Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006140.1 Corchorus capsularis cultivar CVL-1 contig06158, 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: 188578
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:10807 original size:31 final size:31
Alignment explanation
Indices: 10769--10845 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
10759 ACTCAAAAGA
* * * *
10769 CGATCAATTTAGTCCTTATACTTATAAGATT
1 CGATCAATTTAATCCCTATACTCACAAGATT
* *
10800 TGATCAATTTAATCCCTGTACTCACAAGATT
1 CGATCAATTTAATCCCTATACTCACAAGATT
*
10831 CGATCAATTGAATCC
1 CGATCAATTTAATCC
10846 AATCGATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.36
Consensus pattern (31 bp):
CGATCAATTTAATCCCTATACTCACAAGATT
Found at i:14646 original size:34 final size:28
Alignment explanation
Indices: 14581--14640 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
14571 TGTGATCTGG
14581 TGATAGAATGTTGAACTCTTAATTTTAA
1 TGATAGAATGTTGAACTCTTAATTTTAA
14609 TGATAGAATGTTGAACTCTTAATTTTAA
1 TGATAGAATGTTGAACTCTTAATTTTAA
14637 TGAT
1 TGAT
14641 CATGATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (28 bp):
TGATAGAATGTTGAACTCTTAATTTTAA
Found at i:23286 original size:22 final size:22
Alignment explanation
Indices: 23251--23297 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
23241 TATAGGATGC
*
23251 TCTAAATTGAAACAATTTTCTT
1 TCTAAATTGAAACAAATTTCTT
* *
23273 TCTAAGTTGCAACAAATTTCTT
1 TCTAAATTGAAACAAATTTCTT
23295 TCT
1 TCT
23298 TCCATGACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (22 bp):
TCTAAATTGAAACAAATTTCTT
Found at i:25485 original size:9 final size:9
Alignment explanation
Indices: 25461--25514 Score: 90
Period size: 9 Copynumber: 5.9 Consensus size: 9
25451 CGGTGGCGAT
*
25461 CGGTTTCGG
1 CGGTTTTGG
25470 TCGGTTTTGG
1 -CGGTTTTGG
25480 CGGTTTTGG
1 CGGTTTTGG
25489 CGGTTTTGG
1 CGGTTTTGG
25498 CGGTTTTGG
1 CGGTTTTGG
25507 CGGTTTTG
1 CGGTTTTG
25515 ATTTATATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
9 35 0.81
10 8 0.19
ACGTcount: A:0.00, C:0.13, G:0.43, T:0.44
Consensus pattern (9 bp):
CGGTTTTGG
Found at i:26761 original size:22 final size:24
Alignment explanation
Indices: 26736--26788 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
26726 GCGATATCTT
26736 AAGT-AAT-GAACTTTCTTGTATA
1 AAGTCAATCGAACTTTCTTGTATA
*
26758 AAGTCTCAATCGATCTTTCTTGTATA
1 AAG--TCAATCGAACTTTCTTGTATA
26784 AAGTC
1 AAGTC
26789 TCAATCGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
24 3 0.12
25 3 0.12
26 17 0.65
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (24 bp):
AAGTCAATCGAACTTTCTTGTATA
Found at i:26782 original size:26 final size:26
Alignment explanation
Indices: 26746--26799 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
26736 AAGTAATGAA
26746 CTTTCTTGTATAAAGTCTCAATCGAT
1 CTTTCTTGTATAAAGTCTCAATCGAT
26772 CTTTCTTGTATAAAGTCTCAATCGAT
1 CTTTCTTGTATAAAGTCTCAATCGAT
26798 CT
1 CT
26800 GAAATACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (26 bp):
CTTTCTTGTATAAAGTCTCAATCGAT
Found at i:27409 original size:2 final size:2
Alignment explanation
Indices: 27361--27396 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27351 AAGCCTCCTC
27361 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
27397 AATGTCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37836 original size:22 final size:22
Alignment explanation
Indices: 37797--37838 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37787 TAAAAGGAAA
*
37797 TTGGGCCTCGCCATCTTGGATT
1 TTGGGCCTCGCCACCTTGGATT
**
37819 TTGGGCCTTTCCACCTTGGA
1 TTGGGCCTCGCCACCTTGGA
37839 CAAATTTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.29, G:0.26, T:0.36
Consensus pattern (22 bp):
TTGGGCCTCGCCACCTTGGATT
Found at i:49982 original size:2 final size:2
Alignment explanation
Indices: 49975--50057 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
49965 TTGTGTAGGA
49975 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
50017 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
50058 AGAAGGGCCG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56497 original size:2 final size:2
Alignment explanation
Indices: 56490--56542 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
56480 ATATACTACA
*
56490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
56533 AT AT AT AT AT
1 AT AT AT AT AT
56543 TCTCATAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 47 0.98
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:80211 original size:75 final size:76
Alignment explanation
Indices: 80086--80280 Score: 322
Period size: 75 Copynumber: 2.6 Consensus size: 76
80076 CAAATTCTCA
*
80086 TATAAATCATAAGCGAGGTCGAACGTCCTAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
80151 TGGTG-CCCCG
66 TGGTGCCCCCG
*
80161 TTTAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
80226 TGGTGCCCCCG
66 TGGTGCCCCCG
* * * *
80237 TAT-AATCTTAAACGAGGTTGAACGTCCAAGAAGACGTCACCCGC
1 TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGC
80281 GGGAGTCTCC
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
75 105 0.94
76 7 0.06
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (76 bp):
TATAAATCATAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGAC
TGGTGCCCCCG
Found at i:84031 original size:21 final size:21
Alignment explanation
Indices: 84005--84051 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
83995 GTCAGCCCGC
*
84005 CAAAATTCGAAATTTGAATTT
1 CAAAATTCGAAATTCGAATTT
*
84026 CAAAATTTGAAATTCGAATTT
1 CAAAATTCGAAATTCGAATTT
*
84047 AAAAA
1 CAAAA
84052 AAAAAACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (21 bp):
CAAAATTCGAAATTCGAATTT
Found at i:93830 original size:2 final size:2
Alignment explanation
Indices: 93823--93863 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
93813 AAAATAATCA
93823 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93864 TGTGGCTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:99294 original size:53 final size:53
Alignment explanation
Indices: 99236--99338 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
99226 GCCACATGTC
* ** *
99236 ACTTTTTGGCACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGCACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCACG
** * *
99289 ACTTTTTGGTTCATGTGACGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGCACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGC
99339 GTGCCACGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGCACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:102269 original size:6 final size:6
Alignment explanation
Indices: 102258--102287 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
102248 TGAGGCAGAC
*
102258 TGATTT TGATTT TGATTT TGATTT TTATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT
102288 CTACTAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (6 bp):
TGATTT
Found at i:131131 original size:59 final size:58
Alignment explanation
Indices: 131039--131149 Score: 195
Period size: 59 Copynumber: 1.9 Consensus size: 58
131029 CCATTGGGTC
*
131039 CCTATTCGGAAAGCTTTCTGTCAATAGATTGCTTTTGACTAATTATAGCGTTTTAACTT
1 CCTATTCAGAAAGCTTTCTGTCAATAGATTGCTTTTGACTAATTATAG-GTTTTAACTT
*
131098 CCTATTCAGAAAGCTTTCTGTCATTAGATTGCTTTTGACTAATTATAGGTTT
1 CCTATTCAGAAAGCTTTCTGTCAATAGATTGCTTTTGACTAATTATAGGTTT
131150 CTTTATTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
58 4 0.08
59 46 0.92
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (58 bp):
CCTATTCAGAAAGCTTTCTGTCAATAGATTGCTTTTGACTAATTATAGGTTTTAACTT
Found at i:164209 original size:117 final size:118
Alignment explanation
Indices: 164061--164298 Score: 426
Period size: 117 Copynumber: 2.0 Consensus size: 118
164051 TTATAATAGT
*
164061 GAAATCATAGATTCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
1 GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATT-
164126 GTATACCTTGAATTCGGCTATGTAAGT-AAAAAAATGTTGCTTAATATTACTAC
65 GTATACCTTGAATTCGGCTATGTAAGTAAAAAAAATGTTGCTTAATATTACTAC
*
164179 GAAA-CATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAGATGCAGTGAGATTG
1 GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
*
164243 TATACCTTGAATTCGGCTATGTAAGTAAAAAAAATGTTGCTTAATGTTACTAC
66 TATACCTTGAATTCGGCTATGTAAGTAAAAAAAATGTTGCTTAATATTACTAC
164296 GAA
1 GAA
164299 CACAAATATA
Statistics
Matches: 116, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
116 27 0.23
117 85 0.73
118 4 0.03
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (118 bp):
GAAATCATAGATCCATTAACAGAATTTAAATGAACTTTAAGAAACATGAAAATGCAGTGAGATTG
TATACCTTGAATTCGGCTATGTAAGTAAAAAAAATGTTGCTTAATATTACTAC
Found at i:165839 original size:26 final size:26
Alignment explanation
Indices: 165810--165860 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
165800 GGGATATCGT
165810 TCAATTCAAAGTGTTGCCATTTTGGC
1 TCAATTCAAAGTGTTGCCATTTTGGC
165836 TCAATTCAAAGTGTTGCCATTTTGG
1 TCAATTCAAAGTGTTGCCATTTTGG
165861 TTCTGGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.39
Consensus pattern (26 bp):
TCAATTCAAAGTGTTGCCATTTTGGC
Found at i:172133 original size:28 final size:27
Alignment explanation
Indices: 172102--172164 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
172092 CTTATTGTTT
*
172102 AAGTTATTGTAAG-ATGTACTTGTCTTAC
1 AAGTTATTCTAAGAATG--CTTGTCTTAC
*
172130 AAGTTATTCTAAGAATGGTTGTCTTAC
1 AAGTTATTCTAAGAATGCTTGTCTTAC
172157 AAGTTATT
1 AAGTTATT
172165 ATTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 17 0.53
28 12 0.38
29 3 0.09
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (27 bp):
AAGTTATTCTAAGAATGCTTGTCTTAC
Found at i:184040 original size:13 final size:14
Alignment explanation
Indices: 184022--184051 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
184012 ATTATTTTTT
184022 ATTATAATATT-TA
1 ATTATAATATTATA
184035 ATTATAATATTATA
1 ATTATAATATTATA
184049 ATT
1 ATT
184052 TAGAGTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATAATATTATA
Found at i:185139 original size:320 final size:319
Alignment explanation
Indices: 184400--188080 Score: 3198
Period size: 320 Copynumber: 11.3 Consensus size: 319
184390 GATATTTCAA
* * * * *
184400 TTTTGG-ATAAACACTCCTTAAAATATCTATAATCATCTAACCAAATCTCAGCCACAATGGATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
*** * * *
184464 AAGGATTTGTTTTTTACGACCATCTGAATCTTGTTTCGATTTAATAAAAAATAAATTCAGGAAAA
66 AAGGATTTG-CCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAA
* *
184529 AA-GGAAAAAC-A-A-TATAAGCGTGAAAAACCCTTCAATTTTTTTAGCGTTGAATTATATATTT
129 AATGGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTT
* ** * ** *
184590 TTTCTGAGTATTGTGGCAAAGAATAGTAAAAAAAAAAAAATTCCGGTCAGTTTTTGCAAAATTTT
193 TTTATGAGTATTGTGGCAAA-AA-A-TTGAGAAAAAAATTTTCGGGTCAG----T------TTTT
* * * * *
184655 AGCCGAAATCGTTTACT---CATCAAGGTTTTTGGCTAAAAACGCATTCCGGGACTGCGGCTCAG
245 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCT-CGGCTCAG
184717 TTTTGCATGAT
309 TTTTGCATGAT
* * * * * * *
184728 TTTTGACGTAAAGACTCCTTGAAATATCTATATTAATCGAACCAAATCCCAGCCAAATTGGATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
** *** * * *
184793 AACAATTTGATTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA
* * *
184858 TGGAAAAAAGATATTAGAAGCGTGAGAAACCCTTCAATTTTTTTGGCGTTAAATTGTATATTTTT
131 TGGAAAAACGATATTAGAAGCGTGA-AAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTT
* *
184923 TATGAGTATTGTGGCAAAAAATTGAGAAAAAAGTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTA
195 TATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTA
* * * * *
184988 CTAATCATCACGATTTTTGGCTAAAAATGCGTTTCGGGACCTCGACTCAG-TTTGCATGGT
260 CTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGG-CCTCGGCTCAGTTTTGCATGAT
* * *
185048 TTTTGGCATAAAGACTCTTTAAAATATCTATATTCATCTAACCAAATCTCAGCTACATTGCATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* * * * * *
185113 AAGAATTTGCCATTACGAGCATCTAAATCTTATTTTGATTTAAGTAGAAATAAATTC--AGAAAA
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA
*
185176 ---AAAAA--A-ATT-GAATCGTGAAAACCCCTTC-ATTTTTTTGGCGGTT-AATTATATATTTT
131 TGGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGGC-GTTGAATTATATATTTT
** * ** * * *
185232 TTCGGAGTATTATGGCAAAAAACGGAGGAAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCG
194 TTATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTC-A-----G----TTTTTAGCC
* * * * * *
185297 GAAATAGTGTACTAACCATCATGAGTTTTTGGCTAAAAGCGCGTTTCAAGGCCCCGGCTCAATTT
249 GAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGCGTTTC-GGGCCTCGGCTCAGTTT
185362 TGCATGAT
312 TGCATGAT
* * *
185370 TTTTGGCATAAAGACTCCTTGAAATATCTATACTCATCTAACCAAATCTCAGTCACATTGGATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* *** * * ** ***
185435 AAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCAATTTAATTAGAAATTACTTTTAAAAAAA
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA-TA-AATTCGGAAAA
** * *
185500 AATGGAAAAACGATATTAGAA-CTGTGAAAAATACGTCAATCTTTTTGGCGTTGAATTATATATT
129 AATGGAAAAACGATATTAGAAGC-GTG-AAAACCCTTCAATTTTTTTGGCGTTGAATTATATATT
* * * * *
185564 TTTTCTGAATATT-T-G-AAAAAACTTGAGATAAAAACTTTTCGGGTCAGTTTTTAATCCAAAAT
192 TTTTATGAGTATTGTGGCAAAAAA-TTGAGA-AAAAAATTTTCGGGTCAGTTTTT-AGCCGAAAT
* * * *** * * * * *
185626 TGTTTACGATATTTTC-GGGTCAATTTTTGGCTAAAAACTCGTTTCGAGGCATTGGCTTAGTTTT
254 CGTGTACTA-ACCATCACGG----TTTTTGGCTAAAAACGCGTTTCG-GGCCTCGGCTCAGTTTT
*
185690 GCATAAT
313 GCATGAT
* * * * * * * *
185697 TTCTGGCAGT-AAGACTCCATAAAATATCTATAGTCATCGATCCAAATCTCAGCCACAATGGATT
1 TTTTGGCA-TAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATT
*** *
185761 TAAGGATTTGTTTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAATAAATTCAGAGAA
65 TAAGGATTTG-CCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G-GAA
* * *
185826 AAAA--GAAAAACGATAATAGAAGTGTGAAAAACCCTTGAATTTTTTTTGGCGTTGAATGATATA
127 AAAATGGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAA-TTTTTTTGGCGTTGAAT--TATA
* * * * * ** * *
185889 TATTTTTT-CGAGTATTGTGACAAAGAATAGTA-AAAAAAAATTTCTTGTCGGTTTTT-G-CAAA
188 TATTTTTTATGAGTATTGTGGCAAAAAATTG-AGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAA
* * * ** * * * ** *
185950 ATTTTAGTTGAAATCATTTACTCATCACGGTTTTTGATTAAAAACGCATTCCGGGGCCCCGATTG
252 A---TCG-TG---T-ACTAAC-CATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCTCGGCTC
*
186015 AGTTTCGCATGAT
307 AGTTTTGCATGAT
* * * * * *
186028 TTTTGG-AGTAAAGACTCCTTGAAATATCTATATTCTTCAAACCAAATCCCAGTCAGATTGGATT
1 TTTTGGCA-TAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATT
* * *** * * *
186092 TAACGATATGATTTTACGAGCATCTG-ATCTTGTTTCGATTTAGTTAGAAATTAATTCGAAAAAA
65 TAAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCG-GAAAA
* * * * *
186156 AATTGAAAAACGATATTAGAAACGTGAAAAACCCTGCAATCTTTTTGGCGTTGAATTATATAATT
129 AATGGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTT
* *
186221 TTTATGAGAATTGTGGC-AAAAATTGAGAAAAAAACTTTTCGGGTCTA-TTTTTAACCGAAATCG
193 TTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAA-TTTTCGGGTC-AGTTTTTAGCCGAAATCG
* * * * ***
186284 TGTACTAACCATCACAGTTTTTAGCTAAAAACGCGTTTCGGGGCCTCGACACAG-AAAGCATTG-
256 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCTCGGCTCAGTTTTGCA-TGA
186347 T
319 T
* *
186348 TTTTGGCATAAAGACTCCTTAAAATATATATATTCATCTAACCAAATCTCAGCCACATTGCATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* * * * *
186413 AAGGATTTTCCATTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAATCAATTCAGAAATAA
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAA-AA
*
186478 A-GGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAAATTTTTTGGCGTTGAATTATATATTTT
130 ATGGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGGCGTTGAATTATATATTTT
* *
186542 TTATGAGTATTGTGGCGAAAAATTGAGAAAAAGAAATTTT-GAGTCAGTTTTTAGCCGAAATCGT
194 TTATGAGTATTGTGGCAAAAAATTGAG-AAAA-AAATTTTCGGGTCAGTTTTTAGCCGAAATCGT
* *
186606 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTAGGGCCTTGGCTCAGTTTT-CAATGAT
257 GTACTAACCATCACGGTTTTTGGCTAAAAACGCG-TTTCGGGCCTCGGCTCAGTTTTGC-ATGAT
* * *
186670 TTTTGGCATAAAGACTCCTTGAAATATCTATATTTATCTAACC-AACCTCAGCCATATTGCATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* * * *
186734 AAGGATTTGCCATTACGAGCATCTGAATCTTATTTCGATTGAATTAGAAATAAATTTAGAAAAAT
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA-TTCG--GAA-
* * *
186799 AAAATGGAAAAACGATATTAGATGCCTGAAAACCCCTT-AAATTTTTTGGCGGTT-AATCATACA
127 AAAATGGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGGC-GTTGAAT--T--A
* * * * * * *
186862 TTTTTTTTTTCTGAGTACTGTGACAAAAAA-TG-GAAGCAAAACTTTTCGGGTCAATTTGGACAA
186 TATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAA--AAAAATTTTCGGGTC-AGTT------
* * * * * ** * * * *
186925 AATTTAACGGAAATCATGTACTAAACATCATGGGGTTTGGCAAAAAATGTGTTTTCGGGCCCCGG
242 --TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG-TTTCGGGCCTCGG
* *
186990 CTTAGTTTTGCATGGT
304 CTCAGTTTTGCATGAT
* *
187006 TTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATC-AACCAAATCTCAGCCACATTGGATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* *** * * * *
187070 AAGCATTTGTTTTTACGAGCATCTGAATCTTGTTCCGATTTAATTGGAAATTACTTCGGAAAAAA
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG--AAAA
** * * * * * * *
187135 AATGGAAAAACGATA-TAGAAGAATGAAAAACACGTCAATCTTTTAGCCGCTGAATTATATGTTT
129 AATGGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTT
* * * * * *
187199 TTTATAAATGTT-TTGCAAAAAATTGAGAAAAAAACATTTCGGGTCAGTTTTTCGCCGAAATC--
193 TTTATGAGTATTGTGGCAAAAAATTGAGAAAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGT
* * * ** * *
187261 -CACTAACCATCACTGTTTTTGGCTAAAAATGCGTTTCGTGGCCTCAACTAAGTTTTGCATGGT
257 GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCG-GGCCTCGGCTCAGTTTTGCATGAT
* * * * * *
187324 TTTTGACATAAACACTCCTTGAAATATCTATATTCGTCGAACCAAATCTCAGTCACATTGCATTA
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* * * * *
187389 AAGGATTT-CACATTACAAGCATCTTAATCTTGTTTCTATTTAATTAGAAATACATTCAGAAAAA
66 AAGGATTTGC-CATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAA
* * *
187453 AAGG-AAAACGATATTAGAAGCGTGAAAACTCCTTTAATCTTTTTGGCGTTGAATTATATATTTT
130 ATGGAAAAACGATATTAGAAGCGTGAAAAC-CCTTCAATTTTTTTGGCGTTGAATTATATATTTT
* * * *
187517 TTATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTAGGGTCAGTTTTTAACCAAAATAGTGT
194 TTATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGT
* * * * *
187582 ATTAACCATCACGGGTTTTT-GCTAAAAACGCGTTTCGATGCCTCGGCTTAGTTTTGAAAT-TT
259 ACTAACCATCAC-GGTTTTTGGCTAAAAACGCGTTTCG-GGCCTCGGCTCAGTTTTG-CATGAT
* *
187644 TTTTGGCATAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACATTGCATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
***
187709 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTC-ATTTTAATTAGAAATAAATTTATAAAAA
66 AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATAAA-TT-CGGAAA
** *
187773 AAATAAAAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATCTTTTTT-GAGTTGAATTATATA
128 AAAT-GGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAAT-TTTTTTGGCGTTGAATTATATA
* * * *
187837 TTTTTTTTGAGTATTGTGGAAAAAAAATTGA-AAAAACAAATTTCGGGTCAGTTTTTAGTCGAAA
190 TTTTTTATGAGTATTGTGG-CAAAAAATTGAGAAAAA-AATTTTCGGGTCAGTTTTTAGCCGAAA
* * * * *
187901 TAGTGTACTAATCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCTTCGGTTCAGTTTTGAA
253 TCGTGTACTAACCATCACGG-TTTTTGGCTAAAAACGCGTTTC-GGGCCTCGGCTCAGTTTTGCA
187966 TGAT
316 TGAT
* * * * * *
187970 TTTTGGCCTAAAGACTCCTAGAAATATATATATTCATCTAATCAAAGCTCAGTCACATTGCATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
* *
188035 AAGGAATTT-ACATTACGAGCATCCGAATCTTGTTTCGATTTAATTA
66 AAGG-ATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTA
188081 TAAGGAAATT
Statistics
Matches: 2732, Mismatches: 468, Indels: 308
0.78 0.13 0.09
Matches are distributed among these distances:
310 62 0.02
311 18 0.01
312 3 0.00
313 1 0.00
315 5 0.00
316 15 0.01
317 77 0.03
318 125 0.05
319 73 0.03
320 434 0.16
321 295 0.11
322 179 0.07
323 11 0.00
324 106 0.04
325 102 0.04
326 176 0.06
327 168 0.06
328 179 0.07
329 155 0.06
330 84 0.03
331 168 0.06
332 11 0.00
333 42 0.02
334 71 0.03
335 11 0.00
336 160 0.06
337 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (319 bp):
TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGCATTT
AAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAA
TGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTT
ATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTAC
TAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCTCGGCTCAGTTTTGCATGAT
Found at i:187720 original size:975 final size:965
Alignment explanation
Indices: 184400--187885 Score: 2867
Period size: 975 Copynumber: 3.6 Consensus size: 965
184390 GATATTTCAA
* * * * * *
184400 TTTTGG-ATAAACACTCCTTAAAATATCTATAATCATCTAACCAAATCTCAGCCACAATGGATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACATTGCATTT
*** * * * * * * *
184464 AAGGATTTGTTTTTTACGACCATCTGAATCTTGTTTCGATTTAATAAAAAATAAATTCAGGAAAA
66 AAGGA-TT-TCCATTACGAGCATCTTAATCTTGTTTCAATTTAATTAGAAATACATTCAGAAAAA
* * * *
184529 AAGGAAAAAC-A-A-TATAAGCGTGAAAAAC-CCTTCAATTTTTTTAGCGTTGAATTATATATTT
129 AAGGAAAAACGATATTAGAAGCGTG-AAAACTCCTTAAATCTTTTTGGCGTTGAATTATATATTT
* ** * * **
184590 TTTCTGAGTATTGTGGCAAAGAATAGTAAAAAAAAAAAAATTCCGGTCAGTTTTTGCAAAATTTT
193 TTTATGAGTATTGTGGCAAA-AA-A-T-TGAGAAAAAAATTTTGGGTCAGTTTTT-----A----
* * * * * * * *
184655 AGCCGAAAT-CGT-TT-ACTCATCA-AGGTTTTTGGCTAAAAACGCATTCCG-GGACTGCGGCTC
245 A-CCAAAATGTGTATTAAC-CATCACGGGTTTTTGGCTAAAAACGCGTTTCGAGGCCT-TGGCTT
* * * * *
184715 AGTTTTG-CATGATTTTTGACGTAAAGACTCCTTGAAATATCTATATTAATCGAACCAAATCCCA
307 AGTTTTGAAAT--TTTTTGGCATAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCA
* * ** *** * *
184779 GCCAAATTGGATTTAACAATTTGATTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAGAAAT
370 GCCACATTGCATTTAAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * *
184844 TAA-TTCG-GAAAAAATGGAAAAAAGATATTAGAAGCGTGAGAAA-CCCTTCAATTTTTTTGGCG
435 AAATTTAGAAAAAAAAT-GAAAAACGATATTAGAAGCGTGA-AAACCCCTT-AAATTTTTTGGCG
* * * * * * ** *
184906 TTAAAT--TGTATATTTTTTATGAGTATTGTGGCAAAAAAT-TGAGAAAAAAGTTTTCAGGTC--
497 TTGAATCATATATATTTTTT-CGAGTACTGTGACAAAAAATAGGA-AAAAAAAATTTCGGGTCGA
* * * *** * * * * *
184966 AGTT-------TTT-AGCCGAAATCGTGTACTAATCATCACGATTTTTGGCTAAAAATGCGTTTC
560 ATTTGGCAAAATTTAAG-TGAAATCATGTAC---TCATCACGGGGTTTGACAAAAAACGCATTCC
* * * * * * * *
185023 GGGACCTCGACTCAGTTT-GCATGGTTTTTGGCA-TAAAGACTCTTTAAAATATCTATATTCATC
621 GGGGCCCCGATTGAGTTTCGCATGATTTTTGG-AGAAAAGACTCCTTGAAATATCTATATTCATC
* * * * * *** * * **
185086 TAACCAAATCTCAGCTACATTGCATTTAA-GAATTTGCCATTACGAGCATCTAAATCTTATTTTG
685 AAACCAAATCCCAGCCACATTGGATTTAACG-ATATGATTTTACGAGCATCT-GATCTTGTTCCG
* * * * * * *
185150 ATTTAAGTAGAAATAAATTC---AGAAAA---AAAAA--A-ATT-GAATCGTGAAAACCCCTTC-
748 ATTTAATTAGAAATTAATTCGAAAAAAAATGGAAAAACGATATTAGAAACATGAAAAACCCTGCA
* * * * * * ** * * ** * *
185204 ATTTTTTTGGCGGTTAATTATATATTTTTTCGGAGTATTATGGCAAAAAACGGAGGAAAAAA-TT
813 ATCTTTTAGCCGCTGAATTATATAATTTTTATGAGAATTGTGGC-AAAAATTGAGAAAAAAACAT
* * * *
185268 TTCGGGTCAATTTTTGCAAAATTTTAGCGGAAATAGTGTACTAACCATCA-TGAGTTTTTGGCTA
877 TTCGGGTCTATTTTT-----A----A-CCGAAAT--CGCACTAACCATCACT--GTTTTTGGCTA
* * * * *
185332 AAAGCGCGTTTCAAGGCCCCGGCTCAA-TTTTGCATGAT
928 AAAACGCGTTTCGAGGCCTCGACT-AAGTTTTGCATGGT
* *
185370 TTTTGGCATAAAGACTCCTTGAAATATCTATACTCATCTAACCAAATCTCAGTCACATTGGATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACATTGCATTT
* *** * * *
185435 AAGAATTTGTTTTTACGAGCAT-TTGAATCTTGTTTCAATTTAATTAGAAATTACTTTTAAAAAA
66 AAGGATTT-CCATTACGAGCATCTT-AATCTTGTTTCAATTTAATTAGAAA-TACATTCAGAAAA
* * * *
185499 AAATGGAAAAACGATATTAGAA-CTGTGAAAAATACGTCAATCTTTTTGGCGTTGAATTATATAT
128 AAA-GGAAAAACGATATTAGAAGC-GTGAAAACTCCTTAAATCTTTTTGGCGTTGAATTATATAT
* * *
185563 TTTTTCTGAATATT-T-G-AAAAAACTTGAGATAAAAACTTTTCGGGTCAGTTTTTAATCCAAAA
191 TTTTTATGAGTATTGTGGCAAAAAA-TTGAGA-AAAAAATTTT-GGGTCAGTTTTTAA-CCAAAA
* * *
185625 T-TGT-TT-ACGAT-ATTTTCGGGTCAATTTTTGGCTAAAAACTCGTTTCGAGGCATTGGCTTAG
252 TGTGTATTAACCATCA----CGGG----TTTTTGGCTAAAAACGCGTTTCGAGGCCTTGGCTTAG
* * * * * * *
185686 TTTTGCATAA-TTTCTGGCAGT-AAGACTCCATAAAATATCTATAGTCATCGATCCAAATCTCAG
309 TTTTG-A-AATTTTTTGGCA-TAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAG
* * *** *
185749 CCACAATGGATTTAAGGATTTGTTTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAAT
371 CCACATTGCATTTAAGGATTTG-CCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * * *
185814 AAATTCAGAGAAAAAA-GAAAAACGATAATAGAAGTGTGAAAAACCCTTGAATTTTTTTTGGCGT
435 AAATTTAGAAAAAAAATGAAAAACGATATTAGAAGCGTGAAAACCCCTT-AA-ATTTTTTGGCGT
* * * * ** **
185878 TGAATGATATATATTTTTTCGAGTATTGTGACAAAGAATAGTAAAAAAAAATTTCTTGTCGGTTT
498 TGAATCATATATATTTTTTCGAGTACTGTGACAAAAAATAGGAAAAAAAAATTTCGGGTCGAATT
* * * ** **
185943 TTGCAAAATTTTAGTTGAAATCATTTACTCATCACGGTTTTTGATTAAAAACGCATTCCGGGGCC
563 TGGCAAAATTTAAG-TGAAATCATGTACTCATCACGGGGTTTGACAAAAAACGCATTCCGGGGCC
* *
186008 CCGATTGAGTTTCGCATGATTTTTGGAGTAAAGACTCCTTGAAATATCTATATTCTTCAAACCAA
627 CCGATTGAGTTTCGCATGATTTTTGGAGAAAAGACTCCTTGAAATATCTATATTCATCAAACCAA
* * * *
186073 ATCCCAGTCAGATTGGATTTAACGATATGATTTTACGAGCATCTGATCTTGTTTCGATTTAGTTA
692 ATCCCAGCCACATTGGATTTAACGATATGATTTTACGAGCATCTGATCTTGTTCCGATTTAATTA
* * *
186138 GAAATTAATTCGAAAAAAAATTGAAAAACGATATTAGAAACGTGAAAAACCCTGCAATCTTTTTG
757 GAAATTAATTCGAAAAAAAATGGAAAAACGATATTAGAAACATGAAAAACCCTGCAATCTTTTAG
* * *
186203 GCGTTGAATTATATAATTTTTATGAGAATTGTGGCAAAAATTGAGAAAAAAACTTTTCGGGTCTA
822 CCGCTGAATTATATAATTTTTATGAGAATTGTGGCAAAAATTGAGAAAAAAACATTTCGGGTCTA
* * * *
186268 TTTTTAACCGAAATCGTGTACTAACCATCACAGTTTTTAGCTAAAAACGCGTTTCGGGGCCTCGA
887 TTTTTAACCGAAATC--GCACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGGCCTCGA
*** *
186333 C-ACAG-AAAGCATTGT
950 CTA-AGTTTTGCATGGT
* * *
186348 TTTTGGCATAAAGACTCCTTAAAATATATATATTCATCTAACCAAATCTCAGCCACATTGCATTT
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACATTGCATTT
* * * * *
186413 AAGGATTTTCCATTACGAGCATCTGAATATTGTTTCGATTTAATTAAAAAT-CAATTCAGAAATA
66 AAGGA-TTTCCATTACGAGCATCTTAATCTTGTTTCAATTTAATTAGAAATAC-ATTCAGAAAAA
*
186477 AAGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAAAT-TTTTTGGCGTTGAATTATATATTT
129 AAGGAAAAACGATATTAGAAGCGTGAAAACTCCTT-AAATCTTTTTGGCGTTGAATTATATATTT
* * * *
186541 TTTATGAGTATTGTGGCGAAAAATTGAGAAAAAGAAATTTTGAGTCAGTTTTTAGCCGAAATCGT
193 TTTATGAGTATTGTGGCAAAAAATTGAG-AAAA-AAATTTTGGGTCAGTTTTTAACCAAAAT-GT
* * * *
186606 GTACTAACCATCAC-GGTTTTTGGCTAAAAACGCGTTT-TAGGGCCTTGGCTCAGTTTT-CAATG
255 GTATTAACCATCACGGGTTTTTGGCTAAAAACGCGTTTCGA-GGCCTTGGCTTAGTTTTGAAAT-
* * *
186668 ATTTTTGGCATAAAGACTCCTTGAAATATCTATATTTATCTAACC-AACCTCAGCCATATTGCAT
318 -TTTTTGGCATAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACATTGCAT
* *
186732 TTAAGGATTTGCCATTACGAGCATCTGAATCTTATTTCGATTGAATTAGAAATAAATTTAGAAAA
382 TTAAGGATTTGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTAG-AAA
* *
186797 ATAAAATGGAAAAACGATATTAGATGCCTGAAAACCCCTTAAATTTTTTGGCGGTT-AATCATAC
446 A-AAAAT-GAAAAACGATATTAGAAGCGTGAAAACCCCTTAAATTTTTTGGC-GTTGAATCAT--
* * * **
186861 ATTTTTTTTTTCTGAGTACTGTGACAAAAAAT-GGAAGCAAAACTTTTCGGGTC-AATTTGGACA
506 ATATATTTTTTC-GAGTACTGTGACAAAAAATAGGAA-AAAAAAATTTCGGGTCGAATTTGG-CA
* * * ** *
186924 AAATTTAACG-GAAATCATGTACTAAACATCATGGGGTTTGGCAAAAAATGTGTTTTC-GGGCCC
568 AAATTTAA-GTGAAATCATGTACT---CATCACGGGGTTTGACAAAAAACG-CATTCCGGGGCCC
* * *
186987 CGGCTT-AGTTTTGCATGGTTTTTGGCA-AAAAGACTCCTTGAAATATCTATATTCATC-AACCA
628 C-GATTGAGTTTCGCATGATTTTTGG-AGAAAAGACTCCTTGAAATATCTATATTCATCAAACCA
* * *
187049 AATCTCAGCCACATTGGATTTAA-GCATTTGTTTTTACGAGCATCTGAATCTTGTTCCGATTTAA
691 AATCCCAGCCACATTGGATTTAACG-ATATGATTTTACGAGCATCTG-ATCTTGTTCCGATTTAA
* * *
187113 TTGGAAATTACTTCGGAAAAAAAATGGAAAAACGATA-TAGAAGA-ATGAAAAACAC-GTCAATC
754 TTAGAAATTAATTC-GAAAAAAAATGGAAAAACGATATTAGAA-ACATGAAAAACCCTG-CAATC
** * *
187175 TTTTAGCCGCTGAATTATATGTTTTTTAT-A-AATGTTTTGCAAAAAATTGAGAAAAAAACATTT
816 TTTTAGCCGCTGAATTATATAATTTTTATGAGAAT-TGTGGC-AAAAATTGAGAAAAAAACATTT
** * *
187238 CGGGTC-AGTTTTTCGCCGAAATC-CACTAACCATCACTGTTTTTGGCTAAAAATGCGTTTCGTG
879 CGGGTCTA-TTTTTAACCGAAATCGCACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAG
*
187301 GCCTCAACTAAGTTTTGCATGGT
943 GCCTCGACTAAGTTTTGCATGGT
* * * * *
187324 TTTTGACATAAACACTCCTTGAAATATCTATATTCGTCGAACCAAATCTCAGTCACATTGCATTA
1 TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACATTGCATTT
* *
187389 AAGGATTTCACATTACAAGCATCTTAATCTTGTTTCTATTTAATTAGAAATACATTCAGAAAAAA
66 AAGGATTTC-CATTACGAGCATCTTAATCTTGTTTCAATTTAATTAGAAATACATTCAGAAAAAA
*
187454 AGG-AAAACGATATTAGAAGCGTGAAAACTCCTTTAATCTTTTTGGCGTTGAATTATATATTTTT
130 AGGAAAAACGATATTAGAAGCGTGAAAACTCCTTAAATCTTTTTGGCGTTGAATTATATATTTTT
187518 TATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTAGGGTCAGTTTTTAACCAAAATAGTGTA
195 TATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTT-GGGTCAGTTTTTAACCAAAAT-GTGTA
* *
187583 TTAACCATCACGGGTTTTT-GCTAAAAACGCGTTTCGATGCCTCGGCTTAGTTTTGAAATTTTTT
258 TTAACCATCACGGGTTTTTGGCTAAAAACGCGTTTCGAGGCCTTGGCTTAGTTTTGAAA-TTTTT
*
187647 TGGCATAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACATTGCATTTAAG
322 TGGCATAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACATTGCATTTAAG
*
187712 GATTTGCCATTACGAGCATCTGAATCTTGTTTC-ATTTTAATTAGAAATAAATTTATAAAAAAAA
387 GATTTGCCATTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATAAATTTAGAAAAAAAA
* * * * *
187776 TAAAAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATCTTTTTTGAGTTGAATTATATAT-TT
451 T--GAAAAACGATATTAGAAGCGTGAAAACCCCTTAAAT-TTTTTGGCGTTGAATCATATATATT
* * * *
187840 TTTTTGAGTATTGTGGAAAAAAAAT-TGAAAAAACAAATTTCGGGTC
513 TTTTCGAGTACTGT-GACAAAAAATAGGAAAAAA-AAATTTCGGGTC
187886 AGTTTTTAGT
Statistics
Matches: 2071, Mismatches: 319, Indels: 250
0.78 0.12 0.09
Matches are distributed among these distances:
960 1 0.00
961 2 0.00
962 13 0.01
965 2 0.00
966 1 0.00
969 98 0.05
970 124 0.06
971 153 0.07
972 108 0.05
973 117 0.06
974 166 0.08
975 324 0.16
976 223 0.11
977 77 0.04
978 303 0.15
979 142 0.07
980 98 0.05
981 9 0.00
982 18 0.01
985 6 0.00
987 1 0.00
988 3 0.00
989 30 0.01
990 52 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (965 bp):
TTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTCACATTGCATTT
AAGGATTTCCATTACGAGCATCTTAATCTTGTTTCAATTTAATTAGAAATACATTCAGAAAAAAA
GGAAAAACGATATTAGAAGCGTGAAAACTCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTT
ATGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTGGGTCAGTTTTTAACCAAAATGTGTATTA
ACCATCACGGGTTTTTGGCTAAAAACGCGTTTCGAGGCCTTGGCTTAGTTTTGAAATTTTTTGGC
ATAAAGACTCCTTGAAATATCTATATTAATCTAACCAAATCTCAGCCACATTGCATTTAAGGATT
TGCCATTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTAGAAAAAAAATGAAA
AACGATATTAGAAGCGTGAAAACCCCTTAAATTTTTTGGCGTTGAATCATATATATTTTTTCGAG
TACTGTGACAAAAAATAGGAAAAAAAAATTTCGGGTCGAATTTGGCAAAATTTAAGTGAAATCAT
GTACTCATCACGGGGTTTGACAAAAAACGCATTCCGGGGCCCCGATTGAGTTTCGCATGATTTTT
GGAGAAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCCCAGCCACATTGGATTTAACG
ATATGATTTTACGAGCATCTGATCTTGTTCCGATTTAATTAGAAATTAATTCGAAAAAAAATGGA
AAAACGATATTAGAAACATGAAAAACCCTGCAATCTTTTAGCCGCTGAATTATATAATTTTTATG
AGAATTGTGGCAAAAATTGAGAAAAAAACATTTCGGGTCTATTTTTAACCGAAATCGCACTAACC
ATCACTGTTTTTGGCTAAAAACGCGTTTCGAGGCCTCGACTAAGTTTTGCATGGT
Found at i:188104 original size:13 final size:13
Alignment explanation
Indices: 188086--188116 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
188076 AATTATAAGG
188086 AAATTGAGAAAAA
1 AAATTGAGAAAAA
188099 AAATTGAGAAAAA
1 AAATTGAGAAAAA
188112 AAATT
1 AAATT
188117 TTCAGGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (13 bp):
AAATTGAGAAAAA
Found at i:188314 original size:240 final size:238
Alignment explanation
Indices: 187855--188320 Score: 774
Period size: 240 Copynumber: 1.9 Consensus size: 238
187845 GAGTATTGTG
*
187855 GAAAAAAAATTGAAAAAACAAATTTCGGGTCAGTTTTTAGTCGAAATAGTGTACTAATCATCACG
1 GAAAAAAAATTGAAAAAACAAATTTCAGGTCAGTTTTTAGTCGAAATAGTGTACTAATCATCACG
* * *
187920 GTTTTTTGGCTAAAAACGCGTTTCGGGGCTTCGGTTCAGTTTTGAATGATTTTTGGCCTAAAGAC
66 GTTTTTTGGCTAAAAACACGTTTCGGGGCTTCGGCTCAGTTTTGAAAGATTTTTGGCCTAAAGAC
* * * * *
187985 TCCTAGAAATATATATATTCATCTAATCAAAGCTCAGTCACATTGCATTTAAGGAATTTACATTA
131 CCCTAGAAATATATATATTCATCCAACCAAAGCGCAGCCACATTGCATTTAAGGAATTTACATTA
188050 CGAGCATCCGAATCTTGTTTCGATTTAATTATAAGGAAATTGA
196 CGAGCATCCGAATCTTGTTTCGATTTAATTATAAGGAAATTGA
188093 GAAAAAAAATTGAGAAAAA-AAATTTTCAGGTCAGTTTTTAGTCGAAATAGTGTACTAATCATCA
1 GAAAAAAAATTGA-AAAAACAAA-TTTCAGGTCAGTTTTTAGTCGAAATAGTGTACTAATCATCA
188157 CGG-TTTTTGGCTAAAAACACGTTTCGGGGCTTCGGCTCAGTTTTGAAAGATTTTTGGCCTAAAG
64 CGGTTTTTTGGCTAAAAACACGTTTCGGGGCTTCGGCTCAGTTTTGAAAGATTTTTGGCCTAAAG
* * *
188221 ACCCCTTGAAATATATATATATTCATCCAACCAAATCGCAGCCACATTGCATTTAAGGATTTTAC
129 ACCCCTAG-AA-ATATATATATTCATCCAACCAAAGCGCAGCCACATTGCATTTAAGGAATTTAC
188286 ATTACGAGCATCCGAATCTTGTTTCGATTTAATTA
192 ATTACGAGCATCCGAATCTTGTTTCGATTTAATTA
188321 GAAATAAATT
Statistics
Matches: 212, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
238 80 0.38
239 50 0.24
240 82 0.39
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (238 bp):
GAAAAAAAATTGAAAAAACAAATTTCAGGTCAGTTTTTAGTCGAAATAGTGTACTAATCATCACG
GTTTTTTGGCTAAAAACACGTTTCGGGGCTTCGGCTCAGTTTTGAAAGATTTTTGGCCTAAAGAC
CCCTAGAAATATATATATTCATCCAACCAAAGCGCAGCCACATTGCATTTAAGGAATTTACATTA
CGAGCATCCGAATCTTGTTTCGATTTAATTATAAGGAAATTGA
Done.