Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000012.1 Hibiscus syriacus cultivar Beakdansim tig00000022_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: 88030
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2440 original size:64 final size:63
Alignment explanation
Indices: 2358--2562 Score: 193
Period size: 65 Copynumber: 3.2 Consensus size: 63
2348 CTAAGAGTGA
* *
2358 ATCGATGCATGAAGTGCATTCGATTTTTCAAAATAGCCTGAGTGCATCGATGCATGGATTGTGC
1 ATCGATGCATCAAATGCATTCGATTTTTCAAAATA-CCTGAGTGCATCGATGCATGGATTGTGC
* **
2422 ATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-ACCTGAGTGCATCAATGCATGGAGAGTG
1 ATCGATGCATCAAATGCATTCGAT-TTTTCA--AAATACCTGAGTGCATCGATGCATGGATTGTG
2486 C
63 C
* * * * * *
2487 CTCGATGCAT-AAACTGCATTTGA-TGTTCAATTTATTCATTG-GTGCATCGATGCATGGATTGG
1 ATCGATGCATCAAA-TGCATTCGATTTTTCAA--AATAC-CTGAGTGCATCGATGCATGGATT-G
2549 TGC
61 TGC
*
2552 ATCGTTGCATC
1 ATCGATGCATC
2563 CCTTTGAAAA
Statistics
Matches: 115, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
61 1 0.01
63 6 0.05
64 42 0.37
65 62 0.54
66 1 0.01
67 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATTTTTCAAAATACCTGAGTGCATCGATGCATGGATTGTGC
Found at i:2476 original size:65 final size:64
Alignment explanation
Indices: 2351--2513 Score: 197
Period size: 65 Copynumber: 2.5 Consensus size: 64
2341 CGGTGCACTA
* * *
2351 AGAGTGAATCGATGCATGAAGTGCATTCGAT-TTTTCAAAATAGCCTGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCAT-AAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCAATGCATGG
**
2415 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-A-CCTGAGTGCATCAATGCAT
1 AGAGTGCATCGATGCAT-AAATGCATTCGATGTTTTCA--AAATAGCCTGAGTGCATCAATGCAT
2478 GG
63 GG
* *
2480 AGAGTGCCTCGATGCATAAACTGCATTTGATGTT
1 AGAGTGCATCGATGCATAAA-TGCATTCGATGTT
2514 CAATTTATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 29 0.34
65 52 0.61
66 1 0.01
67 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
AGAGTGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCAATGCATGG
Found at i:2549 original size:20 final size:20
Alignment explanation
Indices: 2524--2561 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2514 CAATTTATTC
2524 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2544 ATTGGTGCATCGTTGCAT
1 ATTGGTGCATCGATGCAT
2562 CCCTTTGAAA
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:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:5234 original size:21 final size:22
Alignment explanation
Indices: 5181--5241 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
5171 TGGCCTTGTG
5181 AATCGATGCACATTCAAGGCGT
1 AATCGATGCACATTCAAGGCGT
* * * *
5203 ACATCGGTGCACCTTCATGGTGT
1 A-ATCGATGCACATTCAAGGCGT
5226 -ATCGATGCACATTCAA
1 AATCGATGCACATTCAA
5242 AGGGATGCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 13 0.42
22 1 0.03
23 17 0.55
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (22 bp):
AATCGATGCACATTCAAGGCGT
Found at i:11137 original size:19 final size:19
Alignment explanation
Indices: 11113--11164 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
11103 AATAGACTGA
11113 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
*
11132 GTGCATTGATGCATGGATT
1 GTGCATCGATGCATGGATT
11151 GTGCATCGATGCAT
1 GTGCATCGATGCAT
11165 CAAATACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATGGATT
Found at i:11203 original size:46 final size:46
Alignment explanation
Indices: 11151--11256 Score: 212
Period size: 46 Copynumber: 2.3 Consensus size: 46
11141 TGCATGGATT
11151 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
1 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
11197 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
1 GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
11243 GTGCATCGATGCAT
1 GTGCATCGATGCAT
11257 GGAGAGTGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTTTATTAAAACCTGA
Found at i:26827 original size:19 final size:20
Alignment explanation
Indices: 26805--26842 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
26795 TTACATCTCC
*
26805 AAATCCTGC-TAACATCATT
1 AAATCCTGCAAAACATCATT
*
26824 AAATCGTGCAAAACATCAT
1 AAATCCTGCAAAACATCAT
26843 CACATTCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (20 bp):
AAATCCTGCAAAACATCATT
Found at i:29428 original size:64 final size:63
Alignment explanation
Indices: 29294--29448 Score: 226
Period size: 64 Copynumber: 2.4 Consensus size: 63
29284 CACTCGCCAT
* *
29294 ATCGAATGCATTTTATGCATCGATGCACTACATTGCATCGATACACTCATGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACAACATTGCATCGATACACTCAGGTTTTATGAAAAC
*
29357 ATCGAATGCATTTTATGCATCGATGCACAAGCCA-TGCATCGATGCACTCAGGCTTGTT-TG-AA
1 ATCGAATGCATTTTATGCATCGATGCACAA--CATTGCATCGATACACTCAGG-TT-TTATGAAA
29419 AC
62 AC
29421 ATCGAATGCATTTTATGCATCGATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
29449 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
63 29 0.34
64 48 0.56
65 6 0.07
66 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACAACATTGCATCGATACACTCAGGTTTTATGAAAAC
Found at i:29464 original size:64 final size:61
Alignment explanation
Indices: 29294--29468 Score: 210
Period size: 64 Copynumber: 2.7 Consensus size: 61
29284 CACTCGCCAT
* *
29294 ATCGAATGCATTTTATGCATCGATGCACTACATTGCATCGATACACTCATGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACT-CA-TGCATCGATGCACTCAGGTTTTATGAAAAC
*
29357 ATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTT-TG-AAA
1 ATCGAATGCATTTTATGCATCGATGCAC---TCATGCATCGATGCACTCAGG-TT-TTATGAAAA
29420 C
61 C
*
29421 ATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 ATCGAATGCATTTTATGCATCGATGCACTC--A-TGCATCGATGCACT
29469 AAGGGTTCCA
Statistics
Matches: 99, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
61 1 0.01
63 29 0.29
64 61 0.62
65 6 0.06
66 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (61 bp):
ATCGAATGCATTTTATGCATCGATGCACTCATGCATCGATGCACTCAGGTTTTATGAAAAC
Found at i:30742 original size:75 final size:75
Alignment explanation
Indices: 30619--30770 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
30609 GAGTTACTTA
*
30619 CCTTAAAGATAACTCTTCACAAACGATTTCTTACAATGAAAAATTTATTGAAGAGTAATATACCT
1 CCTTAAAGATAACTCTTCACAAACGATTTCCTACAATGAAAAATTTATTGAAGAGTAATATACCT
30684 TTTGAAGAAC
66 TTTGAAGAAC
*
30694 CCTTAAAGATAACTCTTCACCAACGATTTCCTACAATGAAAAATTTATTGAAGAGTAATATACCT
1 CCTTAAAGATAACTCTTCACAAACGATTTCCTACAATGAAAAATTTATTGAAGAGTAATATACCT
30759 TTTGAAGAAC
66 TTTGAAGAAC
30769 CC
1 CC
30771 ATTTATGTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (75 bp):
CCTTAAAGATAACTCTTCACAAACGATTTCCTACAATGAAAAATTTATTGAAGAGTAATATACCT
TTTGAAGAAC
Found at i:35201 original size:600 final size:601
Alignment explanation
Indices: 34061--35863 Score: 2990
Period size: 600 Copynumber: 3.0 Consensus size: 601
34051 TAGGTGAGTG
* * * * * *
34061 TAATGAGCTAGCTAGACAAGTAAGAGCTGGTTGTGATAAAACTTTCTAGTCGTGACATTATAAGT
1 TAATGAGCTAGCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTCTAAGT
34126 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
66 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
*
34191 TGACTCCTCCAACTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGCTTTTCTTAAGTC
131 TGACTCCTCCAGCTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGCTTTTCTTAAGTC
34256 -TCAATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCC
196 TTCAATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCC
* *
34320 CAAGCTACCATAGGATGCGTCATCCCTTAATGTACCTACATAAATAAACAAACTAAGGTAAAATA
261 CAAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATA
34385 AAGGAAATGAGATGAAATAAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTAT
326 AAGGAAATGAGATGAAATAAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTAT
34450 GAATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGG
391 GAATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGG
34515 AGCTGAATTTAACATGCCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTA
456 AGCTGAATTTAACATGCCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTA
34580 ATGAAATCATATTAAATGAATGTAAAAATCAATGAAAATTAATAATAAATTAAGTAAAGATGTGA
521 ATGAAATCATATTAAATGAATGTAAAAATCAATGAAAATTAATAATAAATTAAGTAAAGATGTGA
34645 ATTAATATCATGCAGC
586 ATTAATATCATGCAGC
34661 TAATGAGCTAGCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTCTAAGT
1 TAATGAGCTAGCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTCTAAGT
34726 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
66 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
*
34791 TGACTCCTCCAGCCAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGCTTTTCTTAAGTC
131 TGACTCCTCCAGCTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGCTTTTCTTAAGTC
*
34856 TTC-ATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGTTGCCATGCTTTTTCAAATAGTTTCC
196 TTCAATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCC
34920 CAAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATA
261 CAAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATA
*
34985 AAGGAAATGAGATGAAATTAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTAT
326 AAGGAAATGAGATGAAATAAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTAT
*
35050 GAATGAATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGG
391 GAATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGG
* *
35115 AGCTGAATTTAACATGTCATAAGTTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTA
456 AGCTGAATTTAACATGCCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTA
35180 ATGAAATCATATTAAATGAATGTAAAAATCAATGAAAATTAATAATAAATTAAGTAAAGATGTGA
521 ATGAAATCATATTAAATGAATGTAAAAATCAATGAAAATTAATAATAAATTAAGTAAAGATGTGA
35245 ATTAATATCATGCAGC
586 ATTAATATCATGCAGC
* * *
35261 TAATGAGCTAGCTAGCCAAATAAGGGTTGGTCGTGATAAAAATTTCTAGCCGTGACCTTCTAAGT
1 TAATGAGCTAGCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTCTAAGT
* *
35326 TCTTTAGCATCACCTTCAGCTACTTTTAGCTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
66 TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
* * * *
35391 TGACTCCTCCAGCTAGGTTCAGTTACATGCT-AGCTCCTCCAGCTAAATTGAGCTCTTCTTAAGT
131 TGACTCCTCCAGCTAGGTTCAGCTACATGCTCA-CTTCTCCAGCTGAATTGAGCTTTTCTTAAGT
** * * * * **
35455 -TTCTGTGAGCTGCTTGAATCTTTGTGAGCTGACTGTGAGCTGACATGCTTTGCCAAATAGTTTC
195 CTTCAATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTC
* * * *
35519 CCAGGCTACCATAGGACATGT-TC-TCCCTTTATATACCTACATAGATAAAAAAAAACTAAGGTA
260 CCAAGCTACCATAGG--ATGTGTCATCCCTTAATGTACCTACATAGAT--AAACAAACTAAGGTA
* * * * * * ** *
35582 AAATGAAGGAAATTAGCTGAAATAAAATAAAATGCATTCTG-TCGTGAATGTATAAGTGTTTGTG
321 AAATAAAGGAAATGAGATGAAATAAAACATAATACATGATGAT-GTGAATGTATAAGTGCTTGTG
* * * *
35646 AGGTATGAATGCATGCCATGAGCTAATTATATAAGGATGAAATGTTAATGAGCTAATGTATATAC
385 AGCTATGAATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATAC
* * * *
35711 TTTATGAGTTGAATTTAACATGCCATAAGCTAAATAAATAATAAATAACAGGCTTCCATATTATG
450 TTTAGGAGCTGAATTTAACATGCCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATG
* * * *
35776 AATGTAATGAAATCATATTAAATGAATGTAAAAATGAATGCAAATCAATAATAAATTAAGTAAAT
515 AATGTAATGAAATCATATTAAATGAATGTAAAAATCAATGAAAATTAATAATAAATTAAGTAAAG
35841 ATGTGAATTAATATCATGCAGC
580 ATGTGAATTAATATCATGCAGC
35863 T
1 T
35864 TTACTAATGA
Statistics
Matches: 1133, Mismatches: 62, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
599 4 0.00
600 851 0.75
601 5 0.00
602 273 0.24
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (601 bp):
TAATGAGCTAGCTAGACAAATAAGGGCTGGTCGTGATAAAACTTTCTAGCCGTGACCTTCTAAGT
TCTTTAGCATCACCTTCAGCTACTTTCAACTAATTTTTCATCACTTTCAACAACTTAGGTTCAAA
TGACTCCTCCAGCTAGGTTCAGCTACATGCTCACTTCTCCAGCTGAATTGAGCTTTTCTTAAGTC
TTCAATGAGTTGATTGAATCTTTGTGAGCAGACTGTGAGCTGCCATGCTTTTTCAAATAGTTTCC
CAAGCTACCATAGGATGTGTCATCCCTTAATGTACCTACATAGATAAACAAACTAAGGTAAAATA
AAGGAAATGAGATGAAATAAAACATAATACATGATGATGTGAATGTATAAGTGCTTGTGAGCTAT
GAATGCATACCATGAGCTAAGTATATAAGGATGCAATGTTAATGAGCTAATGTATATACTTTAGG
AGCTGAATTTAACATGCCATAAGCTAAAGAAATAATAAATAACATGCTTCCATATTATGAATGTA
ATGAAATCATATTAAATGAATGTAAAAATCAATGAAAATTAATAATAAATTAAGTAAAGATGTGA
ATTAATATCATGCAGC
Found at i:35839 original size:32 final size:32
Alignment explanation
Indices: 35776--35844 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
35766 CCATATTATG
*
35776 AATGTAATGAAATCATATTAAATGAATGTAAA
1 AATGTAATGAAATCATAATAAATGAATGTAAA
*
35808 AATG-AATGCAAATCAATAATAAATTAA-GTAAA
1 AATGTAATG-AAATC-ATAATAAATGAATGTAAA
*
35840 TATGT
1 AATGT
35845 GAATTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
31 4 0.13
32 17 0.55
33 10 0.32
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.30
Consensus pattern (32 bp):
AATGTAATGAAATCATAATAAATGAATGTAAA
Found at i:40172 original size:19 final size:19
Alignment explanation
Indices: 40148--40187 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40138 ACACTTCTCC
40148 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
40167 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
40186 CA
1 CA
40188 CACTTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:42481 original size:20 final size:20
Alignment explanation
Indices: 42452--42489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42442 CCTATTCAAA
*
42452 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
42472 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
42490 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:50978 original size:45 final size:45
Alignment explanation
Indices: 50906--50991 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
50896 AACGTGACGA
*
50906 CAACTTCACTTGCCACGACAACATCATTAATTCTACTTGCCTTGG
1 CAACTTCACTTGCCACGACAACATCATTAACTCTACTTGCCTTGG
* * *
50951 CAACTTCACTTGCCATGGCAACGTCATTAACTCTACTTGCC
1 CAACTTCACTTGCCACGACAACATCATTAACTCTACTTGCC
50992 ACTACAACGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.30
Consensus pattern (45 bp):
CAACTTCACTTGCCACGACAACATCATTAACTCTACTTGCCTTGG
Found at i:51161 original size:36 final size:36
Alignment explanation
Indices: 51103--51207 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
51093 TTCAATTAAT
51103 CTTCAATAAG-AAAATACCCAAATTTCTTATGAAAC
1 CTTCAATAAGAAAAATACCCAAATTTCTTATGAAAC
* **
51138 CTTTAATAAGAAAAATATTCAAATTTCTTATGAAAC
1 CTTCAATAAGAAAAATACCCAAATTTCTTATGAAAC
*
51174 CTTCAATAGGAAAAATACCCAAATTTCTTATGAA
1 CTTCAATAAGAAAAATACCCAAATTTCTTATGAA
51208 GCTAATTACT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 9 0.15
36 53 0.85
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (36 bp):
CTTCAATAAGAAAAATACCCAAATTTCTTATGAAAC
Found at i:56076 original size:33 final size:31
Alignment explanation
Indices: 56021--56088 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
56011 ATTTTATATA
56021 ATATATAGTTTTAAAAATATTTTGGAAAACT
1 ATATATAGTTTTAAAAATATTTTGGAAAACT
* *
56052 CATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAACT
56085 ATAT
1 ATAT
56089 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATATTTTGGAAAACT
Found at i:56216 original size:18 final size:18
Alignment explanation
Indices: 56195--56233 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56185 ATTATTTCTT
*
56195 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
56213 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
56231 TTC
1 TTC
56234 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:57489 original size:14 final size:13
Alignment explanation
Indices: 57467--57498 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
57457 GTCAATTCCA
57467 TTTTTTTTTTATT
1 TTTTTTTTTTATT
57480 TTTTTATTTTTATT
1 TTTTT-TTTTTATT
57494 TTTTT
1 TTTTT
57499 GGTCCCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:63204 original size:106 final size:106
Alignment explanation
Indices: 61447--63195 Score: 3133
Period size: 106 Copynumber: 16.5 Consensus size: 106
61437 AGAGTAAATT
*
61447 ACAAATTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
61512 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
61553 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
61618 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
61659 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
61724 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
61765 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
61830 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* *
61871 ACAACTTCTCAATTTCATAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
61936 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
61977 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
62042 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * *
62083 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGC
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
62148 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGCAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * *
62189 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGC
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
62254 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
62295 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
62360 AAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
62401 ACAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
62466 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
62507 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
62572 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
62613 ACAACTTCTCAATTTCAGAGCCAATTTCAGCTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
62678 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
62719 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATA-TGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
62783 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
62824 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
62889 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
62930 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
*
62995 AAGTTCAACTTCAGGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * * *
63036 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAATGC
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
63101 AAGTTCAACTTCACGACGAAGGGA-CGACTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAA
* * * * * * * *
63142 ACAATTTCCCAGTTCCAAAGCCAATTTCAACTTCACGACGGAGGATAGTGGACT
1 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
63196 TGAAACAATA
Statistics
Matches: 1593, Mismatches: 48, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
105 107 0.07
106 1486 0.93
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
Found at i:64033 original size:39 final size:41
Alignment explanation
Indices: 63967--64043 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
63957 AATATAGTTT
* *
63967 TTTTTAAAAACGTTTCTAAAAACTTATAT-ACAATATATAAG
1 TTTTAAAAAACATTTCTAAAAACTTATATAAC-ATATATAAG
*
64008 TTTTAAAAAACATTT-TGAAAA-TTATATAACATATAT
1 TTTTAAAAAACATTTCTAAAAACTTATATAACATATAT
64044 TTTTGAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 12 0.38
40 7 0.22
41 13 0.41
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (41 bp):
TTTTAAAAAACATTTCTAAAAACTTATATAACATATATAAG
Found at i:64133 original size:37 final size:35
Alignment explanation
Indices: 63968--64232 Score: 149
Period size: 31 Copynumber: 7.4 Consensus size: 35
63958 ATATAGTTTT
* *
63968 TTTTAAAAACGTTTCTAAAAACTTATATACAATATATAAG
1 TTTTAAAAACATTT-TGAAAA-TTATAT--AATATAT-AG
* *
64008 TTTTAAAAAACATTTTGAAAATTATATAACATATAT
1 TTTT-AAAAACATTTTGAAAATTATATAATATATAG
* * *
64044 TTTTGAAATCATTTTG-AAA--ATATAATGTATAG
1 TTTTAAAAACATTTTGAAAATTATATAATATATAG
64076 TTTAAAATAAAAACATTTTTGAAAATTTTATATAATATATAG
1 TTT----TAAAAACA-TTTTGAAAA--TTATATAATATATAG
* *
64118 TTTTAAAAATATTTTGGAAAACTCATAT-A-ATAT--
1 TTTTAAAAACATTTT-GAAAA-TTATATAATATATAG
* **
64151 TTTTAAAATA-ATTTTTGAAAACTATATGGTATATAG
1 TTTTAAAA-ACA-TTTTGAAAATTATATAATATATAG
* *
64187 TTTTGAAAACATTTT--TAA--ATATAATATATAG
1 TTTTAAAAACATTTTGAAAATTATATAATATATAG
* *
64218 TTTAAAAAATATTTT
1 TTTTAAAAACATTTT
64233 TTGGGATATA
Statistics
Matches: 181, Mismatches: 25, Indels: 47
0.72 0.10 0.19
Matches are distributed among these distances:
31 23 0.13
32 17 0.09
33 16 0.09
34 12 0.07
35 19 0.10
36 20 0.11
37 20 0.11
38 15 0.08
39 6 0.03
40 9 0.05
41 9 0.05
42 15 0.08
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (35 bp):
TTTTAAAAACATTTTGAAAATTATATAATATATAG
Found at i:64165 original size:33 final size:31
Alignment explanation
Indices: 64110--64177 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
64100 ATTTTATATA
64110 ATATATAGTTTTAAAAATATTTTGGAAAACT
1 ATATATAGTTTTAAAAATATTTTGGAAAACT
* *
64141 CATATAATA-TTTTTAAAATAATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAACT
64174 ATAT
1 ATAT
64178 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATATTTTGGAAAACT
Found at i:64303 original size:18 final size:18
Alignment explanation
Indices: 64282--64320 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
64272 ATTATTTCTT
*
64282 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
64300 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
64318 TTC
1 TTC
64321 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:65571 original size:14 final size:13
Alignment explanation
Indices: 65552--65584 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
65542 GTCAATTCCA
65552 TTTTTTTTTATTAT
1 TTTTTTTTTATT-T
65566 TTTTTTTTTATTT
1 TTTTTTTTTATTT
65579 TTTTTT
1 TTTTTT
65585 GGTCCCCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTATTT
Found at i:65583 original size:11 final size:11
Alignment explanation
Indices: 65553--65584 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
65543 TCAATTCCAT
65553 TTTTTTTTATTA
1 TTTTTTTT-TTA
65565 TTTTTTTTTTA
1 TTTTTTTTTTA
65576 TTTTTTTTT
1 TTTTTTTTT
65585 GGTCCCCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:67674 original size:44 final size:44
Alignment explanation
Indices: 67595--67784 Score: 208
Period size: 44 Copynumber: 4.4 Consensus size: 44
67585 ATTTTGTTCT
* * * *
67595 AACTCCTTATTTGAT--AA-CGAGCGAACTGGTAATGTTGATCC
1 AACTCCTTATGTGATGGAATCGAGCGAAATGATAATGCTGATCC
* * * * *
67636 AACTCCTTATGTGATGAAATCGAGCAAAATGTTTATGTTGATCC
1 AACTCCTTATGTGATGGAATCGAGCGAAATGATAATGCTGATCC
* * * * * *
67680 AACTCTTTATGGGATGGAATCTAACGAAAT-ATGATCCTGATCC
1 AACTCCTTATGTGATGGAATCGAGCGAAATGATAATGCTGATCC
*
67723 AACTCCTTATGTGATGGAATCGAGCGAAGTGATAATGCTGATCC
1 AACTCCTTATGTGATGGAATCGAGCGAAATGATAATGCTGATCC
67767 AACTCCTTATGTGATGGA
1 AACTCCTTATGTGATGGA
67785 TGTGCCAAGG
Statistics
Matches: 123, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 14 0.11
43 36 0.29
44 73 0.59
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (44 bp):
AACTCCTTATGTGATGGAATCGAGCGAAATGATAATGCTGATCC
Found at i:67966 original size:116 final size:116
Alignment explanation
Indices: 67762--68015 Score: 481
Period size: 116 Copynumber: 2.2 Consensus size: 116
67752 TGATAATGCT
*
67762 GATCCAACTCCTTATGTGATGGATGTGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTC
1 GATCCACCTCCTTATGTGATGGATGTGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTC
67827 TCCTTCATCGAACGAGTTCTTCTCATTATGAACCCCTCCATTGAAAATGTG
66 TCCTTCATCGAACGAGTTCTTCTCATTATGAACCCCTCCATTGAAAATGTG
67878 GATCCACCTCCTTATGTGATGGATGTGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTC
1 GATCCACCTCCTTATGTGATGGATGTGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTC
67943 TCCTTCATCGAACGAGTTCTTCTCATTATGAACCCCTCCATTGAAAATGTG
66 TCCTTCATCGAACGAGTTCTTCTCATTATGAACCCCTCCATTGAAAATGTG
* *
67994 GATCCACCTCCTTCTGGGATGG
1 GATCCACCTCCTTATGTGATGG
68016 TATCGAATCT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 135 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (116 bp):
GATCCACCTCCTTATGTGATGGATGTGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTC
TCCTTCATCGAACGAGTTCTTCTCATTATGAACCCCTCCATTGAAAATGTG
Found at i:68608 original size:20 final size:20
Alignment explanation
Indices: 68577--68625 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
68567 AAAATATCAT
*
68577 GCCCGAAGGTCTTAGAGATG
1 GCCCGAATGTCTTAGAGATG
*
68597 GTCCGAATGTCTTAGAGATG
1 GCCCGAATGTCTTAGAGATG
68617 GCCCGAATG
1 GCCCGAATG
68626 ACTTGCTCAT
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:0.20, G:0.33, T:0.22
Consensus pattern (20 bp):
GCCCGAATGTCTTAGAGATG
Found at i:71429 original size:60 final size:60
Alignment explanation
Indices: 71361--71517 Score: 174
Period size: 59 Copynumber: 2.6 Consensus size: 60
71351 TTTGGATGAA
* **
71361 TTTGGGGATGAAATTAAAAGATCTAAAAGTTTAGGGACCAATTTAGAATGAGATTCATAG
1 TTTGGGGATGAAATTAAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGCCATAG
* * * *
71421 TTTGGGGATGAAATTCAAATGTTC-AAAAG-TTAAGGACTAGTTTAGAATGAGAGCCATAG
1 TTTGGGGATGAAATT-AAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGCCATAG
* ** * * *
71480 TGTAAGGATGAAATCAAAATATTTAAAAGTTTAAGGAC
1 TTTGGGGATGAAATTAAAAGATCTAAAAGTTTAAGGAC
71518 TAAGTTAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
58 4 0.05
59 41 0.52
60 28 0.35
61 6 0.08
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (60 bp):
TTTGGGGATGAAATTAAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGCCATAG
Found at i:71634 original size:21 final size:22
Alignment explanation
Indices: 71591--71634 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
71581 ATTTACTTTG
*
71591 AACTACTAAAATAACTTTCCAA
1 AACTACTAAAATAACTTTACAA
* *
71613 AACTATTAAATTAA-TTTACAA
1 AACTACTAAAATAACTTTACAA
71634 A
1 A
71635 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
AACTACTAAAATAACTTTACAA
Found at i:73306 original size:14 final size:13
Alignment explanation
Indices: 73286--73320 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
73276 GTTTAATTTC
*
73286 ATTTTTTTTTTGA
1 ATTTTTTTTTTTA
73299 ATTTTTTTTTTTA
1 ATTTTTTTTTTTA
*
73312 CTTTTTTTT
1 ATTTTTTTT
73321 AAGTTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.83
Consensus pattern (13 bp):
ATTTTTTTTTTTA
Found at i:73537 original size:23 final size:22
Alignment explanation
Indices: 73502--73544 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
73492 ATAATTATTT
73502 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
73524 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
73545 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:76418 original size:16 final size:16
Alignment explanation
Indices: 76394--76442 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
76384 AGGTTGTTTG
*
76394 AGTTCGGGTTATTTTC
1 AGTTCGGGTTAATTTC
* **
76410 AGTTTGGGTTGCTTTC
1 AGTTCGGGTTAATTTC
*
76426 GGTTCGGGTTAATTTC
1 AGTTCGGGTTAATTTC
76442 A
1 A
76443 ATTTGGATTG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (16 bp):
AGTTCGGGTTAATTTC
Found at i:76996 original size:12 final size:12
Alignment explanation
Indices: 76979--77003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
76969 AGTGGTAAAA
76979 TGAAATGTTGTT
1 TGAAATGTTGTT
76991 TGAAATGTTGTT
1 TGAAATGTTGTT
77003 T
1 T
77004 TTTTAAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TGAAATGTTGTT
Found at i:84719 original size:7 final size:7
Alignment explanation
Indices: 84707--84732 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
84697 AGATTCATTC
84707 AAAATTG
1 AAAATTG
84714 AAAATTG
1 AAAATTG
84721 AAAATTG
1 AAAATTG
84728 AAAAT
1 AAAAT
84733 GACTCACTTT
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:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
AAAATTG
Done.