Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold382
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: 2572505
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 7 of 16
Found at i:1037451 original size:3 final size:3
Alignment explanation
Indices: 1037443--1037499 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1037433 TAATTACACA
1037443 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1037491 AAT AAT AAT
1 AAT AAT AAT
1037500 TGTCGCTACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1038624 original size:131 final size:124
Alignment explanation
Indices: 1038474--1038866 Score: 386
Period size: 131 Copynumber: 3.1 Consensus size: 124
1038464 ACGGGGCTAG
* *
1038474 AGTATCCCCGATTATGGAAAATCGGTGTTCTAGAAATAAAAATCAGGGTTGGAGTATCCCCTCAA
1 AGTATCCCCGATTGTGGAAAAT-GGTGTT-TAGAAAT-AAAATCGGGGTTGGAGTATCCCCTCAA
* *
1038539 AAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATCAGTATTTTGAAAATAAAATCGGAGTTG
63 AAATAAC-GGGTTGGAGTATCCC-GATTGT-GAAAATCAGTGTTTTGAAAATAAAATC-GAGTTG
1038604 A
124 A
* * *
1038605 AGTATCCCCGATTGTGGAAAAT--TG----GTAATAAAATCGGGGTTGGAGTATCCCCTTAGAAA
1 AGTATCCCCGATTGTGGAAAATGGTGTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAA
* ** * *
1038664 TAACGGGGTTGGAGTAACCCCGATTGTGAGAAATTGGTGTTTTTAGAAATAAAACTAGAGTTGGA
66 TAAC-GGGTTGGAGT-ATCCCGATTGTGA-AAATCAGTGTTTTGA-AAATAAAA-TCGAGTT-GA
* * * *
1038729 A-TATCTCCGATTGTGGAAAATTGGTATTTTAGAAATAAAATCGGGGTTGAAGTATCCCCTCGAA
1 AGTATCCCCGATTGTGGAAAA-TGGT-GTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAAA
* * * *
1038793 AATAACGGGATTAGAGTATTCCCGATTGTGAAAAACTAGTGTTTTGAGAATAAAATCGAGGTTGG
64 AATAACGGG-TTGGAGTA-TCCCGATTGTGAAAATC-AGTGTTTTGAAAATAAAATCGA-GTTGA
1038858 AGTATCCCC
1 AGTATCCCC
1038867 TCAAAAATAA
Statistics
Matches: 214, Mismatches: 30, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
121 2 0.01
122 57 0.27
123 39 0.18
124 5 0.02
126 1 0.00
128 2 0.01
129 5 0.02
130 23 0.11
131 80 0.37
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (124 bp):
AGTATCCCCGATTGTGGAAAATGGTGTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAA
TAACGGGTTGGAGTATCCCGATTGTGAAAATCAGTGTTTTGAAAATAAAATCGAGTTGA
Found at i:1038847 original size:79 final size:79
Alignment explanation
Indices: 1038730--1038897 Score: 230
Period size: 79 Copynumber: 2.1 Consensus size: 79
1038720 AGAGTTGGAA
* * * * * *
1038730 TATCTCCGATTGTGGAAAATTGGTATTTTAGAAATAAAATCGGGGTTGAAGTATCCCCTCGAAAA
1 TATCCCCGATTGTGAAAAACTAGTATTTTAGAAATAAAATCGAGGTTGAAGTATCCCCTCAAAAA
*
1038795 TAACGGGATTAGAG
66 TAACGGGATTAAAG
* * *
1038809 TATTCCCGATTGTGAAAAACTAGTGTTTT-GAGAATAAAATCGAGGTTGGAGTATCCCCTCAAAA
1 TATCCCCGATTGTGAAAAACTAGTATTTTAGA-AATAAAATCGAGGTTGAAGTATCCCCTCAAAA
1038873 ATAACGGGATTAAAG
65 ATAACGGGATTAAAG
1038888 TATCCCCGAT
1 TATCCCCGAT
1038898 GAAATAACAG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 2 0.03
79 75 0.97
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (79 bp):
TATCCCCGATTGTGAAAAACTAGTATTTTAGAAATAAAATCGAGGTTGAAGTATCCCCTCAAAAA
TAACGGGATTAAAG
Found at i:1038917 original size:28 final size:27
Alignment explanation
Indices: 1038852--1038922 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 27
1038842 ATAAAATCGA
1038852 GGTTGGAGTATCCCCTCAAAAATAACG
1 GGTTGGAGTATCCCCTCAAAAATAACG
** * *
1038879 GGATTAAAGTATCCCC-GATGAAATAACAG
1 GG-TTGGAGTATCCCCTCA-AAAATAAC-G
*
1038908 GGTTGGAGTACCCCC
1 GGTTGGAGTATCCCC
1038923 AATTATGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 3 0.09
28 28 0.82
29 3 0.09
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (27 bp):
GGTTGGAGTATCCCCTCAAAAATAACG
Found at i:1038998 original size:28 final size:28
Alignment explanation
Indices: 1038957--1039030 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
1038947 AGATATAAAG
*
1038957 CGGGGTTTGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCCCT-GAGAAATAA
*
1038985 TGGGGTTGGAGTAT-CCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCCTGA-GAAATAA
1039013 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1039031 AAGATGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 31 0.77
29 3 0.08
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTGAGAAATAA
Found at i:1041207 original size:20 final size:21
Alignment explanation
Indices: 1041182--1041240 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
1041172 AAAATGCCTG
*
1041182 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATGTAGA
* *
1041202 AATGTATCAATACAATG-AGC
1 AATGTATCGATACAATGTAGA
1041222 AATGTATCGATACAATGTA
1 AATGTATCGATACAATGTA
1041241 TCGATACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAATGTAGA
Found at i:1041237 original size:13 final size:13
Alignment explanation
Indices: 1041221--1041251 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1041211 ATACAATGAG
1041221 CAATGTATCGATA
1 CAATGTATCGATA
1041234 CAATGTATCGATA
1 CAATGTATCGATA
1041247 CAATG
1 CAATG
1041252 CAAAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1041248 original size:33 final size:33
Alignment explanation
Indices: 1041202--1041269 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1041192 TACATTGTAA
*
1041202 AATGTATCAATACAATG-AGCAATGTATCGATAC
1 AATGTATCAATACAATGCA-AAATGTATCGATAC
*
1041235 AATGTATCGATACAATGCAAAATGTATCGATAC
1 AATGTATCAATACAATGCAAAATGTATCGATAC
1041268 AA
1 AA
1041270 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (33 bp):
AATGTATCAATACAATGCAAAATGTATCGATAC
Found at i:1041260 original size:20 final size:20
Alignment explanation
Indices: 1041182--1041269 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1041172 AAAATGCCTG
* *
1041182 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATGCAA
* *
1041202 AATGTATCAATACAATG-AGC
1 AATGTATCGATACAATGCA-A
1041222 AATGTATCGAT---A--C--
1 AATGTATCGATACAATGCAA
1041235 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
1041255 AATGTATCGATACAA
1 AATGTATCGATACAA
1041270 ATTGTGAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
13 11 0.20
16 1 0.02
17 1 0.02
18 1 0.02
19 1 0.02
20 40 0.73
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:1041549 original size:3 final size:3
Alignment explanation
Indices: 1041541--1041578 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1041531 AGGTGTCTAC
1041541 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1041579 CAAATCTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1042227 original size:20 final size:20
Alignment explanation
Indices: 1042202--1042243 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1042192 ACAAACAAAG
1042202 AAAGAAATATCACTGAAGAA
1 AAAGAAATATCACTGAAGAA
1042222 AAAGAAATATCACTGAAGAA
1 AAAGAAATATCACTGAAGAA
1042242 AA
1 AA
1042244 GCTTACTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAGAAATATCACTGAAGAA
Found at i:1042913 original size:88 final size:89
Alignment explanation
Indices: 1042796--1042973 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
1042786 GGCCATAGGC
1042796 AGCATGATCTTTTCTTCTTTTCTTTTCTTTTTTTA-TTTTAATATTTTTAAGAAAAAATTATTTA
1 AGCATGATCTTTTCTTCTTTTCTTTTCTTTTTTTATTTTTAATATTTTTAAGAAAAAATTATTTA
1042860 TTTATTTATTTATTTTTATCTTAG
66 TTTATTTATTTATTTTTATCTTAG
*
1042884 AGCATGATCTTTTCTTCTTTTCTTTTCTTTTTTTATTTTTAATATTTTTAAGAAAAATTTATTTA
1 AGCATGATCTTTTCTTCTTTTCTTTTCTTTTTTTATTTTTAATATTTTTAAGAAAAAATTATTTA
1042949 TTTATTTATTTATTTTTATCTTAG
66 TTTATTTATTTATTTTTATCTTAG
1042973 A
1 A
1042974 TTTTAACTAT
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
88 35 0.40
89 53 0.60
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (89 bp):
AGCATGATCTTTTCTTCTTTTCTTTTCTTTTTTTATTTTTAATATTTTTAAGAAAAAATTATTTA
TTTATTTATTTATTTTTATCTTAG
Found at i:1043570 original size:15 final size:15
Alignment explanation
Indices: 1043524--1043576 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1043514 ATTAAGTTAT
1043524 TTAAATTTTAAAAT-
1 TTAAATTTTAAAATA
**
1043538 TT-AA-TAAAAAATA
1 TTAAATTTTAAAATA
1043551 TTAAATTATTAAAA-A
1 TTAAATT-TTAAAATA
1043566 TTAAATTTTAA
1 TTAAATTTTAA
1043577 CAAAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
12 6 0.19
13 4 0.13
14 8 0.26
15 9 0.29
16 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATTTTAAAATA
Found at i:1043992 original size:22 final size:21
Alignment explanation
Indices: 1043945--1044001 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
1043935 TAATAAATTC
* *
1043945 AATTAAATTTAAATATTTAAAT
1 AATTTAATTTAAA-AATTAAAT
1043967 -ATTTAATTTAAAAATTAAAT
1 AATTTAATTTAAAAATTAAAT
1043987 AAATTTAATTTAAAA
1 -AATTTAATTTAAAA
1044002 TATATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 7 0.23
21 11 0.35
22 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTAATTTAAAAATTAAAT
Found at i:1044011 original size:22 final size:22
Alignment explanation
Indices: 1043945--1044012 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
1043935 TAATAAATTC
* *
1043945 AATTAAATTT-AAATAT-TTAA
1 AATTTAATTTAAAATATATTTA
**
1043965 ATATTTAATTTAAAA-ATTAAATA
1 A-ATTTAATTTAAAATA-TATTTA
1043988 AATTTAATTTAAAATATATTTA
1 AATTTAATTTAAAATATATTTA
1044010 AAT
1 AAT
1044013 ATATAGTAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 1 0.03
21 9 0.24
22 24 0.65
23 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTAATTTAAAATATATTTA
Found at i:1045167 original size:16 final size:17
Alignment explanation
Indices: 1045112--1045176 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
1045102 TATTTTATTA
1045112 AAAATAAA-ATTTAAAC
1 AAAATAAATATTTAAAC
*
1045128 ATTAAATAAATA-TTAAAT
1 A--AAATAAATATTTAAAC
*
1045146 ATAATAAATATTTAAA-
1 AAAATAAATATTTAAAC
*
1045162 AAAATATATATTTAA
1 AAAATAAATATTTAA
1045177 TTAAATGGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 22 0.54
17 5 0.12
18 13 0.32
19 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAAATATTTAAAC
Found at i:1045182 original size:16 final size:16
Alignment explanation
Indices: 1045130--1045182 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1045120 ATTTAAACAT
1045130 TAAATAAATA-TTAAA
1 TAAATAAATATTTAAA
1045145 TATAATAAATATTTAAA
1 TA-AATAAATATTTAAA
* * *
1045162 AAAATATATATTTAAT
1 TAAATAAATATTTAAA
1045178 TAAAT
1 TAAAT
1045183 GGAACGATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 2 0.06
16 24 0.75
17 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATAAATATTTAAA
Found at i:1048063 original size:121 final size:121
Alignment explanation
Indices: 1047891--1048225 Score: 394
Period size: 121 Copynumber: 2.8 Consensus size: 121
1047881 ATCATTATCA
* * *
1047891 TAATCATAATCAT--AGTGACAGCCTTTTGATCTGTTGATAATATGTTGAATTTTTAATTTC-AG
1 TAATCATAATCATACAGTGACAGCCTTTTGATCTATTGATAAAATG-TAAATTTTTAATTTCGA-
* ** *
1047953 TAATCAAGATTCAATCAAGACTTTTAGTGCGAGATTCTTAGTTTTGAT-AAAATTAAT
64 TAATCAAGATTCAATCAAGACTCTTAGTGCGAGATTCTTAGTTTCAATAAAAACTAAT
* ** * *
1048010 TAATTATAATCATACAGTGACAAACTTTTGATCTATTGATAAAATGCTAAATTTTTAGTTTCGTT
1 TAATCATAATCATACAGTGACAGCCTTTTGATCTATTGATAAAATG-TAAATTTTTAATTTCGAT
* *
1048075 AATCAAGATTCAATCAAGACTCTTAGCGCTAGATTCTTAGTTTCAATAAAAACTAAT
65 AATCAAGATTCAATCAAGACTCTTAGTGCGAGATTCTTAGTTTCAATAAAAACTAAT
* * * * *
1048132 TAATCATAATCATACAATGACAGCCCTTTAATCTATT-A-AAAAGGTGTCAGACTTTTAATTTCG
1 TAATCATAATCATACAGTGACAGCCTTTTGATCTATTGATAAAA--TGT-AAATTTTTAATTTCG
*
1048195 ATAATCAAAATTCAATCAAGACTCTTAGTGC
63 ATAATCAAGATTCAATCAAGACTCTTAGTGC
1048226 TGCACTCTTA
Statistics
Matches: 182, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
119 12 0.07
120 4 0.02
121 85 0.47
122 81 0.45
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (121 bp):
TAATCATAATCATACAGTGACAGCCTTTTGATCTATTGATAAAATGTAAATTTTTAATTTCGATA
ATCAAGATTCAATCAAGACTCTTAGTGCGAGATTCTTAGTTTCAATAAAAACTAAT
Found at i:1048194 original size:122 final size:120
Alignment explanation
Indices: 1047941--1048239 Score: 345
Period size: 122 Copynumber: 2.5 Consensus size: 120
1047931 TATGTTGAAT
* * ** *
1047941 TTTTAATTTCAGTAATCAAGATTCAATCAAGACTTTTAGTGCGAGATTCTTAGTTTTGATAAAAT
1 TTTTAATTTC-GTAATCAAGATTCAATCAAGACTCTTAGTGCTAGATTCTTAGTTTCAATAAAAC
* * * * *
1048006 TAATTAATTATAATCATACAGTGACAAACTTTTGATCTATTGATAAAATGCTAAAT
65 TAATTAATCATAATCATACAATGACAAACCTTTAATCTATTGATAAAATGCTAAAC
* *
1048062 TTTTAGTTTCGTTAATCAAGATTCAATCAAGACTCTTAGCGCTAGATTCTTAGTTTCAATAAAAA
1 TTTTAATTTCG-TAATCAAGATTCAATCAAGACTCTTAGTGCTAGATTCTTAGTTTCAAT-AAAA
** *
1048127 CTAATTAATCATAATCATACAATGACAGCCCTTTAATCTATT-A-AAAAGGTG-TCAGAC
64 CTAATTAATCATAATCATACAATGACAAACCTTTAATCTATTGATAAAA--TGCT-AAAC
* *
1048184 TTTTAATTTCGATAATCAAAATTCAATCAAGACTCTTAGTGCT-GCACTCTTAGTTT
1 TTTTAATTTCG-TAATCAAGATTCAATCAAGACTCTTAGTGCTAG-ATTCTTAGTTT
1048240 AGAAAAAGAA
Statistics
Matches: 152, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
120 5 0.03
121 55 0.36
122 92 0.61
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (120 bp):
TTTTAATTTCGTAATCAAGATTCAATCAAGACTCTTAGTGCTAGATTCTTAGTTTCAATAAAACT
AATTAATCATAATCATACAATGACAAACCTTTAATCTATTGATAAAATGCTAAAC
Found at i:1052198 original size:14 final size:14
Alignment explanation
Indices: 1052179--1052206 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1052169 CATATTAAAA
1052179 AATATTTTTATATT
1 AATATTTTTATATT
1052193 AATATTTTTATATT
1 AATATTTTTATATT
1052207 TTATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1052843 original size:20 final size:20
Alignment explanation
Indices: 1052818--1053023 Score: 137
Period size: 20 Copynumber: 9.7 Consensus size: 20
1052808 TTTTACCCAG
1052818 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1052838 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1052858 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1052878 ATGTATTGATACATTCTGTTTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
*
1052908 GATATATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * * *
1052929 ATGTATCAATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1052949 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
* *
1052969 ATGTATTG--ACTTTTTTCCCA
1 ATGTATCGATACATTTTT--CA
1052989 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
*
1053010 ATATATCGATACAT
1 ATGTATCGATACAT
1053024 CTAGCTAAAA
Statistics
Matches: 141, Mismatches: 29, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
18 6 0.04
20 95 0.67
21 11 0.08
23 7 0.05
24 5 0.04
27 4 0.03
30 2 0.01
31 11 0.08
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1052965 original size:91 final size:91
Alignment explanation
Indices: 1052807--1052977 Score: 315
Period size: 91 Copynumber: 1.9 Consensus size: 91
1052797 AAAAGTCACA
* * *
1052807 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATATAT
1 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACAT
1052872 TCTTCAATGTATTGATACATTCTGTT
66 TCTTCAATGTATTGATACATTCTGTT
1052898 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACAT
1052963 TCTTCAATGTATTGA
66 TCTTCAATGTATTGA
1052978 CTTTTTTCCC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (91 bp):
TTTTTACCCAGATATATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACAT
TCTTCAATGTATTGATACATTCTGTT
Found at i:1053955 original size:22 final size:24
Alignment explanation
Indices: 1053930--1053973 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1053920 TGTCCAGCAT
1053930 CTCATTGAATG-TTATC-CATTAG
1 CTCATTGAATGATTATCACATTAG
*
1053952 CTCATTGTATGATTATCACATT
1 CTCATTGAATGATTATCACATT
1053974 TTCCATGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (24 bp):
CTCATTGAATGATTATCACATTAG
Found at i:1056743 original size:14 final size:14
Alignment explanation
Indices: 1056726--1056759 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1056716 CTTCATATAG
1056726 TGAACCTTGCAAGC
1 TGAACCTTGCAAGC
*
1056740 TGAACCTTGCGAGC
1 TGAACCTTGCAAGC
*
1056754 TAAACC
1 TGAACC
1056760 ATGTCAAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (14 bp):
TGAACCTTGCAAGC
Found at i:1060068 original size:21 final size:21
Alignment explanation
Indices: 1060014--1060081 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
1060004 CAAAATGATG
1060014 AAAAAGT-CAAAAGTAAAAGCACA
1 AAAAAGTGCAAAAG-AAAA--ACA
1060037 AAAAA-TG-AAAAGAAAAACA
1 AAAAAGTGCAAAAGAAAAACA
*
1060056 AAAAAGTGCAAAA-ACAAAATA
1 AAAAAGTGCAAAAGA-AAAACA
1060077 AAAAA
1 AAAAA
1060082 AGGGAACAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 8 0.20
20 3 0.08
21 18 0.45
22 6 0.15
23 5 0.12
ACGTcount: A:0.74, C:0.09, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAGTGCAAAAGAAAAACA
Found at i:1061847 original size:19 final size:19
Alignment explanation
Indices: 1061825--1061862 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1061815 AAATTAGGTG
1061825 TCTTTTTTACAATTAATTT
1 TCTTTTTTACAATTAATTT
1061844 TCTTTTTTACAATTAATTT
1 TCTTTTTTACAATTAATTT
1061863 GTACTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTTTTTTACAATTAATTT
Found at i:1072648 original size:38 final size:38
Alignment explanation
Indices: 1072544--1072648 Score: 138
Period size: 38 Copynumber: 2.8 Consensus size: 38
1072534 GGAATTTCCT
*
1072544 AGTCACCAGCTAAATCCAAATTGAATTTCCTAGCCACC
1 AGTCACCAGCTAAATCCAAATTGAATTTGCTAGCCACC
* * **
1072582 AGTTACCAGCCAAATCCAAATTGAATTTGCTAGCTGCC
1 AGTCACCAGCTAAATCCAAATTGAATTTGCTAGCCACC
* * *
1072620 AGTCGCTAGCTAAATTCAAATTGAATTTG
1 AGTCACCAGCTAAATCCAAATTGAATTTG
1072649 ATTTAGTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (38 bp):
AGTCACCAGCTAAATCCAAATTGAATTTGCTAGCCACC
Found at i:1077253 original size:31 final size:31
Alignment explanation
Indices: 1077199--1077279 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1077189 ATTCAATTTG
* **
1077199 AAATTTCTTAACCACCAGTCAAATCT-AAATT
1 AAATTTCCTAACCACCAACCAAAT-TAAAATT
*
1077230 AAA-TTCTCTAGCCACCAACCAAATTAAAATT
1 AAATTTC-CTAACCACCAACCAAATTAAAATT
*
1077261 GAATTTCCTAACCACCAAC
1 AAATTTCCTAACCACCAAC
1077280 TGCTAGTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 4 0.10
31 34 0.83
32 3 0.07
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (31 bp):
AAATTTCCTAACCACCAACCAAATTAAAATT
Found at i:1077782 original size:25 final size:25
Alignment explanation
Indices: 1077720--1077789 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
1077710 AATAAAAATT
*
1077720 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
1077744 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
1077769 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
1077790 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:1077835 original size:27 final size:27
Alignment explanation
Indices: 1077774--1077844 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1077764 AAACAAGCCT
* *
1077774 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
1077802 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
1077829 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1077845 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:1077847 original size:24 final size:24
Alignment explanation
Indices: 1077722--1077847 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
1077712 TAAAAATTAG
* *
1077722 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
1077746 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
1077770 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
1077799 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
1077826 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
1077848 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:1082375 original size:25 final size:25
Alignment explanation
Indices: 1082313--1082439 Score: 105
Period size: 27 Copynumber: 4.9 Consensus size: 25
1082303 AATAAAAATT
*
1082313 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
1082337 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
* *
1082362 AGCCTCC-ATATTTGACAAATACAAAGGA
1 AGCCACCAAT-TTTGACAAAT--AAA-CA
* * * *
1082390 AACCACCATTTTTGACAAACACAAAA
1 AGCCACCAATTTTGACAAATA-AACA
* *
1082416 TAACCACCATTTTTGACAAATAAA
1 -AGCCACCAATTTTGACAAATAAA
1082440 TGGGTGGCTT
Statistics
Matches: 86, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
24 21 0.24
25 20 0.23
26 4 0.05
27 25 0.29
28 15 0.17
29 1 0.01
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:1082406 original size:28 final size:27
Alignment explanation
Indices: 1082315--1082437 Score: 105
Period size: 25 Copynumber: 4.7 Consensus size: 27
1082305 TAAAAATTAG
* * *
1082315 CCACCAATTTTGAC-AA-ACAACA-AG
1 CCACCATTTTTGACAAATACAAAATAA
* * *
1082339 CCACCAATTTTGACAAATA-AACA-AG
1 CCACCATTTTTGACAAATACAAAATAA
* *
1082364 CCTCCATATTTGACAAATACAAAGGA-AA
1 CCACCATTTTTGACAAATACAAA--ATAA
*
1082392 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGACAAATACAAAATAA
1082419 CCACCATTTTTGACAAATA
1 CCACCATTTTTGACAAATA
1082438 AATGGGTGGC
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.17
25 24 0.29
26 4 0.05
27 20 0.24
28 22 0.26
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAATACAAAATAA
Found at i:1082440 original size:24 final size:24
Alignment explanation
Indices: 1082315--1082440 Score: 83
Period size: 24 Copynumber: 4.9 Consensus size: 24
1082305 TAAAAATTAG
* * *
1082315 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAATAA-ATAA
* *
1082339 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAATAAATAA
* * *
1082363 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGACAAAT--AAA--TAA
*
1082392 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-A-TAAATAA
1082419 CCACCATTTTTGACAAATAAAT
1 CCACCATTTTTGACAAATAAAT
1082441 GGGTGGCTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 16 0.20
26 2 0.02
27 19 0.23
28 12 0.15
29 7 0.09
30 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (24 bp):
CCACCATTTTTGACAAATAAATAA
Found at i:1082774 original size:22 final size:22
Alignment explanation
Indices: 1082728--1082783 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1082718 ATTTTATTTT
* *
1082728 TATTATTTATTAAATTATTAAAA
1 TATTATTTA-TATATTAATAAAA
*
1082751 TATTATTTATATATTAATATAA
1 TATTATTTATATATTAATAAAA
1082773 TA-TATTT-TATA
1 TATTATTTATATA
1082784 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 5 0.17
22 12 0.40
23 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATTTATATATTAATAAAA
Found at i:1084001 original size:28 final size:28
Alignment explanation
Indices: 1083945--1084021 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
1083935 GAAATAAAGC
*
1083945 CGGGGTTGGAGTATCTCCTC-A-GAAGTAA
1 CGGGGTTGGAGTATC-CC-CGATGAAATAA
1083973 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
** *
1084001 CAAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1084022 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 39 0.91
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1084094 original size:52 final size:52
Alignment explanation
Indices: 1084005--1084338 Score: 157
Period size: 52 Copynumber: 6.3 Consensus size: 52
1083995 AAATAACAAG
* ** * *
1084005 GTTGGAGTATCCTCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGT-GTTTTGGAAATAAAATCGGA
* * * *
1084057 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCACGA
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAATC-GGA
* ** * * ** * *
1084110 -TTGGAGTATCTCCGATT-GTGGAAAAATTAGTGTTTTAGCGATAAAACCGGG
1 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGTGTTTTGGAAATAAAATCGGA
* * ** * *** * * *
1084161 GTTGGAGTATCCCCTCAGAAATAACGG--GGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTAT-CCC-C-G-ATTAAAGGAAAATTGGTGT-T-TTGGA-AATAAAATCGGA
*
1084216 GTTGGAGTATCCCCGATTGTGAA-G-AAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGA-T-TAAAGGAAAATTGGTG--TTTTGGAAATAAAATCGGA
* * * *
1084270 GTTAGAGTATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAATCGGA
*
1084321 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1084339 GTGGAGAATT
Statistics
Matches: 210, Mismatches: 52, Indels: 41
0.69 0.17 0.14
Matches are distributed among these distances:
51 38 0.18
52 83 0.40
53 34 0.16
54 28 0.13
55 17 0.08
56 5 0.02
57 5 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:1084220 original size:27 final size:28
Alignment explanation
Indices: 1084157--1084232 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
1084147 GCGATAAAAC
*
1084157 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1084185 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1084212 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1084233 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 26 0.58
28 19 0.42
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1084311 original size:212 final size:212
Alignment explanation
Indices: 1083938--1084343 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
1083928 ATGATTAGAA
* * *
1083938 ATAAAGCCGGGGTTGGAGTATCTCCTCAGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACA
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACA
* *
1084003 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * *
1084068 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCACGA-TTGGAGTATCTCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-CGAGTTGGAATATCCCCGATTGTGGA
1084132 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
* *
1084150 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACA
* *
1084214 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
1084279 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCCGAGTTGGAATATCCCCGATTGTGG
1084343 A
194 A
1084344 GAATTGATAA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 30 0.17
212 106 0.61
213 39 0.22
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACA
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCCGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:1084316 original size:51 final size:53
Alignment explanation
Indices: 1084220--1084338 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1084210 AACGGGGTTG
* * *
1084220 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1084274 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
1084325 GAATATCCCCGATT
1 GAGTATCCCCGATT
1084339 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1086723 original size:13 final size:13
Alignment explanation
Indices: 1086705--1086730 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1086695 ACAAAGATCC
1086705 ATGTATCGATACA
1 ATGTATCGATACA
1086718 ATGTATCGATACA
1 ATGTATCGATACA
1086731 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1086726 original size:33 final size:33
Alignment explanation
Indices: 1086684--1086750 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1086674 AAAATTTCCA
***
1086684 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1086717 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1086750 A
1 A
1086751 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1086794 original size:19 final size:18
Alignment explanation
Indices: 1086770--1086837 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1086760 CAGTAGCTAA
1086770 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1086789 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1086804 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1086821 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1086838 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1086810 original size:13 final size:13
Alignment explanation
Indices: 1086792--1086816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1086782 ACAATACTTA
1086792 TGTATCGATACAT
1 TGTATCGATACAT
1086805 TGTATCGATACA
1 TGTATCGATACA
1086817 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1086814 original size:32 final size:32
Alignment explanation
Indices: 1086773--1086835 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1086763 TAGCTAATTA
*
1086773 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1086805 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1086836 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1087325 original size:6 final size:6
Alignment explanation
Indices: 1087308--1087418 Score: 83
Period size: 6 Copynumber: 18.8 Consensus size: 6
1087298 GAATATACTA
**
1087308 AAATAT -AATAT AAATAT -AATAT AAAATATT AAAATATT AAA-AT TTATAT
1 AAATAT AAATAT AAATAT AAATAT -AAATA-T -AAATA-T AAATAT AAATAT
* * *
1087357 -AATAT AAATAT AATATTT AAATAT AATTAT AAATAT AAA-A- ATATAT
1 AAATAT AAATAT AA-ATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1087403 AAATAT -AATAT AAATA
1 AAATAT AAATAT AAATA
1087419 CATAAATAGG
Statistics
Matches: 86, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
4 2 0.02
5 23 0.27
6 40 0.47
7 12 0.14
8 9 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
AAATAT
Found at i:1087406 original size:8 final size:8
Alignment explanation
Indices: 1087299--1087409 Score: 54
Period size: 8 Copynumber: 13.8 Consensus size: 8
1087289 TGTAAATAAG
1087299 AATATACTA
1 AATATA-TA
1087308 AA-ATATA
1 AATATATA
*
1087315 ATATAAATA
1 A-ATATATA
1087324 TAATATA-A
1 -AATATATA
1087332 AATAT-TA
1 AATATATA
1087339 AA-ATATTA
1 AATATA-TA
*
1087347 AA-ATTTA
1 AATATATA
*
1087354 TATAATATA
1 AAT-ATATA
1087363 AATATAATA
1 AATAT-ATA
** *
1087372 TTTAAATA
1 AATATATA
1087380 TAAT-TATA
1 -AATATATA
*
1087388 AATATAAA
1 AATATATA
1087396 AATATATA
1 AATATATA
1087404 AATATA
1 AATATA
1087410 ATATAAATAC
Statistics
Matches: 77, Mismatches: 14, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
6 2 0.03
7 17 0.22
8 35 0.45
9 22 0.29
10 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (8 bp):
AATATATA
Found at i:1087423 original size:19 final size:18
Alignment explanation
Indices: 1087308--1087426 Score: 68
Period size: 19 Copynumber: 6.3 Consensus size: 18
1087298 GAATATACTA
1087308 AAATATAATATAAAT-AT
1 AAATATAATATAAATAAT
* *
1087325 AATATAAAATATTAAAATATT
1 AA-ATATAATA-T-AAATAAT
*
1087346 AAA-AT-TTATATAAT-AT
1 AAATATAATATA-AATAAT
1087362 AAATATAATATTTAAAT-AT
1 AAATATAATA--TAAATAAT
*
1087381 AATTATAAATATAAAAATATAT
1 AAATAT-AATAT--AAATA-AT
1087403 AAATATAATATAAATACAT
1 AAATATAATATAAATA-AT
1087422 AAATA
1 AAATA
1087427 GGATATAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
16 5 0.06
17 8 0.10
18 12 0.15
19 24 0.30
20 15 0.19
21 8 0.10
22 7 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATATAATATAAATAAT
Found at i:1087432 original size:19 final size:19
Alignment explanation
Indices: 1087395--1087435 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1087385 ATAAATATAA
* *
1087395 AAATATATAAATATAATAT
1 AAATACATAAATAGAATAT
*
1087414 AAATACATAAATAGGATAT
1 AAATACATAAATAGAATAT
1087433 AAA
1 AAA
1087436 ATTTAATTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATACATAAATAGAATAT
Found at i:1089046 original size:17 final size:18
Alignment explanation
Indices: 1089005--1089049 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
1088995 CTAACAAAAT
1089005 AAATTAAAGGATGACTATG
1 AAATTAAAGGATGACTA-G
1089024 AAATTAAAGGATGACTA-
1 AAATTAAAGGATGACTAG
1089041 AAATTAAAG
1 AAATTAAAG
1089050 TTCTTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (18 bp):
AAATTAAAGGATGACTAG
Found at i:1090624 original size:157 final size:154
Alignment explanation
Indices: 1090376--1090695 Score: 586
Period size: 157 Copynumber: 2.1 Consensus size: 154
1090366 TAATTCCCAG
1090376 TATTTTTATTTTATTCCCAAACAAAAAGCCTAAAAAAAAAAATCCTAACATAAGAAAAATAGATT
1 TATTTTTATTTTATTCCCAAACAAAAAGCCTAAAAAAAAAAATCCTAACATAAGAAAAATAGATT
1090441 TGAAAAGATAAAAAAAGATTAACTTTTTTACTAAATTAATATAGTTTATTAAATTAATTACTAAA
66 TGAAAAGATAAAAAAAGATTAACTTTTTTACTAAATTAATATAGTTTATTAAATTAATTACTAAA
1090506 ATATTAGATTTGAGGTTTCGTAAA
131 ATATTAGATTTGAGGTTTCGTAAA
1090530 TATTTTTATTTTATTCCCAAACAAAAAGCCTAAAAATAAAAAAAATCCTAACATAAGAAAAATAG
1 TATTTTTATTTTATTCCCAAACAAAAAGCCT--AAA-AAAAAAAATCCTAACATAAGAAAAATAG
* *
1090595 ATTTGAAAAGATAAATAAAGATTAACTTTTTTACTAAATTAATATATTTTATTAAATTAATTACT
63 ATTTGAAAAGATAAAAAAAGATTAACTTTTTTACTAAATTAATATAGTTTATTAAATTAATTACT
1090660 AAAATATTAGATTTGAGGTTTCGTAAA
128 AAAATATTAGATTTGAGGTTTCGTAAA
*
1090687 CATTTTTAT
1 TATTTTTAT
1090696 ACGTCAAAGC
Statistics
Matches: 160, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 31 0.19
156 3 0.02
157 126 0.79
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (154 bp):
TATTTTTATTTTATTCCCAAACAAAAAGCCTAAAAAAAAAAATCCTAACATAAGAAAAATAGATT
TGAAAAGATAAAAAAAGATTAACTTTTTTACTAAATTAATATAGTTTATTAAATTAATTACTAAA
ATATTAGATTTGAGGTTTCGTAAA
Found at i:1093157 original size:19 final size:20
Alignment explanation
Indices: 1093113--1093166 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1093103 TTGCCAGTTT
**
1093113 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
1093133 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1093152 CATGTATCGATACAA
1 CATGTATCGATACAA
1093167 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1093510 original size:11 final size:12
Alignment explanation
Indices: 1093493--1093526 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1093483 TTTAAGATAT
1093493 TATATATTTAAA
1 TATATATTTAAA
1093505 -ATATATTTAAA
1 TATATATTTAAA
*
1093516 TAAATATTTAA
1 TATATATTTAA
1093527 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATTTAAA
Found at i:1093890 original size:28 final size:28
Alignment explanation
Indices: 1093834--1093891 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1093824 CACATGGGCA
* **
1093834 AAAACAATTGTATTTTGATAAATGTTTT
1 AAAACAATAGTATTTTGATAAATAATTT
* *
1093862 AAAATAATAGTATTTTGATAATTAATTT
1 AAAACAATAGTATTTTGATAAATAATTT
1093890 AA
1 AA
1093892 TAAACAACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (28 bp):
AAAACAATAGTATTTTGATAAATAATTT
Found at i:1096112 original size:18 final size:18
Alignment explanation
Indices: 1096089--1096126 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1096079 CCTTTCAAAG
1096089 TAAACTTTCACAATGACT
1 TAAACTTTCACAATGACT
*
1096107 TAAACTTTTACAATGACT
1 TAAACTTTCACAATGACT
1096125 TA
1 TA
1096127 TAAACAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
TAAACTTTCACAATGACT
Found at i:1098377 original size:65 final size:65
Alignment explanation
Indices: 1098291--1098412 Score: 140
Period size: 65 Copynumber: 1.9 Consensus size: 65
1098281 TGAAATTTAC
* ** *
1098291 AAGATAAAAATTTTACGTCATACTGCAAACAAATTTAT-TTAAACATTATGATTGACACAATAGA
1 AAGATAAAAATTGTACGTCATACTGCAAACAAATAGATCTCAAA-ATTATGATTGACACAATAGA
1098355 A
65 A
* * * *
1098356 AAGATGAAAATTGTA-GATCATATTGTAAATAAATAGATCTCAAAATTATGATTGACA
1 AAGATAAAAATTGTACG-TCATACTGCAAACAAATAGATCTCAAAATTATGATTGACA
1098413 TTATCTACTC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
64 1 0.02
65 42 0.89
66 4 0.09
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (65 bp):
AAGATAAAAATTGTACGTCATACTGCAAACAAATAGATCTCAAAATTATGATTGACACAATAGAA
Found at i:1098679 original size:20 final size:21
Alignment explanation
Indices: 1098639--1098683 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
1098629 GATATGATTA
1098639 AATGTTTTTCAAGCATAAAAAT
1 AATGTTTTTCAAG-ATAAAAAT
1098661 AATGTTTTTCAAG-TAAAAAT
1 AATGTTTTTCAAGATAAAAAT
1098681 AAT
1 AAT
1098684 TCAAAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.43
22 13 0.57
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (21 bp):
AATGTTTTTCAAGATAAAAAT
Found at i:1109369 original size:21 final size:21
Alignment explanation
Indices: 1109328--1109370 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1109318 AATTAAAGAC
* *
1109328 AATAAATAATTATTTTCAAAA
1 AATAAAAAATCATTTTCAAAA
1109349 AATAAAAAATCATCTTT-AAAA
1 AATAAAAAATCAT-TTTCAAAA
1109370 A
1 A
1109371 TTTAAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAAAAAATCATTTTCAAAA
Found at i:1112451 original size:15 final size:16
Alignment explanation
Indices: 1112426--1112463 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1112416 ACTTATTACC
1112426 ATATCAAAATAT-TTAA
1 ATAT-AAAATATCTTAA
1112442 ATATAAAATATCTTAA
1 ATATAAAATATCTTAA
1112458 ATATAA
1 ATATAA
1112464 TTTTAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAAAATATCTTAA
Found at i:1114049 original size:580 final size:578
Alignment explanation
Indices: 1113264--1114994 Score: 2601
Period size: 580 Copynumber: 3.0 Consensus size: 578
1113254 CATGCAATCT
* * *
1113264 AAATAGGCAAAATTCTATTCGTATTGCAAGCAATTTTTTCTTATAAAATGACTCATAAATTTAAA
1 AAATAAGCAAAATTCTATCCGTATTGCAAGCAATTTTTTCTTATGAAATGACTCATAAATTT---
* *
1113329 AAAAAAAATTCTAAAATATTAGATTTGAGGTTTCATCTAACATGTGAAACATCTTTTATCCCTTA
63 AAAAAAAA-T-TAAAATATTAGATTTGAGGTTTCATCTAACATGTGAAACGTCTTTTATCCCTCA
*
1113394 AAGCAGCTTATATTCCAAGTGGAATAGCAATAGTGTTTCAACAGCCATATTCATCATAATTATCA
126 AAGTAGCTTATATTCCAAGTGGAATAGCAATAGTGTTTCAACAGCCATATTCATCATAATTATCA
* *
1113459 TATGAATATGAGGTATGAATACCATGGTTGTTGTAATCAAAAGCAGAAAATTCAACCTCATATTG
191 TATGAATATGAGGTATGAATACCATGGTTGTTGTAATCAAAAGCAAAAAATTCAACCCCATATTG
1113524 CAAGTTATTTTATTTTTCCATAT-CCTATAAGGGACTATTATTAATTTTATGATTTGGACTCTCC
256 CAAGTTATTTTATTTTTCCAT-TGCCTATAAGGGACTATTATTAATTTTATGATTTGGACTCTCC
* *
1113588 AAGACAGTGATTGATGGATTGACAAGACAAAATTTCTTCATCATATAGCAAGCAAATTTATTTAA
320 AAGATAGTGATTGATGAATTGACAAGACAAAATTTCTTCATCATATAGCAAGCAAATTTATTTAA
*
1113653 TTGACGTAATGAAAAGAATTACAATTCTACACCATATTGCAAGCAAATTGATTTCAAAATTATGA
385 TTGACGCAATGAAAAGAATTACAATTCTACACCATATTGCAAGCAAATTGATTTCAAAATTATGA
* *
1113718 TTGACGTTATGAAAAGGATTAAAATTCTATTCATATTGCAGGCAATTATGTCTTTCTTTCTTTTT
450 TTGACGTTATGAAAAGGAATAAAATTCTATTCATATTGCAGGC-A--AT-TCTTTCTTTTTTTTT
* *
1113783 GATGTAGTAATTGGATTACGAATATATTTTAAAAAA-ATGCTAAACATTTAATTTAGTAATGGAT
511 GATGTAGTAATTGGATTACGAATATATTTAAAAAAACATGCTAAACATTTAATTTAATAATGGAT
1113847 ATC
576 ATC
* * * *
1113850 AAATAAGTAAAATTCTATCCATATTGGAAGCAATTTTTTCTTATGAAATGACTCAGAAA-TTAAA
1 AAATAAGCAAAATTCTATCCGTATTGCAAGCAATTTTTTCTTATGAAATGACTCATAAATTTAAA
* *
1113914 AAAAATTAAAATATTAGATTTGAGGTTTCATCTAACATGTGAAACGTCTTTTATCTCTCAAAATA
66 AAAAATTAAAATATTAGATTTGAGGTTTCATCTAACATGTGAAACGTCTTTTATCCCTCAAAGTA
* * * *
1113979 GCTTATATTTCAAATGGAATAGCAATAGTATTTCAATAGCCATATTCATCATAATTATCATATGA
131 GCTTATATTCCAAGTGGAATAGCAATAGTGTTTCAACAGCCATATTCATCATAATTATCATATGA
* *
1114044 ATATGAGGTATGAATATCATGGTTGTTGTAATCAAAAGCAAAAAATTCAACCCCATATTGTAAGT
196 ATATGAGGTATGAATACCATGGTTGTTGTAATCAAAAGCAAAAAATTCAACCCCATATTGCAAGT
* * * * *
1114109 TATTTTATTTTTCCATTGCCTATATGAGATTATTATTAATTTTATGATTTGAACTCTGCAAGATA
261 TATTTTATTTTTCCATTGCCTATAAGGGACTATTATTAATTTTATGATTTGGACTCTCCAAGATA
* *
1114174 GTGATTGATAAATTGACAAGACAAAATTTCTTCATCATATAGCAAGCAAATTTTTTTAATTGACG
326 GTGATTGATGAATTGACAAGACAAAATTTCTTCATCATATAGCAAGCAAATTTATTTAATTGACG
* * * **
1114239 CAATGAAAAGAATTACAGTTCTACACCATATTGCAAGAAAATTGATTTCAAAATTATGGTTGGTG
391 CAATGAAAAGAATTACAATTCTACACCATATTGCAAGCAAATTGATTTCAAAATTATGATTGACG
* * ** * *
1114304 TTATGAAAAAGAATAAAATTCTATTTATATTGTGGGCAATTCTTTCTTTATTTTTTGACGTAGCA
456 TTATGAAAAGGAATAAAATTCTATTCATATTGCAGGCAATTCTTTCTTT-TTTTTTGATGTAGTA
* * * *
1114369 ATTAGATTACGAATATATTTAAAAAAACATGCTAAACTTTTAATTTAATAATAGATGTC
520 ATTGGATTACGAATATATTTAAAAAAACATGCTAAACATTTAATTTAATAATGGATATC
* * * *
1114428 AAATAGGCAAAATTCTATCCGTATTGCAAGCAATTTTTTCTTAAGAAATGACTCTTAAATTTTTA
1 AAATAAGCAAAATTCTATCCGTATTGCAAGCAATTTTTTCTTATGAAATGACTCATAAA-TTTAA
** *
1114493 AAAAACCTAAAATATTAGATTTGAGGTTTCATCTAACATGTGGAACGTCTTTTATCCCTCAAAGT
65 AAAAAATTAAAATATTAGATTTGAGGTTTCATCTAACATGTGAAACGTCTTTTATCCCTCAAAGT
* * * *
1114558 AGCTTATATTCCAAGTGGAATAACAACAGTGTTTCAACAACTATATTCATCATAATTATCATATG
130 AGCTTATATTCCAAGTGGAATAGCAATAGTGTTTCAACAGCCATATTCATCATAATTATCATATG
*
1114623 AATATGAGGTATGAATACCATAGTTGTTGTAATCAAAAGCAAAAAATTCAACCCCATATTGCAAG
195 AATATGAGGTATGAATACCATGGTTGTTGTAATCAAAAGCAAAAAATTCAACCCCATATTGCAAG
*
1114688 TTATTTTATTTTTCCATTGTCTATATA-GGACTATTATTAATTTTATGATTTGGACTCTCCAAGA
260 TTATTTTATTTTTCCATTGCCTATA-AGGGACTATTATTAATTTTATGATTTGGACTCTCCAAGA
* *
1114752 TAGTGATTGATGAATTGACAAGATAAAATTTCTTCACCATATAGCAAGCAAATTTATTTAATTGA
324 TAGTGATTGATGAATTGACAAGACAAAATTTCTTCATCATATAGCAAGCAAATTTATTTAATTGA
* *
1114817 CGCAATGAAAAGAATTACAATTCT--A-C--A---C--GCAAATTGTTTTTAAAATTATGATTGA
389 CGCAATGAAAAGAATTACAATTCTACACCATATTGCAAGCAAATTGATTTCAAAATTATGATTGA
* *
1114872 CGTTATGAAAAGGAAAAAAATTCTATTCATATTACAGGCAATTCTTT-TTTTTTTTTGATGTAGT
454 CGTTATGAAAAGGAATAAAATTCTATTCATATTGCAGGCAATTCTTTCTTTTTTTTTGATGTAGT
*
1114936 AATTGGATTACAAATATATTTAAAAAAAAACATGCTAAACATTTAATTTAATAATGGAT
519 AATTGGATTACGAATATATTT--AAAAAAACATGCTAAACATTTAATTTAATAATGGAT
1114995 GTATAGTTGA
Statistics
Matches: 1035, Mismatches: 102, Indels: 32
0.89 0.09 0.03
Matches are distributed among these distances:
568 31 0.03
569 3 0.00
570 96 0.09
572 1 0.00
575 1 0.00
576 9 0.01
577 40 0.04
578 80 0.08
579 2 0.00
580 709 0.69
581 1 0.00
582 8 0.01
585 2 0.00
586 52 0.05
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (578 bp):
AAATAAGCAAAATTCTATCCGTATTGCAAGCAATTTTTTCTTATGAAATGACTCATAAATTTAAA
AAAAATTAAAATATTAGATTTGAGGTTTCATCTAACATGTGAAACGTCTTTTATCCCTCAAAGTA
GCTTATATTCCAAGTGGAATAGCAATAGTGTTTCAACAGCCATATTCATCATAATTATCATATGA
ATATGAGGTATGAATACCATGGTTGTTGTAATCAAAAGCAAAAAATTCAACCCCATATTGCAAGT
TATTTTATTTTTCCATTGCCTATAAGGGACTATTATTAATTTTATGATTTGGACTCTCCAAGATA
GTGATTGATGAATTGACAAGACAAAATTTCTTCATCATATAGCAAGCAAATTTATTTAATTGACG
CAATGAAAAGAATTACAATTCTACACCATATTGCAAGCAAATTGATTTCAAAATTATGATTGACG
TTATGAAAAGGAATAAAATTCTATTCATATTGCAGGCAATTCTTTCTTTTTTTTTGATGTAGTAA
TTGGATTACGAATATATTTAAAAAAACATGCTAAACATTTAATTTAATAATGGATATC
Found at i:1115971 original size:18 final size:18
Alignment explanation
Indices: 1115948--1115982 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1115938 CCTCTCAAAG
1115948 TAAACTTTCACAATGACA
1 TAAACTTTCACAATGACA
*
1115966 TAAACTTTTACAATGAC
1 TAAACTTTCACAATGAC
1115983 TTATAGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
TAAACTTTCACAATGACA
Found at i:1116882 original size:28 final size:28
Alignment explanation
Indices: 1116814--1116882 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
1116804 GTATTCCTAT
*
1116814 TATTTTGAGTTTTAAAATCATATTTAAGA
1 TATTTT-AGATTTAAAATCATATTTAAGA
* *
1116843 TATTATATATTTAAAAT-ATATTTAA-A
1 TATTTTAGATTTAAAATCATATTTAAGA
1116869 TAAATTTTAGATTT
1 T--ATTTTAGATTT
1116883 TTTAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 2 0.06
27 8 0.24
28 18 0.55
29 5 0.15
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (28 bp):
TATTTTAGATTTAAAATCATATTTAAGA
Found at i:1117663 original size:2 final size:2
Alignment explanation
Indices: 1117656--1117706 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
1117646 TGCCATATTC
* *
1117656 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AA ACT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1117697 AT AT AT AT AT
1 AT AT AT AT AT
1117707 TCCAAAGCGG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 40 0.93
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1117939 original size:3 final size:3
Alignment explanation
Indices: 1117931--1117956 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1117921 CTTTGGTTGT
1117931 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1117957 TACAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1118521 original size:29 final size:30
Alignment explanation
Indices: 1118466--1118528 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1118456 AACATGTTTG
* ** *
1118466 TAAACAAATAAAATTATATTCATAAAC-AA
1 TAAACAAATAAAATTAAATAAACAAACAAA
*
1118495 TAAACAAATAAATTTAAATAAACAAACAAA
1 TAAACAAATAAAATTAAATAAACAAACAAA
1118525 TAAA
1 TAAA
1118529 TATGTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (30 bp):
TAAACAAATAAAATTAAATAAACAAACAAA
Found at i:1122609 original size:43 final size:38
Alignment explanation
Indices: 1122504--1122613 Score: 89
Period size: 43 Copynumber: 2.7 Consensus size: 38
1122494 GCGGCTTAAG
1122504 TTATTATTTACATAATAAAAT-AATATATTTTTATTTAAAA
1 TTATT-TTTA-ATAATAAAATAAATA-ATTTTTATTTAAAA
* * * *
1122544 TTAATTATAAATATTAATATAAATAATTTTATATTTTTTAAATA
1 TT-ATTTTTAATAATAAAATAAATAATTTT-TA---TTTAAA-A
1122588 TTATTTTTAATAATAAAATAAA-AATT
1 TTATTTTTAATAATAAAATAAATAATT
1122614 AAATTAATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
39 13 0.24
40 10 0.18
41 3 0.05
42 4 0.07
43 22 0.40
44 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (38 bp):
TTATTTTTAATAATAAAATAAATAATTTTTATTTAAAA
Found at i:1122827 original size:3 final size:3
Alignment explanation
Indices: 1122819--1122857 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1122809 AAGTTAGAAA
* * *
1122819 AAT AAT AAT AAT AAT TAT TAT TAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1122858 TATTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:1122846 original size:21 final size:21
Alignment explanation
Indices: 1122820--1122863 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1122810 AGTTAGAAAA
*
1122820 ATAATAATAATAATTATTATT
1 ATAATAATAATAATAATTATT
1122841 ATAATAATAATAATAATTATT
1 ATAATAATAATAATAATTATT
1122862 AT
1 AT
1122864 TATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATAATAATAATAATTATT
Found at i:1122851 original size:24 final size:24
Alignment explanation
Indices: 1122819--1122866 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1122809 AAGTTAGAAA
1122819 AATAATAATAATAATTATTATTAT
1 AATAATAATAATAATTATTATTAT
1122843 AATAATAATAATAATTATTATTAT
1 AATAATAATAATAATTATTATTAT
1122867 TATTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATAATAATAATAATTATTATTAT
Found at i:1122859 original size:18 final size:18
Alignment explanation
Indices: 1122823--1122860 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1122813 TAGAAAAATA
* *
1122823 ATAATAATAATTATTATT
1 ATAATAATAATAATAATT
1122841 ATAATAATAATAATAATT
1 ATAATAATAATAATAATT
1122859 AT
1 AT
1122861 TATTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATAATAATAATAATT
Found at i:1123118 original size:24 final size:24
Alignment explanation
Indices: 1123091--1123142 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1123081 TGTACTTTCA
1123091 CTAATCTTTACTATATTTAAAGTG
1 CTAATCTTTACTATATTTAAAGTG
1123115 CTAATCTTTACTATATTTAAAGTG
1 CTAATCTTTACTATATTTAAAGTG
1123139 CTAA
1 CTAA
1123143 GTGAATTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (24 bp):
CTAATCTTTACTATATTTAAAGTG
Found at i:1123638 original size:16 final size:16
Alignment explanation
Indices: 1123617--1123647 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1123607 TGATTCAAAA
1123617 TTAAAATAACTTAAAT
1 TTAAAATAACTTAAAT
*
1123633 TTAAAATAATTTAAA
1 TTAAAATAACTTAAA
1123648 ATTTTAATAA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATAACTTAAAT
Found at i:1123822 original size:11 final size:12
Alignment explanation
Indices: 1123798--1123837 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1123788 CAATAACTTT
1123798 AAATATAATATAA
1 AAATATAAT-TAA
1123811 AAAT-TAATT-A
1 AAATATAATTAA
1123821 AAATATAA-TAA
1 AAATATAATTAA
1123832 AAATAT
1 AAATAT
1123838 TATATAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.24
11 11 0.44
12 4 0.16
13 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATAATTAA
Found at i:1123843 original size:34 final size:33
Alignment explanation
Indices: 1123798--1123900 Score: 100
Period size: 36 Copynumber: 3.0 Consensus size: 33
1123788 CAATAACTTT
1123798 AAATATAATATAAAAATTAATTAAAATATAATAA
1 AAATATAATATAAAAATTAATTAAAATATAA-AA
* * *
1123832 AAATATTATATAATACAACTATATAAAAATATAAAA
1 AAATATAATATAA-A-AATTA-ATTAAAATATAAAA
* * * *
1123868 ATATATAATATATAAATT-ATTAATATATTAAA
1 AAATATAATATAAAAATTAATTAAAATATAAAA
1123900 A
1 A
1123901 TTTATAATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
32 12 0.21
34 15 0.27
35 2 0.04
36 16 0.29
37 11 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (33 bp):
AAATATAATATAAAAATTAATTAAAATATAAAA
Found at i:1123907 original size:32 final size:32
Alignment explanation
Indices: 1123860--1123920 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1123850 CTATATAAAA
1123860 ATATAAAAATATATAA-TATATAAATTATTAAT
1 ATATAAAAATATATAATTATAT-AATTATTAAT
* *
1123892 ATATTAAAATTTATAATTATATAATTATT
1 ATATAAAAATATATAATTATATAATTATT
1123921 TAAAACACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATAAAAATATATAATTATATAATTATTAAT
Found at i:1138527 original size:37 final size:36
Alignment explanation
Indices: 1138467--1138536 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1138457 GTATTAAAAT
* * **
1138467 TTATATTAAAAAATATAGAATAATTTAAATATATAA
1 TTATAATAAAAAATATAAAATAATACAAATATATAA
*
1138503 TTATAATAAAAAATTTAAATATAATACAAATATA
1 TTATAATAAAAAATATAAA-ATAATACAAATATA
1138537 AAAATTACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 16 0.57
37 12 0.43
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (36 bp):
TTATAATAAAAAATATAAAATAATACAAATATATAA
Found at i:1139134 original size:31 final size:29
Alignment explanation
Indices: 1139098--1139166 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
1139088 CTTTTTTATT
* *
1139098 TTTTTATTATTGAAAA-TTAATTTTAAAATA
1 TTTTTATTATT-AAAATTTAA-ATAAAAATA
*
1139128 TGTTTTATAATTAAAATTTAAATAAAAATA
1 T-TTTTATTATTAAAATTTAAATAAAAATA
1139158 TTTTTATTA
1 TTTTTATTA
1139167 AAAGAATAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 7 0.21
30 13 0.39
31 13 0.39
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTTTATTATTAAAATTTAAATAAAAATA
Found at i:1140955 original size:28 final size:28
Alignment explanation
Indices: 1140924--1140978 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
1140914 ATTTTTATAT
* * *
1140924 TAATATATATTTAAAAGTAAATTTAAAA
1 TAATATAAATTAAAAAATAAATTTAAAA
* *
1140952 TAATTTAAATTAAAAAATATATTTAAA
1 TAATATAAATTAAAAAATAAATTTAAA
1140979 TTTTACTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
TAATATAAATTAAAAAATAAATTTAAAA
Found at i:1144102 original size:21 final size:23
Alignment explanation
Indices: 1144076--1144122 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
1144066 ATCCTAATAA
1144076 TTTTT-AAAAAAGTGAT-AGTTT
1 TTTTTAAAAAAAGTGATAAGTTT
*
1144097 TTTTTAAAAAAATTGATAAGTTT
1 TTTTTAAAAAAAGTGATAAGTTT
1144120 TTT
1 TTT
1144123 CTAATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
23 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (23 bp):
TTTTTAAAAAAAGTGATAAGTTT
Found at i:1144206 original size:22 final size:22
Alignment explanation
Indices: 1144163--1144206 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1144153 TAACTAATCT
**
1144163 TATAATATTATTATTTAATTTA
1 TATAATATTATTAAATAATTTA
* *
1144185 TATAATATTTTTAAATATTTTA
1 TATAATATTATTAAATAATTTA
1144207 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATAATATTATTAAATAATTTA
Found at i:1144821 original size:11 final size:11
Alignment explanation
Indices: 1144805--1144838 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1144795 ATAATTTATG
1144805 TATTTATTTTA
1 TATTTATTTTA
1144816 TATTTATTTTA
1 TATTTATTTTA
*
1144827 TAATTATATTTA
1 TATTTAT-TTTA
1144839 AAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:1144872 original size:27 final size:28
Alignment explanation
Indices: 1144818--1144873 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1144808 TTATTTTATA
1144818 TTTATTTTATAATTATATTTAAAATATTT
1 TTTATTTTATAA-TATATTTAAAATATTT
*
1144847 TTTATTTATATAA-AT-TTTAATATATTT
1 TTTATTT-TATAATATATTTAAAATATTT
1144874 ATAATTCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 11 0.44
28 2 0.08
29 7 0.28
30 5 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATTTTATAATATATTTAAAATATTT
Found at i:1145216 original size:29 final size:29
Alignment explanation
Indices: 1145174--1145233 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1145164 TGTCCACTAT
1145174 AGACTAAATTGCCAACAGTATTGCAGTTA
1 AGACTAAATTGCCAACAGTATTGCAGTTA
1145203 AGACTAAATTGCCAACAGTATTGCAGTTA
1 AGACTAAATTGCCAACAGTATTGCAGTTA
1145232 AG
1 AG
1145234 TTCATTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (29 bp):
AGACTAAATTGCCAACAGTATTGCAGTTA
Found at i:1146470 original size:18 final size:19
Alignment explanation
Indices: 1146422--1146471 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1146412 TTGTATGGAC
1146422 AAAAT-ATTATATAATTATA
1 AAAATAATTAT-TAATTATA
*
1146441 ATATATAA-TATTAA-TATA
1 A-AAATAATTATTAATTATA
1146459 AAAATAATTATTA
1 AAAATAATTATTA
1146472 CTATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 4 0.15
20 6 0.23
21 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAATTATTAATTATA
Found at i:1149668 original size:75 final size:75
Alignment explanation
Indices: 1149527--1149668 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 75
1149517 GTTTTAAAAG
* ** * * * * *
1149527 AAAATGCTAAAATGACCCTAAATGTTCTATTTTGATATGAAAGTGCTAACATGACCTTAAAGGAT
1 AAAATACTAAAATGACCCTAAAAATGCGATTTTGAAATGAAAGTGCTAACACGACCTTAAAAGAT
1149592 TTTAATGCAA
66 TTTAATGCAA
1149602 AAAATACTAAAATGACCCTAAAAATGCGATTTTGAAATGAAAGTGCTAACACGA-CTCTAAAAGA
1 AAAATACTAAAATGACCCTAAAAATGCGATTTTGAAATGAAAGTGCTAACACGACCT-TAAAAGA
1149666 TTT
65 TTT
1149669 GTTTTTGGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 2 0.03
75 56 0.97
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (75 bp):
AAAATACTAAAATGACCCTAAAAATGCGATTTTGAAATGAAAGTGCTAACACGACCTTAAAAGAT
TTTAATGCAA
Found at i:1149899 original size:37 final size:37
Alignment explanation
Indices: 1149849--1149935 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
1149839 TGTCATTTCC
1149849 TAAGCTTGATCTCAGCTTAAGATACAATCGAACTATT
1 TAAGCTTGATCTCAGCTTAAGATACAATCGAACTATT
*
1149886 TAAGCTTGATCTCAGCTTAAGATATAATCGAACTATT
1 TAAGCTTGATCTCAGCTTAAGATACAATCGAACTATT
1149923 TAAGCTTGA-CTCA
1 TAAGCTTGATCTCA
1149936 ATAAGCTCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 4 0.08
37 45 0.92
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (37 bp):
TAAGCTTGATCTCAGCTTAAGATACAATCGAACTATT
Found at i:1151666 original size:235 final size:235
Alignment explanation
Indices: 1151255--1151717 Score: 899
Period size: 235 Copynumber: 2.0 Consensus size: 235
1151245 CAAGTAACAG
*
1151255 TACCTAAACCTAGATTAAACACATTCCCTGTGGTTGATCTCTGAGTATTACAATCACCTGCATAG
1 TACCTAAACCTAGATTAAACACATTCCCTGTGGTTGATCTCCGAGTATTACAATCACCTGCATAG
1151320 TCAGCATCACAGTATCCTTCAAATTTGCATGTTACTCCACTTTTGTAGAATATACCGAGATGAAG
66 TCAGCATCACAGTATCCTTCAAATTTGCATGTTACTCCACTTTTGTAGAATATACCGAGATGAAG
1151385 TGTACCTCTGATGTATCTCAGAATTCTCCAAACTACTTCCAATTGAGGTTTCTTTAGACTTTGCA
131 TGTACCTCTGATGTATCTCAGAATTCTCCAAACTACTTCCAATTGAGGTTTCTTTAGACTTTGCA
*
1151450 TGAATCTATTGACCACTCCAACTACAACTACAAATACAAC
196 TGAATCTATTGACCACTCCAACTACAAATACAAATACAAC
1151490 TACCTAAACCTAGATTAAACACATTCCCTGTGGTTGATCTCCGAGTATTACAATCACCTGCATAG
1 TACCTAAACCTAGATTAAACACATTCCCTGTGGTTGATCTCCGAGTATTACAATCACCTGCATAG
*
1151555 TCAGCATCATAGTATCCTTCAAATTTGCATGTTACTCCACTTTTGTAGAATATACCGAGATGAAG
66 TCAGCATCACAGTATCCTTCAAATTTGCATGTTACTCCACTTTTGTAGAATATACCGAGATGAAG
1151620 TGTACCTCTGATGTATCTCAGAATTCTCCAAACTACTTCCAATTGAGGTTTCTTTAGACTTTGCA
131 TGTACCTCTGATGTATCTCAGAATTCTCCAAACTACTTCCAATTGAGGTTTCTTTAGACTTTGCA
1151685 TGAATCTATTGACCACTCCAACTACAAATACAA
196 TGAATCTATTGACCACTCCAACTACAAATACAA
1151718 TGTCTGGTCT
Statistics
Matches: 225, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
235 225 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (235 bp):
TACCTAAACCTAGATTAAACACATTCCCTGTGGTTGATCTCCGAGTATTACAATCACCTGCATAG
TCAGCATCACAGTATCCTTCAAATTTGCATGTTACTCCACTTTTGTAGAATATACCGAGATGAAG
TGTACCTCTGATGTATCTCAGAATTCTCCAAACTACTTCCAATTGAGGTTTCTTTAGACTTTGCA
TGAATCTATTGACCACTCCAACTACAAATACAAATACAAC
Found at i:1154097 original size:21 final size:21
Alignment explanation
Indices: 1154071--1154146 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
1154061 ATCCAAGAAT
1154071 ATGTATCGATACATTTGTACA
1 ATGTATCGATACATTTGTACA
**
1154092 ATGTATCGATACATTTGTGGA
1 ATGTATCGATACATTTGTACA
*
1154113 ATGTATCGATACA-TTCTACAA
1 ATGTATCGATACATTTGTAC-A
1154134 ATGTATCGATACA
1 ATGTATCGATACA
1154147 AGGTCCCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACATTTGTACA
Found at i:1154229 original size:19 final size:18
Alignment explanation
Indices: 1154178--1154267 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
1154168 TTGAATTCCA
1154178 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
1154195 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
1154216 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
1154235 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
1154248 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
1154267 A
1 A
1154268 ATGTATCGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:1154242 original size:13 final size:13
Alignment explanation
Indices: 1154224--1154248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1154214 ACATAAGTGT
1154224 TGTATCGATACAA
1 TGTATCGATACAA
1154237 TGTATCGATACA
1 TGTATCGATACA
1154249 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1154244 original size:32 final size:32
Alignment explanation
Indices: 1154203--1154275 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1154193 ACATTCAGTA
1154203 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1154235 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1154267 AATGTATCG
1 AATGTATCG
1154276 CTAGGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1154337 original size:13 final size:13
Alignment explanation
Indices: 1154319--1154344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1154309 CATTTTTCTG
1154319 TGTATCGATACAT
1 TGTATCGATACAT
1154332 TGTATCGATACAT
1 TGTATCGATACAT
1154345 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1154363 original size:34 final size:33
Alignment explanation
Indices: 1154299--1154365 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1154289 GCCAAGGAAA
*
1154299 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
* *
1154332 TGTATCGATACATCTATTCTTTGTATTGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
1154366 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:1156768 original size:51 final size:51
Alignment explanation
Indices: 1156710--1156829 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
1156700 AATTCTCCGC
* * * * *
1156710 AATCGGGGATATTCTC-ACTCTGA-TTTATTTTTCAAAA-CACTAATTTTCTAT
1 AATCGGGGATACTC-CAACTCCGATTTTATTTCTAAAAACCACCAATTTT-T-T
1156761 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAACCACCAATTTTTT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAACCACCAATTTTTT
*
1156812 TATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
1156830 CCCGTTAATC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 37 0.62
52 13 0.22
53 9 0.15
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAACCACCAATTTTTT
Found at i:1156883 original size:28 final size:27
Alignment explanation
Indices: 1156813--1156885 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
1156803 CAATTTTTTT
1156813 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
1156840 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
1156866 TTCGAGGGGATACTCCAACC
1 ATC--GGGGATACTCCAACC
1156886 ATTGCTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
26 4 0.10
27 23 0.55
28 15 0.36
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:1156982 original size:79 final size:78
Alignment explanation
Indices: 1156840--1157010 Score: 202
Period size: 79 Copynumber: 2.2 Consensus size: 78
1156830 CCCGTTAATC
* * * *
1156840 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCATTGCTTTATTCTTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCA-CGCTTTATTCTTAAAAC
** *
1156905 ATTGATTTCTCATA
65 ATCAATTTCCCATA
* *
1156919 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCTAATCC-CGGTTTCATT-TCTAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAA-CCACGCTTT-ATTCT-TAAA
*
1156982 ACATCAATTTCCCTTA
63 ACATCAATTTCCCATA
1156998 ATCGGGGATACTC
1 ATCGGGGATACTC
1157011 TAACTCCGAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 5 0.06
79 72 0.91
80 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCACGCTTTATTCTTAAAACA
TCAATTTCCCATA
Found at i:1157095 original size:52 final size:51
Alignment explanation
Indices: 1156951--1157117 Score: 192
Period size: 51 Copynumber: 3.3 Consensus size: 51
1156941 TATTTCCGAA
* * * * * * *
1156951 GGGATACTCTAA-TCCCGGTTTCATTTCTAAAACATCAATTTCCCTTAATCG
1 GGGATACTCCAACT-CCGATTTTATTTCAAAAACACCAATTTTCCATAATCG
* * *
1157002 GGGATACTCTAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAATCG
1 GGGATACTCCAACTCCGATTTTATTTCAAAAACACCAATTTTCCATAATCG
* *
1157053 GGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCG
1 GGGATACTCCAACTCCGATTTTATTT-CAAAAACACCAATTTTCCATAATCG
*
1157105 AGGATACTCCAAC
1 GGGATACTCCAAC
1157118 CTCATTATTT
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
51 68 0.67
52 34 0.33
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCAAAAACACCAATTTTCCATAATCG
Found at i:1157227 original size:289 final size:287
Alignment explanation
Indices: 1156710--1157256 Score: 819
Period size: 289 Copynumber: 1.9 Consensus size: 287
1156700 AATTCTCCGC
* * * * * *
1156710 AATCGGGGATATTCTCACTCTGATTTATTTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCTAACTCCGATTTATTTCTCAAAACACCAATTTTCCATAATCGGGGATACTC
* ** * *
1156775 CAACTCCGATTTTATTTCTAAAAACCACCAATTTTTTTATCGGGGATACTCCAACCCCGTTAATC
66 CAACTCCGATTTTATTTCCAAAAACCACCAATTTTTCAATCGAGGATACTCCAACCCCATTAATC
** * ** *
1156840 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCATTGCTTTATTCTTAAAAT
131 ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCACGGCTTTATTCCTAAAAT
*
1156905 ATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCTAATCCCGGT
196 ATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGGT
1156970 TTCATTTCTAAAACATCAATTTCCCTT
261 TTCATTTCTAAAACATCAATTTCCCTT
*
1156997 AATCGGGGATACTCTAACTCCGATTTTATTTCT-AAAACACCCATTTTCCATAATCGGGGATACT
1 AATCGGGGATACTCTAACTCCGA-TTTATTTCTCAAAACACCAATTTTCCATAATCGGGGATACT
*
1157061 CCAACTCCGATTTTATTTCCAAAAA-CACCAATTTTTCACAATCGAGGATACTCCAACCTCATTA
65 CCAACTCCGATTTTATTTCCAAAAACCACCAATTTTT--CAATCGAGGATACTCCAACCCCATTA
* *
1157125 TTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTA
128 -ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCACGGCTTTATTCCTA
* * *
1157190 AAATATTGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCC
192 AAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCC
1157255 CG
257 CG
1157257 ATTTTTTTTT
Statistics
Matches: 231, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
286 11 0.05
287 72 0.31
288 29 0.13
289 119 0.52
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (287 bp):
AATCGGGGATACTCTAACTCCGATTTATTTCTCAAAACACCAATTTTCCATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAACCACCAATTTTTCAATCGAGGATACTCCAACCCCATTAATC
ATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCACGGCTTTATTCCTAAAAT
ATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGGT
TTCATTTCTAAAACATCAATTTCCCTT
Found at i:1157277 original size:79 final size:78
Alignment explanation
Indices: 1157131--1157335 Score: 225
Period size: 79 Copynumber: 2.6 Consensus size: 78
1157121 ATTATTTCAT
** *
1157131 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCT-AAATAT
* *
1157196 TGATTTCTCATAAT
65 TGATTTCTCACAAC
* * ** * *
1157210 TGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGATTTTTTTTTCT-AATCA
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCG-GCTTTATTCCTAAAT-A
1157274 TTGATTTCTCACAAC
64 TTGATTTCTCACAAC
* * * *
1157289 CGGGGATACTCCAGCCCTGTTATTT-TCAAGGGGACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCG
1157336 TTATTATCTC
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 4 0.04
79 95 0.90
80 7 0.07
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCTAAATATT
GATTTCTCACAAC
Found at i:1166541 original size:13 final size:13
Alignment explanation
Indices: 1166523--1166548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1166513 TTCCTATCAA
1166523 ACCTGAGTGTAAG
1 ACCTGAGTGTAAG
1166536 ACCTGAGTGTAAG
1 ACCTGAGTGTAAG
1166549 CCCATACAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
ACCTGAGTGTAAG
Found at i:1169684 original size:1 final size:1
Alignment explanation
Indices: 1169680--1169765 Score: 64
Period size: 1 Copynumber: 86.0 Consensus size: 1
1169670 CATTCTTTTT
* * * * * * * * *
1169680 AAAAAAAAACAACAAAAAAAACAACAAAAAAAAACAAAAAACAAAAAAAAAACAAAACAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1169745 AAAGAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
1169766 GAAGAATCTG
Statistics
Matches: 61, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1169698 original size:12 final size:12
Alignment explanation
Indices: 1169681--1169734 Score: 73
Period size: 11 Copynumber: 4.9 Consensus size: 12
1169671 ATTCTTTTTA
1169681 AAAAAAAACAAC
1 AAAAAAAACAAC
1169693 AAAAAAAACAAC
1 AAAAAAAACAAC
1169705 -AAAAAAA-AAC
1 AAAAAAAACAAC
1169715 --AAAAAACAA-
1 AAAAAAAACAAC
1169724 AAAAAAAACAA
1 AAAAAAAACAA
1169735 AACAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.15
10 5 0.13
11 16 0.41
12 12 0.31
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAC
Found at i:1169712 original size:28 final size:27
Alignment explanation
Indices: 1169680--1169765 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
1169670 CATTCTTTTT
*
1169680 AAAAAAAAACAACAAAAAAAACAACAAA
1 AAAAAAAAAAAACAAAAAAAA-AACAAA
1169708 AAAAAACAAAAAACAAAAAAAAAACAAA
1 AAAAAA-AAAAAACAAAAAAAAAACAAA
* * * *
1169736 ACAAAGAAAAAAGAGAAAAAAAAAGAAA
1 AAAAAAAAAAAACA-AAAAAAAAACAAA
1169764 AA
1 AA
1169766 GAAGAATCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.14
28 29 0.58
29 14 0.28
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAACAAAAAAAAAACAAA
Found at i:1169713 original size:17 final size:16
Alignment explanation
Indices: 1169680--1169765 Score: 86
Period size: 17 Copynumber: 5.2 Consensus size: 16
1169670 CATTCTTTTT
*
1169680 AAAAAAAAAC-AACAA
1 AAAAAAAAACAAAAAA
*
1169695 AAAAAACAACAAAAAA
1 AAAAAAAAACAAAAAA
1169711 AAACAAAAAACAAAAAA
1 AAA-AAAAAACAAAAAA
*
1169728 AAAACAAAACAAAGAAA
1 AAAAAAAAACAAA-AAA
*
1169745 AAAGAGAAAAA-AAAAGA
1 AAA-A-AAAAACAAAAAA
1169762 AAAA
1 AAAA
1169766 GAAGAATCTG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.15
16 17 0.28
17 26 0.43
18 4 0.07
19 4 0.07
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAA
Found at i:1170891 original size:100 final size:99
Alignment explanation
Indices: 1170732--1170913 Score: 292
Period size: 100 Copynumber: 1.8 Consensus size: 99
1170722 CCTTCCGCTT
* * *
1170732 TTTAGCCCTCAAAGAGCAGTATGCCTTTCCTTTTAAAGCCCCCACAAGTTGGTGGCACTTCCCAG
1 TTTAGCCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAG
*
1170797 TCCTTAAAGAGCAGGACGCTCTCTCCTTTCGCCC
66 TCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCC
* **
1170831 TTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
1 TTTAGCCCTCAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCA
1170896 GTCCTCAAAGAGCAGGAC
65 GTCCTCAAAGAGCAGGAC
1170914 ACCTTTCAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
99 24 0.32
100 51 0.68
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (99 bp):
TTTAGCCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAG
TCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCC
Found at i:1170944 original size:55 final size:55
Alignment explanation
Indices: 1170860--1171244 Score: 501
Period size: 55 Copynumber: 6.9 Consensus size: 55
1170850 GACGCCTTCT
*
1170860 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* *
1170915 CCTTTCAAAGCCCACACAAATTGATGGCACCTTTT-AGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACA
*
1170970 CCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAGGACG
1 ------CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACA
*
1171031 CCTTTCAAAG-CCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACA
* * **
1171085 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGATG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* * * *
1171140 TCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
* * *
1171195 CCTTTCAAAGCCCACACGAGTTGGTGGAACTTTTTAGTCCTCAAAGAGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
1171245 AGATACACTT
Statistics
Matches: 298, Mismatches: 19, Indels: 26
0.87 0.06 0.08
Matches are distributed among these distances:
52 4 0.01
54 45 0.15
55 189 0.63
56 8 0.03
61 52 0.17
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACA
Found at i:1172027 original size:21 final size:21
Alignment explanation
Indices: 1172003--1172077 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
1171993 TTTTGATCCA
*
1172003 AATGTATCGATACATTTGTAC
1 AATGTATCGATACATTTATAC
**
1172024 AATGTATCGATACATTTATGG
1 AATGTATCGATACATTTATAC
* *
1172045 AATGTATCAATACA-TTCTAC
1 AATGTATCGATACATTTATAC
1172065 AAATGTATCGATA
1 -AATGTATCGATA
1172078 AAAGGTCCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 3 0.07
21 42 0.93
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTATAC
Found at i:1172162 original size:19 final size:18
Alignment explanation
Indices: 1172111--1172200 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
1172101 TTGAATTTCA
1172111 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
1172128 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
1172149 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
1172168 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
1172181 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
1172200 A
1 A
1172201 ATGTATCGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:1172175 original size:13 final size:13
Alignment explanation
Indices: 1172157--1172181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1172147 ACATAAGTGT
1172157 TGTATCGATACAA
1 TGTATCGATACAA
1172170 TGTATCGATACA
1 TGTATCGATACA
1172182 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1172177 original size:32 final size:32
Alignment explanation
Indices: 1172136--1172208 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1172126 ACATTCAGTA
1172136 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1172168 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1172200 AATGTATCG
1 AATGTATCG
1172209 CTAGGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1172270 original size:13 final size:13
Alignment explanation
Indices: 1172252--1172277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1172242 CATTTTTCTG
1172252 TGTATCGATACAT
1 TGTATCGATACAT
1172265 TGTATCGATACAT
1 TGTATCGATACAT
1172278 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1172295 original size:34 final size:33
Alignment explanation
Indices: 1172232--1172298 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1172222 GCCAAGGAAA
*
1172232 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
1172265 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
1172299 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:1172804 original size:20 final size:20
Alignment explanation
Indices: 1172759--1172810 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1172749 GTAGCCAAAC
**
1172759 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
1172779 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1172798 TTGTATCGATACA
1 TTGTATCGATACA
1172811 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1175909 original size:51 final size:51
Alignment explanation
Indices: 1175814--1175917 Score: 140
Period size: 51 Copynumber: 2.0 Consensus size: 51
1175804 GGATATTCTC
* * *
1175814 ACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCA
1 ACTCCGATTTTATTTCCAAAACACCAATTTTCTATAATCAGGGATACTCCA
*
1175865 ACTCCGATTTTATTTCCAAAAAACACCAATTTT-T-TCATCAGGGATACTCCA
1 ACTCCGATTTTATTTCC--AAAACACCAATTTTCTATAATCAGGGATACTCCA
1175916 AC
1 AC
1175918 CCTGTTAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
51 33 0.70
52 1 0.02
53 13 0.28
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (51 bp):
ACTCCGATTTTATTTCCAAAACACCAATTTTCTATAATCAGGGATACTCCA
Found at i:1175936 original size:27 final size:28
Alignment explanation
Indices: 1175899--1175975 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
1175889 ACCAATTTTT
*
1175899 TCATCAGGGATACTCCAACCCTGTTA-A
1 TCATCGGGGATACTCCAACCCTGTTATA
* *
1175926 TCATCGGGGATACTCCAACCCCGTTATT
1 TCATCGGGGATACTCCAACCCTGTTATA
***
1175954 TCCGAGGGGATACTCCAACCCT
1 TCATCGGGGATACTCCAACCCT
1175976 TGCTTTATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (28 bp):
TCATCGGGGATACTCCAACCCTGTTATA
Found at i:1176070 original size:79 final size:78
Alignment explanation
Indices: 1175928--1176102 Score: 219
Period size: 79 Copynumber: 2.2 Consensus size: 78
1175918 CCTGTTAATC
* *
1175928 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTTGCTTTATTCTTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCC-TGCTTTATTCTTAAAAC
**
1175993 ATTGATTTCTCATA
65 ATCAATTTCTCATA
* * *
1176007 ATCGGGGATACTCCAACCCTGTTATTTCCGAAGGGATACTCTAATCCC-GGTTTCATT-TATAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAA-CCCTGCTTT-ATTCT-TAAA
*
1176070 ACATCAATTTCTCTTA
63 ACATCAATTTCTCATA
*
1176086 ATCGAGGATACTCCAAC
1 ATCGGGGATACTCCAAC
1176103 TTCGATTTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
78 5 0.06
79 76 0.90
80 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCTGCTTTATTCTTAAAACA
TCAATTTCTCATA
Found at i:1176121 original size:51 final size:51
Alignment explanation
Indices: 1176061--1176205 Score: 200
Period size: 51 Copynumber: 2.8 Consensus size: 51
1176051 TCCCGGTTTC
* * * * *
1176061 ATTTATAAAACATCAATTTCTCTTAATCGAGGATACTCCAACTTCGATTTT
1 ATTTCTAAAACACCAATTTTTCATAATCGAGGATACTCCAACTCCGATTTT
* *
1176112 ATTTCTAAAACACCCATTTTTCATAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCTAAAACACCAATTTTTCATAATCGAGGATACTCCAACTCCGATTTT
* *
1176163 ATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
1 ATTT-CTAAAACACCAATTTTTCATAATCGAGGATACTCCAAC
1176206 CTCGTTATTT
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 48 0.59
52 34 0.41
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (51 bp):
ATTTCTAAAACACCAATTTTTCATAATCGAGGATACTCCAACTCCGATTTT
Found at i:1176217 original size:31 final size:28
Alignment explanation
Indices: 1176194--1176265 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1176184 TCACAATCGA
*
1176194 GGATACTCCAACCTCGTTATTTCATCAG
1 GGATACTCCAACCCCGTTATTTCATCAG
**
1176222 GGATACTCCAACCCCGTTACCTC--CGAGG
1 GGATACTCCAACCCCGTTATTTCATC-A-G
1176250 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1176266 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 37 0.95
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCATCAG
Found at i:1176335 original size:289 final size:287
Alignment explanation
Indices: 1175818--1176344 Score: 830
Period size: 289 Copynumber: 1.8 Consensus size: 287
1175808 ATTCTCACTC
*
1175818 CGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCA
1 CGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCA
* *
1175883 AAAAACACCAATTTTTTCATCAGGGATACTCCAACCCTGTTAATCATCGGGGATACTCCAACCCC
66 AAAAACACCAATTTTTACATCAGGGATACTCCAACCCTGTTAATCATCAGGGATACTCCAACCCC
** ** **
1175948 GTTATTTCCGAGGGGATACTCCAACCCTTGCTTTATTCTTAAAATATTGATTTCTCATAATCGGG
131 GTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATCGGG
* *
1176013 GATACTCCAACCCTGTTATTTCCGAAGGGATACTCTAATCCCGGTTTCATTTATAAAACATCAAT
196 GATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGGTTTCATTTATAAAACATCAAT
1176078 TTCTCTTAATCGAGGATACTCCAACTT
261 TTCTCTTAATCGAGGATACTCCAACTT
*
1176105 CGATTTTA-TTTCTAAAACACCCATTTT-TCATAATCGGGGATACTCCAACTCCGATTTTATTTC
1 CGATTTTATTTTC-AAAACACCAATTTTCT-ATAATCGGGGATACTCCAACTCCGATTTTATTTC
*
1176168 C-AAAAACACCAATTTTTCACAATC-GAGGATACTCCAA-CCTCGTTATTTCATCAGGGATACTC
64 CAAAAAACACCAATTTTT-AC-ATCAG-GGATACTCCAACCCT-GTTA-ATCATCAGGGATACTC
1176230 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCAT
124 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCAT
*
1176295 AATTGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCG
189 AATCGGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCG
1176345 ATTTTTTTTT
Statistics
Matches: 219, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
286 21 0.10
287 60 0.27
288 18 0.08
289 120 0.55
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (287 bp):
CGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCA
AAAAACACCAATTTTTACATCAGGGATACTCCAACCCTGTTAATCATCAGGGATACTCCAACCCC
GTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATCGGG
GATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGGTTTCATTTATAAAACATCAAT
TTCTCTTAATCGAGGATACTCCAACTT
Found at i:1176370 original size:79 final size:79
Alignment explanation
Indices: 1176221--1176423 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
1176211 TATTTCATCA
** * *
1176221 GGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATATTG
* **
1176286 ATTTCTCATAATTG
66 ATTTCTCACAACCG
* * * ** *
1176300 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCATT
1 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATT
*
1176364 GCTTTCTCACAACCG
65 GATTTCTCACAACCG
* * *
1176379 GGGATACTCCAGCCCCGTTATTTTC-AAGGGGACACTCCAACCCCG
1 GGGATACTCCAACCCCGTTATTTCCGAA-GGGATACTCCAACCCCG
1176424 TTATTATCTC
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 5 0.05
79 99 0.95
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATATTG
ATTTCTCACAACCG
Done.