Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_pilon, whole genome shotgun sequence
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: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:2099644 original size:28 final size:28
Alignment explanation
Indices: 2099609--2099698 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
2099599 TATTTATGTA
2099609 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
2099637 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
2099665 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
2099692 AA-ATTAT
1 AATATTAT
2099699 ATTTTTTTAT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:2099672 original size:30 final size:31
Alignment explanation
Indices: 2099638--2099703 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
2099628 TATATCTATA
*
2099638 ATTTTA-TAAATAAAAAATTATGAT-TATTAT
1 ATTTTATTAAA-AAAAAATTATGATAAATTAT
* *
2099668 ATTTTATTAAAATAAAATTATTATAAATTAT
1 ATTTTATTAAAAAAAAATTATGATAAATTAT
2099699 ATTTT
1 ATTTT
2099704 TTTATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
ATTTTATTAAAAAAAAATTATGATAAATTAT
Found at i:2100343 original size:15 final size:14
Alignment explanation
Indices: 2100317--2100361 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2100307 TACTAGAATA
2100317 ATTTATTTAATATT
1 ATTTATTTAATATT
2100331 ATTTATGTTAATATT
1 ATTTAT-TTAATATT
*
2100346 A-TTATTAAAATATT
1 ATTTATT-TAATATT
2100360 AT
1 AT
2100362 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 17 0.63
15 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:2100370 original size:28 final size:28
Alignment explanation
Indices: 2100339--2100429 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
2100329 TTATTTATGT
2100339 TAATATTATTATTAAAATATTAT-ATCTA
1 TAATATTATTATTAAAATATTATGAT-TA
* * * *
2100367 TAATTTTATAAATAAAAAATTATGATTA
1 TAATATTATTATTAAAATATTATGATTA
* ** *
2100395 TTATATT-TTATTAAAATAAAATTATTA
1 TAATATTATTATTAAAATATTATGATTA
2100422 TAA-ATTAT
1 TAATATTAT
2100430 ATTTATTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 5
0.73 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.35
28 26 0.54
29 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TAATATTATTATTAAAATATTATGATTA
Found at i:2100432 original size:31 final size:31
Alignment explanation
Indices: 2100369--2100437 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2100359 TATATCTATA
*
2100369 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
2100399 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
2100430 A-TTTATTA
1 ATTTTATTA
2100438 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:2100922 original size:198 final size:196
Alignment explanation
Indices: 2100538--2101205 Score: 860
Period size: 198 Copynumber: 3.4 Consensus size: 196
2100528 CACATATGTT
* * * * * * * *
2100538 ACATTGAAACAGATAATTATAATATAATAGCTAAATTTATAATGTAACCAGTATAAATATACCGA
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGT-ACCAGTAGAAATATA-CGG
* * * ** *** *
2100603 TTTTATGAGAGAATATGTCTACATAATGTATCAACACAAATTTAA-AAAGTGTCGATACATTTTG
64 TTTTATGAGAAAATAAGTCTACATAATGTATCGACAC-GTTTTAAGTTTGTGTCGATAC-TTTTT
*
2100667 TCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATC
127 TCCAGAATGAATGCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATC
2100732 CCAAAA
191 CCAAAA
* *
2100738 ACATC-AAACCGATAATTACAATGTAATAGGTAAATTAACAATGTACTCAGTAGAAATATATCAG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-CAGTAGAAATATA-CGG
*
2100802 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
64 TTTTATGAGAAAATAAGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
2100867 CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
129 CAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
2100932 AAAA
193 AAAA
* *
2100936 A-ATCGGAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATACTGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTA-CCAGTAGAAATATAC-GG
2101000 TTTTATGAGAAAATAAGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
64 TTTTATGAGAAAATAAGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTC
* * * *
2101065 TAGAATGAATGCCCAACGAGGTGCACACATAAAATGTCGATACATTTA--AAATTGTATCGATCC
129 CAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC
2101128 CAAAA
192 CAAAA
* * * * ** * *
2101133 ACATCTAAACCAATAATTATAATGTAATATGTAAATTCGCAATGTTACCGGTATAAATATACCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACCAGTAGAAATATA-CGG
2101198 TTTTATGA
64 TTTTATGA
2101206 TAGAATATGT
Statistics
Matches: 419, Mismatches: 39, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
196 3 0.01
197 20 0.05
198 296 0.71
199 96 0.23
200 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (196 bp):
ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCAGTAGAAATATACGGTT
TTATGAGAAAATAAGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTCGATACTTTTTTCCA
GAATGAATGCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAA
A
Found at i:2101265 original size:23 final size:23
Alignment explanation
Indices: 2101209--2101265 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2101199 TTTATGATAG
*
2101209 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGCGCTACCT
* **
2101233 ATTACATTATATAAGCGCTACCT
1 AATATGTTATATAAGCGCTACCT
2101256 AATATGTTAT
1 AATATGTTAT
2101266 TGTGCTTGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGCGCTACCT
Found at i:2101319 original size:23 final size:23
Alignment explanation
Indices: 2101293--2101343 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2101283 CCAGTAATTA
** *
2101293 ACCTATTTTATTAAATAAGCGCT
1 ACCTATTACATTAAATAAACGCT
*
2101316 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTAAATAAACGCT
2101339 ACCTA
1 ACCTA
2101344 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (23 bp):
ACCTATTACATTAAATAAACGCT
Found at i:2101321 original size:87 final size:87
Alignment explanation
Indices: 2101220--2101457 Score: 386
Period size: 87 Copynumber: 2.7 Consensus size: 87
2101210 ATATGTCAAT
*
2101220 ATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGGTAATATTTCC
1 ATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTCC
2101285 AGTAATTAACCTATTTTATTAA
66 AGTAATTAACCTATTTTATTAA
* * **
2101307 ATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATGTTTTT
1 ATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTCC
*
2101372 AGTAATTAACCTATTTTATTAT
66 AGTAATTAACCTATTTTATTAA
* * * *
2101394 ATAAGCGCTACCTATTACATTATATAAGTGCTACCTAATTTGTTATTTTACTTGATAATATTTC
1 ATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTC
2101458 TGATTAAATG
Statistics
Matches: 138, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 138 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (87 bp):
ATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTCC
AGTAATTAACCTATTTTATTAA
Found at i:2101415 original size:23 final size:23
Alignment explanation
Indices: 2101380--2101430 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2101370 TTAGTAATTA
**
2101380 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
2101403 ACCTATTACATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
2101426 ACCTA
1 ACCTA
2101431 ATTTGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:2101439 original size:23 final size:23
Alignment explanation
Indices: 2101380--2101439 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2101370 TTAGTAATTA
*
2101380 ACCTATTTTATTATATAAGCGCT
1 ACCTAATTTATTATATAAGCGCT
* *
2101403 ACCT-ATTACATTATATAAGTGCT
1 ACCTAATT-TATTATATAAGCGCT
*
2101426 ACCTAATTTGTTAT
1 ACCTAATTTATTAT
2101440 TTTACTTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (23 bp):
ACCTAATTTATTATATAAGCGCT
Found at i:2104094 original size:100 final size:103
Alignment explanation
Indices: 2103911--2104120 Score: 354
Period size: 100 Copynumber: 2.0 Consensus size: 103
2103901 ACACGTCAGG
2103911 AAAAATTAATAAGAGGTAATTATAGGGATTAAAATGAAAATGAACTAAAAGTTTGATGACTGTAT
1 AAAAATTAATAAGAGGTAATTATAGGGATT---ATGAAAATGAACTAAAAGTTTGATGACTGTAT
*
2103976 TGTATGTATTAAAGGTTAGATGACCAAAATATAAGTGTCCT
63 TGTATGTATTAAAAGTTAGATGACCAAAATATAAGTGTCCT
2104017 AAAAATTAATAAGAGGTAATTATAGGGA-T-T-AAAATGAACTAAAAGTTTGATGACTGTATTGT
1 AAAAATTAATAAGAGGTAATTATAGGGATTATGAAAATGAACTAAAAGTTTGATGACTGTATTGT
*
2104079 ATGTTTTAAAAGTTAGATGACCAAAATATAAGTGTCCT
66 ATGTATTAAAAGTTAGATGACCAAAATATAAGTGTCCT
2104117 AAAA
1 AAAA
2104121 TTTCAGGGAC
Statistics
Matches: 102, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
100 72 0.71
101 1 0.01
105 1 0.01
106 28 0.27
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (103 bp):
AAAAATTAATAAGAGGTAATTATAGGGATTATGAAAATGAACTAAAAGTTTGATGACTGTATTGT
ATGTATTAAAAGTTAGATGACCAAAATATAAGTGTCCT
Found at i:2110079 original size:24 final size:20
Alignment explanation
Indices: 2110027--2110064 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2110017 TAATGCTTGC
2110027 GAACATGTTTGCTTAAATGT
1 GAACATGTTTGCTTAAATGT
2110047 GAACATGTTTGCTTAAAT
1 GAACATGTTTGCTTAAAT
2110065 ATTCGTGAAC
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:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (20 bp):
GAACATGTTTGCTTAAATGT
Found at i:2118361 original size:32 final size:32
Alignment explanation
Indices: 2118315--2118428 Score: 120
Period size: 32 Copynumber: 3.6 Consensus size: 32
2118305 ATACTAGCAA
*
2118315 TGTCACATTTAGATAATGCACAATAGTGTCAG
1 TGTCACATTCAGATAATGCACAATAGTGTCAG
*
2118347 TGTCACATTCAGATAATGCATAATAGTGTCAG
1 TGTCACATTCAGATAATGCACAATAGTGTCAG
* *** * * * *
2118379 TTTTGTATTCAAATAATGCACGACAATGTCAG
1 TGTCACATTCAGATAATGCACAATAGTGTCAG
* *
2118411 TGTCATATTTAGATAATG
1 TGTCACATTCAGATAATG
2118429 AAAAACAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTCACATTCAGATAATGCACAATAGTGTCAG
Found at i:2123136 original size:15 final size:16
Alignment explanation
Indices: 2123116--2123147 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2123106 TGCTTGATTG
2123116 AAAAT-AAAGAAAGTA
1 AAAATAAAAGAAAGTA
2123131 AAAATAAAAGAAAGTA
1 AAAATAAAAGAAAGTA
2123147 A
1 A
2123148 GTTGAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAATAAAAGAAAGTA
Found at i:2133629 original size:5 final size:5
Alignment explanation
Indices: 2133619--2133644 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2133609 TTAAGGTTTC
2133619 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
2133645 ATATATGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:2134216 original size:19 final size:18
Alignment explanation
Indices: 2134177--2134217 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
2134167 GATAATGTTG
2134177 ATATGTTGTATTCGTAAA
1 ATATGTTGTATTCGTAAA
2134195 ATATGTTGTGCATTCG-AAA
1 ATATGTTGT--ATTCGTAAA
2134214 ATAT
1 ATAT
2134218 TTAATTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (18 bp):
ATATGTTGTATTCGTAAA
Found at i:2146652 original size:19 final size:19
Alignment explanation
Indices: 2146630--2146667 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2146620 TACCTTGAAA
2146630 ACTTTTACTTGTTTACTTT
1 ACTTTTACTTGTTTACTTT
2146649 ACTTTTACTTGTTTACTTT
1 ACTTTTACTTGTTTACTTT
2146668 TGCATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (19 bp):
ACTTTTACTTGTTTACTTT
Found at i:2154584 original size:103 final size:103
Alignment explanation
Indices: 2154380--2154584 Score: 274
Period size: 103 Copynumber: 2.0 Consensus size: 103
2154370 TCACGGGATG
* *
2154380 ACTCTACCTGACTAGCTCGGGGGTGAAAAGTATGCTCCCTTTCACCTAGAGTGTGGGATGGTAGG
1 ACTCTACCTGACTAGCTCGAGGGTGAAAAGTATGCTCCCTTTCACCTAGAGTGTAGGATGGTAGG
* * ** *
2154445 TGTGATAGGCTGACTCCTCTCCAAGTAGTGTTAAAAAA
66 TGTGATAGGATGACTCCCCTAAAAGTAGTATTAAAAAA
* *
2154483 ACTCTACCTGACTAGCTCGAGGGT-AGAAGGTATGCTCCCTTTCACTTAGAGTGTAGGATGGTA-
1 ACTCTACCTGACTAGCTCGAGGGTGA-AAAGTATGCTCCCTTTCACCTAGAGTGTAGGATGGTAG
*
2154546 GTGTGAT-GAGATTACTCCCCTAAAAGTA-TATTAAAAAA
65 GTGTGATAG-GATGACTCCCCTAAAAGTAGTATTAAAAAA
2154584 A
1 A
2154585 GTTGAAGTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
101 11 0.12
102 22 0.24
103 57 0.63
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (103 bp):
ACTCTACCTGACTAGCTCGAGGGTGAAAAGTATGCTCCCTTTCACCTAGAGTGTAGGATGGTAGG
TGTGATAGGATGACTCCCCTAAAAGTAGTATTAAAAAA
Found at i:2162771 original size:29 final size:29
Alignment explanation
Indices: 2162684--2162764 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
2162674 AACATTAAAA
*
2162684 TAGCCATCAAATCAATCATTATTCTCGTG
1 TAGCCATCGAATCAATCATTATTCTCGTG
*
2162713 TAGCCATCGAATCAATCATTATTCTTGTG
1 TAGCCATCGAATCAATCATTATTCTCGTG
2162742 TAGCCATCGAATCAATCATTATT
1 TAGCCATCGAATCAATCATTATT
2162765 GCCGTGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (29 bp):
TAGCCATCGAATCAATCATTATTCTCGTG
Found at i:2168335 original size:45 final size:46
Alignment explanation
Indices: 2168286--2168375 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 46
2168276 TTAAGGAATT
*
2168286 TTCTACGTGGTC-CTTA-GGTACATTT-TATATGGCACTTCGGTGCAA
1 TTCTACGTGG-CAC-TACGGTACATTTCTACATGGCACTTCGGTGCAA
* *
2168331 TTCTACGTGGCACTACGGTGCATTTCTACGTGGCACTTCGGTGCA
1 TTCTACGTGGCACTACGGTACATTTCTACATGGCACTTCGGTGCA
2168376 TTTATATAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
44 3 0.08
45 19 0.49
46 17 0.44
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (46 bp):
TTCTACGTGGCACTACGGTACATTTCTACATGGCACTTCGGTGCAA
Found at i:2168376 original size:23 final size:23
Alignment explanation
Indices: 2168285--2168378 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 23
2168275 CTTAAGGAAT
* *
2168285 TTTCTACGTGGTC-CTTAGGTACA
1 TTTCTACGTGG-CACTTCGGTGCA
**
2168308 TTT-TATATGGCACTTCGGTGCA
1 TTTCTACGTGGCACTTCGGTGCA
* *
2168330 ATTCTACGTGGCACTACGGTGCA
1 TTTCTACGTGGCACTTCGGTGCA
2168353 TTTCTACGTGGCACTTCGGTGCA
1 TTTCTACGTGGCACTTCGGTGCA
2168376 TTT
1 TTT
2168379 ATATAAGCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.02
22 15 0.25
23 43 0.73
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (23 bp):
TTTCTACGTGGCACTTCGGTGCA
Found at i:2172538 original size:25 final size:26
Alignment explanation
Indices: 2172500--2172548 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2172490 AAAATTATTT
*
2172500 TTTTAAATTATAAAATAA-AAATAAA
1 TTTTAAATTATAAAAAAATAAATAAA
*
2172525 TTTTAAATTTTAAAAAAATAAATA
1 TTTTAAATTATAAAAAAATAAATA
2172549 GAACATGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TTTTAAATTATAAAAAAATAAATAAA
Found at i:2173699 original size:18 final size:20
Alignment explanation
Indices: 2173672--2173713 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2173662 TTTTAATTAT
2173672 TTTTTATTTATTTAT-AATA
1 TTTTTATTTATTTATAAATA
*
2173691 TTTTT-TTTATTTTTAAATA
1 TTTTTATTTATTTATAAATA
2173710 TTTT
1 TTTT
2173714 AGATGGCGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTATTTATTTATAAATA
Found at i:2175504 original size:2 final size:2
Alignment explanation
Indices: 2175497--2175533 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2175487 ATTTTTCAAG
2175497 AT AT AT AT 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 AT AT AT AT A
2175534 ATAATAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2180145 original size:38 final size:38
Alignment explanation
Indices: 2180094--2180208 Score: 221
Period size: 38 Copynumber: 3.0 Consensus size: 38
2180084 AATTAGCCAA
2180094 GCATTTAAGTGCAACTTGTCTTGTTTCAAGGCTCAAGG
1 GCATTTAAGTGCAACTTGTCTTGTTTCAAGGCTCAAGG
2180132 GCATTTAAGTGCAACTTGTCTTGTTTCAAGGCTCAAGG
1 GCATTTAAGTGCAACTTGTCTTGTTTCAAGGCTCAAGG
*
2180170 GCATTTAAGTGCAACTTGCCTTGTTTCAAGGCTCAAGG
1 GCATTTAAGTGCAACTTGTCTTGTTTCAAGGCTCAAGG
2180208 G
1 G
2180209 TTTGGTATAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (38 bp):
GCATTTAAGTGCAACTTGTCTTGTTTCAAGGCTCAAGG
Found at i:2183685 original size:11 final size:11
Alignment explanation
Indices: 2183671--2183721 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2183661 AGAAGAGTAA
2183671 AAATTGAAAAT
1 AAATTGAAAAT
2183682 AAA-TGACAAAAT
1 AAATTG--AAAAT
* * *
2183694 AAAATCAAAGT
1 AAATTGAAAAT
2183705 AAATTGAAAAT
1 AAATTGAAAAT
2183716 AAATTG
1 AAATTG
2183722 TGAAGTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
10 2 0.06
11 21 0.66
12 8 0.25
13 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.24
Consensus pattern (11 bp):
AAATTGAAAAT
Found at i:2184094 original size:30 final size:30
Alignment explanation
Indices: 2184058--2184139 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
2184048 ATATATATAT
*
2184058 AATATATATACATAATATAT-GGTTTCGAA
1 AATATATATATATAATATATAGGTTTCGAA
* *
2184087 AAGTATATATATATGATATATAGTTTTCGAA
1 AA-TATATATATATAATATATAGGTTTCGAA
*
2184118 TATATATATATATATATATATA
1 AATATATATATATA-ATATATA
2184140 TATATATAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 2 0.04
30 27 0.60
31 16 0.36
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (30 bp):
AATATATATATATAATATATAGGTTTCGAA
Found at i:2184122 original size:2 final size:2
Alignment explanation
Indices: 2184117--2184147 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2184107 TAGTTTTCGA
2184117 AT 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 AT A
2184148 GGTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2184145 original size:69 final size:67
Alignment explanation
Indices: 2184023--2184157 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 67
2184013 TTACGATATT
*
2184023 TATATTATAATGTATATAGTTTCTAATATATATATAATATATATACATAATATAT-GGTTTCGAA
1 TATATTATAATGTATATAGTTTCGAATATATATATAATATATATACATAATATATAGGTTT-GAA
2184087 AAG
65 AAG
*
2184090 TATA-TATATATGATATATAGTTTTCGAATATATATAT-ATATATATATATATATATATAGGTTT
1 TATATTATA-ATG-TATATAG-TTTCGAATATATATATAATATATATACATA-ATATATAGGTTT
2184153 GAAAA
62 GAAAA
2184158 TATTATTTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
66 4 0.07
67 7 0.11
68 19 0.31
69 26 0.43
70 5 0.08
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (67 bp):
TATATTATAATGTATATAGTTTCGAATATATATATAATATATATACATAATATATAGGTTTGAAA
AG
Found at i:2185375 original size:24 final size:24
Alignment explanation
Indices: 2185342--2185396 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
2185332 GAACATAAAG
*
2185342 CATTCTCCTGGTAATTTTGGGAAA
1 CATTCCCCTGGTAATTTTGGGAAA
2185366 CATTCCCCTGGTAATTTTGGGAAA
1 CATTCCCCTGGTAATTTTGGGAAA
2185390 CATTCCC
1 CATTCCC
2185397 TAAACCGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (24 bp):
CATTCCCCTGGTAATTTTGGGAAA
Found at i:2186109 original size:12 final size:12
Alignment explanation
Indices: 2186092--2186128 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2186082 TTTAATTACC
2186092 TAATAGTTAAAT
1 TAATAGTTAAAT
2186104 TAATAGTTAAAT
1 TAATAGTTAAAT
2186116 TAATAGTTAAAT
1 TAATAGTTAAAT
2186128 T
1 T
2186129 TATATGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (12 bp):
TAATAGTTAAAT
Found at i:2187681 original size:81 final size:80
Alignment explanation
Indices: 2187459--2188060 Score: 638
Period size: 81 Copynumber: 7.5 Consensus size: 80
2187449 AATCACTAAA
* * * * * *
2187459 TGACACCGTTTATGTCAAATGCACTGTTAAGCATTCAGTCTTT-CCTCTAAAGGCATTTAACCTT
1 TGACACC-TTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTC-AAAGGCATTTAACCTT
* *
2187523 TCA--TAACTGGCACGAT
64 TCATCTAAC-AGCATGAT
* * * * * *
2187539 TGGCACCTTTTTGCCAAATACATAGTTA-G-A-TTAGTTTTTAACTAAAAGGCATTTAACCTTTC
1 TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTTTC
2187601 ATCTAACAGCCATGAT
66 ATCTAACAG-CATGAT
*
2187617 TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAATCTTTC
1 TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTTTC
2187682 ATCTAACAGGCATGAT
66 ATCTAACA-GCATGAT
* * *
2187698 T-AGCACCTTTCTACCGAATGCACAGTTAGGCA-TTAGTCTTTAAC-CAAAGTCATTTAACCTTT
1 TGA-CACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTTT
2187760 CATCTAACATGCATGAT
65 CATCTAACA-GCATGAT
* * * * *
2187777 TGACACATTTCTACCAAATGCACAGTTAGGCATTTAGTCTTTATCTCAAAGGTATTTAACTTTTC
1 TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTTTC
2187842 ATCTAACATGCATGAT
66 ATCTAACA-GCATGAT
* * * *
2187858 TGGCACCTTTCCGCCAAATGCACAGTTAGGCATTTAGTC-TTATCTCAAAGGCAATTAACCTTTC
1 TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTTTC
2187922 ATCTAACAGGCATGA-
66 ATCTAACA-GCATGAT
* * * * * * * **
2187937 TGGCACATTTCTTCCCAAATGCACAATTAGACATTTAGTTTTTAACTCAAA--AATTTTAAGTTT
1 TGACACCTTTC-TGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCA-TTTAACCTT
2188000 TCATCTAACAAGCATGAT
64 TCATCTAAC-AGCATGAT
* ** *
2188018 TGGCACAATT-TGCCAAATGCACAGTTAGGCATTTAATCTTTAA
1 TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAA
2188061 TTTTAAAACA
Statistics
Matches: 450, Mismatches: 55, Indels: 35
0.83 0.10 0.06
Matches are distributed among these distances:
76 26 0.06
77 4 0.01
78 34 0.08
79 116 0.26
80 112 0.25
81 157 0.35
82 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (80 bp):
TGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTTTC
ATCTAACAGCATGAT
Found at i:2187796 original size:160 final size:161
Alignment explanation
Indices: 2187474--2188060 Score: 691
Period size: 160 Copynumber: 3.7 Consensus size: 161
2187464 CCGTTTATGT
* * * * * * *
2187474 CAAATGCACTGTTAAGCATTCAGTCTTT-CCTCTAAAGGCATTTAACCTTTCA--TAACTGGCAC
1 CAAATGCACAGTTAGGCATTTAGTCTTTAACTC-AAAGGCATTTAATCTTTCATCTAACAGGCAT
* * * * *
2187536 GATTGGCACCTTTTTGCCAAATACATAGTTA-G-A-TTAGTTTTTAACTAAAAGGCATTTAACCT
65 GATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCT
* *
2187598 TTCATCTAACAGCCATGATTGACACCTTTCTGC
130 TTCATCTAACAG-CATGATTGACACATTTCTAC
2187631 CAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAATCTTTCATCTAACAGGCATG
1 CAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAATCTTTCATCTAACAGGCATG
* * * *
2187696 ATTAGCACCTTTCTACCGAATGCACAGTTAGGCA-TTAGTCTTTAAC-CAAAGTCATTTAACCTT
66 ATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTT
2187759 TCATCTAACATGCATGATTGACACATTTCTAC
131 TCATCTAACA-GCATGATTGACACATTTCTAC
* * *
2187791 CAAATGCACAGTTAGGCATTTAGTCTTTATCTCAAAGGTATTTAA-CTTTTCATCTAACATGCAT
1 CAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAATC-TTTCATCTAACAGGCAT
* * *
2187855 GATTGGCACCTTTCCGCCAAATGCACAGTTAGGCATTTAGTC-TTATCTCAAAGGCAATTAACCT
65 GATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCT
* *
2187919 TTCATCTAACAGGCATGA-TGGCACATTTCTTCC
130 TTCATCTAACA-GCATGATTGACACATTTC-TAC
* * * * *
2187952 CAAATGCACAATTAGACATTTAGTTTTTAACTCAAA--AATTTTAAGT-TTTCATCTAACAAGCA
1 CAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCA-TTTAA-TCTTTCATCTAACAGGCA
** *
2188014 TGATTGGCACAATT-TGCCAAATGCACAGTTAGGCATTTAATCTTTAA
64 TGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAA
2188061 TTTTAAAACA
Statistics
Matches: 374, Mismatches: 42, Indels: 25
0.85 0.10 0.06
Matches are distributed among these distances:
157 43 0.11
158 3 0.01
159 61 0.16
160 183 0.49
161 84 0.22
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (161 bp):
CAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAATCTTTCATCTAACAGGCATG
ATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAACCTT
TCATCTAACAGCATGATTGACACATTTCTAC
Found at i:2188017 original size:241 final size:239
Alignment explanation
Indices: 2187569--2188060 Score: 668
Period size: 241 Copynumber: 2.0 Consensus size: 239
2187559 CATAGTTAGA
* *
2187569 TTAGTTTTTAACTAAAAGGCATTTAACCTTTCATCTAACAGCCATGATTGACACCTTTCTGCCAA
1 TTAGTCTTTAACTAAAAGGCATTTAACCTTTCATCTAACAGCCATGATTGACACCTTTCCGCCAA
* *
2187634 ATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCATTTAATCTTTCATCTAACAGGCATGATT
66 ATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCAATTAACCTTTCATCTAACAGGCATGATT
* * * * *
2187699 AGCACCTTTCTACCGAATGCACAGTTAGGCATTAGTCTTTAACCAAAGTCATTTAACCTTTCATC
131 AGCACATTTCTACCAAATGCACAATTAGACATTAGTCTTTAACCAAAAT-ATTTAACCTTTCATC
* *
2187764 TAACATGCATGATTGACACATTTCTACCAAATGCACAGTTAGGCAT
195 TAACAAGCATGATTGACACAATT-TACCAAATGCACAGTTAGGCAT
* * * * *
2187810 TTAGTCTTTATCTCAAAGGTATTTAACTTTTCATCTAACATG-CATGATTGGCACCTTTCCGCCA
1 TTAGTCTTTAACTAAAAGGCATTTAACCTTTCATCTAACA-GCCATGATTGACACCTTTCCGCCA
*
2187874 AATGCACAGTTAGGCATTTAGTC-TTATCTCAAAGGCAATTAACCTTTCATCTAACAGGCATGA-
65 AATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCAATTAACCTTTCATCTAACAGGCATGAT
* * * **
2187937 TGGCACATTTCTTCCCAAATGCACAATTAGACATTTAGTTTTTAACTCAAAA-ATTTTAAGTTTT
130 TAGCACATTTC-TACCAAATGCACAATTAGACA-TTAGTCTTTAAC-CAAAATA-TTTAACCTTT
* *
2188001 CATCTAACAAGCATGATTGGCACAATTTGCCAAATGCACAGTTAGGCAT
191 CATCTAACAAGCATGATTGACACAATTTACCAAATGCACAGTTAGGCAT
*
2188050 TTAATCTTTAA
1 TTAGTCTTTAA
2188061 TTTTAAAACA
Statistics
Matches: 220, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
239 9 0.04
240 85 0.39
241 121 0.55
242 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (239 bp):
TTAGTCTTTAACTAAAAGGCATTTAACCTTTCATCTAACAGCCATGATTGACACCTTTCCGCCAA
ATGCACAGTTAGGCATTTAGTCTTTAACTCAAAGGCAATTAACCTTTCATCTAACAGGCATGATT
AGCACATTTCTACCAAATGCACAATTAGACATTAGTCTTTAACCAAAATATTTAACCTTTCATCT
AACAAGCATGATTGACACAATTTACCAAATGCACAGTTAGGCAT
Found at i:2196082 original size:19 final size:20
Alignment explanation
Indices: 2196055--2196092 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2196045 ATATGTAGTG
2196055 ATAGAATAT-TGTTTGCATGC
1 ATAGAATATGT-TTTGCATGC
2196075 ATAG-ATATGTTTTGCATG
1 ATAGAATATGTTTTGCATG
2196093 AATCAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (20 bp):
ATAGAATATGTTTTGCATGC
Found at i:2196841 original size:45 final size:45
Alignment explanation
Indices: 2196736--2196880 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 45
2196726 GGTCTAAACA
* * * * *
2196736 TAATCAACCTGAAATTGATGAAGCATAACCAGTTGAAACCAGAAAT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGTTGAGA-CAGAAAT
* * * *
2196782 TAGTGAGCCCGAAATTAATGAACCAGAACCAGCTGAGACAGAAAT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGTTGAGACAGAAAT
* * *
2196827 TAATGAACTTGAAATTAATGAACCAGAACCAGTTGAGCCAAAAAT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGTTGAGACAGAAAT
*
2196872 TAATAAACC
1 TAATGAACC
2196881 AGAACCATCT
Statistics
Matches: 81, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
45 52 0.64
46 29 0.36
ACGTcount: A:0.46, C:0.18, G:0.17, T:0.20
Consensus pattern (45 bp):
TAATGAACCTGAAATTAATGAACCAGAACCAGTTGAGACAGAAAT
Found at i:2197894 original size:89 final size:89
Alignment explanation
Indices: 2197726--2197903 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 89
2197716 GAAGGATGGG
2197726 TTCAAATCAGGATGTAGCTGATTATATGTTTGGATGGGTGTCACCTAAAGGGATTTTTTGGGGGT
1 TTCAAATCAGGATGTAGCTGATTATATGTTTGGATGGGTGTCACCTAAAGGGATTTTTTGGGGGT
2197791 CATCTGCTAGCTACTGTTTGAGTT
66 CATCTGCTAGCTACTGTTTGAGTT
2197815 TTCAAATCAGGATGTAGGCTGATTATATGTTTGGATGGGTGTCACCTAAAGGGATTTTTTGGGGG
1 TTCAAATCAGGATGTA-GCTGATTATATGTTTGGATGGGTGTCACCTAAAGGGATTTTTTGGGGG
2197880 TCAT-TGCTAGCTACTGTTTGAGTT
65 TCATCTGCTAGCTACTGTTTGAGTT
2197904 GATGCAGATT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
89 36 0.41
90 52 0.59
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (89 bp):
TTCAAATCAGGATGTAGCTGATTATATGTTTGGATGGGTGTCACCTAAAGGGATTTTTTGGGGGT
CATCTGCTAGCTACTGTTTGAGTT
Found at i:2198001 original size:44 final size:45
Alignment explanation
Indices: 2197938--2198028 Score: 175
Period size: 44 Copynumber: 2.0 Consensus size: 45
2197928 GCCTTTGTAG
2197938 TTGTAGAGAGTGAGAATCAATCATCATGGTTATGA-TTTTTAGAA
1 TTGTAGAGAGTGAGAATCAATCATCATGGTTATGATTTTTTAGAA
2197982 TTGTAGAGAGTGAGAATCAATCATCATGGTTATGATTTTTTAGAA
1 TTGTAGAGAGTGAGAATCAATCATCATGGTTATGATTTTTTAGAA
2198027 TT
1 TT
2198029 ACTGGGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 35 0.76
45 11 0.24
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (45 bp):
TTGTAGAGAGTGAGAATCAATCATCATGGTTATGATTTTTTAGAA
Found at i:2198945 original size:26 final size:26
Alignment explanation
Indices: 2198888--2198998 Score: 129
Period size: 26 Copynumber: 4.3 Consensus size: 26
2198878 AACTTGCTAA
* * *
2198888 TACATATTCTTCATGCATACTGTAAT
1 TACATATTGTTCATGCATAATGTTAT
2198914 T--ATATTGTTACA-GCATAATGTTAT
1 TACATATTGTT-CATGCATAATGTTAT
* *
2198938 TTCATATTGTTCATGAATAATGTTAT
1 TACATATTGTTCATGCATAATGTTAT
*
2198964 TACATATTGTTCATGCATATTGTTAT
1 TACATATTGTTCATGCATAATGTTAT
*
2198990 TGCATATTG
1 TACATATTG
2198999 GAATAATTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
24 18 0.25
25 4 0.05
26 51 0.70
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (26 bp):
TACATATTGTTCATGCATAATGTTAT
Found at i:2198974 original size:13 final size:13
Alignment explanation
Indices: 2198927--2198998 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
2198917 ATTGTTACAG
* *
2198927 CATAATGTTATTT
1 CATATTGTTATTA
*
2198940 CATATTGTTCATGA
1 CATATTGTT-ATTA
*
2198954 -ATAATGTTATTA
1 CATATTGTTATTA
*
2198966 CATATTGTTCA-TG
1 CATATTGTT-ATTA
*
2198979 CATATTGTTATTG
1 CATATTGTTATTA
2198992 CATATTG
1 CATATTG
2198999 GAATAATTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.08
13 41 0.85
14 3 0.06
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (13 bp):
CATATTGTTATTA
Found at i:2199691 original size:16 final size:17
Alignment explanation
Indices: 2199670--2199712 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2199660 ACTGCCAGTA
2199670 TGTTTTAGATTTAC-TT
1 TGTTTTAGATTTACATT
* *
2199686 TGTTTTAG-CTTGCATT
1 TGTTTTAGATTTACATT
2199702 TGTTTTAGATT
1 TGTTTTAGATT
2199713 GATTGGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.60
Consensus pattern (17 bp):
TGTTTTAGATTTACATT
Found at i:2201352 original size:21 final size:21
Alignment explanation
Indices: 2201328--2201387 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
2201318 ATATATTACT
* * *
2201328 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTATGCTGCCGCTACC
*
2201349 TCTCTCTATGCTGCCGCTACT
1 TCTCTCTATGCTGCCGCTACC
* *
2201370 TCTCTCTCTGCTTCCGCT
1 TCTCTCTATGCTGCCGCT
2201388 GCTGCTCTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.03, C:0.42, G:0.15, T:0.40
Consensus pattern (21 bp):
TCTCTCTATGCTGCCGCTACC
Found at i:2201395 original size:21 final size:21
Alignment explanation
Indices: 2201362--2201447 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
2201352 CTCTATGCTG
* * **
2201362 CCGCTACTTCTCTCTCTGCTT
1 CCGCTGCTGCTCTCTCTAATT
**
2201383 CCGCTGCTGCTCTAGCTAATT
1 CCGCTGCTGCTCTCTCTAATT
**
2201404 CCGCTGCTGCTCTAGCTAATT
1 CCGCTGCTGCTCTCTCTAATT
*
2201425 CCGCTGCTGCTCTCTCTATTT
1 CCGCTGCTGCTCTCTCTAATT
2201446 CC
1 CC
2201448 CTTGCTTCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.09, C:0.38, G:0.15, T:0.37
Consensus pattern (21 bp):
CCGCTGCTGCTCTCTCTAATT
Found at i:2201411 original size:18 final size:21
Alignment explanation
Indices: 2201381--2201437 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
2201371 CTCTCTCTGC
2201381 TTCCGCTGCTGCTCTAGCTAA
1 TTCCGCTGCTGCTCTAGCTAA
2201402 TTCCGCTGCTGCTCTAGCTAA
1 TTCCGCTGCTGCTCTAGCTAA
2201423 TTCCGCTGCTGCTCT
1 TTCCGCTGCTGCTCT
2201438 CTCTATTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.11, C:0.35, G:0.19, T:0.35
Consensus pattern (21 bp):
TTCCGCTGCTGCTCTAGCTAA
Found at i:2208533 original size:42 final size:41
Alignment explanation
Indices: 2208466--2208555 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 41
2208456 TTTATGTCAC
*
2208466 AAACGCCACTAAAGTACAACTTTTTAGGGGCATTTT-TTAAA
1 AAACGCCACTAAAGTACAACTTTTTA-CGGCATTTTCTTAAA
* * *
2208507 AAACGCCACTAAA-TTCAAAGTATTTTACGGCGTTTTCTTAAA
1 AAACGCCACTAAAGTAC-AACT-TTTTACGGCATTTTCTTAAA
*
2208549 ACACGCC
1 AAACGCC
2208556 GTTATAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.05
41 23 0.56
42 16 0.39
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAACTTTTTACGGCATTTTCTTAAA
Found at i:2208955 original size:41 final size:42
Alignment explanation
Indices: 2208888--2209008 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 42
2208878 CGTTTATACA
2208888 AAAAAACGCCACTATTGATT-ACACTATTGTGGCGTTTGT-T
1 AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTCT
* *
2208928 AAAAAACGCCACTATTGATTAAAACTATTGTGGCGTTTATCT
1 AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTCT
**
2208970 -AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGT
1 AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGT
2209009 GGTATAAACG
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 20 0.27
41 52 0.71
42 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (42 bp):
AAAAAACGCCACTATTGATTAACACTATTGTGGCGTTTGTCT
Found at i:2209040 original size:83 final size:80
Alignment explanation
Indices: 2208889--2209061 Score: 179
Period size: 83 Copynumber: 2.1 Consensus size: 80
2208879 GTTTATACAA
** **
2208889 AAAAACGCCACTATTGATTACACTATTGTGGCGTTTGTTAAAAAACGCCACTATTGATTAAAACT
1 AAAAACGCCACTATTGATTACACTATTACGGCGTTTGTTAAAAAACGCCACTATTGACCAAAACT
*
2208954 ATTGTGGCGTTTATCT
66 ATTGCGGCGTTT-TCT
* * * *
2208970 AAAAACGCCACTATTGATTAACACTATTACGGCGTTTGTGGT-ATAAACGCCGCTAATTTACCGA
1 AAAAACGCCACTATTGATT-ACACTATTACGGCGTTTGT--TAAAAAACGCCACT-ATTGACCAA
* *
2209034 TA-TATTGCGGCGTTTTTT
62 AACTATTGCGGCGTTTTCT
2209052 AACAAACGCC
1 AA-AAACGCC
2209062 GCAAGAAACC
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
81 19 0.25
82 21 0.28
83 29 0.38
84 7 0.09
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (80 bp):
AAAAACGCCACTATTGATTACACTATTACGGCGTTTGTTAAAAAACGCCACTATTGACCAAAACT
ATTGCGGCGTTTTCT
Found at i:2218174 original size:15 final size:15
Alignment explanation
Indices: 2218144--2218184 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2218134 GCCTACCTCA
*
2218144 TTCTTCTTCTT-GTT
1 TTCTTCTTCTTCATT
2218158 TTGCTTC-TCTTCATT
1 TT-CTTCTTCTTCATT
2218173 TTCTTCTTCTTC
1 TTCTTCTTCTTC
2218185 CTTCACCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.02, C:0.27, G:0.05, T:0.66
Consensus pattern (15 bp):
TTCTTCTTCTTCATT
Found at i:2220104 original size:20 final size:20
Alignment explanation
Indices: 2220076--2220124 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2220066 TCAGCCATTG
*
2220076 AAGGGAAAATAAGGGAAAAT
1 AAGGAAAAATAAGGGAAAAT
2220096 AAGGAAAAATAAGGGAAAAT
1 AAGGAAAAATAAGGGAAAAT
2220116 AAGGAAAAA
1 AAGGAAAAA
2220125 CTCCCTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.27, T:0.08
Consensus pattern (20 bp):
AAGGAAAAATAAGGGAAAAT
Found at i:2220124 original size:10 final size:10
Alignment explanation
Indices: 2220076--2220123 Score: 80
Period size: 10 Copynumber: 4.9 Consensus size: 10
2220066 TCAGCCATTG
2220076 AAGGGAAAAT
1 AAGGGAAAAT
2220086 AAGGGAAAAT
1 AAGGGAAAAT
*
2220096 AAGGAAAAAT
1 AAGGGAAAAT
2220106 AAGGGAAAAT
1 AAGGGAAAAT
2220116 AA-GGAAAA
1 AAGGGAAAA
2220124 ACTCCCTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
9 6 0.17
10 30 0.83
ACGTcount: A:0.65, C:0.00, G:0.27, T:0.08
Consensus pattern (10 bp):
AAGGGAAAAT
Found at i:2221730 original size:19 final size:19
Alignment explanation
Indices: 2221674--2221724 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
2221664 CTATTTCAAT
2221674 CTCCAAAAACATTTTAATA
1 CTCCAAAAACATTTTAATA
2221693 CTCCAAAAACATTTTAATA
1 CTCCAAAAACATTTTAATA
2221712 CTCCAAAAA-ATTT
1 CTCCAAAAACATTT
2221725 AGAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (19 bp):
CTCCAAAAACATTTTAATA
Found at i:2233409 original size:28 final size:28
Alignment explanation
Indices: 2233355--2233411 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2233345 ATATTATAAT
* *
2233355 ATTATAAAAAAACCCTAATTTCTCTTAA
1 ATTATAAAAAAACCCTAATATCCCTTAA
*
2233383 ATTATAAAATAACCCTTAA-ATCCCTTAA
1 ATTATAAAAAAACCC-TAATATCCCTTAA
2233411 A
1 A
2233412 CCTCAAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.33
Consensus pattern (28 bp):
ATTATAAAAAAACCCTAATATCCCTTAA
Found at i:2234735 original size:179 final size:180
Alignment explanation
Indices: 2234520--2234877 Score: 684
Period size: 181 Copynumber: 2.0 Consensus size: 180
2234510 AACCCCTAAA
2234520 CCACATCGACCATCGCCTTTACCGTCGACAAAGCTCCAGCCAACCT-CCCTTCCTTTGGTGACCA
1 CCACATCGACCATCGCCTTTACCGTCGACAAAGCTCCAGCCAACCTCCCCTTCCTTTGGTGACCA
2234584 GAATCCCCATGAAATTGTGACTGATCGACGGTCGATCGATGACGAAT-AATGTTTTATACCTCGC
66 GAATCCCCATGAAATTGTGACTGATCGACGGTCGATCGATGACGAATAAATGTTTTATACCTCGC
2234648 AAACCCTAGAATGAAAATCTTAATCCCACACAATTCCGACAGCCAATCAC
131 AAACCCTAGAATGAAAATCTTAATCCCACACAATTCCGACAGCCAATCAC
*
2234698 CCACATCGACCATCGCCTTTTACCGTCGACAAAGCTCCAGCCGACCTCCCCTTCCTTTGGTGACC
1 CCACATCGACCATCGCC-TTTACCGTCGACAAAGCTCCAGCCAACCTCCCCTTCCTTTGGTGACC
2234763 AGAATCCCCATGAAATTGTGACTGATCGACGGTCGATCGATGACGAATAAATGTTTTATACCTCG
65 AGAATCCCCATGAAATTGTGACTGATCGACGGTCGATCGATGACGAATAAATGTTTTATACCTCG
2234828 CAAACCCTAGAATGAAAATCTTAATCCCACACAATTCCGACAGCCAATCA
130 CAAACCCTAGAATGAAAATCTTAATCCCACACAATTCCGACAGCCAATCA
2234878 ACTGTCGATC
Statistics
Matches: 176, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
178 17 0.10
179 28 0.16
180 65 0.37
181 66 0.38
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (180 bp):
CCACATCGACCATCGCCTTTACCGTCGACAAAGCTCCAGCCAACCTCCCCTTCCTTTGGTGACCA
GAATCCCCATGAAATTGTGACTGATCGACGGTCGATCGATGACGAATAAATGTTTTATACCTCGC
AAACCCTAGAATGAAAATCTTAATCCCACACAATTCCGACAGCCAATCAC
Found at i:2236129 original size:37 final size:38
Alignment explanation
Indices: 2236083--2236245 Score: 158
Period size: 37 Copynumber: 4.4 Consensus size: 38
2236073 TTATATAAGG
2236083 ATTTATATTAAATTAAAATGAAAATATATTA-TTACAA
1 ATTTATATTAAATTAAAATGAAAATATATTATTTACAA
** * *
2236120 ATTTATATTAGGTTGAAATATG--ATTATATTATTTATAA
1 ATTTATATTAAATT-AAA-ATGAAAATATATTATTTACAA
** **
2236158 ATTTATATTTGATT-AAAT-ACAAATATATTATTTATGA
1 ATTTATATTAAATTAAAATGA-AAATATATTATTTACAA
* *
2236195 ATTTATATTCAATTAAAATAAAAATATATTA-TTACAA
1 ATTTATATTAAATTAAAATGAAAATATATTATTTACAA
*
2236232 ATTTATATTTAATT
1 ATTTATATTAAATT
2236246 GGAATATATT
Statistics
Matches: 105, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
35 2 0.02
36 2 0.02
37 63 0.60
38 34 0.32
39 4 0.04
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (38 bp):
ATTTATATTAAATTAAAATGAAAATATATTATTTACAA
Found at i:2240752 original size:16 final size:17
Alignment explanation
Indices: 2240731--2240764 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2240721 GAGATTCTAA
2240731 GGAAAAAT-AACTTTTT
1 GGAAAAATAAACTTTTT
2240747 GGAAAAATAAACTTTTT
1 GGAAAAATAAACTTTTT
2240764 G
1 G
2240765 CTAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
GGAAAAATAAACTTTTT
Found at i:2242843 original size:21 final size:21
Alignment explanation
Indices: 2242819--2242864 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2242809 GTCATGACCC
* *
2242819 ATGAGGCGAAATTAGGGGTTG
1 ATGAGGCAAAATTAGGGGCTG
2242840 ATGAGGCAAAATTAGGGGCTG
1 ATGAGGCAAAATTAGGGGCTG
2242861 ATGA
1 ATGA
2242865 AGAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.39, T:0.22
Consensus pattern (21 bp):
ATGAGGCAAAATTAGGGGCTG
Found at i:2244681 original size:32 final size:31
Alignment explanation
Indices: 2244604--2244692 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
2244594 CCATAAGGGA
* *
2244604 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAT
1 ACATCTTAGGGCCGTG-GGGCCTACCCAAGAC
* *
2244635 AGAT-TTATGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTA-GGGCCGTGGGGCCTACCCAAG-AC
**
2244667 ACATCTTAGGGCCGTAAGGCCTACCC
1 ACATCTTAGGGCCGTGGGGCCTACCC
2244693 GAGAATGATC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
30 3 0.07
31 19 0.41
32 21 0.46
33 3 0.07
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (31 bp):
ACATCTTAGGGCCGTGGGGCCTACCCAAGAC
Found at i:2245655 original size:29 final size:29
Alignment explanation
Indices: 2245617--2245801 Score: 211
Period size: 29 Copynumber: 6.6 Consensus size: 29
2245607 CACATTCGAA
*
2245617 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
2245646 AATTCTCAGAATGTCACTTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
2245675 AATTCCCAGAATGTCA-CTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
2245703 -ATTCCC-AAATGACA-CTTTTTCAAAA-
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * * *
2245728 AAATCCAAAAAAGGCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
2245757 AATTCTCAAAATATCACCATTTTT-AAAAT
1 AATTCCCAAAATGTCACC-TTTTTCAAAAT
2245786 AATTCCCAAAATGTCA
1 AATTCCCAAAATGTCA
2245802 TCGGGTTGGG
Statistics
Matches: 133, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.16
27 12 0.09
28 22 0.17
29 73 0.55
30 5 0.04
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:2245824 original size:18 final size:17
Alignment explanation
Indices: 2245798--2245838 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2245788 TTCCCAAAAT
* *
2245798 GTCATCGGGTTGGGTCGG
1 GTCAACGGGTCGGGTC-G
2245816 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
2245833 GTCAAC
1 GTCAAC
2245839 ATGAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.12, C:0.22, G:0.44, T:0.22
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCG
Found at i:2253094 original size:29 final size:29
Alignment explanation
Indices: 2252969--2253098 Score: 162
Period size: 29 Copynumber: 4.6 Consensus size: 29
2252959 CACATTCGAA
2252969 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
2252998 AATT-CCAGAATGTCA-CTTTTT-AAAA-
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
* *
2253023 AAATCCCAAAATGTCACCTTTTTCAAAAAT
1 AATTCCCAGAATGTCACCTTTTTC-AAAAT
*
2253053 AATTCCCAGAATGTCACCAGTTTT-AAAAT
1 AATTCCCAGAATGTCACC-TTTTTCAAAAT
* *
2253082 AATTCTCAAAATGTCAC
1 AATTCCCAGAATGTCAC
2253099 GGTCGGGTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.03
26 14 0.16
27 12 0.14
28 11 0.12
29 28 0.32
30 16 0.18
31 4 0.05
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (29 bp):
AATTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:2258062 original size:14 final size:14
Alignment explanation
Indices: 2258042--2258083 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
2258032 GAATAATTCT
2258042 ATTAAAACAATATA
1 ATTAAAACAATATA
*
2258056 TTTAAAAACAATA-A
1 ATT-AAAACAATATA
2258070 ATTAAAAC-ATATA
1 ATTAAAACAATATA
2258083 A
1 A
2258084 AATAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 7 0.29
14 5 0.21
15 9 0.38
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAAACAATATA
Found at i:2258084 original size:14 final size:13
Alignment explanation
Indices: 2258042--2258089 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2258032 GAATAATTCT
2258042 ATTAAAACAATATA
1 ATTAAAACAATA-A
*
2258056 TTTAAAAACAATAA
1 ATT-AAAACAATAA
2258070 ATTAAAACATATAA
1 ATTAAAACA-ATAA
*
2258084 AATAAA
1 ATTAAA
2258090 TGACTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.21
14 14 0.48
15 9 0.31
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (13 bp):
ATTAAAACAATAA
Found at i:2259330 original size:3 final size:3
Alignment explanation
Indices: 2259322--2259441 Score: 154
Period size: 3 Copynumber: 39.3 Consensus size: 3
2259312 TTATTTATTA
*
2259322 AAT AAT AAT AAT AAT AAT ATAT ATAT AAT AAT AAT AAT AAAT ACT AAT
1 AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT -AAT AAT AAT
**
2259370 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
*
2259416 ACT AAT -AT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2259442 TAAAATGGAT
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.04
3 87 0.84
4 13 0.12
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2269394 original size:45 final size:45
Alignment explanation
Indices: 2269325--2269411 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
2269315 ATGTACAAGC
2269325 AAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGTAAGT
1 AAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGTAAGT
*
2269370 AAATTACAAAAACAATTGAGAATGGAAACATAGAAATAAGTA
1 AAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGTA
2269412 CCCCGTTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.20
Consensus pattern (45 bp):
AAATTACAAAAACAATTGAAAATGGAAACATAGAAATAAGTAAGT
Found at i:2269557 original size:38 final size:41
Alignment explanation
Indices: 2269478--2269559 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 41
2269468 CCTTTGATCC
2269478 TCGAATATGAGAAATAACCTTTTACAAGTACTGTTATTTTCCT
1 TCGAATAT-AGAAATAACC-TTTACAAGTACTGTTATTTTCCT
2269521 TCGAATAT-GAAATAACC-TTACAAGTA-TGTTATTTTCCT
1 TCGAATATAGAAATAACCTTTACAAGTACTGTTATTTTCCT
2269559 T
1 T
2269560 TTTTCTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
38 13 0.33
39 9 0.23
41 9 0.23
43 8 0.21
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (41 bp):
TCGAATATAGAAATAACCTTTACAAGTACTGTTATTTTCCT
Found at i:2270037 original size:53 final size:55
Alignment explanation
Indices: 2269928--2270360 Score: 293
Period size: 54 Copynumber: 8.3 Consensus size: 55
2269918 ATACTTGAAA
* * * * *
2269928 AATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCAAGGAGTATAAGACTCGAAC
1 AATCTTCAACA-AACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
*** * *
2269983 AATCTTTGGCAAACGTGTCTGCT-CCTCTGC-TTCAGGGAGTATAAGACTCAAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
* *
2270036 AATCTTCAACAAACGTGTCTGCTCCCTATTCGTTC-GGGAGTATAAGACTCGAAT
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
* * * * * * *
2270090 AATCTTAAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAG-ACTCGAAC
* * * * *
2270145 AATCTTCAACAAAC-TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
* * * * * *
2270195 AATCTTC-ACGAACTTGTCCGCTCCCTATTC-TTCAGAGAGTATAGGACT----C
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
* * * * * *
2270244 AATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
* * * * * * *
2270295 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
2270346 AATCTTCAACAAACG
1 AATCTTCAACAAACG
2270361 AATTTGCTTC
Statistics
Matches: 338, Mismatches: 31, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
49 31 0.09
50 46 0.14
51 82 0.24
53 41 0.12
54 89 0.26
55 48 0.14
56 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (55 bp):
AATCTTCAACAAACGTGTCTGCTCCCTATGCGTTCAGGGAGTATAAGACTCGAAC
Found at i:2270157 original size:109 final size:101
Alignment explanation
Indices: 2270035--2270360 Score: 406
Period size: 100 Copynumber: 3.2 Consensus size: 101
2270025 AAGACTCAAA
* * *
2270035 CAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTC-GGGAGTATAAGACTCGAATAATCTTAAA
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC----AATCTT-AA
* *
2270099 CAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
61 CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
* *
2270140 CGAACAATCTTCAACAAAC-TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAC
1 ----CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTAAC
* * *
2270204 GAACTTGTCCGCTCCCTATT-CTTCAGAGAGTATAGGACT
62 AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
* * *
2270243 CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAA
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTT-AACAAA
* *
2270308 CTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
65 CGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
2270345 CAATCTTCAACAAACG
1 CAATCTTCAACAAACG
2270361 AATTTGCTTC
Statistics
Matches: 201, Mismatches: 12, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
99 15 0.07
100 42 0.21
101 22 0.11
102 34 0.17
103 18 0.09
104 18 0.09
105 6 0.03
108 18 0.09
109 28 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (101 bp):
CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTAACAAAC
GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
Found at i:2270300 original size:51 final size:51
Alignment explanation
Indices: 2270035--2270359 Score: 442
Period size: 51 Copynumber: 6.3 Consensus size: 51
2270025 AAGACTCAAA
* * * * *
2270035 CAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTC-GGGAGTATAAGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
* ** * *
2270085 CGAATAATCTTAAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 C----AATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
2270140 CGAACAATCTTCAACAAAC-TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1 ----CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
*
2270194 CAATCTTC-ACGAACTTGTCCGCTCCCTATT-CTTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
2270243 CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
*
2270294 CAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
2270345 CAATCTTCAACAAAC
1 CAATCTTCAACAAAC
2270360 GAATTTGCTT
Statistics
Matches: 247, Mismatches: 16, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
49 32 0.13
50 45 0.18
51 83 0.34
54 62 0.25
55 24 0.10
59 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (51 bp):
CAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
Found at i:2271687 original size:17 final size:17
Alignment explanation
Indices: 2271665--2271809 Score: 73
Period size: 18 Copynumber: 8.1 Consensus size: 17
2271655 CCCTCCTTTA
2271665 TTTCTCTTTTTTTCATT
1 TTTCTCTTTTTTTCATT
*
2271682 TTTCTCTTTTTGTTTTCATACG
1 TTTCTC--TTT-TTTTCAT--T
* *
2271704 TTT-TATATTTTTCATT
1 TTTCTCTTTTTTTCATT
* *
2271720 TTTC-ATTTTCTTCATT
1 TTTCTCTTTTTTTCATT
**
2271736 TTTCT-TTTTTCACCATT
1 TTTCTCTTTTT-TTCATT
*
2271753 TTTCATTTTTTTTTCTCATT
1 TTTC--TCTTTTTT-TCATT
*
2271773 TTTCAT-TTTCTTTCATT
1 TTTC-TCTTTTTTTCATT
*
2271790 TTTCCTCCTTTTTTCATT
1 TTT-CTCTTTTTTTCATT
2271808 TT
1 TT
2271810 CCTTTTCATT
Statistics
Matches: 99, Mismatches: 15, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
16 21 0.21
17 23 0.23
18 24 0.24
19 7 0.07
20 20 0.20
21 1 0.01
22 3 0.03
ACGTcount: A:0.10, C:0.18, G:0.01, T:0.70
Consensus pattern (17 bp):
TTTCTCTTTTTTTCATT
Found at i:2271765 original size:20 final size:21
Alignment explanation
Indices: 2271740--2271781 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2271730 TTCATTTTTC
2271740 TTTTTTCACCATTTTTCATTT
1 TTTTTTCACCATTTTTCATTT
*
2271761 TTTTTTC-TCATTTTTCATTT
1 TTTTTTCACCATTTTTCATTT
2271781 T
1 T
2271782 CTTTCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTCACCATTTTTCATTT
Found at i:2271809 original size:7 final size:7
Alignment explanation
Indices: 2271710--2271781 Score: 67
Period size: 7 Copynumber: 9.7 Consensus size: 7
2271700 TACGTTTTAT
2271710 ATTTTTC
1 ATTTTTC
2271717 ATTTTTC
1 ATTTTTC
2271724 ATTTTCTTC
1 A-TTT-TTC
2271733 ATTTTTC
1 ATTTTTC
*
2271740 TTTTTTCACC
1 ATTTTT---C
2271750 ATTTTTC
1 ATTTTTC
2271757 ATTTTT-
1 ATTTTTC
2271763 -TTTTCTC
1 ATTTT-TC
2271770 ATTTTTC
1 ATTTTTC
2271777 ATTTT
1 ATTTT
2271782 CTTTCATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
5 4 0.07
6 1 0.02
7 30 0.55
8 10 0.18
9 4 0.07
10 6 0.11
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTC
Found at i:2281512 original size:45 final size:48
Alignment explanation
Indices: 2281445--2281544 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 48
2281435 TGTTATCCAC
*
2281445 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC-TTATTC-A
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCGA
* *
2281491 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGA
2281539 AAAAAG
1 AAAAAG
2281545 GAAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 27 0.57
46 8 0.17
47 6 0.13
48 6 0.13
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (48 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCGA
Found at i:2284417 original size:45 final size:45
Alignment explanation
Indices: 2284353--2284443 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
2284343 ACGCATGTAC
2284353 AAGCAAATTACAAAAACAATTGAAAATAGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATAGAAACATAGAAATAAGT
* *
2284398 AAGCAAATTACAAAAACAATTGAGAATGGAAACATAGAAATAAGT
1 AAGCAAATTACAAAAACAATTGAAAATAGAAACATAGAAATAAGT
2284443 A
1 A
2284444 CCCCTTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.18
Consensus pattern (45 bp):
AAGCAAATTACAAAAACAATTGAAAATAGAAACATAGAAATAAGT
Found at i:2288072 original size:21 final size:21
Alignment explanation
Indices: 2288048--2288098 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
2288038 GACATCAAAT
2288048 TCATATCAAGTTCAGATC-ATG
1 TCATATC-AGTTCAGATCGATG
* *
2288069 TCATTTTCAGTTTAGATCGATG
1 TCA-TATCAGTTCAGATCGATG
2288091 TCAT-TCAG
1 TCATATCAG
2288099 GTTAAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 13 0.50
22 9 0.35
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (21 bp):
TCATATCAGTTCAGATCGATG
Found at i:2288790 original size:11 final size:11
Alignment explanation
Indices: 2288776--2288811 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2288766 ATATAATATA
*
2288776 TATATATAGTT
1 TATATGTAGTT
2288787 TATATGTAGTT
1 TATATGTAGTT
*
2288798 TACATGTAGTT
1 TATATGTAGTT
2288809 TAT
1 TAT
2288812 TAATAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (11 bp):
TATATGTAGTT
Found at i:2288791 original size:13 final size:13
Alignment explanation
Indices: 2288742--2288783 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2288732 TTGAAAAAAG
2288742 TATAATATATATA
1 TATAATATATATA
* * *
2288755 TA-AAGACAAATA
1 TATAATATATATA
2288767 TATAATATATATA
1 TATAATATATATA
2288780 TATA
1 TATA
2288784 GTTTATATGT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
TATAATATATATA
Found at i:2288860 original size:30 final size:28
Alignment explanation
Indices: 2288826--2288881 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
2288816 AAACTATGTA
2288826 ATTTATATATATAAATATATAATATATAAG
1 ATTTATATATAT-AATATAT-ATATATAAG
* *
2288856 ATTTATGTATATAATTTATATATATA
1 ATTTATATATATAATATATATATATA
2288882 GTATATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 6 0.25
30 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (28 bp):
ATTTATATATATAATATATATATATAAG
Found at i:2288866 original size:13 final size:13
Alignment explanation
Indices: 2288824--2288881 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
2288814 ATAAACTATG
2288824 TAATTTATATATA
1 TAATTTATATATA
*
2288837 TAAATATATAATATA
1 T-AATTTAT-ATATA
*
2288852 TAAGATTTATGTATA
1 T-A-ATTTATATATA
2288867 TAATTTATATATA
1 TAATTTATATATA
2288880 TA
1 TA
2288882 GTATATTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 13 0.34
14 7 0.18
15 13 0.34
16 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
TAATTTATATATA
Found at i:2289015 original size:2 final size:2
Alignment explanation
Indices: 2289010--2289139 Score: 78
Period size: 2 Copynumber: 66.0 Consensus size: 2
2289000 AGTATTAAAG
* * *
2289010 TA TA TA -A TT TA TA TA TA TA -A TA TA -A GTT TA TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* *
2289051 TA TA TA TA -A TA TA AA CTA TA TA T- TA TA AA CTA TA TA 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
* * *
2289093 TA GTA TA TA TA AA CT- TA TA -A TT TA TA T- TA TA TA TA TA TA TG
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2289134 TA TA TA
1 TA TA TA
2289140 ACTAATATAA
Statistics
Matches: 98, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
1 8 0.08
2 85 0.87
3 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2289053 original size:30 final size:34
Alignment explanation
Indices: 2289019--2289092 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
2289009 GTATATAATT
*
2289019 TATATATATAATAT-AAGT-T-TA-TATAAACTA
1 TATATATATAATATAAACTATATATTATAAACTA
2289049 TATATATATAATATAAACTATATATTATAAACTA
1 TATATATATAATATAAACTATATATTATAAACTA
2289083 TATATATATA
1 TATATATATA
2289093 TAGTATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 14 0.36
31 3 0.08
32 1 0.03
33 2 0.05
34 19 0.49
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (34 bp):
TATATATATAATATAAACTATATATTATAAACTA
Found at i:2289102 original size:60 final size:63
Alignment explanation
Indices: 2289009--2289148 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 63
2288999 AAGTATTAAA
* *
2289009 GTATATAATTTATATATATAATATAAGTTTATATAAAC-TATATATATATAATATAAACTATATA
1 GTATATAA-CTATATATATAATATAAGTATATATAAACTTATA-ATATATAATATAAA-TATATA
2289073 T
63 T
* * *
2289074 -TATA-AACTATATATAT-ATAT-AGTATATATAAACTTATAATTTATATTATATATATATAT
1 GTATATAACTATATATATAATATAAGTATATATAAACTTATAATATATAATATAAATATATAT
2289133 GTATATAACTA-ATATA
1 GTATATAACTATATATA
2289149 AGTAATCTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
59 7 0.10
60 32 0.48
61 13 0.19
62 9 0.13
63 2 0.03
64 4 0.06
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.45
Consensus pattern (63 bp):
GTATATAACTATATATATAATATAAGTATATATAAACTTATAATATATAATATAAATATATAT
Found at i:2289111 original size:34 final size:33
Alignment explanation
Indices: 2289040--2289174 Score: 110
Period size: 34 Copynumber: 3.9 Consensus size: 33
2289030 TATAAGTTTA
* *
2289040 TATAAACTATATATATATAATATAAACTATATA-T
1 TATAAACTATATATATAT-ATATATA-TATAAACT
2289074 TATAAACTATATATATATATAGTATATATAAACT
1 TATAAACTATATATATATATA-TATATATAAACT
** *
2289108 TATAATTTATATTATATATATATATGTATATAACT
1 TATAAACTATA-TATATATATATATATATA-AACT
* * * *
2289143 AATATAAGTAATCTATAGATTATATATATATA
1 TATA-AACT-ATATATATA-TATATATATATA
2289175 GTTTATAGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
33 8 0.10
34 38 0.46
35 17 0.20
36 7 0.08
37 13 0.16
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (33 bp):
TATAAACTATATATATATATATATATATAAACT
Found at i:2289426 original size:37 final size:35
Alignment explanation
Indices: 2289365--2289443 Score: 86
Period size: 37 Copynumber: 2.2 Consensus size: 35
2289355 ACAATAGTTA
* * *
2289365 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTACAATACATGTAT--ATGTAAACT
* *
2289402 ATATATGTAACTTACAATACATGTATGTGTAAACT
1 ATATATGTAACCTACAATACATGTATATGTAAACT
*
2289437 ATGTATG
1 ATATATG
2289444 ATATATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 14 0.39
37 22 0.61
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (35 bp):
ATATATGTAACCTACAATACATGTATATGTAAACT
Found at i:2289451 original size:2 final size:2
Alignment explanation
Indices: 2289444--2289516 Score: 130
Period size: 2 Copynumber: 36.5 Consensus size: 2
2289434 ACTATGTATG
2289444 AT AT AT AT A- ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2289486 AT 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 AT A
2289517 ACCTATAGTA
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 67 0.97
3 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2289637 original size:21 final size:21
Alignment explanation
Indices: 2289611--2289658 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2289601 ATTAGTGTAT
* *
2289611 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
2289632 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
2289653 TTTATA
1 TATATA
2289659 TTAATGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:2289719 original size:15 final size:15
Alignment explanation
Indices: 2289669--2289719 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2289659 TTAATGTACT
*
2289669 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
2289684 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
2289699 ACTATAATTTATATTA
1 A-TATAATTTATATTA
2289715 ATATA
1 ATATA
2289720 GTATATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:2290795 original size:23 final size:24
Alignment explanation
Indices: 2290767--2290820 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
2290757 TTATTTTTTC
2290767 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
2290790 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
2290814 TTTACAT
1 TTTACAT
2290821 TTAATCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:2290916 original size:23 final size:25
Alignment explanation
Indices: 2290859--2290916 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 25
2290849 ATTAATCATG
*
2290859 TTTTATATAATTTACATTTAAATAT
1 TTTTATATAATTTACATTTAAATAA
*
2290884 TTTTAT-TAATTT-TA-TTAAATAA
1 TTTTATATAATTTACATTTAAATAA
2290906 TTTTATATAAT
1 TTTTATATAAT
2290917 AAGTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 13 0.43
23 5 0.17
24 6 0.20
25 6 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTATATAATTTACATTTAAATAA
Found at i:2293753 original size:20 final size:20
Alignment explanation
Indices: 2293708--2293759 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2293698 CCCTTCAAGG
*
2293708 AGTATCGATACTCAAGGATC
1 AGTATCGATACTCAAGGACC
* *
2293728 AATATCGATAC-CAGATGACC
1 AGTATCGATACTCA-AGGACC
2293748 AGTATCGATACT
1 AGTATCGATACT
2293760 GAGACATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTCAAGGACC
Found at i:2298720 original size:31 final size:31
Alignment explanation
Indices: 2298649--2298723 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 31
2298639 GGGGCCTAAG
* *
2298649 AGCCTACCCAAGAAAATTCTCGGGGACACAA
1 AGCCTACCCAAGAAAAATCTCAGGGACACAA
***
2298680 AGGCCTACCCAAGAAAAATCTCAGGGTTGCAA
1 A-GCCTACCCAAGAAAAATCTCAGGGACACAA
2298712 AGCCTACCCAAG
1 AGCCTACCCAAG
2298724 GGTGCCTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.13
Consensus pattern (31 bp):
AGCCTACCCAAGAAAAATCTCAGGGACACAA
Found at i:2300144 original size:20 final size:20
Alignment explanation
Indices: 2300119--2300164 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2300109 TGTTATTTGG
2300119 GTATCGGTACACTGAGGAGT
1 GTATCGGTACACTGAGGAGT
2300139 GTATCGGTACACTGAGGAGT
1 GTATCGGTACACTGAGGAGT
2300159 GTATCG
1 GTATCG
2300165 ATACCCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (20 bp):
GTATCGGTACACTGAGGAGT
Found at i:2300198 original size:75 final size:75
Alignment explanation
Indices: 2300063--2300219 Score: 260
Period size: 75 Copynumber: 2.1 Consensus size: 75
2300053 TGAATGAGTC
* * ** *
2300063 TGTATTGGTACCCTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGTTATTTGGGTATCGGTA
1 TGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGCCATTAGGGTATCGGTA
2300128 CACTGAGGAG
66 CACTGAGGAG
*
2300138 TGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGCCATTAGTGTATCGGTA
1 TGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGCCATTAGGGTATCGGTA
2300203 CACTGAGGAG
66 CACTGAGGAG
2300213 TGTATCG
1 TGTATCG
2300220 ATACCCTTGT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (75 bp):
TGTATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAGTGCCATTAGGGTATCGGTA
CACTGAGGAG
Found at i:2301039 original size:21 final size:21
Alignment explanation
Indices: 2301014--2301102 Score: 101
Period size: 21 Copynumber: 4.1 Consensus size: 21
2301004 AGGGTCTTTA
2301014 TGGTCATTCGGGACAATTATG
1 TGGTCATTCGGGACAATTATG
* *
2301035 TGGTCATTCGTGACAAATATG
1 TGGTCATTCGGGACAATTATG
*
2301056 TGG-CACTTCGGTG-CAAACCTATG
1 TGGTCA-TTCGG-GAC-AA-TTATG
2301079 TGGTCATTCGGGACAATTATG
1 TGGTCATTCGGGACAATTATG
2301100 TGG
1 TGG
2301103 CACTTTAGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 34 0.60
22 6 0.11
23 13 0.23
24 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (21 bp):
TGGTCATTCGGGACAATTATG
Found at i:2301081 original size:44 final size:44
Alignment explanation
Indices: 2301031--2301116 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
2301021 TCGGGACAAT
* *
2301031 TATGTGGTCATTCGTGACAAATATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCATTCGGGACAAATATGTGGCACTTCAGTGCAAACC
* *
2301075 TATGTGGTCATTCGGGACAATTATGTGGCACTTTAGTGCAAA
1 TATGTGGTCATTCGGGACAAATATGTGGCACTTCAGTGCAAA
2301117 TTACAAGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TATGTGGTCATTCGGGACAAATATGTGGCACTTCAGTGCAAACC
Found at i:2306922 original size:31 final size:31
Alignment explanation
Indices: 2306882--2306940 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2306872 TCGGCTCAGC
* *
2306882 GGCTCAGCTCGATGACTCTGCTCGGCGGCTT
1 GGCTAAGCTCGATGACTCGGCTCGGCGGCTT
* *
2306913 GGCTAAGCTCGGTGGCTCGGCTCGGCGG
1 GGCTAAGCTCGATGACTCGGCTCGGCGG
2306941 TGAGGTTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.08, C:0.31, G:0.39, T:0.22
Consensus pattern (31 bp):
GGCTAAGCTCGATGACTCGGCTCGGCGGCTT
Found at i:2308403 original size:20 final size:20
Alignment explanation
Indices: 2308378--2308428 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2308368 CACTTCAAGG
*
2308378 AGTATCGATACACAAGGTCT
1 AGTATCGATACACAAGGTCC
*
2308398 AGTATCGATACCCAAGGTCC
1 AGTATCGATACACAAGGTCC
2308418 AGTATCGATAC
1 AGTATCGATAC
2308429 TGAGGCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
AGTATCGATACACAAGGTCC
Found at i:2319464 original size:31 final size:31
Alignment explanation
Indices: 2319426--2319487 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2319416 TAACATATGA
2319426 TTGAAGCTAGCACATAAAGAATTACATCAAT
1 TTGAAGCTAGCACATAAAGAATTACATCAAT
* *
2319457 TTGAAGCTAGCTCATAAAGAATTACGTCAAT
1 TTGAAGCTAGCACATAAAGAATTACATCAAT
2319488 AGGTTTCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (31 bp):
TTGAAGCTAGCACATAAAGAATTACATCAAT
Found at i:2326668 original size:38 final size:36
Alignment explanation
Indices: 2326551--2326669 Score: 100
Period size: 38 Copynumber: 3.3 Consensus size: 36
2326541 TTTTAGGAAC
*
2326551 CAAAGATGGAATTACCATGTGCAAAGTTGGCCACCTA
1 CAAAGATGAAATTACC-TGTGCAAAGTTGGCCACCTA
* * ** *
2326588 CCAAAGATGAATTTTCCAAT---AAGTTGGCCACCAA
1 -CAAAGATGAAATTACCTGTGCAAAGTTGGCCACCTA
* * *
2326622 CCAAGATGAAATTCCCTTGTGCAAAGTTGGTCACCTA
1 CAAAGATGAAATTACC-TGTGCAAAGTTGGCCACCTA
2326659 CTAAAGATGAA
1 C-AAAGATGAA
2326670 TTTTTCAACT
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
33 13 0.21
34 14 0.23
37 14 0.23
38 21 0.34
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (36 bp):
CAAAGATGAAATTACCTGTGCAAAGTTGGCCACCTA
Found at i:2345719 original size:26 final size:26
Alignment explanation
Indices: 2345681--2345733 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
2345671 AATGACTTAA
2345681 GAATATCACCAAGCCTATG-AATGAAT
1 GAATATCACCAAG-CTATGAAATGAAT
*
2345707 GAATATC-CTCAAGCTTTGAAATGAAT
1 GAATATCAC-CAAGCTATGAAATGAAT
2345733 G
1 G
2345734 GAAATACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (26 bp):
GAATATCACCAAGCTATGAAATGAAT
Found at i:2356029 original size:79 final size:79
Alignment explanation
Indices: 2355941--2356093 Score: 216
Period size: 79 Copynumber: 1.9 Consensus size: 79
2355931 AGGTGTTTAC
* * * * *
2355941 AAATTAAGCTCACAAAAACAATCTATGTACAAGAGAAAAGAAATAACAAAGAATTAAAAGTTTTT
1 AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
2356006 CTCGTGATCCTATT
66 CTCGTGATCCTATT
* * * *
2356020 AAATAAAGCTTACAAAAACACTATATGTATAAGAGAAAAGAAAGAACGAAGAATGAAAAGCTTTT
1 AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
*
2356085 CTCTTGATC
66 CTCGTGATC
2356094 ATTGTTGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (79 bp):
AAATAAAGCTCACAAAAACAATATATGTACAAGAGAAAAGAAAGAACAAAGAATGAAAAGCTTTT
CTCGTGATCCTATT
Found at i:2357913 original size:33 final size:32
Alignment explanation
Indices: 2357844--2357922 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
2357834 AAAGTTAACT
* * *
2357844 GGTTTAATATATTTGTCTAGAATTTATAAACC
1 GGTTTAATATCTTTGCCAAGAATTTATAAACC
*
2357876 GGTTTAATATCTTTGCCAAGAATTTGTAAAACC
1 GGTTTAATATCTTTGCCAAGAATTTAT-AAACC
2357909 GGTTTAATATCTTT
1 GGTTTAATATCTTT
2357923 TGACTTTCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 23 0.55
33 19 0.45
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (32 bp):
GGTTTAATATCTTTGCCAAGAATTTATAAACC
Found at i:2357956 original size:27 final size:27
Alignment explanation
Indices: 2357914--2357969 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2357904 AAACCGGTTT
*
2357914 AATATCTTTTGACTTTCGATTAAATTG
1 AATAACTTTTGACTTTCGATTAAATTG
* *
2357941 AATAACTTTTGGCTTTCGATTAGATTG
1 AATAACTTTTGACTTTCGATTAAATTG
2357968 AA
1 AA
2357970 GTTGTGGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (27 bp):
AATAACTTTTGACTTTCGATTAAATTG
Found at i:2359788 original size:18 final size:17
Alignment explanation
Indices: 2359765--2359808 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2359755 CGTTTCTGAG
2359765 GGAATTGAAATATGTGAA
1 GGAATTGAAATATGT-AA
* * *
2359783 GGAATTGGAATCTGTCA
1 GGAATTGAAATATGTAA
2359800 GGAATTGAA
1 GGAATTGAA
2359809 TCCAATTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.39, C:0.05, G:0.30, T:0.27
Consensus pattern (17 bp):
GGAATTGAAATATGTAA
Found at i:2360652 original size:255 final size:256
Alignment explanation
Indices: 2360198--2360754 Score: 806
Period size: 255 Copynumber: 2.2 Consensus size: 256
2360188 AGTTTCACCC
* *
2360198 AACCTGACCCGAAATAATAAAAAAATTGTTTTTATTCAATAAAAATAGTGACTTAATTGGAAAAA
1 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAAT-AAAATAGTGACTTAATTGGAAAAA
* *
2360263 AAATATATAGAGTAGTTTTATTGTAATTATTCCTAAAAATATAAGGTAAAATTATATATATTTTG
65 AAATATATAGAGGAGTATTATTGTAATTATTCCTAAAAATATAAGGTAAAATTATATATATTTT-
* *
2360328 GGTCAGGTCTGGTCGGGTATTTTTCACCCTACACCCGAACCCGACCCGACCCGAAAATCACACTT
129 -GTCAGG-CT-GTCGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAAAATCACACTT
* *
2360393 AAAAAAATTGACCTGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG
191 AAAAAAACTGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAG
2360458 A
256 A
* *
2360459 AATCCGACCCGACCCGA-AATAAAAAAATTATTTTTATTCAATAAAATCAGTGACTTAATT-GAA
1 AACCCGACCCGA---AATAATAAAAAAATTATTTTTATTCAATAAAAT-AGTGACTTAATTGGAA
*
2360522 AAAAATTATATATAGAGGGGTATTATTGTAATTATT-CTAAAATATATAAGGTAAAATTATATAT
62 AAAAA--ATATATAGAGGAGTATTATTGTAATTATTCCTAAAA-ATATAAGGTAAAATTATATAT
* * *
2360586 A-TTT-TCAGG-T-T-GAGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACAT
124 ATTTTGTCAGGCTGTCGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAAAATCACAC
*
2360646 TTAAAAAAACTGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATT
189 TTAAAAAAACTGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATT
2360711 AGA
254 AGA
*
2360714 AACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATA
1 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATA
2360755 TATGAATTAG
Statistics
Matches: 270, Mismatches: 18, Indels: 24
0.87 0.06 0.08
Matches are distributed among these distances:
252 1 0.00
253 25 0.09
255 120 0.44
256 1 0.00
258 1 0.00
260 5 0.02
261 10 0.04
262 13 0.05
263 45 0.17
264 49 0.18
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (256 bp):
AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAATAGTGACTTAATTGGAAAAAA
AATATATAGAGGAGTATTATTGTAATTATTCCTAAAAATATAAGGTAAAATTATATATATTTTGT
CAGGCTGTCGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAAAATCACACTTAAAAA
AACTGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGA
Found at i:2361945 original size:31 final size:31
Alignment explanation
Indices: 2361910--2361971 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2361900 TAACACATGA
2361910 TTGAAGCTAGCACAAAAAGAATTACATCAAT
1 TTGAAGCTAGCACAAAAAGAATTACATCAAT
* * * *
2361941 TTGAAGCTCGCTCATAAAGAATTACGTCAAT
1 TTGAAGCTAGCACAAAAAGAATTACATCAAT
2361972 AGGTTTCGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (31 bp):
TTGAAGCTAGCACAAAAAGAATTACATCAAT
Found at i:2362219 original size:20 final size:20
Alignment explanation
Indices: 2362194--2362253 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
2362184 AAGTGAGAAT
2362194 CCTTACCACTACACGATAAC
1 CCTTACCACTACACGATAAC
2362214 CCTTACCACTACACGATAAC
1 CCTTACCACTACACGATAAC
*
2362234 CCTTACCACTACACTATAAC
1 CCTTACCACTACACGATAAC
2362254 GACTTGATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.22
Consensus pattern (20 bp):
CCTTACCACTACACGATAAC
Found at i:2368097 original size:12 final size:12
Alignment explanation
Indices: 2368054--2368103 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
2368044 CATAGTGTTT
2368054 TTATTTTACTTG
1 TTATTTTACTTG
2368066 TTCATTTT--TTG
1 TT-ATTTTACTTG
2368077 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
2368091 TTATTTTCCTTG
1 TTATTTTACTTG
2368103 T
1 T
2368104 CTTTTTAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:2391093 original size:27 final size:27
Alignment explanation
Indices: 2391063--2391115 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2391053 CCTTAAGATC
*
2391063 TATTCAGTGATGATTCCGAAAATGATA
1 TATTCAGTGATGAGTCCGAAAATGATA
*
2391090 TATTCAGTGATGAGTCCGAAGATGAT
1 TATTCAGTGATGAGTCCGAAAATGAT
2391116 CTATGGATAA
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:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (27 bp):
TATTCAGTGATGAGTCCGAAAATGATA
Found at i:2391405 original size:20 final size:20
Alignment explanation
Indices: 2391380--2391420 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2391370 TGGATAAGCT
2391380 AAATCTGTTCTATTTTAACC
1 AAATCTGTTCTATTTTAACC
2391400 AAATCTGTTCTATTTTAACC
1 AAATCTGTTCTATTTTAACC
2391420 A
1 A
2391421 TGCACGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (20 bp):
AAATCTGTTCTATTTTAACC
Found at i:2396799 original size:20 final size:20
Alignment explanation
Indices: 2396770--2396807 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2396760 ATAAGCTGAC
*
2396770 TCTGTTCTATTTTAACCAAA
1 TCTGTCCTATTTTAACCAAA
2396790 TCTGTCCTATTTTAACCA
1 TCTGTCCTATTTTAACCA
2396808 TGCACGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
TCTGTCCTATTTTAACCAAA
Found at i:2400247 original size:19 final size:20
Alignment explanation
Indices: 2400202--2400249 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2400192 TATACTATGC
* * *
2400202 TTGAAATTAATTTTAGAGTG
1 TTGAAATTGATGTTAGAATG
2400222 TTGAAATTGATGTTAGAATG
1 TTGAAATTGATGTTAGAATG
2400242 -TGAAATTG
1 TTGAAATTG
2400250 GGCCACTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGAAATTGATGTTAGAATG
Found at i:2402031 original size:20 final size:20
Alignment explanation
Indices: 2402006--2402043 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2401996 ATAAGCTGAC
2402006 TCTGTTCTATTTTAACCAAA
1 TCTGTTCTATTTTAACCAAA
2402026 TCTGTTCTATTTTAACCA
1 TCTGTTCTATTTTAACCA
2402044 TGAACGCTAT
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:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (20 bp):
TCTGTTCTATTTTAACCAAA
Found at i:2403516 original size:23 final size:20
Alignment explanation
Indices: 2403470--2403539 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
2403460 TACCAATTTG
*
2403470 TAATATTTATGAACCAATTA
1 TAATATTTATGAATCAATTA
2403490 TAATATTTATGAATCTAATATTA
1 TAATATTTATGAATC--A-ATTA
*
2403513 TAATAATTATGAATCAATTA
1 TAATATTTATGAATCAATTA
2403533 TAATATT
1 TAATATT
2403540 ATATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 24 0.55
21 1 0.02
22 1 0.02
23 18 0.41
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
TAATATTTATGAATCAATTA
Found at i:2406605 original size:20 final size:20
Alignment explanation
Indices: 2406582--2406619 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2406572 CGGGTCGGAC
2406582 CGGGTAGGGTCAGGTCAGAT
1 CGGGTAGGGTCAGGTCAGAT
*
2406602 CGGGTCGGGTCAGGTCAG
1 CGGGTAGGGTCAGGTCAG
2406620 TCAAACAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.18
Consensus pattern (20 bp):
CGGGTAGGGTCAGGTCAGAT
Found at i:2412087 original size:15 final size:15
Alignment explanation
Indices: 2412067--2412097 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2412057 ACATGGCCTT
2412067 AGTTTGGACTCATTC
1 AGTTTGGACTCATTC
2412082 AGTTTGGACTCATTC
1 AGTTTGGACTCATTC
2412097 A
1 A
2412098 TAGTCCGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (15 bp):
AGTTTGGACTCATTC
Found at i:2412799 original size:31 final size:31
Alignment explanation
Indices: 2412764--2412839 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
2412754 CAGGGCCATG
2412764 GGGCCTACCTAAGAAAAATCACAGGGCCGCA
1 GGGCCTACCTAAGAAAAATCACAGGGCCGCA
** ** *
2412795 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAAAATCACAGGGCCGCA
**
2412826 GAACCTACCTAAGA
1 GGGCCTACCTAAGA
2412840 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.30, G:0.26, T:0.12
Consensus pattern (31 bp):
GGGCCTACCTAAGAAAAATCACAGGGCCGCA
Found at i:2415702 original size:20 final size:21
Alignment explanation
Indices: 2415674--2415713 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2415664 TAATGTACCA
2415674 TGTTGGAAATTAATGTTAGAG
1 TGTTGGAAATTAATGTTAGAG
*
2415695 TGTT-GAAATTGATGTTAGA
1 TGTTGGAAATTAATGTTAGA
2415714 ATATGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (21 bp):
TGTTGGAAATTAATGTTAGAG
Found at i:2415722 original size:19 final size:20
Alignment explanation
Indices: 2415679--2415724 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2415669 TACCATGTTG
* * *
2415679 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGAT
2415699 GAAATTGATGTTAGAAT-AT
1 GAAATTGATGTTAGAATGAT
2415718 GAAATTG
1 GAAATTG
2415725 GCCCACATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGAT
Found at i:2422404 original size:20 final size:20
Alignment explanation
Indices: 2422379--2422418 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2422369 GGATAAGCTG
2422379 AATCTGTTCTATTTTAACCA
1 AATCTGTTCTATTTTAACCA
2422399 AATCTGTTCTATTTTAACCA
1 AATCTGTTCTATTTTAACCA
2422419 TGCACGCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (20 bp):
AATCTGTTCTATTTTAACCA
Done.