Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 5 of 54
Found at i:2126839 original size:66 final size:65
Alignment explanation
Indices: 2126806--2126963 Score: 174
Period size: 66 Copynumber: 2.4 Consensus size: 65
2126796 ACAGTTTTTG
* * *
2126806 TTTTTTATTTTTCTGAGTTAAAAGAAAATGAGGAAAGTAGAAACCAATGGAAAAAACGAACAGAG
1 TTTTTTTTTTTTTTGAGTTAAAAGAAAATGAGGAAAG-AGAAACCAAGGGAAAAAACGAACAGAG
2126871 A
65 A
* * *
2126872 TTTTTTTTTTTTTTGAGTTGAAAGAAAATGAGGAAAGCAGAAACCAA-TGACAATAAACCAACAG
1 TTTTTTTTTTTTTTGAGTTAAAAGAAAATGAGGAAAG-AGAAACCAAGGGA-AA-AAACGAACAG
2126936 AGA
63 AGA
* * *
2126939 TGCTTTTCTGTTTTTGAGTTGAAAA
1 T-TTTTTTTTTTTTTGAGTT-AAAA
2126964 ATTGAGTGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.03
66 45 0.58
67 13 0.17
68 15 0.19
69 3 0.04
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (65 bp):
TTTTTTTTTTTTTTGAGTTAAAAGAAAATGAGGAAAGAGAAACCAAGGGAAAAAACGAACAGAGA
Found at i:2138570 original size:40 final size:40
Alignment explanation
Indices: 2138515--2138593 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
2138505 TTGGCTATTT
*
2138515 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
2138555 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTG
2138594 TTTTTCATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:2141649 original size:25 final size:24
Alignment explanation
Indices: 2141621--2141679 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
2141611 ACTTAAATTG
* *
2141621 AAGAAGAAAGAGAAAATTCGAATCA
1 AAGAAGAAAGAG-AAACTAGAATCA
* *
2141646 AAGAAAGCAAGAGAAACTAGAATCG
1 AAG-AAGAAAGAGAAACTAGAATCA
2141671 AAGAAGAAA
1 AAGAAGAAA
2141680 AAGGAAGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 5 0.18
25 15 0.54
26 8 0.29
ACGTcount: A:0.61, C:0.08, G:0.22, T:0.08
Consensus pattern (24 bp):
AAGAAGAAAGAGAAACTAGAATCA
Found at i:2143560 original size:506 final size:506
Alignment explanation
Indices: 2142114--2143658 Score: 2689
Period size: 506 Copynumber: 3.1 Consensus size: 506
2142104 CCAATGGCAC
* * * *
2142114 GATGAGTTGGCCTTTTCCATATGCTCTTCAATGTTGGTAATGACTGTAGCTCCAACCTTCTTAAA
1 GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGGTAATGACTGTAGTTCCAACCTTCTTAAA
* *
2142179 TTTGAGAGTGGTACTGCCTGATTTACCTCACATAAA-AAAAATATAAAATTTATTAATTAATAAA
66 TTTGAGAGTGGTACTGCCTGTTTTACCTCATATAAAGAAAAATATAAAATTTATTAATTAATAAA
* *
2142243 TAATGAAAATGAATTGTTTATACTTGATCTTAATTACTGAGAAGAAATACATTTTGTTAAAAAAA
131 TAATGAAAATGAGTTCTTTATACTTGATCTTAATTACTGAGAAGAAATACATTTTGTTAAAAAAA
*
2142308 AGTAGAAAGAAGTATTAAAAGTTAATAATTTAGAAAGATTAGATAGTAATTATTTATATATTTGA
196 AGTAAAAAGAAGTATTAAAAGTTAATAATTTAGAAAGATTAGATAGTAATTATTTATATATTTGA
* * *
2142373 TAATTCAAAAAAAATCATTAGAAAAACAATATACGAGACCATTATTAAAGGAAAAATGAAGAGAT
261 TAATTC-AAAAAAATCATTAGAAAAACAATATACGAGAGCATTATTAAAAGAAAAATGGAGAGAT
* * *
2142438 AAGAGGTACCTCTAGCTCAGCCATCTCTTTGTCAAAAGCAAAGACTTGCTTTAATTTTTTGCATT
325 AAGAGGTACCTCTAGCTCAGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAATTTTTCGCATT
*
2142503 AAGATATCTCAAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGATAGATTTT
390 TAGATATCTCAAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGATAGATTTT
2142568 AGTTTATCACAACCATCAATTGTTACTTCCTTCAGACTTTGTAGCCTTACAT
455 AGTTTATCACAACCATCAATTGTTACTTCCTTCAGACTTTGTAGCCTTACAT
* *
2142620 GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGGTAATGACTGCAATTCCAACCTTCTTAAA
1 GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGGTAATGACTGTAGTTCCAACCTTCTTAAA
2142685 TTTGAGAGTGGTACTGCCTGTTTTACCTCATATAAAGAAAAATATAAAATTTATTAATTAATAAA
66 TTTGAGAGTGGTACTGCCTGTTTTACCTCATATAAAGAAAAATATAAAATTTATTAATTAATAAA
2142750 TAATGAAAATGAGTTCTTTATACTTGATCTTAATTACTGAGAAGAAATACATTTTGTT-------
131 TAATGAAAATGAGTTCTTTATACTTGATCTTAATTACTGAGAAGAAATACATTTTGTTAAAAAAA
2142808 A--AAAAA-AAGTATTAAAAGTTAATAATTTAGAAAGATTAGATAGTAATTATTTATATATTTGA
196 AGTAAAAAGAAGTATTAAAAGTTAATAATTTAGAAAGATTAGATAGTAATTATTTATATATTTGA
2142870 TAATTCAAAAAAATCATTAGAAAAACAATATACGAGAGCATTATTAAAAGAAAAATGGAGAGATA
261 TAATTCAAAAAAATCATTAGAAAAACAATATACGAGAGCATTATTAAAAGAAAAATGGAGAGATA
2142935 AGAGGTACCTCTAGCTCAGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAATTTTTCGCATTT
326 AGAGGTACCTCTAGCTCAGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAATTTTTCGCATTT
*
2143000 AGATATCTCAAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGATAGATTTCA
391 AGATATCTCAAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGATAGATTTTA
2143065 GTTTATCACAACCATCAATTGTTACTTCCTTCAGACTTTGTAGCCTTACAT
456 GTTTATCACAACCATCAATTGTTACTTCCTTCAGACTTTGTAGCCTTACAT
*
2143116 GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGGTAATGACTGTAGTTTCAACCTTCTTAAA
1 GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGGTAATGACTGTAGTTCCAACCTTCTTAAA
*
2143181 TTTGAGAGTGGTACTACCTGTTTTACCTCATATAAAGAAAAATATAAAATTTATTAATTAATAAA
66 TTTGAGAGTGGTACTGCCTGTTTTACCTCATATAAAGAAAAATATAAAATTTATTAATTAATAAA
* *
2143246 TAATGAAAATGAGTTCTTTATACTTGATCTTAATTACTGAGTAGAAATGCATTTTGTTAAAAAAA
131 TAATGAAAATGAGTTCTTTATACTTGATCTTAATTACTGAGAAGAAATACATTTTGTTAAAAAAA
*
2143311 AGTAAAAAGAAGTATTAAAAGTTAATAATTTAGAAAGATTAGATATTAATTATTTATATATTTGA
196 AGTAAAAAGAAGTATTAAAAGTTAATAATTTAGAAAGATTAGATAGTAATTATTTATATATTTGA
2143376 TAATTCAAAAAAATCATTAGAAAAACAATATACGAGAGCATTATTAAAAGAAAAATGGAGAGATA
261 TAATTCAAAAAAATCATTAGAAAAACAATATACGAGAGCATTATTAAAAGAAAAATGGAGAGATA
* *
2143441 AGAGGTACCTCTGGGTCAGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAATTTTTCGCATTT
326 AGAGGTACCTCTAGCTCAGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAATTTTTCGCATTT
* *
2143506 AGATATCTCGAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGACAGATTTTA
391 AGATATCTCAAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGATAGATTTTA
* * *
2143571 GTTTATCACAACTATCAATTGTTACTTCCTTCAGACTTTGTAACCTTATAT
456 GTTTATCACAACCATCAATTGTTACTTCCTTCAGACTTTGTAGCCTTACAT
* ** *
2143622 GATGAGTTGGCTCTTTCCATATATTCTCTAATGCTGG
1 GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGG
2143659 CAACGACATC
Statistics
Matches: 990, Mismatches: 38, Indels: 22
0.94 0.04 0.02
Matches are distributed among these distances:
496 414 0.42
497 62 0.06
498 4 0.00
500 1 0.00
503 1 0.00
505 5 0.01
506 419 0.42
507 84 0.08
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (506 bp):
GATGAGTTGGCCCTTTCCATATGCTCTCCAATGCTGGTAATGACTGTAGTTCCAACCTTCTTAAA
TTTGAGAGTGGTACTGCCTGTTTTACCTCATATAAAGAAAAATATAAAATTTATTAATTAATAAA
TAATGAAAATGAGTTCTTTATACTTGATCTTAATTACTGAGAAGAAATACATTTTGTTAAAAAAA
AGTAAAAAGAAGTATTAAAAGTTAATAATTTAGAAAGATTAGATAGTAATTATTTATATATTTGA
TAATTCAAAAAAATCATTAGAAAAACAATATACGAGAGCATTATTAAAAGAAAAATGGAGAGATA
AGAGGTACCTCTAGCTCAGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAATTTTTCGCATTT
AGATATCTCAAGTGTTTCTAGATGCAACAGACTTTGAACAAGGTAAGGTGAGAAGATAGATTTTA
GTTTATCACAACCATCAATTGTTACTTCCTTCAGACTTTGTAGCCTTACAT
Found at i:2151192 original size:21 final size:21
Alignment explanation
Indices: 2151158--2151205 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2151148 TGAATGAAAT
2151158 AATTT-TTACAAATAATTCTA
1 AATTTGTTACAAATAATTCTA
*
2151178 AATTTGTTATAAATAATTCTA
1 AATTTGTTACAAATAATTCTA
2151199 AATTTGT
1 AATTTGT
2151206 GGAGAGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (21 bp):
AATTTGTTACAAATAATTCTA
Found at i:2172522 original size:110 final size:109
Alignment explanation
Indices: 2172325--2172570 Score: 294
Period size: 110 Copynumber: 2.2 Consensus size: 109
2172315 TATTATTTTA
* * * * *
2172325 GCGTGTCAAGGTTGTTCCTAGCGTGTCACGGGTTAACTAGTTTTTTGGGTTTTGGGCGTGTCACA
1 GCGTGTCAAGGCTGTTCCTAGCGTGTCACGAGTTAACTAGATTTATGGGTTTGGGGCGTGTCACA
* * ** *
2172390 GCTGTTCTTGACCTATCATGGGTTAATTGGTTTTTTGGTTTTCGG
66 GCTGTTCTTGACATATCATGGGTTAACTGAATTTTAGGTTTT-GG
* * * *
2172435 GCGTGTCACGGCTGTTCCTAGCGTGTCATGAGTTAACTGGATTTATGGGTTTGGGGCGTGTCATA
1 GCGTGTCAAGGCTGTTCCTAGCGTGTCACGAGTTAACTAGATTTATGGGTTTGGGGCGTGTCACA
* * *
2172500 GCTGTTCTTGGCATGTCGTGGGTTAACTGAATTTTAGGTTTTGG
66 GCTGTTCTTGACATATCATGGGTTAACTGAATTTTAGGTTTTGG
* * * *
2172544 GCATGTCATGGCTATTCCTGGCGTGTC
1 GCGTGTCAAGGCTGTTCCTAGCGTGTC
2172571 GTGGGTAAAT
Statistics
Matches: 115, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
109 25 0.22
110 90 0.78
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.39
Consensus pattern (109 bp):
GCGTGTCAAGGCTGTTCCTAGCGTGTCACGAGTTAACTAGATTTATGGGTTTGGGGCGTGTCACA
GCTGTTCTTGACATATCATGGGTTAACTGAATTTTAGGTTTTGG
Found at i:2172571 original size:54 final size:54
Alignment explanation
Indices: 2172325--2172576 Score: 198
Period size: 55 Copynumber: 4.6 Consensus size: 54
2172315 TATTATTTTA
* * * ** ** *
2172325 GCGTGTCAAGGTTGTTCCTAGCGTGTCACGGGTTAACTAGTTTTTTGGGTTTTGG
1 GCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACT-GAATTTTAGGTTTTGG
** * * * * * * ** *
2172380 GCGTGTCACAGCTGTTCTTGACCTATCATGGGTTAATTGGTTTTTTGGTTTTCGG
1 GCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTGAATTTTAGGTTTT-GG
* * * * * * *
2172435 GCGTGTCACGGCTGTTCCTAGCGTGTCATGAGTTAACTGGATTTATGGGTTTGGG
1 GCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTGAATTT-TAGGTTTTGG
* * *
2172490 GCGTGTCATAGCTGTTCTTGGCATGTCGTGGGTTAACTGAATTTTAGGTTTTGG
1 GCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTGAATTTTAGGTTTTGG
* *
2172544 GCATGTCATGGCTATTCCTGGCGTGTCGTGGGT
1 GCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGT
2172577 AAATTGGTTT
Statistics
Matches: 157, Mismatches: 38, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
54 48 0.31
55 103 0.66
56 6 0.04
ACGTcount: A:0.13, C:0.16, G:0.32, T:0.39
Consensus pattern (54 bp):
GCGTGTCATGGCTGTTCCTGGCGTGTCGTGGGTTAACTGAATTTTAGGTTTTGG
Found at i:2172675 original size:23 final size:23
Alignment explanation
Indices: 2172649--2172703 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2172639 TGATTAGCGC
*
2172649 GTCACGACAGTGATGCATGGCGT
1 GTCACGACACTGATGCATGGCGT
*
2172672 GTCACGATACTGATGCATGGCGT
1 GTCACGACACTGATGCATGGCGT
* *
2172695 ATTACGACA
1 GTCACGACA
2172704 TTTGACTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (23 bp):
GTCACGACACTGATGCATGGCGT
Found at i:2172719 original size:31 final size:31
Alignment explanation
Indices: 2172684--2172766 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
2172674 CACGATACTG
* *
2172684 ATGCATGGCGTATTACGACATTTGAC-TTGAT
1 ATGCATGGCGTATTACAACATTTAACGTT-AT
* *
2172715 ATGCATGGCGTGTTACAATATTTAACGTTAT
1 ATGCATGGCGTATTACAACATTTAACGTTAT
* * *
2172746 ATGCATGACGTGTAACAACAT
1 ATGCATGGCGTATTACAACAT
2172767 GACTGACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (31 bp):
ATGCATGGCGTATTACAACATTTAACGTTAT
Found at i:2179568 original size:86 final size:86
Alignment explanation
Indices: 2179468--2179722 Score: 282
Period size: 86 Copynumber: 3.0 Consensus size: 86
2179458 CATGGCACGG
* *
2179468 GCCAATTGTGGTGACACCCTGAGTGCAAGCAAACTTATGGTGTGACACGCTGACTTGTTGCAGTC
1 GCCAATTGTGGTGACACGCTGAGTGCAAGCAAACTTATGGCGTGACACGCTGACTTGTTGCAGTC
** *
2179533 TTGACGGGTAACACTACACAA
66 TTGAAAGGTAACACGACACAA
* ** *
2179554 GCCAATTGTGGTGACACGCTGAGTGCAAGTAAACTTATGGCGTGACACATTGACTTCTTGCAGTC
1 GCCAATTGTGGTGACACGCTGAGTGCAAGCAAACTTATGGCGTGACACGCTGACTTGTTGCAGTC
* * * ***
2179619 TCGAAAGGTGACACGGCAGGG
66 TTGAAAGGTAACACGACACAA
* * ** *
2179640 GCCAATTGTGGTGACACGCTGAGTGCATGCAGAC-T-TGGCGTGACACGCCAAATTGTTGCAGTC
1 GCCAATTGTGGTGACACGCTGAGTGCAAGCAAACTTATGGCGTGACACGCTGACTTGTTGCAGTC
** *
2179703 TTG-TTGGTGACACGACACAA
66 TTGAAAGGTAACACGACACAA
2179723 AATGTTTAAA
Statistics
Matches: 138, Mismatches: 31, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
83 11 0.08
84 24 0.17
85 1 0.01
86 102 0.74
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (86 bp):
GCCAATTGTGGTGACACGCTGAGTGCAAGCAAACTTATGGCGTGACACGCTGACTTGTTGCAGTC
TTGAAAGGTAACACGACACAA
Found at i:2180499 original size:62 final size:62
Alignment explanation
Indices: 2180329--2180740 Score: 445
Period size: 62 Copynumber: 6.6 Consensus size: 62
2180319 AATAAAGAAT
* * * *
2180329 AAATGTTGTGACACACCATTCATAACAAG-CTAAATGTTCTGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACACCATGCATATCAAGTC-AAATGTTGTGACACGCCATGCATATCAAGTA
* * * * * *
2180391 AATCAT-TTGTGACACGCCATACATAACAACTAAAATGTTATGACACGCCATGCATATCAAGTA
1 AA--ATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTA
* * * * *
2180454 AAACGTTGTGACACGCCATGCATATCAAGTCAAATGTTGTCACACGCCATGCATATCGAGTC
1 AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTA
* * * * * *
2180516 AAATGTTGTCACACACCATGCATAACAAGT-AAATCATTTGTGACACGCCATAGTA-AACAAGCA
1 AAATGTTGTGACACACCATGCATATCAAGTCAAAT--GTTGTGACACGCCAT-GCATATCAAGTA
* * * *
2180579 AAATGTTGTGACACACCATGCATATTAAGTAAAACGTTGTGACACGCCATGCATATCAAGCA
1 AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTA
** * * * *
2180641 AAATGTTGTGACACACCATGCATATCAAGTCATTTGTTGTCACACGCCTTGCATATCGAGTC
1 AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTA
* *
2180703 AAATGTTGTGACACACCATGCATGTCGAGTCAAATGTT
1 AAATGTTGTGACACACCATGCATATCAAGTCAAATGTT
2180741 TTCACACAAG
Statistics
Matches: 294, Mismatches: 47, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
61 7 0.02
62 184 0.63
63 96 0.33
64 7 0.02
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (62 bp):
AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTA
Found at i:2180613 original size:156 final size:156
Alignment explanation
Indices: 2180329--2180695 Score: 535
Period size: 156 Copynumber: 2.4 Consensus size: 156
2180319 AATAAAGAAT
* * * *
2180329 AAATGTTGTGACACACCATTCATAACAAG-CTAAATGTTCTGACACGCCATGCATAACAAGTAAA
1 AAATGTTGTGACACACCATGCATATCAAGTC-AAATGTTGTCACACGCCATGCATAACAAGTAAA
*
2180393 TCATTTGTGACACGCCATACATAACAACTAAAATGTTATGACACGCCATGCATATCAAGTAAAAC
65 TCATTTGTGACACGCCATACATAACAACTAAAATGTTATGACACACCATGCATATCAAGTAAAAC
2180458 GTTGTGACACGCCATGCATATCAAGTC-
130 GTTGTGACACGCCATGCATATCAAG-CA
* * * *
2180485 AAATGTTGTCACACGCCATGCATATCGAGTCAAATGTTGTCACACACCATGCATAACAAGTAAAT
1 AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTCACACGCCATGCATAACAAGTAAAT
* * *
2180550 CATTTGTGACACGCCATA-GTAAACAAGC-AAAATGTTGTGACACACCATGCATATTAAGTAAAA
66 CATTTGTGACACGCCATACAT-AACAA-CTAAAATGTTATGACACACCATGCATATCAAGTAAAA
2180613 CGTTGTGACACGCCATGCATATCAAGCA
129 CGTTGTGACACGCCATGCATATCAAGCA
** *
2180641 AAATGTTGTGACACACCATGCATATCAAGTCATTTGTTGTCACACGCCTTGCATA
1 AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTCACACGCCATGCATA
2180696 TCGAGTCAAA
Statistics
Matches: 188, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
155 2 0.01
156 184 0.98
157 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (156 bp):
AAATGTTGTGACACACCATGCATATCAAGTCAAATGTTGTCACACGCCATGCATAACAAGTAAAT
CATTTGTGACACGCCATACATAACAACTAAAATGTTATGACACACCATGCATATCAAGTAAAACG
TTGTGACACGCCATGCATATCAAGCA
Found at i:2180748 original size:31 final size:31
Alignment explanation
Indices: 2180329--2180740 Score: 404
Period size: 31 Copynumber: 13.2 Consensus size: 31
2180319 AATAAAGAAT
* * *
2180329 AAATGTTGTGACACACCATTCATAACAAG-C
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* *
2180359 TAAATGTTCTGACACGCCATGCATAACAAGT-
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
* * * * *
2180390 AAATCATTTGTGACACGCCATACATAACAACTA
1 AAAT--GTTGTGACACGCCATGCATATCAAGTC
* *
2180423 AAATGTTATGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
2180454 AAACGTTGTGACACGCCATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* *
2180485 AAATGTTGTCACACGCCATGCATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* * *
2180516 AAATGTTGTCACACACCATGCATAACAAGT-
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* * *
2180546 AAATCATTTGTGACACGCCATAGTA-AACAAG-C
1 AAAT--GTTGTGACACGCCAT-GCATATCAAGTC
* * *
2180578 AAAATGTTGTGACACACCATGCATATTAAGTA
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
*
2180610 AAACGTTGTGACACGCCATGCATATCAAG-C
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
2180640 AAAATGTTGTGACACACCATGCATATCAAGTC
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
** * * *
2180672 ATTTGTTGTCACACGCCTTGCATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* * *
2180703 AAATGTTGTGACACACCATGCATGTCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
2180734 AAATGTT
1 AAATGTT
2180741 TTCACACAAG
Statistics
Matches: 319, Mismatches: 49, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
30 10 0.03
31 258 0.81
32 41 0.13
33 10 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATATCAAGTC
Found at i:2181813 original size:16 final size:16
Alignment explanation
Indices: 2181789--2181879 Score: 55
Period size: 14 Copynumber: 5.9 Consensus size: 16
2181779 AAAAAGAATT
*
2181789 AATTATATATACAATA
1 AATTGTATATACAATA
2181805 AATTGTATA-A-AATA
1 AATTGTATATACAATA
** *
2181819 AATTGTGCATACAAAAA
1 AATTGTATATAC-AATA
* * * *
2181836 AATTGTGTACAAAATT
1 AATTGTATATACAATA
*
2181852 AATTGTATA-AAAAT-
1 AATTGTATATACAATA
*
2181866 AATTCTATATACAA
1 AATTGTATATACAA
2181880 AAAAATGTAC
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
14 19 0.32
15 10 0.17
16 18 0.31
17 12 0.20
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (16 bp):
AATTGTATATACAATA
Found at i:2181831 original size:52 final size:51
Alignment explanation
Indices: 2181704--2181839 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 51
2181694 CAAATTCTTA
* * * * *
2181704 GTATAAAATGAATTGTGTATATGCAAAAAAATTAATTGTGTATAAATTTAATT
1 GTATAAAATAAATTGTGCATA--CAAAAAAATTAATTATATATAAATTAAATT
* * **
2181757 ATATAAAATATATT-CCCAATACAAAAAGAATTAATTATATATACAA-TAAATT
1 GTATAAAATAAATTGTGC-ATACAAAAA-AATTAATTATATATA-AATTAAATT
2181809 GTATAAAATAAATTGTGCATACAAAAAAATT
1 GTATAAAATAAATTGTGCATACAAAAAAATT
2181840 GTGTACAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
51 10 0.15
52 39 0.59
53 17 0.26
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (51 bp):
GTATAAAATAAATTGTGCATACAAAAAAATTAATTATATATAAATTAAATT
Found at i:2181868 original size:14 final size:15
Alignment explanation
Indices: 2181796--2181874 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 15
2181786 ATTAATTATA
*
2181796 TATACAATA-AATTG
1 TATACAAAATAATTG
2181810 TAT--AAAATAAATTG
1 TATACAAAAT-AATTG
*
2181824 TGCATACAAAAAAATTG
1 T--ATACAAAATAATTG
*
2181841 TGTACAAAATTAATTG
1 TATACAAAA-TAATTG
*
2181857 TATA-AAAATAATTC
1 TATACAAAATAATTG
2181871 TATA
1 TATA
2181875 TACAAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
12 3 0.06
14 18 0.35
15 11 0.21
16 10 0.19
17 6 0.12
18 4 0.08
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (15 bp):
TATACAAAATAATTG
Found at i:2183427 original size:31 final size:31
Alignment explanation
Indices: 2183392--2183571 Score: 245
Period size: 31 Copynumber: 5.8 Consensus size: 31
2183382 TACCACAAAC
*
2183392 CATAACAAGTAAAAAGTTGTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* * *
2183423 CATAACAAGTAAAACGTTGTGACATGCCATT
1 CATAACAAGTAAAATGTTGTGACACGCCATG
2183454 CATAA-AGAGTAAAATGTTGTGACACGCCATG
1 CATAACA-AGTAAAATGTTGTGACACGCCATG
* * * * *
2183485 TATAACAAGCATAATGTTCTGACACGTCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
*
2183516 CATAACAAGTGAAATGTTGTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
*
2183547 CATAACAAGTAAAATGTTGTCACAC
1 CATAACAAGTAAAATGTTGTGACAC
2183572 ATTAACGCTG
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
30 1 0.01
31 126 0.98
32 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (31 bp):
CATAACAAGTAAAATGTTGTGACACGCCATG
Found at i:2185990 original size:31 final size:31
Alignment explanation
Indices: 2185761--2185986 Score: 208
Period size: 31 Copynumber: 7.3 Consensus size: 31
2185751 AATAAGGAAT
* ** * *
2185761 AAATGTTGTGAAACATCATTCATAACAAG-C
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* *
2185791 AAAATGTTGTGACACGCCATGCATAGC-ATTC
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
* * * *
2185822 AAAATGTTGTGACACACCATACATAACAAGTA
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
*
2185854 AAATGTTGTGACACGCCATGCATATTAAGT-
1 AAATGTTGTGACACGCCATGCATATCAAGTC
2185884 ATAATGTTGTGACACGCCATGCATATCAAGTC
1 A-AATGTTGTGACACGCCATGCATATCAAGTC
* * * *
2185916 AAATGTTGTCACATGCCAT-CTACATCGAGTC
1 AAATGTTGTGACACGCCATGC-ATATCAAGTC
* * *
2185947 AAATGTTTTCACACGCCATGCATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
2185978 AAATATTGT
1 AAATGTTGT
2185987 CACATGTTAA
Statistics
Matches: 164, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.02
31 157 0.96
32 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATATCAAGTC
Found at i:2186460 original size:23 final size:23
Alignment explanation
Indices: 2186433--2186548 Score: 58
Period size: 23 Copynumber: 5.0 Consensus size: 23
2186423 CTTTCTCTAT
2186433 TTCAAACCATGACGTGTCAGCTA
1 TTCAAACCATGACGTGTCAGCTA
* * *
2186456 TTCAAGCAAT-ACCGTGTCA-CACA
1 TTCAAACCATGA-CGTGTCAGC-TA
* * *
2186479 CTTTAAACCATGGCGTGTCAGCTT
1 -TTCAAACCATGACGTGTCAGCTA
* * * *
2186503 TTCAAGCAATGCCGTGTCA-CACA
1 TTCAAACCATGACGTGTCAGC-TA
* *
2186526 CTCTAAACCATGCCGTGTCAGCT
1 TTC-AAACCATGACGTGTCAGCT
2186549 TAATAAGCAA
Statistics
Matches: 66, Mismatches: 19, Indels: 15
0.66 0.19 0.15
Matches are distributed among these distances:
22 3 0.05
23 33 0.50
24 28 0.42
25 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (23 bp):
TTCAAACCATGACGTGTCAGCTA
Found at i:2186507 original size:47 final size:47
Alignment explanation
Indices: 2186436--2186591 Score: 217
Period size: 47 Copynumber: 3.3 Consensus size: 47
2186426 TCTCTATTTC
* * * *
2186436 AAACCATGACGTGTCAGCTATTCAAGCAATACCGTGTCACACACTTT
1 AAACCATGGCGTGTCAGCTTTTCAAGCAATGCCGTGTCACACACTCT
2186483 AAACCATGGCGTGTCAGCTTTTCAAGCAATGCCGTGTCACACACTCT
1 AAACCATGGCGTGTCAGCTTTTCAAGCAATGCCGTGTCACACACTCT
* * *
2186530 AAACCATGCCGTGTCAGCTTAAT-AAGCAATGCCATGTCACACACTCT
1 AAACCATGGCGTGTCAGCTT-TTCAAGCAATGCCGTGTCACACACTCT
*
2186577 AAA-CATGGTGTGTCA
1 AAACCATGGCGTGTCA
2186592 CCAACTCTGA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
46 10 0.10
47 88 0.89
48 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (47 bp):
AAACCATGGCGTGTCAGCTTTTCAAGCAATGCCGTGTCACACACTCT
Found at i:2186543 original size:24 final size:24
Alignment explanation
Indices: 2186467--2186545 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
2186457 TCAAGCAATA
2186467 CCGTGTCACACACTTTAAACCATG
1 CCGTGTCACACACTTTAAACCATG
* * * * *
2186491 GCGTGTCA-GC-TTTTCAAGCAATG
1 CCGTGTCACACACTTT-AAACCATG
*
2186514 CCGTGTCACACACTCTAAACCATG
1 CCGTGTCACACACTTTAAACCATG
2186538 CCGTGTCA
1 CCGTGTCA
2186546 GCTTAATAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 3 0.07
23 14 0.34
24 22 0.54
25 2 0.05
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (24 bp):
CCGTGTCACACACTTTAAACCATG
Found at i:2186631 original size:47 final size:47
Alignment explanation
Indices: 2186580--2186906 Score: 372
Period size: 47 Copynumber: 7.0 Consensus size: 47
2186570 ACACTCTAAA
* *
2186580 CATGGTGTGTCACCAACTCTGAACTCTGACTTGTCACA-ATTTCCCTC
1 CATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGA-TTCCCTC
* * *
2186627 CATGGCGTGTCACCAACTCTGAACTTTGGCATGTCACAGATTCCCTC
1 CATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* * * * * *
2186674 CATGGCGTCTCACCAACTTTGAACGCTGGCATGTCACAGGTTCCCTC
1 CATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* *
2186721 CATGTTC-TGTCACCAACTCTGAACTCTAACGTGTCACAGATTCCCTC
1 CATG-GCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* * * * * *
2186768 AATGGCGTCTCACCAACTCTGAACGT-TGACGTGTTATAGATTTCCAC
1 CATGGCGTGTCACCAACTCTGAAC-TCTGACGTGTCACAGATTCCCTC
* *
2186815 CATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTC
1 CATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* * * * *
2186862 CATAGCGTCTCACCAACTCTAAACGCTGACGTGTCACACATTCCC
1 CATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCC
2186907 AACATGACGT
Statistics
Matches: 236, Mismatches: 39, Indels: 10
0.83 0.14 0.04
Matches are distributed among these distances:
46 2 0.01
47 231 0.98
48 3 0.01
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (47 bp):
CATGGCGTGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
Found at i:2191259 original size:20 final size:19
Alignment explanation
Indices: 2191210--2191259 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
2191200 ATCGATACAC
*
2191210 TTTTAA-ATTATTAATTAT
1 TTTTAATATTTTTAATTAT
*
2191228 TTTTTATCATTTTTAATTACT
1 TTTTAAT-ATTTTTAATTA-T
2191249 TTTTAATATTT
1 TTTTAATATTT
2191260 ATTTTTTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
20 14 0.54
21 7 0.27
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAATATTTTTAATTAT
Found at i:2199431 original size:28 final size:28
Alignment explanation
Indices: 2199396--2199467 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
2199386 CATAAAATTT
2199396 AAAACATACCAAAGCTCATTAAAGTTGA
1 AAAACATACCAAAGCTCATTAAAGTTGA
2199424 AAAACATACCAAAGCTCATTAAAGTTGA
1 AAAACATACCAAAGCTCATTAAAGTTGA
2199452 AAAACATACCAAAGCT
1 AAAACATACCAAAGCT
2199468 GTACATGCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.51, C:0.19, G:0.10, T:0.19
Consensus pattern (28 bp):
AAAACATACCAAAGCTCATTAAAGTTGA
Found at i:2199479 original size:27 final size:27
Alignment explanation
Indices: 2199396--2199480 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 27
2199386 CATAAAATTT
* *
2199396 AAAACATACCAAAGCTCATTAAAGTTGA
1 AAAACATACCAAAGCT-AGTAAAGCTGA
* *
2199424 AAAACATACCAAAGCTCATTAAAGTTGA
1 AAAACATACCAAAGCT-AGTAAAGCTGA
*
2199452 AAAACATACCAAAGCT-GTACATGCTGA
1 AAAACATACCAAAGCTAGTA-AAGCTGA
2199479 AA
1 AA
2199481 TTTATCAGAC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 2 0.04
27 7 0.13
28 44 0.83
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAACATACCAAAGCTAGTAAAGCTGA
Found at i:2213740 original size:27 final size:28
Alignment explanation
Indices: 2213710--2213767 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
2213700 AAAAATAGAA
2213710 TAAAAAGAATAA-ATTATT-TATAAAATT
1 TAAAAAGAATAATATT-TTATATAAAATT
* *
2213737 T-AAAATATTAATATTTTATATAAAATT
1 TAAAAAGAATAATATTTTATATAAAATT
2213764 TAAA
1 TAAA
2213768 TATTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 10 0.38
27 14 0.54
28 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAAAAGAATAATATTTTATATAAAATT
Found at i:2213805 original size:15 final size:15
Alignment explanation
Indices: 2213757--2213822 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
2213747 ATATTTTATA
2213757 TAAAAT-TTAAATAT
1 TAAAATATTAAATAT
* *
2213771 TATTAATAGTAATATGAT
1 TA-AAATATTAA-AT-AT
2213789 TAAAATATTAAATAT
1 TAAAATATTAAATAT
* *
2213804 TAATATTTTAAACTAT
1 TAAAATATTAAA-TAT
2213820 TAA
1 TAA
2213823 TGTTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
14 2 0.05
15 15 0.37
16 11 0.27
17 9 0.22
18 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (15 bp):
TAAAATATTAAATAT
Found at i:2213814 original size:23 final size:24
Alignment explanation
Indices: 2213765--2213822 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
2213755 TATAAAATTT
2213765 AAATATTATTAATAGTAATATGATTA
1 AAATATTA--AATAGTAATATGATTA
* *
2213791 AAATATTAAATATTAATAT-TTTA
1 AAATATTAAATAGTAATATGATTA
*
2213814 AACTATTAA
1 AAATATTAA
2213823 TGTTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.38
24 10 0.34
26 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
AAATATTAAATAGTAATATGATTA
Found at i:2213822 original size:16 final size:15
Alignment explanation
Indices: 2213734--2213829 Score: 56
Period size: 16 Copynumber: 6.4 Consensus size: 15
2213724 TATTTATAAA
*
2213734 ATTTAAAATATTAAT
1 ATTTTAAATATTAAT
2213749 ATTTT--ATA-TAA-
1 ATTTTAAATATTAAT
* *
2213760 AATTTAAATATTATT
1 ATTTTAAATATTAAT
** *
2213775 AATAGTAATATGATTAAA
1 -ATTTTAA-AT-ATTAAT
*
2213793 ATATTAAATATTAAT
1 ATTTTAAATATTAAT
2213808 ATTTTAAACTATTAAT
1 ATTTTAAA-TATTAAT
*
2213824 GTTTTA
1 ATTTTA
2213830 TTTATTAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
11 4 0.07
12 3 0.05
13 6 0.10
14 2 0.03
15 16 0.26
16 18 0.30
17 8 0.13
18 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTTAAATATTAAT
Found at i:2213861 original size:16 final size:16
Alignment explanation
Indices: 2213825--2213862 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2213815 ACTATTAATG
2213825 TTTT-ATTTATTAAAT
1 TTTTAATTTATTAAAT
* *
2213840 TATTAATTTATTAACT
1 TTTTAATTTATTAAAT
2213856 TTTTAAT
1 TTTTAAT
2213863 GAATATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAATTTATTAAAT
Found at i:2213928 original size:14 final size:15
Alignment explanation
Indices: 2213911--2213952 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2213901 ATAATATTAA
2213911 ATTA-TAAATAAAAT
1 ATTAGTAAATAAAAT
* *
2213925 ATTATTAATTAAAAT
1 ATTAGTAAATAAAAT
*
2213940 ATTAGTAATTAAA
1 ATTAGTAAATAAA
2213953 TTATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAGTAAATAAAAT
Found at i:2213939 original size:15 final size:15
Alignment explanation
Indices: 2213919--2213961 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2213909 AAATTATAAA
2213919 TAAAATATTATTAAT
1 TAAAATATTATTAAT
*
2213934 TAAAATATTAGTAAT
1 TAAAATATTATTAAT
*
2213949 TAAATTA-TATTAA
1 TAAAATATTATTAA
2213962 AATATTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAAATATTATTAAT
Found at i:2213965 original size:25 final size:25
Alignment explanation
Indices: 2213928--2214167 Score: 79
Period size: 25 Copynumber: 9.2 Consensus size: 25
2213918 ATAAAATATT
2213928 ATTA-ATTAAAATATTAGTAATTAA
1 ATTATATTAAAATATTAGTAATTAA
*
2213952 ATTATATTAAAATATT-GATATTTAA
1 ATTATATTAAAATATTAG-TAATTAA
* * *
2213977 ATTATAAATTATTAATNATTAATTAATTATT
1 ATTAT--ATTA-AAAT-ATT-AGTAATTA-A
* * *
2214008 ATT-TATTAAATTTTTAATGAATATAA
1 ATTATATTAAAATATTAGT-AAT-TAA
* *
2214034 A--A-A-TAAAATTATTAATATTTAA
1 ATTATATTAAAA-TATTAGTAATTAA
* * *
2214056 TCATAATATATTAAATTATAAATAA--AA
1 --AT--TATATTAAAATATTAGTAATTAA
2214083 TATTATTAATTAAAATATTAGTAATTAA
1 -ATTA-T-ATTAAAATATTAGTAATTAA
*
2214111 ATTATATTAAAATATT-GATATTTAA
1 ATTATATTAAAATATTAG-TAATTAA
* * *
2214136 ATTATAATAATTAATATT-TTAATTTA
1 ATTATATTAA--AATATTAGTAATTAA
2214162 ATTATA
1 ATTATA
2214168 AATTATTAAT
Statistics
Matches: 163, Mismatches: 25, Indels: 54
0.67 0.10 0.22
Matches are distributed among these distances:
22 3 0.02
23 6 0.04
24 16 0.10
25 51 0.31
26 33 0.20
27 20 0.12
28 10 0.06
29 11 0.07
30 10 0.06
31 3 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATTATATTAAAATATTAGTAATTAA
Found at i:2214087 original size:14 final size:15
Alignment explanation
Indices: 2214070--2214111 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2214060 AATATATTAA
2214070 ATTA-TAAATAAAAT
1 ATTAGTAAATAAAAT
* *
2214084 ATTATTAATTAAAAT
1 ATTAGTAAATAAAAT
*
2214099 ATTAGTAATTAAA
1 ATTAGTAAATAAA
2214112 TTATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAGTAAATAAAAT
Found at i:2214089 original size:159 final size:161
Alignment explanation
Indices: 2213828--2214198 Score: 569
Period size: 159 Copynumber: 2.3 Consensus size: 161
2213818 ATTAATGTTT
* *
2213828 TATTT-ATTAAATTATTAATTTATTAACTTTTTAATGAATATAAAAAATAAAAATTATTAATATT
1 TATTTAATTTAATTATT-ATTTATTAAATTTTTAATGAATAT-AAAAAT-AAAATTATTAATATT
2213892 TTAATCATAATAATATTAAATTATAAATAAAATATTATTAATTAAAATATTAGTAATTAAATTAT
63 TTAATCATAATAATATTAAATTATAAATAAAATATTATTAATTAAAATATTAGTAATTAAATTAT
*
2213957 ATTAAAATATTGATATTTAAATTATAAATTATTAA
128 ATTAAAATATTGATATTTAAATTAT-AATAATTAA
2213992 TNA-TTAA-TTAATTATTATTTATTAAATTTTTAATGAATATAAAAATAAAATTATTAATA-TTT
1 T-ATTTAATTTAATTATTATTTATTAAATTTTTAATGAATATAAAAATAAAATTATTAATATTTT
2214054 AATCATAAT-ATATTAAATTATAAATAAAATATTATTAATTAAAATATTAGTAATTAAATTATAT
65 AATCATAATAATATTAAATTATAAATAAAATATTATTAATTAAAATATTAGTAATTAAATTATAT
2214118 TAAAATATTGATATTTAAATTATAATAATTAA
130 TAAAATATTGATATTTAAATTATAATAATTAA
* * * *
2214150 TATTTTAATTTAATTATAAATTATT-AATATTTAA--AAAATAAAAATAAAA
1 TA-TTTAATTTAATTATTATTTATTAAATTTTTAATGAATATAAAAATAAAA
2214199 AATAATATAT
Statistics
Matches: 195, Mismatches: 7, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
157 15 0.08
158 9 0.05
159 90 0.46
160 26 0.13
161 13 0.07
162 6 0.03
163 23 0.12
164 11 0.06
165 2 0.01
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (161 bp):
TATTTAATTTAATTATTATTTATTAAATTTTTAATGAATATAAAAATAAAATTATTAATATTTTA
ATCATAATAATATTAAATTATAAATAAAATATTATTAATTAAAATATTAGTAATTAAATTATATT
AAAATATTGATATTTAAATTATAATAATTAA
Found at i:2214098 original size:15 final size:15
Alignment explanation
Indices: 2214078--2214120 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2214068 AAATTATAAA
2214078 TAAAATATTATTAAT
1 TAAAATATTATTAAT
*
2214093 TAAAATATTAGTAAT
1 TAAAATATTATTAAT
*
2214108 TAAATTA-TATTAA
1 TAAAATATTATTAA
2214121 AATATTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAAATATTATTAAT
Found at i:2214152 original size:27 final size:27
Alignment explanation
Indices: 2214096--2214180 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
2214086 TATTAATTAA
*
2214096 AATATTAGTAA-TTAAATTATATTAA--
1 AATATTA-TAATTTAAATTATAATAATT
2214121 AATATTGAT-ATTTAAATTATAATAATT
1 AATATT-ATAATTTAAATTATAATAATT
* *
2214148 AATATTTTAATTT-AATTATAAATTATT
1 AATATTATAATTTAAATTAT-AATAATT
2214175 AATATT
1 AATATT
2214181 TAAAAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
24 1 0.02
25 20 0.39
26 8 0.16
27 22 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AATATTATAATTTAAATTATAATAATT
Found at i:2228168 original size:18 final size:19
Alignment explanation
Indices: 2228145--2228181 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
2228135 AGTGCCAGGA
2228145 ATAATT-ATGAAAAT-ATGT
1 ATAATTCAT-AAAATCATGT
2228163 ATAATTCATAAAATCATGT
1 ATAATTCATAAAATCATGT
2228182 TTACCTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
ATAATTCATAAAATCATGT
Found at i:2235327 original size:25 final size:24
Alignment explanation
Indices: 2235299--2235357 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
2235289 ACTTAAATTG
* *
2235299 AAGAAGAAAGAGAAAATTCGAATCA
1 AAGAAGAAAGAG-AAACTAGAATCA
* *
2235324 AAGAAAGCAAGAGAAACTAGAATCG
1 AAG-AAGAAAGAGAAACTAGAATCA
2235349 AAGAAGAAA
1 AAGAAGAAA
2235358 AAGGAAGCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 5 0.18
25 15 0.54
26 8 0.29
ACGTcount: A:0.61, C:0.08, G:0.22, T:0.08
Consensus pattern (24 bp):
AAGAAGAAAGAGAAACTAGAATCA
Found at i:2236738 original size:502 final size:499
Alignment explanation
Indices: 2235792--2236871 Score: 1301
Period size: 502 Copynumber: 2.1 Consensus size: 499
2235782 CCAATGGCAC
* *
2235792 GATGAGTTGGC-CATTTCCATATGCTCTCCAATGCTGGTAATGACTGCAGCTCCAACCTTCTTAA
1 GATGAGTTGGCTC-TTTCCATATACTCTCCAATGCTGGTAATGA-TGCAGCTCCAAACTTCTTAA
*
2235856 ATTTGAGAGTGGTACTGTCTGATTTACCTCACATAAAGAAAAATATAAAATTTATTAATTAATAA
64 ATTTGAGAATGGTA-TGTCTGATTTACCTCACATAAAGAAAAATATAAAATTTATTAATTAATAA
* * * *
2235921 ATATTGAAAATGAATTCTTTATACTTGATCTTAATTATTCAAAAGAAATACATTTTGTTAAACAA
128 ATATTGAAAATGAAGTC----TACTTGATATTAAATATTCAAAAGAAATA-ATATTGTTAAACAA
* * * **
2235986 AAGTAGAAAGAAGTATTAAAAGTTAATAATTTAAAAGGATTAGATGATAATTATTTATATATTTG
188 AAGTAGAAAGAAGTATTAAAAGTCAATAATGTAAAAGGATTAGATGACAATTATTTATATATTAA
*
2236051 ATAATTAAAAAAAATCATCAGAAAAACAATATACAAGAGCATTATTAAAGGAAAAATGGAGAGAT
253 ATAATTAAAAAAAATAATCAGAAAAACAATATACAAGAGCATTATTAAAGGAAAAATGGAGAGAT
* * *
2236116 AAGAGTTACCTCTAGCTCGGCCATTTCTTTGTCCAAAGGAAAGACTTGCTCTAAATTTTTGCATA
318 AAGAGGTACCTCTAGCTCGGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAAATTTTTGCATA
* *
2236181 AAGATATCCGAAGTTTCTCTAGATGCAATAGACTTTGAGCAAGGTAAGATGAGAAGATAGATTTC
383 AAGATATCCGAAGTTTCTCTAGATGCAACAGACTTTGAGCAAGGCAAGATGAGAAGATAGATTTC
* * * * * **
2236246 ACTTTATCACAACCTTGAATTTTTATTTTCTTTAGACTCTGTAGGCTTACAT
448 ACTTTATCACAACCATGAATTGTTACTTCCTTCAGACTCTGTAACCTTACAT
2236298 GATGAGTTGGCTCTTTCCATATACTCTCCAATGCTGGTAATGATTGCAGCTCCAAACTTCTTAAA
1 GATGAGTTGGCTCTTTCCATATACTCTCCAATGCTGGTAATGA-TGCAGCTCCAAACTTCTTAAA
* * ** *
2236363 TTTGATAATGGT-TGTACTTGATTTTCCTGGCATAAAG-AAAATATATAATGTT-TTAATTAATA
65 TTTGAGAATGGTATGT-C-TGATTTACCTCACATAAAGAAAAATATAAAAT-TTATTAATTAATA
* * ** *
2236425 AATATTGAAATATGAAGTC-A-TTG-TATTAAATATTGAGAAGGCAT-ATATT-TTAAA-AAATG
127 AATATTGAAA-ATGAAGTCTACTTGATATTAAATATTCAAAAGAAATAATATTGTTAAACAAAAG
* *
2236484 TA-AAAGTAAGTGTTAAAAGTCAATAA-GTACGAAA-GATTATAT-AGCAATTATTTATATATTA
191 TAGAAAG-AAGTATTAAAAGTCAATAATGTA--AAAGGATTAGATGA-CAATTATTTATATATTA
* * **
2236545 AATAATTCAATAAAATGAAAGATAATTAGAAAAAGAATATATGAGAGCATTATTAAAGGAAAAAT
252 AATAA-T---TAAAA--AAA-ATAATCAGAAAAACAATATACAAGAGCATTATTAAAGGAAAAAT
* **
2236610 GGAGAGATAAGAGGTACCTCTAGGTTTGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCT-AATT
310 GGAGAGATAAGAGGTACCTCTAGCTCGGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAAATT
** ** *
2236674 TTTCGCATTTAGATATCTTAAGTGTT-TCTAGATGCAACAGACTTTGAGCAAGGCAAGGTGAGAA
375 TTT-GCATAAAGATATCCGAAGT-TTCTCTAGATGCAACAGACTTTGAGCAAGGCAAGATGAGAA
* *
2236738 GATAGATTTCAGTTTATCACAACCATGAATTGTTACTTCCTTCAGACTTTGTAACCTTACAT
438 GATAGATTTCACTTTATCACAACCATGAATTGTTACTTCCTTCAGACTCTGTAACCTTACAT
* * * *
2236800 GATGAGTTGGCTCTTTCCATATATTCTCTAATGCTGGCAATGACGTCAGCTCCAAACTTCTTAAA
1 GATGAGTTGGCTCTTTCCATATACTCTCCAATGCTGGTAATGATG-CAGCTCCAAACTTCTTAAA
*
2236865 TTGGAGA
65 TTTGAGA
2236872 TCGTCCACAT
Statistics
Matches: 497, Mismatches: 58, Indels: 42
0.83 0.10 0.07
Matches are distributed among these distances:
494 7 0.01
495 49 0.10
496 9 0.02
497 4 0.01
499 20 0.04
500 3 0.01
501 12 0.02
502 260 0.52
503 2 0.00
504 3 0.01
505 32 0.06
506 95 0.19
507 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (499 bp):
GATGAGTTGGCTCTTTCCATATACTCTCCAATGCTGGTAATGATGCAGCTCCAAACTTCTTAAAT
TTGAGAATGGTATGTCTGATTTACCTCACATAAAGAAAAATATAAAATTTATTAATTAATAAATA
TTGAAAATGAAGTCTACTTGATATTAAATATTCAAAAGAAATAATATTGTTAAACAAAAGTAGAA
AGAAGTATTAAAAGTCAATAATGTAAAAGGATTAGATGACAATTATTTATATATTAAATAATTAA
AAAAAATAATCAGAAAAACAATATACAAGAGCATTATTAAAGGAAAAATGGAGAGATAAGAGGTA
CCTCTAGCTCGGCCATTTCTTTGTCAAAAGCAAAGACTTGCTCTAAATTTTTGCATAAAGATATC
CGAAGTTTCTCTAGATGCAACAGACTTTGAGCAAGGCAAGATGAGAAGATAGATTTCACTTTATC
ACAACCATGAATTGTTACTTCCTTCAGACTCTGTAACCTTACAT
Found at i:2237670 original size:2 final size:2
Alignment explanation
Indices: 2237663--2237691 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2237653 AAGCTCATGC
2237663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2237692 GTTCGTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2242774 original size:29 final size:29
Alignment explanation
Indices: 2242741--2242799 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2242731 GTGATATGAA
2242741 TGAAGTGACCATCCAGAGATATTCCATTC
1 TGAAGTGACCATCCAGAGATATTCCATTC
* *
2242770 TGAAGTGACTATCCAGAGATATTGCATTC
1 TGAAGTGACCATCCAGAGATATTCCATTC
2242799 T
1 T
2242800 ATCTTTTCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (29 bp):
TGAAGTGACCATCCAGAGATATTCCATTC
Found at i:2261507 original size:24 final size:24
Alignment explanation
Indices: 2261475--2261523 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2261465 ATGACTGGAT
*
2261475 ATTATCTTCCTTCAAATAATCATA
1 ATTACCTTCCTTCAAATAATCATA
2261499 ATTACCTTCCTTCAAATAATCATA
1 ATTACCTTCCTTCAAATAATCATA
2261523 A
1 A
2261524 CTAAGCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTACCTTCCTTCAAATAATCATA
Found at i:2272028 original size:13 final size:13
Alignment explanation
Indices: 2272010--2272034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2272000 TTTTAGAAAA
2272010 TTTATAAAATCAT
1 TTTATAAAATCAT
2272023 TTTATAAAATCA
1 TTTATAAAATCA
2272035 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:2279102 original size:15 final size:14
Alignment explanation
Indices: 2279079--2279130 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
2279069 AACAGTATTC
*
2279079 AATAATTTAAATATT
1 AATATTTTAAA-ATT
2279094 AATATTTT-AAATT
1 AATATTTTAAAATT
*
2279107 AATTTTTTTAAAATT
1 AA-TATTTTAAAATT
2279122 AAATATTTT
1 -AATATTTT
2279131 TATTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 17 0.55
16 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTTTAAAATT
Found at i:2282094 original size:83 final size:83
Alignment explanation
Indices: 2282007--2282164 Score: 235
Period size: 83 Copynumber: 1.9 Consensus size: 83
2281997 ACTATAACAT
* * *
2282007 TTTTTTCAACATGGCGTGTAACAACTTTTTTTAACCATGACATATAACATGTTTTTGCATATGGC
1 TTTTTTCAACATGGCGTGTAACAACCTTTTTTAACCATAACATATAACATATTTTTGCATATGGC
*
2282072 ATGTATCAACAATAATTA
66 ATGTAACAACAATAATTA
* * * *
2282090 TTTTTTCAACATTGCGTGTAACAACCTTTTTTAACCATAACCTATAATATATTTTTGTATATGGC
1 TTTTTTCAACATGGCGTGTAACAACCTTTTTTAACCATAACATATAACATATTTTTGCATATGGC
*
2282155 GTGTAACAAC
66 ATGTAACAAC
2282165 CTTTTTTAAC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (83 bp):
TTTTTTCAACATGGCGTGTAACAACCTTTTTTAACCATAACATATAACATATTTTTGCATATGGC
ATGTAACAACAATAATTA
Found at i:2282145 original size:50 final size:50
Alignment explanation
Indices: 2282083--2282177 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
2282073 TGTATCAACA
*
2282083 ATAATTATTTTTTCAACATTGCGTGTAACAACCTTTTTTAACCATAACCT
1 ATAATTATTTTTTCAACATGGCGTGTAACAACCTTTTTTAACCATAACCT
*
2282133 ATAATATATTTTTGT--ATATGGCGTGTAACAACCTTTTTTAACCAT
1 ATAAT-TATTTTT-TCAACATGGCGTGTAACAACCTTTTTTAACCAT
2282178 GACGTGTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
50 33 0.80
51 7 0.17
52 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (50 bp):
ATAATTATTTTTTCAACATGGCGTGTAACAACCTTTTTTAACCATAACCT
Found at i:2282154 original size:133 final size:133
Alignment explanation
Indices: 2282017--2282256 Score: 381
Period size: 133 Copynumber: 1.8 Consensus size: 133
2282007 TTTTTTCAAC
* * * *
2282017 ATGGCGTGTAACAACTTTTTTTAACCATGACATATAACATGTTTTTGCATATGGCATGTATCAAC
1 ATGGCGTGTAACAACCTTTTTTAACCATGACATATAACATGTTTTTGCACATGACATGTAACAAC
* *
2282082 AATAATTATTTTTTCAACATTGCGTGTAACAACCTTTTTTAACCATAACCTATAATATATTTTTG
66 AATAATTATTTTTTCAACATGGCATGTAACAACCTTTTTTAACCATAACCTATAATATATTTTTG
2282147 TAT
131 TAT
* * *
2282150 ATGGCGTGTAACAACCTTTTTTAACCATGACGTGTAACATGTTTTTGTACATGACATGTAACAAC
1 ATGGCGTGTAACAACCTTTTTTAACCATGACATATAACATGTTTTTGCACATGACATGTAACAAC
* *
2282215 AATAATTTTTTTTTCAACATGGCATGTAACAACTTTTTTTAA
66 AATAATTATTTTTTCAACATGGCATGTAACAACCTTTTTTAA
2282257 TTATGACGTG
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 96 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (133 bp):
ATGGCGTGTAACAACCTTTTTTAACCATGACATATAACATGTTTTTGCACATGACATGTAACAAC
AATAATTATTTTTTCAACATGGCATGTAACAACCTTTTTTAACCATAACCTATAATATATTTTTG
TAT
Found at i:2282183 original size:26 final size:26
Alignment explanation
Indices: 2282104--2282188 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
2282094 TTCAACATTG
*
2282104 CGTGTAACAACCTTTTTTAACCATAA
1 CGTGTAACAACCTTTTTTAACCATGA
* * * * *
2282130 CCTATAATATA--TTTTTGT-A-TATGG
1 CGTGTAACA-ACCTTTTT-TAACCATGA
2282154 CGTGTAACAACCTTTTTTAACCATGA
1 CGTGTAACAACCTTTTTTAACCATGA
2282180 CGTGTAACA
1 CGTGTAACA
2282189 TGTTTTTGTA
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
23 1 0.02
24 9 0.21
25 12 0.29
26 19 0.45
27 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (26 bp):
CGTGTAACAACCTTTTTTAACCATGA
Found at i:2282195 original size:50 final size:50
Alignment explanation
Indices: 2282098--2282214 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
2282088 TATTTTTTCA
* *
2282098 ACATTGCGTGTAACAACCTTTTTTAACCATAACCTATAATATATTTTTGT
1 ACATGGCGTGTAACAACCTTTTTTAACCATAACCTATAACATATTTTTGT
* * * * *
2282148 ATATGGCGTGTAACAACCTTTTTTAACCATGACGTGTAACATGTTTTTGT
1 ACATGGCGTGTAACAACCTTTTTTAACCATAACCTATAACATATTTTTGT
* *
2282198 ACATGACATGTAACAAC
1 ACATGGCGTGTAACAAC
2282215 AATAATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.38
Consensus pattern (50 bp):
ACATGGCGTGTAACAACCTTTTTTAACCATAACCTATAACATATTTTTGT
Found at i:2282292 original size:133 final size:133
Alignment explanation
Indices: 2282015--2282293 Score: 369
Period size: 133 Copynumber: 2.1 Consensus size: 133
2282005 ATTTTTTTCA
* * * *
2282015 ACATGGCGTGTAACAACTTTTTTTAACCATGACATATAACATGTTTTTGCATATGGCATGTATCA
1 ACATGGCGTGTAACAACCTTTTTTAACCATGACATATAACATGTTTTTGCACATGACATGTAACA
* * * *
2282080 ACAATAATTATTTTTTCAACATTGCGTGTAACAACCTTTTTTAACCATAACCTATAATATATTTT
66 ACAATAATTATTTTTTCAACATGGCATGTAACAACCTTTTTTAACCATAACCTATAACATAATTT
2282145 TGT
131 TGT
* * * *
2282148 ATATGGCGTGTAACAACCTTTTTTAACCATGACGTGTAACATGTTTTTGTACATGACATGTAACA
1 ACATGGCGTGTAACAACCTTTTTTAACCATGACATATAACATGTTTTTGCACATGACATGTAACA
* * ** * * *
2282213 ACAATAATTTTTTTTTCAACATGGCATGTAACAACTTTTTTTAATTATGACGTGTAACATAATTT
66 ACAATAATTATTTTTTCAACATGGCATGTAACAACCTTTTTTAACCATAACCTATAACATAATTT
2282278 TGT
131 TGT
* *
2282281 ACGTGGTGTGTAA
1 ACATGGCGTGTAA
2282294 TATCATGGGG
Statistics
Matches: 124, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
133 124 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (133 bp):
ACATGGCGTGTAACAACCTTTTTTAACCATGACATATAACATGTTTTTGCACATGACATGTAACA
ACAATAATTATTTTTTCAACATGGCATGTAACAACCTTTTTTAACCATAACCTATAACATAATTT
TGT
Found at i:2287850 original size:34 final size:34
Alignment explanation
Indices: 2287807--2287908 Score: 195
Period size: 34 Copynumber: 3.0 Consensus size: 34
2287797 ATAGTGAATC
*
2287807 AAAGGAAAGAGCCTAACTTCCCCTGCCTCGCTTT
1 AAAGGAAAGAGCCTAACTTCCCCTGCCCCGCTTT
2287841 AAAGGAAAGAGCCTAACTTCCCCTGCCCCGCTTT
1 AAAGGAAAGAGCCTAACTTCCCCTGCCCCGCTTT
2287875 AAAGGAAAGAGCCTAACTTCCCCTGCCCCGCTTT
1 AAAGGAAAGAGCCTAACTTCCCCTGCCCCGCTTT
2287909 TGTAGGATCA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (34 bp):
AAAGGAAAGAGCCTAACTTCCCCTGCCCCGCTTT
Found at i:2289179 original size:22 final size:22
Alignment explanation
Indices: 2289133--2289179 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2289123 AATAAAGAAA
*
2289133 AATAAAAATTATACTAATATTTT
1 AATAAAAATTATA-TAAAATTTT
2289156 AATAATAAATTAT-TAAAATTTT
1 AATAA-AAATTATATAAAATTTT
2289178 AA
1 AA
2289180 ATTTTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 5 0.23
24 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAAAAATTATATAAAATTTT
Found at i:2289756 original size:15 final size:15
Alignment explanation
Indices: 2289736--2289770 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2289726 CTGTTATGTG
* *
2289736 AATTTTATTTTTTAT
1 AATTTTAATTTTTAA
2289751 AATTTTAATTTTTAA
1 AATTTTAATTTTTAA
2289766 AATTT
1 AATTT
2289771 AATAAATTAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTAATTTTTAA
Found at i:2291550 original size:23 final size:23
Alignment explanation
Indices: 2291495--2291555 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2291485 GTGAAATACG
*
2291495 TTTGTTGAAACACAATAAACACA
1 TTTGTTAAAACACAATAAACACA
* * ** *
2291518 TTTATAAAAACACAATAGCCATA
1 TTTGTTAAAACACAATAAACACA
2291541 TTTGTTAAAACACAA
1 TTTGTTAAAACACAA
2291556 CAGGCACAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (23 bp):
TTTGTTAAAACACAATAAACACA
Found at i:2299988 original size:17 final size:16
Alignment explanation
Indices: 2299961--2299992 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2299951 CATTTCCTGT
2299961 CTTCTTTTTGCTTACC
1 CTTCTTTTTGCTTACC
2299977 CTTCTATTTTGCTTAC
1 CTTCT-TTTTGCTTAC
2299993 AACATTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.28, G:0.06, T:0.56
Consensus pattern (16 bp):
CTTCTTTTTGCTTACC
Found at i:2300669 original size:17 final size:17
Alignment explanation
Indices: 2300647--2300690 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2300637 AATTAATTAT
2300647 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
*
2300664 ATTAAAAAAATATAAAA
1 ATTAAAAATATATAAAA
*
2300681 GTTAAAAATA
1 ATTAAAAATA
2300691 ATTAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:2317996 original size:20 final size:20
Alignment explanation
Indices: 2317951--2317988 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2317941 TTTTGGCCCC
2317951 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
2317971 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
2317989 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:2319231 original size:13 final size:13
Alignment explanation
Indices: 2319213--2319237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2319203 AGAGAAATTG
2319213 TGATTTTATAAAA
1 TGATTTTATAAAA
2319226 TGATTTTATAAA
1 TGATTTTATAAA
2319238 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:2321386 original size:68 final size:70
Alignment explanation
Indices: 2321277--2321434 Score: 257
Period size: 70 Copynumber: 2.3 Consensus size: 70
2321267 CCAACATTCA
*
2321277 GAAAAATATTGGCAACGTGGTGATTAATAATCAATTGATTA-T-TAATAACAGTAGGCGTAGGAC
1 GAAAAATATTGGCAACTTGGTGATTAATAATCAATTGATTATTATAATAACAGTAGGCGTAGGAC
2321340 ATACC
66 ATACC
* * **
2321345 GAAAAATATTGCCAACTTGGTGATTAATAATCAATTGATTATTATAATAAGAGTAGGTTTAGGAC
1 GAAAAATATTGGCAACTTGGTGATTAATAATCAATTGATTATTATAATAACAGTAGGCGTAGGAC
2321410 ATACC
66 ATACC
2321415 GAAAAATATTGGCAACTTGG
1 GAAAAATATTGGCAACTTGG
2321435 GTCAACGTCG
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
68 39 0.48
69 1 0.01
70 42 0.51
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.30
Consensus pattern (70 bp):
GAAAAATATTGGCAACTTGGTGATTAATAATCAATTGATTATTATAATAACAGTAGGCGTAGGAC
ATACC
Found at i:2324212 original size:70 final size:68
Alignment explanation
Indices: 2324087--2324227 Score: 219
Period size: 70 Copynumber: 2.0 Consensus size: 68
2324077 GTTGGGAACG
2324087 TGGTGATTAATAATCAATTGATTATTAATAAGAGTAGGCGTAGGACATATCGAAAAATATTGCCA
1 TGGTGATTAATAATCAATTGATTATTAATAAGAGTAGGCGTAGGACATATCGAAAAATATTGCCA
2324152 ACT
66 ACT
* * ** *
2324155 TGGTGATTAATAATCAATTGATTGTTATAATAGGAGTAGGTTTAGGACATATCGAAAAATATTGG
1 TGGTGATTAATAATCAATTGATT-AT-TAATAAGAGTAGGCGTAGGACATATCGAAAAATATTGC
2324220 CAACT
64 CAACT
2324225 TGG
1 TGG
2324228 GTCAACGTCG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 23 0.35
69 1 0.02
70 42 0.64
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (68 bp):
TGGTGATTAATAATCAATTGATTATTAATAAGAGTAGGCGTAGGACATATCGAAAAATATTGCCA
ACT
Found at i:2333280 original size:18 final size:18
Alignment explanation
Indices: 2333257--2333295 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2333247 TAATATTTCT
*
2333257 TTAATAATTTTTGATTCA
1 TTAATAATTTATGATTCA
2333275 TTAATAATTTATGATTCA
1 TTAATAATTTATGATTCA
2333293 TTA
1 TTA
2333296 TTTTTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
TTAATAATTTATGATTCA
Found at i:2333423 original size:57 final size:57
Alignment explanation
Indices: 2333331--2333438 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 57
2333321 TAGCACTGAG
* * *
2333331 AAAAATATTGGCAACTTGGTGATTAGTAATCAATTGATTATTAATAAGAGTTTGGAA
1 AAAAATATTGGCAACTCGGTGATGAATAATCAATTGATTATTAATAAGAGTTTGGAA
* *
2333388 AAAAATATTGGCAACTCGGTGGTGAATAATGAATTGATTATTAATAAGAGT
1 AAAAATATTGGCAACTCGGTGATGAATAATCAATTGATTATTAATAAGAGT
2333439 AGGTGTAGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (57 bp):
AAAAATATTGGCAACTCGGTGATGAATAATCAATTGATTATTAATAAGAGTTTGGAA
Found at i:2335905 original size:42 final size:43
Alignment explanation
Indices: 2335826--2335924 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
2335816 TTAATGCCTA
2335826 TGGCATAGGTCATAATCATAACAGAAACCACAATTAACCCCAG
1 TGGCATAGGTCATAATCATAACAGAAACCACAATTAACCCCAG
* * * * *
2335869 TGGTATAGGTCATTATCATATC-GAAACCACAATTAACGCTAG
1 TGGCATAGGTCATAATCATAACAGAAACCACAATTAACCCCAG
*
2335911 TGGCATGGGTCATA
1 TGGCATAGGTCATA
2335925 GGTATATCAG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 29 0.60
43 19 0.40
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (43 bp):
TGGCATAGGTCATAATCATAACAGAAACCACAATTAACCCCAG
Found at i:2339139 original size:577 final size:561
Alignment explanation
Indices: 2338060--2339198 Score: 2055
Period size: 577 Copynumber: 2.0 Consensus size: 561
2338050 TTTGTAACAG
2338060 TTGGTATCAGAGCAGACTCTGAGTACTAGCAATGTGCCACTAAGGATAGTAGGCCCTTGTTGAAG
1 TTGGTATCAGAGCAGACTCTGAGTACTAGCAATGTGCCACTAAGGATAGTAGGCCCTTGTTGAAG
* * *
2338125 TGGGGGAAGATGTCACGGTCCTCGTCTGGATGTGAATCCCACATCGTCAAGATAATGCTCCCTAG
66 TGGGGGAAGATGTCACAGTCCTCGTCTGGATGTGAATCCCACATCATCAAGATAATGCTCCCAAG
* **
2338190 TGAGTTGAGCTAGGGAGAAACTCCTAGTGGGGAGTAAGGGAGAATGTCGTAGTCCTAGAGAGAGA
131 TGAGCTGAGCTAAAGAGAAACTCCTAGTGGGGAGTAAGGGAGAATGTCGTAGTCCTAGAGAGAGA
2338255 AGTCATAAATCTCACATCGACTATCTACTGGAGTGATACTGGGAGTATAAGAATTTACACCACCT
196 AGTCATAAATCTCACATCGACTATCTACTGGAGTGATACTGGGAGTATAAGAATTTACACCACCT
2338320 TCAACCTATGAGGTGCTTTTTGCAGGACAAAACCGTGAGGACAACAAGCCAAAGTGGACAATACC
261 TCAACCTATGAGGTGCTTTTTGCAGGACAAAACCGTGAGGACAACAAGCCAAAGTGGACAATACC
2338385 TCACAGGGGTTAGTGTGGACCGTGACACCTTTGACAAAATTTTAATTCTACTAATCGAGTTAAAA
326 TCACAGGGGTTAGTGTGGACCGTGACACCTTTGACAAAATTTTAATTCTACTAATCGAGTTAAAA
2338450 ACTCACCGAGGATGTGTAGAATAATAGTCCTGAAAATAATCCCTTTGTTTTTACAATCGAGGGAC
391 ACTCACCGAGGATGTGTAGAATAATAGTCCTGAAAATAATCCCTTTGTTTTTACAATCGAGGGAC
2338515 ATTGATCTTTACATGCATTAGTAATGAAGATTTGTTGCTTTTCCTCCTAGCATTTTGTGCTTAAT
456 ATTGATCTTTACATGCATTAGTAATGAAGATTTGTTGCTTTTCCTCCTAGCATTTTGTGCTTAAT
2338580 TACATGCTTTTGTTCGACTTATATATATATATATAGTATATA
521 TACATGCTTTTGTTCGACTTATATATATATATATA-TATATA
*
2338622 NTTGGTATCAGAGCAGACTTTGAGTACTAGCAATGTGCCACTAAGGATAGTAGGCCCTTGTTGAA
1 -TTGGTATCAGAGCAGACTCTGAGTACTAGCAATGTGCCACTAAGGATAGTAGGCCCTTGTTGAA
2338687 GTGGGGGAAGATGTCACAGTCCTCG-CATGGATGTGAATCCCACATCATCAAGATAATGCTCCTA
65 GTGGGGGAAGATGTCACAGTCCTCGTC-TGGATGTGAATCCCACATCATCAAGATAATGCTCC--
2338751 GCAAGTTGAGCTGCAAAGTCCCACATCAAAGAGAAACTCCTAGTGGGGAGTAAGGGAGAATGTCG
127 -CAAG-TGAGCTG---AG-----C-T-AAAGAGAAACTCCTAGTGGGGAGTAAGGGAGAATGTCG
2338816 TAGTCCTAGAGAGAGAAGTCATAAATCTCACATCGACTATCTACTGGAGTGATACTGGGAGTATA
180 TAGTCCTAGAGAGAGAAGTCATAAATCTCACATCGACTATCTACTGGAGTGATACTGGGAGTATA
2338881 AGAATTTACACCACCTTCAACCTATGAGGTGCTTTTTGCAGGACAAAACCGTGAGGACAACAAGC
245 AGAATTTACACCACCTTCAACCTATGAGGTGCTTTTTGCAGGACAAAACCGTGAGGACAACAAGC
2338946 CAAAGTGGACAATACCTCACAGGGGTTAGTGTGGACCGTGACACCTTTGACAAAATTTTAATTCT
310 CAAAGTGGACAATACCTCACAGGGGTTAGTGTGGACCGTGACACCTTTGACAAAATTTTAATTCT
2339011 ACTAATCGAGTTAAAAACTCACCGAGGATGTGTAGAATAATAGTCCTGAAAATAATCCCTTTGTT
375 ACTAATCGAGTTAAAAACTCACCGAGGATGTGTAGAATAATAGTCCTGAAAATAATCCCTTTGTT
2339076 TTTACAATCGAGGGACATTGATCTTTACATGCATTAGTAATGAAGATTTGTTGCTTTTCCTCCTA
440 TTTACAATCGAGGGACATTGATCTTTACATGCATTAGTAATGAAGATTTGTTGCTTTTCCTCCTA
2339141 GCATTTTGTGCTTAATTACATGCTTTTGTTCGACTTATATATATATATATATATATA
505 GCATTTTGTGCTTAATTACATGCTTTTGTTCGACTTATATATATATATATATATATA
2339198 T
1 T
2339199 ATATATATAT
Statistics
Matches: 554, Mismatches: 7, Indels: 18
0.96 0.01 0.03
Matches are distributed among these distances:
562 1 0.00
563 121 0.22
566 3 0.01
567 6 0.01
570 2 0.00
575 2 0.00
576 7 0.01
577 412 0.74
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (561 bp):
TTGGTATCAGAGCAGACTCTGAGTACTAGCAATGTGCCACTAAGGATAGTAGGCCCTTGTTGAAG
TGGGGGAAGATGTCACAGTCCTCGTCTGGATGTGAATCCCACATCATCAAGATAATGCTCCCAAG
TGAGCTGAGCTAAAGAGAAACTCCTAGTGGGGAGTAAGGGAGAATGTCGTAGTCCTAGAGAGAGA
AGTCATAAATCTCACATCGACTATCTACTGGAGTGATACTGGGAGTATAAGAATTTACACCACCT
TCAACCTATGAGGTGCTTTTTGCAGGACAAAACCGTGAGGACAACAAGCCAAAGTGGACAATACC
TCACAGGGGTTAGTGTGGACCGTGACACCTTTGACAAAATTTTAATTCTACTAATCGAGTTAAAA
ACTCACCGAGGATGTGTAGAATAATAGTCCTGAAAATAATCCCTTTGTTTTTACAATCGAGGGAC
ATTGATCTTTACATGCATTAGTAATGAAGATTTGTTGCTTTTCCTCCTAGCATTTTGTGCTTAAT
TACATGCTTTTGTTCGACTTATATATATATATATATATATA
Found at i:2339183 original size:2 final size:2
Alignment explanation
Indices: 2339176--2339216 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2339166 TTGTTCGACT
*
2339176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2339217 GCTTTCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2342665 original size:70 final size:68
Alignment explanation
Indices: 2342582--2342712 Score: 199
Period size: 70 Copynumber: 1.9 Consensus size: 68
2342572 TAAACTATTG
* * *
2342582 GAAAAATATTGGCAACGTGGTGATTAATAATCAATTGATTATCATAATAAGAGTAGGTGTAGGAC
1 GAAAAATATTGGCAACGTGGTGATCAAAAATCAATTGATCAT--TAATAAGAGTAGGTGTAGGAC
2342647 ATATC
64 ATATC
* *
2342652 GAAAAATATTGGCAACTTGGTGATCAAAAATGAATTGATCATTAATAAGAGTAGGTGTAGG
1 GAAAAATATTGGCAACGTGGTGATCAAAAATCAATTGATCATTAATAAGAGTAGGTGTAGG
2342713 GTTAGGACGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 19 0.34
70 37 0.66
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (68 bp):
GAAAAATATTGGCAACGTGGTGATCAAAAATCAATTGATCATTAATAAGAGTAGGTGTAGGACAT
ATC
Found at i:2346212 original size:23 final size:23
Alignment explanation
Indices: 2346186--2346231 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2346176 ATACAATAAC
*
2346186 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
2346209 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
2346232 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:2370163 original size:27 final size:27
Alignment explanation
Indices: 2370133--2370185 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2370123 ATATAGAGGA
2370133 AATAAAGAAGATTATCATGAATCTTTT
1 AATAAAGAAGATTATCATGAATCTTTT
* *
2370160 AATAAGGAAGATTATCCTGAATCTTT
1 AATAAAGAAGATTATCATGAATCTTT
2370186 AAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (27 bp):
AATAAAGAAGATTATCATGAATCTTTT
Found at i:2372304 original size:18 final size:18
Alignment explanation
Indices: 2372281--2372319 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2372271 ATAATAAAAA
* *
2372281 TAATGAATTAGAAATTAT
1 TAATGAATAAAAAATTAT
2372299 TAATGAATAAAAAATTAT
1 TAATGAATAAAAAATTAT
2372317 TAA
1 TAA
2372320 AGAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (18 bp):
TAATGAATAAAAAATTAT
Found at i:2373550 original size:2 final size:2
Alignment explanation
Indices: 2373543--2373592 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2373533 GATGGTGTCT
*
2373543 CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2373585 CA CA CA CA
1 CA CA CA CA
2373593 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:2373597 original size:2 final size:2
Alignment explanation
Indices: 2373592--2373631 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2373582 ACACACACAC
* * *
2373592 AT AT AT AT AT AT AT AT AT AT AT NT GT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2373632 GACTGAATAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2374047 original size:21 final size:21
Alignment explanation
Indices: 2374007--2374047 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2373997 AAAAAACTTT
*
2374007 AAAAATTTTATATAATATGGA
1 AAAAATTTTATAAAATATGGA
2374028 AAAAATTTTA-AAAATCATGG
1 AAAAATTTTATAAAAT-ATGG
2374048 CCCCCATCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (21 bp):
AAAAATTTTATAAAATATGGA
Found at i:2383886 original size:70 final size:68
Alignment explanation
Indices: 2383773--2383931 Score: 228
Period size: 70 Copynumber: 2.3 Consensus size: 68
2383763 CGATGTTGAC
2383773 CCAAGTTGCCAATATTTTTCGATATGTCCTAAACCTACTCTTATTATAATAATCAATTGATTATT
1 CCAAGTTGCCAATATTTTTCGATATGTCCTAAACCTACTCTTA-T-TAATAATCAATTGATTATT
2383838 AATCA
64 AATCA
** ** *
2383843 CCAAGTTGGTAATATTTTTCGATATGTCCTACGCCTACTCTTATTAATAATGAATTGATTATTAA
1 CCAAGTTGCCAATATTTTTCGATATGTCCTAAACCTACTCTTATTAATAATCAATTGATTATTAA
2383908 TCA
66 TCA
* *
2383911 CCACGATTGCCAACATTTTTC
1 CCAAG-TTGCCAATATTTTTC
2383932 TCAATGCTGG
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
68 27 0.34
69 13 0.16
70 39 0.49
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (68 bp):
CCAAGTTGCCAATATTTTTCGATATGTCCTAAACCTACTCTTATTAATAATCAATTGATTATTAA
TCA
Found at i:2391180 original size:514 final size:508
Alignment explanation
Indices: 2390002--2391399 Score: 1694
Period size: 514 Copynumber: 2.7 Consensus size: 508
2389992 AAAATAGCTA
* * *
2390002 CTCACGTTGCCTTGCTCAAAGTGTGATGCATCTAGAACAACTCAAGATATCTACATAC-AGTAAA
1 CTCACCTTGCCTTGCTCAAAGTCTGATGCATCTAGAACAACTCAAGATATCT-CATGCAAG-AAA
* * **
2390066 TTAGAACACGTCTTTGCGTTTGCCAAAGAAATGGTTGAGCAAGAGGTACCTCTTCTCTCTCCATT
64 TTAGAACAAGTCTTTGCTTTTGCCAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATT
* * * *
2390131 TTTCCTTCAATAATGCTCTCATCTGTTCTTTATTTAATCAT-TTTCTTTGTTAAATTATCAAATA
129 TTTCCTTTAATAATGCTATCATCTATTCTTTATCTAATCATGTTT-TTTGTTAAATTATCAAATA
*
2390195 TATAAATAATT-GCTATCTAAT-TCTTCTAAATTATTGACTTTTAACACTTCTTTTTTTTTTGAA
193 TATAAATAATTAG-TATCTAATCT-TTCTAAATTATTGACTTTTAACA---C-TTTCTTTTT-AA
* *
2390258 -ATTTTTTTAAAAAATGCATTTCTTTCTCAATATTTAAATACTTTTTTATCAAGTACAATAAATT
251 CATTTTTTTAAAAAATGCATGTC-TTCTC-A-A--T-AAT--TTTTTGATCAAGTACAATAAATT
* * * * ** * *
2390322 CATATTTTAGTATTTATTAATTAATATATTTTATATTTTTCTTTATAAGTGGAAAATCAATAGCT
308 TATAATTCAGTATTTATTAATTAATAAATTTTATATTTTT-TTTATTTGAGGAAAATCAACAGCT
* *
2390387 TAACGTTCAAATTTAACTTGTTTGAAGTAGAGCTTGTTACCAACATTGGAGAGTATATTGAAAGA
372 TAACGTTCAAATTTAACTTGTTTGAAGTAGAGCTTATTACCAACATTGGAGAGTATATGGAAAGA
* * * * **
2390452 ACCAACTCAGGCAAGCTTACAAAGTTTGAAGGATGTAACAATTCAGAAATGTGATGGACTGAAAT
437 ACCAACTCAGGCAAGCCTACAAAGTCTAAAGGAAGTAACAATTCAGAAATGTGATAAACTGAAAT
2390517 CTATCTT
502 CTATCTT
* ** *
2390524 CTCACCTTGGCTTGCTCAAAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAAT
1 CTCACCTTGCCTTGCTCAAAGTCTGATGCATCTAGAACAACTCAAGATATCTC-ATGCAAGAAAT
* * * *
2390589 TAGAACAAGTATTCGCTTTCGCCCAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTT
65 TAGAACAAGTCTTTGCTTTTGCCAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTT
* *
2390654 TTCCTATAATAATGCTATCATCAATTCTTTATCTAATCATGTTTTTTGTTAAATTATCAAATATA
130 TTCCTTTAATAATGCTATCATCTATTCTTTATCTAATCATGTTTTTTGTTAAATTATCAAATATA
*
2390719 TAAATAATTAGTATCTAATCTTTCTAAATTATTGACTTTTAACACTTTCTTTTTAACATCATCTT
195 TAAATAATTAGTATCTAATCTTTCTAAATTATTGACTTTTAACACTTTCTTTTTAACAT--TTTT
2390784 TTAAAAAATGCATGTCTTCTCAATAATTTTTTGATCAAGTACAATAAATTTATAATTCAGTATTT
258 TTAAAAAATGCATGTCTTCTCAATAATTTTTTGATCAAGTACAATAAATTTATAATTCAGTATTT
*
2390849 ATTAATTAATAAATTTTATA-TTTTTTTATTTGAGGAAAATCAGGCAGCATT-AC-TCTCAAATT
323 ATTAATTAATAAATTTTATATTTTTTTTATTTGAGGAAAATCA-ACAGC-TTAACGT-TCAAATT
*
2390911 TAACTTGTTTGAAGCT-GAG-TTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATC
385 TAACTTGTTTGAAG-TAGAGCTT-ATTACCAACATTGGAGAGTATATGGAAAGAACCAA--C-TC
* * * * * ** *
2390974 ATGTAAGCCTACAAAGTCTAAAGGAAGTAATAGTTTATG-GTTGTGATAAATTGAAATCTATCTT
445 AGGCAAGCCTACAAAGTCTAAAGGAAGTAACAATTCA-GAAATGTGATAAACTGAAATCTATCTT
* * * * *
2391038 CTCACCTTACCTTACTCAAAGTTTGTTGCATTTAGAACAACTCAAGATATCTGCATGCAAGAAAT
1 CTCACCTTGCCTTGCTCAAAGTCTGATGCATCTAGAACAACTCAAGATATCT-CATGCAAGAAAT
* * * * * *
2391103 TAGAGCAAGTCTTTGCTTTTGACAAAGAAATGGCAAACCTAGAGGTACCTCTTATCTCTCCATTT
65 TAGAACAAGTCTTTGCTTTTGCCAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTT
2391168 TTCCTTTAATAATGCTATCATCTATTCTTTATCTAATCATGTTTTTTGTTAAATTATCAAATATA
130 TTCCTTTAATAATGCTATCATCTATTCTTTATCTAATCATGTTTTTTGTTAAATTATCAAATATA
* * * * *
2391233 TAAATAATTAATATCTAATCTTTCTAAATTATTAACTTTTAATAC-TTCTTTCT-ACTTTTTTTT
195 TAAATAATTAGTATCTAATCTTTCTAAATTATTGACTTTTAACACTTTCTTTTTAAC-ATTTTTT
* * * * * * *
2391296 TAAAAAAT--ATGTCTTCTTAGTACTTTTCTGGTCAAGTACAATGAATTTATAATTCAGTACTTA
259 TAAAAAATGCATGTCTTCTCAATAATTTTTTGATCAAGTACAATAAATTTATAATTCAGTATTTA
2391359 TTAATTAATAAATTTATATATATTTTTTTTATTTGA-GAAAA
324 TTAATTAATAAA-TT-T-TATATTTTTTTTATTTGAGGAAAA
2391400 GGAGATTCGA
Statistics
Matches: 768, Mismatches: 85, Indels: 56
0.84 0.09 0.06
Matches are distributed among these distances:
509 60 0.08
510 20 0.03
511 78 0.10
512 67 0.09
513 22 0.03
514 267 0.35
515 3 0.00
517 3 0.00
518 11 0.01
519 6 0.01
520 18 0.02
521 1 0.00
522 206 0.27
523 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (508 bp):
CTCACCTTGCCTTGCTCAAAGTCTGATGCATCTAGAACAACTCAAGATATCTCATGCAAGAAATT
AGAACAAGTCTTTGCTTTTGCCAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTTT
TCCTTTAATAATGCTATCATCTATTCTTTATCTAATCATGTTTTTTGTTAAATTATCAAATATAT
AAATAATTAGTATCTAATCTTTCTAAATTATTGACTTTTAACACTTTCTTTTTAACATTTTTTTA
AAAAATGCATGTCTTCTCAATAATTTTTTGATCAAGTACAATAAATTTATAATTCAGTATTTATT
AATTAATAAATTTTATATTTTTTTTATTTGAGGAAAATCAACAGCTTAACGTTCAAATTTAACTT
GTTTGAAGTAGAGCTTATTACCAACATTGGAGAGTATATGGAAAGAACCAACTCAGGCAAGCCTA
CAAAGTCTAAAGGAAGTAACAATTCAGAAATGTGATAAACTGAAATCTATCTT
Found at i:2395171 original size:516 final size:513
Alignment explanation
Indices: 2394181--2396336 Score: 2550
Period size: 516 Copynumber: 4.2 Consensus size: 513
2394171 TATTTTTAAC
* * * *
2394181 TTTTATATTTTTTTAATTTGAGGAAAATCAGGCAGCGTTACTCTCAAATTTAACTTGTTTGAAGC
1 TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
* *
2394246 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAATCAACACATCATGTAAGCCTACAAAGT
66 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGTAAGCCTACAAAGT
* ** * * * *
2394311 TTGAAGGAAGTAATAATTCATGGTTGTGATAAACTGAAATCTATCTTCACACTTGGGCTTGCTCA
131 CTGAAGGAAGTAA-AATTCATAATTGTGATAAACTAAAATCTATCTTCTCACCTGGCCTTGCTCA
*
2394376 AAGTCTGATGCATCTAGAACAACTTGAGATATCTAAATGCGAA-AAATTAGAGCAAGTCTTTGCT
195 AAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGC-AACAAATTAGAGCAAGTCTTTGCT
* * * * *
2394440 TTTGCCGAAGAAATGGCAAAGCAAGAGGTACCTCTTCTGTCTCCATTTTTCCTTTAATAATGCTA
259 TTT-ACAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTTTTCGTTTAATAATGCTA
* * ** *
2394505 TCGTCTATT-CTTTATCTAATCATG-TTTTTTGTTAAATTATCAAATATATAAATAATTAGTATA
323 TCATATATTACTTTATCTAATCATGTTTTTTTGTTAAATTATCAAATATATAAATAATTTCTATC
* *
2394568 TAATCTTTTTAAATTATTGACTTTTAACACTTTCTTTTTAACATTATCTTTTAAAAAATGTATGT
388 TAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATT-T-TTTTAGAAAATGTATG-
** * * * * *
2394633 TTTCC-CAGTA-TTTTTTGGTCAAGTACAATGAGTTTATAATTCAAAGTATTTATTAATTAATAA
450 TCCCCTCAATACTTTTTCGGTCAAGCACAATGAATTCATAATTC-AA-TATTTATTAATTAATAA
2394696 A
513 A
* * * * *
2394697 TTTTATAGTTTTTTTATTTGAGAAAAATCAAGCAGCATTACTCTCAAATTTAACTTGTTTGAAGC
1 TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
* *
2394762 TGAGTTCATTACCAGCATTGGAGAGTGTATGGAAAGAACCAACTCATCATGTAAGCCTATAAAGT
66 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGTAAGCCTACAAAGT
** * * * *
2394827 CTGAAGGAAGTAAGAATTCATGGTTGTCATAAGCTAAAATCTATCTTCTCACCTGGGCTTACTCA
131 CTGAAGGAAGTAA-AATTCATAATTGTGATAAACTAAAATCTATCTTCTCACCTGGCCTTGCTCA
*
2394892 AAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAAGAAATTAGAGCAAGTCTTTGCTT
195 AAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTTGCTT
* * * * *
2394957 TTACCCAGGAAATGGCAGAGCAAGAAGTACCTCTTCTCTCTCGATTTGTTC-TTTAATAATACTA
260 TTA-CAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTT-TTCGTTTAATAATGCTA
* *
2395021 TCATCTATT-CTTTATCTAATCATGTTTTTTTGTTAAATTATCAAATATATAAATAATTTTTATC
323 TCATATATTACTTTATCTAATCATGTTTTTTTGTTAAATTATCAAATATATAAATAATTTCTATC
2395085 TAATCTTTTTAAATTATTGACTTTTAACACTTCC-TTTTAACATTTTTGTTAGAAAATGTATGTC
388 TAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATTTTT-TTAGAAAATGTATGTC
* *
2395149 CCCTCAATACTTTTTCGGTCAAGTACAATGAATTTATAATTCAATATTTATTAATTAATAAA
452 CCCTCAATACTTTTTCGGTCAAGCACAATGAATTCATAATTCAATATTTATTAATTAATAAA
* *
2395211 TGTTATATTTTTTTTATGTGAGGGAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
1 TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
* * * * *
2395276 TAAGTTCATTACCAGCATTGGAGAATATATGGAAAGAACCAACGCATCACGCAAGCCTACAAAGT
66 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGTAAGCCTACAAAGT
* * * * *
2395341 CTGAAGGATGTAAATGTTCATAATTGTGATAAACTGAAATCTATCTTCTCACCTTGCCTTGCTGA
131 CTGAAGGAAGTAAA-ATTCATAATTGTGATAAACTAAAATCTATCTTCTCACCTGGCCTTGCTCA
* * * *
2395406 AAGTCTGTTGCATCTAGAACAACTTGAGATATCTCAATGCAACCAATTAAAGCAAGTCTTTACTT
195 AAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTTGCTT
* * * * * *
2395471 TTGACAAAAAAATGGCTGAGCTAA-AGGTACCTGTTCTGTCT-CTTTTATTCTTTTAATAATGCT
260 TT-ACAAAGAAATGGCAGAGC-AAGAGGTACCTCTTCTCTCTCCATTT-TTCGTTTAATAATGCT
* * * * * * *
2395534 CTCATATATTCCTTTTTCTAATTATCTTGTCTTTTGTTGAATTTTCAAATATATAAATAATTTCT
322 ATCATATATTACTTTATCTAATCATGTT-T-TTTTGTTAAATTATCAAATATATAAATAATTTCT
*
2395599 ATCTAATCTTTTTAAATTATGGACTTTTAACACTTCCTTTTTAACATTTTTTTAGAAAA-GTATG
385 ATCTAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATTTTTTTAGAAAATGTATG
** * * * * *
2395663 TCTTCTCAATACTTTTTCAGTCAAGCACAGTGAATTCATATTTTAGTATTTATTAATTAATAAA
450 TCCCCTCAATACTTTTTCGGTCAAGCACAATGAATTCATAATTCAATATTTATTAATTAATAAA
* * *
2395727 TTTTATTTTTTTCTTTATGTGAGGAAAATCAGGTAACATTACTCTCAAATTTAACTTATTTGAAG
1 TTTTATATTTTT-TTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAG
* * *
2395792 CTGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAGCTAACTCATCATG-CAGCCCTACACA
65 CTGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGTAAG-CCTACA-A
* * * ** *
2395856 A-TCTGAAGTACGTAAAAGTTCATAACTGTGATAAACTGAAAAT-TATCTTCTCACCTTTCCTTT
128 AGTCTGAAGGAAGTAAAA-TTCATAATTGTGATAAACT-AAAATCTATCTTCTCACCTGGCCTTG
* * * * *
2395919 TTCGAAGTATGTTGCATCTAGAACAACTTGAGATATCTCAATGCAACCAATTAGAGCAAGTCTTT
191 CTCAAAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTT
* * * * *
2395984 GCTGTTGACAAAGAAATGGTTA-ACCTAGAGGTACCTCTTCTCTCTCCATTCTTCGTTTAATAAT
256 GCT-TTTACAAAGAAATGG-CAGAGCAAGAGGTACCTCTTCTCTCTCCATTTTTCGTTTAATAAT
* * * * * * *
2396048 GCTCTCATATATTATTTTTTCTAATTATATTTTATTG---AATTATCAAAGATATAAATAATTTC
319 GCTATCATATATTACTTTATCTAATCATGTTTTTTTGTTAAATTATCAAATATATAAATAATTTC
* * * * * *
2396110 TATTTACTCTGTCTAAATTATTGACTTTTAACACTTCCTTTTTTACATTTTTTATTAAGAAAGTG
384 TATCTAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACA-TTTTT-TT-AGAAAATG
* * * * * *
2396175 CATGTCTTCTCGATATTGAATTACTTTTTTGATCAAGCACAATGAATTCATATTTCAATATTTAT
446 TATGTC--C-C----CTCAA-TACTTTTTCGGTCAAGCACAATGAATTCATAATTCAATATTTAT
2396240 TAATTAATAAA
503 TAATTAATAAA
* * ** * * *
2396251 TTTTATATTTTTCTTTATGTGAGAAAAATCAGGTACCACCACTCTCAAATTTAATTTATTTGGAG
1 TTTTATATTTTT-TTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAG
* *
2396316 CTAAAG-TCATTACCAGAATTG
65 CT-GAGTTCATTACCAGCATTG
2396337 AGCTCCATAT
Statistics
Matches: 1438, Mismatches: 165, Indels: 66
0.86 0.10 0.04
Matches are distributed among these distances:
512 64 0.04
513 12 0.01
514 301 0.21
515 48 0.03
516 434 0.30
517 427 0.30
518 24 0.02
523 3 0.00
524 123 0.09
525 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (513 bp):
TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGTAAGCCTACAAAGT
CTGAAGGAAGTAAAATTCATAATTGTGATAAACTAAAATCTATCTTCTCACCTGGCCTTGCTCAA
AGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTTGCTTT
TACAAAGAAATGGCAGAGCAAGAGGTACCTCTTCTCTCTCCATTTTTCGTTTAATAATGCTATCA
TATATTACTTTATCTAATCATGTTTTTTTGTTAAATTATCAAATATATAAATAATTTCTATCTAA
TCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATTTTTTTAGAAAATGTATGTCCCCT
CAATACTTTTTCGGTCAAGCACAATGAATTCATAATTCAATATTTATTAATTAATAAA
Found at i:2395813 original size:517 final size:513
Alignment explanation
Indices: 2394181--2396336 Score: 2579
Period size: 517 Copynumber: 4.2 Consensus size: 513
2394171 TATTTTTAAC
* * * *
2394181 TTTTATATTTTTTTAATTTGAGGAAAATCAGGCAGCGTTACTCTCAAATTTAACTTGTTTGAAGC
1 TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
* * *
2394246 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAATCAACACATCATGTAAGCCTACAAAGT
66 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGCAAGCCTACAAAGT
* ** * *
2394311 TTGAAGGAAGT-AATAATTCATGGTTGTGATAAACTGAAATCTATCTTCACA-CTTGGGCTTGCT
131 CTGAAGGAAGTAAAT-ATTCATAATTGTGATAAACTGAAATCTATCTTCTCACCTT-GCCTTGCT
*
2394374 CAAAGTCTGATGCATCTAGAACAACTTGAGATATCTAAATGCGAA-AAATTAGAGCAAGTCTTTG
194 CAAAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGC-AACAAATTAGAGCAAGTCTTTG
* * *
2394438 CTTTTGCCGAAGAAATGGCAAAGCAAGAGGTACCTCTTCTGTCTCCATTTTTCCTTTAATAATGC
258 CTTTTGACAAAGAAATGGCAAAGCAAGAGGTACCTCTTCTCTCT-CATTTTT-CTTTAATAATGC
* * * * **
2394503 TATCGTCTATTCTTTATCTAATCAT-GTTTTTTGTTAAATTATCAAATATATAAATAATTAGTAT
321 TATCATATATTCTTTATCTAATTATCTTTTTTTGTTAAATTATCAAATATATAAATAATTTCTAT
* * *
2394567 ATAATCTTTTTAAATTATTGACTTTTAACACTTTCTTTTTAACATTATCTT-TTAAAAAATGTAT
386 CTAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATT-T-TTATTAGAAAATGTAT
* * * * * * * *
2394631 GTTTTCCCAGTA-TTTTTTGGTCAAGTACAATGAGTTTATAATTCAAAGTATTTATTAATTAATA
449 GTCTTCTCAATACTTTTTCGGTCAAGCACAATGAATTCATATTTC-AA-TATTTATTAATTAATA
2394695 AA
512 AA
* * * * *
2394697 TTTTATAGTTTTTTTATTTGAGAAAAATCAAGCAGCATTACTCTCAAATTTAACTTGTTTGAAGC
1 TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
* * *
2394762 TGAGTTCATTACCAGCATTGGAGAGTGTATGGAAAGAACCAACTCATCATGTAAGCCTATAAAGT
66 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGCAAGCCTACAAAGT
** * * * * * *
2394827 CTGAAGGAAGTAAGA-ATTCATGGTTGTCATAAGCTAAAATCTATCTTCTCACCTGGGCTTACTC
131 CTGAAGGAAGTAA-ATATTCATAATTGTGATAAACTGAAATCTATCTTCTCACCTTGCCTTGCTC
*
2394891 AAAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAAGAAATTAGAGCAAGTCTTTGCT
195 AAAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTTGCT
* * * * *
2394956 TTT-ACCCAGGAAATGGCAGAGCAAGAAGTACCTCTTCTCTCTCGATTTGTTCTTTAATAATACT
260 TTTGA-CAAAGAAATGGCAAAGCAAGAGGTACCTCTTCTCTCTC-ATTT-TTCTTTAATAATGCT
* * * *
2395020 ATCATCTATTCTTTATCTAATCATGTTTTTTTGTTAAATTATCAAATATATAAATAATTTTTATC
322 ATCATATATTCTTTATCTAATTATCTTTTTTTGTTAAATTATCAAATATATAAATAATTTCTATC
*
2395085 TAATCTTTTTAAATTATTGACTTTTAACACTTCC-TTTTAACATTTTTGTTAGAAAATGTATGTC
387 TAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATTTTTATTAGAAAATGTATGTC
** * * *
2395149 CCCTCAATACTTTTTCGGTCAAGTACAATGAATTTATAATTCAATATTTATTAATTAATAAA
452 TTCTCAATACTTTTTCGGTCAAGCACAATGAATTCATATTTCAATATTTATTAATTAATAAA
* *
2395211 TGTTATATTTTTTTTATGTGAGGGAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
1 TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
* * * *
2395276 TAAGTTCATTACCAGCATTGGAGAATATATGGAAAGAACCAACGCATCACGCAAGCCTACAAAGT
66 TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGCAAGCCTACAAAGT
* * *
2395341 CTGAAGGATGTAAATGTTCATAATTGTGATAAACTGAAATCTATCTTCTCACCTTGCCTTGCTGA
131 CTGAAGGAAGTAAATATTCATAATTGTGATAAACTGAAATCTATCTTCTCACCTTGCCTTGCTCA
* * * *
2395406 AAGTCTGTTGCATCTAGAACAACTTGAGATATCTCAATGCAACCAATTAAAGCAAGTCTTTACTT
196 AAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTTGCTT
* ** * * * *
2395471 TTGACAAAAAAATGGCTGAGCTAA-AGGTACCTGTTCTGTCTCTTTTATTCTTTTAATAATGCTC
261 TTGACAAAGAAATGGCAAAGC-AAGAGGTACCTCTTCTCTCTCATTT-TTC-TTTAATAATGCTA
* * *
2395535 TCATATATTCCTTTTTCTAATTATCTTGTCTTTTGTTGAATTTTCAAATATATAAATAATTTCTA
323 TCATATATT-CTTTATCTAATTATCTT-T-TTTTGTTAAATTATCAAATATATAAATAATTTCTA
*
2395600 TCTAATCTTTTTAAATTATGGACTTTTAACACTTCCTTTTTAACATTTTT-TTAGAAAA-GTATG
385 TCTAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATTTTTATTAGAAAATGTATG
* * * *
2395663 TCTTCTCAATACTTTTTCAGTCAAGCACAGTGAATTCATATTTTAGTATTTATTAATTAATAAA
450 TCTTCTCAATACTTTTTCGGTCAAGCACAATGAATTCATATTTCAATATTTATTAATTAATAAA
* * *
2395727 TTTTATTTTTTTCTTTATGTGAGGAAAATCAGGTAACATTACTCTCAAATTTAACTTATTTGAAG
1 TTTTATATTTTT-TTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAG
* *
2395792 CTGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAGCTAACTCATCATGC-AGCCCTACACA
65 CTGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGCAAG-CCTACA-A
* * * *
2395856 A-TCTGAAGTACGTAAA-AGTTCATAACTGTGATAAACTGAAAAT-TATCTTCTCACCTTTCCTT
128 AGTCTGAAGGAAGTAAATA-TTCATAATTGTGATAAACTG-AAATCTATCTTCTCACCTTGCCTT
** * * * *
2395918 TTTCGAAGTATGTTGCATCTAGAACAACTTGAGATATCTCAATGCAACCAATTAGAGCAAGTCTT
191 GCTCAAAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTT
* ** * * *
2395983 TGCTGTTGACAAAGAAATGGTTAACCTAGAGGTACCTCTTCTCTCTCCATTCTTCGTTTAATAAT
256 TGCTTTTGACAAAGAAATGGCAAAGCAAGAGGTACCTCTTCTCTCT-CATTTTTC-TTTAATAAT
* * * * * *
2396048 GCTCTCATATATTATTTTTTCTAATTATATTTTATTG---AATTATCAAAGATATAAATAATTTC
319 GCTATCATATATT-CTTTATCTAATTATCTTTTTTTGTTAAATTATCAAATATATAAATAATTTC
* * * * * *
2396110 TATTTACTCTGTCTAAATTATTGACTTTTAACACTTCCTTTTTTACATTTTTTATTAAGAAAGTG
383 TATCTAATCTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACA-TTTTTATT-AGAAAATG
* * *
2396175 CATGTCTTCTCGATATTGAATTACTTTTTTGATCAAGCACAATGAATTCATATTTCAATATTTAT
446 TATGTCTTCTC-------AA-TACTTTTTCGGTCAAGCACAATGAATTCATATTTCAATATTTAT
2396240 TAATTAATAAA
503 TAATTAATAAA
* * ** * * *
2396251 TTTTATATTTTTCTTTATGTGAGAAAAATCAGGTACCACCACTCTCAAATTTAATTTATTTGGAG
1 TTTTATATTTTT-TTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAG
* *
2396316 CTAAAG-TCATTACCAGAATTG
65 CT-GAGTTCATTACCAGCATTG
2396337 AGCTCCATAT
Statistics
Matches: 1443, Mismatches: 159, Indels: 68
0.86 0.10 0.04
Matches are distributed among these distances:
512 64 0.04
513 12 0.01
514 299 0.21
515 51 0.04
516 432 0.30
517 435 0.30
518 23 0.02
523 2 0.00
524 123 0.09
525 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (513 bp):
TTTTATATTTTTTTTATGTGAGGAAAATCAGGTAGCATTACTCTCAAATTTAACTTGTTTGAAGC
TGAGTTCATTACCAGCATTGGAGAGTATATGGAAAGAACCAACTCATCATGCAAGCCTACAAAGT
CTGAAGGAAGTAAATATTCATAATTGTGATAAACTGAAATCTATCTTCTCACCTTGCCTTGCTCA
AAGTCTGATGCATCTAGAACAACTTGAGATATCTCAATGCAACAAATTAGAGCAAGTCTTTGCTT
TTGACAAAGAAATGGCAAAGCAAGAGGTACCTCTTCTCTCTCATTTTTCTTTAATAATGCTATCA
TATATTCTTTATCTAATTATCTTTTTTTGTTAAATTATCAAATATATAAATAATTTCTATCTAAT
CTTTTTAAATTATTGACTTTTAACACTTCCTTTTTAACATTTTTATTAGAAAATGTATGTCTTCT
CAATACTTTTTCGGTCAAGCACAATGAATTCATATTTCAATATTTATTAATTAATAAA
Found at i:2396729 original size:24 final size:24
Alignment explanation
Indices: 2396702--2396748 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2396692 TCTTCGGCAT
*
2396702 GGCAAAAAAAATGGATGGGCACGA
1 GGCAAAAAAAATGGATAGGCACGA
*
2396726 GGCAAAAGAAATGGATAGGCACG
1 GGCAAAAAAAATGGATAGGCACG
2396749 TTATTGAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.13, G:0.34, T:0.09
Consensus pattern (24 bp):
GGCAAAAAAAATGGATAGGCACGA
Found at i:2409509 original size:18 final size:18
Alignment explanation
Indices: 2409481--2409522 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2409471 CCTACTATAG
2409481 CCATCAGCTGTTCCTGTCT
1 CCAT-AGCTGTTCCTGTCT
2409500 CCATAGCTGTTCCTGTCT
1 CCATAGCTGTTCCTGTCT
2409518 CCATA
1 CCATA
2409523 CTCCACTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (18 bp):
CCATAGCTGTTCCTGTCT
Found at i:2434183 original size:18 final size:18
Alignment explanation
Indices: 2434160--2434197 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2434150 TGTAGAAATG
*
2434160 GACATTCTTGGCTATTTT
1 GACATTCTTGACTATTTT
2434178 GACATTCTTGACTATTTT
1 GACATTCTTGACTATTTT
2434196 GA
1 GA
2434198 TAATGGAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (18 bp):
GACATTCTTGACTATTTT
Found at i:2435566 original size:30 final size:30
Alignment explanation
Indices: 2435492--2435566 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
2435482 TTGGATTGAT
* *
2435492 AGGCAT-AGTGTGCAGTAATTTAGGATTTTG
1 AGGCATGA-TGTGTAGTAATTTAGGATTTTC
* ***
2435522 ATGCATGGCATGTAGTAATTTAGGATTTTC
1 AGGCATGATGTGTAGTAATTTAGGATTTTC
2435552 AGGCATGATGTGTAG
1 AGGCATGATGTGTAG
2435567 CAACCAAAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.36
Consensus pattern (30 bp):
AGGCATGATGTGTAGTAATTTAGGATTTTC
Found at i:2456680 original size:27 final size:27
Alignment explanation
Indices: 2456650--2456703 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2456640 CTCGAGTACT
*
2456650 TAACTGCAAACAAGGGTCCAGAAGAAG
1 TAACAGCAAACAAGGGTCCAGAAGAAG
*
2456677 TAACAGCAAACAAGGGTGCAGAAGAAG
1 TAACAGCAAACAAGGGTCCAGAAGAAG
2456704 GAGGAAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.28, T:0.09
Consensus pattern (27 bp):
TAACAGCAAACAAGGGTCCAGAAGAAG
Found at i:2465056 original size:2 final size:2
Alignment explanation
Indices: 2465049--2465099 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
2465039 TTCTCATGAA
* *
2465049 CT CT CT CT CG CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2465091 CT CT CT CT C
1 CT CT CT CT C
2465100 ATCTAGATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.04, T:0.47
Consensus pattern (2 bp):
CT
Found at i:2471282 original size:50 final size:50
Alignment explanation
Indices: 2471216--2471343 Score: 150
Period size: 50 Copynumber: 2.5 Consensus size: 50
2471206 GGAAACAAAA
* * * *
2471216 AAAAAAGATGAGATTTTGAGGAAATTGGATTCTATAGATT-TAAACAAGG
1 AAAAAAGATGGGATTTTGAGGAAATGGGATTCTAGAGATTGCAAACAAGG
* * *
2471265 AGAAAAAGATGGGATTTTGAGGAAATGGGGTTGTAGAGATTGGAGCAAAGAAGG
1 A-AAAAAGATGGGATTTTGAGGAAATGGGATTCTAGAGATT---GCAAACAAGG
2471319 AAAAAAGATGGGATTTTGAGGAAAT
1 AAAAAAGATGGGATTTTGAGGAAAT
2471344 AGGAAAGTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
49 1 0.01
50 34 0.51
53 24 0.36
54 8 0.12
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.24
Consensus pattern (50 bp):
AAAAAAGATGGGATTTTGAGGAAATGGGATTCTAGAGATTGCAAACAAGG
Found at i:2481695 original size:23 final size:24
Alignment explanation
Indices: 2481669--2481726 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2481659 TACCAACGAA
* *
2481669 ATTCAGATTAT-TCATTACTAAGC
1 ATTCAGATTATGCCAATACTAAGC
*
2481692 ATTCAGGTTATGCCAATACTAAGC
1 ATTCAGATTATGCCAATACTAAGC
2481716 ATTCAGATTAT
1 ATTCAGATTAT
2481727 CCATGCTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (24 bp):
ATTCAGATTATGCCAATACTAAGC
Found at i:2490677 original size:2 final size:2
Alignment explanation
Indices: 2490670--2490697 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2490660 CGTTCTGCAT
2490670 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2490698 TGAAAATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2496561 original size:2 final size:2
Alignment explanation
Indices: 2496554--2496578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2496544 ATTGTTTGTC
2496554 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2496579 AACCGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2503821 original size:4 final size:4
Alignment explanation
Indices: 2503812--2503838 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2503802 AAATTACAAC
2503812 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2503839 TACCATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2505488 original size:2 final size:2
Alignment explanation
Indices: 2505481--2505509 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2505471 GACAATGGAC
2505481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2505510 AATCTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2510309 original size:18 final size:18
Alignment explanation
Indices: 2510286--2510328 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2510276 AGATATTATC
2510286 CAAAAATTAAAAAAAAAA
1 CAAAAATTAAAAAAAAAA
* *
2510304 CAAAAAGTTTAATAAAAAA
1 CAAAAA-TTAAAAAAAAAA
2510323 -AAAAAT
1 CAAAAAT
2510329 CTCAAAAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 10 0.45
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (18 bp):
CAAAAATTAAAAAAAAAA
Found at i:2524539 original size:2 final size:2
Alignment explanation
Indices: 2524534--2524566 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2524524 TATGTGTGTG
2524534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2524567 NGTAGGTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2524613 original size:2 final size:2
Alignment explanation
Indices: 2524608--2524640 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2524598 TATGTGTGTG
2524608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2524641 GATTAAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2525952 original size:80 final size:80
Alignment explanation
Indices: 2525819--2525975 Score: 296
Period size: 80 Copynumber: 2.0 Consensus size: 80
2525809 ATGCTTTCAA
2525819 AATCTTTTCCAGGGCATGAAGAGACATGCTCACATGCTAATGGAGGGTTTAAATTAACCCTGCAA
1 AATCTTTTCCAGGGCATGAAGAGACATGCTCACATGCTAATGGAGGGTTTAAATTAACCCTGCAA
2525884 GAAGCTTTTCCAAAT
66 GAAGCTTTTCCAAAT
*
2525899 AATCTTTTCCAGGGCATGAAGGGACATGCTCACATGCTAATGGAGGGTTTAAATTAACCCTGCAA
1 AATCTTTTCCAGGGCATGAAGAGACATGCTCACATGCTAATGGAGGGTTTAAATTAACCCTGCAA
*
2525964 GTAGCTTTTCCA
66 GAAGCTTTTCCA
2525976 CATGCTTTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (80 bp):
AATCTTTTCCAGGGCATGAAGAGACATGCTCACATGCTAATGGAGGGTTTAAATTAACCCTGCAA
GAAGCTTTTCCAAAT
Found at i:2533684 original size:43 final size:43
Alignment explanation
Indices: 2533618--2533704 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
2533608 TTCCTTATTT
*
2533618 ACAATAAACTAAGGAGATAGTTACATATATATTAAGTTAACAC
1 ACAACAAACTAAGGAGATAGTTACATATATATTAAGTTAACAC
2533661 ACAACAAACTAAGGAGATAGTTACATATATATTAAGTTAACAC
1 ACAACAAACTAAGGAGATAGTTACATATATATTAAGTTAACAC
2533704 A
1 A
2533705 AGGATAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.26
Consensus pattern (43 bp):
ACAACAAACTAAGGAGATAGTTACATATATATTAAGTTAACAC
Found at i:2551658 original size:25 final size:25
Alignment explanation
Indices: 2551624--2551676 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2551614 ACCTGAACAA
*
2551624 ATTATATGGATTTAGAACAAATCAT
1 ATTATATGGAATTAGAACAAATCAT
* *
2551649 ATTATATGGAATTAGAACTAATTAT
1 ATTATATGGAATTAGAACAAATCAT
2551674 ATT
1 ATT
2551677 GAATTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (25 bp):
ATTATATGGAATTAGAACAAATCAT
Found at i:2553028 original size:24 final size:25
Alignment explanation
Indices: 2553001--2553054 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
2552991 TATACAGTTC
2553001 TCTTTCAATACAGAAAACCCTG-TT
1 TCTTTCAATACAGAAAACCCTGTTT
* *
2553025 TCTTTCAATTCAGAGAACCCTGTTT
1 TCTTTCAATACAGAAAACCCTGTTT
2553050 TCTTT
1 TCTTT
2553055 GACTGAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (25 bp):
TCTTTCAATACAGAAAACCCTGTTT
Found at i:2553927 original size:15 final size:18
Alignment explanation
Indices: 2553909--2553948 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
2553899 ATTTTTTAAC
2553909 TTAAAATATT-AATA-T-
1 TTAAAATATTCAATACTA
*
2553924 TTAAATTATTCAATACTA
1 TTAAAATATTCAATACTA
2553942 TTAAAAT
1 TTAAAAT
2553949 TAAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAAATATTCAATACTA
Found at i:2554133 original size:31 final size:30
Alignment explanation
Indices: 2554098--2554199 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
2554088 TTACACAATT
2554098 CATAAATATTGATATTTTTATAGTGAATACA
1 CATAAATATTGA-ATTTTTATAGTGAATACA
* * **
2554129 CATAAATA-T-AAGTTTTAGA-TGTCTCACAA
1 CATAAATATTGAATTTTTATAGTGAAT-AC-A
*
2554158 TTGATAAATATTGACATTTTTATAGTGAATACA
1 --CATAAATATTGA-ATTTTTATAGTGAATACA
2554191 CATAAATAT
1 CATAAATAT
2554200 AGGTTTTGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
27 3 0.06
28 9 0.17
29 2 0.04
30 1 0.02
31 23 0.43
32 1 0.02
33 2 0.04
34 9 0.17
35 3 0.06
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (30 bp):
CATAAATATTGAATTTTTATAGTGAATACA
Found at i:2554159 original size:62 final size:63
Alignment explanation
Indices: 2554070--2554243 Score: 262
Period size: 62 Copynumber: 2.7 Consensus size: 63
2554060 ATATAAGTAT
* *
2554070 ATATAAATTTTGGATGTCTTACACAATTCATAAATATTGATATTTTTATAGTGAATACACATAA
1 ATATAAGTTTT-GATGTCTTACACAATTGATAAATATTGATATTTTTATAGTGAATACACATAA
*
2554134 ATATAAGTTTTAGATGTC-T-CACAATTGATAAATATTGACATTTTTATAGTGAATACACATAA
1 ATATAAGTTTT-GATGTCTTACACAATTGATAAATATTGATATTTTTATAGTGAATACACATAA
* *
2554196 ATATAGGTTTTGTATGTCTTATACAATTGATAAATATTGATATTTTTA
1 ATATAAGTTTTG-ATGTCTTACACAATTGATAAATATTGATATTTTTA
2554244 GAGTTATGGT
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
61 1 0.01
62 56 0.56
63 2 0.02
64 41 0.41
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (63 bp):
ATATAAGTTTTGATGTCTTACACAATTGATAAATATTGATATTTTTATAGTGAATACACATAA
Found at i:2554788 original size:33 final size:33
Alignment explanation
Indices: 2554746--2554812 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2554736 TTCAACCAAC
2554746 CCACATGTCATTCAACTGAACCTCTAAACGACA
1 CCACATGTCATTCAACTGAACCTCTAAACGACA
2554779 CCACATGTCATTCAACTGAACCTCTAAACGACA
1 CCACATGTCATTCAACTGAACCTCTAAACGACA
2554812 C
1 C
2554813 AAACTATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.34, G:0.09, T:0.21
Consensus pattern (33 bp):
CCACATGTCATTCAACTGAACCTCTAAACGACA
Found at i:2554952 original size:78 final size:78
Alignment explanation
Indices: 2554823--2554979 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
2554813 AAACTATCAC
2554823 TGATGCAAGGATAAGACACTAAAAGCTTCCTTTTATATATAGTTATAGATATATTGATTTTACCA
1 TGATGCAAGGATAAGACACTAAAAGCTTCCTTTTATATATAGTTATAGATATATTGATTTTACCA
2554888 ATTTTCATATCCA
66 ATTTTCATATCCA
*
2554901 TGATGCAAGGATAAGACACTAAAAGCTTCCTTTTATATATGGTTATAGATATATTGATTTTACCA
1 TGATGCAAGGATAAGACACTAAAAGCTTCCTTTTATATATAGTTATAGATATATTGATTTTACCA
2554966 ATTTTCATATCCA
66 ATTTTCATATCCA
2554979 T
1 T
2554980 TATTTATTTT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (78 bp):
TGATGCAAGGATAAGACACTAAAAGCTTCCTTTTATATATAGTTATAGATATATTGATTTTACCA
ATTTTCATATCCA
Found at i:2555671 original size:24 final size:25
Alignment explanation
Indices: 2555610--2555673 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
2555600 TCAAGCGCAT
*
2555610 ACAAGACACATATAGCTAGACTGAGAC
1 ACAAGACATATATAGCTAGACT--GAC
2555637 ACAAGACATATATAGCTAGACT-AC
1 ACAAGACATATATAGCTAGACTGAC
**
2555661 TTAAGACATATAT
1 ACAAGACATATAT
2555674 TGTTAGTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.38
27 21 0.62
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (25 bp):
ACAAGACATATATAGCTAGACTGAC
Found at i:2558149 original size:52 final size:52
Alignment explanation
Indices: 2558075--2558173 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 52
2558065 TGGTTGGCCA
* * *
2558075 AACCAAAATACTAGAACTTCTTTCTCTTTATATTCTTTATTAATTCGCCAAT
1 AACCAAAACACTAGAACCTCTTTCTCTTGATATTCTTTATTAATTCGCCAAT
* *
2558127 AACCAAAACATTATAACCTCTTTCTCTTGATATTCTTTATTAATTCG
1 AACCAAAACACTAGAACCTCTTTCTCTTGATATTCTTTATTAATTCG
2558174 TCAAGAGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.42
Consensus pattern (52 bp):
AACCAAAACACTAGAACCTCTTTCTCTTGATATTCTTTATTAATTCGCCAAT
Found at i:2558402 original size:41 final size:41
Alignment explanation
Indices: 2558345--2558423 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
2558335 GCGTCAGTAG
*
2558345 TACTCTTGTATCAAGAGAGTTAGGATTCCATTAGCTAGAAA
1 TACTCTTGTATCAAGAGAGTTAGAATTCCATTAGCTAGAAA
2558386 TACTCTTGTATCAAGAGAGTTAGAATTCCATTAGCTAG
1 TACTCTTGTATCAAGAGAGTTAGAATTCCATTAGCTAG
2558424 CAAAAGTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (41 bp):
TACTCTTGTATCAAGAGAGTTAGAATTCCATTAGCTAGAAA
Found at i:2558525 original size:18 final size:18
Alignment explanation
Indices: 2558502--2558537 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2558492 TTAGGAGAGT
2558502 TAGAATTCCATTAGCTGC
1 TAGAATTCCATTAGCTGC
*
2558520 TAGAATTCCATTGGCTGC
1 TAGAATTCCATTAGCTGC
2558538 AAGGGCCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (18 bp):
TAGAATTCCATTAGCTGC
Found at i:2561534 original size:24 final size:24
Alignment explanation
Indices: 2561504--2561550 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2561494 GCAATTTATT
2561504 TTTTATAAAAAAGCCAATCAATTC
1 TTTTATAAAAAAGCCAATCAATTC
*
2561528 TTTTATAAAAAAGCCTATCAATT
1 TTTTATAAAAAAGCCAATCAATT
2561551 GCACTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (24 bp):
TTTTATAAAAAAGCCAATCAATTC
Found at i:2561558 original size:24 final size:24
Alignment explanation
Indices: 2561507--2561558 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2561497 ATTTATTTTT
**
2561507 TATAAAAAAGCCAATCAATTCTTT
1 TATAAAAAAGCCAATCAATTCTAC
*
2561531 TATAAAAAAGCCTATCAATTGC-AC
1 TATAAAAAAGCCAATCAATT-CTAC
2561555 TATA
1 TATA
2561559 TAAGGATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (24 bp):
TATAAAAAAGCCAATCAATTCTAC
Found at i:2572220 original size:3 final size:3
Alignment explanation
Indices: 2572212--2572253 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2572202 GTCAAAATCT
*
2572212 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2572254 CATAAAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2582378 original size:2 final size:2
Alignment explanation
Indices: 2582371--2582402 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2582361 TATTTGAACC
2582371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2582403 TATTTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2586634 original size:33 final size:33
Alignment explanation
Indices: 2586572--2586634 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
2586562 CTTTATTCGT
* * *
2586572 AATGTCGAGTACTTGAATATTATATAATCGTTG
1 AATGTCGAGTACTTGAACACTATACAATCGTTG
*
2586605 AATGTCGAGTACTTGAACCCTATACAATCG
1 AATGTCGAGTACTTGAACACTATACAATCG
2586635 GGTTGGATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (33 bp):
AATGTCGAGTACTTGAACACTATACAATCGTTG
Found at i:2597551 original size:287 final size:286
Alignment explanation
Indices: 2597026--2597598 Score: 1121
Period size: 287 Copynumber: 2.0 Consensus size: 286
2597016 CAATGACAAA
2597026 TCAAAATGAGAAATCATGATTTGGAAGTCACATGTTTTAGTTGCAGAAGCAATTAATCTCTCTAT
1 TCAAAATGAGAAATCATGATTTGGAAGTCACATGTTTTAGTTGCAGAAGCAATTAATCTCTCTAT
2597091 TAAGGGTAAGATTGTGCTATCTTACCCTCCTCACACCTCGTAATTAACAAAGAAATATCGGGCTT
66 TAAGGGTAAGATTGTGCTATCTTACCCTCCTCACACCTCGTAATTAACAAAGAAATATCGGGCTT
2597156 TACGTAAACAATGTTATTCGAGGTGTGAGGAGGGTAAGATATCTTTTTTTTTACATATCTTTTTT
131 TACGTAAACAATGTTATTCGAGGTGTGAGGAGGGTAAGATATCTTTTTTTTTACATATCTTTTTT
2597221 TTCGTAGATCAATTCTATTACGCAAACAATGCATATCTTTTTTTTTTTGTCATAGATGAAGTAAT
196 TTCGTAGATCAATTCTATTACGCAAACAATGCATATCTTTTTTTTTTTGTCATAGATGAAGTAAT
2597286 AGAATTGATCTATTAAAGAAAAATTT
261 AGAATTGATCTATTAAAGAAAAATTT
2597312 NTCAAAATGAGAAATCATGATTTGGAAGTCACATGTTTTAGTTGCAGAAGCAATTAATCTCTCTA
1 -TCAAAATGAGAAATCATGATTTGGAAGTCACATGTTTTAGTTGCAGAAGCAATTAATCTCTCTA
2597377 TTAAGGGTAAGATTGTGCTATCTTACCCTCCTCACACCTCGTAATTAACAAAGAAATATCGGGCT
65 TTAAGGGTAAGATTGTGCTATCTTACCCTCCTCACACCTCGTAATTAACAAAGAAATATCGGGCT
2597442 TTACGTAAACAATGTTATTCGAGGTGTGAGGAGGGTAAGATATC-TTTTTTTTACATATCTTTTT
130 TTACGTAAACAATGTTATTCGAGGTGTGAGGAGGGTAAGATATCTTTTTTTTTACATATCTTTTT
2597506 TTTCGTAGATCAATTCTATTACGCAAACAATGCATATCTTTTTTTTTTTTGTCATAGATGAAGTA
195 TTTCGTAGATCAATTCTATTACGCAAACAATGCATATC-TTTTTTTTTTTGTCATAGATGAAGTA
2597571 ATAGAATTGATCTATTAAAGAAAAATTT
259 ATAGAATTGATCTATTAAAGAAAAATTT
2597599 GTAAAACAAT
Statistics
Matches: 285, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
286 58 0.20
287 227 0.80
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (286 bp):
TCAAAATGAGAAATCATGATTTGGAAGTCACATGTTTTAGTTGCAGAAGCAATTAATCTCTCTAT
TAAGGGTAAGATTGTGCTATCTTACCCTCCTCACACCTCGTAATTAACAAAGAAATATCGGGCTT
TACGTAAACAATGTTATTCGAGGTGTGAGGAGGGTAAGATATCTTTTTTTTTACATATCTTTTTT
TTCGTAGATCAATTCTATTACGCAAACAATGCATATCTTTTTTTTTTTGTCATAGATGAAGTAAT
AGAATTGATCTATTAAAGAAAAATTT
Found at i:2600330 original size:2 final size:2
Alignment explanation
Indices: 2600323--2600354 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2600313 ACATACATAC
2600323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2600355 GTATNTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2600442 original size:2 final size:2
Alignment explanation
Indices: 2600435--2600466 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2600425 ACATACATAC
2600435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2600467 GTATTGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2600445 original size:112 final size:111
Alignment explanation
Indices: 2600237--2600471 Score: 443
Period size: 112 Copynumber: 2.1 Consensus size: 111
2600227 TGATTCTCGT
* *
2600237 TATAAATGTAATCATTCACTTTCTTCATTATCATATCTTATTTTTTTTTTACAGTTTCTTTATAG
1 TATATATGTATTCATTCACTTTCTTCATTATCATATCTTATTTTTTTTTTACAGTTTCTTTATAG
2600302 CATTAAAATGTACATACATACATATATATATATATATATATATATA
66 CATTAAAATGTACATACATACATATATATATATATATATATATATA
2600348 TATATATGTATNTCATTCACTTTCTTCATTATCATATCTTATTTTTTTTTTACAGTTTCTTTATA
1 TATATATGTAT-TCATTCACTTTCTTCATTATCATATCTTATTTTTTTTTTACAGTTTCTTTATA
2600413 GCATTAAAATGTACATACATACATATATATATATATATATATATATA
65 GCATTAAAATGTACATACATACATATATATATATATATATATATATA
2600460 TATATATGTATT
1 TATATATGTATT
2600472 GATATTTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
111 10 0.08
112 111 0.92
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (111 bp):
TATATATGTATTCATTCACTTTCTTCATTATCATATCTTATTTTTTTTTTACAGTTTCTTTATAG
CATTAAAATGTACATACATACATATATATATATATATATATATATA
Found at i:2601932 original size:92 final size:92
Alignment explanation
Indices: 2601673--2601951 Score: 323
Period size: 92 Copynumber: 3.0 Consensus size: 92
2601663 TTATTTAATC
* * * *
2601673 ATTTTTAATGAAAAATCTTACGAAGTTTACTT-AAATCTTGCTCCAAT-TGTTGTCTCCCAT-AA
1 ATTTTTAATGAAAAATCTTACGAAGTTTA-TTCAAGTCTTGCCCCGATCT-TTGTCTCTCATAAA
* **
2601735 TACTTACCAATTTACCAATTGGTGTTTAAA
64 T-CTTACCAATTTACCAATTGATACTTAAA
* * * * * * * **
2601765 ATTTTTAATGAAAAA-CATACAAAATTTTTTCAAGTCTTGTCACGATCTTTGTTTCTTGTAAATC
1 ATTTTTAATGAAAAATCTTACGAAGTTTATTCAAGTCTTGCCCCGATCTTTGTCTCTCATAAATC
*
2601829 TTATCAATTTACCAATTGATACTTAAA
66 TTACCAATTTACCAATTGATACTTAAA
** *
2601856 ATTTTTAATGAAAAATCTTACGAAGTTTATTCAAGTCTAACCCCGATCTTTATCTCTCATAAATC
1 ATTTTTAATGAAAAATCTTACGAAGTTTATTCAAGTCTTGCCCCGATCTTTGTCTCTCATAAATC
2601921 TTACCAATTTACCAATTGATACTTAAA
66 TTACCAATTTACCAATTGATACTTAAA
2601948 ATTT
1 ATTT
2601952 ACAAATTTAC
Statistics
Matches: 153, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
90 2 0.01
91 65 0.42
92 86 0.56
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (92 bp):
ATTTTTAATGAAAAATCTTACGAAGTTTATTCAAGTCTTGCCCCGATCTTTGTCTCTCATAAATC
TTACCAATTTACCAATTGATACTTAAA
Found at i:2603836 original size:2 final size:2
Alignment explanation
Indices: 2603829--2603877 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2603819 NNNNNTGCAC
*
2603829 TA TA TA TA TA TA TA TA TA T- TA TA TA TC TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2603869 TA TA TA TA T
1 TA TA TA TA T
2603878 GTTATCAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2603853 original size:15 final size:15
Alignment explanation
Indices: 2603829--2603877 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
2603819 NNNNNTGCAC
2603829 TATA-TATATATATA
1 TATATTATATATATA
*
2603843 TATATTATATATCTA
1 TATATTATATATATA
2603858 TATATTATATATATA
1 TATATTATATATATA
2603873 TATAT
1 TATAT
2603878 GTTATCAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 4 0.12
15 28 0.88
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:2604788 original size:2 final size:2
Alignment explanation
Indices: 2604740--2604773 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2604730 AAATCTTAAA
2604740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2604774 TGGAATTCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2615896 original size:25 final size:24
Alignment explanation
Indices: 2615850--2615905 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
2615840 TCTTTGTACC
* * * **
2615850 ATTTAAAATTTGTTAATTTTTTGT
1 ATTTTAAATTTGATAATATTTTAA
2615874 ATTTTAAATTTGATAATAATTTTAA
1 ATTTTAAATTTGATAAT-ATTTTAA
2615899 ATTTTAA
1 ATTTTAA
2615906 TTTTTAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
ATTTTAAATTTGATAATATTTTAA
Found at i:2629769 original size:144 final size:143
Alignment explanation
Indices: 2629524--2630290 Score: 825
Period size: 144 Copynumber: 5.3 Consensus size: 143
2629514 GGTTCAAAAT
* * * * * **
2629524 TGCCCTAATCTGAAGGATTTGCCCGACTGGATACTCAATCTCACTTCCCTTAGAAGTCTTCAAAT
1 TGCCCTAATTTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCTTAAAACACTTCAAAT
**** * * * *
2629589 CAATGAGTGCCTTGAATTACAGTCCATTCCAGAAGGGACGCCTCAGCTTACATCTTTAGAAGAAT
66 TTGGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGACACATCAGCTTACATCTTTAGAAGAAT
* ** *
2629654 TATCTGTTCAGAAT
131 TGT-TGTAGAGAAA
* * * *
2629668 TGTCATAATTTGAGGGCTTTGCCAGAGTGGATACTCAATCTCACTTCCCTTAAAACACTTCGAAT
1 TGCCCTAATTTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCTTAAAACACTTCAAAT
* * *
2629733 TTGGGAGTGCCTTGAATTACAGTACATGCCAAAAGGGACACATCAGCTTACCTCTTTAAAAGAAT
66 TTGGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGACACATCAGCTTACATCTTTAGAAGAAT
*
2629798 TGTTCGTAGGGAAA
131 TGTT-GTAGAGAAA
* * *
2629812 TGCCCTAATCTGAGGGCTTTGCCAGATTGGATACTCAATCTCACTTCCCTTAAAACACTTCGAAT
1 TGCCCTAATTTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCTTAAAACACTTCAAAT
* * *
2629877 TTGGGAGTGCCTTGAATTACAGTACATGCCAAAAGGGACACATCAGCTTACTTCTTTAAAAGAAT
66 TTGGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGACACATCAGCTTACATCTTTAGAAGAAT
*
2629942 TGTTAGTAGGGAAA
131 TGTT-GTAGAGAAA
* * *
2629956 TGCCCTAATCTGAGGGCTTTGCCTGACTGGATACTCAATCTCACTTCCCTTACAAA-ACTTCATA
1 TGCCCTAATTTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCTTA-AAACACTTCAAA
** * *
2630020 TTCAGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGACGCATCAGCTTACCTCTTT-GAAAGA
65 TTTGGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGACACATCAGCTTACATCTTTAG-AAGA
** *
2630084 ATTGTCCATTGA-AAA
129 ATTGT-TGTAGAGAAA
* * * *
2630099 TTGCCCTCATCTT-AGGGCTTTGCCTGACTGGATACTCAATCTCACTTCTCTTGAAACACTTCAA
1 -TGCCCTAAT-TTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCTTAAAACACTTCAA
* * * ** *
2630163 ATTTGGAATTGCCTTGAATTACAGTACATGCCAGTAGGGATTTC-TCGGCTTACAT-TCTTAGAA
64 ATTTGGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGA-CACATCAGCTTACATCT-TTAGAA
* *
2630226 GAATTATATGCT---G-AC
127 GAATTGT-TG-TAGAGAAA
* * *
2630241 CGCCATAATTTGAGGGCTTTGCAAGACTGGATACTCAATCTCACTTCCCT
1 TGCCCTAATTTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCT
2630291 CAAAGATCTT
Statistics
Matches: 538, Mismatches: 72, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
140 2 0.00
141 41 0.08
142 1 0.00
143 8 0.01
144 479 0.89
145 7 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (143 bp):
TGCCCTAATTTGAGGGCTTTGCCAGACTGGATACTCAATCTCACTTCCCTTAAAACACTTCAAAT
TTGGGAGTGCCTTGAATTACAGTACATGCCAGAAGGGACACATCAGCTTACATCTTTAGAAGAAT
TGTTGTAGAGAAA
Done.