Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_pilon, whole genome shotgun sequence
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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1669948 original size:183 final size:181
Alignment explanation
Indices: 1669597--1669997 Score: 431
Period size: 183 Copynumber: 2.2 Consensus size: 181
1669587 ATTTAAAAAA
* *
1669597 TGATAATTACAATAATTATCTTTCTTTTAAATATA-AAAAATCTATCTCAACTCATATTAGATTA
1 TGATAATTACAATAATTATCTTT-TTTTAAATATATAAAAA-CTATCTCAACTCAAATAAGATTA
* * *
1669661 TATATATATATATATTATTAAAGTTTGATAATTATAATAATTATCACTCTTTTAAATATATAAAC
64 TATATAAATATATATTATTAAAATTTGATAATTACAATAATTATCACTCTTTTAAATATATAAAC
* * * * *
1669726 TTATTCCAAAGTAGATAATGTTTTATCATATAAATATATATATAAATAGAGAT
129 TTATTCCAAACTAGATAAGGTTCTATCATATAAATATATATATAAATAAAGAC
* * * * *
1669779 TGATATTTACAATAATTATCTTTTTTTAAATATATAAACA-TATTTTAACTCAAATAAGGTTTTA
1 TGATAATTACAATAATTATCTTTTTTTAAATATATAAAAACTATCTCAACTCAAATAA-G-ATTA
*
1669843 TAATATAAATATATATT-TTAATATAATTTGATAATTACAATAATTAT-A-TTTTTTAAATATAT
64 T-ATATAAATATATATTATT-A-A-AATTTGATAATTACAATAATTATCACTCTTTTAAATATAT
* * * *
1669905 AAA-TCTATTTC-AACTAAGATTAGGTTCTAT-ATGATATATATATATATATATAAAGAC
125 AAACT-TATTCCAAACT-AGATAAGGTTCTATCAT-ATAAATATATATATAAATAAAGAC
* ** *
1669962 TGATAATTACAATAATTACCTCCTTTTAAATGTATA
1 TGATAATTACAATAATTATCTTTTTTTAAATATATA
1669998 TAATTATTCA
Statistics
Matches: 184, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
180 13 0.07
181 12 0.07
182 38 0.21
183 98 0.53
184 2 0.01
185 21 0.11
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (181 bp):
TGATAATTACAATAATTATCTTTTTTTAAATATATAAAAACTATCTCAACTCAAATAAGATTATA
TATAAATATATATTATTAAAATTTGATAATTACAATAATTATCACTCTTTTAAATATATAAACTT
ATTCCAAACTAGATAAGGTTCTATCATATAAATATATATATAAATAAAGAC
Found at i:1669966 original size:91 final size:90
Alignment explanation
Indices: 1669597--1669979 Score: 336
Period size: 91 Copynumber: 4.2 Consensus size: 90
1669587 ATTTAAAAAA
* * * * * * *
1669597 TGATAATTACAATAATTATCTTTCTTTTAAATATA-AAAAATCTATCTCAACTCATATTA-GATT
1 TGATAATTACAATAATTATCATT-TTTTAAATATATAAACA--TATTTCAACTAAGATAAGGTTT
*
1669660 ATATATATATATATAT-TAT-TAAAGTT
63 ATATATATATATATATATATATAAAGAT
* * * * * *
1669686 TGATAATTATAATAATTATCACTCTTTTAAATATATAAACTTATTCCAAAGT-AGATAATGTTTT
1 TGATAATTACAATAATTATCA-TTTTTTAAATATATAAACATATTTC-AACTAAGATAA-GGTTT
* * *
1669750 ATCATATAAATATATATATAAATAGAGAT
63 AT-ATATATATATATATATATATAAAGAT
* * *
1669779 TGATATTTACAATAATTATCTTTTTTTAAATATATAAACATATTTTAACTCAA-ATAAGGTTT-T
1 TGATAATTACAATAATTATCATTTTTTAAATATATAAACATATTTCAACT-AAGATAAGGTTTAT
* * *
1669842 ATAATATAAATATATATTTTAATATAA-TT
65 AT-ATATATATATATA-TAT-ATA-AAGAT
*
1669871 TGATAATTACAATAATTAT-ATTTTTTAAATATATAAATC-TATTTCAACTAAGATTAGGTTCTA
1 TGATAATTACAATAATTATCATTTTTTAAATATATAAA-CATATTTCAACTAAGATAAGGTT-TA
*
1669934 TATGATATATATATATATATATAAAGAC
64 TAT-ATATATATATATATATATAAAGAT
1669962 TGATAATTACAATAATTA
1 TGATAATTACAATAATTA
1669980 CCTCCTTTTA
Statistics
Matches: 235, Mismatches: 40, Indels: 36
0.76 0.13 0.12
Matches are distributed among these distances:
88 8 0.03
89 35 0.15
90 24 0.10
91 75 0.32
92 53 0.23
93 40 0.17
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (90 bp):
TGATAATTACAATAATTATCATTTTTTAAATATATAAACATATTTCAACTAAGATAAGGTTTATA
TATATATATATATATATATAAAGAT
Found at i:1671609 original size:97 final size:97
Alignment explanation
Indices: 1671497--1671692 Score: 392
Period size: 97 Copynumber: 2.0 Consensus size: 97
1671487 CAAAATCTGA
1671497 TTGTGATTGTGAATCATTCTTATTAGTTTGAAAGGTAGCATACGTGTAACCATTTACACTAAGCA
1 TTGTGATTGTGAATCATTCTTATTAGTTTGAAAGGTAGCATACGTGTAACCATTTACACTAAGCA
1671562 CTTCTTCACCTCCATATATTAAAAATGTGTCC
66 CTTCTTCACCTCCATATATTAAAAATGTGTCC
1671594 TTGTGATTGTGAATCATTCTTATTAGTTTGAAAGGTAGCATACGTGTAACCATTTACACTAAGCA
1 TTGTGATTGTGAATCATTCTTATTAGTTTGAAAGGTAGCATACGTGTAACCATTTACACTAAGCA
1671659 CTTCTTCACCTCCATATATTAAAAATGTGTCC
66 CTTCTTCACCTCCATATATTAAAAATGTGTCC
1671691 TT
1 TT
1671693 TGTCCTTCTC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 99 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (97 bp):
TTGTGATTGTGAATCATTCTTATTAGTTTGAAAGGTAGCATACGTGTAACCATTTACACTAAGCA
CTTCTTCACCTCCATATATTAAAAATGTGTCC
Found at i:1673652 original size:19 final size:19
Alignment explanation
Indices: 1673628--1673676 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 19
1673618 AGAATTGCTC
*
1673628 TTATTTTAATAACTCAAAT
1 TTATTTTAATAAATCAAAT
1673647 TTATTTTATTAATAAATCAAAT
1 TTA--TT-TTAATAAATCAAAT
1673669 TTATTTTA
1 TTATTTTA
1673677 TTAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 2 0.08
22 16 0.62
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTTTAATAAATCAAAT
Found at i:1673661 original size:22 final size:22
Alignment explanation
Indices: 1673633--1673682 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1673623 TGCTCTTATT
*
1673633 TTAATAACTCAAATTTATTTTA
1 TTAATAAATCAAATTTATTTTA
1673655 TTAATAAATCAAATTTATTTTA
1 TTAATAAATCAAATTTATTTTA
1673677 TTAATA
1 TTAATA
1673683 TTTTAATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATAAATCAAATTTATTTTA
Found at i:1676838 original size:2 final size:2
Alignment explanation
Indices: 1676826--1676872 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1676816 CAAGTAAATT
1676826 TA TA T- 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
1676867 TA TA TA
1 TA TA TA
1676873 ATAGTAGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1678260 original size:39 final size:39
Alignment explanation
Indices: 1678204--1679039 Score: 1323
Period size: 39 Copynumber: 21.4 Consensus size: 39
1678194 CAAGCGAGGC
**
1678204 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGGCAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* * *
1678243 ATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAGACAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* *
1678282 ATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* * *
1678321 ATCTTCTGTTTCGAGGGAAACTATCTCAAGAGAGACAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* *
1678360 ATCTTCTGTTTCAAGGGAAATTATCTCAAGCGAGACAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* * *
1678399 ATCTTATGTTTCAAGGAAAACTATCTCAAGCGAGACAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
*
1678438 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1678477 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
** *
1678516 AAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* *
1678555 ATCTTATGTTTTAAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1678594 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
*
1678633 ATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
*
1678672 ATCTT-TGTTTCGAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
**
1678710 ATCTTCTGTTTCAATAGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* *
1678749 ATCTTCTGTTTCGAGGGAAACTATCTTAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1678788 ATCTTCTGTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTC--TGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
** *
1678829 ATCTTCTGTTTCAATAGAAACTATCTCAAGCAAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
* *
1678868 ATCTTTTGTTTCAAGGGAAACTATCTCATGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
*
1678907 ATCTTCTGTTTCAATGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1678946 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
**
1678985 ATCTTCTGTTTCAATAGAAACTATCTCAAGCGAGATAAA
1 ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
*
1679024 ATCTTTTGTTTCAAGG
1 ATCTTCTGTTTCAAGG
1679040 AAAAACAATA
Statistics
Matches: 744, Mismatches: 50, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
38 38 0.05
39 669 0.90
41 37 0.05
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (39 bp):
ATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAA
Found at i:1679134 original size:76 final size:76
Alignment explanation
Indices: 1679053--1679273 Score: 193
Period size: 76 Copynumber: 2.9 Consensus size: 76
1679043 AACAATATTG
* ** * *
1679053 AGTGAAAT-AAATCTTCTTATTTCGTGTAAAAAATGTCTCTAGCGAGACAAATCTTGCTTTAAGA
1 AGTGAAATGAAAT-ATCTTATTTCGAATAAAAAATGTCCCAAGCGAGACAAATCTTGCTTTAAGA
1679117 AAAACATAATAT
65 AAAACATAATAT
* * ** *
1679129 AGTGAAATGAAATATCTTGTTTTGAATAAAACCTGTCCCAAGCGAGACAAATCTTGTTTTAAGAA
1 AGTGAAATGAAATATCTTATTTCGAATAAAAAATGTCCCAAGCGAGACAAATCTTGCTTTAAGAA
*
1679194 AAAC--AATCT
66 AAACATAATAT
* * * * * * *
1679203 CCAGTCAAATGAAATGTCTTCTTTC-AAGTAAAACA-GTCTCAAGTGAGACAAAGT-TTGTTTTA
1 --AGTGAAATGAAATATCTTATTTCGAA-TAAAAAATGTCCCAAGCGAGACAAA-TCTTGCTTTA
1679265 AGAAAAACA
62 AGAAAAACA
1679274 ATCTTCAGTC
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
74 4 0.03
75 33 0.27
76 80 0.66
77 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (76 bp):
AGTGAAATGAAATATCTTATTTCGAATAAAAAATGTCCCAAGCGAGACAAATCTTGCTTTAAGAA
AAACATAATAT
Found at i:1679266 original size:151 final size:151
Alignment explanation
Indices: 1679078--1679357 Score: 331
Period size: 151 Copynumber: 1.9 Consensus size: 151
1679068 CTTATTTCGT
* *
1679078 GTAAAAAATGTCTCTAGCGAGACAAATCTTGCTTTAAGAAAAACATAAT-AT-AGTGAAATGAAA
1 GTAAAAAATGTCTCAAGCGAGACAAATCTTGCTTTAAGAAAAAC--AATCATCAGTCAAATGAAA
* *
1679141 TATCTTGTTTTGAA-TAAAACCT-GTCCCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAATCT
64 TATCTT-CTTTCAAGT-AAA-CTAGTCCCAAGCGAGACAAAGTC-TGTTTTAAGAAAAACAATCT
1679203 CCAGTCAAATGAAATGTCTTCTTTCAA
125 CCAGTCAAATGAAATGTCTTCTTTCAA
* * * *
1679230 GTAAAACA-GTCTCAAGTGAGACAAAGT-TTGTTTTAAGAAAAACAATCTTCAGTCAAATGAAAT
1 GTAAAAAATGTCTCAAGCGAGACAAA-TCTTGCTTTAAGAAAAACAATCATCAGTCAAATGAAAT
* * * * *
1679293 ATCTTCTTTCAAGTAAAGTAGTCTCAAGTGAGACAAAGTCTGTTTTAAGAAATACAATCTTCAGT
65 ATCTTCTTTCAAGTAAACTAGTCCCAAGCGAGACAAAGTCTGTTTTAAGAAAAACAATCTCCAGT
1679358 GAGATAAATC
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
149 4 0.04
150 47 0.43
151 50 0.46
152 8 0.07
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (151 bp):
GTAAAAAATGTCTCAAGCGAGACAAATCTTGCTTTAAGAAAAACAATCATCAGTCAAATGAAATA
TCTTCTTTCAAGTAAACTAGTCCCAAGCGAGACAAAGTCTGTTTTAAGAAAAACAATCTCCAGTC
AAATGAAATGTCTTCTTTCAA
Found at i:1679274 original size:75 final size:75
Alignment explanation
Indices: 1679028--1679357 Score: 312
Period size: 75 Copynumber: 4.4 Consensus size: 75
1679018 GATAAAATCT
* * * * * * ** *
1679028 TTTGTTTCAAGGAAAAACAATATTGAGTGAAAT-AAATCTTCTTATTTCGTGTAAAAAATGTCTC
1 TTTGTTTTAA-GAAAAACAATCTTCAGTCAAATGAAAT-ATCTTCTTTCAAGTAAAACA-GTCTC
* *
1679092 TAGCGAGACAAA-
63 AAGTGAGACAAAG
* * * * * *
1679104 TCTTGCTTTAAGAAAAACATAAT-AT-AGTGAAATGAAATATCTTGTTTTGAA-TAAAACCTGTC
1 T-TTGTTTTAAGAAAAAC--AATCTTCAGTCAAATGAAATATCTT-CTTTCAAGTAAAA-CAGTC
* *
1679166 CCAAGCGAGACAAA-
61 TCAAGTGAGACAAAG
* *
1679180 TCTTGTTTTAAGAAAAACAATCTCCAGTCAAATGAAATGTCTTCTTTCAAGTAAAACAGTCTCAA
1 T-TTGTTTTAAGAAAAACAATCTTCAGTCAAATGAAATATCTTCTTTCAAGTAAAACAGTCTCAA
1679245 GTGAGACAAAG
65 GTGAGACAAAG
**
1679256 TTTGTTTTAAGAAAAACAATCTTCAGTCAAATGAAATATCTTCTTTCAAGTAAAGTAGTCTCAAG
1 TTTGTTTTAAGAAAAACAATCTTCAGTCAAATGAAATATCTTCTTTCAAGTAAAACAGTCTCAAG
1679321 TGAGACAAAG
66 TGAGACAAAG
* *
1679331 TCTGTTTTAAGAAATACAATCTTCAGT
1 TTTGTTTTAAGAAAAACAATCTTCAGT
1679358 GAGATAAATC
Statistics
Matches: 216, Mismatches: 28, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
74 3 0.01
75 116 0.54
76 79 0.37
77 15 0.07
78 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (75 bp):
TTTGTTTTAAGAAAAACAATCTTCAGTCAAATGAAATATCTTCTTTCAAGTAAAACAGTCTCAAG
TGAGACAAAG
Found at i:1683557 original size:27 final size:28
Alignment explanation
Indices: 1683527--1683579 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
1683517 ATGAAAAATG
*
1683527 ACACAAACAAAAG-AAAGAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAGTGT
1683554 ACACAAACAAAAGAAAAGAAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAGT
1683580 TAGTACAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.13
Consensus pattern (28 bp):
ACACAAACAAAAGAAAAGAAATTAGTGT
Found at i:1685048 original size:2 final size:2
Alignment explanation
Indices: 1685036--1685076 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1685026 CAAGTAAATT
1685036 TA TA T- 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
1685077 ACAGTAGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1687722 original size:91 final size:90
Alignment explanation
Indices: 1687585--1687805 Score: 231
Period size: 91 Copynumber: 2.4 Consensus size: 90
1687575 TTAAAAAAAA
* * * *
1687585 TTGATAATTATAATAATTATCTTTCTTTTAAAATATAAACTTATTTTAAC-CTATATAA-ATGTT
1 TTGA-AATTACAATAATGATCTCT-TTTTAAAATATAAACTTATTTTAACTC-AGATAAGATGTT
*
1687648 A-TATATATATATATATATT-AATAGAA-T
63 ATTATATAAATATATAT-TTCAATA-AAGT
*
1687675 TTGACAATTACAATAATGATCTCTGTTTTGAAAATATAAA-TATATTTTAACTCAGATAAGATTT
1 TTGA-AATTACAATAATGATCTCT-TTTT-AAAATATAAACT-TATTTTAACTCAGATAAGATGT
1687739 TATTATATAAATATATATTTCAATAAAGT
62 TATTATATAAATATATATTTCAATAAAGT
*
1687768 TTGAAATTACAGTAATTG-TCTCTTTTTTAAAATATAAA
1 TTGAAATTACAATAA-TGATCTC-TTTTTAAAATATAAA
1687806 AACCTATTTC
Statistics
Matches: 113, Mismatches: 9, Indels: 17
0.81 0.06 0.12
Matches are distributed among these distances:
90 25 0.22
91 34 0.30
92 28 0.25
93 26 0.23
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.45
Consensus pattern (90 bp):
TTGAAATTACAATAATGATCTCTTTTTAAAATATAAACTTATTTTAACTCAGATAAGATGTTATT
ATATAAATATATATTTCAATAAAGT
Found at i:1687842 original size:93 final size:92
Alignment explanation
Indices: 1687647--1687851 Score: 222
Period size: 93 Copynumber: 2.2 Consensus size: 92
1687637 ATATAAATGT
*
1687647 TATATATATATATATATATTAATAGAATTTGACAATTACAATAATGATCTCTGTTTTGAAAATAT
1 TATATATAAATATATATATTAATAGAATTTGACAATTACAATAATGATCTCTGTTTTGAAAATAT
* * *
1687712 AAATATATTTTAACTCAGATAAGATTT
66 AAAAATATTTCAACTCAGATAAGATTC
* *
1687739 TATTATATAAATATATAT-TTCAATA-AAGTTTGA-AATTACAGTAATTG-TCTCT-TTTTTAAA
1 TA-TATATAAATATATATATT-AATAGAA-TTTGACAATTACAATAA-TGATCTCTGTTTTGAAA
* * * *
1687799 ATATAAAAACCTATTTCAATTGAGATTAGGTTC
62 ATATAAAAA--TATTTCAACTCAGATAAGATTC
1687832 TATATCATAAATATATATAT
1 TATAT-ATAAATATATATAT
1687852 AAAATTACAA
Statistics
Matches: 95, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
91 15 0.16
92 24 0.25
93 55 0.58
94 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (92 bp):
TATATATAAATATATATATTAATAGAATTTGACAATTACAATAATGATCTCTGTTTTGAAAATAT
AAAAATATTTCAACTCAGATAAGATTC
Found at i:1690442 original size:21 final size:21
Alignment explanation
Indices: 1690416--1690455 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1690406 TATTTTTTTA
1690416 ATGATGACATGACATTATCTT
1 ATGATGACATGACATTATCTT
1690437 ATGATGACATGACATTATC
1 ATGATGACATGACATTATC
1690456 ACTGTTAATT
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:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
ATGATGACATGACATTATCTT
Found at i:1693189 original size:2 final size:2
Alignment explanation
Indices: 1693182--1693216 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1693172 TTCTTCAACA
1693182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1693217 ATGAATTATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1694594 original size:13 final size:13
Alignment explanation
Indices: 1694573--1694612 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1694563 GGACCATTTC
*
1694573 AACACATATTATT
1 AACAAATATTATT
1694586 AACAAATATTATT
1 AACAAATATTATT
1694599 AACAAA-ATTATT
1 AACAAATATTATT
1694611 AA
1 AA
1694613 AATTTTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (13 bp):
AACAAATATTATT
Found at i:1699008 original size:2 final size:2
Alignment explanation
Indices: 1699001--1699041 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1698991 TTAATGGGTT
1699001 TA TA TA 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 TA TA TA T
1699042 GTAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1700166 original size:18 final size:19
Alignment explanation
Indices: 1700143--1700185 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1700133 CATTAATCTT
* *
1700143 ATTCC-CTGGTAATTTTTC
1 ATTCCACTGGTAATCTTAC
1700161 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
1700181 ATTCC
1 ATTCC
1700186 GTAAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:1700173 original size:20 final size:20
Alignment explanation
Indices: 1700148--1700185 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1700138 ATCTTATTCC
* *
1700148 CTGGTAATTTTTCATTCCCA
1 CTGGTAATCTTACATTCCCA
1700168 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1700186 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1701618 original size:24 final size:23
Alignment explanation
Indices: 1701574--1701620 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1701564 ATTTTGAAAT
*
1701574 TAAAATAAATAAATAATATAATA
1 TAAAATAAATAAATAAGATAATA
*
1701597 TAAAATAAAATAATTAAGATAATA
1 TAAAAT-AAATAAATAAGATAATA
1701621 ATATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAATAAATAAATAAGATAATA
Found at i:1702149 original size:14 final size:15
Alignment explanation
Indices: 1702116--1702149 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1702106 TAACTTATAG
1702116 GTTTTGTCCATTTTA
1 GTTTTGTCCATTTTA
*
1702131 GTTTTGTCCTTTTTA
1 GTTTTGTCCATTTTA
1702146 -TTTT
1 GTTTT
1702150 ATTAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.68
Consensus pattern (15 bp):
GTTTTGTCCATTTTA
Found at i:1710280 original size:36 final size:37
Alignment explanation
Indices: 1710205--1710282 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 37
1710195 AGTTTGAAGG
* * * *
1710205 GAAACAATCTCAAGTGATATAAATTTGAGTTTTCAAGA
1 GAAAAAATCTCAAGGGAGATAAACTT-AGTTTTCAAGA
1710243 GAAAAAATCTCAAGGGAGATAAACTT-GTTTTCAAGA
1 GAAAAAATCTCAAGGGAGATAAACTTAGTTTTCAAGA
1710279 GAAA
1 GAAA
1710283 TAGTTTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 14 0.39
38 22 0.61
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (37 bp):
GAAAAAATCTCAAGGGAGATAAACTTAGTTTTCAAGA
Found at i:1710434 original size:37 final size:37
Alignment explanation
Indices: 1710301--1710578 Score: 159
Period size: 37 Copynumber: 7.8 Consensus size: 37
1710291 AGGGAAATAA
* * *
1710301 TCTCAAGTGAGATAAAATTTTATTTTGATAAAAATTG
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGAAAAATTG
** ** * *
1710338 TCTCAAGTGAGACGAAA-TTTGAGTTAAG-AAAACTA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGAAAAATTG
* *
1710373 TCTCAATTGAGATAAAATTGTTGTTTTCAGAAAAATTG
1 TCTCAAGTGAGATAAAATT-TTGTTTTAAGAAAAATTG
* * * * ****
1710411 TATCAAGTGAGATGAAATTTTGTTTCAAGAGAAGCCA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGAAAAATTG
* * *
1710448 TCTTAAGTGAG-----ATTTTGTTTTTAGAAAAAATG
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGAAAAATTG
* * *
1710480 TCTCAAGTGAGA-CAAA-TTT-TTTTAAGGAAAATTA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGAAAAATTG
* * **
1710514 TCTCAAGTGAGATAAACTTTTTGTTTCAAGGGAAA-T-
1 TCTCAAGTGAGATAAA-ATTTTGTTTTAAGAAAAATTG
* * *
1710550 TCTCGAGTGAGACAAAA-TTTGTTTCAAGA
1 TCTCAAGTGAGATAAAATTTTGTTTTAAGA
1710579 GCAACGATCT
Statistics
Matches: 181, Mismatches: 49, Indels: 25
0.71 0.19 0.10
Matches are distributed among these distances:
32 24 0.13
34 34 0.19
35 24 0.13
36 22 0.12
37 46 0.25
38 31 0.17
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (37 bp):
TCTCAAGTGAGATAAAATTTTGTTTTAAGAAAAATTG
Found at i:1710523 original size:34 final size:35
Alignment explanation
Indices: 1710474--1710577 Score: 108
Period size: 34 Copynumber: 3.0 Consensus size: 35
1710464 GTTTTTAGAA
1710474 AAAATGTCTCAAGTGAGACAAA-TTTT-TTT-AAGG
1 AAAAT-TCTCAAGTGAGACAAACTTTTGTTTCAAGG
*
1710507 AAAATTATCTCAAGTGAGATAAACTTTTTGTTTCAAGG
1 AAAA-T-TCTCAAGTGAGACAAAC-TTTTGTTTCAAGG
* * *
1710545 GAAATTCTCGAGTGAGACAAA-ATTTGTTTCAAG
1 AAAATTCTCAAGTGAGACAAACTTTTGTTTCAAG
1710578 AGCAACGATC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
33 4 0.07
34 27 0.45
36 18 0.30
37 4 0.07
38 7 0.12
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (35 bp):
AAAATTCTCAAGTGAGACAAACTTTTGTTTCAAGG
Found at i:1713476 original size:16 final size:16
Alignment explanation
Indices: 1713452--1713483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1713442 TTTTCATGAT
1713452 AAATACAAATGTAGAA
1 AAATACAAATGTAGAA
*
1713468 AAATGCAAATGTAGAA
1 AAATACAAATGTAGAA
1713484 TGCAAAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.19
Consensus pattern (16 bp):
AAATACAAATGTAGAA
Found at i:1716794 original size:96 final size:96
Alignment explanation
Indices: 1716689--1716873 Score: 282
Period size: 96 Copynumber: 1.9 Consensus size: 96
1716679 TCGATAATAT
* * * *
1716689 GAGGAAGGTAACTATACCATTGATTTATAGAATGCAGAAATGGTATCGATACCGTAATAGAGTAT
1 GAGGAAGGTAACGATACCATTGATTTACAGAATGCAGAAATGGTATCGATACCGAAAGAGAGTAT
1716754 C-AGTACCATAATATAGAAGTATCGGTACTGA
66 CGA-TACCATAATATAGAAGTATCGGTACTGA
* * * *
1716785 GAGGAAGGTATCGATACCATTGATTTACAGAATGCCGAAATGGTATCGATACTGAAAGGGAGTAT
1 GAGGAAGGTAACGATACCATTGATTTACAGAATGCAGAAATGGTATCGATACCGAAAGAGAGTAT
1716850 CGATACCATAATATAGAAGTATCG
66 CGATACCATAATATAGAAGTATCG
1716874 ATACCATAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 79 0.99
97 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (96 bp):
GAGGAAGGTAACGATACCATTGATTTACAGAATGCAGAAATGGTATCGATACCGAAAGAGAGTAT
CGATACCATAATATAGAAGTATCGGTACTGA
Found at i:1717284 original size:45 final size:45
Alignment explanation
Indices: 1717233--1717535 Score: 462
Period size: 45 Copynumber: 6.7 Consensus size: 45
1717223 ATAAATAGGA
*
1717233 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
1717278 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * *
1717323 CATTAAAGGCATGAAAAGATGTCGTAAATGAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* **
1717368 CATTAAAGGCATGAAAGAATGCCATAAATGAAATGCATAATAGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * *
1717413 CATTAAAGGCATGACATGATGCCGTAAATGAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * * *
1717458 TATTAAAGGCATGAAATGATGTCATAAATAAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* *
1717503 CATTAAAGGCATGAAAGGATGTCATAACTGAAA
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAA
1717536 ATAATGAATA
Statistics
Matches: 233, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 233 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (45 bp):
CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
Found at i:1717990 original size:21 final size:21
Alignment explanation
Indices: 1717947--1717990 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1717937 ATCCGAACAT
*
1717947 TCGGATATCCGAAATTTCAGA
1 TCGGATATCCGAAATTCCAGA
*
1717968 TCGGATATCC-AAATATCCGGA
1 TCGGATATCCGAAAT-TCCAGA
1717989 TC
1 TC
1717991 CAAATCCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (21 bp):
TCGGATATCCGAAATTCCAGA
Found at i:1720552 original size:22 final size:21
Alignment explanation
Indices: 1720526--1720566 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1720516 GGCTGCGGAA
1720526 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
1720548 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
1720567 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:1725674 original size:21 final size:19
Alignment explanation
Indices: 1725650--1725708 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 19
1725640 CTTGGCTTGC
1725650 TTTCTTTTTTACTTTTTTCTT
1 TTTCTTTTTT-CTTTTTT-TT
1725671 TTTCTTTTTTTCTACTTTTTTT
1 TTTC-TTTTTTCT--TTTTTTT
*
1725693 TATCTTTTTTCTTTTT
1 TTTCTTTTTTCTTTTT
1725709 GTACTCCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 4 0.12
21 14 0.41
22 11 0.32
23 5 0.15
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCTTTTTTCTTTTTTTT
Found at i:1725681 original size:14 final size:14
Alignment explanation
Indices: 1725662--1725708 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1725652 TCTTTTTTAC
1725662 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
*
1725676 TTTTTTCTACTTT-T
1 TTTTTTCT-TTTTCT
*
1725690 TTTTATCTTTTTTCT
1 TTTTTTC-TTTTTCT
1725705 TTTT
1 TTTT
1725709 GTACTCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:1725700 original size:27 final size:26
Alignment explanation
Indices: 1725650--1725713 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
1725640 CTTGGCTTGC
*
1725650 TTTCTTTTT-TACTTTTTTCT-TTTT
1 TTTCTTTTTCTACTTTTTTTTATTTT
*
1725674 CTT-TTTTTCTACTTTTTTTTATCTTT
1 TTTCTTTTTCTACTTTTTTTTAT-TTT
*
1725700 TTTCTTTTTGTACT
1 TTTCTTTTTCTACT
1725714 CCAATTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 5 0.16
24 12 0.38
25 1 0.03
26 5 0.16
27 9 0.28
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTCTTTTTCTACTTTTTTTTATTTT
Found at i:1726045 original size:22 final size:21
Alignment explanation
Indices: 1726009--1726049 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1725999 GGCTGCGGAA
1726009 TTGATGGTCTCGATGGATGATG
1 TTGATGGTCTCGAT-GATGATG
* *
1726031 TTGATGGTGTTGATGATGA
1 TTGATGGTCTCGATGATGA
1726050 AATGGAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.05, G:0.37, T:0.39
Consensus pattern (21 bp):
TTGATGGTCTCGATGATGATG
Found at i:1730296 original size:45 final size:45
Alignment explanation
Indices: 1730240--1730537 Score: 461
Period size: 45 Copynumber: 6.6 Consensus size: 45
1730230 ATAAATAGGA
* * *
1730240 CATTAAAAGGCATGAAAAGATGTCATAAATAAAATGCAGAACGGTG
1 CATT-AAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
*
1730286 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
* *
1730331 CATTGAAGGCATGAAAGGATGCCATAAATAACATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
* * *
1730376 CATTAAAGGCATTAAAGGATGCCATAAATTAAATGCATAATGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
* *
1730421 CATTAAAGGCATGAAAGGATGCCATAAATGAATTGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
* *
1730466 CATTAAAGGCATGAAATGATGCCATAAATAAAATGCATAACGATG
1 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
*
1730511 CATTAAAGGCATGAAATGATGCCATAA
1 CATTAAAGGCATGAAAGGATGCCATAA
1730538 CTGAAAATAA
Statistics
Matches: 232, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
45 228 0.98
46 4 0.02
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (45 bp):
CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGTG
Found at i:1740971 original size:8 final size:9
Alignment explanation
Indices: 1740941--1740969 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1740931 CAATTGACCT
1740941 AAACCCAAA
1 AAACCCAAA
1740950 AAACCCAAA
1 AAACCCAAA
1740959 AAACCCAAA
1 AAACCCAAA
1740968 AA
1 AA
1740970 CCGACAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACCCAAA
Found at i:1741798 original size:21 final size:20
Alignment explanation
Indices: 1741771--1741824 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
1741761 CATTCTTTTT
*
1741771 TTATTTTAATTTAG-TCACTG
1 TTATTTTAATTTAGCT-ACTA
*
1741791 TTAATTTTTTATTTAGCTACTA
1 TT-A-TTTTAATTTAGCTACTA
1741813 TTATTTTAATTT
1 TTATTTTAATTT
1741825 TTTCATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 10 0.36
21 2 0.07
22 15 0.54
23 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.06, T:0.61
Consensus pattern (20 bp):
TTATTTTAATTTAGCTACTA
Found at i:1741842 original size:29 final size:28
Alignment explanation
Indices: 1741791--1741848 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
1741781 TTAGTCACTG
1741791 TTAATTTTTTATTTAGCTACTA-TTATT
1 TTAATTTTTTATTTAGCTACTATTTATT
* *
1741818 TTAATTTTTTCATTTTGGTCACTATTTATT
1 TTAATTTTTT-ATTTAGCT-ACTATTTATT
1741848 T
1 T
1741849 CTTATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 6 0.23
29 4 0.15
30 6 0.23
ACGTcount: A:0.22, C:0.09, G:0.05, T:0.64
Consensus pattern (28 bp):
TTAATTTTTTATTTAGCTACTATTTATT
Found at i:1743899 original size:34 final size:32
Alignment explanation
Indices: 1743842--1743904 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
1743832 CTAATCATTT
*
1743842 TGACTAACTTGATTGTTTTTGTCTTGTTTCTA
1 TGACTAACTTGATTGTTTTTGTCTGGTTTCTA
1743874 TGACTAACATTGATT-TCCTTTTGTCTGGTTT
1 TGACTAAC-TTGATTGT--TTTTGTCTGGTTT
1743905 TATTGCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 9 0.33
33 6 0.22
34 12 0.44
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (32 bp):
TGACTAACTTGATTGTTTTTGTCTGGTTTCTA
Found at i:1746929 original size:76 final size:76
Alignment explanation
Indices: 1746677--1747114 Score: 512
Period size: 76 Copynumber: 5.8 Consensus size: 76
1746667 AATACAGAAA
* * ** *
1746677 ATTT-ATTTCACTACATATTGTTTTTCTTAATACAAGATTCGTCTAACTTGAGATAGTTTTTTAC
1 ATTTCATTTCACTACATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAG-TTTTTAC
1746741 TCGAAACAAGAC
65 TCGAAACAAGAC
* * ** * *
1746753 AATTCATTTCACTACATATTGTTTTTATTAAAACAAGATTCATCTCGTTTGAGATAGTTTTTTAC
1 ATTTCATTTCACTACATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAG-TTTTTAC
1746818 TCGAAACAAGAC
65 TCGAAACAAGAC
* * *
1746830 ATTTCATTTCACTACAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGATACAGTTTTTACT
1 ATTTCATTTCACTACATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACT
1746895 CGAAACAAGAC
66 CGAAACAAGAC
* * * * *
1746906 ATTTCATTTTACAACATATTGTTTTTCTTAAAACAAGATTTGTTTCACTTGAGACAATTTTTACT
1 ATTTCATTTCACTACATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACT
*
1746971 CGAAAGAAGAC
66 CGAAACAAGAC
* * * * **
1746982 ATTTCATTTCACT-CAAGATCGTTTTTCTTAAAACAATATTTGTCTTGCTTGAGACAACTTTTAC
1 ATTTCATTTCACTAC-ATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTAC
*
1747046 TCGAAAGAAGAC
65 TCGAAACAAGAC
* * *
1747058 ATTTCATTTCACT-CA-A--GATTATTT-TTAAAACAATATTTTTCTCGCTTGAGATAGTTT
1 ATTTCATTTCACTACATATTG-TT-TTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTT
1747115 CACTTGAAAC
Statistics
Matches: 321, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
72 1 0.00
73 30 0.09
74 4 0.01
75 2 0.01
76 168 0.52
77 116 0.36
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (76 bp):
ATTTCATTTCACTACATATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACT
CGAAACAAGAC
Found at i:1747141 original size:39 final size:39
Alignment explanation
Indices: 1747092--1747627 Score: 734
Period size: 39 Copynumber: 13.6 Consensus size: 39
1747082 TTAAAACAAT
* *
1747092 ATTTT-TCTCGCTTGAGATAGTTTCACTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
1747130 ATTTTATCTCGCTTGATATAGTTTCACTCGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * *
1747169 ATTTTATTTCGCTTGAGATTGTTTCACTCAAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
1747208 ATTTTATCTCCCATGAGATAGTTTCACTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * *
1747247 ATTTTATCTCGCTTGAGATAGTTTTACTTGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * *
1747286 ATTATATCTCTCTAGCTTGAGATAGTTTTACGCGAAACAGAAG
1 ATT-T-TATCTC--GCTTGAGATAGTTTCACTCGAAACAGAAG
1747329 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
1747368 ATTTTATCTCGCTGGAGATAGTTTCACTCGAAACATAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* * *
1747407 ATTTTATCTCGCTTGAGATAGTTTTACTAGAAATAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
**
1747446 ATTTTATCTCGCTTGAGATAGTTTCACTTAAAACAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
1747485 ATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACGGGAG
1 A-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
* *
1747525 ATTTAATCTCAG-TTGAGATAGTTTCACTTGAAACAGAAG
1 ATTTTATCTC-GCTTGAGATAGTTTCACTCGAAACAGAAG
** *
1747564 ATTTTATCTCGCTTGAGATAGTTTCACTTAAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
*
1747603 ATTTTATCTCACTTGAGATAGTTTC
1 ATTTTATCTCGCTTGAGATAGTTTC
1747628 TGATGTAGGC
Statistics
Matches: 443, Mismatches: 47, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
38 6 0.01
39 360 0.81
40 37 0.08
41 10 0.02
42 1 0.00
43 29 0.07
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
Found at i:1747848 original size:22 final size:21
Alignment explanation
Indices: 1747822--1747863 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1747812 TGGCTACGAA
1747822 ATTGATGGTCTTGATGGATGAT
1 ATTGATGGTCTTGAT-GATGAT
*
1747844 ATTGATGGTGTTGATGATGA
1 ATTGATGGTCTTGATGATGA
1747864 AATGGATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.24, C:0.02, G:0.33, T:0.40
Consensus pattern (21 bp):
ATTGATGGTCTTGATGATGAT
Found at i:1752383 original size:22 final size:21
Alignment explanation
Indices: 1752357--1752397 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1752347 GGTTGCGTAA
1752357 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
1752379 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
1752398 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:1753776 original size:42 final size:42
Alignment explanation
Indices: 1753730--1753839 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
1753720 CTTCGAATCA
*
1753730 GCTTAAGTCCTTCGGGCCATC-AGTAAGTATTTCGAGCATGAT
1 GCTTAAGTCCTTCGGGCCATCTA-TAAGTATTTCGAGCAAGAT
* * ** *
1753772 GCTTAAATCCTTCAGTTCATCTATAAGTCTTTCGAGCAAGAT
1 GCTTAAGTCCTTCGGGCCATCTATAAGTATTTCGAGCAAGAT
* *
1753814 G-ATAAGTCCTTCGGGCCATCCATAAG
1 GCTTAAGTCCTTCGGGCCATCTATAAG
1753840 ACCTTCGGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 19 0.35
42 35 0.64
43 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (42 bp):
GCTTAAGTCCTTCGGGCCATCTATAAGTATTTCGAGCAAGAT
Found at i:1756897 original size:21 final size:21
Alignment explanation
Indices: 1756856--1756897 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1756846 TTATGTTGTT
* **
1756856 TTACTGTTTTTTTATTTTTTA
1 TTACTGTTTTTTCATAGTTTA
1756877 TTACTGTTTTTTCATAGTTTA
1 TTACTGTTTTTTCATAGTTTA
1756898 AATTCTAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (21 bp):
TTACTGTTTTTTCATAGTTTA
Found at i:1760206 original size:35 final size:34
Alignment explanation
Indices: 1760160--1760272 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1760150 AAAACAATCC
*
1760160 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
1760195 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
1760230 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
1760265 TCAATTTC
1 TCAATTTC
1760273 TGTCTTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.90
36 6 0.08
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1761425 original size:34 final size:34
Alignment explanation
Indices: 1761346--1761456 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
1761336 ATTCCTCCTT
* *
1761346 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
1761381 TAATTGAATTATTTTGGAATTTAGGGTTTA-AATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
1761415 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
1761450 AAATTGA
1 AAATTGA
1761457 TGATGTTTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 31 0.46
35 34 0.50
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:1762851 original size:297 final size:299
Alignment explanation
Indices: 1762302--1762878 Score: 903
Period size: 297 Copynumber: 1.9 Consensus size: 299
1762292 ATATGGTTTA
* * * * *
1762302 TAAAAAAATATGAAAACATTTCGGTAATTTAAAACATGCAATCAAATCATAGATATAACAGTGAC
1 TAAAAAAATAAGAAAACATTTCGATAATTTAAAACAAGCAAACAAATCATAGATATAACAGTAAC
*
1762367 TAGAGATCATAATTTTAAAACATATAATTAAATTAGACATTCAGAGTAATTTAGATAAATAAACA
66 CAGAGATCATAATTTTAAAACATATAATTAAATTAGACATTCAGAGTAATTTAGATAAATAAACA
* *
1762432 TGAACGGTAATTTAACGGTAAGGAACACACCTTAATTGGCTGAAGGTTTGACAGAGAAATCTACT
131 TGAACAGTAATTTAACGGTAAGGAACACAACTTAATTGGCTGAAGGTTTGACAGAGAAATCTACT
* *
1762497 GAGTGATATGACGATCACGATCAACTCCGGTGTCAGAATCTAAGTACAAAAGAAAACAAACCACT
196 GAGTGATATGACGATCACGATCAACTACGGTGTCAGAACCTAAGTACAAAAGAAAACAAACCACT
*
1762562 ATTCTTATGTAACTAATCTTTAATTTATAAAAAAAAATC
261 ATTCTTATGTAACAAATCTTTAATTTATAAAAAAAAATC
* *
1762601 TAAAAAAA-AAGAAAACATTTTGATAATTTAAAACAAGCAAACAAATCATAGATATAACGGTAAC
1 TAAAAAAATAAGAAAACATTTCGATAATTTAAAACAAGCAAACAAATCATAGATATAACAGTAAC
* *
1762665 CAGATATCATAATTTTAAAACATATAATTAAATTAG-TATTCAGAGTAATTTAGATAAATAAATC
66 CAGAGATCATAATTTTAAAACATATAATTAAATTAGACATTCAGAGTAATTTAGATAAATAAA-C
* *
1762729 -TGAACAGTAATTTAA-TGTAAGGAACACAACTTAATTGGCTGAGGAGTTTGACAGAGAAATCTA
130 ATGAACAGTAATTTAACGGTAAGGAACACAACTTAATTGGCTGAAG-GTTTGACAGAGAAATCTA
* * * *
1762792 CTGAGTGATATGACGATCAC-AGTCAACTACGGTGTCAGAGCCTAAGTACCAATGAAAACAAATC
194 CTGAGTGATATGACGATCACGA-TCAACTACGGTGTCAGAACCTAAGTACAAAAGAAAACAAACC
1762856 ACTATTCTTATGTAACAAATCTT
258 ACTATTCTTATGTAACAAATCTT
1762879 GGGAATCGTG
Statistics
Matches: 254, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
296 27 0.11
297 135 0.53
298 84 0.33
299 8 0.03
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (299 bp):
TAAAAAAATAAGAAAACATTTCGATAATTTAAAACAAGCAAACAAATCATAGATATAACAGTAAC
CAGAGATCATAATTTTAAAACATATAATTAAATTAGACATTCAGAGTAATTTAGATAAATAAACA
TGAACAGTAATTTAACGGTAAGGAACACAACTTAATTGGCTGAAGGTTTGACAGAGAAATCTACT
GAGTGATATGACGATCACGATCAACTACGGTGTCAGAACCTAAGTACAAAAGAAAACAAACCACT
ATTCTTATGTAACAAATCTTTAATTTATAAAAAAAAATC
Found at i:1765187 original size:24 final size:25
Alignment explanation
Indices: 1765150--1765196 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1765140 AATAAAGTAA
* *
1765150 AATATATAAGATATATACTAATAGT
1 AATATATAAAATATATACAAATAGT
1765175 AATA-ATAAAATATATACAAATA
1 AATATATAAAATATATACAAATA
1765197 AAAAAAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
AATATATAAAATATATACAAATAGT
Found at i:1767146 original size:99 final size:99
Alignment explanation
Indices: 1767010--1767388 Score: 580
Period size: 99 Copynumber: 3.8 Consensus size: 99
1767000 GAAATTGTTT
* **
1767010 GTTGACGGTCAGCCGCCCCTTCGCCATGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
1 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
*
1767075 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA
1767109 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
1 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
* *
1767174 ATTGTGAAGTTAAAATTGGCTCTGAAATTGGAAA
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA
*
1767208 GTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
1 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
*
1767273 GTTGTGAAGTTGAAATTGGCTCTGAAATCGGAAA
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA
* * * * * * *
1767307 GTTGACAGTCAACTGCCCTTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGTGTGCACGAT-TCCC
1 GTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGT-C-CAATAT-CC
*
1767371 TTCGTCGTGAAGTTGAAA
63 TTCGTTGTGAAGTTGAAA
1767389 CCGCGGGTTG
Statistics
Matches: 258, Mismatches: 19, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
99 234 0.91
100 2 0.01
101 22 0.09
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (99 bp):
GTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTC
GTTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA
Found at i:1768423 original size:6 final size:6
Alignment explanation
Indices: 1768407--1768464 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
1768397 ACCCACCTTA
*
1768407 TTTTC- TTTTCT TTTTCT TTTGT-T TTTT-T TTTCTCT TTTTCT CTTTTCC
1 TTTTCT TTTTCT TTTTCT TTT-TCT TTTTCT TTT-TCT TTTTCT -TTTTCT
1768455 TTTTCT TTTT
1 TTTTCT TTTT
1768465 TCAATTTAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
5 10 0.22
6 26 0.57
7 10 0.22
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:1768572 original size:59 final size:59
Alignment explanation
Indices: 1768455--1768572 Score: 130
Period size: 59 Copynumber: 2.0 Consensus size: 59
1768445 TCTCTTTTCC
* * * ** **
1768455 TTTTCTTTTTTCAATTTAGGCGCCCTTTCGGGTTTTCACCCTAAATGATTTTTTTTTTT
1 TTTTCTTTTTTCAACTTAGGCGCCCTCTCGGGTTTTCACCCTAAACGATAGTACTTTTT
* * *
1768514 TTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAGCGA-AGTACTTTTT
1 TTTTCTTTTTTCAACTTAGG-CGCCCTCTCGGGTTTTCACCCTAAACGATAGTACTTTTT
1768573 GACTACATCG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 24 0.50
60 24 0.50
ACGTcount: A:0.15, C:0.20, G:0.14, T:0.51
Consensus pattern (59 bp):
TTTTCTTTTTTCAACTTAGGCGCCCTCTCGGGTTTTCACCCTAAACGATAGTACTTTTT
Found at i:1768572 original size:60 final size:59
Alignment explanation
Indices: 1768455--1768572 Score: 137
Period size: 60 Copynumber: 2.0 Consensus size: 59
1768445 TCTCTTTTCC
* * * ** **
1768455 TTTTCTTTTTTCAATTTAGGCGCCCTTTCGGGTTTTCACCCTAAATGATTTTTTTTTTT
1 TTTTCTTTTTTCAACTTAGGCGCCCTCTCGGGTTTTCACCCTAAACGAAGTACTTTTTT
* * *
1768514 TTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAGCGAAGTACTTTTT
1 TTTTCTTTTTTCAACTTAGG-CGCCCTCTCGGGTTTTCACCCTAAACGAAGTACTTTTT
1768573 GACTACATCG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 18 0.38
60 30 0.62
ACGTcount: A:0.15, C:0.20, G:0.14, T:0.51
Consensus pattern (59 bp):
TTTTCTTTTTTCAACTTAGGCGCCCTCTCGGGTTTTCACCCTAAACGAAGTACTTTTTT
Found at i:1779513 original size:24 final size:25
Alignment explanation
Indices: 1779476--1779522 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1779466 AATAAAGTAA
* *
1779476 AATATATAAGATATATACTAATAGT
1 AATATATAAAATATATACAAATAGT
1779501 AATA-ATAAAATATATACAAATA
1 AATATATAAAATATATACAAATA
1779523 AAAAAAACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
AATATATAAAATATATACAAATAGT
Found at i:1785422 original size:30 final size:30
Alignment explanation
Indices: 1785382--1785473 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
1785372 CTACACGGGA
* *
1785382 GACCATCAAACTATGATCAAAAGTCAATGT
1 GACCACCAAACTATGGTCAAAAGTCAATGT
1785412 GACCACCAAACTATGGTCAAAAGTCAATGT
1 GACCACCAAACTATGGTCAAAAGTCAATGT
*
1785442 GACTACCAAACTATGGTCAAAAGTCAATGT
1 GACCACCAAACTATGGTCAAAAGTCAATGT
1785472 GA
1 GA
1785474 TTACCGAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (30 bp):
GACCACCAAACTATGGTCAAAAGTCAATGT
Found at i:1786194 original size:96 final size:92
Alignment explanation
Indices: 1786024--1786317 Score: 283
Period size: 96 Copynumber: 3.3 Consensus size: 92
1786014 AATAATTTTC
* * * * *
1786024 AAATAAATTTCGGTTCGATTAACGGTTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATTTT
1 AAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAAAAATTTATTTGATTCAGTTAATAATTTT
1786089 CAAATAAATTTCT-ATTCGATTAACGGTA
65 CAAATAAATTT-TGATTCGATTAACGGTA
* *
1786117 AAATAATTTCGGTTCAATTAATGGTTAAAGAAAAAAAAATCGGTTGATTTGGTTCAGTTAATGAA
1 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAAAT---TT-ATTTGATTCAGTTAAT-AA
* * *
1786182 -TTTCAAATAAATTTTGGTTCGATTAATGGTC
61 TTTTCAAATAAATTTTGATTCGATTAACGGTA
* *
1786213 AAATAATTTTGGTTCGATTAATGGTTAAAG-----AAAA---A----ATTCGGTTAATAATTTTC
1 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAAATTTATTTGATTCAGTTAATAATTTTC
* * *
1786266 AAATAAATTTCGGTTCGATTAACGGTC
66 AAATAAATTTTGATTCGATTAACGGTA
*
1786293 AAATAATTTCAGTTCGATTAATGGT
1 AAATAATTTCGGTTCGATTAATGGT
1786318 CAAATAATTC
Statistics
Matches: 176, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
79 2 0.01
80 61 0.35
84 1 0.01
91 4 0.02
92 32 0.18
93 4 0.02
95 3 0.02
96 67 0.38
97 2 0.01
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (92 bp):
AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAAAATTTATTTGATTCAGTTAATAATTTTC
AAATAAATTTTGATTCGATTAACGGTA
Found at i:1786224 original size:26 final size:26
Alignment explanation
Indices: 1786184--1786341 Score: 158
Period size: 26 Copynumber: 6.0 Consensus size: 26
1786174 TTAATGAATT
*
1786184 TCAAATAAATTTTGGTTCGATTAATGG
1 TCAAAT-AATTTCGGTTCGATTAATGG
*
1786211 TCAAATAATTTTGGTTCGATTAATGG
1 TCAAATAATTTCGGTTCGATTAATGG
* * * * **
1786237 TTAAAGAAAAAATTCGGTT--AATAATTT
1 -T-CA-AATAATTTCGGTTCGATTAATGG
*
1786264 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAAT-AATTTCGGTTCGATTAATGG
*
1786291 TCAAATAATTTCAGTTCGATTAATGG
1 TCAAATAATTTCGGTTCGATTAATGG
*
1786317 TCAAATAATTCCGGTTCGATTAATG
1 TCAAATAATTTCGGTTCGATTAATG
1786342 TTAAAGAAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
24 2 0.02
25 10 0.09
26 62 0.58
27 22 0.21
28 1 0.01
29 10 0.09
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAATGG
Found at i:1786506 original size:133 final size:133
Alignment explanation
Indices: 1786318--1786565 Score: 403
Period size: 133 Copynumber: 1.9 Consensus size: 133
1786308 GATTAATGGT
* * *
1786318 CAAATAATTCCGGTTCGATTAATGTTAAAGAAAAAAATTTGATTAATTTGGTTCGGTTAATAATT
1 CAAATAATTCCGGTTCAATTAATGTTAAAGAAAAAAATTAGATTAATTCGGTTCGGTTAATAATT
1786383 TTCAAAT-AAATTTCGGTTCGATTAACGGTT-AA-AAAAAATAATTTATTTTATTCGGTTAATAA
66 TTCAAATAAAATTT-GGTTCGATTAACGGTTAAAGAAAAAATAATTTATTTTATTCGGTTAATAA
1786445 TTTC
130 TTTC
* *
1786449 CAAATAAATTTCGGTTCAATTAATGGTTAAAGAAAAAAATTAGGTTAATTCGGTTCGGTTAATAA
1 CAAAT-AATTCCGGTTCAATTAAT-GTTAAAGAAAAAAATTAGATTAATTCGGTTCGGTTAATAA
1786514 TTTTCAAATAAAATTTGGTTCGATTAACGGTTAAAGAAAAAATAATTTATTT
64 TTTTCAAATAAAATTTGGTTCGATTAACGGTTAAAGAAAAAATAATTTATTT
1786566 AAACAAATAA
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
131 5 0.05
132 16 0.15
133 62 0.58
134 8 0.07
135 16 0.15
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (133 bp):
CAAATAATTCCGGTTCAATTAATGTTAAAGAAAAAAATTAGATTAATTCGGTTCGGTTAATAATT
TTCAAATAAAATTTGGTTCGATTAACGGTTAAAGAAAAAATAATTTATTTTATTCGGTTAATAAT
TTC
Found at i:1786524 original size:69 final size:67
Alignment explanation
Indices: 1786317--1786555 Score: 296
Period size: 69 Copynumber: 3.6 Consensus size: 67
1786307 CGATTAATGG
* * *
1786317 TCAAAT-AATTCCGGTTCGATTAA-TGTTAAAGAAAAAAATTTGATTAATTTGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTAG-TTAA-TTGGTTCGGTTAATA
1786380 ATTT
64 ATTT
*
1786384 TCAAATAAATTTCGGTTCGATTAACGGTTAAA-AAAAATAATTTA-TT--TT-ATTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAA-AA-TTAGTTAATTGGTTCGGTTAATA
1786444 ATTT
64 ATTT
* * *
1786448 CCAAATAAATTTCGGTTCAATTAATGGTTAAAGAAAAAAATTAGGTTAATTCGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTA-GTTAATT-GGTTCGGTTAATA
1786513 ATTT
64 ATTT
1786517 TCAAATAAAATTT-GGTTCGATTAACGGTTAAAGAAAAAA
1 TCAAAT-AAATTTCGGTTCGATTAACGGTTAAAGAAAAAA
1786556 TAATTTATTT
Statistics
Matches: 149, Mismatches: 11, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
63 3 0.02
64 46 0.31
65 9 0.06
67 8 0.05
68 23 0.15
69 52 0.35
70 8 0.05
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (67 bp):
TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTAGTTAATTGGTTCGGTTAATAAT
TT
Found at i:1793619 original size:3 final size:3
Alignment explanation
Indices: 1793611--1793643 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1793601 TAGTGTAAAT
1793611 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1793644 GAAAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1794282 original size:65 final size:65
Alignment explanation
Indices: 1794175--1794355 Score: 281
Period size: 65 Copynumber: 2.8 Consensus size: 65
1794165 TTTAGGGATT
* * * * *
1794175 TGTTTCAAGAGAAACTATCTCAAGAGAGAGAAAATTCGTTTCAAGGGAAACGATCTCGAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAGGA
*
1794240 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGAGGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAGGA
* *
1794305 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTCGTTTCAAGGGAAA
1794356 TAGATTCAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 92 0.87
66 14 0.13
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAGGA
Found at i:1794466 original size:36 final size:37
Alignment explanation
Indices: 1794411--1794563 Score: 139
Period size: 36 Copynumber: 4.1 Consensus size: 37
1794401 CGTCTCAAAG
* * *
1794411 GAAAAATGTCCCAAGCGAGACGAAATTTGTTTTGAGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
* *
1794448 G-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
* * * *
1794484 GAAAACTGTCTTAAGCGAGACAAAATTTAATTTTTA-A
1 GAAAATTGTCTCAAGCGAGACAAAATTT-GTTTTGAGA
* * * * *
1794521 GAAAAGTTTTCTCTAGCGAGACGACACTTTGTTTCGAGA
1 GAAAA-TTGTCTCAAGCGAGAC-AAAATTTGTTTTGAGA
1794560 GAAA
1 GAAA
1794564 CCATCTCAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
36 31 0.33
37 31 0.33
38 22 0.23
39 10 0.11
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (37 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
Found at i:1794503 original size:37 final size:37
Alignment explanation
Indices: 1794411--1794525 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 37
1794401 CGTCTCAAAG
* * * * *
1794411 GAAAAATGTCCCAAGCGAGACGAAATTTGTTTTGAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
*
1794448 G-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
* *
1794484 GAAAACTGTCTTAAGCGAGACAAAATTTAATTTTT-AA
1 GAAAACTGTCTCAAGCGAGACAAAATTT-GTTTTTAAA
1794521 GAAAA
1 GAAAA
1794526 GTTTTCTCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 31 0.46
37 32 0.47
38 5 0.07
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (37 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAAA
Found at i:1794539 original size:38 final size:37
Alignment explanation
Indices: 1794424--1794542 Score: 109
Period size: 37 Copynumber: 3.2 Consensus size: 37
1794414 AAATGTCCCA
* * * * * *
1794424 AGCGAGACGAAATTTGTTTTGAGAG-AAATTGTCTCA
1 AGCGAGACAAAATTTATTTTTAAAGAAAACTGTCTCT
*
1794460 AGCGAGACAAAATTTGTTTTTAAAGAAAACTGTCT-T
1 AGCGAGACAAAATTTATTTTTAAAGAAAACTGTCTCT
* *
1794496 AAGCGAGACAAAATTTAATTTTT-AAGAAAAGTTTTCTCT
1 -AGCGAGACAAAATTT-ATTTTTAAAGAAAA-CTGTCTCT
1794535 AGCGAGAC
1 AGCGAGAC
1794543 GACACTTTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
36 22 0.31
37 30 0.43
38 17 0.24
39 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (37 bp):
AGCGAGACAAAATTTATTTTTAAAGAAAACTGTCTCT
Found at i:1798172 original size:12 final size:12
Alignment explanation
Indices: 1798155--1798186 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1798145 AGAATATAAT
*
1798155 GATGCAAATGTA
1 GATGCAAATGCA
1798167 GATGCAAATGCA
1 GATGCAAATGCA
1798179 GATGCAAA
1 GATGCAAA
1798187 AATATTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (12 bp):
GATGCAAATGCA
Found at i:1799380 original size:25 final size:24
Alignment explanation
Indices: 1799352--1799398 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1799342 AAATATTGGG
1799352 AATTACAAACTCCAAAATATATTTA
1 AATTACAAAC-CCAAAATATATTTA
* *
1799377 AATTACGATCCCAAAATATATT
1 AATTACAAACCCAAAATATATT
1799399 CTTATGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AATTACAAACCCAAAATATATTTA
Found at i:1802544 original size:31 final size:32
Alignment explanation
Indices: 1802498--1802579 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 32
1802488 GACCATTTTA
*
1802498 TCCCGAAAGACATAGGTAACA-TGTCCATATG
1 TCCCGAAGGACATAGGTAACACTGTCCATATG
* *
1802529 TTCTGAAGGACATAGGTAA-ACTGTCCATATG
1 TCCCGAAGGACATAGGTAACACTGTCCATATG
*
1802560 TCCCGAAGGACTTAGGTAAC
1 TCCCGAAGGACATAGGTAAC
1802580 CCTCGACTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (32 bp):
TCCCGAAGGACATAGGTAACACTGTCCATATG
Found at i:1805518 original size:11 final size:11
Alignment explanation
Indices: 1805502--1805530 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1805492 TCTGATTACC
1805502 CATCTTTATTA
1 CATCTTTATTA
1805513 CATCTTTATTA
1 CATCTTTATTA
1805524 CATCTTT
1 CATCTTT
1805531 GTAACTCTTA
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:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (11 bp):
CATCTTTATTA
Found at i:1807274 original size:21 final size:21
Alignment explanation
Indices: 1807249--1807288 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1807239 AAGACTCTAT
1807249 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
1807270 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1807289 AAACAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:1813799 original size:64 final size:65
Alignment explanation
Indices: 1813731--1813877 Score: 183
Period size: 64 Copynumber: 2.3 Consensus size: 65
1813721 TCAAATGCAA
* * *
1813731 TTTATGCATCGATGCACAA-ACCATGCATCGATGCACTCTGGCTA-TTTTAAAACATCAAATTGA
1 TTTATGCACCGATGCACAAGA-CATGCATCGATGCACCCTGGATATTTTTAAAACATCAAATTGA
1813794 T
65 T
* **
1813795 TTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGATATTTTTGAAACATCGAAGCTGA
1 TTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGATATTTTTAAAACATC-AAATTGA
1813860 -
65 T
**
1813860 TTTATGCACTAATGCACA
1 TTTATGCACCGATGCACA
1813878 CCCTAGTGCA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 39 0.54
65 28 0.39
66 5 0.07
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (65 bp):
TTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGATATTTTTAAAACATCAAATTGAT
Found at i:1816282 original size:31 final size:31
Alignment explanation
Indices: 1816244--1816334 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
1816234 AGGACCACTA
1816244 TCCATATGTCTCAAAGGACATAGGTAACCTG
1 TCCATATGTCTCAAAGGACATAGGTAACCTG
* *
1816275 TCCATATGTCCTGAAA-GACATAGGTAAACTG
1 TCCATATGT-CTCAAAGGACATAGGTAACCTG
* * * * *
1816306 TTCATATATCCCGAAGGATATAGGTAACC
1 TCCATATGTCTCAAAGGACATAGGTAACC
1816335 CTCGACTCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
30 3 0.06
31 41 0.84
32 5 0.10
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
TCCATATGTCTCAAAGGACATAGGTAACCTG
Found at i:1818868 original size:34 final size:36
Alignment explanation
Indices: 1818799--1818868 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1818789 TTGATGTTGT
* * *
1818799 TTGGTGGTAGGGTAAGCTCGAGGTATGGGGCTGCTG
1 TTGGTGGCAGGATAAGCCCGAGGTATGGGGCTGCTG
*
1818835 TTGGTGGCAGGATAAGCCCG-GG-ATGGGGTTGCTG
1 TTGGTGGCAGGATAAGCCCGAGGTATGGGGCTGCTG
1818869 GCAACAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 11 0.37
35 2 0.07
36 17 0.57
ACGTcount: A:0.14, C:0.13, G:0.47, T:0.26
Consensus pattern (36 bp):
TTGGTGGCAGGATAAGCCCGAGGTATGGGGCTGCTG
Found at i:1819667 original size:26 final size:26
Alignment explanation
Indices: 1819631--1819693 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
1819621 CACTATGTTT
1819631 CGAAGGACCACATATCACATATATCC
1 CGAAGGACCACATATCACATATATCC
1819657 CGAAGGACCACATATCACATATATCC
1 CGAAGGACCACATATCACATATATCC
1819683 CGAAGGACCAC
1 CGAAGGACCAC
1819694 TCCTTAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (26 bp):
CGAAGGACCACATATCACATATATCC
Found at i:1820643 original size:21 final size:21
Alignment explanation
Indices: 1820616--1820668 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
1820606 CGATGTTCGT
1820616 TGGTATCGATACCCTCCACATA
1 TGGTATCGATA-CCTCCACATA
*
1820638 -GGTATCTATA-CTCCACATA
1 TGGTATCGATACCTCCACATA
*
1820657 TGGTATTGATAC
1 TGGTATCGATAC
1820669 TGTTCATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
21 9 0.35
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (21 bp):
TGGTATCGATACCTCCACATA
Found at i:1821615 original size:3 final size:3
Alignment explanation
Indices: 1821607--1821641 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1821597 GTTAGTGTAA
1821607 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1821642 CGTAATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1826254 original size:11 final size:11
Alignment explanation
Indices: 1826225--1826260 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1826215 GTTTATCAAA
* *
1826225 TTATTTTATAA
1 TTATTTTTTAT
1826236 TTATTTTTTAT
1 TTATTTTTTAT
1826247 TTATTTTTTAT
1 TTATTTTTTAT
1826258 TTA
1 TTA
1826261 ATTTGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:1828083 original size:94 final size:95
Alignment explanation
Indices: 1827894--1828090 Score: 234
Period size: 94 Copynumber: 2.1 Consensus size: 95
1827884 TACTGATGGG
* * * * * *
1827894 GTATCGATACTAAGAGGAAGGTATCGATACCATTGATTACAAAATGCAGAAATTGTATCGATATT
1 GTATCGATACTAAGAGAAAAGTATCGATACCATGGATTACAAAATGCACAAATGGTATCGATACT
** * *
1827959 GTAATGGAGTATCGGTACCATAATATAGTA
66 AAAAGGGAGTATCAGTACCATAATATAGTA
* * * *
1827989 GTATCGATACTAGGAGAAAAGTATCGATACCATGGA-TCCAGAATGTACAAATGGTATCGATACT
1 GTATCGATACTAAGAGAAAAGTATCGATACCATGGATTACAAAATGCACAAATGGTATCGATACT
* * *
1828053 AAAAGGGGGTATTAGTACCATAGTATAGTA
66 AAAAGGGAGTATCAGTACCATAATATAGTA
1828083 GTATCGAT
1 GTATCGAT
1828091 GCCATGGTAG
Statistics
Matches: 85, Mismatches: 17, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
94 53 0.62
95 32 0.38
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (95 bp):
GTATCGATACTAAGAGAAAAGTATCGATACCATGGATTACAAAATGCACAAATGGTATCGATACT
AAAAGGGAGTATCAGTACCATAATATAGTA
Found at i:1828638 original size:107 final size:108
Alignment explanation
Indices: 1828438--1828698 Score: 409
Period size: 107 Copynumber: 2.4 Consensus size: 108
1828428 ATGTGTACTA
* * * *
1828438 TAGGTACTATGTGTGCGACCCACGAAATTCATCATATGTTGATGAACAACTGTTTAGGCACTATG
1 TAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACTCTTTAGGCACTATG
1828503 TGTGCAACCCACGTAATTCATCATATGTTGATGAACAACCGTT
66 TGTGCAACCCACGTAATTCATCATATGTTGATGAACAACCGTT
* *
1828546 TAGGCACTATATGTGCAACCCATGGAATTCATCATATGTTGATGAACAAC-CTTTAGGCACTATG
1 TAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACTCTTTAGGCACTATG
1828610 TGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCGTT
66 TGTGCAACCCAC-GTAATTCATCATATGTTGATGAACAACCGTT
* * * *
1828653 TAGGCACTATGTGTGCAACCCACAGAATTCATAATATCTTTATGAA
1 TAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAA
1828699 TGATCGTATT
Statistics
Matches: 140, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
107 94 0.67
108 46 0.33
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (108 bp):
TAGGCACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACTCTTTAGGCACTATG
TGTGCAACCCACGTAATTCATCATATGTTGATGAACAACCGTT
Found at i:1828723 original size:54 final size:54
Alignment explanation
Indices: 1828438--1828698 Score: 402
Period size: 54 Copynumber: 4.9 Consensus size: 54
1828428 ATGTGTACTA
* * *
1828438 TAGGTACTATGTGTGCGACCCAC-GAAATTCATCATATGTTGATGAACAACTGTT
1 TAGGCACTATGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCGTT
1828492 TAGGCACTATGTGTGCAACCCAC-GTAATTCATCATATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACAACCGTT
* **
1828546 TAGGCACTATATGTGCAACCCATGGAATTCATCATATGTTGATGAACAACC-TT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
1828599 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
* * *
1828653 TAGGCACTATGTGTGCAACCCACAGAATTCATAATATCTTTATGAA
1 TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAA
1828699 TGATCGTATT
Statistics
Matches: 193, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
53 50 0.26
54 142 0.74
55 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (54 bp):
TAGGCACTATGTGTGCAACCCACAGAATTCATCATATGTTGATGAACAACCGTT
Found at i:1836778 original size:12 final size:12
Alignment explanation
Indices: 1836754--1836837 Score: 64
Period size: 12 Copynumber: 7.0 Consensus size: 12
1836744 AATTTTATAA
1836754 AATTTAT-TTAT
1 AATTTATGTTAT
1836765 AATTTATGTTAT
1 AATTTATGTTAT
* *
1836777 AAGTTACGTTAT
1 AATTTATGTTAT
* *
1836789 AACTGATGTTA-
1 AATTTATGTTAT
**
1836800 AAAGTATGTTAT
1 AATTTATGTTAT
* *
1836812 TATATTATTTTAT
1 AAT-TTATGTTAT
1836825 AATTTTATGTTAT
1 AA-TTTATGTTAT
1836838 GATCGATATA
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
11 15 0.27
12 23 0.42
13 16 0.29
14 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (12 bp):
AATTTATGTTAT
Found at i:1843558 original size:24 final size:24
Alignment explanation
Indices: 1843531--1843580 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1843521 CTCCTCTCAA
* *
1843531 CAAGAACAATCTGTCTCTGCTGAG
1 CAAGAACAATCTATCTCTACTGAG
* *
1843555 CAAGATCAGTCTATCTCTACTGAG
1 CAAGAACAATCTATCTCTACTGAG
1843579 CA
1 CA
1843581 GGTTCAAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (24 bp):
CAAGAACAATCTATCTCTACTGAG
Found at i:1845448 original size:14 final size:14
Alignment explanation
Indices: 1845429--1845467 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
1845419 TTAAGATCGT
*
1845429 TAGATGAGTGAAAA
1 TAGATGACTGAAAA
1845443 TAGATGACTGAAAA
1 TAGATGACTGAAAA
1845457 TAGATGACTGA
1 TAGATGACTGA
1845468 GATTAACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (14 bp):
TAGATGACTGAAAA
Found at i:1852478 original size:31 final size:31
Alignment explanation
Indices: 1852431--1852497 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1852421 ACAAGCCTTA
* * * *
1852431 GAAAAATTTGGGGACCATTTTG-TAATTTTT
1 GAAAAATTGGGGGACCAATTCGATAATTTTG
1852461 GAAAAAGTTGGGGGACCAATTCGATAATTTTG
1 GAAAAA-TTGGGGGACCAATTCGATAATTTTG
1852493 GAAAA
1 GAAAA
1852498 GGTGTGAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 13 0.42
32 12 0.39
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (31 bp):
GAAAAATTGGGGGACCAATTCGATAATTTTG
Found at i:1853064 original size:24 final size:24
Alignment explanation
Indices: 1853037--1853085 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1853027 TGCATGACAT
1853037 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
1853061 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
1853085 T
1 T
1853086 CAGGAAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:1853661 original size:46 final size:46
Alignment explanation
Indices: 1853609--1853794 Score: 302
Period size: 46 Copynumber: 4.1 Consensus size: 46
1853599 GTAACCATGC
*
1853609 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGCATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
* *
1853655 AAATAAGCTTATGAGCTTACGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
* *
1853701 AAATAAACTTACGAGCTTATGGGATTAAATTGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
* *
1853747 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTTTATTGATA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1853792 AAA
1 AAA
1853795 AATTTATATT
Statistics
Matches: 129, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 21 0.16
46 108 0.84
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
Found at i:1870046 original size:24 final size:24
Alignment explanation
Indices: 1870013--1870067 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1870003 TATTCGATTC
1870013 AAGGATGAACCTTTTAAAGAGAG-
1 AAGGATGAACCTTTTAAAGAGAGT
*
1870036 AGAGGATGAACCTTTTAATGAGAGT
1 A-AGGATGAACCTTTTAAAGAGAGT
1870061 AAGGATG
1 AAGGATG
1870068 GTACTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.29, T:0.24
Consensus pattern (24 bp):
AAGGATGAACCTTTTAAAGAGAGT
Found at i:1871829 original size:24 final size:24
Alignment explanation
Indices: 1871801--1871859 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1871791 CAAGCTATAG
**
1871801 CTCACCTATTTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
*
1871825 TTCACCTAGCTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
1871849 CTCACCTAGCT
1 CTCACCTAGCT
1871860 TACCTTGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.36, G:0.10, T:0.24
Consensus pattern (24 bp):
CTCACCTAGCTAGCTACCAAGACA
Found at i:1872177 original size:19 final size:20
Alignment explanation
Indices: 1872145--1872196 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1872135 TTCGGACAAG
1872145 AACATGTA-TTTCA-TTAAA
1 AACATGTATTTTCATTTAAA
**
1872163 GTCATGTATTTTCATTTAAA
1 AACATGTATTTTCATTTAAA
1872183 AACATGTATTTTCA
1 AACATGTATTTTCA
1872197 ATGGGATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 17 0.61
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (20 bp):
AACATGTATTTTCATTTAAA
Found at i:1885310 original size:13 final size:13
Alignment explanation
Indices: 1885288--1885327 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1885278 CAATAACATG
*
1885288 AAATGAGCGTCAT
1 AAATGCGCGTCAT
1885301 AAATGCGCGTCAT
1 AAATGCGCGTCAT
*
1885314 AAATGCACGTCAT
1 AAATGCGCGTCAT
1885327 A
1 A
1885328 GATTTATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (13 bp):
AAATGCGCGTCAT
Found at i:1897665 original size:19 final size:18
Alignment explanation
Indices: 1897630--1897682 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1897620 TTTCATCAGT
* *
1897630 AAAAGAAAAGAAAAAATTA
1 AAAAAAAAAGCAAAAA-TA
* *
1897649 AAACAAAAGGCAAAAATA
1 AAAAAAAAAGCAAAAATA
1897667 AAAAAAAAAGCAAAAA
1 AAAAAAAAAGCAAAAA
1897683 AATCACAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAGCAAAAATA
Found at i:1897683 original size:19 final size:20
Alignment explanation
Indices: 1897630--1897683 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
1897620 TTTCATCAGT
*
1897630 AAAAGAAAAG-AAAAAATTA
1 AAAAAAAAAGCAAAAAATTA
* *
1897649 AAACAAAAGGC-AAAAA-TA
1 AAAAAAAAAGCAAAAAATTA
1897667 AAAAAAAAAGCAAAAAA
1 AAAAAAAAAGCAAAAAA
1897684 ATCACAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.80, C:0.06, G:0.09, T:0.06
Consensus pattern (20 bp):
AAAAAAAAAGCAAAAAATTA
Found at i:1899217 original size:51 final size:51
Alignment explanation
Indices: 1899153--1899257 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
1899143 CTTTACATCA
* * * * *
1899153 TCTATCACATTCTTGTTCTTGTGTTAGTAGGATTAAAAGATATTACATAGT
1 TCTAACACATTCTTATTCTTATGTTAGTAGGATTAAAAGAGATCACATAGT
* *
1899204 TCTAACACGTTCTTATTCTTATGTTAGTAGGATTAAAAGAGATCACCTAGT
1 TCTAACACATTCTTATTCTTATGTTAGTAGGATTAAAAGAGATCACATAGT
1899255 TCT
1 TCT
1899258 TCTTCCTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (51 bp):
TCTAACACATTCTTATTCTTATGTTAGTAGGATTAAAAGAGATCACATAGT
Found at i:1899800 original size:93 final size:88
Alignment explanation
Indices: 1899636--1899925 Score: 257
Period size: 93 Copynumber: 3.2 Consensus size: 88
1899626 ATATTTAACA
* * * *
1899636 TAAA-ACTTTGATGTTTAGGGACTAAAGATGTTAACTTATACAAGTTGTTACATTG-ATATATGG
1 TAAACACTTTGATGTTTA-CGACTAAAGAGGTTAACTTCT-CAAGTTGTTACA-TGAATAGATGG
* * *
1899699 TAGCTTGAATAGTATTGAAATATCTTGCC
63 AAGATTGAATAGT-CTGAAAT-TCTTG-C
*
1899728 TAAACACTTTGATGTTTACAGACTAAAGAGGTTAACTTCTCGAAGTTGTTACATGAATAGATGAA
1 TAAACACTTTGATGTTTAC-GACTAAAGAGGTTAACTTCTC-AAGTTGTTACATGAATAGATGGA
* * **
1899793 AGTTTGAATAGGTGTGAAATT-AAG-
64 AGATTGAATA-GTCTGAAATTCTTGC
* * * *
1899817 TAAACACTTTGATGTTTACGAACTAAAGAGATTAACTTAC-CAAAGTTGTTATATTAATGGATGG
1 TAAACACTTTGATGTTTACG-ACTAAAGAGGTTAACTT-CTC-AAGTTGTTACATGAATAGATGG
*
1899881 AAGAATGAATAGTGCTGAAATGTCTTGAC
63 AAGATTGAATAGT-CTGAAAT-TCTTG-C
1899910 TAAACACTTTGATGTT
1 TAAACACTTTGATGTT
1899926 AACACGTTAA
Statistics
Matches: 165, Mismatches: 21, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
88 3 0.02
89 69 0.42
90 2 0.01
91 2 0.01
92 8 0.05
93 79 0.48
94 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (88 bp):
TAAACACTTTGATGTTTACGACTAAAGAGGTTAACTTCTCAAGTTGTTACATGAATAGATGGAAG
ATTGAATAGTCTGAAATTCTTGC
Found at i:1899890 original size:89 final size:89
Alignment explanation
Indices: 1899728--1899901 Score: 228
Period size: 89 Copynumber: 2.0 Consensus size: 89
1899718 ATATCTTGCC
* *
1899728 TAAACACTTTGATGTTTACAGACTAAAGAGGTTAACTTCTCGAAGTTGTTACATGAATAGATGAA
1 TAAACACTTTGATGTTTACAGACTAAAGAGATTAACTTCTCAAAGTTGTTACATGAATAGATGAA
**
1899793 AGTTTGAATAGGTG-TGAAATTAAG
66 AGAATGAATA-GTGCTGAAATTAAG
* * *
1899817 TAAACACTTTGATGTTTAC-GAACTAAAGAGATTAACTTAC-CAAAGTTGTTATATTAATGGATG
1 TAAACACTTTGATGTTTACAG-ACTAAAGAGATTAACTT-CTCAAAGTTGTTACATGAATAGATG
*
1899880 GAAGAATGAATAGTGCTGAAAT
64 AAAGAATGAATAGTGCTGAAAT
1899902 GTCTTGACTA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
88 4 0.05
89 69 0.93
90 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (89 bp):
TAAACACTTTGATGTTTACAGACTAAAGAGATTAACTTCTCAAAGTTGTTACATGAATAGATGAA
AGAATGAATAGTGCTGAAATTAAG
Found at i:1899963 original size:84 final size:84
Alignment explanation
Indices: 1899848--1900006 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
1899838 ACTAAAGAGA
* * * *
1899848 TTAACTTACCAAAGTTGTTATATTAATGGATGGAAGAAT-GAATAGTGCTGAAATGTCTT-GACT
1 TTAACTTACCAAAGTTGTTATAATAACGGATGGAAG-ATCGAATACTGCTGAAATGT-TTAAACT
1899911 AAACACTTTGATGTTAACACG
64 AAACACTTTGATGTTAACACG
* * * *
1899932 TTAACTTATCC-ATGTTGTTATAATAGCGGATGGAAGTTCGAATACTGTTGAAATGTTTAAACTA
1 TTAACTTA-CCAAAGTTGTTATAATAACGGATGGAAGATCGAATACTGCTGAAATGTTTAAACTA
1899996 AACACTTTGAT
65 AACACTTTGAT
1900007 TTTTGTAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 3 0.05
84 59 0.92
85 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (84 bp):
TTAACTTACCAAAGTTGTTATAATAACGGATGGAAGATCGAATACTGCTGAAATGTTTAAACTAA
ACACTTTGATGTTAACACG
Found at i:1900119 original size:3 final size:3
Alignment explanation
Indices: 1900111--1900140 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1900101 ATATATAGGT
1900111 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1900141 CAAAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1901864 original size:14 final size:14
Alignment explanation
Indices: 1901845--1901875 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1901835 GCATAATATA
1901845 TATATATATATAAG
1 TATATATATATAAG
*
1901859 TATATATATATATG
1 TATATATATATAAG
1901873 TAT
1 TAT
1901876 GTATCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TATATATATATAAG
Found at i:1904261 original size:19 final size:19
Alignment explanation
Indices: 1904237--1904273 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1904227 TAGCTCAAGA
1904237 AAATGACCCAAACCTCAAC
1 AAATGACCCAAACCTCAAC
1904256 AAATGACCCAAACCTCAA
1 AAATGACCCAAACCTCAA
1904274 GAAAATGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.35, G:0.05, T:0.11
Consensus pattern (19 bp):
AAATGACCCAAACCTCAAC
Found at i:1906612 original size:24 final size:24
Alignment explanation
Indices: 1906584--1906635 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1906574 CAAGATTTCA
* *
1906584 AAGAAATCTTTTCATAGTCTTATC
1 AAGAAATATATTCATAGTCTTATC
* *
1906608 AAGAAATATATTCCTGGTCTTATC
1 AAGAAATATATTCATAGTCTTATC
1906632 AAGA
1 AAGA
1906636 TATGCCAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (24 bp):
AAGAAATATATTCATAGTCTTATC
Found at i:1914612 original size:89 final size:90
Alignment explanation
Indices: 1914493--1914665 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 90
1914483 ATACACCCTT
*
1914493 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATTTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
* *
1914557 AATTAATTGGAATTTAATAATCATC
66 AATTAATTGAAATTAAATAATCATC
* * *
1914582 TTATATCCAAGTTATCCTAATCATATTAGGGATTTTATTATTTGAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1914647 AATTAATTGAAATTAAATA
66 AATTAATTGAAATTAAATA
1914666 TTCGGGATTA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 29 0.38
90 48 0.62
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.45
Consensus pattern (90 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
AATTAATTGAAATTAAATAATCATC
Found at i:1916128 original size:11 final size:11
Alignment explanation
Indices: 1916107--1916140 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1916097 AAATTTGAAG
1916107 AAAAGAAAAAAT
1 AAAA-AAAAAAT
1916119 AAAAAAAAAAT
1 AAAAAAAAAAT
1916130 AAAAATAAAAA
1 AAAAA-AAAAA
1916141 GGAGAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:1916168 original size:19 final size:20
Alignment explanation
Indices: 1916146--1916183 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1916136 AAAAAGGAGA
1916146 GAAAAAAGAGA-GAAAAAAG
1 GAAAAAAGAGAGGAAAAAAG
*
1916165 GAAAAAAGATAGGAAAAAA
1 GAAAAAAGAGAGGAAAAAA
1916184 TGGGGTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (20 bp):
GAAAAAAGAGAGGAAAAAAG
Found at i:1920753 original size:2 final size:2
Alignment explanation
Indices: 1920746--1920791 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
1920736 TAAATGCATG
* *
1920746 TA TA TA TA TA TA TA TA TA TA TA TA TCA TT TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
1920789 TA T
1 TA T
1920792 TTTTTATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1920799 original size:17 final size:17
Alignment explanation
Indices: 1920758--1920815 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 17
1920748 TATATATATA
*
1920758 TATATATATATATCATTT
1 TATATATAAATAT-ATTT
1920776 ATATATATAAATATATTT
1 -TATATATAAATATATTT
*
1920794 TTTATA-AAATAT-TTT
1 TATATATAAATATATTT
1920809 TATATAT
1 TATATAT
1920816 TATATTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 5 0.14
18 4 0.11
19 12 0.34
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATATAAATATATTT
Found at i:1920799 original size:19 final size:20
Alignment explanation
Indices: 1920746--1920815 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 20
1920736 TAAATGCATG
* *
1920746 TATATATATATATATATATA
1 TATATATTTATATATATAAA
1920766 TATATCATTTATATATATAAA
1 TATAT-ATTTATATATATAAA
1920787 TATAT-TTT-T-TATA-AAA
1 TATATATTTATATATATAAA
1920803 TAT-T-TTTATATAT
1 TATATATTTATATAT
1920816 TATATTTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.09
16 7 0.16
17 7 0.16
18 1 0.02
19 3 0.07
20 5 0.11
21 18 0.40
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATATTTATATATATAAA
Found at i:1920807 original size:14 final size:16
Alignment explanation
Indices: 1920746--1920823 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 16
1920736 TAAATGCATG
* * *
1920746 TATATATATATATATA
1 TATAAATATATTTTTA
*
1920762 TATATATATCATTTATATA
1 TATAAATAT-ATTT-T-TA
1920781 TATAAATATATTTTT-
1 TATAAATATATTTTTA
1920796 TATAAA-ATATTTTTA
1 TATAAATATATTTTTA
*
1920811 TAT-ATTATATTTT
1 TATAAATATATTTT
1920824 CATTTAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.17
15 16 0.30
16 10 0.19
17 4 0.08
18 4 0.08
19 10 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
TATAAATATATTTTTA
Found at i:1922653 original size:279 final size:277
Alignment explanation
Indices: 1922303--1923078 Score: 955
Period size: 279 Copynumber: 2.8 Consensus size: 277
1922293 ACAGACTGAG
* * *
1922303 GAGGTTAAATTATCCAA-TTGTTACATTAATGGATAGAAGTTTGAATAGT-ATTGAAATGTCTTA
1 GAGGTTAACTTATCCAAGTTGTTACATTAATGGATGGAAGTTTGAATA-TCGTTGAAATGTCTTA
** * * * * * *
1922366 ACTAAACACTTTGACATTTACGGACAAAAGAGGTTAACCTATGAAAATTTTAACAATAATGCATG
65 ACTAAACACTTTGATGTTTACGGACTAAAGAAGTTAACTTATCAAAGTTTT-ACATTAATG-ATG
* * *
1922431 AAAGTTTGAATAACGTTGAAATGTCTTAACTAAACACTTTGATATTTATGAAGTAAGGAGGTTAA
128 AAAGTTTGAATAACGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGAACTAAAGAGGTTAA
* * * *
1922496 ATTATCCAAGTTTTTACATTAATTGATGAAAGTTTGAATAGGGTTGAAATGACGTAAATAAACAC
193 CTTATCCAAGTTGTTACATTAATGGATGAAAGTTTGAATAGGATTGAAATGACGTAAATAAACAC
** *
1922561 TTTGATGGTTACAGACGAAA
258 TTTGACAGTTACAAACGAAA
* * *
1922581 GAGGTTAACTTATCCAAGTTGTTACAATAATGGATGGTAGTTTGAATATCGTTGAAATGTATTAA
1 GAGGTTAACTTATCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATCGTTGAAATGTCTTAA
* * * * * *
1922646 CTAAACACTTTGATGTTTATGTAGTAAGGATGTTAACTTATCAAAGTTGTCACATTAATGATTGA
66 CTAAACACTTTGATGTTTACGGACTAAAGAAGTTAACTTATCAAAGTT-TTACATTAATGA-TGA
* * * * * * * *
1922711 AAGTCTGAGTAGCGTTGAAATGTATTAACTAAACACTTTGATGTTTATGGATTAAAGAGTTTAGC
129 AAGTTTGAATAACGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGAACTAAAGAGGTTAAC
* * * * * * *
1922776 TTATCCAAGTTGTTAAATTAATGGGTGGAAGTTTGAATAGTATTGAAATGTCTTAACTAAACACT
194 TTATCCAAGTTGTTACATTAATGGATGAAAGTTTGAATAGGATTGAAATGACGTAAATAAACACT
* *
1922841 TTGACATTTACAAACTAAA
259 TTGACAGTTACAAACGAAA
* *
1922860 GAGGTTAACTTATTCAAGTTGTTACATTAATGGATGGAAGTTTGAATAACGTTGAAATGTCTTAA
1 GAGGTTAACTTATCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATCGTTGAAATGTCTTAA
* * *
1922925 CTAAACACTTTGATGTTTACGGACTAAAGAAGTTATCTTATTC-AAGTTGTTACATTAATGGTTA
66 CTAAACACTTTGATGTTTACGGACTAAAGAAGTTAACTTA-TCAAAGTT-TTACATTAATGATGA
* * **
1922989 GAAGTTTGAATAACGTTGGAATGTCTTAACTAAACACTTTTATGTTTACAAACTAAAGAGGTTAA
129 -AAGTTTGAATAACGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGAACTAAAGAGGTTAA
1923054 CTTATCCAAGTTGTTACATTAATGG
193 CTTATCCAAGTTGTTACATTAATGG
1923079 TTGGAATTTA
Statistics
Matches: 420, Mismatches: 72, Indels: 11
0.83 0.14 0.02
Matches are distributed among these distances:
278 20 0.05
279 397 0.95
280 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (277 bp):
GAGGTTAACTTATCCAAGTTGTTACATTAATGGATGGAAGTTTGAATATCGTTGAAATGTCTTAA
CTAAACACTTTGATGTTTACGGACTAAAGAAGTTAACTTATCAAAGTTTTACATTAATGATGAAA
GTTTGAATAACGTTGAAATGTCTTAACTAAACACTTTGATGTTTATGAACTAAAGAGGTTAACTT
ATCCAAGTTGTTACATTAATGGATGAAAGTTTGAATAGGATTGAAATGACGTAAATAAACACTTT
GACAGTTACAAACGAAA
Found at i:1923078 original size:93 final size:92
Alignment explanation
Indices: 1922288--1923100 Score: 860
Period size: 93 Copynumber: 8.8 Consensus size: 92
1922278 TTCTACAAGT
* * * * *
1922288 TGTTTACAGACTGAGGAGGTTAAATTATCCAA-TTGTTACATTAATGGATAGAAGTTTGAATAGT
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGAT-GAAGTTTGAATAGC
*
1922352 ATTGAAATGTCTTAACTAAACACTTTGA
65 GTTGAAATGTCTTAACTAAACACTTTGA
** * * ** * * * *
1922380 CATTTACGGACAAAAGAGGTTAACCTATGAAAATT-TTAACAATAATGCATGAAAGTTTGAATAA
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTT-ACATTAATGGATG-AAGTTTGAATAG
1922444 CGTTGAAATGTCTTAACTAAACACTTTGA
64 CGTTGAAATGTCTTAACTAAACACTTTGA
* * * * * * * * *
1922473 TATTTATGAAGTAAGGAGGTTAAATTATCCAAGTTTTTACATTAATTGATGAAAGTTTGAATAGG
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGATG-AAGTTTGAATAGC
* * *
1922538 GTTGAAATGACGTAAATAAACACTTTGA
65 GTTGAAATGTCTTAACTAAACACTTTGA
* * * * * *
1922566 TGGTTACAGACGAAAGAGGTTAACTTATCCAAGTTGTTACAATAATGGATGGTAGTTTGAATATC
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGAT-GAAGTTTGAATAGC
*
1922631 GTTGAAATGTATTAACTAAACACTTTGA
65 GTTGAAATGTCTTAACTAAACACTTTGA
* * * * * * * * *
1922659 TGTTTATGTAGTAAGGATGTTAACTTATCAAAGTTGTCACATTAAT-GATTGAAAGTCTGAGTAG
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGA-TG-AAGTTTGAATAG
*
1922723 CGTTGAAATGTATTAACTAAACACTTTGA
64 CGTTGAAATGTCTTAACTAAACACTTTGA
* * * * * * *
1922752 TGTTTATGGATTAAAGAGTTTAGCTTATCCAAGTTGTTAAATTAATGGGTGGAAGTTTGAATAGT
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGAT-GAAGTTTGAATAGC
*
1922817 ATTGAAATGTCTTAACTAAACACTTTGA
65 GTTGAAATGTCTTAACTAAACACTTTGA
** ** * *
1922845 CATTTACAAACTAAAGAGGTTAACTTATTCAAGTTGTTACATTAATGGATGGAAGTTTGAATAAC
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGAT-GAAGTTTGAATAGC
1922910 GTTGAAATGTCTTAACTAAACACTTTGA
65 GTTGAAATGTCTTAACTAAACACTTTGA
* * * * *
1922938 TGTTTACGGACTAAAGAAGTTATCTTATTCAAGTTGTTACATTAATGGTTAGAAGTTTGAATAAC
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGAT-GAAGTTTGAATAGC
* *
1923003 GTTGGAATGTCTTAACTAAACACTTTTA
65 GTTGAAATGTCTTAACTAAACACTTTGA
** * *
1923031 TGTTTACAAACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGTTGGAA-TTTAAAATAG
1 TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGAT-GAAGTTT-GAATAG
1923095 CGTTGA
64 CGTTGA
1923101 CTAAACATTT
Statistics
Matches: 595, Mismatches: 116, Indels: 19
0.82 0.16 0.03
Matches are distributed among these distances:
92 31 0.05
93 559 0.94
94 5 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (92 bp):
TGTTTACGGACTAAAGAGGTTAACTTATCCAAGTTGTTACATTAATGGATGAAGTTTGAATAGCG
TTGAAATGTCTTAACTAAACACTTTGA
Found at i:1928840 original size:90 final size:90
Alignment explanation
Indices: 1928687--1928864 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
1928677 CCTAACACAC
*
1928687 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
1928752 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
1928777 CCTTTTATATCCAAGTTACGCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1928842 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
1928865 TTCAAGATTA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:1928844 original size:22 final size:22
Alignment explanation
Indices: 1928819--1928889 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 22
1928809 GGGATTTTAT
1928819 TATTTCAAATTAATTAAATCTA
1 TATTTCAAATTAATTAAATCTA
1928841 TATTT--AATTAATTGAAAT-TA
1 TATTTCAAATTAATT-AAATCTA
* *
1928861 AATATTCAAGATT-ATTAAAACATA
1 TAT-TTCAA-ATTAATTAAATC-TA
1928885 TATTT
1 TATTT
1928890 AATTAACTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
20 12 0.31
21 6 0.15
22 8 0.21
23 6 0.15
24 7 0.18
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (22 bp):
TATTTCAAATTAATTAAATCTA
Found at i:1929765 original size:13 final size:13
Alignment explanation
Indices: 1929747--1929771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1929737 TTATCTTTCA
1929747 GTTTATGTTAAAT
1 GTTTATGTTAAAT
1929760 GTTTATGTTAAA
1 GTTTATGTTAAA
1929772 CACATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
GTTTATGTTAAAT
Found at i:1935884 original size:19 final size:19
Alignment explanation
Indices: 1935860--1935930 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
1935850 AATGCATTTT
1935860 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1935879 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1935898 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1935917 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1935931 TCATGCTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:1943359 original size:21 final size:21
Alignment explanation
Indices: 1943317--1943360 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1943307 ACCCCAGGAG
*
1943317 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1943338 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1943359 CT
1 CT
1943361 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1944515 original size:20 final size:20
Alignment explanation
Indices: 1944486--1944523 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1944476 TTTCAAAGTG
1944486 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1944506 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1944524 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1944594 original size:45 final size:46
Alignment explanation
Indices: 1944545--1944633 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
1944535 ACATCGAATA
* * *
1944545 CATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGTG
1 CATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTCAGTG
*
1944590 CATTTGATGCATTGATGCACAAGACCATGCATCAATGCACTCAG
1 CATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTCAG
1944634 GCTTTTTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (46 bp):
CATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTCAGTG
Found at i:1945812 original size:20 final size:20
Alignment explanation
Indices: 1945758--1945812 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1945748 CCGATTCAAG
*
1945758 TGGTATCGATACCAAGAGGA
1 TGGTATCGATACCATGAGGA
*
1945778 -GAGTATCTATACCATGAGGA
1 TG-GTATCGATACCATGAGGA
1945798 TGGTATCGATACCAT
1 TGGTATCGATACCAT
1945813 TGATCACAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (20 bp):
TGGTATCGATACCATGAGGA
Found at i:1946328 original size:55 final size:56
Alignment explanation
Indices: 1946205--1946328 Score: 137
Period size: 55 Copynumber: 2.2 Consensus size: 56
1946195 ATTATCAAAT
1946205 GGCACTGA-GTGTGCAAAAAGTTAAGAAATTCAAACTAAGTGTATGAATTTCCACATG
1 GGCACT-ATGTGTGCAAAAAG-TAAGAAATTCAAACTAAGTGTATGAATTTCCACATG
* * ** * **
1946262 GGCACTTTGTGTGCAAAAA-TGAGAAATTCATTCTACGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAAAGTAAGAAATTCAAACTAAGTGTATGAATTTCCACATG
1946317 GTG-ACTATGTGT
1 G-GCACTATGTGT
1946329 ACGAACTAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
55 39 0.68
56 1 0.02
57 17 0.30
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (56 bp):
GGCACTATGTGTGCAAAAAGTAAGAAATTCAAACTAAGTGTATGAATTTCCACATG
Found at i:1946626 original size:81 final size:81
Alignment explanation
Indices: 1946517--1947385 Score: 1065
Period size: 81 Copynumber: 10.8 Consensus size: 81
1946507 TGTTCTAAAA
* * * * * *
1946517 TAAATGATAAATAGCCTAACTGTGCATTTGACAAAAAGGTGTAAATTATGCCAGTTAGATGAACT
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA-T
*
1946582 -GTTAAAGACCATTGAG
65 GGTTAAAGACCGTTGAG
* * * *
1946598 TAAAAGATAAATTGCCTAGGTCTACATTTGGCAGAAAGTTGTCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
* *
1946663 GTTAAAGATCATTGAG
66 GTTAAAGACCGTTGAG
* *
1946679 TAAAAGATAAA-TGACCTAGCAGTGCATTTGG-AGAAAAGTGTCAATTATGCCAG-TAGATGAAT
1 TAAAAGATAAATTG-CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAT
* *
1946741 GGTTAAAGATCTTTGAG
65 GGTTAAAGACCGTTGAG
* * * * *
1946758 TAAAAAATAAATGGCCTAGCAGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAAATGAATG
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
*
1946823 GTTAAAGACCGTTCAG
66 GTTAAAGACCGTTGAG
* * *
1946839 TAGAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
*
1946904 ATTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * *
1946920 TAAACGATAAATGGCCTAGCTGTGAATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
1946985 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * *
1947001 TAAAAGATAAATGGCCTAGCTATGCATTTGGCAGAAAGGTGTCAATTATGCAAGTTAGATGAATG
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
*
1947066 GTTAAAGACTGTTGAG
66 GTTAAAGACCGTTGAG
* * ** * * *
1947082 TAAATGATAAATGGATTAGTTGTGCATTTGGTAGAAAGGTATCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
*
1947147 GTTAAAGATCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * *
1947163 TAAAAGATAAA-TGAACTAGCTGTGCCTTTGGCATAAATGTGTCAATTATGCCAGCTAGATG--C
1 TAAAAGATAAATTG-CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAT
* *
1947225 GATTACAGACCGTTGAG
65 GGTTAAAGACCGTTGAG
* * * *
1947242 TAAAAGATAAA-TGTCCTAGCTGTGCATTTAGCATAAAGGTGTCAATTATGCCAGTTAGGTGAAC
1 TAAAAGATAAATTG-CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAT
1947306 GGTTAAAGACCGTTGAG
65 GGTTAAAGACCGTTGAG
** * * *
1947323 TAAAAGATAAA-TGCCCTAATTGTGCATTTGGAAGACAA-GTGTCAATCATGCAAGTTAGATGAA
1 TAAAAGATAAATTG-CCTAGCTGTGCATTTGGCAGA-AAGGTGTCAATTATGCCAGTTAGATGAA
1947386 AAGTAAATGC
Statistics
Matches: 688, Mismatches: 91, Indels: 18
0.86 0.11 0.02
Matches are distributed among these distances:
79 120 0.17
80 46 0.07
81 520 0.76
82 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (81 bp):
TAAAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
GTTAAAGACCGTTGAG
Found at i:1947269 original size:403 final size:402
Alignment explanation
Indices: 1946517--1947385 Score: 1201
Period size: 403 Copynumber: 2.2 Consensus size: 402
1946507 TGTTCTAAAA
* * * * *
1946517 TAAATGATAAATAGCCTAACTGTGCATTTGACAAAAAGGTGTAAATTATGCCAGTTAGATGAACT
1 TAAAAGATAAATGGCCTAACTGTGCATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAACG
* * * *
1946582 GTTAAAGACCATTGAGTAAAAGATAAATTGCCTAGGTCTACATTTGGCAGAAAGTTGTCAATTAT
66 GTTAAAGACCATTGAGTAAAAGATAAATGGCCTAGCTATACATTTGGCAGAAAGGTGTCAATTAT
*
1946647 GCCAGTTAGATGAATGGTTAAAGATCATTGAGTAAAAGATAAATGACCTAGCAGTGCATTTGGAG
131 GCAAGTTAGATGAATGGTTAAAGATCATTGAGTAAAAGATAAATGACCTAGCAGTGCATTTGGAG
* * **
1946712 AAAAGTGTCAATTATGCCAGTAGATGAATGGTTAAAGATCTTTGAGTAAAAAATAAATGGCCTAG
196 AAAAGTATCAATTATGCCAGTAGATGAATGGTTAAAGATCGTTGAGTAAAAAATAAATGAACTAG
* * * * *
1946777 CAGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAAATGAATGGTTAAAGACCGTTCAGTAG
261 CAGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGCTAAATG-ACGATTAAAGACCGTTCAGTAA
* *
1946842 AAGATAAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATT
325 AAGATAAATTGCCTAGCTGTGCATTTAGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATT
1946907 AAAGACCGTTGAG
390 AAAGACCGTTGAG
* * *
1946920 TAAACGATAAATGGCCTAGCTGTGAATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAACTGTGCATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAACG
* *
1946985 GTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAGAAAGGTGTCAATTAT
66 GTTAAAGACCATTGAGTAAAAGATAAATGGCCTAGCTATACATTTGGCAGAAAGGTGTCAATTAT
* * * **
1947050 GCAAGTTAGATGAATGGTTAAAGA-CTGTTGAGTAAATGATAAATGGA-TTAGTTGTGCATTTGG
131 GCAAGTTAGATGAATGGTTAAAGATC-ATTGAGTAAAAGATAAAT-GACCTAGCAGTGCATTTGG
* *
1947113 TAGAAAGGTATCAATTATGCCAGTTAGATGAATGGTTAAAGATCGTTGAGTAAAAGATAAATGAA
194 -AGAAAAGTATCAATTATGCCAG-TAGATGAATGGTTAAAGATCGTTGAGTAAAAAATAAATGAA
* * * * * * *
1947178 CTAGCTGTGCCTTTGGCATAAATGTGTCAATTATGCCAGCTAGATG-CGATTACAGACCGTTGAG
257 CTAGCAGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGCTAAATGACGATTAAAGACCGTTCAG
* *
1947242 TAAAAGATAAA-TGTCCTAGCTGTGCATTTAGCATAAAGGTGTCAATTATGCCAGTTAGGTGAAC
322 TAAAAGATAAATTG-CCTAGCTGTGCATTTAGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAC
*
1947306 GGTTAAAGACCGTTGAG
386 GATTAAAGACCGTTGAG
* * * *
1947323 TAAAAGATAAATGCCCTAATTGTGCATTTGG-AAGACAA-GTGTCAATCATGCAAGTTAGATGAA
1 TAAAAGATAAATGGCCTAACTGTGCATTTGGCAA-A-AAGGTGTCAATTATGCCAGTTAGATGAA
1947386 AAGTAAATGC
Statistics
Matches: 410, Mismatches: 49, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
402 5 0.01
403 305 0.74
404 24 0.06
405 76 0.19
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (402 bp):
TAAAAGATAAATGGCCTAACTGTGCATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAACG
GTTAAAGACCATTGAGTAAAAGATAAATGGCCTAGCTATACATTTGGCAGAAAGGTGTCAATTAT
GCAAGTTAGATGAATGGTTAAAGATCATTGAGTAAAAGATAAATGACCTAGCAGTGCATTTGGAG
AAAAGTATCAATTATGCCAGTAGATGAATGGTTAAAGATCGTTGAGTAAAAAATAAATGAACTAG
CAGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGCTAAATGACGATTAAAGACCGTTCAGTAAA
AGATAAATTGCCTAGCTGTGCATTTAGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTA
AAGACCGTTGAG
Found at i:1947287 original size:322 final size:321
Alignment explanation
Indices: 1946517--1947385 Score: 1167
Period size: 322 Copynumber: 2.7 Consensus size: 321
1946507 TGTTCTAAAA
* * * * * * *
1946517 TAAATGATAAATAGCCTAACTGTGCATTTGACAAAAAGGTGTAAATTATGCCAGTTAGATGAACT
1 TAAAAGATAAATTGACTAGCTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATG-AC-
* * * * * *
1946582 G-TTAAAGACCATTGAGTAAAAGATAAAT-TGCCTAGGTCTACATTTGGCAGAAAGTTGTCAATT
64 GATTAAAGACCGTTGAGTAAAAGATAAATGT-CCTAGCTGTGCATTTGGCAAAAAGGTGTCAATT
* * *
1946645 ATGCCAGTTAGATGAATGGTTAAAGATCATTGAGTAAAAGATAAATGACCTAGC-AGTGCATTTG
128 ATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGACCTAGCTA-TGCATTTG
* *
1946709 GAGAAAAGTGTCAATTATGCCAG-TAGATGAATGGTTAAAGATCTTTGAGTAAAAAATAAATGGC
192 GAG-AAAGTGTCAATTATGCAAGTTAGATGAATGGTTAAAGATCTTTGAGTAAAAAATAAATGGA
*
1946773 CTAGCAGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAAATGAATGGTTAAAGACCGTTCA
256 CTAGCAGTGCATTTGGTAGAAAGGTATCAATTATGCCAGTTAAATGAATGGTTAAAGACCGTTCA
1946838 G
321 G
* * *
1946839 TAGAAGATAAATTGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATTGACTAGCTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATG-ACG
* * *
1946904 ATTAAAGACCGTTGAGTAAACGATAAATGGCCTAGCTGTGAATTTGGCAAAAAGGTGTCAATTAT
65 ATTAAAGACCGTTGAGTAAAAGATAAATGTCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTAT
*
1946969 GCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCA
130 GCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGACCTAGCTATGCATTTGG-A
** *
1947034 GAAAGGTGTCAATTATGCAAGTTAGATGAATGGTTAAAGA-CTGTTGAGTAAATGATAAATGGAT
194 GAAA-GTGTCAATTATGCAAGTTAGATGAATGGTTAAAGATCT-TTGAGTAAAAAATAAATGGAC
** * * *
1947098 TAGTTGTGCATTTGGTAGAAAGGTATCAATTATGCCAGTTAGATGAATGGTTAAAGATCGTTGAG
257 TAGCAGTGCATTTGGTAGAAAGGTATCAATTATGCCAGTTAAATGAATGGTTAAAGACCGTTCAG
* * *
1947163 TAAAAGATAAA-TGAACTAGCTGTGCCTTTGGCATAAATGTGTCAATTATGCCAGCTAGATG-CG
1 TAAAAGATAAATTG-ACTAGCTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGACG
* * *
1947226 ATTACAGACCGTTGAGTAAAAGATAAATGTCCTAGCTGTGCATTTAGCATAAAGGTGTCAATTAT
65 ATTAAAGACCGTTGAGTAAAAGATAAATGTCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTAT
* * ** *
1947291 GCCAGTTAGGTGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGCCCTAATTGTGCATTTGGAA
130 GCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGACCTAGCTATGCATTTGG-A
*
1947356 GACAAGTGTCAATCATGCAAGTTAGATGAA
194 GA-AAGTGTCAATTATGCAAGTTAGATGAA
1947386 AAGTAAATGC
Statistics
Matches: 488, Mismatches: 50, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
321 1 0.00
322 316 0.65
323 24 0.05
324 147 0.30
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (321 bp):
TAAAAGATAAATTGACTAGCTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGACGA
TTAAAGACCGTTGAGTAAAAGATAAATGTCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATG
CCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGACCTAGCTATGCATTTGGAGA
AAGTGTCAATTATGCAAGTTAGATGAATGGTTAAAGATCTTTGAGTAAAAAATAAATGGACTAGC
AGTGCATTTGGTAGAAAGGTATCAATTATGCCAGTTAAATGAATGGTTAAAGACCGTTCAG
Done.