Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 48 of 328
Found at i:13855306 original size:3 final size:3
Alignment explanation
Indices: 13855298--13855530 Score: 74
Period size: 3 Copynumber: 78.7 Consensus size: 3
13855288 AAAAATAGAA
* * * * *
13855298 AAT AAT AAT -AT ATT AAT AAG AAT TAT AAT GAT ATAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * **
13855343 AACA AAT AAT AA- AA- AAT AAC AAT GGGTT AAT AA- AGAT AAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT A-AT AAT AAT AAT
* * * *
13855389 AAT AGA- AGT AAA AAT AAT AAT AAT CAAT -AT AAT AAT AGT AAGG AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA-T AAT
* * * ** *
13855435 -AT AAT AAT AAT AGT AAT AA- AAT AA- AAA AAT GAT GGT AGT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
13855479 AAA AAT AAA AAC AAC AAT AAT AAT AAT AAT GAG GAT ATT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13855526 AAT AA
1 AAT AA
13855531 AATCTAATAT
Statistics
Matches: 169, Mismatches: 43, Indels: 36
0.68 0.17 0.15
Matches are distributed among these distances:
2 19 0.11
3 137 0.81
4 12 0.07
5 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:13855599 original size:24 final size:23
Alignment explanation
Indices: 13855551--13855600 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
13855541 TTTTCTTTTA
* *
13855551 AAATAAAATATGTAAAAGGATAT
1 AAATAAAATATGTAAAAAGAGAT
13855574 AAATAAAATAATG-AAAATAGAGAT
1 AAATAAAAT-ATGTAAAA-AGAGAT
13855598 AAA
1 AAA
13855601 GCACGCGCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (23 bp):
AAATAAAATATGTAAAAAGAGAT
Found at i:13855636 original size:2 final size:2
Alignment explanation
Indices: 13855631--13855682 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
13855621 ACACACACAC
*
13855631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
13855674 -T A- AT AT AT A
1 AT AT AT AT AT A
13855683 AATAGGAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:13855881 original size:3 final size:3
Alignment explanation
Indices: 13855875--13856001 Score: 52
Period size: 3 Copynumber: 43.7 Consensus size: 3
13855865 TAATAAGGGA
* * * * * * *
13855875 AAT AAT AAC AAT AAT -AC AAT AAT GAT AA- AGT AGT AAT AAA AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
13855921 AAT AAC AAT AAT AGT AAA AAT -AT AAT AAT GAT AAT AAAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* *
13855966 AA- AAG AA- AAT AAT AA- AATT AACT AAT -TT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT AA
13856002 AGTAGCTAAA
Statistics
Matches: 90, Mismatches: 25, Indels: 18
0.68 0.19 0.14
Matches are distributed among these distances:
2 11 0.12
3 71 0.79
4 8 0.09
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:13855947 original size:29 final size:31
Alignment explanation
Indices: 13855915--13855987 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
13855905 TAGTAATAAA
13855915 AATAAAAATAACAATAATAGTAAAA-ATATAAT
1 AATAAAAATAACAATAATAGTAAAAGA-A-AAT
* *
13855947 AATGATAAT-A-AATAATAGTAAAAGAAAAT
1 AATAAAAATAACAATAATAGTAAAAGAAAAT
*
13855976 AATAAAATTAAC
1 AATAAAAATAAC
13855988 TAATTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
29 9 0.27
30 15 0.45
31 2 0.06
32 7 0.21
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (31 bp):
AATAAAAATAACAATAATAGTAAAAGAAAAT
Found at i:13859732 original size:23 final size:23
Alignment explanation
Indices: 13859706--13859750 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13859696 TGGGTATGTG
*
13859706 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
13859729 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
13859751 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:13860502 original size:89 final size:89
Alignment explanation
Indices: 13860409--13861118 Score: 444
Period size: 89 Copynumber: 7.9 Consensus size: 89
13860399 CCTTAATCCA
* * * * *
13860409 CTCCACTGCAACTTTAGGGAGATAGGATTAGCTATCTTCAGTCTGCTCCGCTGTAACTTTAGGGA
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
* *
13860474 GATAAGACTTGTGGTTTCGATCTG
66 GATAAGACTTGTGATTTCAATCTG
* * * ** * *
13860498 CTCCACTGCAACTTTAGGAAGATAAGATTTG-TCATGGT-AGACTTGATCCGACCTGCTACAACT
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCT-ATCTTCAGTC-TGCTCC-A-CTG---CAACT
* ** * * *
13860561 TCAGAGG-TATAAGACTCATCGTTTTTAATCCG
59 TCAG-GGAGATAAGACTTGT-GATTTCAATCTG
* * * * * * * *
13860593 CTCCACTGCAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTTTGTTCCGCTGCAACTTTAGGAA
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
* * *
13860658 GATAAGACTTGTAATTTTAACCTG
66 GATAAGACTTGTGATTTCAATCTG
* * * * * * *
13860682 CTCCACTGCAACTTCAGAGAGATAAGGTTTG-T-T-TTGA-TCTGCTCTACTGTAACTTCAGAGA
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
*
13860743 GATAAGA-TATGTAATTATAGCTTCAATCTG
66 GATAAGACT-TG---TGAT---TTCAATCTG
* ** * * * *
13860773 TTCCACTGCAACTTCACAGAAATAAGATTCGCTATCTTTAGTCTACTCCACTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
* *
13860838 GATAAGATTTGTAATTTCAA-CTTG
66 GATAAGACTTGTGATTTCAATC-TG
* ** * * * * * *
13860862 CTCTACTGCAACTTCAGATAGATAAGGTTTGCTATCTTC-GATTTACTCCGCTGTAACTTCAGGG
1 CTCCACTGCAACTTCAGGGAGATAAGATTAGCTATCTTCAG-TCTGCTCCACTGCAACTTCAGGG
13860926 AGATAAGA-TATGCT-ATCTTCAATCTG
65 AGATAAGACT-TG-TGAT-TTCAATCTG
* * ** * *
13860952 CTCCACTACAACTTCAGGGAGATAAGACTT-G-TAACTTCAACCTGCTCCATTGCAACTTCAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
** * *
13861015 AGATAAGGTTTATAGCTTT-AATCTG
65 AGATAAGACTTGT-GATTTCAATCTG
* * * * *
13861040 CTCCACTGCAACTTCAAGGAGATAAGATTCA-CCATCTTTAGTCTGCTCCATTGCAACTTTAGGG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-AGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGG
13861104 AGATAAGACTTGTGA
65 AGATAAGACTTGTGA
13861119 ATTTACTGAT
Statistics
Matches: 478, Mismatches: 105, Indels: 77
0.72 0.16 0.12
Matches are distributed among these distances:
84 1 0.00
85 25 0.05
86 3 0.01
87 3 0.01
88 44 0.09
89 209 0.44
90 50 0.10
91 39 0.08
92 4 0.01
93 4 0.01
94 19 0.04
95 73 0.15
96 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (89 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTAGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGA
GATAAGACTTGTGATTTCAATCTG
Found at i:13860513 original size:44 final size:43
Alignment explanation
Indices: 13860409--13861116 Score: 274
Period size: 45 Copynumber: 15.7 Consensus size: 43
13860399 CCTTAATCCA
*
13860409 CTCCACTGCAACTTTAGGGAGATAGGATTAGCTATCTTCAGTCTG
1 CTCCACTGCAACTTTAGGGAGATAAGATT-G-TATCTTCAGTCTG
* * *
13860454 CTCCGCTGTAACTTTAGGGAGATAAGACTTGTGGT-TTC-GATCTG
1 CTCCACTGCAACTTTAGGGAGATAAGA-TTGT-ATCTTCAG-TCTG
* ** *
13860498 CTCCACTGCAACTTTAGGAAGATAAGATTTGTCATGGT-AGACTTG
1 CTCCACTGCAACTTTAGGGAGATAAGA-TTGT-ATCTTCAGTC-TG
* * * * * *
13860543 ATCCGACCTGCTACAACTTCAGAGG-TATAAGACTCATCGT-T-TTTAATCCG
1 CTCC-A-CTG---CAACTTTAG-GGAGATAAGA-T--T-GTATCTTCAGTCTG
* * * *
13860593 CTCCACTGCAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTTTG
1 CTCCACTGCAACTTTAGGGAGATAAGATT-G-TATCTTCAGTCTG
* * * * **
13860638 TTCCGCTGCAACTTTAGGAAGATAAGACTTGTAAT-TTTAACCTG
1 CTCCACTGCAACTTTAGGGAGATAAGA-TTGT-ATCTTCAGTCTG
* * * *
13860682 CTCCACTGCAACTTCAGAGAGATAAGGTTTGT-T-TTGA-TCTG
1 CTCCACTGCAACTTTAGGGAGATAA-GATTGTATCTTCAGTCTG
* * * * *
13860723 CTCTACTGTAACTTCAGAGAGATAAGATATGTAATTATAGCTTCAATCTG
1 CTCCACTGCAACTTTAGGGAGATAAGAT-TG----TAT--CTTCAGTCTG
* * ** * * *
13860773 TTCCACTGCAACTTCACAGAAATAAGATTCGCTATCTTTAGTCTA
1 CTCCACTGCAACTTTAGGGAGATAAGATT-G-TATCTTCAGTCTG
* *
13860818 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT-TTCA-ACTTG
1 CTCCACTGCAACTTTAGGGAGATAAGA-TTGT-ATCTTCAGTC-TG
* * ** * * *
13860862 CTCTACTGCAACTTCAGATAGATAAGGTTTGCTATCTTC-GATTTA
1 CTCCACTGCAACTTTAGGGAGATAA-GATTG-TATCTTCAG-TCTG
* * * *
13860907 CTCCGCTGTAACTTCAGGGAGATAAGATATGCTATCTTCAATCTG
1 CTCCACTGCAACTTTAGGGAGATAAGAT-TG-TATCTTCAGTCTG
* * * **
13860952 CTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTTAGGGAGATAAGA-TTGTATCTTCAGTCTG
* * * * * *
13860996 CTCCATTGCAACTTCAGAGAGATAAGGTT-TATAGCTTTAATCTG
1 CTCCACTGCAACTTTAGGGAGATAAGATTGTAT--CTTCAGTCTG
* * ** *
13861040 CTCCACTGCAACTTCAAGGAGATAAGATTCACCATCTTTAGTCTG
1 CTCCACTGCAACTTTAGGGAGATAAGATT--GTATCTTCAGTCTG
*
13861085 CTCCATTGCAACTTTAGGGAGATAAGACTTGT
1 CTCCACTGCAACTTTAGGGAGATAAGA-TTGT
13861117 GAATTTACTG
Statistics
Matches: 506, Mismatches: 106, Indels: 103
0.71 0.15 0.14
Matches are distributed among these distances:
40 2 0.00
41 28 0.06
42 8 0.02
43 5 0.01
44 173 0.34
45 208 0.41
46 11 0.02
47 8 0.02
48 3 0.01
49 5 0.01
50 48 0.09
51 4 0.01
52 1 0.00
53 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
CTCCACTGCAACTTTAGGGAGATAAGATTGTATCTTCAGTCTG
Found at i:13860843 original size:45 final size:44
Alignment explanation
Indices: 13860584--13861111 Score: 345
Period size: 45 Copynumber: 11.8 Consensus size: 44
13860574 ACTCATCGTT
* * * *
13860584 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTGTC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GCTATC
* * * * * * *
13860629 TTCAGTTTGTTCCGCTGCAACTTTAGGAAGATAAGACTTG-TAAT-
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCT-ATC
* * * *
13860673 TTTAACCTGCTCCACTGCAACTTCAGAGAGATAAGGTT--TGT-
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTATC
* * * * *
13860714 TTTGATCTGCTCTACTGTAACTTCAGAGAGATAAGATATGTAATTATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG---CTAT--C
* * ** *
13860764 TTCAATCTGTTCCACTGCAACTTCACAGAAATAAGATTCGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GCTATC
* *
13860809 TTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAAT-
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCT-ATC
* * ** *
13860853 TTCAA-CTTGCTCTACTGCAACTTCAGATAGATAAGGTTTGCTATC
1 TTTAATC-TGCTCCACTGCAACTTCAGGGAGATAA-GATTGCTATC
** * * * *
13860898 TTCGATTTACTCCGCTGTAACTTCAGGGAGATAAGATATGCTATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGCTATC
* * *
13860943 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TAAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCTATC
* * * * * ** *
13860987 TTCAACCTGCTCCATTGCAACTTCAGAGAGATAAGGTTTATAGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTATC
* * *
13861031 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCACCATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GCTATC
* * *
13861076 TTTAGTCTGCTCCATTGCAACTTTAGGGAGATAAGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
13861112 CTTGTGAATT
Statistics
Matches: 374, Mismatches: 86, Indels: 46
0.74 0.17 0.09
Matches are distributed among these distances:
41 33 0.09
42 2 0.01
43 5 0.01
44 130 0.35
45 162 0.43
46 5 0.01
47 5 0.01
49 1 0.00
50 31 0.08
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTATC
Found at i:13860956 original size:134 final size:132
Alignment explanation
Indices: 13860679--13861122 Score: 473
Period size: 134 Copynumber: 3.3 Consensus size: 132
13860669 TAATTTTAAC
* ** * * *
13860679 CTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGT--TTTGATCTGCTCTACTGTAACTTCAGAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAATTTCAACTGCTCTACTGCAACTTCAGAG
* * *
13860742 AGATAAGATATGTAATTATAGCTTCAATCTGTTCCACTGCAACTTCACA-GAAATAAGATTCGCT
66 AGATAAG----GT--TTATATCTTCAATCTGCTCCACTGCAACTTCA-AGGAGATAAGATTCGCT
13860806 ATCTTTAGT
124 ATCTTTAGT
* *
13860815 CTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTCAACTTGCTCTACTGCAACTTCAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAATTTCAAC-TGCTCTACTGCAACTTCAGA
* * * * * * * *
13860880 TAGATAAGGTTTGCTATCTTCGATTTACTCCGCTGTAACTTCAGGGAGATAAGATAT-GCTATCT
65 GAGATAAGGTTT-ATATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGAT-TCGCTATCT
* *
13860944 TCAAT
128 TTAGT
* * * *
13860949 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCATTGCAACTTCAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAATTTCAA-CTGCTCTACTGCAACTTCAGA
* * * *
13861014 GAGATAAGGTTTATAGCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCACCATCTTT
65 GAGATAAGGTTTATATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATCTTT
13861079 AGT
130 AGT
* *
13861082 CTGCTCCATTGCAACTTTAGGGAGATAAGACTTGTGAATTT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-AATTT
13861123 ACTGATCTTG
Statistics
Matches: 256, Mismatches: 43, Indels: 20
0.80 0.13 0.06
Matches are distributed among these distances:
132 1 0.00
133 75 0.29
134 113 0.44
135 4 0.02
136 32 0.12
138 5 0.02
139 26 0.10
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (132 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAATTTCAACTGCTCTACTGCAACTTCAGAG
AGATAAGGTTTATATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATCTTTA
GT
Found at i:13865506 original size:39 final size:39
Alignment explanation
Indices: 13865451--13865529 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
13865441 GTAAATTTTG
13865451 TACTCCTTCGTCGGACTATCACCCTTCTATCATCGTGTT
1 TACTCCTTCGTCGGACTATCACCCTTCTATCATCGTGTT
*
13865490 TACTCCTTCGTTGGACTATCACCCTTCTATCATCGTGTT
1 TACTCCTTCGTCGGACTATCACCCTTCTATCATCGTGTT
13865529 T
1 T
13865530 TCTCAGACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.15, C:0.32, G:0.13, T:0.41
Consensus pattern (39 bp):
TACTCCTTCGTCGGACTATCACCCTTCTATCATCGTGTT
Found at i:13867344 original size:3 final size:3
Alignment explanation
Indices: 13867336--13867569 Score: 74
Period size: 3 Copynumber: 78.7 Consensus size: 3
13867326 AAAAATAGAA
* * * * *
13867336 AAT AAT AAT -AT ATT AAT AAG AAT TAT AAT GAT ATAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * **
13867381 AACA AAT AAT AA- AA- AAT AAC AAT GGGTT AAT AA- AGAT AAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT A-AT AAT AAT AAT
* * * *
13867427 AAT AGA- AGT AAA AAT AAT AAT AAT CAAT -AT AAT AAT AGT AAGG AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA-T AAT
* * * * ** *
13867473 -AT AAT AAT AAT AGT AAT AA- AAT AAA AAA AAT GAT GGT AGT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
13867518 AAA AAT AAA AAC AAC AAT AAT AAT AAT AAT GAG GAT ATT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13867565 AAT AA
1 AAT AA
13867570 AATCTAATAT
Statistics
Matches: 170, Mismatches: 44, Indels: 34
0.69 0.18 0.14
Matches are distributed among these distances:
2 17 0.10
3 140 0.82
4 12 0.07
5 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:13867544 original size:29 final size:29
Alignment explanation
Indices: 13867475--13867546 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 29
13867465 TAAGGAATAT
* * *
13867475 AATAATAATAGTAATAAAATAAAAAAAAT
1 AATAATAATAATAAAAAAATAAAAAAAAC
* ** * *
13867504 GATGGTAGTAATAAAAAAATAAAAACAAC
1 AATAATAATAATAAAAAAATAAAAAAAAC
13867533 AATAATAATAATAA
1 AATAATAATAATAA
13867547 TGAGGATATT
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (29 bp):
AATAATAATAATAAAAAAATAAAAAAAAC
Found at i:13867638 original size:24 final size:23
Alignment explanation
Indices: 13867590--13867639 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
13867580 TTTTCTTTTA
* *
13867590 AAATAAAATATGTAAAAGGATAT
1 AAATAAAATATGTAAAAAGAGAT
13867613 AAATAAAATAATG-AAAATAGAGAT
1 AAATAAAAT-ATGTAAAA-AGAGAT
13867637 AAA
1 AAA
13867640 GCACGCGCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (23 bp):
AAATAAAATATGTAAAAAGAGAT
Found at i:13867728 original size:2 final size:2
Alignment explanation
Indices: 13867670--13867710 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
13867660 ACACACACAC
13867670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13867711 AAATGATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13867927 original size:3 final size:3
Alignment explanation
Indices: 13867921--13868047 Score: 61
Period size: 3 Copynumber: 43.7 Consensus size: 3
13867911 TAATAAGGGA
* * * * * * *
13867921 AAT AAT AAC AAT AAT -AC AAT AAT GAT AA- AGT AGT AAT AAA AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
13867967 AAT AAC AAT AAT AGT AA- AAT AAT AAT AAT GAT AAT AAAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* *
13868012 AA- AAG AA- AAT AAT AA- AATT AACT AAT -TT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT AA
13868048 AGTAGCTAAA
Statistics
Matches: 92, Mismatches: 23, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
2 11 0.12
3 73 0.79
4 8 0.09
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:13867993 original size:35 final size:36
Alignment explanation
Indices: 13867936--13868026 Score: 89
Period size: 35 Copynumber: 2.6 Consensus size: 36
13867926 TAACAATAAT
* *
13867936 ACAATAAT-GATAAAGTAGTAATAAAAATAA-AAATA
1 ACAATAATAG-TAAAATAATAATAAAAATAATAAATA
**
13867971 ACAATAATAGTAAAATAATAATAATGATAATAAATA
1 ACAATAATAGTAAAATAATAATAAAAATAATAAATA
* * *
13868007 ATAGTAAAAG-AAAATAATAA
1 ACAATAATAGTAAAATAATAA
13868027 AATTAACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 34 0.72
36 13 0.28
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (36 bp):
ACAATAATAGTAAAATAATAATAAAAATAATAAATA
Found at i:13868004 original size:20 final size:19
Alignment explanation
Indices: 13867955--13868009 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
13867945 ATAAAGTAGT
*
13867955 AATAAAAATAAA-AATAAC
1 AATAATAATAAATAATAAC
* *
13867973 AATAATAGTAAAATAATAAT
1 AATAATAAT-AAATAATAAC
*
13867993 AATGATAATAAATAATA
1 AATAATAATAAATAATA
13868010 GTAAAAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 7 0.23
19 11 0.37
20 12 0.40
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
AATAATAATAAATAATAAC
Found at i:13870362 original size:20 final size:20
Alignment explanation
Indices: 13870337--13870374 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13870327 ACCGAGGCAT
13870337 AAATTTTCATCAAA-ATTTAA
1 AAATTTTCA-CAAACATTTAA
13870357 AAATTTTCACAAACATTT
1 AAATTTTCACAAACATTT
13870375 GTAATGTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTTTCACAAACATTTAA
Found at i:13870585 original size:13 final size:13
Alignment explanation
Indices: 13870567--13870591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13870557 TAATATATTT
13870567 ATTAATTAAAAAC
1 ATTAATTAAAAAC
13870580 ATTAATTAAAAA
1 ATTAATTAAAAA
13870592 AACTTCAAAT
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:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:13875069 original size:2 final size:2
Alignment explanation
Indices: 13875062--13875088 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13875052 ATGTTGTAAT
13875062 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13875089 GAAATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13876469 original size:16 final size:16
Alignment explanation
Indices: 13876440--13876478 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 16
13876430 CGCGACTCAT
13876440 TTTTTTAATAATATATATA
1 TTTTTTAAT-AT-TAT-TA
13876459 TTTTTTAATATTATTA
1 TTTTTTAATATTATTA
13876475 TTTT
1 TTTT
13876479 ATTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 2 0.10
19 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAATATTATTA
Found at i:13876799 original size:46 final size:46
Alignment explanation
Indices: 13876673--13876943 Score: 257
Period size: 46 Copynumber: 6.1 Consensus size: 46
13876663 AAAAAATTTT
* * *
13876673 ATTAAGTTTAATAACTATTTAATATTATTATTTTAATAATGTT---
1 ATTAAGTTTAATAATTTTTTAATATTATTATTTTAATAATTTTGAA
*
13876716 ATTAA-TTT-ATTATTTTTT-ATACTTAAATT-TTTTAATAATTTTGAA
1 ATTAAGTTTAATAATTTTTTAATA-TT--ATTATTTTAATAATTTTGAA
* * *
13876761 ATTAAGTTTCATAATTTTTTAATATTATTATTTGAATAATTCTGAA
1 ATTAAGTTTAATAATTTTTTAATATTATTATTTTAATAATTTTGAA
* *
13876807 ATTATGTTTAATAATTTTTTAATATTATTATTTTAATAATGTT---
1 ATTAAGTTTAATAATTTTTTAATATTATTATTTTAATAATTTTGAA
* *
13876850 ATTAA-TTT-ATTATTTTTT-ATGCTTAAATT-TTTTAATAATTTTGAA
1 ATTAAGTTTAATAATTTTTTAAT-ATT--ATTATTTTAATAATTTTGAA
* *
13876895 ATTAAGGTTAATAA-TTTTTAATATTATTATTTTAATAATTCTGATA
1 ATTAAGTTTAATAATTTTTTAATATTATTATTTTAATAATTTTGA-A
13876941 ATT
1 ATT
13876944 TATTATTTTT
Statistics
Matches: 187, Mismatches: 20, Indels: 39
0.76 0.08 0.16
Matches are distributed among these distances:
40 5 0.03
41 20 0.11
42 30 0.16
43 15 0.08
44 3 0.02
45 27 0.14
46 68 0.36
47 16 0.09
48 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (46 bp):
ATTAAGTTTAATAATTTTTTAATATTATTATTTTAATAATTTTGAA
Found at i:13876820 original size:21 final size:21
Alignment explanation
Indices: 13876746--13876824 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
13876736 ACTTAAATTT
*
13876746 TTTAATAATTTTGAAATTAAG
1 TTTAATAATTTTGAAATTATG
* * *
13876767 TTTCATAATTTTTTAATATTATTA
1 TTTAATAA-TTTTGAA-ATTA-TG
*
13876791 TTTGAATAATTCTGAAATTATG
1 TTT-AATAATTTTGAAATTATG
13876813 TTTAATAATTTT
1 TTTAATAATTTT
13876825 TTAATATTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
21 15 0.33
22 10 0.22
23 8 0.18
24 8 0.18
25 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTAATAATTTTGAAATTATG
Found at i:13876842 original size:25 final size:25
Alignment explanation
Indices: 13876771--13876865 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 25
13876761 ATTAAGTTTC
*
13876771 ATAATTTTTTAATATTATTATTTGA
1 ATAATTTTTTAATATTATTATTTTA
* * *
13876796 ATAA-TTCTGAA-ATTA-T-GTTTA
1 ATAATTTTTTAATATTATTATTTTA
13876817 ATAATTTTTTAATATTATTATTTTA
1 ATAATTTTTTAATATTATTATTTTA
*
13876842 ATAATGTTATTAAT-TTATTATTTT
1 ATAAT-TTTTTAATATTATTATTTT
13876866 TTATGCTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
21 7 0.12
22 6 0.11
23 8 0.14
24 6 0.11
25 23 0.40
26 7 0.12
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (25 bp):
ATAATTTTTTAATATTATTATTTTA
Found at i:13876932 original size:87 final size:87
Alignment explanation
Indices: 13876795--13877021 Score: 309
Period size: 87 Copynumber: 2.6 Consensus size: 87
13876785 TTATTATTTG
* * *
13876795 AATAATTCTGAAATTATGTTTAATAATTTTTTAATATTATTATTTTAATAATGT-T-ATTAATTT
1 AATAATTTTGAAATTAAGGTTAATAATTTTTTAATATTATTATTTTAATAAT-TCTGA-TAATTT
13876858 ATTATTTTTTATGCTTAAATTTTTT
64 ATTA-TTTTTATGCTTAAATTTTTT
13876883 AATAATTTTGAAATTAAGGTTAATAA-TTTTTAATATTATTATTTTAATAATTCTGATAATTTAT
1 AATAATTTTGAAATTAAGGTTAATAATTTTTTAATATTATTATTTTAATAATTCTGATAATTTAT
*
13876947 TATTTTTATGCTTAGATTTTTT
66 TATTTTTATGCTTAAATTTTTT
* * * * *
13876969 AATATTTTTAAAATTAA-GTCTAATAATTTTTTAGTATTATTAATTAAATAATT
1 AATAATTTTGAAATTAAGGT-TAATAATTTTTTAATATTATTATTTTAATAATT
13877022 TTTTATTGGA
Statistics
Matches: 126, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
85 2 0.02
86 41 0.33
87 59 0.47
88 24 0.19
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (87 bp):
AATAATTTTGAAATTAAGGTTAATAATTTTTTAATATTATTATTTTAATAATTCTGATAATTTAT
TATTTTTATGCTTAAATTTTTT
Found at i:13877432 original size:33 final size:33
Alignment explanation
Indices: 13877348--13877434 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
13877338 TGATGAACTC
* *
13877348 GAGCCAGGTGGAGTAGAGAACGGCGCTGGATAT
1 GAGCCAGGAGGAGTAGAGTACGGCGCTGGATAT
* * *
13877381 GGGCCAGGAGGAGTAGAGTACGGTGGTGGATAT
1 GAGCCAGGAGGAGTAGAGTACGGCGCTGGATAT
13877414 GAGCC-GGAAGGAGTAGAGTAC
1 GAGCCAGG-AGGAGTAGAGTAC
13877435 AGATGTGCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.28, C:0.13, G:0.45, T:0.15
Consensus pattern (33 bp):
GAGCCAGGAGGAGTAGAGTACGGCGCTGGATAT
Found at i:13881816 original size:21 final size:20
Alignment explanation
Indices: 13881774--13881833 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
13881764 AACTTATTTA
* **
13881774 TATTTTAATTAATCATGTTT
1 TATTTTAATTAATCTTAATT
13881794 TAGTTTTAATTAATCTTAATT
1 TA-TTTTAATTAATCTTAATT
* *
13881815 TA-CTTAATTAAGCTTAATT
1 TATTTTAATTAATCTTAATT
13881834 ATTAATTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTTAATTAATCTTAATT
Found at i:13884813 original size:27 final size:27
Alignment explanation
Indices: 13884775--13884829 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13884765 GAACAAGCTG
13884775 CGAGTCATGGTTATCTTCCTCCGCTTT
1 CGAGTCATGGTTATCTTCCTCCGCTTT
13884802 CGAGTCATGGTTATCTTCCTCCGCTTT
1 CGAGTCATGGTTATCTTCCTCCGCTTT
13884829 C
1 C
13884830 TTTACAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.31, G:0.18, T:0.40
Consensus pattern (27 bp):
CGAGTCATGGTTATCTTCCTCCGCTTT
Found at i:13886333 original size:46 final size:46
Alignment explanation
Indices: 13886280--13886455 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
13886270 TATTTGGGCA
* *
13886280 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
13886326 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
13886373 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
13886419 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13886456 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:13886429 original size:93 final size:93
Alignment explanation
Indices: 13886276--13886447 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
13886266 GGGATATTTG
* * *
13886276 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
13886341 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
13886369 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
13886434 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
13886448 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:13887691 original size:74 final size:77
Alignment explanation
Indices: 13887585--13887731 Score: 176
Period size: 77 Copynumber: 1.9 Consensus size: 77
13887575 AGAAGATTCT
* * * * * *
13887585 ACAAGTGCTAAAGAGATGGGTAAGACTTTGGA-GA-T-GAACATTGAATTGTTACCAAAGCTTAT
1 ACAAGTCCTAAAGAGATGGGTAAGAATATGGAGGAGTGGAACATCGAATTGATACCAAAGCGTAT
13887647 AGAAGATGTAGA
66 AGAAGATGTAGA
* * *
13887659 ACAAGTCCTAAAGAGATGGGT-CGTAATATGGAGGAGTGGAGCATCGAATTGATATCAAAGCGTA
1 ACAAGTCCTAAAGAGATGGGTAAG-AATATGGAGGAGTGGAACATCGAATTGATACCAAAGCGTA
13887723 TAGAAGATG
65 TAGAAGATG
13887732 CTCCGAGTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
73 1 0.02
74 26 0.43
75 2 0.03
76 1 0.02
77 30 0.50
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.24
Consensus pattern (77 bp):
ACAAGTCCTAAAGAGATGGGTAAGAATATGGAGGAGTGGAACATCGAATTGATACCAAAGCGTAT
AGAAGATGTAGA
Found at i:13889728 original size:12 final size:13
Alignment explanation
Indices: 13889711--13889740 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
13889701 TTCTCATGTA
13889711 TATATTATTAT-T
1 TATATTATTATAT
13889723 TATATTATTATAT
1 TATATTATTATAT
13889736 TATAT
1 TATAT
13889741 ATACCCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTATTATAT
Found at i:13889832 original size:6 final size:6
Alignment explanation
Indices: 13889821--13889853 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
13889811 ACTATTATTA
*
13889821 TATATG TATATG TATATG TATATA TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TAT
13889854 TATTGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:13890084 original size:3 final size:3
Alignment explanation
Indices: 13890076--13890114 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13890066 TTTGTATTTC
13890076 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13890115 ATAATAGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13896778 original size:16 final size:17
Alignment explanation
Indices: 13896745--13896783 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
13896735 AACTTAAATC
13896745 TTTTAAGATTTAGATAA
1 TTTTAAGATTTAGATAA
13896762 TTTTAA-ATTT-GAGTAA
1 TTTTAAGATTTAGA-TAA
13896778 TTTTAA
1 TTTTAA
13896784 CTTCAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (17 bp):
TTTTAAGATTTAGATAA
Found at i:13897581 original size:21 final size:22
Alignment explanation
Indices: 13897538--13897593 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
13897528 AAAGTATATT
* *
13897538 TTAAATATTT-AAATATAACTA
1 TTAAATATTTGTAATATAAATA
13897559 TTAAATATTTGTAAT-TAAATA
1 TTAAATATTTGTAATATAAATA
*
13897580 TTAACACATTTGTA
1 TTAA-ATATTTGTA
13897594 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (22 bp):
TTAAATATTTGTAATATAAATA
Found at i:13909460 original size:15 final size:16
Alignment explanation
Indices: 13909434--13909463 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13909424 TCATAACAAT
13909434 TTTATCATTTTTATAG
1 TTTATCATTTTTATAG
13909450 TTTAT-ATTTTTATA
1 TTTATCATTTTTATA
13909464 ACTTTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTATCATTTTTATAG
Found at i:13911440 original size:2 final size:2
Alignment explanation
Indices: 13911433--13911466 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13911423 AATCATTTAC
13911433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13911467 GTAAATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13918660 original size:31 final size:31
Alignment explanation
Indices: 13918625--13918693 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
13918615 GTTAACAAAC
13918625 CAATGACTTAAATAAAAACTTTTGAATAATT
1 CAATGACTTAAATAAAAACTTTTGAATAATT
* *
13918656 CAATGACTTAAATGAAAACTTTTGAATAGTT
1 CAATGACTTAAATAAAAACTTTTGAATAATT
13918687 CAATGAC
1 CAATGAC
13918694 CAAATTGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTTTTGAATAATT
Found at i:13923815 original size:29 final size:29
Alignment explanation
Indices: 13923781--13923862 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
13923771 AACCTAGTGA
13923781 AATTTTAGCTCGGACGAGCAACCTTGTAT
1 AATTTTAGCTCGGACGAGCAACCTTGTAT
* *
13923810 ACTTTTAGC-CTGGACTGA-CAACCTTGTGT
1 AATTTTAGCTC-GGAC-GAGCAACCTTGTAT
* *
13923839 AATTTTAGCTTGGACAAGCAACCT
1 AATTTTAGCTCGGACGAGCAACCT
13923863 AGTGTGGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 2 0.05
29 40 0.91
30 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (29 bp):
AATTTTAGCTCGGACGAGCAACCTTGTAT
Found at i:13923867 original size:29 final size:28
Alignment explanation
Indices: 13923771--13923867 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 28
13923761 CTAGTAACCT
* *
13923771 AACCTAGTGAAATTTTAGCTCGGACGAGC
1 AACCTAGTGTAATTTTAGCTTGGAC-AGC
* * * * *
13923800 AACCTTGTATACTTTTAGCCTGGACTGAC
1 AACCTAGTGTAATTTTAGCTTGGACAG-C
*
13923829 AACCTTGTGTAATTTTAGCTTGGACAAGC
1 AACCTAGTGTAATTTTAGCTTGGAC-AGC
13923858 AACCTAGTGT
1 AACCTAGTGT
13923868 GGTGTAGTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
28 1 0.02
29 52 0.96
30 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (28 bp):
AACCTAGTGTAATTTTAGCTTGGACAGC
Found at i:13924925 original size:32 final size:32
Alignment explanation
Indices: 13924868--13924930 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
13924858 AAACTATAAT
13924868 AACAAATAATAATGTATAAACATATAAATATC
1 AACAAATAATAATGTATAAACATATAAATATC
* * * * *
13924900 AACATATAATAATTTATTAATATATATATAT
1 AACAAATAATAATGTATAAACATATAAATAT
13924931 ATATTAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (32 bp):
AACAAATAATAATGTATAAACATATAAATATC
Found at i:13925232 original size:23 final size:23
Alignment explanation
Indices: 13925199--13925263 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
13925189 ATGCAGCAAA
*
13925199 AATCCAACCAAACACACCAAAAT
1 AATCCACCCAAACACACCAAAAT
13925222 AATCCACCCAAACACACCAAAAT
1 AATCCACCCAAACACACCAAAAT
*
13925245 AATCCACCTAAACACACCA
1 AATCCACCCAAACACACCA
13925264 GAACAGCACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.09
Consensus pattern (23 bp):
AATCCACCCAAACACACCAAAAT
Found at i:13925464 original size:24 final size:24
Alignment explanation
Indices: 13925416--13925470 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
13925406 TATTCAATTT
13925416 TCATA-TTTCAATTCAATCACTTTC
1 TCATATTTTCAATTCAATCAC-TTC
*
13925440 TCATATTTTCCATTCAAATCA-TTC
1 TCATATTTTCAATTC-AATCACTTC
13925464 TCA-ATTT
1 TCATATTT
13925471 AATCACAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 11 0.39
25 8 0.29
26 5 0.18
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (24 bp):
TCATATTTTCAATTCAATCACTTC
Found at i:13926269 original size:16 final size:16
Alignment explanation
Indices: 13926250--13926280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13926240 TTAGTCTCTA
*
13926250 TTTCTTTTCTTCTTTG
1 TTTCTTTTATTCTTTG
13926266 TTTCTTTTATTCTTT
1 TTTCTTTTATTCTTT
13926281 TATTTATTTC
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:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTTATTCTTTG
Found at i:13926328 original size:3 final size:3
Alignment explanation
Indices: 13926305--13926356 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
13926295 ATGTATTAGT
*
13926305 TAA TAA -AA TTAA TAA -AA TAA TAA TAA TAA TACA TTA TAA TAA T-A
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
13926349 TAA TAA TA
1 TAA TAA TA
13926357 TTTAATTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 6 0.14
3 32 0.76
4 4 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:13926355 original size:8 final size:8
Alignment explanation
Indices: 13926314--13926357 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
13926304 TTAATAAAAT
*
13926314 TAATAAAA
1 TAATAATA
13926322 TAATAATAA
1 TAATAAT-A
13926331 TAATACATTA
1 TAATA-A-TA
13926341 TAATAATA
1 TAATAATA
13926349 TAATAATA
1 TAATAATA
13926357 T
1 T
13926358 TTAATTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 17 0.53
9 7 0.22
10 7 0.22
11 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
TAATAATA
Found at i:13931819 original size:21 final size:21
Alignment explanation
Indices: 13931795--13931836 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13931785 CTTAGCATAA
13931795 CCATTTT-TTTTCTTTCTTCTT
1 CCATTTTCTTTTCTTT-TTCTT
13931816 CCATTTTCTTTTCTTTTTCTT
1 CCATTTTCTTTTCTTTTTCTT
13931837 TTTTCTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (21 bp):
CCATTTTCTTTTCTTTTTCTT
Found at i:13931840 original size:18 final size:18
Alignment explanation
Indices: 13931800--13931843 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
13931790 CATAACCATT
13931800 TTTTTTC-TTTCTTCTTC
1 TTTTTTCTTTTCTTCTTC
** *
13931817 CATTTTCTTTTCTTTTTC
1 TTTTTTCTTTTCTTCTTC
13931835 TTTTTTCTT
1 TTTTTTCTT
13931844 CACATTCTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTTTCTTCTTC
Found at i:13931851 original size:27 final size:27
Alignment explanation
Indices: 13931801--13931857 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
13931791 ATAACCATTT
13931801 TTTTTCTTTCTTCTTCCATTTTCTTTTC
1 TTTTTCTTTCTTCTTCCA-TTTCTTTTC
*
13931829 TTTTTCTTTTTTCTTCACA-TTCTTTTC
1 TTTTTCTTTCTTCTTC-CATTTCTTTTC
13931856 TT
1 TT
13931858 GTGTCTGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.37
28 15 0.56
29 2 0.07
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTCTTTCTTCTTCCATTTCTTTTC
Found at i:13936765 original size:26 final size:26
Alignment explanation
Indices: 13936735--13936837 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 26
13936725 TGAAATTCCC
13936735 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
13936761 ATCATGGAACATTTACCT-A---A-T
1 ATCATGGAACATTTACCTAACCCATT
**
13936782 ATCATAAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
13936808 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
13936834 ATCA
1 ATCA
13936838 ATTTGTATTA
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
21 17 0.25
22 2 0.03
25 2 0.03
26 47 0.69
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:13941808 original size:19 final size:20
Alignment explanation
Indices: 13941786--13941824 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
13941776 GAATTTAATG
13941786 TTAAAATTATA-TTTT-AACT
1 TTAAAA-TATAGTTTTGAACT
13941805 TTAAAATATAGTTTTGAACT
1 TTAAAATATAGTTTTGAACT
13941825 CAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAAATATAGTTTTGAACT
Found at i:13951382 original size:93 final size:93
Alignment explanation
Indices: 13951218--13951386 Score: 214
Period size: 93 Copynumber: 1.8 Consensus size: 93
13951208 TCTCAAACTC
* * * *
13951218 AAAACAAAGTCTAAGTAGAAATGGTAATTTTTCGGATAATAAAAATACTATCAGTTGTAGATGCG
1 AAAACAAAGTCTAAGTAGAAATGGTAATTTTTCGAATAATAAAAATACTATCAGATGCAGATGCA
*
13951283 GTTTTAACCCCATGAATAATGGATAGTA
66 GATTTAACCCCATGAATAATGGATAGTA
* * * * * * *
13951311 AAAATAAAGTCTAGGTAGAGATGAG-AATTTTTCGAATAGTAAAAATATTATCTGATGCGGATGC
1 AAAACAAAGTCTAAGTAGAAATG-GTAATTTTTCGAATAATAAAAATACTATCAGATGCAGATGC
13951375 AGATTTAACCCC
65 AGATTTAACCCC
13951387 TTAAATATCT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
93 62 0.98
94 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (93 bp):
AAAACAAAGTCTAAGTAGAAATGGTAATTTTTCGAATAATAAAAATACTATCAGATGCAGATGCA
GATTTAACCCCATGAATAATGGATAGTA
Found at i:13952964 original size:7 final size:7
Alignment explanation
Indices: 13952954--13952983 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
13952944 ATTATTTTTA
13952954 ATTTAAT
1 ATTTAAT
13952961 ATTTAAT
1 ATTTAAT
13952968 ATTTAAT
1 ATTTAAT
13952975 ATTTAAT
1 ATTTAAT
13952982 AT
1 AT
13952984 AGTTGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTAAT
Found at i:13957611 original size:19 final size:19
Alignment explanation
Indices: 13957589--13957629 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13957579 AGAAAAAAAA
13957589 AAGAAAAA-AGCATAAGTTT
1 AAGAAAAAGAGCATAA-TTT
*
13957608 AAGAAAAAGAGTATAATTT
1 AAGAAAAAGAGCATAATTT
13957627 AAG
1 AAG
13957630 TACTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.59, C:0.02, G:0.17, T:0.22
Consensus pattern (19 bp):
AAGAAAAAGAGCATAATTT
Found at i:13957994 original size:13 final size:13
Alignment explanation
Indices: 13957962--13958011 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
13957952 ATGTAAATAA
13957962 AAAATAA-ATTTT
1 AAAATAATATTTT
*
13957974 -ATATAATATTTT
1 AAAATAATATTTT
*
13957986 AAAATAATATTGT
1 AAAATAATATTTT
*
13957999 AAAA-ATTATTTT
1 AAAATAATATTTT
13958011 A
1 A
13958012 CTAATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 5 0.16
12 12 0.39
13 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
AAAATAATATTTT
Found at i:13964571 original size:40 final size:39
Alignment explanation
Indices: 13964421--13964573 Score: 243
Period size: 39 Copynumber: 3.9 Consensus size: 39
13964411 TAATGTTCGA
* *
13964421 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
13964460 GTGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
13964499 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
13964538 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
13964574 GGTTACCATA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:13964589 original size:40 final size:39
Alignment explanation
Indices: 13964422--13964604 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
13964412 AATGTTCGAG
* * *
13964422 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
13964461 TGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
13964500 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
13964539 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
13964579 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
13964605 GTTTGAACGA
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 87 0.68
40 41 0.32
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:13964640 original size:79 final size:79
Alignment explanation
Indices: 13964428--13964642 Score: 177
Period size: 78 Copynumber: 2.7 Consensus size: 79
13964418 CGAGTGATAT
** * * * * * *
13964428 CCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGACATCCGGGCT-AA-GCCCGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCC-GGATAAACTCCCGAAGGCAATTG
** *
13964491 TGCGAGTTATGATAT
65 TGCGAGTTACCATAA
** * * * * *
13964506 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT
*
13964571 GCGGGTTACCATAA
66 GCGAGTTACCATAA
* **
13964585 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCCGGATAAACT-CCGAAGG
1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGGATAAACTCCCGAAGG
13964643 TATGTGATTC
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
77 3 0.03
78 40 0.35
79 40 0.35
80 30 0.26
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT
GCGAGTTACCATAA
Found at i:13972583 original size:40 final size:39
Alignment explanation
Indices: 13972433--13972585 Score: 243
Period size: 39 Copynumber: 3.9 Consensus size: 39
13972423 AAATGTTCGA
* *
13972433 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
13972472 GTGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
*
13972511 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
* *
13972550 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
13972586 GGTTACCATA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
Found at i:13972601 original size:40 final size:39
Alignment explanation
Indices: 13972434--13972616 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
13972424 AATGTTCGAG
* * *
13972434 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
13972473 TGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
13972512 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
13972551 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
13972591 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
13972617 GTTTGAACGA
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 87 0.68
40 41 0.32
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:13972652 original size:79 final size:79
Alignment explanation
Indices: 13972440--13972654 Score: 177
Period size: 78 Copynumber: 2.7 Consensus size: 79
13972430 CGAGTGATAT
** * * * * * *
13972440 CCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGACATCCGGGCT-AA-GCCCGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCC-GGATAAACTCCCGAAGGCAATTG
** *
13972503 TGCGAGTTATGATAT
65 TGCGAGTTACCATAA
** * * * * *
13972518 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT
*
13972583 GCGGGTTACCATAA
66 GCGAGTTACCATAA
* **
13972597 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCCGGATAAACT-CCGAAGG
1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGGATAAACTCCCGAAGG
13972655 TATGTGATTC
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
77 3 0.03
78 40 0.35
79 40 0.35
80 30 0.26
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT
GCGAGTTACCATAA
Found at i:13974403 original size:20 final size:21
Alignment explanation
Indices: 13974373--13974413 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
13974363 TTTAATCATG
*
13974373 TAAATATATATAATTTAATTA
1 TAAATATATATAATTAAATTA
*
13974394 TAAA-ATATATTATTAAATTA
1 TAAATATATATAATTAAATTA
13974414 ATTAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATATATATAATTAAATTA
Found at i:13974441 original size:25 final size:27
Alignment explanation
Indices: 13974387--13974443 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
13974377 TATATATAAT
*
13974387 TTAATTATAAAATATATTATTAAATTAA
1 TTAATTATAAAATATATTATT-AATGAA
13974415 TTAATTAT-AAATATCA-TATT-ATGAA
1 TTAATTATAAAATAT-ATTATTAATGAA
13974440 TTAA
1 TTAA
13974444 ATTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.30
27 10 0.37
28 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATTATAAAATATATTATTAATGAA
Found at i:13974620 original size:20 final size:20
Alignment explanation
Indices: 13974564--13974626 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
13974554 ATTATTTATC
* *
13974564 ATTATTATTATTATTCTATCAA
1 ATTATAATTATTA-T-TATTAA
13974586 ATTATAATT-TATATTATTAA
1 ATTATAATTAT-TATTATTAA
*
13974606 ATTATGATTATTATTATTAA
1 ATTATAATTATTATTATTAA
13974626 A
1 A
13974627 AATAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 23 0.64
21 3 0.08
22 10 0.28
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATAATTATTATTATTAA
Found at i:13980714 original size:38 final size:39
Alignment explanation
Indices: 13980662--13980811 Score: 241
Period size: 38 Copynumber: 3.9 Consensus size: 39
13980652 AATGTTCGAG
13980662 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
13980701 TGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
13980739 TGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
13980777 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
13980812 GGTTACCATA
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
38 74 0.70
39 14 0.13
40 17 0.16
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
Found at i:13984221 original size:13 final size:12
Alignment explanation
Indices: 13984195--13984236 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
13984185 CTTAATTTAT
*
13984195 CTAACAAAAATC
1 CTAATAAAAATC
13984207 CTAATAAAAATTC
1 CTAATAAAAA-TC
13984220 CTAATAGAAAATC
1 CTAATA-AAAATC
13984233 CTAA
1 CTAA
13984237 GTAGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.33
13 14 0.52
14 4 0.15
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (12 bp):
CTAATAAAAATC
Found at i:13984241 original size:14 final size:13
Alignment explanation
Indices: 13984201--13984241 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
13984191 TTATCTAACA
13984201 AAAATCCTAATA-
1 AAAATCCTAATAG
13984213 AAAATTCCTAATAG
1 AAAA-TCCTAATAG
13984227 AAAATCCTAAGTAG
1 AAAATCCTAA-TAG
13984241 A
1 A
13984242 TAAAAATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 14 0.54
14 8 0.31
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (13 bp):
AAAATCCTAATAG
Found at i:13985412 original size:44 final size:42
Alignment explanation
Indices: 13985347--13985495 Score: 156
Period size: 43 Copynumber: 3.5 Consensus size: 42
13985337 ATATGTGTTA
* *
13985347 TCGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTATGATT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATCGTA-TT-TGATT
* *
13985390 TACGTGTAAGACCATGTTTGGGATATTGGCATCGTATTTGATT
1 T-CGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATT
* * * *
13985433 TCGTGTAAGACCCTGTCTGGGACAATGGCATCAATGTTTGATT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATC-GTATTTGATT
* * *
13985476 ACATGTAAGACCACGTCTGG
1 TCGTGTAAGACCATGTCTGG
13985496 AAAGTTGGCA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
42 27 0.30
43 31 0.35
44 30 0.34
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATT
Found at i:13988115 original size:61 final size:61
Alignment explanation
Indices: 13988014--13988140 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 61
13988004 TGAGAAATTG
* * * *
13988014 ACACGGCCTGGACTTCCGTACACGGGTAGACTACATGCCCGTGTACT-TTCAGCAGACTCTA
1 ACACGGCCTAGACTTCCGTACACGGGTAGACCACACGCCCGTG-ACTATTCAACAGACTCTA
* *
13988075 ACACGGCCTAGACCTT-CTTACACGGGTAGACCACACGCCCGTGGCTATTCAACAGACTCTA
1 ACACGGCCTAGA-CTTCCGTACACGGGTAGACCACACGCCCGTGACTATTCAACAGACTCTA
13988136 ACACG
1 ACACG
13988141 ATTTGAAGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 2 0.03
61 53 0.91
62 3 0.05
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.20
Consensus pattern (61 bp):
ACACGGCCTAGACTTCCGTACACGGGTAGACCACACGCCCGTGACTATTCAACAGACTCTA
Found at i:13995771 original size:6 final size:6
Alignment explanation
Indices: 13995760--13995800 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
13995750 TATTTTACTA
* *
13995760 TTATTT TTATTT TTATTT TTATTT TTGTTT CTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
13995801 CAAATTCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:13997679 original size:61 final size:60
Alignment explanation
Indices: 13997551--13997679 Score: 174
Period size: 61 Copynumber: 2.1 Consensus size: 60
13997541 CATGAGAAAT
*
13997551 TGACACGGCCTGGACTTCTGTACACGGGTAGACCACACGCTCGTGTAGTTTCGACAGACTC
1 TGACACGGCCTGGACTTCTGTACACGGGTAGACCACACGCCCGTGTAG-TTCGACAGACTC
*
13997612 TAACACGGCCTGGACCTTCT-TACACGGGTAGACCACACGCCCGTGGCTA-TTC-ATCAGACTC
1 TGACACGGCCTGGA-CTTCTGTACACGGGTAGACCACACGCCCGT-G-TAGTTCGA-CAGACTC
13997673 TGACACG
1 TGACACG
13997680 ATTTGAAGCA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
60 1 0.02
61 52 0.85
62 6 0.10
63 2 0.03
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (60 bp):
TGACACGGCCTGGACTTCTGTACACGGGTAGACCACACGCCCGTGTAGTTCGACAGACTC
Found at i:14003179 original size:43 final size:42
Alignment explanation
Indices: 14003078--14003181 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
14003068 ATGATTTATG
* * * *
14003078 TGTAAGACCATGTCTGGGATATTGGCATCGTATTTGATTTCG
1 TGTAAGACCACGTCTGGGATAGTGGCATCGTATTTGATTACA
* * * *
14003120 TGTAAAACC-CTATCTGGTATAGTGGCATCGATGTTTGATTACA
1 TGTAAGACCAC-GTCTGGGATAGTGGCATCG-TATTTGATTACA
14003163 TGTAAGACCACGTCTGGGA
1 TGTAAGACCACGTCTGGGA
14003182 CGTTAGCTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
42 24 0.50
43 23 0.48
44 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGATAGTGGCATCGTATTTGATTACA
Found at i:14003657 original size:22 final size:22
Alignment explanation
Indices: 14003603--14003657 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
14003593 GAACAGTACC
* * *
14003603 ACACGTCCGTGTGGCTAATTTA
1 ACACGCCCGTGCGGCTAATATA
*
14003625 ACATGCCCGTGCGGCTAATATA
1 ACACGCCCGTGCGGCTAATATA
*
14003647 ACACGCTCGTG
1 ACACGCCCGTG
14003658 TCCTCAACCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (22 bp):
ACACGCCCGTGCGGCTAATATA
Found at i:14006878 original size:18 final size:18
Alignment explanation
Indices: 14006857--14006906 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
14006847 TCAGCAATAT
* *
14006857 TCATTTATTCAGTATCAG
1 TCATTTATTCAGTAACAA
*
14006875 TCATTTATTCTGTAACAA
1 TCATTTATTCAGTAACAA
*
14006893 TCAATTATTCAGTA
1 TCATTTATTCAGTA
14006907 GCAGACAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (18 bp):
TCATTTATTCAGTAACAA
Found at i:14007054 original size:6 final size:6
Alignment explanation
Indices: 14007038--14007070 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
14007028 CACCATAAGG
*
14007038 GTAACA ATAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
14007071 GTGGTACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:14007877 original size:3 final size:3
Alignment explanation
Indices: 14007808--14007863 Score: 94
Period size: 3 Copynumber: 18.0 Consensus size: 3
14007798 TTTGTTTTAT
14007808 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACTTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA
14007858 ATA ATA
1 ATA ATA
14007864 TACTTATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 48 0.94
5 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:14009638 original size:15 final size:15
Alignment explanation
Indices: 14009618--14009649 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
14009608 TTGTGGATGA
14009618 TGATATTGAATTGTT
1 TGATATTGAATTGTT
14009633 TGATATTGAATTGTT
1 TGATATTGAATTGTT
14009648 TG
1 TG
14009650 CAAATTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (15 bp):
TGATATTGAATTGTT
Found at i:14026159 original size:59 final size:59
Alignment explanation
Indices: 14026072--14026187 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 59
14026062 TATGTAATAC
14026072 TAAAGAAGGTATTAATTGGGTGTAAAAAACTGAAGAAAAATACATAAAGAAGTCTATAT
1 TAAAGAAGGTATTAATTGGGTGTAAAAAACTGAAGAAAAATACATAAAGAAGTCTATAT
*
14026131 TAAAGAAGGTATTAAATTGGGTGTAAAAAATTGAAGAAAAATACATAAAGAAGTCTA
1 TAAAGAAGGTATT-AATTGGGTGTAAAAAACTGAAGAAAAATACATAAAGAAGTCTA
14026188 GTTCTTTCGG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 13 0.24
60 42 0.76
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (59 bp):
TAAAGAAGGTATTAATTGGGTGTAAAAAACTGAAGAAAAATACATAAAGAAGTCTATAT
Found at i:14027080 original size:28 final size:28
Alignment explanation
Indices: 14027040--14027095 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
14027030 TTTGTTTACA
14027040 TGTAAATAAGTCATTTTTCCTGTAAAAT
1 TGTAAATAAGTCATTTTTCCTGTAAAAT
14027068 TGTAAATAAGTCATTTTTCCTGTAAAAT
1 TGTAAATAAGTCATTTTTCCTGTAAAAT
14027096 GACTTACCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (28 bp):
TGTAAATAAGTCATTTTTCCTGTAAAAT
Found at i:14027329 original size:22 final size:22
Alignment explanation
Indices: 14027304--14027345 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
14027294 TAGTCATATA
14027304 ATAAATTATTAATATAATAAGT
1 ATAAATTATTAATATAATAAGT
* * *
14027326 ATAATTTATTATTTTAATAA
1 ATAAATTATTAATATAATAA
14027346 ATTATTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAGT
Found at i:14028669 original size:30 final size:31
Alignment explanation
Indices: 14028633--14028699 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
14028623 GTTTGAATTT
14028633 AGTCACTCAAC-TT-TCAAAAAATAACAAATC
1 AGTCACT-AACGTTCTCAAAAAATAACAAATC
* *
14028663 AGTCACTAACGTTCTCAAAAAGTGACAAATC
1 AGTCACTAACGTTCTCAAAAAATAACAAATC
14028694 AGTCAC
1 AGTCAC
14028700 CCATTAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (31 bp):
AGTCACTAACGTTCTCAAAAAATAACAAATC
Found at i:14029480 original size:18 final size:19
Alignment explanation
Indices: 14029453--14029490 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
14029443 AAATCTTACA
14029453 ACAAAGTGAAATG-TAAAAT
1 ACAAAGTGAAA-GCTAAAAT
14029472 ACAAA-TGAAAGCTAAAAT
1 ACAAAGTGAAAGCTAAAAT
14029490 A
1 A
14029491 GGAATCACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 12 0.67
19 5 0.28
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (19 bp):
ACAAAGTGAAAGCTAAAAT
Found at i:14029529 original size:3 final size:3
Alignment explanation
Indices: 14029521--14029562 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
14029511 CATTTTTTCT
*
14029521 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTT TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
14029563 ATTGCCTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:14032408 original size:14 final size:14
Alignment explanation
Indices: 14032370--14032404 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
14032360 AATAATTTAA
14032370 TTTAAAAA-ATTGT
1 TTTAAAAATATTGT
14032383 TTTAAAAATATT-T
1 TTTAAAAATATTGT
14032396 TTTAAAAAT
1 TTTAAAAAT
14032405 TATTAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 18 0.86
14 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTTAAAAATATTGT
Found at i:14039440 original size:43 final size:43
Alignment explanation
Indices: 14039376--14039498 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
14039366 ATCAAGATGT
* * *
14039376 GATTACATGTAAGA-CACTGTGTGGGACAGTGGCATTG-TATTGC
1 GATTACGTGTAAGACCA-TGTGTGGGACAGTGGCATCGTTAAT-C
*
14039419 GATTACGTGTAAGACCATGTGTGGGACATTGGCATCGTTAATC
1 GATTACGTGTAAGACCATGTGTGGGACAGTGGCATCGTTAATC
* *
14039462 GACTT-CGTGTAAGACCGTGTGTGGGACAGTGGTATCG
1 GA-TTACGTGTAAGACCATGTGTGGGACAGTGGCATCG
14039499 ATATGTGATA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
43 63 0.90
44 7 0.10
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTGTGGGACAGTGGCATCGTTAATC
Found at i:14039516 original size:43 final size:41
Alignment explanation
Indices: 14039376--14039520 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 41
14039366 ATCAAGATGT
*
14039376 GATTACATGTAAGACACTGTGTGGGACAGTGGCATTGTATTGC
1 GATTACATGTAAGAC-CTGTGTGGGACAGTGGCATCGTA-TGC
* *
14039419 GATTACGTGTAAGACCATGTGTGGGACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACC-TGTGTGGGACAGTGGCATCG-T-ATGC
* * *
14039462 GACTT-CGTGTAAGACCGTGTGTGGGACAGTGGTATCGATATGT
1 GA-TTACATGTAAGACC-TGTGTGGGACAGTGGCATCG-TATGC
*
14039505 GATAACATGTAAGACC
1 GATTACATGTAAGACC
14039521 ATATCTAGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
42 4 0.05
43 77 0.90
44 4 0.05
45 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (41 bp):
GATTACATGTAAGACCTGTGTGGGACAGTGGCATCGTATGC
Found at i:14042320 original size:2 final size:2
Alignment explanation
Indices: 14042302--14042370 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
14042292 TACAATATTT
* *
14042302 CA CA CA TA CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
14042344 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
14042371 TCTCTCTCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.48, G:0.01, T:0.01
Consensus pattern (2 bp):
CA
Found at i:14042375 original size:2 final size:2
Alignment explanation
Indices: 14042370--14042407 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14042360 CACACACACA
14042370 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
14042408 ATATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14042412 original size:2 final size:2
Alignment explanation
Indices: 14042407--14042444 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14042397 TCTCTCTCTC
14042407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14042445 CATGTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14045194 original size:31 final size:31
Alignment explanation
Indices: 14045115--14045195 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
14045105 GGTCATTTAG
* * *
14045115 TTAAAAAAGTTACAATTT-AGTCATTAAACTA
1 TTAAAAAATTTTC-ATTTAAGTCACTAAACTA
* *
14045146 TTCAAAAGTTTTCATTTAAGTCACTAAACTA
1 TTAAAAAATTTTCATTTAAGTCACTAAACTA
14045177 TTTAAAAAATTTT-ATTTAA
1 -TTAAAAAATTTTCATTTAA
14045196 ATTACTGGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 4 0.10
31 27 0.66
32 10 0.24
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
TTAAAAAATTTTCATTTAAGTCACTAAACTA
Found at i:14047351 original size:6 final size:6
Alignment explanation
Indices: 14047340--14047364 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14047330 CGCCAAGAAG
14047340 CAAAGC CAAAGC CAAAGC CAAAGC C
1 CAAAGC CAAAGC CAAAGC CAAAGC C
14047365 TCCCACCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.16, T:0.00
Consensus pattern (6 bp):
CAAAGC
Found at i:14053435 original size:25 final size:24
Alignment explanation
Indices: 14053392--14053550 Score: 104
Period size: 25 Copynumber: 6.4 Consensus size: 24
14053382 ATGGCTCCAC
* *
14053392 GAGCTTCCCGATATTTGGCTCTTAT
1 GAGCTTCCCGTTA-ATGGCTCTTAT
* *
14053417 GAGTTTCCTGATTAATGGCTCTCT-T
1 GAGCTTCCCG-TTAATGGCTCT-TAT
* *
14053442 GAGCTTCCCGTTTATGGCTCGTAT
1 GAGCTTCCCGTTAATGGCTCTTAT
** * *
14053466 GAGCTTCCCAATAATTGGCTCGTAA
1 GAGCTTCCCGTTAA-TGGCTCTTAT
* **
14053491 GAGCTTCTCGTTATATGGCTCACAT
1 GAGCTTCCCGTTA-ATGGCTCTTAT
* ** *
14053516 GAGCTTTCCGTTACATGGCTCAAAA
1 GAGCTTCCCGTTA-ATGGCTCTTAT
14053541 GAGCTTCCCG
1 GAGCTTCCCG
14053551 ATTATTTTCT
Statistics
Matches: 105, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 21 0.20
25 79 0.75
26 4 0.04
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCTTAT
Found at i:14053485 original size:49 final size:49
Alignment explanation
Indices: 14053392--14053521 Score: 113
Period size: 49 Copynumber: 2.6 Consensus size: 49
14053382 ATGGCTCCAC
* * * * **
14053392 GAGCTTCCCGATATT-TGGCTCTTATGAGTTTCCTGATTAATGGCTC-TCTT
1 GAGCTTCCCG-T-TTATGGCTCATATGAGCTTCCTCAATAATGGCTCGT-AA
*
14053442 GAGCTTCCCGTTTATGGCTCGTATGAGCTTCC-CAATAATTGGCTCGTAA
1 GAGCTTCCCGTTTATGGCTCATATGAGCTTCCTCAATAA-TGGCTCGTAA
* *
14053491 GAGCTTCTCGTTATATGGCTCACATGAGCTT
1 GAGCTTCCCGTT-TATGGCTCATATGAGCTT
14053522 TCCGTTACAT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
48 6 0.09
49 34 0.51
50 27 0.40
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (49 bp):
GAGCTTCCCGTTTATGGCTCATATGAGCTTCCTCAATAATGGCTCGTAA
Found at i:14053509 original size:74 final size:75
Alignment explanation
Indices: 14053392--14053536 Score: 170
Period size: 74 Copynumber: 1.9 Consensus size: 75
14053382 ATGGCTCCAC
* * * * * * * *
14053392 GAGCTTCCCGATATTTGGCTCTTATGAGTTTCCTGATTAATGGCTCTCTTGAGCTTCCCGTT-TA
1 GAGCTTCCCAATAATTGGCTCGTAAGAGCTTCCTGATTAATGGCTCACATGAGCTTCCCGTTACA
14053456 TGGCTCGTAT
66 TGGCTCGTAT
*
14053466 GAGCTTCCCAATAATTGGCTCGTAAGAGCTT-CTCG-TTATATGGCTCACATGAGCTTTCCGTTA
1 GAGCTTCCCAATAATTGGCTCGTAAGAGCTTCCT-GATTA-ATGGCTCACATGAGCTTCCCGTTA
14053529 CATGGCTC
64 CATGGCTC
14053537 AAAAGAGCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
73 5 0.08
74 47 0.80
75 7 0.12
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (75 bp):
GAGCTTCCCAATAATTGGCTCGTAAGAGCTTCCTGATTAATGGCTCACATGAGCTTCCCGTTACA
TGGCTCGTAT
Found at i:14053535 original size:50 final size:49
Alignment explanation
Indices: 14053442--14053555 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 49
14053432 TGGCTCTCTT
** **
14053442 GAGCTTCCCGTTTATGGCTCGTATGAGCTTCCCAATAATTGGCTCGTAA
1 GAGCTTCCCGTTTATGGCTCACATGAGCTTCCCAATAATTGGCTCAAAA
* * **
14053491 GAGCTTCTCGTTATATGGCTCACATGAGCTTTCCGTTACA-TGGCTCAAAA
1 GAGCTTCCCGTT-TATGGCTCACATGAGCTTCCCAATA-ATTGGCTCAAAA
*
14053541 GAGCTTCCCGATTAT
1 GAGCTTCCCGTTTAT
14053556 TTTCTCGTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 14 0.26
50 38 0.72
51 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (49 bp):
GAGCTTCCCGTTTATGGCTCACATGAGCTTCCCAATAATTGGCTCAAAA
Found at i:14058706 original size:30 final size:30
Alignment explanation
Indices: 14058650--14058707 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
14058640 CACGGCCATG
* *
14058650 ACACACGGGCGTGTGGTCTACTCGTGTGTC
1 ACACACGGGCGTATGGTCTACCCGTGTGTC
14058680 ACACACGGGCGTATGGATC-ACCCGTGTG
1 ACACACGGGCGTATGG-TCTACCCGTGTG
14058708 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (30 bp):
ACACACGGGCGTATGGTCTACCCGTGTGTC
Found at i:14060417 original size:2 final size:2
Alignment explanation
Indices: 14060410--14060457 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
14060400 TGGATATGCT
14060410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14060452 TA TA TA
1 TA TA TA
14060458 CATCCGAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14065181 original size:2 final size:2
Alignment explanation
Indices: 14065174--14065203 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14065164 AAAATGGTTC
14065174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14065204 TCAGCCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14068309 original size:17 final size:17
Alignment explanation
Indices: 14068289--14068323 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14068279 AATTTTAATT
**
14068289 ATAATAAAGTAAATAAA
1 ATAATAAAACAAATAAA
14068306 ATAATAAAACAAATAAA
1 ATAATAAAACAAATAAA
14068323 A
1 A
14068324 GGAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
ATAATAAAACAAATAAA
Found at i:14074301 original size:488 final size:488
Alignment explanation
Indices: 14073378--14074356 Score: 1602
Period size: 488 Copynumber: 2.0 Consensus size: 488
14073368 TCTGCCAAGG
*
14073378 TAACTCTGTGTTAACTCTCACTAAGTTCTTTTGAACTTAGTGTTATGTTTATGATTATGTTTCAG
1 TAACTCTATGTTAACTCTCACTAAGTTCTTTTGAACTTAGTGTTATGTTTATGATTATGTTTCAG
* * *
14073443 GTAGTATAGTATGAGCTTGCGCCAAGAGGGACGACGCCAAAACTATGCCAATGAGGCGACAAATT
66 GAAGTATAGTACGAGCTTGCGCCAAGAGGGACGACGCCAAAACTATGCCAAGGAGGCGACAAATT
* * *
14073508 GGGTTACTATACATATAATGGAAAAGTGGCGTATTGTAGGACTTTACCTTAAGAGTCAATTTTTA
131 GGGTTACTATACATACAATGAAAAAGTGGCGTATTGTAGGACTTTACATTAAGAGTCAATTTTTA
*
14073573 GTAAATGTTTGTATTTTAATGAATTGTAATTGGTCCGATGTAATATTTTATTTCTAAAATACTTT
196 GTAAATGTTTGTATTGTAATGAATTGTAATTGGTCCGATGTAATATTTTATTTCTAAAATACTTT
* * * *
14073638 CTGTTGTTTCTTTAATATTAAGTTTTTGAATGAAATAATAATGAAAAATGTTTTAAGTATAGAAT
261 CTATTGTGTCTTTAATATTAAGTTTTTAAATGAAATAATAATAAAAAATGTTTTAAGTATAGAAT
* * * *
14073703 GTCTGTTAACTGTTTTGAAATTTTGTTATATATTGTTTGTGTAACACCCAAGATCCGAACTTGAT
326 GTCTATCAACTATTTTGAAATTTTGTTATATATTGTTTGTATAACACCCAAGATCCGAACTTGAT
* * *
14073768 GAATCGGGTCGAATTGAGGGCGTTACAAAGACTACCTCATATGAAGAATACACAAAAGCTCAATT
391 GAATCGGGTCGAATTAAGGGCGTCACAAAGACTACCTCATATGAAGAATACACAAAAGCTCAACT
* *
14073833 AGACCAATAAGCAGGAGAGCCTTT-TCAAACTCA
456 AGACCAACAAGCAAGAGAG-CTTTCTCAAACTCA
* *
14073866 TAACTCTATGTTAACTCTCACTAAGTTCTTTTGAACTTAGTGTTATGTTTATGTTTATGTTTTAG
1 TAACTCTATGTTAACTCTCACTAAGTTCTTTTGAACTTAGTGTTATGTTTATGATTATGTTTCAG
* * *
14073931 GAAGTATAGTACGAGTTTGCGCTAAGAGGGACGACGCCAAGACTATGCCAAGGAGGCGACAAATT
66 GAAGTATAGTACGAGCTTGCGCCAAGAGGGACGACGCCAAAACTATGCCAAGGAGGCGACAAATT
* *
14073996 GGGTTATTATACATACAATGAAAAAGTGGCGTATTGTAGGACTTTACATTAAGAGTCAGTTTTTA
131 GGGTTACTATACATACAATGAAAAAGTGGCGTATTGTAGGACTTTACATTAAGAGTCAATTTTTA
*
14074061 GTAAATGTTTGTATTGTAATGAATTGTAATTGGTCTGATGTAATATTTTATTTCTAAAATACTTT
196 GTAAATGTTTGTATTGTAATGAATTGTAATTGGTCCGATGTAATATTTTATTTCTAAAATACTTT
*
14074126 CTATTGTGTCTTTGATATTAAGTTTTTAAATGAAATAATAATAAAAAATGTTTTAAGTATAGAAT
261 CTATTGTGTCTTTAATATTAAGTTTTTAAATGAAATAATAATAAAAAATGTTTTAAGTATAGAAT
*
14074191 GTCTATCAACTATTTTGAAATTTTGTTATATATTGTTTGTATAACACCCGAGATCCGAACTTGAT
326 GTCTATCAACTATTTTGAAATTTTGTTATATATTGTTTGTATAACACCCAAGATCCGAACTTGAT
* * ** *
14074256 GAATCGGGTC-AGATTAAGGGTGTCACAAAGACTACCTCTTATGAAGAATACATGAAAGCTTAAC
391 GAATCGGGTCGA-ATTAAGGGCGTCACAAAGACTACCTCATATGAAGAATACACAAAAGCTCAAC
14074320 TAGACCAACAAGCAAGAGAGCTTTCTCAAACTCA
455 TAGACCAACAAGCAAGAGAGCTTTCTCAAACTCA
14074354 TAA
1 TAA
14074357 ACCTTCTTTT
Statistics
Matches: 453, Mismatches: 36, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
487 5 0.01
488 448 0.99
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (488 bp):
TAACTCTATGTTAACTCTCACTAAGTTCTTTTGAACTTAGTGTTATGTTTATGATTATGTTTCAG
GAAGTATAGTACGAGCTTGCGCCAAGAGGGACGACGCCAAAACTATGCCAAGGAGGCGACAAATT
GGGTTACTATACATACAATGAAAAAGTGGCGTATTGTAGGACTTTACATTAAGAGTCAATTTTTA
GTAAATGTTTGTATTGTAATGAATTGTAATTGGTCCGATGTAATATTTTATTTCTAAAATACTTT
CTATTGTGTCTTTAATATTAAGTTTTTAAATGAAATAATAATAAAAAATGTTTTAAGTATAGAAT
GTCTATCAACTATTTTGAAATTTTGTTATATATTGTTTGTATAACACCCAAGATCCGAACTTGAT
GAATCGGGTCGAATTAAGGGCGTCACAAAGACTACCTCATATGAAGAATACACAAAAGCTCAACT
AGACCAACAAGCAAGAGAGCTTTCTCAAACTCA
Found at i:14075250 original size:17 final size:17
Alignment explanation
Indices: 14075217--14075250 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14075207 TAAAGTTTCA
**
14075217 TGTCATTTTTATTTAAT
1 TGTCATTTTTAACTAAT
14075234 TGTCATTTTTAACTAAT
1 TGTCATTTTTAACTAAT
14075251 GTGGTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (17 bp):
TGTCATTTTTAACTAAT
Found at i:14081895 original size:11 final size:11
Alignment explanation
Indices: 14081821--14081904 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 11
14081811 TTTCTAAATA
*
14081821 TAATATTATTT
1 TAATATTAATT
14081832 TAATAAATTTAATCT
1 TAAT--A-TTAAT-T
14081847 TAA-ATTAAATT
1 TAATATT-AATT
* *
14081858 AAATATTTATT
1 TAATATTAATT
*
14081869 TAGATAATAA-T
1 TA-ATATTAATT
14081880 T--TATTAATT
1 TAATATTAATT
14081889 TAATATTAATT
1 TAATATTAATT
14081900 TAATA
1 TAATA
14081905 CCTATCTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
8 5 0.09
9 2 0.04
11 28 0.50
12 12 0.21
13 1 0.02
14 4 0.07
15 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (11 bp):
TAATATTAATT
Found at i:14081900 original size:19 final size:20
Alignment explanation
Indices: 14081861--14081901 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
14081851 TTAAATTAAA
*
14081861 TATTTATTTAGATAATAATT
1 TATTAATTTAGATAATAATT
*
14081881 TATTAATTTA-ATATTAATT
1 TATTAATTTAGATAATAATT
14081900 TA
1 TA
14081902 ATACCTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTAATTTAGATAATAATT
Found at i:14082292 original size:19 final size:20
Alignment explanation
Indices: 14082250--14082294 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
14082240 GAAAAATGAT
* * *
14082250 TTCTAGAAATTGATTTATTT
1 TTCTGGAAATTGATTTACTC
14082270 TTCTGGAAA-TGATTTACTC
1 TTCTGGAAATTGATTTACTC
14082289 TTCTGG
1 TTCTGG
14082295 TGTTTCAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (20 bp):
TTCTGGAAATTGATTTACTC
Found at i:14082435 original size:2 final size:2
Alignment explanation
Indices: 14082428--14082456 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14082418 TTGAGTTTAT
14082428 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
14082457 TAATAAATTT
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:14085649 original size:55 final size:54
Alignment explanation
Indices: 14085602--14085715 Score: 138
Period size: 55 Copynumber: 2.0 Consensus size: 54
14085592 AGAAATATTT
14085602 AAGAAGTTGAAGAACAGAAGAGAAGAAAAAGACTTACCTGGACGAAGAAGGAGATGG
1 AAGAAGTTGAAGAA-AGAA-AGAAGAAAAAGACTTACCTGGACGAAGAA-GAGATGG
* * * * * *
14085659 AATAAGTTGAAGAATGGAAGAAGAAGAAGACTTACCTGGATGAAGAAGGGGATGG
1 AAGAAGTTGAAGAAAGAAAGAAGAAAAAGACTTACCTGGACGAAGAA-GAGATGG
14085714 AA
1 AA
14085716 AATGTCTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
55 36 0.71
56 2 0.04
57 13 0.25
ACGTcount: A:0.47, C:0.07, G:0.32, T:0.13
Consensus pattern (54 bp):
AAGAAGTTGAAGAAAGAAAGAAGAAAAAGACTTACCTGGACGAAGAAGAGATGG
Found at i:14086606 original size:19 final size:19
Alignment explanation
Indices: 14086560--14086607 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
14086550 GTATATATTT
*
14086560 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGAAGA
*
14086578 TAAATCTTATTTAGGAAGA
1 TAAATTTTATTTAGGAAGA
14086597 TAAATTTTATT
1 TAAATTTTATT
14086608 CAGATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (19 bp):
TAAATTTTATTTAGGAAGA
Found at i:14089601 original size:53 final size:53
Alignment explanation
Indices: 14089520--14089670 Score: 223
Period size: 53 Copynumber: 2.8 Consensus size: 53
14089510 CTTACACGGT
* *
14089520 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
14089575 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
* *
14089628 TCACATTACACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
14089671 GCACACTTAT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 82 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:14091906 original size:24 final size:24
Alignment explanation
Indices: 14091879--14092052 Score: 287
Period size: 24 Copynumber: 7.2 Consensus size: 24
14091869 AAAGGCAATG
*
14091879 CTTTTAATAACTGGGGCAAAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
14091903 CTTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
* *
14091927 CTATTAATAACTAGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
14091951 CTTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
14091975 CTTTTAATAACT-GGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
*
14091998 CTTTTGATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
14092022 CTTTTTTAATAACTGGGGCATAAGCC
1 C--TTTTAATAACTGGGGCATAAGCC
14092048 CTTTT
1 CTTTT
14092053 GCACTTCCTC
Statistics
Matches: 140, Mismatches: 7, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
23 22 0.16
24 95 0.68
26 23 0.16
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGCC
Found at i:14092168 original size:20 final size:20
Alignment explanation
Indices: 14092103--14092161 Score: 118
Period size: 20 Copynumber: 3.0 Consensus size: 20
14092093 TATGAATATA
14092103 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
14092123 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
14092143 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
14092162 ACCATGTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:14099746 original size:24 final size:24
Alignment explanation
Indices: 14099695--14099840 Score: 204
Period size: 24 Copynumber: 6.0 Consensus size: 24
14099685 ACTTTATCAT
*
14099695 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
14099720 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
14099744 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
14099768 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
14099792 ATAATTGGGGCATAAGCTCTTTTTTA
1 ATAACTGGGGCATAAGC-C-CTTTTA
14099818 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
14099841 GCACTTCCTC
Statistics
Matches: 109, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
24 75 0.69
25 14 0.13
26 20 0.18
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:14099915 original size:20 final size:20
Alignment explanation
Indices: 14099890--14099956 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
14099880 TTATGAATAC
*
14099890 ATCATGTGTATATCATACAT
1 ATCATGTGCATATCATACAT
14099910 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
14099930 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
14099950 ACCATGT
1 ATCATGT
14099957 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:14105697 original size:68 final size:64
Alignment explanation
Indices: 14105556--14105706 Score: 171
Period size: 68 Copynumber: 2.3 Consensus size: 64
14105546 TGGAACCATG
* * *
14105556 CATGCGACCTAGCTACATATATCTCGTAGCTCTCTTGTCTAAATGGTGTACACATAGTATCACC
1 CATGCGACCTAGCTACATATATCTCGTAGCTCTCTTGTCTAAATGATGTACACATAGCATCACA
* *
14105620 CATGCGACCTAGCTACATCATAATGTCTCGTAGCTCTCTTGTAC-ACATGATGTGCAC-TCAGCA
1 CATGCGACCTAGCTACAT-AT-A--TCTCGTAGCTCTCTTGT-CTAAATGATGTACACAT-AGCA
*
14105683 TCATA
60 TCACA
*
14105688 CATGTGACCTAGCTACATA
1 CATGCGACCTAGCTACATA
14105707 CCATCTGTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
64 18 0.24
65 2 0.03
66 1 0.01
67 2 0.03
68 50 0.68
69 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (64 bp):
CATGCGACCTAGCTACATATATCTCGTAGCTCTCTTGTCTAAATGATGTACACATAGCATCACA
Found at i:14106205 original size:30 final size:30
Alignment explanation
Indices: 14106171--14106231 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
14106161 TCCTTAACTC
14106171 AAACTTTTGCAAAATTACAATTTTACCCCT
1 AAACTTTTGCAAAATTACAATTTTACCCCT
* * * *
14106201 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTTGCAAAATTACAATTTTACCCCT
14106231 A
1 A
14106232 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTACCCCT
Found at i:14109594 original size:9 final size:8
Alignment explanation
Indices: 14109565--14109614 Score: 57
Period size: 9 Copynumber: 5.9 Consensus size: 8
14109555 ATCCTGTCAA
14109565 ATAAAAAT
1 ATAAAAAT
14109573 AT-AAAAT
1 ATAAAAAT
14109580 ATAAAAAT
1 ATAAAAAT
14109588 CATAAAAAATT
1 -AT-AAAAA-T
14109599 ATAAAAAT
1 ATAAAAAT
14109607 CATAAAAA
1 -ATAAAAA
14109615 ATTATTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 7 0.19
8 8 0.22
9 14 0.38
10 7 0.19
11 1 0.03
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:14109597 original size:10 final size:10
Alignment explanation
Indices: 14109582--14109616 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
14109572 TATAAAATAT
14109582 AAAAATCATA
1 AAAAATCATA
*
14109592 AAAAATTAT-
1 AAAAATCATA
14109601 AAAAATCATA
1 AAAAATCATA
14109611 AAAAAT
1 AAAAAT
14109617 TATTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAATCATA
Found at i:14109603 original size:19 final size:19
Alignment explanation
Indices: 14109575--14109619 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
14109565 ATAAAAATAT
14109575 AAAA-TATAAAAATCATAA
1 AAAATTATAAAAATCATAA
14109593 AAAATTATAAAAATCATAA
1 AAAATTATAAAAATCATAA
14109612 AAAATTAT
1 AAAATTAT
14109620 TAAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATTATAAAAATCATAA
Found at i:14109632 original size:19 final size:19
Alignment explanation
Indices: 14109563--14109632 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
14109553 ATATCCTGTC
*
14109563 AAATAAAAATATAAAATATAA
1 AAATAAAAA-A-AAATTATAA
* *
14109584 AAATCATAAAAAATTATAA
1 AAATAAAAAAAAATTATAA
* * *
14109603 AAATCATAAAAAATTATTA
1 AAATAAAAAAAAATTATAA
*
14109622 AATTAAAAAAA
1 AAATAAAAAAA
14109633 TCAAAACTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 34 0.81
20 1 0.02
21 7 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAAAAAAAATTATAA
Done.