Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold107
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1028272
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 136574 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:735881 original size:81 final size:82
Alignment explanation
Indices: 735708--735885 Score: 240
Period size: 81 Copynumber: 2.2 Consensus size: 82
735698 TCAGCACTTA
* * *
735708 TCAGTAC-TTGTCAGTACTTCTCTACGTTTTTCAATACCGTCAGTAAAAAATGTCAGTAATTTTC
1 TCAGTACATTGTCAGTACTTCTCTAAGTTTCTCAATACCGTCAGTAAAAAACGTCAGTAATTTTC
*
735772 TAAGTTTATCAGTACTG
66 TAAGTTTATCAGTAATG
* * *
735789 TC--TA-AGTTTGTCAGTACTTTTCTAAGTTTCTCAGTACCGTCAGT-AAAAACGTCAGTACTTT
1 TCAGTACA--TTGTCAGTACTTCTCTAAGTTTCTCAATACCGTCAGTAAAAAACGTCAGTAATTT
735850 TCTAAGTTTATCAGTAATG
64 TCTAAGTTTATCAGTAATG
735869 TCAGTACATTGTCAGTA
1 TCAGTACATTGTCAGTA
735886 AATGTCCAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
79 2 0.02
80 35 0.42
81 44 0.52
82 2 0.02
83 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (82 bp):
TCAGTACATTGTCAGTACTTCTCTAAGTTTCTCAATACCGTCAGTAAAAAACGTCAGTAATTTTC
TAAGTTTATCAGTAATG
Found at i:735904 original size:81 final size:80
Alignment explanation
Indices: 735742--735905 Score: 197
Period size: 80 Copynumber: 2.0 Consensus size: 80
735732 CGTTTTTCAA
* * **
735742 TACCGTCAGTAAAAAATGTCAGTAATTTTCTAAGTTTATCAGTACTGTCTAAGTTTGTCAGTACT
1 TACCGTCAGTAAAAAACGTCAGTAATTTTCTAAGTTTATCAGTAATGTCTAAG-TTGTCAGTAAA
* * *
735807 TTTCTAAGTTTCTCAG
65 TGTCCAAGTTTATCAG
*
735823 TACCGTCAGT-AAAAACGTCAGTACTTTTCTAAGTTTATCAGTAATGTCAGTACA-TTGTCAGTA
1 TACCGTCAGTAAAAAACGTCAGTAATTTTCTAAGTTTATCAGTAATGTC--TA-AGTTGTCAGTA
*
735886 AATGTCCAATTTTATCAG
63 AATGTCCAAGTTTATCAG
735904 TA
1 TA
735906 AAAAATGGGA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 35 0.49
81 33 0.46
82 2 0.03
83 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (80 bp):
TACCGTCAGTAAAAAACGTCAGTAATTTTCTAAGTTTATCAGTAATGTCTAAGTTGTCAGTAAAT
GTCCAAGTTTATCAG
Found at i:739966 original size:2 final size:2
Alignment explanation
Indices: 739959--740002 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
739949 NNNNNNNAAA
739959 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
740001 TC
1 TC
740003 ATGATTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:740305 original size:12 final size:12
Alignment explanation
Indices: 740288--740326 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
740278 ACCCTTATGT
740288 GTCTGTCTGTCC
1 GTCTGTCTGTCC
*
740300 GTCTGTCTGTCT
1 GTCTGTCTGTCC
*
740312 GTCAGTCTGTCC
1 GTCTGTCTGTCC
740324 GTC
1 GTC
740327 CGTAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.31, G:0.26, T:0.41
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:740329 original size:4 final size:4
Alignment explanation
Indices: 740287--740322 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
740277 AACCCTTATG
* *
740287 TGTC TGTC TGTC CGTC TGTC TGTC TGTC AGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
740323 CGTCCGTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.03, C:0.28, G:0.25, T:0.44
Consensus pattern (4 bp):
TGTC
Found at i:740633 original size:167 final size:166
Alignment explanation
Indices: 740351--740814 Score: 592
Period size: 165 Copynumber: 2.8 Consensus size: 166
740341 CTGTTGCATT
* * *
740351 TATCTGAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCAT
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTT-AGGCATGCCAT
* * *
740416 ATCGTGGGATATATTTTTGTATCAATCGGACATAAACTTCCTGTTAAATGACGACTTTGCTTATT
65 ATCGTGGGATATATTTTTGTATCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT
* * **
740481 TTTTAACCAAAATTTTCAAACAACTTTTCGTCAAGGA
130 TTTTAACCAAAATTTTCAAACAAATTTTCCTCAAACA
* * *
740518 TATCTCAGCAACTATTAATCGCAGATGTTTGAAATTTTTACACAATATTTGTATAGGCAAGCCAT
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGT-TAGGCATGCCAT
*
740583 ATCGTGGGATATATTTTTGTATCAATCAGACGTCAACTTCCTGTTAAATGA-GTACATTG-TT-T
65 ATCGTGGGATATATTTTTGTATCAATCAGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTAT
* *
740645 ATTTTAGCCAAAATTTTCAAACAAATTTTCCTCAAACA
129 TTTTTAACCAAAATTTTCAAACAAATTTTCCTCAAACA
* * * *
740683 TTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCAT
1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTG-TTAGGCATGCCAT
** * * * * * * * * *
740748 ATTTTGGGATATATTTCTGTACCAATTAGATGCCAGCTTTCTGTTAAATGTCGACTTTGCGTATT
65 ATCGTGGGATATATTTTTGTATCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT
740813 TT
130 TT
740815 GCATATTCAC
Statistics
Matches: 255, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
165 135 0.53
166 6 0.02
167 113 0.44
168 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (166 bp):
TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTTAGGCATGCCATA
TCGTGGGATATATTTTTGTATCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
TTTAACCAAAATTTTCAAACAAATTTTCCTCAAACA
Found at i:745227 original size:13 final size:12
Alignment explanation
Indices: 745194--745242 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
745184 AAATGATATA
*
745194 TTGGGTTGTTTT
1 TTGGGTTTTTTT
745206 TTGGGTTTTTTT
1 TTGGGTTTTTTT
745218 GTT-GG--TTTTT
1 -TTGGGTTTTTTT
*
745228 TGGGGTTTTTTT
1 TTGGGTTTTTTT
745240 TTG
1 TTG
745243 TTCCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.23
12 20 0.67
13 2 0.07
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (12 bp):
TTGGGTTTTTTT
Found at i:752603 original size:179 final size:179
Alignment explanation
Indices: 752090--752630 Score: 597
Period size: 184 Copynumber: 3.0 Consensus size: 179
752080 GAAACCACAG
* * *
752090 TATGCAGTATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTTTTATAAAGAAAAC
1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA---TTTTTTTATAAA-TAATC
* * * *
752155 AGAAACCAAATTTCT-AGCAATATGTACACTTCTGATATATGTACAATTGATCTGCAAAAGAAGC
62 AGAAATCAAATTTCTAAG-AATATGCACATTTCTGATATATGTACAATTGATCTGCAAAAGAACC
* * * ** *
752219 ACTTTCTATATTTAAAACTGTAGGAGAAAATATCTGTACAATGAGGGTACCCTA
126 ACTTCCTATATTAAAAACTGTAGGGGAAGTTATCTGTACAATGAAGGTACCCTA
* * * * *
752273 TATACAATATTTTGCC-AAAAATGATTAAGTTCAAAAGCTGGTATTTTTTTATAAATTATTACAA
1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTATAAATAATCAGAA
* * * * *
752337 ATC-AATATCATAGCAATACATGTATGCACATCTCTAATGA-ATGTACAACTGATCTGCAAAAGA
66 ATCAAATTTC-T---AAGA-A--TATGCACATTTCTGAT-ATATGTACAATTGATCTGCAAAAGA
* *
752400 ACCATTTCCTATATTAAAAACTGTAGGGGAAGTTATCTGTACATTGAAGGTACCCTA
123 ACCACTTCCTATATTAAAAACTGTAGGGGAAGTTATCTGTACAATGAAGGTACCCTA
* * * * * *
752457 TATGCAATATTTTGCCAAAAAAAGACGAAGTTCAATAGCTGGTATTTTATCATGAATAATCAGAA
1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTATAAATAATCAGAA
*
752522 ATCAAATTTCTAAGAATATGCACATTTCTGATATATGTACAATTGATCTGCAAGAGAACCACTTC
66 ATCAAATTTCTAAGAATATGCACATTTCTGATATATGTACAATTGATCTGCAAAAGAACCACTTC
* * * *
752587 CTATCTTGAAAACTGTAGGAGG-AGTTATCCGTACAATGATGGTA
131 CTATATTAAAAACTGTAGG-GGAAGTTATCTGTACAATGAAGGTA
752631 TCCTTTGGCA
Statistics
Matches: 297, Mismatches: 48, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
177 5 0.02
178 8 0.03
179 90 0.30
180 2 0.01
181 2 0.01
182 31 0.10
183 14 0.05
184 97 0.33
185 43 0.14
186 5 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (179 bp):
TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTATAAATAATCAGAA
ATCAAATTTCTAAGAATATGCACATTTCTGATATATGTACAATTGATCTGCAAAAGAACCACTTC
CTATATTAAAAACTGTAGGGGAAGTTATCTGTACAATGAAGGTACCCTA
Found at i:786526 original size:166 final size:168
Alignment explanation
Indices: 786230--786566 Score: 489
Period size: 166 Copynumber: 2.0 Consensus size: 168
786220 GGTGCGAGTC
* * ** *
786230 TTTAAAAATCTTCTTCTCAAGAACAACTCCACCAGAAATGCCAATTTTTTTTCACAAACGCTTGT
1 TTTAAAAATCCTCTTCTCAAGAACAACTCCACCAGAAATGCCAA-TTATTAACACAAAAGCTTGT
** * * ** *
786295 ATATAAAGTGAAGATTTTAAATTGTAAAAATCGTGATCCTCGGATTAAAACTAGGGCCTCAGGCG
65 ATATAAAGTGAAGATTCGAAATTGTAAAAATCGTGACCCCCGGACCAAAACTAGGGCCCCAGGCG
*
786360 GGGTTCAAAGTTTAACATACTAATACATAGG-AAAATGT
130 GGGTTCAAAGTTTAACATACAAATACATAGGAAAAATGT
* *
786398 TTTAAAAATCCTCTTCTCAAGAACCACTGCACCAGAAATGCCAA-TATTAACACAAAAGCTTGTA
1 TTTAAAAATCCTCTTCTCAAGAACAACTCCACCAGAAATGCCAATTATTAACACAAAAGCTTGTA
* * *
786462 TATATAGTGAATATTCGAAATTGTAAAAATCGTGACCCCCGGACCAAAATTAGGGCCCCAGGCGG
66 TATAAAGTGAAGATTCGAAATTGTAAAAATCGTGACCCCCGGACCAAAACTAGGGCCCCAGGCGG
786527 GGTTCAAAGTTTAACATACAAATACATAGGAAAAATGT
131 GGTTCAAAGTTTAACATACAAATACATAGGAAAAATGT
786565 TT
1 TT
786567 ATATTGCTTT
Statistics
Matches: 150, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
166 100 0.67
167 9 0.06
168 41 0.27
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (168 bp):
TTTAAAAATCCTCTTCTCAAGAACAACTCCACCAGAAATGCCAATTATTAACACAAAAGCTTGTA
TATAAAGTGAAGATTCGAAATTGTAAAAATCGTGACCCCCGGACCAAAACTAGGGCCCCAGGCGG
GGTTCAAAGTTTAACATACAAATACATAGGAAAAATGT
Found at i:788859 original size:44 final size:43
Alignment explanation
Indices: 788796--788891 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 43
788786 CCAAGCTGGA
788796 TTAAAAGTTAAATGTAGAAGTATATATGGAAAAAATTTT-AAAAT
1 TTAAAA-TTAAATGTAGAAGTATATATGG-AAAAATTTTGAAAAT
* *
788840 TTAAAATTAAAATGTAGAAGTATGTATGGAAAATTTTTGAAAAT
1 TTAAAATT-AAATGTAGAAGTATATATGGAAAAATTTTGAAAAT
788884 TTAAAATT
1 TTAAAATT
788892 TTTAAAATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
43 10 0.21
44 38 0.79
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (43 bp):
TTAAAATTAAATGTAGAAGTATATATGGAAAAATTTTGAAAAT
Found at i:804931 original size:12 final size:12
Alignment explanation
Indices: 804916--804946 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
804906 ACAAGGTAAA
804916 AAAGACTGAAAT
1 AAAGACTGAAAT
*
804928 AAAGACAGAAAT
1 AAAGACTGAAAT
804940 AAAGACT
1 AAAGACT
804947 ATAATGACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.61, C:0.10, G:0.16, T:0.13
Consensus pattern (12 bp):
AAAGACTGAAAT
Found at i:806009 original size:31 final size:31
Alignment explanation
Indices: 805971--806040 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
805961 ACATGACATT
*
805971 GTGTTGTGCAAAGTTGTGTCAACGCGACAGC
1 GTGTTGTGCAAAGTTGTGTCAACGCAACAGC
* * *
806002 GTGTTGTGCAAAGTTGTGTTAGCGCAACGGC
1 GTGTTGTGCAAAGTTGTGTCAACGCAACAGC
806033 GTGTTGTG
1 GTGTTGTG
806041 TGTTAGCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.19, C:0.16, G:0.36, T:0.30
Consensus pattern (31 bp):
GTGTTGTGCAAAGTTGTGTCAACGCAACAGC
Found at i:806042 original size:23 final size:23
Alignment explanation
Indices: 806016--806086 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
806006 TGTGCAAAGT
* *
806016 TGTGTTAGCGCAACGGCGTGTTG
1 TGTGTTAGCGCGACGGCGCGTTG
*
806039 TGTGTTAGCGTGACGGCGCGTTG
1 TGTGTTAGCGCGACGGCGCGTTG
*
806062 TGTGTTAGCGCGACGGTGCGTTG
1 TGTGTTAGCGCGACGGCGCGTTG
806085 TG
1 TG
806087 CAACGTTGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.10, C:0.17, G:0.42, T:0.31
Consensus pattern (23 bp):
TGTGTTAGCGCGACGGCGCGTTG
Found at i:806097 original size:54 final size:54
Alignment explanation
Indices: 806039--806187 Score: 201
Period size: 54 Copynumber: 2.8 Consensus size: 54
806029 CGGCGTGTTG
* * * *
806039 TGTGTTAGCGTGACGGCGCGTTGTGTGTTAGCGCGACGGTGCGTTGTGCAACGT
1 TGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGCGTTGTGCAAAGT
* * *
806093 TGTGTCAGCGCGATGGCGTGTTGT-TAGTTAGCGCGACCGCGCGTTGTGCAAAGT
1 TGTGTTAGCGCGACGGCGTGTTGTGT-GTTAGCGCGACGGCGCGTTGTGCAAAGT
* *
806147 TGCGTTGGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCG
1 TGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCG
806188 TGTTTATTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 79 0.98
55 1 0.01
ACGTcount: A:0.11, C:0.20, G:0.41, T:0.28
Consensus pattern (54 bp):
TGTGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGCGTTGTGCAAAGT
Found at i:807722 original size:166 final size:167
Alignment explanation
Indices: 807486--808097 Score: 599
Period size: 166 Copynumber: 3.8 Consensus size: 167
807476 TTACACTTGT
* * * *
807486 GTGGAAGCATCCTCAGGTAGTGTAGATTCAAGTTTGTTCAAACCATGGTCCCCGGGGGTAGGGAG
1 GTGGAAGCATCCTCAGATAGTGTATATTCAAGTTTGTTCAAATCATGGTCCCCGGAGGTAGGGAG
*
807551 GGGCCACAAGAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
66 GGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
*
807616 CTCAATAAC-ACTCAGGCC-AGAAAAGCTCAAATTAG-A
131 CTCAAAAACTA-TCAGGCCAAG-AAAGCTCAAATTAGCA
* *
807652 GTGGAAGCATCCTCAGATAGTGTATATTCAAGTTTGTTCAAATCATGGTCCCCGGATGTAGGGTG
1 GTGGAAGCATCCTCAGATAGTGTATATTCAAGTTTGTTCAAATCATGGTCCCCGGAGGTAGGGAG
* *
807717 GGGCCACAATTA-GGGGATCAAGTTTTACATAGGAATATATAGAGATAATCTTTTAAAATCTTCT
66 GGGCCACAA-TAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCT
* *
807781 TCTCAAAAACTATTAGGCCAAGAAAGCTCAAATTGGCA
130 TCTCAAAAACTATCAGGCCAAGAAAGCTCAAATTAGCA
* * * * * *
807819 -TGTAA-CTATCCTCAGATAATGTATATTTAAGTTCGTTCAAATCATGGTCCCTGGAGGTAGGGC
1 GTGGAAGC-ATCCTCAGATAGTGTATATTCAAGTTTGTTCAAATCATGGTCCCCGGAGGTAGGGA
* * * ** **
807882 GGGGCCACAATA--GGGAT--ACTTTT---T---TATGTATAGAGAAAATCTTTGGAAATAATCT
65 GGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCT
* * * *
807937 TCTC-AAAACTATTAGGCCAGGAAAGCCCAAATTTG--
130 TCTCAAAAACTATCAGGCCAAGAAAGCTCAAATTAGCA
* * * * * * * * * * *
807972 GTTGGAAGTATCCCCAGATCGTATACATTCAAGTTTGTTTAAATAATAGT-CCAGG-GGTGGGGT
1 G-TGGAAGCATCCTCAGATAGTGTATATTCAAGTTTGTTCAAATCATGGTCCCCGGAGGTAGGGA
* * * *
808035 GAGTCCACAAT-GGGGGATGAA-TGTTTACATA-GAA-ATGTAGAGAAAATCTTTAAAAATCTTC
65 GGGGCCACAATAGGGGGATCAAGT-TTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTC
808096 TT
129 TT
808098 TTTAAAGACT
Statistics
Matches: 374, Mismatches: 54, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
153 15 0.04
154 9 0.02
155 64 0.17
156 32 0.09
159 2 0.01
160 23 0.06
161 1 0.00
162 5 0.01
164 5 0.01
165 3 0.01
166 210 0.56
167 5 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (167 bp):
GTGGAAGCATCCTCAGATAGTGTATATTCAAGTTTGTTCAAATCATGGTCCCCGGAGGTAGGGAG
GGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTT
CTCAAAAACTATCAGGCCAAGAAAGCTCAAATTAGCA
Found at i:816041 original size:11 final size:11
Alignment explanation
Indices: 816025--816049 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
816015 GGGTGTGATC
816025 AAATCTATCAT
1 AAATCTATCAT
816036 AAATCTATCAT
1 AAATCTATCAT
816047 AAA
1 AAA
816050 GCCCTTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATCTATCAT
Found at i:823582 original size:180 final size:180
Alignment explanation
Indices: 823280--824000 Score: 1282
Period size: 180 Copynumber: 4.0 Consensus size: 180
823270 ACCCTACATG
* *
823280 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTAGCATTTTTTTC-ATAAATTATC
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCGATAAATTATC
823344 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
65 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
823409 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
130 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* *
823460 TATATGCAACATTTTGCCAAAAAATGACTAAGTTTAAAAGCTGGTATTTTTTCGATTAATTATCG
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
* * *
823525 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATATACAATTGATCTGCAAAAGAATAAT
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
823590 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* *
823640 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
* *
823705 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTTATCTGCTAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
823770 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* * *
823820 TATATGCAATAATTTGCCAAAAAATGAGTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
*
823885 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAATAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
823950 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
824000 T
1 T
824001 TTTGGCAGCC
Statistics
Matches: 517, Mismatches: 23, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
179 7 0.01
180 510 0.99
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (180 bp):
TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:827174 original size:2 final size:2
Alignment explanation
Indices: 827167--827200 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
827157 AATTAGTAAA
827167 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
827201 ACAGGATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:828511 original size:21 final size:21
Alignment explanation
Indices: 828487--829038 Score: 504
Period size: 21 Copynumber: 26.3 Consensus size: 21
828477 AGATGATTTT
*
828487 ATTATATGCTGTGGGTCTATT
1 ATTATATGCTGTGGGTCTATA
828508 ATTATATGCTGT-GGTACTATA
1 ATTATATGCTGTGGGT-CTATA
*
828529 ATTATATGCTGTGGGTCTATT
1 ATTATATGCTGTGGGTCTATA
* * *
828550 ATTATATGCTGTAGGTCAATT
1 ATTATATGCTGTGGGTCTATA
* * *
828571 ATTATATGTTGTGGGTTTGTA
1 ATTATATGCTGTGGGTCTATA
* **
828592 ATTATATGCTGTGGTTCCCTA
1 ATTATATGCTGTGGGTCTATA
* *
828613 ATTATATGCTGTGGTTTTATA
1 ATTATATGCTGTGGGTCTATA
* *
828634 ATTATATGCTGTGGTTTTATA
1 ATTATATGCTGTGGGTCTATA
* *
828655 ATTATATGCTGTGGTTCTATT
1 ATTATATGCTGTGGGTCTATA
* *
828676 ATTATATGCTGTGGTTCTAAA
1 ATTATATGCTGTGGGTCTATA
* *
828697 ATTATATGCGGTGGTTCTA-A
1 ATTATATGCTGTGGGTCTATA
* *
828717 ATTATATGCTGTGGGTCTTTT
1 ATTATATGCTGTGGGTCTATA
* *
828738 ATTATATGCTGTGGATCTATC
1 ATTATATGCTGTGGGTCTATA
*
828759 ATTATATGCTATGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
828780 ATTATATGCTGTGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
* * *
828801 ATCATATGCTGT-GGTTTCATT
1 ATTATATGCTGTGGGTCT-ATA
828822 ATTATATGCTGTGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
828843 ATTATATGCTGTGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
* *
828864 ATTATATGTTGT-GGTTTAATA
1 ATTATATGCTGTGGGTCT-ATA
828885 ATTATATGCTGTGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
* *
828906 ATTATATGGTGTGGGT-TCATT
1 ATTATATGCTGTGGGTCT-ATA
* *
828927 ATTATATGCTGT-GGTTTCATT
1 ATTATATGCTGTGGGTCT-ATA
*
828948 CTTATATGCTGTGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
*
828969 ATTATATGCTGTGGGT-TCATT
1 ATTATATGCTGTGGGTCT-ATA
* * *
828990 TTTATATGCTG-GGGTTTCATT
1 ATTATATGCTGTGGGTCT-ATA
*
829011 ATCATATGCTGTGGGT-TCATA
1 ATTATATGCTGTGGGTCT-ATA
829032 ATTATAT
1 ATTATAT
829039 ATGCTGTCGG
Statistics
Matches: 465, Mismatches: 54, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
20 34 0.07
21 415 0.89
22 16 0.03
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (21 bp):
ATTATATGCTGTGGGTCTATA
Found at i:828534 original size:42 final size:43
Alignment explanation
Indices: 828487--829038 Score: 559
Period size: 42 Copynumber: 13.2 Consensus size: 43
828477 AGATGATTTT
* *
828487 ATTATATGCTGTGGGTCTATTATTATATGCTGT-GGTACTATA
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * * *
828529 ATTATATGCTGTGGGTCTATTATTATATGCTGTAGG-TCAATT
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * * **
828571 ATTATATGTTGTGGGTTTGTAATTATATGCTGT-GGTTCCCTA
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * *
828613 ATTATATGCTGTGGTTTTATAATTATATGCTGT-GGTTTTATA
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * *
828655 ATTATATGCTGTGGTTCTATTATTATATGCTGT-GGTTCTAAA
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * * *
828697 ATTATATGCGGTGGTTCTA-AATTATATGCTGTGGG-TCTTTT
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * *
828738 ATTATATGCTGTGGATCTATCATTATATGCTATGGGTTC-ATA
1 ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
* * *
828780 ATTATATGCTGTGGGT-TCATAATCATATGCTGTGGTTTC-ATT
1 ATTATATGCTGTGGGTCT-ATAATTATATGCTGTGGGTTCTATA
828822 ATTATATGCTGTGGGT-TCATAATTATATGCTGTGGGTTC-ATA
1 ATTATATGCTGTGGGTCT-ATAATTATATGCTGTGGGTTCTATA
* *
828864 ATTATATGTTGT-GGTTTAATAATTATATGCTGTGGGTTC-ATA
1 ATTATATGCTGTGGGTCT-ATAATTATATGCTGTGGGTTCTATA
* * * *
828906 ATTATATGGTGTGGGT-TCATTATTATATGCTGTGGTTTC-ATT
1 ATTATATGCTGTGGGTCT-ATAATTATATGCTGTGGGTTCTATA
* *
828948 CTTATATGCTGTGGGT-TCATAATTATATGCTGTGGGTTC-ATT
1 ATTATATGCTGTGGGTCT-ATAATTATATGCTGTGGGTTCTATA
* * * *
828990 TTTATATGCTG-GGGTTTCATTATCATATGCTGTGGGTTC-ATA
1 ATTATATGCTGTGGGTCT-ATAATTATATGCTGTGGGTTCTATA
829032 ATTATAT
1 ATTATAT
829039 ATGCTGTCGG
Statistics
Matches: 445, Mismatches: 56, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
41 42 0.09
42 396 0.89
43 7 0.02
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (43 bp):
ATTATATGCTGTGGGTCTATAATTATATGCTGTGGGTTCTATA
Found at i:828557 original size:63 final size:63
Alignment explanation
Indices: 828485--829038 Score: 646
Period size: 63 Copynumber: 8.8 Consensus size: 63
828475 TTAGATGATT
* *
828485 TTATTATATGCTGTGGGTCTATTATTATATGCTGT-GGTACTATAATTATATGCTGTGGG-TCTA
1 TTATTATATGCTGTGGGTTTATTATTATATGCTGTGGGTTC-ATAATTATATGCTGTGGGTTC-A
* ** * ** *
828548 TTATTATATGCTGTAGGTCAATTATTATATGTTGTGGGTTTGTAATTATATGCTGT-GGTTCCC
1 TTATTATATGCTGTGGGTTTATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTT-CA
* * * * *
828611 TAATTATATGCTGTGGTTTTATAATTATATGCTGTGGTTTTATAATTATATGCTGT-GGTTCTA
1 TTATTATATGCTGTGGGTTTATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTC-A
** *
828674 TTATTATATGCTGT-GGTTCTAAAATTATATGCGGT-GGTTC-TAAATTATATGCTGTGGG-TCT
1 TTATTATATGCTGTGGGTT-TATTATTATATGCTGTGGGTTCAT-AATTATATGCTGTGGGTTC-
*
828735 T
63 A
* * * *
828736 TTATTATATGCTGTGGATCTATCATTATATGCTATGGGTTCATAATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTTATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
* *
828799 TAATCATATGCTGT-GGTTTCATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTT-ATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
* * * *
828862 TAATTATATGTTGT-GGTTTAATAATTATATGCTGTGGGTTCATAATTATATGGTGTGGGTTCA
1 TTATTATATGCTGTGGGTTT-ATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
*
828925 TTATTATATGCTGT-GGTTTCATTCTTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
1 TTATTATATGCTGTGGGTTT-ATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
* *
828988 TTTTTATATGCTG-GGGTTTCATTATCATATGCTGTGGGTTCATAATTATAT
1 TTATTATATGCTGTGGGTTT-ATTATTATATGCTGTGGGTTCATAATTATAT
829039 ATGCTGTCGG
Statistics
Matches: 427, Mismatches: 51, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
61 1 0.00
62 54 0.13
63 365 0.85
64 7 0.02
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (63 bp):
TTATTATATGCTGTGGGTTTATTATTATATGCTGTGGGTTCATAATTATATGCTGTGGGTTCA
Found at i:831125 original size:157 final size:156
Alignment explanation
Indices: 830839--831149 Score: 613
Period size: 157 Copynumber: 2.0 Consensus size: 156
830829 ATATATATAN
830839 TATATATATATTTATGTATGATGTGAAACACTGGTAGGTATGTTTGATATCTTGTAATTGTGCAT
1 TATATATATATTTATGTATGATGTGAAACACTGGTAGGTATGTTTGATATCTTGTAATTGTGCAT
830904 GTATATATCTGAGCAGTCACAGTTATTAAGTGTATCTTTCAACAATATCCAAACATCTTTGAAAA
66 GTATATATCTGAGCAGTCACAGTTATTAAGTGTATCTTTCAACAATATCCAAACATCTTTGAAAA
830969 TCAGCTATTTCCATTACTTTGACANTA
131 TCAGCTATTTCCATTACTTTGACA-TA
830996 TATATATATATTTATGTATGATGTGAAACACTGGTAGGTATGTTTGATATCTTGTAATTGTGCAT
1 TATATATATATTTATGTATGATGTGAAACACTGGTAGGTATGTTTGATATCTTGTAATTGTGCAT
831061 GTATATATCTGAGCAGTCACAGTTATTAAGTGTATCTTTCAACAATATCCAAACATCTTTGAAAA
66 GTATATATCTGAGCAGTCACAGTTATTAAGTGTATCTTTCAACAATATCCAAACATCTTTGAAAA
831126 TCAGCTATTTCCATTACTTTGACA
131 TCAGCTATTTCCATTACTTTGACA
831150 ATCCCTGTGA
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (156 bp):
TATATATATATTTATGTATGATGTGAAACACTGGTAGGTATGTTTGATATCTTGTAATTGTGCAT
GTATATATCTGAGCAGTCACAGTTATTAAGTGTATCTTTCAACAATATCCAAACATCTTTGAAAA
TCAGCTATTTCCATTACTTTGACATA
Found at i:831545 original size:21 final size:21
Alignment explanation
Indices: 831519--831569 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
831509 GTATTAAATA
831519 GTTCGTGTAACGTG-GGTGATC
1 GTTCGTGTAACGTGCGG-GATC
*
831540 GTTCGTATAACGTGCGGGATC
1 GTTCGTGTAACGTGCGGGATC
*
831561 GTGCGTGTA
1 GTTCGTGTA
831570 TCAGGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.16, C:0.16, G:0.37, T:0.31
Consensus pattern (21 bp):
GTTCGTGTAACGTGCGGGATC
Found at i:832573 original size:11 final size:11
Alignment explanation
Indices: 832553--832608 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
832543 TAAGTTAGTG
*
832553 ATCGTCCGTGT
1 ATCGTGCGTGT
832564 ATCGTGCGTG-
1 ATCGTGCGTGT
*
832574 ATCGTTCGTGT
1 ATCGTGCGTGT
832585 ATCGTGCGTG-
1 ATCGTGCGTGT
*
832595 ATCGTTCGTGT
1 ATCGTGCGTGT
832606 ATC
1 ATC
832609 AGAAACGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.38
Consensus pattern (11 bp):
ATCGTGCGTGT
Found at i:832576 original size:21 final size:21
Alignment explanation
Indices: 832550--832608 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
832540 CAGTAAGTTA
*
832550 GTGATCGTCCGTGTATCGTGC
1 GTGATCGTTCGTGTATCGTGC
832571 GTGATCGTTCGTGTATCGTGC
1 GTGATCGTTCGTGTATCGTGC
832592 GTGATCGTTCGTGTATC
1 GTGATCGTTCGTGTATC
832609 AGAAACGTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.10, C:0.20, G:0.32, T:0.37
Consensus pattern (21 bp):
GTGATCGTTCGTGTATCGTGC
Found at i:832583 original size:10 final size:10
Alignment explanation
Indices: 832550--832604 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
832540 CAGTAAGTTA
*
832550 GTGATCGTCC
1 GTGATCGTGC
832560 GTGTATCGTGC
1 GTG-ATCGTGC
*
832571 GTGATCGTTC
1 GTGATCGTGC
832581 GTGTATCGTGC
1 GTG-ATCGTGC
*
832592 GTGATCGTTC
1 GTGATCGTGC
832602 GTG
1 GTG
832605 TATCAGAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.09, C:0.20, G:0.35, T:0.36
Consensus pattern (10 bp):
GTGATCGTGC
Found at i:833695 original size:21 final size:21
Alignment explanation
Indices: 833667--834161 Score: 485
Period size: 21 Copynumber: 23.6 Consensus size: 21
833657 CTAAGTATAC
833667 CAGCATATAATAATGAACCCA
1 CAGCATATAATAATGAACCCA
* * *
833688 CCGCATATAATAATTAAACCA
1 CAGCATATAATAATGAACCCA
* *
833709 CAGTATATAATTATGAACCCA
1 CAGCATATAATAATGAACCCA
* * *
833730 CAGCAT-TTATTATGAACCAA
1 CAGCATATAATAATGAACCCA
*
833750 CAGCATATAATAATGAAACCA
1 CAGCATATAATAATGAACCCA
*
833771 CAGCATATAATTATGAACCCA
1 CAGCATATAATAATGAACCCA
* *
833792 CAGAATATAATTATGAACCCA
1 CAGCATATAATAATGAACCCA
* * * *
833813 CAACATATAGTTATGAAACCA
1 CAGCATATAATAATGAACCCA
*
833834 CAGCATATAATAATGAAACCA
1 CAGCATATAATAATGAACCCA
*
833855 CAGCATATAATTATGAACCCA
1 CAGCATATAATAATGAACCCA
*
833876 CAGCATATAATAATGGAA-CCT
1 CAGCATATAATAAT-GAACCCA
* *
833897 CGGCATATAATAATGAAACCA
1 CAGCATATAATAATGAACCCA
833918 CAGCATATAATAAT-AGACCCA
1 CAGCATATAATAATGA-ACCCA
* * *
833939 AAGCATATCATTATAGAA-CCA
1 CAGCATATAATAAT-GAACCCA
833960 CAGCATATAATAAT-AGACCCA
1 CAGCATATAATAATGA-ACCCA
* * *
833981 CAGCATTTAATTATAAACCCA
1 CAGCATATAATAATGAACCCA
*
834002 CAGCATATAATTATAGAA-CCA
1 CAGCATATAATAAT-GAACCCA
*
834023 CAGTATATAATAAT-AGACCCA
1 CAGCATATAATAATGA-ACCCA
*
834044 CAGCATATATTAAT-AGACCCA
1 CAGCATATAATAATGA-ACCCA
* *
834065 CGGCATATAATTATAGAA-CCA
1 CAGCATATAATAAT-GAACCCA
*
834086 CAGCATATAATAAT-AGACCGA
1 CAGCATATAATAATGA-ACCCA
*
834107 CAGCATATAATTATAGAA-CCA
1 CAGCATATAATAAT-GAACCCA
834128 CAGCATATAA-ATATAGAA-CCA
1 CAGCATATAATA-AT-GAACCCA
834149 CAGCATATAATAA
1 CAGCATATAATAA
834162 AATCACCTAA
Statistics
Matches: 398, Mismatches: 56, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.01
20 25 0.06
21 357 0.90
22 10 0.03
23 3 0.01
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.23
Consensus pattern (21 bp):
CAGCATATAATAATGAACCCA
Found at i:833835 original size:63 final size:63
Alignment explanation
Indices: 833667--834161 Score: 580
Period size: 63 Copynumber: 7.9 Consensus size: 63
833657 CTAAGTATAC
* * * * *
833667 CAGCATATAATAATGAACCCACCGCATATAATAATTA-AACCACAGTATATAATTATGAACCCA
1 CAGCATATAATTATGAACCCACAGCATATAATTA-TAGAACCACAGCATATAATAATGAACCCA
* * * *
833730 CAGCAT-TTATTATGAACCAACAGCATATAATAAT-GAAACCACAGCATATAATTATGAACCCA
1 CAGCATATAATTATGAACCCACAGCATATAATTATAG-AACCACAGCATATAATAATGAACCCA
* * * *
833792 CAGAATATAATTATGAACCCACAACATATAGTTAT-GAAACCACAGCATATAATAATGAAACCA
1 CAGCATATAATTATGAACCCACAGCATATAATTATAG-AACCACAGCATATAATAATGAACCCA
* * * * *
833855 CAGCATATAATTATGAACCCACAGCATATAATAATGGAACCTCGGCATATAATAATGAAACCA
1 CAGCATATAATTATGAACCCACAGCATATAATTATAGAACCACAGCATATAATAATGAACCCA
* * *
833918 CAGCATATAATAAT-AGACCCAAAGCATATCATTATAGAACCACAGCATATAATAAT-AGACCCA
1 CAGCATATAATTATGA-ACCCACAGCATATAATTATAGAACCACAGCATATAATAATGA-ACCCA
* * *
833981 CAGCATTTAATTATAAACCCACAGCATATAATTATAGAACCACAGTATATAATAAT-AGACCCA
1 CAGCATATAATTATGAACCCACAGCATATAATTATAGAACCACAGCATATAATAATGA-ACCCA
* *
834044 CAGCATAT-ATTAAT-AGACCCACGGCATATAATTATAGAACCACAGCATATAATAAT-AGACCG
1 CAGCATATAATT-ATGA-ACCCACAGCATATAATTATAGAACCACAGCATATAATAATGA-ACCC
834106 A
63 A
*
834107 CAGCATATAATTATAGAA-CCACAGCATATAAATATAGAACCACAGCATATAATAA
1 CAGCATATAATTAT-GAACCCACAGCATATAATTATAGAACCACAGCATATAATAA
834162 AATCACCTAA
Statistics
Matches: 382, Mismatches: 38, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
61 1 0.00
62 59 0.15
63 315 0.82
64 6 0.02
65 1 0.00
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.23
Consensus pattern (63 bp):
CAGCATATAATTATGAACCCACAGCATATAATTATAGAACCACAGCATATAATAATGAACCCA
Found at i:834637 original size:2 final size:2
Alignment explanation
Indices: 834632--834683 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
834622 AACCACCCCC
834632 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
834674 CA CA CA CA CA
1 CA CA CA CA CA
834684 AATGGCATGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:844612 original size:1 final size:1
Alignment explanation
Indices: 844606--844630 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
844596 ATGCCCCTCA
844606 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
844631 TTGCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:849244 original size:1 final size:1
Alignment explanation
Indices: 849238--849262 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
849228 CGGATCTAGA
849238 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
849263 CCCCCCCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:856927 original size:4 final size:4
Alignment explanation
Indices: 856918--856958 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
856908 AAGCCAAAAT
856918 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA T
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA T
856959 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (4 bp):
TAGA
Found at i:865197 original size:21 final size:21
Alignment explanation
Indices: 865171--865240 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
865161 GTGCGAGAAA
865171 CGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTTTAG
* * **
865192 CGTTTCGTGTGAATCGTGAAG
1 CGTTTCGTGTAAACCGTTTAG
865213 CGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTTTAG
865234 CGTTTCG
1 CGTTTCG
865241 GGCAAAGCGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTTAG
Found at i:865257 original size:42 final size:42
Alignment explanation
Indices: 865171--865296 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
865161 GTGCGAGAAA
* ** * *
865171 CGTTTCGTGTAAACCGTTTAGCGTTTCGTGTGAATCGTGAAG
1 CGTTTCGTGTAAACCGTTTAGCGTTTCGGGCAAAGCGTGCAG
865213 CGTTTCGTGTAAACCGTTTAGCGTTTCGGGCAAAGCGTGCAG
1 CGTTTCGTGTAAACCGTTTAGCGTTTCGGGCAAAGCGTGCAG
* * * * *
865255 CGTTTCGGGCAAAGCGTGTAAATCGTTTCGGGCAAAGCGTGC
1 CGTTTCGTGTAAACCGT-T-TAGCGTTTCGGGCAAAGCGTGC
865297 GAGAACCGTG
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 51 0.71
43 1 0.01
44 20 0.28
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (42 bp):
CGTTTCGTGTAAACCGTTTAGCGTTTCGGGCAAAGCGTGCAG
Found at i:865285 original size:23 final size:21
Alignment explanation
Indices: 865206--865295 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
865196 TCGTGTGAAT
* * *
865206 CGTGAAGCGTTTCGTGTAAAC
1 CGTGAAGCGTTTCGGGCAAAG
**
865227 CGTTTAGCGTTTCGGGCAAAG
1 CGTGAAGCGTTTCGGGCAAAG
*
865248 CGTGCAGCGTTTCGGGCAAAG
1 CGTGAAGCGTTTCGGGCAAAG
*
865269 CGTGTAAATCGTTTCGGGCAAAG
1 CGTG--AAGCGTTTCGGGCAAAG
865292 CGTG
1 CGTG
865296 CGAGAACCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 39 0.67
23 19 0.33
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (21 bp):
CGTGAAGCGTTTCGGGCAAAG
Found at i:866807 original size:21 final size:21
Alignment explanation
Indices: 866783--866889 Score: 142
Period size: 21 Copynumber: 5.1 Consensus size: 21
866773 GTGCGAGAAT
866783 CGTTTCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
866804 CGTTTCGTGTAAATCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
* * * *
866825 CGTTTCGGGCAAAGCGTGCAG
1 CGTTTCGTGTAAACCGTTCAG
866846 CGTTTCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
866867 CGTTTCGTGTGAACCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
866888 CG
1 CG
866890 AGCGTGTAGC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTCAG
Found at i:866901 original size:11 final size:11
Alignment explanation
Indices: 866885--866918 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
866875 GTGAACCGTT
866885 TAGCGAGCGTG
1 TAGCGAGCGTG
866896 TAGCGAGCGTG
1 TAGCGAGCGTG
*
866907 CAGCGAGCGTG
1 TAGCGAGCGTG
866918 T
1 T
866919 GGTGTAGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (11 bp):
TAGCGAGCGTG
Found at i:866918 original size:63 final size:63
Alignment explanation
Indices: 866788--866918 Score: 151
Period size: 63 Copynumber: 2.1 Consensus size: 63
866778 AGAATCGTTT
* ** **
866788 CGTGTAAACCGTTCAGCGTTTCGTGTAAATCGTTTAGCGTTTCGGGCAAAGCGTGCAGCGTTT
1 CGTGTAAACCGTTCAGCGTTTCGTGTAAACCGTTTAGCGTAGCGGGCAAAGCGTGCAGCGTAG
* *
866851 CGTGTAAACCGTTCAGCGTTTCGTGTGAACCGTTTAGCG-AGCGTGTAGC-GAGCGTGCAGCG-A
1 CGTGTAAACCGTTCAGCGTTTCGTGTAAACCGTTTAGCGTAGCG-G--GCAAAGCGTGCAGCGTA
866913 G
63 G
866914 CGTGT
1 CGTGT
866919 GGTGTAGTAG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.03
63 43 0.74
64 11 0.19
65 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.28
Consensus pattern (63 bp):
CGTGTAAACCGTTCAGCGTTTCGTGTAAACCGTTTAGCGTAGCGGGCAAAGCGTGCAGCGTAG
Found at i:879447 original size:2 final size:2
Alignment explanation
Indices: 879442--879486 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
879432 TCAGATCTAA
879442 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
879484 AC A
1 AC A
879487 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:885089 original size:24 final size:24
Alignment explanation
Indices: 885057--885103 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
885047 AATTTTATCA
885057 ATTTTCTTTCCTTACCAAGGTCCT
1 ATTTTCTTTCCTTACCAAGGTCCT
* *
885081 ATTTTCTTTTCTTATCAAGGTCC
1 ATTTTCTTTCCTTACCAAGGTCC
885104 AGATATTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTTCTTTCCTTACCAAGGTCCT
Found at i:891449 original size:2 final size:2
Alignment explanation
Indices: 891442--891490 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
891432 AGAATTTGAA
891442 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
891484 AG AG AG A
1 AG AG AG A
891491 ATTATAAGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:892209 original size:5 final size:5
Alignment explanation
Indices: 892190--892318 Score: 138
Period size: 5 Copynumber: 26.0 Consensus size: 5
892180 CTGTAAAGTG
*
892190 CGAAA CGAAA TCGAAA CGAAA CGAAA CGAAA TCG-AA CGAAA CGAAA CGAAT
1 CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA
* * * * * *
892241 CCAAT CGAAA CGAAA CGAAA CCAAT CGAAA CCAAA CGAAA CCAAA CGAAA
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
* *
892291 CGAAA CCAAA --AAT CGAAA CGAAA CGAAA
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA
892319 TTGAATTTAA
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
3 2 0.02
4 2 0.02
5 93 0.89
6 7 0.07
ACGTcount: A:0.57, C:0.23, G:0.16, T:0.05
Consensus pattern (5 bp):
CGAAA
Found at i:892567 original size:2 final size:2
Alignment explanation
Indices: 892560--892601 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
892550 TTCAGACGTT
892560 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
892602 TGCCTTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:892626 original size:5 final size:5
Alignment explanation
Indices: 892616--892692 Score: 111
Period size: 5 Copynumber: 15.2 Consensus size: 5
892606 TTAAAACTTG
* *
892616 GTTTC GTTTC GTTTC GATTG GTTTC GTTTC GTTTC GTTTC G-TTC GATTTC
1 GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC GTTTC G-TTTC
892666 GTTTC GTTTC GTTTC GATTTC GTTTC G
1 GTTTC GTTTC GTTTC G-TTTC GTTTC G
892693 CACTTTACAG
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
4 4 0.06
5 52 0.80
6 9 0.14
ACGTcount: A:0.04, C:0.18, G:0.22, T:0.56
Consensus pattern (5 bp):
GTTTC
Found at i:893884 original size:12 final size:12
Alignment explanation
Indices: 893851--893885 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
893841 TTCCGTTAAA
*
893851 TTCCGTTCCACT
1 TTCCGTTCCGCT
*
893863 TTCCGTTCCGTT
1 TTCCGTTCCGCT
893875 TTCCGTTCCGC
1 TTCCGTTCCGC
893886 GTTTTAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.40, G:0.14, T:0.43
Consensus pattern (12 bp):
TTCCGTTCCGCT
Found at i:898844 original size:2 final size:2
Alignment explanation
Indices: 898837--898870 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
898827 TATATGTAAA
898837 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
898871 AGTGTATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:899552 original size:2 final size:2
Alignment explanation
Indices: 899545--899604 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
899535 TTGTTAGAAA
899545 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
899587 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
899605 AAAAAGACGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:901993 original size:12 final size:12
Alignment explanation
Indices: 901969--902001 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
901959 ATCACATTTT
901969 GTCCGTC-GTCC
1 GTCCGTCTGTCC
*
901980 GTCTGTCTGTCC
1 GTCCGTCTGTCC
901992 GTCCGTCTGT
1 GTCCGTCTGT
902002 AAGCTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.00, C:0.36, G:0.27, T:0.36
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:908192 original size:13 final size:15
Alignment explanation
Indices: 908168--908200 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
908158 TACCAAAACA
908168 AAAACAAAACAAC-C
1 AAAACAAAACAACTC
908182 AAAAC-AAACAACTC
1 AAAACAAAACAACTC
908196 AAAAC
1 AAAAC
908201 GCGATCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.70, C:0.27, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAACAAAACAACTC
Found at i:912154 original size:2 final size:2
Alignment explanation
Indices: 912147--912186 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
912137 TAGAATTTAT
912147 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
912187 AAGATGAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:922461 original size:73 final size:73
Alignment explanation
Indices: 922342--922487 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
922332 AAATTGAGGC
922342 GCCATTGAGGTTTGCTTATTTATATCTAAATATTTAATCGTAATACTATGACGGCTTAAAATTAT
1 GCCATTGAGGTTTGCTTATTTATATCTAAATATTTAATCGTAATACTATGACGGCTTAAAATTAT
922407 ATAAATAT
66 ATAAATAT
* *
922415 GCCATTGAGGTTTGCTTATTTATATTTAAATATTTAATCGTAATACTATGATGGCTTAAAATTAT
1 GCCATTGAGGTTTGCTTATTTATATCTAAATATTTAATCGTAATACTATGACGGCTTAAAATTAT
922480 ATAAATAT
66 ATAAATAT
922488 AAGTAATAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (73 bp):
GCCATTGAGGTTTGCTTATTTATATCTAAATATTTAATCGTAATACTATGACGGCTTAAAATTAT
ATAAATAT
Found at i:923127 original size:18 final size:18
Alignment explanation
Indices: 923093--923130 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
923083 CATATTCAGG
*
923093 ATTTTTTAGTAATAACAC
1 ATTTTTTAGTAACAACAC
923111 ATTTTTTA-TGAACAACAC
1 ATTTTTTAGT-AACAACAC
923129 AT
1 AT
923131 GTGCTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (18 bp):
ATTTTTTAGTAACAACAC
Found at i:925144 original size:55 final size:55
Alignment explanation
Indices: 925084--925194 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
925074 ATGGAGTCAT
925084 AATAAAATATATGTGGACAATGTGGTATATTACATGTAGATCCTGTATAAATAAA
1 AATAAAATATATGTGGACAATGTGGTATATTACATGTAGATCCTGTATAAATAAA
925139 AATAAAATATATGTGGACAATGTGGTATATTACATGTAGATCCTGTATAAATAAA
1 AATAAAATATATGTGGACAATGTGGTATATTACATGTAGATCCTGTATAAATAAA
925194 A
1 A
925195 GTCCATTCCC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.32
Consensus pattern (55 bp):
AATAAAATATATGTGGACAATGTGGTATATTACATGTAGATCCTGTATAAATAAA
Found at i:926925 original size:38 final size:38
Alignment explanation
Indices: 926874--926967 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
926864 NNNNNNNNNN
* * *
926874 ACACTTGGCTAGCGAAGATGTGTGTGAAAAGGAATCGG
1 ACACTTGGCTAGCGAAGATGTGTATGAAAACGAATCAG
926912 ACACTTGGCTAGCGAAGATGTGTATGAAAACGAATCAG
1 ACACTTGGCTAGCGAAGATGTGTATGAAAACGAATCAG
*
926950 ACACTTGGCTAGCAAAGA
1 ACACTTGGCTAGCGAAGA
926968 CGGGCTAAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (38 bp):
ACACTTGGCTAGCGAAGATGTGTATGAAAACGAATCAG
Found at i:930118 original size:2 final size:2
Alignment explanation
Indices: 930113--930154 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
930103 ATATGGCATT
930113 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
930155 AGTTCATCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:936656 original size:21 final size:22
Alignment explanation
Indices: 936623--936679 Score: 107
Period size: 21 Copynumber: 2.6 Consensus size: 22
936613 GAGAGAGAGA
936623 GAGAGAGAGAAGGAAGGGGAAG
1 GAGAGAGAGAAGGAAGGGGAAG
936645 GAGAGA-AGAAGGAAGGGGAAG
1 GAGAGAGAGAAGGAAGGGGAAG
936666 GAGAGAGAGAAGGA
1 GAGAGAGAGAAGGA
936680 GAGAGAGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (22 bp):
GAGAGAGAGAAGGAAGGGGAAG
Found at i:938420 original size:37 final size:37
Alignment explanation
Indices: 938379--938892 Score: 469
Period size: 37 Copynumber: 13.9 Consensus size: 37
938369 GGAAGCAAAT
* *
938379 TTTTCTTTCATCTCGTAACCAGTTACTAGTAGCTAGC
1 TTTTCTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
* * *
938416 TTTTCTTAC-TCTTCGTAGCCAGTTACTAGTTGCCAAC
1 TTTTCTTACATC-TCGTAGCCAGTTACTAGTAGCTAGC
* * *
938453 TTTTATTTA-ATCTCGTAGACAGTTACTAGTAGCTAGT
1 TTTT-CTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
*
938490 TTTTCTTAC-TCCTCGTAGCCAGTTACTAGTAGAC-AAC
1 TTTTCTTACAT-CTCGTAGCCAGTTACTAGTAG-CTAGC
* *
938527 TTTTATTTA-ATCTCGTAGACAGTTACTAGTAGCTAGC
1 TTTT-CTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
* *
938564 TTTTCTTAC-TCCTCGTAGCCAGTTACTAGTAGCCAAC
1 TTTTCTTACAT-CTCGTAGCCAGTTACTAGTAGCTAGC
* *
938601 TTTTATTTA-ATCTCGTAGCCAGTTATTAGTAGCTAGC
1 TTTT-CTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
* *
938638 CTTTCTTAC-TCGTCGTAGCCAGTTACTAGTAGAC-AAC
1 TTTTCTTACATC-TCGTAGCCAGTTACTAGTAG-CTAGC
* **
938675 TTTTATTTA-ATCTCGTAGATAGTTACTAGTAGCTAGC
1 TTTT-CTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
*
938712 TTTTCTTAC-TCCTCGTAGCCAGTTACTAGTAGCCAGC
1 TTTTCTTACAT-CTCGTAGCCAGTTACTAGTAGCTAGC
* ** * * *
938749 TTTTATTTTATCCCGTTGCCAGTTACTAGTAGCTAGA
1 TTTTCTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
* * * * * *
938786 ATTTCTTACCTCTCGTAGCTATTTACAAGTAG-TCAAC
1 TTTTCTTACATCTCGTAGCCAGTTACTAGTAGCT-AGC
* * * *
938823 TTTTATTTCATCTCCTAGCCAATTACTAGTAGCTAGC
1 TTTTCTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
* *
938860 TTTTCTAACTAT-TCGTCGCCAGTTACTAGTAGC
1 TTTTCTTAC-ATCTCGTAGCCAGTTACTAGTAGC
938893 CAGTTACTAG
Statistics
Matches: 379, Mismatches: 73, Indels: 50
0.75 0.15 0.10
Matches are distributed among these distances:
36 22 0.06
37 333 0.88
38 24 0.06
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (37 bp):
TTTTCTTACATCTCGTAGCCAGTTACTAGTAGCTAGC
Found at i:938509 original size:74 final size:74
Alignment explanation
Indices: 938388--938894 Score: 721
Period size: 74 Copynumber: 6.9 Consensus size: 74
938378 TTTTTCTTTC
* *
938388 ATCTCGTA-ACCAGTTACTAGTAGCTAGCTTTTCTTACTCTTCGTAGCCAGTTACTAGTTGCCAA
1 ATCTCGTAGA-CAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAA
938452 CTTTTATTTA
65 CTTTTATTTA
* *
938462 ATCTCGTAGACAGTTACTAGTAGCTAGTTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGACAAC
1 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAAC
938527 TTTTATTTA
66 TTTTATTTA
938536 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAAC
1 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAAC
938601 TTTTATTTA
66 TTTTATTTA
* * * * *
938610 ATCTCGTAGCCAGTTATTAGTAGCTAGCCTTTCTTACTCGTCGTAGCCAGTTACTAGTAGACAAC
1 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAAC
938675 TTTTATTTA
66 TTTTATTTA
* *
938684 ATCTCGTAGATAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAGC
1 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAAC
*
938749 TTTTATTTT
66 TTTTATTTA
* * * ** * * * *
938758 ATCCCGTTGCCAGTTACTAGTAGCTAGAATTTCTTAC-CTCTCGTAGCTATTTACAAGTAGTCAA
1 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTC-CTCGTAGCCAGTTACTAGTAGCCAA
*
938822 CTTTTATTTC
65 CTTTTATTTA
* * * * ** *
938832 ATCTCCTAGCCAATTACTAGTAGCTAGCTTTTCTAACTATTCGTCGCCAGTTACTAGTAGCCA
1 ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCA
938895 GTTACTAGTA
Statistics
Matches: 385, Mismatches: 45, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
73 1 0.00
74 383 0.99
75 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (74 bp):
ATCTCGTAGACAGTTACTAGTAGCTAGCTTTTCTTACTCCTCGTAGCCAGTTACTAGTAGCCAAC
TTTTATTTA
Found at i:938896 original size:14 final size:14
Alignment explanation
Indices: 938877--938906 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
938867 ACTATTCGTC
938877 GCCAGTTACTAGTA
1 GCCAGTTACTAGTA
938891 GCCAGTTACTAGTA
1 GCCAGTTACTAGTA
938905 GC
1 GC
938907 TAACTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (14 bp):
GCCAGTTACTAGTA
Found at i:939926 original size:4 final size:4
Alignment explanation
Indices: 939917--939943 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
939907 TTAAATGATT
939917 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
939944 ATTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:940097 original size:1 final size:1
Alignment explanation
Indices: 940081--940127 Score: 76
Period size: 1 Copynumber: 47.0 Consensus size: 1
940071 TAAAATTAGC
* *
940081 AAAAAACAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
940128 CAAATGATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:940449 original size:2 final size:2
Alignment explanation
Indices: 940442--940501 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
940432 TTAACAAAAC
940442 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
940484 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
940502 GTGACAAGGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:946122 original size:18 final size:18
Alignment explanation
Indices: 946099--946196 Score: 160
Period size: 18 Copynumber: 5.4 Consensus size: 18
946089 GTTCCCCCGC
946099 CCACCACCCAAGCACCAA
1 CCACCACCCAAGCACCAA
*
946117 CCACCACCAAAGCACCAA
1 CCACCACCCAAGCACCAA
*
946135 CCACCACTCAAGCACCAA
1 CCACCACCCAAGCACCAA
*
946153 CCACCACCAAAGCACCAA
1 CCACCACCCAAGCACCAA
*
946171 CCACCACCCAGGCACCAA
1 CCACCACCCAAGCACCAA
946189 CCACCACC
1 CCACCACC
946197 ATGCCACCCA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.39, C:0.54, G:0.06, T:0.01
Consensus pattern (18 bp):
CCACCACCCAAGCACCAA
Found at i:946176 original size:15 final size:15
Alignment explanation
Indices: 946119--946176 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 15
946109 AGCACCAACC
946119 ACCACCAAAGCACCA
1 ACCACCAAAGCACCA
946134 ACCACCACTCAAGCACCAA
1 ACCACCA---AAGCACC-A
946153 CCACCACCAAAGCACCA
1 --ACCACCAAAGCACCA
946170 ACCACCA
1 ACCACCA
946177 CCCAGGCACC
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 14 0.38
17 1 0.03
18 14 0.38
19 1 0.03
21 7 0.19
ACGTcount: A:0.43, C:0.50, G:0.05, T:0.02
Consensus pattern (15 bp):
ACCACCAAAGCACCA
Found at i:946214 original size:36 final size:36
Alignment explanation
Indices: 946099--946197 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
946089 GTTCCCCCGC
946099 CCACCACCCAAGCACCAACCACCACCAAAGCACCAA
1 CCACCACCCAAGCACCAACCACCACCAAAGCACCAA
*
946135 CCACCACTCAAGCACCAACCACCACCAAAGCACCAA
1 CCACCACCCAAGCACCAACCACCACCAAAGCACCAA
*
946171 CCACCACCCAGGCACCAACCACCACCA
1 CCACCACCCAAGCACCAACCACCACCA
946198 TGCCACCCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.39, C:0.54, G:0.06, T:0.01
Consensus pattern (36 bp):
CCACCACCCAAGCACCAACCACCACCAAAGCACCAA
Found at i:947186 original size:12 final size:12
Alignment explanation
Indices: 947169--947193 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
947159 TGTAGATTCA
947169 AGTGATGATGTC
1 AGTGATGATGTC
947181 AGTGATGATGTC
1 AGTGATGATGTC
947193 A
1 A
947194 TGCATGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (12 bp):
AGTGATGATGTC
Found at i:948089 original size:1 final size:1
Alignment explanation
Indices: 948085--948114 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
948075 GGGGGGGGGG
948085 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
948115 GGGGGGGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:952071 original size:20 final size:20
Alignment explanation
Indices: 952046--952100 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
952036 ATAACAGTAT
952046 TTTTTTCTGTATCCAAAATA
1 TTTTTTCTGTATCCAAAATA
* * * * *
952066 TTTTTTATGAATCTATACTA
1 TTTTTTCTGTATCCAAAATA
952086 TTTTTTCTGTATCCA
1 TTTTTTCTGTATCCA
952101 TGTATTTTTC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTTTCTGTATCCAAAATA
Found at i:952109 original size:20 final size:20
Alignment explanation
Indices: 952042--952109 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
952032 TCAGATAACA
952042 GTATTTTTTTCTGTATCCA-
1 GTATTTTTTTCTGTATCCAT
** * * *
952061 AAATATTTTTTATGAATCTAT
1 GTAT-TTTTTTCTGTATCCAT
*
952082 ACTA-TTTTTTCTGTATCCAT
1 -GTATTTTTTTCTGTATCCAT
952102 GTATTTTT
1 GTATTTTT
952110 CATGCGCCTG
Statistics
Matches: 34, Mismatches: 11, Indels: 7
0.65 0.21 0.13
Matches are distributed among these distances:
19 4 0.12
20 29 0.85
22 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (20 bp):
GTATTTTTTTCTGTATCCAT
Found at i:955724 original size:2 final size:2
Alignment explanation
Indices: 955717--955763 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
955707 CATAATTATA
955717 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
955759 AG AG A
1 AG AG A
955764 TTAATTTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:960259 original size:112 final size:109
Alignment explanation
Indices: 960039--960259 Score: 284
Period size: 112 Copynumber: 2.0 Consensus size: 109
960029 CACTGGCGAG
* *
960039 AAATGGTACTCGGTGAGAACTGGTTGCACGCCAGTAGTAAAATAATTCTCTATAATTTGCCAACC
1 AAATGGTACTCGGCGAGAACTGGTTGCACGCCAGTAGTAAAATAATTCTATATAATTTGCCAACC
* * ** *
960104 TGAGACGATTTATGATATATGTGTAATTTTTGATTTTTTTTTTT
66 TAAGACGATTTAAGATATATGTGTAATTTTTGAAGTTTATTTTT
* *
960148 AAATGGTACTCGGCGAGAACT-GTTCGCACGCCAGTAGTAAAATTATTTTTTATCATAATTTGCC
1 AAATGGTACTCGGCGAGAACTGGTT-GCACGCCAGTAGTAAAA-TA-ATTCTAT-ATAATTTGCC
* *
960212 AA-CTCAAGATGATTTAAGATATATGTGTAATTTTTTAAGTTTATTTTT
62 AACCT-AAGACGATTTAAGATATATGTGTAATTTTTGAAGTTTATTTTT
960260 TGCAGGATAA
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
108 3 0.03
109 37 0.39
110 2 0.02
111 6 0.06
112 48 0.50
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (109 bp):
AAATGGTACTCGGCGAGAACTGGTTGCACGCCAGTAGTAAAATAATTCTATATAATTTGCCAACC
TAAGACGATTTAAGATATATGTGTAATTTTTGAAGTTTATTTTT
Found at i:963397 original size:20 final size:20
Alignment explanation
Indices: 963372--963439 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
963362 TAAAATTCAG
963372 TTTATGAAGGATTTTATGAT
1 TTTATGAAGGATTTTATGAT
* * * *
963392 TTTATGATA-TACATTTATCAG
1 TTTATGA-AGGA-TTTTATGAT
*
963413 TTTATGGAGGATTTTATGAT
1 TTTATGAAGGATTTTATGAT
963433 TTTATGA
1 TTTATGA
963440 TATACAGATT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTATGAAGGATTTTATGAT
Found at i:963425 original size:41 final size:41
Alignment explanation
Indices: 963368--963445 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
963358 CAGATAAAAT
963368 TCAGTTTATGAAGGATTTTATGATTTTATGATATACATTTA
1 TCAGTTTATGAAGGATTTTATGATTTTATGATATACATTTA
*
963409 TCAGTTTATGGAGGATTTTATGATTTTATGATATACA
1 TCAGTTTATGAAGGATTTTATGATTTTATGATATACA
963446 GATTTCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (41 bp):
TCAGTTTATGAAGGATTTTATGATTTTATGATATACATTTA
Found at i:966155 original size:33 final size:32
Alignment explanation
Indices: 966109--966174 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 32
966099 AGAATTAAAT
966109 TGAATTTTGGGCACAAAAAGATATGTTGTAAG
1 TGAATTTTGGGCACAAAAAGATATGTTGTAAG
*
966141 TNGAATTTTTGGCACAAAAAGATATGTTGTAAG
1 T-GAATTTTGGGCACAAAAAGATATGTTGTAAG
966174 T
1 T
966175 CGTAAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.33
Consensus pattern (32 bp):
TGAATTTTGGGCACAAAAAGATATGTTGTAAG
Found at i:981216 original size:20 final size:20
Alignment explanation
Indices: 981127--981830 Score: 855
Period size: 20 Copynumber: 35.1 Consensus size: 20
981117 TGCAAGTGGC
*
981127 TTACATTAGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
* * * *
981147 TTGCATTAGTGTAAATGGA-T
1 TTACATTGGTGTAGAT-AACT
* * ***
981167 TTATATTGGTGTAGGTGGGT
1 TTACATTGGTGTAGATAACT
* * *
981187 TAACAATGGTGTAGATATCT
1 TTACATTGGTGTAGATAACT
**
981207 TTACATTGGTGTAGATGGCT
1 TTACATTGGTGTAGATAACT
981227 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
981247 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
*
981267 ATACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
* *
981287 TTACTTTGGTGTAAATAACT
1 TTACATTGGTGTAGATAACT
* **
981307 TTACAGTAATGTAGATAACT
1 TTACATTGGTGTAGATAACT
981327 TTACATTGGTGTATAGGA-AACT
1 TTACATTGGTG--TA-GATAACT
981349 TTACATTGGTGTAGATAA-T
1 TTACATTGGTGTAGATAACT
* **
981368 TTAACATTGGTGTAGGTGGCT
1 TT-ACATTGGTGTAGATAACT
* *
981389 TTATAGTT-GTGTAGATATCT
1 TTACA-TTGGTGTAGATAACT
* *
981409 TTACATCGGTGTAGATATCT
1 TTACATTGGTGTAGATAACT
981429 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
*
981449 TTACATTGGTGTAGATATCT
1 TTACATTGGTGTAGATAACT
981469 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
981489 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
*
981509 TTACATTGGTGTAGATAAAT
1 TTACATTGGTGTAGATAACT
* * *
981529 TTACAGTAGTGTAAATAACT
1 TTACATTGGTGTAGATAACT
981549 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
**
981569 TTACATTGGTGTAGATATTT
1 TTACATTGGTGTAGATAACT
981589 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
981609 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
*
981629 TTACATTGGTGTAGATATCT
1 TTACATTGGTGTAGATAACT
*
981649 TTACATTGGTGCAGATAACT
1 TTACATTGGTGTAGATAACT
981669 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
* * *
981689 TTACAGTAGTGTAAATAACT
1 TTACATTGGTGTAGATAACT
* * *
981709 TTACATTCGTGTAGGTGACT
1 TTACATTGGTGTAGATAACT
981729 TTACATTGGTGTAGATAA-T
1 TTACATTGGTGTAGATAACT
**
981748 TTAACATTGGTGTTAG-TGGCT
1 TT-ACATTGGTG-TAGATAACT
*
981769 TTATAGTT-GTGTAGATAACT
1 TTACA-TTGGTGTAGATAACT
*
981789 TTACATCGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
981809 TTACATTGGTGTAGATAACT
1 TTACATTGGTGTAGATAACT
981829 TT
1 TT
981831 TCCCGAAGCA
Statistics
Matches: 586, Mismatches: 82, Indels: 32
0.84 0.12 0.05
Matches are distributed among these distances:
19 14 0.02
20 539 0.92
21 14 0.02
22 17 0.03
23 2 0.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (20 bp):
TTACATTGGTGTAGATAACT
Found at i:983279 original size:20 final size:20
Alignment explanation
Indices: 983250--983605 Score: 358
Period size: 20 Copynumber: 17.9 Consensus size: 20
983240 AGATGCGTGG
983250 CTTTACATTGGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
* * **
983270 CTTAACATTGGTGTAGGTGG
1 CTTTACATTGGTGTAGATAA
*
983290 CTTTACATTGGTGCAGATAA
1 CTTTACATTGGTGTAGATAA
* * ** * **
983310 CTTAAAATTGGTCAACATGG
1 CTTTACATTGGTGTAGATAA
*
983330 CTTAACATTGGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
*
983350 TTTTACATTGGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
*
983370 CTTTACATTTGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
* *
983390 CTTTACATTGGTGTAGGTGA
1 CTTTACATTGGTGTAGATAA
*
983410 CTTTAGATTGGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
*
983430 CTTTACATTGGTATAGATAA
1 CTTTACATTGGTGTAGATAA
*
983450 CTTTACATTGGTGTAGCTAA
1 CTTTACATTGGTGTAGATAA
983470 CTTTACATTGGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
* * **
983490 CGTTACATTGGTGTAGGTGG
1 CTTTACATTGGTGTAGATAA
* *
983510 TTTTATACTT-GTGTAGATAA
1 CTTTACA-TTGGTGTAGATAA
* * **
983530 -TTTAACATTAGTGTAGGTGG
1 CTTT-ACATTGGTGTAGATAA
*
983550 CATTACA-TGGTGTAGATAA
1 CTTTACATTGGTGTAGATAA
* *
983569 CTTAACATTGCTGTAGATAA
1 CTTTACATTGGTGTAGATAA
* *
983589 CTTAACATCGGTGTAGA
1 CTTTACATTGGTGTAGA
983606 CGGCTAGTCA
Statistics
Matches: 270, Mismatches: 61, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
19 18 0.07
20 248 0.92
21 4 0.01
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (20 bp):
CTTTACATTGGTGTAGATAA
Found at i:983926 original size:15 final size:15
Alignment explanation
Indices: 983906--983936 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
983896 AAATGAAATG
983906 GATCTATTTTAGGAT
1 GATCTATTTTAGGAT
983921 GATCTATTTTAGGAT
1 GATCTATTTTAGGAT
983936 G
1 G
983937 GCATTTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (15 bp):
GATCTATTTTAGGAT
Found at i:984917 original size:2 final size:2
Alignment explanation
Indices: 984910--984965 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
984900 TACCAACCAA
984910 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
984952 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
984966 NNNNNNGCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:987961 original size:2 final size:2
Alignment explanation
Indices: 987954--987986 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
987944 ATTAAAGATT
987954 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
987987 CAATTATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:988317 original size:2 final size:2
Alignment explanation
Indices: 988299--988339 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
988289 CATAAACTAA
* *
988299 CT CT CT TT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
988340 CACATAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:990769 original size:12 final size:12
Alignment explanation
Indices: 990735--990771 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
990725 GCACATCACA
990735 TAAATTACTATT
1 TAAATTACTATT
*
990747 TAAA-TAGTATT
1 TAAATTACTATT
990758 TAAATTACTATT
1 TAAATTACTATT
990770 TA
1 TA
990772 CTATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (12 bp):
TAAATTACTATT
Found at i:993552 original size:31 final size:31
Alignment explanation
Indices: 993514--993744 Score: 329
Period size: 31 Copynumber: 7.4 Consensus size: 31
993504 TCCATATAAG
993514 GGCCAAAATGCACGATCCTCTCCCAAACCAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAA
* **
993545 GGCCAAAA-ACATACGATCCTCTCCCAAACTGA
1 GGCCAAAATGC--ACGATCCTCTCCCAAACCAA
* * *
993577 GGCCAAAATGTATGATCCTCTCCCAAACCAT
1 GGCCAAAATGCACGATCCTCTCCCAAACCAA
***
993608 GGCCAAAACATACGATCCTCTCCCAAACCAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAA
993639 GGCCAAAATGCACGATCCTCTCCCAAACCAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAA
**
993670 GGCCAAAATATACGATCCTCTCCCAAACCAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAA
*
993701 GGCCAAAATGCACGATCCTCTCCCAAACCAT
1 GGCCAAAATGCACGATCCTCTCCCAAACCAA
993732 GGCCAAAATGCAC
1 GGCCAAAATGCAC
993745 NAGGCCAACA
Statistics
Matches: 176, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
30 1 0.01
31 149 0.85
32 26 0.15
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.15
Consensus pattern (31 bp):
GGCCAAAATGCACGATCCTCTCCCAAACCAA
Found at i:993740 original size:62 final size:62
Alignment explanation
Indices: 993514--993739 Score: 380
Period size: 62 Copynumber: 3.6 Consensus size: 62
993504 TCCATATAAG
**
993514 GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCCAAAAACATACGATCCTCTCCCAAACTGA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCC-AAAACATACGATCCTCTCCCAAACCAA
* * *
993577 GGCCAAAATGTATGATCCTCTCCCAAACCATGGCCAAAACATACGATCCTCTCCCAAACCAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCCAAAACATACGATCCTCTCCCAAACCAA
*
993639 GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCCAAAATATACGATCCTCTCCCAAACCAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCCAAAACATACGATCCTCTCCCAAACCAA
*
993701 GGCCAAAATGCACGATCCTCTCCCAAACCATGGCCAAAA
1 GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCCAAAA
993740 TGCACNAGGC
Statistics
Matches: 153, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 121 0.79
63 32 0.21
ACGTcount: A:0.36, C:0.36, G:0.12, T:0.15
Consensus pattern (62 bp):
GGCCAAAATGCACGATCCTCTCCCAAACCAAGGCCAAAACATACGATCCTCTCCCAAACCAA
Found at i:1002434 original size:15 final size:16
Alignment explanation
Indices: 1002404--1002452 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
1002394 CATACAGCTT
* *
1002404 ACTCCACTTATATTGA
1 ACTCCGCTTATTTTGA
1002420 ACT-CGCTTATTTTGAA
1 ACTCCGCTTATTTTG-A
*
1002436 ATTCCGCTTATTTTGA
1 ACTCCGCTTATTTTGA
1002452 A
1 A
1002453 ATAGAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 9 0.32
16 8 0.29
17 11 0.39
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (16 bp):
ACTCCGCTTATTTTGA
Found at i:1002535 original size:17 final size:17
Alignment explanation
Indices: 1002515--1002548 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1002505 GGATATAATG
* *
1002515 ATATCGGTTATTTTGAA
1 ATATCGCTTATATTGAA
1002532 ATATCGCTTATATTGAA
1 ATATCGCTTATATTGAA
1002549 GCCACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (17 bp):
ATATCGCTTATATTGAA
Found at i:1012644 original size:6 final size:6
Alignment explanation
Indices: 1012629--1012691 Score: 60
Period size: 6 Copynumber: 11.0 Consensus size: 6
1012619 ACGACGGTTA
* * * * *
1012629 CCTAAC CCTAAT CCTAA- ACTAAC CCTAAT CCTAAC CCTAA- ACTAAT
1 CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC
1012675 CCTAAC CCTAA- CCTAAC
1 CCTAAC CCTAAC CCTAAC
1012692 AGCCTGTCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 13 0.28
6 33 0.72
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (6 bp):
CCTAAC
Found at i:1012652 original size:17 final size:17
Alignment explanation
Indices: 1012630--1012662 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1012620 CGACGGTTAC
1012630 CTAACCCTAATCCTAAA
1 CTAACCCTAATCCTAAA
1012647 CTAACCCTAATCCTAA
1 CTAACCCTAATCCTAA
1012663 CCCTAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.24
Consensus pattern (17 bp):
CTAACCCTAATCCTAAA
Found at i:1012655 original size:23 final size:22
Alignment explanation
Indices: 1012629--1012690 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 22
1012619 ACGACGGTTA
1012629 CCTAACCCTAATCCTAAACTAAC
1 CCTAACCCTAA-CCTAAACTAAC
* *
1012652 CCTAATCCTAACCCTAAACTAAT
1 CCTAACCCTAA-CCTAAACTAAC
1012675 CCTAACCCTAACCTAA
1 CCTAACCCTAACCTAA
1012691 CAGCCTGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.23
Consensus pattern (22 bp):
CCTAACCCTAACCTAAACTAAC
Found at i:1012673 original size:17 final size:17
Alignment explanation
Indices: 1012653--1012690 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1012643 TAAACTAACC
1012653 CTAATCCTAACCCTAAA
1 CTAATCCTAACCCTAAA
*
1012670 CTAATCCTAACCCTAAC
1 CTAATCCTAACCCTAAA
1012687 CTAA
1 CTAA
1012691 CAGCCTGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (17 bp):
CTAATCCTAACCCTAAA
Found at i:1016315 original size:4 final size:4
Alignment explanation
Indices: 1016300--1016349 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
1016290 ATCACCCGTT
* * * *
1016300 GTCC GT-C GTCC GTCC GTCC GCCC GTCC GTCT GTCT GTCT GTCC GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
1016347 GTC
1 GTC
1016350 TGTAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.00, C:0.44, G:0.26, T:0.30
Consensus pattern (4 bp):
GTCC
Found at i:1016796 original size:166 final size:167
Alignment explanation
Indices: 1016522--1017267 Score: 1223
Period size: 166 Copynumber: 4.5 Consensus size: 167
1016512 GCATGTCTTT
*
1016522 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACA
1 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
1016587 TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
66 TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
1016652 CAAA-TTTAACATAGATATACCTTAGGAAAATGTTTA
131 CAAAGTTTAACATAGATATACCTTAGGAAAATGTTTA
* *
1016688 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACATAAGCTTGTATACA
1 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
1016753 TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
66 TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
1016818 CAAA-TTTAACATAGATATACCTTAGGAAAATGTTTA
131 CAAAGTTTAACATAGATATACCTTAGGAAAATGTTTA
1016854 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
1 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
*
1016919 TAGTGAAGATTCTAAATTGTAACAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
66 TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
1016984 CAAAGTTTAACATAGATATACCTTAGGAAAATGTTTA
131 CAAAGTTTAACATAGATATACCTTAGGAAAATGTTTA
*
1017021 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTA
1 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
* * ** * * **
1017086 TAATGAAGATTCTAAATTGTAGAAATCGTGACCCTCAAATCAAAACAGCAGCCCCAGGCGGGGTT
66 TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
* *
1017151 CAAAGTTTAACATAGA-ACTA-CATATGAAAAATGTTT-
131 CAAAGTTTAACATAGATA-TACCTTA-GGAAAATGTTTA
* * * * ** * *
1017187 AAAAATTTTCTTCTCAAAAACCACTTCACCAAAAATGCCAATACATACACAAACGGTTGTATATA
1 AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
*
1017252 TAGTGAAGATTGTAAA
66 TAGTGAAGATTCTAAA
1017268 AATCGTGACC
Statistics
Matches: 550, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
166 370 0.67
167 180 0.33
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (167 bp):
AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATATA
TAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTT
CAAAGTTTAACATAGATATACCTTAGGAAAATGTTTA
Found at i:1017142 original size:333 final size:332
Alignment explanation
Indices: 1016519--1017267 Score: 1225
Period size: 333 Copynumber: 2.3 Consensus size: 332
1016509 GGTGCATGTC
1016519 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
*
1016584 ACATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
66 ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
1016649 GTTCAAATTTAACATAGATATACCTTAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACCACTG
131 GTTCAAATTTAACATAGATATACCTTAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACCACTG
* *
1016714 CACCAGAAATGCCAATATTTACACATAAGCTTGTATACATAGTGAAGATTCTAAATTGTAAAAAT
196 CACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAATGAAGATTCTAAATTGTAAAAAT
** * ** *
1016779 CGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGGTTCAAA-TTTAACATAGATA-TACCT-T
261 CGTGACCCTCAAACCAAAACAGCAGCCCCAGGCGGGGTTCAAAGTTTAACATAGA-ACTACATAT
*
1016841 AGGAAAATG
325 -GAAAAATG
1016850 TTTAAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
1 TTT-AAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTA
*
1016915 TATATAGTGAAGATTCTAAATTGTAACAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
65 TATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGG
1016980 GGTTCAAAGTTTAACATAGATATACCTTAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACCAC
130 GGTTCAAA-TTTAACATAGATATACCTTAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACCAC
** *
1017045 TGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATGTATAATGAAGATTCTAAATTGTAGAA
194 TGCACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAATGAAGATTCTAAATTGTAAAA
*
1017110 ATCGTGACCCTCAAATCAAAACAGCAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATA
259 ATCGTGACCCTCAAACCAAAACAGCAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATA
1017175 TGAAAAATG
324 TGAAAAATG
* * * * ** * *
1017184 TTTAAAAATTTTCTTCTCAAAAACCACTTCACCAAAAATGCCAATACATACACAAACGGTTGTAT
1 TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
*
1017249 ATATAGTGAAGATTGTAAA
66 ATATAGTGAAGATTCTAAA
1017268 AATCGTGACC
Statistics
Matches: 389, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
331 3 0.01
332 132 0.34
333 228 0.59
334 25 0.06
335 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (332 bp):
TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTACACAAAAGCTTGTAT
ATATAGTGAAGATTCTAAATTGTAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
GTTCAAATTTAACATAGATATACCTTAGGAAAATGTTTAAAAAATCTTCTTCTCAAGAACCACTG
CACCAGAAATGCCAATATTTACACAAAAGCTTGTATACATAATGAAGATTCTAAATTGTAAAAAT
CGTGACCCTCAAACCAAAACAGCAGCCCCAGGCGGGGTTCAAAGTTTAACATAGAACTACATATG
AAAAATG
Found at i:1018078 original size:165 final size:165
Alignment explanation
Indices: 1017828--1018235 Score: 455
Period size: 165 Copynumber: 2.5 Consensus size: 165
1017818 CGGTATATAT
* * * * * *
1017828 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAATTTGTCAGATAACTACGTA
1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCA
* * * *
1017892 AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCTGT-GACCTCAATCTAATACTGGGGC
65 AGCATCCTCAAATAATGTAGATTCAAAATAATTAAAA-CTGTAGACCTCAA-CTAATACTGGGGC
* * *
1017955 CCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG
128 CCCAAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * *
1017993 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTATGCAA
1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA
* * * * ** *
1018058 GCATCCTTAGATAATGTAGATTCAAAATAATTAAAACTTTAGCCCTGGACTAATACTGTGGCCCC
66 GCATCCTCAAATAATGTAGATTCAAAATAATTAAAACTGTAGACCTCAACTAATACTGGGGCCCC
* *
1018123 AAGAGGGGTTCAAAGTTTAACATAGAAAGATATAT
131 AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
* * * * *
1018158 TGAAAATGTTTTTAAAAA-GTTTTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTATTATGC
1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGC
*
1018222 AAGGATCCTCAAAT
64 AAGCATCCTCAAAT
1018236 TGTGTAAACT
Statistics
Matches: 200, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
164 3 0.01
165 130 0.65
166 60 0.30
167 7 0.04
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (165 bp):
GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA
GCATCCTCAAATAATGTAGATTCAAAATAATTAAAACTGTAGACCTCAACTAATACTGGGGCCCC
AAGAGGGGTTCAAAGTTTAACATAGAAAGATAGAG
Found at i:1018940 original size:17 final size:19
Alignment explanation
Indices: 1018918--1018958 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1018908 TGAGGTCTAG
1018918 TACCGTATC-GTT-AAAAA
1 TACCGTATCAGTTCAAAAA
*
1018935 TACCGTATCATTTCAAAAA
1 TACCGTATCAGTTCAAAAA
1018954 TACCG
1 TACCG
1018959 GTATGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 2 0.10
19 10 0.48
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (19 bp):
TACCGTATCAGTTCAAAAA
Done.