Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008140.1 Hibiscus syriacus cultivar Beakdansim tig00110698_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: 511555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:440279 original size:15 final size:15
Alignment explanation
Indices: 440241--440289 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
440231 TACAAAAACA
440241 TTTTATTA-TATTAT
1 TTTTATTATTATTAT
*
440255 ATTTATTTATTATTAT
1 TTTTA-TTATTATTAT
440271 TTTTATTATTATTAT
1 TTTTATTATTATTAT
440286 TTTT
1 TTTT
440290 GCAGGCCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 4 0.13
15 17 0.55
16 10 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:440386 original size:33 final size:33
Alignment explanation
Indices: 440344--440421 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
440334 ATAAATCAAC
*
440344 GTATTTGAGTCTTATTGAAACACTAAAACC-AA
1 GTATTTGAGTCCTATTGAAACACTAAAACCGAA
* *
440376 TGTATTTGAGTCCTATTGAAATACTAAAGCCGAA
1 -GTATTTGAGTCCTATTGAAACACTAAAACCGAA
*
440410 GCATTTGAGTCC
1 GTATTTGAGTCC
440422 AAGTAGGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (33 bp):
GTATTTGAGTCCTATTGAAACACTAAAACCGAA
Found at i:445503 original size:20 final size:21
Alignment explanation
Indices: 445449--445511 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
445439 GATTCCCCTG
445449 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
445473 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
445493 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
445512 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:454424 original size:16 final size:16
Alignment explanation
Indices: 454403--454434 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
454393 TCGGGGCTTA
454403 ACTTCACGACAAAGGG
1 ACTTCACGACAAAGGG
*
454419 ACTTCACGACGAAGGG
1 ACTTCACGACAAAGGG
454435 GTTTCCCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.28, T:0.12
Consensus pattern (16 bp):
ACTTCACGACAAAGGG
Found at i:454638 original size:110 final size:110
Alignment explanation
Indices: 454445--454651 Score: 324
Period size: 110 Copynumber: 1.9 Consensus size: 110
454435 GTTTCCCAAT
* ** *
454445 TTCAGAGCCAATTTTAACTTCACAGTGAATAATATTAGACCCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGAATATTAGACCCAAGACAACACAAGCTCAACTTCA
* *
454510 CGATGAAGGGGCGGCTGATTGTCAACAAACAACTTTTCAATTTCA
66 CGACGAAGGGGCGGCTGATTGTCAAAAAACAACTTTTCAATTTCA
* * * *
454555 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTTGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGAATATTAGACCCAAGACAACACAAGCTCAACTTCA
454620 CGACGAAGGGGCGGCTGATTGTCAAAAAACAA
66 CGACGAAGGGGCGGCTGATTGTCAAAAAACAA
454652 TTTCCCAGTT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGAATATTAGACCCAAGACAACACAAGCTCAACTTCA
CGACGAAGGGGCGGCTGATTGTCAAAAAACAACTTTTCAATTTCA
Found at i:455681 original size:23 final size:24
Alignment explanation
Indices: 455637--455685 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
455627 ACAAAACATT
*
455637 TTATTATATTATATTTATTTATTA
1 TTATTATAATATATTTATTTATTA
455661 TTATTAATAATAT-TTTA-TTATTA
1 TTATT-ATAATATATTTATTTATTA
455684 TT
1 TT
455686 TTTGTAGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 9 0.39
25 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTATAATATATTTATTTATTA
Found at i:455780 original size:33 final size:33
Alignment explanation
Indices: 455743--455820 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
455733 ATAAATCAAC
* *
455743 GTATTTGAGTCTTATTAAAACGCTAAAACC-AA
1 GTATTTGAGTCCTATTAAAACACTAAAACCGAA
*
455775 TGTATTTGAGTCCTATTGAAACACTAAAACCGAA
1 -GTATTTGAGTCCTATTAAAACACTAAAACCGAA
*
455809 GCATTTGAGTCC
1 GTATTTGAGTCC
455821 AAGTAGGACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
GTATTTGAGTCCTATTAAAACACTAAAACCGAA
Found at i:456185 original size:2 final size:2
Alignment explanation
Indices: 456178--456217 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
456168 TTTTACATTG
456178 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
456218 TCATTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:459764 original size:12 final size:11
Alignment explanation
Indices: 459735--459762 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
459725 TTGATTTGTG
459735 GTTTTTCAATA
1 GTTTTTCAATA
459746 GTTTTTCAATA
1 GTTTTTCAATA
459757 GTTTTT
1 GTTTTT
459763 TCCCCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.07, G:0.11, T:0.61
Consensus pattern (11 bp):
GTTTTTCAATA
Found at i:460478 original size:21 final size:21
Alignment explanation
Indices: 460453--460492 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
460443 GACTATCGCA
460453 TTGCGATTTTCCAAATTCGTG
1 TTGCGATTTTCCAAATTCGTG
*
460474 TTGCGATTTTCCTAATTCG
1 TTGCGATTTTCCAAATTCG
460493 CAATGCGAAT
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:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGTG
Found at i:460499 original size:21 final size:21
Alignment explanation
Indices: 460448--460500 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
460438 ATTCTGACTA
460448 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
** *
460469 TCGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
460490 TCGCAATGCGA
1 TCGCATTGCGA
460501 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:460518 original size:20 final size:20
Alignment explanation
Indices: 460490--460580 Score: 132
Period size: 20 Copynumber: 4.5 Consensus size: 20
460480 TTTTCCTAAT
*
460490 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACATAAA
*
460510 TCACAATGCGAATACATAAA
1 TCGCAATGCGAATACATAAA
460530 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACATAAA
460550 TCGCAATGCGAAT-C-TAACTA
1 TCGCAATGCGAATACATAA--A
460570 TCGCAATGCGA
1 TCGCAATGCGA
460581 TTTACATAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
18 3 0.05
19 1 0.02
20 62 0.94
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACATAAA
Found at i:460782 original size:22 final size:22
Alignment explanation
Indices: 460757--460820 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
460747 CGACATCCGC
460757 CCCCATCTCCGACGAAATCAGT
1 CCCCATCTCCGACGAAATCAGT
*
460779 CCCCATCTCCGACGATATCAGT
1 CCCCATCTCCGACGAAATCAGT
* *
460801 CTCCATCTCCGGCGAAATCA
1 CCCCATCTCCGACGAAATCA
460821 TTCACGGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCCATCTCCGACGAAATCAGT
Found at i:461285 original size:34 final size:34
Alignment explanation
Indices: 461171--461290 Score: 116
Period size: 34 Copynumber: 3.4 Consensus size: 34
461161 CGATTTTCAT
*
461171 TTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTCTTGCGTTGTGATAGTCAAA
* * * ** *
461205 TTCACTTTGCGATAGTCATTTTCATGTTGTGATTTTC-AT
1 TTCGCGTTGCGAT--TC--TTGC--GTTGTGATAGTCAAA
461244 TTCGCGTTGCGATTCTTGCGTTGTGATAGTCAAA
1 TTCGCGTTGCGATTCTTGCGTTGTGATAGTCAAA
461278 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
461291 AGTCATTTTC
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
33 10 0.15
34 25 0.38
35 3 0.05
36 2 0.03
37 2 0.03
38 3 0.05
39 12 0.18
40 9 0.14
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (34 bp):
TTCGCGTTGCGATTCTTGCGTTGTGATAGTCAAA
Found at i:461288 original size:73 final size:73
Alignment explanation
Indices: 461157--461331 Score: 269
Period size: 73 Copynumber: 2.4 Consensus size: 73
461147 CGATTCTGTC
*
461157 GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAATTCACTTTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAATTCACGTTGCGATAGTC
461222 ATTTTCAT
66 ATTTTCAT
* * *
461230 GTTGTGATTTTCATTTCGCGTTGCGATTCTTGCGTTGTGATAGTCAAATTCGCGTTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAATTCACGTTGCGATAGTC
*
461295 ATTTTCGT
66 ATTTTCAT
** *
461303 GTTGCGATAGTCATTTTCGTGTTGCGATT
1 GTTGCGATTTTCA-TTTCGCGTTGCGATT
461332 TTCATTTTCG
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 78 0.85
74 14 0.15
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.43
Consensus pattern (73 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAATTCACGTTGCGATAGTC
ATTTTCAT
Found at i:461327 original size:40 final size:40
Alignment explanation
Indices: 461190--461350 Score: 147
Period size: 40 Copynumber: 4.2 Consensus size: 40
461180 CGATTCTTGC
* * *
461190 GTTGCGATAGTCAAATTCACTTTGCGATAGTCATTTTCAT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGT
* ** * *
461230 GTTGTGATTTTC-ATTTCGCGTTGCGAT--TC---TT-GC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGT
*
461263 GTTGTGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGT
** * **
461303 GTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGT
461343 GTTGCGAT
1 GTTGCGAT
461351 TTTAAGTTTC
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
33 10 0.10
34 16 0.17
36 2 0.02
37 2 0.02
39 14 0.15
40 52 0.54
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (40 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGT
Found at i:461353 original size:20 final size:20
Alignment explanation
Indices: 461211--461350 Score: 123
Period size: 20 Copynumber: 7.3 Consensus size: 20
461201 CAAATTCACT
*
461211 TTGCGATAGTCATTTTCATG
1 TTGCGATAGTCATTTTCGTG
* ** *
461231 TTGTGATTTTCA-TTTCGCG
1 TTGCGATAGTCATTTTCGTG
*
461250 TTGCGAT--TC---TT-GCG
1 TTGCGATAGTCATTTTCGTG
* ** *
461264 TTGTGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGTG
461284 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
461304 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
**
461324 TTGCGATTTTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
461344 TTGCGAT
1 TTGCGAT
461351 TTTAAGTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.09
15 2 0.02
16 2 0.02
17 2 0.02
19 13 0.13
20 73 0.72
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:462842 original size:6 final size:6
Alignment explanation
Indices: 462831--462866 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
462821 TCTCCCTTTT
462831 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
462867 GGGATGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CTCCAC
Found at i:463273 original size:20 final size:20
Alignment explanation
Indices: 463248--463427 Score: 216
Period size: 20 Copynumber: 8.6 Consensus size: 20
463238 AGAATAGTTT
*
463248 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
463268 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
463288 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
463308 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* *
463328 ACTATCGCAATGAGAAAATCG
1 ACTATCGCAACGCGAAAAT-G
*
463349 CAACAACAAAATCGCAACGCGAAAATG
1 -----AC--TATCGCAACGCGAAAATG
*
463376 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* **
463396 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAAAATG
463416 ACTATCGCAACG
1 ACTATCGCAACG
463428 AAAGAATCGC
Statistics
Matches: 141, Mismatches: 11, Indels: 16
0.84 0.07 0.10
Matches are distributed among these distances:
20 121 0.86
21 1 0.01
22 2 0.01
26 2 0.01
27 1 0.01
28 14 0.10
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:463411 original size:88 final size:88
Alignment explanation
Indices: 463271--463439 Score: 277
Period size: 88 Copynumber: 1.9 Consensus size: 88
463261 GAAAATGACT
463271 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGC
*
463336 AATGAGAA-AATCGCAACAACAAA
66 AACGA-AAGAATCGCAACAACAAA
* * **
463359 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGC
463424 AACGAAAGAATCGCAA
66 AACGAAAGAATCGCAA
463440 TGAGAAATGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
87 2 0.03
88 73 0.97
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (88 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGC
AACGAAAGAATCGCAACAACAAA
Found at i:463497 original size:20 final size:20
Alignment explanation
Indices: 463472--463694 Score: 251
Period size: 20 Copynumber: 11.3 Consensus size: 20
463462 GATTCTCTCG
**
463472 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
463492 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
463512 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
463532 TTGCGATAGTCATTTTCGCGCA
1 TTGCGATAGTCATTTT--CGCA
*
463554 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATTTTCGCA
**
463568 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
463588 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
463608 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
463628 TTGCGATACTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
** *
463648 TTATGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
* *
463668 TTGCGATAGTTATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
463688 TTGCGAT
1 TTGCGAT
463695 TTTAAGTTTC
Statistics
Matches: 177, Mismatches: 18, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
14 10 0.06
16 3 0.02
20 154 0.87
22 10 0.06
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:463606 original size:56 final size:54
Alignment explanation
Indices: 463472--463614 Score: 160
Period size: 56 Copynumber: 2.5 Consensus size: 54
463462 GATTCTCTCG
* ** *
463472 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCATTGCGAT--TC----TCTCATTGCGATAGTCAAATTCGCA
**
463532 TTGCGATAGTCATTTTCGCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATT--CGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCA
463588 TTGCGATAGTCAAATTCGCATTGCGAT
1 TTGCGATAGTCAAATTCGCATTGCGAT
463615 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
54 11 0.15
56 35 0.48
60 16 0.22
62 11 0.15
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (54 bp):
TTGCGATAGTCAAATTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCA
Found at i:463618 original size:96 final size:96
Alignment explanation
Indices: 463454--463646 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 96
463444 AAATGAAAAT
* **
463454 CGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCGAT
1 CGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGAT
* *
463519 AGTCATTTTCGCGTTGCGATAGTCATTTTCG
66 AGTCATTTTCGCATTGCGATACTCATTTTCG
463550 CGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGAT
1 CGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGAT
*
463615 AGTCATTTTTGCATTGCGATACTCATTTTCG
66 AGTCATTTTCGCATTGCGATACTCATTTTCG
463646 C
1 C
463647 ATTATGATAG
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (96 bp):
CGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGAT
AGTCATTTTCGCATTGCGATACTCATTTTCG
Found at i:464169 original size:18 final size:19
Alignment explanation
Indices: 464130--464171 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
464120 CTCACCTGTC
464130 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
464151 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
464169 ATC
1 ATC
464172 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:464219 original size:21 final size:20
Alignment explanation
Indices: 464124--464231 Score: 58
Period size: 21 Copynumber: 5.2 Consensus size: 20
464114 GCCCGACTCA
464124 CCTGTCATCGTTCAAGAGG-
1 CCTGTCATCGTTCAAGAGGC
**
464143 CCTCCCCTATCGTTCAAGAGGCC
1 CCT-GTC-ATCGTTCAAGAGG-C
* ** *
464166 CCTATCATCCCTCAAGAGTC
1 CCTGTCATCGTTCAAGAGGC
* *
464186 TCCT-CCTACCGTTCAAGAGGC
1 -CCTGTC-ATCGTTCAAGAGGC
*
464207 CACTGTCATCGTTGAAGAGGTC
1 C-CTGTCATCGTTCAAGAGG-C
464229 CCT
1 CCT
464232 CCCAACATTC
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
19 3 0.05
20 4 0.06
21 51 0.78
22 4 0.06
23 3 0.05
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:464225 original size:42 final size:43
Alignment explanation
Indices: 464125--464233 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 43
464115 CCCGACTCAC
* * *
464125 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCTCCTCCTACCGTTCAAGAGGCCA
* **
464167 CTATCATCCCTCAAGA-GTCTCCTCCTACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCTACCGTTCAAGAGGCCA
*
464209 CTGTCATCGTTGAAGAGGTC-CCTCC
1 CTGTCATCGTTCAAGAGGTCTCCTCC
464234 CAACATTCTA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 5 0.09
42 47 0.85
43 3 0.05
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.25
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCTCCTCCTACCGTTCAAGAGGCCA
Found at i:465639 original size:14 final size:14
Alignment explanation
Indices: 465620--465655 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
465610 ATTGTTTAAT
465620 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
465634 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
465648 TGATTTGT
1 TGATTTGT
465656 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:465818 original size:33 final size:34
Alignment explanation
Indices: 465761--465855 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 34
465751 AAAACAGACT
* * ** *
465761 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCAGAAATGAAAATCGCAACGAGAGA
*
465795 ATTGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCAGAAATGAAAATCGCAACGAGAGA
*
465828 ATCGCAATGCAAAAATGAAAATCGCAAC
1 ATCGCAATGCAGAAATGAAAATCGCAAC
465856 ACGATACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCAGAAATGAAAATCGCAACGAGAGA
Found at i:465912 original size:14 final size:14
Alignment explanation
Indices: 465893--465946 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
465883 CATTTTCACA
465893 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
465907 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
465924 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
465940 TTGCGAT
1 TTGCGAT
465947 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:465933 original size:33 final size:33
Alignment explanation
Indices: 465872--465966 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
465862 CTAATTTCAT
*
465872 GTTGCGATTTTCATTTTCACATTGCGATTCTCTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCTCTC
465906 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
** *
465939 GTTGCGATAGTCATTTCCGCGTTGCGAT
1 GTTGCGATTTTCATTT-CGCATTGCGAT
465967 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 33 0.59
34 23 0.41
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:465963 original size:20 final size:20
Alignment explanation
Indices: 465938--466071 Score: 207
Period size: 20 Copynumber: 6.7 Consensus size: 20
465928 GCGATTCTCT
465938 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
465958 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
465978 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
465998 TGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
466018 TGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
466038 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
466058 CGTTACGATAGTCA
1 CGTTGCGATAGTCA
466072 AATGAATGTC
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 106 0.98
21 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:468501 original size:24 final size:24
Alignment explanation
Indices: 468467--468520 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
468457 CTAAAAAATC
468467 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
468491 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
468515 ATCAAA
1 ATCAAA
468521 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:468534 original size:24 final size:24
Alignment explanation
Indices: 468467--468534 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
468457 CTAAAAAATC
* * *
468467 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
468491 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
468515 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
468535 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:469387 original size:20 final size:20
Alignment explanation
Indices: 469362--469468 Score: 187
Period size: 20 Copynumber: 5.3 Consensus size: 20
469352 AAATTCAGTA
*
469362 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCTCG
469382 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
469402 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
469422 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
469442 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
469462 TTGCGAT
1 TTGCGAT
469469 TTACGTATTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:469485 original size:20 final size:20
Alignment explanation
Indices: 469462--469567 Score: 185
Period size: 20 Copynumber: 5.3 Consensus size: 20
469452 CAGATTCGCG
469462 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTTGCA
469482 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTTGCA
* *
469502 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTTGCA
469522 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTTGCA
*
469542 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTTGCA
469562 TTGCGA
1 TTGCGA
469568 ATTAGGAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACGTATTTGCA
Found at i:469486 original size:60 final size:60
Alignment explanation
Indices: 469361--469548 Score: 170
Period size: 60 Copynumber: 3.1 Consensus size: 60
469351 GAAATTCAGT
* * * * * *
469361 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGT-CAGAATCT-C
1 ATTGCGATAGTCAGAATCTCGTTGCGATAGTCAGATTCGCGTTGCGAT-TTAC-GTATTTGC
*
469421 GTTGCGATAGTCAGAATCTCGTTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTTGC
1 ATTGCGATAGTCAGAATCTCGTTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTTGC
* * * * * * *
469481 ATTGCGAT--TTACGTATTTGCATTGCGAT-TTACATATTCGCATTGCGATTTACGTATTTGC
1 ATTGCGATAGTCA-GAATCT-CGTTGCGATAGT-CAGATTCGCGTTGCGATTTACGTATTTGC
469541 ATTGCGAT
1 ATTGCGAT
469549 TTACGTATTC
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.02
59 10 0.09
60 96 0.89
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (60 bp):
ATTGCGATAGTCAGAATCTCGTTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTTGC
Found at i:469549 original size:60 final size:60
Alignment explanation
Indices: 469455--469567 Score: 208
Period size: 60 Copynumber: 1.9 Consensus size: 60
469445 CGATAGTCAG
* *
469455 ATTCGCGTTGCGATTTACGTATTTGCATTGCGATTTACGTATTTGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTACGTATTCGCATTGCGATTTACAT
469515 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTACGTATTCGCATTGCGA
469568 ATTAGGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (60 bp):
ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTACGTATTCGCATTGCGATTTACAT
Found at i:469588 original size:21 final size:21
Alignment explanation
Indices: 469564--469609 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
469554 TATTCGCATT
469564 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
469585 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
469606 GCGA
1 GCGA
469610 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:470049 original size:136 final size:137
Alignment explanation
Indices: 469804--470195 Score: 461
Period size: 136 Copynumber: 2.9 Consensus size: 137
469794 TTCGTTGGGT
* * * * * * * * * *
469804 TTTAATACTAGAGCTTTAACATTT-GGTTTTATTTCACTTTAATCCTTAAATTTAAGA-AAATAT
1 TTTAATACTAGAGCCTT--CATTTAGGTTTAATTTCATTTTAGTCTTTTAACTTAGGAGAATTTT
* * * * *
469867 TTAAAATGGTCACCACTTATGCTCAAGATTCCAATTTAATTATTCAATTTAATAAATTTTAAAAT
64 TTAAAATGGCCATCACTTATGCTCGAGGTTCCAATTTAATTATTCAATTTAATAAATTGTAAAAT
469932 TCATTAGAG
129 TCATTAGAG
* *
469941 TTTAATACTAGAGCCTTCATTTTGGGTTTAATTTCATTTTAGTCTTTTAACTTAGGTGAA-TTTT
1 TTTAATACTAGAGCCTTCA-TTTAGGTTTAATTTCATTTTAGTCTTTTAACTTAGGAGAATTTTT
*
470005 T-AAATGGCCATCACTTATGCTCGAGGTTCCAATTTAATTATTCAATTTAATAGATTGTAAAATT
65 TAAAATGGCCATCACTTATGCTCGAGGTTCCAATTTAATTATTCAATTTAATAAATTGTAAAATT
*
470069 CATTAGGG
130 CATTAGAG
* * *
470077 TTTAATAGTAGAGCCTTCATTTAGGTTTAATTTTATTTTAGTCTTTTAATTTAGGAGAATTTTTT
1 TTTAATACTAGAGCCTTCATTTAGGTTTAATTTCATTTTAGTCTTTTAACTTAGGAGAATTTTTT
* * * * * *
470142 AAAATGGTCC-TCACTTATGGTCGAGGTTCTATTTTGATTATTCACTTGAATAAA
66 AAAATGG-CCATCACTTATGCTCGAGGTTCCAATTTAATTATTCAATTTAATAAA
470196 ATCTCTTAAA
Statistics
Matches: 220, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
135 38 0.17
136 90 0.41
137 88 0.40
138 4 0.02
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (137 bp):
TTTAATACTAGAGCCTTCATTTAGGTTTAATTTCATTTTAGTCTTTTAACTTAGGAGAATTTTTT
AAAATGGCCATCACTTATGCTCGAGGTTCCAATTTAATTATTCAATTTAATAAATTGTAAAATTC
ATTAGAG
Found at i:473574 original size:10 final size:10
Alignment explanation
Indices: 473527--473580 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
473517 AAAGGTTCTG
473527 ACCGGTTTG-
1 ACCGGTTTGA
* *
473536 ATCGGTTTCA
1 ACCGGTTTGA
*
473546 ACCGGTTCGA
1 ACCGGTTTGA
473556 ACCGGTTTGA
1 ACCGGTTTGA
473566 ACCGGTTTG-
1 ACCGGTTTGA
473575 ACCGGT
1 ACCGGT
473581 CTGACCCGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
9 13 0.34
10 25 0.66
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.30
Consensus pattern (10 bp):
ACCGGTTTGA
Found at i:473580 original size:9 final size:9
Alignment explanation
Indices: 473520--473586 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
473510 GCCAGTCAAA
473520 GGTTCTGACC
1 GGTT-TGACC
*
473530 GGTTTGATC
1 GGTTTGACC
*
473539 GGTTTCAACC
1 GGTTT-GACC
*
473549 GGTTCGAACC
1 GGTTTG-ACC
473559 GGTTTGAACC
1 GGTTTG-ACC
473569 GGTTTGACC
1 GGTTTGACC
*
473578 GGTCTGACC
1 GGTTTGACC
473587 CGACCGACCG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
9 20 0.42
10 28 0.58
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.30
Consensus pattern (9 bp):
GGTTTGACC
Found at i:473599 original size:8 final size:9
Alignment explanation
Indices: 473583--473631 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
473573 TGACCGGTCT
473583 GACCCGACC
1 GACCCGACC
473592 GA-CCGACC
1 GACCCGACC
473600 GACCCGACC
1 GACCCGACC
473609 GTTGACCCGACCC
1 ---GACCCGA-CC
473622 GACCCGACC
1 GACCCGACC
473631 G
1 G
473632 TTGACCATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 8 0.23
9 11 0.31
10 7 0.20
12 7 0.20
13 2 0.06
ACGTcount: A:0.20, C:0.51, G:0.24, T:0.04
Consensus pattern (9 bp):
GACCCGACC
Found at i:473605 original size:17 final size:18
Alignment explanation
Indices: 473583--473631 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
473573 TGACCGGTCT
473583 GACCCGACCGACCGA-CC
1 GACCCGACCGACCGACCC
**
473600 GACCCGACCG-TTGACCC
1 GACCCGACCGACCGACCC
473617 GACCCGACCCGACCG
1 GACCCGA-CCGACCG
473632 TTGACCATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 19 0.76
18 3 0.12
19 1 0.04
ACGTcount: A:0.20, C:0.51, G:0.24, T:0.04
Consensus pattern (18 bp):
GACCCGACCGACCGACCC
Found at i:473623 original size:22 final size:21
Alignment explanation
Indices: 473594--473637 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
473584 ACCCGACCGA
473594 CCGACCGACCCGACCGTTGAC
1 CCGACCGACCCGACCGTTGAC
473615 CCGACCCGACCCGACCGTTGAC
1 CCGA-CCGACCCGACCGTTGAC
473637 C
1 C
473638 ATTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.18, C:0.50, G:0.23, T:0.09
Consensus pattern (21 bp):
CCGACCGACCCGACCGTTGAC
Found at i:473642 original size:7 final size:7
Alignment explanation
Indices: 473627--473664 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
473617 GACCCGACCC
473627 GACCGTT
1 GACCGTT
*
473634 GACCATT
1 GACCGTT
473641 GACCGTT
1 GACCGTT
473648 GACCGTT
1 GACCGTT
473655 GACCGTT
1 GACCGTT
473662 GAC
1 GAC
473665 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:480865 original size:18 final size:18
Alignment explanation
Indices: 480844--480893 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
480834 GAACCGGTCT
480844 GACCCAACCGACCGACCC
1 GACCCAACCGACCGACCC
**
480862 GACCCAACCG-TTGACCC
1 GACCCAACCGACCGACCC
*
480879 GACCCGACCCGACCG
1 GACCC-AACCGACCG
480894 GACCGTTGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 10 0.40
18 14 0.56
19 1 0.04
ACGTcount: A:0.24, C:0.52, G:0.20, T:0.04
Consensus pattern (18 bp):
GACCCAACCGACCGACCC
Found at i:480887 original size:27 final size:26
Alignment explanation
Indices: 480851--480902 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
480841 TCTGACCCAA
480851 CCGACCGACCCGACCCAACCGTTGAC
1 CCGACCGACCCGACCCAACCGTTGAC
**
480877 CCGACCCGACCCGACCGGACCGTTGA
1 CCGA-CCGACCCGACCCAACCGTTGA
480903 TCGTTGACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.21, C:0.48, G:0.23, T:0.08
Consensus pattern (26 bp):
CCGACCGACCCGACCCAACCGTTGAC
Found at i:483203 original size:20 final size:21
Alignment explanation
Indices: 483165--483203 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
483155 GTCAAAAATT
483165 AAAGAATTTAGAAAGGTTTAA
1 AAAGAATTTAGAAAGGTTTAA
483186 AAAG-ATTTA-AAAGTGTTT
1 AAAGAATTTAGAAAG-GTTT
483204 GGAGTTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (21 bp):
AAAGAATTTAGAAAGGTTTAA
Found at i:484138 original size:62 final size:61
Alignment explanation
Indices: 484020--484147 Score: 139
Period size: 62 Copynumber: 2.1 Consensus size: 61
484010 TTAAAGGACT
* ** *
484020 TAAAATCTAAGGCTCTAATTAATAATCTAAAATCTAACCTAAGTGGCTAAAGTAAAAGAATC
1 TAAAATCTAAAGCTCTAACAAATAATCTAAAATCTAACCTAAGTGACTAAAGTAAAA-AATC
* * * * * * * *
484082 TAAAATCTAAAGTTCTAACAAATAGTCTAAAGTTTAATCTAAGTGACTGAATTAAAAAATT
1 TAAAATCTAAAGCTCTAACAAATAATCTAAAATCTAACCTAAGTGACTAAAGTAAAAAATC
484143 TAAAA
1 TAAAA
484148 ACTATGGCTA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
61 8 0.15
62 46 0.85
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (61 bp):
TAAAATCTAAAGCTCTAACAAATAATCTAAAATCTAACCTAAGTGACTAAAGTAAAAAATC
Found at i:486380 original size:36 final size:36
Alignment explanation
Indices: 486322--486391 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
486312 AAAATTTACA
* **
486322 AAATATGGCAGCACATTTAAATTTAT-TAAAGATGGC
1 AAATATGGAAGCACATCCAAATTTATAT-AAGATGGC
*
486358 AAATATGGAAGCATATCCAAATTTATATAAGATG
1 AAATATGGAAGCACATCCAAATTTATATAAGATG
486392 ACAACATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (36 bp):
AAATATGGAAGCACATCCAAATTTATATAAGATGGC
Found at i:486419 original size:24 final size:24
Alignment explanation
Indices: 486386--486442 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
486376 AAATTTATAT
*
486386 AAGATGACAACATTTTCCTTACAA
1 AAGATAACAACATTTTCCTTACAA
486410 AAGATAACAACATTTTCCTTACAA
1 AAGATAACAACATTTTCCTTACAA
486434 AAGATAACA
1 AAGATAACA
486443 GTATCATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (24 bp):
AAGATAACAACATTTTCCTTACAA
Found at i:486571 original size:33 final size:33
Alignment explanation
Indices: 486427--486591 Score: 113
Period size: 33 Copynumber: 5.0 Consensus size: 33
486417 CAACATTTTC
** * *
486427 CTTACAAAAGATAACAGTATCATGAACAAGTTTA
1 CTTACAAAAGATGGCAGTAACATG-TCAAGTTTA
* * * *
486461 CTTACAAAATATGGCAACT-GCATGTTAAGTTTA
1 CTTACAAAAGATGGC-AGTAACATGTCAAGTTTA
* * * * * * **
486494 CTTTCAAAAAATGACAGCAACAAGTTAAACTTA
1 CTTACAAAAGATGGCAGTAACATGTCAAGTTTA
*
486527 CTTACAGAAGATGGCAGTAACATGTCAAGTTTA
1 CTTACAAAAGATGGCAGTAACATGTCAAGTTTA
*
486560 CTTACAAAAGATTGC---AACATGTCCAAGTTTA
1 CTTACAAAAGATGGCAGTAACATGT-CAAGTTTA
486591 C
1 C
486592 AAAAGAAGGT
Statistics
Matches: 101, Mismatches: 27, Indels: 9
0.74 0.20 0.07
Matches are distributed among these distances:
30 7 0.07
31 9 0.09
32 1 0.01
33 66 0.65
34 16 0.16
35 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
CTTACAAAAGATGGCAGTAACATGTCAAGTTTA
Found at i:486704 original size:108 final size:108
Alignment explanation
Indices: 486515--486732 Score: 418
Period size: 108 Copynumber: 2.0 Consensus size: 108
486505 TGACAGCAAC
*
486515 AAGTTAAACTTACTTACAGAAGATGGCAGTAACATGTCAAGTTTACTTACAAAAGATTGCAACAT
1 AAGTTAAACTTACTTACAGAAGATGGCAGTAACATGTAAAGTTTACTTACAAAAGATTGCAACAT
486580 GTCCAAGTTTACAAAAGAAGGTAGTTGCATGTCCAAATTTACA
66 GTCCAAGTTTACAAAAGAAGGTAGTTGCATGTCCAAATTTACA
486623 AAGTTAAACTTACTTACAGAAGATGGCAGTAACATGTAAAGTTTACTTACAAAAGATTGCAACAT
1 AAGTTAAACTTACTTACAGAAGATGGCAGTAACATGTAAAGTTTACTTACAAAAGATTGCAACAT
*
486688 GTCCAAGTTTACAAAAGATGGTAGTTGCATGTCCAAATTTACA
66 GTCCAAGTTTACAAAAGAAGGTAGTTGCATGTCCAAATTTACA
486731 AA
1 AA
486733 AAATGGCAAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (108 bp):
AAGTTAAACTTACTTACAGAAGATGGCAGTAACATGTAAAGTTTACTTACAAAAGATTGCAACAT
GTCCAAGTTTACAAAAGAAGGTAGTTGCATGTCCAAATTTACA
Found at i:488146 original size:22 final size:23
Alignment explanation
Indices: 488104--488146 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
488094 CCCAACCTTA
488104 ATCCTAATAAAATAATAAATCTG
1 ATCCTAATAAAATAATAAATCTG
* *
488127 ATCCTAA-AAGATAATTAATC
1 ATCCTAATAAAATAATAAATC
488147 ATCCTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (23 bp):
ATCCTAATAAAATAATAAATCTG
Found at i:488150 original size:20 final size:22
Alignment explanation
Indices: 488104--488152 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
488094 CCCAACCTTA
488104 ATCCTAATAAAATAATAAATCTG
1 ATCCTAATAAAATAATAAATC-G
* *
488127 ATCCTAA-AAGATAATTAATC-
1 ATCCTAATAAAATAATAAATCG
488147 ATCCTA
1 ATCCTA
488153 TATTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
22 11 0.46
23 7 0.29
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (22 bp):
ATCCTAATAAAATAATAAATCG
Found at i:491914 original size:15 final size:15
Alignment explanation
Indices: 491890--491928 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
491880 TTTTGGCTCT
491890 TTTTTGTTTTTTTGCC
1 TTTTT-TTTTTTTGCC
491906 -TTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
491920 TTTTTTTTT
1 TTTTTTTTT
491929 GTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:491915 original size:14 final size:14
Alignment explanation
Indices: 491891--491928 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
491881 TTTGGCTCTT
491891 TTTTGTTTTTTTGCC
1 TTTT-TTTTTTTGCC
491906 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
491920 TTTTTTTTT
1 TTTTTTTTT
491929 GTTTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:492304 original size:15 final size:15
Alignment explanation
Indices: 492280--492322 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
492270 ACAACACGAT
492280 AAAA-ATAAATAAAC
1 AAAAGATAAATAAAC
*
492294 AAAAGATAAATAAAT
1 AAAAGATAAATAAAC
*
492309 GAAAGATGAAATAA
1 AAAAGAT-AAATAA
492323 GATAATAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (15 bp):
AAAAGATAAATAAAC
Found at i:497447 original size:17 final size:17
Alignment explanation
Indices: 497422--497460 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
497412 CATTGTTGTA
*
497422 ACAACGCTTACAACATC
1 ACAAGGCTTACAACATC
497439 ACAAGGCTTACAACATC
1 ACAAGGCTTACAACATC
497456 ACAAG
1 ACAAG
497461 AAGACCCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGGCTTACAACATC
Found at i:501863 original size:28 final size:28
Alignment explanation
Indices: 501792--501849 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
501782 TTTCTATCAT
*
501792 AAATTCATATC--TTTGTATATACCTTG
1 AAATTCATATCTTTTTGTATATACATTG
501818 AAATTCATATCTTTTTGTATATACATTG
1 AAATTCATATCTTTTTGTATATACATTG
501846 AAAT
1 AAAT
501850 CAATTTTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 11 0.38
28 18 0.62
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (28 bp):
AAATTCATATCTTTTTGTATATACATTG
Found at i:502690 original size:30 final size:31
Alignment explanation
Indices: 502630--502697 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
502620 TAAAATTGGC
** * *
502630 AACTTTTCAAAAATTATTGATTTGGTCCCTA
1 AACTTTTCAAAAATTACAGATATAGTCCCTA
502661 AACTTTTCAAAAATTACAGA-ATAGTCCCTA
1 AACTTTTCAAAAATTACAGATATAGTCCCTA
*
502691 AAATTTT
1 AACTTTT
502698 TCTAAGGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (31 bp):
AACTTTTCAAAAATTACAGATATAGTCCCTA
Found at i:507161 original size:31 final size:31
Alignment explanation
Indices: 507092--507159 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
507082 TAAAATTTTC
* *
507092 AACTTTTCAAAAATTACCGATTTGGTACCCA
1 AACTTTTCAAAAATTACAGATATGGTACCCA
* *
507123 AACTTTTCAAAAATTATAGA-ATGGTCCCCA
1 AACTTTTCAAAAATTACAGATATGGTACCCA
*
507153 AAATTTT
1 AACTTTT
507160 TCTAAGGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (31 bp):
AACTTTTCAAAAATTACAGATATGGTACCCA
Done.