Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 16 of 47
Found at i:2290479 original size:13 final size:13
Alignment explanation
Indices: 2290461--2290486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2290451 CAATTTTTTA
2290461 TGTATCGATACAT
1 TGTATCGATACAT
2290474 TGTATCGATACAT
1 TGTATCGATACAT
2290487 ACTTGGTGTA
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:2293476 original size:20 final size:20
Alignment explanation
Indices: 2293434--2293477 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2293424 TTTTACTATC
* *
2293434 TAATGCTGTAATAATTTAGG
1 TAATGCTGTAATAATTCAAG
2293454 TAATG-TGTAATAAATTCAAG
1 TAATGCTGTAAT-AATTCAAG
2293474 TAAT
1 TAAT
2293478 ATGATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (20 bp):
TAATGCTGTAATAATTCAAG
Found at i:2294112 original size:20 final size:20
Alignment explanation
Indices: 2294069--2294112 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2294059 TTTTGTTGTC
* *
2294069 TAATATTGTAATAATTTCTA
1 TAATATTGTAATAAATTCAA
2294089 TAATA-TGTAATAAATTCAA
1 TAATATTGTAATAAATTCAA
2294108 GTAAT
1 -TAAT
2294113 TTTATAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (20 bp):
TAATATTGTAATAAATTCAA
Found at i:2294945 original size:20 final size:20
Alignment explanation
Indices: 2294920--2294967 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2294910 ATCGATACAT
* * *
2294920 TGTATCGATATATTTTACTA
1 TGTATCGATACAATGTACTA
2294940 TGTATCGATACAATGTACTA
1 TGTATCGATACAATGTACTA
2294960 TGTATCGA
1 TGTATCGA
2294968 GAGAAACAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATGTACTA
Found at i:2296000 original size:16 final size:16
Alignment explanation
Indices: 2295979--2296014 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2295969 TTCGTTAAGA
**
2295979 AAAGTTAAGTACAAGC
1 AAAGTTAAAAACAAGC
2295995 AAAGTTAAAAACAAGC
1 AAAGTTAAAAACAAGC
2296011 AAAG
1 AAAG
2296015 AAATAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAGTTAAAAACAAGC
Found at i:2297537 original size:31 final size:31
Alignment explanation
Indices: 2297500--2297566 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
2297490 TGACGAAGAT
2297500 TTTGATGAAAAAT-G-AAAAGAAATGATGTAAA
1 TTTGATG-AAAATCGAAAAAGAAATGATG-AAA
*
2297531 TTTGATGAAATTCGAAAAAGAAATGATGAAA
1 TTTGATGAAAATCGAAAAAGAAATGATGAAA
2297562 TTTGA
1 TTTGA
2297567 GATTGAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 4 0.12
31 16 0.48
32 13 0.39
ACGTcount: A:0.51, C:0.01, G:0.19, T:0.28
Consensus pattern (31 bp):
TTTGATGAAAATCGAAAAAGAAATGATGAAA
Found at i:2302261 original size:9 final size:9
Alignment explanation
Indices: 2302233--2302262 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2302223 TCCGAGTCAA
2302233 CTTCATCAT
1 CTTCATCAT
*
2302242 CATCATCAT
1 CTTCATCAT
2302251 CTTCATCAT
1 CTTCATCAT
2302260 CTT
1 CTT
2302263 TGATGGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (9 bp):
CTTCATCAT
Found at i:2303885 original size:33 final size:33
Alignment explanation
Indices: 2303838--2303907 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2303828 GTCGTTAGGC
* * *
2303838 ACAATGTATCGATACATTTTACTATGTATCGAT
1 ACAATGTATCGATACAATATACCATGTATCGAT
*
2303871 ACAATGTATTGATACAATATACCATGTATCGAT
1 ACAATGTATCGATACAATATACCATGTATCGAT
2303904 ACAA
1 ACAA
2303908 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (33 bp):
ACAATGTATCGATACAATATACCATGTATCGAT
Found at i:2303892 original size:20 final size:20
Alignment explanation
Indices: 2303869--2303907 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2303859 CTATGTATCG
*
2303869 ATACAATGTATTGATACAAT
1 ATACAATGTATCGATACAAT
*
2303889 ATACCATGTATCGATACAA
1 ATACAATGTATCGATACAA
2303908 ACAGTGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
ATACAATGTATCGATACAAT
Found at i:2305061 original size:17 final size:16
Alignment explanation
Indices: 2305020--2305055 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2305010 TACTAATTTT
2305020 AAAAAT-ATTTTAAGA
1 AAAAATAATTTTAAGA
2305035 AAAAATAATTTTAA-A
1 AAAAATAATTTTAAGA
2305050 AAAAAT
1 AAAAAT
2305056 CAAATTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAAATAATTTTAAGA
Found at i:2307936 original size:78 final size:78
Alignment explanation
Indices: 2307746--2308702 Score: 724
Period size: 79 Copynumber: 12.2 Consensus size: 78
2307736 TTTTTTTCCA
*** * * * *
2307746 AGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACATTGATTTTTCACTATTGAGGATGCTCCA
1 AGGGGATACTCCAA-CCCGATTTTATTTTC-AAAACACCAATTTTTCACAATCGGGGATACTCCA
*
2307810 ACCTCGTTATTTTCG
64 ACCCCGTTATTTTCG
* * ** * *** *
2307825 ATGAGATACTTTAACCCCGATTTTATTTCCAAAACATTGATTTTTCACAATC-GGGATACTCTAA
1 AGGGGATACTCCAA-CCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
2307889 CCCCGTTATTTTCG
65 CCCCGTTATTTTCG
** * * * *
2307903 AGAAGATACTCTAACTCCGATTTTATTTTCAAAACA-TAAATTTTCTACAAACGGGGATACTCCA
1 AGGGGATACTCCAAC-CCGATTTTATTTTCAAAACACCAATTTTTC-ACAATCGGGGATACTCCA
* *
2307967 ACCTCGTTATTTTTG
64 ACCCCGTTATTTTCG
* * * * *
2307982 AGGGGATACTCCAACCCTAGTTTTA-TTTCACAAACACCAATTTCT-AGAATCAGTGATACTCCA
1 AGGGGATACTCCAACCCGA-TTTTATTTTCA-AAACACCAATTTTTCACAATCGGGGATACTCCA
*
2308045 ACCTCGTTATTTTCG
64 ACCCCGTTATTTTCG
* * * * *
2308060 AGGGGATATTCCAACCTCAATTTTATTTTCAAAACATCAA-TTTTCTACAATTGGGGATACGCCA
1 AGGGGATACTCCAACC-CGATTTTATTTTCAAAACACCAATTTTTC-ACAATCGGGGATACTCCA
*
2308124 ACGCCGTTA-TTTCG
64 ACCCCGTTATTTTCG
* * * *
2308138 AGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCAAA
1 AGGGGATACTCCAACC-CGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * * *
2308203 TCCTGTTATTTCCA
65 CCCCGTTATTTTCG
* * * * * *
2308217 AGTGGATACTCCAACTTCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGAACACTCCAA
1 AGGGGATACTCCAAC-CCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
2308282 CCCCGTTATTTCCA
65 CCCCGTTATTTTCG
* * * * * *
2308296 AGGGGATATTCTAACCCCGGTTTTATTTCCATAACACCAATTTTTCACAATCAGGGATACTCCAA
1 AGGGGATACTCCAA-CCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
2308361 CCCCGTTATTTTCG
65 CCCCGTTATTTTCG
* * * * * *
2308375 ATGGGATACTCTAACCTC-AGTTTTATTTTCAAAACGCCAA-TTCT-ACAATCGAGGATATTCCA
1 AGGGGATACTCCAACC-CGA-TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCA
*
2308437 ATCCC-TTA-TTTCTG
64 ACCCCGTTATTTTC-G
* * * * * **
2308451 AGGGGATACTCTAACCCCGATTTTATTTTTAAAACA-TAGATTTTTCACAATCGAGAATACT-TT
1 AGGGGATACTCCAA-CCCGATTTTATTTTCAAAACACCA-ATTTTTCACAATCGGGGATACTCCA
* *
2308514 ACCTCGTTATTTTCA
64 ACCCCGTTATTTTCG
** * * * * * * **
2308529 AAAGAATACTCCAAGCCTGGTTTTA-TTTCCAAACATCGATTTTTCACAATCGGGGATACTCTGA
1 AGGGGATACTCCAA-CCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* **
2308593 TCTTGTTATTTTCG
65 CCCCGTTATTTTCG
* ** * * *
2308607 AAGGGATA-TCCTAACTTTGGTTTTATTTTTAAAATACCAATTTTTCACAATCGGGGATACTCCA
1 AGGGGATACTCC-AAC-CCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCA
** *
2308671 ACCCTATTA-TTTCTA
64 ACCCCGTTATTTTC-G
*
2308686 ATGGGATACTCCAACCC
1 AGGGGATACTCCAACCC
2308703 TAGTTTTGTC
Statistics
Matches: 709, Mismatches: 137, Indels: 65
0.78 0.15 0.07
Matches are distributed among these distances:
75 5 0.01
76 33 0.05
77 71 0.10
78 253 0.36
79 335 0.47
80 12 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (78 bp):
AGGGGATACTCCAACCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCG
Found at i:2307998 original size:157 final size:156
Alignment explanation
Indices: 2307748--2308700 Score: 742
Period size: 157 Copynumber: 6.1 Consensus size: 156
2307738 TTTTTCCAAG
* *** * * * *
2307748 GGGATACTCCAACCCCGATTTTA-TTTCTAAAACATTGATTTT-TCACTATTGAGGATGCTCCAA
1 GGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTCT-ACAATCGGGGATACTCCAA
* * * ***
2307811 CCTCGTTATTTTCGATGAGATACTTTAACCCCGATTTTATTTCCAAAACATTGATTTTTCACAAT
64 CC-CGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAAT
*
2307876 C-GGGATACTCTAACCCCGTTATTTTCGA
128 CAGGGATACTCCAACCCCGTTATTTTCGA
* * ** *
2307904 GAAGATACTCTAACTCCGATTTTATTTTCAAAACATAAATTTTCTACAAACGGGGATACTCCAAC
1 G-GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAAC
* * * * *
2307969 CTCGTTATTTTTGAGGGGATACTCCAA-CCCTAGTTTTATTT-CACAAACACCAATTTCT-AGAA
65 C-CGTTATTTTCGAGGGGATACTCTAACCCCGA-TTTTATTTCCA-AAACACCAATTTTTCACAA
* *
2308031 TCAGTGATACTCCAACCTCGTTATTTTCGA
127 TCAGGGATACTCCAACCCCGTTATTTTCGA
* * * * *
2308061 GGGGATATTCCAAC-CTCAATTTTATTTTCAAAACATCAATTTTCTACAATTGGGGATACGCCAA
1 -GGGATACTCCAACTC-CGATTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAA
* * * *
2308125 CGCCGTTA-TTTCGAGGGGATACTCCAACCTCGGTTTTATTTCCAAAACACTAATTTTTCACAAT
64 C-CCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAAT
* * * * * *
2308189 CGGGGATACTCAAATCCTGTTATTTCCAA
128 CAGGGATACTCCAACCCCGTTATTTTCGA
* * * * *
2308218 GTGGATACTCCAACTTCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGAACACTCCAAC
1 G-GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAA-
* * * * *
2308283 CCCGTTATTTCCAAGGGGATATTCTAACCCCGGTTTTATTTCCATAACACCAATTTTTCACAATC
64 CCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
2308348 AGGGATACTCCAACCCCGTTATTTTCGA
129 AGGGATACTCCAACCCCGTTATTTTCGA
* * * * *
2308376 TGGGATACTCTAACCTCAG-TTTTATTTTCAAAACGCCAA--TTCTACAATCGAGGATATTCCAA
1 -GGGATACTCCAA-CTCCGATTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAA
** *
2308438 TCCC-TTA-TTTCTGAGGGGATACTCTAACCCCGATTTTATTTTTAAAACA-TAGATTTTTCACA
64 -CCCGTTATTTTC-GAGGGGATACTCTAACCCCGATTTTATTTCCAAAACACCA-ATTTTTCACA
* ** * *
2308500 ATC-GAGAATACT-TTACCTCGTTATTTTCAAA
126 ATCAG-GGATACTCCAACCCCGTTATTTTC-GA
* * * * * * * *
2308531 AGAATACTCCAAGC-CTGGTTTTA-TTTCCAAACATCGATTTT-TCACAATCGGGGATACTCTGA
1 GGGATACTCCAA-CTCCGATTTTATTTTCAAAACACCAATTTTCT-ACAATCGGGGATACTC-CA
* ** * *** * ** *
2308593 TCTTGTTATTTTCGAAGGGATA-TCCTAACTTTGGTTTTATTTTTAAAATACCAATTTTTCACAA
63 ACCCGTTATTTTCGAGGGGATACT-CTAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAA
* ** *
2308657 TCGGGGATACTCCAACCCTATTA-TTTCTAA
127 TCAGGGATACTCCAACCCCGTTATTTTC-GA
2308687 TGGGATACTCCAAC
1 -GGGATACTCCAAC
2308701 CCTAGTTTTG
Statistics
Matches: 638, Mismatches: 125, Indels: 68
0.77 0.15 0.08
Matches are distributed among these distances:
153 12 0.02
154 34 0.05
155 72 0.11
156 132 0.21
157 276 0.43
158 108 0.17
159 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (156 bp):
GGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTACAATCGGGGATACTCCAACC
CGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCAG
GGATACTCCAACCCCGTTATTTTCGA
Found at i:2321056 original size:1 final size:1
Alignment explanation
Indices: 2321052--2321121 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
2321042 TCCTTTTTCT
* * * * ** * * * *
2321052 AAAAATAAAAAAACAAAAAAATAAAAAACAAAAATCAAAAAAATAAAAAAAGAGAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2321117 AAAAA
1 AAAAA
2321122 GAGAAAAGAA
Statistics
Matches: 50, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.04, G:0.04, T:0.06
Consensus pattern (1 bp):
A
Found at i:2321077 original size:15 final size:16
Alignment explanation
Indices: 2321052--2321102 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
2321042 TCCTTTTTCT
2321052 AAAAATAAAAAAACAA
1 AAAAATAAAAAAACAA
2321068 AAAAAT-AAAAAAC--
1 AAAAATAAAAAAACAA
*
2321081 AAAAATCAAAAAAATAA
1 AAAAAT-AAAAAAACAA
2321098 AAAAA
1 AAAAA
2321103 GAGAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 6 0.20
15 13 0.43
16 6 0.20
17 5 0.17
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAATAAAAAAACAA
Found at i:2321084 original size:22 final size:21
Alignment explanation
Indices: 2321051--2321102 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
2321041 TTCCTTTTTC
2321051 TAAAAATAAAAAAACAAAAAAA
1 TAAAAA-AAAAAAACAAAAAAA
*
2321073 TAAAAAACAAAAATCAAAAAAA
1 TAAAAAA-AAAAAACAAAAAAA
2321095 TAAAAAAA
1 TAAAAAAA
2321103 GAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.10
Consensus pattern (21 bp):
TAAAAAAAAAAAACAAAAAAA
Found at i:2321134 original size:20 final size:19
Alignment explanation
Indices: 2321088--2321136 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
2321078 AACAAAAATC
*
2321088 AAAAAAATAAAAAAAGAGA
1 AAAAAAAGAAAAAAAGAGA
2321107 AAAAAAAGAAAAAAAGAGA
1 AAAAAAAGAAAAAAAGAGA
2321126 AAAGAAAAGAA
1 AAA-AAAAGAA
2321137 CCTGTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAGAGA
Found at i:2322277 original size:61 final size:61
Alignment explanation
Indices: 2322102--2322607 Score: 544
Period size: 61 Copynumber: 8.3 Consensus size: 61
2322092 CCTTTTATCT
* *
2322102 TTTCAGTCCTCAAAGAGCAAGACG-TATTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATC
1 TTTCAGTCCTCAAAGAGCAAGACGCT-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * * * *
2322163 TTTTAGTCCTCGAAGAGTAGGACACATCTTTTCTTTTTAAAGCCCACATAAGTTAGTGGCACC
1 TTTCAGTCCTCAAAGAGCAAGACGC-T-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
2322226 TTTCAGTCCTCAAAGAGCATGACGCTTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACC
1 TTTCAGTCCTCAAAGAGCAAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
2322287 TTTCAGTCCTCAAAGAG-TAGAACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGTACC
1 TTTCAGTCCTCAAAGAGCAAG-ACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * *
2322348 TTTTAGTCCTTAAAGAGCAGGACGC-CTTTCTTTTTAAAGCCCATACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
2322408 TTCCAATCCTCAAAGAGCAAGACG--TTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * ** *
2322467 -TTCTAGTCCTCAAAAAACAAGAC-ATTTTCTCCTTGCAAAGCCTACACAAGTTGGTGGCA-C
1 TTTC-AGTCCTCAAAGAGCAAGACGCTTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
2322527 TTTCTAGTCCTCAAAGAGCAGGGCGCTTTCTCCTTGTAAAGCCCATACAAGTTGGTGGCACC
1 TTTC-AGTCCTCAAAGAGCAAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
2322589 -TTCTAGTCCCCAAAGAGCA
1 TTTC-AGTCCTCAAAGAGCA
2322608 GGACACATTT
Statistics
Matches: 378, Mismatches: 56, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
58 2 0.01
59 47 0.12
60 56 0.15
61 216 0.57
62 6 0.02
63 51 0.13
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (61 bp):
TTTCAGTCCTCAAAGAGCAAGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:2322569 original size:241 final size:246
Alignment explanation
Indices: 2322100--2322617 Score: 606
Period size: 241 Copynumber: 2.1 Consensus size: 246
2322090 AACCTTTTAT
* * * *
2322100 CTTTTCAGTCCTCAAAGAGCAAGACGTATTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATCTT
1 CTTTT-AGTCCTCAAAGAGCAGGACGCATTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
** * * * * *
2322165 TTAGTCCTCGAAGAGTAGGACACATCTTTTCTTTTTAAAGCCCACATAAGTTAGTGGCACCTTTC
65 CCAATCCTCGAAGAGTAGCACACATCTTTTCCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTC
* * * * **
2322230 AGTCCTCAAAGAGCATGACGCTTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACCTTTCAGTC
130 AGTCCTCAAAAAACAAGACGATTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTC
* * * *
2322295 CTCAAAGAGTAGAACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGTAC
195 CTCAAAGAGCAGAACGCCTTTTCCTTGTAAAGCCCACACAAGTTGGTGGCAC
* * *
2322347 CTTTTAGTCCTTAAAGAGCAGGACGCCTTTCT-TTTTAAAGCCCATACAAGTTGGTGGCACCTTC
1 CTTTTAGTCCTCAAAGAGCAGGACGCATTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
2322411 CAATCCTC-AA-AG-AGCA-AGA-CGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTC
66 CAATCCTCGAAGAGTAGCACACATC-TTTTCCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTC
* *
2322470 TAGTCCTCAAAAAACAAGAC-ATTTTCTCCTTGCAAAGCCTACACAAGTTGGTGGCA-CTTTCTA
130 -AGTCCTCAAAAAACAAGACGATTTT-TCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTTC-A
** *
2322533 GTCCTCAAAGAGCAGGGCG-CTTTCTCCTTGTAAAGCCCATACAAGTTGGTGGCAC
192 GTCCTCAAAGAGCAGAACGCCTTT-TCCTTGTAAAGCCCACACAAGTTGGTGGCAC
* * *
2322588 CTTCTAGTCCCCAAAGAGCAGGACACATTT
1 CTTTTAGTCCTCAAAGAGCAGGACGCATTT
2322618 AATTTCCTCA
Statistics
Matches: 230, Mismatches: 36, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
240 17 0.07
241 144 0.63
242 3 0.01
243 2 0.01
244 2 0.01
245 35 0.15
246 22 0.10
247 5 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (246 bp):
CTTTTAGTCCTCAAAGAGCAGGACGCATTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
CAATCCTCGAAGAGTAGCACACATCTTTTCCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCA
GTCCTCAAAAAACAAGACGATTTTTCCTTGCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCC
TCAAAGAGCAGAACGCCTTTTCCTTGTAAAGCCCACACAAGTTGGTGGCAC
Found at i:2322660 original size:43 final size:41
Alignment explanation
Indices: 2322599--2322691 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
2322589 TTCTAGTCCC
2322599 CAAAGAGCAGGACACATTTAATTTCCTCATTTTCCTTTATCCT
1 CAAAGAGCAGGACACATTT-ATTTCCT-ATTTTCCTTTATCCT
* ** * * *
2322642 CAAAGAGTAGGATGCATTTTTTTCCTTTTTTCCTTTGTCCT
1 CAAAGAGCAGGACACATTTATTTCCTATTTTCCTTTATCCT
2322683 CAAAGAGCA
1 CAAAGAGCA
2322692 AGATGTACTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 21 0.49
42 6 0.14
43 16 0.37
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (41 bp):
CAAAGAGCAGGACACATTTATTTCCTATTTTCCTTTATCCT
Found at i:2325802 original size:79 final size:79
Alignment explanation
Indices: 2325708--2326303 Score: 583
Period size: 79 Copynumber: 7.5 Consensus size: 79
2325698 ATTCATATTT
* *
2325708 TTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCGATTTTTCACAATCGAGG
1 TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
** * *
2325773 ATACTTTAGTCACG
66 ATACTCCAGCCCCG
* * *
2325787 TTATTTTTGAAGGGATACTCCAACC-CTAATTTTATTTCCAAAACATCAATTTTTCACAATCGAG
1 TTATTTTTGAGGGGATACTCCAACCTC-GATTTTATTTCCAAAACACCAATTTTTCACAATCGAG
* *
2325851 AATACTCCAACCCCG
65 GATACTCCAGCCCCG
* * *
2325866 TTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTTCACAATCGAGG
1 TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
* *
2325931 ATACTCCAACCCTG
66 ATACTCCAGCCCCG
* * * * ** * *
2325945 TTATTTTTGAGGGGATACTCTATCCCCGATTTTATTTCCAAAATACCAATTTCCCATAATTGAGG
1 TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
* *
2326010 ATACTCCAACCCTG
66 ATACTCCAGCCCCG
* * * * * * ** *
2326024 TTATTTTAGAGGGGATATTCTAATCTCGATTTTATTTTCAAAGCACTGATTTTTCACAATCGGGG
1 TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
* *
2326089 ATACT-CTGACCTCG
66 ATACTCCAG-CCCCG
** * * * * * *
2326103 TTATTTTCAAGAGGATGCTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACAA-CTGGG
1 TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATC-GAG
* *
2326167 GATACTTC-GACCCCA
65 GATACTCCAG-CCCCG
*
2326182 TTATTTTTGAGGGGATAC-CCTAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCG-G
1 TTATTTTTGAGGGGATACTCC-AACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAG
* * **
2326245 AGATTCTCCAACCCTA
65 -GATACTCCAGCCCCG
*** * *
2326261 TTATTTCCAAGGGGATACTCCAACCCCGATTTTATCTCCAAAA
1 TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAA
2326304 TATTAAACTT
Statistics
Matches: 426, Mismatches: 81, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
78 6 0.01
79 415 0.97
80 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (79 bp):
TTATTTTTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGG
ATACTCCAGCCCCG
Found at i:2325960 original size:158 final size:158
Alignment explanation
Indices: 2325711--2326303 Score: 685
Period size: 158 Copynumber: 3.7 Consensus size: 158
2325701 CATATTTTTA
* *
2325711 TTTCTGAGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCGATTTTTCACAATCGAGGATA
1 TTTC-GAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATA
** * * * **
2325776 CTTTAGTCAC-GTTATTTTTGAA-GGGATACTCCAACCCTAATTTTATTTCCAAAACATCAATTT
65 CTCCA-ACCCTGTTA-TTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTT
*
2325839 TTCACAATCGAGAATACTCCAACCCCGTTAT
128 TTCACAATCGAGGATACTCCAACCCCGTTAT
*
2325870 TTTCGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATAC
1 TTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATAC
** * * * * **
2325935 TCCAACCCTGTTATTTTTGAGGGGATACTCTATCCCCGATTTTATTTCCAAAATACCAATTTCCC
66 TCCAACCCTGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTC
* * *
2326000 ATAATTGAGGATACTCCAACCCTGTTAT
131 ACAATCGAGGATACTCCAACCCCGTTAT
* * * * * ** *
2326028 TTTAGAGGGGATATTCTAATCTCGATTTTATTTTCAAAGCACTGATTTTTCACAATCGGGGATAC
1 TTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATAC
** * * *
2326093 TCTGA-CCTCGTTATTTTCAAGAGGATGCTCCAACCCCGATTTTATTTCCAAAACATCGATTTTT
66 TCCAACCCT-GTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTT
* * * *
2326157 CACAA-CTGGGGATACTTCGACCCCATTAT
130 CACAATC-GAGGATACTCCAACCCCGTTAT
*
2326186 TTTTGAGGGGATAC-CCTAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCG-GAGAT
1 TTTCGAGGGGATACTCC-AACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAG-GAT
* * * *
2326249 TCTCCAACCCTATTATTTCCAAGGGGATACTCCAACCCCGATTTTATCTCCAAAA
64 ACTCCAACCCTGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAA
2326304 TATTAAACTT
Statistics
Matches: 362, Mismatches: 65, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
157 12 0.03
158 343 0.95
159 7 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (158 bp):
TTTCGAGGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATAC
TCCAACCCTGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTC
ACAATCGAGGATACTCCAACCCCGTTAT
Found at i:2330350 original size:19 final size:18
Alignment explanation
Indices: 2330326--2330406 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 18
2330316 TTTTGAATTT
2330326 CAAACAATTTGTATCGATA
1 CAAA-AATTTGTATCGATA
**
2330345 CAAACAGTAAATGTATCGATA
1 CAAA-A--ATTTGTATCGATA
* *
2330366 CATAAGTGTTGTATCGATA
1 CAAAAAT-TTGTATCGATA
**
2330385 CATAAGTTTTGTATCGATA
1 CA-AAAATTTGTATCGATA
2330404 CAA
1 CAA
2330407 TGTATCGCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
19 31 0.63
20 3 0.06
21 14 0.29
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (18 bp):
CAAAAATTTGTATCGATA
Found at i:2332913 original size:51 final size:51
Alignment explanation
Indices: 2332858--2332994 Score: 152
Period size: 51 Copynumber: 2.7 Consensus size: 51
2332848 TTTCGTTTCC
* *
2332858 AAAACATCAA-TTTCTCTTAATCGAGGATACTCCAACTCCGATTTTATTTGT
1 AAAACACCAATTTTC-CATAATCGAGGATACTCCAACTCCGATTTTATTTGT
* * **
2332909 AAAACACCCATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCC
1 AAAACACCAATTTTCCATAATCGAGGATACTCCAACTCCGATTTTATTTGT
* * * *
2332960 AAAACACCGACTTTT-CACAATTGGGGATACTCCAA
1 AAAACACC-AATTTTCCATAATCGAGGATACTCCAA
2332995 TCCCGTTATT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 66 0.89
52 8 0.11
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (51 bp):
AAAACACCAATTTTCCATAATCGAGGATACTCCAACTCCGATTTTATTTGT
Found at i:2333162 original size:79 final size:78
Alignment explanation
Indices: 2332932--2333187 Score: 257
Period size: 79 Copynumber: 3.2 Consensus size: 78
2332922 TCCATAATCG
* * * * *
2332932 GGGATACTCCAACTCCGATTTTATTTCCAAAACA-CCGACTTTTCACAATTGGGGATACTCCAAT
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACATCC-ATTTTTCACAATCGGGGATACTCCAAC
*
2332996 CCCGTTATTTTCGAG
65 CCCGTTATTTT-GAA
* * * * * * *
2333011 GGGACACTCCAACCCCGGTTTTA-TTTCTAAAACATCAAATTTTTTTTATAGTC-GGGATACTTC
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACATC-CA--TTTTTCACAATCGGGGATACTCC
2333074 AACCCCGTTATTTCTGAA
62 AACCCCGTTATTT-TGAA
* * * *
2333092 GGGATGCTCCAATCCCGATTTTATTTTCAAATCATCCATTTTTCACAACCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACATCCATTTTTCACAATCGGGGATACTCCAACC
*
2333157 CCGTTATTTTCAA
66 CCGTTATTTTGAA
2333170 GGGGATACTCCAACCCCG
1 -GGGATACTCCAACCCCG
2333188 TTATTATCTC
Statistics
Matches: 141, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
78 14 0.10
79 63 0.45
80 3 0.02
81 49 0.35
82 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACATCCATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTGAA
Found at i:2341421 original size:10 final size:10
Alignment explanation
Indices: 2341406--2341455 Score: 64
Period size: 10 Copynumber: 4.7 Consensus size: 10
2341396 CATTCGTACC
2341406 AAAAAAACAA
1 AAAAAAACAA
2341416 AAAAAAACCAA
1 AAAAAAA-CAA
*
2341427 AAAAAACCAAGA
1 AAAAAAAC-A-A
2341439 AAAAAAACAA
1 AAAAAAACAA
2341449 AAAAAAA
1 AAAAAAA
2341456 TGAACAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 16 0.46
11 11 0.31
12 8 0.23
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2341464 original size:23 final size:23
Alignment explanation
Indices: 2341415--2341467 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2341405 CAAAAAAACA
* *
2341415 AAAAAAAACCAAAAAAAACCAAG
1 AAAAAAAACAAAAAAAAACCAAC
**
2341438 AAAAAAAACAAAAAAAAATGAAC
1 AAAAAAAACAAAAAAAAACCAAC
2341461 AAAAAAA
1 AAAAAAA
2341468 GGGTCTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (23 bp):
AAAAAAAACAAAAAAAAACCAAC
Found at i:2342736 original size:28 final size:28
Alignment explanation
Indices: 2342705--2343163 Score: 571
Period size: 28 Copynumber: 16.2 Consensus size: 28
2342695 CATTCATCTC
* * *
2342705 TTCAAAGCCTACAAGTCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
** *
2342733 TTCAAAGTTCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
2342761 TTCAAAGCCCACAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2342789 TTCAAAGCCCACAAGTTAGTGGCACACT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2342817 TTCAAAGCCCACAAGTGAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2342845 TTCAAAGCCCACAAGTGAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2342873 TTCAAAGCCCACAAGTTAGTGGCA-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
2342900 CTTCAAAAGACCACAAGTCAGTGGTATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCACCCT
2342930 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
2342958 TTTAAAGCCCAAAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2342986 TCCAAAGCCCAAAAGTCAGTGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
2343013 TCTCAAAGCCCACAAGTCAGTGGCACCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
2343042 TTCAAAGCCCACAAGACTGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
2343070 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2343098 TTCAAAGTCTACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGC--ACCCT
*
2343128 TTCAAAGCCCACAAGTCGGTGGCAACCCTT
1 TTCAAAGCCCACAAGTCAGTGGC-ACCC-T
2343158 TTCAAA
1 TTCAAA
2343164 TCACCATTTT
Statistics
Matches: 376, Mismatches: 47, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
27 6 0.02
28 307 0.82
29 29 0.08
30 34 0.09
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:2343264 original size:45 final size:46
Alignment explanation
Indices: 2343197--2343325 Score: 125
Period size: 49 Copynumber: 2.7 Consensus size: 46
2343187 TCCGATATCG
* *
2343197 CTGGCATTGAATTAGCATATTGGCACCTTT-ATTAGCCCAATGTCA
1 CTGGCCTTGAATTAGCACATTGGCACCTTTCATTAGCCCAATGTCA
* * * * *
2343242 CTGGCCTTGAATCATCACATTGGTCCACTTTTCCCTTAGCCCAATGTCG
1 CTGGCCTTGAATTAGCACATTGG--CACCTTT-CATTAGCCCAATGTCA
* *
2343291 CTGTCCTTGAATTGGCACATTGGCACTCCTTTCAT
1 CTGGCCTTGAATTAGCACATTGGCA--CCTTTCAT
2343326 CTCTAAGTCT
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
45 19 0.29
47 8 0.12
48 2 0.03
49 36 0.55
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (46 bp):
CTGGCCTTGAATTAGCACATTGGCACCTTTCATTAGCCCAATGTCA
Found at i:2344056 original size:20 final size:20
Alignment explanation
Indices: 2344031--2344090 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
2344021 TTTTACCCAG
* *
2344031 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
2344051 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
2344071 ATGTATCGATACATTCTATC
1 ATGTATCGATACATT-TATC
2344091 TTTTTACCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:2344125 original size:51 final size:49
Alignment explanation
Indices: 2344051--2344186 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 49
2344041 ACATTTTTCA
*
2344051 ATGTATCGATACATGTATGAATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACAT-TAT-AATGTATCGATACATTATATCTTTTTACCCAG
* * *
2344102 ATGTATCGATACATTCTTCAATGTATCGATACATTATGTTTTTTTACCCAG
1 ATGTATCGATACATT-AT-AATGTATCGATACATTATATCTTTTTACCCAG
2344153 ATGTATCGATACATTAAATAATGTATCGATACAT
1 ATGTATCGATACATT--ATAATGTATCGATACAT
2344187 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.01
51 74 0.97
52 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (49 bp):
ATGTATCGATACATTATAATGTATCGATACATTATATCTTTTTACCCAG
Found at i:2345783 original size:21 final size:21
Alignment explanation
Indices: 2345750--2345790 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2345740 CTAAGTAAAA
2345750 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2345771 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2345791 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2345855 original size:20 final size:19
Alignment explanation
Indices: 2345830--2345900 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
2345820 ACCCTGAAAA
2345830 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
2345850 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
2345869 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
2345890 GTATCGATACA
1 GTATCGATACA
2345901 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:2345996 original size:10 final size:10
Alignment explanation
Indices: 2345977--2346007 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2345967 AATCTCATTT
2345977 TCACTGTTCA
1 TCACTGTTCA
*
2345987 TCACTATTCA
1 TCACTGTTCA
2345997 TCACTGTTCA
1 TCACTGTTCA
2346007 T
1 T
2346008 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2346130 original size:13 final size:13
Alignment explanation
Indices: 2346112--2346137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2346102 ACATATTTGT
2346112 GTGTATCGATACA
1 GTGTATCGATACA
2346125 GTGTATCGATACA
1 GTGTATCGATACA
2346138 TCATAAATAG
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:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:2346679 original size:34 final size:35
Alignment explanation
Indices: 2346616--2346682 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2346606 CTAAGTGATT
2346616 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2346652 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2346683 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2357684 original size:79 final size:78
Alignment explanation
Indices: 2357545--2358266 Score: 840
Period size: 79 Copynumber: 9.2 Consensus size: 78
2357535 CAGAGCACCT
* * * * * * *
2357545 CCTCAGAAATAACGGGGTTGGA-TATCCCTAATGGTGGAAAATTGATGTTTTGAAAATAAAATCG
1 CCTCAAAAATAACGGGGTTAGAGTATCCC-GATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
* *
2357609 GGGTTGGAATATCT
65 GGGTTGGAGTATCC
** *
2357623 CCTCAAAAATAATAGGGTTAGAGTATCTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCA
1 CCTCAAAAATAACGGGGTTAGAGTATC-CCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
* *
2357688 GGATTGAAGTATCC
65 GGGTTGGAGTATCC
* * * *
2357702 CCTCGAAAATAACGGGGTTAAAGTATCCACAATTGTGAAAAATTGGTGTTTTGAAAATAAAATCG
1 CCTCAAAAATAACGGGGTTAGAGTATCC-CGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
2357767 GGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* ** * *
2357781 CTTCAAAAATAATAGGGTTAGAGTGTCCCCGATTGTGAAAAATTGGTATTTTGAAAATAAAACCG
1 CCTCAAAAATAACGGGGTTAGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
2357846 AGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* * * * *
2357860 CCTGATAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTT-AGAAATAAAATC
1 CCTCAAAAATAACGGGGTTAGAGTATCC-CGATTGTGAAAAATTGGTGTTTTGA-AAATAAAACC
**
2357924 AAGGTTGGAGTATCC
64 GGGGTTGGAGTATCC
* * * * *
2357939 CCTCGAAAATAACGGGGTTGGAATATCTTCGATTGTGAAAAATCGGTGTTTTGAAAATAAAACCG
1 CCTCAAAAATAACGGGGTTAGAGTATC-CCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
2358004 AGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* ** *
2358018 CCTCAGAAATAACAAGGTT-GAAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAACC
1 CCTCAAAAATAACGGGGTTAG-AGTATCCC-GATTGTGAAAAATTGGTGTTTTGAAAATAAAACC
* *
2358082 GAGGG-TGGAATATCT
64 G-GGGTTGGAGTATCC
* * * *
2358097 CCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGTAAATAAAACCA
1 CCTCAAAAATAACGGGGTTAGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
2358162 GGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* * *
2358176 CCTCAAAAATAACGGGGTTGGAGTGTCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCG
1 CCTCAAAAATAACGGGGTTAGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
2358241 CGGTTGGAGTATCC
65 GGGTTGGAGTATCC
*
2358255 CCTCAGAAATAA
1 CCTCAAAAATAA
2358267 AAACATGAAT
Statistics
Matches: 552, Mismatches: 78, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
78 27 0.05
79 514 0.93
80 11 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (78 bp):
CCTCAAAAATAACGGGGTTAGAGTATCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGG
GGTTGGAGTATCC
Found at i:2362491 original size:21 final size:21
Alignment explanation
Indices: 2362467--2362513 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2362457 CCAAGTATAT
* * *
2362467 GTATCGATACATGTATGTTAG
1 GTATCGAAACACGCATGTTAG
2362488 GTATCGAAACACGCATGTTAG
1 GTATCGAAACACGCATGTTAG
2362509 GTATC
1 GTATC
2362514 AACACATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (21 bp):
GTATCGAAACACGCATGTTAG
Found at i:2363050 original size:14 final size:14
Alignment explanation
Indices: 2363031--2363060 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2363021 CTTTTAAATT
2363031 TCATAACTCTCTAA
1 TCATAACTCTCTAA
*
2363045 TCATAACTTTCTAA
1 TCATAACTCTCTAA
2363059 TC
1 TC
2363061 TCTCTAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (14 bp):
TCATAACTCTCTAA
Found at i:2364146 original size:33 final size:33
Alignment explanation
Indices: 2364083--2364148 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2364073 GCCGTTATAA
* * *
2364083 GCAATGTATCGATACAATTCATCATGTATCGAT
1 GCAAGGTAGCGATACAATTCATCATATATCGAT
*
2364116 GCAAGGTAGCGATACAATGTCCT-ATATATCGAT
1 GCAAGGTAGCGATACAAT-TCATCATATATCGAT
2364149 ACAAACAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (33 bp):
GCAAGGTAGCGATACAATTCATCATATATCGAT
Found at i:2372958 original size:20 final size:20
Alignment explanation
Indices: 2372935--2373007 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2372925 ACAATTCAAA
2372935 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2372955 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2372976 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2372996 GTATCGATACAT
1 GTATCGATACAT
2373008 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2372979 original size:21 final size:21
Alignment explanation
Indices: 2372953--2373028 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2372943 ACATGTTGCA
2372953 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2372974 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2372994 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2373015 ATGTATCGATACAT
1 ATGTATCGATACAT
2373029 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2372986 original size:41 final size:41
Alignment explanation
Indices: 2372935--2373028 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2372925 ACAATTCAAA
*
2372935 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2372976 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2373017 GTATCGATACAT
1 GTATCGATACAT
2373029 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2373085 original size:13 final size:13
Alignment explanation
Indices: 2373067--2373092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2373057 TACAGCAAGT
2373067 ATGTATCGATACA
1 ATGTATCGATACA
2373080 ATGTATCGATACA
1 ATGTATCGATACA
2373093 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:2377173 original size:15 final size:15
Alignment explanation
Indices: 2377153--2377183 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2377143 TAAAAATGTC
*
2377153 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2377168 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2377183 C
1 C
2377184 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:2379276 original size:20 final size:20
Alignment explanation
Indices: 2379197--2379276 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
2379187 AATGTCCAAA
*
2379197 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
2379217 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
2379242 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
2379262 TTGTATCGATACATT
1 ATGTATCGATACATT
2379277 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:2379280 original size:13 final size:13
Alignment explanation
Indices: 2379262--2379300 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2379252 ACATTTTTCT
2379262 TTGTATCGATACA
1 TTGTATCGATACA
2379275 TTGTATCGATACA
1 TTGTATCGATACA
*
2379288 CTGTATCGATACA
1 TTGTATCGATACA
2379301 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:2381763 original size:20 final size:20
Alignment explanation
Indices: 2381740--2381812 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2381730 ACAATTCAAA
2381740 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2381760 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2381781 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2381801 GTATCGATACAT
1 GTATCGATACAT
2381813 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2381784 original size:21 final size:21
Alignment explanation
Indices: 2381758--2381833 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2381748 ACATGTTGCA
2381758 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2381779 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2381799 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2381820 ATGTATCGATACAT
1 ATGTATCGATACAT
2381834 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2381791 original size:41 final size:41
Alignment explanation
Indices: 2381740--2381833 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2381730 ACAATTCAAA
*
2381740 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2381781 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2381822 GTATCGATACAT
1 GTATCGATACAT
2381834 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2381890 original size:13 final size:13
Alignment explanation
Indices: 2381872--2381897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2381862 TACAGCAAGT
2381872 ATGTATCGATACA
1 ATGTATCGATACA
2381885 ATGTATCGATACA
1 ATGTATCGATACA
2381898 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:2383206 original size:13 final size:13
Alignment explanation
Indices: 2383188--2383213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2383178 TACACCAAGT
2383188 ATGTATCGATACA
1 ATGTATCGATACA
2383201 ATGTATCGATACA
1 ATGTATCGATACA
2383214 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:2383211 original size:32 final size:33
Alignment explanation
Indices: 2383170--2383233 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2383160 TAGCCAAACT
* **
2383170 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2383202 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2383234 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:2383735 original size:34 final size:35
Alignment explanation
Indices: 2383672--2383738 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2383662 CTAAGTGATT
2383672 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2383708 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2383739 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2385419 original size:84 final size:84
Alignment explanation
Indices: 2385259--2385419 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 84
2385249 ACTCAAAGAA
* * * *
2385259 GAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
* *
2385324 TATGAAAGAGTTACAAAAT
66 AAAGAAAGAGTTACAAAAT
* *
2385343 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--AGAAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
2385404 AGAAAAGAAATGAGTT
64 AG-AAAGAAA-GAGTT
2385420 GCAAGTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
82 11 0.17
83 6 0.09
84 48 0.74
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
AAAGAAAGAGTTACAAAAT
Found at i:2386950 original size:13 final size:13
Alignment explanation
Indices: 2386932--2386956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2386922 TTTTCCAGAT
2386932 TGTATCGATACAA
1 TGTATCGATACAA
2386945 TGTATCGATACA
1 TGTATCGATACA
2386957 TTGCTTCAGT
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:2388124 original size:12 final size:12
Alignment explanation
Indices: 2388107--2388132 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2388097 TTATATGCAA
2388107 ATAAATTTTGAT
1 ATAAATTTTGAT
2388119 ATAAATTTTGAT
1 ATAAATTTTGAT
2388131 AT
1 AT
2388133 GTGTGAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATAAATTTTGAT
Found at i:2388876 original size:13 final size:13
Alignment explanation
Indices: 2388858--2388883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2388848 TACACCAAGT
2388858 ATGTATCGATACA
1 ATGTATCGATACA
2388871 ATGTATCGATACA
1 ATGTATCGATACA
2388884 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:2388881 original size:32 final size:33
Alignment explanation
Indices: 2388840--2388903 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2388830 TAGCCAAACT
* **
2388840 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2388872 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2388904 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:2389405 original size:34 final size:35
Alignment explanation
Indices: 2389342--2389408 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2389332 CTAAGTGATT
2389342 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2389378 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2389409 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2391877 original size:51 final size:50
Alignment explanation
Indices: 2391820--2391986 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 50
2391810 TTTTCATCTC
* *
2391820 GGGGATACTCCAAC-CTCGGTTCCATTTCCAAAACATCAATTTTTCCTAATT
1 GGGGATACTCCAACTC-CGATTTCATTTCCAAAACATCAATTTTTCC-AATT
* * * ** *
2391871 GGGGATACTCCAACTCCGATTTCATTTCTAAAGCATCGATTTACCGCAATC
1 GGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTC-CAATT
* * * *
2391922 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTTACAATT
1 GGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAA-TTTTTCCAATT
2391973 GGGGATACTCCAAC
1 GGGGATACTCCAAC
2391987 CCCGTTATTT
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 90 0.95
52 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (50 bp):
GGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCCAATT
Found at i:2392041 original size:28 final size:28
Alignment explanation
Indices: 2391973--2392045 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 28
2391963 TTTTACAATT
*
2391973 GGGGATACTCCAACCCCGTTATTTCATA
1 GGGGATACTCCAACCCCGTTATTTCAGA
* *
2392001 -GGGATACTCCAACCGCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
2392028 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2392046 ACTTTATATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAGA
Found at i:2392197 original size:51 final size:51
Alignment explanation
Indices: 2392139--2392307 Score: 184
Period size: 51 Copynumber: 3.3 Consensus size: 51
2392129 TTATTTCCGA
*
2392139 GGGGATACTCCAACCTCGATTTTATTTCTAAAATACTAATTTTCCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAATACTGATTTTCCACAATC
* * *
2392190 GGGGATACTCCAA-CTCTGATTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCTC-GATTTTATTTCTAAAATACTGATTTTC-CACAATC
* * ** *
2392241 GGGTGATACTTCAACCCCGACCTTATTTCT-AAAT-CATCGATTTTTCACAATC
1 GGG-GATACTCCAACCTCGATTTTATTTCTAAAATAC-T-GATTTTCCACAATC
2392293 GGGGATACTCCAACC
1 GGGGATACTCCAACC
2392308 CCGTTATTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
50 7 0.07
51 57 0.58
52 29 0.30
53 5 0.05
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAATACTGATTTTCCACAATC
Found at i:2392457 original size:79 final size:77
Alignment explanation
Indices: 2392252--2392470 Score: 233
Period size: 79 Copynumber: 2.8 Consensus size: 77
2392242 GGTGATACTT
** *
2392252 CAACCCCGACCTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT
1 CAACCCCGATTTTATTTCTAAA-CACCGATTTTTCACAATC-GGGATACTCCAACCCCGTTATTT
*
2392317 TTGAGAGGATACTC
64 TTGAGAGGAAACTC
* * * * **
2392331 CAACCTCGATTTTATTTTCAAAATACCGA-TTTTCTATAATCAGGGATACTCCAACCTTGTTATT
1 CAACCCCGATTTTA-TTTCTAAACACCGATTTTTC-ACAATC-GGGATACTCCAACCCCGTTATT
* *
2392395 TTTGAGGGGAAATTC
63 TTTGAGAGGAAACTC
* **
2392410 CAACCCCGATTTTATTTCTAGAACACCAATTTTTCACAATCGTGGATACTCCGGCCCCGTT
1 CAACCCCGATTTTATTTCTA-AACACCGATTTTTCACAATCG-GGATACTCCAACCCCGTT
2392471 GTTATCTCAA
Statistics
Matches: 113, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
78 11 0.10
79 90 0.80
80 12 0.11
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (77 bp):
CAACCCCGATTTTATTTCTAAACACCGATTTTTCACAATCGGGATACTCCAACCCCGTTATTTTT
GAGAGGAAACTC
Found at i:2406067 original size:55 final size:55
Alignment explanation
Indices: 2406002--2406250 Score: 275
Period size: 55 Copynumber: 4.4 Consensus size: 55
2405992 TTCACCCTTT
* *
2406002 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGTCCACACAAGTTGGTGGCACGTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
* * * *
2406057 AGTCCTCAAAGAGCAAGATGTCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TC
1 AGTCCTCAAAGAGCAGGACG-C-----C-TTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCC
* * * ***
2406119 AGTCCTCAAACAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCC
* * *
2406175 AATCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
2406230 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
2406251 TCTCTCCTTT
Statistics
Matches: 160, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
55 67 0.42
56 47 0.29
61 2 0.01
62 42 0.26
63 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
Found at i:2406207 original size:56 final size:55
Alignment explanation
Indices: 2406086--2406250 Score: 206
Period size: 56 Copynumber: 3.0 Consensus size: 55
2406076 GTCTTTTTCT
* *
2406086 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAACAGTAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAACAGCAGGACGCC
* ** * * *
2406141 TTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTAATCCTCAAAGAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CCTTTCAATCCTCAAACAGCAGGACGCC
* * *
2406197 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TCAATCCTCAAACAGCAGGACGC
2406251 TCTCTCCTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 2 0.02
55 45 0.48
56 47 0.50
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (55 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAACAGCAGGACGCC
Found at i:2406248 original size:111 final size:113
Alignment explanation
Indices: 2406002--2406250 Score: 317
Period size: 111 Copynumber: 2.2 Consensus size: 113
2405992 TTCACCCTTT
* *
2406002 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGTCCACACAAGTTGGTGGCACGTCCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACGTCCCAATCCTCAAA
*
2406067 GAGCAAGATGTCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
66 GAGCAAGATGTC----TCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC
* * ** ***
2406119 AGTCCTCAAACAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTAATCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CGTCCCAATCCTCAA
*
2406184 AGAGCAGGATG-C-C-TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCC
65 AGAGCAAGATGTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CC
2406230 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
2406251 TCTCTCCTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
110 3 0.03
111 47 0.40
112 1 0.01
117 47 0.40
118 19 0.16
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (113 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACGTCCCAATCCTCAAA
GAGCAAGATGTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC
Found at i:2406402 original size:61 final size:60
Alignment explanation
Indices: 2406293--2406589 Score: 313
Period size: 61 Copynumber: 4.9 Consensus size: 60
2406283 AGGACGTCTT
2406293 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTG
1 TTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT-CTG
* *
2406355 TTAAAGCCCACACAAG-TGGATGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TTTC--
1 TTAAAGCCCACACAAGTTGG-TGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTG
* * * * *
2406412 --AAAGCCCACACAAGTCGGTGGCATTTTCCAAATCCTCAAAGAGCAGGATG-CTTTCTCTC
1 TTAAAGCCCACACAAGTTGGTGGCATTTT-CTAGTCCTCAAAGAGCAGGACGCCTTT-TCTG
* ** * *
2406471 TGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCTTCAAAGAGCAGGACGCCTTTTCTT
1 T-TAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTG
** * *
2406532 TTCAAAGCCCACATGAGTTGGTGGCACTTTT-TAGTCCTCACAGAGCAAGACGCACTTT
1 TT-AAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGC-CTTT
2406590 ATTTTCCTCT
Statistics
Matches: 198, Mismatches: 23, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
55 24 0.12
56 22 0.11
57 2 0.01
59 1 0.01
60 3 0.02
61 91 0.46
62 55 0.28
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (60 bp):
TTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTG
Found at i:2406410 original size:150 final size:146
Alignment explanation
Indices: 2406113--2406411 Score: 379
Period size: 150 Copynumber: 2.0 Consensus size: 146
2406103 GTTGGTGGCA
* * *
2406113 CCTTTCAGTCCTCAAACAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTAAT
1 CCTTTCAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAAT
*
2406178 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
66 CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
*
2406243 CAGGACGCTCTCTCCTTTCGC
131 CAGGA----C-CACCTTTCGC
* * *
2406264 CCTTT-AGTCCTCAAACAGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGT
1 CCTTTCAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAAT
* *
2406328 CCTCAAAGAGCAGGACGCCTTTTCCTGTTAAAGCCCACACAAG-TGGATGGCATTTTCCAGTCCT
66 CCTCAAAGAGCAGGACGCC---T--T-TTAAAGCCCACACAAGTTGG-TGGCACTTCCCAGTCCT
2406392 CAAAGAGCAGGA-CACCTTTC
124 CAAAGAGCAGGACCACCTTTC
2406412 AAAGCCCACA
Statistics
Matches: 131, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
150 78 0.60
151 5 0.04
153 1 0.01
155 4 0.03
156 43 0.33
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (146 bp):
CCTTTCAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAAT
CCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAG
CAGGACCACCTTTCGC
Found at i:2406412 original size:267 final size:268
Alignment explanation
Indices: 2405930--2406523 Score: 856
Period size: 267 Copynumber: 2.2 Consensus size: 268
2405920 CGCCTTCTCT
2405930 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
* *
2405995 ACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGTCCACACAAGTTGGTGGCACGTCCCAGT
66 ACCCTTTAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACGTCCCAGT
* * * *
2406060 CCTCAAAGAGCAAGATGTCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCT
131 CCTCAAAGAGCAAGACGTCCTTTTCCTGTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCT
* * * ***
2406125 CAAACAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTTAATCCTCAAAGAGCA
196 CAAACAGCAGGACACCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCAAATCCTCAAAGAGCA
2406190 GGATGC-C
261 GGATGCTC
*
2406197 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
* * * * * *
2406261 CGCCCTTTAGTCCTCAAACAGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTA
65 CACCCTTTAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC-GTCCCA
* *
2406326 GTCCTCAAAGAGCAGGACG-CCTTTTCCTGTTAAAGCCCACACAAG-TGGATGGCA-TTTTCCAG
129 GTCCTCAAAGAGCAAGACGTCCTTTTCCTGTTAAAGCCCACACAAGTTGG-TGGCACCTTT-CAG
*
2406388 TCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCAAATCCTCAAAG
192 TCCTCAAACAGCAGGACACCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCAAATCCTCAAAG
2406453 AGCAGGATGCTTTC
257 AGCAGGATGC--TC
* *
2406467 TCTCTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCTTCAAAGAGCAGGACGC
1 T-T-T-TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGC
2406524 CTTTTCTTTT
Statistics
Matches: 291, Mismatches: 25, Indels: 16
0.88 0.08 0.05
Matches are distributed among these distances:
266 9 0.03
267 211 0.73
268 20 0.07
270 2 0.01
271 1 0.00
272 1 0.00
273 44 0.15
274 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (268 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
ACCCTTTAGTCCTCAAACAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACGTCCCAGT
CCTCAAAGAGCAAGACGTCCTTTTCCTGTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCT
CAAACAGCAGGACACCTTTCAAAGCCCACACAAGTCGGTGGCATTTTCCAAATCCTCAAAGAGCA
GGATGCTC
Found at i:2406478 original size:117 final size:117
Alignment explanation
Indices: 2406269--2406527 Score: 337
Period size: 117 Copynumber: 2.2 Consensus size: 117
2406259 TTCGCCCTTT
* * * * * *
2406269 AGTCCTCAAACAGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTTTCAAATCCTCAA
* **
2406334 AGAGCAGGACGCCTTTTCCTGTTAAAGCCCACACAAG-TGGATGGCATTTTCC
66 AGAGCAGGACGCCTTTTCCTGTCAAAGCCCACACAAGTTGG-TGGCACCTTCC
*
2406386 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTCGGTGGCA-TTTTCCAAATCCTCA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTTT-CAAATCCTCA
* *
2406450 AAGAGCAGGATG-CTTTCTCTCTG-CAAAGCCCACACAAGTTGGTGGCACCTTCT
65 AAGAGCAGGACGCCTTT-TC-CTGTCAAAGCCCACACAAGTTGGTGGCACCTTCC
*
2406503 AGTCTTCAAAGAGCAGGACGCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTT
2406528 TCTTTTCAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
116 8 0.06
117 110 0.89
118 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (117 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTCGGTGGCACTTTTCAAATCCTCAA
AGAGCAGGACGCCTTTTCCTGTCAAAGCCCACACAAGTTGGTGGCACCTTCC
Found at i:2406722 original size:46 final size:45
Alignment explanation
Indices: 2406560--2406766 Score: 185
Period size: 46 Copynumber: 4.6 Consensus size: 45
2406550 TGGTGGCACT
* * * *
2406560 TTTTAGTCCTCACAGAGCAAGACGCACTTT-ATTT-TCCTCTT-T-C
1 TTTT-GTCCTCAAAGAGCAGGACGCA-TTTCATTTCTTCTTTTCTCC
* * *
2406603 TTTTGTCCTCAAAAAGCAGGACGCATTTCGTTT-TCCTTTTCTCC
1 TTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCTTCTTTTCTCC
*** *
2406647 -TTTGTCCTCAAAGAGCAGGACATGTTTCATTCTCTTATTTTCTCC
1 TTTTGTCCTCAAAGAGCAGGACGCATTTCATT-TCTTCTTTTCTCC
*
2406692 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTC-CC
1 TTTTGTCCTCAAAGAGCAGGACGCATTTCATTT-CTTCTTTTCTCC
* * *
2406737 TTCTAGTCCTTAAAGAGCAGGACACATTTC
1 TT-TTGTCCTCAAAGAGCAGGACGCATTTC
2406767 GTTTTCCCTT
Statistics
Matches: 135, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
41 3 0.02
42 27 0.20
43 31 0.23
44 2 0.01
45 14 0.10
46 58 0.43
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (45 bp):
TTTTGTCCTCAAAGAGCAGGACGCATTTCATTTCTTCTTTTCTCC
Found at i:2406780 original size:46 final size:45
Alignment explanation
Indices: 2406604--2406787 Score: 173
Period size: 46 Copynumber: 4.1 Consensus size: 45
2406594 TCCTCTTTCT
* *
2406604 TTTGTCCTCAAAAAGCAGGACGCATTTCGTTTTCC--TTTTCTCC
1 TTTGTCCTCAAAGAGCAGGACACATTTCGTTTTCCTATTTTCTCC
** * * *
2406647 TTTGTCCTCAAAGAGCAGGACATGTTTCATTCTCTTATTTTCTCC
1 TTTGTCCTCAAAGAGCAGGACACATTTCGTTTTCCTATTTTCTCC
* * * *
2406692 TTTTGTCCTCAAAGAGCAGGACGCACTTC-ATTTCCTTCTTTTC-CC
1 -TTTGTCCTCAAAGAGCAGGACACATTTCGTTTTCC-TATTTTCTCC
* *
2406737 TTCTAGTCCTTAAAGAGCAGGACACATTTCGTTTTCC-CTTTT-TCC
1 TT-T-GTCCTCAAAGAGCAGGACACATTTCGTTTTCCTATTTTCTCC
2406782 TTTGTC
1 TTTGTC
2406788 ATCGAAAAGC
Statistics
Matches: 114, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
43 31 0.27
44 3 0.03
45 23 0.20
46 52 0.46
47 5 0.04
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (45 bp):
TTTGTCCTCAAAGAGCAGGACACATTTCGTTTTCCTATTTTCTCC
Found at i:2406786 original size:89 final size:86
Alignment explanation
Indices: 2406565--2406803 Score: 214
Period size: 89 Copynumber: 2.7 Consensus size: 86
2406555 GCACTTTTTA
* * * * *
2406565 GTCCTCACAGAGCAAGACGCACTTT-ATTTT-CCTCTTTCTTTTGTCCTCAAAAAGCAGGACGCA
1 GTCCTCAAAGAGCAGGACACA-TTTCATTTTCCCTTTTTCCTTTGTCCTCAAAAAGCAGGACGCA
* *
2406628 TTTCGTTTTCCTTTTCTCCTTT
65 CTTCATTTTCCTTTTCTCCTTT
** * ** *
2406650 GTCCTCAAAGAGCAGGACATGTTTCATTCTCTTATTTTCTCCTTTTGTCCTCAAAGAGCAGGACG
1 GTCCTCAAAGAGCAGGACACATTTCATTTTC-CCTTTT-TCC-TTTGTCCTCAAAAAGCAGGACG
*
2406715 CACTTCA-TTTCCTTCTTTTCCCTTCT
63 CACTTCATTTTCCTT-TTCT-CCTT-T
* * * * *
2406741 AGTCCTTAAAGAGCAGGACACATTTCGTTTTCCCTTTTTCCTTTGTCATCGAAAAGCAAGACG
1 -GTCCTCAAAGAGCAGGACACATTTCATTTTCCCTTTTTCCTTTGTCCTCAAAAAGCAGGACG
2406804 TACTCTTTTC
Statistics
Matches: 120, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
84 3 0.03
85 20 0.17
87 3 0.03
88 9 0.08
89 47 0.39
90 7 0.06
91 5 0.04
92 26 0.22
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (86 bp):
GTCCTCAAAGAGCAGGACACATTTCATTTTCCCTTTTTCCTTTGTCCTCAAAAAGCAGGACGCAC
TTCATTTTCCTTTTCTCCTTT
Found at i:2407538 original size:13 final size:13
Alignment explanation
Indices: 2407522--2407551 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2407512 ATACATTGTT
*
2407522 CATTGTATCGATA
1 CATTATATCGATA
2407535 CATTATATCGATA
1 CATTATATCGATA
2407548 CATT
1 CATT
2407552 TTAGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:2407592 original size:20 final size:20
Alignment explanation
Indices: 2407567--2407618 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2407557 TTTACCCAGA
*
2407567 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
2407587 TGTATCAATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
2407607 TGTATCGATACA
1 TGTATCGATACA
2407619 ATTTCAGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:2410001 original size:51 final size:52
Alignment explanation
Indices: 2409923--2410075 Score: 156
Period size: 51 Copynumber: 3.0 Consensus size: 52
2409913 TTTTTCATCT
* * *
2409923 TCGGG-ATACTCCAACCCCGATTCCATTTCCAAAACATCAATTTTTCC-TAA
1 TCGGGAATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCCACAA
* * * * *
2409973 TCGGGAATACTCCAACTCCAATTTCATTTCTAAAGCATCGA-TTTACCACAA
1 TCGGGAATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCCACAA
* *
2410024 TC-GGAGATACTCCAACTCCGATTTTATTTTCAAAACA-CTAATTTTT-CACAA
1 TCGGGA-ATACTCCAACTCCGATTTCATTTCCAAAACATC-AATTTTTCCACAA
2410075 T
1 T
2410076 TAGAGATACT
Statistics
Matches: 83, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
50 14 0.17
51 66 0.80
52 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (52 bp):
TCGGGAATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCCACAA
Found at i:2410136 original size:28 final size:27
Alignment explanation
Indices: 2410080--2410150 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
2410070 CACAATTAGA
* *
2410080 GATACTCTAACGCCGTTATTTCATCGGG
1 GATACTCCAACCCCGTTATTTCA-CGGG
2410108 GATACTCCAACCCCGTTATTTTCGA-GGG
1 GATACTCCAACCCCGTTA-TTTC-ACGGG
2410136 GATACTCCAACCCCG
1 GATACTCCAACCCCG
2410151 GCTTTATGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.27
Consensus pattern (27 bp):
GATACTCCAACCCCGTTATTTCACGGG
Found at i:2410217 original size:28 final size:28
Alignment explanation
Indices: 2410184--2410260 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
2410174 TTTTTTCATA
* *
2410184 ATCGGGGGTATTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2410212 ATCGGGGATACTCCAATCCCGTTATTT-
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
2410239 -TCGAGGGGATACTCTAACCCCG
1 ATC--GGGGATACTCCAACCCCG
2410261 ATTTTATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:2410321 original size:110 final size:108
Alignment explanation
Indices: 2410029--2410307 Score: 339
Period size: 110 Copynumber: 2.6 Consensus size: 108
2410019 CACAATCGGA
* * * ** * *
2410029 GATACTCCAACTCCGATTTTATTT-TCAAAACACTAATTTTTCACAAT-TAGAGATACTCTAACG
1 GATACTCCAACCCCGATTTTATTTCTAAAAATACTAATTTTTCACAATCGGGA-ATACTCCAACC
2410092 CCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGG
65 CCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGG
** * * * * ** *
2410136 GATACTCCAACCCCGGCTTTATGTCTAAAAATATTGATTTTTTTCATAATCGGGGGTATTCCAAC
1 GATACTCCAACCCCGATTTTATTTCTAAAAATACT-A-ATTTTTCACAATCGGGAATACTCCAAC
*
2410201 CCCGTTATTTCATCGGGGATACTCCAATCCCGTTATTTTCGAGGG
64 CCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGG
* *
2410246 GATACTCTAACCCCGATTTTATTTCT-AAAATACTAATTTTCCACAATCGGGAATACTCCAAC
1 GATACTCCAACCCCGATTTTATTTCTAAAAATACTAATTTTTCACAATCGGGAATACTCCAAC
2410308 TCCGATTTTA
Statistics
Matches: 140, Mismatches: 28, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
107 41 0.29
108 8 0.06
109 8 0.06
110 82 0.59
111 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (108 bp):
GATACTCCAACCCCGATTTTATTTCTAAAAATACTAATTTTTCACAATCGGGAATACTCCAACCC
CGTTATTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGG
Found at i:2410345 original size:51 final size:51
Alignment explanation
Indices: 2410247--2410363 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 51
2410237 TTTCGAGGGG
* *
2410247 ATACTCTAACCCCGATTTTATTTCTAAAATACTAATTTTCCACAATCGGGA
1 ATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTCCACAATCGGGA
* * * * *
2410298 ATACTCCAACTCCGATTTTATTTCCAAAATATTGA-TTTCTCATAATCGGGGG
1 ATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTC-CACAATC-GGGA
*
2410350 ATACTTCAACCCCG
1 ATACTCCAACCCCG
2410364 GCCTTGTTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
50 4 0.07
51 36 0.65
52 15 0.27
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (51 bp):
ATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTCCACAATCGGGA
Found at i:2410481 original size:79 final size:80
Alignment explanation
Indices: 2410370--2410530 Score: 236
Period size: 79 Copynumber: 2.0 Consensus size: 80
2410360 CCCGGCCTTG
* * * *
2410370 TTTCTAAATCATCGATTTTTCATAATCGGGGATATTCCAACCCCGTTATTTTCGAGGGGATACTC
1 TTTCAAAATCATCGATTTTTCATAATCAGGGATACTCCAACCCCATTATTTTCGAGGGGATACTC
2410435 CAACCCCAATTTTAT
66 CAACCCCAATTTTAT
* *
2410450 TTTCAAAAT-ATCGA-TTTTCTATAATTAGGGATACTCCAACCCTATTATTTTCGAGGGGATACT
1 TTTCAAAATCATCGATTTTTC-ATAATCAGGGATACTCCAACCCCATTATTTTCGAGGGGATACT
*
2410513 CCAACCCCGATTTTAT
65 CCAACCCCAATTTTAT
2410529 TT
1 TT
2410531 CTAGAACACC
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 5 0.07
79 60 0.82
80 8 0.11
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (80 bp):
TTTCAAAATCATCGATTTTTCATAATCAGGGATACTCCAACCCCATTATTTTCGAGGGGATACTC
CAACCCCAATTTTAT
Found at i:2410561 original size:79 final size:78
Alignment explanation
Indices: 2410384--2410565 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 78
2410374 TAAATCATCG
* * *
2410384 ATTTTTCATAATCGGGGATATTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTA
1 ATTTTCCATAATC-GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAATTTTA
* * *
2410449 TTTTCAAAATATCG
65 TTTTCAAAACACCA
* * * *
2410463 ATTTTCTATAATTAGGGATACTCCAACCCTATTATTTTCGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTCCATAA-TCGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAATTTTA
*
2410528 -TTTCTAGAACACCA
65 TTTTC-AAAACACCA
*
2410542 ATTTTCCACAATCGTGGATACTCC
1 ATTTTCCATAATCG-GGATACTCC
2410566 GGCCCCGTTG
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
78 6 0.07
79 79 0.92
80 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (78 bp):
ATTTTCCATAATCGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAATTTTAT
TTTCAAAACACCA
Found at i:2412615 original size:22 final size:22
Alignment explanation
Indices: 2412587--2412629 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2412577 CTATACTTAC
2412587 AACATTAGTAATCCATTCTTTT
1 AACATTAGTAATCCATTCTTTT
2412609 AACATTAGTAATCCATTCTTT
1 AACATTAGTAATCCATTCTTT
2412630 CAGCCGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (22 bp):
AACATTAGTAATCCATTCTTTT
Found at i:2416175 original size:21 final size:22
Alignment explanation
Indices: 2416146--2416191 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2416136 TGTTCAGACA
** *
2416146 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2416168 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2416189 AGT
1 AGT
2416192 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2419029 original size:20 final size:20
Alignment explanation
Indices: 2419004--2419042 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2418994 TCAAGCTTAA
*
2419004 CAAAAGTCGTTCTCAATGGC
1 CAAAAGTCATTCTCAATGGC
2419024 CAAAAGTCATTCTCAATGG
1 CAAAAGTCATTCTCAATGG
2419043 GTTGAGAGAT
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:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
CAAAAGTCATTCTCAATGGC
Found at i:2420217 original size:89 final size:89
Alignment explanation
Indices: 2420062--2420226 Score: 240
Period size: 89 Copynumber: 1.9 Consensus size: 89
2420052 TCAAAACATT
* * * *
2420062 ACATAATCAGCGATTTTGCCATACTATTATTCTTTAAAGATAAAAACATAATATTGCTAAACATA
1 ACATAATCAACGATTTTGCCATACTATCATTCTCTAAAGATAAAAACATAATATTACTAAACATA
2420127 TCTTCTTATTAATTCAAAATGCAA
66 TCTTCTTATTAATTCAAAATGCAA
* * * * *
2420151 ACATAATCAACGATTTTGTCATAGTATCGTTCTCTAAAGATAAAAGCATAATATTACTAAATATA
1 ACATAATCAACGATTTTGCCATACTATCATTCTCTAAAGATAAAAACATAATATTACTAAACATA
*
2420216 TCTTTTTATTA
66 TCTTCTTATTA
2420227 TTTCGATATG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 66 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.38
Consensus pattern (89 bp):
ACATAATCAACGATTTTGCCATACTATCATTCTCTAAAGATAAAAACATAATATTACTAAACATA
TCTTCTTATTAATTCAAAATGCAA
Found at i:2421012 original size:2 final size:2
Alignment explanation
Indices: 2421007--2421041 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2420997 GGTATGTGTG
2421007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2421042 GTGTGTGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2424420 original size:18 final size:17
Alignment explanation
Indices: 2424378--2424420 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2424368 ATATAAAATT
*
2424378 TAAAATTTTACATCATA
1 TAAAATTTTACAACATA
* *
2424395 TGAGATTTTATCAACATA
1 TAAAATTTTA-CAACATA
2424413 TAAAATTT
1 TAAAATTT
2424421 AACTATTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (17 bp):
TAAAATTTTACAACATA
Found at i:2430798 original size:20 final size:21
Alignment explanation
Indices: 2430767--2430805 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2430757 AGGTCAAAAT
2430767 CCTAGAAAGTATCGATACAAG
1 CCTAGAAAGTATCGATACAAG
2430788 CCTAG-AAGTATCGATACA
1 CCTAGAAAGTATCGATACA
2430806 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAAG
Found at i:2430832 original size:13 final size:13
Alignment explanation
Indices: 2430814--2430838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2430804 CATATTGCTT
2430814 TGTATCGATACAA
1 TGTATCGATACAA
2430827 TGTATCGATACA
1 TGTATCGATACA
2430839 TCTTCATTGT
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:2430854 original size:32 final size:33
Alignment explanation
Indices: 2430795--2430857 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
2430785 AAGCCTAGAA
*
2430795 GTATCGATACATATTGCTTTGTATCGATACAAT
1 GTATCGATACATATTGCATTGTATCGATACAAT
*
2430828 GTATCGATACATCTT-CATTGTATCGATACA
1 GTATCGATACATATTGCATTGTATCGATACA
2430858 TGAAACTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
GTATCGATACATATTGCATTGTATCGATACAAT
Found at i:2435510 original size:34 final size:34
Alignment explanation
Indices: 2435472--2435539 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2435462 GCCATAGTTG
* * *
2435472 CCTTATGGTTTTCCTTTATATTAGCCCTAATCAT
1 CCTTATAGTCTTCCTCTATATTAGCCCTAATCAT
2435506 CCTTATAGTCTTCCTCTATATTAGCCCTAATCAT
1 CCTTATAGTCTTCCTCTATATTAGCCCTAATCAT
2435540 GGCTATCTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (34 bp):
CCTTATAGTCTTCCTCTATATTAGCCCTAATCAT
Found at i:2439823 original size:9 final size:9
Alignment explanation
Indices: 2439809--2439834 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2439799 CCATCGTAAA
2439809 ATAATTTTT
1 ATAATTTTT
2439818 ATAATTTTT
1 ATAATTTTT
2439827 ATAATTTT
1 ATAATTTT
2439835 GGAAATCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATAATTTTT
Found at i:2441695 original size:35 final size:35
Alignment explanation
Indices: 2441649--2441729 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
2441639 ATAGCATTAG
*
2441649 AGGCAGTGATTAGGCAAAATGCATACGATGCATTT
1 AGGCAGAGATTAGGCAAAATGCATACGATGCATTT
*
2441684 AGGTAGAGATTAGGCAAAATGCATACGATGCATTT
1 AGGCAGAGATTAGGCAAAATGCATACGATGCATTT
2441719 AGGCAGAGATT
1 AGGCAGAGATT
2441730 TGCCACCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (35 bp):
AGGCAGAGATTAGGCAAAATGCATACGATGCATTT
Found at i:2442087 original size:15 final size:16
Alignment explanation
Indices: 2442058--2442090 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2442048 GAGCTAACGG
2442058 TAATCTCTAACTCATA
1 TAATCTCTAACTCATA
*
2442074 TAAT-TCTAATTCATA
1 TAATCTCTAACTCATA
2442089 TA
1 TA
2442091 GTTTTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATCTCTAACTCATA
Found at i:2442406 original size:133 final size:133
Alignment explanation
Indices: 2442168--2442409 Score: 448
Period size: 133 Copynumber: 1.8 Consensus size: 133
2442158 AAAAGTTTCA
*
2442168 AAATTAAAAGTTGAAAATGATTTATTATTGAAATCAAAAATTGATTTAGAAAATCAAAATAAAGA
1 AAATTAAAAGTTGAAAATGATTTATCATTGAAATCAAAAATTGATTTAGAAAATCAAAATAAAGA
2442233 TTTGAAAAATAATTTGATATTTCTAATGAAAAAAATTAAGTTTTTAATTTTATGTTTCTAATGAA
66 TTTGAAAAATAATTTGATATTTCTAATGAAAAAAATTAAGTTTTTAATTTTATGTTTCTAATGAA
2442298 ATC
131 ATC
*
2442301 AAATTAAAAGTTGAAAATGATTTATCGTTGAAATCAAAAATTGATTTAGAAAATCAAAATAAAGA
1 AAATTAAAAGTTGAAAATGATTTATCATTGAAATCAAAAATTGATTTAGAAAATCAAAATAAAGA
* *
2442366 TTTGAAAAATAATTTTATGTTTCTAATGAAAAAAATTAAGTTTT
66 TTTGAAAAATAATTTGATATTTCTAATGAAAAAAATTAAGTTTT
2442410 GAGAAAAAAA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 105 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (133 bp):
AAATTAAAAGTTGAAAATGATTTATCATTGAAATCAAAAATTGATTTAGAAAATCAAAATAAAGA
TTTGAAAAATAATTTGATATTTCTAATGAAAAAAATTAAGTTTTTAATTTTATGTTTCTAATGAA
ATC
Found at i:2443848 original size:166 final size:167
Alignment explanation
Indices: 2443566--2443886 Score: 511
Period size: 166 Copynumber: 1.9 Consensus size: 167
2443556 GATTGTATTA
*
2443566 ATACCTTTAAGCAAACTTGGCCTTTTCAAGTTGTTTTTGGTCTAAAATTCCATTTTGATCATTTT
1 ATACCTTTAAGCAAACTTGACCTTTTCAAGTTGTTTTTGGTCTAAAATTCCATTTTGATCATTTT
* * *
2443631 AGTGAGATTTTGCTTCAAATGTTTCATTTTTATCAATCTTAAATCATAATTAAAATCATTT-TTA
66 AATGAGATTTTGCTTCAAATGCTTCATTTTTATCAATCCTAAATCATAATTAAAATCATTTCTTA
2443695 ACTCATCACATGCTTATGTATAACATTGGATAAATTG
131 ACTCATCACATGCTTATGTATAACATTGGATAAATTG
* *
2443732 ATACCTTTAAGTAAATTTGACCTTTTCAAGTTGTTTTTGGTCTAAAATGT-CATTTTGATCATTT
1 ATACCTTTAAGCAAACTTGACCTTTTCAAGTTGTTTTTGGTCTAAAAT-TCCATTTTGATCATTT
* * * *
2443796 TAATGGGATTTTGCTTCAAATGCTTCGTTTTTATCAATCCTAAATTATAATTAATATCATTTCTT
65 TAATGAGATTTTGCTTCAAATGCTTCATTTTTATCAATCCTAAATCATAATTAAAATCATTTCTT
* *
2443861 GACTTATCACATGCTTATGTATAACA
130 AACTCATCACATGCTTATGTATAACA
2443887 AATGCATGAT
Statistics
Matches: 141, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
166 114 0.81
167 27 0.19
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (167 bp):
ATACCTTTAAGCAAACTTGACCTTTTCAAGTTGTTTTTGGTCTAAAATTCCATTTTGATCATTTT
AATGAGATTTTGCTTCAAATGCTTCATTTTTATCAATCCTAAATCATAATTAAAATCATTTCTTA
ACTCATCACATGCTTATGTATAACATTGGATAAATTG
Found at i:2444695 original size:20 final size:20
Alignment explanation
Indices: 2444649--2444704 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2444639 ACTGCCAAGG
*
2444649 AAATGTATCGATATATTAAT
1 AAATGTATCGATACATTAAT
*
2444669 AAATGTATCGATACATTTAT
1 AAATGTATCGATACATTAAT
* * *
2444689 CATTGTACCGATACAT
1 AAATGTATCGATACAT
2444705 CTGGGGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTAAT
Found at i:2450862 original size:21 final size:21
Alignment explanation
Indices: 2450836--2450877 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2450826 ATGTACAAGG
2450836 GCACAGGATCTAGCCTCCATA
1 GCACAGGATCTAGCCTCCATA
2450857 GCACAGGATCTAGCCTCCATA
1 GCACAGGATCTAGCCTCCATA
2450878 TATCAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (21 bp):
GCACAGGATCTAGCCTCCATA
Found at i:2458470 original size:21 final size:21
Alignment explanation
Indices: 2458418--2458463 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2458408 TTGCCAATTG
2458418 AAGTTGAGATGCCTTCTCTCA
1 AAGTTGAGATGCCTTCTCTCA
2458439 AAGTTGAGATGCCTTCTCTCA
1 AAGTTGAGATGCCTTCTCTCA
2458460 AAGT
1 AAGT
2458464 CTTGATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (21 bp):
AAGTTGAGATGCCTTCTCTCA
Found at i:2458918 original size:15 final size:15
Alignment explanation
Indices: 2458870--2458954 Score: 73
Period size: 18 Copynumber: 5.2 Consensus size: 15
2458860 TAATAATAAC
2458870 AAAAAAATAACAAAA
1 AAAAAAATAACAAAA
*
2458885 AAACAAAAGCAA-AAAA
1 AAA-AAAA-TAACAAAA
2458901 AAATATCAAATAACAAAA
1 AAA-A--AAATAACAAAA
2458919 AAAAAAATAACAAATA
1 AAAAAAATAACAAA-A
*
2458935 ACCAAAAAAAAACAAAA
1 A--AAAAAATAACAAAA
2458952 AAA
1 AAA
2458955 TGGTCTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
15 15 0.26
16 14 0.24
17 7 0.12
18 22 0.38
ACGTcount: A:0.81, C:0.11, G:0.01, T:0.07
Consensus pattern (15 bp):
AAAAAAATAACAAAA
Found at i:2458945 original size:23 final size:22
Alignment explanation
Indices: 2458895--2458946 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2458885 AAACAAAAGC
*
2458895 AAAAAAAAATATCAAATAACAA
1 AAAAAAAAATAACAAATAACAA
*
2458917 AAAAAAAAATAACAAATAACCA
1 AAAAAAAAATAACAAATAACAA
2458939 AAAAAAAA
1 AAAAAAAA
2458947 CAAAAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.81, C:0.10, G:0.00, T:0.10
Consensus pattern (22 bp):
AAAAAAAAATAACAAATAACAA
Found at i:2458955 original size:22 final size:20
Alignment explanation
Indices: 2458864--2458955 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 20
2458854 TAATAATAAT
2458864 AATAACAAAAAAATAACAAAAA
1 AATAACAAAAAAA-AA-AAAAA
* *
2458886 AACAA-AAGCAAAAAAAAATATCA
1 AATAACAA--AAAAAAAAA-A-AA
2458909 AATAACAAAAAAAAAAATAACA
1 AATAACAAAAAAAAAAA-AA-A
2458931 AATAACCAAAAAAAAACAAAAA
1 AATAA-CAAAAAAAAA-AAAAA
2458953 AAT
1 AAT
2458956 GGTCTGAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
21 4 0.07
22 28 0.48
23 22 0.38
24 4 0.07
ACGTcount: A:0.79, C:0.11, G:0.01, T:0.09
Consensus pattern (20 bp):
AATAACAAAAAAAAAAAAAA
Found at i:2460580 original size:53 final size:54
Alignment explanation
Indices: 2460517--2460642 Score: 150
Period size: 53 Copynumber: 2.4 Consensus size: 54
2460507 AAATTTTCAT
2460517 GTTCGAGTCATTTTAGGTTCGGGTCAATCAG-GTTTAACACTCAAGTT-AATC-A
1 GTTCGAGTCATTTTAGGTTCGGGTCAAT-AGAGTTTAACACTCAAGTTAAATCGA
* * * * * *
2460569 GGTTCGGGTCATTCTAGATTCGGGTCAATTGAGTTTAACATTTAAGTTAAATCGA
1 -GTTCGAGTCATTTTAGGTTCGGGTCAATAGAGTTTAACACTCAAGTTAAATCGA
*
2460624 GTTCAAGTCATTTTAGGTT
1 GTTCGAGTCATTTTAGGTT
2460643 TAGGTTTAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
52 1 0.02
53 39 0.65
54 19 0.32
55 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (54 bp):
GTTCGAGTCATTTTAGGTTCGGGTCAATAGAGTTTAACACTCAAGTTAAATCGA
Found at i:2461367 original size:16 final size:16
Alignment explanation
Indices: 2461345--2461389 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
2461335 AATTGTCCGG
2461345 GTCATTTTGGGTTCG-
1 GTCATTTTGGGTTCGA
2461360 GATCATTTTGGGTTCGA
1 G-TCATTTTGGGTTCGA
2461377 GTCATTTTGGGTT
1 GTCATTTTGGGTT
2461390 TCAGGTCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.11, C:0.11, G:0.31, T:0.47
Consensus pattern (16 bp):
GTCATTTTGGGTTCGA
Found at i:2461557 original size:32 final size:32
Alignment explanation
Indices: 2461513--2461752 Score: 183
Period size: 32 Copynumber: 7.7 Consensus size: 32
2461503 AGTTGTTGGT
*
2461513 ATCCTTTCTTTCAAAGCCCATGACTCTGTGGC
1 ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
* ** *
2461545 ATGCTTTCTTTCAAAGTTCACGACTCCGTGGC
1 ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
* * *
2461577 ATTCTTTCTTTTAAAGCCCACAACTCTGTGGC
1 ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
* ** *
2461609 ATCCTTTCTTTCAAAGCCCACAACTCCATGGA
1 ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
* *
2461641 AT-CTTTC-CT-AAAGCCCACGACTCCGTGGC
1 ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
** * * *
2461670 ACTTTTTTCTTTTCAAAACCCACAACTTTGTGGC
1 A-TCCTTTC-TTTCAAAGCCCACGACTCTGTGGC
* * *
2461704 A-CC---CTTT-TAAGTCCACAACTCTGTGGC
1 ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
2461731 A-CCTTCTCTTTCTAAAGCCCAC
1 ATCCTT-TCTTTC-AAAGCCCAC
2461753 ACAAGTTGGT
Statistics
Matches: 163, Mismatches: 34, Indels: 21
0.75 0.16 0.10
Matches are distributed among these distances:
27 19 0.12
28 3 0.02
29 19 0.12
30 2 0.01
31 13 0.08
32 82 0.50
33 8 0.05
34 17 0.10
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (32 bp):
ATCCTTTCTTTCAAAGCCCACGACTCTGTGGC
Found at i:2461635 original size:64 final size:63
Alignment explanation
Indices: 2461516--2461753 Score: 211
Period size: 64 Copynumber: 3.8 Consensus size: 63
2461506 TGTTGGTATC
* ** * ** *
2461516 CTTTCTTTCAAAGCCCATGACTCTGTGGCATGCTTTCTTTCAAAGTTCACGACTCCGTGGCATT
1 CTTTCTTTTAAAGCCCACAACTCTGTGGCATCCTTTCTTTCAAAGCCCACAACTCCGTGGCA-T
* *
2461580 CTTTCTTTTAAAGCCCACAACTCTGTGGCATCCTTTCTTTCAAAGCCCACAACTCCATGGAAT
1 CTTTCTTTTAAAGCCCACAACTCTGTGGCATCCTTTCTTTCAAAGCCCACAACTCCGTGGCAT
* * * ** * **
2461643 CTTTC--CTAAAGCCCACGACTCCGTGGCACTTTTTTCTTTTCAAAACCCACAACTTTGTGGCA-
1 CTTTCTTTTAAAGCCCACAACTCTGTGGCA-TCCTTTC-TTTCAAAGCCCACAACTCCGTGGCAT
* *
2461705 C--CCTTTT-AAGTCCACAACTCTGTGGCA-CCTTCTCTTTCTAAAGCCCACA
1 CTTTCTTTTAAAGCCCACAACTCTGTGGCATCCTT-TCTTTC-AAAGCCCACA
2461754 CAAGTTGGTG
Statistics
Matches: 141, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
59 6 0.04
60 12 0.09
61 37 0.26
62 7 0.05
63 26 0.18
64 53 0.38
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (63 bp):
CTTTCTTTTAAAGCCCACAACTCTGTGGCATCCTTTCTTTCAAAGCCCACAACTCCGTGGCAT
Found at i:2461776 original size:31 final size:32
Alignment explanation
Indices: 2461738--2461822 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 32
2461728 GGCACCTTCT
** *
2461738 CTTTCTAAAGCCCACACAAGTTGGTGGCAA-C
1 CTTTCTAAAGCCCACACAAGTCAGTAGCAACC
*
2461769 CTTTCTAAAGCCCACACAAGTCAGTAGTAACC
1 CTTTCTAAAGCCCACACAAGTCAGTAGCAACC
* *
2461801 CTTTCAAAAGCCTACACAAGTC
1 CTTTCTAAAGCCCACACAAGTC
2461823 GATGACATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 26 0.55
32 21 0.45
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (32 bp):
CTTTCTAAAGCCCACACAAGTCAGTAGCAACC
Found at i:2462084 original size:52 final size:52
Alignment explanation
Indices: 2461907--2462100 Score: 174
Period size: 52 Copynumber: 3.7 Consensus size: 52
2461897 CTAATACCGC
* * * ** *
2461907 TGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCCAATATCGT
1 TGGCCTTAAATCAGCATATTGGCATCTTTAACATTTTTAAGCCCAATATCGT
* ** * **
2461959 TGGCCTTAAATCAGCATATTGACATCTTTAACATTCCTAAGCCCAATGTCAC
1 TGGCCTTAAATCAGCATATTGGCATCTTTAACATTTTTAAGCCCAATATCGT
* * ** *
2462011 TGGCCTTGAATCAGCACATTGGCAT-TCTTCGCATTTTTAAGCCTAATATCGT
1 TGGCCTTAAATCAGCATATTGGCATCT-TTAACATTTTTAAGCCCAATATCGT
** * * *
2462063 TGGCCTTAAATCAATATATTGGCACCGTTACCATTTTT
1 TGGCCTTAAATCAGCATATTGGCATCTTTAACATTTTT
2462101 TCCCATCTTT
Statistics
Matches: 109, Mismatches: 31, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
51 1 0.01
52 108 0.99
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (52 bp):
TGGCCTTAAATCAGCATATTGGCATCTTTAACATTTTTAAGCCCAATATCGT
Found at i:2465708 original size:19 final size:21
Alignment explanation
Indices: 2465683--2465735 Score: 83
Period size: 19 Copynumber: 2.6 Consensus size: 21
2465673 GTAGCCAAAC
*
2465683 TTGTATCGATACAC-AAAATA
1 TTGTATCGATACACAAAAAAA
2465703 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACACAAAAAAA
2465723 TTGTATCGATACA
1 TTGTATCGATACA
2465736 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 5 0.17
21 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (21 bp):
TTGTATCGATACACAAAAAAA
Found at i:2467323 original size:13 final size:13
Alignment explanation
Indices: 2467305--2467331 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2467295 TTATGAATAG
2467305 TATGCATTTAAAC
1 TATGCATTTAAAC
2467318 TATGCATTTAAAC
1 TATGCATTTAAAC
2467331 T
1 T
2467332 GCAAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TATGCATTTAAAC
Found at i:2467720 original size:21 final size:21
Alignment explanation
Indices: 2467696--2467737 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2467686 ATATCTCATG
2467696 CATATGAATTATGTTGTATGT
1 CATATGAATTATGTTGTATGT
2467717 CATATGAATTATGTTGTATGT
1 CATATGAATTATGTTGTATGT
2467738 ATGCGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.48
Consensus pattern (21 bp):
CATATGAATTATGTTGTATGT
Found at i:2468103 original size:111 final size:111
Alignment explanation
Indices: 2467908--2468352 Score: 756
Period size: 111 Copynumber: 4.0 Consensus size: 111
2467898 TTAACTATGA
* * *
2467908 AATTAATCTCGATTTTGATATAA-TAAAAATATAAGCTCAATTAGCTTGTGTTTAAATATTTTCA
1 AATTAATTTCAATTTTGA-ATAACGAAAAAT-TAAGCTCAATTAGCTTGTGTTTAAATATTTTCA
2467972 AATTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
64 AATTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
2468020 AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTCAAA
1 AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTCAAA
2468085 TTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
66 TTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
2468131 AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTCAAA
1 AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTCAAA
2468196 TTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
66 TTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
*
2468242 AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTTAAA
1 AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTCAAA
* * *
2468307 TTAGTAT-TTT--TTCGAATCATTTTGAAAATACTTT-AGAAAATACT
66 TTAGTATGTTTCCTT-AAATCATTTTGAAAACAGTTTGA-AAAATACT
2468351 AA
1 AA
2468353 CATATTTTTG
Statistics
Matches: 323, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
108 3 0.01
109 28 0.09
110 3 0.01
111 267 0.83
112 22 0.07
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (111 bp):
AATTAATTTCAATTTTGAATAACGAAAAATTAAGCTCAATTAGCTTGTGTTTAAATATTTTCAAA
TTAGTATGTTTCCTTAAATCATTTTGAAAACAGTTTGAAAAATACT
Found at i:2470006 original size:13 final size:13
Alignment explanation
Indices: 2469988--2470013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2469978 TACAGCAAGT
2469988 ATGTATCGATACA
1 ATGTATCGATACA
2470001 ATGTATCGATACA
1 ATGTATCGATACA
2470014 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:2472264 original size:21 final size:21
Alignment explanation
Indices: 2472231--2472275 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2472221 TTGCAAGTTG
*
2472231 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2472253 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2472273 AAA
1 AAA
2472276 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:2474099 original size:15 final size:15
Alignment explanation
Indices: 2474079--2474109 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2474069 TAAAAATGTC
*
2474079 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2474094 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2474109 C
1 C
2474110 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:2478755 original size:13 final size:13
Alignment explanation
Indices: 2478737--2478762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2478727 TACAGCAAGT
2478737 ATGTATCGATACA
1 ATGTATCGATACA
2478750 ATGTATCGATACA
1 ATGTATCGATACA
2478763 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:2487995 original size:21 final size:21
Alignment explanation
Indices: 2487970--2488016 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2487960 TATATTTAAA
2487970 AGAAAGACTCAATATAAAATT
1 AGAAAGACTCAATATAAAATT
*
2487991 AGAAAGACTCAATATAGAATT
1 AGAAAGACTCAATATAAAATT
2488012 AGAAA
1 AGAAA
2488017 AGTATGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (21 bp):
AGAAAGACTCAATATAAAATT
Found at i:2491496 original size:9 final size:10
Alignment explanation
Indices: 2491469--2491495 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2491459 ACCTAAACAT
2491469 TCATTTTTCA
1 TCATTTTTCA
2491479 TCATTTTTCA
1 TCATTTTTCA
2491489 TCATTTT
1 TCATTTT
2491496 CCCACTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.63
Consensus pattern (10 bp):
TCATTTTTCA
Found at i:2499153 original size:16 final size:15
Alignment explanation
Indices: 2499121--2499173 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
2499111 TAGATTTTGA
*
2499121 TATATTTATAAA-CT
1 TATATTTATAAATAT
2499135 TATATTGTATAAATAT
1 TATATT-TATAAATAT
* *
2499151 TATTTTTATATTATAT
1 TATATTTATA-AATAT
2499167 TATATTT
1 TATATTT
2499174 TAATTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.19
15 10 0.31
16 16 0.50
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TATATTTATAAATAT
Done.