Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005278.1 Hibiscus syriacus cultivar Beakdansim tig00011935_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: 119768
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:273 original size:26 final size:26
Alignment explanation
Indices: 224--295 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
214 ATGCACTTTT
224 TACAACACTTTTC-AAAGCTAGTTTC
1 TACAACACTTTTCAAAAGCTAGTTTC
249 TACAACACTTTTCAAAAGCTAGTTTC
1 TACAACACTTTTCAAAAGCTAGTTTC
*
275 TACAATACTTTTCAAAAGCTA
1 TACAACACTTTTCAAAAGCTA
296 TACCAAACTG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 13 0.29
26 32 0.71
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (26 bp):
TACAACACTTTTCAAAAGCTAGTTTC
Found at i:2788 original size:14 final size:16
Alignment explanation
Indices: 2763--2800 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2753 TTTTATATCG
*
2763 ATTATGTTTTAT-AGA
1 ATTATATTTTATCAGA
2778 ATT-TATTTTATCAGA
1 ATTATATTTTATCAGA
2793 ATTATATT
1 ATTATATT
2801 ATGTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 9 0.45
16 4 0.20
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (16 bp):
ATTATATTTTATCAGA
Found at i:5391 original size:75 final size:76
Alignment explanation
Indices: 5308--5522 Score: 233
Period size: 77 Copynumber: 2.8 Consensus size: 76
5298 TTTTAGGCAT
* * * * * *
5308 AACCCATTTTATTAATTAAAATATTAACATT-TAGATCGCAA-CTATTTCTTAGTGAGCCATGAC
1 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCACAACCTATTTCTTAGTGAACAATGAC
*
5371 ATTTTCTT-ACGC
66 A--TTCTTGACAC
*
5383 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCATAACCTATTTCTTAGTGAACAATGAC
1 AACCCATTTTATTAATAAAAATATTAACATTCCAAATCACAACCTATTTCTTAGTGAACAATGAC
*
5448 ATTCTTGGGCAC
66 ATTCTT-GACAC
* ** * *
5460 AACCCATTTTATTAATAAAAATATTATA-ATTCCATATC-CAATTTATTTTTTAGTGAACCATGA
1 AACCCATTTTATTAATAAAAATATTA-ACATTCCAAATCACAACCTATTTCTTAGTGAACAATGA
5523 TATTTTTTTA
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
75 35 0.29
76 26 0.22
77 58 0.48
78 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (76 bp):
AACCCATTTTATTAATAAAAATATTAACATTCCAAATCACAACCTATTTCTTAGTGAACAATGAC
ATTCTTGACAC
Found at i:8578 original size:3 final size:3
Alignment explanation
Indices: 8559--8598 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
8549 TGCACAAATG
*
8559 TAA TAA TAT TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
8599 ATAAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:8613 original size:9 final size:10
Alignment explanation
Indices: 8560--8610 Score: 56
Period size: 9 Copynumber: 5.5 Consensus size: 10
8550 GCACAAATGT
*
8560 AATAATATTA
1 AATAATAATA
*
8570 ATTAATAAT-
1 AATAATAATA
8579 AATAATAAT-
1 AATAATAATA
8588 AATAATAATA
1 AATAATAATA
8598 AAT-A-AATA
1 AATAATAATA
8606 AATAA
1 AATAA
8611 AATGTTTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
8 7 0.19
9 19 0.53
10 10 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATAATAATA
Found at i:9492 original size:241 final size:240
Alignment explanation
Indices: 9056--9917 Score: 1279
Period size: 241 Copynumber: 3.6 Consensus size: 240
9046 ATTCCCTTCA
* * * *
9056 TCGTGAAGTTGAAA-CTGTGGATGGCCCCTCCGTCGTGAAGTTGAGACTTGAATTTG-ATATCCT
1 TCGTGGAGTTGAAATC-GTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTG-ACTTGAATATCCT
* * * * *
9119 TCGTCATGAAGTTGAAATCCAATTAAGTTATATTGTTTCGATTCTAATATCCTCCGCCGTGAAGT
64 TCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGT
* * * *
9184 TGAAATTGGCTCTGAAATTGGGAAGCCCCTTCGTCATGAATTTAAGCCTCAAATGGCACGGTATC
129 TGAAATTGGCTCTGAAACTGGGAAG-CCCTTCGTCATGAAATTGAGCCTCAAATGGCACGATATC
*
9249 CTCTATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
193 CTCCATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
9297 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
1 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
9362 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
66 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
* * *
9427 AAATTGGCTCTGAAACTGGGAAGCCCTTTCATCATGAAGTTGAGCCTCAAATAGCACGATATCCT
131 AAATTGGCTCTGAAACTGGGAAGCCC-TTCGTCATGAAATTGAGCCTCAAATGGCACGATATCCT
*
9492 CCATCGTGGAGTTGAAATCGTGGATATGTGGGTACGATATCCTCCG
195 CCATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
* **
9538 TTGTGGAGTTGAAATTATGGAT-GCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
1 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
* ** *
9602 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTAGAGTTTAATATCCTCCACCGTGAAGTTG
66 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
* *
9667 AAATTGGCTCTGAAACT-GGAAGCTCCTTCGTCGTGAAATTGAGCCTCAAATGGCATGATATCCT
131 AAATTGGCTCTGAAACTGGGAAGC-CCTTCGTCATGAAATTGAGCCTCAAATGGCACGATATCCT
* * * *
9731 CCGTTGTGGAGTTGAAATCGTGGATGTGTGGATACGATATCCTCTG
195 CCATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
* *
9777 TTGTGGATTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
1 TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
* * * **
9842 GTCGTGAAGTTGAAATCCAAGT-A--TGTATTGTTTCAAGCCCAATATCCTTCGTTGTGAAGTTG
66 GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
*
9904 AAATTGACTCTGAA
131 AAATTGGCTCTGAA
9918 CGAAATTGAA
Statistics
Matches: 569, Mismatches: 47, Indels: 14
0.90 0.07 0.02
Matches are distributed among these distances:
237 43 0.08
239 100 0.18
240 193 0.34
241 232 0.41
242 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (240 bp):
TCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTC
GTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTG
AAATTGGCTCTGAAACTGGGAAGCCCTTCGTCATGAAATTGAGCCTCAAATGGCACGATATCCTC
CATCGTGGAGTTGAAATCGTGGATGTGTGGGTACGATATCCTCCG
Found at i:19628 original size:20 final size:20
Alignment explanation
Indices: 19586--19634 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19576 TTAACTTTTC
*
19586 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
19606 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
19625 TTTTACCTTT
1 TTTTATCTTT
19635 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:32442 original size:15 final size:14
Alignment explanation
Indices: 32416--32455 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
32406 TAAGTCGAAG
32416 AAAG-AAAAAAAAA
1 AAAGAAAAAAAAAA
*
32429 AGAGAAAAATAAAAA
1 AAAGAAAAA-AAAAA
32444 AAAGAAAAAAAA
1 AAAGAAAAAAAA
32456 GTATTTAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 3 0.13
14 7 0.30
15 13 0.57
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAAA
Found at i:32442 original size:17 final size:16
Alignment explanation
Indices: 32413--32453 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
32403 TCCTAAGTCG
*
32413 AAGAAAGAA-AAAAAA
1 AAGAAAAAATAAAAAA
32428 AAGAGAAAAATAAAAAA
1 AAGA-AAAAATAAAAAA
32445 AAGAAAAAA
1 AAGAAAAAA
32454 AAGTATTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 9 0.39
17 10 0.43
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (16 bp):
AAGAAAAAATAAAAAA
Found at i:35918 original size:2 final size:2
Alignment explanation
Indices: 35911--35942 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35901 TTTTATTTCT
35911 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
35943 CTTTTGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35989 original size:2 final size:2
Alignment explanation
Indices: 35982--36028 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
35972 TATTTTACCT
35982 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
36024 TA TA T
1 TA TA T
36029 TTTTATTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36068 original size:38 final size:35
Alignment explanation
Indices: 36026--36121 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 35
36016 TATATATATA
36026 TATTTTTATTTTATTTACTTATTTATCTATTTTATTTT
1 TATTTTTATTTT-TTTACTTATTTATCT-TTTTA-TTT
* *
36064 TATTTTTA-TTCTCTA-TT-TTTATCTTTTTATTT
1 TATTTTTATTTTTTTACTTATTTATCTTTTTATTT
**
36096 TCCTTTTATTTGTTTTACTTATTTAT
1 TATTTTTATTT-TTTTACTTATTTAT
36122 TTATCTGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
32 9 0.19
33 7 0.15
34 10 0.21
35 4 0.08
36 8 0.17
37 2 0.04
38 8 0.17
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (35 bp):
TATTTTTATTTTTTTACTTATTTATCTTTTTATTT
Found at i:36092 original size:33 final size:32
Alignment explanation
Indices: 36026--36106 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
36016 TATATATATA
36026 TATTTTTATTTTATTTACTTATTTATCTATTT
1 TATTTTTATTTTATTTACTTATTTATCTATTT
*
36058 TATTTTTATTTTTATTCT-CTATTTTTATCT-TTT
1 TATTTTTA-TTTTATT-TACT-TATTTATCTATTT
**
36091 TATTTTCCTTTTATTT
1 TATTTTTATTTTATTT
36107 GTTTTACTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.02
32 15 0.35
33 18 0.42
34 9 0.21
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (32 bp):
TATTTTTATTTTATTTACTTATTTATCTATTT
Found at i:36203 original size:4 final size:4
Alignment explanation
Indices: 36194--36307 Score: 53
Period size: 4 Copynumber: 27.8 Consensus size: 4
36184 TTTTCTTCAT
*
36194 TTTA TTTA TTTTA TTTA TTCTA TTCA TTT- TTATA TTTA CTTTA -TT-
1 TTTA TTTA -TTTA TTTA TT-TA TTTA TTTA TT-TA TTTA -TTTA TTTA
* *
36239 TTTA TCTTA TTTA TTT- TTTA -TTA CTTTC CTTA TTTCA TTCGT- TTTA
1 TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT-A TT--TA TTTA
*
36285 CTTTC TTTA -TTA TTTA TTTA TTT
1 -TTTA TTTA TTTA TTTA TTTA TTT
36308 CTTCTAACAC
Statistics
Matches: 85, Mismatches: 8, Indels: 34
0.67 0.06 0.27
Matches are distributed among these distances:
3 16 0.19
4 40 0.47
5 28 0.33
7 1 0.01
ACGTcount: A:0.19, C:0.10, G:0.01, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:36204 original size:9 final size:9
Alignment explanation
Indices: 36192--36254 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
36182 ATTTTTCTTC
36192 ATTTTATTT
1 ATTTTATTT
36201 ATTTTATTT
1 ATTTTATTT
* *
36210 ATTCTATTC
1 ATTTTATTT
*
36219 ATTTT-TAT
1 ATTTTATTT
36227 A-TTTACTTT
1 ATTTTA-TTT
36236 ATTTTTATCTT
1 A-TTTTAT-TT
36247 A-TTTATTT
1 ATTTTATTT
36255 TTTATTACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 28 0.65
10 1 0.02
11 7 0.16
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (9 bp):
ATTTTATTT
Found at i:36237 original size:30 final size:31
Alignment explanation
Indices: 36193--36265 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
36183 TTTTTCTTCA
*
36193 TTTTATTTATTTTATTTAT-TC-TATTCATT
1 TTTTATTTACTTTATTTATATCTTATTCATT
* *
36222 TTTATATTTACTTTATTTTTATCTTATTTATT
1 TTT-TATTTACTTTATTTATATCTTATTCATT
36254 TTTTA-TTACTTT
1 TTTTATTTACTTT
36266 CCTTATTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 21 0.55
31 4 0.11
32 10 0.26
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTTATTTACTTTATTTATATCTTATTCATT
Found at i:36272 original size:23 final size:23
Alignment explanation
Indices: 36244--36306 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
36234 TTATTTTTAT
36244 CTTATTTATTTTTTATTACTTTC
1 CTTATTTATTTTTTATTACTTTC
**
36267 CTTATTTCATTCGTT-TTACTTTC
1 CTTATTT-ATTTTTTATTACTTTC
*
36290 TTTA-TTATTTATTTATT
1 CTTATTTATTT-TTTATT
36307 TCTTCTAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 3 0.09
22 4 0.12
23 20 0.62
24 5 0.16
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (23 bp):
CTTATTTATTTTTTATTACTTTC
Found at i:38403 original size:3 final size:3
Alignment explanation
Indices: 38395--38456 Score: 63
Period size: 3 Copynumber: 19.3 Consensus size: 3
38385 CTGCATAAAT
*
38395 ATA ATA ATA TTA ATTA ATTA ATA ATA ATTA ATA ATA ATTA A-A ATTA
1 ATA ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA A-TA ATA A-TA
38441 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
38457 ATAAATAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 2 0.04
3 35 0.67
4 15 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:38422 original size:10 final size:10
Alignment explanation
Indices: 38396--38456 Score: 71
Period size: 10 Copynumber: 6.6 Consensus size: 10
38386 TGCATAAATA
38396 TAATAAT-AT
1 TAATAATAAT
38405 TAAT--TAAT
1 TAATAATAAT
38413 TAATAATAAT
1 TAATAATAAT
38423 TAATAATAAT
1 TAATAATAAT
38433 TAA-AATTAA-
1 TAATAA-TAAT
38442 TAATAATAA-
1 TAATAATAAT
38451 TAATAA
1 TAATAA
38457 ATAAATAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
7 1 0.02
8 6 0.13
9 18 0.38
10 22 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATAATAAT
Found at i:38459 original size:10 final size:10
Alignment explanation
Indices: 38389--38468 Score: 62
Period size: 10 Copynumber: 8.3 Consensus size: 10
38379 GTCGGCCTGC
38389 ATAAAT-ATA
1 ATAAATAATA
*
38398 AT-AATATTA
1 ATAAATAATA
*
38407 ATTAATTAATA
1 A-TAAATAATA
*
38418 ATAATTAATA
1 ATAAATAATA
*
38428 ATAATTAA-A
1 ATAAATAATA
*
38437 ATTAATAATA
1 ATAAATAATA
38447 AT-AATAATAA
1 ATAAATAAT-A
38457 ATAAATAA-A
1 ATAAATAATA
38466 ATA
1 ATA
38469 TTTTCGTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
8 3 0.05
9 22 0.37
10 24 0.40
11 11 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAATAATA
Found at i:45369 original size:20 final size:20
Alignment explanation
Indices: 45325--45632 Score: 260
Period size: 20 Copynumber: 15.2 Consensus size: 20
45315 AATGACCAAC
*
45325 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
45344 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
45364 AAAATCGCAACGTGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
45384 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
45404 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
45424 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
45445 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
45466 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
45487 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
45508 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
45530 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
45548 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
45570 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
45588 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
45610 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
45628 AAAAT
1 AAAAT
45633 GAGTAAATTC
Statistics
Matches: 241, Mismatches: 25, Indels: 45
0.77 0.08 0.14
Matches are distributed among these distances:
18 10 0.04
19 15 0.06
20 166 0.69
21 15 0.06
22 35 0.15
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:45395 original size:40 final size:39
Alignment explanation
Indices: 45325--45632 Score: 293
Period size: 40 Copynumber: 7.6 Consensus size: 39
45315 AATGACCAAC
* *
45325 AAAATCGCAACGCGA--AATAAAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGATTAA-GAAAATCGCAACGCGATTCA
* * * **
45363 GAAAATCGCAACGTGATTTAGAAAATCGCAACGTTGA-AAA
1 -AAAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTCA
*
45403 GAAAATCGCAACG-G-TCAAAAGAAAATCGCAACGCGATATTCCA
1 -AAAATCGCAACGCGAT--TAAGAAAATCGCAACGCG--ATT-CA
* * *
45446 AGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TT-CA
* * *
45488 AGAATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
*
45528 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
*
45568 AGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCA
1 AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATT-CA
*
45608 AGAATCGCAACGCGATTAAGAAAAT
1 AAAATCGCAACGCGATTAAGAAAAT
45633 GAGTAAATTC
Statistics
Matches: 237, Mismatches: 19, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
38 1 0.00
39 16 0.07
40 149 0.63
41 4 0.02
42 64 0.27
43 2 0.01
44 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (39 bp):
AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCA
Found at i:46254 original size:6 final size:6
Alignment explanation
Indices: 46243--46294 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
46233 TCTCGTCTCG
46243 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
46291 GGTC
1 GGTC
46295 ATACGTGTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:46414 original size:20 final size:20
Alignment explanation
Indices: 46389--46636 Score: 224
Period size: 20 Copynumber: 12.2 Consensus size: 20
46379 AAATTTACTC
46389 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
46409 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
46429 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
46449 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
46469 ATTTTCTGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
46489 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
46511 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
46531 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
46553 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
46573 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
46593 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
46613 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
46632 ATTTT
1 ATTTT
46637 GTTGGTCATT
Statistics
Matches: 192, Mismatches: 19, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.01
18 2 0.01
19 16 0.08
20 133 0.69
21 12 0.06
22 27 0.14
25 1 0.01
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:46575 original size:42 final size:42
Alignment explanation
Indices: 46418--46560 Score: 193
Period size: 42 Copynumber: 3.5 Consensus size: 42
46408 GATTTTCTTA
* * *
46418 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTT-GGAAG
* *
46458 ATCGCGTTGCGATTTTCTGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAG
*
46500 ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAT
1 ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAG
*
46542 ATCGCGTTGCGATTTTCTT
1 ATCGCGTTGCGATTCTCTT
46561 TTGACCGTTG
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.35
41 3 0.03
42 57 0.61
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (42 bp):
ATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCTTGGAAG
Found at i:53206 original size:15 final size:15
Alignment explanation
Indices: 53186--53223 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
53176 AAGCTCCTTT
53186 GGAGCCATACGATAA
1 GGAGCCATACGATAA
53201 GGAGCCATACGATAA
1 GGAGCCATACGATAA
53216 GGAGCCAT
1 GGAGCCAT
53224 CGAAATCGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.29, T:0.13
Consensus pattern (15 bp):
GGAGCCATACGATAA
Found at i:57714 original size:21 final size:21
Alignment explanation
Indices: 57682--57721 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
57672 AACTGCTTAG
57682 TACAGAGGGTATCGATACTCC
1 TACAGAGGGTATCGATACTCC
*
57703 TACA-AGGAGTATCGGTACT
1 TACAGAGG-GTATCGATACT
57722 ACCTTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
TACAGAGGGTATCGATACTCC
Found at i:61345 original size:20 final size:20
Alignment explanation
Indices: 61320--61395 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
61310 CAATGCTGGT
*
61320 AGTATCGATACTACCTAGTG
1 AGTATCGATACTTCCTAGTG
61340 AGTATCGATACTTCCTAGTG
1 AGTATCGATACTTCCTAGTG
*
61360 AGTATCGATACTTCTTAGTG
1 AGTATCGATACTTCCTAGTG
61380 AGTATCGATACTTCCT
1 AGTATCGATACTTCCT
61396 TTACCTTTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTTCCTAGTG
Found at i:61961 original size:39 final size:39
Alignment explanation
Indices: 61869--61963 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
61859 TATTTCACTC
**
61869 TAACATTCTAAATTCCTAATTTCTTAAATTTTACTACCA
1 TAACATTCTAAATTTTTAATTTCTTAAATTTTACTACCA
* * * **
61908 TAACATTCAAAATTTTTAATTTCTTATATTATT-TTACGT
1 TAACATTCTAAATTTTTAATTTCTTAAATT-TTACTACCA
61947 TAACATTCTAAATTTTT
1 TAACATTCTAAATTTTT
61964 TTTTAAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 45 0.96
40 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.01, T:0.49
Consensus pattern (39 bp):
TAACATTCTAAATTTTTAATTTCTTAAATTTTACTACCA
Found at i:62106 original size:2 final size:2
Alignment explanation
Indices: 62099--62125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62089 AATTTTAAAT
62099 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
62126 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63139 original size:20 final size:20
Alignment explanation
Indices: 63114--63151 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
63104 TTTGTTTCAC
*
63114 GGAATGTAAGATTACCAGTG
1 GGAATGTAAAATTACCAGTG
63134 GGAATGTAAAATTACCAG
1 GGAATGTAAAATTACCAG
63152 GGAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATGTAAAATTACCAGTG
Found at i:74463 original size:35 final size:35
Alignment explanation
Indices: 74420--74486 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
74410 CAAAGTCTAT
74420 TATAGTTCTTTTATGTAGATAAGAAAAGATGTTTA
1 TATAGTTCTTTTATGTAGATAAGAAAAGATGTTTA
74455 TATAGTTCTTTTATGTAGATAAGAAAAGATGT
1 TATAGTTCTTTTATGTAGATAAGAAAAGATGT
74487 CATTATAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (35 bp):
TATAGTTCTTTTATGTAGATAAGAAAAGATGTTTA
Found at i:74494 original size:35 final size:34
Alignment explanation
Indices: 74417--74495 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 34
74407 AATCAAAGTC
74417 TATTATAGTTCTTTTATGTAGATAAGAAAAGATG
1 TATTATAGTTCTTTTATGTAGATAAGAAAAGATG
*
74451 TTTATATAGTTCTTTTATGTAGATAAGAAAAGATG
1 TAT-TATAGTTCTTTTATGTAGATAAGAAAAGATG
74486 TCATTATAGT
1 T-ATTATAGT
74496 AGATTGGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 2 0.05
35 38 0.93
36 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (34 bp):
TATTATAGTTCTTTTATGTAGATAAGAAAAGATG
Found at i:76065 original size:2 final size:2
Alignment explanation
Indices: 76058--76125 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
76048 ACTAATGCAT
76058 TA TA TA TA TA TA T- TA TA -A 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
76098 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
76126 CCTGTGTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 62 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:79012 original size:3 final size:3
Alignment explanation
Indices: 79004--79103 Score: 173
Period size: 3 Copynumber: 33.3 Consensus size: 3
78994 AATTAAAAAT
* *
79004 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
79052 ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
79100 ATA A
1 ATA A
79104 AGATAGTAGG
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:79439 original size:134 final size:133
Alignment explanation
Indices: 79255--80053 Score: 825
Period size: 134 Copynumber: 6.1 Consensus size: 133
79245 GCTGTCACTC
* * * *
79255 AGGGAGTATCAAATATGGGGATGTTGATCCATTCCGCTATCACTTAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTGGGGA-GTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGGGGC
* * * * *
79320 AGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTT-GAAAGAGAGGGATATGTTCTTCTTTT
65 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAA-AGAGGGACATGTTCTGCTTCT
*
79384 TCTGG
129 TCTGA
* * * *
79389 AGGGAATATCATATATGGGGTAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCTGGGC
1 AGGGAATATCAGATCTGGGG-AGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGGGGC
* * * * * *
79454 AGAATTGTTCTGCTATCACTCAGGGAATATCAAAAT-TTGGAAAGGAGGGATATGTT-TCGCTTT
65 AGACTTGTTCCGCTGTCACTCAGGGAATATC-AAATCTTGGAAAAGAGGGACATGTTCT-GCTTC
79517 TTCTGA
128 TTCTGA
* * *
79523 AGGGAATATCAGATCTGGATGAGTTAATCCATTCTC-CTATCACTCATGGAAGATTGAATCGGGG
1 AGGGAATATCAGATCTGG-GGAGTTGATCCATTC-CGCTATCACTCAGGGAAGATTGAATCGGGG
* * *
79587 CAGACTTGTTCCGCTGTCACTCAGGGAATAGC---TCTTGGAAAAGAGGGACATATTCCGCTTCT
64 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCTGCTTCT
79649 TCTGA
129 TCTGA
* *
79654 AGGGAATATCAGATCTGGAGGAGTTG-T-CA-----C--T---T-AGGGAAGATCGAATCGGGGT
1 AGGGAATATCAGATCTGG-GGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGGGGC
** * * * * *
79706 AGACTTGTTCTACTGTCACTTAGGGAATATCAAATCTTGGAAAAGAGGAACCTGTTCCGTTTCTT
65 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCTGCTTCTT
*
79771 TTGA
130 CTGA
* * * * * * *
79775 AGAGAATATCA-AGTCTGGAGAAGTTTATCCATTCCGCTGTTACCCAAGGAAGATTGAATCGGGG
1 AGGGAATATCAGA-TCTGG-GGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGGGG
* * * * *
79839 CAGACTTGTTCCGCTGTTACTCAGAGAATATCTAATCTTGGAAAATATGGACATGTT-TCGCTTC
64 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCT-GCTTC
79903 TTCTGA
128 TTCTGA
** *
79909 AGGGAATATCAGATCTGAGGGAGTTGATCCATTCTACTTTCACTCAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTG-GGGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGGGGC
* * * *
79974 AGGCTTGTTCCGTTATCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACCTGTTCCT-CTTCT
65 AGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTT-CTGCTTCT
80038 TCTGA
129 TCTGA
80043 AGGGAATATCA
1 AGGGAATATCA
80054 AATATGTAAA
Statistics
Matches: 554, Mismatches: 81, Indels: 60
0.80 0.12 0.09
Matches are distributed among these distances:
118 44 0.08
119 1 0.00
120 1 0.00
121 51 0.09
122 2 0.00
123 2 0.00
124 1 0.00
128 1 0.00
129 2 0.00
130 3 0.01
131 51 0.09
133 1 0.00
134 380 0.69
135 13 0.02
136 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (133 bp):
AGGGAATATCAGATCTGGGGAGTTGATCCATTCCGCTATCACTCAGGGAAGATTGAATCGGGGCA
GACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCTGCTTCTTC
TGA
Found at i:103021 original size:17 final size:17
Alignment explanation
Indices: 103001--103034 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
102991 AAGTGGCAAC
103001 CATTCTATACATTTTTG
1 CATTCTATACATTTTTG
*
103018 CATTCTTTACATTTTTG
1 CATTCTATACATTTTTG
103035 TATATTCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.56
Consensus pattern (17 bp):
CATTCTATACATTTTTG
Found at i:105046 original size:8 final size:8
Alignment explanation
Indices: 105033--105111 Score: 81
Period size: 8 Copynumber: 9.8 Consensus size: 8
105023 ACACTTGAAG
105033 AAAAGAAA
1 AAAAGAAA
105041 AAAAGAAA
1 AAAAGAAA
*
105049 AATAGAAA
1 AAAAGAAA
105057 AAAAGAAA
1 AAAAGAAA
105065 AAGAA-AAA
1 AA-AAGAAA
* *
105073 AGAAGGGAA
1 A-AAAGAAA
105082 AAAAGAAA
1 AAAAGAAA
*
105090 GAAAA-TAA
1 -AAAAGAAA
105098 AAAAGAAA
1 AAAAGAAA
105106 AAAAGA
1 AAAAGA
105112 GAGGAGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
7 4 0.07
8 44 0.76
9 10 0.17
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:105082 original size:12 final size:12
Alignment explanation
Indices: 105067--105126 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
105057 AAAAGAAAAA
105067 GAAAAAAGAAGG
1 GAAAAAAGAAGG
*
105079 GAAAAAAGAA-A
1 GAAAAAAGAAGG
* *
105090 GAAAATAAAAAAG
1 GAAAA-AAGAAGG
*
105103 AAAAAAAGAGAGG
1 GAAAAAAGA-AGG
105116 AGAAAAAAGAA
1 -GAAAAAAGAA
105127 ATAAAATAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
11 5 0.14
12 17 0.46
13 7 0.19
14 8 0.22
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (12 bp):
GAAAAAAGAAGG
Found at i:105133 original size:38 final size:35
Alignment explanation
Indices: 105044--105134 Score: 114
Period size: 38 Copynumber: 2.5 Consensus size: 35
105034 AAAGAAAAAA
*
105044 AGAAAAATAGAAAAAAA-GAAAAAGAAAAAAGAAGG
1 AGAAAAA-AGAAAAAAATAAAAAAGAAAAAAGAAGG
105079 -GAAAAAAGAAAGAAAATAAAAAAGAAAAAAAGAGAGG
1 AGAAAAAAGAAA-AAAATAAAAAAG-AAAAAAGA-AGG
105116 AGAAAAAAGAAATAAAATA
1 AGAAAAAAGAAA-AAAATA
105135 GGGTTCAAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
33 5 0.10
34 10 0.20
35 6 0.12
36 8 0.16
37 3 0.06
38 17 0.35
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (35 bp):
AGAAAAAAGAAAAAAATAAAAAAGAAAAAAGAAGG
Found at i:107181 original size:24 final size:24
Alignment explanation
Indices: 107137--107186 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
107127 ATAAAGAACC
*
107137 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
107161 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
107185 AA
1 AA
107187 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:107859 original size:18 final size:18
Alignment explanation
Indices: 107836--107877 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
107826 TTGCTATTCC
107836 CTGCACACCACAAACAAA
1 CTGCACACCACAAACAAA
***
107854 CTGCACTTTACAAACAAA
1 CTGCACACCACAAACAAA
107872 CTGCAC
1 CTGCAC
107878 TTTTTCCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.36, G:0.07, T:0.14
Consensus pattern (18 bp):
CTGCACACCACAAACAAA
Found at i:107878 original size:18 final size:18
Alignment explanation
Indices: 107845--107880 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
107835 CCTGCACACC
107845 ACAAACAAACTGCACTTT
1 ACAAACAAACTGCACTTT
107863 ACAAACAAACTGCACTTT
1 ACAAACAAACTGCACTTT
107881 TTCCTCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (18 bp):
ACAAACAAACTGCACTTT
Found at i:110537 original size:19 final size:21
Alignment explanation
Indices: 110506--110558 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
110496 TGAAGGAAAG
* *
110506 AGAAAAAGTAAAAGTTAA-AA
1 AGAAAGAGAAAAAGTTAATAA
*
110526 TA-AAAGAGAAAAAATTAATAA
1 -AGAAAGAGAAAAAGTTAATAA
110547 AGAAAGAGAAAA
1 AGAAAGAGAAAA
110559 GAAAAAGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (21 bp):
AGAAAGAGAAAAAGTTAATAA
Done.