Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 73 of 193
Found at i:23337904 original size:18 final size:20
Alignment explanation
Indices: 23337875--23337923 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
23337865 ATAAAAGTAG
*
23337875 AGAAGAAGAAAAAGAA-AGC
1 AGAAGAAAAAAAAGAATAGC
23337894 A-AAG-AAAAAAAGAATAGC
1 AGAAGAAAAAAAAGAATAGC
23337912 AGAA-AAAAAAAA
1 AGAAGAAAAAAAA
23337924 TATTGCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.35
18 7 0.27
19 10 0.38
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (20 bp):
AGAAGAAAAAAAAGAATAGC
Found at i:23339672 original size:148 final size:147
Alignment explanation
Indices: 23339419--23340030 Score: 626
Period size: 148 Copynumber: 4.2 Consensus size: 147
23339409 AAGTTCTGAA
* * * *
23339419 TAGTGTTTTTCTTTAAAAAAAGAAATTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTTATT
1 TAGTGATTTTCATTAAAAAAAGAAA-TTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCATT
* * * *
23339484 TCAAAGAAAAAGTTTAAAATTTTAAA-TAAAGTTTTGATTTTTTTTAACTATTTTAAAAT-AAAA
65 TTAAAGAAAAAGTTTAAATTTTTAAACAAAAG-TTTGATTTTTTTTAACTATTTCAAAATAAAAA
* *
23339547 GTCAAATTTTTTAAGTAAAG
129 GTTAGA-TTTTTAAGTAAAG
* *
23339567 TAGTGATTTTCATTAAAAAAATAAAGTTTAGATTTTTAAAACTAAAAATCTGTTTTTTAGTCATT
1 TAGTGATTTTCATTAAAAAAAGAAA-TTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCATT
* * * *
23339632 TTAAAGAAAAAGTTTAAATTTTTTAACAAAATTTTGA-TTTTTTAAACTATTTCGAAATAAAAAG
65 TTAAAGAAAAAGTTTAAATTTTTAAACAAAAGTTTGATTTTTTTTAACTATTTCAAAATAAAAAG
* *
23339696 TTTGGATTTCTAAGTAAAG
130 -TTAGATTTTTAAGTAAAG
* * *
23339715 TAGTGATTTTCATTAAAAAAAAAGAAACTTTAGATTTTTTAAAATAAAAATTTGTTTTTTGGTCA
1 TAGTGATTTTCATT--AAAAAAAGAAA-TTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCA
* * *
23339780 TTTTAAAG-AAAATTTTAAATTTTTTAAA-TAAAGTTT-CTCTTTTTTTAACTATTTCAAAATAA
63 TTTTAAAGAAAAAGTTTAAA-TTTTTAAACAAAAGTTTGAT-TTTTTTTAACTATTTCAAAATAA
* *
23339842 AAATTTAGATTTTTAAGTAAAT
126 AAAGTTAGATTTTTAAGTAAAG
* ** *
23339864 TATTGATTTT--TT-TTAAAA-AAA--TAGATTTTTAAAAATAAAAAAATCTATTTTTTAGGT-A
1 TAGTGATTTTCATTAAAAAAAGAAATTTAGATTTTTAAAAAT--AAAAATCTGTTTTTTA-GTCA
* * *
23339922 TTTTAAAAGAAAAAGTTT-AATTTTTAAAC-AAAGTTTGATATTTTTTAAGTATTTCGAAAT-AA
63 TTTT-AAAGAAAAAGTTTAAATTTTTAAACAAAAGTTTGATTTTTTTTAACTATTTCAAAATAAA
* * *
23339984 AAGTTTTGATTTTTAAGAAAAA
127 AAG-TTAGATTTTTAAGTAAAG
** *
23340006 TAGTGATTTTGTTTTAAAAAAGAAA
1 TAGTGATTTTCATTAAAAAAAGAAA
23340031 AAACTTTTTA
Statistics
Matches: 389, Mismatches: 55, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
140 14 0.04
141 4 0.01
142 75 0.19
143 12 0.03
144 13 0.03
145 4 0.01
146 3 0.01
147 20 0.05
148 117 0.30
149 45 0.12
150 82 0.21
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (147 bp):
TAGTGATTTTCATTAAAAAAAGAAATTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCATTT
TAAAGAAAAAGTTTAAATTTTTAAACAAAAGTTTGATTTTTTTTAACTATTTCAAAATAAAAAGT
TAGATTTTTAAGTAAAG
Found at i:23345364 original size:21 final size:21
Alignment explanation
Indices: 23345338--23345377 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23345328 TAACCAAGCC
23345338 AAATTTTATTTATTTACATCT
1 AAATTTTATTTATTTACATCT
23345359 AAATTTTATTTATTTACAT
1 AAATTTTATTTATTTACAT
23345378 AATTTGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTTTATTTATTTACATCT
Found at i:23359619 original size:33 final size:33
Alignment explanation
Indices: 23359582--23359652 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
23359572 CATTACTTGC
* * *
23359582 ATGTACTTATATTTAATTAATGTA-TTAGAGTAG
1 ATGTACCTA-ATTTAATGAATGTATTTAGAGAAG
*
23359615 ATGTACCTAGTTTAATGAATGTATTTAGAGAAG
1 ATGTACCTAATTTAATGAATGTATTTAGAGAAG
23359648 ATGTA
1 ATGTA
23359653 TCTAGTAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (33 bp):
ATGTACCTAATTTAATGAATGTATTTAGAGAAG
Found at i:23359630 original size:32 final size:33
Alignment explanation
Indices: 23359593--23359658 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
23359583 TGTACTTATA
* *
23359593 TTTAATTAATGTA-TTAGAGTAGATGTACCTAG
1 TTTAATGAATGTATTTAGAGAAGATGTACCTAG
*
23359625 TTTAATGAATGTATTTAGAGAAGATGTATCTAG
1 TTTAATGAATGTATTTAGAGAAGATGTACCTAG
23359658 T
1 T
23359659 AGTCATGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.41
Consensus pattern (33 bp):
TTTAATGAATGTATTTAGAGAAGATGTACCTAG
Found at i:23363367 original size:17 final size:17
Alignment explanation
Indices: 23363320--23363367 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
23363310 TATATATATG
*
23363320 AAAATGCAATGACAATG
1 AAAATGCAATGACAATA
* * **
23363337 TAGATGCAGCGACAATA
1 AAAATGCAATGACAATA
23363354 AAAATGCAATGACA
1 AAAATGCAATGACA
23363368 TTAATAATGT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.17
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:23365266 original size:13 final size:13
Alignment explanation
Indices: 23365248--23365272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23365238 AAAACAATGT
23365248 AAAAGGAAACAAA
1 AAAAGGAAACAAA
23365261 AAAAGGAAACAA
1 AAAAGGAAACAA
23365273 GTTAGTGACG
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:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGGAAACAAA
Found at i:23367559 original size:66 final size:66
Alignment explanation
Indices: 23367456--23367580 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
23367446 TTGTAAATGC
* * *
23367456 AGTTCGTCATACTTTCTTTGAGACTCTGCTTCCCTCGCTGCTACCTTGGCTTCAAGTTGTAGCTG
1 AGTTCATCATACTTTCTTTGAGACTCTACTTCCCTCGCTGCTACCTTCGCTTCAAGTTGTAGCTG
23367521 A
66 A
* * * * *
23367522 AGTTCATCATATTTTCTTTGAGCCTCTACTTCTCTCGCTGCTGCCTTCGCTTTAAGTTG
1 AGTTCATCATACTTTCTTTGAGACTCTACTTCCCTCGCTGCTACCTTCGCTTCAAGTTG
23367581 AGCAATTTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (66 bp):
AGTTCATCATACTTTCTTTGAGACTCTACTTCCCTCGCTGCTACCTTCGCTTCAAGTTGTAGCTG
A
Found at i:23370382 original size:34 final size:34
Alignment explanation
Indices: 23370339--23370405 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
23370329 GCCTAGCTGC
23370339 TAGTTCAAATACTAAAATTCAACTTTGGGTATTG
1 TAGTTCAAATACTAAAATTCAACTTTGGGTATTG
* *
23370373 TAGTTCAAATACTAAAATTCAGCTTTGTGTATT
1 TAGTTCAAATACTAAAATTCAACTTTGGGTATT
23370406 ACAGTACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (34 bp):
TAGTTCAAATACTAAAATTCAACTTTGGGTATTG
Found at i:23373887 original size:83 final size:82
Alignment explanation
Indices: 23373713--23373890 Score: 209
Period size: 83 Copynumber: 2.2 Consensus size: 82
23373703 TTTTATCATA
** * * *
23373713 AAACGTCACTAAT-GCTCTTTATCTATTATGGCGTTTTTCATAAAAGTTGCTATTGCTTAATTTT
1 AAACGTCGTTAATGGCTCTTAATCTATTATGACGTTTTTCATAAAAGTCGCTATTGCTTAATTTT
*
23373777 TATCGATATTTTTTTAT
66 TATCGACATTTTTTTAT
* * *
23373794 AAACGTCGTTAATGGCTCTTAATCTATTGTGACGTTTTTTCATAAACGTCGTTATTGCTTAACTT
1 AAACGTCGTTAATGGCTCTTAATCTATTATGACG-TTTTTCATAAAAGTCGCTATTGCTTAA-TT
* *
23373859 TTTA-CGGCGTTCTTTTTAT
64 TTTATCGACATT-TTTTTAT
23373878 AAACG-CGTTAATG
1 AAACGTCGTTAATG
23373891 TTATTTTTAT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
81 11 0.13
82 17 0.21
83 36 0.44
84 18 0.22
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (82 bp):
AAACGTCGTTAATGGCTCTTAATCTATTATGACGTTTTTCATAAAAGTCGCTATTGCTTAATTTT
TATCGACATTTTTTTAT
Found at i:23374090 original size:10 final size:10
Alignment explanation
Indices: 23374077--23374101 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23374067 TCATAAAAAA
23374077 ATTTAAATTT
1 ATTTAAATTT
23374087 ATTTAAATTT
1 ATTTAAATTT
23374097 ATTTA
1 ATTTA
23374102 TAATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:23374584 original size:36 final size:36
Alignment explanation
Indices: 23374532--23374607 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
23374522 GTGGAAGTTG
*
23374532 ACTCTACAGATGTCGACTTTCACTCTGTAAATACCT
1 ACTCCACAGATGTCGACTTTCACTCTGTAAATACCT
*
23374568 ACTCCACAGATGTCGACTTTCACTTTGTAAATACCT
1 ACTCCACAGATGTCGACTTTCACTCTGTAAATACCT
23374604 ACTC
1 ACTC
23374608 TCATTCCTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.33
Consensus pattern (36 bp):
ACTCCACAGATGTCGACTTTCACTCTGTAAATACCT
Found at i:23375379 original size:18 final size:17
Alignment explanation
Indices: 23375358--23375407 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
23375348 AAATAATTTA
23375358 AAAATTATAAAAATAGTC
1 AAAATTATAAAAATA-TC
* *
23375376 AAAATAATAATAAT-TC
1 AAAATTATAAAAATATC
23375392 AAAATTCA-AAAAATAT
1 AAAATT-ATAAAAATAT
23375408 TATAAAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 12 0.46
17 2 0.08
18 12 0.46
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (17 bp):
AAAATTATAAAAATATC
Found at i:23376130 original size:41 final size:41
Alignment explanation
Indices: 23376085--23376235 Score: 141
Period size: 41 Copynumber: 3.7 Consensus size: 41
23376075 ACGGCATTTT
* *
23376085 TAAACGCCGTTAATTCTCTTACCTTTTGCGGTGTTTTCTCA
1 TAAACACCGCTAATTCTCTTACCTTTTGCGGTGTTTTCTCA
* ** *
23376126 TAAACACCACTAATAT-TCTTACCTTTTGTAGCGTTTTCTCA
1 TAAACACCGCTAAT-TCTCTTACCTTTTGCGGTGTTTTCTCA
* * *
23376167 TAAACGA-TGTTAATTCTCTTACCTTTTGCGACAT-TTTTCTCA
1 TAAAC-ACCGCTAATTCTCTTACCTTTTGCG--GTGTTTTCTCA
23376209 TAAACACCGCT-ATTGCT-TTACCTTTTG
1 TAAACACCGCTAATT-CTCTTACCTTTTG
23376236 TGGCGTTTAT
Statistics
Matches: 88, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.01
41 68 0.77
42 19 0.22
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.43
Consensus pattern (41 bp):
TAAACACCGCTAATTCTCTTACCTTTTGCGGTGTTTTCTCA
Found at i:23376190 original size:82 final size:81
Alignment explanation
Indices: 23376093--23376243 Score: 216
Period size: 82 Copynumber: 1.8 Consensus size: 81
23376083 TTTAAACGCC
* *
23376093 GTTAATTCTCTTACCTTTTGCG-GTGTTTTCTCATAAACACCACTAATATTC-TTACCTTTTGTA
1 GTTAATTCTCTTACCTTTTGCGAAT-TTTTCTCATAAACACCACT-AT-TGCTTTACCTTTTGTA
23376156 GCGTTTTCTCATAAACGAT
63 GCGTTTTCTCATAAACGAT
* *
23376175 GTTAATTCTCTTACCTTTTGCGACATTTTTCTCATAAACACCGCTATTGCTTTACCTTTTGTGGC
1 GTTAATTCTCTTACCTTTTGCGA-ATTTTTCTCATAAACACCACTATTGCTTTACCTTTTGTAGC
23376240 GTTT
65 GTTT
23376244 ATGAAAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
81 2 0.03
82 41 0.66
83 18 0.29
84 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (81 bp):
GTTAATTCTCTTACCTTTTGCGAATTTTTCTCATAAACACCACTATTGCTTTACCTTTTGTAGCG
TTTTCTCATAAACGAT
Found at i:23380216 original size:24 final size:23
Alignment explanation
Indices: 23380169--23380217 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
23380159 CTTCTTGTAA
*
23380169 TTTAGGTTTAGTTATTTTCTTTC
1 TTTAGGTTTAGTTATTTTCATTC
23380192 TTTAGGTTTTAGTTATTGTT-ATTC
1 TTTAGG-TTTAGTTATT-TTCATTC
23380216 TT
1 TT
23380218 GTTTTATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 15 0.65
25 2 0.09
ACGTcount: A:0.14, C:0.06, G:0.14, T:0.65
Consensus pattern (23 bp):
TTTAGGTTTAGTTATTTTCATTC
Found at i:23387163 original size:13 final size:14
Alignment explanation
Indices: 23387145--23387174 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23387135 GGGGAGAAAG
23387145 AAAAG-AAAAGGAA
1 AAAAGAAAAAGGAA
23387158 AAAAGAAAAAGGAA
1 AAAAGAAAAAGGAA
23387172 AAA
1 AAA
23387175 CTAGGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGGAA
Found at i:23389881 original size:32 final size:33
Alignment explanation
Indices: 23389845--23389906 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
23389835 TGTAGTTATA
* *
23389845 TTTAATTAATGTA-TTAGAGTAGATGTATCCAG
1 TTTAATGAATGTATTTAGAGAAGATGTATCCAG
23389877 TTTAATGAATGTATTTAGAGAAGATGTATC
1 TTTAATGAATGTATTTAGAGAAGATGTATC
23389907 TAGTAGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (33 bp):
TTTAATGAATGTATTTAGAGAAGATGTATCCAG
Found at i:23392099 original size:2 final size:2
Alignment explanation
Indices: 23392092--23392127 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23392082 TTAAAATCTA
23392092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23392128 TCATAGCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23392688 original size:21 final size:21
Alignment explanation
Indices: 23392640--23392690 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
23392630 CATTATTTTT
*
23392640 TAATTTTTTTTTAAATTTATA
1 TAATTTTATTTTAAATTTATA
**
23392661 TTGTTTTATTTTAATATTTA-A
1 TAATTTTATTTTAA-ATTTATA
23392682 TAATTTTAT
1 TAATTTTAT
23392691 CATTTTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TAATTTTATTTTAAATTTATA
Found at i:23394815 original size:29 final size:29
Alignment explanation
Indices: 23394756--23394814 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
23394746 TTTGGTTTAA
*
23394756 TGTGCAATTGTATAAATGAATTTTAATTT
1 TGTGCAATTGTATAAATAAATTTTAATTT
* * *
23394785 TGTGCAATTTTATACATCAAATTTTGATTT
1 TGTGCAATTGTATAAAT-AAATTTTAATTT
23394815 GATCCAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (29 bp):
TGTGCAATTGTATAAATAAATTTTAATTT
Found at i:23395603 original size:15 final size:13
Alignment explanation
Indices: 23395583--23395627 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
23395573 CCTGGCCACC
23395583 AATATTAATTTCTTT
1 AATATT-ATTT-TTT
23395598 AATATTATTTTTT
1 AATATTATTTTTT
23395611 ATATATATATTTTTT
1 A-ATAT-TATTTTTT
23395626 AA
1 AA
23395628 AAATATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.14
14 9 0.32
15 15 0.54
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTATTTTTT
Found at i:23395801 original size:19 final size:18
Alignment explanation
Indices: 23395762--23395801 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
23395752 TGCTTCTCAC
23395762 ATAATAATAAAATTAACA
1 ATAATAATAAAATTAACA
23395780 ATAA-AATAAAAGTTATACA
1 ATAATAATAAAA-TTA-ACA
23395799 ATA
1 ATA
23395802 TGCAAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
ATAATAATAAAATTAACA
Found at i:23396630 original size:51 final size:50
Alignment explanation
Indices: 23396570--23396704 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 50
23396560 ACACCAATAG
* *
23396570 TCACTCAACTTT-GACATGGGAAAACAAACAGTCACCTGGTTTACATTTCAA
1 TCACTCAACTTTAAAAAT-GGAAAA-AAACAGTCACCTGGTTTACATTTCAA
* *
23396621 TCACTCAACTTTAAAAATGTAACAAAACAGTCACCTGGTTTACATTTCAA
1 TCACTCAACTTTAAAAATGGAAAAAAACAGTCACCTGGTTTACATTTCAA
* *
23396671 TCACTCAACTTTAAAAATGTAACAAAACAGTCAC
1 TCACTCAACTTTAAAAATGGAAAAAAACAGTCAC
23396705 TCAACTTTGA
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
50 60 0.76
51 16 0.20
52 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (50 bp):
TCACTCAACTTTAAAAATGGAAAAAAACAGTCACCTGGTTTACATTTCAA
Found at i:23396656 original size:50 final size:50
Alignment explanation
Indices: 23396595--23396704 Score: 220
Period size: 50 Copynumber: 2.2 Consensus size: 50
23396585 ATGGGAAAAC
23396595 AAACAGTCACCTGGTTTACATTTCAATCACTCAACTTTAAAAATGTAACA
1 AAACAGTCACCTGGTTTACATTTCAATCACTCAACTTTAAAAATGTAACA
23396645 AAACAGTCACCTGGTTTACATTTCAATCACTCAACTTTAAAAATGTAACA
1 AAACAGTCACCTGGTTTACATTTCAATCACTCAACTTTAAAAATGTAACA
23396695 AAACAGTCAC
1 AAACAGTCAC
23396705 TCAACTTTGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (50 bp):
AAACAGTCACCTGGTTTACATTTCAATCACTCAACTTTAAAAATGTAACA
Found at i:23402098 original size:22 final size:23
Alignment explanation
Indices: 23402063--23402108 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
23402053 AGAAATAAAT
23402063 AAACTAAAACCTAAA-GAAAGAA
1 AAACTAAAACCTAAATGAAAGAA
23402085 AAACTGAAAA-CTAAATGAAAGAA
1 AAACT-AAAACCTAAATGAAAGAA
23402108 A
1 A
23402109 TAAAATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (23 bp):
AAACTAAAACCTAAATGAAAGAA
Found at i:23408875 original size:17 final size:17
Alignment explanation
Indices: 23408855--23408887 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23408845 TATCACTTGC
*
23408855 TATTTCAATAGCATTTT
1 TATTTCAATAACATTTT
23408872 TATTTCAATAACATTT
1 TATTTCAATAACATTT
23408888 CCCTATTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (17 bp):
TATTTCAATAACATTTT
Found at i:23413829 original size:66 final size:66
Alignment explanation
Indices: 23413751--23413884 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
23413741 TTGCACTTCT
*
23413751 CTAATTTGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
1 CTAATTAGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
23413816 A
66 A
* *
23413817 CTAATTAGATCAACCAACACTGGTTTAACTCTTAATTTAACCATCAAGTTACCATCACCACTAAT
1 CTAATTAGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
23413882 A
66 A
23413883 CT
1 CT
23413885 TATTCAAGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (66 bp):
CTAATTAGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
A
Found at i:23421076 original size:66 final size:66
Alignment explanation
Indices: 23420998--23421131 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
23420988 TTGCACTTCT
*
23420998 CTAATTTGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
1 CTAATTAGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
23421063 A
66 A
*
23421064 CTAATTAGATCAACCAACACTGGTTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
1 CTAATTAGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
23421129 A
66 A
23421130 CT
1 CT
23421132 TATTCAAGTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.37, C:0.28, G:0.05, T:0.30
Consensus pattern (66 bp):
CTAATTAGATCAACCAACACTGATTTAACTCTTAATTCAACCATCAAGTTACCATCACCACTAAT
A
Found at i:23431939 original size:29 final size:29
Alignment explanation
Indices: 23431882--23431956 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
23431872 TGTGACCTCT
* *
23431882 TTATAAAAAGTAATATTAAAAAATTAATTAA
1 TTATAAAAA-TAA-AATAAAAAATAAATTAA
23431913 TTATAAAAATAAAATAAAAAATAAATTAA
1 TTATAAAAATAAAATAAAAAATAAATTAA
*
23431942 TTACAAAAATAAAAT
1 TTATAAAAATAAAAT
23431957 GTTTGCTACG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 29 0.71
30 3 0.07
31 9 0.22
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (29 bp):
TTATAAAAATAAAATAAAAAATAAATTAA
Found at i:23431952 original size:17 final size:16
Alignment explanation
Indices: 23431896--23431954 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
23431886 AAAAAGTAAT
*
23431896 ATTAAAAAATTAATTA
1 ATTAAAAAATAAATTA
23431912 ATTATAAAAAT-AA--A
1 ATTA-AAAAATAAATTA
23431926 A-TAAAAAATAAATTA
1 ATTAAAAAATAAATTA
23431941 ATTACAAAAATAAA
1 ATTA-AAAAATAAA
23431955 ATGTTTGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 6 0.16
13 4 0.11
14 2 0.05
15 2 0.05
16 8 0.22
17 15 0.41
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTAAAAAATAAATTA
Found at i:23432381 original size:28 final size:28
Alignment explanation
Indices: 23432329--23432383 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
23432319 ACATTTTCCC
*
23432329 TGCATTTAATGTTTTAGTGGTTTTTTCA
1 TGCATTTAATGTTTTAATGGTTTTTTCA
23432357 TGCATTTAATGTTTTAAT-GTCTTTTTC
1 TGCATTTAATGTTTTAATGGT-TTTTTC
23432384 TTATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (28 bp):
TGCATTTAATGTTTTAATGGTTTTTTCA
Found at i:23432391 original size:28 final size:28
Alignment explanation
Indices: 23432331--23432394 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
23432321 ATTTTCCCTG
* *
23432331 CATTTAATGTTTTAGTGGTTTTTTCATG
1 CATTTAATGTTTTAATGGTTTTTTCATA
*
23432359 CATTTAATGTTTTAAT-GTCTTTTTCTTA
1 CATTTAATGTTTTAATGGT-TTTTTCATA
*
23432387 TATTTAAT
1 CATTTAAT
23432395 CTCTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.59
Consensus pattern (28 bp):
CATTTAATGTTTTAATGGTTTTTTCATA
Found at i:23432877 original size:20 final size:19
Alignment explanation
Indices: 23432854--23432925 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
23432844 AAAAATTACA
*
23432854 AAAAATTCAAGATAATTTT
1 AAAAATTCAAAATAATTTT
*
23432873 CAAAAATTGAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
23432893 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
23432912 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
23432926 TTATATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
18 4 0.09
19 19 0.42
20 22 0.49
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:23432914 original size:18 final size:18
Alignment explanation
Indices: 23432875--23432930 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
23432865 ATAATTTTCA
* *
23432875 AAAATTGAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
23432894 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
23432912 AAAAATTCTAAA-ATTTAT
1 -AAAATTCAAAATATTTAT
23432930 A
1 A
23432931 TTTTTATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 1 0.03
18 11 0.33
19 21 0.64
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:23432945 original size:19 final size:19
Alignment explanation
Indices: 23432921--23432960 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
23432911 TAAAAATTCT
23432921 AAAATTTAT-ATTTTTATAA
1 AAAATTTATAATTTTT-TAA
23432940 AAAATTTATAATTTTTTAA
1 AAAATTTATAATTTTTTAA
23432959 AA
1 AA
23432961 TCCAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTTATAATTTTTTAA
Found at i:23435321 original size:28 final size:27
Alignment explanation
Indices: 23435282--23435336 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
23435272 CAAATATTTA
*
23435282 AAAATAATATTTTAAATGATAATTTTT
1 AAAATAATATTTGAAATGATAATTTTT
* * *
23435309 AAAATTATCATTTGAATTTATAATTTTT
1 AAAATAAT-ATTTGAAATGATAATTTTT
23435337 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
AAAATAATATTTGAAATGATAATTTTT
Found at i:23451494 original size:12 final size:12
Alignment explanation
Indices: 23451479--23451517 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
23451469 AGACAAGGAT
23451479 GAAGAAAAAGAA
1 GAAGAAAAAGAA
* *
23451491 GAAGGAAAGGAA
1 GAAGAAAAAGAA
*
23451503 GAAGAGAAAGAA
1 GAAGAAAAAGAA
23451515 GAA
1 GAA
23451518 ACAGAACCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:23454585 original size:22 final size:23
Alignment explanation
Indices: 23454557--23454612 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
23454547 TCAAAGGATT
*
23454557 AATTGAAGT-AAAAAAAAAAATC
1 AATTGAAATAAAAAAAAAAAATC
23454579 AATTGAAATAAAAAAAAAAAAATC
1 AATTGAAAT-AAAAAAAAAAAATC
23454603 AATTGAAATA
1 AATTGAAATA
23454613 GAAGGGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 8 0.26
23 1 0.03
24 22 0.71
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (23 bp):
AATTGAAATAAAAAAAAAAAATC
Found at i:23454598 original size:24 final size:24
Alignment explanation
Indices: 23454566--23454612 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
23454556 TAATTGAAGT
23454566 AAAAAAAAAAATCAATTGAAATAA
1 AAAAAAAAAAATCAATTGAAATAA
23454590 AAAAAAAAAAATCAATTGAAATA
1 AAAAAAAAAAATCAATTGAAATA
23454613 GAAGGGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAAAAAAATCAATTGAAATAA
Found at i:23454952 original size:19 final size:19
Alignment explanation
Indices: 23454930--23454987 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
23454920 ATAATTTTAG
23454930 TAATTTTAAAATTTTAAAA
1 TAATTTTAAAATTTTAAAA
* ***
23454949 TAATTTT-ATATTTTTTTA
1 TAATTTTAAAATTTTAAAA
23454967 TGAATTTTAAAATTTTTAAAA
1 T-AATTTTAAAA-TTTTAAAA
23454988 ATTAATTAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
18 8 0.29
19 13 0.46
20 2 0.07
21 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATTTTAAAATTTTAAAA
Found at i:23457977 original size:17 final size:17
Alignment explanation
Indices: 23457952--23458001 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
23457942 TACAATGACA
*
23457952 AATGGAAATGCAATGAT
1 AATGAAAATGCAATGAT
* * *
23457969 AATGCAAATGTAGTGAT
1 AATGAAAATGCAATGAT
*
23457986 AATTAAAATGCAATGA
1 AATGAAAATGCAATGA
23458002 CAAAGGGGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (17 bp):
AATGAAAATGCAATGAT
Found at i:23470034 original size:9 final size:9
Alignment explanation
Indices: 23469994--23470048 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
23469984 GTATTGAGGC
23469994 AGAAGAAAA
1 AGAAGAAAA
*
23470003 GGAAAGAAAA
1 AG-AAGAAAA
23470013 GATGAAGAAAA
1 -A-GAAGAAAA
*
23470024 AGAAGAGAA
1 AGAAGAAAA
*
23470033 AGACGAAAA
1 AGAAGAAAA
23470042 AGAAGAA
1 AGAAGAA
23470049 GATGTTGCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 21 0.57
10 8 0.22
11 7 0.19
12 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (9 bp):
AGAAGAAAA
Found at i:23470034 original size:21 final size:22
Alignment explanation
Indices: 23469995--23470050 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
23469985 TATTGAGGCA
* *
23469995 GAAGAAAAGGAA-AGAAAAGAT
1 GAAGAAAAAGAAGAGAAAAGAC
23470016 GAAGAAAAAGAAGAG-AAAGAC
1 GAAGAAAAAGAAGAGAAAAGAC
23470037 GAA-AAAGAAGAAGA
1 GAAGAAA-AAGAAGA
23470051 TGTTGCCCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.02
Consensus pattern (22 bp):
GAAGAAAAAGAAGAGAAAAGAC
Found at i:23470593 original size:13 final size:13
Alignment explanation
Indices: 23470575--23470605 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23470565 GTTTGGGGGG
*
23470575 AATGTGGAATGGA
1 AATGTGGAATCGA
23470588 AATGTGGAATCGA
1 AATGTGGAATCGA
23470601 AATGT
1 AATGT
23470606 AATTGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (13 bp):
AATGTGGAATCGA
Found at i:23472717 original size:24 final size:24
Alignment explanation
Indices: 23472641--23472705 Score: 114
Period size: 24 Copynumber: 2.7 Consensus size: 24
23472631 CAATCAATAC
23472641 ATTTTATATTACATTTGCACTGAA
1 ATTTTATATTACATTTGCACTGAA
23472665 ATTTTATATTACATTTGCACT-AA
1 ATTTTATATTACATTTGCACTGAA
23472688 TATTTTATATTACATTTG
1 -ATTTTATATTACATTTG
23472706 GCTGACAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 2 0.05
24 38 0.95
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTTTATATTACATTTGCACTGAA
Found at i:23491568 original size:21 final size:22
Alignment explanation
Indices: 23491539--23491583 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
23491529 AGAGGTAATC
*
23491539 AGGACAAGGATCAAGAAAAGGA
1 AGGACAAGGAACAAGAAAAGGA
* *
23491561 AGGA-AAGGAAGAAGAGAAGGA
1 AGGACAAGGAACAAGAAAAGGA
23491582 AG
1 AG
23491584 AATTAGAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.56, C:0.04, G:0.38, T:0.02
Consensus pattern (22 bp):
AGGACAAGGAACAAGAAAAGGA
Found at i:23523461 original size:21 final size:20
Alignment explanation
Indices: 23523423--23523461 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23523413 AAGCATGCCC
*
23523423 AGAAAACAAAAAATAAGAAA
1 AGAAAACAAAAAAGAAGAAA
*
23523443 AGAAAAGAAAAAAGGAAGA
1 AGAAAACAAAAAA-GAAGA
23523462 GGAGGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AGAAAACAAAAAAGAAGAAA
Found at i:23523515 original size:20 final size:21
Alignment explanation
Indices: 23523481--23523524 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
23523471 AAAAGTATTG
*
23523481 AAGAAGAAAGATGAATAAGAC
1 AAGAAGAAAGATGAAGAAGAC
*
23523502 AAGAA-AAAGTTGAAGAAGAC
1 AAGAAGAAAGATGAAGAAGAC
23523522 AAG
1 AAG
23523525 GAATGGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.61, C:0.05, G:0.25, T:0.09
Consensus pattern (21 bp):
AAGAAGAAAGATGAAGAAGAC
Found at i:23526817 original size:17 final size:18
Alignment explanation
Indices: 23526795--23526832 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23526785 ATTAAATATT
*
23526795 TTAAATT-ATCGGAATGA
1 TTAAATTGATCGGAATCA
*
23526812 TTAAATTGATGGGAATCA
1 TTAAATTGATCGGAATCA
23526830 TTA
1 TTA
23526833 TCTAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (18 bp):
TTAAATTGATCGGAATCA
Found at i:23534262 original size:11 final size:11
Alignment explanation
Indices: 23534246--23534289 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
23534236 AACCTCTCCA
23534246 TTTTCTTTCTC
1 TTTTCTTTCTC
23534257 TTTTCTCTTTCTC
1 -TTT-TCTTTCTC
*
23534270 TTTTCTTTTTC
1 TTTTCTTTCTC
*
23534281 TTTTTTTTC
1 TTTTCTTTC
23534290 AGGTGAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 14 0.50
12 6 0.21
13 8 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:23534286 original size:13 final size:13
Alignment explanation
Indices: 23534249--23534284 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
23534239 CTCTCCATTT
23534249 TCTTTCTCTTTTC
1 TCTTTCTCTTTTC
23534262 TCTTTCTCTTTTC
1 TCTTTCTCTTTTC
23534275 T-TTT-TCTTTT
1 TCTTTCTCTTTT
23534285 TTTTCAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.26
12 3 0.13
13 14 0.61
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TCTTTCTCTTTTC
Found at i:23536359 original size:13 final size:14
Alignment explanation
Indices: 23536341--23536370 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23536331 GTCAACGCAA
23536341 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
23536354 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
23536368 TCA
1 TCA
23536371 TTGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:23537071 original size:7 final size:7
Alignment explanation
Indices: 23537059--23537092 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
23537049 TCTTGATAAT
23537059 TTCTTCA
1 TTCTTCA
23537066 TTCTTCA
1 TTCTTCA
23537073 TTCTTCA
1 TTCTTCA
23537080 TTCTTCA
1 TTCTTCA
23537087 TTCTTC
1 TTCTTC
23537093 TATTTATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:23543311 original size:13 final size:14
Alignment explanation
Indices: 23543284--23543312 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23543274 TTTATTTATA
23543284 TTTGTTTTTTGTTC
1 TTTGTTTTTTGTTC
23543298 TTTGTTTTTT-TTC
1 TTTGTTTTTTGTTC
23543311 TT
1 TT
23543313 CTGTGCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (14 bp):
TTTGTTTTTTGTTC
Found at i:23544750 original size:3 final size:3
Alignment explanation
Indices: 23544744--23544781 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
23544734 TATTATTATT
* *
23544744 ATC ATC ACC ATC ACC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
23544782 TAGGGTTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:23545347 original size:52 final size:51
Alignment explanation
Indices: 23545290--23545497 Score: 133
Period size: 52 Copynumber: 4.1 Consensus size: 51
23545280 ATAAAAAATA
* *
23545290 TTTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAATAAATTTTTGAT
1 TTTTTTTA-TCATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTATTGAT
* * * * * *
23545342 TTTTTTTAACTATTTCGAAATAAAAA-TTTAGATTTTTAAGTAAAGTAGTGAT
1 TTTTTTTATC-ATTT-TAAAGAAAAAGTTTAAATTTTTAAATAAAGTATTGAT
** **** * * ***
23545394 TTTCATTA--AAGAAAAAAAAGAAAGTTTAGATTTTT-AA-AAA-TAAAAAT
1 TTTTTTTATCATTTTAAAGAA-AAAGTTTAAATTTTTAAATAAAGTATTGAT
* *
23545441 GTTTTTTAGTCATTTTAAAGAAAAAGTTTAAA-TTTTAAATAAAGTTTTGAT
1 TTTTTTTA-TCATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTATTGAT
23545492 TTTTTT
1 TTTTTT
23545498 AACTATTTCG
Statistics
Matches: 113, Mismatches: 33, Indels: 21
0.68 0.20 0.13
Matches are distributed among these distances:
47 9 0.08
48 12 0.11
49 16 0.14
50 20 0.18
51 9 0.08
52 39 0.35
53 8 0.07
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (51 bp):
TTTTTTTATCATTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTATTGAT
Found at i:23545697 original size:142 final size:141
Alignment explanation
Indices: 23545187--23545687 Score: 620
Period size: 142 Copynumber: 3.5 Consensus size: 141
23545177 GATCTTGAGA
* * * *
23545187 AAAGTTTTGATTTTTTTAACAATTTCGAAATAAAAGTTTTAATTTTTAAGAAAAATAATGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
*
23545252 CTGT-AAAAAAATGTTTAGA-TTTTTAATAATAAAAAATATTTTTTTAGTCATTTTAAAGAAAAA
66 -T-TAAAAAAAAAGTTTAGATTTTTTAA-AATAAAAAATA-TTTTTTAGTCATTTTAAAGAAAAA
23545315 GTTTAAATTTTTAAAT
127 GTTTAAA-TTTTAAAT
* * * *
23545331 AAATTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATTT
1 AAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTT
* *
23545396 TCATTAAAGAAAAAAAAGAAAGTTTAGATTTTTAAAAAT-AAAAATGTTTTTTAGTCATTTTAAA
65 T--TT------AAAAAA-AAAGTTTAGATTTTTTAAAATAAAAAATATTTTTTAGTCATTTTAAA
23545460 GAAAAAGTTTAAATTTTAAAT
121 GAAAAAGTTTAAATTTTAAAT
* * *
23545481 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTTTATGTAAAGTAGTGGTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGAAAAGTAGTGATTT
*
23545545 TTTAAAAAAAACGTTTAGATTTTTTAAAATAAAAAATCTATTTTTTAAGT-ATTTTAAAAGAAAA
65 TTTAAAAAAAAAGTTTAGATTTTTTAAAATAAAAAA--TATTTTTT-AGTCATTTT-AAAGAAAA
*
23545609 AGTTT-AATTTTAAAC
126 AGTTTAAATTTTAAAT
*
23545624 AAA-ATTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
23545688 GTTTTAAAAA
Statistics
Matches: 314, Mismatches: 25, Indels: 38
0.83 0.07 0.10
Matches are distributed among these distances:
140 19 0.06
141 11 0.04
142 52 0.17
143 28 0.09
144 25 0.08
145 49 0.16
146 1 0.00
147 2 0.01
148 3 0.01
149 47 0.15
150 17 0.05
151 31 0.10
152 11 0.04
153 12 0.04
154 6 0.02
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (141 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
TTAAAAAAAAAGTTTAGATTTTTTAAAATAAAAAATATTTTTTAGTCATTTTAAAGAAAAAGTTT
AAATTTTAAAT
Found at i:23545722 original size:142 final size:142
Alignment explanation
Indices: 23545187--23545698 Score: 541
Period size: 145 Copynumber: 3.5 Consensus size: 142
23545177 GATCTTGAGA
* * * *
23545187 AAAGTTTTGATTTTTTTAACAATTTCGAAATAAAAGTTTTAATTTTTAAGAAAAATAATGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
* * * * *
23545252 CTGTAAAAAAATGTTTAGATTTTTAATAATAAAAAATATTTTTTTAGTCATTTTAAAGAAAAAGT
66 CTTTAAAAAAACGATAAAATTTTTAAT-ATAAAAAATATTTTTTTAGTCATTTTAAAGAAAAAGT
23545317 TTAAATTTTTAAAT
130 TTAAA-TTTTAAAT
* * * *
23545331 AAATTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAGTGATTT
1 AAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTT
* * * ** * *
23545396 TCATTAAAGAAAA-AAAAGAAAGTTTAGATTTTTAAAAATAAAAATGTTTTTTAGTCATTTTAAA
65 TCTTTAAA-AAAACGATA-AAA-TTT---TTAATATAAA-AAATAT-TTTTTTAGTCATTTTAAA
23545460 GAAAAAGTTTAAATTTTAAAT
122 GAAAAAGTTTAAATTTTAAAT
* * *
23545481 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAG-TTTGAATTTTTATGTAAAGTAGTGGTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTG-ATTTTTAAGAAAAGTAGTGATTT
* * * * * *
23545545 T-TTAAAAAAAACGTTTAGATTTTTTAAAATAAAAAATCTATTTTTTAAGT-ATTTTAAAAGAAA
65 TCTTTAAAAAAACG-ATAAAATTTTTAATATAAAAAA--TATTTTTTTAGTCATTTT-AAAGAAA
*
23545608 AAGTTT-AATTTTAAAC
126 AAGTTTAAATTTTAAAT
*
23545624 AAA-ATTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
* *
23545688 GTTTTAAAAAA
66 CTTTAAAAAAA
23545699 GAGAAAACTT
Statistics
Matches: 307, Mismatches: 44, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
142 52 0.17
143 32 0.10
144 36 0.12
145 55 0.18
146 6 0.02
147 10 0.03
148 8 0.03
149 52 0.17
150 25 0.08
151 31 0.10
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (142 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
CTTTAAAAAAACGATAAAATTTTTAATATAAAAAATATTTTTTTAGTCATTTTAAAGAAAAAGTT
TAAATTTTAAAT
Found at i:23546305 original size:26 final size:27
Alignment explanation
Indices: 23546259--23546312 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
23546249 TATTTATTCT
*
23546259 TATTTCATCTTTATTTATTTTCATATA
1 TATTTCATATTTATTTATTTTCATATA
*
23546286 TATTT-ATATTTATGTT-TTTTTATATA
1 TATTTCATATTTAT-TTATTTTCATATA
23546312 T
1 T
23546313 TCCCCTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (27 bp):
TATTTCATATTTATTTATTTTCATATA
Found at i:23549203 original size:2 final size:2
Alignment explanation
Indices: 23549196--23549230 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23549186 TGAGATTTAT
23549196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23549231 TTGGAGTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23552300 original size:24 final size:24
Alignment explanation
Indices: 23552273--23552321 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
23552263 CTAATATCAC
*
23552273 TTTCATTCATTTCATTTTCATCTT
1 TTTCATTCATTTCACTTTCATCTT
23552297 TTTCATTCATTTCACTTTCATCTT
1 TTTCATTCATTTCACTTTCATCTT
23552321 T
1 T
23552322 CTTAGCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCATTCATTTCACTTTCATCTT
Found at i:23558727 original size:42 final size:42
Alignment explanation
Indices: 23558675--23558795 Score: 224
Period size: 42 Copynumber: 2.9 Consensus size: 42
23558665 GATGTTTCGA
* *
23558675 ATCTTTCCACATGAAGAAAAAAGGGAAATGATAATTTCATCG
1 ATCTCTCCACATGAAGAAGAAAGGGAAATGATAATTTCATCG
23558717 ATCTCTCCACATGAAGAAGAAAGGGAAATGATAATTTCATCG
1 ATCTCTCCACATGAAGAAGAAAGGGAAATGATAATTTCATCG
23558759 ATCTCTCCACATGAAGAAGAAAGGGAAATGATAATTT
1 ATCTCTCCACATGAAGAAGAAAGGGAAATGATAATTT
23558796 TATCTTTTAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (42 bp):
ATCTCTCCACATGAAGAAGAAAGGGAAATGATAATTTCATCG
Found at i:23564438 original size:10 final size:10
Alignment explanation
Indices: 23564423--23564447 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23564413 AAAATTGCAA
23564423 TTTAACCAAT
1 TTTAACCAAT
23564433 TTTAACCAAT
1 TTTAACCAAT
23564443 TTTAA
1 TTTAA
23564448 GTTCTGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAACCAAT
Found at i:23566134 original size:21 final size:20
Alignment explanation
Indices: 23566088--23566136 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
23566078 GGGGTCCAAA
23566088 CCGTGTGACAGGATACACGG
1 CCGTGTGACAGGATACACGG
* *
23566108 CTGTGTGACTAAGG-TACATGG
1 CCGTGTGAC--AGGATACACGG
23566129 CCGTGTGA
1 CCGTGTGA
23566137 GCAATCGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.33
21 13 0.54
22 3 0.12
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (20 bp):
CCGTGTGACAGGATACACGG
Found at i:23567703 original size:19 final size:20
Alignment explanation
Indices: 23567669--23567706 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
23567659 ATAAATTATT
23567669 AATATTCATAATTTAAACAA
1 AATATTCATAATTTAAACAA
*
23567689 AATATT-ATTATTTAAACA
1 AATATTCATAATTTAAACA
23567707 TTAATGCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATTCATAATTTAAACAA
Found at i:23569593 original size:3 final size:3
Alignment explanation
Indices: 23569585--23569617 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
23569575 GTTGCTTCCA
*
23569585 TTG TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
23569618 CAGTCCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:23570198 original size:3 final size:3
Alignment explanation
Indices: 23570190--23570217 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
23570180 ATTTTCATCC
23570190 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
23570218 TGGGTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23575146 original size:18 final size:18
Alignment explanation
Indices: 23575123--23575164 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
23575113 AATAAGTTTA
23575123 TAATTAAATAAATTT-AAT
1 TAATTAAA-AAATTTAAAT
*
23575141 TAATTAAAAATTTTAAAT
1 TAATTAAAAAATTTAAAT
23575159 TAATTA
1 TAATTA
23575165 CACTTTGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTAAAAAATTTAAAT
Found at i:23577097 original size:94 final size:95
Alignment explanation
Indices: 23576954--23577136 Score: 262
Period size: 94 Copynumber: 1.9 Consensus size: 95
23576944 TTTCTCTAGT
* *
23576954 GTTTTGATTTTTTTTATTTTTAAATCAATCATTTATATTTATTTACTTATTTATTAACTATTAAC
1 GTTTTGATTTTTTATATTTTTAAATC-A-CATTTATATTTATTTACTTATATATTAACTATTAAC
* * * *
23577019 TTGTTTAGTTTATGTATTATATATATATCACC
64 TTATTTAGCTTATATATTAAATATATATCACC
*
23577051 GTTTTGATTCTTTTAT-TTTTTAAATC-CTTTTATATTTATTTACTTATATATTAACTATTAACT
1 GTTTTGATT-TTTTATATTTTTAAATCACATTTATATTTATTTACTTATATATTAACTATTAACT
23577114 TATTTAGCTTATATATTAAATAT
65 TATTTAGCTTATATATTAAATAT
23577137 GCATATATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
94 54 0.69
97 19 0.24
98 5 0.06
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (95 bp):
GTTTTGATTTTTTATATTTTTAAATCACATTTATATTTATTTACTTATATATTAACTATTAACTT
ATTTAGCTTATATATTAAATATATATCACC
Found at i:23578222 original size:32 final size:32
Alignment explanation
Indices: 23578155--23578223 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
23578145 ATTTATATAT
* * **
23578155 ATAATCCTTTGCATTTTTTATTAAATATTACG
1 ATAATCCTTTGCATTTTCTATGAAATACCACG
* *
23578187 ATAATCCTTTGTATTTTCTATGAAATACCATG
1 ATAATCCTTTGCATTTTCTATGAAATACCACG
23578219 ATAAT
1 ATAAT
23578224 ATTATCGCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (32 bp):
ATAATCCTTTGCATTTTCTATGAAATACCACG
Found at i:23581499 original size:13 final size:14
Alignment explanation
Indices: 23581466--23581514 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
23581456 AACACTAATA
*
23581466 AAAGAAGAGATAAA-
1 AAAGAAAAGA-AAAG
*
23581480 AAA-AAAAGAGAAG
1 AAAGAAAAGAAAAG
23581493 -AAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
23581506 AAAGAAAAG
1 AAAGAAAAG
23581515 GTCAAGATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.48
14 11 0.38
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:23581499 original size:17 final size:17
Alignment explanation
Indices: 23581465--23581511 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
23581455 AAACACTAAT
*
23581465 AAAAGAAGAGATA-AAAAA
1 AAAAGAA-AGA-AGAAAAG
23581483 AAAAGAGAAGAAGAAAAG
1 AAAAGA-AAGAAGAAAAG
23581501 AAAAGAAAGAA
1 AAAAGAAAGAA
23581512 AAGGTCAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 19 0.73
19 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAGAAAAG
Found at i:23581587 original size:61 final size:65
Alignment explanation
Indices: 23581480--23581605 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 65
23581470 AAGAGATAAA
* * *
23581480 AAAAAAAGAGAAGAAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACTCGCAAAGGGTATCTT
1 AAAAAAA-AGAAGAAGAAAAG-AAAGAAAGAAAAGGTCAAGATGAAAACCCACAAAGGGCATCTT
23581545 TT
64 TT
23581547 AAAAAAAAGAAGAAGAAAAG-AA-AAAG-AAA-GTCAAGATGAAAACCCACAAAGGGCATCTT
1 AAAAAAAAGAAGAAGAAAAGAAAGAAAGAAAAGGTCAAGATGAAAACCCACAAAGGGCATCTT
23581606 GAAAAATCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
61 27 0.48
62 3 0.05
63 4 0.07
64 2 0.04
66 13 0.23
67 7 0.12
ACGTcount: A:0.59, C:0.10, G:0.21, T:0.11
Consensus pattern (65 bp):
AAAAAAAAGAAGAAGAAAAGAAAGAAAGAAAAGGTCAAGATGAAAACCCACAAAGGGCATCTTTT
Found at i:23582452 original size:11 final size:10
Alignment explanation
Indices: 23582429--23582467 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
23582419 GATTTTACCC
23582429 AAAAAAAGAA
1 AAAAAAAGAA
23582439 AAAAATAAGGAA
1 AAAAA-AA-GAA
23582451 AAAGAAAAGAA
1 AAA-AAAAGAA
23582462 AAAAAA
1 AAAAAA
23582468 TAAAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.31
11 8 0.31
12 8 0.31
13 2 0.08
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:23583612 original size:49 final size:49
Alignment explanation
Indices: 23583550--23584279 Score: 511
Period size: 49 Copynumber: 15.0 Consensus size: 49
23583540 ACGAATAAGG
*
23583550 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * *
23583599 AGGGAAAGATTTAAGCCGCAACGGCGAA-TTTAGTA-C-CA-AGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTT-GTACCTCAGAAACATGA
* * * *
23583645 AGGGAAGGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * * * *
23583694 AGGGAAACATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* *
23583743 AGGGAAA-ATTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGT
1 AGGGAAAGA-TTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * ** * * * * *
23583792 AGGAAAATATTTAAGCCATAACGGGGAATCTAGTACCACA-AAGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * *
23583841 AGGAAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAACATGTA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATG-A
* * * * * * * * *
23583891 A-GGAAAGACTTAAGCCGTAATGACGAATCTGGTACCACA-AAGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * *
23583939 AGGGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTCAAAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * * *
23583988 AGTGAAAGATTTAAGCCGCAACGACGAATCC-AGTA--TCACGAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GAA-ACATGA
* * * *
23584037 AGGGAAAGGTTTAAGTCGTAACGGCGAA-CTTATACCTTAGAAACATTG-
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACA-TGA
* * * * * * * *
23584085 AGGGATATATTTAAGTCGCAACTGCGAATCTGGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * * *
23584134 AGGGAAAGGTTTAAGTCCCAACAGCGAGCCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * ** ** * * * *
23584183 AGGGAAAGATTGAAGCCGCAACGATGAGTCTGGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * * * *
23584232 AGGGAAAGGTTTAAGTTGCGACGACGAACCTTGTACCTTAGAAACATG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATG
23584280 CTGGGAAGGA
Statistics
Matches: 517, Mismatches: 136, Indels: 56
0.73 0.19 0.08
Matches are distributed among these distances:
46 32 0.06
47 9 0.02
48 51 0.10
49 405 0.78
50 20 0.04
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (49 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
Found at i:23583788 original size:98 final size:98
Alignment explanation
Indices: 23583504--23584325 Score: 994
Period size: 98 Copynumber: 8.4 Consensus size: 98
23583494 GAGATGAGAT
* * * *
23583504 GGGAAAGATTTAAGCCACAACGGTGAATCCAGTACCACG-A-ATAAGGAGGGAAAGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
23583567 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
66 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
* *
23583600 GGGAAAGATTTAAGCCGCAACGGCGAATTTAGTA-C-C-AAGATATGGAGGGAAGGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* *
23583662 GCAATGGCGAACCTTGTACCTCAAAAACATGAA
66 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
* **
23583695 GGGAAACATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAATTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* *
23583760 GCAACGACGAACCTTGTACCTCAGAAACATGTA
66 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
* * ** * * * *
23583793 GGAAAATATTTAAGCCATAACGGGGAATCTAGTACCACAAAGATATGAAGGAAAAGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
*
23583858 GCAACGGCGAACCTTGTACCTCAAAAACATGTAA
66 GCAACGGCGAACCTTGTACCTCAGAAACATG-AA
* * * * * * *
23583892 -GGAAAGACTTAAGCCGTAATGACGAATCTGGTACCACAAAGATATGAAGGGAAAGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* *
23583956 GTAACGGCGAACCTTGTACCTCAAAAACATGAA
66 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
* * * *
23583989 GTGAAAGATTTAAGCCGCAACGACGAATCCAGTATCACGAAGATATGGAGGGAAAGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* * *
23584054 GTAACGGCGAA-CTTATACCTTAGAAACATTG-A
66 GCAACGGCGAACCTTGTACCTCAGAAACA-TGAA
* * * * *
23584086 GGGATATATTTAAGTCGCAACTGCGAATCTGGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* * *
23584151 CCAACAGCGAGCCTTGTACCTCAGAAACATGAA
66 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
* ** * * *
23584184 GGGAAAGATTGAAGCCGCAACGATGAGTCTGGTACCACGAAGATATGGAGGGAAAGGTTTAAGTT
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* * * **
23584249 GCGACGACGAACCTTGTACCTTAGAAACATGCT
66 GCAACGGCGAACCTTGTACCTCAGAAACATGAA
* * * * * * *
23584282 GGGAAGGATTGAGGCTGCAACGGCGAATCCAATACCATGAAGAT
1 GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGAT
23584326 GCGACGAAAA
Statistics
Matches: 622, Mismatches: 94, Indels: 18
0.85 0.13 0.02
Matches are distributed among these distances:
94 2 0.00
95 85 0.14
96 31 0.05
97 83 0.13
98 420 0.68
99 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (98 bp):
GGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTC
GCAACGGCGAACCTTGTACCTCAGAAACATGAA
Found at i:23589172 original size:28 final size:28
Alignment explanation
Indices: 23589139--23589192 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
23589129 TACAACACAG
*
23589139 TAACATAAGTGACTAAAATGTAACATTT
1 TAACATAAATGACTAAAATGTAACATTT
23589167 TAACATAAATGACTAAAATGTAACAT
1 TAACATAAATGACTAAAATGTAACAT
23589193 GAATCTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (28 bp):
TAACATAAATGACTAAAATGTAACATTT
Found at i:23591065 original size:97 final size:97
Alignment explanation
Indices: 23590890--23591421 Score: 748
Period size: 96 Copynumber: 5.5 Consensus size: 97
23590880 TAAAAAATTT
* * *
23590890 ATATGTTGAGAAATTTCAGATTTCTTT-ATTGTAGGTTTGAAACC-ATATATATTTCTATTTTTT
1 ATATGCTGAGAAATTTCAGATTT-TTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTT
*
23590953 ATTTTGACATAAGTATGAAAATTCAATAGATTC
65 ATTTTGACATGAGTATGAAAATTCAATAGATTC
* **
23590986 ATATGCTGATAAATTTTGGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
1 ATATGCTGAGAAATTTCAGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
23591051 TTTTGACATGAGTATGAAAATTCAATAGATTC
66 TTTTGACATGAGTATGAAAATTCAATAGATTC
* * * * * * *
23591083 ATATGCCGAGAAA-TTCGGGTTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTA
1 ATATGCTGAGAAATTTCAGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
** *
23591147 TTTTGACATGAGGCTGAATATTCAATAGATTC
66 TTTTGACATGAGTATGAAAATTCAATAGATTC
*
23591179 ATATGCTGAGAAATTTTAGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
1 ATATGCTGAGAAATTTCAGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
23591244 TTTTGACATGAGTATGAAAATTCAATAGATTC
66 TTTTGACATGAGTATGAAAATTCAATAGATTC
* * * * * * *
23591276 ATATGCCGAGAAA-TTCGGGTTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTA
1 ATATGCTGAGAAATTTCAGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
** *
23591340 TTTTGACATGAGGCTGAATATTCAATAGATTC
66 TTTTGACATGAGTATGAAAATTCAATAGATTC
* * *
23591372 ATATGCTGAGAAATTTTAGATTTTTTTATTGTAGATTTTAAATCAATATA
1 ATATGCTGAGAAATTTCAGATTTTTTCATTGTAGATTTTAAACCAATATA
23591422 ATGGAGTTAG
Statistics
Matches: 383, Mismatches: 49, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
95 3 0.01
96 205 0.54
97 175 0.46
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (97 bp):
ATATGCTGAGAAATTTCAGATTTTTTCATTGTAGATTTTAAACCAATATATATTTCTATTTTTTA
TTTTGACATGAGTATGAAAATTCAATAGATTC
Found at i:23591226 original size:193 final size:193
Alignment explanation
Indices: 23590910--23591421 Score: 900
Period size: 193 Copynumber: 2.7 Consensus size: 193
23590900 AAATTTCAGA
* * * * * * ** *
23590910 TTTCTTTATTGTAGGTTTGAAACC-ATATATATTTCTATTTTTTATTTTGACATAAGTATGAAAA
1 TTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTATTTTGACATGAGGCTGAATA
* *
23590974 TTCAATAGATTCATATGCTGATAAATTTTGGATTTTTTCATTGTAGATTTTAAACCAATATATAT
66 TTCAATAGATTCATATGCTGAGAAATTTTAGATTTTTTCATTGTAGATTTTAAACCAATATATAT
23591039 TTCTATTTTTTATTTTGACATGAGTATGAAAATTCAATAGATTCATATGCCGAGAAATTCGGG
131 TTCTATTTTTTATTTTGACATGAGTATGAAAATTCAATAGATTCATATGCCGAGAAATTCGGG
23591102 TTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTATTTTGACATGAGGCTGAATA
1 TTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTATTTTGACATGAGGCTGAATA
23591167 TTCAATAGATTCATATGCTGAGAAATTTTAGATTTTTTCATTGTAGATTTTAAACCAATATATAT
66 TTCAATAGATTCATATGCTGAGAAATTTTAGATTTTTTCATTGTAGATTTTAAACCAATATATAT
23591232 TTCTATTTTTTATTTTGACATGAGTATGAAAATTCAATAGATTCATATGCCGAGAAATTCGGG
131 TTCTATTTTTTATTTTGACATGAGTATGAAAATTCAATAGATTCATATGCCGAGAAATTCGGG
23591295 TTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTATTTTGACATGAGGCTGAATA
1 TTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTATTTTGACATGAGGCTGAATA
* *
23591360 TTCAATAGATTCATATGCTGAGAAATTTTAGATTTTTTTATTGTAGATTTTAAATCAATATA
66 TTCAATAGATTCATATGCTGAGAAATTTTAGATTTTTTCATTGTAGATTTTAAACCAATATA
23591422 ATGGAGTTAG
Statistics
Matches: 306, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
192 20 0.07
193 286 0.93
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.45
Consensus pattern (193 bp):
TTTCTTCAATGTAGATTTTAAACCGATATATATTTCTATTATTTATTTTGACATGAGGCTGAATA
TTCAATAGATTCATATGCTGAGAAATTTTAGATTTTTTCATTGTAGATTTTAAACCAATATATAT
TTCTATTTTTTATTTTGACATGAGTATGAAAATTCAATAGATTCATATGCCGAGAAATTCGGG
Found at i:23594484 original size:19 final size:19
Alignment explanation
Indices: 23594449--23594506 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 19
23594439 ATATTATTAC
23594449 AAAAATGTAAAAGAAATTGT-
1 AAAAAT-TAAAA-AAATTGTA
*
23594469 AAAAATTATAAAAAATGTTTA
1 AAAAATTA-AAAAAAT-TGTA
23594490 AAAAATTAAAAATAATT
1 AAAAATTAAAAA-AATT
23594507 TTTTTACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 6 0.18
20 16 0.48
21 11 0.33
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAATTAAAAAAATTGTA
Found at i:23594637 original size:23 final size:23
Alignment explanation
Indices: 23594594--23594643 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
23594584 TATTTTGAAT
**
23594594 TTTTACAATTTATAATTATA-TA
1 TTTTACAATTTATAAAAATATTA
*
23594616 TTTTAGAATCTTATAAAAATATTA
1 TTTTACAAT-TTATAAAAATATTA
23594640 TTTT
1 TTTT
23594644 TATTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 9 0.39
24 6 0.26
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTACAATTTATAAAAATATTA
Found at i:23595029 original size:21 final size:19
Alignment explanation
Indices: 23594995--23595043 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
23594985 TATTTTAAGT
23594995 ATTAAAT-TAAAATAAAAA
1 ATTAAATATAAAATAAAAA
23595013 ATTTAAATATCAAAATAAAAA
1 A-TTAAATAT-AAAATAAAAA
*
23595034 AATAAATATA
1 ATTAAATATA
23595044 CTTCAAGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 7 0.26
20 8 0.30
21 11 0.41
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATTAAATATAAAATAAAAA
Found at i:23601183 original size:18 final size:19
Alignment explanation
Indices: 23601148--23601186 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
23601138 AATAAATAGA
23601148 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
23601167 AATA-AATTATAAA-TTAAT
1 AATACAATT-TAAATTTAAT
23601185 AA
1 AA
23601187 AAGCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:23605949 original size:248 final size:247
Alignment explanation
Indices: 23605501--23605985 Score: 799
Period size: 248 Copynumber: 2.0 Consensus size: 247
23605491 ACCCAGTCTG
*
23605501 AGGTTATTTCTTCTTCTTGAAGTCTTTCTTGACTTCCGCCACATTTGCCTTAGTCACATTAACAT
1 AGGTTATTTCTTCTTCTTGAAGTCTTTCTTGACTTCCGCCACATTTGCCTTAGACACATTAACAT
* *
23605566 TGACTGCTTGTTAAGCTTTTTGGCTGCACTTCTATTGTCTTCTTCAATCCAAAGTTTGACAATCA
66 TGACTGCTTGTTAAGCTTTTTGGCTGCACTTCTATTGTCTTCTTCAATCCAAAGTCTAACAATCA
*
23605631 AATCTTCCACTGTCATTTCCTTTCTTTTATGCTTCAGATAGTTCTTGAAGTCATTCCAAGCACGG
131 AATCTTCCACTGCCATTTCCTTTCTTTTATGCTTCAGATAGTTCTTGAAGTCATTCCAAGCACGG
*
23605696 GGTAACTTTTCGATAATGGCTACCACCTGAAAGGTTCACTTATTGAAGTTCA
196 GGTAACTTCTCGATAATGGCTACCACCTGAAAGGTTCACTTATTGAAGTTCA
* * * * *
23605748 AGGTTGTTTCTTCTTCTTGAAGTCTTTCTTGACTTCTGCCACATTTGCTTTAGACACTTTAAGAT
1 AGGTTATTTCTTCTTCTTGAAGTCTTTCTTGACTTCCGCCACATTTGCCTTAGACACATTAACAT
* * ***
23605813 TGACTGCTTTGTTGAGCTTTTTGGCTGTACTTCTATTGTCTTCTTCAATTTGAAGTCTAACAATC
66 TGACTGC-TTGTTAAGCTTTTTGGCTGCACTTCTATTGTCTTCTTCAATCCAAAGTCTAACAATC
* *
23605878 AAATCTTCCATTGCCATTTCCTTTCTTTTATGCTTCAGATAGTTCTTGAAGTCATTCCAAGCACT
130 AAATCTTCCACTGCCATTTCCTTTCTTTTATGCTTCAGATAGTTCTTGAAGTCATTCCAAGCACG
*
23605943 GGGTAACTTCTCGATAATGGCTGCCACCTGAAAGGTTCACTTA
195 GGGTAACTTCTCGATAATGGCTACCACCTGAAAGGTTCACTTA
23605986 CAACCACCCC
Statistics
Matches: 219, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
247 66 0.30
248 153 0.70
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (247 bp):
AGGTTATTTCTTCTTCTTGAAGTCTTTCTTGACTTCCGCCACATTTGCCTTAGACACATTAACAT
TGACTGCTTGTTAAGCTTTTTGGCTGCACTTCTATTGTCTTCTTCAATCCAAAGTCTAACAATCA
AATCTTCCACTGCCATTTCCTTTCTTTTATGCTTCAGATAGTTCTTGAAGTCATTCCAAGCACGG
GGTAACTTCTCGATAATGGCTACCACCTGAAAGGTTCACTTATTGAAGTTCA
Found at i:23606931 original size:18 final size:19
Alignment explanation
Indices: 23606903--23606939 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
23606893 GAATACAATT
*
23606903 TAAATTTAATAATAAAATG
1 TAAATTTAATAAAAAAATG
23606922 TAAA-TTAATAAAAAAATG
1 TAAATTTAATAAAAAAATG
23606940 AACAAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAATTTAATAAAAAAATG
Found at i:23615337 original size:29 final size:29
Alignment explanation
Indices: 23615304--23615359 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
23615294 TTTACTTAAA
*
23615304 TTTTATAAT-AAATATTTTTAATTATTTAT
1 TTTTA-AATAAAATATTTTAAATTATTTAT
*
23615333 TTTTAGATAAAATATTTTAAATTATTT
1 TTTTAAATAAAATATTTTAAATTATTT
23615360 CGTTTCTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAAATAAAATATTTTAAATTATTTAT
Found at i:23617063 original size:3 final size:3
Alignment explanation
Indices: 23617055--23617102 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
23617045 CTTGAGAGTG
* * * *
23617055 AGA AGA AGA AGA AGA AGA AGA CGA CGA CGA AGA AGA AG- AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
23617102 A
1 A
23617103 TCAAGCGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.58, C:0.06, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:23621422 original size:16 final size:18
Alignment explanation
Indices: 23621401--23621433 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23621391 TGATAAAAAT
23621401 ATTAAT-TA-ATTTGATG
1 ATTAATATATATTTGATG
23621417 ATTAATATATATTTGAT
1 ATTAATATATATTTGAT
23621434 AATTTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (18 bp):
ATTAATATATATTTGATG
Found at i:23641537 original size:23 final size:22
Alignment explanation
Indices: 23641485--23641537 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
23641475 AAATCAGATT
*
23641485 TTTATTATTTTTTGATATTTTC
1 TTTATTTTTTTTTGATATTTTC
23641507 TGATT-TTTTTTGTTT-ATATTTTC
1 T--TTATTTTTT-TTTGATATTTTC
23641530 TTTATTTT
1 TTTATTTT
23641538 AGTTAGTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 14 0.54
24 5 0.19
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTATTTTTTTTTGATATTTTC
Found at i:23646298 original size:67 final size:67
Alignment explanation
Indices: 23646190--23646327 Score: 213
Period size: 67 Copynumber: 2.1 Consensus size: 67
23646180 GCCCAAACCA
* * *
23646190 ATTATTCAGCCACTGAAAAAGAACTTTTAGCTATTGTATTTGCTTTGGAAAATTTTAGATCATAT
1 ATTATTCAACCACTGAAAAAGAACTTTTAGCTATTGTATTTGCTTTGGAAAAATTTAAATCATAT
23646255 TT
66 TT
* * * *
23646257 ATTATTCAACCATTGAGAAAGAACTTTTAGCTATTTTATTTGCTTTGGAAAAATTTAAATTATAT
1 ATTATTCAACCACTGAAAAAGAACTTTTAGCTATTGTATTTGCTTTGGAAAAATTTAAATCATAT
23646322 TT
66 TT
23646324 ATTA
1 ATTA
23646328 GGCAGTAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (67 bp):
ATTATTCAACCACTGAAAAAGAACTTTTAGCTATTGTATTTGCTTTGGAAAAATTTAAATCATAT
TT
Found at i:23651476 original size:4 final size:4
Alignment explanation
Indices: 23651469--23651495 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23651459 ATTTGGTGCT
23651469 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
23651496 TTGACTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:23654091 original size:21 final size:21
Alignment explanation
Indices: 23654051--23654091 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
23654041 TTATATTAAG
23654051 TAAAAAATTTAAAATGATTAT
1 TAAAAAATTTAAAATGATTAT
23654072 TAAACAAATTTAAAAT-ATTA
1 TAAA-AAATTTAAAATGATTA
23654092 AAAGTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAAAATTTAAAATGATTAT
Found at i:23654781 original size:3 final size:3
Alignment explanation
Indices: 23654773--23654800 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
23654763 ATTTCAACTT
23654773 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23654801 CAATTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23656435 original size:28 final size:28
Alignment explanation
Indices: 23656381--23656457 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
23656371 CTATAGATTA
* *
23656381 CACCACGAAGGCATTCCTTT-CCAAAGAT
1 CACCACAAAGGC-TTCCTTTAACAAAGAT
*
23656409 CACCACAAAGGCTTCCTTTAACTAAGAT
1 CACCACAAAGGCTTCCTTTAACAAAGAT
23656437 -AGCCACGAAA-GCTTCCTTTAA
1 CA-CCAC-AAAGGCTTCCTTTAA
23656458 TGAGATAGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
27 8 0.19
28 32 0.74
29 3 0.07
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (28 bp):
CACCACAAAGGCTTCCTTTAACAAAGAT
Found at i:23656506 original size:28 final size:26
Alignment explanation
Indices: 23656413--23656506 Score: 66
Period size: 28 Copynumber: 3.4 Consensus size: 26
23656403 AAAGATCACC
* * *
23656413 ACAAAGGCTTCCTTTAACTAAGATAGCC
1 ACAAA-GCTTCC-TTAAATGAGATAGCT
*
23656441 ACGAAAGCTTCCTTTAATGAGATAGTCAT
1 AC-AAAGCTTCCTTAAATGAGATAG-C-T
23656470 A-ACAA-CTTCCTTGAAATGAGATAGCT
1 ACA-AAGCTTCCTT-AAATGAGATAGCT
23656496 ACAAAGGCTTC
1 ACAAA-GCTTC
23656507 TTTTTAGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
26 4 0.08
27 20 0.38
28 25 0.47
29 4 0.08
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (26 bp):
ACAAAGCTTCCTTAAATGAGATAGCT
Found at i:23656923 original size:21 final size:21
Alignment explanation
Indices: 23656882--23656926 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23656872 CACCTAGACA
**
23656882 CTCTCATTTTTTGCTGTCCTC
1 CTCTCATTTTTTGCTCCCCTC
23656903 CTCTC-TTTTTTGCCTCCCCTC
1 CTCTCATTTTTTG-CTCCCCTC
23656924 CTC
1 CTC
23656927 CTTGCTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.02, C:0.42, G:0.07, T:0.49
Consensus pattern (21 bp):
CTCTCATTTTTTGCTCCCCTC
Found at i:23671207 original size:35 final size:35
Alignment explanation
Indices: 23671167--23671244 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
23671157 ATTCGTATTG
*
23671167 AGCATGAT-ATTATTCTGATTATGATTTGCATGTTA
1 AGCATG-TCATTATTCTGATTATAATTTGCATGTTA
*
23671202 AGCATGTCATTATTCTGATTCTAATTTGCATGTTA
1 AGCATGTCATTATTCTGATTATAATTTGCATGTTA
*
23671237 AACATGTC
1 AGCATGTC
23671245 CCTATGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 1 0.03
35 38 0.97
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (35 bp):
AGCATGTCATTATTCTGATTATAATTTGCATGTTA
Found at i:23677680 original size:32 final size:32
Alignment explanation
Indices: 23677643--23677708 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
23677633 AAATTGATAT
* * *
23677643 ATGATCCTTTGCATTTTCTGTGAGATATTATG
1 ATGATCCTTTGCATTTTCTATGAAATATCATG
*
23677675 ATGATCCTTTTCATTTTCTATGAAATATCATG
1 ATGATCCTTTGCATTTTCTATGAAATATCATG
23677707 AT
1 AT
23677709 AATATTGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (32 bp):
ATGATCCTTTGCATTTTCTATGAAATATCATG
Found at i:23679272 original size:12 final size:12
Alignment explanation
Indices: 23679255--23679280 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23679245 CTTAGTCATC
23679255 TTCCCTAATGTG
1 TTCCCTAATGTG
23679267 TTCCCTAATGTG
1 TTCCCTAATGTG
23679279 TT
1 TT
23679281 AGGGCACGTA
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (12 bp):
TTCCCTAATGTG
Found at i:23685216 original size:26 final size:25
Alignment explanation
Indices: 23685163--23685220 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
23685153 CCATTTACAA
* *
23685163 TTTACCATTTATTTTTTGCATTTAG
1 TTTATCATTTATTTTTTGCACTTAG
* *
23685188 TTTATCATTTATTTTTTCGTACTTGG
1 TTTATCATTTATTTTTT-GCACTTAG
23685214 TTTATCA
1 TTTATCA
23685221 ACTATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60
Consensus pattern (25 bp):
TTTATCATTTATTTTTTGCACTTAG
Found at i:23687406 original size:29 final size:31
Alignment explanation
Indices: 23687344--23687406 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
23687334 TATGAGGAAG
*
23687344 TTGAATCAAAATTAAAATTTTATACATATAA
1 TTGAATCAAAATTAAAATTTTACACATATAA
* *
23687375 TTGAA-CAAAATTAAAA-TTTACATATATTA
1 TTGAATCAAAATTAAAATTTTACACATATAA
23687404 TTG
1 TTG
23687407 CGCATTGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.45
30 11 0.38
31 5 0.17
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (31 bp):
TTGAATCAAAATTAAAATTTTACACATATAA
Found at i:23687672 original size:13 final size:12
Alignment explanation
Indices: 23687637--23687674 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
23687627 TGCATGACAA
23687637 AATTTTT-TTAT
1 AATTTTTATTAT
*
23687648 TATTTTTATTAT
1 AATTTTTATTAT
23687660 AATTTTATATTAT
1 AATTTT-TATTAT
23687673 AA
1 AA
23687675 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 6 0.26
12 9 0.39
13 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTTTATTAT
Found at i:23690830 original size:21 final size:21
Alignment explanation
Indices: 23690777--23690830 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
23690767 TTAGTATCCT
23690777 TAAACCTTAAAATATTAAACCC
1 TAAACCTT-AAATATTAAACCC
23690799 TAAA-CTATAAATATT-AACCTC
1 TAAACCT-TAAATATTAAACC-C
23690820 TAAACCTTAAA
1 TAAACCTTAAA
23690831 CCCTAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACCTTAAATATTAAACCC
Found at i:23697709 original size:31 final size:31
Alignment explanation
Indices: 23697674--23697733 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
23697664 AACCGCTAAA
** *
23697674 GTTTTAGATCATTTTTATTTTGGTCACTCAC
1 GTTTTAGATCATTCCTATTTTGGCCACTCAC
*
23697705 GTTTTAGATCGTTCCTATTTTGGCCACTC
1 GTTTTAGATCATTCCTATTTTGGCCACTC
23697734 TCTGTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (31 bp):
GTTTTAGATCATTCCTATTTTGGCCACTCAC
Found at i:23701440 original size:72 final size:72
Alignment explanation
Indices: 23701324--23701482 Score: 187
Period size: 72 Copynumber: 2.2 Consensus size: 72
23701314 CCCATATGCC
** *** *
23701324 CCCTGTAACTTAACTTACAAAACAGTATGTACACATGGTCTGGCACATGCAT-GTGTGCCCAGCC
1 CCCTGTAACTTATTTTACAAAACAGTATGTACACACCATCTGGCACACGC-TCGTGTGCCCAGCC
* *
23701388 TGTGTG-G
65 CGTGTGTA
* *
23701395 CCTCTGTAACTTATTTTACAAAACAGTATGTACACACCATTTGGCACACGCTCGTGTGTCCAGCC
1 CC-CTGTAACTTATTTTACAAAACAGTATGTACACACCATCTGGCACACGCTCGTGTGCCCAGCC
23701460 CGTGTGTA
65 CGTGTGTA
*
23701468 CCCTGTAGCTTATTT
1 CCCTGTAACTTATTT
23701483 AAATGGCACA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 3 0.04
72 69 0.93
73 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.30
Consensus pattern (72 bp):
CCCTGTAACTTATTTTACAAAACAGTATGTACACACCATCTGGCACACGCTCGTGTGCCCAGCCC
GTGTGTA
Found at i:23704953 original size:21 final size:20
Alignment explanation
Indices: 23704927--23704978 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
23704917 ATCCTAAAAT
23704927 TTTTAAACTTATAACATATAA
1 TTTTAAACTTATAA-ATATAA
* *
23704948 TTTTAAACTTTTTAATTATAA
1 TTTTAAAC-TTATAAATATAA
23704969 TTTTAAACTT
1 TTTTAAACTT
23704979 TTTATAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 21 0.75
22 5 0.18
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTAAACTTATAAATATAA
Found at i:23704979 original size:21 final size:21
Alignment explanation
Indices: 23704943--23704982 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23704933 ACTTATAACA
23704943 TATAATTTTAAACTTTTTAAT
1 TATAATTTTAAACTTTTTAAT
23704964 TATAATTTTAAACTTTTTA
1 TATAATTTTAAACTTTTTA
23704983 TAATAGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TATAATTTTAAACTTTTTAAT
Found at i:23714093 original size:23 final size:23
Alignment explanation
Indices: 23714063--23714114 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
23714053 AACGGTCAAT
23714063 GGTCCGTTTTGGACAAAGTTAAC
1 GGTCCGTTTTGGACAAAGTTAAC
23714086 GGTCCGTTTTGGACAAAGTTAAC
1 GGTCCGTTTTGGACAAAGTTAAC
23714109 GGTCCG
1 GGTCCG
23714115 GTTCGAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (23 bp):
GGTCCGTTTTGGACAAAGTTAAC
Found at i:23714136 original size:17 final size:17
Alignment explanation
Indices: 23714114--23714146 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23714104 TTAACGGTCC
23714114 GGTTCGAGTT-GATCAAT
1 GGTTCGA-TTCGATCAAT
23714131 GGTTCGATTCGATCAA
1 GGTTCGATTCGATCAA
23714147 AGTCAACGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (17 bp):
GGTTCGATTCGATCAAT
Found at i:23720488 original size:21 final size:22
Alignment explanation
Indices: 23720464--23720508 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
23720454 TTTTTTTGCT
*
23720464 AATTTCATCGTTACTTT-GGGA
1 AATTTCATCATTACTTTAGGGA
23720485 AATTTCATCATTACTTTAGGGA
1 AATTTCATCATTACTTTAGGGA
23720507 AA
1 AA
23720509 AATTCACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (22 bp):
AATTTCATCATTACTTTAGGGA
Found at i:23729448 original size:16 final size:17
Alignment explanation
Indices: 23729427--23729459 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
23729417 TAAGAGATTG
23729427 TCATCCT-CAAACAAAC
1 TCATCCTGCAAACAAAC
23729443 TCATCCTGGCAAACAAA
1 TCATCCT-GCAAACAAA
23729460 GCCCTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.33, G:0.06, T:0.18
Consensus pattern (17 bp):
TCATCCTGCAAACAAAC
Found at i:23734142 original size:81 final size:81
Alignment explanation
Indices: 23734016--23734179 Score: 265
Period size: 81 Copynumber: 2.0 Consensus size: 81
23734006 TCTCATGATA
* * *
23734016 ATATATATATTTATCAGGGTTCACAGTATAATTATCATATCATATTAAGTTAACCACATTCCGTT
1 ATATATATATATATCAGAGTTCACAGTATAATTATCACATCATATTAAGTTAACCACATTCCGTT
23734081 GAACATGCATGACAAT
66 GAACATGCATGACAAT
* * * *
23734097 ATATATATATATATTAGAGTTCACAGTATAATTATCACATTATATTAAGTTAACCATATTTCGTT
1 ATATATATATATATCAGAGTTCACAGTATAATTATCACATCATATTAAGTTAACCACATTCCGTT
23734162 GAACATGCATGACAAT
66 GAACATGCATGACAAT
23734178 AT
1 AT
23734180 CAACATGCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (81 bp):
ATATATATATATATCAGAGTTCACAGTATAATTATCACATCATATTAAGTTAACCACATTCCGTT
GAACATGCATGACAAT
Found at i:23734779 original size:19 final size:19
Alignment explanation
Indices: 23734755--23734792 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23734745 TCAATCCAAA
*
23734755 AAGTCAACTATCAACGGTC
1 AAGTCAACGATCAACGGTC
*
23734774 AAGTCAACGATCAATGGTC
1 AAGTCAACGATCAACGGTC
23734793 TGGCTCAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (19 bp):
AAGTCAACGATCAACGGTC
Found at i:23737550 original size:72 final size:72
Alignment explanation
Indices: 23737474--23737613 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
23737464 TGTTAGCCTC
* * *
23737474 TTGTACCTTAACTTACAAAACAGTATGTACACATGGTCTGGCACATGCCTGAGTGCCCAGCCCAT
1 TTGTAACTTAACTTACAAAACAGTATGTACACATCGTCTGGCACACGCCTGAGTGCCCAGCCCAT
23737539 GTGGCAT
66 GTGGCAT
** * *
23737546 TTGTAACTTATTTTACAAAATAGTATGTACACATCGTCTGGCACACGCCTGTGTGCCCAGCCCAT
1 TTGTAACTTAACTTACAAAACAGTATGTACACATCGTCTGGCACACGCCTGAGTGCCCAGCCCAT
23737611 GTG
66 GTG
23737614 TCCCCTGTAG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (72 bp):
TTGTAACTTAACTTACAAAACAGTATGTACACATCGTCTGGCACACGCCTGAGTGCCCAGCCCAT
GTGGCAT
Found at i:23737628 original size:72 final size:72
Alignment explanation
Indices: 23737486--23737630 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 72
23737476 GTACCTTAAC
* * **
23737486 TTACAAAACAGTATGTACACATGGTCTGGCACATGCCTGAGTGCCCAGCCCATGTGGCATTTGTA
1 TTACAAAACAGTATGTACACATCGTCTGGCACACGCCTGAGTGCCCAGCCCATGTGGCACCTGTA
23737551 ACTTATT
66 ACTTATT
* * * *
23737558 TTACAAAATAGTATGTACACATCGTCTGGCACACGCCTGTGTGCCCAGCCCATGTGTCCCCTGTA
1 TTACAAAACAGTATGTACACATCGTCTGGCACACGCCTGAGTGCCCAGCCCATGTGGCACCTGTA
*
23737623 GCTTATT
66 ACTTATT
23737630 T
1 T
23737631 AAATGGCACA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (72 bp):
TTACAAAACAGTATGTACACATCGTCTGGCACACGCCTGAGTGCCCAGCCCATGTGGCACCTGTA
ACTTATT
Found at i:23740152 original size:27 final size:27
Alignment explanation
Indices: 23740112--23740164 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
23740102 TAATCTTTTG
*
23740112 ACCAAAATAAAAATGCTCTAAAACGTA
1 ACCAAAATAAAAATGATCTAAAACGTA
*
23740139 ACCAAAATAGAAATGATCTAAAACGT
1 ACCAAAATAAAAATGATCTAAAACGT
23740165 TAGTGACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.55, C:0.17, G:0.09, T:0.19
Consensus pattern (27 bp):
ACCAAAATAAAAATGATCTAAAACGTA
Found at i:23740576 original size:11 final size:11
Alignment explanation
Indices: 23740560--23740602 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
23740550 ATAATTTTAT
23740560 ATATTTTAATA
1 ATATTTTAATA
*
23740571 ATATTTTAACA
1 ATATTTTAATA
*
23740582 ATTATTTTATATC
1 A-TATTTTA-ATA
23740595 ATATTTTA
1 ATATTTTA
23740603 TTCATGCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 11 0.41
12 14 0.52
13 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:23741377 original size:18 final size:18
Alignment explanation
Indices: 23741356--23741390 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23741346 TTTAAAATTA
*
23741356 AAAATTATTAAAAATATG
1 AAAATTATAAAAAATATG
23741374 AAAATTATAAAAAATAT
1 AAAATTATAAAAAATAT
23741391 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATTATAAAAAATATG
Found at i:23741378 original size:37 final size:37
Alignment explanation
Indices: 23741305--23741381 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 37
23741295 TTTAATTATT
23741305 TTTTTAAAATTTTAAAAATTTTAAAAAGCTATAAAATTA
1 TTTTTAAAA-TTTAAAAATTTTAAAAA-CTATAAAATTA
23741344 TTTTTAAAA-TTAAAAATTATTAAAAA-TATGAAAATTA
1 TTTTTAAAATTTAAAAATT-TTAAAAACTAT-AAAATTA
23741381 T
1 T
23741382 AAAAAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
36 3 0.08
37 17 0.47
38 7 0.19
39 9 0.25
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (37 bp):
TTTTTAAAATTTAAAAATTTTAAAAACTATAAAATTA
Done.