Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006498.1 Hibiscus syriacus cultivar Beakdansim tig00015810_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: 88166
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1377 original size:14 final size:15
Alignment explanation
Indices: 1358--1398 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
1348 TGTTACTTCA
1358 GAATGATTAAACGC-
1 GAATGATTAAACGCT
*
1372 GAATGATTCAAATGCT
1 GAATGATT-AAACGCT
1388 GAATGATTAAA
1 GAATGATTAAA
1399 GGCTCTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 8 0.33
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (15 bp):
GAATGATTAAACGCT
Found at i:13045 original size:2 final size:2
Alignment explanation
Indices: 13034--13063 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13024 ACCTTCCCCC
*
13034 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13064 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:21674 original size:29 final size:29
Alignment explanation
Indices: 21641--21696 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
21631 ACCAATATCT
* *
21641 AAATATAAAATTTAAAAATTCAAAATACA
1 AAATACAAAATCTAAAAATTCAAAATACA
* *
21670 AAATACAAAATCTAATAATTCATAATA
1 AAATACAAAATCTAAAAATTCAAAATA
21697 TAAATAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (29 bp):
AAATACAAAATCTAAAAATTCAAAATACA
Found at i:21717 original size:19 final size:16
Alignment explanation
Indices: 21683--21713 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21673 TACAAAATCT
21683 AATAATTCATAATATA
1 AATAATTCATAATATA
*
21699 AATAATTCATTATAT
1 AATAATTCATAATAT
21714 TATATTATAT
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:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:30496 original size:107 final size:107
Alignment explanation
Indices: 30365--30641 Score: 475
Period size: 107 Copynumber: 2.6 Consensus size: 107
30355 AACAATTTGG
**
30365 TATCACTAAATCTATTCTAATAACGTGTAG-GATCATCTTGTTCACTGATAGTGCATAACATTAT
1 TATCACTAAATCTATTCTAATAACG-CCAGTGATCATCTTGTTCACTGATAGTGCATAACATTAT
*
30429 ATACCATCAGTCCATATCGATATTTCACTCATAAACAACTACC
65 ATACCATCAGTCAATATCGATATTTCACTCATAAACAACTACC
30472 TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTATA
1 TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTATA
30537 TACCATCAGTCAATATCGATATTTCACTCATAAACAACTACC
66 TACCATCAGTCAATATCGATATTTCACTCATAAACAACTACC
* * * *
30579 TACCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGAAAGAGCATAAAATTA
1 TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTA
30642 ACCCAAATCA
Statistics
Matches: 162, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
106 2 0.01
107 160 0.99
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.32
Consensus pattern (107 bp):
TATCACTAAATCTATTCTAATAACGCCAGTGATCATCTTGTTCACTGATAGTGCATAACATTATA
TACCATCAGTCAATATCGATATTTCACTCATAAACAACTACC
Found at i:31022 original size:108 final size:106
Alignment explanation
Indices: 30819--31314 Score: 451
Period size: 107 Copynumber: 4.7 Consensus size: 106
30809 ATAAAGCGGG
* * * * * *
30819 TGATCATCTTGTTCACTGATGGGGCATAAAATTATATACAGTTAGTCCATATCGGTATTTCACTC
1 TGATCATCTTATTCACTGATAGTGCATAAAATTATATAAAGTCAGTCCATATCGATATTTCACTC
* * * *
30884 GTAAATAATTATGCATCACTAAATCCATTCTAATAACACGCA
66 GTAAACAATTACGTATCACTAAATCTATTCTAATAACA-GCA
* * *
30926 TGATCATCTTGTTCGCTGATAGTGCATAAACTTATATAAATGTCAGTCCATATCGATATTTCACT
1 TGATCATCTTATTCACTGATAGTGCATAAAATTATATAAA-GTCAGTCCATATCGATATTTCACT
* * * **
30991 CGTGAAA-AATTACGTATCACTAAATCAATTCTAATAGCGTGTG
65 CGT-AAACAATTACGTATCACTAAATCTATTCTAATAAC-AGCA
* * *
31034 TGATCATCTTATTCACTGAT-GATGCAT-AAATTATATACAGCCAGTCCGTATCGATATTTCACT
1 TGATCATCTTATTCACTGATAG-TGCATAAAATTATATAAAGTCAGTCCATATCGATATTTCACT
* * * * *
31097 CATAAACAATTACATATCGCTAAATCTATTCTAATAGAGAGCG
65 CGTAAACAATTACGTATCACTAAATCTATTCTAATA-ACAGCA
* * ** * * *
31140 TGATCATC----TC-GTG--A-TGCATAAAATCATATACCGACAGTCGATATCGGTATTTCACT-
1 TGATCATCTTATTCACTGATAGTGCATAAAATTATATAAAGTCAGTCCATATCGATATTTCACTC
* *
31196 GATAAACAATTTCGTATCACTAAATCTATTCTAACAA-AGCGA
66 G-TAAACAATTACGTATCACTAAATCTATTCTAATAACAGC-A
* ** *
31238 GTGATCATCTTATTCACTGATAGAGCATAAAATTATATATTGTCAGTCGATATCGATATTTCACT
1 -TGATCATCTTATTCACTGATAGTGCATAAAATTATATAAAGTCAGTCCATATCGATATTTCACT
* *
31303 CATAAAAAATTA
65 CGTAAACAATTA
31315 AAGCAAACAA
Statistics
Matches: 318, Mismatches: 51, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
97 3 0.01
98 6 0.02
99 68 0.21
101 2 0.01
102 2 0.01
103 2 0.01
104 2 0.01
105 3 0.01
106 61 0.19
107 90 0.28
108 76 0.24
109 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (106 bp):
TGATCATCTTATTCACTGATAGTGCATAAAATTATATAAAGTCAGTCCATATCGATATTTCACTC
GTAAACAATTACGTATCACTAAATCTATTCTAATAACAGCA
Found at i:31204 original size:99 final size:98
Alignment explanation
Indices: 31053--31247 Score: 257
Period size: 99 Copynumber: 2.0 Consensus size: 98
31043 TATTCACTGA
* * *
31053 TGATGCATAAATTATATACAGCCAGTCCGTATCGATATTTCACTCATAAACAATTACATATCGCT
1 TGATGCATAAATCATATACAGACAGTCCGTATCGATATTTCACTCATAAACAATTACATATCACT
* * *
31118 AAATCTATTCTAATAGAGAGCGTGATCATCTCG
66 AAATCTATTCTAACAAAGAGAGTGATCATCTCG
* * * * *
31151 TGATGCATAAAATCATATACCGACAGT-CGATATCGGTATTTCACTGATAAACAATTTCGTATCA
1 TGATGCAT-AAATCATATACAGACAGTCCG-TATCGATATTTCACTCATAAACAATTACATATCA
*
31215 CTAAATCTATTCTAACAAAGCGAGTGATCATCT
64 CTAAATCTATTCTAACAAAGAGAGTGATCATCT
31248 TATTCACTGA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
98 10 0.12
99 73 0.88
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (98 bp):
TGATGCATAAATCATATACAGACAGTCCGTATCGATATTTCACTCATAAACAATTACATATCACT
AAATCTATTCTAACAAAGAGAGTGATCATCTCG
Found at i:34212 original size:24 final size:24
Alignment explanation
Indices: 34185--34238 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
34175 AAACAAAAAT
*
34185 TAAACTTTAGATATGTTTCTTAAC
1 TAAACTTTAGATATGTTTATTAAC
34209 TAAACTTTAGATATGTTTATTAAC
1 TAAACTTTAGATATGTTTATTAAC
*
34233 TCAACT
1 TAAACT
34239 CGATTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (24 bp):
TAAACTTTAGATATGTTTATTAAC
Found at i:35437 original size:230 final size:225
Alignment explanation
Indices: 35025--35472 Score: 770
Period size: 230 Copynumber: 2.0 Consensus size: 225
35015 GTAAATTATC
* *
35025 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
35090 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATATTTTTTG
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAATTTTG
35155 TGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
131 TGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
35220 ACATAAATTACATAACTTTCAAAAAAGTATA
196 ACATAAATTACATAACTTT-AAAAAAGTATA
*
35251 TATCATTTTTATAAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTG
1 TATCATTTTTAT-AAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTA
*
35316 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAAT
64 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTAT-AAATATCAAAACAATCAAAT-AAAT
* * *
35381 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGGAACACTATTAAATAAAT
127 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
35446 TGAAACATAAATTACATAACTTTAAAA
192 TGAAACATAAATTACATAACTTTAAAA
35473 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
226 12 0.06
227 25 0.12
228 61 0.29
229 24 0.11
230 87 0.42
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (225 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAATTTTG
TGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
ACATAAATTACATAACTTTAAAAAAGTATA
Found at i:35559 original size:20 final size:20
Alignment explanation
Indices: 35536--35581 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
35526 CGATATACCA
*
35536 GGTAAAAATATGATAAAACC
1 GGTAAAAAAATGATAAAACC
35556 GGTAAAAAAATGATAAAACC
1 GGTAAAAAAATGATAAAACC
35576 GGTAAA
1 GGTAAA
35582 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAAAATGATAAAACC
Found at i:35724 original size:19 final size:18
Alignment explanation
Indices: 35702--35747 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
35692 CGATATAACA
35702 GGTAAAATATGATAAAACC
1 GGTAAAATATGAT-AAACC
*
35721 GGTAACAAAATGATAAACC
1 GGTAA-AATATGATAAACC
35740 GGTAAAAT
1 GGTAAAAT
35748 GATACCGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.20
Consensus pattern (18 bp):
GGTAAAATATGATAAACC
Found at i:38133 original size:32 final size:32
Alignment explanation
Indices: 38070--38129 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
38060 AAATAGATGG
*
38070 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
*
38102 AGTGGTGAAAGAAGTTG-GGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
38130 GTGATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:39942 original size:19 final size:19
Alignment explanation
Indices: 39918--39966 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
39908 AATGTCGAGT
39918 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
39937 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
*
39956 TATTTTTGTAT
1 TAATTTTGTAT
39967 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:39975 original size:18 final size:19
Alignment explanation
Indices: 39918--39978 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
39908 AATGTCGAGT
* *
39918 TAATTTTGTATAAGATTTA
1 TAATTTTGTATATGATATA
*
39937 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGATATA
* *
39956 TATTTTTGTATGTGA-ATA
1 TAATTTTGTATATGATATA
39974 TAATT
1 TAATT
39979 ATGAATGAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
18 6 0.16
19 31 0.84
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATATGATATA
Found at i:40721 original size:197 final size:199
Alignment explanation
Indices: 40089--41647 Score: 2898
Period size: 199 Copynumber: 7.9 Consensus size: 199
40079 ATGGCCACAG
* * *
40089 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAA
40154 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
65 AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA
40219 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
130 TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAA
40284 AACAA
195 AACAA
40289 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
40354 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
40419 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
40484 ACAA
196 ACAA
40488 GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
40552 GTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCAGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
40616 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
40681 ACAA
196 ACAA
40685 GGTGCACCCA-AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
40749 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
40813 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-AAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
40877 A-AA
196 ACAA
40880 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
40945 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
* * **
41010 GTCTAAATAATGTGTCGACACAAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
41075 ACAA
196 ACAA
41079 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
41144 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
* ** **
41209 GTCTAAATAATGTGTCGACACTAATATAGCTTGTGTCGATATTTTTTCCCCAGAATGAATGGAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
41274 ACAA
196 ACAA
41278 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
41343 GTATAATGTAATATGTAATTTTTCAATCTAACCTGTACAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
**
41408 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAAGAATGAATGGAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCC-AGAATGAATTAAA
41472 AACAA
195 AACAA
41477 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
1 GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
*
41542 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGAGAATAT
66 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
41607 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
41648 CTAATTTAAA
Statistics
Matches: 1335, Mismatches: 17, Indels: 15
0.98 0.01 0.01
Matches are distributed among these distances:
195 12 0.01
196 122 0.09
197 332 0.25
198 89 0.07
199 726 0.54
200 54 0.04
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (199 bp):
GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAA
ACAA
Found at i:43128 original size:18 final size:18
Alignment explanation
Indices: 43107--43174 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
43097 AGCGGTCGCA
43107 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
43125 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
43146 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
43167 GAAGATGA
1 GAAGATGA
43175 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:43131 original size:6 final size:6
Alignment explanation
Indices: 43107--43204 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
43097 AGCGGTCGCA
* * * * * *
43107 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
43155 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
43203 GA
1 GA
43205 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:43142 original size:3 final size:3
Alignment explanation
Indices: 43122--43208 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
43112 TGAAGCTGAC
* * * * * ** *
43122 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
43170 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
43209 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:43157 original size:42 final size:42
Alignment explanation
Indices: 43110--43200 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
43100 GGTCGCAGAA
*
43110 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
43152 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
43194 GATGAAG
1 GATGAAG
43201 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:43208 original size:18 final size:18
Alignment explanation
Indices: 43107--43204 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
43097 AGCGGTCGCA
* *
43107 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
43125 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
43143 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
43161 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
43179 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
43197 GAAGATGA
1 GAAGATGA
43205 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:45179 original size:180 final size:180
Alignment explanation
Indices: 44677--45198 Score: 868
Period size: 182 Copynumber: 2.9 Consensus size: 180
44667 CTTTCAACAT
** * * *
44677 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGAT-AATTTGTAATATAACCGGTATAAATATACCGGT-TTATGAGCGAATA
*
44742 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
64 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
44807 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCA
129 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCA
*
44859 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAGCGAATA
1 ATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAAATATACCG-GTTTATGAGCGAATA
44924 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
64 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
44989 AATATGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
129 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCC--A
45043 ATTATAATGTAATAGATAATTTGTAATATAACC-GTATAAATATA-CGGTTTATGAGCGAATAGG
1 ATTATAATGTAATAGATAATTTGTAATATAACCGGTATAAATATACCGGTTTATGAGCGAATAGG
* *
45106 TCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAAAA
66 TCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
* *
45171 TGTGTCGATACCATTGAAAAAAGTGTCG
131 TGTGTCGATACGATTTAAAAAAGTGTCG
45199 GTAATTTGAA
Statistics
Matches: 322, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
180 104 0.32
181 4 0.01
182 179 0.56
183 15 0.05
184 20 0.06
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (180 bp):
ATTATAATGTAATAGATAATTTGTAATATAACCGGTATAAATATACCGGTTTATGAGCGAATAGG
TCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
TGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCA
Found at i:47691 original size:25 final size:25
Alignment explanation
Indices: 47657--47721 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
47647 TTATCATTAA
47657 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
47682 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
47707 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
47722 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:48040 original size:23 final size:23
Alignment explanation
Indices: 48009--48072 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
47999 ATAGGTAAAC
*
48009 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
48032 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
48055 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
48073 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:48079 original size:23 final size:23
Alignment explanation
Indices: 48009--48081 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
47999 ATAGGTAAAC
* **
48009 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
48032 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
48055 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
48078 ATAT
1 ATAT
48082 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:48381 original size:25 final size:25
Alignment explanation
Indices: 48347--48397 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
48337 ACAACAAATC
*
48347 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
48372 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
48397 A
1 A
48398 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:48713 original size:18 final size:18
Alignment explanation
Indices: 48692--48728 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48682 GTAATTGGAG
48692 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
48710 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
48728 T
1 T
48729 ATTTATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:48736 original size:24 final size:23
Alignment explanation
Indices: 48683--48733 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
48673 ATTTCATATG
*
48683 TAATTGGAGTTTGAATTTAAATT
1 TAATTTGAGTTTGAATTTAAATT
48706 TCAATTTGAGTTTGAATTTCAATATT
1 T-AATTTGAGTTTGAATTT-AA-ATT
48732 TA
1 TA
48734 TTTCGGCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.04
24 16 0.67
25 3 0.12
26 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (23 bp):
TAATTTGAGTTTGAATTTAAATT
Found at i:49438 original size:23 final size:23
Alignment explanation
Indices: 49407--49470 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
49397 ATAGGTAAAC
*
49407 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
49430 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
49453 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
49471 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:49477 original size:23 final size:23
Alignment explanation
Indices: 49407--49479 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
49397 ATAGGTAAAC
* **
49407 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
49430 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
49453 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
49476 ATAT
1 ATAT
49480 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:54265 original size:39 final size:39
Alignment explanation
Indices: 54215--54292 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
54205 AAAATAAAGA
*
54215 TTTATAATAGACGTGAATGTTCTTGATATTAATAATATT
1 TTTATAATAGACGTGAAAGTTCTTGATATTAATAATATT
*
54254 TTTATAGTAGACGTGAAAGTTCTTGATATTAATAATATT
1 TTTATAATAGACGTGAAAGTTCTTGATATTAATAATATT
54293 AAATATGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (39 bp):
TTTATAATAGACGTGAAAGTTCTTGATATTAATAATATT
Found at i:54452 original size:13 final size:15
Alignment explanation
Indices: 54421--54453 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
54411 TGAAAAAAAT
54421 TAAAAGTATGATGAG
1 TAAAAGTATGATGAG
54436 TAAAA-TATGAT-AG
1 TAAAAGTATGATGAG
54449 TAAAA
1 TAAAA
54454 AAAAGTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
TAAAAGTATGATGAG
Found at i:56676 original size:2 final size:2
Alignment explanation
Indices: 56669--56733 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
56659 TTTATCCAAT
56669 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
56711 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
56734 GAATAAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58875 original size:2 final size:2
Alignment explanation
Indices: 58868--58893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58858 TAGCAAAAGA
58868 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
58894 GAATTAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60370 original size:2 final size:2
Alignment explanation
Indices: 60322--60352 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60312 GACTAAAATA
60322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60353 CTTTAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63081 original size:60 final size:59
Alignment explanation
Indices: 63004--63127 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 59
62994 TAACGTAATC
* * *
63004 AAATGATTATTCGACTATAGAATATTATTTTATTAATTAATATAACTATTAAAAGTTATA
1 AAATGATAATTCAACTATA-AATATTATTTTATTAAGTAATATAACTATTAAAAGTTATA
* * * * * * *
63064 AAATGATAATTCAACTATAAATATTGTTTTGTTGAGTCATCTGACTATTCAAAGTTATA
1 AAATGATAATTCAACTATAAATATTATTTTATTAAGTAATATAACTATTAAAAGTTATA
63123 AAATG
1 AAATG
63128 GTCGGTTAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 37 0.69
60 17 0.31
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (59 bp):
AAATGATAATTCAACTATAAATATTATTTTATTAAGTAATATAACTATTAAAAGTTATA
Found at i:63337 original size:23 final size:23
Alignment explanation
Indices: 63307--63351 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
63297 TGCTCTTGGT
63307 GGGCTCTCCCCTTTACCATACAA
1 GGGCTCTCCCCTTTACCATACAA
63330 GGGCTCTCCCCTTTACCATACA
1 GGGCTCTCCCCTTTACCATACA
63352 GTCAAGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.40, G:0.13, T:0.27
Consensus pattern (23 bp):
GGGCTCTCCCCTTTACCATACAA
Found at i:63802 original size:14 final size:14
Alignment explanation
Indices: 63785--63814 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
63775 TTTACATCCT
63785 TTCATTTATGTTCG
1 TTCATTTATGTTCG
*
63799 TTCATTTGTGTTCG
1 TTCATTTATGTTCG
63813 TT
1 TT
63815 TATCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.17, T:0.60
Consensus pattern (14 bp):
TTCATTTATGTTCG
Found at i:73703 original size:102 final size:102
Alignment explanation
Indices: 73527--73746 Score: 255
Period size: 102 Copynumber: 2.2 Consensus size: 102
73517 CAAGTTGAAC
* * * * * * *
73527 AAGTTGGCAGATGAATGTCTTCCTCTTGAACTTGAAGGCATAGTGACATATGAGTTTTGTACAGA
1 AAGTTGGCAGATGAATGCCTTCCTATTAAACTTGAAGGCATAATGACATATGAGTTTTGAAAAAA
73592 CAGTTGTGTCAATGGT-ATCTCGATATTAAGGTCCAAG
66 CAGTTGTGTCAATGGTAAT-TCGATATTAAGGTCCAAG
* * * *
73629 AAGTTGGCAGATGAATGCCTTCGC-ATTAAACTTGAATGTATAATGTCATATGGGTTTTGAAAAA
1 AAGTTGGCAGATGAATGCCTTC-CTATTAAACTTGAAGGCATAATGACATATGAGTTTTGAAAAA
* * * * *
73693 ACTGTTGTGTCGATGGTAATTCTATGTTAAGGTCGAAG
65 ACAGTTGTGTCAATGGTAATTCGATATTAAGGTCCAAG
*
73731 AAGTTGACAGATGAAT
1 AAGTTGGCAGATGAAT
73747 ATTTTCCTCT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
102 96 0.97
103 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (102 bp):
AAGTTGGCAGATGAATGCCTTCCTATTAAACTTGAAGGCATAATGACATATGAGTTTTGAAAAAA
CAGTTGTGTCAATGGTAATTCGATATTAAGGTCCAAG
Found at i:74954 original size:60 final size:60
Alignment explanation
Indices: 74842--74972 Score: 138
Period size: 60 Copynumber: 2.2 Consensus size: 60
74832 GACATGATAG
** * * * *
74842 AGATTCTTTGCAAAAGCTGAAAGTGTTACTTGTGAAAATAGTTTTCCCTTTTATTGTTAA
1 AGATTCTTTGCAAAAGCTGAAAACGTTACTTGTGAAAAGAGTCTTCCCTTTTACTGTCAA
* * ** *
74902 AGATTCTTTGCAAAAGGTGAAAACGCTT-CTTGTGAGAAGAGTCTTCTTTTTTACTGTCAT
1 AGATTCTTTGCAAAAGCTGAAAACG-TTACTTGTGAAAAGAGTCTTCCCTTTTACTGTCAA
*
74962 AGAATCTTTGC
1 AGATTCTTTGC
74973 TTTTCTTAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
60 56 0.97
61 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (60 bp):
AGATTCTTTGCAAAAGCTGAAAACGTTACTTGTGAAAAGAGTCTTCCCTTTTACTGTCAA
Found at i:74964 original size:231 final size:222
Alignment explanation
Indices: 74452--74994 Score: 547
Period size: 231 Copynumber: 2.4 Consensus size: 222
74442 AGAGATTCCA
* * * *
74452 TGCAAAAGTTGAAAGCGCTTCTTGTGAAAACAAAGAGTCTTCTCTTTTT-TGTCAGATATTCTTT
1 TGCAAAAGGTGAAAGCGCTTCTTGTG---A-GAAGAGTCTTCT-TTTTTATGTCATAGATTCTTT
* *
74516 GTATTATTAAGTCAATTATATGCACAGTTGTTGTCTGCAATCGGGAACTATTCATGTCAACACCT
61 GT-TTATTAAGTCAATTATATGCAAAGTTGTTGTCTCCAATCGGGAACTATTCATGTCAACACCT
* * * *
74581 CCTATGTCTGATGGGATGAGACCGTTTGACATGACAGAGATTTTCTATAAAAGGACCTCTTATGA
125 CATATGTCTGATAGGATGAGACCATTTGACATGACAGAGATTTTCTACAAAAGGACCTCTTATGA
74646 AAATAGGCTTCCCTTTTATTGTCAAAGATTCTT
190 AAATAGGCTTCCCTTTTATTGTCAAAGATTCTT
* * * * * *
74679 TGCAAAAAGTGAAAGTGTTTCTTGTGAGAA-AGGTTTTCTCTTTTATTATCATAGATTCTTTGTT
1 TGCAAAAGGTGAAAGCGCTTCTTGTGAGAAGA-GTCTTCTTTTTTA-TGTCATAGATTCTTTGTT
* * * * *
74743 TATTCAGTCAATTATATGCAAAGTTTTTGT-TCCTAGTTGGGGAACTATTCATGTCCACACCTCA
64 TATTAAGTCAATTATATGCAAAGTTGTTGTCTCC-A-ATCGGGAACTATTCATGTCAACACCTCA
* * * * * **
74807 TATGTTTTATAGGATGAGTCCATTTGACATGATAGAGATTCTT-TGCAAAAGCTGAAAGTGTTAC
127 TATGTCTGATAGGATGAGACCATTTGACATGACAGAGATT-TTCTACAAAAG--G--A--CCT-C
* ** *
74871 TTGTGAAAATAGTTTTCCCTTTTATTGTTAAAGATTCTT
184 TTATGAAAATAGGCTTCCCTTTTATTGTCAAAGATTCTT
* *
74910 TGCAAAAGGTGAAAACGCTTCTTGTGAGAAGAGTCTTCTTTTTTACTGTCATAGAATCTTTGCTT
1 TGCAAAAGGTGAAAGCGCTTCTTGTGAGAAGAGTCTTCTTTTTTA-TGTCATAGATTCTTTG-TT
*
74975 T-TCTTAGTCAATTATATGCA
64 TAT-TAAGTCAATTATATGCA
74995 CAACTACTAT
Statistics
Matches: 258, Mismatches: 42, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
222 7 0.03
223 37 0.14
224 79 0.31
225 2 0.01
226 1 0.00
227 22 0.09
228 1 0.00
230 1 0.00
231 88 0.34
232 20 0.08
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (222 bp):
TGCAAAAGGTGAAAGCGCTTCTTGTGAGAAGAGTCTTCTTTTTTATGTCATAGATTCTTTGTTTA
TTAAGTCAATTATATGCAAAGTTGTTGTCTCCAATCGGGAACTATTCATGTCAACACCTCATATG
TCTGATAGGATGAGACCATTTGACATGACAGAGATTTTCTACAAAAGGACCTCTTATGAAAATAG
GCTTCCCTTTTATTGTCAAAGATTCTT
Found at i:80158 original size:63 final size:63
Alignment explanation
Indices: 80049--80188 Score: 172
Period size: 63 Copynumber: 2.2 Consensus size: 63
80039 ATGAGCATTT
* * * * *
80049 CCGGGATCCACAGGTTGTTCTTCGACAACCCCGTCACCTACATCTTGATTCGGTTGCTCAATC
1 CCGGCATCCACGGGTTGTTCTTCGACAAACCCGTCACCTACATCTTGATTCGGGTGCTCAACC
* * * * * **
80112 CCGGCATCCACGGGTTGTTCTTCGACAAACCTGTCACTTGCTTCTTGATTTGGGTGCTTGACC
1 CCGGCATCCACGGGTTGTTCTTCGACAAACCCGTCACCTACATCTTGATTCGGGTGCTCAACC
80175 CCGGCATCCACGGG
1 CCGGCATCCACGGG
80189 AATGGATTCT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.16, C:0.32, G:0.23, T:0.29
Consensus pattern (63 bp):
CCGGCATCCACGGGTTGTTCTTCGACAAACCCGTCACCTACATCTTGATTCGGGTGCTCAACC
Found at i:81048 original size:2 final size:2
Alignment explanation
Indices: 81041--81085 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
81031 GTTTGACGTG
81041 AT AT AT AT AT AT AT AT 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
81083 AT A
1 AT A
81086 AGCGAGCACT
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:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84600 original size:14 final size:15
Alignment explanation
Indices: 84581--84610 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
84571 AATCTGGTGA
84581 TTTTAAAAT-TTATT
1 TTTTAAAATATTATT
84595 TTTTAAAATATTATT
1 TTTTAAAATATTATT
84610 T
1 T
84611 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAAAATATTATT
Done.