Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 183 of 240
Found at i:56376014 original size:77 final size:77
Alignment explanation
Indices: 56375875--56376196 Score: 310
Period size: 77 Copynumber: 4.1 Consensus size: 77
56375865 TTTAAATTTT
* ** * ** * * *
56375875 GAAACAAAATCAAAATTAGTTCTGTTAAATGGCAAGATTAAATCTCGATACA-AAGTTATTTAAT
1 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAACAGAA-TTATTTAAT
*
56375939 AAAATCTTGTTTG
65 TAAATCTTGTTTG
* *
56375952 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAATAGAATTCTTTAATT
1 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTTAATT
*
56376017 AAATATTGTTTG
66 AAATCTTGTTTG
* * * * * *
56376029 AAAACAAAACCAAAATGAAATCTGTTAAATGGTGGGAATAAATCCC-ATAACACAATTATTTAAT
1 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGA-AACAGAATTATTTAAT
*
56376093 TAAATCTTCATTTG
65 TAAATCTT-GTTTG
* *
56376107 GAAACAAAATCAAAATCAAATCAAACCTGTTAAACGGT-AGGAATAAATCCCGATACAG-ATTAT
1 GAAACAAAATCAAAAT---A--AAATCTGTTAAACGGTGA-GAATAAATCCCGAAACAGAATTAT
* **
56376170 TCAATTATTTCTTGTTTG
60 TTAATTAAATCTTGTTTG
56376188 GAAACAAAA
1 GAAACAAAA
56376197 AAAAGGAATA
Statistics
Matches: 200, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
76 1 0.00
77 122 0.61
78 20 0.10
81 13 0.06
82 15 0.08
83 28 0.14
84 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (77 bp):
GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTTAATT
AAATCTTGTTTG
Found at i:56376056 original size:154 final size:156
Alignment explanation
Indices: 56375872--56376159 Score: 363
Period size: 154 Copynumber: 1.8 Consensus size: 156
56375862 GAATTTAAAT
* * ** * *
56375872 TTTGAAACAAAATCAAAATTAGTTCTGTTAAATGGCAAGATTAAATCTCGAT-ACA-AAGTTATT
1 TTTGAAACAAAACCAAAATGAAATCTGTTAAATGGCAAGAATAAATC-CCATAACACAA-TTATT
* *
56375935 TAATAAAATCTT-GTTTGGAAACAAAATCAAAAT-A-AAATCTGTTAAACGGT-GAGAATAAATC
64 TAATAAAATCTTCATTTGGAAACAAAATCAAAATAACAAACCTGTTAAACGGTAG-GAATAAATC
56375996 CCGAAATAGAATTCTTTAATTAAATATTG
128 CCGAAATAGAATTCTTTAATTAAATATTG
***
56376025 TTTGAAAACAAAACCAAAATGAAATCTGTTAAATGGTGGGAATAAATCCCATAACACAATTATTT
1 TTTG-AAACAAAACCAAAATGAAATCTGTTAAATGGCAAGAATAAATCCCATAACACAATTATTT
*
56376090 AATTAAATCTTCATTTGGAAACAAAATCAAAATCAAATCAAACCTGTTAAACGGTAGGAATAAAT
65 AATAAAATCTTCATTTGGAAACAAAATCAAAAT--AA-CAAACCTGTTAAACGGTAGGAATAAAT
56376155 CCCGA
127 CCCGA
56376160 TACAGATTAT
Statistics
Matches: 113, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
153 7 0.06
154 54 0.48
155 22 0.19
158 1 0.01
160 28 0.25
161 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (156 bp):
TTTGAAACAAAACCAAAATGAAATCTGTTAAATGGCAAGAATAAATCCCATAACACAATTATTTA
ATAAAATCTTCATTTGGAAACAAAATCAAAATAACAAACCTGTTAAACGGTAGGAATAAATCCCG
AAATAGAATTCTTTAATTAAATATTG
Found at i:56376211 original size:83 final size:83
Alignment explanation
Indices: 56376040--56376211 Score: 188
Period size: 83 Copynumber: 2.1 Consensus size: 83
56376030 AAACAAAACC
* * * * *
56376040 AAAATGAAATCTGTTAAATGGTGGGAATAAATCCCATAACACAATTATTTAATTAAATCTTCATT
1 AAAATCAAACCTGTTAAACGGTAGGAATAAATCCCATAACACAATTATTCAATTAAATCTTCATT
**
56376105 TGGAAACAAAATCAAAAT
66 TGGAAACAAAAAAAAAAT
* * ** *
56376123 CAAATCAAACCTGTTAAACGGTAGGAATAAATCCCGAT-ACA-GATTATTCAATTATTTCTT-GT
1 AAAATCAAACCTGTTAAACGGTAGGAATAAATCCC-ATAACACAATTATTCAATTAAATCTTCAT
56376185 TTGGAAACAAAAAAAAGGAAT
65 TTGGAAACAAAAAAAA--AAT
56376206 AAAATC
1 AAAATC
56376212 CATTGAACAG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
81 15 0.21
82 15 0.21
83 41 0.56
84 2 0.03
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (83 bp):
AAAATCAAACCTGTTAAACGGTAGGAATAAATCCCATAACACAATTATTCAATTAAATCTTCATT
TGGAAACAAAAAAAAAAT
Found at i:56388901 original size:20 final size:20
Alignment explanation
Indices: 56388878--56388917 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
56388868 TGTGCCTTTA
*
56388878 TTTGTACTTTGGTGCCCCTG
1 TTTGTACTTCGGTGCCCCTG
56388898 TTTGTACTTCGGTGCCCCTG
1 TTTGTACTTCGGTGCCCCTG
56388918 AATAGCACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.28, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTGTACTTCGGTGCCCCTG
Found at i:56390940 original size:18 final size:19
Alignment explanation
Indices: 56390913--56390948 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
56390903 CAATATAGTG
*
56390913 TCATTGATTTC-ACTTAAA
1 TCATTCATTTCAACTTAAA
56390931 TCATTCATTTCAACTTAA
1 TCATTCATTTCAACTTAA
56390949 GCAAACAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (19 bp):
TCATTCATTTCAACTTAAA
Found at i:56391457 original size:33 final size:33
Alignment explanation
Indices: 56391417--56391482 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
56391407 AGGTATGACT
56391417 CGAAAGCACATATGTTTCAGTAGATTCAATAGA
1 CGAAAGCACATATGTTTCAGTAGATTCAATAGA
56391450 CGAAAGCACATATGTTTCAGTAGATTCAATAGA
1 CGAAAGCACATATGTTTCAGTAGATTCAATAGA
56391483 TTTGGCTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (33 bp):
CGAAAGCACATATGTTTCAGTAGATTCAATAGA
Found at i:56395862 original size:21 final size:22
Alignment explanation
Indices: 56395816--56395862 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
56395806 CAGACAGAAA
* *
56395816 ACCAGCCCAAACCAACCAATAG
1 ACCAGCCCAAACCAACCAACAC
*
56395838 ACCA-CCCATACCAACCAACAC
1 ACCAGCCCAAACCAACCAACAC
56395859 ACCA
1 ACCA
56395863 TGTGGGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.45, C:0.47, G:0.04, T:0.04
Consensus pattern (22 bp):
ACCAGCCCAAACCAACCAACAC
Found at i:56396312 original size:27 final size:25
Alignment explanation
Indices: 56396231--56396367 Score: 105
Period size: 27 Copynumber: 5.2 Consensus size: 25
56396221 TAAAACGGTA
*
56396231 ATTTTACCC-TAGGGGTATTTTGGTC
1 ATTTTACCCTTTGGGGTA-TTTGGTC
* * * *
56396256 ATTTTACACTTTGAGGATATTTCAGAC
1 ATTTTACCCTTTG-GGGTATTT-GGTC
*
56396283 ATTTTACCCTTCGGGGTTACTTTGGTC
1 ATTTTACCCTTTGGGG-TA-TTTGGTC
* *
56396310 ATTTTAACCTTTGGTGGTATTTCAGTC
1 ATTTTACCCTTTGG-GGTATTT-GGTC
*
56396337 ATTTTACCTTTTGAGGGTATTTTGGTC
1 ATTTTACCCTTTG-GGGTA-TTTGGTC
56396364 ATTT
1 ATTT
56396368 AACGACCCTT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
25 8 0.09
26 10 0.11
27 60 0.69
28 9 0.10
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (25 bp):
ATTTTACCCTTTGGGGTATTTGGTC
Found at i:56396312 original size:54 final size:53
Alignment explanation
Indices: 56396231--56396367 Score: 163
Period size: 54 Copynumber: 2.6 Consensus size: 53
56396221 TAAAACGGTA
56396231 ATTTTACCC-TAGGGGTATTTTGGTCATTTT-ACACTTTGAG-GATATTTCAGAC
1 ATTTTACCCTTAGGGGTATTTTGGTCATTTTAAC-CTTTG-GTGATATTTCAGAC
* * * *
56396283 ATTTTACCCTTCGGGGTTACTTTGGTCATTTTAACCTTTGGTGGTATTTCAGTC
1 ATTTTACCCTTAGGGG-TATTTTGGTCATTTTAACCTTTGGTGATATTTCAGAC
* *
56396337 ATTTTACCTTTTGAGGGTATTTTGGTCATTT
1 ATTTTACCCTTAG-GGGTATTTTGGTCATTT
56396368 AACGACCCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
52 9 0.12
53 6 0.08
54 53 0.73
55 5 0.07
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (53 bp):
ATTTTACCCTTAGGGGTATTTTGGTCATTTTAACCTTTGGTGATATTTCAGAC
Found at i:56402749 original size:284 final size:284
Alignment explanation
Indices: 56402239--56402784 Score: 806
Period size: 284 Copynumber: 1.9 Consensus size: 284
56402229 TGAGCCATCC
*
56402239 CAGCCAAGAATAAATTTTAACCCTAATTATTAATTAAGTCAACAATAACCTTTAATTAAGTATTT
1 CAGCCAAGAATAAATTTTAACCCTAATTATTAACTAAGTCAACAATAACCTTTAATTAAGTATTT
* * * * *
56402304 ACTACTCTTAGCTAAGAATACCCTCTTGGTTTCATCTTCACTAAGAATTACCATCTAAGATGCCC
66 ACTACCCTTAGCTAAGAATACCCTCTCGGTTTCATCTTCACCAAGAATTACAACCTAAGATGCCC
* * * *
56402369 TCTCAGTCTCACCTAGGCATACGGATACTCTATTGGTCCCATAACTTGGTACGAGTTCTACTGAA
131 TCTCAGTCTCACCTAGGCAAACGGATACTCTATTAGTCCCACAACTTGGTACGAGTTCTACTCAA
* * * * *
56402434 CAAGATACCCTCTCGGTCTCACTTGTCTAGATCTTCTACTAGGGTGTCATTTCCCTGTATATTAA
196 CAAGACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCCTGTATATTAA
56402499 GTCAAGAATCAATTTTAGCCCTCT
261 GTCAAGAATCAATTTTAGCCCTCT
* * * *
56402523 CAGCCAAGAATCAATTTTAGCCCTAATTATTAACTAAGTCAACAATGACCTTTGATTAAGTATTT
1 CAGCCAAGAATAAATTTTAACCCTAATTATTAACTAAGTCAACAATAACCTTTAATTAAGTATTT
* * * *
56402588 ACTACCCTTAGTTTAGAATACCCTCTCGGTTTCATCTTCACCGATAATTACAACCTAAGATGCCC
66 ACTACCCTTAGCTAAGAATACCCTCTCGGTTTCATCTTCACCAAGAATTACAACCTAAGATGCCC
* * * * * *
56402653 TCTCGGTCTCAGCTAGGCAAACGGGTACTCTCTTAGTCCCACCACTTGGTACGAGTTCTATTCAA
131 TCTCAGTCTCACCTAGGCAAACGGATACTCTATTAGTCCCACAACTTGGTACGAGTTCTACTCAA
*
56402718 -AATGACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCTTGTATATTA
196 CAA-GACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCCTGTATATTA
56402782 AGT
260 AGT
56402785 ATTCTCGAAT
Statistics
Matches: 231, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
283 2 0.01
284 229 0.99
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (284 bp):
CAGCCAAGAATAAATTTTAACCCTAATTATTAACTAAGTCAACAATAACCTTTAATTAAGTATTT
ACTACCCTTAGCTAAGAATACCCTCTCGGTTTCATCTTCACCAAGAATTACAACCTAAGATGCCC
TCTCAGTCTCACCTAGGCAAACGGATACTCTATTAGTCCCACAACTTGGTACGAGTTCTACTCAA
CAAGACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCCTGTATATTAA
GTCAAGAATCAATTTTAGCCCTCT
Found at i:56415386 original size:41 final size:41
Alignment explanation
Indices: 56415340--56415442 Score: 116
Period size: 49 Copynumber: 2.3 Consensus size: 41
56415330 TAAGCATGTA
* *
56415340 TTGGTTGATTAATTAATTAGTTAGAGGACGAGAGGTTATAG
1 TTGGTTAATTAATTAATTAGTTAGAGGACGAGAGGTAATAG
56415381 TTGGTTAATTAATAGCTAAGTTAATTAGTTAGAGGACGAGAGGTAATAG
1 TTGG----TTAAT---TAA-TTAATTAGTTAGAGGACGAGAGGTAATAG
56415430 TTGGTTAATTAAT
1 TTGGTTAATTAAT
56415443 AGCTAACTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
41 5 0.10
42 3 0.06
45 9 0.17
48 3 0.06
49 32 0.62
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (41 bp):
TTGGTTAATTAATTAATTAGTTAGAGGACGAGAGGTAATAG
Found at i:56415408 original size:49 final size:49
Alignment explanation
Indices: 56415352--56415448 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
56415342 GGTTGATTAA
*
56415352 TTAATTAGTTAGAGGACGAGAGGTTATAGTTGGTTAATTAATAGCTAAG
1 TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAAG
56415401 TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAA
1 TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAA
56415449 CTCAATAAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (49 bp):
TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAAG
Found at i:56424239 original size:25 final size:25
Alignment explanation
Indices: 56424148--56424242 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 25
56424138 ACGAATACTC
56424148 CACAGCTCGTA-AGAGCATACTGATT
1 CACAGCTCGTATA-AGCATACTGATT
*** * *
56424173 TGTAGCTCGTGAT-TGCATATTGA-T
1 CACAGCTCGT-ATAAGCATACTGATT
*
56424197 CTACAGCTCG-AGTGAGCATACTGATT
1 C-ACAGCTCGTA-TAAGCATACTGATT
56424223 CACAGCTCGTATAAGCATAC
1 CACAGCTCGTATAAGCATAC
56424243 ATGTACATGA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
23 1 0.02
24 2 0.04
25 45 0.87
26 4 0.08
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (25 bp):
CACAGCTCGTATAAGCATACTGATT
Found at i:56424402 original size:17 final size:17
Alignment explanation
Indices: 56424380--56424417 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
56424370 AATATATGAA
56424380 CTTACTAAGCTTAAATG
1 CTTACTAAGCTTAAATG
56424397 CTTACTAAGCTTAAATG
1 CTTACTAAGCTTAAATG
56424414 CTTA
1 CTTA
56424418 AATGTTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (17 bp):
CTTACTAAGCTTAAATG
Found at i:56425996 original size:53 final size:54
Alignment explanation
Indices: 56425934--56426046 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
56425924 GGTATAACAG
* * * * ** *
56425934 TCATGTTACCCTACGA-GGTGTTTCAGTCATTTTATCCTTCGGGGGTATTTTGA
1 TCATTTTACCCTACGAGGGTATTTCAGTCATTTTACCCTTCGAGCATATTTCGA
* *
56425987 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGCATATTTCGA
1 TCATTTTACCCTACGAGGGTATTTCAGTCATTTTACCCTTCGAGCATATTTCGA
56426041 TCATTT
1 TCATTT
56426047 GCCCACGAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 14 0.28
54 36 0.72
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (54 bp):
TCATTTTACCCTACGAGGGTATTTCAGTCATTTTACCCTTCGAGCATATTTCGA
Found at i:56425999 original size:27 final size:27
Alignment explanation
Indices: 56425934--56426046 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
56425924 GGTATAACAG
* * *
56425934 TCATGTTACCCTACGA-GGTGTTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
56425959 GTCATTTTATCCTTCGGGGGTATTTTGA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
*
56425987 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
**
56426014 TCATTTTACCCTTCGAGCATATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
56426041 TCATTT
1 TCATTT
56426047 GCCCACGAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
26 12 0.17
27 59 0.82
28 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:56428840 original size:102 final size:104
Alignment explanation
Indices: 56428657--56428848 Score: 316
Period size: 102 Copynumber: 1.9 Consensus size: 104
56428647 CGGTGGATTG
* *
56428657 AGCACTTAGCAACCCCTTTTCACATTAAAAAATACGGTTGAATCAGCACTTAGCAACCACCAATG
1 AGCACTTAGCAACCCCTCTTCACATTAAAAAATACGGTGGAATCAGCACTTAGCAACCACCAATG
** *
56428722 AATTGGGGAATTAGCACTTAGCAACCCCTTGCAGGAATC
66 AATCAGGGAATCAGCACTTAGCAACCCCTTGCAGGAATC
*
56428761 AGCACTTAGCAACCCC-CTTCACATT-TAAAATACGGTGGAATCAGCACTTAGCAACCACCAATG
1 AGCACTTAGCAACCCCTCTTCACATTAAAAAATACGGTGGAATCAGCACTTAGCAACCACCAATG
56428824 AATCAGGGAATCAGCACTTAGCAAC
66 AATCAGGGAATCAGCACTTAGCAAC
56428849 TATATTCAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 58 0.71
103 8 0.10
104 16 0.20
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.21
Consensus pattern (104 bp):
AGCACTTAGCAACCCCTCTTCACATTAAAAAATACGGTGGAATCAGCACTTAGCAACCACCAATG
AATCAGGGAATCAGCACTTAGCAACCCCTTGCAGGAATC
Found at i:56469295 original size:27 final size:27
Alignment explanation
Indices: 56469209--56469279 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
56469199 CTAGGAGGTC
* * *
56469209 GTAATAAGTACCGTAATACCCCTATAGG
1 GTAA-AAGGACCGTAATACCCTTGTAGG
*
56469237 GTAAAATGACCGTAATACCCTTGTAGG
1 GTAAAAGGACCGTAATACCCTTGTAGG
56469264 GTAAAAGGACCGTAAT
1 GTAAAAGGACCGTAAT
56469280 GCCTTTGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAAAAGGACCGTAATACCCTTGTAGG
Found at i:56469391 original size:24 final size:24
Alignment explanation
Indices: 56469364--56469409 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
56469354 GAATTTTTTG
* *
56469364 TGATATAAATGATTGATTTGTCCT
1 TGATACAAATGACTGATTTGTCCT
* *
56469388 TGATGCAAATGACTGCTTTGTC
1 TGATACAAATGACTGATTTGTC
56469410 TGTGTTTGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATACAAATGACTGATTTGTCCT
Found at i:56469654 original size:32 final size:33
Alignment explanation
Indices: 56469600--56469770 Score: 151
Period size: 32 Copynumber: 5.4 Consensus size: 33
56469590 GCTGCGATGC
*
56469600 TACTGATGGCTT-TGTG-CTGATCATGTTACCGT
1 TACTGATGGCTTGTGTGTC-GATCATATTACCGT
* *
56469632 TATTGATGGCTTGT-TGTCGATCATATTACTGT
1 TACTGATGGCTTGTGTGTCGATCATATTACCGT
* *
56469664 TACT-ATGGCTT-TGTGCCAATCATATTACCGT
1 TACTGATGGCTTGTGTGTCGATCATATTACCGT
* * *
56469695 TACTGATGGC-TGTGTGTCGATCATATCACTGC
1 TACTGATGGCTTGTGTGTCGATCATATTACCGT
* * * * *
56469727 TACTAATGGCTT-TGTGCCAATCACATTACTG-
1 TACTGATGGCTTGTGTGTCGATCATATTACCGT
*
56469758 TACTTATGGCTTG
1 TACTGATGGCTTG
56469771 CAGCCATTCT
Statistics
Matches: 114, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.01
31 38 0.33
32 72 0.63
33 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (33 bp):
TACTGATGGCTTGTGTGTCGATCATATTACCGT
Found at i:56469678 original size:63 final size:64
Alignment explanation
Indices: 56469597--56469768 Score: 224
Period size: 63 Copynumber: 2.7 Consensus size: 64
56469587 TTTGCTGCGA
* ** * * *
56469597 TGCTACTGATGGCTTTGTGCTGATCATGTTACCGTTATTGATGGCT-TGTTGTCGATCATATTAC
1 TGCTACTAATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTGTG-TGTCGATCATATCAC
*
56469661 TGTTACT-ATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTGTGTGTCGATCATATCAC
1 TGCTACTAATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTGTGTGTCGATCATATCAC
* * *
56469724 TGCTACTAATGGCTTTGTGCCAATCACATTACTG-TACTTATGGCT
1 TGCTACTAATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCT
56469769 TGCAGCCATT
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 64 0.67
64 32 0.33
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (64 bp):
TGCTACTAATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTGTGTGTCGATCATATCAC
Found at i:56469786 original size:22 final size:22
Alignment explanation
Indices: 56469761--56469825 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
56469751 ATTACTGTAC
**
56469761 TTATGGCTTGCAGCCATTCTGT
1 TTATGGCTTATAGCCATTCTGT
* * * *
56469783 TTATAGCTTATAGCTATCCTAT
1 TTATGGCTTATAGCCATTCTGT
*
56469805 TTATGGCTTTTAGCCATTCTG
1 TTATGGCTTATAGCCATTCTG
56469826 ACTACCGGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (22 bp):
TTATGGCTTATAGCCATTCTGT
Found at i:56470012 original size:28 final size:28
Alignment explanation
Indices: 56469980--56470045 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
56469970 GCTGCACCAT
*
56469980 ACTGTTACTGTATCGGGCTTAGGCCCAC
1 ACTGTTACTGTATCGGGCTAAGGCCCAC
* * *
56470008 ACTGTTTCTATATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATCGGGCTAAGGCCCAC
56470036 ACTG-TACTGT
1 ACTGTTACTGT
56470046 TACTTTTATC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (28 bp):
ACTGTTACTGTATCGGGCTAAGGCCCAC
Found at i:56480613 original size:27 final size:27
Alignment explanation
Indices: 56480575--56480982 Score: 485
Period size: 27 Copynumber: 15.1 Consensus size: 27
56480565 TTCCCATGTA
*
56480575 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
56480602 ATTTTACCCTATGAGGGTATTTCTGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * * *
56480629 GTTTTACTCTATGGAGGTATTTCTGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
56480656 ATTCTACCTTATGGTGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
56480683 ATTCTACCCTATTGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
56480710 ATTTTACCATATGGGGGTCTTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
56480737 ATTTTACCCTATGAGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
56480764 ATTTTACCTTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* **
56480791 ATTCTACCCTATAAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* **
56480818 ATTCTACCCTATAAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
56480845 ATTCTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
** *
56480872 ATTTTGTCCTACGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
56480899 ATTTTACCCTAT-AGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
56480925 ATTTTACCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
56480952 ATTTTACCCTATGGGGGTATATCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
56480979 ATTT
1 ATTT
56480983 ATCGACCTCT
Statistics
Matches: 332, Mismatches: 48, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
26 25 0.08
27 307 0.92
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:56481665 original size:12 final size:12
Alignment explanation
Indices: 56481648--56481689 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
56481638 ATCCCAATAT
56481648 TCTCTCCTAAAA
1 TCTCTCCTAAAA
56481660 TCTCTCC-AAATA
1 TCTCTCCTAAA-A
* *
56481672 TCCCTCCTCAAA
1 TCTCTCCTAAAA
56481684 TCTCTC
1 TCTCTC
56481690 TATGACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.80
13 2 0.08
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCTCCTAAAA
Found at i:56490424 original size:8 final size:8
Alignment explanation
Indices: 56490411--56490435 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
56490401 TTTTAAATAC
56490411 TATTTTAT
1 TATTTTAT
56490419 TATTTTAT
1 TATTTTAT
56490427 TATTTTAT
1 TATTTTAT
56490435 T
1 T
56490436 GTTTAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:56500942 original size:27 final size:26
Alignment explanation
Indices: 56500892--56501301 Score: 343
Period size: 27 Copynumber: 15.2 Consensus size: 26
56500882 GGTCGATATC
***
56500892 TGACCGAAATACCTTTATAGGGTAAAA
1 TGACCGAAATACCCCCATA-GGTAAAA
* *
56500919 TCACCGAAATACCCCCAAATGGTAAAA
1 TGACCGAAATACCCCCATA-GGTAAAA
* *
56500946 TGATCAAAATACCCCCATAGGGTAAAA
1 TGACCGAAATACCCCCATA-GGTAAAA
* *
56500973 TGACCGAAATACCCTCATAGGGTAGAA
1 TGACCGAAATACCCCCATA-GGTAAAA
*
56501000 TGACCAAAATACCCCCATAGTGTAAAA
1 TGACCGAAATACCCCCATAG-GTAAAA
*
56501027 TGACCGAAATACCCCCATAGGATAGAA
1 TGACCGAAATACCCCCATAGG-TAAAA
**
56501054 TGATTGAAATACCCCCATAGGGTAAAA
1 TGACCGAAATACCCCCATA-GGTAAAA
* * * *
56501081 TGACTGAAATACTCCTATAAGATAAAA
1 TGACCGAAATACCCCCAT-AGGTAAAA
*
56501108 TGATCGAAATACCCCCATAGGTTAAAA
1 TGACCGAAATACCCCCATAGG-TAAAA
* * * *
56501135 TGACTGAAATATCCTCATAAGGTAGAA
1 TGACCGAAATACCCCCAT-AGGTAAAA
* *
56501162 TAACCGAAATACCCCCCATAGGGTAGAA
1 TGACCGAAATA-CCCCCATA-GGTAAAA
* * **
56501190 TGACCAAAATAACCCTGTAGGCTAAAA
1 TGACCGAAATACCCCCATAGG-TAAAA
* * * * * *
56501217 TGAGCAAAACATCCCCACAGGGTAGAA
1 TGACCGAAATACCCCCATA-GGTAAAA
* *
56501244 TGACTGAAATACCCTCATAGGGTAAAA
1 TGACCGAAATACCCCCATA-GGTAAAA
*
56501271 TGACCGAAATACCCCTATAAGGTAAAA
1 TGACCGAAATACCCCCAT-AGGTAAAA
56501298 TGAC
1 TGAC
56501302 TGTTATATCC
Statistics
Matches: 307, Mismatches: 65, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
26 6 0.02
27 271 0.88
28 30 0.10
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (26 bp):
TGACCGAAATACCCCCATAGGTAAAA
Found at i:56501027 original size:81 final size:81
Alignment explanation
Indices: 56500892--56501301 Score: 426
Period size: 81 Copynumber: 5.0 Consensus size: 81
56500882 GGTCGATATC
* * * * * * * *
56500892 TGACCGAAATACCTTTATAGGGTAAAATCACCGAAATACCCCCAAATGGTAAAATGATCAAAATA
1 TGACCGAAATACCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATA
56500957 CCCCCATAGGGTAAAA
66 CCCCCATAGGGTAAAA
* *
56500973 TGACCGAAATACCCTCATAGGGTAGAATGACCAAAATACCCCCATAGTGTAAAATGACCGAAATA
1 TGACCGAAATACCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATA
* *
56501038 CCCCCATAGGATAGAA
66 CCCCCATAGGGTAAAA
** * * * * * * * *
56501054 TGATTGAAATACCCCCATAGGGTAAAATGACTGAAATACTCCTATAAGATAAAATGATCGAAATA
1 TGACCGAAATACCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATA
*
56501119 CCCCCATAGGTTAAAA
66 CCCCCATAGGGTAAAA
* * * * * *
56501135 TGACTGAAATATCCTCATAAGGTAGAATAACCGAAATACCCCCCATAGGGTAGAATGACCAAAAT
1 TGACCGAAATACCCTCATAGGGTAGAATGACCGAAATA-CCCCCATAGGGTAAAATGACCGAAAT
* ** *
56501200 AACCCTGTAGGCTAAAA
65 ACCCCCATAGGGTAAAA
* * * * * *
56501217 TGAGCAAAACATCCC-CACAGGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACCGAAAT
1 TGACCGAAATA-CCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAAT
* *
56501281 ACCCCTATAAGGTAAAA
65 ACCCCCATAGGGTAAAA
56501298 TGAC
1 TGAC
56501302 TGTTATATCC
Statistics
Matches: 266, Mismatches: 61, Indels: 4
0.80 0.18 0.01
Matches are distributed among these distances:
81 206 0.77
82 58 0.22
83 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (81 bp):
TGACCGAAATACCCTCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATA
CCCCCATAGGGTAAAA
Found at i:56501303 original size:54 final size:54
Alignment explanation
Indices: 56500892--56501301 Score: 419
Period size: 54 Copynumber: 7.6 Consensus size: 54
56500882 GGTCGATATC
*** * * * *
56500892 TGACCGAAATACCTTTATAGGGTAAAATCACCGAAATACCCCCAAATGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
* * *
56500946 TGATCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAGAA
1 TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
* * * * *
56501000 TGACCAAAATACCCCCATAGTGTAAAATGACCGAAATACCCCCATAGGATAGAA
1 TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
** * * *
56501054 TGATTGAAATACCCCCATAGGGTAAAATGACTGAAATACTCCT-ATAAGATAAAA
1 TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATAC-CCTCATAGGGTAAAA
* * * * * *
56501108 TGATCGAAATACCCCCATAGGTTAAAATGACTGAAATATCCTCATAAGGTAGAA
1 TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
* * * * *
56501162 TAACCGAAATACCCCCCATAGGGTAGAATGACCAAAATAACCCT-GTAGGCTAAAA
1 TGACCGAAATA-CCCCCATAGGGTAAAATGACCGAAAT-ACCCTCATAGGGTAAAA
* * * * * * *
56501217 TGAGCAAAACATCCCCACAGGGTAGAATGACTGAAATACCCTCATAGGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
* *
56501271 TGACCGAAATACCCCTATAAGGTAAAATGAC
1 TGACCGAAATACCCCCATAGGGTAAAATGAC
56501302 TGTTATATCC
Statistics
Matches: 295, Mismatches: 56, Indels: 10
0.82 0.16 0.03
Matches are distributed among these distances:
53 8 0.03
54 245 0.83
55 38 0.13
56 4 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (54 bp):
TGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAA
Found at i:56503811 original size:40 final size:40
Alignment explanation
Indices: 56503766--56503912 Score: 141
Period size: 40 Copynumber: 3.7 Consensus size: 40
56503756 AGAGCATTCT
* * * *
56503766 TTTCAGTAGATTCAGTAGTTATGGATCGAAAGAGCATATG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
* * * * * *
56503806 TTTCAGAAAATTTAGTAGGTGTGGCTCAAAATCGCATACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
* ** * *
56503846 TTTCAGTAGATTTAGTAAATATGGCTCGAAGGCGCATGCG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
* *
56503886 TTTTAGTAGATTCAGAAGGTATGGCTC
1 TTTCAGTAGATTCAGTAGGTATGGCTC
56503913 TTCTGAGCAC
Statistics
Matches: 83, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
Found at i:56505787 original size:40 final size:40
Alignment explanation
Indices: 56505736--56505898 Score: 191
Period size: 40 Copynumber: 4.1 Consensus size: 40
56505726 ATTTCTTTTA
* * *
56505736 CTCGATAGAGCATTCTTTTCAGTAGATTCAGTAGGTATGG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
* * *
56505776 CTTGAAAGAGCATACGTTTCAGTAAATTCAGTAGGTGTGG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
* * * * *
56505816 CTCAAAAGCGCATACGTTTCAGTAGATTTAGTAAGTATTG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
* * * *
56505856 CTCGAAGGCGCATGCGTTTTAGTAGATTCAGTAGGTATGG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
56505896 CTC
1 CTC
56505899 TTCTGAGTAC
Statistics
Matches: 102, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (40 bp):
CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
Found at i:56508573 original size:20 final size:22
Alignment explanation
Indices: 56508548--56508595 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
56508538 CGAATCTGCC
56508548 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
56508568 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
56508590 AAAAAT
1 AAAAAT
56508596 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:56518488 original size:15 final size:15
Alignment explanation
Indices: 56518470--56518506 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
56518460 TGGTGGTAGA
*
56518470 GGTGCTGGTCGGCGT
1 GGTGCTGGTCAGCGT
*
56518485 GGTGCTGGTCAGTGT
1 GGTGCTGGTCAGCGT
56518500 GGTGCTG
1 GGTGCTG
56518507 CTCAATGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.03, C:0.16, G:0.51, T:0.30
Consensus pattern (15 bp):
GGTGCTGGTCAGCGT
Found at i:56518515 original size:15 final size:15
Alignment explanation
Indices: 56518483--56518517 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56518473 GCTGGTCGGC
* *
56518483 GTGGTGCTGGTCAGT
1 GTGGTGCTGCTCAAT
56518498 GTGGTGCTGCTCAAT
1 GTGGTGCTGCTCAAT
56518513 GTGGT
1 GTGGT
56518518 AATAGTGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.14, G:0.43, T:0.34
Consensus pattern (15 bp):
GTGGTGCTGCTCAAT
Found at i:56519932 original size:107 final size:108
Alignment explanation
Indices: 56519775--56520050 Score: 351
Period size: 111 Copynumber: 2.5 Consensus size: 108
56519765 ATCGAAACTT
* * *
56519775 AGCATATTAGGGCACG-TTCCTCGAATTTCCAAACGCAAAATATAAT-CTTACTTTGAAATTTTA
1 AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATAT-TTCCTTACTTTGAAATTTTA
* * * *
56519838 AAAGGTTATTTGGTTATTTGGTCGAATG-AAAAAATCGATACCC
65 AAAGGATATTTGGCTATTTGGTCGAATGAAAAAAATAGAAACCC
* *
56519881 ATCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTTCCTTACTTTGAAATTTTAA
1 AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTTCCTTACTTTGAAATTTTAA
* * *
56519946 TAGGATATTTTGCTGTTTGGTCGAATGAAAAAAAAAATAGAAACCC
66 AAGGATATTTGGCTATTTGGTCGAATG---AAAAAAATAGAAACCC
* * * *
56519992 AGCAGATTAGGGCGCATTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
1 AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTTCCTTACTTTGAAA
56520051 AATTTTCCTT
Statistics
Matches: 146, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
106 15 0.10
107 65 0.45
111 66 0.45
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (108 bp):
AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTTCCTTACTTTGAAATTTTAA
AAGGATATTTGGCTATTTGGTCGAATGAAAAAAATAGAAACCC
Found at i:56520028 original size:111 final size:107
Alignment explanation
Indices: 56519735--56520050 Score: 341
Period size: 111 Copynumber: 2.9 Consensus size: 107
56519725 GAGATTTATG
* ** * * * ** * * *
56519735 AGGATATTTAGCTATTTGGTTAAACG-AGAAATCGAAACTTAGCATATTAGGGCAC-GTTCCTCG
1 AGGATATTTGGCTATTTGGTCGAATGAAAAAATAGAAACCCAGCACATTAGGGCACATTTTCTCG
*
56519798 AATTTCCAAACGCAAAATATAAT-CTTACTTTGAAATTTTAAA
66 AATTTCCAAACGCAAAATAT-TTCCTTACTTTGAAATTTTAAA
* * * * * *
56519840 AGGTTATTTGGTTATTTGGTCGAATGAAAAAATCGATACCCATCACATTAGGGCACGTTTTCTCG
1 AGGATATTTGGCTATTTGGTCGAATGAAAAAATAGAAACCCAGCACATTAGGGCACATTTTCTCG
* *
56519905 AATTTCCAAACGCAAAACATTTCCTTACTTTGAAATTTTAAT
66 AATTTCCAAACGCAAAATATTTCCTTACTTTGAAATTTTAAA
* * * *
56519947 AGGATATTTTGCTGTTTGGTCGAATGAAAAAAAAAATAGAAACCCAGCAGATTAGGGCGCATTTT
1 AGGATATTTGGCTATTTGGTCGAATG----AAAAAATAGAAACCCAGCACATTAGGGCACATTTT
*
56520012 CTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
62 CTCGAATTTCCAAACGCAAAATATTTCCTTACTTTGAAA
56520051 AATTTTCCTT
Statistics
Matches: 175, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
105 20 0.11
106 24 0.14
107 65 0.37
111 66 0.38
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (107 bp):
AGGATATTTGGCTATTTGGTCGAATGAAAAAATAGAAACCCAGCACATTAGGGCACATTTTCTCG
AATTTCCAAACGCAAAATATTTCCTTACTTTGAAATTTTAAA
Found at i:56520692 original size:3 final size:3
Alignment explanation
Indices: 56520672--56520817 Score: 132
Period size: 3 Copynumber: 49.0 Consensus size: 3
56520662 AAATGGAAAT
* * * * * *
56520672 ATA ATG ATA ATA ACA ATA ATA TTA ACA ATA ATA CTA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** * * *
56520720 AGG ATA ATA ATA ATA ATA ATA ATA ATA ATA CTT ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** * *
56520768 ATA A-A CTA ATT AGC TTA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56520815 ATA
1 ATA
56520818 GGACTAAATT
Statistics
Matches: 109, Mismatches: 33, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
2 1 0.01
3 108 0.99
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56521739 original size:20 final size:20
Alignment explanation
Indices: 56521714--56521753 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
56521704 GATGGGCGGT
*
56521714 GACGTGACCATGGCGGTGGC
1 GACGTGACCATGGCAGTGGC
*
56521734 GACGTGACCGTGGCAGTGGC
1 GACGTGACCATGGCAGTGGC
56521754 AGGGTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (20 bp):
GACGTGACCATGGCAGTGGC
Found at i:56522394 original size:44 final size:44
Alignment explanation
Indices: 56522333--56522436 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
56522323 CGGCCTACTG
* * * *
56522333 CAACTTCAGAGG-TATAGGATTTATCATTTTAATCTGCTCCACTA
1 CAACTTCAG-GGAGATAGGATTAATCACTTCAATCTGCTCCACTA
* ** * *
56522377 CAACTTTAGGGAGATAGGATTAATTGCTTCAATCTGCTCCAGTG
1 CAACTTCAGGGAGATAGGATTAATCACTTCAATCTGCTCCACTA
56522421 CAACTTCAGGGAGATA
1 CAACTTCAGGGAGATA
56522437 AGACTGGATG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
43 2 0.04
44 47 0.96
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATTAATCACTTCAATCTGCTCCACTA
Found at i:56522465 original size:41 final size:41
Alignment explanation
Indices: 56522408--56522609 Score: 145
Period size: 41 Copynumber: 4.8 Consensus size: 41
56522398 AATTGCTTCA
* *
56522408 ATCTGCTCCAGTGCAACTTCAGGGAGATAAGACTGGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATGCG
* * * * ***
56522449 ATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGA-C--TGGATGCG
* * * * * * *
56522493 ATCCGGTCCACTACAACTTCAGGGAGATAGGATTGGTTTATTCTG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGG---ATGC-G
* * *
56522538 -TCTTCTCTAATGCAACTTCAGGGAGATAAGACTAGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATGCG
**
56522578 ATCTGCTCTACTGCAACTTCAAAGAGATAAGA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGA
56522610 TCTATGGTTT
Statistics
Matches: 119, Mismatches: 34, Indels: 16
0.70 0.20 0.09
Matches are distributed among these distances:
40 1 0.01
41 61 0.51
42 1 0.01
44 56 0.47
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (41 bp):
ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATGCG
Found at i:56522561 original size:129 final size:129
Alignment explanation
Indices: 56522327--56522699 Score: 487
Period size: 129 Copynumber: 2.9 Consensus size: 129
56522317 TTAATCCGGC
* * * ** * *
56522327 CTACTGCAACTTCAGAG-GTATAGGATTTATCATTTTAATCTGCTCCACTACAACTTTAGGGAGA
1 CTACTGCAACTTCAAAGAG-ATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGA
** * ** * *
56522391 TAGGATTAATTGCTTCAATCTGCTCCAGTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCT
65 TAGGATTGGTTTCTTCTGTCTGCTCCAATGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
* * * * *
56522456 CTATTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGGTCCACTACAACTTCAGGGAGAT
1 CTACTGCAACTTCAAAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGAT
* * *
56522521 AGGATTGGTTTATTCTGTCTTCTCTAATGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
66 AGGATTGGTTTCTTCTGTCTGCTCCAATGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
* *
56522585 CTACTGCAACTTCAAAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGCGAGAT
1 CTACTGCAACTTCAAAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGAT
* * *
56522650 AGGATTGGTTTCTTCTGTCTGCTCCACTGCAAGTTCAGAGAGATAAGACT
66 AGGATTGGTTTCTTCTGTCTGCTCCAATGCAACTTCAGGGAGATAAGACT
56522700 TGTATCTTCA
Statistics
Matches: 210, Mismatches: 33, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
129 209 1.00
130 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (129 bp):
CTACTGCAACTTCAAAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGAT
AGGATTGGTTTCTTCTGTCTGCTCCAATGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
Found at i:56522649 original size:44 final size:44
Alignment explanation
Indices: 56522359--56522740 Score: 204
Period size: 44 Copynumber: 8.8 Consensus size: 44
56522349 GGATTTATCA
* * * *
56522359 TTTTAATCTGCTCCACTACAACTTTAGGGAGATAGGAT-TAATTG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-ATGG
* * *
56522403 CTTCAATCTGCTCCAGTGCAACTTCAGGGAGATAAGA-C--TGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
* *** * * * * *
56522444 ATGCGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
* * * *
56522488 TTTTAATCCGGTCCACTACAACTTCAGGGAGATAGGA--T-TGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
* *
56522529 -TTTATTCTGTCTTCTCTAATGCAACTTCAGGGAGATAAGA-CTA--G
1 TTTTAATCTG-C-TC-C-ACTGCAACTTCAGGGAGATAAGATCTATGG
* *** * **
56522573 ATGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
* * *
56522617 TTTTAATCCGCTCCACTGCAACTTCAGCGAGATAGGA--T-TGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
** * *
56522658 TTTCTTCTGTCTGCTCCACTGCAAGTTCAGAGAGATAAGA-CT-T-G
1 -TT-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
* *
56522702 TATCTTCAATCTGCCCCACTGCAACTTCAGGGGGATAAG
1 T-T-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAG
56522741 GTTTGATATG
Statistics
Matches: 258, Mismatches: 61, Indels: 38
0.72 0.17 0.11
Matches are distributed among these distances:
40 7 0.03
41 58 0.22
42 10 0.04
43 6 0.02
44 169 0.66
45 8 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATGG
Found at i:56522982 original size:45 final size:45
Alignment explanation
Indices: 56522757--56522981 Score: 306
Period size: 45 Copynumber: 5.0 Consensus size: 45
56522747 TATGATATTT
* * * * *
56522757 GATCTACTTCGCTGCCAATACAGGAAAACAAGACCTACTAGCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
56522802 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * * *
56522847 GATCTGCTTCACTACCAATACAAGAAGAAAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
*
56522892 GATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * * *
56522937 AATCTACTTTGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
56522982 ACTGATTTGT
Statistics
Matches: 160, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 160 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (45 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
Found at i:56534786 original size:106 final size:106
Alignment explanation
Indices: 56534624--56535027 Score: 510
Period size: 108 Copynumber: 3.8 Consensus size: 106
56534614 GAGATTTATG
* * * * * *
56534624 AGGATATTTAGCTATTTGGTTAAACAAGAAATCGAAACTCAGCACATTACGGCACG-TTCCTCGA
1 AGGATATTTAGCTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAA
* *
56534688 ATTTCCAAACGCAAAATATAGTCTTACTTTCAAATTTTAAA
66 ATTTCCAAACGCAAAATATAGCCTTACTTTGAAATTTTAAA
** * *
56534729 AGTTTATTTGGCTATTTGGTCAAACGAAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTCA
1 AGGATATTTAGCTATTTGGTCAAAC-AAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCA
* *
56534794 AATTTCCAAACACAAAATATTA-CCTTACTTTGAAAATTTAAA
65 AATTTCCAAACGCAAAATA-TAGCCTTACTTTGAAATTTTAAA
*
56534836 AGGATATTTAGCTATTTGGTCGAATGA-AAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCT
1 AGGATATTTAGCTATTTGGTC-AA--ACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
* * * * *
56534900 CGAATTTCCAAACGCAAAACATTGCCTTACTTTGGAATTTTAAT
63 CAAATTTCCAAACGCAAAATATAGCCTTACTTTGAAATTTTAAA
* * * *
56534944 AGGATATTTTGCTATTTGGACGAAA-AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCA
1 AGGATATTTAGCTATTTGGTC-AAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCA
56535008 AATTTCCAAACGCAAAATAT
65 AATTTCCAAACGCAAAATAT
56535028 TGACTTCGTT
Statistics
Matches: 261, Mismatches: 31, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
105 21 0.08
106 82 0.31
107 59 0.23
108 98 0.38
110 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (106 bp):
AGGATATTTAGCTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAA
ATTTCCAAACGCAAAATATAGCCTTACTTTGAAATTTTAAA
Found at i:56534998 original size:214 final size:211
Alignment explanation
Indices: 56534624--56535046 Score: 566
Period size: 214 Copynumber: 2.0 Consensus size: 211
56534614 GAGATTTATG
* * *
56534624 AGGATATTTAGCTATTTGGTTAAACAAGAAATCGAAACTCAGCACATTACGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTGAAACAAAAAATCGAAACCCAGCACATTACGGCACGTTCCTCGAA
* * ** *
56534689 TTTCCAAACGCAAAATATAGTCTTACTTTCAAATTTTAAAAGTTTATTTGGCTATTTGGTCAAAC
66 TTTCCAAACGCAAAACATAGCCTTACTTTCAAATTTTAAAAGGATATTTGGCTATTTGGACAAAC
* * *
56534754 GAAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACACAAAATATT-ACC
131 -AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACACAAAATATTGA-C
56534818 TTAC-TTTGAAAATTTAAA
194 TT-CGTTTGAAAATTTAAA
* * *
56534836 AGGATATTTAGCTATTTGGTCGAATGA-AAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCT
1 AGGATATTTAGCTATTTGGT-GAA--ACAAAAAATCGAAACCCAGCACATTACGGCACG-TTCCT
* ** * *
56534900 CGAATTTCCAAACGCAAAACATTGCCTTACTTTGGAATTTTAATAGGATATTTTGCTATTTGGAC
62 CGAATTTCCAAACGCAAAACATAGCCTTACTTTCAAATTTTAAAAGGATATTTGGCTATTTGGAC
*
56534965 GAAA-AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACGCAAAATATT
127 -AAACAAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACACAAAATATT
56535029 GACTTCGTTTGAAAATTT
191 GACTTCGTTTGAAAATTT
56535047 TTCCTTTTTG
Statistics
Matches: 184, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
212 20 0.11
213 3 0.02
214 97 0.53
215 61 0.33
216 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (211 bp):
AGGATATTTAGCTATTTGGTGAAACAAAAAATCGAAACCCAGCACATTACGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATAGCCTTACTTTCAAATTTTAAAAGGATATTTGGCTATTTGGACAAAC
AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACACAAAATATTGACTT
CGTTTGAAAATTTAAA
Found at i:56535093 original size:21 final size:20
Alignment explanation
Indices: 56535069--56535113 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
56535059 GCATGGTGTT
56535069 AATATGCATAAT-GGAATAATA
1 AATATG-ATAATAGGAATAA-A
*
56535090 AATATGATAATATGAATAAA
1 AATATGATAATAGGAATAAA
56535110 AATA
1 AATA
56535114 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (20 bp):
AATATGATAATAGGAATAAA
Found at i:56535249 original size:19 final size:19
Alignment explanation
Indices: 56535222--56535262 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56535212 ATGAATAAAT
56535222 AAATAAATGA-ACATAAAGTA
1 AAATAAATGACA-ATAAAG-A
56535242 AAAT-AATGACAATAAAGA
1 AAATAAATGACAATAAAGA
56535260 AAA
1 AAA
56535263 CAGATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (19 bp):
AAATAAATGACAATAAAGA
Found at i:56535691 original size:3 final size:3
Alignment explanation
Indices: 56535658--56535797 Score: 59
Period size: 3 Copynumber: 47.0 Consensus size: 3
56535648 AAATGGAAAT
* * * * * *
56535658 ATA ATG ATA ATTA ACA ATA ATA TTA ACA ATA ATA CTA CTA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * * * * *
56535704 GTA AGG ATA ATA ATA ATG ATA ATA TTA ATA ATA CTT CTA ATA ATA ATC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * ** * *
56535752 GT- ATA ATA A-A CTA ATT AGC TTA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56535798 GGACTAAATA
Statistics
Matches: 96, Mismatches: 38, Indels: 6
0.69 0.27 0.04
Matches are distributed among these distances:
2 2 0.02
3 91 0.95
4 3 0.03
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:56539300 original size:49 final size:50
Alignment explanation
Indices: 56539246--56539342 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
56539236 TGATAACGTA
* *
56539246 TTATAAAATAAA-AAGAGATGGA-AGAATAAAGAACTAAGAAAATATGATG
1 TTATAAAATAAAGAA-AGATGGAGAGAATAAAAAACAAAGAAAATATGATG
* *
56539295 TTATAAACTAAAGAAATATGGAGAGAATAAAAAACAAAGAAAATATGA
1 TTATAAAATAAAGAAAGATGGAGAGAATAAAAAACAAAGAAAATATGA
56539343 AAGCAATAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 17 0.40
50 25 0.60
ACGTcount: A:0.61, C:0.03, G:0.16, T:0.20
Consensus pattern (50 bp):
TTATAAAATAAAGAAAGATGGAGAGAATAAAAAACAAAGAAAATATGATG
Found at i:56539350 original size:27 final size:27
Alignment explanation
Indices: 56539299--56539350 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
56539289 ATGATGTTAT
*
56539299 AAACTAAAGAAATATGGAGAGAATAAA
1 AAACTAAAGAAATATGGAAAGAATAAA
56539326 AAAC-AAAGAAAATAT-GAAAGCAATA
1 AAACTAAAG-AAATATGGAAAG-AATA
56539351 GAGGATGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.13
Consensus pattern (27 bp):
AAACTAAAGAAATATGGAAAGAATAAA
Found at i:56540948 original size:22 final size:22
Alignment explanation
Indices: 56540888--56540945 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
56540878 AGTCTTCAAG
56540888 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
56540907 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
56540929 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
56540946 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:56543630 original size:19 final size:19
Alignment explanation
Indices: 56543606--56543650 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
56543596 TCTTTCTTTT
*
56543606 TGCATT-CATTCCATGCATC
1 TGCATTACATTCCAT-CATA
*
56543625 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
56543644 TGCATTA
1 TGCATTA
56543651 GACTTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:56551974 original size:45 final size:45
Alignment explanation
Indices: 56551919--56552132 Score: 259
Period size: 45 Copynumber: 4.8 Consensus size: 45
56551909 AAAAAAACAG
* * *
56551919 ATCTTGTCTTCCTATATTGGCAGTGAAGTAGATCAAAGATAGTAA
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAA
* * *
56551964 ATCCTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAA
* * * **
56552009 ATCTTGTCTTCCTGTATTGGCAACGAAGTAGATCGAAGTTAGCGG
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAA
* ** *
56552054 ATCTTGTCTTTCTGTATTAACAGCGAAGTAGATCAAAGATAGTAGA
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCA-A
* *
56552100 A-CTTGTCTTCCTGTACTGGCAGCAAAGTAGATC
1 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
56552133 GATGTCACCA
Statistics
Matches: 144, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
45 143 0.99
46 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (45 bp):
ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAGATAGCAA
Found at i:56552069 original size:90 final size:90
Alignment explanation
Indices: 56551916--56552134 Score: 285
Period size: 90 Copynumber: 2.4 Consensus size: 90
56551906 TTGAAAAAAA
* * * *
56551916 CAGATCTTGTCTTCCTATATTGGCAGTGAAGTAGATCAAAGATAGTAAATCCTGTCTTCCTGTAT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTAT
** *
56551981 TGGCAGCGAAGTAGATCGAAGATAG
66 TAACAGCGAAGTAGATCAAAGATAG
* * ** * *
56552006 CAGATCTTGTCTTCCTGTATTGGCAACGAAGTAGATCGAAGTTAGCGGATCTTGTCTTTCTGTAT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTAT
56552071 TAACAGCGAAGTAGATCAAAGATAG
66 TAACAGCGAAGTAGATCAAAGATAG
* * * *
56552096 TAGAACTTGTCTTCCTGTACTGGCAGCAAAGTAGATCGA
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
56552135 TGTCACCAGT
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 111 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (90 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTAT
TAACAGCGAAGTAGATCAAAGATAG
Found at i:56553451 original size:23 final size:23
Alignment explanation
Indices: 56553421--56553465 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
56553411 CTAAAATATA
56553421 AAAAAGGGAGAAGAGAAACTTAT
1 AAAAAGGGAGAAGAGAAACTTAT
56553444 AAAAAGGGAGAAGAGAAACTTA
1 AAAAAGGGAGAAGAGAAACTTA
56553466 CCTGTTCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.27, T:0.11
Consensus pattern (23 bp):
AAAAAGGGAGAAGAGAAACTTAT
Found at i:56556864 original size:73 final size:71
Alignment explanation
Indices: 56556745--56556900 Score: 204
Period size: 73 Copynumber: 2.2 Consensus size: 71
56556735 GATGTTTTCC
* ** * *
56556745 AGAAAGCGCCGCAAAAACCTAAGCCCAATTACGCCGTTTTCGGAGCTTTCAGAGATTTAGCGGCG
1 AGAAAGCGCCACAAAAACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCAGAGATTTAGAGGCA
56556810 TTTTTA
66 TTTTTA
* * * *
56556816 AGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTTTCGGGGATTTAGAGG
1 AGAAAGCGCCAC--AAAAACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCAGAGATTTAGAGG
56556881 CATTTTTA
64 CATTTTTA
*
56556889 AGAGAGCGCCAC
1 AGAAAGCGCCAC
56556901 TAATGCTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 11 0.15
73 62 0.85
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (71 bp):
AGAAAGCGCCACAAAAACCTAAGCCCAACGACGCCGTTTTCGGAGCTTTCAGAGATTTAGAGGCA
TTTTTA
Found at i:56557112 original size:192 final size:187
Alignment explanation
Indices: 56556745--56557205 Score: 651
Period size: 192 Copynumber: 2.5 Consensus size: 187
56556735 GATGTTTTCC
** * *
56556745 AGAAAGCGCCGC--AAAAACCTAAGCCCAATTACGCCGTTTTCGGAGCTTTCAGAGATTTAGCGG
1 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGG
* *
56556808 CGTTTTTAAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTTTCGGGGA
66 CGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCAGTTTTCTGAGCTTTCGGGGA
* *
56556873 TTTAGAGGCATTTTTAAGAGAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTTG
131 TTTAGAGGCATTTTTAACAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTTG
* *
56556930 AGAAAGCGCCGCAAAAAAACCTAGGCCCAACGACGCCGTTTTCTGAGCTATGCTCAGGGCTTTTT
1 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT-T--TCAGGG--ATTT
* *
56556995 AGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCGACGACGCAGTTTTCTGAGCTTT-
61 AGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCAGTTTTCTGAGCTTTC
* * * *
56557059 GGGGATTTAGCGGCGTTTTTAACAAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTTG
126 GGGGATTTAGAGGCATTTTTAACAAAGCGCCACTAATGCTCAAGGC-TTTAGCGGCGTTTTTG
* * * * *
56557122 TGAAAGCGCCGCAAAAAAACCTAAGCCCGACGAAGCCGTTTTTTGAGCTTT-GGGGATTTAGCGG
1 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGG
56557186 CGTTTTTAAGAAAGCGCCGC
66 CGTTTTTAAGAAAGCGCCGC
56557206 TAATGCTCAG
Statistics
Matches: 244, Mismatches: 24, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
185 12 0.05
186 27 0.11
187 31 0.13
188 4 0.02
189 1 0.00
190 5 0.02
191 41 0.17
192 123 0.50
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (187 bp):
AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGGGATTTAGCGG
CGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCAGTTTTCTGAGCTTTCGGGGA
TTTAGAGGCATTTTTAACAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTTG
Found at i:56557180 original size:114 final size:115
Alignment explanation
Indices: 56556979--56557445 Score: 681
Period size: 114 Copynumber: 4.1 Consensus size: 115
56556969 TTTCTGAGCT
*
56556979 ATGCTCAGGGCTTTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCGACGACGC
1 ATGCTCAGGGCTTTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGC
* *
56557044 AGTTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAACAAAGCGCCGCTA
66 CGTTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
* * *
56557094 ATGCTCAGGGC-TTTTAGCGGCGTTTTTGTGAAAGCGCCGCAAAAAAACCTAAGCCCGACGAAGC
1 ATGCTCAGGGCTTTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGC
*
56557158 CGTTTTTTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
66 CGTTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
* * *
56557208 ATGCTCAGGGC-TTTTAGCGGCGTTTTTGTGAAAGCGGCGC-AAAAAACCTTAAGTCCAACGACG
1 ATGCTCAGGGCTTTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACG
* ** * *
56557271 CCGTTTTCTGAGCTTTGGTGATTTAGCCACGTTTTTAAGAAAACGCCTCTA
65 CCGTTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
* * * *
56557322 ATGCTCAAGGCTTTTTAGCGACATTTTCGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACG
1 ATGCTCAGGGCTTTTTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACG
* *
56557387 CCGGTTTT-TGAGCTTTTGGGGATTTAGCGGTGTTTTTATGAAAGCGCCGCTA
65 CC-GTTTTCTGAGC-TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
56557439 ATGCTCA
1 ATGCTCA
56557446 AATAGTTATA
Statistics
Matches: 317, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
113 8 0.03
114 203 0.64
115 35 0.11
116 20 0.06
117 51 0.16
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (115 bp):
ATGCTCAGGGCTTTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGC
CGTTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
Found at i:56557673 original size:7 final size:7
Alignment explanation
Indices: 56557661--56557891 Score: 89
Period size: 7 Copynumber: 32.4 Consensus size: 7
56557651 GGTTAGGAGC
56557661 TTAGGGT
1 TTAGGGT
*
56557668 TTAGGGG
1 TTAGGGT
*
56557675 TTATGGGC
1 TTA-GGGT
56557683 TTAGGGT
1 TTAGGGT
*
56557690 CTATGGG-
1 TTA-GGGT
*
56557697 TTAGTGGC
1 TTAG-GGT
*
56557705 TTATGGT
1 TTAGGGT
56557712 TTAGGGT
1 TTAGGGT
*
56557719 TTA--AT
1 TTAGGGT
* *
56557724 TAAGAGT
1 TTAGGGT
* *
56557731 TTATGAT
1 TTAGGGT
56557738 TTAGGGGT
1 TTA-GGGT
56557746 TTAGGGGT
1 TTA-GGGT
56557754 TTAGGGGT
1 TTA-GGGT
* *
56557762 TTATGCT
1 TTAGGGT
56557769 TTAGAGGT
1 TTAG-GGT
* *
56557777 TTAAGTT
1 TTAGGGT
*
56557784 TTAAGGT
1 TTAGGGT
56557791 TTAGGGT
1 TTAGGGT
56557798 TTAGGGGT
1 TTA-GGGT
56557806 TTA-GG-
1 TTAGGGT
* *
56557811 TTATCGGC
1 TTA-GGGT
56557819 TTAGGGT
1 TTAGGGT
*
56557826 CTAAGGG-
1 -TTAGGGT
*
56557833 TTATTGGT
1 TTA-GGGT
* *
56557841 TTATGAT
1 TTAGGGT
*
56557848 TTAGTGT
1 TTAGGGT
*
56557855 TTATGGT
1 TTAGGGT
56557862 TTAGGGT
1 TTAGGGT
56557869 TTAGGGT
1 TTAGGGT
*
56557876 GTA-GGT
1 TTAGGGT
*
56557882 TTATGGT
1 TTAGGGT
56557889 TTA
1 TTA
56557892 AAGTATGCAG
Statistics
Matches: 169, Mismatches: 39, Indels: 32
0.70 0.16 0.13
Matches are distributed among these distances:
5 6 0.04
6 10 0.06
7 97 0.57
8 56 0.33
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:56557676 original size:22 final size:21
Alignment explanation
Indices: 56557651--56557717 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
56557641 AGTGTGTAAA
56557651 GGTTAGGAGCTTAGGGTTTAGG
1 GGTTAGG-GCTTAGGGTTTAGG
* *
56557673 GGTTATGGGCTTAGGGTCTATG
1 GGTTA-GGGCTTAGGGTTTAGG
*
56557695 GGTTAGTGGCTTATGGTTTAGG
1 GGTTAG-GGCTTAGGGTTTAGG
56557717 G
1 G
56557718 TTTAATTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.92
23 2 0.05
ACGTcount: A:0.15, C:0.06, G:0.43, T:0.36
Consensus pattern (21 bp):
GGTTAGGGCTTAGGGTTTAGG
Found at i:56557750 original size:8 final size:8
Alignment explanation
Indices: 56557737--56557810 Score: 66
Period size: 8 Copynumber: 9.8 Consensus size: 8
56557727 GAGTTTATGA
56557737 TTTAGGGG
1 TTTAGGGG
56557745 TTTAGGGG
1 TTTAGGGG
56557753 TTTAGGGG
1 TTTAGGGG
* *
56557761 TTTA-TGC
1 TTTAGGGG
*
56557768 TTTAGAGG
1 TTTAGGGG
* *
56557776 TTTA-AGT
1 TTTAGGGG
*
56557783 TTTA-AGG
1 TTTAGGGG
56557790 TTTA-GGG
1 TTTAGGGG
56557797 TTTAGGGG
1 TTTAGGGG
56557805 TTTAGG
1 TTTAGG
56557811 TTATCGGCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
7 23 0.40
8 34 0.60
ACGTcount: A:0.18, C:0.01, G:0.38, T:0.43
Consensus pattern (8 bp):
TTTAGGGG
Found at i:56557777 original size:15 final size:15
Alignment explanation
Indices: 56557737--56557810 Score: 78
Period size: 15 Copynumber: 4.9 Consensus size: 15
56557727 GAGTTTATGA
56557737 TTTAGGGGTTTAGGGG
1 TTTAGGGGTTTA-GGG
* *
56557753 TTTAGGGGTTTATGC
1 TTTAGGGGTTTAGGG
* * *
56557768 TTTAGAGGTTTAAGT
1 TTTAGGGGTTTAGGG
*
56557783 TTTA-AGGTTTAGGG
1 TTTAGGGGTTTAGGG
56557797 TTTAGGGGTTTAGG
1 TTTAGGGGTTTAGG
56557811 TTATCGGCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
14 12 0.24
15 25 0.51
16 12 0.24
ACGTcount: A:0.18, C:0.01, G:0.38, T:0.43
Consensus pattern (15 bp):
TTTAGGGGTTTAGGG
Found at i:56557967 original size:62 final size:63
Alignment explanation
Indices: 56557833--56557981 Score: 171
Period size: 62 Copynumber: 2.4 Consensus size: 63
56557823 GGTCTAAGGG
* * *
56557833 TTATTGGTTTATGATTTAGTGTTTATGGTTTAGGGTTTAGGGTGTAGGTTTATGGTTTAAAGTAT
1 TTATT-GTTTATGATTTAGTGTTTATGGTTTAGCGTGTAGGCTGTAGGTTTATGGTTT-AAGTAT
** * *
56557898 GCA--GTTTATGATTTAGTGTTTATGGTTTAGCGTGTAGGCTGTGGGTTTATGGTTT-AGTTT
1 TTATTGTTTATGATTTAGTGTTTATGGTTTAGCGTGTAGGCTGTAGGTTTATGGTTTAAGTAT
*
56557958 TTATTGTTTATTG-TTTAGGGTTTA
1 TTATTGTTTA-TGATTTAGTGTTTA
56557982 GCTAGTAGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
60 5 0.07
62 63 0.89
63 2 0.03
65 1 0.01
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.52
Consensus pattern (63 bp):
TTATTGTTTATGATTTAGTGTTTATGGTTTAGCGTGTAGGCTGTAGGTTTATGGTTTAAGTAT
Found at i:56557974 original size:14 final size:15
Alignment explanation
Indices: 56557942--56557982 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
56557932 TAGGCTGTGG
56557942 GTTTATGGTTTAGTT
1 GTTTATGGTTTAGTT
*
56557957 -TTTATTGTTTA-TT
1 GTTTATGGTTTAGTT
*
56557970 GTTTAGGGTTTAG
1 GTTTATGGTTTAG
56557983 CTAGTAGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.10
14 19 0.90
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (15 bp):
GTTTATGGTTTAGTT
Found at i:56557981 original size:21 final size:21
Alignment explanation
Indices: 56557829--56557981 Score: 53
Period size: 21 Copynumber: 7.4 Consensus size: 21
56557819 TTAGGGTCTA
*
56557829 AGGG-TTATTGGTTTATGATTT
1 AGGGTTTATT-GTTTATGGTTT
* * *
56557850 AGTGTTTATGGTTTAGGGTTT
1 AGGGTTTATTGTTTATGGTTT
* *
56557871 AGGGTGTA-GGTTTATGGTTT
1 AGGGTTTATTGTTTATGGTTT
** * *** *
56557891 AAAGTATGCAGTTTATGATTT
1 AGGGTTTATTGTTTATGGTTT
* * *
56557912 AGTGTTTATGGTTTA-GCGTGT
1 AGGGTTTATTGTTTATG-GTTT
* * **
56557933 AGGCTGT-GGGTTTATGGTTT
1 AGGGTTTATTGTTTATGGTTT
** *
56557953 AGTTTTTATTGTTTATTGTTT
1 AGGGTTTATTGTTTATGGTTT
56557974 AGGGTTTA
1 AGGGTTTA
56557982 GCTAGTAGCT
Statistics
Matches: 93, Mismatches: 34, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
20 29 0.31
21 60 0.65
22 4 0.04
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.50
Consensus pattern (21 bp):
AGGGTTTATTGTTTATGGTTT
Found at i:56558048 original size:103 final size:103
Alignment explanation
Indices: 56557970--56558177 Score: 355
Period size: 103 Copynumber: 2.0 Consensus size: 103
56557960 ATTGTTTATT
* * *
56557970 GTTTAGGGTTTAGCTAGTAGCTTAGAGTTTAGGGATTAATATGGGCATAGGGTATATGGGTTAAG
1 GTTTAGGGTTTAGCTAATAGCTTAGAGTTTAGGGATTAATACGGGAATAGGGTATATGGGTTAAG
56558035 AGGGCATATGGTTTAGGGTTTAAATTTTATATTTTAGG
66 AGGGCATATGGTTTAGGGTTTAAATTTTATATTTTAGG
* *
56558073 GTTTAGGGTTTAGGTAATAGCTTAGAGTTTTGGGATTAATACGGGAATAGGGTATATGGGTTAAG
1 GTTTAGGGTTTAGCTAATAGCTTAGAGTTTAGGGATTAATACGGGAATAGGGTATATGGGTTAAG
*
56558138 AGGGCATATGG-TTAGGGTTTAAATTGTATATTTTAGG
66 AGGGCATATGGTTTAGGGTTTAAATTTTATATTTTAGG
56558175 GTT
1 GTT
56558178 AGGATTATGG
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 28 0.28
103 71 0.72
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.38
Consensus pattern (103 bp):
GTTTAGGGTTTAGCTAATAGCTTAGAGTTTAGGGATTAATACGGGAATAGGGTATATGGGTTAAG
AGGGCATATGGTTTAGGGTTTAAATTTTATATTTTAGG
Found at i:56558057 original size:24 final size:24
Alignment explanation
Indices: 56557996--56558054 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
56557986 GTAGCTTAGA
*
56557996 GTTTAGGGATTAATATGGGCATAGG
1 GTTTAGGG-TTAAGATGGGCATAGG
* *
56558021 GTATATGGGTTAAGA-GGGCATATG
1 GTTTA-GGGTTAAGATGGGCATAGG
56558045 GTTTAGGGTT
1 GTTTAGGGTT
56558055 TAAATTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 5 0.17
24 12 0.41
25 9 0.31
26 3 0.10
ACGTcount: A:0.25, C:0.03, G:0.37, T:0.34
Consensus pattern (24 bp):
GTTTAGGGTTAAGATGGGCATAGG
Found at i:56560218 original size:9 final size:9
Alignment explanation
Indices: 56560204--56560485 Score: 214
Period size: 9 Copynumber: 32.3 Consensus size: 9
56560194 TAATTATGTA
56560204 TACATAACT
1 TACATAACT
56560213 TACATAACT
1 TACATAACT
* *
56560222 TAAATATCT
1 TACATAACT
* *
56560231 TAGACAACT
1 TACATAACT
*
56560240 TACATAACC
1 TACATAACT
56560249 TACATAA--
1 TACATAACT
56560256 TACATTTAACT
1 TACA--TAACT
*
56560267 TAAATAACT
1 TACATAACT
56560276 TACATAA--
1 TACATAACT
*
56560283 TACAAAACT
1 TACATAACT
56560292 TACATAACT
1 TACATAACT
* *
56560301 TAAATATCT
1 TACATAACT
*
56560310 TACACAACT
1 TACATAACT
* *
56560319 TGCATAACC
1 TACATAACT
56560328 TACATAA--
1 TACATAACT
56560335 TACATTTAACT
1 TACA--TAACT
56560346 TACATAACT
1 TACATAACT
56560355 TACATAACT
1 TACATAACT
56560364 TAC--AACT
1 TACATAACT
*
56560371 TACATAACA
1 TACATAACT
*
56560380 TACATTACT
1 TACATAACT
**
56560389 TTGATAACT
1 TACATAACT
56560398 TACATAACT
1 TACATAACT
56560407 TACATAA--
1 TACATAACT
*
56560414 TACACAACT
1 TACATAACT
* *
56560423 TGCATAGCT
1 TACATAACT
* *
56560432 GACTTAA--
1 TACATAACT
56560439 TACATAACT
1 TACATAACT
56560448 TACATAA--
1 TACATAACT
*
56560455 TACATACACA
1 TACATA-ACT
56560465 TACATAACT
1 TACATAACT
*
56560474 TACATAATT
1 TACATAACT
56560483 TAC
1 TAC
56560486 TTAATACATA
Statistics
Matches: 213, Mismatches: 41, Indels: 38
0.73 0.14 0.13
Matches are distributed among these distances:
7 38 0.18
8 1 0.00
9 161 0.76
10 6 0.03
11 7 0.03
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:56560295 original size:79 final size:78
Alignment explanation
Indices: 56560203--56560417 Score: 299
Period size: 79 Copynumber: 2.7 Consensus size: 78
56560193 TTAATTATGT
56560203 ATACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
1 ATACA-AACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
56560268 AAATAACTTACATA
65 AAATAACTTACATA
* *
56560282 ATACAAAACTTACATAACTTAAATATCTTACACAACTTGCATAACCTACATAATACATTTAACTT
1 ATAC-AAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
*
56560347 ACATAACTTACATA
65 AAATAACTTACATA
* * * * *
56560361 ACTTAC-AACTTACATAACATACAT-TACTTTGATAACTTACATAACTTACATAATACA
1 A--TACAAACTTACATAACTTAAATAT-CTTAGACAACTTACATAACCTACATAATACA
56560418 CAACTTGCAT
Statistics
Matches: 122, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.01
79 117 0.96
80 1 0.01
81 3 0.02
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (78 bp):
ATACAAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTTA
AATAACTTACATA
Found at i:56560319 original size:43 final size:43
Alignment explanation
Indices: 56560205--56560485 Score: 185
Period size: 43 Copynumber: 6.7 Consensus size: 43
56560195 AATTATGTAT
* * *
56560205 ACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCT
1 ACATAACTTACATAACTTAAATAACTTACATAACTTACATAA--T
*
56560250 ACATAA--TAC---A-TT---TAACTTAAATAACTTACATAAT
1 ACATAACTTACATAACTTAAATAACTTACATAACTTACATAAT
* * * *
56560284 ACAAAACTTACATAACTTAAATATCTTACACAACTTGCATAACCT
1 ACATAACTTACATAACTTAAATAACTTACATAACTTACATAA--T
* *
56560329 ACATAA--TACATTTAACTTACATAACTTACATAACTTACA-ACTT
1 ACATAACTTACA--TAACTTAAATAACTTACATAACTTACATA-AT
* * **
56560372 ACATAACATACATTACTTTGATAACTTACATAACTTACATAAT
1 ACATAACTTACATAACTTAAATAACTTACATAACTTACATAAT
* * * * **
56560415 ACACAACTTGCATAGCTGACTTAA--TACATAACTTACATAAT
1 ACATAACTTACATAACTTAAATAACTTACATAACTTACATAAT
* * *
56560456 ACATACACATACATAACTTACATAATTTAC
1 ACATA-ACTTACATAACTTAAATAACTTAC
56560486 TTAATACATA
Statistics
Matches: 183, Mismatches: 33, Indels: 41
0.71 0.13 0.16
Matches are distributed among these distances:
34 6 0.03
36 21 0.11
39 3 0.02
40 3 0.02
41 21 0.11
42 14 0.08
43 71 0.39
44 5 0.03
45 39 0.21
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (43 bp):
ACATAACTTACATAACTTAAATAACTTACATAACTTACATAAT
Found at i:56560319 original size:52 final size:51
Alignment explanation
Indices: 56560204--56560496 Score: 202
Period size: 52 Copynumber: 5.6 Consensus size: 51
56560194 TAATTATGTA
* * * * * * *
56560204 TACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATA-A
1 TACACAACTTACATAACTTACATA--ATACATAACTTACATAACTTACATACT
* * * *
56560256 TACATTTAACTTAAATAACTTACATAATACAAAACTTACATAACTTAAATATCT
1 TACA--CAACTTACATAACTTACATAATACATAACTTACATAACTTACATA-CT
* *
56560310 TACACAACTTGCATAACCTACATAATACATTTAACTTACATAACTTACATAACT
1 TACACAACTTACATAACTTACATAATACA--TAACTTACATAACTTACAT-ACT
* * ** *
56560364 T--ACAACTTACATAACATACATTACTTTGATAACTTACATAACTTACATA-A
1 TACACAACTTACATAACTTACA-TA-ATACATAACTTACATAACTTACATACT
* * * * *
56560414 TACACAACTTGCATAGCTGACTTAATACATAACTTACATAA--TACATACACA
1 TACACAACTTACATAACTTACATAATACATAACTTACATAACTTACAT--ACT
* * *
56560465 TACATAACTTACATAATTTACTTAATACATAA
1 TACACAACTTACATAACTTACATAATACATAA
56560497 ATATATATCA
Statistics
Matches: 194, Mismatches: 33, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
48 5 0.03
50 16 0.08
51 31 0.16
52 95 0.49
53 2 0.01
54 44 0.23
55 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.32
Consensus pattern (51 bp):
TACACAACTTACATAACTTACATAATACATAACTTACATAACTTACATACT
Found at i:56566036 original size:21 final size:21
Alignment explanation
Indices: 56566012--56566060 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
56566002 GGCAACGAAG
56566012 GAAGCAGAGGCTGCAGCGAGA
1 GAAGCAGAGGCTGCAGCGAGA
* *
56566033 GAAGCAAAGGCTGCAGCGCGA
1 GAAGCAGAGGCTGCAGCGAGA
56566054 GAAGCAG
1 GAAGCAG
56566061 CGAGGGAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.41, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGGCTGCAGCGAGA
Found at i:56566564 original size:42 final size:41
Alignment explanation
Indices: 56566443--56566754 Score: 374
Period size: 42 Copynumber: 7.4 Consensus size: 41
56566433 AATTCCAAAA
* * *
56566443 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATTA-CTT
1 TTAGCGGCGTTTTTT-T-TAAGCGCCGCTAAAGAACATGATC-T
* **
56566486 TTAGCGGCGTTTGTGATGAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTT-T-TTTTAAGCGCCGCTAAAGAACATGATCT
*
56566529 TTAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTT-TTTTTAAGCGCCGCTAAAGAACATGATCT
* * *
56566571 TTAGCGACGTCTTTTTTAAGCGCCGCTAAAGAACATAATCT
1 TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
*
56566612 TTAGCGGCGTTTTTTTCTAAGTGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGATCT
* *
56566654 TAAGCGGTGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCG--TTTTTTTTAAGCGCCGCTAAAGAACATGATCT
* * *
56566697 TTAGCGGTGTTTTTTATTAAGCGCCGCTAAGGAACATGACCT
1 TTAGCGGCGTTTTTT-TTAAGCGCCGCTAAAGAACATGATCT
*
56566739 TTAGTGGCGTTTTTTT
1 TTAGCGGCGTTTTTTT
56566755 CTGTAAATGC
Statistics
Matches: 239, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
41 48 0.20
42 103 0.43
43 78 0.33
44 9 0.04
45 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
Found at i:56566709 original size:85 final size:82
Alignment explanation
Indices: 56566505--56566735 Score: 345
Period size: 83 Copynumber: 2.8 Consensus size: 82
56566495 TTTGTGATGA
*
56566505 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTTAAGCGCCGCTAAAGAACATGATC
*
56566570 TTTAGCGACGTCTTTTTT
65 TTAAGCGACGTCTTTTTT
* *
56566588 AAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTTTTTCTAAGTGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGATC
**
56566653 TTAAGCGGTGTCTTTTTTTT
65 TTAAGCGACGTC--TTTTTT
* *
56566673 AAGCGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTTTATTAAGCGCCGCTAAGGAACATGA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TTAAGCGCCGCTAAAGAACATGA
56566736 CCTTTAGTGG
Statistics
Matches: 134, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
82 3 0.02
83 67 0.50
85 63 0.47
86 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (82 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
TAAGCGACGTCTTTTTT
Found at i:56566754 original size:85 final size:86
Alignment explanation
Indices: 56566443--56566754 Score: 373
Period size: 85 Copynumber: 3.7 Consensus size: 86
56566433 AATTCCAAAA
* * * * * ** **
56566443 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTGTGATGAAAG
1 TTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTAAG
56566508 CGCCGCTAAAGAACATGATCT
66 CGCCGCTAAAGAACATGATCT
* * * * *
56566529 TTAGCGGCG-TTTCTATTTAAGCGCCGCTAAAGAACATGATCTTTAGCGACG--TCTTTTTTAAG
1 TTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTAAG
*
56566591 CGCCGCTAAAGAACATAATCT
66 CGCCGCTAAAGAACATGATCT
* * * * * *
56566612 TTAGCGGCGTTTTTT-TCTAAGTGCCGCTAAAGAACATGATCTTAAGCGGTGTCTTTTTTTTAAG
1 TTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTAAG
56566676 CGCCGCTAAAGAACATGATCT
66 CGCCGCTAAAGAACATGATCT
* * *
56566697 TTAGCGGTGTTTTTTAT-TAAGCGCCGCTAAGGAACATGACCTTTAGTGGCGTTTTTTT
1 TTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTT
56566755 CTGTAAATGC
Statistics
Matches: 192, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
83 66 0.34
84 4 0.02
85 113 0.59
86 9 0.05
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (86 bp):
TTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTTTTAAG
CGCCGCTAAAGAACATGATCT
Found at i:56566805 original size:17 final size:17
Alignment explanation
Indices: 56566783--56566816 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56566773 TTAGTGACGT
56566783 TGTAATGAATATTCTTG
1 TGTAATGAATATTCTTG
56566800 TGTAATGAATATTCTTG
1 TGTAATGAATATTCTTG
56566817 AAGCATTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
TGTAATGAATATTCTTG
Found at i:56568549 original size:45 final size:44
Alignment explanation
Indices: 56568448--56568607 Score: 167
Period size: 45 Copynumber: 3.6 Consensus size: 44
56568438 TGAGAAATAT
* * * ** ***
56568448 CATAGTTGAAAGATATTATGGCATTAAACCGGAGTGAATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCCAAAACAAATAAGAC
* * * *
56568492 TATAGTTGAAAGATACGATGGCACTAATCCGAAAATATATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCC-AAAACAAATAAGAC
* * *
56568537 CATGGTTGAAAGATACTATGGCATTAAATCCAATACAAATAAGAC
1 CATAGTTGAAAGATACTATGGCACT-AATCCAAAACAAATAAGAC
56568582 CATAGTTGAAAGATACTATGGCACTA
1 CATAGTTGAAAGATACTATGGCACTA
56568608 GTTCAGGAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 26 0.27
45 64 0.67
46 5 0.05
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (44 bp):
CATAGTTGAAAGATACTATGGCACTAATCCAAAACAAATAAGAC
Found at i:56568624 original size:45 final size:44
Alignment explanation
Indices: 56568448--56568628 Score: 150
Period size: 45 Copynumber: 4.0 Consensus size: 44
56568438 TGAGAAATAT
* * * * * *
56568448 CATAGTTGAAAGATATTATGGCATTAAACCGGAGTGAATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCAGGAATAAATAAGAC
* * * * *
56568492 TATAGTTGAAAGATACGATGGCACTAATCCGAAAATATATAAGAC
1 CATAGTTGAAAGATACTATGGCACTAATCAG-GAATAAATAAGAC
* * *
56568537 CATGGTTGAAAGATACTATGGCATTAAATCCA--ATACAAATAAGAC
1 CATAGTTGAAAGATACTATGGCACT-AAT-CAGGA-ATAAATAAGAC
* **
56568582 CATAGTTGAAAGATACTATGGCACTAGTTCAGGAATGTATAAGAC
1 CATAGTTGAAAGATACTATGGCACTA-ATCAGGAATAAATAAGAC
56568627 CA
1 CA
56568629 GGGTTAGAAG
Statistics
Matches: 108, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
44 30 0.28
45 73 0.68
46 4 0.04
47 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (44 bp):
CATAGTTGAAAGATACTATGGCACTAATCAGGAATAAATAAGAC
Found at i:56568648 original size:90 final size:90
Alignment explanation
Indices: 56568484--56568649 Score: 219
Period size: 90 Copynumber: 1.8 Consensus size: 90
56568474 AACCGGAGTG
* * *
56568484 AATAAGACTATAGTTGAAAGATACGATGGCACTAATCCGAAAATATATAAGACCATGGTTGAAAG
1 AATAAGACCATAGTTGAAAGATACGATGGCACTAATCAGAAAATATATAAGACCAGGGTTGAAAG
* *
56568549 ATACTATGGCATTAAATCCAATACA
66 AAACCATGGCATTAAATCCAATACA
* * * *
56568574 AATAAGACCATAGTTGAAAGATACTATGGCACTAGTTCAG-GAATGTATAAGACCAGGGTT-AGA
1 AATAAGACCATAGTTGAAAGATACGATGGCACTA-ATCAGAAAATATATAAGACCAGGGTTGA-A
56568637 AGAAACCATGGCA
64 AGAAACCATGGCA
56568650 CCCTTTGGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 1 0.02
90 61 0.94
91 3 0.05
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (90 bp):
AATAAGACCATAGTTGAAAGATACGATGGCACTAATCAGAAAATATATAAGACCAGGGTTGAAAG
AAACCATGGCATTAAATCCAATACA
Found at i:56569104 original size:10 final size:10
Alignment explanation
Indices: 56569089--56569113 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56569079 GTAACCCCTG
56569089 TTTCAAAAAT
1 TTTCAAAAAT
56569099 TTTCAAAAAT
1 TTTCAAAAAT
56569109 TTTCA
1 TTTCA
56569114 TGTTTTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTCAAAAAT
Found at i:56570662 original size:40 final size:40
Alignment explanation
Indices: 56570613--56570752 Score: 190
Period size: 40 Copynumber: 3.5 Consensus size: 40
56570603 TATATGATCT
* * * *
56570613 GGGGTACGTATGTGAAATCAGGGGTGCCGAAGTACAAGTA
1 GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
* *
56570653 GGGGCACGTATCTGCAATCAGGGGTACTGAAGTACAAATA
1 GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
* * *
56570693 GGGGCACGTATGTGCAATTAGGGTTACCAAAGTACAAATA
1 GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
*
56570733 GGGCCACGTATGTGCAATCA
1 GGGGCACGTATGTGCAATCA
56570753 TTCAATAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (40 bp):
GGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATA
Found at i:56570714 original size:20 final size:20
Alignment explanation
Indices: 56570651--56570715 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
56570641 GAAGTACAAG
*
56570651 TAGGGGCACGTATCTGCAAT
1 TAGGGGCACGTATGTGCAAT
* * * * *
56570671 CAGGGGTAC-TGAAGTACAAA
1 TAGGGGCACGT-ATGTGCAAT
56570691 TAGGGGCACGTATGTGCAAT
1 TAGGGGCACGTATGTGCAAT
56570711 TAGGG
1 TAGGG
56570716 TTACCAAAGT
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (20 bp):
TAGGGGCACGTATGTGCAAT
Found at i:56580281 original size:63 final size:63
Alignment explanation
Indices: 56580165--56580291 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
56580155 TTACATGACT
* * *
56580165 TGGACACACGCCCATGTCCCTGGCCCGTGTGACCTTGAATTCAAAACTGTGAGTTATACGGCC
1 TGGACACACGCCCATGTCCCTAGCCCGTGTGACCTTGAATTCAAAACTATGAGTTACACGGCC
* * *
56580228 TGGACACACGCCTATGTCCCTAGCCCTTGTG-TCTCT-AATTCGAAAA-TAATGAGTTACACGGC
1 TGGACACACGCCCATGTCCCTAGCCCGTGTGACCT-TGAATTC-AAAACT-ATGAGTTACACGGC
56580290 C
63 C
56580291 T
1 T
56580292 AACACACTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
62 8 0.15
63 47 0.85
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (63 bp):
TGGACACACGCCCATGTCCCTAGCCCGTGTGACCTTGAATTCAAAACTATGAGTTACACGGCC
Found at i:56581132 original size:20 final size:21
Alignment explanation
Indices: 56581093--56581132 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56581083 CGATCTCATA
56581093 CACATAAACAAAGTACTTAAC
1 CACATAAACAAAGTACTTAAC
*
56581114 CACATATACAAAG-ACTTAA
1 CACATAAACAAAGTACTTAA
56581133 TTATTGACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.20
Consensus pattern (21 bp):
CACATAAACAAAGTACTTAAC
Found at i:56583838 original size:15 final size:14
Alignment explanation
Indices: 56583818--56583864 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
56583808 GTCATCAATC
56583818 TTTCTTGTCTCTTTT
1 TTTCTT-TCTCTTTT
*
56583833 TTTCTTCCTCTTTT
1 TTTCTTTCTCTTTT
56583847 TTGT-TTTCT-TTTT
1 TT-TCTTTCTCTTTT
56583860 TTTCT
1 TTTCT
56583865 GTTTTTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 7 0.25
14 13 0.46
15 7 0.25
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTCTTTCTCTTTT
Found at i:56592259 original size:20 final size:20
Alignment explanation
Indices: 56592234--56592277 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
56592224 ACCTGAACCC
*
56592234 AAAAGATTTAAACTCGAATT
1 AAAAGATTTAAACTCAAATT
56592254 AAAAGATTTAAACTCAAATT
1 AAAAGATTTAAACTCAAATT
56592274 AAAA
1 AAAA
56592278 TCCCAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAAGATTTAAACTCAAATT
Found at i:56598097 original size:74 final size:75
Alignment explanation
Indices: 56597907--56598116 Score: 323
Period size: 74 Copynumber: 2.8 Consensus size: 75
56597897 TATCCGTTAT
* * *
56597907 CGGTGGATTCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGTAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
56597972 ATTTAAGAAA
66 ATCTAAGAAA
* * *
56597982 CAGTGGCATTAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* *
56598047 A-CTCAGATA
66 ATCTAAGAAA
*
56598056 CGGTGGAACCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
56598117 GGGGGAATCA
Statistics
Matches: 122, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
74 62 0.51
75 60 0.49
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATCTAAGAAA
Found at i:56598125 original size:27 final size:28
Alignment explanation
Indices: 56598091--56598144 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
56598081 CCAATGATTC
56598091 GGGGAATCAGCACTTAGCAA-CCCCTTG
1 GGGGAATCAGCACTTAGCAATCCCCTTG
56598118 GGGGAATCAGCACTTAGCAATCCCCTT
1 GGGGAATCAGCACTTAGCAATCCCCTT
56598145 TTACTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (28 bp):
GGGGAATCAGCACTTAGCAATCCCCTTG
Found at i:56598176 original size:104 final size:101
Alignment explanation
Indices: 56598017--56598245 Score: 350
Period size: 104 Copynumber: 2.2 Consensus size: 101
56598007 CCAATGATTC
*
56598017 GGGGAATCAGCACTTAGCAACCCCTTTCACACTCAGATACGGTGGAACCAGCACTTAGCAACCAC
1 GGGGAATCAGCACTTAGCAACCCCTTTCACACTAAGATACGGTGGAACCAGCACTTAGCAACCAC
56598082 CAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
* ** **
56598118 GGGGAATCAGCACTTAGCAATCCCCTTTTACTTTTAAAGATACGGTGGAGTCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAA-CCCCTTTCAC-ACT-AAGATACGGTGGAACCAGCACTTAGCAAC
*
56598183 CACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTG
63 CACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
* *
56598222 AGGGAATTAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
56598246 CTTTATATTC
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 20 0.17
102 9 0.08
103 5 0.04
104 82 0.71
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (101 bp):
GGGGAATCAGCACTTAGCAACCCCTTTCACACTAAGATACGGTGGAACCAGCACTTAGCAACCAC
CAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:56605072 original size:33 final size:33
Alignment explanation
Indices: 56605017--56605223 Score: 137
Period size: 33 Copynumber: 5.7 Consensus size: 33
56605007 TTATCCGTTA
*
56605017 TCGGTGGATTCAGCACTTAGCAACCACCCATGAG
1 TCGG-GGAATCAGCACTTAGCAACCACCCATGAG
* * *
56605051 TCGGGGAATCAACACTTAGCAACCCCTTTCACATTTAAG
1 TCGGGGAATCAGCACTTAGCAACCAC---C-CA--TGAG
* * * *
56605090 ATACGGTGGGATCAGCGCTTAGCAACCACCAATGAT
1 -T-CGG-GGAATCAGCACTTAGCAACCACCCATGAG
* *
56605126 TCGGGGAATCAGCACTTAGCAACCCCTTTCACACTCAG
1 TCGGGGAATCAGCACTTAGCAACCAC---C-CA-TGAG
*
56605164 ATACGGTGGAATCAGCACTTAGCAACCACCAATGA-
1 -T-CGG-GGAATCAGCACTTAGCAACCACCCATGAG
56605199 TCTGGGGAATCAGCACTTAGCAACC
1 TC-GGGGAATCAGCACTTAGCAACC
56605224 CCTTAGGGGG
Statistics
Matches: 135, Mismatches: 20, Indels: 37
0.70 0.10 0.19
Matches are distributed among these distances:
33 59 0.44
34 10 0.07
35 1 0.01
36 6 0.04
37 4 0.03
38 4 0.03
39 5 0.04
40 4 0.03
41 24 0.18
42 18 0.13
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCCATGAG
Found at i:56605195 original size:74 final size:74
Alignment explanation
Indices: 56605018--56605227 Score: 323
Period size: 74 Copynumber: 2.8 Consensus size: 74
56605008 TATCCGTTAT
* * *
56605018 CGGTGGATTCAGCACTTAGCAACCACCCATGAGTCGGGGAATCAACACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGA-TCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
56605083 ATTTAAGATA
65 ATCTAAGATA
* *
56605093 CGGTGGGATCAGCGCTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGA-TCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
56605158 A-CTCAGATA
65 ATCTAAGATA
56605167 CGGTGGAATCAGCACTTAGCAACCACCAATGATCTGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATC-GGGGAATCAGCACTTAGCAACCCCTT
56605228 AGGGGGATTT
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
73 2 0.02
74 62 0.50
75 60 0.48
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (74 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATCGGGGAATCAGCACTTAGCAACCCCTTTCACA
TCTAAGATA
Found at i:56605233 original size:28 final size:28
Alignment explanation
Indices: 56605202--56605255 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
56605192 CCAATGATCT
56605202 GGGGAATCAGCACTTAGCAACCCCTTAG
1 GGGGAATCAGCACTTAGCAACCCCTTAG
* *
56605230 GGGGATTTAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
56605256 TTACATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (28 bp):
GGGGAATCAGCACTTAGCAACCCCTTAG
Found at i:56605290 original size:104 final size:101
Alignment explanation
Indices: 56605128--56605361 Score: 344
Period size: 104 Copynumber: 2.3 Consensus size: 101
56605118 CCAATGATTC
* *
56605128 GGGGAATCAGCACTTAGCAACCCCTTTCACACTCAGATACGGTGGAATCAGCACTTAGCAACCAC
1 GGGGAATCAGCACTTAGCAACCCCTTTTACACTAAGATACGGTGGAATCAGCACTTAGCAACCAC
*
56605193 CAATGA-TCTGGGGAATCAGCACTTAGCAACCCCTTAG
66 CAATGATTC-GGGGAATCAACACTTAGCAACCCCTT-G
* * * *
56605230 GGGGATTTAGCACTTAGCAACCCCTTTTACATTTAAAGATACGGTGGAGTCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCTTTTACA-CT-AAGATACGGTGGAATCAGCACTTAGCAACC
*
56605295 ACCAGTGATTCGGGGAATCAACACTTAGCAACCCCTTG
64 ACCAATGATTCGGGGAATCAACACTTAGCAACCCCTTG
*
56605333 GGGGAATCAGCACTTAGCAACCCCCTTTA
1 GGGGAATCAGCACTTAGCAACCCCTTTTA
56605362 TATTCAATAT
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
102 28 0.24
103 28 0.24
104 60 0.51
105 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (101 bp):
GGGGAATCAGCACTTAGCAACCCCTTTTACACTAAGATACGGTGGAATCAGCACTTAGCAACCAC
CAATGATTCGGGGAATCAACACTTAGCAACCCCTTG
Found at i:56605982 original size:11 final size:12
Alignment explanation
Indices: 56605954--56605987 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
56605944 GCCCAAACGT
56605954 CGAAATTTTTGAA
1 CGAAATTTTT-AA
56605967 CGAAATTTTT-A
1 CGAAATTTTTAA
56605978 CGAAATTTTT
1 CGAAATTTTT
56605988 CGGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:56607254 original size:23 final size:23
Alignment explanation
Indices: 56607210--56607254 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
56607200 CTTTTCAATA
*
56607210 TATAAAAATAATAAAATATTAAG
1 TATAAAAATAATAAAAGATTAAG
* * *
56607233 TATATAAATAATATAAGGTTAA
1 TATAAAAATAATAAAAGATTAA
56607255 TAGATCAAGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (23 bp):
TATAAAAATAATAAAAGATTAAG
Found at i:56607332 original size:14 final size:15
Alignment explanation
Indices: 56607305--56607333 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56607295 TAGTCATTAT
56607305 ACTTAAATATTTTTA
1 ACTTAAATATTTTTA
56607320 ACTTAAA-ATTTTTA
1 ACTTAAATATTTTTA
56607334 GTCCAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
ACTTAAATATTTTTA
Found at i:56613190 original size:11 final size:11
Alignment explanation
Indices: 56613169--56613212 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
56613159 ATCTTAATGG
56613169 AATTGAATTAAA
1 AATT-AATTAAA
56613181 AATTAATTAAA
1 AATTAATTAAA
* *
56613192 AAATAATAAAA
1 AATTAATTAAA
56613203 AATTAATTAA
1 AATTAATTAA
56613213 CTTGAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 24 0.86
12 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AATTAATTAAA
Found at i:56613193 original size:12 final size:12
Alignment explanation
Indices: 56613169--56613212 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
56613159 ATCTTAATGG
56613169 AATTGAATT-AAA
1 AATT-AATTAAAA
56613181 AATTAATTAAAA
1 AATTAATTAAAA
56613193 AA-TAA-TAAAA
1 AATTAATTAAAA
56613203 AATTAATTAA
1 AATTAATTAA
56613213 CTTGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.24
11 10 0.34
12 12 0.41
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
AATTAATTAAAA
Found at i:56613281 original size:18 final size:18
Alignment explanation
Indices: 56613257--56613307 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
56613247 ATTCAACTGA
56613257 ATTTTA-TTATTTTTAAT
1 ATTTTATTTATTTTTAAT
56613274 ATTTTTATTTTATTTTTAAT
1 A-TTTTA-TTTATTTTTAAT
*
56613294 AATTTATTTATTTT
1 ATTTTATTTATTTT
56613308 AAATTAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.03
18 13 0.43
19 4 0.13
20 12 0.40
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTATTTATTTTTAAT
Found at i:56613283 original size:23 final size:23
Alignment explanation
Indices: 56613263--56613308 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 23
56613253 CTGAATTTTA
56613263 TTATTTTTAAT-A-TT-TTTATT
1 TTATTTTTAATAATTTATTTATT
56613283 TTATTTTTAATAATTTATTTATT
1 TTATTTTTAATAATTTATTTATT
56613306 TTA
1 TTA
56613309 AATTAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 2 0.09
23 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTTTTAATAATTTATTTATT
Found at i:56614833 original size:8 final size:8
Alignment explanation
Indices: 56614820--56614849 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
56614810 TGACTTGGGG
56614820 AGAAGAGA
1 AGAAGAGA
56614828 AGAAGAGA
1 AGAAGAGA
*
56614836 GGAAGAGA
1 AGAAGAGA
56614844 AGAAGA
1 AGAAGA
56614850 AATAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
AGAAGAGA
Found at i:56616306 original size:11 final size:11
Alignment explanation
Indices: 56616292--56616316 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56616282 TAATATATTG
56616292 TTAAACAATAT
1 TTAAACAATAT
56616303 TTAAACAATAT
1 TTAAACAATAT
56616314 TTA
1 TTA
56616317 GAATAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAACAATAT
Found at i:56642886 original size:43 final size:43
Alignment explanation
Indices: 56642821--56642936 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
56642811 TGATAAATGA
*
56642821 TTTT-GTGTAGGACCATGTCTGGGACGTTGGCATCGA-CTTGTG
1 TTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATC-TGTG
**
56642863 TTTTCGTGTAAGACCACATCTGGGACAG-TGGCATCGATCTGTG
1 TTTTCGTGTAAGACCATGTCTGGGAC-GTTGGCATCGATCTGTG
* * *
56642906 TTTACATGTAAGACCATGTTTGGGACGTTGG
1 TTTTCGTGTAAGACCATGTCTGGGACGTTGG
56642937 TGTTGTACGA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 5 0.08
43 55 0.89
44 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (43 bp):
TTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATCTGTG
Found at i:56649575 original size:16 final size:18
Alignment explanation
Indices: 56649556--56649593 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56649546 AGTTTTATTG
56649556 TTTAT-ATGTT-TATAAT
1 TTTATAATGTTATATAAT
*
56649572 TTTATAATTTTATATAAT
1 TTTATAATGTTATATAAT
56649590 TTTA
1 TTTA
56649594 ATTTAGAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 4 0.21
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTATAATGTTATATAAT
Found at i:56649912 original size:15 final size:17
Alignment explanation
Indices: 56649881--56649912 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
56649871 AAATTTTTTA
56649881 ATTTATAAATGATTATT
1 ATTTATAAATGATTATT
56649898 ATTT-TAAAT-ATTATT
1 ATTTATAAATGATTATT
56649913 TACATTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTATAAATGATTATT
Found at i:56652363 original size:22 final size:23
Alignment explanation
Indices: 56652337--56652379 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
56652327 GGTTGCTGCC
56652337 ATTATTTTTATTC-AATTTTGCT
1 ATTATTTTTATTCTAATTTTGCT
*
56652359 ATTATTTTTTTTCTAATTTTG
1 ATTATTTTTATTCTAATTTTG
56652380 GGGTTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (23 bp):
ATTATTTTTATTCTAATTTTGCT
Found at i:56658352 original size:45 final size:45
Alignment explanation
Indices: 56658285--56658373 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
56658275 TAGTTGGGAG
56658285 GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTAA
1 GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTAA
* * *
56658330 GAGTTTTTGCTGTTAGCTGAGTTCACCTACAATAGCAGTTTCTA
1 GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTA
56658374 CTCCAGTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (45 bp):
GAGTTTCTGCCGTTAGCCGAGTTCACCTACAATAGCAGTTTCTAA
Found at i:56659293 original size:5 final size:5
Alignment explanation
Indices: 56659285--56659311 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
56659275 ATTTGGGTGG
56659285 TTTGT TTTGT TTTGT TTTGT TTTGT TT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TT
56659312 ATAACGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTGT
Found at i:56661801 original size:36 final size:36
Alignment explanation
Indices: 56661754--56661827 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
56661744 AAACGAAATG
56661754 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
1 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
56661790 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
1 TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
56661826 TA
1 TA
56661828 CACAACAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (36 bp):
TATAATTATTTCAGAAAACTTCCTACCCAACTCTAC
Found at i:56671495 original size:27 final size:27
Alignment explanation
Indices: 56671309--56671484 Score: 255
Period size: 27 Copynumber: 6.5 Consensus size: 27
56671299 ATAGATACCT
*
56671309 ATAGGGTAAAATGACTGAAATACCCTC
1 ATAGGGTAAAATGACTGAAATACCCCC
*
56671336 ATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
** * *
56671363 ATAGATTAAAGTGA-TCGAAATACCCTC
1 ATAGGGTAAAATGACT-GAAATACCCCC
*
56671390 ATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
*
56671417 ATAGGGTAAAATGACTGAAATACCCCT
1 ATAGGGTAAAATGACTGAAATACCCCC
*
56671444 ATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCCC
56671471 ATAGGGTAAAATGA
1 ATAGGGTAAAATGA
56671485 TTGTTATACC
Statistics
Matches: 132, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 130 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (27 bp):
ATAGGGTAAAATGACTGAAATACCCCC
Found at i:56671508 original size:54 final size:53
Alignment explanation
Indices: 56671309--56671510 Score: 255
Period size: 54 Copynumber: 3.7 Consensus size: 53
56671299 ATAGATACCT
*
56671309 ATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGACTAAAATACCCCC
1 ATAGGGTAAAATGACTGAAATACCCT-ATAGGGTAAAATGACTGAAATACCCCC
** * *
56671363 ATAGATTAAAGTGA-TCGAAATACCCTCATAGGGTAAAATGATTGAAATACCCCC
1 ATAGGGTAAAATGACT-GAAATACCCT-ATAGGGTAAAATGACTGAAATACCCCC
*
56671417 ATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACTGAAATA-CCCTATAGGGTAAAATGACTGAAATACCCCC
* **
56671471 ATAGGGTAAAATGATTGTTATACCCT-TAGGAGATAAAATG
1 ATAGGGTAAAATGACTGAAATACCCTATAGG-G-TAAAATG
56671511 GCTGTTATGG
Statistics
Matches: 130, Mismatches: 13, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
52 4 0.03
53 6 0.05
54 115 0.88
55 5 0.04
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (53 bp):
ATAGGGTAAAATGACTGAAATACCCTATAGGGTAAAATGACTGAAATACCCCC
Found at i:56671508 original size:81 final size:79
Alignment explanation
Indices: 56671309--56671510 Score: 251
Period size: 81 Copynumber: 2.5 Consensus size: 79
56671299 ATAGATACCT
* * *
56671309 ATAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGACTAAAATACCCCCATAGATTAAAG
1 ATAGGGTAAAATGATTGAAATACCCT--TAGGGTAAAATGACTAAAATACCCCCATAGAGTAAAA
* *
56671374 TGATCGAAATACCCTC
64 TGACCGAAATACCCCC
* * * *
56671390 ATAGGGTAAAATGATTGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAA
1 ATAGGGTAAAATGATTGAAATA--CCCTTAGGGTAAAATGACTAAAATACCCCCATAGAGTAAAA
56671455 TGACCGAAATACCCCC
64 TGACCGAAATACCCCC
**
56671471 ATAGGGTAAAATGATTGTTATACCCTTAGGAGATAAAATG
1 ATAGGGTAAAATGATTGAAATACCCTTAGG-G-TAAAATG
56671511 GCTGTTATGG
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
79 7 0.07
80 1 0.01
81 94 0.90
83 3 0.03
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (79 bp):
ATAGGGTAAAATGATTGAAATACCCTTAGGGTAAAATGACTAAAATACCCCCATAGAGTAAAATG
ACCGAAATACCCCC
Found at i:56671786 original size:26 final size:26
Alignment explanation
Indices: 56671719--56671795 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
56671709 TGTGCCACAT
*
56671719 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTTGCAGCTTTGCTGCG
*
56671745 ATACTGA-TA-TTGGCAGCTCTGCTGCG
1 ATACT-ATTACTT-GCAGCTTTGCTGCG
* *
56671771 ATGCTATTACTTGCAGTTTTGCTGC
1 ATACTATTACTTGCAGCTTTGCTGC
56671796 AATATTGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 2 0.05
26 37 0.88
27 3 0.07
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.36
Consensus pattern (26 bp):
ATACTATTACTTGCAGCTTTGCTGCG
Found at i:56685655 original size:29 final size:29
Alignment explanation
Indices: 56685596--56685664 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
56685586 CAGTTGAACA
56685596 TAAATTTTAAAAATAAAAAATAGAGTAAT
1 TAAATTTTAAAAATAAAAAATAGAGTAAT
* *
56685625 TAAATTTCTATAAATAAAAAA-ATA-TATAT
1 TAAATTT-TAAAAATAAAAAATAGAGTA-AT
56685654 TAAATTTTAAA
1 TAAATTTTAAA
56685665 TTTACTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.14
29 18 0.51
30 12 0.34
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAATTTTAAAAATAAAAAATAGAGTAAT
Found at i:56685801 original size:3 final size:3
Alignment explanation
Indices: 56685788--56685826 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
56685778 TAAAATGAAT
56685788 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56685827 TGCAGTAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:56686495 original size:29 final size:29
Alignment explanation
Indices: 56686462--56686517 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
56686452 CTCAAAGGAA
*
56686462 TTTTAGAATATTTTCACATGTGTCATTAT
1 TTTTAGAATATTTTCAAATGTGTCATTAT
* * *
56686491 TTTTAGATTTTTTTTAAATGTGTCATT
1 TTTTAGAATATTTTCAAATGTGTCATT
56686518 TTACTCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (29 bp):
TTTTAGAATATTTTCAAATGTGTCATTAT
Found at i:56689502 original size:25 final size:25
Alignment explanation
Indices: 56689455--56689503 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
56689445 GTTCACTTTT
*
56689455 TTACAAAAATAATATAAACAATTAA
1 TTACAAAAATAATATAAAAAATTAA
*
56689480 TTACAAAAATAGGTA-AAAAAATTA
1 TTACAAAAATA-ATATAAAAAATTA
56689504 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
TTACAAAAATAATATAAAAAATTAA
Found at i:56693693 original size:24 final size:24
Alignment explanation
Indices: 56693666--56693717 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56693656 TTTCTAGGAG
* **
56693666 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
56693690 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
56693714 ATTT
1 ATTT
56693718 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:56697121 original size:16 final size:16
Alignment explanation
Indices: 56697100--56697131 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56697090 AAATTGTACC
56697100 TAAGTCAGAAGGGGCA
1 TAAGTCAGAAGGGGCA
56697116 TAAGTCAGAAGGGGCA
1 TAAGTCAGAAGGGGCA
56697132 CATTGAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (16 bp):
TAAGTCAGAAGGGGCA
Found at i:56698135 original size:24 final size:24
Alignment explanation
Indices: 56698073--56698124 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
56698063 TTTCTAGAAG
* **
56698073 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGTATTTATTAACATAATAT
56698097 ATTTAGTATTTATTAACATAATAT
1 ATTTAGTATTTATTAACATAATAT
56698121 ATTT
1 ATTT
56698125 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGTATTTATTAACATAATAT
Done.