCTAATCGCA-TATACGTGCCCCTGT
1 CCTGATCGCACATACGTGCCCCTGTTGTACTTCGATACTCCTAAT-GCACT-TACGTGCCCCTGT
* * * * *
12345929 CGTACTTCGGTACTCCTGATCGCACATACGTTCCCCTGTTGTACTCCGGTGTC
64 CGTACTTCGGTACCCCTAATCGCACATACGTGCCCCTATTGTACTCCGGTCTC
* * * * *
12345982 CCTGATCCCACATACGTGCCCCTGTAGTACTTCAATACTCCTAAT-CATACATATGTGCCCCTGT
1 CCTGATCGCACATACGTGCCCCTGTTGTACTTCGATACTCCTAATGC--ACTTACGTGCCCCTG-
** * **
12346046 TC-TACTTCGGTACCCCTAATTTCACATACGTGCCCTTATTGTACTTTGGTACT-
63 TCGTACTTCGGTACCCCTAATCGCACATACGTGCCCCTATTGTACTCCGGT-CTC
* *
12346099 CTTGATCGCACATACGTGCCCCTGTTGTACTTCGATAC-CTCTGACTGCACTTACGTGCC
1 CCTGATCGCACATACGTGCCCCTGTTGTACTTCGATACTC-CT-AATGCACTTACGTGCC
12346158 TTGTTTACAT
Statistics
Matches: 142, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
115 1 0.01
116 1 0.01
117 134 0.94
118 5 0.04
119 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.32
Consensus pattern (116 bp):
CCTGATCGCACATACGTGCCCCTGTTGTACTTCGATACTCCTAATGCACTTACGTGCCCCTGTCG
TACTTCGGTACCCCTAATCGCACATACGTGCCCCTATTGTACTCCGGTCTC
Found at i:12371431 original size:13 final size:13
Alignment explanation
Indices: 12371413--12371437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12371403 TAAAAGAGTT
12371413 ATTAATTAAAAAG
1 ATTAATTAAAAAG
12371426 ATTAATTAAAAA
1 ATTAATTAAAAA
12371438 ACTTGAAAAC
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:12376013 original size:129 final size:130
Alignment explanation
Indices: 12375863--12376121 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
12375853 GAAGCTTTCA
12375863 ACTAATTTTGTATTATCAGATATTGGAATATTCAATACCAAATAAGATAAATATTTTCTATCTAT
1 ACTAATTTTGTATTATCAGATATTGGAATATTCAATACCAAATAAGATAAATATTTTCTATCTAT
12375928 AATGATAGAATTCATTACTACATTTTTATATCATTCCTCAAATAATATTAACATAAACGAAATAT
66 AATGATAGAATTCATTACTACATTTTTATATCATTCCTCAAATAATATTAACATAAACGAAATAT
12375993 ACTAATTTTG-ATTATCAGATATTGGAATATTCAATACCAAATAAGATAAATATTTTCTATCTAT
1 ACTAATTTTGTATTATCAGATATTGGAATATTCAATACCAAATAAGATAAATATTTTCTATCTAT
12376057 AATGATAGAATTCATTACTACATTTTTATATCATTCCTCAAATAATATTAACATAAACGAAATAT
66 AATGATAGAATTCATTACTACATTTTTATATCATTCCTCAAATAATATTAACATAAACGAAATAT
12376122 TTGGGCATAT
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 119 0.92
130 10 0.08
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (130 bp):
ACTAATTTTGTATTATCAGATATTGGAATATTCAATACCAAATAAGATAAATATTTTCTATCTAT
AATGATAGAATTCATTACTACATTTTTATATCATTCCTCAAATAATATTAACATAAACGAAATAT
Found at i:12381296 original size:22 final size:22
Alignment explanation
Indices: 12381268--12381326 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
12381258 TGATAAAGGT
**
12381268 GATATCGTGATACCCGGAAGAG
1 GATATCGTGATACCAAGAAGAG
*
12381290 GATATCGTGACACCAAGAAGAG
1 GATATCGTGATACCAAGAAGAG
*
12381312 GATATCGCGATACCA
1 GATATCGTGATACCA
12381327 CTGAAGGGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (22 bp):
GATATCGTGATACCAAGAAGAG
Found at i:12381960 original size:85 final size:86
Alignment explanation
Indices: 12381806--12381974 Score: 216
Period size: 85 Copynumber: 2.0 Consensus size: 86
12381796 AGATAAAAAC
* * * * * * *
12381806 ATTTGTAATTACTGCCACTTGTTGTGAGTGCACAACATGGTTGCAGATTAAATAAATTGTC-GTT
1 ATTTGTAATTACTACCACTTGTTGTGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTA
*
12381870 GGGTTTGTGGACGAGCCACAT
66 GGTTTTGTGGACGAGCCACAT
* *
12381891 ATTTGTAGTTACTATCACTTGTTGTGAGTGCACAACAT-ATTCGCAGATTAAACAAACTGCCACT
1 ATTTGTAATTACTACCACTTGTTGTGAGTGCACAACATGATT-GCAGATTAAACAAACTGCCACT
*
12381955 AGGTTTTGTGGATGAGCCAC
65 AGGTTTTGTGGACGAGCCAC
12381975 CACTTGTTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
84 2 0.03
85 51 0.72
86 18 0.25
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (86 bp):
ATTTGTAATTACTACCACTTGTTGTGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTA
GGTTTTGTGGACGAGCCACAT
Found at i:12386285 original size:7 final size:7
Alignment explanation
Indices: 12386275--12386299 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12386265 ATTCGATTGA
12386275 TATTTAG
1 TATTTAG
12386282 TATTTAG
1 TATTTAG
12386289 TATTTAG
1 TATTTAG
12386296 TATT
1 TATT
12386300 ATGTATTATG
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:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:12386676 original size:18 final size:17
Alignment explanation
Indices: 12386650--12386683 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12386640 TCGGGAACCA
*
12386650 ATCATCGTTCCGGAATT
1 ATCATCGTTCCAGAATT
12386667 ATCATGCGTTCCAGAAT
1 ATCAT-CGTTCCAGAAT
12386684 ACATGCCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
ATCATCGTTCCAGAATT
Found at i:12387501 original size:35 final size:35
Alignment explanation
Indices: 12387462--12387572 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 35
12387452 TTTGAGTTAT
12387462 TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
1 TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
* * *** * * *
12387497 TTTGATGTAATAAAAT-AAAAAAAATTTCG-AG-TTA
1 TTTGATATTATTTGATGTAATAAAA--TAGAAGTTTA
12387531 TTTTGATATTATTTGATGTAATAAAATAGAAGTTTA
1 -TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
12387567 TTTGAT
1 TTTGAT
12387573 GTAATACAAA
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
34 11 0.20
35 32 0.59
36 11 0.20
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (35 bp):
TTTGATATTATTTGATGTAATAAAATAGAAGTTTA
Found at i:12387503 original size:25 final size:25
Alignment explanation
Indices: 12387469--12387578 Score: 90
Period size: 25 Copynumber: 4.6 Consensus size: 25
12387459 TATTTTGATA
12387469 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
**
12387494 TTATTTGATGTAATAAAATA-AAAA
1 TTATTTGATGTAATAAAATAGAAGT
** ** *
12387518 AAATTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
12387538 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
12387564 TTATTTGATGTAATA
1 TTATTTGATGTAATA
12387579 CAAACCCTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
20 2 0.03
21 9 0.14
22 1 0.02
23 1 0.02
24 11 0.17
25 38 0.60
26 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:12387545 original size:70 final size:69
Alignment explanation
Indices: 12387425--12387578 Score: 281
Period size: 70 Copynumber: 2.2 Consensus size: 69
12387415 TATTTTGATA
* *
12387425 TTATTTTATGTAAAAAAATAAAAAAAATTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAATAAAAAAAATTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
12387490 AAGT
66 AAGT
12387494 TTATTTGATGTAATAAAATAAAAAAAATTTCGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAAAAAAAATTT-GAGTTATTTTGATATTATTTGATGTAATAAAATA
12387559 GAAGT
65 GAAGT
12387564 TTATTTGATGTAATA
1 TTATTTGATGTAATA
12387579 CAAACCCTAA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
69 28 0.34
70 54 0.66
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (69 bp):
TTATTTGATGTAATAAAATAAAAAAAATTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
AAGT
Found at i:12387640 original size:29 final size:29
Alignment explanation
Indices: 12387597--12388166 Score: 630
Period size: 29 Copynumber: 20.4 Consensus size: 29
12387587 AACCTAATTT
*
12387597 AACCCTAAATCCTAACCTAATTTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
12387627 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
12387656 AATCCTAACCCTAACCTAATTTAACTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
12387685 AACCCTAACCCCTAACCTAAATTAACTAAA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
*
12387715 AACCCTAACCCCTAACCTAATTTAATTACA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
12387745 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12387774 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
12387803 CACCCTAACCCCTAACCTAATTTAATTACA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
*
12387833 AACCCTAACCCTAACCTAATTTAGTTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
**
12387862 AACCCTAACATTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
12387891 AACTCTAACCCCTTAACTTAA---AATT--A
1 AACCCTAA-CCC-TAACCTAATTTAATTAAA
*
12387917 AA----AACCCTAACCTAATTTAACTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12387942 AACCCTAA--C---CC-AATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
12387965 AACCCTAACCCTAACCTAAGTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
12387994 AACCCTAAACCCT----T-A---ACTTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
12388016 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12388045 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
12388074 AACCCTAAACACTTAACTTAA---AATT--A
1 AACCCT-AAC-CCTAACCTAATTTAATTAAA
*
12388100 AA----AACCCTAACCTAATTGAATT-AA
1 AACCCTAACCCTAACCTAATTTAATTAAA
12388124 AACCCTTAACCCTAACCTAATTTAATTAAA
1 AACCC-TAACCCTAACCTAATTTAATTAAA
12388154 AACCCTAAACCCT
1 AACCCT-AACCCT
12388167 TAACTTAAAA
Statistics
Matches: 465, Mismatches: 34, Indels: 82
0.80 0.06 0.14
Matches are distributed among these distances:
20 15 0.03
21 11 0.02
22 14 0.03
23 26 0.06
24 5 0.01
25 6 0.01
26 8 0.02
27 1 0.00
28 10 0.02
29 243 0.52
30 111 0.24
31 15 0.03
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:12387664 original size:23 final size:23
Alignment explanation
Indices: 12387584--12387665 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 23
12387574 TAATACAAAC
****
12387584 CCTAACCTAATTTAACCCTAAAT
1 CCTAACCTAATTTAATTAAAAAT
12387607 CCTAACCTAATTTAATTAAAAACCCT
1 CCTAACCTAATTTAATTAAAAA---T
12387633 AACCCTAACCTAATTTAATTAAAAAT
1 ---CCTAACCTAATTTAATTAAAAAT
12387659 CCTAACC
1 CCTAACC
12387666 CTAACCTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
23 25 0.51
26 2 0.04
29 22 0.45
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.29
Consensus pattern (23 bp):
CCTAACCTAATTTAATTAAAAAT
Found at i:12387789 original size:88 final size:87
Alignment explanation
Indices: 12387597--12388166 Score: 630
Period size: 88 Copynumber: 6.8 Consensus size: 87
12387587 AACCTAATTT
* *
12387597 AACCCTAAATCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAATCCT
1 AACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT
*
12387662 AACCCTAACCTAATTTAACTAAA
65 AACCCTAACCTAATTTAATTAAA
* * *
12387685 AACCCTAACCCCTAACCTAAATTAACTAAAAACCCTAACCCCTAACCTAATTTAATTACAAACCC
1 AACCCTAA-CCCTAACCTAATTTAATTAAAAACCCTAA-CCCTAACCTAATTTAATTAAAAACCC
12387750 TAACCCTAACCTAATTTAATTAAA
64 TAACCCTAACCTAATTTAATTAAA
* *
12387774 AACCCTAACCCTAACCTAATTTAATTAAACACCCTAACCCCTAACCTAATTTAATTACAAACCCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCCTAACCTAATTTAATTAAAAACCCT
*
12387839 AACCCTAACCTAATTTAGTTAAA
65 AACCCTAACCTAATTTAATTAAA
** * *
12387862 AACCCTAACATTAACCTAATTTAATTAAAAACTCTAACCCCTTAACTTAA---AATT--AAA---
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCC-TAACCTAATTTAATTAAAAACCC
*
12387919 -AACCCTAACCTAATTTAACTAAA
64 TAACCCTAACCTAATTTAATTAAA
*
12387942 AACCCTAA--C---CC-AATTTAATTAAAAACCCTAACCCTAACCTAAGTTAATTAAAAACCCTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-
*
12388001 AACCCT----T-A---ACTTAAA
65 AACCCTAACCTAATTTAATTAAA
*
12388016 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-
* *
12388081 AACACTTAACTTAA---AATT--A
65 AAC-CCTAACCTAATTTAATTAAA
*
12388100 AA----AACCCTAACCTAATTGAATT-AAAACCCTTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCC-TAACCCTAACCTAATTTAATTAAAAACCCT
12388160 AAACCCT
65 -AACCCT
12388167 TAACTTAAAA
Statistics
Matches: 427, Mismatches: 29, Indels: 61
0.83 0.06 0.12
Matches are distributed among these distances:
72 7 0.02
73 3 0.01
74 32 0.07
75 6 0.01
77 4 0.01
78 1 0.00
79 11 0.03
80 131 0.31
81 2 0.00
82 6 0.01
84 6 0.01
85 1 0.00
86 8 0.02
87 2 0.00
88 145 0.34
89 62 0.15
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (87 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTA
ACCCTAACCTAATTTAATTAAA
Found at i:12387928 original size:51 final size:51
Alignment explanation
Indices: 12387736--12388195 Score: 311
Period size: 51 Copynumber: 8.6 Consensus size: 51
12387726 CTAACCTAAT
* *
12387736 TTAA-TTACAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAC
1 TTAACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCC---C
* * * *
12387789 CTAATTTAATTAAACACCCTAACCCCTAACCTAATTTAATTACAAACCCTAACCCTAACC
1 TTAACTT-A--AAA-ACCATAA-CCCTAACCTAATTTAATTAAAAACCCTAA-CC---CC
* * * ** *
12387849 TAATTTAGTTAAAAACCCTAACATTAACCTAATTTAATTAAAAACTCTAACCCC
1 ---TTAACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCCC
*** * * *
12387903 TTAACTTAAAATTAAAAACCCTAACCTAATTTAACTAAAAACCCTAACCCAAT
1 TTAACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCC--C
* * *
12387956 TTAA-TTAAAAACCCTAACCCTAACCTAAGTTAATTAAAAACCCTAAACCC
1 TTAACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCCC
* *
12388006 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTAAC
1 TTAACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCC---C
* * * * **
12388060 CTAATTTAATTAA--A-AACCCTAAACACTTAACTTAAAATTAAAAACCCTAACCTAA
1 TTAACTTAA-AAACCATAACCCT-AAC-C-TAA-TT-TAATTAAAAACCCTAACC-CC
* * *
12388115 TTGAA-TTAAAACCCTTAACCCTAACCTAATTTAATTAAAAACCCTAAACCC
1 TT-AACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCCC
* * *
12388166 TTAACTTAAAAACCCTAACCTTAACGTAAT
1 TTAACTTAAAAACCATAACCCTAACCTAAT
12388196 GTTAGATTTG
Statistics
Matches: 322, Mismatches: 54, Indels: 64
0.73 0.12 0.15
Matches are distributed among these distances:
50 6 0.02
51 104 0.32
52 58 0.18
53 12 0.04
54 17 0.05
55 12 0.04
56 7 0.02
57 27 0.08
58 32 0.10
59 35 0.11
60 6 0.02
62 1 0.00
63 5 0.02
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (51 bp):
TTAACTTAAAAACCATAACCCTAACCTAATTTAATTAAAAACCCTAACCCC
Found at i:12387934 original size:80 final size:78
Alignment explanation
Indices: 12387662--12388195 Score: 429
Period size: 80 Copynumber: 6.5 Consensus size: 78
12387652 TAAAAATCCT
* * * *
12387662 AACCCTAACCTAATTTAACTAAAAACCCTAACCCCTAACCTAAATTAACTAAAAACCCTAACCCC
1 AACCCTAACCTAATTTAATTAAAAACCCTAA--CTTAACCTAATTTAATTAAAAACCCTAA-CCC
12387727 TAACCTAATTTAATTACAAA
63 TAACCTAA--TAATT--AAA
* *
12387747 CCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAACACCCTAAC
1 ----AACCCTAACCTAATTTAATTAAAAACCCTAA-CTTAACCTAATTTAATTAAAAACCCTAA-
12387812 CCCTAACCTAATTTAATTACAAA
60 CCCTAACCTAA--TAATT--AAA
* *
12387835 CCCTAACCCTAACCTAATTTAGTTAAAAACCCTAACATTAACCTAATTTAATTAAAAACTCTAAC
1 ----AACCCTAACCTAATTTAATTAAAAACCCTAAC-TTAACCTAATTTAATTAAAAACCCTAA-
*
12387900 CCCTTAACTTAA-AATTAAA
60 CCC-TAACCTAATAATTAAA
*
12387919 AACCCTAACCTAATTTAACTAAAAACCCTAAC----CC-AATTTAATTAAAAACCCTAACCCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACTTAACCTAATTTAATTAAAAACCCTAACCCTAA
12387979 CCTAAGTTAATTAAA
66 CCTAA--TAATTAAA
*
12387994 AACCCTAAACC---CTTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCC
1 AACCCT-AACCTAATTTAA-TTAAAAACCCTAA-CTTAACCTAATTTAATTAAAAACCCTAACCC
12388056 TAACCTAATTTAATTAAA
63 TAACCTAA--TAATTAAA
* *
12388074 AACCCTAAACACTTAACTTAAAATTAAAAA-CC---C-TAACCTAATTGAATT-AAAACCCTTAA
1 AACCCT-AAC-C-TAA-TT-TAATTAAAAACCCTAACTTAACCTAATTTAATTAAAAACCC-TAA
12388133 CCCTAACCTAATTTAATTAAA
60 CCCTAACCTAA--TAATTAAA
* *
12388154 AACCCTAAACC---CTTAACTTAAAAACCCTAACCTTAACGTAAT
1 AACCCT-AACCTAATTTAA-TTAAAAACCCTAA-CTTAACCTAAT
12388196 GTTAGATTTG
Statistics
Matches: 395, Mismatches: 22, Indels: 65
0.82 0.05 0.13
Matches are distributed among these distances:
72 7 0.02
73 9 0.02
74 39 0.10
75 18 0.05
76 4 0.01
79 11 0.03
80 136 0.34
81 2 0.01
84 3 0.01
85 2 0.01
86 12 0.03
87 3 0.01
88 112 0.28
89 37 0.09
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (78 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACTTAACCTAATTTAATTAAAAACCCTAACCCTAA
CCTAATAATTAAA
Found at i:12388017 original size:22 final size:20
Alignment explanation
Indices: 12387985--12388030 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
12387975 CTAACCTAAG
12387985 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AA-CC
12388006 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
12388026 TTAAC
1 TTAAC
12388031 CTAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:12388075 original size:183 final size:184
Alignment explanation
Indices: 12387618--12388166 Score: 663
Period size: 183 Copynumber: 2.8 Consensus size: 184
12387608 CTAACCTAAT
* *
12387618 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAATCCTAACCCTAACCTAATTTAACTA
1 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
* *
12387683 AAAACCCTAACCCC-TAACCTAAATTAACTAAAAACCCTAACCCCTAACCTAATTTAATTACAAA
66 AAAACCCTAACCCCTTAA-CTTAA--AA-T-TAAA----AA-CCCTAACCTAATTTAATTA-AAA
* * *
12387747 CCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAACACCCTAAC
120 --C-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAGTTAATTAAAAACCCTAAA
12387812 CCC
182 CCC
* **
12387815 TAACCTAATTTAATTACAAACCCTAACCCTAACCTAATTTAGTTAAAAACCCTAACATTAACCTA
1 T----TAA-TT-A--A-AAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTA
* *
12387880 ATTTAATTAAAAACTCTAACCCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAACT-AAA-A
57 ATTTAATTAAAAACCCTAACCCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAATTAAAACA
*
12387943 ACCCTAACCCAATTTAATTAAAAACCCTAACCCTAACCTAAGTTAATTAAAAACCCTAAACCC
122 ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAAGTTAATTAAAAACCCTAAACCC
*
12388006 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
1 TTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATT
* * *
12388071 AAAAACCCTAAACACTTAACTTAAAATTAAAAACCCTAACCTAATTGAATTAAAACCCTTAACCC
65 AAAAACCCTAACCCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAATTAAAA--C--AACCC
12388136 TAACCTAATTTAATTAAAAACCCTAAACCCT
126 TAACCTAATTTAATTAAAAACCCT-AACCCT
12388167 TAACTTAAAA
Statistics
Matches: 311, Mismatches: 24, Indels: 41
0.83 0.06 0.11
Matches are distributed among these distances:
183 98 0.32
184 4 0.01
186 1 0.00
187 5 0.02
189 28 0.09
190 6 0.02
191 61 0.20
195 3 0.01
197 18 0.06
198 2 0.01
201 3 0.01
202 5 0.02
203 2 0.01
204 2 0.01
205 1 0.00
206 69 0.22
207 3 0.01
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (184 bp):
TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
AAAACCCTAACCCCTTAACTTAAAATTAAAAACCCTAACCTAATTTAATTAAAACAACCCTAACC
TAATTTAATTAAAAACCCTAACCCTAACCTAAGTTAATTAAAAACCCTAAACCC
Found at i:12388177 original size:22 final size:20
Alignment explanation
Indices: 12388145--12388190 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
12388135 CTAACCTAAT
12388145 TTAA-TTAAAAACCCTAAACCC
1 TTAACTTAAAAACCCT-AA-CC
12388166 TTAACTTAAAAACCCTAACC
1 TTAACTTAAAAACCCTAACC
12388186 TTAAC
1 TTAAC
12388191 GTAATGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:12391720 original size:126 final size:124
Alignment explanation
Indices: 12391394--12391744 Score: 537
Period size: 126 Copynumber: 2.8 Consensus size: 124
12391384 CCCAAACATG
**
12391394 CTACTGTAGCAAAAGTGCGTCCACGAAGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAA-GCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
12391459 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC--AAAAAAATTATTTCTTACATGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* *
12391517 CTACTGTAGCAAAAGCTCG-CTGACGAAGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCACGTC-CACGAAG-CGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
12391581 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCTTGAC
64 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
*
12391643 CTACTGTAGCAAAAGCACGTCCACGAGAGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCACGTCCACGA-AGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* **
12391708 AAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
12391745 CTCGAAATTA
Statistics
Matches: 209, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
122 2 0.01
123 92 0.44
125 5 0.02
126 107 0.51
127 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCACGTCCACGAAGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:12396375 original size:9 final size:9
Alignment explanation
Indices: 12396361--12396415 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
12396351 TATAGTTTGA
12396361 TATTCGAAT
1 TATTCGAAT
12396370 TATTCGAAT
1 TATTCGAAT
*
12396379 TATTCGAGT
1 TATTCGAAT
12396388 TATTCGAAT
1 TATTCGAAT
*
12396397 TATTCGAGT
1 TATTCGAAT
*
12396406 TATTCAAAT
1 TATTCGAAT
12396415 T
1 T
12396416 CGAAAACTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12396384 original size:18 final size:18
Alignment explanation
Indices: 12396361--12396415 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
12396351 TATAGTTTGA
*
12396361 TATTCGAATTATTCGAAT
1 TATTCGAGTTATTCGAAT
12396379 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
*
12396397 TATTCGAGTTATTCAAAT
1 TATTCGAGTTATTCGAAT
12396415 T
1 T
12396416 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:12415240 original size:21 final size:21
Alignment explanation
Indices: 12415216--12415283 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
12415206 ATTTGCAGCA
12415216 TTAATTATAAAAAATAATATT
1 TTAATTATAAAAAATAATATT
* * *
12415237 TTAA-TAAAAATAAATAAAATAA
1 TTAATTATAAA-AAATAATAT-T
* *
12415259 TAAATT-TTAAAAATAATATT
1 TTAATTATAAAAAATAATATT
12415279 TTAAT
1 TTAAT
12415284 GTAAAATGAG
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
20 9 0.26
21 20 0.57
22 5 0.14
23 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAATTATAAAAAATAATATT
Found at i:12415253 original size:28 final size:28
Alignment explanation
Indices: 12415222--12415276 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12415212 AGCATTAATT
12415222 ATAAAA-AATAATATTTTAATAAA-AATAA
1 ATAAAATAATAA-ATTTTAA-AAATAATAA
12415250 ATAAAATAATAAATTTTAAAAATAATA
1 ATAAAATAATAAATTTTAAAAATAATA
12415277 TTTTAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 17 0.68
29 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAATAATAAATTTTAAAAATAATAA
Found at i:12418298 original size:24 final size:24
Alignment explanation
Indices: 12418266--12418311 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12418256 ATGACAGTAA
12418266 AACTTAATGTTTGATTCAAATGTC
1 AACTTAATGTTTGATTCAAATGTC
*
12418290 AACTTAATGTTTGGTTCAAATG
1 AACTTAATGTTTGATTCAAATG
12418312 GTTGGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (24 bp):
AACTTAATGTTTGATTCAAATGTC
Found at i:12423569 original size:30 final size:30
Alignment explanation
Indices: 12423535--12423600 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
12423525 GGCCAATATA
12423535 ACGAGACTGTAGTCTGTTAAGACAGTAAAC
1 ACGAGACTGTAGTCTGTTAAGACAGTAAAC
12423565 ACGAGACTGTAGTCTGTTAAGACAGTAAAC
1 ACGAGACTGTAGTCTGTTAAGACAGTAAAC
12423595 ACGAGA
1 ACGAGA
12423601 AAAGGCCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (30 bp):
ACGAGACTGTAGTCTGTTAAGACAGTAAAC
Found at i:12423943 original size:76 final size:76
Alignment explanation
Indices: 12423800--12424048 Score: 293
Period size: 76 Copynumber: 3.3 Consensus size: 76
12423790 AACCAAACCT
* * * * * * *
12423800 AGCCTTTGTGGTGAGTTATCTGAAAGGCCTATGTGGCGTAGTATTCGAAAAACCTTAGTGGCAAA
1 AGCCCTTGTGGTGAATTATCTAAAAGGCCTATGTGGCGTATTATTCAAAAAACCATAGTAGCAAA
12423865 GTTATCTAGGA
66 GTTATCTAGGA
* * * **
12423876 AGCCCTTGTGGTGAATTCTCTAAAAGGCCTATGTGGTGTATTATTCAAAAAACCATATTAGTGAA
1 AGCCCTTGTGGTGAATTATCTAAAAGGCCTATGTGGCGTATTATTCAAAAAACCATAGTAGCAAA
12423941 GTTATCTAGGA
66 GTTATCTAGGA
** * * * *
12423952 AGCCCTTGTGGCAAATTATCTAAAAGGCTTATGTGGCATATTATTCAAAAAACCTTAGTGGCAAA
1 AGCCCTTGTGGTGAATTATCTAAAAGGCCTATGTGGCGTATTATTCAAAAAACCATAGTAGCAAA
12424017 GTTATCTTA-GA
66 GTTATC-TAGGA
* * *
12424028 AGCTCTTGTGGCGAGTTATCT
1 AGCCCTTGTGGTGAATTATCT
12424049 GGAAAGTCTG
Statistics
Matches: 146, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
76 144 0.99
77 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (76 bp):
AGCCCTTGTGGTGAATTATCTAAAAGGCCTATGTGGCGTATTATTCAAAAAACCATAGTAGCAAA
GTTATCTAGGA
Found at i:12423986 original size:25 final size:25
Alignment explanation
Indices: 12423958--12424023 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
12423948 AGGAAGCCCT
**
12423958 TGTGGCAAATTATCTAAAAGGCTTA
1 TGTGGCAAATTATCTAAAAACCTTA
* *
12423983 TGTGGCATATTATTCAAAAAACCTTA
1 TGTGGCAAATTA-TCTAAAAACCTTA
12424009 -GTGGCAAAGTTATCT
1 TGTGGCAAA-TTATCT
12424024 TAGAAGCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (25 bp):
TGTGGCAAATTATCTAAAAACCTTA
Found at i:12425369 original size:59 final size:58
Alignment explanation
Indices: 12425282--12425424 Score: 144
Period size: 59 Copynumber: 2.4 Consensus size: 58
12425272 GTCTAAACTT
* * * * * * * * *
12425282 TTTTTTTGTCCAACTTAGGCCCTAAACTTGACAATTGTTTCAATATTGGGGCCTGAAC
1 TTTTTTTGTCCAAGTTAAGCCTTGAACTTGACAAATGTTCCAACATTGGGACCTCAAC
* * *
12425340 TTTTTTTGGTCCAAGTTAAGCCTTGAACTTGGCAAATGTTCCCACATTGGGACTTCAAC
1 TTTTTTT-GTCCAAGTTAAGCCTTGAACTTGACAAATGTTCCAACATTGGGACCTCAAC
*
12425399 TTTTTTTATCCAAGTT-AGTCCTTGAA
1 TTTTTTTGTCCAAGTTAAG-CCTTGAA
12425425 AACCCTAAAG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 2 0.03
58 22 0.31
59 46 0.66
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (58 bp):
TTTTTTTGTCCAAGTTAAGCCTTGAACTTGACAAATGTTCCAACATTGGGACCTCAAC
Found at i:12425586 original size:90 final size:90
Alignment explanation
Indices: 12425431--12425613 Score: 224
Period size: 90 Copynumber: 2.0 Consensus size: 90
12425421 TGAAAACCCT
* * * * *
12425431 AAAGTTCAAGCCTTAATGTGGAAACAATTGTCAAGTTTAGGCCCCAATGTGGGAACAATTACCAA
1 AAAGTTCAAGCCTCAATATGGAAACAATTGCCAAGTCTAGGCCCCAATGTGGAAACAATTACCAA
* *
12425496 GTTCAAGGCCTAATTTGGACAAAAA
66 GTTCAAGACCTAACTTGGACAAAAA
* * * * *
12425521 AAAGTTCAAGTCTCAATATGGGAAA-AGTTGCCAAGTCTAGGTCCCATTGTGGAAACAATTGCCA
1 AAAGTTCAAGCCTCAATAT-GGAAACAATTGCCAAGTCTAGGCCCCAATGTGGAAACAATTACCA
* *
12425585 AGTTTATGACCTAACTTGGACAAAAA
65 AGTTCAAGACCTAACTTGGACAAAAA
12425611 AAA
1 AAA
12425614 AATTAGACCC
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
90 73 0.94
91 5 0.06
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (90 bp):
AAAGTTCAAGCCTCAATATGGAAACAATTGCCAAGTCTAGGCCCCAATGTGGAAACAATTACCAA
GTTCAAGACCTAACTTGGACAAAAA
Found at i:12425635 original size:90 final size:90
Alignment explanation
Indices: 12425435--12425641 Score: 204
Period size: 90 Copynumber: 2.3 Consensus size: 90
12425425 AACCCTAAAG
** * * * *
12425435 TTCAAGCCTTAATG-TGGAAACAATTGTCAAGTTTAGGCCCCAATGTGGGAACAATTACCAAGTT
1 TTCAAGCCCCAATGTTGGAAA-AGTTGCCAAGTCTAGGCCCCAATGTGGAAACAATTACCAAGTT
* * *
12425499 CAAGGCCTAATTTGGACAAAAAAAAG
65 CAAGACCTAACTTGGACAAAAAAAAA
* * * * * * * *
12425525 TTCAAGTCTCAATATGGGAAAAGTTGCCAAGTCTAGGTCCCATTGTGGAAACAATTGCCAAGTTT
1 TTCAAGCCCCAATGTTGGAAAAGTTGCCAAGTCTAGGCCCCAATGTGGAAACAATTACCAAGTTC
*
12425590 ATGACCTAACTTGGACAAAAAAAAAA
66 AAGACCTAACTTGGAC-AAAAAAAAA
12425616 TT--AGACCCCAATGTTGGAAAAGTTGC
1 TTCAAG-CCCCAATGTTGGAAAAGTTGC
12425642 TAAATTTAGG
Statistics
Matches: 94, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
89 2 0.02
90 77 0.82
91 15 0.16
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (90 bp):
TTCAAGCCCCAATGTTGGAAAAGTTGCCAAGTCTAGGCCCCAATGTGGAAACAATTACCAAGTTC
AAGACCTAACTTGGACAAAAAAAAA
Found at i:12425749 original size:3 final size:3
Alignment explanation
Indices: 12425741--12425768 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12425731 GAGCCTAACA
12425741 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12425769 GACTCCCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12428983 original size:21 final size:21
Alignment explanation
Indices: 12428962--12429154 Score: 131
Period size: 21 Copynumber: 9.2 Consensus size: 21
12428952 CTTTCCGTTT
* * *
12428962 AGCTCTTACGAGCTTCTATTT
1 AGCTCTTATGAGCTTCTGTTC
* * * *
12428983 AACTCATATGAGTTTCCGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
12429004 AAG-TCTT-TCGAGCTTCTATTC
1 -AGCTCTTAT-GAGCTTCTGTTC
* *
12429025 AACTCTTATGAGTTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
12429046 AGCTCTTATGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* * *
12429067 AACTCATATGAG-TTTTCGTTC
1 AGCTCTTATGAGCTTCT-GTTC
* *
12429088 AGCTCTTACGAGCTTCTATTC
1 AGCTCTTATGAGCTTCTGTTC
* * * * *
12429109 AACCCTTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTC
* *
12429130 AGCTCTCATGAACTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
12429151 AGCT
1 AGCT
12429155 TTCGAGCTTT
Statistics
Matches: 125, Mismatches: 41, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
20 5 0.04
21 115 0.92
22 5 0.04
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:12429000 original size:42 final size:42
Alignment explanation
Indices: 12428953--12429135 Score: 224
Period size: 42 Copynumber: 4.4 Consensus size: 42
12428943 CGTGTTTTAC
* *
12428953 TTTCCGTTTAGCTCTTACGAGCTTCTATTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
* *
12428995 TTTCCGTTCAAG-TCTTTCGAGCTTCTATTCAACTCTTATGAG
1 TTTCCGTTC-AGCTCTTACGAGCTTCTATTCAACTCATATGAG
* * * *
12429037 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
* * * *
12429079 TTTTCGTTCAGCTCTTACGAGCTTCTATTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
* *
12429121 TTTCTGTTTAGCTCT
1 TTTCCGTTCAGCTCT
12429136 CATGAACTTC
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 114 0.97
43 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTACGAGCTTCTATTCAACTCATATGAG
Found at i:12429068 original size:84 final size:84
Alignment explanation
Indices: 12428953--12429149 Score: 288
Period size: 84 Copynumber: 2.3 Consensus size: 84
12428943 CGTGTTTTAC
* * * *
12428953 TTTCCGTTTAGCTCTTACGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAAG-TCTTTCGAGC
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTTAACTCATATGAGTTTCCGTTC-AGCTCTTACGAGC
*
12429017 TTCTATTCAACTCTTATGAG
65 TTCTATTCAACCCTTATGAG
* *
12429037 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCATATGAGTTTTCGTTCAGCTCTTACGAGCT
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTCTTACGAGCT
*
12429102 TCTATTCAACCCTTATGGG
66 TCTATTCAACCCTTATGAG
* *
12429121 TTTCTGTTTAGCTCTCATGAACTTCTGTT
1 TTTCTGTTTAGCTCTTATGAGCTTCTGTT
12429150 CAGCTTTCGA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
83 2 0.02
84 99 0.98
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.44
Consensus pattern (84 bp):
TTTCTGTTTAGCTCTTATGAGCTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTCTTACGAGCT
TCTATTCAACCCTTATGAG
Found at i:12432761 original size:20 final size:20
Alignment explanation
Indices: 12432719--12432768 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12432709 TACATATTAT
* * * *
12432719 CACTGTTAATGATTTGACTC
1 CACTGTTCATGACTTAACCC
12432739 CACTGTTCATGACTTAACCC
1 CACTGTTCATGACTTAACCC
*
12432759 CACTATTCAT
1 CACTGTTCAT
12432769 AGGGCTGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (20 bp):
CACTGTTCATGACTTAACCC
Found at i:12435832 original size:16 final size:17
Alignment explanation
Indices: 12435801--12435833 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12435791 ACTTTCCACA
*
12435801 AACTTAAGCAAAGTTTT
1 AACTTAAACAAAGTTTT
12435818 AACTTAAAC-AAGTTTT
1 AACTTAAACAAAGTTTT
12435834 GGATACTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (17 bp):
AACTTAAACAAAGTTTT
Found at i:12447205 original size:104 final size:104
Alignment explanation
Indices: 12447022--12447215 Score: 293
Period size: 104 Copynumber: 1.9 Consensus size: 104
12447012 NNNNNNNNNN
* * * *
12447022 GGGGAATCAGCATATAGCAACCCCCTTTTCATTTCAAAAATACGGTGGATATCGCACTTAGCACC
1 GGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAAATACGGTGGATATCGCACCTAACACC
12447087 ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTTG
** *
12447126 GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGGTATGGTGGATCA-CGCACCTAACA
1 GGGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAAATACGGTGGAT-ATCGCACCTAACA
12447190 CCACCAATG-AATCGGGGAATCAGCAC
64 CCACCAATGAAATCGGGGAATCAGCAC
12447216 ACAGTAACCC
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
104 44 0.54
105 36 0.44
106 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (104 bp):
GGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAAATACGGTGGATATCGCACCTAACACC
ACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:12447923 original size:70 final size:69
Alignment explanation
Indices: 12447807--12448126 Score: 316
Period size: 70 Copynumber: 4.7 Consensus size: 69
12447797 ACAACAATTG
* * *
12447807 GGAGCCTTAGCCCTCTCTAACTA-TTTAGAGGTTGTGGTATTAAACCTGCGAGCCCTAAGATCAT
1 GGAGCCTTAGCTCTCGCTAACTATTTTAGA-GTTGTGGTATTGAACCTGCGAGCCCTAAGATCAT
12447871 ATCTA
65 ATCTA
* * * *
12447876 GGAGCCTTAGGTCTCGCTAACTATTTTAGAGTCTGTGGTATTGAACCTGCAAGCCCTACGATCAC
1 GGAGCCTTAGCTCTCGCTAACTATTTTAGAGT-TGTGGTATTGAACCTGCGAGCCCTAAGATCAT
*
12447941 AGCTTA
65 ATC-TA
* * * * * *
12447947 -AAGACTTAGCTCTCACTAACTA-TTTAGA-----GGTACTGAACTTGTGAGCCCTAAGATCATA
1 GGAGCCTTAGCTCTCGCTAACTATTTTAGAGTTGTGGTATTGAACCTGCGAGCCCTAAGATCATA
* **
12448005 ACGG
66 TCTA
* * * * *
12448009 GGAGCCTTAGCTCTCGTTAACTATTTTAGAGGCTGCGGTATTGAACCTGCGAGCCTTAAGATTAT
1 GGAGCCTTAGCTCTCGCTAACTATTTTAGA-GTTGTGGTATTGAACCTGCGAGCCCTAAGATCAT
*
12448074 AGT-TG
65 A-TCTA
12448079 GGAGCCTTAGCTCTCGCTAACTATTTTAGAGGTTGTGGTATTGAACCT
1 GGAGCCTTAGCTCTCGCTAACTATTTTAGA-GTTGTGGTATTGAACCT
12448127 CGAACCTTAG
Statistics
Matches: 204, Mismatches: 35, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
63 43 0.21
64 6 0.03
69 28 0.14
70 125 0.61
71 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (69 bp):
GGAGCCTTAGCTCTCGCTAACTATTTTAGAGTTGTGGTATTGAACCTGCGAGCCCTAAGATCATA
TCTA
Found at i:12448088 original size:133 final size:134
Alignment explanation
Indices: 12447856--12448111 Score: 345
Period size: 133 Copynumber: 1.9 Consensus size: 134
12447846 TTAAACCTGC
* * * * *
12447856 GAGCCCTAAGATCATATCTAGGAGCCTTAGGTCTCGCTAACTATTTTAGAGTCTGTGGTATTGAA
1 GAGCCCTAAGATCATAACGAGGAGCCTTAGCTCTCGCTAACTATTTTAGAGGCTGCGGTATTGAA
*
12447921 CCTGCAAGCCCTACGATCACAGCTTAAAGACTTAGCTCTCACTAACTA-TTTAGAGGTACTGAAC
66 CCTGCAAGCCCTAAGATCACAGCTTAAAGACTTAGCTCTCACTAACTATTTTAGAGGTACTGAAC
12447985 TTGT
131 TTGT
* *
12447989 GAGCCCTAAGATCATAACGGGGAGCCTTAGCTCTCGTTAACTATTTTAGAGGCTGCGGTATTGAA
1 GAGCCCTAAGATCATAACGAGGAGCCTTAGCTCTCGCTAACTATTTTAGAGGCTGCGGTATTGAA
* * * * ** * *
12448054 CCTGCGAGCCTTAAGATTATAG-TTGGGAGCCTTAGCTCTCGCTAACTATTTTAGAGGT
66 CCTGCAAGCCCTAAGATCACAGCTT-AAAGACTTAGCTCTCACTAACTATTTTAGAGGT
12448112 TGTGGTATTG
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
132 2 0.02
133 94 0.90
134 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (134 bp):
GAGCCCTAAGATCATAACGAGGAGCCTTAGCTCTCGCTAACTATTTTAGAGGCTGCGGTATTGAA
CCTGCAAGCCCTAAGATCACAGCTTAAAGACTTAGCTCTCACTAACTATTTTAGAGGTACTGAAC
TTGT
Found at i:12448176 original size:50 final size:49
Alignment explanation
Indices: 12448083--12448186 Score: 122
Period size: 48 Copynumber: 2.1 Consensus size: 49
12448073 TAGTTGGGAG
* *
12448083 CCTTAGCTCTCGCTAACTATTTTAGAGGTTGTGGTATTGAACCT-CGAA
1 CCTTAGCTCTCGCTAACTATTTTAGAGGCTGTGGTATTAAACCTGCGAA
* * *
12448131 CCTTAGCTCTCTCTAACTATGTTTTGAGGGCTGCT-GTATTAAACCTGCGAG
1 CCTTAGCTCTCGCTAACTAT-TTTAGA-GGCTG-TGGTATTAAACCTGCGAA
12448182 CCTTA
1 CCTTA
12448187 AGATCACAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 19 0.40
49 5 0.11
50 14 0.30
51 9 0.19
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (49 bp):
CCTTAGCTCTCGCTAACTATTTTAGAGGCTGTGGTATTAAACCTGCGAA
Found at i:12448226 original size:120 final size:118
Alignment explanation
Indices: 12448013--12448230 Score: 285
Period size: 120 Copynumber: 1.8 Consensus size: 118
12448003 TAACGGGGAG
* * * **
12448013 CCTTAGCTCTCGTTAACTATTTTAGAGGCTGCGGTATTGAACCTGCGAGCCTTAAGATTATAGTT
1 CCTTAGCTCTCGTTAACTATTTTAGAGGCTGCGGTATTAAACCTGCGAGCCTTAAGATCACAACT
* * * *
12448078 GGGAGCCTTAGCTCTCGCTAACTATTTTAGAGGTTGTGGTATTGAACCTCGAA
66 AGGAACCTTAGCTCCCACTAACTATTTTAGAGGTTGTGGTATTGAACCTCGAA
* *
12448131 CCTTAGCTCTC-TCTAACTATGTTTTGAGGGCTGCTGTATTAAACCTGCGAGCCTTAAGATCACA
1 CCTTAGCTCTCGT-TAACTAT-TTTAGA-GGCTGCGGTATTAAACCTGCGAGCCTTAAGATCACA
* *
12448195 ACTAGGAACCTTAGCTCCCACTAATTGTTTTAGAGG
63 ACTAGGAACCTTAGCTCCCACTAACTATTTTAGAGG
12448231 CTGTTATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
117 1 0.01
118 18 0.21
119 5 0.06
120 60 0.71
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (118 bp):
CCTTAGCTCTCGTTAACTATTTTAGAGGCTGCGGTATTAAACCTGCGAGCCTTAAGATCACAACT
AGGAACCTTAGCTCCCACTAACTATTTTAGAGGTTGTGGTATTGAACCTCGAA
Found at i:12448311 original size:70 final size:71
Alignment explanation
Indices: 12448131--12448436 Score: 222
Period size: 70 Copynumber: 4.3 Consensus size: 71
12448121 GAACCTCGAA
* ** *
12448131 CCTTAGCTCTCTCTAACTATGTTTT-GAGGGCT-GCTGTATT-AAACCTGCGAGCCTTAAGATCA
1 CCTTAGCTCTCTCTAACTAT-TTTTAGA-GGCTAG-AGTATTGAAA-CTATGAACCTTAAGATCA
* * * *
12448193 CAACTAGGAA
62 TAGCTGGGAG
* * *
12448203 CCTTAGCTCCCACTAA-T-TGTTTTAGAGGCT-GTTA-TATTGAATCTATGAACCTTAAGATCAT
1 CCTTAGCTCTCTCTAACTAT-TTTTAGAGGCTAG--AGTATTGAAACTATGAACCTTAAGATCAT
*
12448264 AGTTGGGAG
63 AGCTGGGAG
* * * * * * * * *
12448273 CTTTAGCTCTCTCTAGCTATTTTTAG-GGCTACG-GTATTGAACCTGTGAGCCCTAAGATAACAA
1 CCTTAGCTCTCTCTAACTATTTTTAGAGGCTA-GAGTATTGAAACTATGAACCTTAAGATCATAG
12448336 CTGGGAG
65 CTGGGAG
* * *
12448343 CCTTAGCTCTCACTAACT-GTTTTAGAGGCTAGAGTATT-AAAC-CTGCAAGCCTTAAGATCATA
1 CCTTAGCTCTCTCTAACTATTTTTAGAGGCTAGAGTATTGAAACTATG-AA-CCTTAAGATCATA
12448405 GCTGGGAG
64 GCTGGGAG
12448413 CCTTAGCTCTCTCTAACTATTTTT
1 CCTTAGCTCTCTCTAACTATTTTT
12448437 TTAGGGGAGG
Statistics
Matches: 183, Mismatches: 38, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
68 2 0.01
69 11 0.06
70 138 0.75
71 16 0.09
72 16 0.09
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (71 bp):
CCTTAGCTCTCTCTAACTATTTTTAGAGGCTAGAGTATTGAAACTATGAACCTTAAGATCATAGC
TGGGAG
Found at i:12448396 original size:140 final size:140
Alignment explanation
Indices: 12448131--12448436 Score: 395
Period size: 140 Copynumber: 2.2 Consensus size: 140
12448121 GAACCTCGAA
* * * *
12448131 CCTTAGCTCTCTCTAACTATGTTTTGAGGGCTGCTGTATTAAACCTGCGAGCCTTAAGATCACAA
1 CCTTAGCTCTCTCTAACTAT-TTTTGAGGGCTACGGTATTAAACCTGCGAGCCCTAAGATAACAA
* *
12448196 CTAGGAACCTTAGCTCCCACTAATTGTTTTAGAGGCTGTTATATTGAATCTATGAACCTTAAGAT
65 CTAGGAACCTTAGCTCCCACTAACTGTTTTAGAGGCTG-TATATTGAAACTATGAACCTTAAGAT
*
12448261 CATAGTTGGGAG
129 CATAGCTGGGAG
* * * *
12448273 CTTTAGCTCTCTCTAGCTATTTTT-AGGGCTACGGTATTGAACCTGTGAGCCCTAAGATAACAAC
1 CCTTAGCTCTCTCTAACTATTTTTGAGGGCTACGGTATTAAACCTGCGAGCCCTAAGATAACAAC
* * * *
12448337 TGGGAGCCTTAGCTCTCACTAACTGTTTTAGAGGCTAG-AGTATT-AAAC-CTGCAAGCCTTAAG
66 TAGGAACCTTAGCTCCCACTAACTGTTTTAGAGGCT-GTA-TATTGAAACTATG-AA-CCTTAAG
12448399 ATCATAGCTGGGAG
127 ATCATAGCTGGGAG
12448413 CCTTAGCTCTCTCTAACTATTTTT
1 CCTTAGCTCTCTCTAACTATTTTT
12448437 TTAGGGGAGG
Statistics
Matches: 143, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
138 2 0.01
139 6 0.04
140 112 0.78
141 5 0.03
142 18 0.13
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (140 bp):
CCTTAGCTCTCTCTAACTATTTTTGAGGGCTACGGTATTAAACCTGCGAGCCCTAAGATAACAAC
TAGGAACCTTAGCTCCCACTAACTGTTTTAGAGGCTGTATATTGAAACTATGAACCTTAAGATCA
TAGCTGGGAG
Found at i:12455278 original size:24 final size:24
Alignment explanation
Indices: 12455250--12455315 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
12455240 GAGTTTCTTT
* *
12455250 TATTATTATTTTAAGTTTTA-TATG
1 TATTATTATTTGAA-ATTTACTATG
12455274 TATTATTATTTGAAATTTACTATG
1 TATTATTATTTGAAATTTACTATG
*
12455298 TATTACTATTT-AAATTTA
1 TATTATTATTTGAAATTTA
12455316 ACATAGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (24 bp):
TATTATTATTTGAAATTTACTATG
Found at i:12457798 original size:40 final size:40
Alignment explanation
Indices: 12457742--12457821 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
12457732 TCATAGGACA
*
12457742 GACACTCTGAATAGGCCTCGAGCATGTTGGACATGTGTAT
1 GACACTCTGAACAGGCCTCGAGCATGTTGGACATGTGTAT
*
12457782 GACACTCTGAGCAGGCCTCGAGCATGTTGGACATGTGTAT
1 GACACTCTGAACAGGCCTCGAGCATGTTGGACATGTGTAT
12457822 CGTTTCAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
GACACTCTGAACAGGCCTCGAGCATGTTGGACATGTGTAT
Found at i:12467864 original size:17 final size:18
Alignment explanation
Indices: 12467832--12467872 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12467822 TCACACGGGC
* *
12467832 TGGGCCAATTTGGGCGTG
1 TGGGCCAATATGGGCGTA
12467850 TGGGCC-ATATGGGCGTA
1 TGGGCCAATATGGGCGTA
12467867 TGGGCC
1 TGGGCC
12467873 CATACGAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.12, C:0.20, G:0.44, T:0.24
Consensus pattern (18 bp):
TGGGCCAATATGGGCGTA
Found at i:12470236 original size:45 final size:44
Alignment explanation
Indices: 12470187--12470349 Score: 184
Period size: 45 Copynumber: 3.6 Consensus size: 44
12470177 AATTAAAAAT
* * **
12470187 ACCATAGTTGAAAGATACTATGGCACTAAATCGGCAAT-GTGTAAG
1 ACCATAGTTGAAAGATATTATGGCACTAAATC--TAATAGAATAAG
* ** *
12470232 ACCATAATTGAAAGATATTATGGCTTTAAATCTAATACAAATAAG
1 ACCATAGTTGAAAGATATTATGGCACTAAATCTAATA-GAATAAG
* **
12470277 ACCATATTTGAAAGATATTATGGCTTTAAATCTAATACGAATAAG
1 ACCATAGTTGAAAGATATTATGGCACTAAATCTAATA-GAATAAG
12470322 ACCATAGTTGAAAGATATTATGGCACTA
1 ACCATAGTTGAAAGATATTATGGCACTA
12470350 CTTCGGGAAT
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
43 3 0.03
45 100 0.97
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (44 bp):
ACCATAGTTGAAAGATATTATGGCACTAAATCTAATAGAATAAG
Found at i:12481550 original size:132 final size:133
Alignment explanation
Indices: 12481404--12481669 Score: 525
Period size: 132 Copynumber: 2.0 Consensus size: 133
12481394 AAAATATTTA
12481404 TAAAAATTATTAGAAATGAATTAAAAAACCATAAAATTTTATTAAAAAAAGTATATAAATATTAT
1 TAAAAATTATTAGAAATGAATTAAAAAACCATAAAATTTTATTAAAAAAAGTATATAAATATTAT
12481469 CTTAGAATGCATTATATTACTCTTAATATCTTTATTGTTAATAGTATATGTTTCTCATTTTTAAC
66 CTTAGAATGCATTATATTACTCTTAATATCTTTATTGTTAATAGTATATGTTTCTCATTTTTAAC
12481534 TAT
131 TAT
12481537 TAAAAATTA-TAGAAATGAATTAAAAAACCATAAAATTTTATTAAAAAAAGTATATAAATATTAT
1 TAAAAATTATTAGAAATGAATTAAAAAACCATAAAATTTTATTAAAAAAAGTATATAAATATTAT
12481601 CTTAGAATGCATTATATTACTCTTAATATCTTTATTGTTAATAGTATATGTTTCTCATTTTTAAC
66 CTTAGAATGCATTATATTACTCTTAATATCTTTATTGTTAATAGTATATGTTTCTCATTTTTAAC
12481666 TAT
131 TAT
12481669 T
1 T
12481670 TTCATATTTT
Statistics
Matches: 133, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 124 0.93
133 9 0.07
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (133 bp):
TAAAAATTATTAGAAATGAATTAAAAAACCATAAAATTTTATTAAAAAAAGTATATAAATATTAT
CTTAGAATGCATTATATTACTCTTAATATCTTTATTGTTAATAGTATATGTTTCTCATTTTTAAC
TAT
Found at i:12482267 original size:58 final size:58
Alignment explanation
Indices: 12482200--12482316 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
12482190 TAAATGAACC
**
12482200 TAATCAACCATTTCTTCAGATTTATTATATCATGTCATCAATCAATGAAAATGTGGCA
1 TAATCAACCATTTCTTCAGATTTATTATATCACATCATCAATCAATGAAAATGTGGCA
*
12482258 TAATCAACCATTTGTTCAGATTTATTATATCACATCATCAATCAATGAAAATGTGGCA
1 TAATCAACCATTTCTTCAGATTTATTATATCACATCATCAATCAATGAAAATGTGGCA
12482316 T
1 T
12482317 TATTAACGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (58 bp):
TAATCAACCATTTCTTCAGATTTATTATATCACATCATCAATCAATGAAAATGTGGCA
Found at i:12484229 original size:69 final size:69
Alignment explanation
Indices: 12484118--12484248 Score: 192
Period size: 69 Copynumber: 1.9 Consensus size: 69
12484108 ATAGTACCTC
* * * *
12484118 CATTTCTTTGAGCCCCTCGCCGCTTTTCTGGAAACCCTGGAGGAGCTTTAACTTCACTCTCCCGT
1 CATTTCTTTCAGCCCCTCGCCGCTTATCTGGAAACCCCGGAGGAGCTTCAACTTCACTCTCCCGT
12484183 CCAT
66 CCAT
* *
12484187 CATTTCTTTCA-CTCCCTCGCCGCTTATCTGGAAACCCCGGAGGAGGTTCAACTTCAGTCTCC
1 CATTTCTTTCAGC-CCCTCGCCGCTTATCTGGAAACCCCGGAGGAGCTTCAACTTCACTCTCC
12484249 TGACCACCGG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 1 0.02
69 54 0.98
ACGTcount: A:0.17, C:0.35, G:0.18, T:0.31
Consensus pattern (69 bp):
CATTTCTTTCAGCCCCTCGCCGCTTATCTGGAAACCCCGGAGGAGCTTCAACTTCACTCTCCCGT
CCAT
Found at i:12485418 original size:19 final size:18
Alignment explanation
Indices: 12485383--12485422 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
12485373 TTTATTATTA
12485383 ATATTTTAATATATAAACT
1 ATATTTTAATATATAAA-T
12485402 ATATTTTAA-ATATTAAAT
1 ATATTTTAATATA-TAAAT
12485420 ATA
1 ATA
12485423 ATCAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTTAATATATAAAT
Found at i:12486164 original size:15 final size:15
Alignment explanation
Indices: 12486146--12486193 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12486136 TAAGAGAGGG
12486146 AAAAAGAACAAATAA
1 AAAAAGAACAAATAA
*
12486161 AAAAAGGACAAA-AA
1 AAAAAGAACAAATAA
*
12486175 AAATTAGAA-AAATAA
1 AAA-AAGAACAAATAA
12486190 AAAA
1 AAAA
12486194 TAAGAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.08
Consensus pattern (15 bp):
AAAAAGAACAAATAA
Found at i:12486201 original size:15 final size:15
Alignment explanation
Indices: 12486155--12486210 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
12486145 GAAAAAGAAC
*
12486155 AAATAAAAAA-AGGA
1 AAATAAAAAATAAGA
* *
12486169 CAA-AAAAAATTAGAA
1 AAATAAAAAATAAG-A
12486184 AAATAAAAAATAAGA
1 AAATAAAAAATAAGA
12486199 AAATAAATAAAT
1 AAATAAA-AAAT
12486211 GTATCATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.18
14 3 0.09
15 11 0.33
16 13 0.39
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATAAAAAATAAGA
Found at i:12498349 original size:21 final size:21
Alignment explanation
Indices: 12498309--12498372 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
12498299 GGCGTGACAC
*
12498309 GCAG-CCTGTGTTGACCCATA
1 GCAGACCTGTGTTGAGCCATA
*
12498329 GCA-ACCTTGTGTTGAGTCATA
1 GCAGACC-TGTGTTGAGCCATA
* *
12498350 GTAGTCCTGTGTTGAGCCATA
1 GCAGACCTGTGTTGAGCCATA
12498371 GC
1 GC
12498373 CTGAATGTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 5 0.14
21 28 0.80
22 2 0.06
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (21 bp):
GCAGACCTGTGTTGAGCCATA
Found at i:12500086 original size:6 final size:6
Alignment explanation
Indices: 12500072--12500104 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
12500062 GAGATTTACA
12500072 CATACAT CATAAT CATAAT CATAAT CATAAT CA
1 CATA-AT CATAAT CATAAT CATAAT CATAAT CA
12500105 CATCAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (6 bp):
CATAAT
Found at i:12501333 original size:3 final size:3
Alignment explanation
Indices: 12501325--12501365 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
12501315 TAATATTTTC
** *
12501325 ATT ATT ATT ATT ACA ATT ATT ATT AGT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12501366 ATATCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Done.