Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold113
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: 3764034
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 4009 characters in sequence are not A, C, G, or T
File 14 of 23
Found at i:2092739 original size:31 final size:31
Alignment explanation
Indices: 2092664--2092747 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
2092654 TGACACTATC
*
2092664 TTTC-AAGGCTAAGATAAAAACCTCCATATCTT
1 TTTCAAAGGCTAAGAT-AGAA-CTCCATATCTT
* *
2092696 TTT-ACAGGCTAAGATAGAACTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAACTCCATATCTT
2092726 TTTCAAAGGCTAAGATAGAACT
1 TTTCAAAGGCTAAGATAGAACT
2092748 TCTCAATCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 13 0.28
31 20 0.43
32 13 0.28
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (31 bp):
TTTCAAAGGCTAAGATAGAACTCCATATCTT
Found at i:2093228 original size:13 final size:13
Alignment explanation
Indices: 2093210--2093247 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2093200 ACATTTCACC
2093210 ATGTATCGATACA
1 ATGTATCGATACA
2093223 ATGTATCGATACA
1 ATGTATCGATACA
*
2093236 CTGTATCGATAC
1 ATGTATCGATAC
2093248 TTAGTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2093481 original size:20 final size:21
Alignment explanation
Indices: 2093456--2093499 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2093446 ATACTTTGAG
2093456 TTATTTTTA-CTTGAAAAACA
1 TTATTTTTAGCTTGAAAAACA
2093476 TTATTTTTATGCTTGAAAAACA
1 TTATTTTTA-GCTTGAAAAACA
2093498 TT
1 TT
2093500 TAATCTTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (21 bp):
TTATTTTTAGCTTGAAAAACA
Found at i:2097681 original size:73 final size:72
Alignment explanation
Indices: 2097510--2098509 Score: 628
Period size: 73 Copynumber: 13.9 Consensus size: 72
2097500 TATTTTGCTC
* * * * * * *
2097510 TAGTCCTTAAAAAGCAAGATGC-TTTCTTTACAC-ACCCTAAAGCCTACAAAAGCTGGTGGCACA
1 TAGTCCTCAAAGAGCAAGACGCTTTTC-TTAC-CTACCTTAAAGCCCACACAAGCTGGTGGCACC
* *
2097573 TATTTACCC
64 TATCTACCT
* * * * * * * *
2097582 TAGTCTTAAAAAACCAAGACGTTTTTCTTACCTATCTTAAAGCCCACACAAACTAGTGGCACCTA
1 TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCTA
2097647 TCTACCTT
66 TCTACC-T
* * * * *
2097655 TATTCCTCAAAGAGTAAGACGCTTTTCTTACCTACCATAAAGCCCACATAAGTTGGTGGCACCTA
1 TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCTA
2097720 TCTACCCT
66 TCTA-CCT
* * * * * *
2097728 TAGTCTTCAAAAAGCAAGACGCTTTTCTTACCTACCTTAAAGCCTACACAAGTTGGTGGCGCTTA
1 TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCTA
2097793 TCTACCT
66 TCTACCT
* * * * ** * *
2097800 TCAATCCTTAAAGAACAGGACATTTTTCTTACCTACAC-TAAAGCCCGCACAAGCTAGTGGCA-C
1 T-AGTCCTCAAAGAGCAAGACGCTTTTCTTACCTAC-CTTAAAGCCCACACAAGCTGGTGGCACC
2097863 TAATCTACCCT
64 T-ATCTA-CCT
* * * * * * *
2097874 TAGTCTTTAAAGAGCATGATGCTTTTCTTACCTACAC-TAAAACCCACATAAGTTGGTGAG-ACC
1 TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTAC-CTTAAAGCCCACACAAGCTGGTG-GCACC
*
2097937 TATCTACCCC
64 TATCTA-CCT
* * * * * * * * *
2097947 TAATCC-CTAAAAAGTAAGATGCTTTTCTTACCTACCTTAAAGCTCATATAAGCTAGTGACACCT
1 TAGTCCTC-AAAGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCT
2098011 ATCTACCT
65 ATCTACCT
* * * * * * * *
2098019 CCAGTCCTCAAAGAGTAGGATGCTTTTCCTACCTACCTTAAAGTCTACACAAGCTGGTGGCATCT
1 -TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCT
*
2098084 ACCTA-C-
65 ATCTACCT
* * * * * **
2098090 TAGTCCTCAAAGAGTAAGACAG-TTTTTTTACCTACCATAAGGCCCACATAAGCTGGTGATACCT
1 TAGTCCTCAAAGAGCAAGAC-GCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCT
2098154 ATCTA--T
65 ATCTACCT
* * * * * ** *
2098160 TAGTTCTCAATA-AGCAGGACGTTTTTCTCACCTACCATAAAGCCCACACAAGCTAATGGTACCT
1 TAGTCCTCAA-AGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCT
*
2098224 ATTTATCAC-
65 ATCTA-C-CT
* * ** * *** * *
2098233 CAGTCCTTAAAGAATAGGATAATTTTTCTTACCTACCTTAAAGCCCACAAAAGTTGGTGGCACCT
1 TAGTCCTCAAAGAGCAAGA-CGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCT
2098298 ATCTACC-
65 ATCTACCT
* * * ** *
2098305 TA-TCCTCAAAGAGCATGATGCTTTTCTTATCTA--TTGCAAAGCTTACACAAGCTGGTGGCACT
1 TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCTT--AAAGCCCACACAAGCTGGTGGCACC
2098367 TATCTATCAC-
64 TATCTA-C-CT
* * *
2098377 TAGTCCTCAAAGAGCATA-ATGCTTTTCTTACCTACTTTAAAGCCCACATC-AG-TTGTGGCACC
1 TAGTCCTCAAAGAGCA-AGACGCTTTTCTTACCTACCTTAAAGCCCACA-CAAGCTGGTGGCACC
*
2098439 TATTTACC-
64 TATCTACCT
* * * * * * * * * *
2098447 -AATCCTCAAAGAGTAGGATGTTTTTTTTCCCTA-CTATAAAGCCCACATAAGCTAGTGACACCT
1 TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCT-TAAAGCCCACACAAGCTGGTGGCACCT
2098510 GTTCGAACAA
Statistics
Matches: 729, Mismatches: 161, Indels: 78
0.75 0.17 0.08
Matches are distributed among these distances:
68 3 0.00
69 40 0.05
70 154 0.21
71 17 0.02
72 79 0.11
73 382 0.52
74 52 0.07
75 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (72 bp):
TAGTCCTCAAAGAGCAAGACGCTTTTCTTACCTACCTTAAAGCCCACACAAGCTGGTGGCACCTA
TCTACCT
Found at i:2097900 original size:219 final size:217
Alignment explanation
Indices: 2097510--2098446 Score: 757
Period size: 219 Copynumber: 4.3 Consensus size: 217
2097500 TATTTTGCTC
* * *
2097510 TAGTCCTT-AAAAAGCAAGATGC-TTTCTTTACAC-ACCCTAAAGCCTACAAAAGCTGGTGGCAC
1 TAGT-CTTCAAAAAGCAAGATGCTTTTC-TTAC-CTACCTTAAAGCCTACACAAGCTAGTGGCAC
* * * * * * * *
2097572 ATATTTACC-CTAGT-CTTAAAAAACCAAGACGTTTTTCTTACCTATCTTAAAGCCCACACAAAC
63 CTATCTACCTCCAGTCCTTAAAGAA-CAGGACATTTTTCTTACCTACCTTAAAGCCCACACAAGC
* * *
2097635 TAGTGGCACCTATCTACCTTTATTCCTCAAAGAGTAAGACGCTTTTCTTACCTACCATAAAGCCC
127 TAGTGGCACCTATCTACC--TAGTCCTCAAAGAGCAAGATGCTTTTCTTACCTACCATAAAGCCC
*
2097700 ACATAAGTTGGTGGCACCTATCTACCCT
190 ACATAAGCTGGTGGCACCTATCTACCCT
* * * * *
2097728 TAGTCTTCAAAAAGCAAGACGCTTTTCTTACCTACCTTAAAGCCTACACAAGTTGGTGGCGCTTA
1 TAGTCTTCAAAAAGCAAGATGCTTTTCTTACCTACCTTAAAGCCTACACAAGCTAGTGGCACCTA
* * *
2097793 TCTACCTTCAATCCTTAAAGAACAGGACATTTTTCTTACCTACAC-TAAAGCCCGCACAAGCTAG
66 TCTACCTCCAGTCCTTAAAGAACAGGACATTTTTCTTACCTAC-CTTAAAGCCCACACAAGCTAG
* * * *
2097857 TGGCA-CTAATCTACCCTTAGTCTTTAAAGAGCATGATGCTTTTCTTACCTA-CACTAAAACCCA
130 TGGCACCT-ATCTA-CC-TAGTCCTCAAAGAGCAAGATGCTTTTCTTACCTACCA-TAAAGCCCA
* *
2097920 CATAAGTTGGTGAG-ACCTATCTACCCC
191 CATAAGCTGGTG-GCACCTATCTACCCT
* * * * * *
2097947 TAATC-CCTAAAAAGTAAGATGCTTTTCTTACCTACCTTAAAG-CTCATATAAGCTAGTGACACC
1 TAGTCTTC-AAAAAGCAAGATGCTTTTCTTACCTACCTTAAAGCCT-ACACAAGCTAGTGGCACC
* ** *** * * * *
2098010 TATCTACCTCCAGTCCTCAAAGAGTAGGATGCTTTTCCTACCTACCTTAAAGTCTACACAAGCTG
64 TATCTACCTCCAGTCCTTAAAGAACAGGACATTTTTCTTACCTACCTTAAAGCCCACACAAGCTA
* * * * * *
2098075 GTGGCATCTACCTA-CTAGTCCTCAAAGAGTAAGACAG-TTTTTTTACCTACCATAAGGCCCACA
129 GTGGCACCTATCTACCTAGTCCTCAAAGAGCAAGA-TGCTTTTCTTACCTACCATAAAGCCCACA
**
2098138 TAAGCTGGTGATACCTATCTA---T
193 TAAGCTGGTGGCACCTATCTACCCT
* * * * * * * * *
2098160 TAGT-TCTCAATAAGCAGGACGTTTTTCTCACCTACCATAAAGCCCACACAAGCTAATGGTACCT
1 TAGTCT-TCAAAAAGCAAGATGCTTTTCTTACCTACCTTAAAGCCTACACAAGCTAGTGGCACCT
* * * * * * * *
2098224 ATTTATCACCAGTCCTTAAAGAATAGGATAATTTTTCTTACCTACCTTAAAGCCCACAAAAGTTG
65 ATCTACCTCCAGTCCTTAAAGAACAGGA-CATTTTTCTTACCTACCTTAAAGCCCACACAAGCTA
* * **** ** *
2098289 GTGGCACCTATCTACCTA-TCCTCAAAGAGCATGATGCTTTTCTTATCTATTGCAAAGCTTACAC
129 GTGGCACCTATCTACCTAGTCCTCAAAGAGCAAGATGCTTTTCTTACCTACCATAAAGCCCACAT
* *
2098353 AAGCTGGTGGCACTTATCTATCAC-
194 AAGCTGGTGGCACCTATCTA-CCCT
* * * * *
2098377 TAGTCCTCAAAGAGCATA-ATGCTTTTCTTACCTACTTTAAAGCCCACATC-AG-TTGTGGCACC
1 TAGTCTTCAAAAAGCA-AGATGCTTTTCTTACCTACCTTAAAGCCTACA-CAAGCTAGTGGCACC
*
2098439 TATTTACC
64 TATCTACC
2098447 AATCCTCAAA
Statistics
Matches: 570, Mismatches: 119, Indels: 62
0.76 0.16 0.08
Matches are distributed among these distances:
213 68 0.12
214 90 0.16
215 3 0.01
216 67 0.12
217 47 0.08
218 62 0.11
219 219 0.38
220 14 0.02
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (217 bp):
TAGTCTTCAAAAAGCAAGATGCTTTTCTTACCTACCTTAAAGCCTACACAAGCTAGTGGCACCTA
TCTACCTCCAGTCCTTAAAGAACAGGACATTTTTCTTACCTACCTTAAAGCCCACACAAGCTAGT
GGCACCTATCTACCTAGTCCTCAAAGAGCAAGATGCTTTTCTTACCTACCATAAAGCCCACATAA
GCTGGTGGCACCTATCTACCCT
Found at i:2100996 original size:72 final size:77
Alignment explanation
Indices: 2100874--2101078 Score: 231
Period size: 72 Copynumber: 2.7 Consensus size: 77
2100864 TTTTGGAGAT
* * * *
2100874 AAAAACGGGGTTGGAGTATCCTCTATGGTGAAAAATTGATGTTTTGGAAATAAACTC-GA-AG-G
1 AAAAACGAGGTTAGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAACTCGGATAGAG
2100936 TATCCCC-T-CA
66 TATCCCCTTGCA
* * * *
2100946 AAAAACGAGGTTAGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAGTCGGAGTTAG
1 AAAAACGAGGTTAGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAACTCGGA--TAG
*
2101011 AGTATCCCCTTGGA
64 AGTATCCCCTTGCA
* * * * *
2101025 AATAACGAGGTTAGAGTATCCTTGATGGTGAAAACTCGATGTTTTTGAAATAAA
1 AAAAACGAGGTTAGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAA
2101079 ATTGAGGTTA
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
72 49 0.45
73 2 0.02
76 2 0.02
77 8 0.07
78 1 0.01
79 47 0.43
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (77 bp):
AAAAACGAGGTTAGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAACTCGGATAGAG
TATCCCCTTGCA
Found at i:2101067 original size:79 final size:78
Alignment explanation
Indices: 2100877--2101124 Score: 242
Period size: 79 Copynumber: 3.2 Consensus size: 78
2100867 TGGAGATAAA
* * * *
2100877 AACGGGGTTGGAGTATCCTCT-ATGGTGAAAAATTGATGTTTTGGAAATAAACTCGA---AG-GT
1 AACGAGGTTAGAGTATCCT-TGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGAGTTAGAGT
*
2100937 ATCCCC-TCAAAA-
65 ATCCCCTTGAAAAT
** * * *
2100949 AACGAGGTTAGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAGTCGGAGTTAGAGT
1 AACGAGGTTAGAGTATCCTTGATGGTGAAAAATTGATGTTTTAGAAATAAAATC-GAGTTAGAGT
*
2101014 ATCCCCTTGGAAAT
65 ATCCCCTTGAAAAT
* * * *
2101028 AACGAGGTTAGAGTATCCTTGATGGTGAAAACTCGATGTTTTTGAAATAAAATTGAGGTTAGAGT
1 AACGAGGTTAGAGTATCCTTGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGA-GTTAGAGT
* *
2101093 ATCCTCTCGAAAAT
65 ATCCCCTTGAAAAT
*
2101107 AACG-GGTTTGGAGTATCC
1 AACGAGG-TTAGAGTATCC
2101125 CCTCAAAAAT
Statistics
Matches: 143, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
72 45 0.31
73 2 0.01
76 2 0.01
77 8 0.06
78 8 0.06
79 78 0.55
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (78 bp):
AACGAGGTTAGAGTATCCTTGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGAGTTAGAGTA
TCCCCTTGAAAAT
Found at i:2101122 original size:28 final size:28
Alignment explanation
Indices: 2101084--2101154 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2101074 ATAAAATTGA
*
2101084 GGTTAGAGTATCCTCTCGAAAATAACGG
1 GGTTAGAGTATCCTCTCAAAAATAACGG
* * * *
2101112 GTTTGGAGTATCCCCTCAAAAATAATGG
1 GGTTAGAGTATCCTCTCAAAAATAACGG
*
2101140 GGTTATAGTATCCTC
1 GGTTAGAGTATCCTC
2101155 AATTATGAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (28 bp):
GGTTAGAGTATCCTCTCAAAAATAACGG
Found at i:2101264 original size:187 final size:184
Alignment explanation
Indices: 2100935--2101312 Score: 470
Period size: 187 Copynumber: 2.0 Consensus size: 184
2100925 AAACTCGAAG
* *
2100935 GTATCCCCTCAAAAAACGAGGTTAGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAA
1 GTATCCCCTCAAAAAACGAGGTTAGAGTATCCCCAATTATGAAAAATTAATGTTTTAGAAATAAA
* * * * * *
2101000 GTCGGAGTTAGAGTATCCCCTTGGAAATAACGAGGTTAGAGTATCCTTGATGGTGAAAACTCGAT
66 ATCGGAGTTAGAGTATCCCCTTGAAAATAACGAGGCTAGAGTATCCTCGATAGTGAAAAATCGAT
* * * * *
2101065 GTTTTTGAAATAAAATTGAGGTTAGAGTATCCTCTCGAAAATAACGGGTTTGGA
131 GTTTTAGAAATAAAATCGAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGA
* * * * * *
2101119 GTATCCCCTCAAAAATAATGGGGTTATAGTATCCTCAATTATGAAAAAATTAGTGTTTTGGAAAT
1 GTATCCCCTC-AAAA-AACGAGGTTAGAGTATCCCCAATTATG-AAAAATTAATGTTTTAGAAAT
* * * * * *
2101184 AAAATCGGGGTTGGAGTATCCTCTTGAAAATAGC-AGTGCTGGGGTATCCTCGATAGTGAAAAAT
63 AAAATCGGAGTTAGAGTATCCCCTTGAAAATAACGAG-GCTAGAGTATCCTCGATAGTGAAAAAT
* *
2101248 CGGTGTTTTAGAAATAAAATCGAGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGA
127 CGATGTTTTAGAAATAAAATCGAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGA
2101306 GTATCCC
1 GTATCCC
2101313 TCATTGTGGA
Statistics
Matches: 163, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
184 10 0.06
185 4 0.02
186 23 0.14
187 126 0.77
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (184 bp):
GTATCCCCTCAAAAAACGAGGTTAGAGTATCCCCAATTATGAAAAATTAATGTTTTAGAAATAAA
ATCGGAGTTAGAGTATCCCCTTGAAAATAACGAGGCTAGAGTATCCTCGATAGTGAAAAATCGAT
GTTTTAGAAATAAAATCGAGGTTAGAGTATCCCCTCAAAAATAACGGGGTTGGA
Found at i:2101277 original size:79 final size:78
Alignment explanation
Indices: 2101114--2101583 Score: 430
Period size: 79 Copynumber: 5.9 Consensus size: 78
2101104 AATAACGGGT
* ** ** * * ** *
2101114 TTGGAGTATCCCCTCAAAAATAATGGGGTTATAGTATCCTCAATTATGAAAAAATTAGTGTTTTG
1 TTGGAGTATCCCCTCGAAAATAA-CAGGTTGGAGTATCCTCGATTGTG-AAAAATCGGTGTTTTA
*
2101179 GAAATAAAATCGGGG
64 GAAATAAAATCGAGG
* * * * * *
2101194 TTGGAGTATCCTCTTGAAAATAGCAGTGCTGGGGTATCCTCGATAGTGAAAAATCGGTGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACAG-GTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAG
2101259 AAATAAAATCGAGG
65 AAATAAAATCGAGG
* * * *
2101273 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTC-ATTGTGGAAAATCGATGTTTT-
1 TTGGAGTATCCCCTCGAAAATAAC-AGGTTGGAGTAT-CCTCGATTGTGAAAAATCGGTGTTTTA
2101336 GAAAATAAAA-CTGAGG
64 G-AAATAAAATC-GAGG
** * *
2101352 TTAAAGTATCCCCTCGAAAATATCATGGTTGGAGTATCCCCGATTGTGAAAAATCGGTGTTTTAG
1 TTGGAGTATCCCCTCGAAAATAACA-GGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAG
2101417 AAATAAAATC-AGGG
65 AAATAAAATCGA-GG
* * * *
2101431 TTGGAATATCCCGTCGAAAATAACAAGGTTGGAGTATCCCCGATTGTGAAAAATTGAAGT-TTTT
1 TTGGAGTATCCCCTCGAAAATAAC-AGGTTGGAGTATCCTCGATTGTGAAAAATCG--GTGTTTT
** **
2101495 TTAAATAAAGCCGAGG
63 AGAAATAAAATCGAGG
* * ** *
2101511 TTGGAGTATCCCCTTGAAAATAACAAGGTTGGAGTAT-CTCCGATAGTGAAAAATTTGTATTTTA
1 TTGGAGTATCCCCTCGAAAATAAC-AGGTTGGAGTATCCT-CGATTGTGAAAAATCGGTGTTTTA
2101575 GAAATAAAA
64 GAAATAAAA
2101584 ACATGAATGA
Statistics
Matches: 320, Mismatches: 54, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
78 8 0.03
79 206 0.64
80 103 0.32
81 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGAAAATAACAGGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTTAGA
AATAAAATCGAGG
Found at i:2101403 original size:158 final size:157
Alignment explanation
Indices: 2101114--2101583 Score: 518
Period size: 158 Copynumber: 3.0 Consensus size: 157
2101104 AATAACGGGT
* ** * *
2101114 TTGGAGTATCCCCTCAAAAATAATGGGGTTATAGTAT-CCTCAATTATGAAAAAATTAGTGTTTT
1 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTCAATTGTG-AAAAATGA-TGTTTT
* * * * * * *
2101178 GGAAATAAAA-TCGGGGTTGGAGTATCCTCTTGAAAATAGCAGTGCTGGGGTATCCTCGATAGTG
64 GAAAATAAAACT-GAGGTTGGAGTATCCCCTTGAAAATAACAG-GTTGGAGTATCCCCGATAGTG
2101242 AAAAATCGGTGTTTTAGAAATAAAATC-GAGG
127 AAAAATCGGTGTTTTAGAAATAAAATCAG-GG
*
2101273 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTC-ATTGTGGAAAATCGATGTTTTG
1 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTCAATTGTGAAAAAT-GATGTTTTG
** * * *
2101337 AAAATAAAACTGAGGTTAAAGTATCCCCTCGAAAATATCATGGTTGGAGTATCCCCGATTGTGAA
65 AAAATAAAACTGAGGTTGGAGTATCCCCTTGAAAATAACA-GGTTGGAGTATCCCCGATAGTGAA
2101402 AAATCGGTGTTTTAGAAATAAAATCAGGG
129 AAATCGGTGTTTTAGAAATAAAATCAGGG
* * * ** * *
2101431 TTGGAATATCCCGTCGAAAATAACAAGGTTGGAGTATCCC-CGATTGTGAAAAATTGAAGTTTTT
1 TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTCAATTGTGAAAAA-TGATG-TTTT
** * * *
2101495 TTAAATAAAGCCGAGGTTGGAGTATCCCCTTGAAAATAACAAGGTTGGAGTATCTCCGATAGTGA
64 GAAAATAAAACTGAGGTTGGAGTATCCCCTTGAAAATAAC-AGGTTGGAGTATCCCCGATAGTGA
** *
2101560 AAAATTTGTATTTTAGAAATAAAA
128 AAAATCGGTGTTTTAGAAATAAAA
2101584 ACATGAATGA
Statistics
Matches: 265, Mismatches: 37, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
157 1 0.00
158 137 0.52
159 122 0.46
160 5 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (157 bp):
TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCTCAATTGTGAAAAATGATGTTTTGA
AAATAAAACTGAGGTTGGAGTATCCCCTTGAAAATAACAGGTTGGAGTATCCCCGATAGTGAAAA
ATCGGTGTTTTAGAAATAAAATCAGGG
Found at i:2103983 original size:20 final size:21
Alignment explanation
Indices: 2103938--2103994 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
2103928 CAAAAATGCC
* *
2103938 AGAATGTATTGATATATTGAT
1 AGAATGTATTGATACAATGAT
2103959 A-AATGTATTGATACAATGA-
1 AGAATGTATTGATACAATGAT
*
2103978 AGAATGTATCGATACAA
1 AGAATGTATTGATACAA
2103995 ATTGTGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (21 bp):
AGAATGTATTGATACAATGAT
Found at i:2107424 original size:27 final size:27
Alignment explanation
Indices: 2107394--2107453 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2107384 ATATCTAATT
2107394 TTATTTATCGA-GGATACTCCAACCCCA
1 TTATTTAT-GAGGGATACTCCAACCCCA
*
2107421 TTATTT-TGAGGGGATACTCTAACCCCA
1 TTATTTATGA-GGGATACTCCAACCCCA
2107448 TT-TTTA
1 TTATTTA
2107454 AACTTGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 2 0.07
26 4 0.14
27 23 0.79
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (27 bp):
TTATTTATGAGGGATACTCCAACCCCA
Found at i:2109783 original size:84 final size:84
Alignment explanation
Indices: 2109663--2109820 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
2109653 TAATAATTTT
* *
2109663 ATTTTTGGAAAACTCCATCCCCACTATATTGAGGGGATACTCTAACCCCGATC-TTCAAACAACT
1 ATTTTTGGAAAACTCCATCCCCACTATATCGAGGGGATACTCTAACCCCGATCTTTCAAACAAAT
2109727 CAAACTTTTTCTTTATGTA
66 CAAACTTTTTCTTTATGTA
* * * * * *
2109746 ATTTTTGGAGAAATTCTATCCCTACTCAT-TCGAGGGGATATTCTAACCTCGATCTTTGAAACAA
1 ATTTTTGGA-AAACTCCATCCCCACT-ATATCGAGGGGATACTCTAACCCCGATCTTTCAAACAA
2109810 ATCAAACTTTT
64 ATCAAACTTTT
2109821 ACTTCGTATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 9 0.14
84 35 0.55
85 20 0.31
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (84 bp):
ATTTTTGGAAAACTCCATCCCCACTATATCGAGGGGATACTCTAACCCCGATCTTTCAAACAAAT
CAAACTTTTTCTTTATGTA
Found at i:2112428 original size:32 final size:32
Alignment explanation
Indices: 2112392--2112454 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
2112382 TTTTCTCAAC
* * * *
2112392 TAATAGATTTTGCCTTAGTTGTCTCTTTTGAT
1 TAATAGATTTCGCCCTAATTATCTCTTTTGAT
*
2112424 TAATAGGTTTCGCCCTAATTATCTCTTTTGA
1 TAATAGATTTCGCCCTAATTATCTCTTTTGA
2112455 CTAAAGGTTT
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:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (32 bp):
TAATAGATTTCGCCCTAATTATCTCTTTTGAT
Found at i:2112617 original size:95 final size:94
Alignment explanation
Indices: 2112377--2112640 Score: 253
Period size: 95 Copynumber: 2.8 Consensus size: 94
2112367 TTTACCTTGG
* * * * * * * *
2112377 TCACCTTTTCTCAACTAATAGATTTTGCCTTAGTTGTCTCTTTTGATTAATAGGTTTCGCCCTAA
1 TCACTTTTTCTCGACTAATAGGTTTTGCCCTAGTCGTCTC-TTTAATTAATAGGTTTCACCCTAG
*
2112442 TTATCTCTTTTGACTAAAGGTTTCACACTA
65 TCATCTCTTTTGACTAAAGGTTTCACACTA
* * * * * * *
2112472 TCACTTTTTCTTGACAAATAGGCTTTACCCTAGTCGCCTTTTTTAATTAATAAGTTTCACCCTAG
1 TCACTTTTTCTCGACTAATAGGTTTTGCCCTAGTCGTC-TCTTTAATTAATAGGTTTCACCCTAG
** *
2112537 TCAT-TCCTTTTGACTAAAGGTTTTGCTCTAA
65 TCATCT-CTTTTGACTAAAGGTTTCACACT-A
* ** *
2112568 TTCA-TTTTTCTCGACTAATAGGTTTTGCCCTAGTCATCTCTTTCCTTAATAGGTTTCACCTTAG
1 -TCACTTTTTCTCGACTAATAGGTTTTGCCCTAGTCGTCTCTTTAATTAATAGGTTTCACCCTAG
*
2112632 TCACCTCTT
65 TCATCTCTT
2112641 ATTACAACTA
Statistics
Matches: 133, Mismatches: 31, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
94 1 0.01
95 98 0.74
96 31 0.23
97 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (94 bp):
TCACTTTTTCTCGACTAATAGGTTTTGCCCTAGTCGTCTCTTTAATTAATAGGTTTCACCCTAGT
CATCTCTTTTGACTAAAGGTTTCACACTA
Found at i:2112840 original size:30 final size:31
Alignment explanation
Indices: 2112786--2112844 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
2112776 CTAGATTTTG
*
2112786 ACCTAGTCATCTCTTTTTGACTATTGGTTCT
1 ACCTAGTCATCTCTTTTAGACTATTGGTTCT
2112817 ACCTAGATCAT-TC-TTTAGACTATTGGTT
1 ACCTAG-TCATCTCTTTTAGACTATTGGTT
2112845 TTGCCCTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 14 0.54
31 8 0.31
32 4 0.15
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (31 bp):
ACCTAGTCATCTCTTTTAGACTATTGGTTCT
Found at i:2112950 original size:30 final size:30
Alignment explanation
Indices: 2112916--2112985 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2112906 TTTTACCGAG
* * *
2112916 GTCATTTTTCCAACTATTGGTTTTGCCTAA
1 GTCATTTTACCAACTATTGGTTTAGCCAAA
* *
2112946 GTCATTTTACTAATTATTGGTTTAGCCAAA
1 GTCATTTTACCAACTATTGGTTTAGCCAAA
*
2112976 GTCATCTTAC
1 GTCATTTTAC
2112986 AAATAGGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (30 bp):
GTCATTTTACCAACTATTGGTTTAGCCAAA
Found at i:2113863 original size:33 final size:33
Alignment explanation
Indices: 2113825--2114168 Score: 109
Period size: 32 Copynumber: 10.6 Consensus size: 33
2113815 ATTTATAGAA
2113825 TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
1 TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
* * * * * *
2113858 TCAAACATATATCCTTCTAAACATG-TCAAAAG
1 TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
* * * * ** *
2113890 TTAAACTTGTATCATTATGAACAGGACAATAA-
1 TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
*
2113922 TCAAACTTGTAT-CTTTTAAACAAGTT-AAAAG
1 TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
** * * * * *
2113953 TTTGAACATGTATCCTTTTAAACATGTCAAGAA-
1 -TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
** ** * * *
2113986 T-TGACTTGTATTGTTCT-AAGCAAATTAGAAAG
1 TCAAACTTGTATCCTTTTGAA-CAAGTTAAAAAG
** * **
2114018 TTGAACCTACATCCTTTTGAACAAG-TAAAGAA-
1 TCAAACTTGTATCCTTTTGAACAAGTTAAA-AAG
* ** *
2114050 TCGAACTCATATCCTTTTGAACAAGTTAAAGAG
1 TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
* * * ** * *
2114083 TCGAACTCGTAT-CTTTCTAAATGAG-TCAAGAG
1 TCAAACTTGTATCCTTT-TGAACAAGTTAAAAAG
* * * *
2114115 TTAAAGTTGTATCATTTTGAACAAGTCAAAGAA-
1 TCAAACTTGTATCCTTTTGAACAAGTTAAA-AAG
* *
2114148 TCAAGCATGTATCCTTTTGAA
1 TCAAACTTGTATCCTTTTGAA
2114169 TAGGTCAAAA
Statistics
Matches: 218, Mismatches: 77, Indels: 32
0.67 0.24 0.10
Matches are distributed among these distances:
30 5 0.02
31 24 0.11
32 94 0.43
33 89 0.41
34 6 0.03
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (33 bp):
TCAAACTTGTATCCTTTTGAACAAGTTAAAAAG
Found at i:2114069 original size:32 final size:33
Alignment explanation
Indices: 2114028--2114095 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2114018 TTGAACCTAC
2114028 ATCCTTTTGAACAAG-TAAAGAATCGAACTCAT
1 ATCCTTTTGAACAAGTTAAAGAATCGAACTCAT
* *
2114060 ATCCTTTTGAACAAGTTAAAGAGTCGAACTCGT
1 ATCCTTTTGAACAAGTTAAAGAATCGAACTCAT
2114093 ATC
1 ATC
2114096 TTTCTAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 15 0.45
33 18 0.55
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (33 bp):
ATCCTTTTGAACAAGTTAAAGAATCGAACTCAT
Found at i:2114961 original size:21 final size:22
Alignment explanation
Indices: 2114927--2114968 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2114917 TTTTTTCATA
2114927 AAAATATATATTAATAAAAATT
1 AAAATATATATTAATAAAAATT
* *
2114949 AAAATTTA-ATTAATTAAAAT
1 AAAATATATATTAATAAAAAT
2114969 GATTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATATATATTAATAAAAATT
Found at i:2114974 original size:17 final size:15
Alignment explanation
Indices: 2114945--2114978 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
2114935 TATTAATAAA
2114945 AATTAAAATTTAATT
1 AATTAAAATTTAATT
2114960 AATTAAAATGATTAATT
1 AATTAAAAT--TTAATT
2114977 AA
1 AA
2114979 AAATAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTAAAATTTAATT
Found at i:2115202 original size:34 final size:36
Alignment explanation
Indices: 2115158--2115241 Score: 117
Period size: 30 Copynumber: 2.5 Consensus size: 36
2115148 TTTTTTCACG
*
2115158 GGCTAAGATAGAACCTCTCTCCCTATCTTTTGC-AA
1 GGCTAAGATAGAACCTCTCTCCCTATCTTTTACAAA
2115193 -GCTAAGATAGAA---C-CTCCCTATCTTTTACAAA
1 GGCTAAGATAGAACCTCTCTCCCTATCTTTTACAAA
2115224 GGCTAAGATAGAACCTCT
1 GGCTAAGATAGAACCTCT
2115242 ACACTATCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
30 14 0.33
31 3 0.07
32 12 0.29
34 12 0.29
35 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (36 bp):
GGCTAAGATAGAACCTCTCTCCCTATCTTTTACAAA
Found at i:2115212 original size:30 final size:32
Alignment explanation
Indices: 2115158--2115240 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 32
2115148 TTTTTTCACG
*
2115158 GGCTAAGATAGAACCTCTCTCCCTATCTTTTGC-AA
1 GGCTAAGATAGAA---C-CTCCCTATCTTTTACAAA
2115193 -GCTAAGATAGAACCTCCCTATCTTTTACAAA
1 GGCTAAGATAGAACCTCCCTATCTTTTACAAA
2115224 GGCTAAGATAGAACCTC
1 GGCTAAGATAGAACCTC
2115241 TACACTATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
30 14 0.31
31 3 0.07
32 16 0.36
34 12 0.27
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (32 bp):
GGCTAAGATAGAACCTCCCTATCTTTTACAAA
Found at i:2119637 original size:19 final size:20
Alignment explanation
Indices: 2119597--2119637 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2119587 ACTCCTCAAC
*
2119597 AAAATGGACTCTTGAGAGGA
1 AAAATGGACTCTTGAGAAGA
2119617 AAAATTGGACT-TTG-GAAGA
1 AAAA-TGGACTCTTGAGAAGA
2119636 AA
1 AA
2119638 TGGCTAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (20 bp):
AAAATGGACTCTTGAGAAGA
Found at i:2124674 original size:32 final size:32
Alignment explanation
Indices: 2124626--2124781 Score: 171
Period size: 32 Copynumber: 4.8 Consensus size: 32
2124616 TCTAAGTGAT
*
2124626 TGAGAGATTCTATCTTAGCCTTG-AAAGATAG
1 TGAGAGGTTCTATCTTAGCCTTGAAAAGATAG
*
2124657 TGCAGAGGTTCTATCTTAGCCTTTGTAAGAGATAG
1 TG-AGAGGTTCTATCTTAGCC-TTG-AAAAGATAG
*
2124692 -G-GAGGTTCTATCTTAG-CATGCAAAAGATAG
1 TGAGAGGTTCTATCTTAGCCTTG-AAAAGATAG
2124722 TGAGAGAGGTTCTATCTTAGCCTATGAAAAGATAG
1 T--GAGAGGTTCTATCTTAGCCT-TGAAAAGATAG
2124757 -G-GAGGTTTCTATCTTAGCCTTGAAA
1 TGAGAGG-TTCTATCTTAGCCTTGAAA
2124782 GTTAGTGTTG
Statistics
Matches: 108, Mismatches: 6, Indels: 22
0.79 0.04 0.16
Matches are distributed among these distances:
30 10 0.09
31 12 0.11
32 47 0.44
33 4 0.04
34 16 0.15
35 17 0.16
36 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (32 bp):
TGAGAGGTTCTATCTTAGCCTTGAAAAGATAG
Found at i:2124808 original size:66 final size:64
Alignment explanation
Indices: 2124633--2124788 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 64
2124623 GATTGAGAGA
* * *
2124633 TTCTATCTTAGCCTTGAAAGATAGTGCAGAGGTTCTATCTTAGCCTTTGTAAGAGATAGGGAGG
1 TTCTATCTTAGCCTTGAAAGATAGTGGAGAGGTTCTATCTTAGCCTATGTAAAAGATAGGGAGG
*
2124697 TTCTATCTTAG-CATGCAAAAGATAGTGAGAGAGGTTCTATCTTAGCCTATG-AAAAGATAGGGA
1 TTCTATCTTAGCCTTG--AAAGATAGTG-GAGAGGTTCTATCTTAGCCTATGTAAAAGATAGGGA
2124760 GG
63 GG
*
2124762 TTTCTATCTTAGCCTTGAAAGTTAGTG
1 -TTCTATCTTAGCCTTGAAAGATAGTG
2124789 TTGTGAGGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
63 3 0.04
64 11 0.14
65 32 0.40
66 32 0.40
67 3 0.04
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (64 bp):
TTCTATCTTAGCCTTGAAAGATAGTGGAGAGGTTCTATCTTAGCCTATGTAAAAGATAGGGAGG
Found at i:2126324 original size:21 final size:21
Alignment explanation
Indices: 2126300--2126358 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
2126290 GAATAATATT
*
2126300 CTAGAAAAGAAATTAAATGAA
1 CTAGAAAAGAAAATAAATGAA
2126321 CTAGAAAAGAAAATAAATG-A
1 CTAGAAAAGAAAATAAATGAA
* *
2126341 GTTGAAAAAGAAAATAAA
1 CTAG-AAAAGAAAATAAA
2126359 CGAGTTGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.64, C:0.03, G:0.15, T:0.17
Consensus pattern (21 bp):
CTAGAAAAGAAAATAAATGAA
Found at i:2126363 original size:21 final size:22
Alignment explanation
Indices: 2126325--2126377 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
2126315 AATGAACTAG
*
2126325 AAAAGAAAATAAATGAGTTG-A
1 AAAAGAAAATAAACGAGTTGCA
2126346 AAAAGAAAATAAACGAGTTGCA
1 AAAAGAAAATAAACGAGTTGCA
*
2126368 AGAAGAAAAT
1 AAAAGAAAAT
2126378 GATGAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.62, C:0.04, G:0.19, T:0.15
Consensus pattern (22 bp):
AAAAGAAAATAAACGAGTTGCA
Found at i:2128639 original size:20 final size:21
Alignment explanation
Indices: 2128601--2128643 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2128591 AAGTTTGCAT
*
2128601 AAAATTTGTATTAAAGGGGAG
1 AAAATTTATATTAAAGGGGAG
*
2128622 AAAATTTATATTAAGGGGGAG
1 AAAATTTATATTAAAGGGGAG
2128643 A
1 A
2128644 GGTTGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (21 bp):
AAAATTTATATTAAAGGGGAG
Found at i:2130112 original size:32 final size:32
Alignment explanation
Indices: 2130071--2130195 Score: 109
Period size: 32 Copynumber: 3.9 Consensus size: 32
2130061 AAGTGATTAA
*
2130071 GAGG-TTCTATCTTAGCCTTTGTAAAAGATATG
1 GAGGTTTCTATCTTAGCCTTTG-AAAAGATAAG
* **
2130103 GAGG-TTCTATCTTAGCC--TGCAAAATATGGGG
1 GAGGTTTCTATCTTAGCCTTTG-AAAAGAT-AAG
**
2130134 AGAGAGTTTCTATCTTAGCCCATGAAAAGATAAG
1 -GAG-GTTTCTATCTTAGCCTTTGAAAAGATAAG
2130168 GAGGTTTCTATCTTAGCC-TTG-AAAGATA
1 GAGGTTTCTATCTTAGCCTTTGAAAAGATA
2130196 GTGTTGTAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
30 15 0.19
31 3 0.04
32 35 0.44
33 4 0.05
34 14 0.18
35 6 0.08
36 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (32 bp):
GAGGTTTCTATCTTAGCCTTTGAAAAGATAAG
Found at i:2130749 original size:85 final size:86
Alignment explanation
Indices: 2130631--2130804 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 86
2130621 TAATGTACAT
* *
2130631 TATATTTTTAATTAATATTAATGATATAGTTCTTTATCCATAAGATTTTTTAGTAATTGTA-ATT
1 TATATTTTTAATTAATATTAATGAAATAGTTCTTTATCCATAAGATTTTTTAATAATTGTATA-T
*
2130695 CATA-TCTTATGTAGATAAAGCC
65 CATACT-TTATGTAGATAAAACC
* * * *
2130717 TATA-TTTTAATTAATGTTAATGAAATATTTCTTTGTCCATAAGATTTTTTAATAATTGTTTATC
1 TATATTTTTAATTAATATTAATGAAATAGTTCTTTATCCATAAGATTTTTTAATAATTGTATATC
2130781 ATACTTTATGTAGATAAAACC
66 ATACTTTATGTAGATAAAACC
2130802 TAT
1 TAT
2130805 GAAACACATT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
85 73 0.92
86 6 0.08
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (86 bp):
TATATTTTTAATTAATATTAATGAAATAGTTCTTTATCCATAAGATTTTTTAATAATTGTATATC
ATACTTTATGTAGATAAAACC
Found at i:2137757 original size:13 final size:13
Alignment explanation
Indices: 2137739--2137764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2137729 TACACAAAGT
2137739 ATGTATCGATACA
1 ATGTATCGATACA
2137752 ATGTATCGATACA
1 ATGTATCGATACA
2137765 CAAAAAATTG
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:2137762 original size:32 final size:33
Alignment explanation
Indices: 2137721--2137784 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2137711 TAGCCAAACT
**
2137721 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2137753 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2137785 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2140018 original size:21 final size:21
Alignment explanation
Indices: 2139985--2140034 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2139975 TTGCAAGTTG
*
2139985 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2140007 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
2140028 AAATAAA
1 AAATAAA
2140035 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2141842 original size:15 final size:15
Alignment explanation
Indices: 2141822--2141852 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2141812 TAAAAATGTC
*
2141822 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2141837 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2141852 C
1 C
2141853 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2143955 original size:13 final size:13
Alignment explanation
Indices: 2143933--2143970 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2143923 CATTTTTCTT
*
2143933 TGTATTGATACAA
1 TGTATCGATACAA
*
2143946 TGTATCGATACAC
1 TGTATCGATACAA
2143959 TGTATCGATACA
1 TGTATCGATACA
2143971 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2144125 original size:20 final size:20
Alignment explanation
Indices: 2144082--2144127 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2144072 AAATATTTTG
2144082 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2144103 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2144123 CAAAA
1 CAAAA
2144128 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2145793 original size:12 final size:12
Alignment explanation
Indices: 2145776--2145801 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2145766 TAAATTTTTG
2145776 ATATGTGTGTAA
1 ATATGTGTGTAA
2145788 ATATGTGTGTAA
1 ATATGTGTGTAA
2145800 AT
1 AT
2145802 TATCTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (12 bp):
ATATGTGTGTAA
Found at i:2146562 original size:13 final size:13
Alignment explanation
Indices: 2146544--2146569 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2146534 TACACAAAGT
2146544 ATGTATCGATACA
1 ATGTATCGATACA
2146557 ATGTATCGATACA
1 ATGTATCGATACA
2146570 CAAAAAATTG
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:2146567 original size:32 final size:33
Alignment explanation
Indices: 2146526--2146589 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2146516 TAGCCAAACT
**
2146526 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2146558 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2146590 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2152586 original size:16 final size:17
Alignment explanation
Indices: 2152551--2152588 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2152541 AATAAATAAT
* *
2152551 GAAAATTTTTAATTTCA
1 GAAAATATTTAATTTAA
2152568 GAAAATATTT-ATTTAA
1 GAAAATATTTAATTTAA
2152584 GAAAA
1 GAAAA
2152589 GAATAAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (17 bp):
GAAAATATTTAATTTAA
Found at i:2163557 original size:28 final size:29
Alignment explanation
Indices: 2163488--2163560 Score: 100
Period size: 27 Copynumber: 2.6 Consensus size: 29
2163478 CTTCACAATC
2163488 GGGGATACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCGTTAATCATCGA
*
2163517 --GGATACTCCAACCCCGTT-AT-TTCTGA
1 GGGGATACTCCAACCCCGTTAATCATC-GA
2163543 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2163561 ACTTTATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
27 18 0.45
28 16 0.40
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTAATCATCGA
Found at i:2163668 original size:52 final size:51
Alignment explanation
Indices: 2163376--2163765 Score: 217
Period size: 51 Copynumber: 7.4 Consensus size: 51
2163366 CTCAATTCTC
* * * *
2163376 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACCAA-TTTT
1 CACAATCGAGGATACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTT
* * * *
2163426 CTATAATCGGGGATACTCCAACTCCGATTTTATT-TCCAAAAAATACCAATTTCTT
1 C-ACAATCGAGGATACTCCAACCCCGATTTTATTCT-C--AAAACACCAATTT-TT
* * * *
2163481 CACAATCGGGGATACTCCAACCCCG---TTAATCATCGAGGATACTCCAACCCCGTTATTT
1 CACAATCGAGGATACTCCAACCCCGATTTTATTC-TC-A--AAACACCAA-----TT-TTT
** * * * * ***
2163539 C-TGA--GGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTT
1 CACAATCGAGGATACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTT
* * * * *
2163587 CATAATCGGGGATACTCCAACCCTGGTTTTATTGCT-AAAACACTAATTTTT
1 CACAATCGAGGATACTCCAACCCCGATTTTATT-CTCAAAACACCAATTTTT
* *
2163638 CCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAA-TTTT
1 -CACAATCGAGGATACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTT
* * * *
2163689 CCCTTTAATCGGGGATACTCCAACTCCGATTTTATT-TCCAAAAATACCAATTTTT
1 CAC---AATCGAGGATACTCCAACCCCGATTTTATTCT-C-AAAACACCAATTTTT
2163744 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
2163766 TCGTTATTTC
Statistics
Matches: 268, Mismatches: 41, Indels: 60
0.73 0.11 0.16
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 4 0.01
51 76 0.28
52 59 0.22
53 44 0.16
54 36 0.13
55 27 0.10
56 1 0.00
57 3 0.01
58 9 0.03
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CACAATCGAGGATACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTT
Found at i:2163751 original size:105 final size:103
Alignment explanation
Indices: 2163545--2163765 Score: 275
Period size: 105 Copynumber: 2.1 Consensus size: 103
2163535 ATTTCTGAGG
* *** *
2163545 GGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTCCATAATCGGGGATACTCCAACCC
* * * *
2163610 TGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGA
66 TGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
** *
2163648 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCCTTTAATCGGGGATACTCCAAC
1 GGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTT-CC-ATAATCGGGGATACTCCAAC
*
2163713 TCC-GATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
64 -CCTGATTTTA-TTCCAAAAACACCAATTTTTCCACAATCGA
2163753 GGATACTCCAACC
1 GGATACTCCAACC
2163766 TCGTTATTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
103 35 0.35
104 1 0.01
105 47 0.47
106 18 0.18
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (103 bp):
GGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTCCATAATCGGGGATACTCCAACCC
TGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:2163799 original size:28 final size:29
Alignment explanation
Indices: 2163748--2163822 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
2163738 ATTTTTCACA
* **
2163748 ATCGAGGATACTCCAA-CCTCGTTATTTC
1 ATCGGGGATACTCCAACCCTCGTTACATC
2163776 ATCGGGGATACTCCAACCCT-GTTACATC
1 ATCGGGGATACTCCAACCCTCGTTACATC
***
2163804 CGAGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
2163823 CGGCTTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 37 0.93
29 3 0.08
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCTCGTTACATC
Found at i:2163843 original size:264 final size:263
Alignment explanation
Indices: 2163374--2163873 Score: 797
Period size: 264 Copynumber: 1.9 Consensus size: 263
2163364 TTCTCAATTC
* * *
2163374 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
2163439 TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
** *
2163504 CGTTAATCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTAATCATCGAGGATACTCCAACCCCGTTACATCCGAGGGGATACTCCAACCCCGACTTTATT
** *
2163569 TTCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCTGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCTGGTTTTATTGCTAAAACACTAAT
2163634 TTT
261 TTT
* *
2163637 TCCACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT--CTATAATCGGG
2163702 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * * *
2163765 CTCGTTATTTCATCGGGGATACTCCAACCCTGTTACATCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGAGGATACTCCAACCCCGTTACATCCGAGGGGATACTCCAACCCCGACTTT
*
2163830 ATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCC
193 ATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCC
2163874 CGTTATTTTC
Statistics
Matches: 216, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
263 76 0.35
264 104 0.48
265 36 0.17
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (263 bp):
TCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGAGGATACTCCAACCCCGTTACATCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCTGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:2163890 original size:107 final size:107
Alignment explanation
Indices: 2163699--2163898 Score: 251
Period size: 107 Copynumber: 1.9 Consensus size: 107
2163689 CCCTTTAATC
* * *
2163699 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
2163764 CCTCGTTATTTCATCGGGGATACTCCAACCCTGTTACATCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCTGTTACATCCGA
* * *** * * *
2163807 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
2163871 CCCCGTTATTTTCGA-GGGGATACTCCAA
66 CCCCGTTA-TTTC-ACGGGGATACTCCAA
2163899 TCCCGATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
107 52 0.67
108 25 0.32
109 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCTGTTACATCCGA
Found at i:2163898 original size:28 final size:29
Alignment explanation
Indices: 2163858--2163912 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2163848 TCTCATAATT
2163858 GGGGATACTCCAACCCCG-TTATTTTCGA
1 GGGGATACTCCAACCCCGATTATTTTCGA
* *
2163886 GGGGATACTCCAATCCCGATTTTTTTC
1 GGGGATACTCCAACCCCGATTATTTTC
2163913 TAATTATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGATTATTTTCGA
Found at i:2163952 original size:77 final size:78
Alignment explanation
Indices: 2163776--2163980 Score: 241
Period size: 77 Copynumber: 2.6 Consensus size: 78
2163766 TCGTTATTTC
* ** * *
2163776 ATCGGGGATACTCCAACCCTGTTACATCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAAT
* *
2163841 ATTGATTTCTCATA
65 ATCGATTTCTCACA
* * ** * *
2163855 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT-TTTTCTAATTA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATA
2163919 TCGATTTCTCACA
66 TCGATTTCTCACA
* * * *
2163932 ATCGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
2163981 TTATTATCTC
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
77 61 0.57
78 4 0.04
79 42 0.39
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATA
TCGATTTCTCACA
Found at i:2171373 original size:14 final size:14
Alignment explanation
Indices: 2171356--2171382 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2171346 GAGTGTTTGA
2171356 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
2171370 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
2171383 TTCCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:2171375 original size:13 final size:13
Alignment explanation
Indices: 2171357--2171381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2171347 AGTGTTTGAA
2171357 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
2171370 AAAAAAAAAAAA
1 AAAAAAAAAAAA
2171382 ATTCCAAATG
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:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:2171414 original size:21 final size:20
Alignment explanation
Indices: 2171382--2171442 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
2171372 AAAAAAAAAA
2171382 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
2171401 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
2171422 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
2171442 A
1 A
2171443 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 17 0.49
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:2171434 original size:20 final size:19
Alignment explanation
Indices: 2171382--2171442 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
2171372 AAAAAAAAAA
2171382 ATTCCAAATGTATCGATAC
1 ATTCCAAATGTATCGATAC
**
2171401 ATTTGTAGAATGTATCGATAC
1 A-TTCCA-AATGTATCGATAC
2171422 ATTCACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATAC
2171442 A
1 A
2171443 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 15 0.43
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTCCAAATGTATCGATAC
Found at i:2171502 original size:19 final size:19
Alignment explanation
Indices: 2171478--2171545 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2171468 AATTCAACGA
2171478 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2171497 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2171512 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2171529 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2171546 TTAGTTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2171516 original size:32 final size:32
Alignment explanation
Indices: 2171480--2171542 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2171470 TTCAACGATT
*
2171480 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2171512 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2171543 TAATTAGTTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2171517 original size:13 final size:13
Alignment explanation
Indices: 2171499--2171523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2171489 ACATAAGTTT
2171499 TGTATCGATACAA
1 TGTATCGATACAA
2171512 TGTATCGATACA
1 TGTATCGATACA
2171524 TAAGTATTGT
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:2171607 original size:33 final size:33
Alignment explanation
Indices: 2171565--2171631 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2171555 GCCAAGGAAA
***
2171565 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
2171598 TGTATCGATACGTGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2171631 T
1 T
2171632 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2174093 original size:52 final size:52
Alignment explanation
Indices: 2173974--2174106 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 52
2173964 TTGAGTTTCT
* * * * *
2173974 CAATTCTCCACAATCGGGGATATTCCAA-TCCCGGTTTTATTTTCAAAACGC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCCGATTTTATTTCCAAAACAC
** *
2174025 CAATTTTCCTTTAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTCCCGATTTTATTTCC-AAAACAC
* *
2174078 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
2174107 CTCGTTATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
51 8 0.12
52 45 0.67
53 14 0.21
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCCGATTTTATTTCCAAAACAC
Found at i:2174126 original size:28 final size:28
Alignment explanation
Indices: 2174090--2174166 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
2174080 ATTTTTCACA
* * *
2174090 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2174118 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*
2174146 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
2174167 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2174233 original size:107 final size:107
Alignment explanation
Indices: 2174041--2174245 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 107
2174031 TCCTTTAATC
* * *
2174041 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
2174106 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCTGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCTGA
* * *** * * *
2174149 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
2174213 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
2174246 ATTTTTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
105 3 0.04
107 58 0.71
108 21 0.26
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCTGA
Found at i:2174269 original size:79 final size:79
Alignment explanation
Indices: 2174120--2174322 Score: 214
Period size: 79 Copynumber: 2.6 Consensus size: 79
2174110 GTTATTTCAT
* * *
2174120 CGGGGATACTCCAACCCCGTTA-CTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTTC-GAAGGGATACTCCAACCCCGGATTTATTCCCAAAATA
* * *
2174184 TTGATTTCTCATAAT
65 TCGATTTCTCACAAC
* * * ****
2174199 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCC-GATTTTTTTTTTAAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
2174263 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * *
2174278 CGGGGATACTTCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
2174323 TGTTATTATC
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 15 0.15
79 85 0.83
80 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:2186742 original size:13 final size:12
Alignment explanation
Indices: 2186723--2186755 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2186713 ACCTTCTCTT
2186723 CAAAAAAAAAAG
1 CAAAAAAAAAAG
2186735 CAAAAAAAAAAG
1 CAAAAAAAAAAG
*
2186747 GAAAAAAAA
1 CAAAAAAAA
2186756 CAAAAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAG
Found at i:2188167 original size:26 final size:26
Alignment explanation
Indices: 2188082--2188777 Score: 85
Period size: 28 Copynumber: 25.3 Consensus size: 26
2188072 AAGTTGGTGG
*
2188082 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
2188108 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
2188137 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
2188163 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* * *
2188192 CA-TTTTCCAGTCCTCAAAGAACAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
2188218 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
* * *
2188247 CGCCTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
2188273 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
* *
2188302 CACCTTTCCAGTCCTCAACGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
2188329 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
2188358 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
2188384 CACCTATTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
2188413 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* **
2188439 CACCTTTCAAAG-CCTACACAAGTTGGTGG-
1 CACCTTTC--AGTCC-ACA-AAG-AGCAGGA
* *
2188468 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
2188494 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
* *
2188523 CATCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
2188549 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
2188578 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
2188604 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
* *
2188633 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * **
2188659 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
2188688 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
2188714 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
2188743 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
2188769 CACCTTTCA
1 CACCTTTCA
2188778 AAGCCCACCC
Statistics
Matches: 445, Mismatches: 160, Indels: 130
0.61 0.22 0.18
Matches are distributed among these distances:
25 32 0.07
26 93 0.21
27 90 0.20
28 111 0.25
29 84 0.19
30 35 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:2189163 original size:55 final size:55
Alignment explanation
Indices: 2187759--2189154 Score: 2158
Period size: 55 Copynumber: 25.3 Consensus size: 55
2187749 TTCCGCCTTT
*
2187759 CAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
2187814 CAGTCCTCAAAGAGCAGGACACC-CTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
2187869 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
2187924 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
*
2187979 CAGTCCTCAAAGAGTAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
* *
2188034 CAGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
* *
2188089 CAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
2188144 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
* ***
2188199 CAGTCCTCAAAGAACAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
*
2188254 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
* *
2188310 CAGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * *
2188365 CAGTCCCCAAAGAGCAGGACACCTATTAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
*
2188420 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCTACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
2188475 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAT-TTTC
* *
2188530 CAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
*
2188585 CAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
2188640 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
*
2188695 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * *
2188750 CAGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCATCTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
***
2188805 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
*
2188860 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
***
2188916 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTC
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
* * *
2188971 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * *
2189026 CAGTCCCCGAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
* * *
2189081 CAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
2189136 CAGTCCTCAAAGAGCAGGA
1 CAGTCCTCAAAGAGCAGGA
2189155 TGCTTTTTAT
Statistics
Matches: 1261, Mismatches: 53, Indels: 54
0.92 0.04 0.04
Matches are distributed among these distances:
54 28 0.02
55 1096 0.87
56 137 0.11
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:2189615 original size:12 final size:11
Alignment explanation
Indices: 2189586--2189614 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2189576 AGAGTGTTTG
2189586 AAAAAAACAAA
1 AAAAAAACAAA
2189597 AAAAAAACAAA
1 AAAAAAACAAA
2189608 AAAAAAA
1 AAAAAAA
2189615 AAATTCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:2189649 original size:21 final size:20
Alignment explanation
Indices: 2189617--2189677 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
2189607 AAAAAAAAAA
2189617 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
2189636 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
2189657 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
2189677 A
1 A
2189678 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.09
20 15 0.43
21 17 0.49
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:2189669 original size:20 final size:19
Alignment explanation
Indices: 2189617--2189677 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
2189607 AAAAAAAAAA
2189617 ATTCCAAATGTATCGATAC
1 ATTCCAAATGTATCGATAC
**
2189636 ATTTGTAGAATGTATCGATAC
1 A-TTCCA-AATGTATCGATAC
2189657 ATTCACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATAC
2189677 A
1 A
2189678 GGGTCCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 15 0.43
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
ATTCCAAATGTATCGATAC
Found at i:2189737 original size:19 final size:19
Alignment explanation
Indices: 2189713--2189780 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2189703 AATTCAACGA
2189713 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2189732 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2189747 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2189764 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2189781 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2189751 original size:32 final size:32
Alignment explanation
Indices: 2189715--2189777 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2189705 TTCAACGATT
*
2189715 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2189747 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2189778 TAATTAGCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2189752 original size:13 final size:13
Alignment explanation
Indices: 2189734--2189758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2189724 ACATAAGTTT
2189734 TGTATCGATACAA
1 TGTATCGATACAA
2189747 TGTATCGATACA
1 TGTATCGATACA
2189759 TAAGTATTGT
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:2189842 original size:33 final size:33
Alignment explanation
Indices: 2189800--2189866 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2189790 GCCAAGGAAA
***
2189800 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
2189833 TGTATCGATACGTGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2189866 T
1 T
2189867 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2192329 original size:52 final size:52
Alignment explanation
Indices: 2192210--2192342 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 52
2192200 TTGAGTTTCT
* * * * *
2192210 CAATTCTCCACAATCGGGGATATTCCAA-TCCCGGTTTTATTTTCAAAACGC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCCGATTTTATTTCCAAAACAC
** *
2192261 CAATTTTCCTTTAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTCCCGATTTTATTTCC-AAAACAC
* *
2192314 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
2192343 CTCGTTATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
51 8 0.12
52 45 0.67
53 14 0.21
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCCGATTTTATTTCCAAAACAC
Found at i:2192362 original size:28 final size:28
Alignment explanation
Indices: 2192326--2192402 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2192316 ATTTTTCACA
* * *
2192326 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2192354 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2192382 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2192403 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2192468 original size:106 final size:107
Alignment explanation
Indices: 2192277--2192480 Score: 252
Period size: 106 Copynumber: 1.9 Consensus size: 107
2192267 TCCTTTAATC
* * *
2192277 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
2192342 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * *
2192385 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTG-GGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
2192448 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
2192481 ATTTTTTTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 3 0.04
106 37 0.45
107 21 0.26
108 21 0.26
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:2202602 original size:28 final size:28
Alignment explanation
Indices: 2202570--2202669 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
2202560 AAAAAAAAAT
2202570 CGGGATTGGAGTATCCCCTCGAAAATAA
1 CGGGATTGGAGTATCCCCTCGAAAATAA
* *
2202598 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGATTGGAGTATCCCCTCGAAAATAA
*
2202626 CGGGGTTGGAGTAT-CCC-CGATGAAATAA
1 CGGGATTGGAGTATCCCCTCGA--AAATAA
2202654 CGAGG-TTGGAGTATCC
1 CG-GGATTGGAGTATCC
2202670 TCGATTGTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.03
27 3 0.05
28 55 0.87
29 3 0.05
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (28 bp):
CGGGATTGGAGTATCCCCTCGAAAATAA
Found at i:2202767 original size:53 final size:52
Alignment explanation
Indices: 2202657--2202880 Score: 236
Period size: 52 Copynumber: 4.3 Consensus size: 52
2202647 GAAATAACGA
* * * * * * *
2202657 GGTTGGAGTATCCTCGATTGT-CAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGT-GTTTTGAAAATAAAACCGG
* * * *
2202709 AGTTGGAGTATCCCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAAATTAGTGTTTTGAAAATAAAACCGG
* *
2202762 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTGA-AAATAAAACCGG
* * * * **
2202814 GGTTGGAGTATCCCCGATTATGAAAAAATCAATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTGAAAATAAAACCGG
2202866 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2202881 TCGGAAATAA
Statistics
Matches: 145, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
51 1 0.01
52 100 0.69
53 35 0.24
54 9 0.06
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTGAAAATAAAACCGG
Found at i:2202768 original size:105 final size:104
Alignment explanation
Indices: 2202657--2202880 Score: 270
Period size: 105 Copynumber: 2.1 Consensus size: 104
2202647 GAAATAACGA
* * * * *
2202657 GGTTGGAGTATCCTCGATTGT-CAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGCAAAAATTAGT-GTTTTAGAAATAAAACCGGAGTTGGAGTATC
** *** *
2202721 CCCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGG
65 CCCGATT-AAGAAAAAATCAATATTTTGAAAATAAAACCGG
* * *
2202762 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGCAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAGTATCC
* **
2202827 CCGATTATGAAAAAATCAATATTTTGAAAATAAAGTCGG
66 CCGATTAAGAAAAAATCAATATTTTGAAAATAAAACCGG
2202866 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2202881 TCGGAAATAA
Statistics
Matches: 101, Mismatches: 17, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
104 39 0.39
105 53 0.52
106 9 0.09
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTGTGCAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAGTATCC
CCGATTAAGAAAAAATCAATATTTTGAAAATAAAACCGG
Found at i:2202926 original size:27 final size:28
Alignment explanation
Indices: 2202863--2202935 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
2202853 AAAATAAAGT
**
2202863 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
* *
2202891 CGGGGTTGGAGTATCCCCAATG-ATTAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
*
2202918 CGGGGTTGGAATATCCCC
1 CGGGGTTGGAGTATCCCC
2202936 GATTGTGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCAAGGAAATAA
Found at i:2202989 original size:56 final size:52
Alignment explanation
Indices: 2202922--2203054 Score: 142
Period size: 51 Copynumber: 2.5 Consensus size: 52
2202912 GATTAACGGG
* * * *
2202922 GTTGGAATATCCCCGATTGTGAAGAAATTGGTATTTTTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGTG-AGAAAAT--TA-GTGTTTTGAAAATAAAATCGGA
* * *
2202978 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATTGGA
1 GTTGGAATATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
2203029 GTTAGAATATCCCCGATTGTGGAGAA
1 GTTGGAATATCCCCGATTGT-GAGAA
2203055 TTGAGAAACT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
51 35 0.54
52 2 0.03
53 4 0.06
54 6 0.09
56 18 0.28
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (52 bp):
GTTGGAATATCCCCGATTGTGAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:2205435 original size:13 final size:13
Alignment explanation
Indices: 2205417--2205442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2205407 ATAAAGATCC
2205417 ATGTATCGATACA
1 ATGTATCGATACA
2205430 ATGTATCGATACA
1 ATGTATCGATACA
2205443 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:2205506 original size:19 final size:19
Alignment explanation
Indices: 2205482--2205555 Score: 139
Period size: 19 Copynumber: 3.9 Consensus size: 19
2205472 CAGTAGCTAA
2205482 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
2205501 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
*
2205520 TTATGTATCGATACAACAC
1 TTATGTATCGATACAATAC
2205539 TTATGTATCGATACAAT
1 TTATGTATCGATACAAT
2205556 TTACTGAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:2205617 original size:21 final size:21
Alignment explanation
Indices: 2205591--2205667 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2205581 GTTGGGACCC
* *
2205591 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
2205612 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
2205633 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
2205654 TGTATCGATACATT
1 TGTATCGATACATT
2205668 TGGATAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:2208043 original size:27 final size:25
Alignment explanation
Indices: 2208003--2208072 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
2207993 AGACAACGCA
*
2208003 AACACAATTA-AAAAATAATTAAAATAT
1 AACACAA-TACAAAAATAA-T-AAATAC
2208030 AACACAATACAAAAA-AATAAATAC
1 AACACAATACAAAAATAATAAATAC
2208054 AACACGAATACACAAAATA
1 AACAC-AATACA-AAAATA
2208073 TATCAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 10 0.26
25 7 0.18
26 8 0.21
27 13 0.34
ACGTcount: A:0.67, C:0.14, G:0.01, T:0.17
Consensus pattern (25 bp):
AACACAATACAAAAATAATAAATAC
Found at i:2208057 original size:24 final size:25
Alignment explanation
Indices: 2208024--2208070 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2208014 AAAATAATTA
*
2208024 AAATATAACAC-AATACAAAAAAAT
1 AAATACAACACGAATACAAAAAAAT
*
2208048 AAATACAACACGAATACACAAAA
1 AAATACAACACGAATACAAAAAA
2208071 TATATCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.68, C:0.17, G:0.02, T:0.13
Consensus pattern (25 bp):
AAATACAACACGAATACAAAAAAAT
Found at i:2208139 original size:17 final size:19
Alignment explanation
Indices: 2208117--2208155 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2208107 TAATAATAAA
2208117 TTATTTAAAAAT-TA-ATT
1 TTATTTAAAAATATAGATT
*
2208134 TTATTTATAAATATAGATT
1 TTATTTAAAAATATAGATT
2208153 TTA
1 TTA
2208156 ATAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTATTTAAAAATATAGATT
Found at i:2208213 original size:29 final size:28
Alignment explanation
Indices: 2208119--2208213 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 28
2208109 ATAATAAATT
*
2208119 ATTTAAAAATTAATTTTATTTATAAAT-ATA
1 ATTTAAAAA--AA-TTTATTTAAAAATAATA
* * * *
2208149 GATTTTAATAAATATATATTAAAAATAA-C
1 -ATTTAAAAAAATTTAT-TTAAAAATAATA
2208178 ATATTAACAAAAATTTATTTAAAAATAATA
1 AT-TTAA-AAAAATTTATTTAAAAATAATA
2208208 ATTTAA
1 ATTTAA
2208214 TAATTTTCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 6 0.12
29 26 0.52
30 11 0.22
31 7 0.14
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
ATTTAAAAAAATTTATTTAAAAATAATA
Found at i:2210338 original size:2 final size:2
Alignment explanation
Indices: 2210331--2210377 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2210321 CCTTCCTAGT
2210331 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
2210373 TA TA T
1 TA TA T
2210378 GAAAGTATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2212753 original size:16 final size:16
Alignment explanation
Indices: 2212732--2212762 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2212722 ATAAATAAAT
*
2212732 ATCTTATATTTTAATA
1 ATCTTATATATTAATA
2212748 ATCTTATATATTAAT
1 ATCTTATATATTAAT
2212763 GAATTTTTAT
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:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
ATCTTATATATTAATA
Found at i:2213134 original size:22 final size:22
Alignment explanation
Indices: 2213092--2213134 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2213082 AAAAAATGTT
* *
2213092 TGATAATATATTAGTATATGAA
1 TGATAATATAGTAATATATGAA
2213114 TGATAATATAGTACATA-ATGA
1 TGATAATATAGTA-ATATATGA
2213135 CTAATAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (22 bp):
TGATAATATAGTAATATATGAA
Found at i:2218196 original size:38 final size:37
Alignment explanation
Indices: 2218145--2218222 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
2218135 AGTATTTTAC
* *
2218145 AATAAAAATTATTATTTTAAATTGATAATATGATTCAA
1 AATAAAAATTATTATTTTAAATTAATAATATAATT-AA
*
2218183 AATAAAAATTATTATTTTAAATTAATGATATAATTAA
1 AATAAAAATTATTATTTTAAATTAATAATATAATTAA
2218220 AAT
1 AAT
2218223 CGATTTCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (37 bp):
AATAAAAATTATTATTTTAAATTAATAATATAATTAA
Found at i:2218204 original size:19 final size:19
Alignment explanation
Indices: 2218137--2218204 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
2218127 TAGTACAAAG
2218137 TATTTTACAATAAAAATTAT
1 TATTTTA-AATAAAAATTAT
* *
2218157 TATTTTAAATTGATAA-TAT
1 TATTTTAAA-TAAAAATTAT
* **
2218176 GATTCAAAATAAAAATTAT
1 TATTTTAAATAAAAATTAT
2218195 TATTTTAAAT
1 TATTTTAAAT
2218205 TAATGATATA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
18 4 0.11
19 21 0.58
20 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTTAAATAAAAATTAT
Found at i:2220840 original size:51 final size:51
Alignment explanation
Indices: 2220785--2220940 Score: 226
Period size: 51 Copynumber: 3.1 Consensus size: 51
2220775 CTCCAGCTCT
* *
2220785 GATTTTATTTCTAAAATACCAATTTTTCACCATTAGGGATACTCCAACCCC
1 GATTTTATTTCTAAAACACCGATTTTTCACCATTAGGGATACTCCAACCCC
**
2220836 GATTTTATTTCTAAAACACCGA-TTTTCTACCATCGGGGATACTCCAACCCC
1 GATTTTATTTCTAAAACACCGATTTTTC-ACCATTAGGGATACTCCAACCCC
* *
2220887 GATTTTATTTCTAAAACACCGATTTTTCACCA-TCGGGAATACTCCAACCTC
1 GATTTTATTTCTAAAACACCGATTTTTCACCATTAGGG-ATACTCCAACCCC
2220938 GAT
1 GAT
2220941 ATTTCTAATG
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
50 8 0.08
51 82 0.86
52 5 0.05
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
GATTTTATTTCTAAAACACCGATTTTTCACCATTAGGGATACTCCAACCCC
Found at i:2221002 original size:79 final size:78
Alignment explanation
Indices: 2220871--2221095 Score: 265
Period size: 79 Copynumber: 2.9 Consensus size: 78
2220861 TCTACCATCG
*
2220871 GGGATACTCCAACCCCGATTTTATTTCTAAAACACCGATTTTTCACCATCGGGAATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAACC
*
2220936 TCGATA-TTTCTAA
66 CCGATACTTT-TAA
* * * * * *
2220949 TGGGATACTCTAACCTCAATTTTATTTCTAAAACACTGATTTTTTACCATCGGGGATACTCCGAC
1 -GGGATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAAC
* *
2221014 CCCGTTACTTTTGA
65 CCCGATACTTTTAA
* * * * *
2221028 GAGGATACTCCAACCCCGATTTTGTTTCCAAAA-ATTCGATTTTTCACCATCGAGAATACTCTAA
1 G-GGATACTCCAACCCCGATTTTATTTCTAAAACACT-GATTTTTCACCATCGGGAATACTCCAA
2221092 CCCC
64 CCCC
2221096 ATTTTTATTT
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
78 3 0.02
79 116 0.95
80 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAACC
CCGATACTTTTAA
Found at i:2221120 original size:51 final size:51
Alignment explanation
Indices: 2221032--2221147 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
2221022 TTTTGAGAGG
* *
2221032 ATACTCCAACCCCGATTTTGTTTCCAAAAATTCGATTTTTCACCATCGAGA
1 ATACTCCAACCCCGATTTTATTTCCAAAAATTCGATTTATCACCATCGAGA
* * *
2221083 ATACTCTAACCCC-ATTTTTATTTCTAAAATATT-GATTTATCACCATCGAGG
1 ATACTCCAACCCCGA-TTTTATTTCCAAAA-ATTCGATTTATCACCATCGAGA
2221134 ATACTCCAACCCCG
1 ATACTCCAACCCCG
2221148 TTGTTTTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.02
51 52 0.93
52 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.34
Consensus pattern (51 bp):
ATACTCCAACCCCGATTTTATTTCCAAAAATTCGATTTATCACCATCGAGA
Found at i:2222626 original size:21 final size:23
Alignment explanation
Indices: 2222601--2222648 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
2222591 AATACTTTGG
*
2222601 ATTATTTTTA-CTTG-AAAACAT
1 ATTATTTATAGCTTGAAAAACAT
2222622 ATTATTTATAGCTTGAAAAACAT
1 ATTATTTATAGCTTGAAAAACAT
2222645 -TTAT
1 ATTAT
2222649 ACTTAACTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 7 0.29
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (23 bp):
ATTATTTATAGCTTGAAAAACAT
Found at i:2223230 original size:26 final size:27
Alignment explanation
Indices: 2223197--2223251 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
2223187 TTTGTTATCT
*
2223197 CCCTTTTTATTTCAAAAAT-ATTTTCC
1 CCCTTTTTATTTCAAAAATAATCTTCC
*
2223223 CCCTTTTTGTTTCAAAAATAATCTTCC
1 CCCTTTTTATTTCAAAAATAATCTTCC
2223250 CC
1 CC
2223252 TTTATAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (27 bp):
CCCTTTTTATTTCAAAAATAATCTTCC
Found at i:2233020 original size:14 final size:14
Alignment explanation
Indices: 2233001--2233039 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2232991 CTCCTTTCTT
2233001 TCTAGAATCCTTTC
1 TCTAGAATCCTTTC
*
2233015 TCTAGAATCTTTTC
1 TCTAGAATCCTTTC
2233029 -CTTAGAATCCT
1 TC-TAGAATCCT
2233040 GTCCCTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.44
Consensus pattern (14 bp):
TCTAGAATCCTTTC
Found at i:2241077 original size:48 final size:48
Alignment explanation
Indices: 2241015--2241146 Score: 201
Period size: 48 Copynumber: 2.8 Consensus size: 48
2241005 AGAGGAGTGC
** *
2241015 CAATGTGCCAATTCAAGGCCAGCGACATCGAGCTAAGGGAAAAATGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATGGA
* *
2241063 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATGGA
* *
2241111 AAATGTGCTGATTCAAGGCTAGCGACATTGAGCTAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA
2241147 TAAAGGTGCC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATGGA
Found at i:2241465 original size:30 final size:29
Alignment explanation
Indices: 2241279--2242002 Score: 537
Period size: 28 Copynumber: 24.4 Consensus size: 29
2241269 TATGTAGGCA
*
2241279 TTGAAGGGGATGCCACTGACTTGTG-GGCT
1 TTGAAAGGG-TGCCACTGACTTGTGTGGCT
* * * * *
2241308 TTGAAGGGGTACCACGGACTTATG-GCCT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
* * *
2241336 GTGGAAGGGTGCCACTGACTTGTG-GGCA
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
2241364 TTGAAAGGGTGCCACTGACTTGTG-GGCT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
* **
2241392 TTGGAAGGGTGCCACTGACTTGT-AAGCT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
*
2241420 TTGGAAA-GGTGCCACTGATTTGTGTAGGCT
1 TT-GAAAGGGTGCCACTGACTTGTGT-GGCT
* * *
2241450 TTGAAAGGGTACCACTAACTTGT-AGGCT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
* * * *
2241478 TTGGAAGGGTGCCACTGATTTATATGGGCT
1 TTGAAAGGGTGCCACTGACTTGTGT-GGCT
**
2241508 TTGAAAGGGGTTGCCACCAACTTGTGTTGGCT
1 TTGAAA-GGG-TGCCACTGACTTGTG-TGGCT
2241540 TTGAAAGGGTGCCACTGACTTGTG-GGCT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
* * *
2241568 TTGAAAAGAGTTGCCACCGACTTGTGTGGGT
1 TTG-AAAG-GGTGCCACTGACTTGTGTGGCT
* *
2241599 TTGAAAGGGTGCCACCGACTTGTG-GTCGT
1 TTGAAAGGGTGCCACTGACTTGTGTGGC-T
*
2241628 TTG-AAGAGATGCCACTGACTTGTG-GGCT
1 TTGAAAG-GGTGCCACTGACTTGTGTGGCT
*
2241656 TTGAGAAGAGTTGCCACTGACTTGTGTAGGCT
1 TTGA-AAG-GGTGCCACTGACTTGTGT-GGCT
* **
2241688 TTGAAAGGATGCCACTGACTTGTG-AACT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
* *
2241716 TTTAAAGAGATGCCACTGACTTGTG-GGCT
1 TTGAAAG-GGTGCCACTGACTTGTGTGGCT
* *
2241745 TTGAAAAGAGTTGCCACCGACTTGTGTGGGCT
1 TTG-AAAG-GGTGCCACTGACTTGTGT-GGCT
* * **
2241777 TTCAAATGAGTTGCCACCAACTTGTGTGGGCT
1 TTGAAA-G-GGTGCCACTGACTTGTGT-GGCT
*
2241809 TTGAAATGGGTTGCCATTGACTTGTG-GGCT
1 TTGAAA-GGG-TGCCACTGACTTGTGTGGCT
* * *
2241839 TTAAAAGGATGCCACTGACTTGTG-GCCT
1 TTGAAAGGGTGCCACTGACTTGTGTGGCT
*
2241867 TTGAAATGGGTTGCCACCGACTTGTGTGGACT
1 TTGAAA-GGG-TGCCACTGACTTGTGTGG-CT
*
2241899 TTGAAATGGGTTG-CACCGACTTGTGTGCGCT
1 TTGAAA-GGG-TGCCACTGACTTGTGTG-GCT
* * * *
2241930 TTCAAATAAGTTGCCACCGACTTGTGTGGGCT
1 TT-GAA-AGGGTGCCACTGACTTGTGT-GGCT
* *
2241962 TTGAAATGAGTTGCCACCGACTTGTG-GGCT
1 TTGAAA-G-GGTGCCACTGACTTGTGTGGCT
* *
2241992 TTAAAATGGTG
1 TTGAAAGGGTG
2242003 TTGCCACGGA
Statistics
Matches: 578, Mismatches: 81, Indels: 73
0.79 0.11 0.10
Matches are distributed among these distances:
28 172 0.30
29 82 0.14
30 148 0.26
31 42 0.07
32 131 0.23
33 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (29 bp):
TTGAAAGGGTGCCACTGACTTGTGTGGCT
Found at i:2242036 original size:27 final size:27
Alignment explanation
Indices: 2242004--2242407 Score: 512
Period size: 27 Copynumber: 14.7 Consensus size: 27
2241994 AAAATGGTGT
*
2242004 TGCCACGGAGTCGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
2242031 TGCCACAGAGTTGTGGACTTAAAA-GA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2242057 GTGCCACAGAGTGGTGGACTTTAAAA-GA
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
2242085 GTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGA
*
2242113 TGCCACGGAGTGGTGGACATTAAAA-GA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
2242140 GTGCCACGGAGTTGTGGACTTTAAAAGG-
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
2242168 TGCCACGGAGTTGTAGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
2242195 TGCCACGGAGTTGTGGACTTTAAAAGG-
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
2242222 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2242249 TGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2242276 TGCCATGAAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
**
2242304 TATCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
2242331 TGCCACGAAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2242358 TGCCACGAAGTTGTGGACTTTGAAAAGAAA
1 TGCCACGGAGTTGTGGAC-TT-AAAAG-GA
* *
2242388 TGCCACTGAATTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
2242408 TGAAGAGGTC
Statistics
Matches: 337, Mismatches: 27, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
26 18 0.05
27 208 0.62
28 87 0.26
29 8 0.02
30 16 0.05
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:2242045 original size:153 final size:153
Alignment explanation
Indices: 2241356--2241997 Score: 603
Period size: 153 Copynumber: 4.3 Consensus size: 153
2241346 GCCACTGACT
* * * ** * *
2241356 TGTGGGCATTGAAA-G-GGTGCCACTGACTTGTG-GGCTTTGGAAGGGTGCCACTGACTTGT-AA
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGCTTTAAAAGGATGCCACTGACTTGTGGA
* * * * ** *
2241417 GCTTTGGAAAG-G-TGCCACTGATTTGTGTAGGCTTTGAAAGGG-TACCACTAACTTGT-AG-GC
66 -CTTTGAAAAGAGATGCCACCGACTTGTGT-GGCTTTGAAAGGGTTGCCACCGACTTGTGTGCGC
** * * * *
2241477 TTTGGAA-G-GGTGCCACTGATTTA
129 TTTCAAATGAGTTGCCACCGACTTG
* * * * * *
2241500 TATGGGCTTTGAAAGGGGTTGCCACCAACTTGTGTTGGCTTTGAAAGGGTGCCACTGACTTGTGG
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTGTG-TGGCTTTAAAAGGATGCCACTGACTTGTGG
* * *
2241565 GCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGTTTGAAAGGG-TGCCACCGACTTGTG-GTCG-
65 ACTTTGAAAAGAGATGCCACCGACTTGTGTGGCTTTGAAAGGGTTGCCACCGACTTGTGTG-CGC
* * *
2241627 TTT-GAA-GAGATGCCACTGAC-T-
129 TTTCAAATGAGTTGCCACCGACTTG
* *
2241648 TGTGGGCTTTGAGAA-GAGTTGCCACTGACTTGTGTAGGCTTTGAAAGGATGCCACTGACTTGTG
1 TGTGGGCTTTGA-AATGAGTTGCCACCGACTTGTGT-GGCTTTAAAAGGATGCCACTGACTTGTG
* * * * *
2241712 AACTTT-TAAAGAGATGCCACTGACTTGTG-GGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGG
64 GACTTTGAAAAGAGATGCCACCGACTTGTGTGGCTTTG-AAAGGGTTGCCACCGACTTGTGTGCG
*
2241775 CTTTCAAATGAGTTGCCACCAACTTG
128 CTTTCAAATGAGTTGCCACCGACTTG
* ** *
2241801 TGTGGGCTTTGAAATGGGTTGCCATTGACTTGTG-GGCTTTAAAAGGATGCCACTGACTTGTGGC
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGCTTTAAAAGGATGCCACTGACTTGTGGA
* * *
2241865 CTTTGAAATGGGTTGCCACCGACTTGTGTGGACTTTGAAATGGGTTG-CACCGACTTGTGTGCGC
66 CTTTGAAAAGAGATGCCACCGACTTGTGTGG-CTTTGAAA-GGGTTGCCACCGACTTGTGTGCGC
*
2241929 TTTCAAATAAGTTGCCACCGACTTG
129 TTTCAAATGAGTTGCCACCGACTTG
2241954 TGTGGGCTTTGAAATGAGTTGCCACCGACTTGTG-GGCTTTAAAA
1 TGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGCTTTAAAA
2241998 TGGTGTTGCC
Statistics
Matches: 421, Mismatches: 51, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
144 12 0.03
145 1 0.00
146 20 0.05
147 26 0.06
148 109 0.26
149 36 0.09
150 29 0.07
151 43 0.10
152 21 0.05
153 114 0.27
154 10 0.02
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (153 bp):
TGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGCTTTAAAAGGATGCCACTGACTTGTGGA
CTTTGAAAAGAGATGCCACCGACTTGTGTGGCTTTGAAAGGGTTGCCACCGACTTGTGTGCGCTT
TCAAATGAGTTGCCACCGACTTG
Found at i:2242097 original size:55 final size:53
Alignment explanation
Indices: 2242004--2242377 Score: 518
Period size: 55 Copynumber: 6.9 Consensus size: 53
2241994 AAAATGGTGT
* *
2242004 TGCCACGGAGTCGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAG-G
* *
2242058 TGCCACAGAGTGGTGGACTTTAAAA-GAGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA-TGCCACGGAGTTGTGGACTTAAAA-GG
*
2242113 TGCCACGGAGTGGTGGACATTAAAA-GAGTGCCACGGAGTTGTGGACTTTAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA-TGCCACGGAGTTGTGGAC-TTAAAAGG
*
2242168 TGCCACGGAGTTGTAGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTAAAAGG
*
2242222 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAA-GG
* * **
2242276 TGCCATGAAGTTGTGGACTTTAAAAGGATATCACGGAGTTGTGGACTTAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGG
* *
2242330 ATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTT
1 -TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
2242378 TGAAAAGAAA
Statistics
Matches: 294, Mismatches: 18, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
53 6 0.02
54 140 0.48
55 141 0.48
56 7 0.02
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (53 bp):
TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGG
Found at i:2242102 original size:82 final size:81
Alignment explanation
Indices: 2242004--2242407 Score: 535
Period size: 82 Copynumber: 4.9 Consensus size: 81
2241994 AAAATGGTGT
* * *
2242004 TGCCACGGAGTCGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGAGTGCCACAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAG-GTGCCACGGAG
*
2242068 TGGTGGACTTTAAAA-GA
65 TTGTGGAC-TTAAAAGGA
* * *
2242085 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTGGTGGACATTAAAAGAGTGCCACGGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAG-GTGCCACGGA
2242150 GTTGTGGACTTTAAAAGG-
64 GTTGTGGAC-TTAAAAGGA
*
2242168 TGCCACGGAGTTGTAGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGTGCCACGGAGT
2242233 TGTGGACTTAAAAGGA
66 TGTGGACTTAAAAGGA
* * * * **
2242249 TGCCACGAAGTTGTGGACTTAAAAGGGTGCCATGAAGTTGTGGACTTTAAAAGGATATCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGG-TGCCACGGAG
2242314 TTGTGGACTTAAAAGGA
65 TTGTGGACTTAAAAGGA
* * * *
2242331 TGCCACGAAGTTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTGAAAAGAAATGCCACTG
1 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAG--GTGCCACGG
*
2242396 AATTGTGGACTT
63 AGTTGTGGACTT
2242408 TGAAGAGGTC
Statistics
Matches: 291, Mismatches: 24, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
80 8 0.03
81 68 0.23
82 161 0.55
83 37 0.13
84 17 0.06
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGTGCCACGGAGT
TGTGGACTTAAAAGGA
Found at i:2254986 original size:17 final size:17
Alignment explanation
Indices: 2254960--2255006 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
2254950 TTATCTAATT
*
2254960 TTATAATTATTAGATAA
1 TTATATTTATTAGATAA
*
2254977 TTATATTTATTAGGTAA
1 TTATATTTATTAGATAA
*
2254994 ATATTATTTATTA
1 TTA-TATTTATTA
2255007 AGTTAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTATATTTATTAGATAA
Found at i:2267082 original size:15 final size:16
Alignment explanation
Indices: 2267064--2267093 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2267054 TCTATACAAA
2267064 TATAAA-TTTTAAAAT
1 TATAAATTTTTAAAAT
2267079 TATAAATTTTTAAAA
1 TATAAATTTTTAAAA
2267094 ATCAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATTTTTAAAAT
Found at i:2268455 original size:2 final size:2
Alignment explanation
Indices: 2268448--2268506 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
2268438 ATGTTTATTT
* * * *
2268448 TA TA TA TA TA TA CA TA TA TG TA TA TA TA TA TA AA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2268490 TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA T
2268507 TATGTCTTGC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2268506 original size:22 final size:22
Alignment explanation
Indices: 2268448--2268511 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2268438 ATGTTTATTT
2268448 TATATATATATAC--ATATATG
1 TATATATATATACATATATATG
*
2268468 TATATATATATAAATATATATG
1 TATATATATATACATATATATG
2268490 TATATATATATACATAT-TATG
1 TATATATATATACATATATATG
2268511 T
1 T
2268512 CTTGCTTCAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.30
21 5 0.12
22 23 0.57
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (22 bp):
TATATATATATACATATATATG
Found at i:2280594 original size:6 final size:5
Alignment explanation
Indices: 2280580--2280616 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
2280570 CTTTCGCCGC
*
2280580 TTCTT TTCTTT TTCTT TTCTT TTCTT TTCAT TTCTT T
1 TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TTCTT T
2280617 GCTCTTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:2285080 original size:22 final size:23
Alignment explanation
Indices: 2285038--2285085 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2285028 TATGTACTGT
*
2285038 AAAAAATTAATTATAATAAATTA
1 AAAAAATTAAGTATAATAAATTA
2285061 AAAAAATTAACGTA-AA-AAATTA
1 AAAAAATTAA-GTATAATAAATTA
2285083 AAA
1 AAA
2285086 TTGGACATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 12 0.52
24 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAAAATTAAGTATAATAAATTA
Found at i:2285343 original size:13 final size:13
Alignment explanation
Indices: 2285327--2285351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2285317 ATAGTAGTTT
2285327 TAAAAAGTATATA
1 TAAAAAGTATATA
2285340 TAAAAAGTATAT
1 TAAAAAGTATAT
2285352 CAATTAATTT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
TAAAAAGTATATA
Found at i:2285611 original size:18 final size:18
Alignment explanation
Indices: 2285570--2285613 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2285560 GAATTTGTAG
2285570 TTATATAATAAAAAATTA
1 TTATATAATAAAAAATTA
* *
2285588 TAATATAATTAATAAATT-
1 TTATATAA-TAAAAAATTA
2285606 TTATATAA
1 TTATATAA
2285614 GAATTTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATATAATAAAAAATTA
Found at i:2288391 original size:19 final size:20
Alignment explanation
Indices: 2288367--2288404 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2288357 ATCCAAACAT
2288367 AAAAAATCTC-TATTTTTTG
1 AAAAAATCTCGTATTTTTTG
*
2288386 AAAAAATTTCGTATTTTTT
1 AAAAAATCTCGTATTTTTT
2288405 CAGAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (20 bp):
AAAAAATCTCGTATTTTTTG
Found at i:2297055 original size:23 final size:23
Alignment explanation
Indices: 2297035--2297087 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
2297025 AGTTAAAAGT
* *
2297035 AAAAACACACACAAAAAAAAAAC
1 AAAAACAAAAACAAAAAAAAAAC
2297058 AAAAACAAAAACAAAAAAAACACAC
1 AAAAACAAAAACAAAAAAAA-A-AC
2297083 AAAAA
1 AAAAA
2297088 AAGAGTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAACAAAAACAAAAAAAAAAC
Found at i:2297056 original size:6 final size:6
Alignment explanation
Indices: 2297035--2297087 Score: 56
Period size: 6 Copynumber: 8.8 Consensus size: 6
2297025 AGTTAAAAGT
* *
2297035 AAAAAC ACACAC AAAAA- AAAAAC AAAAAC AAAAAC AAAAA- AAACACAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAA-A-AC
2297083 AAAAA
1 AAAAA
2297088 AAGAGTGCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.21
6 26 0.67
7 2 0.05
8 3 0.08
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:2297059 original size:11 final size:11
Alignment explanation
Indices: 2297045--2297089 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 11
2297035 AAAAACACAC
2297045 ACAAAAAAAAA
1 ACAAAAAAAAA
2297056 ACAAAAACAAAA
1 ACAAAAA-AAAA
2297068 ACAAAAAAAACA
1 ACAAAAAAAA-A
2297080 CACAAAAAAA
1 -ACAAAAAAA
2297090 GAGTGCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.32
12 12 0.39
13 9 0.29
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:2298372 original size:32 final size:31
Alignment explanation
Indices: 2298295--2298567 Score: 302
Period size: 30 Copynumber: 8.7 Consensus size: 31
2298285 ATCTCTCTTC
*
2298295 TCAAAGTCCATGACTCAGTGGCATCTTTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
2298325 TCTAAGTCCACGACTCAGGGGCATCATTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC-TTTTCT
* * *
2298357 TCCAAGTCCATGACTCAGTGGCATTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCA-TCTTTTCT
* *
2298389 TCAAAGTCCATGACTCAGTGGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
2298419 CCAAAGTCCACGACTCAGTGGTATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
*
2298450 TCAAAGTCCACGACTCAGTGGCAATCTCTT-T
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCT
*
2298481 TCAAAGTCCACGACTCAGTGGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
2298511 CCAAAGTCCACGACTCTGTGGCACCTTTTTCTTT
1 TCAAAGTCCACGACTCAGTGGCATC-TTTTC--T
* * *
2298545 TCAAAGTTCACAACTCTGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
2298568 CCCTTTTAAG
Statistics
Matches: 209, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
30 77 0.37
31 56 0.27
32 55 0.26
33 1 0.00
34 20 0.10
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (31 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCT
Found at i:2298465 original size:61 final size:61
Alignment explanation
Indices: 2298288--2298533 Score: 300
Period size: 62 Copynumber: 4.0 Consensus size: 61
2298278 TCTTCAAATC
* * * *
2298288 TCTCTTCTCAAAGTCCATGACTCAGTGGCATCTTTT-TTCTAAGTCCACGACTCAGGGGCA
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * * *
2298348 TCATTTTCTTCC-AAGTCCATGACTCAGTGGCATTTTTTTCTTCAAAGTCCATGACTCAGTGGCA
1 TC-TCTTC--CCAAAGTCCACGACTCAGTGGCA-TCTTTTCTTCAAAGTCCACGACTCAGTGGCA
*
2298412 TCTCTTCCCAAAGTCCACGACTCAGTGGTATCTTTTCTTCAAAGTCCACGACTCAGTGGCAA
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGC-A
** * * *
2298474 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTC-CCAAAGTCCACGACTCTGTGGCA
1 TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
2298534 CCTTTTTCTT
Statistics
Matches: 162, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
60 3 0.02
61 54 0.33
62 72 0.44
63 10 0.06
64 23 0.14
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (61 bp):
TCTCTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
Found at i:2298601 original size:27 final size:27
Alignment explanation
Indices: 2298548--2298601 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2298538 TTTCTTTTCA
* *
2298548 AAGTTCACAACTCTGTGGCACCCTTTT
1 AAGTTCACAACTCCGTGGCACCATTTT
*
2298575 AAGTTCACAACTCCGTGGCACTATTTT
1 AAGTTCACAACTCCGTGGCACCATTTT
2298602 TTTTAAGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (27 bp):
AAGTTCACAACTCCGTGGCACCATTTT
Found at i:2298652 original size:34 final size:33
Alignment explanation
Indices: 2298514--2298857 Score: 276
Period size: 34 Copynumber: 10.8 Consensus size: 33
2298504 TCTCTTCCCA
* *
2298514 AAGTCCACGACTCTGTGGCACCTTTTT-CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
2298546 CAAAGTTCACAACTCTGTGGCA-C-----CCTTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
2298575 AAGTTCACAACTCCGTGGCA-CTATTTT--TTTT
1 AAGTCCACAACTCCGTGGCACCT-TTTTCCTTTT
* *
2298606 AAGCCCACAACTCCATGGCACTCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* * *
2298640 AAGTCCATAACTCCATGGTA-C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
2298667 AAGTCCACAACTCTGTGGTATCTTTTT-CTTTGT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTT-T
* * *
2298700 AAGTCCACAACTCCATGGCATCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
2298733 AAGTCCACAACTCCGTGGCACC-TTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
2298765 AAGTCCACGACTTCGTGGCACCTTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT-CCTTTT
* * * *
2298799 AAGCCCACACCTTCGTGGCATCCCTTTTT-CTTGT
1 AAGTCCACAACTCCGTGGCA--CCTTTTTCCTTTT
2298833 AAGTCCACAACTCCGTGGCACCTTT
1 AAGTCCACAACTCCGTGGCACCTTT
2298858 AAGTCTAATA
Statistics
Matches: 257, Mismatches: 30, Indels: 48
0.77 0.09 0.14
Matches are distributed among these distances:
27 43 0.17
28 1 0.00
29 5 0.02
31 21 0.08
32 42 0.16
33 52 0.20
34 86 0.33
36 7 0.03
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
Done.