Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397296.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_84.0, 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: 311483
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.27
Warning! 58532 characters in sequence are not A, C, G, or T
Found at i:4073 original size:30 final size:30
Alignment explanation
Indices: 4037--4102 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
4027 CTTGCATTTT
4037 AAATCATTTAACAAATGAATTTAACTATGC
1 AAATCATTTAACAAATGAATTTAACTATGC
*
4067 AAATCATTTAACAAATGCATTTAACTATGC
1 AAATCATTTAACAAATGAATTTAACTATGC
*
4097 ATATCA
1 AAATCA
4103 CACAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (30 bp):
AAATCATTTAACAAATGAATTTAACTATGC
Found at i:8086 original size:27 final size:28
Alignment explanation
Indices: 8043--8097 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
8033 GCCTAGGCAC
* * *
8043 ATATAACAACCTGTGG-CCTTGCCATGT
1 ATATAACAAACTATGGCCCTAGCCATGT
8070 ATATAACAAACTATGGCCCTAGCCATGT
1 ATATAACAAACTATGGCCCTAGCCATGT
8098 CTAATAGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (28 bp):
ATATAACAAACTATGGCCCTAGCCATGT
Found at i:16500 original size:18 final size:18
Alignment explanation
Indices: 16474--16508 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
16464 AAAGATGAAG
16474 AAAAGGAAAAGAAAGAAAC
1 AAAAGGAAAAG-AAGAAAC
16493 AAAA-GAAAAGAAGAAA
1 AAAAGGAAAAGAAGAAA
16509 AATTTAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAGGAAAAGAAGAAAC
Found at i:38065 original size:19 final size:19
Alignment explanation
Indices: 38041--38082 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38031 AAGTTATCTC
* *
38041 AATTAGGATCTAGCTTTAA
1 AATTAGCATCAAGCTTTAA
*
38060 AATTAGCATCAAGCTTTAT
1 AATTAGCATCAAGCTTTAA
38079 AATT
1 AATT
38083 GTCTATTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
AATTAGCATCAAGCTTTAA
Found at i:38792 original size:18 final size:19
Alignment explanation
Indices: 38766--38813 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
38756 GTGATAAGTG
*
38766 AAAAGAATATTTT-GAAAT
1 AAAATAATATTTTAGAAAT
*
38784 AAAATAATATTTTATAAAT
1 AAAATAATATTTTAGAAAT
*
38803 AAAATATTATT
1 AAAATAATATT
38814 AAAATATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTAGAAAT
Found at i:52990 original size:16 final size:16
Alignment explanation
Indices: 52969--53001 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52959 CCTTAGGGAT
52969 TAGCAATCACATGGAC
1 TAGCAATCACATGGAC
52985 TAGCAATCACATGGAC
1 TAGCAATCACATGGAC
53001 T
1 T
53002 CCTTTAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (16 bp):
TAGCAATCACATGGAC
Found at i:62434 original size:38 final size:37
Alignment explanation
Indices: 62384--62457 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
62374 GTATCCACTT
62384 TTTTTAAGAAAAAGAGTTTTTCTTACT-TTAAAATTTTG
1 TTTTTAAGAAAAAGA-TTTTTCTTA-TATTAAAATTTTG
*
62422 TTTTTATA-AAAAATATTTTTCTTATATTAAAATTTT
1 TTTTTA-AGAAAAAGATTTTTCTTATATTAAAATTTT
62458 TTATATTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 1 0.03
37 19 0.58
38 12 0.36
39 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (37 bp):
TTTTTAAGAAAAAGATTTTTCTTATATTAAAATTTTG
Found at i:62458 original size:18 final size:18
Alignment explanation
Indices: 62400--62459 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
62390 AGAAAAAGAG
62400 TTTTTCTTACT-TTAAAAT
1 TTTTTCTTA-TATTAAAAT
* *
62418 TTTGTTTTTATA-AAAAAT
1 TTT-TTCTTATATTAAAAT
62436 ATTTTTCTTATATTAAAAT
1 -TTTTTCTTATATTAAAAT
62455 TTTTT
1 TTTTT
62460 ATATTAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTCTTATATTAAAAT
Found at i:62471 original size:37 final size:37
Alignment explanation
Indices: 62384--62471 Score: 92
Period size: 37 Copynumber: 2.3 Consensus size: 37
62374 GTATCCACTT
62384 TTTTTAAGAAAAAGAGTTTTTCTTACTTTAAAATTTTG
1 TTTTT-AGAAAAAGAGTTTTTCTTACTTTAAAATTTTG
* *
62422 TTTTTATAAAAA-ATATTTTTCTTA-TATTAAAATTTT-
1 TTTTTAGAAAAAGA-GTTTTTCTTACT-TTAAAATTTTG
62458 TTATATTAGAAAAA
1 TT-T-TTAGAAAAA
62472 AGGAGGAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
36 4 0.09
37 26 0.60
38 13 0.30
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (37 bp):
TTTTTAGAAAAAGAGTTTTTCTTACTTTAAAATTTTG
Found at i:65150 original size:35 final size:35
Alignment explanation
Indices: 65105--65264 Score: 221
Period size: 35 Copynumber: 4.6 Consensus size: 35
65095 CCAAGTTTTT
* *
65105 ACAATGGCTTTTCACAGGCTCAGCCACAACCTTCT
1 ACAATGGCTTTTCAAAGGCTCAGCCACAACCTTCA
*
65140 ACAATGGCTTTTCAAAGGCTCAGCTACAACCTTCA
1 ACAATGGCTTTTCAAAGGCTCAGCCACAACCTTCA
* ** * *
65175 ACAATGGGTTTTCAAAACCTGAACCACAACCTTCA
1 ACAATGGCTTTTCAAAGGCTCAGCCACAACCTTCA
* *
65210 ACAATGGCTTTTCAAAAGCTCAGCCATAACCTTCA
1 ACAATGGCTTTTCAAAGGCTCAGCCACAACCTTCA
*
65245 ACAATGGTTTTTCAAAGGCT
1 ACAATGGCTTTTCAAAGGCT
65265 GANNNNNNNN
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 109 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (35 bp):
ACAATGGCTTTTCAAAGGCTCAGCCACAACCTTCA
Found at i:69873 original size:19 final size:20
Alignment explanation
Indices: 69849--69886 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
69839 TCCCTTAAGG
69849 TTTAAACA-AATTCTAAAAC
1 TTTAAACATAATTCTAAAAC
*
69868 TTTAAACATAGTTCTAAAA
1 TTTAAACATAATTCTAAAA
69887 TGTCCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (20 bp):
TTTAAACATAATTCTAAAAC
Found at i:77953 original size:68 final size:68
Alignment explanation
Indices: 77632--77937 Score: 461
Period size: 68 Copynumber: 4.5 Consensus size: 68
77622 TCTCATAAGG
* * * *
77632 TATATAGAAT-TACATCATATACATAATCTCATGGCATTCTTCATACTTTTTCAATCATCTCATG
1 TATATGGAATATACATCATATACATAATCTAATGGCATTCATCATACTTTCTCAATCATCTCATG
77696 TAA
66 TAA
* * * *
77699 TATATGGAATAGACATCATATACACAATCTAATGGCATTCATCATGCTTTCTCAATAATCTCATG
1 TATATGGAATATACATCATATACATAATCTAATGGCATTCATCATACTTTCTCAATCATCTCATG
*
77764 TAG
66 TAA
* * * *
77767 TATATGGAATATATATCATATACATAATCTAATGGCATTCATCATTCTTTCTTAATCATCTCACG
1 TATATGGAATATACATCATATACATAATCTAATGGCATTCATCATACTTTCTCAATCATCTCATG
*
77832 TAG
66 TAA
*
77835 TATATGGAATATACATCATATACATAATCTAATGGCATTCATCATGCTTTCTCAATCATCTCATG
1 TATATGGAATATACATCATATACATAATCTAATGGCATTCATCATACTTTCTCAATCATCTCATG
77900 TAA
66 TAA
*
77903 TATATGGAATATACATCATATACATAATTTAATGG
1 TATATGGAATATACATCATATACATAATCTAATGG
77938 ATTTCTTTAT
Statistics
Matches: 216, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
67 9 0.04
68 207 0.96
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (68 bp):
TATATGGAATATACATCATATACATAATCTAATGGCATTCATCATACTTTCTCAATCATCTCATG
TAA
Found at i:92305 original size:18 final size:19
Alignment explanation
Indices: 92278--92324 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
92268 CGATGGGCGG
92278 AAAA-AATATTTT-TGAAT
1 AAAATAATATTTTATGAAT
92295 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATGAAT
92314 AAAATAATATT
1 AAAATAATATT
92325 AAANNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 4 0.14
18 8 0.29
19 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATGAAT
Found at i:110451 original size:24 final size:23
Alignment explanation
Indices: 110411--110455 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
110401 ATTATTAACC
*
110411 TAAACTAAACATTTAAACATAAAT
1 TAAACTAAACATATAAA-ATAAAT
110435 TAAACTAAAC-TAATAAAATAA
1 TAAACTAAACAT-ATAAAATAA
110456 CTGAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAACTAAACATATAAAATAAAT
Found at i:116464 original size:28 final size:28
Alignment explanation
Indices: 116431--116540 Score: 98
Period size: 28 Copynumber: 3.9 Consensus size: 28
116421 AAGATATTTC
* *
116431 TTTTGTTACACGCCTTGTATGATTTCTA
1 TTTTGTTACACACCTTGTATAATTTCTA
* * *
116459 TTTTGTTAGACACATTTTATAATTTCTA
1 TTTTGTTACACACCTTGTATAATTTCTA
** ** *
116487 TTTCATTACATGCCCTG-ACTAATTTCTA
1 TTTTGTTACACACCTTGTA-TAATTTCTA
116515 TTTTGTTACACACCTTG-ACTAATTTC
1 TTTTGTTACACACCTTGTA-TAATTTC
116541 CACTTTTGGT
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
27 1 0.02
28 62 0.98
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (28 bp):
TTTTGTTACACACCTTGTATAATTTCTA
Found at i:116854 original size:28 final size:28
Alignment explanation
Indices: 116821--116886 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
116811 AACATATTTC
* ** *
116821 TTTTGTTACACGCTTTGACTGATTTCTA
1 TTTTGTTACACACCCTGACTAATTTCTA
116849 TTTTGTTACACACCCTGACTAATTTCTA
1 TTTTGTTACACACCCTGACTAATTTCTA
*
116877 TTTTCTTACA
1 TTTTGTTACA
116887 TGCCATTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.48
Consensus pattern (28 bp):
TTTTGTTACACACCCTGACTAATTTCTA
Found at i:129151 original size:18 final size:19
Alignment explanation
Indices: 129125--129172 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
129115 GTAACAAGTA
*
129125 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
129143 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
*
129162 AAAATATTATT
1 AAAATAATATT
129173 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:129447 original size:77 final size:77
Alignment explanation
Indices: 129360--129504 Score: 263
Period size: 77 Copynumber: 1.9 Consensus size: 77
129350 ACACGTTGAT
129360 GGGTGCAAACTTTATATTATATTTATACACATATAAAGGAAGGAGAATATAAGAAAATTAGAATT
1 GGGTGCAAACTTTATATTATATTTATACACATATAAAGGAAGGAGAATATAAGAAAATTAGAATT
129425 TAAAGATTAATG
66 TAAAGATTAATG
* * *
129437 GGGTGTAAACTTTATATTATATTTGTACACATGTAAAGGAAGGAGAATATAAGAAAATTAGAATT
1 GGGTGCAAACTTTATATTATATTTATACACATATAAAGGAAGGAGAATATAAGAAAATTAGAATT
129502 TAA
66 TAA
129505 GGAATGATGG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 65 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.32
Consensus pattern (77 bp):
GGGTGCAAACTTTATATTATATTTATACACATATAAAGGAAGGAGAATATAAGAAAATTAGAATT
TAAAGATTAATG
Found at i:133340 original size:16 final size:16
Alignment explanation
Indices: 133319--133351 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
133309 AATGATATTC
133319 TGAAAAAT-TATAACTT
1 TGAAAAATATAT-ACTT
133335 TGAAAAATATATACTT
1 TGAAAAATATATACTT
133351 T
1 T
133352 CATACTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TGAAAAATATATACTT
Found at i:145970 original size:22 final size:22
Alignment explanation
Indices: 145939--145981 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
145929 AATAATAACT
145939 TTTGTTGAAAATGTATCGATACA
1 TTTGTTG-AAATGTATCGATACA
145962 TTTG-TGAAATGTATCGATAC
1 TTTGTTGAAATGTATCGATAC
145982 TTTTAGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.70
22 2 0.10
23 4 0.20
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
TTTGTTGAAATGTATCGATACA
Found at i:146003 original size:61 final size:59
Alignment explanation
Indices: 145875--146004 Score: 136
Period size: 61 Copynumber: 2.1 Consensus size: 59
145865 AGGGTTTTGA
*** * *
145875 CATTTTGCTTAAAATGTATCGATACATATGTCTGTGTATTGATACTTTTGAGATAATAAT
1 CATTTTG-TTAAAATGTATCGATACATATGTAAATGTATCGATACTTTTGAGATAATAAG
* * *
145935 AACTTTTGTTGAAAATGTATCGATACATTTGTGAAATGTATCGATACTTTT-AGGTCAATAAG
1 CA-TTTTGTT-AAAATGTATCGATACATATGT-AAATGTATCGATACTTTTGAGAT-AATAAG
145997 CATTTTGT
1 CATTTTGT
146005 CTTAATTCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
60 3 0.05
61 34 0.60
62 20 0.35
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (59 bp):
CATTTTGTTAAAATGTATCGATACATATGTAAATGTATCGATACTTTTGAGATAATAAG
Found at i:146780 original size:32 final size:32
Alignment explanation
Indices: 146739--146803 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
146729 CTGAAGGCCA
146739 TGTAATATCAGTAAATGAAACCCAAAATAAAC
1 TGTAATATCAGTAAATGAAACCCAAAATAAAC
146771 TGTAATATCAGTAAATGAAACCCAAAATAAAC
1 TGTAATATCAGTAAATGAAACCCAAAATAAAC
146803 T
1 T
146804 ATCATGAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.23
Consensus pattern (32 bp):
TGTAATATCAGTAAATGAAACCCAAAATAAAC
Found at i:149919 original size:35 final size:35
Alignment explanation
Indices: 149857--149934 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
149847 NNNNNNNNNN
* *
149857 ATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTG
1 ATTAAA-TTATTTAATCAAATTATTGGGCCTAATTG
* *
149893 ATTAAATTATTTAATTAAATTTTTGGGCCTAATTG
1 ATTAAATTATTTAATCAAATTATTGGGCCTAATTG
149928 ATTAAAT
1 ATTAAAT
149935 CAAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
35 32 0.84
36 6 0.16
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (35 bp):
ATTAAATTATTTAATCAAATTATTGGGCCTAATTG
Found at i:152865 original size:16 final size:18
Alignment explanation
Indices: 152842--152881 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
152832 ATTACATCGT
152842 ATAAAACCATTA-ATTAA
1 ATAAAACCATTAGATTAA
152859 A-AAAACCATTAGATTAA
1 ATAAAACCATTAGATTAA
152876 ATAAAA
1 ATAAAA
152882 TAAATATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (18 bp):
ATAAAACCATTAGATTAA
Found at i:158105 original size:31 final size:31
Alignment explanation
Indices: 158041--158374 Score: 188
Period size: 31 Copynumber: 10.8 Consensus size: 31
158031 TTATGTGGTC
* * * * *
158041 ACACGCTGAGTGGTGGCAGATTTGTGCCATG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* *
158072 ACATGCTGAGTGCTAGCAGATATATGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * * ***
158103 ACATGTTGAGTGCTACCAGATTTAAAACGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * ** **
158134 ACACGTTGGGTGAAAGCAGATTTATGG-GACC
1 ACACGCTGAGTGCTAGCAGATTTATGGCG-TG
* * * *
158165 ACACGGTGAGTGGTGGCA-A-ATATGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * * * * *
158194 AAACTCTAAGTGCTACCAAATATATGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* ** * *
158225 ACACACTGAGTGAAAGCAGATTTATGGGGTC
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * * * * *
158256 ACACTCTGAGTGATGGCAGATTTGTGCCATG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * *
158287 ACACGCTAAGTGCTAGCAGATATATGGCATG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
** * *
158318 ACACATTGAGTGCTACCAGATTTAGGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* **
158349 ACACGCTGGGTGAAAGCAGATTTATG
1 ACACGCTGAGTGCTAGCAGATTTATG
158375 AGGTCACACA
Statistics
Matches: 222, Mismatches: 77, Indels: 8
0.72 0.25 0.03
Matches are distributed among these distances:
29 16 0.07
30 4 0.02
31 202 0.91
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (31 bp):
ACACGCTGAGTGCTAGCAGATTTATGGCGTG
Found at i:158259 original size:91 final size:93
Alignment explanation
Indices: 158143--158329 Score: 234
Period size: 93 Copynumber: 2.0 Consensus size: 93
158133 GACACGTTGG
* * * *
158143 GTGAAAGCAGATTTATGGGACCACACGGTGAGTGGTGGCAAATATG-G-CGTGAAACTCTAAGTG
1 GTGAAAGCAGATTTATGGGACCACACGCTGAGTGATGGCAAATATGTGCCATGAAACGCTAAGTG
*
158206 CTACCAAATATATGGCGTGACACACTGA
66 CTACCAAATATATGGCATGACACACTGA
** * * * *
158234 GTGAAAGCAGATTTATGGGGTCACACTCTGAGTGATGGCAGATTTGTGCCATGACACGCTAAGTG
1 GTGAAAGCAGATTTATGGGACCACACGCTGAGTGATGGCAAATATGTGCCATGAAACGCTAAGTG
* * *
158299 CTAGCAGATATATGGCATGACACATTGA
66 CTACCAAATATATGGCATGACACACTGA
158327 GTG
1 GTG
158330 CTACCAGATT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
91 39 0.49
92 1 0.01
93 40 0.50
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (93 bp):
GTGAAAGCAGATTTATGGGACCACACGCTGAGTGATGGCAAATATGTGCCATGAAACGCTAAGTG
CTACCAAATATATGGCATGACACACTGA
Found at i:158368 original size:93 final size:93
Alignment explanation
Indices: 158199--158371 Score: 222
Period size: 93 Copynumber: 1.9 Consensus size: 93
158189 GCGTGAAACT
* * *
158199 CTAAGTGCTACCAAATATATGGCGTGACACACTGAGTGAAAGCAGATTTATGGGGTCACACTCTG
1 CTAAGTGCTACCAAATATATGGCATGACACACTGAGTGAAACCAGATTTATGGGGTCACACGCTG
**
158264 AGTGATGGCAGATTTGTGCCATGACACG
66 AGTGAAAGCAGATTTGTGCCATGACACG
* * * ** *
158292 CTAAGTGCTAGCAGATATATGGCATGACACATTGAGTGCTACCAGATTTA-GGGCGTGACACGCT
1 CTAAGTGCTACCAAATATATGGCATGACACACTGAGTGAAACCAGATTTATGGG-GTCACACGCT
*
158356 GGGTGAAAGCAGATTT
65 GAGTGAAAGCAGATTT
158372 ATGAGGTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 3 0.04
93 64 0.96
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (93 bp):
CTAAGTGCTACCAAATATATGGCATGACACACTGAGTGAAACCAGATTTATGGGGTCACACGCTG
AGTGAAAGCAGATTTGTGCCATGACACG
Found at i:158420 original size:215 final size:215
Alignment explanation
Indices: 158031--158522 Score: 646
Period size: 215 Copynumber: 2.3 Consensus size: 215
158021 NNNNNNNNNN
* * * *
158031 TTATGTGGTCACACGCTGAGTGGTGGCAGATTTGTGCCATGACATGCTGAGTGCTAGCAGATATA
1 TTATGGGGTCACACTCTGAGTGATGGCAGATTTGTGCCATGACACGCTGAGTGCTAGCAGATATA
* ** *
158096 TGGCGTGACATGTTGAGTGCTACCAGATTTAAAACGTGACACGTTGGGTGAAAGCAGATTTATGG
66 TGGCATGACACATTGAGTGCTACCAGATTTAAAACGTGACACGCTGGGTGAAAGCAGATTTATGG
* *
158161 GACCACACGGTGAGTGGTGGCAAATATGGCGTGAAACTCTAAGTGCTACCAAATATATGGCGTGA
131 GACCACACAGTGAGTGGTGGCAAATATGGCGTGAAACTCTAAGTGCTACCAAATATATGGCATGA
*
158226 CACACTGAGTGAAAGCAGAT
196 CACACTAAGTGAAAGCAGAT
*
158246 TTATGGGGTCACACTCTGAGTGATGGCAGATTTGTGCCATGACACGCTAAGTGCTAGCAGATATA
1 TTATGGGGTCACACTCTGAGTGATGGCAGATTTGTGCCATGACACGCTGAGTGCTAGCAGATATA
***
158311 TGGCATGACACATTGAGTGCTACCAGATTTAGGGCGTGACACGCTGGGTGAAAGCAGATTTATGA
66 TGGCATGACACATTGAGTGCTACCAGATTTAAAACGTGACACGCTGGGTGAAAGCAGATTTATG-
* * ********** * *
158376 GG-TCACACATTGAGTGGTGGCAAATATGNNNNNNNNNNCTAAGTGCTAGCAGATATATGGCATG
130 GGACCACACAGTGAGTGGTGGCAAATATGGCGTGAAACTCTAAGTGCTACCAAATATATGGCATG
158440 ACACACTAAGTGAAAGCAGAT
195 ACACACTAAGTGAAAGCAGAT
* * * * *
158461 TTATGGAGTCACACGT-TGAGTGCTGGCAGATTTGTACCGTGACACACTGAGTGCTAGCAGAT
1 TTATGGGGTCACAC-TCTGAGTGATGGCAGATTTGTGCCATGACACGCTGAGTGCTAGCAGAT
158523 NNNNNNNNNN
Statistics
Matches: 240, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
215 237 0.99
216 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.25
Consensus pattern (215 bp):
TTATGGGGTCACACTCTGAGTGATGGCAGATTTGTGCCATGACACGCTGAGTGCTAGCAGATATA
TGGCATGACACATTGAGTGCTACCAGATTTAAAACGTGACACGCTGGGTGAAAGCAGATTTATGG
GACCACACAGTGAGTGGTGGCAAATATGGCGTGAAACTCTAAGTGCTACCAAATATATGGCATGA
CACACTAAGTGAAAGCAGAT
Found at i:158597 original size:29 final size:30
Alignment explanation
Indices: 158555--158629 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
158545 NNNNNNNNNN
* * *
158555 TATGGGATCACACGCTGAGTGGTGGCAG-A
1 TATGGCATGACACGCTAAGTGGTGGCAGAA
158584 TATGGCATGACACGCTAAGTGGTGGCAGATA
1 TATGGCATGACACGCTAAGTGGTGGCAGA-A
*
158615 TATGGCGTGACACGC
1 TATGGCATGACACGC
158630 CANNNNNNNN
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (30 bp):
TATGGCATGACACGCTAAGTGGTGGCAGAA
Found at i:160458 original size:31 final size:31
Alignment explanation
Indices: 160423--160648 Score: 281
Period size: 31 Copynumber: 7.3 Consensus size: 31
160413 NNNNNNNNNN
* * *
160423 TTGACTTGTTATGCATTGTGTGTAACAACAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
* *
160454 TTGACTGGATATGCATGGTGTGTAACAACAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
* * *
160485 TTGGCTTGTTATGCATGGCGTGTAATAACAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
*
160516 TTGACTTGATATGCATGGCGTATAACAACAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
* ** * *
160547 TTGACTTGTTATGCATTACATGTAACAGCAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
* * *
160578 TTTACTTGATATGCATGGTGTGTAACAGCAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
*
160609 TTTACTTGATATGCATGGCGTGTAACAACAT
1 TTGACTTGATATGCATGGCGTGTAACAACAT
*
160640 TTTACTTGA
1 TTGACTTGA
160649 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 169 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (31 bp):
TTGACTTGATATGCATGGCGTGTAACAACAT
Found at i:167139 original size:73 final size:73
Alignment explanation
Indices: 166984--167158 Score: 226
Period size: 73 Copynumber: 2.4 Consensus size: 73
166974 ATAGATCATT
* * *** *
166984 GCTTGCCCTGTTGTTTAACACAACGTTCTGCTCTAACTCATTACTATTGTCTGTCTTCGTTTCTT
1 GCTTGCTCTGTTGTTTAACACAACGTTCTGCTCTAACTCATCACTATTGTCTGTCTTCCCGTCCT
* *
167049 TTTGTTTC
66 TTTATATC
* * *
167057 GCTTTCTCTGTTGTTTAAGACGACGTTCTGCTCTAACTCATCACTATTGTCT-TCCTTCCCGTCC
1 GCTTGCTCTGTTGTTTAACACAACGTTCTGCTCTAACTCATCACTATTGTCTGT-CTTCCCGTCC
*
167121 TTTTATATG
65 TTTTATATC
167130 GCTTGCTCTGTTGTTTAACACAACGTTCT
1 GCTTGCTCTGTTGTTTAACACAACGTTCT
167159 TTGTTTTCAT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 1 0.01
73 85 0.99
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.45
Consensus pattern (73 bp):
GCTTGCTCTGTTGTTTAACACAACGTTCTGCTCTAACTCATCACTATTGTCTGTCTTCCCGTCCT
TTTATATC
Found at i:177595 original size:19 final size:18
Alignment explanation
Indices: 177547--177600 Score: 90
Period size: 18 Copynumber: 2.9 Consensus size: 18
177537 AGAAAGAATT
177547 TTTTTGAATAAAATAATA
1 TTTTTGAATAAAATAATA
*
177565 TTTTTAAATAAAATAATA
1 TTTTTGAATAAAATAATA
177583 TTTTATGAATAAAATAAT
1 TTTT-TGAATAAAATAAT
177601 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
18 21 0.64
19 12 0.36
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTTTTGAATAAAATAATA
Found at i:193860 original size:15 final size:15
Alignment explanation
Indices: 193840--193868 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
193830 TCATGTAAAG
193840 ATCTCTTTTGTCGAA
1 ATCTCTTTTGTCGAA
193855 ATCTCTTTTGTCGA
1 ATCTCTTTTGTCGA
193869 TTTTAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
ATCTCTTTTGTCGAA
Found at i:219564 original size:68 final size:68
Alignment explanation
Indices: 219455--219591 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 68
219445 ACATATAACT
* * *
219455 AAGGAAATATTTCCTAGCTTAGTGAGCAAGTTTTCAAGCCTAACTTTAACTTAAAGAATGTGGCC
1 AAGGAAATATTCCCTAGCTTAGTGAGCAAGTTTCCAAGCCTAACTTCAACTTAAAGAATGTGGCC
219520 CCC
66 CCC
* **
219523 AAGGAAATATTCCCTAGCTTGGTGAGCAAGTTTCCAAGCCTAACTTCAGTTTAAAGAATGTGGCC
1 AAGGAAATATTCCCTAGCTTAGTGAGCAAGTTTCCAAGCCTAACTTCAACTTAAAGAATGTGGCC
219588 CCC
66 CCC
219591 A
1 A
219592 TGCAACCTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (68 bp):
AAGGAAATATTCCCTAGCTTAGTGAGCAAGTTTCCAAGCCTAACTTCAACTTAAAGAATGTGGCC
CCC
Found at i:223167 original size:21 final size:21
Alignment explanation
Indices: 223141--223192 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
223131 GGTTCACATG
223141 AATAGATGAAA-AACATCTATT
1 AATAGAT-AAAGAACATCTATT
223162 AATAGATAAAGAACATCTATT
1 AATAGATAAAGAACATCTATT
*
223183 AATAAATAAA
1 AATAGATAAA
223193 CTCTAATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (21 bp):
AATAGATAAAGAACATCTATT
Found at i:227058 original size:14 final size:14
Alignment explanation
Indices: 227039--227086 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
227029 NNNNNNNNTT
*
227039 CTTTCTTTCCTCTC
1 CTTTCTTTCATCTC
* *
227053 CTTTCTCTT-TTCTT
1 CTTTCT-TTCATCTC
227067 CTTTCTTTCATCTC
1 CTTTCTTTCATCTC
227081 CTTTCT
1 CTTTCT
227087 CTTTCTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTCTTTCATCTC
Found at i:227071 original size:28 final size:27
Alignment explanation
Indices: 227037--227096 Score: 102
Period size: 28 Copynumber: 2.2 Consensus size: 27
227027 NNNNNNNNNN
*
227037 TTCTTTCTTTCCTCTCCTTTCTCTTTTC
1 TTCTTTCTTTCATCTCCTTTCTC-TTTC
227065 TTCTTTCTTTCATCTCCTTTCTCTTTC
1 TTCTTTCTTTCATCTCCTTTCTCTTTC
227092 TTCTT
1 TTCTT
227097 GGTTATGGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (27 bp):
TTCTTTCTTTCATCTCCTTTCTCTTTC
Found at i:230422 original size:18 final size:20
Alignment explanation
Indices: 230385--230422 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
230375 TCCAAAATTA
*
230385 ATATTTTTTCCTTGTTAAAT
1 ATATTTTTTCCTTGTGAAAT
230405 ATATTTTTT-CTTG-GAAAT
1 ATATTTTTTCCTTGTGAAAT
230423 TTATAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (20 bp):
ATATTTTTTCCTTGTGAAAT
Found at i:246013 original size:22 final size:22
Alignment explanation
Indices: 245971--246013 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
245961 GGTGGTCCAA
*
245971 TAAGAAACTAAAGAAACAAAAC
1 TAAGAAACTAAAAAAACAAAAC
*
245993 TAAGAAA-TAACAAAAAGAAAA
1 TAAGAAACTAA-AAAAACAAAA
246014 GGGAAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.09
Consensus pattern (22 bp):
TAAGAAACTAAAAAAACAAAAC
Found at i:256716 original size:45 final size:46
Alignment explanation
Indices: 256527--256702 Score: 174
Period size: 47 Copynumber: 3.8 Consensus size: 46
256517 NNNNNNNNNN
* * * ** * * *
256527 GACATGTCAAGGTTTAGGGTTTGTGACACACCATGGAGGGAATCTAT
1 GACATGTCAGGGTTCAGAGTTT-TGACATGCCATAGAAGGAATCTGT
* *
256574 GACACGTCAGGGTTCAGAGTTTATGACATGCCATAAAAGGAATCTGT
1 GACATGTCAGGGTTCAGAGTTT-TGACATGCCATAGAAGGAATCTGT
* * ** *
256621 GACATGCCTGGGTTCAGAGTTTTTGACATGCCACGGAGGGAATCTGT
1 GACATGTCAGGGTTCAGAG-TTTTGACATGCCATAGAAGGAATCTGT
*
256668 GACATGTAAGGGTTCAGAG-TTTGACATGCCATAGA
1 GACATGTCAGGGTTCAGAGTTTTGACATGCCATAGA
256703 TGAAATTCTT
Statistics
Matches: 105, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
45 14 0.13
47 88 0.84
48 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (46 bp):
GACATGTCAGGGTTCAGAGTTTTGACATGCCATAGAAGGAATCTGT
Found at i:256755 original size:92 final size:94
Alignment explanation
Indices: 256539--256765 Score: 255
Period size: 92 Copynumber: 2.4 Consensus size: 94
256529 CATGTCAAGG
** * * *
256539 TTTAGGGTTTGTGACACACCATGGAGGGAATCTATGACACGTCAGGGTTCAGAGTTTATGACATG
1 TTTAGGGTTTGTGACATGCCATGGAGGGAATCTGTGACATGTAAGGGTTCAGAGTTTATGACATG
* * **
256604 CCATAAAAGGAATCTGTGACATGCCTGGG
66 CCATAAAAGAAATCTGTGACATGCCAGCA
* * * *
256633 TTCAGAGTTTTTGACATGCCACGGAGGGAATCTGTGACATGTAAGGGTTCAGAG-TT-TGACATG
1 TTTAGGGTTTGTGACATGCCATGGAGGGAATCTGTGACATGTAAGGGTTCAGAGTTTATGACATG
* *
256696 CCATAGATGAAATTCT-TGACACT-CCAGCA
66 CCATAAAAGAAA-TCTGTGACA-TGCCAGCA
* *
256725 TTTAGGGTTTGTGACATGCCATGGATGGAATTTGTGACATG
1 TTTAGGGTTTGTGACATGCCATGGAGGGAATCTGTGACATG
256766 CCATGGATGG
Statistics
Matches: 110, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
92 59 0.54
93 6 0.05
94 45 0.41
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (94 bp):
TTTAGGGTTTGTGACATGCCATGGAGGGAATCTGTGACATGTAAGGGTTCAGAGTTTATGACATG
CCATAAAAGAAATCTGTGACATGCCAGCA
Found at i:256759 original size:23 final size:23
Alignment explanation
Indices: 256732--256791 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
256722 GCATTTAGGG
256732 TTTGTGACATGCCATGGATGGAA
1 TTTGTGACATGCCATGGATGGAA
256755 TTTGTGACATGCCATGGATGGAA
1 TTTGTGACATGCCATGGATGGAA
256778 TTTGTGACATGCCA
1 TTTGTGACATGCCA
256792 AGGTTTAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (23 bp):
TTTGTGACATGCCATGGATGGAA
Found at i:260325 original size:23 final size:22
Alignment explanation
Indices: 260299--260453 Score: 166
Period size: 23 Copynumber: 6.8 Consensus size: 22
260289 ATTATGGCGT
260299 AATGGGGTGACACGCCATGTCCC
1 AATGGGGTGACACGCCATG-CCC
* *
260322 AATGGGGTGACATGCTATGCGCC
1 AATGGGGTGACACGCCATGC-CC
* *
260345 AACGGGGTGACATGCCATGCCAC
1 AATGGGGTGACACGCCATGCC-C
*
260368 AATGGGGTGACACACCATGTCCC
1 AATGGGGTGACACGCCATG-CCC
***
260391 AATGTCCTGACACGCCATGCCCC
1 AATGGGGTGACACGCCATG-CCC
260414 AATGGGGTGACACGCCATGCCCC
1 AATGGGGTGACACGCCATG-CCC
* *
260437 AATTGGGTGACATGCCA
1 AATGGGGTGACACGCCA
260454 CATTGGACAT
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.02
23 108 0.96
24 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.17
Consensus pattern (22 bp):
AATGGGGTGACACGCCATGCCC
Found at i:260391 original size:69 final size:69
Alignment explanation
Indices: 260299--260448 Score: 201
Period size: 69 Copynumber: 2.2 Consensus size: 69
260289 ATTATGGCGT
* ** * * * *
260299 AATGGGGTGACACGCCATGTCCCAATGGGGTGACATGCTATGCGCCAACGGGGTGACATGCCATG
1 AATGGGGTGACACACCATGTCCCAATGGCCTGACACGCCATGCCCCAACGGGGTGACACGCCATG
260364 CCAC
66 CCAC
* *
260368 AATGGGGTGACACACCATGTCCCAATGTCCTGACACGCCATGCCCCAATGGGGTGACACGCCATG
1 AATGGGGTGACACACCATGTCCCAATGGCCTGACACGCCATGCCCCAACGGGGTGACACGCCATG
*
260433 CCCC
66 CCAC
*
260437 AATTGGGTGACA
1 AATGGGGTGACA
260449 TGCCACATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.17
Consensus pattern (69 bp):
AATGGGGTGACACACCATGTCCCAATGGCCTGACACGCCATGCCCCAACGGGGTGACACGCCATG
CCAC
Found at i:264264 original size:31 final size:31
Alignment explanation
Indices: 264226--264457 Score: 234
Period size: 31 Copynumber: 7.5 Consensus size: 31
264216 NNNNNNNNNN
264226 TGTTGTTACATGCCATGCATATCAAGAT-AAA
1 TGTTGTTACATGCCATGCATATCAAG-TCAAA
* * **
264257 TGTTGTTACACGCCATGGATATCAAGGAAAA
1 TGTTGTTACATGCCATGCATATCAAGTCAAA
* ** *
264288 TGTTGTTACATGCAATGCATATTGAGTAAAA
1 TGTTGTTACATGCCATGCATATCAAGTCAAA
* ** * * *
264319 TGTTGTCACACACTATGCATATCGAGTAAAA
1 TGTTGTTACATGCCATGCATATCAAGTCAAA
* * *
264350 TATTGTTACATGCAATGCATAACAAGTCAAA
1 TGTTGTTACATGCCATGCATATCAAGTCAAA
* *
264381 TGTTGTTACACAG-CATGCATAACAAGTCAAA
1 TGTTGTTACA-TGCCATGCATATCAAGTCAAA
* * *
264412 TGTTGTTACACGCAACGCATATCAAGTCAAA
1 TGTTGTTACATGCCATGCATATCAAGTCAAA
264443 TGTTGTTACATGCCA
1 TGTTGTTACATGCCA
264458 ACGCTGACAT
Statistics
Matches: 167, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.01
31 165 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (31 bp):
TGTTGTTACATGCCATGCATATCAAGTCAAA
Found at i:264296 original size:62 final size:62
Alignment explanation
Indices: 264226--264457 Score: 279
Period size: 62 Copynumber: 3.7 Consensus size: 62
264216 NNNNNNNNNN
* * *
264226 TGTTGTTACATGCCATGCATATCAAGAT-AAATGTTGTTACACGCCATGGATATCAAGGAAAA
1 TGTTGTTACATGCAATGCATATCAAG-TCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
** * * * * *
264288 TGTTGTTACATGCAATGCATATTGAGTAAAATGTTGTCACACACTATGCATATCGAGTAAAA
1 TGTTGTTACATGCAATGCATATCAAGTCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
* * * *
264350 TATTGTTACATGCAATGCATAACAAGTCAAATGTTGTTACACAG-CATGCATAACAAGTCAAA
1 TGTTGTTACATGCAATGCATATCAAGTCAAATGTTGTTACAC-GCCATGCATATCAAGTAAAA
* * *
264412 TGTTGTTACACGCAACGCATATCAAGTCAAATGTTGTTACATGCCA
1 TGTTGTTACATGCAATGCATATCAAGTCAAATGTTGTTACACGCCA
264458 ACGCTGACAT
Statistics
Matches: 142, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
61 2 0.01
62 140 0.99
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (62 bp):
TGTTGTTACATGCAATGCATATCAAGTCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
Found at i:270942 original size:22 final size:22
Alignment explanation
Indices: 270894--271058 Score: 145
Period size: 23 Copynumber: 7.3 Consensus size: 22
270884 GCACAGGGCG
*
270894 TGTAACATGTTGTGAACATGGCA
1 TGTAACAT-TTTTGAACATGGCA
*
270917 TGTAACAATTTTTGAAC-TTGCA
1 TGTAAC-ATTTTTGAACATGGCA
* *
270939 TGTAACACTTTTGAACATGGCG
1 TGTAACATTTTTGAACATGGCA
270961 TGTAACATTTTTGAACATGGCA
1 TGTAACATTTTTGAACATGGCA
* * *
270983 TGTATCATATTTTAAACATCGC-
1 TGTAACAT-TTTTGAACATGGCA
* * *
271005 GGCTAACAATTTTTGAAAATGGCG
1 TG-TAAC-ATTTTTGAACATGGCA
** *
271029 TGTAACATAATTGAAAAATGGCA
1 TGTAACATTTTTG-AACATGGCA
271052 TGTAACA
1 TGTAACA
271059 ACATNNNNNN
Statistics
Matches: 116, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
21 9 0.08
22 46 0.40
23 56 0.48
24 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
TGTAACATTTTTGAACATGGCA
Found at i:278043 original size:21 final size:21
Alignment explanation
Indices: 278017--278057 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
278007 ATGCAAAGAA
278017 AAAAGAAAAGAAAATAATGGC
1 AAAAGAAAAGAAAATAATGGC
* *
278038 AAAAGAAAAGACAATGATGG
1 AAAAGAAAAGAAAATAATGG
278058 TGGCGGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.22, T:0.10
Consensus pattern (21 bp):
AAAAGAAAAGAAAATAATGGC
Found at i:278331 original size:18 final size:20
Alignment explanation
Indices: 278290--278336 Score: 71
Period size: 18 Copynumber: 2.4 Consensus size: 20
278280 GGATCAGCTT
278290 GAAAGCAAAGTGAGAAAGGAA
1 GAAAG-AAAGTGAGAAAGGAA
278311 GAAAGAAAG-GAGAAA-GAA
1 GAAAGAAAGTGAGAAAGGAA
278329 GAAAGAAA
1 GAAAGAAA
278337 AGAAGACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
20 4 0.15
21 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (20 bp):
GAAAGAAAGTGAGAAAGGAA
Found at i:291182 original size:115 final size:115
Alignment explanation
Indices: 290976--291209 Score: 337
Period size: 115 Copynumber: 2.0 Consensus size: 115
290966 TATTTATTAT
* *
290976 ATATATAATAAAAACTAATCATTTGATGCAATTAATTAGAATATTTATTTACAAATTAGGTAAAT
1 ATATATAATAAAAACTAATCATTTGATGC-A--AATTAGAAAAGTTATTTACAAATTAGGTAAAT
* *
291041 CTTATTATTAGTTATAGTAAAAAAAGTTAAAAATGGTAATGT-AAAAATATAATA
63 CTTATTATAAGTTATAATAAAAAAAGTT-AAAATGGTAAT-TAAAAAATATAATA
* *
291095 ATATATTATGAAAACTAATCATTTGATGC-AATTAGAAAAGTTATTTACAAATTAGGTAAATCTT
1 ATATATAATAAAAACTAATCATTTGATGCAAATTAGAAAAGTTATTTACAAATTAGGTAAATCTT
* *
291159 ATTATAATTTATAATAAAAAAAGTTCAAATGGTAATTAAAAAATATAATA
66 ATTATAAGTTATAATAAAAAAAGTTAAAATGGTAATTAAAAAATATAATA
291209 A
1 A
291210 ATAAATGTCT
Statistics
Matches: 106, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
113 1 0.01
114 23 0.22
115 55 0.52
119 27 0.25
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (115 bp):
ATATATAATAAAAACTAATCATTTGATGCAAATTAGAAAAGTTATTTACAAATTAGGTAAATCTT
ATTATAAGTTATAATAAAAAAAGTTAAAATGGTAATTAAAAAATATAATA
Found at i:304483 original size:13 final size:13
Alignment explanation
Indices: 304465--304502 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
304455 GTAATAGACA
304465 AAGAAAGGAAATT
1 AAGAAAGGAAATT
304478 AAGAAAGGAAATT
1 AAGAAAGGAAATT
*
304491 AAGAAATGAAAT
1 AAGAAAGGAAAT
304503 CTATAGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (13 bp):
AAGAAAGGAAATT
Done.