Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001961.1 Hibiscus syriacus cultivar Beakdansim tig00003965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 76033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3859 original size:15 final size:15
Alignment explanation
Indices: 3835--3865 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3825 ACACATAGTT
*
3835 TTTATGAAAACAACA
1 TTTATAAAAACAACA
3850 TTTATAAAAACAACA
1 TTTATAAAAACAACA
3865 T
1 T
3866 ATTAAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (15 bp):
TTTATAAAAACAACA
Found at i:8262 original size:88 final size:88
Alignment explanation
Indices: 8158--8334 Score: 345
Period size: 88 Copynumber: 2.0 Consensus size: 88
8148 TTCAAATTTC
*
8158 ATTTTTGAGAGTTCTAAATCCTTCTTCAATATTTCATTTTGATTTTCAAAATCCATTTTCATTTC
1 ATTTTTGAGAGTTCTAAATCCTTCTTCAAGATTTCATTTTGATTTTCAAAATCCATTTTCATTTC
8223 TAGAAGAAGTTTGTTTAATTTGA
66 TAGAAGAAGTTTGTTTAATTTGA
8246 ATTTTTGAGAGTTCTAAATCCTTCTTCAAGATTTCATTTTGATTTTCAAAATCCATTTTCATTTC
1 ATTTTTGAGAGTTCTAAATCCTTCTTCAAGATTTCATTTTGATTTTCAAAATCCATTTTCATTTC
8311 TAGAAGAAGTTTGTTTAATTTGA
66 TAGAAGAAGTTTGTTTAATTTGA
8334 A
1 A
8335 AATTTCTTTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (88 bp):
ATTTTTGAGAGTTCTAAATCCTTCTTCAAGATTTCATTTTGATTTTCAAAATCCATTTTCATTTC
TAGAAGAAGTTTGTTTAATTTGA
Found at i:9776 original size:20 final size:20
Alignment explanation
Indices: 9738--9776 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9728 TGTTGAACAG
**
9738 TGGGGGGAATCGGTACCCTC
1 TGGGGGGAATCAATACCCTC
*
9758 TGGGGGGAATCAATTCCCT
1 TGGGGGGAATCAATACCCT
9777 TCGAGCATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (20 bp):
TGGGGGGAATCAATACCCTC
Found at i:10191 original size:17 final size:17
Alignment explanation
Indices: 10169--10204 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10159 TTAGAGTAAG
10169 TATGAATACATTATTAT
1 TATGAATACATTATTAT
10186 TATGAATACATTATTAT
1 TATGAATACATTATTAT
10203 TA
1 TA
10205 CTTTTAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
TATGAATACATTATTAT
Found at i:10217 original size:17 final size:17
Alignment explanation
Indices: 10197--10232 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10187 ATGAATACAT
*
10197 TATTATTACTTTTAGAG
1 TATTAGTACTTTTAGAG
*
10214 TATTCGTACTTTTAGAG
1 TATTAGTACTTTTAGAG
10231 TA
1 TA
10233 AGTATTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (17 bp):
TATTAGTACTTTTAGAG
Found at i:10553 original size:23 final size:23
Alignment explanation
Indices: 10491--10562 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
10481 AAGTAGCTAG
* *
10491 TTTAACGTAATAGGTAACACTTA
1 TTTAACGTAATAGGTAGCGCTTA
*
10514 TTTAACGTAATAGGTAGTGCTTA
1 TTTAACGTAATAGGTAGCGCTTA
* *
10537 TTTAACATAATAGGTAGCGCCTA
1 TTTAACGTAATAGGTAGCGCTTA
10560 TTT
1 TTT
10563 TATTTTACCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCGCTTA
Found at i:10639 original size:75 final size:75
Alignment explanation
Indices: 10537--10699 Score: 236
Period size: 75 Copynumber: 2.2 Consensus size: 75
10527 GTAGTGCTTA
* *
10537 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGATTACATTATTAATAACCTTTAAACAAAC
1 TTTAACATAATAGATAGCGCCTATTTTATTTTACCGATTACATTATTAATAACCTTCAAACAAAC
10602 CGGTAGATAT
66 CGGTAGATAT
* * * * *
10612 TTTAACGTAATAGATAGCGCCTCTTTTATTTTGCCGTTTACATTATTAATAACCTTCAAACAAAT
1 TTTAACATAATAGATAGCGCCTATTTTATTTTACCGATTACATTATTAATAACCTTCAAACAAAC
*
10677 CGGTAGATAG
66 CGGTAGATAT
* *
10687 TTTGATATAATAG
1 TTTAACATAATAG
10700 GTAACACTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (75 bp):
TTTAACATAATAGATAGCGCCTATTTTATTTTACCGATTACATTATTAATAACCTTCAAACAAAC
CGGTAGATAT
Found at i:10720 original size:23 final size:23
Alignment explanation
Indices: 10693--10746 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
10683 ATAGTTTGAT
*
10693 ATAATAGGTAACACTTATTTAAC
1 ATAATAGGTAACACCTATTTAAC
* *
10716 GTAATAGGTAGCACCTATTTAAC
1 ATAATAGGTAACACCTATTTAAC
10739 ATAATAGG
1 ATAATAGG
10747 CAACGTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (23 bp):
ATAATAGGTAACACCTATTTAAC
Found at i:10744 original size:121 final size:121
Alignment explanation
Indices: 10612--10833 Score: 266
Period size: 121 Copynumber: 1.8 Consensus size: 121
10602 CGGTAGATAT
* * * * * *
10612 TTTAACGTAATAGATAGCGCCTCTTTTATTTTGCCGTTTACATTATTAATAACCTTCAAACAAAT
1 TTTAACATAATAGACAACGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
* * *
10677 CGGTAGATAGTTTG-ATATAATAGGTAACACTTATTTAACGTAATAGGTAGCACCTA
66 CAGTAGATA-TTTGAATATAATAAGTAACACCTATTTAACGTAATAGGTAGCACCTA
* ** ** * *
10733 TTTAACATAATAGGCAACGTTTATTTTATTTTATTGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGACAACGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
* *
10798 CAGTAGGTATTTGAATATAATAAGTAGCACCTATTT
66 CAGTAGATATTTGAATATAATAAGTAACACCTATTT
10834 TATTTTACTG
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
120 4 0.05
121 78 0.95
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (121 bp):
TTTAACATAATAGACAACGCCTATTTTATTTTACCGTTTACATTATTAATAACCTTCAAACAAAC
CAGTAGATATTTGAATATAATAAGTAACACCTATTTAACGTAATAGGTAGCACCTA
Found at i:10788 original size:196 final size:195
Alignment explanation
Indices: 10442--11290 Score: 1117
Period size: 196 Copynumber: 4.3 Consensus size: 195
10432 AAGTTGTATA
* * * * *
10442 TATTTTACCATTTACATTATTATTAACCTTTAAACAAACAAGTAGCTAGTTTAACGTAATAGGTA
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC-AGTAGATAGTTTAACATAATAGGTA
** * *
10507 ACACTTATTTAACGTAATAGGTAGTGCTTATTTAACATAATAGGTAGCGCCTATTTTATTTTACC
65 ACACTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAACGCCTATTTTATTTTACC
* * * * *
10572 GATTACATTATTAATAACCTTTAAACAAACCGGTAGATATTTTAACGTAATAGATAGCGCCTCTT
130 GTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATAGATAGCACCTATT
10637 T
195 T
* * * * *
10638 TATTTTGCCGTTTACATTATTAATAACCTTCAAACAAATCGGTAGATAGTTTGATATAATAGGTA
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAA-CAGTAGATAGTTTAACATAATAGGTA
* ** **
10703 ACACTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGCAACGTTTATTTTATTTTATT
65 ACACTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAACGCCTATTTTATTTTACC
* * **
10768 GTTTACATTATTAGTAACCTTTAAACAAACCAGTAGGTATTTGAATATAATA-AGTAGCACCTAT
130 GTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATAGA-TAGCACCTAT
10832 TT
194 TT
* *
10834 TATTTTACTGTTTACATTATTAGTAACCTTCAAACAAACCAGTATG-TAATTTAACATAATAGGT
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAA-CAGTA-GATAGTTTAACATAATAGGT
* ** * ** *
10898 AGCGTTTATTTAACGTAATATGTAATACCTATTTAACATAATAGGTAGCGCCTATTTTATTTTAC
64 AACACTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAACGCCTATTTTATTTTAC
* *
10963 CGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATGGGTAGCACCTAT
129 CGTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATAGATAGCACCTAT
11028 TT
194 TT
* * * *
11030 TATTTTACCGTTTACATTATTAGTATCCTTCAAACAAACTGGTAGGTAGTTTAACATAATAGGTG
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC-AGTAGATAGTTTAACATAATAGGTA
* ** * ** *
11095 GCGTTTATTTAATGTAATAGGTAGCGTCTATTTAACATAATAGGTAACACCTATTTTATTTTACC
65 ACACTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAACGCCTATTTTATTTTACC
* * * *
11160 GTTTACATTATTAGTAACCTTTAAACAAACTGGTATGTATTTTAACGTAATAGGTAGCACCTCTT
130 GTTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATAGATAGCACCTATT
11225 T
195 T
* *
11226 TATTTTACCATTTACATTATTAGTAACCTTCAAACAAAATAGTAGATAGTTTAACATAATAGGTA
1 TATTTTACCGTTTACATTATTAGTAACCTTCAAAC-AAACAGTAGATAGTTTAACATAATAGGTA
11291 GCGTCTATTT
Statistics
Matches: 570, Mismatches: 76, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
195 3 0.01
196 562 0.99
197 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (195 bp):
TATTTTACCGTTTACATTATTAGTAACCTTCAAACAAACAGTAGATAGTTTAACATAATAGGTAA
CACTTATTTAACGTAATAGGTAGCACCTATTTAACATAATAGGTAACGCCTATTTTATTTTACCG
TTTACATTATTAGTAACCTTTAAACAAACCGGTAGGTATTTTAACGTAATAGATAGCACCTATTT
Found at i:10908 original size:23 final size:23
Alignment explanation
Indices: 10882--10954 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
10872 CCAGTATGTA
**
10882 ATTTAACATAATAGGTAGCGTTT
1 ATTTAACATAATAGGTAGCGCCT
* * ***
10905 ATTTAACGTAATATGTAATACCT
1 ATTTAACATAATAGGTAGCGCCT
10928 ATTTAACATAATAGGTAGCGCCT
1 ATTTAACATAATAGGTAGCGCCT
10951 ATTT
1 ATTT
10955 TATTTTACCG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (23 bp):
ATTTAACATAATAGGTAGCGCCT
Found at i:10908 original size:75 final size:74
Alignment explanation
Indices: 10731--10908 Score: 248
Period size: 75 Copynumber: 2.4 Consensus size: 74
10721 AGGTAGCACC
* * * *
10731 TATTTAACATAATAGGCAACGTTTATTTTATTTTATTGTTTACATTATTAGTAACCTTTAAACAA
1 TATTTAACATAATAGGTAGCGTTTATTTTATTTTACTGTTTACATTATTAGTAACCTTCAAACAA
10796 ACCAGTAGG
66 ACCAGTAGG
* * ***
10805 TATTTGAATATAATAAGTAGCACCTATTTTATTTTACTGTTTACATTATTAGTAACCTTCAAACA
1 TATTT-AACATAATAGGTAGCGTTTATTTTATTTTACTGTTTACATTATTAGTAACCTTCAAACA
*
10870 AACCAGTATG
65 AACCAGTAGG
10880 TAATTTAACATAATAGGTAGCGTTTATTT
1 T-ATTTAACATAATAGGTAGCGTTTATTT
10909 AACGTAATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
74 5 0.06
75 78 0.90
76 4 0.05
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (74 bp):
TATTTAACATAATAGGTAGCGTTTATTTTATTTTACTGTTTACATTATTAGTAACCTTCAAACAA
ACCAGTAGG
Found at i:11029 original size:121 final size:122
Alignment explanation
Indices: 10805--11029 Score: 326
Period size: 121 Copynumber: 1.9 Consensus size: 122
10795 AACCAGTAGG
* *
10805 TATTTGAATATAATAAGTAGCACCTATTTTATTTTACTGTTTACATTATTAGTAACCTTCAAACA
1 TATTTGAACATAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACA
* ***
10870 AACCAGTATGTAATTTAACATAATAGGTAGCGTTTATTTAACGTAATATGTAATACC
66 AACCAGTAGGTAATTTAACATAATAGGTAGCACCTATTTAACGTAATATGTAATACC
* * *
10927 TATTT-AACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACA
1 TATTTGAACATAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACA
* * * *
10991 AACCGGTAGGTATTTTAACGTAATGGGTAGCACCTATTT
66 AACCAGTAGGTAATTTAACATAATAGGTAGCACCTATTT
11030 TATTTTACCG
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
121 85 0.94
122 5 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (122 bp):
TATTTGAACATAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACA
AACCAGTAGGTAATTTAACATAATAGGTAGCACCTATTTAACGTAATATGTAATACC
Found at i:11104 original size:75 final size:75
Alignment explanation
Indices: 10929--11093 Score: 267
Period size: 75 Copynumber: 2.2 Consensus size: 75
10919 GTAATACCTA
*
10929 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
*
10994 CGGTAGGTAT
66 CGGTAGGTAG
* * * *
11004 TTTAACGTAATGGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTATCCTTCAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
*
11069 TGGTAGGTAG
66 CGGTAGGTAG
11079 TTTAACATAATAGGT
1 TTTAACATAATAGGT
11094 GGCGTTTATT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAACAAAC
CGGTAGGTAG
Found at i:11112 original size:23 final size:23
Alignment explanation
Indices: 11079--11140 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
11069 TGGTAGGTAG
* *
11079 TTTAACATAATAGGTGGCGTTTA
1 TTTAACATAATAGGTAGCGTCTA
**
11102 TTTAATGTAATAGGTAGCGTCTA
1 TTTAACATAATAGGTAGCGTCTA
11125 TTTAACATAATAGGTA
1 TTTAACATAATAGGTA
11141 ACACCTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (23 bp):
TTTAACATAATAGGTAGCGTCTA
Found at i:11248 original size:75 final size:75
Alignment explanation
Indices: 11125--11307 Score: 260
Period size: 75 Copynumber: 2.4 Consensus size: 75
11115 GTAGCGTCTA
* * * *
11125 TTTAACATAATAGGTAACACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAAA
* *
11190 TGGTATG-TAT
66 TAGTA-GATAG
* *
11200 TTTAACGTAATAGGTAGCACCTCTTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAAA
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAAA
11265 TAGTAGATAG
66 TAGTAGATAG
**
11275 TTTAACATAATAGGTAGCGTCTATTTTATTTTA
1 TTTAACATAATAGGTAGCACCTATTTTATTTTA
11308 ACCGATTAGG
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 1 0.01
75 94 0.99
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCACCTATTTTATTTTACCATTTACATTATTAGTAACCTTCAAACAAAA
TAGTAGATAG
Found at i:12179 original size:16 final size:16
Alignment explanation
Indices: 12154--12184 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12144 TATTAATTAT
12154 AAATTAAATATTATAA
1 AAATTAAATATTATAA
*
12170 AAATTTAATATTATA
1 AAATTAAATATTATA
12185 TAAACTCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTAAATATTATAA
Found at i:16304 original size:105 final size:105
Alignment explanation
Indices: 16121--16328 Score: 328
Period size: 105 Copynumber: 2.0 Consensus size: 105
16111 ATACTCCTAT
* *
16121 ATTCTGATGTCAACATCTATTCCTAAAGAACTTGCTAGCAATACCTCTCTTTGACTTCAGTCAAC
1 ATTCTGATGTCAACATCTATTCCTAAACAACTTGCTAGAAATACCTCTCTTTGACTTCAGTCAAC
* *
16186 AATTAGATAATGACAACTTCCTAACTAGCAACAGTAAACA
66 AATTAGATAATGACAACTTCATAACTAACAACAGTAAACA
* *
16226 ATTCTGATGTCAGCATCTATTTCTAAACAAC-TGACTAGAAATACCTCTCTTTGACTTCAGTCAA
1 ATTCTGATGTCAACATCTATTCCTAAACAACTTG-CTAGAAATACCTCTCTTTGACTTCAGTCAA
* *
16290 CAATTAGATGATGACAACTTCATAACTAACACCAGTAAA
65 CAATTAGATAATGACAACTTCATAACTAACAACAGTAAA
16329 TAAAATGCAG
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 2 0.02
105 92 0.98
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (105 bp):
ATTCTGATGTCAACATCTATTCCTAAACAACTTGCTAGAAATACCTCTCTTTGACTTCAGTCAAC
AATTAGATAATGACAACTTCATAACTAACAACAGTAAACA
Found at i:23400 original size:18 final size:18
Alignment explanation
Indices: 23351--23403 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
23341 TTAAAATTTT
* *
23351 TCCCGAAGGACCATTTTG
1 TCCCGAAGGACCACTATG
*
23369 TCCCGAATGACCACTATG
1 TCCCGAAGGACCACTATG
*
23387 TCCCAAAGGACCACTAT
1 TCCCGAAGGACCACTAT
23404 AACCCTCGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:32154 original size:51 final size:51
Alignment explanation
Indices: 32074--32172 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
32064 AATACTTCGC
* * * *
32074 TTAGGATGAAAACCTGAAAGGGCATCCTAAGTCGAAAAAAAGGAAAAACGT
1 TTAGGATGAAAACCCGAAACGGCACCCTAAATCGAAAAAAAGGAAAAACGT
* * *
32125 TTAGGGTGAAAACCCGAAACGGCACCCTAAATTGAAAAAAATGAAAAA
1 TTAGGATGAAAACCCGAAACGGCACCCTAAATCGAAAAAAAGGAAAAA
32173 GAGAAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (51 bp):
TTAGGATGAAAACCCGAAACGGCACCCTAAATCGAAAAAAAGGAAAAACGT
Found at i:32825 original size:14 final size:14
Alignment explanation
Indices: 32806--32832 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32796 GATCAAAACT
32806 TCAAGATTCCAGAG
1 TCAAGATTCCAGAG
32820 TCAAGATTCCAGA
1 TCAAGATTCCAGA
32833 CAGATTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAG
Found at i:33035 original size:106 final size:106
Alignment explanation
Indices: 32845--33612 Score: 992
Period size: 106 Copynumber: 7.4 Consensus size: 106
32835 GATTTTAGCT
* *
32845 AGAGTCAATTTCAACTTCACAGT-AAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
1 AGAGTCAATTTCAACTTCACA-TCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
*
32909 ATGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
65 ACGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
* ** * *
32951 AGAGCCAATTTCAACTTCACATCGAAGGATGCTGGACTCGGGACAACACAAGTTTAACTTCACAA
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
*
33016 CGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
* *
33057 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* *
33122 CGAAGGGAC-AGCTGGTTGTCAACAAACAATCTCCCAATTTC
66 CGAAGGGACGA-CTGGTTGTCAACAAATAATTTCCCAATTTC
* * *
33163 AAAG-C-----CAA--T---AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * * *
33217 CGAAGGGATGGCTGGTTGTCAACAAACAAGTTCCTAATTTC
66 CGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
*
33258 AGGGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC--CACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
*
33321 CGAAGGGACAACTGGTTGTCAACAAATAATTTCCCAATTTC
66 CGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
* * *
33362 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAA
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * *
33427 CGAAGGGACGACTGGTTGTTAATAAATAATTTCCCAATTTT
66 CGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
* * * * * *
33468 AGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGATAACACAAGCTCAACTTCATAA
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
* * * * * *
33533 CGAAGGGGC-AGTTGGTTGTCAACAAACAATTTTCCAGTTCC
66 CGAAGGGACGA-CTGGTTGTCAACAAATAATTTCCCAATTTC
* ** *
33574 AGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTC
33613 AGAACAATAC
Statistics
Matches: 580, Mismatches: 65, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
95 80 0.14
96 1 0.00
98 1 0.00
100 3 0.01
101 3 0.01
103 1 0.00
104 95 0.16
105 4 0.01
106 392 0.68
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (106 bp):
AGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAATTTC
Found at i:33240 original size:95 final size:97
Alignment explanation
Indices: 33076--33466 Score: 430
Period size: 104 Copynumber: 3.9 Consensus size: 97
33066 TTCAACTTCA
* * *
33076 CAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGT
1 CAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGT
*
33141 CAACAAACAATCTCCCAATTTCAAAGCCAA-T
66 CAACAAACAATTTCCCAATTTCAAAGCCAACT
***
33172 -AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGT
1 CAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGT
* * **
33236 CAACAAACAAGTTCCTAATTTCAGGGTCAATTTCAACTT
66 CAACAAACAATTTCCCAATTTCA-----AA-GCCAAC-T
*
33275 CACATCGAAGGATATTGGACTCGAGAC--CACAAGTTCAACTTCACAACGAAGGGACAACTGGTT
1 --CAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACAACTGGTT
* *
33338 GTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAACTT
64 GTCAACAAACAATTTCCCAATTTCAAAG-C-----CAAC-T
*
33379 CACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTT
1 --CAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACAACTGGTT
* * *
33444 GTTAATAAATAATTTCCCAATTT
64 GTCAACAAACAATTTCCCAATTT
33467 TAGGGTCAAT
Statistics
Matches: 253, Mismatches: 23, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
95 80 0.32
99 1 0.00
100 2 0.01
101 3 0.01
103 1 0.00
104 87 0.34
106 79 0.31
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (97 bp):
CAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGT
CAACAAACAATTTCCCAATTTCAAAGCCAACT
Found at i:33422 original size:305 final size:306
Alignment explanation
Indices: 32869--33612 Score: 972
Period size: 305 Copynumber: 2.4 Consensus size: 306
32859 CTTCACAGTA
*
32869 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTGGTTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
* * * *
32934 AATAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGCTGGACTCGGGACAACA
66 AACAAGTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATACTGGACTCGAGAC-ACA
* * *
32999 CAAGTTTAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCA
130 CAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
33064 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
195 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
33129 AC-AGCTGGTTGTCAACAAACAATCTCCCAATTTCAAAGCCAATAGCG
260 ACGA-CTGGTTGTCAACAAACAATCTCCCAATTTCAAAGCCAATAGCG
* * * *
33176 AAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
* * * *
33241 AACAAGTTCCTAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC-CAC
66 AACAAGTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATACTGGACTCGAGACACAC
*
33305 AAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAA
131 AAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
* *
33370 TTTCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGA
196 TTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGA
* * * * *** *
33435 CGACTGGTTGTTAATAAATAATTTCCCAATTTTAGGGTCAATTTCAACTTCACATCG
261 CGACTGGTTGTCAACAAACAATCTCCCAA--TT----TCAAAGCCAA--T---AGCG
* * * * * *
33492 AAGGATATTAGACTCAAGATAACACAAGCTCAACTTCATAACGAAGGGGC-AGTTGGTTGTCAAC
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGA-CTGGTTGTCAAC
* * * * ** * *
33556 AAACAATTTTCCAGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
65 AAACAAGTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATACTGGACTC
33613 AGAACAATAC
Statistics
Matches: 377, Mismatches: 47, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
305 150 0.40
306 1 0.00
307 115 0.31
311 7 0.02
313 1 0.00
316 103 0.27
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (306 bp):
AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
AACAAGTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATACTGGACTCGAGACACAC
AAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGA
CGACTGGTTGTCAACAAACAATCTCCCAATTTCAAAGCCAATAGCG
Found at i:34162 original size:34 final size:35
Alignment explanation
Indices: 34097--34167 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
34087 CCAAAAAAGA
34097 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
34132 AGAGTTGGATTAGGACTCAAA-ACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
34166 AG
1 AG
34168 GATTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:34502 original size:2 final size:2
Alignment explanation
Indices: 34495--34543 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
34485 ATTTTATTAT
34495 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34537 TA TA TA T
1 TA TA TA T
34544 TTTTAATATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34723 original size:2 final size:2
Alignment explanation
Indices: 34718--34742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34708 CTTATAACTT
34718 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34743 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34903 original size:41 final size:39
Alignment explanation
Indices: 34858--34934 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
34848 ATGACCCATT
* *
34858 TTTTTGTTTTATTTCTAACTAAAGTCTCTCTCACTTTTCTC
1 TTTTTGTCTTATTTCTAACTAAAG-CCCTC-CACTTTTCTC
*
34899 TTTTTGTCTTATTTCTGACTAAAGCCCTCCACTTTT
1 TTTTTGTCTTATTTCTAACTAAAGCCCTCCACTTTT
34935 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.21
40 4 0.12
41 22 0.67
ACGTcount: A:0.17, C:0.23, G:0.06, T:0.53
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCTCCACTTTTCTC
Found at i:35001 original size:38 final size:40
Alignment explanation
Indices: 34950--35029 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
34940 AGTGAGAGGG
*
34950 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
34988 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
35028 TA
1 TA
35030 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:35025 original size:2 final size:2
Alignment explanation
Indices: 35018--35058 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35008 TACTTTGATG
35018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35059 TTCCTTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40414 original size:21 final size:21
Alignment explanation
Indices: 40356--40420 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
40346 TTAGTGCAGA
40356 GGGAATCGATACCCCCT-TAAAG
1 GGGAATCGATACCCCCTGT--AG
*
40378 GGGAACCGATTA-CCCCTGTAG
1 GGGAATCGA-TACCCCCTGTAG
40399 GGGAATCGATACCCCCTG-AG
1 GGGAATCGATACCCCCTGTAG
40419 GG
1 GG
40421 TTCTGGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 6 0.16
21 16 0.42
22 13 0.34
23 3 0.08
ACGTcount: A:0.26, C:0.28, G:0.29, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGTAG
Found at i:43565 original size:19 final size:19
Alignment explanation
Indices: 43521--43565 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
43511 AAATTTGTAT
*
43521 TGTTCTATTTGGGAGAGAG
1 TGTTCTCTTTGGGAGAGAG
43540 TGTTCTCTTTGGGAGAGAG
1 TGTTCTCTTTGGGAGAGAG
43559 TGTTCTC
1 TGTTCTC
43566 AAGAATTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.11, G:0.33, T:0.40
Consensus pattern (19 bp):
TGTTCTCTTTGGGAGAGAG
Found at i:46959 original size:45 final size:45
Alignment explanation
Indices: 46909--46998 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
46899 TGATCAAACA
46909 AATCATCAATTCTAGGGAGGGGATACTTATTCTTGATGGTCACTT
1 AATCATCAATTCTAGGGAGGGGATACTTATTCTTGATGGTCACTT
46954 AATCATCAATTCTAGGGAGGGGATACTTATTCTTGATGGTCACTT
1 AATCATCAATTCTAGGGAGGGGATACTTATTCTTGATGGTCACTT
46999 TATTGAGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (45 bp):
AATCATCAATTCTAGGGAGGGGATACTTATTCTTGATGGTCACTT
Found at i:50354 original size:20 final size:20
Alignment explanation
Indices: 50326--50371 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
50316 ATTTGAAGTA
50326 GTATCGGTACCCCTTATAGG
1 GTATCGGTACCCCTTATAGG
* *
50346 GTATTGGTACCCCTTATATG
1 GTATCGGTACCCCTTATAGG
50366 GTATCG
1 GTATCG
50372 ATACTTCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
GTATCGGTACCCCTTATAGG
Found at i:53902 original size:16 final size:17
Alignment explanation
Indices: 53870--53912 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
53860 TCAAAGTTCT
*
53870 TTTTCTTTTCATTTACG
1 TTTTCTTTACATTTACG
53887 TTTTCTTTAC-TTTACG
1 TTTTCTTTACATTTACG
*
53903 TTTTTTTTAC
1 TTTTCTTTAC
53913 CTTTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTCTTTACATTTACG
Found at i:54509 original size:15 final size:17
Alignment explanation
Indices: 54485--54522 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
54475 CTTGAGGTGA
*
54485 TTTCATCATTA-TTAT-
1 TTTCAACATTATTTATG
54500 TTTCAACATTATTTATG
1 TTTCAACATTATTTATG
54517 TTTCAA
1 TTTCAA
54523 TTTCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 4 0.20
17 6 0.30
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTCAACATTATTTATG
Found at i:60856 original size:3 final size:3
Alignment explanation
Indices: 60842--60890 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
60832 TCTACAAAAA
60842 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
60889 AT
1 AT
60891 ACTTAATTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:61944 original size:2 final size:2
Alignment explanation
Indices: 61939--61977 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
61929 CCTAAGAGAT
61939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61978 TAGGCAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62182 original size:19 final size:20
Alignment explanation
Indices: 62142--62182 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
62132 TATTTTAGTA
*
62142 TTTTTTTACATATTATGTAT
1 TTTTTTTACATATTATGAAT
62162 TTTTTGTTA-ATATT-TGAAT
1 TTTTT-TTACATATTATGAAT
62181 TT
1 TT
62183 GGCCATGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
20 10 0.53
21 3 0.16
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTTTTACATATTATGAAT
Found at i:62441 original size:29 final size:28
Alignment explanation
Indices: 62397--62526 Score: 84
Period size: 28 Copynumber: 4.5 Consensus size: 28
62387 TGTTAGGACC
*
62397 ATTTTAGACCCTTTAAGATTCTATTTTACT
1 ATTTTAG-TCCTTTAA-ATTCTATTTTACT
* *
62427 ATTTTAGTCCTTTAATTATCTA-TTTGCT
1 ATTTTAGTCCTTTAAAT-TCTATTTTACT
* * * *
62455 ATTTTAATCCCTTAAATGTATGTTTTACT
1 ATTTTAGTCCTTTAAAT-TCTATTTTACT
* * * **
62484 ATTTTGGACTTTTAAATTTCTATTTTTGT
1 ATTTTAGTCCTTTAAA-TTCTATTTTACT
*
62513 -TTTTGGTCCTTTAA
1 ATTTTAGTCCTTTAA
62527 GTTTCTGTAT
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
28 34 0.45
29 34 0.45
30 8 0.11
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.55
Consensus pattern (28 bp):
ATTTTAGTCCTTTAAATTCTATTTTACT
Found at i:62525 original size:28 final size:30
Alignment explanation
Indices: 62483--62556 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
62473 TATGTTTTAC
* * *
62483 TATTTTGGACTTTTAAATTTCTATTTTTG-
1 TATTTTGGTCCTTTAAATTTCTATATTTGT
* *
62512 T-TTTTGGTCCTTTAAGTTTCTGTATTTGT
1 TATTTTGGTCCTTTAAATTTCTATATTTGT
62541 TATTTTGGTCCTTTAA
1 TATTTTGGTCCTTTAA
62557 CGTTATGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 22 0.58
29 2 0.05
30 14 0.37
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (30 bp):
TATTTTGGTCCTTTAAATTTCTATATTTGT
Found at i:65897 original size:20 final size:20
Alignment explanation
Indices: 65872--65912 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
65862 TGACATTCCC
*
65872 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTAAAACAT
65892 TCTTTGAGACCTTAAAACAT
1 TCTTTGAGACCTTAAAACAT
65912 T
1 T
65913 GGATTTATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TCTTTGAGACCTTAAAACAT
Found at i:67008 original size:20 final size:20
Alignment explanation
Indices: 66984--67030 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
66974 TAAGTAGTAA
66984 CGATACTGAAGGAGTATTAT
1 CGATACTGAAGGAGTATTAT
*
67004 TGATACTGAAGGAGTATTAT
1 CGATACTGAAGGAGTATTAT
67024 CGATACT
1 CGATACT
67031 AGGGGTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (20 bp):
CGATACTGAAGGAGTATTAT
Found at i:67992 original size:21 final size:22
Alignment explanation
Indices: 67964--68090 Score: 116
Period size: 21 Copynumber: 5.8 Consensus size: 22
67954 CTTAAGGAGA
*
67964 ATTCTATGTGGTCATTCGGGAC
1 ATTCTATGTGGTCCTTCGGGAC
*
67986 A-TATATGTGGTCCTTCGGGAC
1 ATTCTATGTGGTCCTTCGGGAC
* *
68007 ATT-TATACGTGTTCCTTTGGGAC
1 ATTCTAT--GTGGTCCTTCGGGAC
* * *
68030 ATTTCTACGTGTTCCTTTGGGAC
1 A-TTCTATGTGGTCCTTCGGGAC
* *
68053 A-TCTATGTGGTCATTCGAGAC
1 ATTCTATGTGGTCCTTCGGGAC
*
68074 ATTCTATGTGGTACTTC
1 ATTCTATGTGGTCCTTC
68091 AGTGAAATTA
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
21 38 0.44
22 15 0.17
23 30 0.34
24 2 0.02
25 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (22 bp):
ATTCTATGTGGTCCTTCGGGAC
Found at i:68022 original size:23 final size:23
Alignment explanation
Indices: 67978--68054 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
67968 TATGTGGTCA
* *
67978 TTCGGGACA--TATATGTGGTCC
1 TTCGGGACATTTATACGTGTTCC
67999 TTCGGGACATTTATACGTGTTCC
1 TTCGGGACATTTATACGTGTTCC
* *
68022 TTTGGGACATTTCTACGTGTTCC
1 TTCGGGACATTTATACGTGTTCC
*
68045 TTTGGGACAT
1 TTCGGGACAT
68055 CTATGTGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.18
23 41 0.82
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (23 bp):
TTCGGGACATTTATACGTGTTCC
Found at i:69698 original size:14 final size:13
Alignment explanation
Indices: 69681--69732 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
69671 ATAAATTATT
69681 AATAAATTAAAATA
1 AATAAA-TAAAATA
*
69695 AATAAAGAAAATGA
1 AATAAATAAAAT-A
*
69709 AATGAATAAAATA
1 AATAAATAAAATA
69722 AA-AAAGTAAAA
1 AATAAA-TAAAA
69733 GAGTAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 2 0.06
13 13 0.41
14 17 0.53
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:74334 original size:20 final size:19
Alignment explanation
Indices: 74301--74340 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
74291 CATTGTAGGA
74301 ATTTATGGCATCAACAAAG
1 ATTTATGGCATCAACAAAG
*
74320 ATTTCATGGCCTCAACAAAG
1 ATTT-ATGGCATCAACAAAG
74340 A
1 A
74341 CCTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (19 bp):
ATTTATGGCATCAACAAAG
Done.