Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1079
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: 410574
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:305128 original size:79 final size:80
Alignment explanation
Indices: 304994--305144 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 80
304984 TAAAATCAGA
** * * ** * *
304994 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAATATCCCCGATTAAGAAAAATTAATGTTTTAAAAATAAAACCGGAGTTGGAGTATCCCC
305059 TC-AAAAGTAACGGG
66 TCGAAAAGTAACGGG
*
305073 GTTGGAATATCCCCGATTAAGAAAAATTAATGTTTTAAAAATAAAACCGGAGTTGGAGTATCCTC
1 GTTGGAATATCCCCGATTAAGAAAAATTAATGTTTTAAAAATAAAACCGGAGTTGGAGTATCCCC
305138 TCGAAAA
66 TCGAAAA
305145 ATCTAGAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
79 58 0.94
80 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (80 bp):
GTTGGAATATCCCCGATTAAGAAAAATTAATGTTTTAAAAATAAAACCGGAGTTGGAGTATCCCC
TCGAAAAGTAACGGG
Found at i:307583 original size:19 final size:21
Alignment explanation
Indices: 307559--307607 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
307549 GATACACTGC
307559 ATCGATACA-TTACT-TATGT
1 ATCGATACATTTACTGTATGT
*
307578 ATCGATACATTTACTGTTTGT
1 ATCGATACATTTACTGTATGT
307599 ATCGATACA
1 ATCGATACA
307608 AATTATTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 13 0.48
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
ATCGATACATTTACTGTATGT
Found at i:309468 original size:11 final size:11
Alignment explanation
Indices: 309452--309512 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 11
309442 GGCGTCATCT
309452 ACAAAAAAAAA
1 ACAAAAAAAAA
*
309463 ACAAAAAAACA
1 ACAAAAAAAAA
*
309474 A-AAAAATAAA
1 ACAAAAAAAAA
* *
309484 A-AACAAACAA
1 ACAAAAAAAAA
*
309494 AC-AAAAAACA
1 ACAAAAAAAAA
309504 ACAAAAAAA
1 ACAAAAAAA
309513 GGGGGAAGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 22 0.56
11 17 0.44
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:309470 original size:8 final size:8
Alignment explanation
Indices: 309457--309512 Score: 69
Period size: 8 Copynumber: 6.9 Consensus size: 8
309447 CATCTACAAA
309457 AAAAAAAC
1 AAAAAAAC
309465 AAAAAAAC
1 AAAAAAAC
309473 AAAAAAA-
1 AAAAAAAC
*
309480 TAAAAAAC
1 AAAAAAAC
*
309488 AAACAAAC
1 AAAAAAAC
309496 AAAAAACAAC
1 -AAAAA-AAC
309506 AAAAAAA
1 AAAAAAA
309513 GGGGGAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
7 6 0.15
8 23 0.56
9 9 0.22
10 3 0.07
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:309478 original size:15 final size:15
Alignment explanation
Indices: 309457--309510 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
309447 CATCTACAAA
309457 AAAAAAACAAAAAAAC
1 AAAAAAAC-AAAAAAC
*
309473 AAAAAAATAAAAAAC
1 AAAAAAACAAAAAAC
*
309488 AAACAAACAAAAAAC
1 AAAAAAACAAAAAAC
309503 AACAAAAA
1 AA-AAAAA
309511 AAGGGGGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (15 bp):
AAAAAAACAAAAAAC
Found at i:309488 original size:23 final size:22
Alignment explanation
Indices: 309454--309510 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
309444 CGTCATCTAC
309454 AAAAAAAAAACAAAAAAACAAA
1 AAAAAAAAAACAAAAAAACAAA
*
309476 AAAATAAAAAACAAACAAACAAA
1 AAAA-AAAAAACAAAAAAACAAA
309499 AAACAACAAAAA
1 AAA-AA-AAAAA
309511 AAGGGGGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 4 0.13
23 21 0.68
24 6 0.19
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAACAAAAAAACAAA
Found at i:310858 original size:28 final size:28
Alignment explanation
Indices: 310818--310889 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
310808 TTCTCAAAGC
*
310818 CCACTAGTTAGTGGCACCTCTTCGAAGT
1 CCACAAGTTAGTGGCACCTCTTCGAAGT
* * *
310846 CCACAAGTTAGTGGCATCTTTTTGAAGT
1 CCACAAGTTAGTGGCACCTCTTCGAAGT
*
310874 CCACAA-TCAGTGGCAC
1 CCACAAGTTAGTGGCAC
310890 TTGCTGTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (28 bp):
CCACAAGTTAGTGGCACCTCTTCGAAGT
Found at i:311145 original size:32 final size:32
Alignment explanation
Indices: 311061--311359 Score: 360
Period size: 32 Copynumber: 9.4 Consensus size: 32
311051 CTAGTGGAAA
*
311061 AACCTTC-TCTAAAGCCCACACAAGTTGGTAGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
311093 AACCTTCTTCAAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
*
311126 AACCTTCTTCAAAGCCCACACAAGTTAGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * *
311158 AATCC--CTCCAAAGCCCATACAAGTCGGTGGC
1 AA-CCTTCTTCAAAGCCCACACAAGTTGGTGGC
* * *
311189 GATCCTT-TTAAAAGCCCACACAAGTTGTTGGC
1 -AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
*
311221 AACTTTC-TCTAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGC
* *
311253 AACCTTCTTCAAAGCCCATACAAGTCGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* *
311285 AACC-CCTCCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
* *
311316 AACCTTCTTTAAAGCCCACACAAGTCGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
*
311348 AACCCT-TTCAAA
1 AACCTTCTTCAAA
311360 AGCCTGCATA
Statistics
Matches: 228, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
31 61 0.27
32 130 0.57
33 37 0.16
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.21
Consensus pattern (32 bp):
AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
Found at i:311203 original size:63 final size:62
Alignment explanation
Indices: 311061--311353 Score: 365
Period size: 63 Copynumber: 4.6 Consensus size: 62
311051 CTAGTGGAAA
* *
311061 AACCTTC-TCTAAAGCCCACACAAGTTGGTAGCAACCTTCTTCAAAAGCCCACACAAGTTGGTGG
1 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGCAACC--C-TCCAAAGCCCACACAAGTTGGTGG
311125 C
62 C
* * *
311126 AACCTTCTTCAAAGCCCACACAAGTTAGTGGCAATCCCTCCAAAGCCCATACAAGTCGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGCAA-CCCTCCAAAGCCCACACAAGTTGGTGGC
* * * * *
311189 GATCCTT-TTAAAAGCCCACACAAGTTGTTGGCAACTTTCTCTAAAGCCCACACAAGTTGGTGGC
1 -AACCTTCTTCAAAGCCCACACAAGTTGGTGGCAAC--CCTCCAAAGCCCACACAAGTTGGTGGC
* *
311253 AACCTTCTTCAAAGCCCATACAAGTCGGTGGCAACCCCTCCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGCAA-CCCTCCAAAGCCCACACAAGTTGGTGGC
* *
311316 AACCTTCTTTAAAGCCCACACAAGTCGGTGGCAACCCT
1 AACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCT
311354 TTCAAAAGCC
Statistics
Matches: 199, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
62 5 0.03
63 108 0.54
64 52 0.26
65 30 0.15
66 4 0.02
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (62 bp):
AACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCCTCCAAAGCCCACACAAGTTGGTGGC
Found at i:311363 original size:95 final size:94
Alignment explanation
Indices: 311071--311359 Score: 382
Period size: 95 Copynumber: 3.0 Consensus size: 94
311061 AACCTTCTCT
* * * *
311071 AAAGCCCACACAAGTTGGTAGCAACCTTCTTCAAAAGCCCACACAAGTTGGTGGCAACCTTCTTC
1 AAAGCCCATACAAGTCGGTGGCAACC--CTTCAAAAGCCCACACAAGTTGGTGGCAACCTTCTTT
* *
311136 AAAGCCCACACAAGTTAGTGGCAATCCC-TCC
64 AAAGCCCACACAAGTTGGTGGCAA-CCCTTTC
* * * * * *
311167 AAAGCCCATACAAGTCGGTGGCGATCCTTTTAAAAGCCCACACAAGTTGTTGGCAACTTTCTCTA
1 AAAGCCCATACAAGTCGGTGGC-AACCCTTCAAAAGCCCACACAAGTTGGTGGCAACCTTCTTTA
*
311232 AAGCCCACACAAGTTGGTGGCAACCTTCTTC
65 AAGCCCACACAAGTTGGTGGCAACCCT-TTC
* *
311263 AAAGCCCATACAAGTCGGTGGCAACCCCTCCAAAGCCCACACAAGTTGGTGGCAACCTTCTTTAA
1 AAAGCCCATACAAGTCGGTGGCAACCCTTCAAAAGCCCACACAAGTTGGTGGCAACCTTCTTTAA
*
311328 AGCCCACACAAGTCGGTGGCAACCCTTTC
66 AGCCCACACAAGTTGGTGGCAACCCTTTC
311357 AAA
1 AAA
311360 AGCCTGCATA
Statistics
Matches: 167, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
94 8 0.05
95 113 0.68
96 43 0.26
97 3 0.02
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (94 bp):
AAAGCCCATACAAGTCGGTGGCAACCCTTCAAAAGCCCACACAAGTTGGTGGCAACCTTCTTTAA
AGCCCACACAAGTTGGTGGCAACCCTTTC
Found at i:311373 original size:127 final size:128
Alignment explanation
Indices: 311061--311363 Score: 441
Period size: 127 Copynumber: 2.4 Consensus size: 128
311051 CTAGTGGAAA
* *
311061 AACCTTCTCTAAAGCCCACACAAGTTGGTAGCAACCTTCTTCAAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTTAAAGCCCACACAAGTTGGTGGCAACCTT-TTCAAAAGCCCACACAAGTTGGTGGC
* * *
311126 AACCTTCTTCAAAGCCCACACAAGTTAGTGGCAATCCCTCCAAAGCCCATACAAGTCGGTGGCG
65 AACCTTCTTCAAAGCCCACACAAGTCAGTGGCAACCCCTCCAAAGCCCACACAAGTCGGTGGCG
* * * *
311190 ATCCTT-TTAAAAGCCCACACAAGTTGTTGGCAA-CTTTCTCTAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTTAAAGCCCACACAAGTTGGTGGCAACCTTT-TCAAAAGCCCACACAAGTTGGTGGC
* * *
311253 AACCTTCTTCAAAGCCCATACAAGTCGGTGGCAACCCCTCCAAAGCCCACACAAGTTGGTGGC-
65 AACCTTCTTCAAAGCCCACACAAGTCAGTGGCAACCCCTCCAAAGCCCACACAAGTCGGTGGCG
* *
311316 AACCTTCTTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAAGCC
1 AACCTTCTTTAAAGCCCACACAAGTTGGTGGCAACCTTTTCAAAAGCC
311364 TGCATAAGTT
Statistics
Matches: 153, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
126 6 0.04
127 116 0.76
128 26 0.17
129 5 0.03
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (128 bp):
AACCTTCTTTAAAGCCCACACAAGTTGGTGGCAACCTTTTCAAAAGCCCACACAAGTTGGTGGCA
ACCTTCTTCAAAGCCCACACAAGTCAGTGGCAACCCCTCCAAAGCCCACACAAGTCGGTGGCG
Found at i:311532 original size:49 final size:51
Alignment explanation
Indices: 311426--311934 Score: 182
Period size: 52 Copynumber: 9.8 Consensus size: 51
311416 AACACATTGG
** * * * ** * *
311426 CATCTTTAAGTCCAATGTCGTTGGCCTTTAATCGGCGTATTAGCA-CT-TT
1 CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCATCTCAT
* * *
311475 CATTTTTAAGTCCAATGTCACTGTCCTTAAATCAGAACATTGGCA-C-CAT
1 CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCATCTCAT
** * * *
311524 CATCTTTAAGTTTAATGTCGCTGGT-CGTGAATCAGCACATTGACATTCTTCAT
1 CATCTTTAAGTCCAATGTCACT-GTCCTTGAATCAGCACATTGGCA-TC-TCAT
** *
311577 -ATCTTTAAACCCAATGTCACTGGCCTTGAATCAGCACATTGGCATTCTTC-T
1 CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCA-TC-TCAT
* * * ** * * * ** *
311628 CATCTTCAAGTCTAACGTTGCTGGCCGTGAATCAACACATTTACAT-TCTTT
1 CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCATCTC-AT
* * * * * * *
311679 GCATCTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCAT
1 -CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCA----TCTCAT
* * * * *
311735 CCTCCTCAACCTTAAGTCTAATGTCGCTGGCCTTGAATCATCACATTGGCA-C-CAT
1 CAT-CT-----TTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCATCTCAT
* * * * * * * * *
311790 CATCTTTAAGTCCACTATCGCTGGCCTTAAATTAGCATATTGGCATCTTTAA
1 CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCATC-TCAT
* * *
311842 CAT-TCCTAAG-CCTAATGTCACTGGCCTTAAATCAGCACATTGGCATTCTTC-T
1 CATCT-TTAAGTCC-AATGTCACTGTCCTTGAATCAGCACATTGGCA-TC-TCAT
* * * *
311894 TATCTTCAAGTCTAATGTCACTAG-CCGTGAATCAGCACATT
1 CATCTTTAAGTCCAATGTCACT-GTCCTTGAATCAGCACATT
311935 AACATTCTTT
Statistics
Matches: 346, Mismatches: 83, Indels: 59
0.71 0.17 0.12
Matches are distributed among these distances:
49 106 0.31
50 3 0.01
51 8 0.02
52 170 0.49
53 10 0.03
54 2 0.01
55 7 0.02
56 4 0.01
57 2 0.01
61 34 0.10
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (51 bp):
CATCTTTAAGTCCAATGTCACTGTCCTTGAATCAGCACATTGGCATCTCAT
Found at i:311593 original size:52 final size:51
Alignment explanation
Indices: 311537--311982 Score: 227
Period size: 52 Copynumber: 8.5 Consensus size: 51
311527 CTTTAAGTTT
* *
311537 AATGTCGCTGGTCGTGAATCAGCACATTGACATTCTTCATATCTTTAAACCC
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTC-TATCTTTAAGCCC
* * * * * *
311589 AATGTCACTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCT
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTCT-ATCTTTAAGCCC
* * * *
311641 AACGTTGCTGGCCGTGAATCAACACATTTACATTCTT-TGCATCTTTAAGCCC
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTCT--ATCTTTAAGCCC
* * * * * * * * *
311693 AATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCATCCTCCTCAACCTTAAGTCT
1 AATGTCGCTGGCCGTGAATCAGCACATT-G-A-C---AT--T-CTTCT-ATCTTTAAGCCC
* * * * * *
311754 AATGTCGCTGGCCTTGAATCATCACATTGGCA-CCATC-ATCTTTAAGTCC
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTCTATCTTTAAGCCC
* * * * * * * * *
311803 ACTATCGCTGGCCTTAAATTAGCATATTGGCA-TCTT-TAACATTCCTAAGCCT
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTCTATC-TT--TAAGCCC
* * * * * * *
311855 AATGTCACTGGCCTTAAATCAGCACATTGGCATTCTTCTTATCTTCAAGTCT
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTC-TATCTTTAAGCCC
* * * *
311907 AATGTCACTAGCCGTGAATCAGCACATTAACATTCTTTGTATCTTTAAGCCC
1 AATGTCGCTGGCCGTGAATCAGCACATTGACATTC-TTCTATCTTTAAGCCC
* * * *
311959 AATATTGCTTGCCTTGAATCAGCA
1 AATGTCGCTGGCCGTGAATCAGCA
311983 TATTAGCACA
Statistics
Matches: 299, Mismatches: 75, Indels: 40
0.72 0.18 0.10
Matches are distributed among these distances:
49 39 0.13
50 2 0.01
51 4 0.01
52 199 0.67
53 6 0.02
54 3 0.01
55 5 0.02
58 3 0.01
60 2 0.01
61 35 0.12
62 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (51 bp):
AATGTCGCTGGCCGTGAATCAGCACATTGACATTCTTCTATCTTTAAGCCC
Found at i:311674 original size:104 final size:101
Alignment explanation
Indices: 311486--311726 Score: 277
Period size: 104 Copynumber: 2.4 Consensus size: 101
311476 ATTTTTAAGT
* * * * * * *
311486 CCAATGTCACTGTCCTTAAATCAGAACATTGGCACCATCATCTTTAAGTTTAATGTCGCTGGTCG
1 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACCATCATCTTCAAGTCTAACGTCGCTGGCCG
* *
311551 TGAATCAGCACATTGACATTCTTCATATCTTTAAAC
66 TGAATCAACACATTGACATTCTTCACATCTTTAAAC
*
311587 CCAATGTCACTGGCCTTGAATCAGCACATTGGCATTCTTC-TCATCTTCAAGTCTAACGTTGCTG
1 CCAATGTCACTGGCCTTGAATCAGCACATTGGCA--C--CATCATCTTCAAGTCTAACGTCGCTG
* ** *
311651 GCCGTGAATCAACACATTTACATTCTTTGCATCTTTAAGC
62 GCCGTGAATCAACACATTGACATTCTTCACATCTTTAAAC
* * * *
311691 CCAATATCGCTGGCCTTGAATTAGCATATTGGCACC
1 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACC
311727 TTTATCATCC
Statistics
Matches: 118, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
100 1 0.01
101 31 0.26
102 1 0.01
103 1 0.01
104 83 0.70
105 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (101 bp):
CCAATGTCACTGGCCTTGAATCAGCACATTGGCACCATCATCTTCAAGTCTAACGTCGCTGGCCG
TGAATCAACACATTGACATTCTTCACATCTTTAAAC
Found at i:311735 original size:104 final size:102
Alignment explanation
Indices: 311522--311891 Score: 298
Period size: 104 Copynumber: 3.5 Consensus size: 102
311512 CATTGGCACC
* * * * *
311522 ATCATCTTTAAGTTTAATGTCGCTGGTCGTGAATCAGCACATTGACATTC-TTCATATCTTTAAA
1 ATCATCTTCAAGTCTAATGTCGCTGGCCGTGAATCAACACATTGACATTCTTTC--ATCTTTAAG
* * * * *
311586 CCCAATGTCACTGGCCTTGAATCAGCACATTGGCATTCTT
64 CCCAATATCGCTGGCCTTGAATTAGCATATTGGCACT-TT
* * * *
311626 CTCATCTTCAAGTCTAACGTTGCTGGCCGTGAATCAACACATTTACATTCTTTGCATCTTTAAGC
1 ATCATCTTCAAGTCTAATGTCGCTGGCCGTGAATCAACACATTGACATTCTTT-CATCTTTAAGC
311691 CCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTT
65 CCAATATCGCTGGCCTTGAATTAGCATATTGGCA-CTTT
* * * **
311730 ATCATCCTCCTCAACCTTAAGTCTAATGTCGCTGGCCTTGAATCATCACATTGGCA--CCATCAT
1 ATCAT-CT--T----C--AAGTCTAATGTCGCTGGCCGTGAATCAACACATTGACATTCTTTCAT
* * *
311793 CTTTAAGTCCACTATCGCTGGCCTTAAATTAGCATATTGGCATCTTT
57 CTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCA-CTTT
* * * * * * * *
311840 AACAT-TCCTAAGCCTAATGTCACTGGCCTTAAATCAGCACATTGGCATTCTT
1 ATCATCTTC-AAGTCTAATGTCGCTGGCCGTGAATCAACACATTGACATTCTT
311892 CTTATCTTCA
Statistics
Matches: 217, Mismatches: 35, Indels: 29
0.77 0.12 0.10
Matches are distributed among these distances:
101 35 0.16
102 1 0.00
103 1 0.00
104 87 0.40
105 5 0.02
106 1 0.00
107 1 0.00
108 1 0.00
110 50 0.23
111 3 0.01
113 32 0.15
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (102 bp):
ATCATCTTCAAGTCTAATGTCGCTGGCCGTGAATCAACACATTGACATTCTTTCATCTTTAAGCC
CAATATCGCTGGCCTTGAATTAGCATATTGGCACTTT
Found at i:312691 original size:20 final size:21
Alignment explanation
Indices: 312645--312698 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
312635 GTTTCGATAC
312645 AATGTATCGATACATAAGTTT
1 AATGTATCGATACATAAGTTT
312666 --TGTATCGATACATAA-TTT
1 AATGTATCGATACATAAGTTT
312684 AATGTATCGATACAT
1 AATGTATCGATACAT
312699 TACCCAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.10
19 15 0.48
20 13 0.42
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATAAGTTT
Found at i:318517 original size:13 final size:13
Alignment explanation
Indices: 318499--318524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318489 TACAGCAAGT
318499 ATGTATCGATACA
1 ATGTATCGATACA
318512 ATGTATCGATACA
1 ATGTATCGATACA
318525 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:320770 original size:21 final size:21
Alignment explanation
Indices: 320737--320781 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
320727 TTGCAAGTTG
*
320737 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
320759 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
320779 AAA
1 AAA
320782 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:324590 original size:13 final size:13
Alignment explanation
Indices: 324572--324622 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
324562 GGAAATTCTA
324572 TGTATCGATACAT
1 TGTATCGATACAT
324585 TGTATCGATACAT
1 TGTATCGATACAT
*
324598 TGTATCGATACAC
1 TGTATCGATACAT
324611 TGTATCGATACA
1 TGTATCGATACA
324623 GGGTGATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:327092 original size:20 final size:20
Alignment explanation
Indices: 327069--327142 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
327059 ACAATTCAAA
327069 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
327089 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
327110 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
327130 GTATCGATACATG
1 GTATCGATACATG
327143 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:327113 original size:21 final size:21
Alignment explanation
Indices: 327087--327162 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
327077 ACATGTTGCA
327087 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
327108 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
327128 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
327149 ATGTATCGATACAT
1 ATGTATCGATACAT
327163 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:327120 original size:41 final size:41
Alignment explanation
Indices: 327069--327162 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
327059 ACAATTCAAA
327069 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
327110 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
327151 GTATCGATACAT
1 GTATCGATACAT
327163 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:327219 original size:13 final size:13
Alignment explanation
Indices: 327201--327226 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
327191 TACAGCAAGT
327201 ATGTATCGATACA
1 ATGTATCGATACA
327214 ATGTATCGATACA
1 ATGTATCGATACA
327227 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:334942 original size:51 final size:50
Alignment explanation
Indices: 334861--334982 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 50
334851 AATAGATGTA
*
334861 TGAATAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 TGAA-AATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCAATACAT
*
334912 TGAAGAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
1 TGAA-AATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCAATACAT
* *
334963 TCAAACATGTATTGATACAT
1 TGAAA-ATGTATCGATACAT
334983 TGAAAAATGT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 1 0.02
51 64 0.98
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (50 bp):
TGAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCAATACAT
Found at i:334974 original size:20 final size:20
Alignment explanation
Indices: 334948--335002 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
334938 AAAAAGATAG
*
334948 AATGTATCAATACATTCAAA
1 AATGTATCGATACATTCAAA
* * *
334968 CATGTATTGATACATTGAAA
1 AATGTATCGATACATTCAAA
334988 AATGTATCGATACAT
1 AATGTATCGATACAT
335003 CTAGGTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:340054 original size:15 final size:16
Alignment explanation
Indices: 340034--340063 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
340024 TAAAGGGTAG
340034 GAGATGA-CACCTATC
1 GAGATGAGCACCTATC
340049 GAGATGAGCACCTAT
1 GAGATGAGCACCTAT
340064 GAGTCCCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (16 bp):
GAGATGAGCACCTATC
Found at i:341390 original size:18 final size:17
Alignment explanation
Indices: 341359--341456 Score: 83
Period size: 18 Copynumber: 5.5 Consensus size: 17
341349 AATACTATGC
*
341359 ATAAAAAAA-GAAAAAA
1 ATAAAAAAACAAAAAAA
341375 ATAAAAAAACCAAAAAAA
1 ATAAAAAAA-CAAAAAAA
* *
341393 AGAATAAACAAAAAACAAAA
1 ATAA-AAA-AACAAA-AAAA
341413 ATAAATAAAA-AATAAAAA
1 ATAAA-AAAACAA-AAAAA
*
341431 ATAAATAAAACAAAATAA
1 ATAAA-AAAACAAAAAAA
341449 ATAAAAAA
1 ATAAAAAA
341457 TCTAATGAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
16 9 0.13
17 3 0.04
18 34 0.49
19 12 0.17
20 11 0.16
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (17 bp):
ATAAAAAAACAAAAAAA
Found at i:341405 original size:24 final size:24
Alignment explanation
Indices: 341361--341431 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
341351 TACTATGCAT
*
341361 AAAA-AAAGAAAAAAATAAAAAAACCA
1 AAAATAAAG-AAAAAA-CAAAAAA-CA
*
341387 AAAA-AAAGAATAAACAAAAAACA
1 AAAATAAAGAAAAAACAAAAAACA
* *
341410 AAAATAAATAAAAAATAAAAAA
1 AAAATAAAGAAAAAACAAAAAA
341432 TAAATAAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 6 0.15
24 20 0.51
25 5 0.13
26 8 0.21
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.07
Consensus pattern (24 bp):
AAAATAAAGAAAAAACAAAAAACA
Found at i:341420 original size:4 final size:4
Alignment explanation
Indices: 341411--341457 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
341401 CAAAAAACAA
*
341411 AAAT AAAT AAA- AAAT AAA- AAAT AAAT AAA- ACA- AAAT AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
341454 AAAT
1 AAAT
341458 CTAATGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 13 0.35
4 24 0.65
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:341423 original size:32 final size:32
Alignment explanation
Indices: 341388--341457 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
341378 AAAAAACCAA
* *
341388 AAAAAAGAATAAAC-AA-AAAACAAAAATAAAT
1 AAAAAATAAAAAACAAATAAAAC-AAAATAAAT
*
341419 AAAAAATAAAAAATAAATAAAACAAAATAAAT
1 AAAAAATAAAAAACAAATAAAACAAAATAAAT
341451 AAAAAAT
1 AAAAAAT
341458 CTAATGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 11 0.32
32 18 0.53
33 5 0.15
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.13
Consensus pattern (32 bp):
AAAAAATAAAAAACAAATAAAACAAAATAAAT
Found at i:341450 original size:14 final size:14
Alignment explanation
Indices: 341369--341456 Score: 67
Period size: 14 Copynumber: 6.3 Consensus size: 14
341359 ATAAAAAAAG
341369 AAAAAAATAAA-AA
1 AAAAAAATAAATAA
*
341382 AACCAAAAA-AAAGAA
1 AA--AAAAATAAATAA
* *
341397 TAAACAAA-AAACAA
1 -AAAAAAATAAATAA
*
341411 AAATAAATAAA-AA
1 AAAAAAATAAATAA
341424 ATAAAAAATAAATAA
1 A-AAAAAATAAATAA
*
341439 AACAAAATAAATAA
1 AAAAAAATAAATAA
341453 AAAA
1 AAAA
341457 TCTAATGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
13 11 0.18
14 39 0.63
15 10 0.16
16 2 0.03
ACGTcount: A:0.83, C:0.06, G:0.01, T:0.10
Consensus pattern (14 bp):
AAAAAAATAAATAA
Found at i:341773 original size:58 final size:57
Alignment explanation
Indices: 341673--341792 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 57
341663 AGATGGTATT
341673 AGTGCATCAAATAACCTGAATTCCCAAAGGGCAAAAGCACCTGGTTCTTTAAT-AGAC
1 AGTGCATCAAATAACCTGAATTCCCAAAGGGCAAAAGCACCTGGTTCTTTAATGA-AC
*
341730 AGTGCATCAAATAACTTGAATTGCCCAAAGGGCAAAAGCACCTGGTTCTTTAATGAAC
1 AGTGCATCAAATAACCTGAATT-CCCAAAGGGCAAAAGCACCTGGTTCTTTAATGAAC
341788 AGTGC
1 AGTGC
341793 CAGATACAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
57 21 0.35
58 38 0.63
59 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (57 bp):
AGTGCATCAAATAACCTGAATTCCCAAAGGGCAAAAGCACCTGGTTCTTTAATGAAC
Found at i:342376 original size:42 final size:42
Alignment explanation
Indices: 342327--342532 Score: 114
Period size: 42 Copynumber: 4.9 Consensus size: 42
342317 CCCGAGAGAC
* * *
342327 ACCTTTACCCTTATGGTGACCTGTCAACTCAGTCTCCGATTA
1 ACCTTTACCCTTATGGTGACCTATCAACTCAGTCTCCAATAA
** * * ** *
342369 ACCTTTA-CCTTATTATTTACCTGTCGGCTCAGTC-CTCGATAA
1 ACCTTTACCCTTA-TGGTGACCTATCAACTCAGTCTC-CAATAA
* * * * * * * *
342411 ACCCATTACCCATATGGTAACCTATTAGCTTAGTCTCTAATTA
1 A-CCTTTACCCTTATGGTGACCTATCAACTCAGTCTCCAATAA
* * * *
342454 ACCTTTATCTCC-T-TGTTTACCTATCGACTCAGTCCCCAATAA
1 ACCTTTA-C-CCTTATGGTGACCTATCAACTCAGTCTCCAATAA
* *
342496 ACCCCTTACCCCTATGGTGACCTATCAACTCAGTCTC
1 A-CCTTTACCCTTATGGTGACCTATCAACTCAGTCTC
342533 TGGTCAACCT
Statistics
Matches: 121, Mismatches: 33, Indels: 19
0.70 0.19 0.11
Matches are distributed among these distances:
41 8 0.07
42 57 0.47
43 49 0.40
44 7 0.06
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.34
Consensus pattern (42 bp):
ACCTTTACCCTTATGGTGACCTATCAACTCAGTCTCCAATAA
Found at i:342427 original size:85 final size:85
Alignment explanation
Indices: 342331--343184 Score: 691
Period size: 85 Copynumber: 10.0 Consensus size: 85
342321 AGAGACACCT
* * * * * *
342331 TTACCCTTATGGTGACCTGTCAACTCAGTCTCCGATTAACCTTTA-CCTTATTATTTACCTGTCG
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCC-CATTGTTTACCTATCA
* *
342395 GCTCAGTCCTCGATAAACCCA
65 GCTCAGTCCTCGGTAAACCCC
* * * * * * ** *
342416 TTACCCATATGGTAACCTATTAGCTTAGTCTCTAATTAACCTTTATCTCC-TTGTTTACCTATC-
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATC-CCATTGTTTACCTATCA
* **
342479 GACTCAGTCCCCAATAAACCCC
65 G-CTCAGTCCTCGGTAAACCCC
* * * * ** *
342501 TTACCCCTATGGTGACCTATCAACTCAGTCTCTGGTCAACCTTTATCCCCTCATTAACCTATCAG
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCCCATTGTTTACCTATCAG
***
342566 CTCAGTCCTTAATAAACCCC
66 CTCAGTCCTCGGTAAACCCC
* * * * * * *
342586 TTACCCCTATGGTGACCTATTAGCTTAGTCTCCGGTCAACCTTTATCCCAATGTTTACCTCTC-G
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCCCATTGTTTACCTATCAG
* * * **
342650 ACTTAGACCTCGGTAAATGCTT
66 -CTCAGTCCTCGGTAAA-CCCC
* * * * * * *
342672 TTACCCCTATGGTGACCTGTTAGCTTAGTTTTCGATCAACCTTCATCCCATTGTTTACCTATCTG
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCCCATTGTTTACCTATCAG
* *
342737 CTCAATCCTTGGTAAACCCC
66 CTCAGTCCTCGGTAAACCCC
* * * * *
342757 TTACCTCTATGGTGACCTGTCAACTCAGTCTTCGGTCAACCTTCATCCTC-TTGTTTACCTACCA
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCC-CATTGTTTACCTATCA
* * *
342821 ACTCAGTCTTCGATAAACCCC
65 GCTCAGTCCTCGGTAAACCCC
* * * * * *
342842 TTACCCCTATAGTGACTTGTCAGCTCAGTCTTCCG-TCAACCTTCATCTCATTGTTTACCTGTCA
1 TTACCCCTATGGTGACCTGTCAACTCAGTC-TCCGATCAACCTTTATCCCATTGTTTACCTATCA
342906 GCTCAGTCCTCGGTAAACCCC
65 GCTCAGTCCTCGGTAAACCCC
* * * * * * * * *
342927 TTTACTCCTATGCTGACTTGT-AAGCTCAGTCTCTGATGAACCTTCATCCCATTATTTACTTGTC
1 -TTACCCCTATGGTGACCTGTCAA-CTCAGTCTCCGATCAACCTTTATCCCATTGTTTACCTATC
*
342991 AGCTCGGT-CTCTGGTAAACCCC
64 AGCTCAGTCCTC-GGTAAACCCC
* * * * * **
343013 TTACCCTTATGGGGACCTGTCAACTTAGTCTCCGATCAACCTTTATCCTATTGTTTACCTGTTGG
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCCCATTGTTTACCTATCAG
* *
343078 CTCAGTCCTTGGTAAACCCA
66 CTCAGTCCTCGGTAAACCCC
* * * * * * * * *
343098 TTACCCCTATGGTGACCTATTAGCTCAGTCTTC-AGTCACCCTTCATCTCATTGTTTACCTGTCG
1 TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGA-TCAACCTTTATCCCATTGTTTACCTATCA
* *
343162 GCTTAGTCCTTGGTAAACCCC
65 GCTCAGTCCTCGGTAAACCCC
343183 TT
1 TT
343185 CATCTTAGTG
Statistics
Matches: 627, Mismatches: 124, Indels: 36
0.80 0.16 0.05
Matches are distributed among these distances:
84 6 0.01
85 475 0.76
86 144 0.23
87 2 0.00
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (85 bp):
TTACCCCTATGGTGACCTGTCAACTCAGTCTCCGATCAACCTTTATCCCATTGTTTACCTATCAG
CTCAGTCCTCGGTAAACCCC
Found at i:342551 original size:43 final size:43
Alignment explanation
Indices: 342504--342634 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
342494 AAACCCCTTA
*
342504 CCCCTATGGTGACCTATCAACTCAGTCTCTGGTCAACCTTTAT
1 CCCCTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTTAT
* ** * *
342547 CCCCTCAT--TAACCTATCAGCTCAGTC-CTTAATAAACCCCTTA-
1 CCCCT-ATGGTGACCTATCAGCTCAGTCTC-TGGTCAA-CCTTTAT
* * *
342589 CCCCTATGGTGACCTATTAGCTTAGTCTCCGGTCAACCTTTAT
1 CCCCTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTTAT
342632 CCC
1 CCC
342635 AATGTTTACC
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
41 3 0.04
42 30 0.45
43 31 0.46
44 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.11, T:0.31
Consensus pattern (43 bp):
CCCCTATGGTGACCTATCAGCTCAGTCTCTGGTCAACCTTTAT
Found at i:342593 original size:42 final size:42
Alignment explanation
Indices: 342395--342615 Score: 114
Period size: 43 Copynumber: 5.2 Consensus size: 42
342385 TTACCTGTCG
** * * *
342395 GCTCAGTCCTCGATAAACCCATTACCCATATGGTAACCTATTA
1 GCTCAGTCCTTAATAAACCCCTTACCCCTAT-GTAACCTATCA
* * * * *
342438 GCTTAGT-CTCTAATTAA-CCTTTATCTCCT-TGTTTACCTATC-
1 GCTCAGTCCT-TAATAAACCCCTTA-CCCCTATG-TAACCTATCA
** *
342479 GACTCAGTCCCCAATAAACCCCTTACCCCTATGGTGACCTATCA
1 G-CTCAGTCCTTAATAAACCCCTTACCCCTAT-GTAACCTATCA
* ** * *
342523 ACTCAGT-CTCTGGTCAA-CCTTTATCCCCTCAT-TAACCTATCA
1 GCTCAGTCCT-TAATAAACCCCTTA-CCCCT-ATGTAACCTATCA
* *
342565 GCTCAGTCCTTAATAAACCCCTTACCCCTATGGTGACCTATTA
1 GCTCAGTCCTTAATAAACCCCTTACCCCTAT-GTAACCTATCA
*
342608 GCTTAGTC
1 GCTCAGTC
342616 TCCGGTCAAC
Statistics
Matches: 130, Mismatches: 32, Indels: 32
0.67 0.16 0.16
Matches are distributed among these distances:
41 4 0.03
42 59 0.45
43 64 0.49
44 3 0.02
ACGTcount: A:0.25, C:0.33, G:0.10, T:0.32
Consensus pattern (42 bp):
GCTCAGTCCTTAATAAACCCCTTACCCCTATGTAACCTATCA
Found at i:342769 original size:256 final size:254
Alignment explanation
Indices: 342331--343184 Score: 824
Period size: 256 Copynumber: 3.3 Consensus size: 254
342321 AGAGACACCT
* * * * * * * * * *
342331 TTACCCTTATGGTGACCTGTCAACTCAGTCTCCGATTAACCTTTACCTTATTATTTACCTGTCGG
1 TTACCCCTATGGTGACCTATTAGCTCAGTCTCCG-TCAACCTTCATCTCATTGTTTACCTGTCGA
* * * * * * * * * * * *
342396 CTCAGTCCTCGATAAA-CCCATTACCCATATGGTAACCTATTAGCTTAGTCTCTAATTAACCTTT
65 CTTAGTCCTCGGTAAACCCCTTTACCCCTATGCTGACCTGTAAGCTCAGTCTCTGATCAACCTTC
* * * *** *
342460 ATCTCC-TTGTTTACCTATC-GACTCAGTCCCCAATAAACCCCTTACCCCTATGGTGACCTATCA
130 ATC-CCATTATTTACCTATCAG-CTCAATCTCTGGTAAACCCCTTA-CCCTATGGTGACCTGTCA
* ** * *
342523 ACTCAGTCTCTGGTCAACCTTTATCCCCTCATTAACCTATCAGCTCAGTCCTTAATAAACCCC
192 ACTCAGTCTCTGGTCAACCTTTATCCTCTTGTTTACCTATCAGCTCAGTCCTTGATAAACCCC
* * * * *
342586 TTACCCCTATGGTGACCTATTAGCTTAGTCTCCGGTCAACCTTTATCCCAATGTTTACCTCTCGA
1 TTACCCCTATGGTGACCTATTAGCTCAGTCTCC-GTCAACCTTCATCTCATTGTTTACCTGTCGA
* ** * * * * *
342651 CTTAGACCTCGGTAAATGCTTTTACCCCTATGGTGACCTGTTAGCTTAGT-TTTCGATCAACCTT
65 CTTAGTCCTCGGTAAACCCCTTTACCCCTATGCTGACCTGTAAGCTCAGTCTCT-GATCAACCTT
* *
342715 CATCCCATTGTTTACCTATCTGCTCAATC-CTTGGTAAACCCCTTACCTCTATGGTGACCTGTCA
129 CATCCCATTATTTACCTATCAGCTCAATCTC-TGGTAAACCCCTTACC-CTATGGTGACCTGTCA
* * *
342779 ACTCAGTCT-TCGGTCAACCTTCATCCTCTTGTTTACCTACCAACTCAGT-CTTCGATAAACCCC
192 ACTCAGTCTCT-GGTCAACCTTTATCCTCTTGTTTACCTATCAGCTCAGTCCTT-GATAAACCCC
* * * *
342842 TTACCCCTATAGTGACTTGTCAGCTCAGTCTTCCGTCAACCTTCATCTCATTGTTTACCTGTC-A
1 TTACCCCTATGGTGACCTATTAGCTCAGTC-TCCGTCAACCTTCATCTCATTGTTTACCTGTCGA
* * * *
342906 GCTCAGTCCTCGGTAAACCCCTTTACTCCTATGCTGACTTGTAAGCTCAGTCTCTGATGAACCTT
65 -CTTAGTCCTCGGTAAACCCCTTTACCCCTATGCTGACCTGTAAGCTCAGTCTCTGATCAACCTT
* * ** *
342971 CATCCCATTATTTACTTGTCAGCTCGGTCTCTGGTAAACCCCTTACCCTTATGGGGACCTGTCAA
129 CATCCCATTATTTACCTATCAGCTCAATCTCTGGTAAACCCCTTACCC-TATGGTGACCTGTCAA
* * * * * ** * *
343036 CTTAGTCTCCGATCAACCTTTATCCTATTGTTTACCTGTTGGCTCAGTCCTTGGTAAACCCA
193 CTCAGTCTCTGGTCAACCTTTATCCTCTTGTTTACCTATCAGCTCAGTCCTTGATAAACCCC
* * *
343098 TTACCCCTATGGTGACCTATTAGCTCAGTCTTCAGTCACCCTTCATCTCATTGTTTACCTGTCGG
1 TTACCCCTATGGTGACCTATTAGCTCAGTC-TCCGTCAACCTTCATCTCATTGTTTACCTGTCGA
*
343163 CTTAGTCCTTGGTAAACCCCTT
65 CTTAGTCCTCGGTAAACCCCTT
343185 CATCTTAGTG
Statistics
Matches: 494, Mismatches: 88, Indels: 33
0.80 0.14 0.05
Matches are distributed among these distances:
255 76 0.15
256 408 0.83
257 10 0.02
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (254 bp):
TTACCCCTATGGTGACCTATTAGCTCAGTCTCCGTCAACCTTCATCTCATTGTTTACCTGTCGAC
TTAGTCCTCGGTAAACCCCTTTACCCCTATGCTGACCTGTAAGCTCAGTCTCTGATCAACCTTCA
TCCCATTATTTACCTATCAGCTCAATCTCTGGTAAACCCCTTACCCTATGGTGACCTGTCAACTC
AGTCTCTGGTCAACCTTTATCCTCTTGTTTACCTATCAGCTCAGTCCTTGATAAACCCC
Found at i:342910 original size:42 final size:42
Alignment explanation
Indices: 342771--342913 Score: 114
Period size: 42 Copynumber: 3.4 Consensus size: 42
342761 CTCTATGGTG
*
342771 ACCTGTCAACTCAGTCTTCGGTCAACCTTCATCCTC-TTGTTT
1 ACCTGTCAACTCAGTCTTCCGTCAACCTTCAT-CTCATTGTTT
** * * * * *
342813 ACCTACCAACTCAGTCTT-CGATAAACCCCTT-ACCCCTATAG-TG
1 ACCTGTCAACTCAGTCTTCCG-TCAA--CCTTCATCTC-ATTGTTT
* *
342856 ACTTGTCAGCTCAGTCTTCCGTCAACCTTCATCTCATTGTTT
1 ACCTGTCAACTCAGTCTTCCGTCAACCTTCATCTCATTGTTT
*
342898 ACCTGTCAGCTCAGTC
1 ACCTGTCAACTCAGTC
342914 CTCGGTAAAC
Statistics
Matches: 75, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
41 8 0.11
42 40 0.53
43 19 0.25
44 8 0.11
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (42 bp):
ACCTGTCAACTCAGTCTTCCGTCAACCTTCATCTCATTGTTT
Found at i:343181 original size:341 final size:340
Alignment explanation
Indices: 342331--343184 Score: 896
Period size: 341 Copynumber: 2.5 Consensus size: 340
342321 AGAGACACCT
* * * *
342331 TTACCCTTATGGTGACCTGTCAACTCAGTCTCCGATTAACCTTTA-CCTTATTATTTACCTGTCG
1 TTACCCTTATGGTGACCTGTCAACTTAGTCTCCGATCAACCTTTATCC-TATTGTTTACCTGTTG
* * * * * * *
342395 GCTCAGTCCTCGATAAACCCATTACCCATATGGTAACCTATTAGCTTAGTC-TCTAATTAACCTT
65 GCTCAGTCCTTGGTAAACCCATTACCCCTATGGTGACCTATTAGCTCAGTCTTC-AGTCAACCTT
* *** *
342459 TATCTCCTTGTTTACCTATCGACTCAGTCCCCAATAAACCCCTTACCCCTATGGTGACCTATCAA
129 CATCT-CTTGTTTACCTATCGACTCAGTCCTTGATAAACCCCTTACCCCTATAGTGACCTATCAA
* * * *
342524 CTCAGTCTCTGGTCAACCTTTATCCCCTCATTAACCTATCAGCTCAGTCCTTAATAAACCCCTTA
193 CTCAGTCTCTCGTCAACCTTCATCCCATCATTAACCTATCAGCTCAGTCCTCAATAAACCCCTTA
* * * * * * *
342589 CCCCTATGGTGACCTATTAGCTTAGTCTCCGGTCAACCTTTATCCCAATGTTTACCTCTCGACTT
258 CCCCTATGCTGACCTATAAGCTCAGTCTCCGATCAACCTTCATCCCAATATTTACCTCTCGACTC
* **
342654 AGACCTCGGTAAATGCTT
323 AGACCTCGGTAAATCCCC
* * * * * * * *
342672 TTACCCCTATGGTGACCTGTTAGCTTAGTTTTCGATCAACCTTCATCCCATTGTTTACCTATCT-
1 TTACCCTTATGGTGACCTGTCAACTTAGTCTCCGATCAACCTTTATCCTATTGTTTACCTGT-TG
* * * * * * *
342736 GCTCAATCCTTGGTAAACCCCTTACCTCTATGGTGACCTGTCAACTCAGTCTTCGGTCAACCTTC
65 GCTCAGTCCTTGGTAAACCCATTACCCCTATGGTGACCTATTAGCTCAGTCTTCAGTCAACCTTC
* * * * *
342801 ATCCTCTTGTTTACCTACCAACTCAGT-CTTCGATAAACCCCTTACCCCTATAGTGACTTGTCAG
130 AT-CTCTTGTTTACCTATCGACTCAGTCCTT-GATAAACCCCTTACCCCTATAGTGACCTATCAA
* ** * * **
342865 CTCAGTCT-TCCGTCAACCTTCATCTCATTGTTTACCTGTCAGCTCAGTCCTCGGTAAACCCCTT
193 CTCAGTCTCT-CGTCAACCTTCATCCCATCATTAACCTATCAGCTCAGTCCTCAATAAACCCC-T
* * * * * * * *
342929 TACTCCTATGCTGACTTGTAAGCTCAGTCTCTGATGAACCTTCATCCCATTATTTACTTGTC-AG
256 TACCCCTATGCTGACCTATAAGCTCAGTCTCCGATCAACCTTCATCCCAATATTTACCTCTCGA-
**
342993 CTC-GGTCTCTGGTAAA-CCCC
320 CTCAGACCTC-GGTAAATCCCC
*
343013 TTACCCTTATGGGGACCTGTCAACTTAGTCTCCGATCAACCTTTATCCTATTGTTTACCTGTTGG
1 TTACCCTTATGGTGACCTGTCAACTTAGTCTCCGATCAACCTTTATCCTATTGTTTACCTGTTGG
*
343078 CTCAGTCCTTGGTAAACCCATTACCCCTATGGTGACCTATTAGCTCAGTCTTCAGTCACCCTTCA
66 CTCAGTCCTTGGTAAACCCATTACCCCTATGGTGACCTATTAGCTCAGTCTTCAGTCAACCTTCA
* * * *
343143 TCTCATTGTTTACCTGTCGGCTTAGTCCTTGGTAAACCCCTT
131 TCTC-TTGTTTACCTATCGACTCAGTCCTTGATAAACCCCTT
343185 CATCTTAGTG
Statistics
Matches: 411, Mismatches: 90, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
340 6 0.01
341 339 0.82
342 66 0.16
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (340 bp):
TTACCCTTATGGTGACCTGTCAACTTAGTCTCCGATCAACCTTTATCCTATTGTTTACCTGTTGG
CTCAGTCCTTGGTAAACCCATTACCCCTATGGTGACCTATTAGCTCAGTCTTCAGTCAACCTTCA
TCTCTTGTTTACCTATCGACTCAGTCCTTGATAAACCCCTTACCCCTATAGTGACCTATCAACTC
AGTCTCTCGTCAACCTTCATCCCATCATTAACCTATCAGCTCAGTCCTCAATAAACCCCTTACCC
CTATGCTGACCTATAAGCTCAGTCTCCGATCAACCTTCATCCCAATATTTACCTCTCGACTCAGA
CCTCGGTAAATCCCC
Found at i:343199 original size:44 final size:44
Alignment explanation
Indices: 343136--343244 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 44
343126 TCTTCAGTCA
* * **
343136 CCCTTCATCTCATTGTTTACCTGTCGGCTTAGTCCTTGGTAAAC
1 CCCTTCATCTTAGTGTTTACCTGTCGGCTTAGTCCTTACTAAAC
* *
343180 CCCTTCATCTTAGTGTTTACTTGTCGGCTTAGTCTTTACTAAAC
1 CCCTTCATCTTAGTGTTTACCTGTCGGCTTAGTCCTTACTAAAC
* *
343224 CTCTTCATCCT-GTGTTTACCT
1 CCCTTCATCTTAGTGTTTACCT
343245 ATCAGCTCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
43 9 0.16
44 47 0.84
ACGTcount: A:0.16, C:0.28, G:0.14, T:0.42
Consensus pattern (44 bp):
CCCTTCATCTTAGTGTTTACCTGTCGGCTTAGTCCTTACTAAAC
Found at i:343417 original size:41 final size:42
Alignment explanation
Indices: 343367--343452 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
343357 ACCTCTCTGC
* * *
343367 TTAGTCCCTGGTGAATCTTTTA-CCCTTCGTTGACTTATCAGT
1 TTAGTCCCTGGTCAACCCTTTATCCCTT-GTTGACTTATCAGT
*
343409 TTAG-CCCTGGTCAACCCTTTATCCCTTGTTTACTTATCAGT
1 TTAGTCCCTGGTCAACCCTTTATCCCTTGTTGACTTATCAGT
343450 TTA
1 TTA
343453 ATGCCTGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 30 0.77
42 9 0.23
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (42 bp):
TTAGTCCCTGGTCAACCCTTTATCCCTTGTTGACTTATCAGT
Found at i:344945 original size:150 final size:150
Alignment explanation
Indices: 344724--345114 Score: 421
Period size: 165 Copynumber: 2.5 Consensus size: 150
344714 ATTTTCAAGA
* * * * *
344724 GTTTAAAATTTTTAAAATTCATTAAATATTATTATTTAATCACCATTAAATCAATTTTGAAGAA-
1 GTTTTAAATTTTTAAAATTCATCAAATATTATTATTTAATCA-TATTAAATC-ATTTTTAAAAAT
* * *
344788 TTCATTCATTTTTTTTC-TTGAAATTTTTCTATT-TCCAAAATATAGAGTTTTCTACTCCATAAA
64 TTCATTCATTTTTTTTCTTTGAAATTCTTCT-TTCCCCAAAAAATAGAGTTTTCTACTCCATAAA
*
344851 TTTTTTTGAGAGGATTTTTCTTG
128 TATTTTTGAGAGGATTTTTCTTG
* *
344874 GTTTCT-AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATTATTTTTCAAAAA
1 GTTT-TAAATTTTTAAAATTCATCAAATATTATTATTTA-ATCATATTAAATCATTTTT-AAAAA
*
344938 TTTATTCATTTTCATGAGTTTGAATTTTTTCTTTGAAATTCTTCTTTCCCCAAAAAATTGAGTTT
63 --T-TTCA--TTC---A--TT---TTTTTTCTTTGAAATTCTTCTTTCCCCAAAAAATAGAGTTT
*
345003 TCTATTCCATAAATATTTTTGAGAGGATTTTTCTTG
115 TCTACTCCATAAATATTTTTGAGAGGATTTTTCTTG
* * *
345039 GTTTTAAATTTTTAAAATTCATCAAATATCATCATTTAAGTCATATTAAATCATTTTTGAAAATT
1 GTTTTAAATTTTTAAAATTCATCAAATATTATTATTTAA-TCATATTAAATCATTTTTAAAAATT
*
345104 TCATTTATTTT
65 TCATTCATTTT
345115 CATGAGTTTT
Statistics
Matches: 201, Mismatches: 19, Indels: 41
0.77 0.07 0.16
Matches are distributed among these distances:
149 5 0.02
150 46 0.23
151 5 0.02
154 6 0.03
156 4 0.02
159 3 0.01
161 6 0.03
162 1 0.00
164 14 0.07
165 111 0.55
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.50
Consensus pattern (150 bp):
GTTTTAAATTTTTAAAATTCATCAAATATTATTATTTAATCATATTAAATCATTTTTAAAAATTT
CATTCATTTTTTTTCTTTGAAATTCTTCTTTCCCCAAAAAATAGAGTTTTCTACTCCATAAATAT
TTTTGAGAGGATTTTTCTTG
Found at i:345234 original size:164 final size:165
Alignment explanation
Indices: 344797--345297 Score: 641
Period size: 165 Copynumber: 3.0 Consensus size: 165
344787 ATTCATTCAT
* * * *
344797 TTTTTTTC-TTGAAATTTTTCTATTT-CCAAAATATAGAGTTTTCTACTCCATAAATTTTTTTGA
1 TTTTTTTCTTTGAAA-TTTTCTTTTTCCCAAAA-ATTGAGTTTTCTATTCCATAAATATTTTTGA
* * **
344860 GAGGATTTTTCTTGGTTTCTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAAT
64 GAGGATTTTTCTTGGTTTCTAATTTTTAAAATTCATCAAATATCATCATTTAAGTCATATTAAAT
* * *
344925 TATTTTTCAAAAATTT-ATTCATTTTCATGAGTTTGAA
129 CATTTTT-AAAAATTTCATTTATTTTCATGAGTTTTAA
*
344962 -TTTTTTCTTTGAAATTCTTC-TTTCCCCAAAAAATTGAGTTTTCTATTCCATAAATATTTTTGA
1 TTTTTTTCTTTGAAATT-TTCTTTTTCCC-AAAAATTGAGTTTTCTATTCCATAAATATTTTTGA
345025 GAGGATTTTTCTTGGTTT-TAAATTTTTAAAATTCATCAAATATCATCATTTAAGTCATATTAAA
64 GAGGATTTTTCTTGGTTTCT-AATTTTTAAAATTCATCAAATATCATCATTTAAGTCATATTAAA
*
345089 TCATTTTTGAAAATTTCATTTATTTTCATGAGTTTTAA
128 TCATTTTTAAAAATTTCATTTATTTTCATGAGTTTTAA
*
345127 TTTTTTTCTTTGAAATTTTCTTGTTTCCCAAAAATTGAGTTTT-TATTCCATAAATATTTTCGAT
1 TTTTTTTCTTTGAAATTTTCTT-TTTCCCAAAAATTGAGTTTTCTATTCCATAAATATTTTTGA-
*
345191 G-GGA-TTTTCTTGGTTTCTAATTTTTAAAATTCATAAAATATCATCATTT-AGTTC-TCATTAA
64 GAGGATTTTTCTTGGTTTCTAATTTTTAAAATTCATCAAATATCATCATTTAAG-TCAT-ATTAA
* * *
345252 ATCAGTTTCAAGAAA-TTCAATTTA-TTTCATGAATTTTAA
127 ATCATTTTTAA-AAATTTC-ATTTATTTTCATGAGTTTTAA
345291 TTTTTTT
1 TTTTTTT
345298 GTATACATTA
Statistics
Matches: 301, Mismatches: 20, Indels: 31
0.86 0.06 0.09
Matches are distributed among these distances:
163 3 0.01
164 100 0.33
165 157 0.52
166 36 0.12
167 5 0.02
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (165 bp):
TTTTTTTCTTTGAAATTTTCTTTTTCCCAAAAATTGAGTTTTCTATTCCATAAATATTTTTGAGA
GGATTTTTCTTGGTTTCTAATTTTTAAAATTCATCAAATATCATCATTTAAGTCATATTAAATCA
TTTTTAAAAATTTCATTTATTTTCATGAGTTTTAA
Found at i:345617 original size:10 final size:10
Alignment explanation
Indices: 345602--345650 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
345592 GGAACTCAAC
*
345602 AGAAAAAGAG
1 AGAAAAAAAG
345612 AGAAAAAAAG
1 AGAAAAAAAG
*
345622 AAGAAAAAAAA
1 -AGAAAAAAAG
345633 AGAAAAAATAG
1 AGAAAAAA-AG
*
345644 TGAAAAA
1 AGAAAAA
345651 TAGTTGGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 17 0.52
11 16 0.48
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:345626 original size:11 final size:11
Alignment explanation
Indices: 345604--345640 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
345594 AACTCAACAG
345604 AAAAAGAGAGAA
1 AAAAAGA-AGAA
345616 AAAAAGAAGAA
1 AAAAAGAAGAA
345627 AAAAA-AAGAA
1 AAAAAGAAGAA
345637 AAAA
1 AAAA
345641 TAGTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.36
11 9 0.36
12 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:345630 original size:13 final size:13
Alignment explanation
Indices: 345604--345640 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
345594 AACTCAACAG
*
345604 AAAAAG-AGAGAA
1 AAAAAGAAGAAAA
345616 AAAAAGAAGAAAA
1 AAAAAGAAGAAAA
345629 AAAAAGAA-AAAA
1 AAAAAGAAGAAAA
345641 TAGTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAAAA
Found at i:347462 original size:13 final size:13
Alignment explanation
Indices: 347444--347469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
347434 ACATTTTGGG
347444 ATGTATCGATACA
1 ATGTATCGATACA
347457 ATGTATCGATACA
1 ATGTATCGATACA
347470 TATTGTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:347574 original size:20 final size:21
Alignment explanation
Indices: 347530--347581 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
347520 GCCAATCACC
*
347530 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
347551 TGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
347571 TGTATCGATAC
1 TGTATCGATAC
347582 TGTTGAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:348185 original size:3 final size:3
Alignment explanation
Indices: 348179--348224 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
348169 AAAAAAGATG
*
348179 ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
348225 AGTTTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:351111 original size:19 final size:20
Alignment explanation
Indices: 351065--351117 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
351055 GTTACAAGCC
*
351065 GATGTATCGATACATTTTGG
1 GATGTATCGATACATATTGG
*
351085 GATGTATCGATACATATTGT
1 GATGTATCGATACATATTGG
351105 G-TGTATCGATACA
1 GATGTATCGATACA
351118 AATAGTTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (20 bp):
GATGTATCGATACATATTGG
Found at i:353237 original size:20 final size:22
Alignment explanation
Indices: 353198--353240 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
353188 GCTGTGAGTG
*
353198 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
353220 TGGGGG-TG-CCGGTCGCGACC
1 TGGGGGCTGCCCGGTCGCGACC
353240 T
1 T
353241 AGTGAGTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.05, C:0.30, G:0.47, T:0.19
Consensus pattern (22 bp):
TGGGGGCTGCCCGGTCGCGACC
Found at i:353755 original size:20 final size:20
Alignment explanation
Indices: 353730--353784 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
353720 AGTTTTCCAG
353730 ATGTATCGATACATTTGAAC
1 ATGTATCGATACATTTGAAC
353750 ATGTATCGATACATTTGAAC
1 ATGTATCGATACATTTGAAC
353770 ATGTATCGATACATT
1 ATGTATCGATACATT
353785 CTGGAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTGAAC
Found at i:354462 original size:13 final size:13
Alignment explanation
Indices: 354444--354469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
354434 TACAGCAAGT
354444 ATGTATCGATACA
1 ATGTATCGATACA
354457 ATGTATCGATACA
1 ATGTATCGATACA
354470 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:356721 original size:21 final size:21
Alignment explanation
Indices: 356688--356732 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
356678 TTGCAAGTTG
*
356688 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
356710 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
356730 AAA
1 AAA
356733 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:358556 original size:15 final size:15
Alignment explanation
Indices: 358536--358566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
358526 TAAAAATGTC
*
358536 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
358551 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
358566 C
1 C
358567 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:360650 original size:20 final size:20
Alignment explanation
Indices: 360622--360660 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
360612 CATCTGGAAA
360622 TTCTATGTATCGATACATTT
1 TTCTATGTATCGATACATTT
*
360642 TTCTTTGTATCGATACATT
1 TTCTATGTATCGATACATT
360661 GTATCGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.51
Consensus pattern (20 bp):
TTCTATGTATCGATACATTT
Found at i:360664 original size:13 final size:13
Alignment explanation
Indices: 360646--360684 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
360636 ACATTTTTCT
360646 TTGTATCGATACA
1 TTGTATCGATACA
360659 TTGTATCGATACA
1 TTGTATCGATACA
*
360672 CTGTATCGATACA
1 TTGTATCGATACA
360685 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:360829 original size:21 final size:21
Alignment explanation
Indices: 360805--360851 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
360795 AAATCTTTTG
360805 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
360826 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
360846 CAAAAT
1 CAAAAT
360852 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:360848 original size:20 final size:19
Alignment explanation
Indices: 360807--360849 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
360797 ATCTTTTGCA
360807 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
360827 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
360847 AAA
1 AAA
360850 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:369809 original size:33 final size:32
Alignment explanation
Indices: 369762--369829 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
369752 CGTTACAAGC
* *
369762 CAATGTATCTATACATTTTGGGATGTATCAATA
1 CAATGTATCGATACATATTGGG-TGTATCAATA
* *
369795 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCAATA
369827 CAA
1 CAA
369830 ACAGTTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCAATA
Found at i:369859 original size:11 final size:11
Alignment explanation
Indices: 369843--369875 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
369833 GTTAAGGGTG
*
369843 GCTACTACCAA
1 GCTACTGCCAA
369854 GCTACTGCCAA
1 GCTACTGCCAA
369865 GCTACTGCCAA
1 GCTACTGCCAA
369876 TCACCTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.30, C:0.36, G:0.15, T:0.18
Consensus pattern (11 bp):
GCTACTGCCAA
Found at i:370569 original size:3 final size:3
Alignment explanation
Indices: 370563--370629 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
370553 AAAAAAGATG
* *
370563 ATA ATA ATA GTA ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
370611 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
370630 AGTTTTTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:373451 original size:20 final size:20
Alignment explanation
Indices: 373414--373467 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
373404 TTCTACAACT
373414 TGTATTGATACAATAAGTGAA
1 TGTATTGATAC-ATAAGTGAA
373435 TGTATTGATACATAAGTGAA
1 TGTATTGATACATAAGTGAA
*
373455 TATATTGATACAT
1 TGTATTGATACAT
373468 GTTTGAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATTGATACATAAGTGAA
Found at i:373611 original size:51 final size:50
Alignment explanation
Indices: 373524--373714 Score: 220
Period size: 51 Copynumber: 3.7 Consensus size: 50
373514 TCTGGAAAGA
* * *
373524 AAATGTAGCAATACATTTTTTATTGTATCGATACATTCTGGGTTTGATCC
1 AAATGTATCGATACATTTTTTATTGTATCGATACATTCTGGGTTTGACCC
*
373574 AAATGTATCGATACATTTTTTCTTCGTATCGATACATTCTGGGTTTTTGACCC
1 AAATGTATCGATACATTTTTTATT-GTATCGATACATTCTGGG--TTTGACCC
* * * * * *
373627 AAATGTATCGATACATTATTCATTATATCTATACATTTTGGCTTTTGACCC
1 AAATGTATCGATACATTTTTTATTGTATCGATACATTCTGG-GTTTGACCC
* * * *
373678 AAATGTAACTATACATTCTTTAATGTATCGATACATT
1 AAATGTATCGATACATTTTTTATTGTATCGATACATT
373715 TAGTTAAATT
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 21 0.18
51 56 0.47
52 14 0.12
53 28 0.24
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (50 bp):
AAATGTATCGATACATTTTTTATTGTATCGATACATTCTGGGTTTGACCC
Found at i:373661 original size:103 final size:103
Alignment explanation
Indices: 373524--373714 Score: 240
Period size: 103 Copynumber: 1.9 Consensus size: 103
373514 TCTGGAAAGA
* * * * *
373524 AAATGTAGCAATACATTTTTTATTGTATCGATACATTCTGG-GTTTGATCCAAATGTATCGATAC
1 AAATGTAGCAATACATTATTCATTATATCGATACATTCTGGCGTTTGACCCAAATGTAACGATAC
* **
373588 ATTTTTTCTTCGTATCGATACATTCTGGGTTTTTGACCC
66 ATTCTTTAAT-GTATCGATACATTCTGGGTTTTTGACCC
* * * * * *
373627 AAATGTATCGATACATTATTCATTATATCTATACATTTTGGCTTTTGACCCAAATGTAACTATAC
1 AAATGTAGCAATACATTATTCATTATATCGATACATTCTGGCGTTTGACCCAAATGTAACGATAC
373692 ATTCTTTAATGTATCGATACATT
66 ATTCTTTAATGTATCGATACATT
373715 TAGTTAAATT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
103 47 0.64
104 26 0.36
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (103 bp):
AAATGTAGCAATACATTATTCATTATATCGATACATTCTGGCGTTTGACCCAAATGTAACGATAC
ATTCTTTAATGTATCGATACATTCTGGGTTTTTGACCC
Found at i:376099 original size:27 final size:27
Alignment explanation
Indices: 376053--376125 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
376043 TTATTTATCT
* *
376053 GGGATACTCCAGCCCCATTCTTCCG-A
1 GGGATACTCCAACCCTATTCTTCCGAA
* *
376079 GGAGATACTCTAACCCTATTCTTCTGAA
1 GG-GATACTCCAACCCTATTCTTCCGAA
*
376107 GGGATAGTCCAACCCTATT
1 GGGATACTCCAACCCTATT
376126 TTTTTAACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.05
27 34 0.87
28 3 0.08
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (27 bp):
GGGATACTCCAACCCTATTCTTCCGAA
Found at i:384678 original size:78 final size:78
Alignment explanation
Indices: 384562--384767 Score: 234
Period size: 79 Copynumber: 2.6 Consensus size: 78
384552 GAGATAATAA
* * * * * * * *
384562 CGGGGTTGGAGTGTTCCCTTGAAAATAACAGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
384627 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* * *
384640 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCGCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
384705 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
*
384719 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
384768 GATTAACGGG
Statistics
Matches: 106, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 52 0.49
79 53 0.50
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:384782 original size:27 final size:28
Alignment explanation
Indices: 384719--384794 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
384709 GGAATAAAGC
***
384719 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
384747 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
384774 CGGGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
384795 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:384876 original size:51 final size:51
Alignment explanation
Indices: 384778--385153 Score: 268
Period size: 51 Copynumber: 7.4 Consensus size: 51
384768 GATTAACGGG
* * * * *
384778 GTTGGAGTATCCTCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTAG--TGTTTTGAAAATAAAATCGGA
*
384832 GTTGGAGTATCCCTGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
* * * * *
384883 GTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGGG
1 GTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * * * *
384935 GTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* ** * ** * *** *
384986 GTTGGAGTGTCCCC---TCGGAAATAA--CG-GGGTTG-GAATATCCTCGGG
1 GTTGGAGTATCCCCGATTATGAAA-AATTAGTGTTTTGAAAATAAAATCGGA
* * * * *
385031 GTTGGAATATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTAG--TGTTTTGAAAATAAAATCGGA
* *
385085 GTTGGAGTATCCTCGATTAT-AGAAAATTAGTGGTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
*
385136 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
385154 GTGGAGAATT
Statistics
Matches: 251, Mismatches: 54, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
45 21 0.08
46 3 0.01
48 11 0.04
49 3 0.01
50 1 0.00
51 107 0.43
52 43 0.17
53 18 0.07
54 44 0.18
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:384999 original size:103 final size:104
Alignment explanation
Indices: 384774--384999 Score: 269
Period size: 103 Copynumber: 2.2 Consensus size: 104
384764 CGATGATTAA
* * * * *
384774 CGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGAGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAG-ATGTTTTAGAAATAAAACCGGAGTTGGAG
* * * *
384839 TATCCCTGATTATAGAAAATTAGTGTTTTGAAAATAAAAT
65 TATCCCCGATTATAGAAAATCAATATTTTGAAAATAAAAT
* * * *
384879 CGGAGTTGGAATATCCCCGATTGTGGAA-AAATTAG-TGTTTTAGCAATAAAACCGGGGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTGT-GAAGAAATTAGATGTTTTAGAAATAAAACCGGAGTTGGAG
*
384942 TATCCCCGATTAT-GAAAAATCAATATTTTGAAAATAAAGT
65 TATCCCCGATTATAG-AAAATCAATATTTTGAAAATAAAAT
*
384982 CGGGGTTGGAGTGTCCCC
1 CGGGGTTGGAGTATCCCC
385000 TCGGAAATAA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
102 1 0.01
103 71 0.70
105 27 0.26
106 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (104 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTAGATGTTTTAGAAATAAAACCGGAGTTGGAGT
ATCCCCGATTATAGAAAATCAATATTTTGAAAATAAAAT
Found at i:385032 original size:17 final size:17
Alignment explanation
Indices: 385010--385042 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
385000 TCGGAAATAA
385010 CGGGGTTGGAATATCCT
1 CGGGGTTGGAATATCCT
385027 CGGGGTTGGAATATCC
1 CGGGGTTGGAATATCC
385043 CCGATTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (17 bp):
CGGGGTTGGAATATCCT
Found at i:385126 original size:253 final size:256
Alignment explanation
Indices: 384668--385158 Score: 783
Period size: 253 Copynumber: 1.9 Consensus size: 256
384658 TCGAAAATAA
* * **
384668 CGGGGTTGGAGTATCCGCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAAAATAAAGCCGGGGTTGGAGTAT
* * *
384733 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCTCGATTGT
66 CCCCTCGGAAATAACGGGGTTGGAATAT-CCC----A-T-ACGGGGTTGGAATATCCCCGATTGT
384798 GAAGAAATTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCTGATTATAGAAAATTAGT
124 GAAGAAATTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCTGATTATAGAAAATTAGT
*
384863 GTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
189 GGTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
384928 AAC
254 AAC
* * *
384931 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAGTCGGGGTTGGAGTGT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAAAATAAAGCCGGGGTTGGAGTAT
384996 CCCCTCGGAAATAACGGGGTTGGAATAT-CC-T-CGGGGTTGGAATATCCCCGATTGTGAAGAAA
66 CCCCTCGGAAATAACGGGGTTGGAATATCCCATACGGGGTTGGAATATCCCCGATTGTGAAGAAA
385058 TTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTAT-CCTCGATTATAGAAAATTAGTGGTTTG
131 TTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCT-GATTATAGAAAATTAGTGGTTTG
385122 AAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
195 AAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
385159 GAATTAAGAA
Statistics
Matches: 216, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
252 3 0.01
253 125 0.58
255 1 0.00
261 2 0.01
263 85 0.39
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (256 bp):
CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGAAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAATATCCCATACGGGGTTGGAATATCCCCGATTGTGAAGAAA
TTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCTGATTATAGAAAATTAGTGGTTTGA
AAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
Found at i:387539 original size:13 final size:13
Alignment explanation
Indices: 387521--387546 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387511 ACAAAGATCC
387521 ATGTATCGATACA
1 ATGTATCGATACA
387534 ATGTATCGATACA
1 ATGTATCGATACA
387547 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:387542 original size:33 final size:33
Alignment explanation
Indices: 387500--387566 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
387490 AAAATTTCCA
***
387500 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
387533 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
387566 A
1 A
387567 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:387610 original size:19 final size:17
Alignment explanation
Indices: 387584--387655 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 17
387574 GGCAGTAGGT
387584 AATTATGTATCGATACA
1 AATTATGTATCGATACA
387601 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
387619 -A-T-TGTATCGATACAA
1 AATTATGTATCGATAC-A
387634 AATTTATGTATCGATACA
1 AA-TTATGTATCGATACA
387652 AATT
1 AATT
387656 GTTGAATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.23
14 1 0.02
16 2 0.04
17 3 0.06
18 5 0.11
19 25 0.53
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (17 bp):
AATTATGTATCGATACA
Found at i:387626 original size:13 final size:13
Alignment explanation
Indices: 387608--387632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
387598 ACAATACTTA
387608 TGTATCGATACAT
1 TGTATCGATACAT
387621 TGTATCGATACA
1 TGTATCGATACA
387633 AAATTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:387630 original size:32 final size:32
Alignment explanation
Indices: 387589--387651 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
387579 TAGGTAATTA
*
387589 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
387621 TGTATCGATACAAAATTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
387652 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:387733 original size:21 final size:21
Alignment explanation
Indices: 387709--387761 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
387699 CATTTGTAGG
387709 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
* **
387730 ATGTATCAATACATTGTACAA
1 ATGTATCGATACATTCCACAA
387751 ATGTATCGATA
1 ATGTATCGATA
387762 TATTTGGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:389038 original size:13 final size:13
Alignment explanation
Indices: 389020--389045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
389010 TCAAGGTTTT
389020 GGCAAAAAAGAAA
1 GGCAAAAAAGAAA
389033 GGCAAAAAAGAAA
1 GGCAAAAAAGAAA
389046 CCCCTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (13 bp):
GGCAAAAAAGAAA
Found at i:389642 original size:13 final size:13
Alignment explanation
Indices: 389624--389657 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
389614 TAAATTTTTG
389624 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
*
389637 AAAAAAGAAGAAA
1 AAAAAAAAAGAAA
389650 AGAAAAAA
1 A-AAAAAA
389658 TTGAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:390042 original size:17 final size:17
Alignment explanation
Indices: 390022--390070 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
390012 AAAATAGAAA
390022 AAAACAAAAAAAGAATG
1 AAAACAAAAAAAGAATG
*
390039 AAAATCAAGAAAAG-ATG
1 AAAA-CAAAAAAAGAATG
390056 AAAA-AAAATAAAGAA
1 AAAACAAAA-AAAGAA
390071 AAAAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 3 0.11
16 4 0.15
17 12 0.44
18 8 0.30
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.08
Consensus pattern (17 bp):
AAAACAAAAAAAGAATG
Found at i:390071 original size:50 final size:48
Alignment explanation
Indices: 389980--390077 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 48
389970 TTTCTTTGTG
* *
389980 AAAAAAGAAAAAATGAAGAATGAGATGAAAGAAAAATAGAAAAAAACA
1 AAAAAAGAAAAAATCAAGAATAAGATGAAAGAAAAATAGAAAAAAACA
390028 AAAAAAGAATGAAAATCAAGAA-AAGATGAAA-AAAAATAAAGAAAAAAACA
1 AAAAAAGAA--AAAATCAAGAATAAGATGAAAGAAAAAT--AGAAAAAAACA
390078 TGTTGTGTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
48 15 0.34
49 8 0.18
50 21 0.48
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.08
Consensus pattern (48 bp):
AAAAAAGAAAAAATCAAGAATAAGATGAAAGAAAAATAGAAAAAAACA
Found at i:392055 original size:164 final size:168
Alignment explanation
Indices: 391776--392094 Score: 457
Period size: 164 Copynumber: 1.9 Consensus size: 168
391766 ATGGATTTCA
* * * * **
391776 TGGGGCAAGGATATTCTGACCACTCATTCCCAATCACATCATTTTCTTTTAGCCACTATTTGGTA
1 TGGGGCAAGGATATCCCGACCACTCATTCCCAAT-ACATCA-TTCCCTTTAGCCACTAGATGGTA
* *
391841 TTAATGCATCACATGACCATAAAGGGTACAGCTCACACATTCCCAATCATATCCCCTTCACCCAA
64 TTAATGCATCACATGACCACAAAGGGTACAGCCCACACATTCCCAATCATATCCCCTTCACCCAA
*
391906 CCACTAGATGGTATTGATGCATCACAAAGCCTGATTTCCT
129 CCACTAGATGGTATTGATACATCACAAAGCCTGATTTCCT
391946 TGGGGCAAGGATATCCCGACCACTCATTCCCAAT-CAT-A-TCCCTTT-GCCACTAGATGGTATT
1 TGGGGCAAGGATATCCCGACCACTCATTCCCAATACATCATTCCCTTTAGCCACTAGATGGTATT
* * * * *
392007 GATGCATCACATGACCACAAAGGGTATAGCCCATACATTCCTAATCATATCCCTTTCACCCAACC
66 AATGCATCACATGACCACAAAGGGTACAGCCCACACATTCCCAATCATATCCCCTTCACCCAACC
*
392072 ATTAGATGGTATTGATACATCAC
131 ACTAGATGGTATTGATACATCAC
392095 TTAACCCCCT
Statistics
Matches: 134, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
164 93 0.69
165 5 0.04
167 1 0.01
168 3 0.02
170 32 0.24
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (168 bp):
TGGGGCAAGGATATCCCGACCACTCATTCCCAATACATCATTCCCTTTAGCCACTAGATGGTATT
AATGCATCACATGACCACAAAGGGTACAGCCCACACATTCCCAATCATATCCCCTTCACCCAACC
ACTAGATGGTATTGATACATCACAAAGCCTGATTTCCT
Found at i:392600 original size:44 final size:43
Alignment explanation
Indices: 392454--392606 Score: 108
Period size: 44 Copynumber: 3.4 Consensus size: 43
392444 GGCGTTAAGA
** * *
392454 CCTGGTCAAACTATCTTTATTCATTTGGCTATGTTGGCGTTAGT
1 CCTGGTCAAACT-TCTTCCTTCATTTGGTTATGTTGGCATTAGT
* * ** * * * * *
392498 CTTGGTCAAACTTTTTCCATTTTTTTTTGATTCTATTGGCATTTGAA
1 CCTGGTCAAACTTCTTCC---TTCATTTGGTTATGTTGGCATTAG-T
* *
392545 CCTTGTCAAACTGTCTTCCTTCATTTGGTTGTGTTGGCATTAGT
1 CCTGGTCAAACT-TCTTCCTTCATTTGGTTATGTTGGCATTAGT
*
392589 CCTGGTCAAACTTTTTCC
1 CCTGGTCAAACTTCTTCC
392607 ACCCTCATTT
Statistics
Matches: 79, Mismatches: 25, Indels: 11
0.69 0.22 0.10
Matches are distributed among these distances:
43 8 0.10
44 22 0.28
45 18 0.23
46 16 0.20
47 10 0.13
48 5 0.06
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (43 bp):
CCTGGTCAAACTTCTTCCTTCATTTGGTTATGTTGGCATTAGT
Found at i:392618 original size:91 final size:91
Alignment explanation
Indices: 392453--392628 Score: 217
Period size: 91 Copynumber: 1.9 Consensus size: 91
392443 TGGCGTTAAG
* * * *
392453 ACCTGGTCAAACTATCTTTATTCATTTGGCTATGTTGGCGTTAGTCTTGGTCAAACTTTTTCCAT
1 ACCTGGTCAAACTATCTTCATTCATTTGGCTATGTTGGCATTAGTCCTGGTCAAACTTTTTCCAC
** ** *
392518 TTTTTTTTGATTCTATTGGCATTTGA
66 CCTCATTTGACTCTATTGGCATTTGA
* * * * *
392544 ACCTTGTCAAACTGTCTTCCTTCATTTGGTTGTGTTGGCATTAGTCCTGGTCAAACTTTTTCCAC
1 ACCTGGTCAAACTATCTTCATTCATTTGGCTATGTTGGCATTAGTCCTGGTCAAACTTTTTCCAC
*
392609 CCTCATTTGACTGTATTGGC
66 CCTCATTTGACTCTATTGGC
392629 GTAGGACCTA
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (91 bp):
ACCTGGTCAAACTATCTTCATTCATTTGGCTATGTTGGCATTAGTCCTGGTCAAACTTTTTCCAC
CCTCATTTGACTCTATTGGCATTTGA
Found at i:392628 original size:46 final size:45
Alignment explanation
Indices: 392578--392680 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 45
392568 TTTGGTTGTG
* *
392578 TTGGCATTAGTCCTGGTCAAACTTTTTCCACCCTCATTTGACTGTA
1 TTGGC-TTAGTCCTAGTCAAACTTTTTCCACCCTCATTTAACTGTA
* * * **
392624 TTGGCGTAGGACCTAGTTAAACTTTTTCCACCCTTTTTTAACTGTA
1 TTGGCTTA-GTCCTAGTCAAACTTTTTCCACCCTCATTTAACTGTA
*
392670 TTTGCGTTAGT
1 TTGGC-TTAGT
392681 GTAGACACCT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
45 2 0.04
46 41 0.91
47 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (45 bp):
TTGGCTTAGTCCTAGTCAAACTTTTTCCACCCTCATTTAACTGTA
Found at i:393914 original size:33 final size:32
Alignment explanation
Indices: 393872--393936 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
393862 ACACACCCAG
393872 ATGTATCGATACATATTGC-TTAGTATCGATACA
1 ATGTATCGATACATATT-CATTA-TATCGATACA
* *
393905 ATGTATCGATGCATGTTCATTATATCGATACA
1 ATGTATCGATACATATTCATTATATCGATACA
393937 TCATGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGTATCGATACATATTCATTATATCGATACA
Found at i:394040 original size:24 final size:24
Alignment explanation
Indices: 394006--394057 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
393996 ATTACTGTTC
*
394006 ATCACTCTTCATCACTGCTCATGT
1 ATCACTATTCATCACTGCTCATGT
*
394030 ATCACTATTCATCACTGTTCATGT
1 ATCACTATTCATCACTGCTCATGT
394054 ATCA
1 ATCA
394058 ATACAGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (24 bp):
ATCACTATTCATCACTGCTCATGT
Found at i:394581 original size:35 final size:36
Alignment explanation
Indices: 394514--394603 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
394504 AGTGATTGTG
*
394514 AGGTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAA
1 AGGTTCTATCTTAGCCTGTGAAAAAGATAGGGAGAA
394550 AGGTTCTATCTTAG-CTCGTG-AAAAGATAGGGAG--
1 AGGTTCTATCTTAGCCT-GTGAAAAAGATAGGGAGAA
*
394583 -GTTTCTATCTTAGCCT-TGAAA
1 AGGTTCTATCTTAGCCTGTGAAA
394604 GATAGTGTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
31 2 0.04
32 14 0.29
33 2 0.04
35 15 0.31
36 16 0.33
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (36 bp):
AGGTTCTATCTTAGCCTGTGAAAAAGATAGGGAGAA
Found at i:400019 original size:155 final size:156
Alignment explanation
Indices: 399702--400034 Score: 377
Period size: 155 Copynumber: 2.1 Consensus size: 156
399692 GTTCTAATGC
* * *
399702 AAAATTACCAAAATG-CCTTTGAAATAGACCTTTGACATTAAAGTATCTCAGTAAACCTAAAAGA
1 AAAATTACCAAAATGCCCTTAGAAATAGACCTTCGACATGAAAGTATCTCAGTAAACCTAAAAGA
* ** * * *
399766 TTTGGAAAATGATCATAACAGGGTAAACCTATCCTAAATGCATACCTTTGGCATAAAAACATCTC
66 CTTGGAAAACAATCATAAAAAGGTAAACCTATCCTAAATGCATACCTTTGCCATAAAAACATCTC
* * *
399831 GATGACTACATCAGATTCGGTTCTAA
131 AATAACTACATCAAATTCGGTTCTAA
* * * ** *
399857 AATAATTAACAAAATGCCCTTAG-AGTATACCTTCGACATGAAAGTATCTTGGTAACCCTAAAAG
1 AA-AATTACCAAAATGCCCTTAGAAATAGACCTTCGACATGAAAGTATCTCAGTAAACCTAAAAG
* * * *
399921 ACTT-GAAAACAATCATAAAAAGGTGAACCTATCCTAGATGCATACTTTTGCCATAAAAGCATCT
65 ACTTGGAAAACAATCATAAAAAGGTAAACCTATCCTAAATGCATACCTTTGCCATAAAAACATCT
* * *
399985 TAATAACTACATCAAACTT-GATTTTTAA
130 CAATAACTACATCAAA-TTCG-GTTCTAA
*
400013 AAAATTACCAAAATGCCTTTAG
1 AAAATTACCAAAATGCCCTTAG
400035 GGACTACCTT
Statistics
Matches: 147, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
155 84 0.57
156 58 0.39
157 5 0.03
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (156 bp):
AAAATTACCAAAATGCCCTTAGAAATAGACCTTCGACATGAAAGTATCTCAGTAAACCTAAAAGA
CTTGGAAAACAATCATAAAAAGGTAAACCTATCCTAAATGCATACCTTTGCCATAAAAACATCTC
AATAACTACATCAAATTCGGTTCTAA
Found at i:400061 original size:155 final size:156
Alignment explanation
Indices: 399729--400078 Score: 348
Period size: 155 Copynumber: 2.2 Consensus size: 156
399719 TTTGAAATAG
* * * ** * * ** * *
399729 ACCTTTGACATTAAAGTATCTCAGTAAACCTAAAAGATTTGGAAAATGATCATAACAGGGTAAAC
1 ACCTTCGACATCAAAGCATCTTGGTAACCCTAAAAGACTTGGAAAACAATCATAAAAAGGTAAAC
* * * *
399794 CTATCCTAAATGCATACCTTTGGCATAAAAACATCTCGATGACTACATCAGATTCGGTTCTAAAA
66 CTATCCTAAATGCATACCTTTGCCATAAAAACATCTCAATAACTACATCAAATTCGGTTCTAAAA
*
399859 TAATTAACAAAATGCCCTTAGAGTAT
131 TAATTAACAAAATGCCCTTAGAGGAT
* * *
399885 ACCTTCGACATGAAAGTATCTTGGTAACCCTAAAAGACTT-GAAAACAATCATAAAAAGGTGAAC
1 ACCTTCGACATCAAAGCATCTTGGTAACCCTAAAAGACTTGGAAAACAATCATAAAAAGGTAAAC
* * * * * *
399949 CTATCCTAGATGCATACTTTTGCCATAAAAGCATCTTAATAACTACATCAAACTT-GATTTTTAA
66 CTATCCTAAATGCATACCTTTGCCATAAAAACATCTCAATAACTACATCAAA-TTCG-GTTCTAA
* *
400013 AA-AATTACCAAAATGCCTTTAG-GGACT
129 AATAATTAACAAAATGCCCTTAGAGGA-T
* * * * * *
400040 ACCTTTGTCTTCTAAGCATCTTGGTGACCCTAAAGGACT
1 ACCTTCGACATCAAAGCATCTTGGTAACCCTAAAAGACT
400079 AAGAAATAAT
Statistics
Matches: 159, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
154 2 0.01
155 114 0.72
156 43 0.27
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (156 bp):
ACCTTCGACATCAAAGCATCTTGGTAACCCTAAAAGACTTGGAAAACAATCATAAAAAGGTAAAC
CTATCCTAAATGCATACCTTTGCCATAAAAACATCTCAATAACTACATCAAATTCGGTTCTAAAA
TAATTAACAAAATGCCCTTAGAGGAT
Found at i:400915 original size:17 final size:18
Alignment explanation
Indices: 400893--400927 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
400883 TTTTATTTGA
400893 TTTATTTCG-TTTGATTT
1 TTTATTTCGATTTGATTT
*
400910 TTTATTTTGATTTGATTT
1 TTTATTTCGATTTGATTT
400928 AAATTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.03, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTATTTCGATTTGATTT
Found at i:402194 original size:13 final size:13
Alignment explanation
Indices: 402176--402200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402166 CATTTTATGG
402176 TGTATCGATACAA
1 TGTATCGATACAA
402189 TGTATCGATACA
1 TGTATCGATACA
402201 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:402195 original size:33 final size:32
Alignment explanation
Indices: 402153--402218 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
402143 CGTTACAAGC
**
402153 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTAT-GTGTATCGATA
*
402186 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
402218 C
1 C
402219 CAGTTTAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:402300 original size:20 final size:20
Alignment explanation
Indices: 402275--402336 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
402265 CTTTTTCAAA
402275 TATCGATACTGTGCAACATG
1 TATCGATACTGTGCAACATG
402295 TATCGATA-----C-A-ATG
1 TATCGATACTGTGCAACATG
402308 TATCGATACTGTGCAACATG
1 TATCGATACTGTGCAACATG
402328 TATCGATAC
1 TATCGATAC
402337 AATTAAATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 20 0.57
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACTGTGCAACATG
Found at i:402310 original size:13 final size:13
Alignment explanation
Indices: 402292--402316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402282 ACTGTGCAAC
402292 ATGTATCGATACA
1 ATGTATCGATACA
402305 ATGTATCGATAC
1 ATGTATCGATAC
402317 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:402312 original size:33 final size:33
Alignment explanation
Indices: 402275--402339 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
402265 CTTTTTCAAA
402275 TATCGATACTGTGCAACATGTATCGATACAATG
1 TATCGATACTGTGCAACATGTATCGATACAATG
402308 TATCGATACTGTGCAACATGTATCGATACAAT
1 TATCGATACTGTGCAACATGTATCGATACAAT
402340 TAAATGTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (33 bp):
TATCGATACTGTGCAACATGTATCGATACAATG
Found at i:404805 original size:13 final size:13
Alignment explanation
Indices: 404783--404821 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
404773 ATAATCCCCC
*
404783 TGTATCGATACAG
1 TGTATCGATACAA
*
404796 TGTATTGATACAA
1 TGTATCGATACAA
404809 TGTATCGATACAA
1 TGTATCGATACAA
404822 AGAATGATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:406909 original size:15 final size:15
Alignment explanation
Indices: 406889--406918 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
406879 GTTCATCAAT
406889 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
406904 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
406919 CTCAATTCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Done.