Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397278.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_7.0, 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: 2181410
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.18
Warning! 1087948 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:1638165 original size:173 final size:168
Alignment explanation
Indices: 1637561--1638304 Score: 587
Period size: 172 Copynumber: 4.4 Consensus size: 168
1637551 TGTTTTCGAC
* * * * * * *
1637561 AGCCTTGTTAGTCGCTTGAGGTTGATTTATAATTTTTGTAA-TGATTTTAGATTGAATGTGTTTT
1 AGCCTTGTTACTCGCTTTAAGTGGATTTATAACTTTT-TAATTGATTTTAAATT-AAT-TTTTTT
* ** * * * * **
1637625 AC--ATTTTTCATTAAAAC-GCATCGTAATTTGATGTTTGCATTGAGAAACATCAAGCCAAA-GC
63 TCTTATTTTTGGTTAAAACAG-ATCATAATTTGATATTTGCATAGA-AAACATGAAGTAAAAGGC
* * * * * *
1637686 AATCCATTGACAAAAAAACTCCGTTTATAGTCACTTATGCTTTCAAA
126 -ATCCATTGACAAGAAAAGT-C-ATTAT-GTCACTCAAGCCTTCAAA
* * * * * * * *
1637733 AGTCTTGTTACTCGCTTTAAGTAGAATTATAGCTTTATAAATGATTTTAAATTAAATTTTTTT-A
1 AGCCTTGTTACTCGCTTTAAGTGGATTTATAACTTTTTAATTGATTTTAAATTAATTTTTTTTCT
* * * * * * * *
1637797 TAGTTTTGGTTAAAATAGATCATAATTTGATATTAGCATGGGAAACATGAAGCAAAGGGCACCCA
66 TATTTTTGGTTAAAACAGATCATAATTTGATATTTGCATAGAAAACATGAAGTAAAAGGCATCCA
* *
1637862 TTGACAAGAAAAGTC--CAT-TCACTCATA-CCTTTAAA
131 TTGACAAGAAAAGTCATTATGTCACTCA-AGCCTTCAAA
* * * * *
1637897 ACCCTTCTTACTAGCTTTAAGTGGATTTATAAGTTTTTTAATTGATTTTAAATTGATTTTGTTTT
1 AGCCTTGTTACTCGCTTTAAGTGGATTTATAA-CTTTTTAATTGATTTTAAATTAATTTT-TTTT
* * * * *
1637962 C--ATTTTTGATTAAAACATATCATAATTTGATATTTTCATTAGAAAACGTGTAGTAAAAGGCAT
64 CTTATTTTTGGTTAAAACAGATCATAATTTGATATTTGCA-TAGAAAACATGAAGTAAAAGGCAT
*
1638025 CCATTGACAAGAAAAGTCTATGTATAGTCGCTCAAGCCTTCAAA
128 CCATTGACAAGAAAAGTC-AT-TAT-GTCACTCAAGCCTTCAAA
* *
1638069 AGCCTTGTTCCTCGCTTTAAGTGGATTTATAAATTTTTAATTGATTTTAAATTAATTTTTTTTCT
1 AGCCTTGTTACTCGCTTTAAGTGGATTTATAACTTTTTAATTGATTTTAAATTAATTTTTTTTC-
* * * **
1638134 TTATTTTTGGTTATAACAGATCATAATTTGATGTTTGCACCA-AGAAACATGAAGTAAAAATCAT
65 TTATTTTTGGTTAAAACAGATCATAATTTGATATTTGCA-TAGA-AAACATGAAGTAAAAGGCAT
* * *
1638198 CCATTGATAAGAAAAGTCCATTATTGTCACTCATGCCTTCGAA
128 CCATTGACAAGAAAAGT-CATTA-TGTCACTCAAGCCTTCAAA
* * * * * * * *
1638241 AGTCTTATTGCTTGCTTGAGGTGGATTTCTAACTTTTTAATTGATTTTAAATTGATTTTTTTTC
1 AGCCTTGTTACTCGCTTTAAGTGGATTTATAACTTTTTAATTGATTTTAAATTAATTTTTTTTC
1638305 ATTTTTATTA
Statistics
Matches: 458, Mismatches: 91, Indels: 46
0.77 0.15 0.08
Matches are distributed among these distances:
164 37 0.08
165 53 0.12
166 41 0.09
169 1 0.00
170 40 0.09
171 63 0.14
172 154 0.34
173 68 0.15
174 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (168 bp):
AGCCTTGTTACTCGCTTTAAGTGGATTTATAACTTTTTAATTGATTTTAAATTAATTTTTTTTCT
TATTTTTGGTTAAAACAGATCATAATTTGATATTTGCATAGAAAACATGAAGTAAAAGGCATCCA
TTGACAAGAAAAGTCATTATGTCACTCAAGCCTTCAAA
Found at i:1641353 original size:86 final size:86
Alignment explanation
Indices: 1641207--1641375 Score: 232
Period size: 86 Copynumber: 2.0 Consensus size: 86
1641197 CTCATTTGAA
** ** * * *
1641207 GTGGATTTATAATTTTTTAAATGATTTTAGGTTGAATTCTTTTATATTTTTGGTTAAAACATATC
1 GTGGATTTATAACATTTTAAATGATTTTAAATTGAATTCTTTTACATTATTGCTTAAAACATATC
1641272 ATAATTTGATGTTTGCATTAG
66 ATAATTTGATGTTTGCATTAG
* * *
1641293 GTGGATTTATAACATTTTAAATGA-TTTAAATTGATTTTTTTCTACATTATTGCTTTAAACATAT
1 GTGGATTTATAACATTTTAAATGATTTTAAATTGAATTCTTT-TACATTATTGCTTAAAACATAT
1641357 CATAATTTGATGTTTGCAT
65 CATAATTTGATGTTTGCAT
1641376 AAGGAAAACT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 13 0.18
86 59 0.82
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (86 bp):
GTGGATTTATAACATTTTAAATGATTTTAAATTGAATTCTTTTACATTATTGCTTAAAACATATC
ATAATTTGATGTTTGCATTAG
Found at i:1651992 original size:167 final size:157
Alignment explanation
Indices: 1651728--1652042 Score: 310
Period size: 167 Copynumber: 1.9 Consensus size: 157
1651718 ATAAAAGTCT
* ** * *
1651728 ATTTATAGTCACTTATACCTTCAAAAGCCTTGTTACTTGCCTTAAGTGGATTTGTAACTTTTTAA
1 ATTTATAGTCACTTATACCTTCAAAAGCATTGTTACTCACCTTAAATGGATTTATAACTTTTTAA
* ** *
1651793 ATAATTTTCAATTGAATTTCTTTTGTATTTTTGATTAAAATGGATCATAATTAGATGTCTGCATT
66 ATAATTTTAAATTGAATTTCTTTTCAATTTTTGATTAAAATGGATCATAATTAGATGTCTGCATC
*
1651858 AGGAAACATGAAGCAAAAACCACNNNNNNNNNNGTCC
131 AAGAAACATGAAGCAAAAACCAC----------GTCC
* * * * * *
1651895 ATTTATAGTCACTTATGCCTTCTAAAGCATTTTTACTCACTTTAAATGGGTTTATACCTTTTTTA
1 ATTTATAGTCACTTATACCTTCAAAAGCATTGTTACTCACCTTAAATGGATTTATAAC-TTTTTA
* * * * * *
1651960 AATGATTTTAAATT-AATTT-TGTTTCAATTTTTGGTTACAATGGGTCATAATTTGATGTTTGCA
65 AATAATTTTAAATTGAATTTCT-TTTCAATTTTTGATTAAAATGGATCATAATTAGATGTCTGCA
1652023 TCAAGAAACATGAAGCAAAA
129 TCAAGAAACATGAAGCAAAA
1652043 GCCATCCATT
Statistics
Matches: 124, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
166 1 0.01
167 105 0.85
168 18 0.15
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.40
Consensus pattern (157 bp):
ATTTATAGTCACTTATACCTTCAAAAGCATTGTTACTCACCTTAAATGGATTTATAACTTTTTAA
ATAATTTTAAATTGAATTTCTTTTCAATTTTTGATTAAAATGGATCATAATTAGATGTCTGCATC
AAGAAACATGAAGCAAAAACCACGTCC
Found at i:1653201 original size:169 final size:171
Alignment explanation
Indices: 1652891--1653492 Score: 474
Period size: 169 Copynumber: 3.5 Consensus size: 171
1652881 CTTAGAATGT
* *
1652891 CTTGTTACTCACTTTAAGTGAATTTATAAC-TTTCAAATAATTTTGAATTGGATTTTTTTTTATA
1 CTTGTTACTCACTTTAAGTGGATTTATAACTTTTCAAATAATTTTGAATT-GA-TTTTTTTAATA
* * * * ** ** *
1652955 TTTTTAGTTAAAACATATCATAATTTGATGGTTTCAATGGGAAACATGAAGTGAAGGCCATCCAT
64 TTTTTAGTTAAAACAGATCATAATTTGATGGTTTCAATAGAAAAAATGAAGCAAAAACCACCCAT
* *
1653020 TGACAAGAAAAG-TCTATTTATAGTCGCTCATACCTTCAAAACC
129 TAACAAGAAAAGTTC-ATTTATAGTCACTCATACCTTCAAAACC
*
1653063 CTTGTTACTCACTTTAAGTGGATTTATAACTTTTCAAATAATTTTTAATT-A-TTTTTTAATATT
1 CTTGTTACTCACTTTAAGTGGATTTATAACTTTTCAAATAATTTTGAATTGATTTTTTTAATATT
* * *
1653126 TTTTGTTAAAACAGATCTTAATTTG-TTGTTTGC-ATCAGAAAAAATGAAGCAAAAACCACCCAT
66 TTTAGTTAAAACAGATCATAATTTGATGGTTT-CAAT-AGAAAAAATGAAGCAAAAACCACCCAT
* * ** *
1653189 TAACAAGAAAAGTTCATTTGTAGTCACTCATATCTTTGAAAGC
129 TAACAAGAAAAGTTCATTTATAGTCACTCATACCTTCAAAACC
* * * * * *
1653232 ATTGTTACT-AGCTTTAAGTGGATTTATAGCTTTTTAACTTAA-TGTAAATTGATTTTTTTAAT-
1 CTTGTTACTCA-CTTTAAGTGGATTTATAACTTTTCAA-ATAATTTTGAATTGATTTTTTTAATA
* * * * * ** * * ** * * * * *
1653294 CTTTCA-CT-AAACGGGTCATAATTTGAT-GTTTACGTTGGGAAGCATAAAGCGAAAGCTATCCA
64 TTTTTAGTTAAAACAGATCATAATTTGATGGTTT-CAATAGAAAAAATGAAGCAAAAACCACCCA
* ** * * * *
1653356 TTGACAAGGGAAGTTTATTTATAGTTACTCATAACTTCAAAAGC
128 TTAACAAGAAAAGTTCATTTATAGTCACTCATACCTTCAAAACC
* ** * * * * *
1653400 CTTCTTACTCGTTTTAAATGGATTTATAACTTTTTAAATGATGTTAAATTGAATTGTTTTT-ATA
1 CTTGTTACTCACTTTAAGTGGATTTATAACTTTTCAAATAATTTTGAATTG-ATT-TTTTTAATA
* *
1653464 CTTTTAGTTAAAACATATCATAATTTGAT
64 TTTTTAGTTAAAACAGATCATAATTTGAT
1653493 ATTTGCACTA
Statistics
Matches: 343, Mismatches: 70, Indels: 34
0.77 0.16 0.08
Matches are distributed among these distances:
167 2 0.01
168 116 0.34
169 132 0.38
170 19 0.06
171 11 0.03
172 45 0.13
173 18 0.05
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (171 bp):
CTTGTTACTCACTTTAAGTGGATTTATAACTTTTCAAATAATTTTGAATTGATTTTTTTAATATT
TTTAGTTAAAACAGATCATAATTTGATGGTTTCAATAGAAAAAATGAAGCAAAAACCACCCATTA
ACAAGAAAAGTTCATTTATAGTCACTCATACCTTCAAAACC
Found at i:1672445 original size:172 final size:171
Alignment explanation
Indices: 1672110--1672446 Score: 374
Period size: 172 Copynumber: 2.0 Consensus size: 171
1672100 NNNNNNNNAG
* ** * *
1672110 ATGGCTTTCGTTACATATTTCTCTGTGCAAACATCAAATTATGATCTATTTTAACTAAAAATGTA
1 ATGGCTTTCCTTACATATTTCTCTGTGCAAACATCAAATTATGATCTACATTAACCAAAAATATA
* * * * * *
1672175 AAAAAATTTAATTAAAAATTATTTAAAAAGTTATAAATTCTCTTAAATCGAGTAACAAGGCTTTT
66 AAAAAATTCAATTAAAAATCATTTAAAAAGTTATAAATCCTCTTAAATCAAGTAACAAAGATTTT
* * * *
1672240 GAAGGTATGAGTGACTATAAATAAACTTTTCTTGTCAAAAA
131 AAAGGCATGAGTGACAATAAATAAACCTTTCTTGTCAAAAA
* * *
1672281 ATGGCTTTCACTT-CATGTTTCT-TGATGCAAACATTAAATTATGATCTACATTAACCAGAAATA
1 ATGGCTTTC-CTTACATATTTCTCTG-TGCAAACATCAAATTATGATCTACATTAACCAAAAATA
* * * * * *
1672344 TAAAAACTATTCAATTCAAAATCGTTTAAAAAGTTATAAATCCTTTTAAGGT-AAGTAATAAAGA
64 TAAAAA-AATTCAATTAAAAATCATTTAAAAAGTTATAAATCCTCTTAA-ATCAAGTAACAAAGA
* **
1672408 TTTTAAAGGCATGAGTGACAATGAATGGACCTTTCTTGT
127 TTTTAAAGGCATGAGTGACAATAAATAAACCTTTCTTGT
1672447 TAATTGTAAC
Statistics
Matches: 135, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
170 2 0.01
171 55 0.41
172 77 0.57
173 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (171 bp):
ATGGCTTTCCTTACATATTTCTCTGTGCAAACATCAAATTATGATCTACATTAACCAAAAATATA
AAAAAATTCAATTAAAAATCATTTAAAAAGTTATAAATCCTCTTAAATCAAGTAACAAAGATTTT
AAAGGCATGAGTGACAATAAATAAACCTTTCTTGTCAAAAA
Found at i:1675570 original size:25 final size:26
Alignment explanation
Indices: 1675541--1675592 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1675531 TCCTTTTCGT
* *
1675541 TTTTTTTTCCTTTTTTCCATT-CTCTC
1 TTTTCTTT-CTTTCTTCCATTCCTCTC
*
1675567 TTTTCTTTCTTTCTTCCTTTCCTCTC
1 TTTTCTTTCTTTCTTCCATTCCTCTC
1675593 CTTCCCTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTCTTTCTTTCTTCCATTCCTCTC
Found at i:1677910 original size:18 final size:19
Alignment explanation
Indices: 1677878--1677921 Score: 72
Period size: 18 Copynumber: 2.3 Consensus size: 19
1677868 NNTTTAAAAA
1677878 TATTTTATTCATAAAAATAT
1 TATTTTATT-ATAAAAATAT
1677898 TATTTTATT-TAAAAATAT
1 TATTTTATTATAAAAATAT
1677916 TATTTT
1 TATTTT
1677922 TAACTATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 15 0.62
20 9 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTATTATAAAAATAT
Found at i:1677923 original size:15 final size:16
Alignment explanation
Indices: 1677870--1677924 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 16
1677860 NNNNNNNNNN
1677870 TTTAAAAATATT-TTA
1 TTTAAAAATATTATTA
1677885 TTCATAAAAATATTATTTTA
1 TT--TAAAAATATTA--TTA
1677905 TTTAAAAATATTATT-
1 TTTAAAAATATTATTA
1677920 TTTAA
1 TTTAA
1677925 CTATCACCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 10 0.29
18 11 0.31
20 5 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAAATATTATTA
Found at i:1679762 original size:18 final size:20
Alignment explanation
Indices: 1679739--1679777 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1679729 TAAAAAAATT
*
1679739 AATTTA-AAAT-TATTTAAA
1 AATTTATAAATCTACTTAAA
1679757 AATTTATAAATCTACTTAAA
1 AATTTATAAATCTACTTAAA
1679777 A
1 A
1679778 CGAGTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTATAAATCTACTTAAA
Found at i:1680135 original size:172 final size:170
Alignment explanation
Indices: 1679690--1680866 Score: 957
Period size: 172 Copynumber: 6.9 Consensus size: 170
1679680 ACATTTCTCG
* * * * *
1679690 ATGCAAACATCAAATCATGATTTGTTTTAATAAAAAATAT-AAAAAAATT-AATTTAAAATTATT
1 ATGCAAACATCAAATTATGATATG-TTTAACAAAAAATGTAAAAAAAATTAAATTTAAAATGATT
* * ** ** *
1679753 TAAAAATTTATAAATCTACTTAAAACGAGTAACAAGGCTTTCGATGGTATGAAAGACTATAAATC
65 TAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTC-AAAGTATGAGTGACTATAAATG
* * * * * *
1679818 AACTTTTCTAGTGAATGGATGGCTTT-GCATCACATTTCCCA
129 GACTTTTCTTGTCAATGGATGGCTTTCGCTTCACGTTTCCTA
* * * * * * * *
1679859 ATGCAAACATTAAATTGTGTTCTACTTTAACTAAAAATGTAAAAGAAATTAAA-TTAACATGATT
1 ATGCAAACATCAAATTATGATAT-GTTTAACAAAAAATGTAAAAAAAATTAAATTTAAAATGATT
* * * ** * *
1679923 TAAAAAGTTATAAAT-TCAATTAAAGTGGGTAATTAGGCTTTGCAAACTATGAGTGACTGTAAAT
65 TAAAAAGTTATAAATCT-ACTTAAAGCGAGTAACAAGGCTTT-CAAAGTATGAGTGACTATAAAT
* *
1679987 GGACTTTTCTTATCAATGGATGGCTTTCGCTTCACGCTTCCTA
128 GGACTTTTCTTGTCAATGGATGGCTTTCGCTTCACGTTTCCTA
* * * * *
1680030 ATG-AAGACATCAAATTATAATATGTTTAAACCAAAAATATAAAAAAAATTAAATTAAAAATCAT
1 ATGCAA-ACATCAAATTATGATATGTTT-AACAAAAAATGTAAAAAAAATTAAATTTAAAATGAT
* * * * * *
1680094 TTAAAAAGCTATAAATCCACTTGAAGCGAGTAACAAGGCTTTCGAAGGTATGAGTGTCTGTAAAT
64 TTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTC-AAAGTATGAGTGACTATAAAT
* * * * *
1680159 GGACTTTTCTTGTCAATGGATCGCTTTTGCTTCATGTTTCTTG
128 GGACTTTTCTTGTCAATGGATGGCTTTCGCTTCACGTTTCCTA
* * * * * * * *
1680202 ATACAAATATTC-AATTATGATCTATATTAACTAAAAATGTAAAAACAATTCAATTCAAAATGAT
1 ATGCAAACA-TCAAATTATGATATGT-TTAACAAAAAATGTAAAAAAAATTAAATTTAAAATGAT
* * * * *
1680266 TTAAAAAGTTATAAATCCT-CTTAAAGCAAGTAATAAGGTTTTCAAAGGTAT-AG-GCAGTCATG
64 TTAAAAAGTTATAAAT-CTACTTAAAGCGAGTAACAAGGCTTTCAAA-GTATGAGTG-ACT-ATA
* * * * * * * *
1680328 TATGGAATTTTTTTGAT-AATAGATAGTTTTCGTTTCACATTT-CTCA
125 AATGGACTTTTCTTG-TCAATGGATGGCTTTCGCTTCACGTTTCCT-A
** * * * * *
1680374 ATATAAACATTAAATTATGATCTGTTTTAATAAAAAATGTAAAAAAAATT-AATTTAAAGTGAAT
1 ATGCAAACATCAAATTATGATATG-TTTAACAAAAAATGTAAAAAAAATTAAATTTAAAATGATT
* **
1680438 TAAAAAGTTATAAATCTACTTAAAGCAAGTAACAAGGCTTTCAAAGGTAAAAGTGACTATAAATG
65 TAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCAAA-GTATGAGTGACTATAAATG
* * ** * *
1680503 GACTTTTCTTGCCGATATATGGCTTTCGCTTCTCGTTTCCCA
129 GACTTTTCTTGTCAATGGATGGCTTTCGCTTCACGTTTCCTA
* * * * *
1680545 AAGCAAACATCAAATTATGATATGTTTCAACAAAAAATGTAAAAAAACTTCAATTCAAAATCATT
1 ATGCAAACATCAAATTATGATATGTTT-AACAAAAAATGTAAAAAAAATTAAATTTAAAATGATT
* * * * * * * *
1680610 TAAAAAGTTATAAATCTACTTAAAACGAGTAATATGACTTTTGAAAATATGAGTGACCACAAATG
65 TAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGC-TTTCAAAGTATGAGTGACTATAAATG
* * *
1680675 GACTTTTCTTGTTAATGGATGACTCTT-GCTTCACGTTTCCCTC
129 GACTTTTCTTGTCAATGGATGGCT-TTCGCTTCACGTTT-CCTA
* * * *
1680718 A-GCAAACATCAAATTATGATATGTTTTAAGC-AAAACTATAAAAAAAATTAAATTTTAAATTAT
1 ATGCAAACATCAAATTATGATATG-TTTAA-CAAAAAATGTAAAAAAAATTAAATTTAAAATGAT
* * ** * *
1680781 TTAAAAATTTATAAATCTTCTTAAAGTAAGTAACAAGGCTTTTGAAAATCATGAGTGACTATAAA
64 TTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGC-TTTCAAAGT-ATGAGTGACTATAAA
*
1680846 TAGG-CTTTTGTTGTCAATGGA
127 T-GGACTTTTCTTGTCAATGGA
1680867 GGACTTTTGT
Statistics
Matches: 797, Mismatches: 175, Indels: 68
0.77 0.17 0.07
Matches are distributed among these distances:
169 31 0.04
170 97 0.12
171 186 0.23
172 427 0.54
173 54 0.07
174 2 0.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
ATGCAAACATCAAATTATGATATGTTTAACAAAAAATGTAAAAAAAATTAAATTTAAAATGATTT
AAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCAAAGTATGAGTGACTATAAATGGA
CTTTTCTTGTCAATGGATGGCTTTCGCTTCACGTTTCCTA
Found at i:1680453 original size:343 final size:337
Alignment explanation
Indices: 1679676--1680875 Score: 1041
Period size: 343 Copynumber: 3.5 Consensus size: 337
1679666 GATTTTTTTA
* * * *
1679676 CTTCACATTTCTCGATGCAAACATCAAATCATGATTTGTTTTAATAAAAAATAT-AAAAAAATTA
1 CTTCACATTTCTCAAT-AAAACATCAAATTATGATATGTTTTAATAAAAAATATAAAAAAAATTA
* * * *
1679740 ATTTAAAATTATTTAAAAATTTATAAATCTACTTAAAACGAGTAACAAGGCTTTCGATGGTATGA
65 ATTTAAAATCATTTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCGAAGGTATGA
** ** * * * ** *
1679805 AAGACTATAAATCAACTTTTCTAGTGAATGGATGGC-TTTGCATCACATTTCCCAATGCAAACAT
130 GTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCATGTTT-CCAATACAAACAT
* * * * *
1679869 TAAATTGTGTTCTACTTTAACTAAAAATGTAAAAGAAATTAAATT-AACATGATTTAAAAAGTTA
194 TCAATTATGATCTA-TTTAACTAAAAATGTAAAA-AAATTCAATTCAAAATGATTTAAAAAGTTA
* * * * *
1679933 TAAAT-TCAATTAAAGTGGGTAATTAGGCTTTGCAAACTATGAGTGACTGTAAATGGACTTTTCT
257 TAAATCTC--TTAAAGCGAGTAATAAGGCTTTGCAAACTATGAGTCACTGT-AATGGAATTTTCT
* *
1679997 TATCAATGGATGGCTTTCG
319 TATCAATAGATAGCTTTCG
** * * * **
1680016 CTTCACGCTTC-CTAATGAAGACATCAAATTATAATATGTTTAAACCAAAAATATAAAAAAAATT
1 CTTCACATTTCTC-AAT-AAAACATCAAATTATGATATGTTTTAATAAAAAATATAAAAAAAATT
* * * *
1680080 AAATTAAAAATCATTTAAAAAGCTATAAATCCACTTGAAGCGAGTAACAAGGCTTTCGAAGGTAT
64 -AATTTAAAATCATTTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCGAAGGTAT
* * * ** *
1680145 GAGTGTCTGTAAATGGACTTTTCTTGTCAATGGATCGCTTTTGCTTCATGTTTCTTGATACAAAT
128 GAGTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCATGTTTC-CAATACAAAC
1680210 ATTCAATTATGATCTATATTAACTAAAAATGTAAAAACAATTCAATTCAAAATGATTTAAAAAGT
192 ATTCAATTATGATCTAT-TTAACTAAAAATGTAAAAA-AATTCAATTCAAAATGATTTAAAAAGT
* * *
1680275 TATAAATCCTCTTAAAGCAAGTAATAAGG-TTTTCAAAGGTATAGGCAGTCA-TGT-ATGGAATT
255 TATAAAT-CTCTTAAAGCGAGTAATAAGGCTTTGCAAA-CTAT--G-AGTCACTGTAATGGAATT
* *
1680337 TTTTTGAT-AATAGATAGTTTTCG
315 TTCTT-ATCAATAGATAGCTTTCG
* * * *
1680360 TTTCACATTTCTCAATATAAACATTAAATTATGATCTGTTTTAATAAAAAATGTAAAAAAAATTA
1 CTTCACATTTCTCAATA-AAACATCAAATTATGATATGTTTTAATAAAAAATATAAAAAAAATTA
* * * * * **
1680425 ATTTAAAGTGAATTAAAAAGTTATAAATCTACTTAAAGCAAGTAACAAGGCTTTCAAAGGTAAAA
65 ATTTAAAATCATTTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCGAAGGTATGA
* * ** *
1680490 GTGACTATAAATGGACTTTTCTTGCCGATATATGGCTTTCGCTTC-TCGTTTCCCAA-AGCAAAC
130 GTGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCAT-GTTT-CCAATA-CAAAC
* * * *
1680553 A-TCAAATTATGATATGTTTCAACAAAAAATGTAAAAAAACTTCAATTCAAAATCATTTAAAAAG
192 ATTC-AATTATGATCTATTT-AACTAAAAATGTAAAAAAA-TTCAATTCAAAATGATTTAAAAAG
* * * * * *** *
1680617 TTATAAATCTACTTAAAACGAGTAATATGACTTTTG-AAAATATGAGTGACCACAAATGGACTTT
254 TTATAAATCT-CTTAAAGCGAGTAATAAGGC-TTTGCAAACTATGAGTCA-CTGTAATGGAATTT
* * *
1680681 TCTTGTTAATGGAT-GACTCTT-G
316 TCTTATCAATAGATAG-CT-TTCG
* ** ** *
1680703 CTTCACGTTTCCCTC-AGCAAACATCAAATTATGATATGTTTTAAGCAAAACTATAAAAAAAATT
1 CTTCACATTT--CTCAATAAAACATCAAATTATGATATGTTTTAATAAAAAATATAAAAAAAATT
* * * * ** * **
1680767 AAATTTTAAATTATTTAAAAATTTATAAATCTTCTTAAAGTAAGTAACAAGGCTTTTGAAAATCA
64 -AATTTAAAATCATTTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCGAAGGT-A
*
1680832 TGAGTGACTATAAATAGG-CTTTTGTTGTCAATGGA-GGACTTTTG
127 TGAGTGACTATAAAT-GGACTTTTCTTGTCAATGGATGG-CTTTTG
1680876 TCTTAACCAA
Statistics
Matches: 689, Mismatches: 133, Indels: 71
0.77 0.15 0.08
Matches are distributed among these distances:
339 1 0.00
340 45 0.07
341 10 0.01
342 100 0.15
343 309 0.45
344 172 0.25
345 40 0.06
346 8 0.01
347 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (337 bp):
CTTCACATTTCTCAATAAAACATCAAATTATGATATGTTTTAATAAAAAATATAAAAAAAATTAA
TTTAAAATCATTTAAAAAGTTATAAATCTACTTAAAGCGAGTAACAAGGCTTTCGAAGGTATGAG
TGACTATAAATGGACTTTTCTTGTCAATGGATGGCTTTTGCTTCATGTTTCCAATACAAACATTC
AATTATGATCTATTTAACTAAAAATGTAAAAAAATTCAATTCAAAATGATTTAAAAAGTTATAAA
TCTCTTAAAGCGAGTAATAAGGCTTTGCAAACTATGAGTCACTGTAATGGAATTTTCTTATCAAT
AGATAGCTTTCG
Found at i:1706936 original size:18 final size:19
Alignment explanation
Indices: 1706910--1706957 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1706900 GTAATGGCTG
*
1706910 AAAAGAATATTTTA-GAAT
1 AAAATAATATTTTATGAAT
* *
1706928 AAAATAATAATTTATTAAT
1 AAAATAATATTTTATGAAT
1706947 AAAATAATATT
1 AAAATAATATT
1706958 AAAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTTATGAAT
Found at i:1708114 original size:18 final size:19
Alignment explanation
Indices: 1708071--1708119 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1708061 TTAATATTTT
*
1708071 AATAATATTTTATTCATAAA
1 AATATTATTTTATT-ATAAA
1708091 AATATTATTTTATT-TAAA
1 AATATTATTTTATTATAAA
* *
1708109 ACTATTGTTTT
1 AATATTATTTT
1708120 TACCTATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTATAAA
Found at i:1715337 original size:18 final size:19
Alignment explanation
Indices: 1715298--1715346 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1715288 TTAATATTTT
*
1715298 AATAATATTTTATTCATAAA
1 AATATTATTTTATT-ATAAA
1715318 AATATTATTTTATT-TAAA
1 AATATTATTTTATTATAAA
*
1715336 AATATTGTTTT
1 AATATTATTTT
1715347 TACCTATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTATAAA
Found at i:1746718 original size:170 final size:171
Alignment explanation
Indices: 1746434--1747508 Score: 770
Period size: 171 Copynumber: 6.3 Consensus size: 171
1746424 CTTTCGAACA
* * ** *
1746434 CATGAGCGACTATAAATAGAC-TTTCTTTGTTAATCAATAGCTTTTGCTT--CATGTTTCTTGAT
1 CATGAGTGACTATAAATAGACTTTTC-TTGTCAATGGATGGCTTTTGCTTCACAT-TTTC-T-AT
* * * * *
1746496 GCAAATATCAAATTATGATCCGTTTTAACCAAAAATGAAAAAAAAA-TCAATTTAAAATCAGTTA
62 GAAAACATCAAATTATGATCTGTTTTAAACAAAAATGAAAAAAAAATTCAATTTAAAATCATTTA
* * * * * *
1746560 CAAAGTTATCAATACACTTAAAGTGAGTAACAAGGCTTTTAAAAG
127 AAAAGTTATAAATCCACTTAAAGTGAGCAACAAGGCTTTTGAAGG
* * * * * *
1746605 CTTGAGCGACTATAAATGGACTTTTCTTGTCAATAGATGGCGTTGGCTTCACATTTTCTATGAAA
1 CATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTCACATTTTCTATGAAA
* * * * *
1746670 ACATCAAATTATGATATGTTTTAAATACAAAT-ATAAGAAAATTCAATTTAAAATCATTTCAAAA
66 ACATCAAATTATGATCTGTTTTAAACAAAAATGAAAAAAAAATTCAATTTAAAATCATTT-AAAA
* *
1746734 A-TTATAAATCCACTTCAAA-CGAACAACAAGGCTTTTGAAGG
130 AGTTATAAATCCACTT-AAAGTGAGCAACAAGGCTTTTGAAGG
** * * * * * **
1746775 CATGAACGAATATAAATAGACCTTTCTTCTCAATGGATGGTTTTTGC-T-ACATGGTTTCCAACA
1 CATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTCACAT--TTTCTATGA
* * * * *
1746838 TAAATATCAAATTATGATTTGTTTT-AACAAAAAATGAAAACAAAAGTCAATTTAAAATCAATT-
64 -AAACATCAAATTATGATCTGTTTTAAAC-AAAAATGAAAAAAAAATTCAATTTAAAATCATTTA
* * * * *
1746901 AAAAGTTATGAGTCCACTTCAAGCT-AGAAAAAAGGCTTTTGAAGG
127 AAAAGTTATAAATCCACTTAAAG-TGAGCAACAAGGCTTTTGAAGG
* * * * * ** *
1746946 CATGAATGACTATAAATAGACCTTTCTTCTCAATGGATAGCTTTAGCTTCATGTTTTCTAGTGCA
1 CATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTCACATTTTCTA-TGAA
* * * * *
1747011 AACATCAAAATATAATCTGTTGTAAATAAAAATGTAAAAAAAAAATTCAATTCAAAATCATTTAA
65 AACATCAAATTATGATCTGTTTTAAACAAAAATG--AAAAAAAAATTCAATTTAAAATCATTTAA
* * * * * *
1747076 AAAGTTACAAATCCACTTAGAG-GAAGTAATAAGGCTTTCGAAAG
128 AAAGTTATAAATCCACTTAAAGTG-AGCAACAAGGCTTTTGAAGG
* * * * * ** * *
1747120 CATGAGTGACTACAAATATACTTTTTTTGTCAATGGATGACTTTCGCTTCATGTTTTCCAATGCA
1 CATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTCACATTTT-CTATGAA
* * * * * * *
1747185 AACATTAAATCATGAT-TCATTTTAACCAAAAATGTAAGAAAAGAATTTAATTGAAAATCATTTA
65 AACATCAAATTATGATCT-GTTTTAAACAAAAATG-AA-AAAAAAATTCAATTTAAAATCATTTA
* * * *
1747249 AAAAGTTATAAATCCTCTTAATGTGAGCAACAAGGCTTTCGTAGG
127 AAAAGTTATAAATCCACTTAAAGTGAGCAACAAGGCTTTTGAAGG
* * *
1747294 CATAAGTGACTATAAAT-GAACTTTTCTTGTTAATGGAGGGCTTTTGCTTCACA-TTTCTAGATG
1 CATGAGTGACTATAAATAG-ACTTTTCTTGTCAATGGATGGCTTTTGCTTCACATTTTCT--ATG
* * ** * * * **
1747357 CAGACATCAAGCTATGATCCGTTTTAACCAAAATTG--GTAAAAATTCAATTCTAAAATCATTT-
63 AAAACATCAAATTATGATCTGTTTTAAACAAAAATGAAAAAAAAATTCAATT-TAAAATCATTTA
* * * * * *
1747419 ATAAGATTATAAAACCAATTAAAGCGA-CAAACTAGGCTTTCGAAGG
127 AAAAG-TTATAAATCCACTTAAAGTGAGC-AACAAGGCTTTTGAAGG
* * * * * *
1747465 AATGAGAGACTATAACT-GAACTTTTCCTATCGATGGATGGCTTT
1 CATGAGTGACTATAAATAG-ACTTTTCTTGTCAATGGATGGCTTT
1747509 CACTTCATAT
Statistics
Matches: 715, Mismatches: 155, Indels: 68
0.76 0.17 0.07
Matches are distributed among these distances:
168 4 0.01
169 8 0.01
170 142 0.20
171 249 0.35
172 35 0.05
173 34 0.05
174 240 0.34
175 3 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (171 bp):
CATGAGTGACTATAAATAGACTTTTCTTGTCAATGGATGGCTTTTGCTTCACATTTTCTATGAAA
ACATCAAATTATGATCTGTTTTAAACAAAAATGAAAAAAAAATTCAATTTAAAATCATTTAAAAA
GTTATAAATCCACTTAAAGTGAGCAACAAGGCTTTTGAAGG
Found at i:1776266 original size:171 final size:169
Alignment explanation
Indices: 1775759--1776907 Score: 850
Period size: 171 Copynumber: 6.7 Consensus size: 169
1775749 NNNNNNNNNN
** * *
1775759 GTAACAAGGAGTTCGAAGGCATGAGCGACTATAAATGGACTTTTCTTGTCAATGAATGGCTTTTG
1 GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAATGGAC-TTTCTTGTCAATGGATGGCTTTTG
* * *
1775824 CTTTATGTTTCTT-GATGCAAATATCAAATTATGATCTTTTTAACTAAAA-ATACAAAACAAATC
65 CTTCATGTTT-TTCAATGCAAATATCAAATTATGATCTTTTTAACCAAAATATA-AAAA-AAATC
* *
1775887 CAATTTAAAATCATTTAAAATA-TTATAAATCTACTTAAAGCGA
127 TAATTTAAAATCATTTAAAA-AGTTATAAATCCACTTAAAGCGA
** * * ** * * * * * * *
1775930 GTAACAAGATTTTTGAAGGGATGA-ACAATAATAAATAGAGTTCTCTTGTTAATGAATGACCTTT
1 GTAACAAGGCTTTCGAAGGCATGAGTGACT-ATAAATGGACTT-TCTTGTCAATGGATGGCTTTT
* * * * * * * *
1775994 GCTTCATGTTTTGT-AATGAAAATATCAAAATATGATCTATTTGACGAAAATTTAGAACAAATCT
64 GCTTCATGTTTT-TCAATGCAAATATCAAATTATGATCTTTTTAACCAAAATATAAAAAAAATCT
* *
1776058 AA-TTGAAATCATTTAAAATGTTATAAATCCACTTAAAGCGA
128 AATTTAAAATCATTTAAAAAGTTATAAATCCACTTAAAGCGA
* * * * * * * *
1776099 GTAATAAGGCTTTCAAAAGTATTAGTGACAATAAATGGAGTTGTCTTGTCAATGGATTGCTTTTG
1 GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTT-TCTTGTCAATGGATGGCTTTTG
* * * * * * *
1776164 CTTCATATTTTTCGATACAAACATCAAATTATGATATGTTTTGACCAAAATGTAAAAAAAATCTA
65 CTTCATGTTTTTCAATGCAAATATCAAATTATGATCT-TTTTAACCAAAATATAAAAAAAATCTA
* *
1776229 ATTCAAAATCATTTAAAAAGTTATAAATCCACTTAAAGTGA
129 ATTTAAAATCATTTAAAAAGTTATAAATCCACTTAAAGCGA
* * * * ** * *
1776270 GTAACAAGGCTTTCGAATGCATG-TTTACTATAACTAAACTTTTTCTATCAATGGATGGCTTTTG
1 GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTCT-TGTCAATGGATGGCTTTTG
* * * * *
1776334 CTTTATGTTTCTCAATGCAAATATCAAATTATGATCCATTTTAATCTAAAATGTAAAAAAAAAT-
65 CTTCATGTTTTTCAATGCAAATATCAAATTATGAT-CTTTTTAA-CCAAAATAT-AAAAAAAATC
* * * ** * *
1776398 TATTTTAAAACCATTTAAAATGTTATAGGTCCACTTGAAGCAA
127 TAATTTAAAATCATTTAAAAAGTTATAAATCCACTTAAAGCGA
* * * * ** *
1776441 GTAACAAAGCTTTTGAAGGTATGAGTGACTATAAACT-AACTTTGCTCATCAATGGATGACTTTT
1 GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAA-TGGACTTT-CTTGTCAATGGATGGCTTTT
** * * * *
1776505 GCTTCACATTTTCCAATGCAAATATTAAATTATAATTTCTTTTAACCAAAA-ATATAAAAAAATC
64 GCTTCATGTTTTTCAATGCAAATATCAAATTATGATCT-TTTTAACCAAAATATA-AAAAAAATC
** * * **
1776569 -AATTTAAAATCATTTAAAATCTCATAAACCCACTTAAAATGA
127 TAATTTAAAATCATTTAAAAAGTTATAAATCCACTTAAAGCGA
* * * *
1776611 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAATGAACTTTTCTTGTCAATGGATGGCCTTCG
1 GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAATGGAC-TTTCTTGTCAATGGATGGCTTTTG
** ** * * * * * * *
1776676 CTTCACATTTCCCATTGCAAACATAAAATTATGATCTATCTTAACCAAAAATATAAAACAATTTT
65 CTTCATGTTTTTCAATGCAAATATCAAATTATGATCT-TTTTAACC-AAAATATAAAAAAAATCT
* * * * * *
1776741 ATTTTAAAACCTTTTGAAATA-TTATAAATCCACTTGAAGTGA
128 AATTTAAAATCATTT-AAAAAGTTATAAATCCACTTAAAGCGA
** * * * * * * *
1776783 GTAGTAAGGCTTTCAAAGGCATAAGTAACGATAAACT-GAGTTTCCTTTTCAATGGATGGGTTTT
1 GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAA-TGGACTTT-CTTGTCAATGGATGGCTTTT
* * * * * *
1776847 GCTTCAGGTTTCTT-GATGCAAACATCAAATTATGATCTGTTCAACCAAAAACATAAAAAAA
64 GCTTCATGTTT-TTCAATGCAAATATCAAATTATGATCTTTTTAACC-AAAATATAAAAAAA
1776908 TTCAATNNNN
Statistics
Matches: 769, Mismatches: 181, Indels: 56
0.76 0.18 0.06
Matches are distributed among these distances:
168 1 0.00
169 111 0.14
170 227 0.30
171 241 0.31
172 183 0.24
173 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (169 bp):
GTAACAAGGCTTTCGAAGGCATGAGTGACTATAAATGGACTTTCTTGTCAATGGATGGCTTTTGC
TTCATGTTTTTCAATGCAAATATCAAATTATGATCTTTTTAACCAAAATATAAAAAAAATCTAAT
TTAAAATCATTTAAAAAGTTATAAATCCACTTAAAGCGA
Found at i:1776524 original size:172 final size:171
Alignment explanation
Indices: 1775759--1776883 Score: 656
Period size: 170 Copynumber: 6.6 Consensus size: 171
1775749 NNNNNNNNNN
** * * ** ** *
1775759 GTAACAAGGAGTTCGAAGGCATGAGCGACTATAAA-TGGACTTTTCTTGTCAATGAATGGCTTTT
1 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAAC-TTTCTCATCAATGGATGGCTTTT
* ** * * * *
1775823 GCTT--TATGTTTCTTGATGCAAATATCAAATTATGAT-CTTTTTAACTAAAA-ATACAAAACAA
65 GCTTCACAT-TTTC-CAATGCAAACATCAAATTATGATCCATTTTAACCAAAATATA-AAAAAAA
* * * * *
1775884 ATCCAATTTAAAATCATTTAAAATATTATAAATCTACTTAAAGCGA
127 AT-TAATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
** * * ** * * * ** * * * *
1775930 GTAACAAGATTTTTGAAGGGATGA-ACAATAATAAA-TAGAGTTCTCTTGTTAATGAATGACCTT
1 GTAACAAGGCTTTCGAAGGAATGAGTGACT-ATAAACTAAACTT-TCTCATCAATGGATGGCTTT
** ** * * * * * * * * *
1775993 TGCTTCATGTTTTGTAATGAAAATATCAAAATATGATCTA-TTTGACGAAAAT-TTAGAACAAAT
64 TGCTTCACATTTTCCAATGCAAACATCAAATTATGATCCATTTTAACCAAAATATAAAAAAAAAT
* * *
1776056 CTAA-TTGAAATCATTTAAAATGTTATAAATCCACTTAAAGCGA
129 -TAATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
* * * * * * ** * ** *
1776099 GTAATAAGGCTTTCAAAAGTATTAGTGACAATAAA-TGGAGTTGTCTTGTCAATGGATTGCTTTT
1 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAACTT-TCTCATCAATGGATGGCTTTT
* * * * *** * *
1776163 GCTTCATATTTTTCGATACAAACATCAAATTATGATATGTTTTGACCAAAATGT-AAAAAAAATC
65 GCTTCACATTTTCCAATGCAAACATCAAATTATGATCCATTTTAACCAAAATATAAAAAAAAAT-
* * *
1776227 TAATTCAAAATCATTTAAAAAGTTATAAATCCACTTAAAGTGA
129 TAATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
* * * * *
1776270 GTAACAAGGCTTTCGAATGCATG-TTTACTAT-AACTAAACTTTTTCTATCAATGGATGGCTTTT
1 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAACTTTCTC-ATCAATGGATGGCTTTT
* * * *
1776333 GCTT--TATGTTTCTCAATGCAAATATCAAATTATGATCCATTTTAATCTAAAATGTAAAAAAAA
65 GCTTCACAT-TTTC-CAATGCAAACATCAAATTATGATCCATTTTAA-CCAAAATATAAAAAAAA
* ** * **
1776396 ATTATTTTAAAACCATTTAAAATGTTATAGGTCCACTTGAAGCAA
127 ATTAATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
* * * *
1776441 GTAACAAAGCTTTTGAAGGTATGAGTGACTATAAACT-AACTTTGCTCATCAATGGATGACTTTT
1 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAACTTT-CTCATCAATGGATGGCTTTT
* * * * *
1776505 GCTTCACATTTTCCAATGCAAATATTAAATTATAATTTC-TTTTAACCAAAA-ATATAAAAAAAT
65 GCTTCACATTTTCCAATGCAAACATCAAATTATGA-TCCATTTTAACCAAAATATAAAAAAAAAT
* * * * * *
1776568 CAATTTAAAATCATTTAAAATCTCATAAACCCACTTAAAATGA
129 TAATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
* ** * *
1776611 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAA-TGAACTTTTCTTGTCAATGGATGGCCTTC
1 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAAC-TTTCTCATCAATGGATGGCTTTT
* * * * * * **
1776675 GCTTCACATTTCCCATTGCAAACATAAAATTATGATCTATCTTAACCAAAAATATAAAACAATTT
65 GCTTCACATTTTCCAATGCAAACATCAAATTATGATCCATTTTAACC-AAAATATAAAAAAAAAT
* * * * *
1776740 TATTTTAAAACCTTTTGAAATATTATAAATCCACTTGAAGTGA
129 TAATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
** * * * * * * * ** *
1776783 GTAGTAAGGCTTTCAAAGGCATAAGTAACGATAAACT-GAGTTTCCTTTTCAATGGATGGGTTTT
1 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAACTTT-CTCATCAATGGATGGCTTTT
** **
1776847 GCTTCA-GGTTTCTTGATGCAAACATCAAATTATGATC
65 GCTTCACATTTTC-CAATGCAAACATCAAATTATGATC
1776884 TGTTCAACCA
Statistics
Matches: 750, Mismatches: 174, Indels: 59
0.76 0.18 0.06
Matches are distributed among these distances:
168 3 0.00
169 117 0.16
170 219 0.29
171 212 0.28
172 182 0.24
173 15 0.02
174 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (171 bp):
GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAACTAAACTTTCTCATCAATGGATGGCTTTTG
CTTCACATTTTCCAATGCAAACATCAAATTATGATCCATTTTAACCAAAATATAAAAAAAAATTA
ATTTAAAACCATTTAAAATGTTATAAATCCACTTAAAGTGA
Found at i:1776868 original size:342 final size:335
Alignment explanation
Indices: 1775800--1776913 Score: 1002
Period size: 342 Copynumber: 3.3 Consensus size: 335
1775790 TAAATGGACT
* * * * *
1775800 TTTCTTGTCAATGAATGGCTTTTGCTTTATGTTTCTTGATGCAAATATCAAATTATGA-TCTTTT
1 TTTCTTATCAATGGATGGCTTTTGCTTCATATTT-TTGATGCAAACATCAAATTATGATTC-TTT
* * * *
1775864 TAACTAAAAATACAAAACAAATCCAATTTAAAATCATTTAAAATATTATAAATCTACTTAAAGCG
64 TAACCAAAAATATAAAA-AAAT-CAATTTAAAATCATTTAAAATATTATAAATCCACTTAAAGTG
** * * * * * * * * *
1775929 AGTAACAAGATTTTTGAAGGGATGAACAATAATAAATAGAGTTCTCTTGTTAATGAATGACCTTT
127 AGTAACAAGGCTTTCGAAGGAATGATCACT-ATAAATA-ACTTTTCTTGTCAATGGATGGCCTTT
*** * * * * * *
1775994 GCTTCATGTTTTGTAATGAAAATATCAAAA-TATGATCTATTTGACGAAAATTTAGAACAAATCT
190 GCTTCATGTTTCCCAATGCAAATAT-AAAATTATGATCTATTTAACAAAAATATAAAACAAATTT
* * * * * *
1776058 A-ATTGAAATCATTTAAAATGTTATAAATCCACTTAAAGCGAGTAATAAGGCTTTCAAAAGTATT
254 ATTTTAAAACCATTTAAAATGTTATAAATCCACTTGAAGCGAGTAATAAGGCTTTCAAAGGTATA
1776122 AGTGACAATAAA-TGGAG
319 AGTGACAATAAACT-GAG
* * * *
1776139 TTGTCTTGTCAATGGATTGCTTTTGCTTCATATTTTTCGATACAAACATCAAATTATGATATGTT
1 TT-TCTTATCAATGGATGGCTTTTGCTTCATATTTTT-GATGCAAACATCAAATTATGAT-TCTT
* * *
1776204 TTGACC-AAAATGTAAAAAAAATCTAATTCAAAATCATTTAAAA-AGTTATAAATCCACTTAAAG
63 TTAACCAAAAATAT-AAAAAAATC-AATTTAAAATCATTTAAAATA-TTATAAATCCACTTAAAG
* * * * * * *
1776267 TGAGTAACAAGGCTTTCGAATGCATGTTTACTATAACTAAACTTTT-TCTATCAATGGATGGCTT
125 TGAGTAACAAGGCTTTCGAAGGAATGATCACTATAAAT-AACTTTTCT-TGTCAATGGATGGCCT
* * * * * * *
1776331 TTGCTTTATGTTTCTCAATGCAAATATCAAATTATGATCCATTTTAATCTAAAATGTAAAAAAAA
188 TTGCTTCATGTTTCCCAATGCAAATATAAAATTATGATCTA-TTTAA-CAAAAATATAAAACAAA
* ** * * * **
1776396 ATTATTTTAAAACCATTTAAAATGTTATAGGTCCACTTGAAGCAAGTAACAAAGCTTTTGAAGGT
251 TTTATTTTAAAACCATTTAAAATGTTATAAATCCACTTGAAGCGAGTAATAAGGCTTTCAAAGGT
* * * *
1776461 ATGAGTGACTATAAACTAAC
316 ATAAGTGACAATAAACTGAG
* * * ** * * *
1776481 TTTGCTCATCAATGGATGACTTTTGCTTCACATTTTCCAATGCAAATATTAAATTATAATTTCTT
1 TTT-CTTATCAATGGATGGCTTTTGCTTCATATTTT-TGATGCAAACATCAAATTATGA-TTCTT
* * * *
1776546 TTAACCAAAAATATAAAAAAATCAATTTAAAATCATTTAAAATCTCATAAACCCACTTAAAATGA
63 TTAACCAAAAATATAAAAAAATCAATTTAAAATCATTTAAAATATTATAAATCCACTTAAAGTGA
* *
1776611 GTAACAAGGCTTTCGAAGGAATGAGTGACTATAAATGAACTTTTCTTGTCAATGGATGGCCTTCG
128 GTAACAAGGCTTTCGAAGGAATGA-TCACTATAAAT-AACTTTTCTTGTCAATGGATGGCCTTTG
** * * *
1776676 CTTCACATTTCCCATTGCAAACATAAAATTATGATCTATCTTAACCAAAAATATAAAACAATTTT
191 CTTCATGTTTCCCAATGCAAATATAAAATTATGATCTAT-TTAA-CAAAAATATAAAACAAATTT
* * * * * *
1776741 ATTTTAAAACCTTTTGAAATATTATAAATCCACTTGAAGTGAGTAGTAAGGCTTTCAAAGGCATA
254 ATTTTAAAACCATTTAAAATGTTATAAATCCACTTGAAGCGAGTAATAAGGCTTTCAAAGGTATA
* *
1776806 AGTAACGATAAACTGAG
319 AGTGACAATAAACTGAG
* * **
1776823 TTTCCTTTTCAATGGATGGGTTTTGCTTCAGGTTTCTTGATGCAAACATCAAATTATGA-TCTGT
1 TTT-CTTATCAATGGATGGCTTTTGCTTCATATTT-TTGATGCAAACATCAAATTATGATTCT-T
* *
1776887 TCAACCAAAAACATAAAAAAATTCAAT
63 TTAACCAAAAATATAAAAAAA-TCAAT
1776914 NNNNNNNNNN
Statistics
Matches: 615, Mismatches: 135, Indels: 47
0.77 0.17 0.06
Matches are distributed among these distances:
338 4 0.01
339 56 0.09
340 121 0.20
341 104 0.17
342 320 0.52
343 10 0.02
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (335 bp):
TTTCTTATCAATGGATGGCTTTTGCTTCATATTTTTGATGCAAACATCAAATTATGATTCTTTTA
ACCAAAAATATAAAAAAATCAATTTAAAATCATTTAAAATATTATAAATCCACTTAAAGTGAGTA
ACAAGGCTTTCGAAGGAATGATCACTATAAATAACTTTTCTTGTCAATGGATGGCCTTTGCTTCA
TGTTTCCCAATGCAAATATAAAATTATGATCTATTTAACAAAAATATAAAACAAATTTATTTTAA
AACCATTTAAAATGTTATAAATCCACTTGAAGCGAGTAATAAGGCTTTCAAAGGTATAAGTGACA
ATAAACTGAG
Found at i:1792882 original size:15 final size:17
Alignment explanation
Indices: 1792852--1792888 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1792842 GATTTATAAC
1792852 ATTTTAAATGGTTTTAA
1 ATTTTAAATGGTTTTAA
*
1792869 ATTTT-AAT-GTTTTAC
1 ATTTTAAATGGTTTTAA
1792884 ATTTT
1 ATTTT
1792889 CGTCAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (17 bp):
ATTTTAAATGGTTTTAA
Found at i:1796215 original size:170 final size:169
Alignment explanation
Indices: 1795920--1796711 Score: 655
Period size: 171 Copynumber: 4.6 Consensus size: 169
1795910 TTAGTCATGT
* * * * * *
1795920 CTTTAAAAGCCTTGTTACTTGCTTTACGTGGATTTAT-AATATTTTAAATGGTTTTAAATTTCAA
1 CTTTAAAAGCCTTATTACTTGCTTTAAGTAGATTTATAAAT-TTTTAAATGATTTTAGA-TTGAA
* * * **
1795984 TGTTTTTATATTTTTGTTAAAACAGATCATAATTTGATAATTGCATTGGG-AACTGTGAAGCAAA
64 TTTTTTTATTTTTTTATTAAAACAGATCATAATTTGATGTTTGCATTGGGAAACTGTGAAGCAAA
*
1796048 AGCCATATATTGATAGAAAAAGTCTAGTTATTGTCACATATGC
129 AGCAAT-TATTGATAGAAAAAGTCTAGTTATTGTCAC-TATGC
* * * * *
1796091 CTTTGAAAGCCTTATTACTTACTTTAAGTTAG-TTCATAAATTTTTAAATGACTTTAAATT-AGA
1 CTTTAAAAGCCTTATTACTTGCTTTAAG-TAGATTTATAAATTTTTAAATGATTTTAGATTGA-A
* *
1796154 TTTTTTTATTTTTTTATTAAAACATATCATAATTTGATGTTTGCTTTGGGAAACT-TGAAGCAAA
64 TTTTTTTATTTTTTTATTAAAACAGATCATAATTTGATGTTTGCATTGGGAAACTGTGAAGCAAA
* * * * *
1796218 AGTAATCCATTGACA-ATAAAACTCT-GTTTATTGTCACTCATAC
129 AGCAAT-TATTGATAGA-AAAAGTCTAG-TTATTGTCACT-ATGC
* *
1796261 CTTTAAAAGCCTTATTGCTTGCTTTAAGTAGATTTATAAGTTTTTAAATGATTTTAGATTGAATT
1 CTTTAAAAGCCTTATTACTTGCTTTAAGTAGATTTATAAATTTTTAAATGATTTTAGATTGAA-T
* * *
1796326 TTTTTTACATTTTTTATTAAAACATATCATAATTTGATGTTTGCATTGGGAAA-TGTGAAGTAAA
65 TTTTTTA-TTTTTTTATTAAAACAGATCATAATTTGATGTTTGCATTGGGAAACTGTGAAGCAAA
* * * * *
1796390 GGCTATTCATTGATAAGAAAATG-C-ATTTATAGTCACTTATGC
129 AGCAATT-ATTGAT-AGAAAAAGTCTAGTTATTGTCAC-TATGC
* * * *
1796432 CTTAAAAAGCCTTGTTACTCGTTTTAAGTAGATTTATAAATTTTTAAATGATTTTAGATTGAATT
1 CTTTAAAAGCCTTATTACTTGCTTTAAGTAGATTTATAAATTTTTAAATGATTTTAGATTGAATT
* * * * * *
1796497 TTTTTATATATTTTTAGTTAAAATAGATCATAACTTGATG-TTGCATT-AGAAACAG-AAAGTAA
66 TTTTTAT-T-TTTTTA-TTAAAACAGATCATAATTTGATGTTTGCATTGGGAAACTGTGAAGCAA
* * * * * * ** * *
1796559 AAGCCATCCATTAACA-AGAAAAGTCCATTTACAGTCGCTCATCC
128 AAGCAAT-TATTGATAGA-AAAAGTCTAGTTATTGTCACT-ATGC
* * * * * * *
1796603 CTTCAAAAGCCTTGTTACTCGCTCTAAGT-GCTTTTATAAATTTTTCAATGATTTTAAATTG-AT
1 CTTTAAAAGCCTTATTACTTGCTTTAAGTAG-ATTTATAAATTTTTAAATGATTTTAGATTGAAT
* ** * *
1796666 TTTGCTTA-CATTTTAGTTAAAACATATCATAATTTGTTGTTTGCAT
65 TTT-TTTATTTTTTTA-TTAAAACAGATCATAATTTGATGTTTGCAT
1796712 CAAGAAATAT
Statistics
Matches: 515, Mismatches: 77, Indels: 60
0.79 0.12 0.09
Matches are distributed among these distances:
168 26 0.05
169 18 0.03
170 171 0.33
171 209 0.41
172 86 0.17
173 4 0.01
174 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (169 bp):
CTTTAAAAGCCTTATTACTTGCTTTAAGTAGATTTATAAATTTTTAAATGATTTTAGATTGAATT
TTTTTATTTTTTTATTAAAACAGATCATAATTTGATGTTTGCATTGGGAAACTGTGAAGCAAAAG
CAATTATTGATAGAAAAAGTCTAGTTATTGTCACTATGC
Found at i:1796480 original size:171 final size:170
Alignment explanation
Indices: 1795903--1796786 Score: 803
Period size: 170 Copynumber: 5.2 Consensus size: 170
1795893 ACAAACTCAT
* * * * *
1795903 TTTATAGTTAGTCATGTCTTTAAAAGCCTTGTTACTTGCTTTACGTGGATTTAT-AATATTTTAA
1 TTTATAGTCACTCATGCCTTTAAAAGCCTTGTTACTTGCTTTAAGTAGATTTATAAAT-TTTTAA
* * * * * * **
1795967 ATGGTTTTAAATTTCAATGTTTTTATA-TTTTTGTTAAAACAGATCATAATTTGATAATTGCATT
65 ATGATTTTAAA-TTGAATTTTTTTACATTTTTTATTAAAACATATCATAATTTGATGTTTGCATT
* *
1796031 GGGAACTGTGAAGCAAAAGCCATAT-ATTGA-TAGAAAAAGTCTA
129 GGGAAATGTGAAGCAAAAGCCAT-TCATTGACAAG-AAAA-TCTA
* * * * * *
1796074 GTTATTGTCACAT-ATGCCTTTGAAAGCCTTATTACTTACTTTAAGTTAG-TTCATAAATTTTTA
1 TTTATAGTCAC-TCATGCCTTTAAAAGCCTTGTTACTTGCTTTAAG-TAGATTTATAAATTTTTA
* * *
1796137 AATGACTTTAAATT-AGATTTTTTTA-TTTTTTTATTAAAACATATCATAATTTGATGTTTGCTT
64 AATGATTTTAAATTGA-ATTTTTTTACATTTTTTATTAAAACATATCATAATTTGATGTTTGCAT
** * * *
1796200 TGGGAAACT-TGAAGCAAAAGTAATCCATTGACAATAAAACTCTG
128 TGGGAAA-TGTGAAGCAAAAGCCATTCATTGACAAGAAAA-TCTA
* * * * *
1796244 TTTATTGTCACTCATACCTTTAAAAGCCTTATTGCTTGCTTTAAGTAGATTTATAAGTTTTTAAA
1 TTTATAGTCACTCATGCCTTTAAAAGCCTTGTTACTTGCTTTAAGTAGATTTATAAATTTTTAAA
*
1796309 TGATTTTAGATTGAATTTTTTTTACATTTTTTATTAAAACATATCATAATTTGATGTTTGCATTG
66 TGATTTTAAATTGAA-TTTTTTTACATTTTTTATTAAAACATATCATAATTTGATGTTTGCATTG
* * * *
1796374 GGAAATGTGAAGTAAAGGCTATTCATTGATAAGAAAATGC-A
130 GGAAATGTGAAGCAAAAGCCATTCATTGACAAGAAAAT-CTA
* * * *
1796415 TTTATAGTCACTTATGCCTTAAAAAGCCTTGTTACTCGTTTTAAGTAGATTTATAAATTTTTAAA
1 TTTATAGTCACTCATGCCTTTAAAAGCCTTGTTACTTGCTTTAAGTAGATTTATAAATTTTTAAA
* * * * *
1796480 TGATTTTAGATTGAATTTTTTTATATATTTTTAGTTAAAATAGATCATAACTTGATG-TTGCATT
66 TGATTTTAAATTGAATTTTTTTACAT-TTTTTA-TTAAAACATATCATAATTTGATGTTTGCATT
* * * * * * *
1796544 -AGAAACAG-AAAGTAAAAGCCATCCATTAACAAGAAAAGTCCA
129 GGGAAA-TGTGAAGCAAAAGCCATTCATTGACAAGAAAA-TCTA
* * * * * * * *
1796586 TTTACAGTCGCTCATCCCTTCAAAAGCCTTGTTACTCGCTCTAAGT-GCTTTTATAAATTTTTCA
1 TTTATAGTCACTCATGCCTTTAAAAGCCTTGTTACTTGCTTTAAGTAG-ATTTATAAATTTTTAA
* *
1796650 ATGATTTTAAATTG-ATTTTGCTTACA--TTTTAGTTAAAACATATCATAATTTGTTGTTTGCAT
65 ATGATTTTAAATTGAATTTT-TTTACATTTTTTA-TTAAAACATATCATAATTTGATGTTTGCAT
*** * * **
1796712 CAAGAAATATGAAGCAAAGGCCATTCATTGACCGGAAAAATCTA
128 TGGGAAATGTGAAGCAAAAGCCATTCATTGACAAG-AAAATCTA
* *
1796756 TTTATAGTCACTCATTCCTTTGAAAGCCTTG
1 TTTATAGTCACTCATGCCTTTAAAAGCCTTG
1796787 ACACTCGCAT
Statistics
Matches: 587, Mismatches: 100, Indels: 53
0.79 0.14 0.07
Matches are distributed among these distances:
168 25 0.04
169 11 0.02
170 231 0.39
171 227 0.39
172 93 0.16
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (170 bp):
TTTATAGTCACTCATGCCTTTAAAAGCCTTGTTACTTGCTTTAAGTAGATTTATAAATTTTTAAA
TGATTTTAAATTGAATTTTTTTACATTTTTTATTAAAACATATCATAATTTGATGTTTGCATTGG
GAAATGTGAAGCAAAAGCCATTCATTGACAAGAAAATCTA
Found at i:1816925 original size:171 final size:160
Alignment explanation
Indices: 1816748--1817056 Score: 316
Period size: 171 Copynumber: 1.9 Consensus size: 160
1816738 NNNNNNAATA
* * * *
1816748 ACAAGAAAA-TTTCATTTATAACCACACATGCCTTTGAAAGCTTTGTTACTCACCTTAAGTGGAT
1 ACAAGAAAAGTCT-ATTTATAACCACACATGCCTATGAAAGCCTTGTTACTCACATTAAGTGGAT
* *
1816812 TTATAACTTTTTAAATAATTTTAAATTAAATTTTTTTATA-TTGTTAGTTAAAACATATCATAAT
65 CTATAACTTTTTAAATAATTTTAAATTAAATTTTTTTA-AGTTGTTA-TTAAAACAGATCATAAT
*
1816876 TTGATGTTTGTGTTGGGAAATGTGNNNNNNNNNNCATCCATTG
128 TTGATATTTGTGTTGGGAAATGTG----------CATCCATTG
* * * ** *
1816919 ACAAGAAAAGTCTATTTATAATCACTCATGCCTATGTAAGCCTTGTTACTCGTATTAAGTGGGTC
1 ACAAGAAAAGTCTATTTATAACCACACATGCCTATGAAAGCCTTGTTACTCACATTAAGTGGATC
* * * * *
1816984 TATAACTTTTTAAATGATTTTAAATTGATTTTTTTTAAGTTTTTTATTAAAATAGATCATAATTT
66 TATAACTTTTTAAATAATTTTAAATTAAATTTTTTTAAG-TTGTTATTAAAACAGATCATAATTT
1817049 GATATTTG
130 GATATTTG
1817057 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
170 1 0.01
171 109 0.93
172 7 0.06
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.42
Consensus pattern (160 bp):
ACAAGAAAAGTCTATTTATAACCACACATGCCTATGAAAGCCTTGTTACTCACATTAAGTGGATC
TATAACTTTTTAAATAATTTTAAATTAAATTTTTTTAAGTTGTTATTAAAACAGATCATAATTTG
ATATTTGTGTTGGGAAATGTGCATCCATTG
Found at i:1825350 original size:20 final size:18
Alignment explanation
Indices: 1825325--1825362 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
1825315 TGTTACTTAC
1825325 TTTAAATGGATTTATAAATT
1 TTTAAATGG-TTT-TAAATT
1825345 TTTAAATGGTTTTAAATT
1 TTTAAATGGTTTTAAATT
1825363 GATTTTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTAAATGGTTTTAAATT
Found at i:1829560 original size:21 final size:20
Alignment explanation
Indices: 1829526--1829564 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1829516 GAAAAATCTA
1829526 TTTAAATAGATTTATAATTTT
1 TTTAAATAGATTTA-AATTTT
1829547 TTTAAAT-GATTTTAAATT
1 TTTAAATAGA-TTTAAATT
1829565 GAATTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTAAATAGATTTAAATTTT
Found at i:1847701 original size:5 final size:5
Alignment explanation
Indices: 1847691--1847730 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
1847681 CTTAAAGAAG
*
1847691 ATGAA ATGAA ATGCAA ATTGAA ATGAA ATGAA AGGAA ATG
1 ATGAA ATGAA ATG-AA A-TGAA ATGAA ATGAA ATGAA ATG
1847731 GTGCCGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 23 0.74
6 6 0.19
7 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.20
Consensus pattern (5 bp):
ATGAA
Found at i:1872008 original size:19 final size:20
Alignment explanation
Indices: 1871967--1872007 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1871957 TTTTACTCGC
1871967 TTTAAATAGATTTATAACTT
1 TTTAAATAGATTTATAACTT
*
1871987 TTTAAAT-GATTT-TAAATT
1 TTTAAATAGATTTATAACTT
1872005 TTT
1 TTT
1872008 TTTTTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTAAATAGATTTATAACTT
Found at i:1880973 original size:172 final size:160
Alignment explanation
Indices: 1880779--1881111 Score: 348
Period size: 172 Copynumber: 2.0 Consensus size: 160
1880769 GATGTTTGCA
* * *
1880779 TCAAGAAACATGAAGGAAAAGCCATCCATTGACAAGAA-AAGTTCATTCATAATTACTCATGCAT
1 TCAAGAAACACGAAGCAAAAGCCATCCATTGAC-AGAACAAGTTCATTCATAATCACTCATGCAT
* * * *
1880843 TC-AAAAGCCTTTTTACTCGCTTTAAATAGATTTATAACTTTTTAAATGATATTGAATTGAACT-
65 TCGAAAA-CCTTGTTAATCGCGTTAAATAGATTTATAACTTTTTAAATGAT-TTGAAATGAA-TG
* *
1880906 TTTTTTACATTTTTATTTAAAACATATCATAATTT
127 TTTTTT-CATTTTTAGTTAAAACAGATCATAATTT
* * *
1880941 NNNNNNNNNNTCAAGAAGCACGAAGCAAAAGCCATCCATTGACAGAACAAGTTCATTTATAGTCA
1 ----------TCAAGAAACACGAAGCAAAAGCCATCCATTGACAGAACAAGTTCATTCATAATCA
* * * * *
1881006 CTCATGCCTTCGAAAACCTTGTTAATCTCGTTAAGTGGATTTATAACTTTTTAAATGATTTTAAA
56 CTCATGCATTCGAAAACCTTGTTAATCGCGTTAAATAGATTTATAACTTTTTAAATGATTTGAAA
1881071 TGAATGGTTTTTTCATTTTTAGTTAAAACAGATCATAATTT
121 TGAAT-GTTTTTTCATTTTTAGTTAAAACAGATCATAATTT
1881112 GTTGTTTGCA
Statistics
Matches: 140, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
170 1 0.01
171 38 0.27
172 97 0.69
173 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (160 bp):
TCAAGAAACACGAAGCAAAAGCCATCCATTGACAGAACAAGTTCATTCATAATCACTCATGCATT
CGAAAACCTTGTTAATCGCGTTAAATAGATTTATAACTTTTTAAATGATTTGAAATGAATGTTTT
TTCATTTTTAGTTAAAACAGATCATAATTT
Found at i:1881171 original size:171 final size:169
Alignment explanation
Indices: 1880613--1881679 Score: 713
Period size: 171 Copynumber: 6.3 Consensus size: 169
1880603 TTTTCAACAA
* * * * *
1880613 GAAACATGAAGCGAAAGCCATCCATTGATAGGAAAAGTCCATTTATAGTCACTAATG-CTTC-AA
1 GAAACGTGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAA
** * * * * * * *
1880676 AAGCCTAATTAGTAAC-TGTAAATAGTTTTATAA-TCTTATAAATGGTTTTAAAATTG-ATTTTT
66 AA-CCTTGTTAATTACGT-TAAGTGGATTTATAACT-TTTTAAATGATTTT-AAA-TGAATTTTT
** * * **
1880738 TCT-CAAGTTTGGTTAAAACAAATCATAATTTGATGTTTGCATCAA
126 T-TACATTTTTGGTTAAAACAGATCATAATTTGATATTTGCAT-TG
* * * * * * *
1880783 GAAACATGAAGGAAAAGCCATCCATTGACAAGAAAAGTTCATTCATAATTACTCATGCATTC-AA
1 GAAACGTGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAA
* * ** * * * * *
1880847 AAGCCTTTTTACTCGCTTTAAATAGATTTATAACTTTTTAAATGATATTGAATTGAACTTTTTTT
66 AA-CCTTGTTAATTACGTTAAGTGGATTTATAACTTTTTAAATGAT-TTTAAATGAA-TTTTTTT
** * ********** **
1880912 ACATTTTTATTTAAAACATATCATAATTTNNNNNNNNNNTCAA
128 ACATTTTTGGTTAAAACAGATCATAATTTGATATTTGCAT-TG
* ** *
1880955 GAAGCACGAAGCAAAAGCCATCCATTGAC-AGAACAAGTTCATTTATAGTCACTCATGCCTTCGA
1 GAAACGTGAAGCAAAAGCCATCCATTGACAAGAA-AAGTCCATTTATAGTCACTCATGCCTTCGA
1881019 AAACCTTGTTAATCT-CGTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATGAATGGTTTTT
65 AAACCTTGTTAAT-TACGTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATGAAT--TTTTT
* * *
1881083 T-CATTTTTAGTTAAAACAGATCATAATTTGTTGTTTGCATTG
127 TACATTTTTGGTTAAAACAGATCATAATTTGATATTTGCATTG
* * * *
1881125 GCAAATGTGAAGCGAAAGCCATCCATTAACAAGAAAAGTCCATTTATAGTCACTCATGTCTTC-A
1 G-AAACGTGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGA
* * *
1881189 AAAGCCTTGTT-ACT-CGTTTTAAGTGGATTTATAACTTTTT-AATAATTTT-AAT-TATTTTTT
65 AAA-CCTTGTTAATTACG--TTAAGTGGATTTATAACTTTTTAAATGATTTTAAATGAATTTTTT
* * * * **
1881249 TATATTTTTGGGTAAATCAGA-CATAATTTGATGTTTGCATCAA
127 TACATTTTTGGTTAAAACAGATCATAATTTGATATTTGCAT-TG
* ** * * * *
1881292 GAAACGTGAGGTGAAAGCCAAT-CATTGATATG-AAA-TCTCATTTATAGTCTCTGTAT--CTTC
1 GAAACGTGAAGCAAAAGCC-ATCCATTGACAAGAAAAGTC-CATTTATAGTCACT-CATGCCTTC
* * * * * * ** *
1881352 GAAAACCTAGTTAGTTACTTTAAATAGTTTTATAACCATATAAATGATTTTGAAATTGAATTTTT
63 GAAAACCTTGTTAATTACGTTAAGTGGATTTATAACTTTTTAAATGATTTT-AAA-TGAATTTTT
* * * * * *
1881417 CTCCA-TTTTGGTTAAATCAGATTATAATTTGATATTTGTATCG
126 TTACATTTTTGGTTAAAACAGATCATAATTTGATATTTGCATTG
* * * * * * **
1881460 AGAAATGTGATGCAAAAGCCATCCATTAACAGGAAAATTCCATTTATAGTCGCTCAACCCTTCGA
1 -GAAACGTGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGA
* * * * * **
1881525 AAGCCATGTTACTTGCCTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATTTATTTTTTTAC
65 AAACCTTGTTAATTACGTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATGAATTTTTTTAC
* *
1881590 ATTTTTGATTAAAACATATCATAATTTGATATTTGCATTG
130 ATTTTTGGTTAAAACAGATCATAATTTGATATTTGCATTG
* * *
1881630 GTAAACATGAAGCAAAAGTCATCCATTGACAAGAAAAGTCTATTTATAGT
1 G-AAACGTGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGT
1881680 TAGTATTAAC
Statistics
Matches: 707, Mismatches: 151, Indels: 78
0.76 0.16 0.08
Matches are distributed among these distances:
164 28 0.04
165 29 0.04
166 49 0.07
167 20 0.03
168 20 0.03
169 64 0.09
170 156 0.22
171 204 0.29
172 133 0.19
173 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (169 bp):
GAAACGTGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAA
AACCTTGTTAATTACGTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATGAATTTTTTTACA
TTTTTGGTTAAAACAGATCATAATTTGATATTTGCATTG
Found at i:1881504 original size:335 final size:336
Alignment explanation
Indices: 1880596--1881679 Score: 1050
Period size: 335 Copynumber: 3.2 Consensus size: 336
1880586 GACCAACAAG
* *
1880596 TTTGATGTTTTCAACAAGAAACATGAAGCGAAAGCCATCCATTGATAGGAAAAGTC-CATTTATA
1 TTTGATGTTTGCATCAAGAAACATGAAGCGAAAGCCATCCATTGATA-GAAAAGTCTCATTTATA
* * * * *
1880660 GTCACTAATGCTTC-AAAAGCCTAATTAGTAACTGTAAATAGTTTTATAATCTTATAAATGGTTT
65 GTCACTAATGCTTCGAAAA-CCTAGTTAGTTACTTTAAATAGTTTTATAACCTTATAAATGATTT
* * * * * **
1880724 TAAAATTGATTTTTTCTCAAGTTTGGTTAAAACAAATCATAATTTGATGTTTGCATCAAGAAACA
129 T-AAATTGAATTTTTCTCCATTTTGGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAATG
* * * * *
1880789 TGAAGGAAAAGCCATCCATTGACAAGAAAAGTT-CATTCATAATTACTCATGCATTCAAAAGCCT
193 TGAAGCAAAAGCCATCCATTAACAAGAAAA-TTCCATTTATAGTCACTCATGC-TTCAAAAGCCT
* * * *
1880853 TTTTACTCGCTTTAAATAGATTTATAACTTTTTAAATGATATTGAATTGAACTTTTTTTACATTT
256 TGTTACTCGCTTTAAGTGGATTTATAACTTTTTAAATGAT-TTTAATT--A-TTTTTTTACATTT
1880918 TT-ATTTAAAACATATCATAA
317 TTGA-TTAAAACATATCATAA
********** * * * *
1880938 TTTNNNNNNNNNNTCAAGAAGCACGAAGCAAAAGCCATCCATTGACAGAACAAGT-TCATTTATA
1 TTTGATGTTTGCATCAAGAAACATGAAGCGAAAGCCATCCATTGATAGAA-AAGTCTCATTTATA
* * * * * * * * *
1881002 GTCACTCATGCCTTCGAAAACCTTGTTAATCT-CGTTAAGTGGATTTATAACTTTTTAAATGATT
65 GTCACTAATG-CTTCGAAAACCTAGTTAGT-TACTTTAAATAGTTTTATAACCTTATAAATGATT
* * * *
1881066 TTAAA-TGAATGGTTTT-TTCATTTTTAGTTAAAACAGATCATAATTTGTTGTTTGCATTG-GCA
128 TTAAATTGAAT--TTTTCTCCA-TTTTGGTTAAAACAGATCATAATTTGATGTTTGCATCGAG-A
* *
1881128 AATGTGAAGCGAAAGCCATCCATTAACAAGAAAAGTCCATTTATAGTCACTCATGTCTTCAAAAG
189 AATGTGAAGCAAAAGCCATCCATTAACAAGAAAATTCCATTTATAGTCACTCATG-CTTCAAAAG
* * *
1881193 CCTTGTTACTCGTTTTAAGTGGATTTATAACTTTTT-AATAATTTTAATTATTTTTTTATATTTT
253 CCTTGTTACTCGCTTTAAGTGGATTTATAACTTTTTAAATGATTTTAATTATTTTTTTACATTTT
** * *
1881257 TGGGTAAATCAGA-CATAA
318 TGATTAAAACATATCATAA
* * *
1881275 TTTGATGTTTGCATCAAGAAACGTGAGGTGAAAGCCAAT-CATTGATATG-AAA-TCTCATTTAT
1 TTTGATGTTTGCATCAAGAAACATGAAGCGAAAGCC-ATCCATTGATA-GAAAAGTCTCATTTAT
* * *
1881337 AGTCTCTGTAT-CTTCGAAAACCTAGTTAGTTACTTTAAATAGTTTTATAACCATATAAATGATT
64 AGTCACT-AATGCTTCGAAAACCTAGTTAGTTACTTTAAATAGTTTTATAACCTTATAAATGATT
* * * *
1881401 TTGAAATTGAATTTTTCTCCATTTTGGTTAAATCAGATTATAATTTGATATTTGTATCGAGAAAT
128 TT-AAATTGAATTTTTCTCCATTTTGGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAAT
* * * ** * *
1881466 GTGATGCAAAAGCCATCCATTAACAGGAAAATTCCATTTATAGTCGCTCAACCCTTCGAAAGCCA
192 GTGAAGCAAAAGCCATCCATTAACAAGAAAATTCCATTTATAGTCACTC-ATGCTTCAAAAGCCT
* *
1881531 TGTTACTTGCCTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATTTATTTTTTTACATTTTT
256 TGTTACTCGCTTTAAGTGGATTTATAACTTTTTAAATGATTTT-AA-TTATTTTTTTACATTTTT
1881596 GATTAAAACATATCATAA
319 GATTAAAACATATCATAA
* ** * * *
1881614 TTTGATATTTGCAT-TGGTAAACATGAAGCAAAAGTCATCCATTGACAAGAAAAGTCT-ATTTAT
1 TTTGATGTTTGCATCAAG-AAACATGAAGCGAAAGCCATCCATTGA-TAGAAAAGTCTCATTTAT
1881677 AGT
64 AGT
1881680 TAGTATTAAC
Statistics
Matches: 590, Mismatches: 121, Indels: 64
0.76 0.16 0.08
Matches are distributed among these distances:
334 1 0.00
335 168 0.28
336 32 0.05
337 42 0.07
338 52 0.09
339 39 0.07
340 13 0.02
341 16 0.03
342 65 0.11
343 157 0.27
344 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (336 bp):
TTTGATGTTTGCATCAAGAAACATGAAGCGAAAGCCATCCATTGATAGAAAAGTCTCATTTATAG
TCACTAATGCTTCGAAAACCTAGTTAGTTACTTTAAATAGTTTTATAACCTTATAAATGATTTTA
AATTGAATTTTTCTCCATTTTGGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAATGTGA
AGCAAAAGCCATCCATTAACAAGAAAATTCCATTTATAGTCACTCATGCTTCAAAAGCCTTGTTA
CTCGCTTTAAGTGGATTTATAACTTTTTAAATGATTTTAATTATTTTTTTACATTTTTGATTAAA
ACATATCATAA
Found at i:1883776 original size:172 final size:172
Alignment explanation
Indices: 1881893--1883776 Score: 1493
Period size: 171 Copynumber: 11.0 Consensus size: 172
1881883 NNNNNNTTGG
* * * *
1881893 ATTTGTTTTACATTTTT-GATT-AAATAGATCATAATTTGATATTTGCA-TCGAGAAACATGAAA
1 ATTTTTTTTACATTTTTAG-TTAAAACAGATCATAATTTGATGTTTGCATTAG-GAAACAT-AAA
* * * * * * *
1881955 -CAAAAGCTATCCATTGACAAGAAAAGTCTATCTATAGTCATTCATGCCTTTGAAAGCTTTATTA
63 GCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTA
* * * * * *
1882019 CCCACTTTGAGTGGATTTATAACTTTTTAAATGATTTTAAGTCG-
128 CTCGCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTGA
** * * * *
1882063 ATTAGTTTTA-ATATTTT-GCATAAAATCATATCATAGTTTGATGTTTGCATTAGGAAATATGAA
1 ATTTTTTTTACAT-TTTTAG-TTAAAA-CAGATCATAATTTGATGTTTGCATTAGGAAACAT-AA
* * * * * * **
1882126 A-CGAAAGCTATCTATTGACAGGAAAAGTTCATTTGTAGTCACTCATGCCTTTAAAAGCCTAT-T
62 AGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCT-TGT
* ** * * * *
1882189 TAGTCATTTTAAATAGTTTTATAA-TATTATAAATCATTTTAAAATTGA
126 TACTCGCTTTAAATGGATTTATAACT-TTTTAAATGATTTT-AAATTGA
* * * * * * * * * *
1882237 A-TTTCTCT-CAATTTTGGTTAAAACGGATCAAAATTAGATGTTTGCATTGGGAAATATGAAGCA
1 ATTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
* * ** * *
1882300 AAA-CCCTTCACTT-ACAAGAAAAGTCCATCGATAGTCACTCATACCTTCGAAAGCCTTATT-CT
66 AAAGCCATCCA-TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTAC-
** * * *
1882362 TCAATTTAAAAGAATTTATAACTTTTTAAATGATTTTGAATTGAA
129 TCGCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTG-A
* * * * * ** *
1882407 ATTTTTTTTTACATTCTTGGCTAAAACAGATAATAATTTGATGTTTGCATCAAAAAACCTAAAGC
1 A-TTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGC
* * * *
1882472 AAAA-CCTATCCATTAACAAGACAAGCCCATTTATAGTCACTCATGCCCTT-GAAATCCTTGTTA
65 AAAAGCC-ATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATG-CCTTCGAAAGCCTTGTTA
* * * * * *
1882535 CTCGCTCTAAGTGGATTTATGACTTGTTAAATGATCTTAGATTGA
128 CTCGCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTGA
* *
1882580 ATTTTTTTTACATTGTTAGTTAAAACAAATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
1 ATTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
* * * * * *
1882645 AAAGCTATCCATTGACAAGAAAAGAT-TATTTATAGTCACTCATACTTTTG-AAGTCCTTATTAC
66 AAAGCCATCCATTGACAAGAAAAG-TCCATTTATAGTCACTCATGCCTTCGAAAG-CCTTGTTAC
* * * * *
1882708 TTGTTTTAAGTGGATTTATGA-TTTTTCAAATGATTTTAGATTG-
129 TCGCTTTAAATGGATTTATAACTTTTT-AAATGATTTTAAATTGA
* * * *
1882751 ATTTTTTCGTTAAATTTTTGGTTAAAACAAATCATAATTTGATGTTTGCCTT-GAGAAACATAAA
1 ATTTTTT--TTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAG-GAAACATAAA
* * * * * *
1882815 CCAAAAACCACCCATTGACAAGAAAAGTCTATTTATAGTCACTCATGCCTTCAAAAGCCTAGTTA
63 GCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTA
* * * * *
1882880 GTCGGTTTAAATAGTTTTATAA-TCTTATAAATGATTTTAAAATTGA
128 CTCGCTTTAAATGGATTTATAACT-TTTTAAATGATTTT-AAATTGA
* * * * * * * * * * *
1882926 ATTTCTCTTA-A-TTTTGGTTCAAACGGATCATAATTTGACGTTAGCTTTGGGAAACGTAAAGTA
1 ATTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
* * * * ** * *
1882989 AAAACCTTCTATTGACAACAAAAGTCCATTTATAGTCACTCATATCTTCAAAAGCCTTGTTACTT
66 AAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTACTC
*
1883054 GCTTTAAGTGGATTTATAACTTTTTAAATGATTTTAAATT-A
131 GCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTGA
* * * * ** *
1883095 ATTTTTGTTATATTTTTTA-TTAAAATAGATCATAATTTGATGTTTACATCGGGAAACATGAAGC
1 ATTTTTTTTACA-TTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGC
** * * * *
1883159 AAAAGCCATCCATTGACAAGAAAAGTATATTTATAGCCACTAATGCCTTTGAAAGCCTTGTTAAT
65 AAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTACT
* * *
1883224 TGCTTTAAGTGGATTTATAACTTTTTAAACGATTTTAAATTGA
130 CGCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTGA
* * * * * ** *
1883267 A-TTTTTTT-CTATTTTTTGTTTAAAACAAATCATAATTTGTTGTTTGCATCAAGAAATGTGAAG
1 ATTTTTTTTAC-ATTTTTAG-TTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAG
*** * * * * * *
1883330 -AAAAAAAATCTATTGAAAAGAAAAGTCCACTTATAATCACTCATGCCTTCAAAAGCCATGTTAC
64 CAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTAC
** * * * *
1883394 TCATTTTTAGTGGATTTATAACTTTTTAAATAATTATT-AATTAA
129 TCGCTTTAAATGGATTTATAACTTTTTAAATGATT-TTAAATTGA
* * * * *
1883438 ATTTTTTTTACATTTTTAGTTTAAACAAATCATAATTTGATGTTTGCATCAAGAAGCAT-AAGCA
1 ATTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
* * ** * *
1883502 AAAGCCATCCATTAACAAGAAAAGTCCATTTCCT-GTCACTCATGCCTTTTAAAGCCTAGTTACA
66 AAAGCCATCCATTGACAAGAAAAGTCCATTT-ATAGTCACTCATGCCTTCGAAAGCCTTGTTACT
*
1883566 CGCTTTAAATGGATTTATAACTTTTTAAATCATTTTAAA-TGTA
130 CGCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTG-A
* * * * *
1883609 ATTTTTTTTACATTTTTAGTTAAAATAGATCATAATTTAATGTTTGCATTGGGAAATATAAAACA
1 ATTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
** * * * *
1883674 AAAGCCATCCATTGACTCG-AAAGATTCATTTATAGTCAC-CAATACCTTCGAAAGTCTTGTTAG
66 AAAGCCATCCATTGACAAGAAAAG-TCCATTTATAGTCACTC-ATGCCTTCGAAAGCCTTGTTAC
* * * *
1883737 TCACTTTAAATAGTTTTATAA-TCTTATAAATGATTTTAAA
129 TCGCTTTAAATGGATTTATAACT-TTTTAAATGATTTTAAA
1883777 ATTNNNNNNN
Statistics
Matches: 1370, Mismatches: 287, Indels: 112
0.77 0.16 0.06
Matches are distributed among these distances:
169 17 0.01
170 104 0.08
171 569 0.42
172 397 0.29
173 191 0.14
174 82 0.06
175 10 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (172 bp):
ATTTTTTTTACATTTTTAGTTAAAACAGATCATAATTTGATGTTTGCATTAGGAAACATAAAGCA
AAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTGTTACTC
GCTTTAAATGGATTTATAACTTTTTAAATGATTTTAAATTGA
Found at i:1890292 original size:35 final size:35
Alignment explanation
Indices: 1890252--1890334 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
1890242 CCAAGCTTTT
* * * *
1890252 ACAATGGCTTTTCACAA-GCTCAGCCATAACTTTCA
1 ACAATGGTTTTTCA-AAGGCTCAACCACAACCTTCA
* *
1890287 ACAATGATTTTTGAAAGGCTCAACCACAACCTTCA
1 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTCA
1890322 ACAATGGTTTTTC
1 ACAATGGTTTTTC
1890335 CTGGGATCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 2 0.05
35 37 0.95
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (35 bp):
ACAATGGTTTTTCAAAGGCTCAACCACAACCTTCA
Found at i:1890798 original size:22 final size:22
Alignment explanation
Indices: 1890766--1890852 Score: 149
Period size: 22 Copynumber: 4.0 Consensus size: 22
1890756 ATAGAATGCT
1890766 CTTAGTCGACTAATCGATTTCA
1 CTTAGTCGACTAATCGATTTCA
*
1890788 CTTAGTTGACTAATCGATTTCA
1 CTTAGTCGACTAATCGATTTCA
1890810 CTTAGTCGACTAATCGATTTCA
1 CTTAGTCGACTAATCGATTTCA
1890832 CTTAGTCGACTAAGTCG-TTTC
1 CTTAGTCGACTAA-TCGATTTC
1890853 TATCTCTGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
22 59 0.95
23 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (22 bp):
CTTAGTCGACTAATCGATTTCA
Found at i:1901370 original size:22 final size:22
Alignment explanation
Indices: 1901338--1901383 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1901328 GCAAATATTG
*
1901338 AATTATGATATGTTTTAACTAA
1 AATTATGATATATTTTAACTAA
*
1901360 AATTATTATATATTTTAACTAA
1 AATTATGATATATTTTAACTAA
1901382 AA
1 AA
1901384 ATGTAAACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
AATTATGATATATTTTAACTAA
Found at i:1906566 original size:20 final size:20
Alignment explanation
Indices: 1906529--1906566 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1906519 TTCTTGTCAC
*
1906529 TCATTTTAAGTGAATTTACA
1 TCATTTTAAATGAATTTACA
*
1906549 TCATTTTAAATGATTTTA
1 TCATTTTAAATGAATTTA
1906567 AATTGGATNN
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:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (20 bp):
TCATTTTAAATGAATTTACA
Found at i:1941371 original size:172 final size:172
Alignment explanation
Indices: 1940982--1941385 Score: 420
Period size: 172 Copynumber: 2.3 Consensus size: 172
1940972 NNNNNTTCAT
* *
1940982 TTCTGGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAACATAAACCAAAAATCATCCATT
1 TTCTAGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAACATAAAGCAAAAATCATCCATT
*
1941047 GATAAGCAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCTTATTAATTGCTTTAAGTGGAT
66 GATAAGCAAAGTCCATCTATAGTCACCCATGGCTTCAAAAGCCTTATTAATTGCTTTAAGTGGAT
********** *
1941112 TTATAACTTTTTAAATAGTTTTAAATNNNNNNNNNNTTATAG
131 TTATAACTTTTTAAATAGTTTTAAATAATTTTTTTTTTACAG
* *
1941154 TTCTGGTTAAAACAGATTATAATTTGATGTTTGCATCGAGAAACATAAAGCAAAAA-CTATCCAT
1 TTCTAGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAACATAAAGCAAAAATC-ATCCAT
* ******
1941218 TGATAAGCAAAGTCCATCTATAGTCACCCAT-GCGTTCAAAAGCCTTATTACTTGCTTTNNNNNN
65 TGATAAGCAAAGTCCATCTATAGTCACCCATGGC-TTCAAAAGCCTTATTAATTGCTTTAAGTGG
**** * *
1941282 NNNNATAACTTTTTAAATGGTTTTAAATTAATTTTTTTTTTACAT
129 ATTTATAACTTTTTAAATAGTTTTAAA-TAATTTTTTTTTTACAG
* * * * * * *
1941327 TTTTAGTTAAAACAGAACATAATTT-ATATTTACATCTG-GAAACATGAAGCGAAAGTCAT
1 TTCTAGTTAAAACAGATCATAATTTGATGTTTGCATC-GAGAAACATAAAGCAAAAATCAT
1941386 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
171 3 0.02
172 160 0.84
173 28 0.15
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.35
Consensus pattern (172 bp):
TTCTAGTTAAAACAGATCATAATTTGATGTTTGCATCGAGAAACATAAAGCAAAAATCATCCATT
GATAAGCAAAGTCCATCTATAGTCACCCATGGCTTCAAAAGCCTTATTAATTGCTTTAAGTGGAT
TTATAACTTTTTAAATAGTTTTAAATAATTTTTTTTTTACAG
Found at i:1963022 original size:123 final size:114
Alignment explanation
Indices: 1962856--1963085 Score: 191
Period size: 123 Copynumber: 1.9 Consensus size: 114
1962846 TACATTTTTA
** * *
1962856 GTTTAAACATATCATAATTTGATATTTGCGTTAGGAATAGTGAAGC-AAAGGCCATCCATTGA-T
1 GTTTAAACATATCATAATTTGATATTTGCACTAGGAAAAGTGAAACGAAA-GCCATCCATTGATT
* *
1962919 -AAGAAAAGTTCATTTCTAGTCACTCATACCTTCGAAAGCCTGGTTACNNNNNNNNNNTT
65 AAAGAAAAGTTCATTTATAGTCACTCATACATTCGAAAGCCTGGTTAC----------TT
**
1962978 GTTTAAAACATATCATAATTT-ATTATTTGCACT-GGAAAATGTGAAACGAAAGCCATTTATTGA
1 GTTT-AAACATATCATAATTTGA-TATTTGCACTAGGAAAA-GTGAAACGAAAGCCATCCATTGA
*
1963041 TTGACAAAGAAAAGTTCATTTATAGTCACTCATGCATTCGAAAGC
63 TT---AAAGAAAAGTTCATTTATAGTCACTCATACATTCGAAAGC
1963086 TTAAGTTGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
122 10 0.11
123 40 0.44
124 4 0.04
128 36 0.40
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.31
Consensus pattern (114 bp):
GTTTAAACATATCATAATTTGATATTTGCACTAGGAAAAGTGAAACGAAAGCCATCCATTGATTA
AAGAAAAGTTCATTTATAGTCACTCATACATTCGAAAGCCTGGTTACTT
Found at i:1963959 original size:2 final size:2
Alignment explanation
Indices: 1963954--1963982 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1963944 GTATATAACT
1963954 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1963983 ATATGGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1965032 original size:22 final size:22
Alignment explanation
Indices: 1964988--1965028 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1964978 CGAACGAACC
*
1964988 TTCTTTTCTCTCTTTTCTTTCT
1 TTCTTTTCTCTCTTCTCTTTCT
1965010 TTCTTTTCTC-CTTCTCTTT
1 TTCTTTTCTCTCTTCTCTTT
1965029 TCTTCTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTTTCTCTCTTCTCTTTCT
Found at i:1965034 original size:21 final size:21
Alignment explanation
Indices: 1964987--1965035 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1964977 CCGAACGAAC
*
1964987 CTTCTTTTCTCTCTTTTCTTT
1 CTTCTTTTCTCTCTTCTCTTT
1965008 CTTTCTTTTCTC-CTTCTCTTTT
1 C-TTCTTTTCTCTCTTCTC-TTT
1965030 CTTCTT
1 CTTCTT
1965036 GGTTGTGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
CTTCTTTTCTCTCTTCTCTTT
Found at i:1970522 original size:14 final size:14
Alignment explanation
Indices: 1970480--1970514 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1970470 AATTTTGGAA
*
1970480 TAAAATAATATTAT
1 TAAAATAATAATAT
*
1970494 TAATATAATAATAT
1 TAAAATAATAATAT
1970508 TAAAATA
1 TAAAATA
1970515 TTAGTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATAATAATAT
Found at i:1984236 original size:12 final size:11
Alignment explanation
Indices: 1984222--1984260 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1984212 ATTTATAAAT
1984222 TTTTTAATTAA
1 TTTTTAATTAA
1984233 TTTTTAATTAA
1 TTTTTAATTAA
* *
1984244 ATTTTATTTACA
1 TTTTTAATTA-A
1984256 TTTTT
1 TTTTT
1984261 TGTTAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTTAATTAA
Found at i:1990662 original size:11 final size:10
Alignment explanation
Indices: 1990646--1990680 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1990636 AATTTATAAC
1990646 TTTTTAAATT
1 TTTTTAAATT
*
1990656 ATTTTTAATTT
1 -TTTTTAAATT
1990667 TTTTTAAATT
1 TTTTTAAATT
1990677 TTTT
1 TTTT
1990681 GTTGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:1991934 original size:172 final size:170
Alignment explanation
Indices: 1990960--1991967 Score: 812
Period size: 170 Copynumber: 5.9 Consensus size: 170
1990950 NNNNNNNNNN
* * * * * *
1990960 ATTGCAAACATTAAATTATGATCCATTTTC-ACCAAAATTGTAAAACAAATTCAATTC-AAATAA
1 ATTGCAAACATCAAATTATGATCTA-TTTCAACAAAAAATGTAAAAAAAATT-AATTCAAAATCA
* * *
1991023 TTTACAAAGTTATAAATCCACTTAAAGCAAGGAACAAGGCTTTCGAAGGTATGAGCGACTATAAA
64 TTTA-AAAGTTATAAATCCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAA
* * * * * *
1991088 TGGACATTTCTTGTCAATGGATGGCTATT-GCTTAATGTTTTCC
128 TAGACTTTTCTTATCAATGGATAGCT-TTCGCTTCATGTTTCCC
* * * * *
1991131 ACTACAAACATCAAATTATGATATGTTTTCAACAAAAAAT-T-AAAAAAA--AA-TAAAAATCAT
1 ATTGCAAACATCAAATTATGATCT-ATTTCAACAAAAAATGTAAAAAAAATTAATTCAAAATCAT
*
1991191 TTAAAAAGTTATAAATTCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAAT
65 TT-AAAAGTTATAAATCCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAAT
* * * *
1991256 AGACTTTTCTTATCAAAGGATGGCTTTTGTTTCATGTTTCCC
129 AGACTTTTCTTATCAATGGATAGCTTTCGCTTCATGTTTCCC
* * * * * * *
1991298 -TATGCAAACATTAAATTATAAT-TTTTTTAA-AAAAAGTTTTAAAAAAAATTAATTTAAAGA-C
1 AT-TGCAAACATCAAATTATGATCTATTTCAACAAAAA-ATGTAAAAAAAATTAATTCAAA-ATC
* * * * ** * ** * * *
1991359 ATTTATAAGTTATAAATTCACTTAAGGAGAATAATAAGGCTTTTTAACGTATGAGTGACTTTAAA
63 ATTTAAAAGTTATAAATCCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAA
* * * **
1991424 TGGA-TTGTTCTTATCAACGGATAGTTTTCGCTTCATGTTTCTT
128 TAGACTT-TTCTTATCAATGGATAGCTTTCGCTTCATGTTTCCC
* * * * * *
1991467 AATGCAACCATCAAATTATGATCTGTTTAAACAAAAAATATAAAAAAAATTAA-TCTAAAATAAT
1 ATTGCAAACATCAAATTATGATCTATTTCAACAAAAAATGTAAAAAAAATTAATTC-AAAATCAT
* * * * * * * * *
1991531 TAAAAAGTAATAAATCCATTTAAAGTGAGGGATAAGGTTTTTGAAGGCACGAGTGACTATAAATA
65 TTAAAAGTTATAAATCCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAATA
* * * * * **
1991596 GACTTTGCTTATCGATGAAT-GTTTTTCGCTGCACAT-TTTCGA
130 GACTTTTCTTATCAATGGATAG-CTTTCGCT--TCATGTTTCCC
* * * * *
1991638 ATTG-AAACATCAAATTATGATCTCTTTTAACCAAAAATGTAAAAAAAAAATCAATTTAAAATCA
1 ATTGCAAACATCAAATTATGATCTATTTCAACAAAAAATGT--AAAAAAAATTAATTCAAAATCA
* * * ** *
1991702 TTTATAAAGTTATAAATCCACATAAAGTC-AAGAATAATACTTTCGAAGGCATGAGTGACTATAT
64 TTTA-AAAGTTATAAATCCACTTAAAG-CGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAA
* * * **
1991766 ATAGACTTTTCTTATCAATGGATAGCTTCCACTTAACATTTCCC
127 ATAGACTTTTCTTATCAATGGATAGCTTTCGCTTCATGTTTCCC
* * * *
1991810 ATTGCAAACATCAAATTGTGATCTATTTCAACTAAAATTGTAAAAACAATTCAATTCAAAATCAT
1 ATTGCAAACATCAAATTATGATCTATTTCAACAAAAAATGTAAAAAAAATT-AATTCAAAATCAT
* * * * *
1991875 TTAAATACTTATAAATCTACTGAAAGCGAGGAACAAGGTTTTCGAAGGTATGAGTGACTATAAAT
65 TTAAA-AGTTATAAATCCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAAT
**
1991940 AGA-TATTTCTTGCCAATGGATAGCTTTC
129 AGACT-TTTCTTATCAATGGATAGCTTTC
1991968 ACATAATGTT
Statistics
Matches: 665, Mismatches: 137, Indels: 69
0.76 0.16 0.08
Matches are distributed among these distances:
164 5 0.01
165 7 0.01
166 5 0.01
167 123 0.18
168 3 0.00
169 104 0.16
170 140 0.21
171 52 0.08
172 122 0.18
173 103 0.15
174 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (170 bp):
ATTGCAAACATCAAATTATGATCTATTTCAACAAAAAATGTAAAAAAAATTAATTCAAAATCATT
TAAAAGTTATAAATCCACTTAAAGCGAGGAACAAGGCTTTCGAAGGCATGAGTGACTATAAATAG
ACTTTTCTTATCAATGGATAGCTTTCGCTTCATGTTTCCC
Found at i:2015671 original size:15 final size:15
Alignment explanation
Indices: 2015651--2015689 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2015641 CTTTGAAAGC
2015651 CATATCATGGGGAAA
1 CATATCATGGGGAAA
2015666 CATATCATGGGGAAA
1 CATATCATGGGGAAA
2015681 CATATCATG
1 CATATCATG
2015690 ATTTGATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (15 bp):
CATATCATGGGGAAA
Found at i:2020104 original size:171 final size:174
Alignment explanation
Indices: 2019891--2020285 Score: 421
Period size: 172 Copynumber: 2.3 Consensus size: 174
2019881 AATGATTTTA
* * ** * *
2019891 AAATTGAA-ATTTTTTTA-GTTTTGAT-TAAAATTGATTATAATTTGATGTTTGCAT-TGGGAAA
1 AAATTGAATTTTTTTTTACATTTTGATATAAAACAGATCATAATTTGATGTTTGCATCTAGGAAA
* ** *
2019952 CGTGAAGTGAAAGCCATCCATTGATAAGAAAAGT-TCATGTAGAGTCACACATGCCTTCGAAATC
66 CATGAAGAAAAAGCCATCCATTGACAAGAAAAGTCT-ATGTAGAGTCACACATGCCTTCGAAA-C
** * *
2020016 G-TTGTTACTCTTTTTAAGTGGATTTATAACTTTTTAAACAACTTT
129 GATTGTTACTCGCTTTAAGTAGATTTATAAATTTTTAAACAACTTT
* *
2020061 AAATT-AGA-TTTTTTTTATATTTTGA-ATAAAACATATCATAATTTGATGTTTGCATCTAGGAA
1 AAATTGA-ATTTTTTTTTACATTTTGATATAAAACAGATCATAATTTGATGTTTGCATCTAGGAA
* * * * ** * *
2020123 ACATGAAGAAAAAGTCATCCATTGACAAGAAAAGTCTATTTATATTCATTCATGTCTTCGAAAGG
65 ACATGAAGAAAAAGCCATCCATTGACAAGAAAAGTCTATGTAGAGTCACACATGCCTTCGAAACG
* *
2020188 ATTGTTACTCGCTTTAAGTAGATTTATAAATTTTTAAATAATTTT
130 ATTGTTACTCGCTTTAAGTAGATTTATAAATTTTTAAACAACTTT
* * * * *
2020233 TAATTGAATTTTTTTTTACATTTTTATTTTAACCAGATCATAATTTGATGTTT
1 AAATTGAATTTTTTTTTACATTTTGATATAAAACAGATCATAATTTGATGTTT
2020286 CCNNNNNNNN
Statistics
Matches: 184, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
169 1 0.01
170 14 0.08
171 32 0.17
172 98 0.53
173 17 0.09
174 22 0.12
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (174 bp):
AAATTGAATTTTTTTTTACATTTTGATATAAAACAGATCATAATTTGATGTTTGCATCTAGGAAA
CATGAAGAAAAAGCCATCCATTGACAAGAAAAGTCTATGTAGAGTCACACATGCCTTCGAAACGA
TTGTTACTCGCTTTAAGTAGATTTATAAATTTTTAAACAACTTT
Found at i:2030182 original size:13 final size:13
Alignment explanation
Indices: 2030146--2030185 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 13
2030136 AAAATTTAGA
2030146 AAAATTTAATTTT
1 AAAATTTAATTTT
2030159 AAAATCATTAATTTT
1 AAAAT--TTAATTTT
2030174 AAAATTTAATTT
1 AAAATTTAATTT
2030186 AATTTAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.48
15 13 0.52
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAATTTAATTTT
Found at i:2044768 original size:173 final size:162
Alignment explanation
Indices: 2044585--2044914 Score: 369
Period size: 173 Copynumber: 2.0 Consensus size: 162
2044575 TGTTTAAAAG
* *
2044585 CCTTGTTATTCATTTTAAGAGAATTTATAACATTTTAAATGATTTTGAATTGAA-TTTTTTTTTA
1 CCTTGTTATTCACTTTAAGAGAATTTATAAC-TTTTAAATGATTTTAAATTGAACTTTTTTTTTA
** *
2044649 CA-TTTTTAG-TAAAAAAAGATCATAATTTGATGTTTGCATTGGGAAACATAAAGCAAAAGCTAT
65 -ATTTTTTAGTTAAAAAAA-ATCATAATTTGATGTTTGCATTAAGAAA-ATAAAGCAAAAACTAT
* *
2044712 CCATTGAGAAGAAAAGTCTATTTATAGTCANNNNNNNNNNTGAAAT
127 CCATTGACAAGAAAAGCCTATTTATAGTCA----------TGAAAT
* * * *
2044758 CCTTGTTATTCGCTTTAAGTGGATTTATGACTTTTAAATGATTTTAAATTGAACTTTTTTTTTAA
1 CCTTGTTATTCACTTTAAGAGAATTTATAACTTTTAAATGATTTTAAATTGAACTTTTTTTTTAA
* * * *
2044823 TTTTTTTGGTTAAAAGAAATCATAATTTGATGTTTGCATTAAGAAAATTAAGCAAAAACTATCTA
66 -TTTTTTAGTTAAAAAAAATCATAATTTGATGTTTGCATTAAGAAAATAAAGCAAAAACTATCCA
2044888 TTGACAAGAAAAGCCTATTTATAGTCA
130 TTGACAAGAAAAGCCTATTTATAGTCA
2044915 CTTATGCTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
172 22 0.16
173 77 0.56
174 32 0.23
175 7 0.05
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.40
Consensus pattern (162 bp):
CCTTGTTATTCACTTTAAGAGAATTTATAACTTTTAAATGATTTTAAATTGAACTTTTTTTTTAA
TTTTTTAGTTAAAAAAAATCATAATTTGATGTTTGCATTAAGAAAATAAAGCAAAAACTATCCAT
TGACAAGAAAAGCCTATTTATAGTCATGAAAT
Found at i:2044937 original size:173 final size:170
Alignment explanation
Indices: 2044499--2045168 Score: 500
Period size: 172 Copynumber: 3.9 Consensus size: 170
2044489 AAACGGATTG
* * * * * *
2044499 TAATTTGATGTTTGCATTGTAA-AACATGAAGC-AGAACTCTCCATTGATAAGAAATGTCC-ATT
1 TAATTTGATGTTTGCA-T-TAAGAAAATAAAGCAAAAACTATCCATTGACAAGAAAAG-CCTATT
* * * * *
2044561 GATAGTCACTCATGTGTTTAAAAGCCTTGTTATTCATTTTAAGAGAATTTATAACATTTTAAATG
63 TATAGTCACTCA--TGTTTCAAAGCCTTGTTATTCACTTTAAGTGGATTTATAAC-TTTTAAATG
*
2044626 ATTTTGAATTGAA-TTTTTTTTTACATTTTTAGTAAAAAAAGATCA
125 ATTTTAAATTGAACTTTTTTTTTACATTTTTAGTAAAAAAAGATCA
** * * *
2044671 TAATTTGATGTTTGCATTGGGAAACATAAAGCAAAAGCTATCCATTGAGAAGAAAAGTCTATTTA
1 TAATTTGATGTTTGCATTAAGAAA-ATAAAGCAAAAACTATCCATTGACAAGAAAAGCCTATTTA
******** * * * *
2044736 TAGTCANNNNNNNNNNTGAAATCCTTGTTATTCGCTTTAAGTGGATTTATGACTTTTAAATGATT
65 TAGTCA--CTCATGTTTCAAAGCCTTGTTATTCACTTTAAGTGGATTTATAACTTTTAAATGATT
* *
2044801 TTAAATTGAACTTTTTTTTTA-ATTTTTTTGGTTAAAAGAA-ATCA
128 TTAAATTGAACTTTTTTTTTACA--TTTTTAG-TAAAAAAAGATCA
* *
2044845 TAATTTGATGTTTGCATTAAGAAAATTAAGCAAAAACTATCTATTGACAAGAAAAGCCTATTTAT
1 TAATTTGATGTTTGCATTAAGAAAATAAAGCAAAAACTATCCATTGACAAGAAAAGCCTATTTAT
* * *
2044910 AGTCACTTATGCTTTCAAAGGCCTTGTTATTCTCTTTAAGTGGATTTCTAACTTTATAAATGATT
66 AGTCACTCATG-TTTCAAA-GCCTTGTTATTCACTTTAAGTGGATTTATAACTTT-TAAATGATT
* * * ** * *
2044975 TTAAATTG-AC-TGTTTTTTACATTATTGGTTTAAACAGATCC
128 TTAAATTGAACTTTTTTTTTACATTTTTAGTAAAAAAAGATCA
* * * * * * ** * * *
2045016 TTATTTGATGTTTTCATCCAA-AAATGTGATGTGAAAGCTATCCATAGACAAGAAATGTCC-ATT
1 TAATTTGATGTTTGCAT-TAAGAAA-ATAAAGCAAAAACTATCCATTGACAAGAAAAG-CCTATT
* ** * * * *
2045079 TATAGTCTCTCATACCTTCGAAAGCCTTATTACTCACTTTAAGAGGATTTACAACTATTTAAATG
63 TATAGTCACTCAT-GTTTC-AAAGCCTTGTTATTCACTTTAAGTGGATTTATAACT-TTTAAATG
* *
2045144 ATTTTGAATTGAA--TTGTTTTTACAT
125 ATTTTAAATTGAACTTTTTTTTTACAT
2045169 NNNNNNNNNN
Statistics
Matches: 395, Mismatches: 81, Indels: 44
0.76 0.16 0.08
Matches are distributed among these distances:
170 5 0.01
171 30 0.08
172 152 0.38
173 152 0.38
174 49 0.12
175 7 0.02
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.40
Consensus pattern (170 bp):
TAATTTGATGTTTGCATTAAGAAAATAAAGCAAAAACTATCCATTGACAAGAAAAGCCTATTTAT
AGTCACTCATGTTTCAAAGCCTTGTTATTCACTTTAAGTGGATTTATAACTTTTAAATGATTTTA
AATTGAACTTTTTTTTTACATTTTTAGTAAAAAAAGATCA
Found at i:2054231 original size:24 final size:23
Alignment explanation
Indices: 2054203--2054248 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2054193 AATTTATAAC
2054203 TTTTTAAATTATTTTTAATTAAAT
1 TTTTTAAA-TATTTTTAATTAAAT
* *
2054227 TTTTTTAATATTTTTTATTAAA
1 TTTTTAAATATTTTTAATTAAA
2054249 ACATATCANN
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTAAATATTTTTAATTAAAT
Found at i:2054233 original size:14 final size:15
Alignment explanation
Indices: 2054206--2054235 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2054196 TTATAACTTT
2054206 TTAAATTATTTTTAA
1 TTAAATTATTTTTAA
2054221 TTAAATT-TTTTTAA
1 TTAAATTATTTTTAA
2054235 T
1 T
2054236 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAAATTATTTTTAA
Found at i:2079243 original size:18 final size:20
Alignment explanation
Indices: 2079220--2079257 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2079210 AAAAAAATTC
2079220 AATTTC-AAATC-ATTTAAA
1 AATTTCTAAATCAATTTAAA
2079238 AATTTCTAAATCAATTTAAA
1 AATTTCTAAATCAATTTAAA
2079258 GTGAGTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTCTAAATCAATTTAAA
Found at i:2094136 original size:31 final size:32
Alignment explanation
Indices: 2094101--2094160 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
2094091 ATGACACTTG
2094101 GAAAA-GTGGGACTCAATTTATGATTATGATT
1 GAAAAGGTGGGACTCAATTTATGATTATGATT
** **
2094132 GAAAAGGTGGGTGTTGATTTATGATTATG
1 GAAAAGGTGGGACTCAATTTATGATTATG
2094161 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 5 0.21
32 19 0.79
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (32 bp):
GAAAAGGTGGGACTCAATTTATGATTATGATT
Found at i:2103768 original size:17 final size:17
Alignment explanation
Indices: 2103742--2103775 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2103732 CCCTTAATTG
*
2103742 TAACTTAAACAGTTTAC
1 TAACTCAAACAGTTTAC
2103759 TAACTCAAACAGTTTAC
1 TAACTCAAACAGTTTAC
2103776 ACTCACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (17 bp):
TAACTCAAACAGTTTAC
Found at i:2123251 original size:35 final size:35
Alignment explanation
Indices: 2123205--2123311 Score: 142
Period size: 35 Copynumber: 3.1 Consensus size: 35
2123195 ATTAAGTTGT
* * *
2123205 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
1 GCCTAATTAATTAAATTATATAATTAAGTTATTGG
* *
2123240 GCTTAATTAATTAAATTATCTAATTAAGTTATTGG
1 GCCTAATTAATTAAATTATATAATTAAGTTATTGG
* * *
2123275 ACCTACTTAATTAAATTAAATAATTAAGTTATTGG
1 GCCTAATTAATTAAATTATATAATTAAGTTATTGG
2123310 GC
1 GC
2123312 ATNNNNNNNN
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (35 bp):
GCCTAATTAATTAAATTATATAATTAAGTTATTGG
Found at i:2149212 original size:18 final size:19
Alignment explanation
Indices: 2149172--2149214 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2149162 ATATTATTTT
*
2149172 AATATTATTTTGTTTAAAA
1 AATATTATTTTATTTAAAA
*
2149191 AATATTATTTTATTT-CAA
1 AATATTATTTTATTTAAAA
2149209 AATATT
1 AATATT
2149215 TCTTTCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTTAAAA
Found at i:2153881 original size:30 final size:29
Alignment explanation
Indices: 2153808--2153886 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
2153798 AACATGTTTG
2153808 GTCTTAATTTAGACAAG-AAAATAGATAT
1 GTCTTAATTTAGACAAGAAAAATAGATAT
* ** *
2153836 GTTTTAATTTAAGACAAGAAAAATATTTTTT
1 GTCTTAATTT-AGACAAGAAAAATA-GATAT
*
2153867 GTCTTAATCTAGACAAGAAA
1 GTCTTAATTTAGACAAGAAA
2153887 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 9 0.21
29 7 0.17
30 16 0.38
31 10 0.24
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (29 bp):
GTCTTAATTTAGACAAGAAAAATAGATAT
Found at i:2177238 original size:29 final size:29
Alignment explanation
Indices: 2177181--2177238 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2177171 NNNNNNNNNN
**
2177181 TCTAAATTAAGACCAAACATGTTTTCTTG
1 TCTAAATTAAGACCAAACATGTTAACTTG
2177210 TCTAAATTAAGA-CAAACATGTTAAACTTG
1 TCTAAATTAAGACCAAACATGTT-AACTTG
2177239 CCATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (29 bp):
TCTAAATTAAGACCAAACATGTTAACTTG
Done.