Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1017
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: 65279
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6699 original size:35 final size:35
Alignment explanation
Indices: 6653--6722 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
6643 CTTAACTTAG
*
6653 ATTTGTTTCAAGGGTTTTGGAAACTTGATCTTGAA
1 ATTTGCTTCAAGGGTTTTGGAAACTTGATCTTGAA
* *
6688 ATTTGCTTCAAGGGTTTTTGAGACTTGATCTTGAA
1 ATTTGCTTCAAGGGTTTTGGAAACTTGATCTTGAA
6723 TCAATAGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.43
Consensus pattern (35 bp):
ATTTGCTTCAAGGGTTTTGGAAACTTGATCTTGAA
Found at i:6835 original size:35 final size:35
Alignment explanation
Indices: 6795--6866 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
6785 CTTGATCATG
*
6795 AATCTTGCTTTAAGGGTCATT-AAACTTCATCTTGA
1 AATCTTGCTTCAAGGGTC-TTCAAACTTCATCTTGA
*
6830 AATCTTGCTTCAAGGGTCTTCAAACTTGATCTTGA
1 AATCTTGCTTCAAGGGTCTTCAAACTTCATCTTGA
6865 AA
1 AA
6867 AACAAAGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (35 bp):
AATCTTGCTTCAAGGGTCTTCAAACTTCATCTTGA
Found at i:7308 original size:41 final size:41
Alignment explanation
Indices: 7263--7400 Score: 134
Period size: 46 Copynumber: 3.3 Consensus size: 41
7253 AAATTAATTT
* * *
7263 TTAATTTAATTAAAGATAAAACTCTTTTATTTATCCCTTGA
1 TTAATTTAATTAAAGATAAAATTCTTTTATTTATCTCTTAA
* * *
7304 TTAATTTAATTGAATCAGAGATAAAATTCTTTGATTCATCTTTTAA
1 TTAATTTAATT--A--A-AGATAAAATTCTTTTATTTATCTCTTAA
* * *
7350 TTAATTTAATTAGAGAT-AAATTATTTTATTTATGTCTTAA
1 TTAATTTAATTAAAGATAAAATTCTTTTATTTATCTCTTAA
*
7390 TTAATATAATT
1 TTAATTTAATT
7401 TAATTAGAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
40 28 0.35
41 15 0.19
43 1 0.01
44 1 0.01
45 1 0.01
46 33 0.42
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (41 bp):
TTAATTTAATTAAAGATAAAATTCTTTTATTTATCTCTTAA
Found at i:8212 original size:78 final size:78
Alignment explanation
Indices: 8052--8307 Score: 270
Period size: 78 Copynumber: 3.3 Consensus size: 78
8042 TTGAGTAGGT
* * ** * *
8052 AGTTTAAGCTCGTGCTTAGGAG-TATCATAATAGTTTAAGCTTTTGTTTAGGAGCGACAA--CTT
1 AGTTTAAGCTCATGCTTAGGAGCAAT-ATAATAGTTTAAGCTCGTGTTTAGGAGC-ATAATTATT
*
8114 TT-TTTTTTGGAGGAAC
64 TTGTTTTTTTGA--AAC
* *
8130 AGTTTGAGCTCATGCTTAGGAGCAATATAACAGTTTAAGCTCGTGTTTAGGAGCATAATTATTTT
1 AGTTTAAGCTCATGCTTAGGAGCAATATAATAGTTTAAGCTCGTGTTTAGGAGCATAATTATTTT
*
8195 GTTTTTTTGAAAT
66 GTTTTTTTGAAAC
* * * * ** *
8208 AGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGTTTAGGAGTGTCATTATTTT
1 AGTTTAAGCTCATGCTTAGGAGCAATATAATAGTTTAAGCTCGTGTTTAGGAGCATAATTATTTT
8273 G-TTTTTTGAAAC
66 GTTTTTTTGAAAC
* *
8285 AGTTTAAGCTTATGTTTAGGAGC
1 AGTTTAAGCTCATGCTTAGGAGC
8308 TTAATCATAT
Statistics
Matches: 152, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
77 34 0.22
78 104 0.68
79 6 0.04
80 8 0.05
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (78 bp):
AGTTTAAGCTCATGCTTAGGAGCAATATAATAGTTTAAGCTCGTGTTTAGGAGCATAATTATTTT
GTTTTTTTGAAAC
Found at i:8391 original size:119 final size:117
Alignment explanation
Indices: 8198--8420 Score: 295
Period size: 119 Copynumber: 1.9 Consensus size: 117
8188 TTATTTTGTT
* * * **
8198 TTTTTGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGTTTAGGAGTG
1 TTTTAGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGCTTAAGAGCA
* * *
8263 TCATTATTTTGTTTTTTGAAACAGTTTAAGCTTATGTTTAGGAGCTTAATCATA
66 TCATCA-TTT-TTTTTTGAAACAATTTAAGCTCATGTTTAGGAGCTTAATCATA
* * **
8317 TTTTAGAAATAGTTTAAGCTCGTGTTTAGGAGTGATATAGTAGTTTGAGCAT-GTGCTTAAGAGC
1 TTTTAGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGC-TCGTGCTTAAGAGC
*
8381 ATCATCATTTTTTTTTGAAATAATTTAAGCTCATGTTTAG
65 ATCATCATTTTTTTTTGAAACAATTTAAGCTCATGTTTAG
8421 AAGGATATAA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
117 27 0.30
118 3 0.03
119 59 0.66
120 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (117 bp):
TTTTAGAAATAGTTTAAGCTCATGTTTAGAAGCAATATAGTAGTTTGAGCTCGTGCTTAAGAGCA
TCATCATTTTTTTTTGAAACAATTTAAGCTCATGTTTAGGAGCTTAATCATA
Found at i:8963 original size:109 final size:108
Alignment explanation
Indices: 8772--8985 Score: 401
Period size: 109 Copynumber: 2.0 Consensus size: 108
8762 TAAAGAAAAA
*
8772 GATTGGCTTTATTCCCTTAGAGATCCACCATTATACTTATGCTTTGAGCTAGAATAATAAGATTA
1 GATTGGCTTTATTCCCTTAGAGATCCACCATCATACTTATGCTTTGAGCTAGAATAATAAGATTA
8837 AAAGAGTCAAATTTTATGGTTCTATTGAACTGATTAGATTGCAT
66 AAAGAGTCAAATTTTATGGTTCTATT-AACTGATTAGATTGCAT
*
8881 GATTGGCTTTATTCCCTTAGAGATCCACCATCGTACTTATGCTTTGAGCTAGAATAATAAGATTA
1 GATTGGCTTTATTCCCTTAGAGATCCACCATCATACTTATGCTTTGAGCTAGAATAATAAGATTA
8946 AAAGAGTCAAATTTTATGGTTCTATTAACTGATTAGATTG
66 AAAGAGTCAAATTTTATGGTTCTATTAACTGATTAGATTG
8986 AAAAACCATG
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 14 0.14
109 89 0.86
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (108 bp):
GATTGGCTTTATTCCCTTAGAGATCCACCATCATACTTATGCTTTGAGCTAGAATAATAAGATTA
AAAGAGTCAAATTTTATGGTTCTATTAACTGATTAGATTGCAT
Found at i:11911 original size:14 final size:14
Alignment explanation
Indices: 11890--11923 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11880 TGGGGCAAAT
11890 AAGATACCCTTGGA
1 AAGATACCCTTGGA
*
11904 AGGATACCCTTGGA
1 AAGATACCCTTGGA
11918 AAGATA
1 AAGATA
11924 TTTTGACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (14 bp):
AAGATACCCTTGGA
Found at i:13614 original size:17 final size:17
Alignment explanation
Indices: 13571--13613 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
13561 CTAGTTAGGT
* *
13571 AAGACAAAAAGAAGATG
1 AAGAAAAAAAGAAGATA
*
13588 AAGAAGAAAAGAAGA-A
1 AAGAAAAAAAGAAGATA
13604 AAGAAAAAAA
1 AAGAAAAAAA
13614 ACATATGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (17 bp):
AAGAAAAAAAGAAGATA
Found at i:15322 original size:97 final size:96
Alignment explanation
Indices: 15163--15409 Score: 334
Period size: 97 Copynumber: 2.5 Consensus size: 96
15153 AATTTTATTT
* * * *
15163 ATCGGGGATACTCCAACCCTATTCCTCTAATGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1 ATCGGGGACACTTCAACCC-ATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
*
15228 GTTTAAATCTTATTCTTAGTTAAATTGCCACC
65 GTTTAAATCTTATTCTTACTTAAATTGCCACC
**
15260 ATCGGGGACACTTCAACTCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAAGGCATCAAA
1 ATCGGGGACACTTCAAC-CCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
* * *
15325 GTTTAAATTTTATTCTTACTTAAATTGTCATC
65 GTTTAAATCTTATTCTTACTTAAATTGCCACC
* * *
15357 ATCGGGGACA-TTCCAACCCCATTCCTCCGAGGGGATACTTCAACCCCGTTTTT
1 ATCGGGGACACTT-CAA-CCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTT
15410 CAATCAAAAA
Statistics
Matches: 134, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
96 2 0.01
97 129 0.96
98 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (96 bp):
ATCGGGGACACTTCAACCCATTCCTCTGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAG
TTTAAATCTTATTCTTACTTAAATTGCCACC
Found at i:20169 original size:37 final size:36
Alignment explanation
Indices: 20128--20202 Score: 82
Period size: 37 Copynumber: 2.0 Consensus size: 36
20118 AAAAAATGTC
*
20128 AAAA-GCAAAAGTACAAAATATGAAAA-GAAAAACAAAA
1 AAAAGGCAAAAG--CAAAATA-AAAAAGGAAAAACAAAA
*
20165 AAAAGTGCAAAAGCAAAATAAAAAAGGAACAACAAAA
1 AAAAG-GCAAAAGCAAAATAAAAAAGGAAAAACAAAA
20202 A
1 A
20203 TCCAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
36 4 0.12
37 22 0.67
39 7 0.21
ACGTcount: A:0.72, C:0.09, G:0.12, T:0.07
Consensus pattern (36 bp):
AAAAGGCAAAAGCAAAATAAAAAAGGAAAAACAAAA
Found at i:20209 original size:45 final size:46
Alignment explanation
Indices: 20114--20214 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 46
20104 CATCATAATG
* *
20114 ACAAAAAAAA-TGTCAAAAGCAAAAGTACAAAATATGAAAAGAAAA
1 ACAAAAAAAAGTGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAA
20159 ACAAAAAAAAGTG-CAAAAGCAAAA-TA-AAAA-AGGAACAACAAAA
1 ACAAAAAAAAGTGTCAAAAGCAAAAGTACAAAATAGGAA-AACAAAA
20202 ATCCAAAAAAAAG
1 A--CAAAAAAAAG
20215 ACATGAATGC
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
42 4 0.08
43 11 0.22
44 2 0.04
45 31 0.62
46 2 0.04
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.08
Consensus pattern (46 bp):
ACAAAAAAAAGTGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAA
Found at i:21509 original size:27 final size:27
Alignment explanation
Indices: 21474--21746 Score: 352
Period size: 27 Copynumber: 10.0 Consensus size: 27
21464 TTTCTTTTCA
21474 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
21501 ATGTCCACAACTCCGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
21528 AAAGTCTAAAACTTCGTGGCA-CTCTTTT
1 -AAGTCCACAACTCCGTGGCATC-CTTTT
*
21556 AAAGTCCACAACTCCGTGGCATCTTTTT
1 -AAGTCCACAACTCCGTGGCATCCTTTT
*
21584 AAGTCCACAACTCCGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* * *
21611 AAATCCACAACTCCGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
21638 AAGTCCACAACTCCGTGGCACCCGTTTC
1 AAGTCCACAACTCCGTGGCATCC-TTTT
* *
21666 AAGTCCACAACTCTGTGGCGTTCCTTTT
1 AAGTCCACAACTCCGTGGC-ATCCTTTT
21694 AAG-CCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
21720 AAGTCCACAACTTCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
21747 TACGCCCACA
Statistics
Matches: 216, Mismatches: 24, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
26 10 0.05
27 134 0.62
28 69 0.32
29 3 0.01
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:21701 original size:109 final size:109
Alignment explanation
Indices: 21474--21745 Score: 375
Period size: 109 Copynumber: 2.5 Consensus size: 109
21464 TTTCTTTTCA
* ** *
21474 AAGTCCACAACTCCGTGGCATCCTTTTATGTCCACAACTCCGTGGCATCTTTTTAAAGTCTAAAA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTAAAGTCCAAAA
* * * *
21539 CTTCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCATCTTTTT
65 CTCCGTGGCACCCGTTTAAAGTCCACAACTCCGTGGCATCCTTTT
* * *
21584 AAGTCCACAACTCCGTGGCATCTTTTTAAATCCACAACTCCGTGGCACCCTTTAAAGTCCACAAC
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCAAAAC
* * *
21649 TCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCCTTTT
66 TCCGTGGCACCCGTTTAAAGTCCACAACTCCGTGGC-ATCCTTTT
* *
21694 AAG-CCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
21746 TTACGCCCAC
Statistics
Matches: 143, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
109 90 0.63
110 53 0.37
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (109 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCAAAAC
TCCGTGGCACCCGTTTAAAGTCCACAACTCCGTGGCATCCTTTT
Found at i:21756 original size:55 final size:54
Alignment explanation
Indices: 21474--21811 Score: 351
Period size: 55 Copynumber: 6.2 Consensus size: 54
21464 TTTCTTTTCA
*
21474 AAGTCCACAACTCCGTGGCATCCTTTTATGTCCACAACTCCGTGGCATCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * *
21528 AAAGTCTAAAACTTCGTGGCA-CTCTTTTAAAGTCCACAACTCCGTGGCATCTTTTT
1 -AAGTCCACAACTCCGTGGCATC-CTTTT-AAGTCCACAACTCCGTGGCATCTTTTT
* * * * *
21584 AAGTCCACAACTCCGTGGCATCTTTTTAAATCCACAACTCCGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * * * *
21638 AAGTCCACAACTCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCCTTTT
1 AAGTCCACAACTCCGTGGCATCC-TTTTAAGTCCACAACTCCGTGGC-ATCTTTTT
*
21694 AAG-CCACAACTCCGTGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCAT-CTTTTT
* * * * ** * * *
21748 ACGCCCACAAGTCAGTGGCA--CTATCCAAAGTCCATAACTTCGTGGCATTTTTTT
1 AAGTCCACAACTCCGTGGCATCCT-T-TTAAGTCCACAACTCCGTGGCATCTTTTT
*
21802 AAGCCCACAA
1 AAGTCCACAA
21812 GTCAATGGCA
Statistics
Matches: 240, Mismatches: 34, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
53 3 0.01
54 87 0.36
55 115 0.48
56 35 0.15
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (54 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
Found at i:21756 original size:82 final size:81
Alignment explanation
Indices: 21474--21767 Score: 360
Period size: 82 Copynumber: 3.6 Consensus size: 81
21464 TTTCTTTTCA
* * *
21474 AAGTCCACAACTCCGTGGCATCC-TTTTATGTCCACAACTCCGTGGCATCTTTTTAAAGTCTAAA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAAG-CCACA
*
21538 ACTTCGTGGCACTCTTTT
65 ACTCCGTGGCAC-CTTTT
*
21556 AAAGTCCACAACTCCGTGGCAT-CTTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAATCCACA
1 -AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAAGCCACA
*
21620 ACTCCGTGGCACCCTTTA
65 ACTCCGTGGCA-CCTTTT
* * * * * *
21638 AAGTCCACAACTCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCCTTTT-AAGCCACA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGC-ATCTTTTTAAAGCCACA
21702 ACTCCGTGGCATCCTTTT
65 ACTCCGTGGCA-CCTTTT
* * * * *
21720 AAGTCCACAACTTCGTGGCATCCTTTTTACGCCCACAAGTCAGTGGCA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCA
21768 CTATCCAAAG
Statistics
Matches: 183, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
81 20 0.11
82 102 0.56
83 61 0.33
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (81 bp):
AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAAGCCACAA
CTCCGTGGCACCTTTT
Found at i:21792 original size:82 final size:83
Alignment explanation
Indices: 21474--21811 Score: 341
Period size: 82 Copynumber: 4.1 Consensus size: 83
21464 TTTCTTTTCA
* ** * *
21474 AAGTCCACAACTCCGTGGCATCC-TTTTATGTCCACAACTCCGTGGCATCTTTTTAAAGTCTAAA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTCCAAAGTCCACA
*
21538 ACTTCGTGGCA-CTCTTTT
66 ACTCCGTGGCATC-CTTTT
**
21556 AAAGTCCACAACTCCGTGGCAT-CTTTTTAAGTCCACAACTCCGTGGCATCTTTTTAAA-TCCAC
1 -AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTCCAAAGTCCAC
* *
21619 AACTCCGTGGCACCCTTTA
65 AACTCCGTGGCATCCTTTT
* * * * * *
21638 AAGTCCACAACTCCGTGGCACCCGTTTCAAGTCCACAACTCTGTGGCGTTCCTTT--TAAG-CCA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGC-AT-CTTTCCAAAGTCCA
21700 CAACTCCGTGGCATCCTTTT
64 CAACTCCGTGGCATCCTTTT
* * * * * * *
21720 AAGTCCACAACTTCGTGGCATCCTTTTTACGCCCACAAGTCAGTGGCA-CTATCCAAAGTCCATA
1 AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTCCAAAGTCCACA
* **
21784 ACTTCGTGGCATTTTTTT
66 ACTCCGTGGCATCCTTTT
*
21802 AAGCCCACAA
1 AAGTCCACAA
21812 GTCAATGGCA
Statistics
Matches: 217, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
79 3 0.01
81 23 0.11
82 131 0.60
83 56 0.26
84 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (83 bp):
AAGTCCACAACTCCGTGGCATCCTTTTTAAGTCCACAACTCCGTGGCATCTTTCCAAAGTCCACA
ACTCCGTGGCATCCTTTT
Found at i:22049 original size:28 final size:28
Alignment explanation
Indices: 21455--22362 Score: 644
Period size: 28 Copynumber: 31.9 Consensus size: 28
21445 AGTTCATGAT
* * *
21455 TCAGTGGCATTTCTTTTCAAAGTCCACAAC
1 TCAGTGGCA--TCCTTTCAAAGCCCACAAG
* * * * *
21485 TCCGTGGCATCCTTT-TATGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * * * * *
21512 TCCGTGGCATCTTTTTAAAGTCTAAAACT
1 TCAGTGGCATCCTTTCAAAGCCCACAA-G
* * *
21541 TC-GTGGCA-CTCTTTTAAAGTCCACAAC
1 TCAGTGGCATC-CTTTCAAAGCCCACAAG
* ** * *
21568 TCCGTGGCAT-CTTTTTAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * * *
21595 TCCGTGGCATCTTTTTAAA-TCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * *
21622 TCCGTGGCACCCTTT-AAAGTCCACAAC
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * *
21649 TCCGTGGCACCCGTTTC-AAGTCCACAAC
1 TCAGTGGCATCC-TTTCAAAGCCCACAAG
* * * *
21677 TCTGTGGCGTTCCTTT-TAAG-CCACAAC
1 TCAGTGGC-ATCCTTTCAAAGCCCACAAG
* * * *
21704 TCCGTGGCATCCTTT-TAAGTCCACAACT
1 TCAGTGGCATCCTTTCAAAGCCCACAA-G
** *
21732 TC-GTGGCATCCTTTTTACGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * * *
21759 TCAGTGGCA--CTATCCAAAGTCCATAACT
1 TCAGTGGCATCCT-TTCAAAGCCCACAA-G
* **
21787 TC-GTGGCAT-TTTTTTAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* * *
21813 TCAATGGCACCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* ** *
21841 TCAGTGGCACCCCTTTTTAAGCCCATAAG
1 TCAGTGGCA-TCCTTTCAAAGCCCACAAG
**
21870 TCAGTGGCATTATTTCAAAGCCCACACAAG
1 TCAGTGGCATCCTTTCAAAG-CC-CACAAG
** * *
21900 TTGGTGGCAACTCATTTGAAAGCCGACACAAG
1 TCAGTGGC-A-TCCTTTCAAAGCC--CACAAG
* *
21932 TCGGTGGCAACCCATTTCAAAGCCCACATAAG
1 TCAGTGGC-ATCC-TTTCAAAGCCCAC--AAG
*
21964 TC-GTTGGCAACCCATTTCAAAGCCCACAAG
1 TCAG-TGGC-ATCC-TTTCAAAGCCCACAAG
*
21994 TCAATGGCATCCTTCTCAAAGCCCACAAG
1 TCAGTGGCATCCTT-TCAAAGCCCACAAG
22023 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
22051 TTAGTGGCATCCTTCTCAAAGCCCACACAAA
1 TCAGTGGCATCCTT-TCAAAG-CC-CACAAG
* *
22082 TCAGTGACATCTTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
22110 TCAGTGGCATCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
22138 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
22166 TTAGTGGCATCCTTTTAAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
* *
22194 TTAGTGGCATCCTTCTCAAAGCTCACACAAA
1 TCAGTGGCATCCTT-TCAAAGC-C-CACAAG
* *
22225 TC-GATGGCATCTTTTCAAAGCCCATAAG
1 TCAG-TGGCATCCTTTCAAAGCCCACAAG
*
22253 TCAGTGGCATCCTTTCAAAGCCCATAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
**
22281 TCAGTGGCATCCTTTTGAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
*
22309 TCAGTGGCATCCTTTCGAAGCCCACAAG
1 TCAGTGGCATCCTTTCAAAGCCCACAAG
22337 TCAGTGGCATCCTTTCAAAGCCCACA
1 TCAGTGGCATCCTTTCAAAGCCCACA
22363 CAAGTTAATG
Statistics
Matches: 746, Mismatches: 92, Indels: 82
0.81 0.10 0.09
Matches are distributed among these distances:
26 17 0.02
27 156 0.21
28 349 0.47
29 78 0.10
30 48 0.06
31 36 0.05
32 62 0.08
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (28 bp):
TCAGTGGCATCCTTTCAAAGCCCACAAG
Found at i:22153 original size:115 final size:112
Alignment explanation
Indices: 21707--22360 Score: 590
Period size: 115 Copynumber: 5.7 Consensus size: 112
21697 CCACAACTCC
* * * *
21707 GTGGCATCCTTTT-AAGTCCACAACTTC-GTGGCATCCTTTT-TACGCCCACAAGTCAGTGGCA-
1 GTGGCATCCTTTTAAAGCCCACAA-GTCAGTGGCAT-CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * * ** *
21768 -CTATCCAAAGTCCATAACTTC-GTGGCAT-TTTTTTAAGCCCACAAGTCA
64 CCT-TTCAAAGCCCATAA-GTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
* * * * * * *
21816 ATGGCACCCTTTCAAAGCCCATAAGTCAGTGGCACCCCTTTT-TAAGCCCATAAGTCAGTGGCAT
1 GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCA--TCTTTTCAAAGCCCACAAGTCAGTGGCAT
** * ** * * **
21880 TATTTCAAAGCCCACACAAGTTGGTGGCAACTCATTTGAAAGCCGACACAAGTCG
64 CCTTTCAAAG-CC-CATAAGTCAGTGGC-A-TCCTTTCAAAGCC--CACAAGTTA
* * * * *
21935 GTGGCAACCCATTTCAAAGCCCACATAAGTC-GTTGGCAACCCATTTCAAAGCCCACAAGTCAAT
1 GTGGC-ATCC-TTTTAAAGCCCAC--AAGTCAG-TGGC-A-TCTTTTCAAAGCCCACAAGTCAGT
*
21999 GGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
59 GGCATCCTT-TCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
* * *
22054 GTGGCATCCTTCTCAAAGCCCACACAAATCAGTGACATCTTTTCAAAGCCCACAAGTCAGTGGCA
1 GTGGCATCCTT-TTAAAG-CC-CACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCA
22119 TCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
63 TCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
* * *
22169 GTGGCATCCTTTTAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCTCACACAAATC-GATGGC
1 GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCAT-CTTTTCAAAGC-C-CACAAGTCAG-TGGC
* * *
22233 ATCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCA
62 ATCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
* * *
22284 GTGGCATCCTTTTGAAGCCCACAAGTCAGTGGCATCCTTTCGAAGCCCACAAGTCAGTGGCATCC
1 GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCC
22349 TTTCAAAGCCCA
66 TTTCAAAGCCCA
22361 CACAAGTTAA
Statistics
Matches: 458, Mismatches: 56, Indels: 59
0.80 0.10 0.10
Matches are distributed among these distances:
109 12 0.03
110 14 0.03
111 24 0.05
112 45 0.10
113 17 0.04
114 24 0.05
115 148 0.32
116 31 0.07
117 11 0.02
118 16 0.03
119 27 0.06
120 7 0.02
121 23 0.05
122 2 0.00
123 27 0.06
124 24 0.05
125 6 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (112 bp):
GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCC
TTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTA
Found at i:22180 original size:143 final size:141
Alignment explanation
Indices: 21787--22365 Score: 721
Period size: 143 Copynumber: 4.0 Consensus size: 141
21777 GTCCATAACT
** *
21787 TCGTGGCAT-TTTTTTAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCATAAGTCAGTGGCAC
1 TCGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCA-
* ** * ** * *
21851 CCCTTTTTAAGCCCATAAGTCAGTGGCATTATTTCAAAGCCCACACAAGTTGGTGGCAACTCATT
65 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGTTAGTGGC-A-TCCTT
* * *
21916 TGAAAGCCGACACAAG
126 TCAAAGCCCACACAAA
* * *
21932 TCGGTGGCAACCCATTTCAAAGCCCACATAAGTC-GTTGGCAACCCATTTCAAAGCCCACAAGTC
1 TC-GTGGC-A-TCTTTTCAAAGCCCAC--AAGTCAG-TGGC-ACCC-TTTCAAAGCCCATAAGTC
*
21996 AATGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAT
58 AGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAT
22061 CCTTCTCAAAGCCCACACAAA
122 CCTT-TCAAAGCCCACACAAA
* *
22082 TCAGTGACATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCA
1 TC-GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCA
* *
22147 TCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTTAGTGGCATCCTTCTCA
65 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTT-TCA
*
22212 AAGCTCACACAAA
129 AAGCCCACACAAA
* *
22225 TCGATGGCATCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCA
1 TCG-TGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCA
** * *
22290 TCCTTTTGAAGCCCACAAGTCAGTGGCATCCTTTCGAAGCCCACAAGTCAGTGGCATCCTTTCAA
65 TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAA
22355 AGCCCACACAA
130 AGCCCACACAA
22366 GTTAATGGCT
Statistics
Matches: 384, Mismatches: 37, Indels: 29
0.85 0.08 0.06
Matches are distributed among these distances:
142 15 0.04
143 186 0.48
144 28 0.07
145 5 0.01
146 14 0.04
147 2 0.01
148 14 0.04
149 16 0.04
150 20 0.05
151 22 0.06
152 10 0.03
153 52 0.14
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (141 bp):
TCGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCAT
CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAA
GCCCACACAAA
Found at i:22526 original size:45 final size:47
Alignment explanation
Indices: 22475--22591 Score: 139
Period size: 48 Copynumber: 2.5 Consensus size: 47
22465 AAGTCTGATA
* *
22475 TCGCTGGCATTGAATCAGCATATTG-GCACCTTT-ATTAGCTTAATG
1 TCGCTGGCCTTGAATCAGCACATTGTGCACCTTTCATTAGCTTAATG
* * *
22520 TCGCTGGCCTTGAATCAGCACATTGTTCACTTTTCCCTTAGCTTAATG
1 TCGCTGGCCTTGAATCAGCACATTGTGCACCTTT-CATTAGCTTAATG
* **
22568 TTGCTGGCCTTGAATTGGCACATT
1 TCGCTGGCCTTGAATCAGCACATT
22592 AGCACTCCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 23 0.38
46 6 0.10
48 32 0.52
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (47 bp):
TCGCTGGCCTTGAATCAGCACATTGTGCACCTTTCATTAGCTTAATG
Found at i:25146 original size:97 final size:97
Alignment explanation
Indices: 25014--25253 Score: 322
Period size: 97 Copynumber: 2.5 Consensus size: 97
25004 AATTTTAATT
**
25014 ATCGGGGATAC-TCTAACCCTATTCCTCCAAGGGGATACTCCAACCCAGCTTTTAAACACATCAA
1 ATCGGGGATACTTC-AACCCTATTCCTCTGAGGGGATACTCCAACCCAGCTTTTAAACACATCAA
* *
25078 ATTTTAAATCTTATTCTCACTTAAATTGTCACC
65 AGTTTAAATCTTATTCTAACTTAAATTGTCACC
* *
25111 ATCGGGGATACTTCAACCCTATTCCTCTGAGGGGATACTCCAACCCTGCTTTTAAACGCATCAAA
1 ATCGGGGATACTTCAACCCTATTCCTCTGAGGGGATACTCCAACCCAGCTTTTAAACACATCAAA
* *
25176 GTTTAAATTTTATTCTAACTTAAATTGTCATC
66 GTTTAAATCTTATTCTAACTTAAATTGTCACC
* * * * * *
25208 ATCGAGGACACTCCAACCCCATT-CTTTCGAGAGGATACTCCAACCC
1 ATCGGGGATACTTCAACCCTATTCCTCT-GAGGGGATACTCCAACCC
25254 CATTTTTCAA
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
96 3 0.02
97 122 0.96
98 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (97 bp):
ATCGGGGATACTTCAACCCTATTCCTCTGAGGGGATACTCCAACCCAGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTAACTTAAATTGTCACC
Found at i:25247 original size:27 final size:26
Alignment explanation
Indices: 25211--25261 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
25201 TGTCATCATC
25211 GAGGACACTCCAACCCCATTCTTTCGA
1 GAGGACACTCCAACCCCATT-TTTCGA
*
25238 GAGGATACTCCAACCCCATTTTTC
1 GAGGACACTCCAACCCCATTTTTC
25262 AATCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.25, C:0.35, G:0.14, T:0.25
Consensus pattern (26 bp):
GAGGACACTCCAACCCCATTTTTCGA
Found at i:34089 original size:11 final size:12
Alignment explanation
Indices: 34057--34097 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
34047 TTGGAAAGGT
*
34057 AATTTCATG-AA
1 AATTTTATGAAA
*
34068 ATTTTTATGAAA
1 AATTTTATGAAA
34080 AATTTT-TGAAA
1 AATTTTATGAAA
34091 AATTTTA
1 AATTTTA
34098 AAAAATCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (12 bp):
AATTTTATGAAA
Found at i:35804 original size:20 final size:20
Alignment explanation
Indices: 35779--35853 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
35769 GTAAAAAGAC
35779 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
** *
35799 AGAATGTATCGATATGTTCA
1 AGAATGTATCGATACATTGA
* *
35819 TA-CATTTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
35839 AAAATGTATCCATAC
1 AGAATGTATCGATAC
35854 TCTGGGTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:35894 original size:89 final size:91
Alignment explanation
Indices: 35736--35901 Score: 291
Period size: 89 Copynumber: 1.8 Consensus size: 91
35726 ACTAGATGTG
* *
35736 TCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAG
1 TCGATACATTGAAAAATGTATCCATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAA
35801 AATGTATCGATATGTTCATACATTTA
66 AATGTATCGATATGTTCATACATTTA
*
35827 TCGATACATTGAAAAATGTATCCATAC-TCTGGGT-AAAAGACAGAATGTATTGATACATTGAAA
1 TCGATACATTGAAAAATGTATCCATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAA
35890 AATGTATCGATA
66 AATGTATCGATA
35902 CATCTGGGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
89 39 0.54
90 7 0.10
91 26 0.36
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (91 bp):
TCGATACATTGAAAAATGTATCCATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAA
AATGTATCGATATGTTCATACATTTA
Found at i:38165 original size:68 final size:68
Alignment explanation
Indices: 38039--38166 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 68
38029 CTTGACTCGA
* * * * * **
38039 ACTTAGGTGCCACCAGCTTGTGTGGGCATTGACTCAAGTGCTGCCAGCTTGTGCAGGCTTTAACT
1 ACTTAGGTGCCACCAACTTATGTGGGCATTGACTCAAGTACCGCCAACTCCTGCAGGCTTTAACT
38104 CAG
66 CAG
* * *
38107 ACTTAGGTGCCACCAACTTATGTGGGCTTTGACTCAGGTACCGCCAACTCCTGTAGGCTT
1 ACTTAGGTGCCACCAACTTATGTGGGCATTGACTCAAGTACCGCCAACTCCTGCAGGCTT
38167 AGACTCGGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 50 1.00
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.28
Consensus pattern (68 bp):
ACTTAGGTGCCACCAACTTATGTGGGCATTGACTCAAGTACCGCCAACTCCTGCAGGCTTTAACT
CAG
Found at i:38264 original size:31 final size:30
Alignment explanation
Indices: 38220--38400 Score: 89
Period size: 31 Copynumber: 5.7 Consensus size: 30
38210 AAGAGCTACT
* **
38220 AGCTTGTGTGGGCTTTGACTCAGGTGCTGCC
1 AGCTTGT-AGGGCTTTGACTCAGGTGCCACC
38251 AGCTTGTACGGGCTTTGACT-AGGGTGCCACC
1 AGCTTGTA-GGGCTTTGACTCA-GGTGCCACC
* * *
38282 AACTCGTAAGGCTTTGACTCAGGTTTAGGTGCCACC
1 AGCTTGTAGGGCTTTGACTC------AGGTGCCACC
* * * *
38318 AGCTTGT-GTAGCTTTGACTTAGGTGCCGCT
1 AGCTTGTAG-GGCTTTGACTCAGGTGCCACC
* * * *
38348 AACTCGTGT-GGGCTTAGACTTAGGTGCAACC
1 AGCT--TGTAGGGCTTTGACTCAGGTGCCACC
*
38379 AGCTTGTACGAGCTTTGACTCA
1 AGCTTGTA-GGGCTTTGACTCA
38401 AGCTTAGGTG
Statistics
Matches: 113, Mismatches: 23, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
29 3 0.03
30 22 0.19
31 60 0.53
32 4 0.04
36 23 0.20
37 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.30
Consensus pattern (30 bp):
AGCTTGTAGGGCTTTGACTCAGGTGCCACC
Found at i:38396 original size:196 final size:195
Alignment explanation
Indices: 38093--38596 Score: 580
Period size: 196 Copynumber: 2.6 Consensus size: 195
38083 CAGCTTGTGC
* * * * * *
38093 AGGCTTTAACTCAGACTTAGGTGCCACCAACTTATGTGGGCTTTGACTCAGGTACCGCCAACTCC
1 AGGCTTTGACTCAGGCTTAGGTGCCACCAACTTGTGT-AGCTTTGACTCAGGTGCCGCCAACTCA
* ** * * * * *
38158 TGTAGGCTTAGACTCGGGTGTCGCTAGTTTGTGCGGGCTTTGACTCAAGCTTAAGAGCTACTAGC
65 TGTGGGCTTAGACTTAGGTG-CACCAGCTTGTGCGAGCTTTGACTCAAGCTTAAGAGCCACTAGC
** * * *
38223 TTGTGTGGGCTTTGACTCAGGT-GCTGCCAGCTTGTACGGGCTTTGACTAGGGTGCCACCAACTC
129 TTGTGTAAGCTTTGACTCAAGTATC-GCCAGCTTGTACAGGCTTTGACTAGGGTGCCACCAACTC
38287 GTA
193 GTA
* * * * *
38290 AGGCTTTGACTCAGGTTTAGGTGCCACCAGCTTGTGTAGCTTTGACTTAGGTGCCGCTAACTCGT
1 AGGCTTTGACTCAGGCTTAGGTGCCACCAACTTGTGTAGCTTTGACTCAGGTGCCGCCAACTCAT
* * * *
38355 GTGGGCTTAGACTTAGGTGCAACCAGCTTGTACGAGCTTTGACTCAAGCTTAGGTGCCATTAGCT
66 GTGGGCTTAGACTTAGGTGC-ACCAGCTTGTGCGAGCTTTGACTCAAGCTTAAGAGCCACTAGCT
**
38420 TGTGTAAGCTTTGACTCAAGTATCGCCAGCTTGTGTAGGCTTTGACTAGGGTGCCACCAACTCGT
130 TGTGTAAGCTTTGACTCAAGTATCGCCAGCTTGTACAGGCTTTGACTAGGGTGCCACCAACTCGT
*
38485 G
195 A
* * * * * *
38486 TGGAATTTGACTCAGGCTTAGGTGCCACCAACTTGTGTAGGTTTTAACTCAAGTGCCACCAACTC
1 AGG-CTTTGACTCAGGCTTAGGTGCCACCAACTTGTGTA-GCTTTGACTCAGGTGCCGCCAACTC
*
38551 ATAG-GGGCTTAGACTTAGGTGGCTCCAGCTTGTGCGAGCTTTGACT
64 AT-GTGGGCTTAGACTTAGGT-GCACCAGCTTGTGCGAGCTTTGACT
38597 TAGGTGCTGC
Statistics
Matches: 258, Mismatches: 43, Indels: 11
0.83 0.14 0.04
Matches are distributed among these distances:
195 1 0.00
196 132 0.51
197 65 0.25
198 57 0.22
199 3 0.01
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (195 bp):
AGGCTTTGACTCAGGCTTAGGTGCCACCAACTTGTGTAGCTTTGACTCAGGTGCCGCCAACTCAT
GTGGGCTTAGACTTAGGTGCACCAGCTTGTGCGAGCTTTGACTCAAGCTTAAGAGCCACTAGCTT
GTGTAAGCTTTGACTCAAGTATCGCCAGCTTGTACAGGCTTTGACTAGGGTGCCACCAACTCGTA
Found at i:38594 original size:99 final size:98
Alignment explanation
Indices: 38082--38596 Score: 362
Period size: 99 Copynumber: 5.2 Consensus size: 98
38072 TCAAGTGCTG
* * * * * *
38082 CCAGCTTGTGC-AGGCTTTAACTCAGACTTAGGTGCCACCAACTTATGTGGGCTTTGACTCAGGT
1 CCAGCTTGTGCGA-GCTTTGACTCAGGCTTAGGTGCCACCAGCTTGTGT-AGCTTTGACTCAAGT
* * * ** * *
38146 ACCGCCAACTCCTGTAGGCTTAGACTCGGGTGTCG
64 GCCGCCAACTCGTGTGGGCTTAGACTTAGGTGGCA
* * * * * * * * * *
38181 CTAGTTTGTGCGGGCTTTGACTCAAGCTTAAGAGCTACTAGCTTGTGTGGGCTTTGACTCAGGTG
1 CCAGCTTGTGCGAGCTTTGACTCAGGCTTAGGTGCCACCAGCTTGTGT-AGCTTTGACTCAAGTG
* * * ** * *
38246 CTGCCAGCTTGTACGGGCTTTGAC-TAGGGTGCCA
65 CCGCCAACTCGTGTGGGCTTAGACTTA-GGTGGCA
* * ** * * *
38280 CCAACTCGTAAG-GCTTTGACTCAGGTTTAGGTGCCACCAGCTTGTGTAGCTTTGACTTAGGTGC
1 CCAGCTTGTGCGAGCTTTGACTCAGGCTTAGGTGCCACCAGCTTGTGTAGCTTTGACTCAAGTGC
*
38344 CGCTAACTCGTGTGGGCTTAGACTTAGGT-GCAA
66 CGCCAACTCGTGTGGGCTTAGACTTAGGTGGC-A
* * ** *
38377 CCAGCTTGTACGAGCTTTGACTCAAGCTTAGGTGCCATTAGCTTGTGTAAGCTTTGACTCAAGTA
1 CCAGCTTGTGCGAGCTTTGACTCAGGCTTAGGTGCCACCAGCTTGTGT-AGCTTTGACTCAAGTG
* * * * * *
38442 TCGCCAGCTTGTGTAGGCTTTGAC-TAGGGTGCCA
65 CCGCCAACTCGTGTGGGCTTAGACTTA-GGTGGCA
* * * * *
38476 CCAACTCGTGTG-GA-ATTTGACTCAGGCTTAGGTGCCACCAACTTGTGTAGGTTTTAACTCAAG
1 CCAGCT--TGTGCGAGCTTTGACTCAGGCTTAGGTGCCACCAGCTTGTGTA-GCTTTGACTCAAG
* * *
38539 TGCCACCAACTCATAG-GGGCTTAGACTTAGGTGGCT
63 TGCCGCCAACTCGT-GTGGGCTTAGACTTAGGTGGCA
38575 CCAGCTTGTGCGAGCTTTGACT
1 CCAGCTTGTGCGAGCTTTGACT
38597 TAGGTGCTGC
Statistics
Matches: 316, Mismatches: 85, Indels: 30
0.73 0.20 0.07
Matches are distributed among these distances:
96 1 0.00
97 48 0.15
98 67 0.21
99 191 0.60
100 6 0.02
101 3 0.01
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.30
Consensus pattern (98 bp):
CCAGCTTGTGCGAGCTTTGACTCAGGCTTAGGTGCCACCAGCTTGTGTAGCTTTGACTCAAGTGC
CGCCAACTCGTGTGGGCTTAGACTTAGGTGGCA
Found at i:38600 original size:31 final size:31
Alignment explanation
Indices: 38556--38627 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
38546 AACTCATAGG
*
38556 GGCTTAGACTTAGGTGGCT-CCAGCTTGTGC-
1 GGCTTTGACTTAGGT-GCTGCCAGCTTGTGCA
*
38586 GAGCTTTGACTTAGGTGCTGCTAGCTTGTGCA
1 G-GCTTTGACTTAGGTGCTGCCAGCTTGTGCA
38618 GGCTTTGACT
1 GGCTTTGACT
38628 AGGGTGCCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.11
31 32 0.86
32 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.32, T:0.33
Consensus pattern (31 bp):
GGCTTTGACTTAGGTGCTGCCAGCTTGTGCA
Found at i:51476 original size:53 final size:53
Alignment explanation
Indices: 51396--51503 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
51386 TTTAGAGTTC
*
51396 ATTAATAGGGTCCGAGAGTCGGTTACACGTGGGGAAGGATCATCACCTCTACG
1 ATTAATAGGGTCCGAGAGTCGGTTACACGTGGGGAAGGATCAACACCTCTACG
51449 ATTAATAGGGTCCGAGAGTCGGTTACACGTGGGGAAGGATCAACACCTCTACG
1 ATTAATAGGGTCCGAGAGTCGGTTACACGTGGGGAAGGATCAACACCTCTACG
51502 AT
1 AT
51504 GCCCAAAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (53 bp):
ATTAATAGGGTCCGAGAGTCGGTTACACGTGGGGAAGGATCAACACCTCTACG
Found at i:55400 original size:20 final size:19
Alignment explanation
Indices: 55371--55409 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
55361 AGGTCAAAAC
55371 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
55390 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
55410 GAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:55437 original size:13 final size:13
Alignment explanation
Indices: 55419--55443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55409 AGAATGCACA
55419 GTATCGATACATT
1 GTATCGATACATT
55432 GTATCGATACAT
1 GTATCGATACAT
55444 GATCAAATGT
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):
GTATCGATACATT
Found at i:55456 original size:20 final size:21
Alignment explanation
Indices: 55431--55483 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
55421 ATCGATACAT
*
55431 TGTATCGATACATG-ATCA-AA
1 TGTATCGATACATGCA-AAGAA
*
55451 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
55472 TGTATCGATACA
1 TGTATCGATACA
55484 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:55456 original size:33 final size:33
Alignment explanation
Indices: 55398--55461 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
55388 CACCTTCAAA
*
55398 TGTATCGATACAGAATGCACAGTATCGATACAT
1 TGTATCGATACAGAATGCAAAGTATCGATACAT
55431 TGTATCGATACATG-AT-CAAATGTATCGATAC
1 TGTATCGATACA-GAATGCAAA-GTATCGATAC
55462 TTGCAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 24 0.86
34 1 0.04
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (33 bp):
TGTATCGATACAGAATGCAAAGTATCGATACAT
Found at i:55562 original size:13 final size:13
Alignment explanation
Indices: 55544--55569 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55534 ACACACAATA
55544 TGTATCGATACAT
1 TGTATCGATACAT
55557 TGTATCGATACAT
1 TGTATCGATACAT
55570 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:55585 original size:33 final size:32
Alignment explanation
Indices: 55524--55591 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
55514 CCTTAATTCT
* *
55524 TTGTATTGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
55556 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
55589 TTG
1 TTG
55592 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:62045 original size:13 final size:13
Alignment explanation
Indices: 62027--62052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62017 TACACCAAGT
62027 ATGTATCGATACA
1 ATGTATCGATACA
62040 ATGTATCGATACA
1 ATGTATCGATACA
62053 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:62045 original size:32 final size:33
Alignment explanation
Indices: 62009--62072 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
61999 TAGCCAAACT
* **
62009 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
62041 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
62073 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:63677 original size:9 final size:9
Alignment explanation
Indices: 63645--63675 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
63635 TCAACCATCA
63645 AAGACGATG
1 AAGACGATG
63654 AAGACGATG
1 AAGACGATG
*
63663 AAGATGATG
1 AAGACGATG
63672 AAGA
1 AAGA
63676 TGTTGATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.06, G:0.32, T:0.13
Consensus pattern (9 bp):
AAGACGATG
Found at i:64310 original size:21 final size:21
Alignment explanation
Indices: 64277--64326 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
64267 TTGCAAGTTG
*
64277 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
64299 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
64320 AAATAAA
1 AAATAAA
64327 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Done.