Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007389.1 Hibiscus syriacus cultivar Beakdansim tig00019892_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: 104546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:371 original size:54 final size:54
Alignment explanation
Indices: 289--460 Score: 220
Period size: 54 Copynumber: 3.2 Consensus size: 54
279 GTTATCACAT
* * * *
289 ACTTAGTGTCGAAACAGTTATTCATCCACATAGGGTGAATTCCGTGAAATGCAC
1 ACTTAGTGCCGAAACAGTTATTCATCCACATAGGATAAATTCAGTGAAATGCAC
* ** * *
343 ACTTAGTGCCGAAATAACTATTCATCCACATAGGATAAATTCTGGGAAATGCAC
1 ACTTAGTGCCGAAACAGTTATTCATCCACATAGGATAAATTCAGTGAAATGCAC
* * *
397 ACTTAGTGCCAAAACGGTTATTCATCCACATAGGATTAATTCAGTGAAATGCAC
1 ACTTAGTGCCGAAACAGTTATTCATCCACATAGGATAAATTCAGTGAAATGCAC
451 A-TTAAGTGCC
1 ACTT-AGTGCC
461 TTGGGTAATG
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 2 0.02
54 99 0.98
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
ACTTAGTGCCGAAACAGTTATTCATCCACATAGGATAAATTCAGTGAAATGCAC
Found at i:891 original size:94 final size:95
Alignment explanation
Indices: 780--1000 Score: 260
Period size: 94 Copynumber: 2.3 Consensus size: 95
770 GGCCCTTCAA
*
780 TATCGATA-CCTCTACCATGGTATCGATACTACCCTAT-TAGGGTATCGATACCC-C-TTCTGAT
1 TATCGATACCCTC-ACCATGGTATCGATACTACCCTATCT-GGGTACCGATACCCTCTTTC-GAT
* * *
841 ATCGTTACCAAAATT-AGATTTGATGTGT-CTTCG
63 ATCGATACCAAAATTAAG-TTTGATAT-TACCTCG
* *
874 TATCGATACCCTCACCATGGCATCGATAATA--CTATGCTGGGTACCGATACCCTCTTTCGATAT
1 TATCGATACCCTCACCATGGTATCGATACTACCCTAT-CTGGGTACCGATACCCTCTTTCGATAT
*
937 CGATACCAAAATTAAGTTTGATATTACCTGG
65 CGATACCAAAATTAAGTTTGATATTACCTCG
*
968 TATCGATACCCTCACCATTGTATCGATACTACC
1 TATCGATACCCTCACCATGGTATCGATACTACC
1001 TCATCAGTAC
Statistics
Matches: 108, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
92 4 0.04
93 14 0.13
94 81 0.75
95 9 0.08
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (95 bp):
TATCGATACCCTCACCATGGTATCGATACTACCCTATCTGGGTACCGATACCCTCTTTCGATATC
GATACCAAAATTAAGTTTGATATTACCTCG
Found at i:7149 original size:54 final size:54
Alignment explanation
Indices: 7091--7390 Score: 350
Period size: 54 Copynumber: 5.6 Consensus size: 54
7081 TAAGAAAATT
** * * * *
7091 ATGAATTTCGTGATTTGCACACGTAATGCCAAAATGGTTATTCATCCTCATATG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
* * * *
7145 ATGAATTCCATGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
* ** * *
7199 ATGAATTTTGTGAAACACACACTTAGTGCCAAAATAGCTATTCATCCACATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
* * *
7253 ATGAA-TTCTGTGAAATGTACACTTAGTGCTAAAATGATTATTCATCCACATAGG
1 ATGAATTTC-GTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
* * * * *
7307 ATGAATTTCGTGAAATGCACGCTTAGTGTCGAAACGGTTATTCATCCACATTGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
* * *
7361 ATGAATTCCGTGAAAGGCACATTTAGTGCC
1 ATGAATTTCGTGAAATGCACACTTAGTGCC
7391 TATTGGGTAA
Statistics
Matches: 204, Mismatches: 40, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
53 2 0.01
54 199 0.98
55 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (54 bp):
ATGAATTTCGTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
Found at i:7838 original size:95 final size:96
Alignment explanation
Indices: 7734--7937 Score: 249
Period size: 95 Copynumber: 2.1 Consensus size: 96
7724 CTCTATCATC
* * *
7734 ATATTGATACTACCCTAT-TATGGTA-TCGATACCCCCTCCCAGTATCGATACCAAAATT-GGCT
1 ATATCGATACTACCCTATCTAGGGTACT-GATACCCCATCCCAGTATCGATACCAAAATTAGG-T
*
7796 TCGATGTGT-CTTGGTATCGATACCATCACCATG
64 TCGATGT-TACTTGGTATCGATACCATCAACATG
* * *
7829 ATATCGATACTA--TTATGCTAGGGTACTGATACCCCATTCCGGTATCGATACCAAAATTAGGTT
1 ATATCGATACTACCCTAT-CTAGGGTACTGATACCCCATCCCAGTATCGATACCAAAATTAGGTT
*
7892 CGATGTTACTTGGTATCGATACCCTCAACATG
65 CGATGTTACTTGGTATCGATACCATCAACATG
*
7924 GTATCGATACTACC
1 ATATCGATACTACC
7938 TCATCAATAC
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
93 3 0.03
94 1 0.01
95 86 0.92
96 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (96 bp):
ATATCGATACTACCCTATCTAGGGTACTGATACCCCATCCCAGTATCGATACCAAAATTAGGTTC
GATGTTACTTGGTATCGATACCATCAACATG
Found at i:20063 original size:74 final size:75
Alignment explanation
Indices: 19926--20069 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 75
19916 ATTACTAAGG
*
19926 AACATCGAATCCAATTTTGGTATCGATATCAATAGGGGGTATCGGTACCATAGTAGGGTAGTATC
1 AACATCGAATCCAATTTTGGTATCGATATCAATAGGGGGTATCGGTACCATAGTAGGATAGTATC
19991 GATACCAGGC
66 GATACCAGGC
* * * *
20001 AACATCGAA-CCTATTTTTGGTATCGATACTCGA-A-GGGGTATCGGTATCATAGTA-TATAAGT
1 AACATCGAATCC-AATTTTGGTATCGATA-TCAATAGGGGGTATCGGTACCATAGTAGGAT-AGT
20062 ATCGATAC
63 ATCGATAC
20070 TAGGATAGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
73 1 0.02
74 32 0.52
75 25 0.41
76 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (75 bp):
AACATCGAATCCAATTTTGGTATCGATATCAATAGGGGGTATCGGTACCATAGTAGGATAGTATC
GATACCAGGC
Found at i:20089 original size:28 final size:28
Alignment explanation
Indices: 20050--20111 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
20040 ATCGGTATCA
*
20050 TAGTATATAAGTATCGATACTAGGATAG
1 TAGTATAGAAGTATCGATACTAGGATAG
*
20078 TAGTATAGAAGTATCGATACTAGGGTAG
1 TAGTATAGAAGTATCGATACTAGGATAG
20106 TAGTAT
1 TAGTAT
20112 CAATACTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (28 bp):
TAGTATAGAAGTATCGATACTAGGATAG
Found at i:20539 original size:55 final size:56
Alignment explanation
Indices: 20469--20933 Score: 499
Period size: 55 Copynumber: 8.5 Consensus size: 56
20459 CAAATCCTTG
*
20469 GAATTCATCATGAGTTGATGAATCACCGTACATGCA-CTTCGTGTGCATATTCACA
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
* * * *
20524 TAATTCATCATGAGTTGATGAATCACCATACAGGCACCTT-GTGTGC-TAATCCATA
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCAT-ATTCACA
*** * * * *
20579 GAATTCATCATGAGTTGATGAATCATTTTATAGACA-CTTCATGTGTATATTCACA
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
* * * * * *
20634 GAATTCAACATGAGTTGACGAATCACCGTACAAGCACCTTC-TGTGCAAATCCACG
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
* *
20689 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTT-GTGTGCAAATCCACA
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
** * *
20744 GAATTCATCATGAGTTGATGAATCACCGTACAGG-AAATTCGTGTGAATATTCA-T
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
* * * * **
20798 GAAATTCATCATGAG-T--TGAATCACCGTACGGGCACCTT-GTGTACAAATCCATG
1 G-AATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
*
20851 GAATTCATCATGAGTTGATGAATCACTGTACAGGCA-CTTCGTGTGCATATTCAC-
1 GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
* **
20905 GAAGTTCATAATTCGTTGATGAATCACCG
1 GAA-TTCATCATGAGTTGATGAATCACCG
20934 GAGAGGTACT
Statistics
Matches: 340, Mismatches: 55, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
52 37 0.11
53 5 0.01
54 15 0.04
55 275 0.81
56 8 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (56 bp):
GAATTCATCATGAGTTGATGAATCACCGTACAGGCACCTTCGTGTGCATATTCACA
Found at i:20749 original size:165 final size:163
Alignment explanation
Indices: 20469--20933 Score: 564
Period size: 165 Copynumber: 2.8 Consensus size: 163
20459 CAAATCCTTG
* * * **
20469 GAATTCATCATGAGTTGATGAATCACCGTACATGCA-CTTCGTGTGCATATTCACATAATTCATC
1 GAATTCATCATGAGTTGA-GAATCACCGTACAAGCACCTTC-TGTGCAAATCCACGGAATTCATC
* * *
20533 ATGAGTTGATGAATCACCATACAGGCACCTTGTGTGCTAATCCATAGAATTCATCATGAGTTGAT
64 ATGAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCACAGAATTCATCATGAGTTGAT
*** * * *
20598 GAATCATTTTATA-GACACTTCATGTGTATATTCACA
129 GAATCACCGTACAGGA-AATTCATGTGAATATTCA-A
*
20634 GAATTCAACATGAGTTGACGAATCACCGTACAAGCACCTTCTGTGCAAATCCACGGAATTCATCA
1 GAATTCATCATGAGTTGA-GAATCACCGTACAAGCACCTTCTGTGCAAATCCACGGAATTCATCA
20699 TGAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCACAGAATTCATCATGAGTTGATG
65 TGAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCACAGAATTCATCATGAGTTGATG
* *
20764 AATCACCGTACAGGAAATTCGTGTGAATATTCAT
130 AATCACCGTACAGGAAATTCATGTGAATATTCAA
** * * *
20798 GAAATTCATCATGAGTT--GAATCACCGTACGGGCACCTTGTGTACAAATCCATGGAATTCATCA
1 G-AATTCATCATGAGTTGAGAATCACCGTACAAGCACCTTCTGTGCAAATCCACGGAATTCATCA
* * * * **
20861 TGAGTTGATGAATCACTGTACAGGCA-CTTCGTGTGCATATTCAC-GAAGTTCATAATTCGTTGA
65 TGAGTTGATGAATCACCGTACAGGCACCTT-GTGTGCAAATCCACAGAA-TTCATCATGAGTTGA
20924 TGAATCACCG
128 TGAATCACCG
20934 GAGAGGTACT
Statistics
Matches: 265, Mismatches: 30, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
161 6 0.02
162 100 0.38
164 1 0.00
165 152 0.57
166 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (163 bp):
GAATTCATCATGAGTTGAGAATCACCGTACAAGCACCTTCTGTGCAAATCCACGGAATTCATCAT
GAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCACAGAATTCATCATGAGTTGATGA
ATCACCGTACAGGAAATTCATGTGAATATTCAA
Found at i:31238 original size:19 final size:19
Alignment explanation
Indices: 31210--31278 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
31200 ATGCAAAAAT
* *
31210 AGTATGGATACCGTAATAG
1 AGTATCGATACCATAATAG
*
31229 AGTATCGATACAATAATATAG
1 AGTATCGATACCAT-A-ATAG
**
31250 TAGTATCGATACCATGGTAG
1 -AGTATCGATACCATAATAG
31270 AGTATCGAT
1 AGTATCGAT
31279 GTTGTTGAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 20 0.49
20 4 0.10
21 4 0.10
22 13 0.32
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
AGTATCGATACCATAATAG
Found at i:31693 original size:54 final size:55
Alignment explanation
Indices: 31593--31696 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 55
31583 AATCGCACCA
* *
31593 TGTGTACACAACTAATAAATTCATAATAAGTTTATGAATTTCTGTATTGGTAGGG
1 TGTGTACACAACCAATAAATTCATAATAAGATTATGAATTTCTGTATTGGTAGGG
* *
31648 TGTGTACA-AACCACATAAATT-TTAATAAGATTGTGAATTAT-TGTATTGG
1 TGTGTACACAACCA-ATAAATTCATAATAAGATTATGAATT-TCTGTATTGG
31697 CACTACGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
54 27 0.63
55 16 0.37
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (55 bp):
TGTGTACACAACCAATAAATTCATAATAAGATTATGAATTTCTGTATTGGTAGGG
Found at i:31927 original size:81 final size:81
Alignment explanation
Indices: 31791--32554 Score: 933
Period size: 81 Copynumber: 9.5 Consensus size: 81
31781 TAAAATTAAT
* * * * * *
31791 GATTAATGGCCTAGCAGTGCATTTGGCAAAAAGATGTCAATTATGCCACTTAGATGAAATGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
31856 ATACCTTTGAGTAAAA
66 ATACCTTTGAGTAAAA
* * * * *
31872 TATTAATGGCCTAGGTATGCATTTGGCATAAAGGTGTCAATTATGCTAGTTAGATGAAACGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
*
31937 ATACCTTTCAGTAAAA
66 ATACCTTTGAGTAAAA
* * * * *
31953 GATTAATGGCCTAGTTGTACATTTGGCAGAAAGGTGTCAATTATACTAGTTAGATGAAATGCT-A
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
32017 A-ACCTTTGAGTAAAA
66 ATACCTTTGAGTAAAA
* * * *** * * *
32032 TATTAATGGACTAGTTGTGCATTTATAAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
32097 ATACCTTTTGAGTAAAA
66 ATACC-TTTGAGTAAAA
* * * * * * * *
32114 AATTAATGGCCTAGCTCTGCTTTTGGCAGAAAGGTGTCAATAACGCCACTTAGATGAAAGATTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
32179 ATACCTTTGAGTAAAA
66 ATACCTTTGAGTAAAA
* * * * *
32195 GATTAATGGCCTAGCTATGCATTTGGCAGAAAGGTGGCAATCATG-TCAATTAGAAGAAAGGTTA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAAGGTTA
32259 AATACCTTTGAGTAAAA
65 AATACCTTTGAGTAAAA
* *
32276 GATTAATGGCCTAGCTGTGCATTTGGCAGAAACGTGTCAATTATGCTAGTTATATGAAAGGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
32341 ATACCTTTGAGTAAAA
66 ATACCTTTGAGTAAAA
* * * * * * * *
32357 GATTAATGACCTAGCTGTGTATTTGGCAGAAAGGTGACAATTGTGC-AGTTATAGGAAATGTTAG
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
32421 ATACCTTTGAGTAAAA
66 ATACCTTTGAGTAAAA
* * * * * * *
32437 TATTAGTGGTCTAGTTGTGCATTTGGCATAAAGGTGTTAATTATTCTAGTTAGATGAAAGGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
* *
32502 ATACGTTTTAGTAAAA
66 ATACCTTTGAGTAAAA
* * *
32518 GATTAATGGCCTAACTGTGAATTTGGCAGAAATGTGT
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT
32555 AAGTTATTCT
Statistics
Matches: 583, Mismatches: 94, Indels: 12
0.85 0.14 0.02
Matches are distributed among these distances:
79 64 0.11
80 70 0.12
81 380 0.65
82 69 0.12
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (81 bp):
GATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGTTAA
ATACCTTTGAGTAAAA
Found at i:32432 original size:323 final size:322
Alignment explanation
Indices: 31792--32549 Score: 966
Period size: 323 Copynumber: 2.3 Consensus size: 322
31782 AAAATTAATG
* *
31792 ATTAATGGCCTAGCAGTGCATTTGGCAAAAAGATGTCAATTATGCCACTTAGATGAAATGTTAAA
1 ATTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATGCCACTTAGATGAAA-GTTAAA
* * * * * *
31857 TACCTTTGAGTAAAATATTAATGGCCTAGGTATGCATTTGGCATAAAGGTGTCAATTATGCTAGT
65 TACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAAAGGTGGCAATCATGCTAAT
* * *
31922 TAGATGAAACGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGTTGTACATTTGGCAGAAAGG
130 TAGAAGAAACGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGCTGTACATTTGGCAGAAACG
* * *
31987 TGTCAATTATACTAGTTAGATGAAATGCTAAACCTTTGAGTAAAATATTAATGGACTAGTTGTGC
195 TGTCAATTATACTAGTTAGATGAAAGGCTAAACCTTTGAGTAAAAGATTAATGGACTAGCTGTGC
* * * *
32052 ATTTATAAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAAATACCTTTTGAGTAAAAA
260 ATTTAGAAGAAAGGTGACAATTATGCCAATTAGAGGAAAGGTTAAATACCTTTTGAGTAAAAA
* * * * *
32115 ATTAATGGCCTAGCTCTGCTTTTGGCAGAAAGGTGTCAATAACGCCACTTAGATGAAAGATTAAA
1 ATTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATGCCACTTAGATGAAAG-TTAAA
32180 TACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAAAGGTGGCAATCATG-TCAA
65 TACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAAAGGTGGCAATCATGCT-AA
* * *
32244 TTAGAAGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAC
129 TTAGAAGAAACGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGCTGTACATTTGGCAGAAAC
* * *
32309 GTGTCAATTATGCTAGTTATATGAAAGGTTAAATACCTTTGAGTAAAAGATTAAT-GACCTAGCT
194 GTGTCAATTATACTAGTTAGATGAAAGGCT-AA-ACCTTTGAGTAAAAGATTAATGGA-CTAGCT
* * * * * * * *
32373 GTGTATTTGGCAGAAAGGTGACAATTGTG-CAGTTATAGGAAATGTTAGATACC-TTTGAGTAAA
256 GTGCATTTAGAAGAAAGGTGACAATTATGCCAATTAGAGGAAAGGTTAAATACCTTTTGAGTAAA
*
32436 AT
321 AA
* * * * * * * *
32438 ATTAGTGGTCTAGTTGTGCATTTGGCATAAAGGTGTTAATTATTCTAGTTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATGCCACTTAGATGAAA-GTTAAA
* * * * *
32503 TACGTTTTAGTAAAAGATTAATGGCCTAACTGTGAATTTGGCAGAAA
65 TACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAAA
32550 TGTGTAAGTT
Statistics
Matches: 374, Mismatches: 55, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
322 2 0.01
323 301 0.80
324 24 0.06
325 47 0.13
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (322 bp):
ATTAATGGCCTAGCTGTGCATTTGGCAAAAAGGTGTCAATTATGCCACTTAGATGAAAGTTAAAT
ACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAAAGGTGGCAATCATGCTAATT
AGAAGAAACGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGCTGTACATTTGGCAGAAACGT
GTCAATTATACTAGTTAGATGAAAGGCTAAACCTTTGAGTAAAAGATTAATGGACTAGCTGTGCA
TTTAGAAGAAAGGTGACAATTATGCCAATTAGAGGAAAGGTTAAATACCTTTTGAGTAAAAA
Found at i:32544 original size:242 final size:241
Alignment explanation
Indices: 31791--32554 Score: 962
Period size: 242 Copynumber: 3.2 Consensus size: 241
31781 TAAAATTAAT
* * * *
31791 GATTAATGGCCTAGCAGTGCATTTGGCA-AAAAGATGTCAATTATGCCACTTAGATGAAATGTTA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAATG-TGTCAATTATGCCAATTAGATGAAAGGTTA
* * * *
31855 AATACCTTTGAGTAAAATATTAATGGCCTAGGTATGCATTTGGCATAAAGGTGTCAATTATGCTA
65 AATACCTTTGAGTAAAAAATTAATGGCCTAGCTATGTATTTGGCAGAAAGGTGTCAATTATGC-A
* *
31920 GTTAGATGAAACGTTAAATACCTTTCAGTAAAAGATTAATGGCCTAGTTGTACATTTGGCAGAAA
129 GTTAGATGAAA-GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAA
* * *
31985 GGTGTCAATTATACTAGTTAGATGAAATGCT-AA-ACCTTTGAGTAAAA
193 GGTGTCAATTATTCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
* * * ***
32032 TATTAATGGACTAGTTGTGCATTTATAAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAA
* * *
32097 ATACCTTTTGAGTAAAAAATTAATGGCCTAGCTCTGCT-TTTGGCAGAAAGGTGTCAATAACGCC
66 ATACC-TTTGAGTAAAAAATTAATGGCCTAGCTATG-TATTTGGCAGAAAGGTGTCAATTATG-C
* * *
32161 ACTTAGATGAAAGATTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAA
128 AGTTAGATGAAAG-TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAA
* * * *
32226 AGGTGGCAATCATGTC-AATTAGAAGAAAGGTTAAATACCTTTGAGTAAAA
192 AGGTGTCAATTAT-TCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
* * * *
32276 GATTAATGGCCTAGCTGTGCATTTGGCAGAAACGTGTCAATTATGCTAGTTATATGAAAGGTTAA
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAA
* * * * *
32341 ATACCTTTGAGTAAAAGATTAATGACCTAGCTGTGTATTTGGCAGAAAGGTGACAATTGTGCAGT
66 ATACCTTTGAGTAAAAAATTAATGGCCTAGCTATGTATTTGGCAGAAAGGTGTCAATTATGCAGT
* * * * * * *
32406 TATAGGAAATGTTAGATACCTTTGAGTAAAATATTAGTGGTCTAGTTGTGCATTTGGCATAAAGG
131 TAGATGAAA-GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGG
* * *
32471 TGTTAATTATTCTAGTTAGATGAAAGGTTAAATACGTTTTAGTAAAA
195 TGTCAATTATTCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
* *
32518 GATTAATGGCCTAACTGTGAATTTGGCAGAAATGTGT
1 GATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGT
32555 AAGTTATTCT
Statistics
Matches: 446, Mismatches: 66, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
241 58 0.13
242 262 0.59
243 52 0.12
244 74 0.17
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (241 bp):
GATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAATTAGATGAAAGGTTAA
ATACCTTTGAGTAAAAAATTAATGGCCTAGCTATGTATTTGGCAGAAAGGTGTCAATTATGCAGT
TAGATGAAAGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGT
GTCAATTATTCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAA
Found at i:35196 original size:12 final size:12
Alignment explanation
Indices: 35179--35209 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35169 ACCCTACTTT
35179 CATCATCGCTTA
1 CATCATCGCTTA
35191 CATCATCGCTTA
1 CATCATCGCTTA
35203 CATCATC
1 CATCATC
35210 ATGAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (12 bp):
CATCATCGCTTA
Found at i:36041 original size:23 final size:23
Alignment explanation
Indices: 36015--36059 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
36005 AGACCATATA
*
36015 TATTCACTATCTCATGTAAACCT
1 TATTCACTATCTCAGGTAAACCT
36038 TATTCACTATCTCAGGTAAACC
1 TATTCACTATCTCAGGTAAACC
36060 AATGAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (23 bp):
TATTCACTATCTCAGGTAAACCT
Found at i:44374 original size:45 final size:45
Alignment explanation
Indices: 44276--44602 Score: 465
Period size: 45 Copynumber: 7.2 Consensus size: 45
44266 AAACGAATGA
* *
44276 ATAAATGAAATGCATAAAGGTGCATTTAATGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCA-TTAAAGGCATGAAAGGATGCC
*
44322 ATGAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
* * ***
44367 ATAAATGAAATGCATAACGATGCATTAAAGGTATGAAAGGATTAT
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
* *
44412 ATAAATGAAATGCATAATGGTACATTTAAAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCA-TTAAAGGCATGAAAGGATGCC
* * * *
44458 ATAAATGAAATCCATAATGATACATTAAAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
*
44503 ATAAATGAAATGCATAACGGTGCATTAATGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
* * *
44548 ATAAATGAAATGCATAATGGTGCATTAAAGGAATGAAAGGATGGC
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
*
44593 ATAACTGAAA
1 ATAAATGAAA
44603 ATAATAAATA
Statistics
Matches: 252, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
45 191 0.76
46 61 0.24
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
Found at i:44484 original size:136 final size:136
Alignment explanation
Indices: 44272--44602 Score: 495
Period size: 136 Copynumber: 2.4 Consensus size: 136
44262 TCTAAAACGA
* * * *
44272 ATGA-ATAAATGAAATGCATAAAGGTGCATTTAATGGCATGAAAGGATGCCATGAATGAAATGCA
1 ATGACATAAATGAAATGCATAATGGTGCATTTAAAGGCATGAAAGGATGCCATAAATGAAATCCA
* * *
44336 TAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGATGCATTAAAGGTAT
66 TAACGATACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGATGCATTAAAGGCAT
44401 GAAAGG
131 GAAAGG
* * *
44407 ATTATATAAATGAAATGCATAATGGTACATTTAAAGGCATGAAAGGATGCCATAAATGAAATCCA
1 ATGACATAAATGAAATGCATAATGGTGCATTTAAAGGCATGAAAGGATGCCATAAATGAAATCCA
* * *
44472 TAATGATACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAATGGCAT
66 TAACGATACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGATGCATTAAAGGCAT
44537 GAAAGG
131 GAAAGG
* * * *
44543 ATGCCATAAATGAAATGCATAATGGTGCA-TTAAAGGAATGAAAGGATGGCATAACTGAAA
1 ATGACATAAATGAAATGCATAATGGTGCATTTAAAGGCATGAAAGGATGCCATAAATGAAA
44603 ATAATAAATA
Statistics
Matches: 176, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
135 31 0.18
136 145 0.82
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (136 bp):
ATGACATAAATGAAATGCATAATGGTGCATTTAAAGGCATGAAAGGATGCCATAAATGAAATCCA
TAACGATACATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGATGCATTAAAGGCAT
GAAAGG
Found at i:67470 original size:16 final size:15
Alignment explanation
Indices: 67445--67478 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
67435 GATGAATGAT
*
67445 TTTGATATTTGGTTG
1 TTTGATATTTGGATG
67460 TTTGAATATTTGGATG
1 TTTG-ATATTTGGATG
67476 TTT
1 TTT
67479 TGGTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (15 bp):
TTTGATATTTGGATG
Found at i:68087 original size:20 final size:20
Alignment explanation
Indices: 68059--68116 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
68049 TCAATAGGGT
* *
68059 AGTACCGATACTCCCTTATC
1 AGTATCGATACCCCCTTATC
68079 AGTATCGATACCCCCTTATC
1 AGTATCGATACCCCCTTATC
68099 AGTATCGATACCCCCTTA
1 AGTATCGATACCCCCTTA
68117 CATCGAATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.34, G:0.10, T:0.29
Consensus pattern (20 bp):
AGTATCGATACCCCCTTATC
Found at i:71052 original size:81 final size:80
Alignment explanation
Indices: 70911--71563 Score: 808
Period size: 81 Copynumber: 8.1 Consensus size: 80
70901 TGTTAAGAAT
* *
70911 TTAATCTTTTACTCAAAGGCATTTTGCCTTTCATCTAACTGACAATATTGCCACCTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCA-TTTACCTTTCATCTAACTGACAATATTGACACCTTTCTGCCAA
*
70976 ATGCACAACTAGGCCA
65 ATGCACAGCTAGGCCA
* * *
70992 ATAATATTTTACTCAAAGGCATCTACCATTTCATCTAACTGACAATATTGACACCTTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTACC-TTTCATCTAACTGACAATATTGACACCTTTCTGCCAA
* * *
71057 ATGCACAACTATGCTA
65 ATGCACAGCTAGGCCA
* * * * * * * *
71073 ATAATATTTTACTCAAAGGTATTTAGCTTGTCATCTATCT-AGCAATATTGATACCTTTTTGCCT
1 TTAATCTTTTACTCAAAGGCATTTACCTT-TCATCTAACTGA-CAATATTGACACCTTTCTGCCA
71137 AATGCACAGCTAGGCCA
64 AATGCACAGCTAGGCCA
* ** * *
71154 TTAATCTTTTACTCAAAGTCATTTAGTGTTTCATCTAACTGGA-AATATTGACACATTTCTACCA
1 TTAATCTTTTACTCAAAGGCATTTA-CCTTTCATCTAACT-GACAATATTGACACCTTTCTGCCA
*
71218 AATGCACAACTAGGCCA
64 AATGCACAGCTAGGCCA
* * * *
71235 TTAATCTTTTACTCAAAGGCATTTACCCTTTCATCTAACT-AGTAATATTGGCACTTTTATGCCA
1 TTAATCTTTTACTCAAAGGCATTTA-CCTTTCATCTAACTGA-CAATATTGACACCTTTCTGCCA
*
71299 AATACACAGCTAGGCCA
64 AATGCACAGCTAGGCCA
* * *
71316 TTAATCTTTTACTCAAAGGCATTTATCCTTTCATCTAACTGTCAATATGGACACCTTTCTGACAA
1 TTAATCTTTTACTCAAAGGCATTTA-CCTTTCATCTAACTGACAATATTGACACCTTTCTGCCAA
* *
71381 ATGAACATCTAGGCCA
65 ATGCACAGCTAGGCCA
* * *
71397 TTAATCTTTTACTTAAAGGCATTTAGCCTTTCATCTAACTGGCAATATTGACACATTTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTA-CCTTTCATCTAACTGACAATATTGACACCTTTCTGCCAA
71462 ATGCACAGCTAGGCCA
65 ATGCACAGCTAGGCCA
* * * * * *
71478 TTATTCTTTTACTCAAAGGCTTTTAGCCTTTCATCTAATTGGCAATATTGACAACATTCTGCCAA
1 TTAATCTTTTACTCAAAGGCATTTA-CCTTTCATCTAACTGACAATATTGACACCTTTCTGCCAA
71543 ATGCACAGCTAGGCCA
65 ATGCACAGCTAGGCCA
71559 TTAAT
1 TTAAT
71564 TTGTCATTTT
Statistics
Matches: 496, Mismatches: 67, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.00
80 7 0.01
81 485 0.98
82 2 0.00
83 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (80 bp):
TTAATCTTTTACTCAAAGGCATTTACCTTTCATCTAACTGACAATATTGACACCTTTCTGCCAAA
TGCACAGCTAGGCCA
Found at i:77876 original size:23 final size:22
Alignment explanation
Indices: 77850--77920 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
77840 AGAGTGCACT
*
77850 GATGTACATTCAAGGAGTGCATC
1 GATGCACATTCAAGG-GTGCATC
* * *
77873 GATGCACCTTC-ATGGTGTATC
1 GATGCACATTCAAGGGTGCATC
77894 GATGCACATTCAAGGGATGCATC
1 GATGCACATTCAAGGG-TGCATC
77917 GATG
1 GATG
77921 TACGATCTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 16 0.41
22 5 0.13
23 18 0.46
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (22 bp):
GATGCACATTCAAGGGTGCATC
Found at i:80761 original size:12 final size:12
Alignment explanation
Indices: 80744--80773 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
80734 AAAGAAAGAG
80744 TAATGCTCATCT
1 TAATGCTCATCT
80756 TAATGCTCATCT
1 TAATGCTCATCT
80768 TAATGC
1 TAATGC
80774 ACTTGAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (12 bp):
TAATGCTCATCT
Found at i:82302 original size:90 final size:89
Alignment explanation
Indices: 82178--82354 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 89
82168 TATTTCCAAA
* * *
82178 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAC
*
82243 TAGGGTAACTTGGATATAAAAGGAT
65 GAGGGTAACTTGGATATAAAAGGAT
* *
82268 TATTAAATTCCAATTCATTAAATATAGATTTAATTAATTTGAATTAATAAAACCCTAATATGACG
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACG
*
82333 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
82355 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 32 0.40
90 48 0.60
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACG
AGGGTAACTTGGATATAAAAGGAT
Found at i:89060 original size:16 final size:15
Alignment explanation
Indices: 89019--89060 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
89009 TCCCAAATAT
89019 TTAATTTAAA-TTAA
1 TTAATTTAAATTTAA
*
89033 TTAAATATAAATTTAA
1 TT-AATTTAAATTTAA
89049 TTAATTTGAAAT
1 TTAATTT-AAAT
89061 AATAAATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TTAATTTAAATTTAA
Found at i:89169 original size:89 final size:89
Alignment explanation
Indices: 89027--89189 Score: 290
Period size: 89 Copynumber: 1.8 Consensus size: 89
89017 ATTTAATTTA
*
89027 AATTAATTAAATATAAATTTAATTAATTTGAAATAATAAATCCCTAATATGATTAGGGTAACTTA
1 AATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTA
89092 GATATAAAAGGATTATTAAATTCC
66 GATATAAAAGGATTATTAAATTCC
* *
89116 AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
1 AATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTA
*
89181 GCTATAAAA
66 GATATAAAA
89190 AGGTGTGCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (89 bp):
AATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTA
GATATAAAAGGATTATTAAATTCC
Found at i:89879 original size:17 final size:17
Alignment explanation
Indices: 89857--89964 Score: 65
Period size: 17 Copynumber: 6.2 Consensus size: 17
89847 TTAATTATTT
*
89857 ACTAGTTAAATGAATGA
1 ACTAGTTAAATCAATGA
*
89874 ACTAGTTTAATCAATGA
1 ACTAGTTAAATCAATGA
* * *
89891 ACTAACTTTATTCAATGA
1 ACT-AGTTAAATCAATGA
* * * *
89909 ACTTG-TAGACTTGAATTA
1 ACTAGTTA-A-ATCAATGA
* * *
89927 ACTACTTTAATTAATGA
1 ACTAGTTAAATCAATGA
*
89944 ACTAGTTTAATCAATGA
1 ACTAGTTAAATCAATGA
89961 ACTA
1 ACTA
89965 CTGGTATGAT
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
16 1 0.01
17 43 0.61
18 25 0.36
19 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (17 bp):
ACTAGTTAAATCAATGA
Found at i:92235 original size:16 final size:17
Alignment explanation
Indices: 92214--92254 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
92204 TACAAATATT
92214 TTTAAAACAA-TAGCAA
1 TTTAAAACAAGTAGCAA
*
92230 TTTAAAA-AAGTAGCAG
1 TTTAAAACAAGTAGCAA
92246 TTTAAAACA
1 TTTAAAACA
92255 TATTTACCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (17 bp):
TTTAAAACAAGTAGCAA
Found at i:92407 original size:38 final size:38
Alignment explanation
Indices: 92338--92410 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
92328 TGGAAAACGA
*
92338 TAAGGTCTTATCCTGTCCAAACAATAGAGGAGCCTGGG
1 TAAGGTCTTATCCTGTCCAAACAATAAAGGAGCCTGGG
* * *
92376 TAAGGTCTTAT-CTCGTGCACACAGTAAAGGAGCCT
1 TAAGGTCTTATCCT-GTCCAAACAATAAAGGAGCCT
92411 TGGGAAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.07
38 28 0.93
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (38 bp):
TAAGGTCTTATCCTGTCCAAACAATAAAGGAGCCTGGG
Found at i:94765 original size:20 final size:20
Alignment explanation
Indices: 94706--94768 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
94696 TAAAAAATAG
*
94706 AAATAGAGTTTAATTGCAAA
1 AAATAGAGTTTAATTGCGAA
94726 AAATAGAGTTTAATTGCGAA
1 AAATAGAGTTTAATTGCGAA
*
94746 AAATAGAGTTTAATTACGAA
1 AAATAGAGTTTAATTGCGAA
94766 AAA
1 AAA
94769 CATATCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.29
Consensus pattern (20 bp):
AAATAGAGTTTAATTGCGAA
Found at i:96912 original size:45 final size:45
Alignment explanation
Indices: 96805--96975 Score: 159
Period size: 45 Copynumber: 3.9 Consensus size: 45
96795 CAAAGCATAT
** * * * * * *
96805 GAGCCTGCAAAAAGGGTAAGGTCTTACCCT-TGCATATAGCAAAA
1 GAGCCTGGGAAAATGGTAAGGTCTTATCCTGTGCACATAACAGAC
* * * * *
96849 GAGCCT-AGAAAATTGTAAGGTCTTTTCATGTGCACATAACAGTC
1 GAGCCTGGGAAAATGGTAAGGTCTTATCCTGTGCACATAACAGAC
* * *
96893 GAGCCTGGGAAAATGGTAAGGTCTTATCCTGTGCACACAGCAGAG
1 GAGCCTGGGAAAATGGTAAGGTCTTATCCTGTGCACATAACAGAC
* *
96938 GAGTCTGGGCAAATGGTAAGGTCTTATCCT-TGCACATA
1 GAGCCTGGGAAAATGGTAAGGTCTTATCCTGTGCACATA
96976 GCAAAGTAGC
Statistics
Matches: 102, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
43 16 0.16
44 28 0.27
45 58 0.57
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (45 bp):
GAGCCTGGGAAAATGGTAAGGTCTTATCCTGTGCACATAACAGAC
Found at i:97012 original size:39 final size:39
Alignment explanation
Indices: 96969--97049 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
96959 TCTTATCCTT
* * *
96969 GCACATAGCAAAGTAGCCTGCGATAAGGACTTACCCTGA
1 GCACATAACAAAGGAGCCTGCGATAAGGACTTACCCTAA
* *
97008 GCACATAACCAAGGAGCCTGCGGTAAGGACTTACCCTAA
1 GCACATAACAAAGGAGCCTGCGATAAGGACTTACCCTAA
97047 GCA
1 GCA
97050 TAAAGCCGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.16
Consensus pattern (39 bp):
GCACATAACAAAGGAGCCTGCGATAAGGACTTACCCTAA
Found at i:100823 original size:17 final size:17
Alignment explanation
Indices: 100801--100906 Score: 63
Period size: 17 Copynumber: 6.1 Consensus size: 17
100791 CAATTAGAGT
100801 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
100818 TAGTTTAATTAATTATC
1 TAGTTTAATAAATGAAC
*
100835 TAAGTTTAATCAATGAAC
1 T-AGTTTAATAAATGAAC
* *
100853 T--TATAATATTGAAAGAAC
1 TAGTTTAATA---AATGAAC
* * * *
100871 TACTTTGATGAATTAAC
1 TAGTTTAATAAATGAAC
*
100888 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
100905 TA
1 TA
100907 CTTAGTTAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
15 5 0.08
17 35 0.54
18 21 0.32
20 4 0.06
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Done.