Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004622.1 Hibiscus syriacus cultivar Beakdansim tig00010344_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: 131793
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1292 original size:49 final size:50
Alignment explanation
Indices: 1202--1297 Score: 140
Period size: 49 Copynumber: 1.9 Consensus size: 50
1192 ATGTTAAAAC
* * * *
1202 AAAGAGTAAATTCAATAGGGAGTATCAATACGCCTTCAAGGAGTATCGAT
1 AAAGAGTAAATTCAACAGAGAGTATCAATACACATTCAAGGAGTATCGAT
*
1252 AAAGAGTAAATTCAACA-AGAGTATCGATACACATTCAAGGAGTATC
1 AAAGAGTAAATTCAACAGAGAGTATCAATACACATTCAAGGAGTATC
1298 AATACTGCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 25 0.61
50 16 0.39
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.23
Consensus pattern (50 bp):
AAAGAGTAAATTCAACAGAGAGTATCAATACACATTCAAGGAGTATCGAT
Found at i:2604 original size:35 final size:37
Alignment explanation
Indices: 2565--2636 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
2555 TAATGCGTTA
* *
2565 GGTTTGTCGTT-TTATATTCTTAATGTAAT-TTTTAT
1 GGTTTGTCATTATTATATCCTTAATGTAATGTTTTAT
* *
2600 GGTTTGTTATTATTATCTCCTTAATGTAATGTTTTAT
1 GGTTTGTCATTATTATATCCTTAATGTAATGTTTTAT
2637 ATTTTAGGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 9 0.29
36 16 0.52
37 6 0.19
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.58
Consensus pattern (37 bp):
GGTTTGTCATTATTATATCCTTAATGTAATGTTTTAT
Found at i:6542 original size:182 final size:181
Alignment explanation
Indices: 6235--6727 Score: 673
Period size: 182 Copynumber: 2.7 Consensus size: 181
6225 TGACGGTTTA
* * * * *
6235 TGTCGATACTTTAAAAAAATGTATCGATCCATATCAATATAACAAGTAAAAATATGATAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAA-CG
* *
6300 GTCTCGAAAAGATAAAACCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATA
65 GTCTCGAAAAGACAAAATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATA
* * *
6365 AGTATCGACAC-TGTGTGAATTTAAAAGAGAAATAGTTTTAGCGCCTACAAAG
130 AGTATCGACACAT-TGTGAATTTAAAAAAGAAACAATTTTAGCGCCTACAAAG
* *
6417 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACAG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAAC-G
* * * * * *
6482 GTCTCTAAAGGACAAAATCGATATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
65 GTCTCGAAAAGACAAAATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATA
* * * *
6547 AGTATCGATACATTGTGAATTTAAAAAAGAAGCAATTTTAGTGCCTATAAAG
130 AGTATCGACACATTGTGAATTTAAAAAAGAAACAATTTTAGCGCCTACAAAG
* * *
6599 TATCGATGCTTTATAAAAATGTATCGATCCATAATGATATAACAGGTAAAAAATATGACAAAATC
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGT-AAAAATATGACAAAA-C
* * * *
6664 GGTCTCGAAATGACAAAATCGGTAAAGCGCTATCGGATATATTGAAATTGTCGATACTTTAATA
64 GGTCTCGAAAAGACAAAATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATA
6728 AATACGCGTA
Statistics
Matches: 271, Mismatches: 36, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
181 1 0.00
182 198 0.73
183 71 0.26
184 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (181 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACGG
TCTCGAAAAGACAAAATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATATAA
GTATCGACACATTGTGAATTTAAAAAAGAAACAATTTTAGCGCCTACAAAG
Found at i:9136 original size:21 final size:21
Alignment explanation
Indices: 9112--9155 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
9102 AAGACAATCA
9112 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
9133 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
9154 AG
1 AG
9156 GCATAATGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:9231 original size:33 final size:33
Alignment explanation
Indices: 9189--9254 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
9179 AAATAGATGG
*
9189 AGTGGTGAAAGAAGTTGAGGTGTTGACGGGTGA
1 AGTGCTGAAAGAAGTTGAGGTGTTGACGGGTGA
*
9222 AGTGCTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGCTGAAAGAAGTTGAGGTGTTGACGGGTGA
9255 CTTATGGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGCTGAAAGAAGTTGAGGTGTTGACGGGTGA
Found at i:11049 original size:19 final size:19
Alignment explanation
Indices: 11025--11073 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
11015 AATGTAGGGT
11025 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
11044 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
11063 TAATTTTGTAT
1 TAATTTTGTAT
11074 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:11407 original size:15 final size:15
Alignment explanation
Indices: 11384--11422 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11374 TGTCCATATG
11384 GTTCCCAAACGTAAA
1 GTTCCCAAACGTAAA
*
11399 GTTCTCAAACGTAAA
1 GTTCCCAAACGTAAA
*
11414 GTTTCCAAA
1 GTTCCCAAA
11423 AAATAGGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (15 bp):
GTTCCCAAACGTAAA
Found at i:11964 original size:199 final size:200
Alignment explanation
Indices: 11439--12587 Score: 1344
Period size: 200 Copynumber: 5.8 Consensus size: 200
11429 GTAAGCAGAT
* * * *
11439 GTGTCGATACATTTATAAAAAATATCGATACCAAAAACATAGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * *
11504 GGTAATTTTGTAATATAACCGGTATAAGTATACCAGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTATATGAGAATAGGTCTACATAATGT
* * * * * *
11569 ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGATTGCCCCAAATGATGAACGC
131 ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGACCAAAATGGTGCACCC
11634 ATAAA
196 ATAAA
11639 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * ** * * *
11704 GGTAAATTTATAATGTAACTAGTATAACTACACCGGTTTTATGA-GAGAATAGGTCTACATAATG
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTAT-ATGAGAATAGGTCTACATAATG
* * * * * * *
11768 TATCAACACTTTTGGAATTTGTGTCGATACTGTTTGTCCTGAAGGAATGACCAAAAGGGTGCACC
130 TATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGACCAAAATGGTGCACC
11833 CATAAA
195 CATAAA
* ** * *
11839 GTGTCGATACATTT-TTAAAAGTGCCGATCCCAGAGACATCGAAACCCATAATTATAATTTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
*
11903 GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTATATGAGAATAGGTATACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTATATGAGAATAGGTCTACATAATGT
** * * * * *
11968 ATCGACACAATTGAAATTGGTGTCGATCCTTTTTGTCCAGAATGAAAGCCCAAAATGGTGAACGC
131 ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGACCAAAATGGTGCACCC
12033 ATAAA
196 ATAAA
* * * * *
12038 GTGTCGATACATTTTTTAAAAGTGTCGATCCCAGAGATATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
12103 GGTAATTTTGAAATGTAACCAGTATAAATATACCTGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTATATGAGAATAGGTCTACATAATGT
* * * **
12168 ATCAACAC-TTT---A------TCGATACATTTTGTCCAAAATGAATGCAAAAAAAAATGGTGCA
131 ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATG---ACCAAAATGGTGCA
*
12223 CACATAAA
193 CCCATAAA
* * * *
12231 GTGTCTATACATTTATAAAAAGTATAGATCCCAGAAACATCGAAACACATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
12296 GGTAATTTT-TCAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCAGTTTTATATGAGAATAGGTCTACATAATG
* * * * * *
12360 TATCGACACTTATGGAATTCGTGTCGATACTTTTTATCTAGAATG-ATG-CCAAAAGGGTGCACC
130 TATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGACCAAAATGGTGCACC
*
12423 CATTAA
195 CATAAA
* * ** * *
12429 GTGTCAATACATTTTTAAAAAGTGCCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* ** * * *
12494 GGTAAATTTCCAATGTAACCGATATAAATATACCAGTTTTATGA-GAAAATAGGTC-AGCATAAA
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTAT-ATGAGAATAGGTCTA-CATAAT
* *
12557 GTATCGACAATTGTT-AAATTTGTGTCGATAC
129 GTATCGACACTT-TTGAAATTGGTGTCGATAC
12588 CATTTTAAAA
Statistics
Matches: 809, Mismatches: 119, Indels: 44
0.83 0.12 0.05
Matches are distributed among these distances:
190 22 0.03
193 139 0.17
194 2 0.00
196 1 0.00
197 2 0.00
198 148 0.18
199 173 0.21
200 301 0.37
202 3 0.00
203 18 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACCAGTTTTATATGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGACCAAAATGGTGCACCC
ATAAA
Found at i:15388 original size:24 final size:24
Alignment explanation
Indices: 15337--15389 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
15327 TTTCATATGT
* * *
15337 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
* *
15361 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
15385 AATTT
1 AATTT
15390 CGGCTCCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:16965 original size:200 final size:199
Alignment explanation
Indices: 16607--17574 Score: 1224
Period size: 200 Copynumber: 4.8 Consensus size: 199
16597 TAAAGTTTCC
** * *
16607 CATAAAGTGTCGATACATGCTTAAAAAATATCGATCCCAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * ** * * *
16672 GTAATAGGTAAATTTACAATGTAACCGATATAAATTTATTGGTTTTTTGAGAAAATAGATATACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
* *
16737 TAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGGT
131 TAATGTATCAACACTT-TTGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGGT
16802 GCACG
195 GCACG
*
16807 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* ** * * * * *
16872 GTAATAGGTAATTTTGTAATATAACCGGTATAAATATATCAGTTTTATGTGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
* * * * * *
16937 TAATGTGTCAACAGTTTTGAATTTTGTGTCGATACTTTTTGTCTAGAATGATTGGCCAAA-ATGG
131 TAATGTATCAACACTTTTGAA-TTTGTGTCGATACTTTTTGTCCAAAATGAAT-GCCAAACGTGG
*
17001 TGAACG
194 TGCACG
* * * *
17007 CATAAAGTGTCGATACATTTATAAAAAGTATCGACCCCAGAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * *
17072 GTAATAGGTAAATTTACAATGTAACCGATATAATTATACCGGTTTTATGAGATAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
* * * * *
17137 TAATGTATCGACACTTGTGGAATTTGTATCGATACATTTTGTCCAAAATGAATGCCAAAAG-GGT
131 TAATGTATCAACACTT-TTGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGG-
*
17201 TGCACA
194 TGCACG
* * *
17207 CATAAAGTGTCGATACAGTTTTAAAAAGTATAGATCCCAAAAACATTGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * **
17272 GTAATAGGTAAATTTACAATGTAACCGGTATAAATTTACCAGTTTTTTGAGAAAATAGGTGAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
* * * *
17337 TAATGTATCGACACATTTT-AGATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGGGG
131 TAATGTATCAACAC-TTTTGA-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGG
*
17401 TGCAGG
194 TGCACG
* * * ** * * * *
17407 TAGAAAGTGTCGATACA-TTTGAAATTGTATCAATCCAAAAAACATCGAAACTGATAATTATAAC
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* *
17471 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
* * *
17536 TAATGTATCAACCCTTTTAAATTTTTGTCGATACTTTTT
131 TAATGTATCAACACTTTTGAATTTGTGTCGATACTTTTT
17575 AAATAACACG
Statistics
Matches: 666, Mismatches: 93, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
198 21 0.03
199 124 0.19
200 507 0.76
201 14 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCTACA
TAATGTATCAACACTTTTGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGTGGTG
CACG
Found at i:22053 original size:199 final size:199
Alignment explanation
Indices: 21608--22323 Score: 883
Period size: 199 Copynumber: 3.6 Consensus size: 199
21598 CCTAAATATA
* *
21608 TGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAACATCAAAACCAATAATTATAAGGTAATA
1 TGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* * * * * * *
21671 GGTAAATTAACAATGTAACCGATATAAATATACCG-GTTAATTAGAAAACAAGTCAACATAATGT
65 GGTAAATTTACAATGTAACCAATATAAATATACCGAGTTTATGAGAAAATAGGTCAGCATAATGT
** *
21735 ATCGACACTTGTGCAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGTACG
130 ATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATG-CCAAACGAGGTGCACG
21800 CATAAAG
193 CATAAAG
*
21807 TATCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCAAAACCGATAATTATAATGTAATA
1 TGTCGATACATTTATTAAAAGTATCGATCCCAA-AAACATCAAAACCGATAATTATAATGTAATA
* ** * * *
21871 TGTAAATTTACAATGTAACCGGTATAAATATATCGATTTTATGAGAAAATAGGTCAGCATAAAGT
65 GGTAAATTTACAATGTAACCAATATAAATATACCGAGTTTATGAGAAAATAGGTCAGCATAATGT
*
21936 ATCGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACG-GGTGCACGC
130 ATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACGC
22000 ATAAAG
194 ATAAAG
* * * *
22006 TGTCAATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGTGATAG
1 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAG
* * * * *
22071 GTAAATTTATAATGTACCCAATAGAAATATACCG-GTTTTATGAGAAAATAGGTCTGAATAATGT
66 GTAAATTTACAATGTAACCAATATAAATATACCGAG-TTTATGAGAAAATAGGTCAGCATAATGT
* * * * *
22135 ATCGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGTGGTGCACGCA
130 ATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
22200 TAAAG
195 TAAAG
** * * * *
22205 TGTCGATACATTTCA--AATTGTATCGATCCAAAAAACATCGAAATCGATAATTATAATATAATA
1 TGTCGATACATTT-ATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
* * * * * *
22268 GGTAAATTTGCAATGTTACCAGTATAAATATATC-AGTTTACTTATAAAATAGGTCA
65 GGTAAATTTACAATGTAACCAATATAAATATACCGAGTTTA-TGAGAAAATAGGTCA
22324 ATATAAACGC
Statistics
Matches: 449, Mismatches: 57, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
197 4 0.01
198 106 0.24
199 200 0.45
200 70 0.16
201 67 0.15
202 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (199 bp):
TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCAATATAAATATACCGAGTTTATGAGAAAATAGGTCAGCATAATGTA
TCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCAT
AAAG
Found at i:22422 original size:87 final size:87
Alignment explanation
Indices: 22324--22486 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
22314 AAATAGGTCA
*
22324 ATATAAACGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATAAAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
*
22389 TCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* ** *
22411 ATATAAGCGCTACCTATTACATTATAAAAGCGTTTCCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATAAAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
22476 CCGGTTAAATG
66 CCGGTTAAATG
22487 ATATAACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATAAAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:23926 original size:14 final size:14
Alignment explanation
Indices: 23907--23934 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23897 TAAGTGTAAA
23907 TATAATTTTAATTT
1 TATAATTTTAATTT
23921 TATAATTTTAATTT
1 TATAATTTTAATTT
23935 ACAACACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATAATTTTAATTT
Found at i:29938 original size:24 final size:24
Alignment explanation
Indices: 29907--29954 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
29897 AAACACAATA
*
29907 ATTTGAAAA-TTAACAATTTTTTT
1 ATTTGAAAATTTAAAAATTTTTTT
29930 ATTTCGAAAATTTAAAAATTTTTTT
1 ATTT-GAAAATTTAAAAATTTTTTT
29955 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
25 13 0.59
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTGAAAATTTAAAAATTTTTTT
Found at i:30392 original size:20 final size:21
Alignment explanation
Indices: 30339--30400 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
30329 GATTCCCCTG
30339 TGGGGGGATCGGTTCCCATTCAA
1 TGGGGGGATCGGTTCCC--TCAA
* *
30362 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
30382 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
30401 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
23 15 0.44
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:36942 original size:23 final size:21
Alignment explanation
Indices: 36889--36968 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 21
36879 CGGTGTTTGA
36889 GTGCATGGATGCAC-TGCATG
1 GTGCATGGATGCACTTGCATG
*
36909 GTGCATCGATGCACTAGTGGCA-G
1 GTGCATGGATGCACT--T-GCATG
*
36932 GTGCATGGATGCAC-TGCAAGG
1 GTGCATGGATGCACTTGC-ATG
36953 GTGCATGGATGCACTT
1 GTGCATGGATGCACTT
36969 TGACACCCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
19 2 0.04
20 15 0.29
21 15 0.29
22 1 0.02
23 15 0.29
24 3 0.06
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTTGCATG
Found at i:38124 original size:23 final size:23
Alignment explanation
Indices: 38091--38134 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
38081 GAGTAGAGGG
38091 TCTACGCGGTCCTTTGGGACAAT
1 TCTACGCGGTCCTTTGGGACAAT
*
38114 TCTACGTGGTCCTTTGGGACA
1 TCTACGCGGTCCTTTGGGACA
38135 TATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
TCTACGCGGTCCTTTGGGACAAT
Found at i:38317 original size:24 final size:23
Alignment explanation
Indices: 38247--38311 Score: 103
Period size: 24 Copynumber: 2.8 Consensus size: 23
38237 TAATTTTATA
*
38247 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
38270 TGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGC-AATTCTACG
*
38294 TGGCACTTCAGTGCAATT
1 TGGCACTTCGGTGCAATT
38312 TATACGAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 17 0.44
24 22 0.56
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:38842 original size:21 final size:21
Alignment explanation
Indices: 38805--38848 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
38795 GAGCTGAAAT
* *
38805 ACTGTAGTAGTGCATCGGTAC
1 ACTGTAGTAGTACATCGATAC
*
38826 ACTGTAGTAGTATATCGATAC
1 ACTGTAGTAGTACATCGATAC
38847 AC
1 AC
38849 AATTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (21 bp):
ACTGTAGTAGTACATCGATAC
Found at i:42156 original size:20 final size:19
Alignment explanation
Indices: 42133--42180 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
42123 CGATATAACA
*
42133 GGTAAAAATATGATAAAACT
1 GGTAAAAA-ATGATAAAACC
* *
42153 GGTATCAAAATGATGAAACC
1 GGTA-AAAAATGATAAAACC
42173 GGTAAAAA
1 GGTAAAAA
42181 GCTACCGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 17 0.74
21 3 0.13
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:42277 original size:181 final size:183
Alignment explanation
Indices: 41921--42395 Score: 704
Period size: 182 Copynumber: 2.6 Consensus size: 183
41911 GATCCAAATT
* * * * * **
41921 AAAAATGTATCGATCCACAACGATATAACAAGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
** * * * *
41986 AAACCGGTAAAGCGGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAAAGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
42051 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT-CA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
* * *
42103 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
42168 AAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAAAGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
42232 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
42285 AAAAATGTATCGATCAAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
42350 AAAACCGG-AAAAATGATACCGGATAAATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAAA-GATACCGGATATATTAAAAGTGTCGATACTTT
42396 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 67 0.25
182 113 0.43
183 83 0.32
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.26
Consensus pattern (183 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAAAGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
Found at i:42339 original size:20 final size:20
Alignment explanation
Indices: 42316--42363 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42306 CGATATAACA
42316 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
*
42336 GGTATCAAA-ATGATAAAACC
1 GGTA-AAAATATGATAAAACC
42356 GG-AAAAAT
1 GGTAAAAAT
42364 GATACCGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 17 0.71
21 3 0.12
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:44708 original size:182 final size:182
Alignment explanation
Indices: 44228--45069 Score: 1463
Period size: 182 Copynumber: 4.6 Consensus size: 182
44218 TTTTACCTTT
* *
44228 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
44293 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTTGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
44358 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGAAACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * *
44410 TTTAAAAGAGAAG-AGTTATAGAGCCAATAAAGTGTCGATACTTTATAAAAATGTATCAATCTAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
44474 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
44539 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
44591 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
44656 AACAATATAACAGGTAATAATATGACAATACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
44721 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCAACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
44773 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
44838 AACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
44903 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
44955 -TTAATAAGATAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * * * **
45019 TAATAATATAACATGTAAAAATATAATAAAACCGGTTTATAAATGACAAAA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
45070 GGTGAACGCA
Statistics
Matches: 628, Mismatches: 30, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
181 176 0.28
182 452 0.72
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:45972 original size:11 final size:11
Alignment explanation
Indices: 45955--46006 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
45945 GCAACAGATC
45955 ATAACAAACTA
1 ATAACAAACTA
*
45966 CTAACAAACTA
1 ATAACAAACTA
45977 ATAACAAACTA
1 ATAACAAACTA
* *
45988 AGT-CCTAACTA
1 A-TAACAAACTA
45999 ATAACAAA
1 ATAACAAA
46007 AACTAACTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 1 0.03
11 31 0.94
12 1 0.03
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:46149 original size:36 final size:36
Alignment explanation
Indices: 46107--46248 Score: 248
Period size: 36 Copynumber: 3.9 Consensus size: 36
46097 CAATACATCT
*
46107 TTCCGTTCGACTTGAATCGGAAGTGTCAATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCC
* *
46143 TTCCGTTCGACTTGAATCGAAAGTGCCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCC
*
46179 TTCCGTTCGACTTGAATTGGAAGTGTCGATGCTTCC
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCC
46215 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTT
1 TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTT
46249 TCTTTCATTC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (36 bp):
TTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTCC
Found at i:48273 original size:27 final size:26
Alignment explanation
Indices: 48231--48281 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
48221 TTTTTTATAT
*
48231 ATTTGAGAAATATTTAGGGTTTTTAG
1 ATTTGAGAAATATTTAGGATTTTTAG
48257 ATTTGAGAAA-AGTTTTAGGATTTTT
1 ATTTGAGAAATA--TTTAGGATTTTT
48282 TTGAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 1 0.05
26 10 0.45
27 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (26 bp):
ATTTGAGAAATATTTAGGATTTTTAG
Found at i:51507 original size:6 final size:6
Alignment explanation
Indices: 51496--51523 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
51486 CATAGTATTA
51496 ATAAAT ATAAAT ATAAAT ATAAAT ATAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAA
51524 TTTATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:59075 original size:15 final size:16
Alignment explanation
Indices: 59057--59088 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
59047 CTATTAATAG
59057 TGACAAAACT-AATTT
1 TGACAAAACTAAATTT
59072 TGACAAAACTAAATTT
1 TGACAAAACTAAATTT
59088 T
1 T
59089 TCACAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (16 bp):
TGACAAAACTAAATTT
Found at i:66710 original size:20 final size:20
Alignment explanation
Indices: 66687--66735 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
66677 ATGTTAACTG
66687 TTTAAATTTAGTGTTTACTA
1 TTTAAATTTAGTGTTTACTA
* *
66707 TTTAAATTTTGTGTTTACTG
1 TTTAAATTTAGTGTTTACTA
*
66727 TTTCAATTT
1 TTTAAATTT
66736 GCAAATATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTAAATTTAGTGTTTACTA
Found at i:70320 original size:22 final size:22
Alignment explanation
Indices: 70290--70332 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
70280 GAAATAAACT
* *
70290 GTACTGTGAATAGTAATGAACA
1 GTACCGTGAACAGTAATGAACA
*
70312 GTACCGTGAACAGTGATGAAC
1 GTACCGTGAACAGTAATGAAC
70333 GACTCTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
GTACCGTGAACAGTAATGAACA
Found at i:70915 original size:21 final size:21
Alignment explanation
Indices: 70866--70926 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 21
70856 ATATGAAATT
*
70866 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
70887 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
70909 TTGTCCCGAAGAACCTAT
1 TTGTCCCGAAGGACCTAT
70927 AAAACCCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:77274 original size:22 final size:22
Alignment explanation
Indices: 77231--77279 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
77221 ACTATACGGT
**
77231 ATGAACAGTACTGTGAGAAGTA
1 ATGAACAGTACCATGAGAAGTA
77253 ATGAACAGTACCATGA-ACAGTA
1 ATGAACAGTACCATGAGA-AGTA
77275 ATGAA
1 ATGAA
77280 TGACTCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (22 bp):
ATGAACAGTACCATGAGAAGTA
Found at i:88977 original size:21 final size:21
Alignment explanation
Indices: 88953--88998 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
88943 TAAAGCGAGG
88953 GAAGCAGCAGAAGCAGAGAGA
1 GAAGCAGCAGAAGCAGAGAGA
* * *
88974 GAAGTAGGAGAATCAGAGAGA
1 GAAGCAGCAGAAGCAGAGAGA
88995 GAAG
1 GAAG
88999 TATCATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.39, T:0.04
Consensus pattern (21 bp):
GAAGCAGCAGAAGCAGAGAGA
Found at i:88999 original size:21 final size:21
Alignment explanation
Indices: 88961--89000 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
88951 GGGAAGCAGC
88961 AGAAGCAGAGAGAGAAGTAGG
1 AGAAGCAGAGAGAGAAGTAGG
*
88982 AGAATCAGAGAGAGAAGTA
1 AGAAGCAGAGAGAGAAGTA
89001 TCATATCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.38, T:0.07
Consensus pattern (21 bp):
AGAAGCAGAGAGAGAAGTAGG
Found at i:89620 original size:27 final size:27
Alignment explanation
Indices: 89581--89668 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
89571 TCTCGATATT
*
89581 TTGCGGCATTTGTTATCTCTTCACCTA
1 TTGCGGCGTTTGTTATCTCTTCACCTA
* *
89608 TTACGGCGTTTGTTATCTTTTCACCTA
1 TTGCGGCGTTTGTTATCTCTTCACCTA
89635 TTGCGGCGTTTGTTATCTCTTCACCTA
1 TTGCGGCGTTTGTTATCTCTTCACCTA
89662 TTGCGGC
1 TTGCGGC
89669 ATTTATTCCA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.44
Consensus pattern (27 bp):
TTGCGGCGTTTGTTATCTCTTCACCTA
Found at i:94875 original size:4 final size:4
Alignment explanation
Indices: 94866--94890 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
94856 TTCAACTATG
94866 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
94891 TATACATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:95622 original size:15 final size:15
Alignment explanation
Indices: 95576--95623 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
95566 ACTATGTTTA
95576 TAAATTAAAATATAG
1 TAAATTAAAATATAG
* **
95591 TAATTTTCAA-A-AG
1 TAAATTAAAATATAG
95604 TAAATTAAAATATAG
1 TAAATTAAAATATAG
95619 TAAAT
1 TAAAT
95624 GATTTTAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 9 0.36
14 2 0.08
15 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (15 bp):
TAAATTAAAATATAG
Found at i:102744 original size:24 final size:22
Alignment explanation
Indices: 102707--102761 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 22
102697 GGTAAAAGAG
102707 GAAGAGCAAGAAGAAGAA-AATAAA
1 GAAGAG-AAGAAGAA-AACAA-AAA
102731 GAAGAGAAGAAAGAAAACAAAAA
1 GAAGAGAAG-AAGAAAACAAAAA
102754 GCAAGAGA
1 G-AAGAGA
102762 TCCTCTACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.67, C:0.05, G:0.25, T:0.02
Consensus pattern (22 bp):
GAAGAGAAGAAGAAAACAAAAA
Found at i:109188 original size:22 final size:22
Alignment explanation
Indices: 109160--109212 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
109150 ATTTTCCACA
*
109160 AAAAGGATCGATCCTTTTTTGC
1 AAAAGGATCGATCCCTTTTTGC
*
109182 AAAAGGATCAATCCCTTTTTGC
1 AAAAGGATCGATCCCTTTTTGC
*
109204 GAAA-GATCG
1 AAAAGGATCG
109213 GTCATTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
AAAAGGATCGATCCCTTTTTGC
Found at i:109743 original size:7 final size:7
Alignment explanation
Indices: 109731--109756 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
109721 TGAATGTTAT
109731 GTTTAGG
1 GTTTAGG
109738 GTTTAGG
1 GTTTAGG
109745 GTTTAGG
1 GTTTAGG
109752 GTTTA
1 GTTTA
109757 TGTATTAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:112027 original size:20 final size:20
Alignment explanation
Indices: 112002--112075 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
111992 AATAGGTTTT
112002 GGATCGATCCCTTCGA-AAAA
1 GGATCGATCCC-TCGAGAAAA
112022 GGATCGATCCCTCGAGGAAAA
1 GGATCGATCCCTCGA-GAAAA
* *
112043 TGATAGATCCCTCGATGAAAA
1 GGATCGATCCCTCGA-GAAAA
* *
112064 GTATTGATCCCT
1 GGATCGATCCCT
112076 TCCCCTAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.09
20 11 0.24
21 31 0.67
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (20 bp):
GGATCGATCCCTCGAGAAAA
Found at i:114747 original size:20 final size:20
Alignment explanation
Indices: 114722--114795 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
114712 AATAGGTTTT
114722 GGATCGATCCCTTCGA-AAAA
1 GGATCGATCCC-TCGAGAAAA
114742 GGATCGATCCCTCGAGGAAAA
1 GGATCGATCCCTCGA-GAAAA
* *
114763 TGATAGATCCCTCGATGAAAA
1 GGATCGATCCCTCGA-GAAAA
* *
114784 GTATTGATCCCT
1 GGATCGATCCCT
114796 TCCCCTAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.09
20 11 0.24
21 31 0.67
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (20 bp):
GGATCGATCCCTCGAGAAAA
Found at i:116921 original size:24 final size:24
Alignment explanation
Indices: 116886--116941 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
116876 AACTATCTCG
*
116886 TTAACATTTATAGGAAACACAATA
1 TTAACATCTATAGGAAACACAATA
116910 TTAACATCTATAGGAAACACAATA
1 TTAACATCTATAGGAAACACAATA
116934 TTAACATC
1 TTAACATC
116942 CCATACCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (24 bp):
TTAACATCTATAGGAAACACAATA
Found at i:127156 original size:13 final size:13
Alignment explanation
Indices: 127140--127164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127130 TTAAAATTAA
127140 AAAATAAAGAAAT
1 AAAATAAAGAAAT
127153 AAAATAAAGAAA
1 AAAATAAAGAAA
127165 AATAAACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAATAAAGAAAT
Found at i:128898 original size:15 final size:15
Alignment explanation
Indices: 128878--128908 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
128868 CATTTGTGAA
128878 GCAATTCTTTATAGC
1 GCAATTCTTTATAGC
*
128893 GCAATTCTTTGTAGC
1 GCAATTCTTTATAGC
128908 G
1 G
128909 GTCCCATCAC
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:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (15 bp):
GCAATTCTTTATAGC
Done.