Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397276.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_106.0, 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: 2845708
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.30
Warning! 346660 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:2627122 original size:31 final size:30
Alignment explanation
Indices: 2627069--2627133 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
2627059 GCTAGGAAGC
2627069 AAAAGAAGAAAGAAAGAAAGGAGAAAGGAAA
1 AAAAGAAGAAAGAAAGAAAGGAGAAA-GAAA
* * * *
2627100 AAAGGAAGTAAGGAAGAGAGGAGAAAGAAA
1 AAAAGAAGAAAGAAAGAAAGGAGAAAGAAA
2627130 AAAA
1 AAAA
2627134 AGGTAAGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (30 bp):
AAAAGAAGAAAGAAAGAAAGGAGAAAGAAA
Found at i:2633637 original size:21 final size:21
Alignment explanation
Indices: 2633598--2633637 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2633588 ACTCTTTGTC
* **
2633598 TTCTTCCAATTCTCCTCTCTT
1 TTCTTCCAATTATAATCTCTT
2633619 TTCTTCCAATTATAATCTC
1 TTCTTCCAATTATAATCTC
2633638 ACTCTATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (21 bp):
TTCTTCCAATTATAATCTCTT
Found at i:2635172 original size:447 final size:443
Alignment explanation
Indices: 2634228--2635278 Score: 1043
Period size: 447 Copynumber: 2.3 Consensus size: 443
2634218 ATGACGAGTT
* * * * * *
2634228 GCTTGGTTTGATTGCCAAGTTCAGTTAACCTAAGAAACAAAAAGTCTCTTTACTTAAAGATTATT
1 GCTTGGTCTCATTGCCAAGTTCAGTCAACCCAAAAAACAAAAAGTCTCTTTA-TTAAAGATAATT
* * * * * * *
2634293 TACATATTTGCCATTTTGAAATTGCCAAGTTGATGTCGATAATTGAAAAAGTTCATACTACCAAT
65 CAAATATTTACCATTTTGAAATTGCCAAGTTGATCTCGATAATTGAAGAAGTTCAAACTATCAAT
* *
2634358 TGCTAA-TGAAGTGAAA-AAGACTAATTGCTTGAGTCTATGACTCACATTCGGCCCAATCAATTG
130 TGC-AAGTGAAGT-AAAGAAGACTTATTGCTTGAGTCTATGACTCACATTCGACCCAATCAATTG
* ** * * * * **
2634421 TCAATTCTTGAAGTGTTGCAATGCATGAATATTAGTTCTTCCTCAGTAAAAGTTTAAACTGCCAA
193 ACAATTCTTGAAGCATTGCAATGCATGAATATTAATTCCTCCTCAATAAAAGCTTAAACTGAAAA
* *
2634486 TAAAAAATAGCCTGTTCAACCAAAAATCCTTAATACGATGGCTTAGGCAAAATTAAGTCCCATAA
258 TAAAAAATAGCCTGTTCAACCAAAAATCCTTAAAACGATAGCTTAGGCAAAATTAAGTCCCATAA
* ** *
2634551 AAAAGGAATTACTATTAAGTTGAAAATCCCTAAAAAGACAACTTAGGCAAAAGTTAAAATGTAAA
323 AAAAGAAAGAACTATTAAGTTGAAAATCCCTAAAAAGACAACTTAGGCAAAAGTT--AATGGAAA
*
2634616 GAAAAAAAAACAAGAACTACATTACAACTTGATCCTTCGTATTAGAAGGAACGTAGGCA
386 GAAAAAAAAACAAG-ACTACATTACAACTTGATCCTTCATATTAGAAGGAACGTAGGCA
* *
2634675 GTTTGGTCTCATTGCCAAGTTCAGTCAACCCAAAAAACAAAAACTCTCTTTGATTAAAGATAATT
1 GCTTGGTCTCATTGCCAAGTTCAGTCAACCCAAAAAACAAAAAGTCTCTTT-ATTAAAGATAATT
* * * * * * *
2634740 CAAATCTTTTCCATTTTGAAGTTGCCAAGTTGGTCTCTACAATTGAAGAAGTTCACACTATCAAT
65 CAAATATTTACCATTTTGAAATTGCCAAGTTGATCTCGATAATTGAAGAAGTTCAAACTATCAAT
* *
2634805 TGCAAGTGAAGTAAAGAAGACTTATTGCTTGAGTCTACT-CCTCACAATT-GATCCAATCAA-TG
130 TGCAAGTGAAGTAAAGAAGACTTATTGCTTGAGTCTA-TGACTCAC-ATTCGACCCAATCAATTG
* * * * * * *
2634867 ACAAATTCTTGATGCATTAG-AGTGCTTGGATATTAATTCCTCCTTAATAAGAGCTTAAATTGAA
193 AC-AATTCTTGAAGCATT-GCAATGCATGAATATTAATTCCTCCTCAATAAAAGCTTAAACTGAA
* * * * * * *
2634931 AATAAAAAATAGTCT-TTTAAGCCAAAAATTCTTAAAAGGATAGCTTAGGCAAAAATTACGTTCT
256 AATAAAAAATAGCCTGTTCAA-CCAAAAATCCTTAAAACGATAGCTTAGGC-AAAATTAAGTCCC
* * ** **
2634995 GTAGAAAAAGAAAGAAC-ATTGAGTTGAAAATCTTTAAAATA-ATGACTTAGGCAAAAGTT-A-G
319 ATA-AAAAAGAAAGAACTATTAAGTTGAAAATCCCTAAAA-AGACAACTTAGGCAAAAGTTAATG
*** * * *
2635056 GACCTAAAAAAAAA-AAG-CTACATTACGACTTGATCTTTCATATTA-AGAGGTACGTAGGCA
382 GAAAGAAAAAAAAACAAGACTACATTACAACTTGATCCTTCATATTAGA-AGGAACGTAGGCA
* * * ** *
2635116 GCTTGTTCTCATTGTCAAGTTTAGTCAACTGATGAAAAAGGATGAAAAAGTCTCTTTTATTAAAG
1 GCTTGGTCTCATTGCCAAGTTCAGTCAAC---CCAAAAA--A-CAAAAAGTCTC-TTTATTAAAG
* * * * *
2635181 ATAATTCAAATATTTACGATGTTGAAATTGCCAA-ATGAACGTCGATAATTGAAGAAGTTTAAAC
59 ATAATTCAAATATTTACCATTTTGAAATTGCCAAGTTGATC-TCGATAATTGAAGAAGTTCAAAC
**
2635245 TATCAAATTGCAAGTGAAGCCAAGAAGACTTATT
123 TATC-AATTGCAAGTGAAGTAAAGAAGACTTATT
2635279 TCTACTTGGT
Statistics
Matches: 495, Mismatches: 88, Indels: 41
0.79 0.14 0.07
Matches are distributed among these distances:
440 1 0.00
441 62 0.13
443 3 0.01
444 16 0.03
445 1 0.00
446 16 0.03
447 302 0.61
448 83 0.17
449 11 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (443 bp):
GCTTGGTCTCATTGCCAAGTTCAGTCAACCCAAAAAACAAAAAGTCTCTTTATTAAAGATAATTC
AAATATTTACCATTTTGAAATTGCCAAGTTGATCTCGATAATTGAAGAAGTTCAAACTATCAATT
GCAAGTGAAGTAAAGAAGACTTATTGCTTGAGTCTATGACTCACATTCGACCCAATCAATTGACA
ATTCTTGAAGCATTGCAATGCATGAATATTAATTCCTCCTCAATAAAAGCTTAAACTGAAAATAA
AAAATAGCCTGTTCAACCAAAAATCCTTAAAACGATAGCTTAGGCAAAATTAAGTCCCATAAAAA
AGAAAGAACTATTAAGTTGAAAATCCCTAAAAAGACAACTTAGGCAAAAGTTAATGGAAAGAAAA
AAAAACAAGACTACATTACAACTTGATCCTTCATATTAGAAGGAACGTAGGCA
Found at i:2640620 original size:21 final size:21
Alignment explanation
Indices: 2640594--2640636 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2640584 TGACACAGAG
*
2640594 TAATGAATACATGGCCAAGAA
1 TAATGAATACATGGCAAAGAA
*
2640615 TAATGAATAGATGGCAAAGAA
1 TAATGAATACATGGCAAAGAA
2640636 T
1 T
2640637 GATGCCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (21 bp):
TAATGAATACATGGCAAAGAA
Found at i:2642590 original size:23 final size:23
Alignment explanation
Indices: 2642563--2642609 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2642553 TTTCATTTCA
*
2642563 TGTTTGG-GGGTGTTTTTAGATTT
1 TGTTTGGTGGGTGTCTTTAG-TTT
2642586 TGTTTGGTGGGTGTCTTTAGTTT
1 TGTTTGGTGGGTGTCTTTAGTTT
2642609 T
1 T
2642610 AAGATTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.06, C:0.02, G:0.34, T:0.57
Consensus pattern (23 bp):
TGTTTGGTGGGTGTCTTTAGTTT
Found at i:2644359 original size:15 final size:16
Alignment explanation
Indices: 2644340--2644381 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
2644330 ATATATTTGT
2644340 ATTTTT-TATAAT-TA
1 ATTTTTATATAATATA
2644354 ATTTTTATATAATATA
1 ATTTTTATATAATATA
*
2644370 ATCTCTTATATA
1 AT-TTTTATATA
2644382 TTTTTTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 6 0.25
16 4 0.17
17 8 0.33
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTTATATAATATA
Found at i:2646300 original size:31 final size:30
Alignment explanation
Indices: 2646260--2646337 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
2646250 ATTTGGCTAG
2646260 GAAGCAAAGGAAGAAAGAAAGAAAGGAGAAA
1 GAAG-AAAGGAAGAAAGAAAGAAAGGAGAAA
* * *
2646291 GAAAGAAAGGAAGAATGGAAGAGAGGAGAAA
1 G-AAGAAAGGAAGAAAGAAAGAAAGGAGAAA
*
2646322 GAAGAAAAG-AGAAAGA
1 GAAGAAAGGAAGAAAGA
2646338 GAAGGTTCGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.12
30 7 0.17
31 25 0.62
32 3 0.08
ACGTcount: A:0.63, C:0.01, G:0.35, T:0.01
Consensus pattern (30 bp):
GAAGAAAGGAAGAAAGAAAGAAAGGAGAAA
Found at i:2646310 original size:8 final size:8
Alignment explanation
Indices: 2646258--2646341 Score: 77
Period size: 8 Copynumber: 10.8 Consensus size: 8
2646248 AGATTTGGCT
2646258 AGGAAGCAA
1 AGGAAG-AA
2646267 AGGAAGAA
1 AGGAAGAA
*
2646275 AGAAAGAA
1 AGGAAGAA
2646283 AGG-AGAA
1 AGGAAGAA
*
2646290 AGAAAGAA
1 AGGAAGAA
2646298 AGGAAGAA
1 AGGAAGAA
* *
2646306 TGGAAGAG
1 AGGAAGAA
2646314 AGG-AGAA
1 AGGAAGAA
2646321 A-GAAGAA
1 AGGAAGAA
*
2646328 AAG-AGAA
1 AGGAAGAA
2646335 AGAGAAG
1 AG-GAAG
2646342 GTTCGGCCTA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
6 1 0.02
7 20 0.33
8 32 0.52
9 8 0.13
ACGTcount: A:0.62, C:0.01, G:0.36, T:0.01
Consensus pattern (8 bp):
AGGAAGAA
Found at i:2651867 original size:17 final size:17
Alignment explanation
Indices: 2651845--2651888 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2651835 AAGATTAATG
2651845 TAAAAATATAAAT-AAAA
1 TAAAAA-ATAAATGAAAA
*
2651862 TAAAAAATAACTGAAAA
1 TAAAAAATAAATGAAAA
2651879 TAAAAAATAA
1 TAAAAAATAA
2651889 GAGGTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
TAAAAAATAAATGAAAA
Found at i:2657268 original size:21 final size:21
Alignment explanation
Indices: 2657221--2657268 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2657211 TGACATAGAG
* * *
2657221 TAATGAATACATGGCCAATAA
1 TAATGCATACATGGCAAAGAA
2657242 TAATGCATACATGGCAAAGAA
1 TAATGCATACATGGCAAAGAA
*
2657263 TGATGC
1 TAATGC
2657269 CATCATTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (21 bp):
TAATGCATACATGGCAAAGAA
Found at i:2659221 original size:23 final size:23
Alignment explanation
Indices: 2659194--2659240 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2659184 TTTCTTTTCA
*
2659194 TGTTTGG-GGGTGTTTTTAGATTT
1 TGTTTGGTGGGTGTCTTTAG-TTT
2659217 TGTTTGGTGGGTGTCTTTAGTTT
1 TGTTTGGTGGGTGTCTTTAGTTT
2659240 T
1 T
2659241 AATATTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.06, C:0.02, G:0.34, T:0.57
Consensus pattern (23 bp):
TGTTTGGTGGGTGTCTTTAGTTT
Found at i:2664595 original size:17 final size:18
Alignment explanation
Indices: 2664573--2664615 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2664563 AAGATTAATG
2664573 TAAAAATATAAAT-AAAA
1 TAAAAATATAAATGAAAA
*
2664590 TAAAAA-ATAATTGAAAA
1 TAAAAATATAAATGAAAA
2664607 TGAAAAATA
1 T-AAAAATA
2664616 AGAGGTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 5 0.23
19 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
TAAAAATATAAATGAAAA
Found at i:2669351 original size:445 final size:444
Alignment explanation
Indices: 2668493--2669591 Score: 1214
Period size: 445 Copynumber: 2.5 Consensus size: 444
2668483 NNNGTTGACA
* * * * * *
2668493 CAAGCAATAAGTCTTCTTT-ACTTCAGTTGCAATTGATAGTGTGAACTTCTTCAATTGTAGAGAC
1 CAAGCAATTAGTCTT-TTTCACTTCA-TTGCAATTGATAGTATGAACTTCTTCAATTATCGACAT
* * *
2668557 CAACTTGGCAACCTCAAAATGGCAAAGATTTTAATTATCTTTAATCAAAGAGAGTTTTTGTTTTT
64 CAACTTGGCAATCTCAAAATGGCAAAGATTTAAATTATCTTTAATCAAAGAGACTTTTTGTTTTT
* *
2668622 TGGGTTGACTAAACTTGGCAATGAAACCAAACTGCCTACGTACCTTCTAATATGAAGGATCAAGT
129 TGGGTTGACTGAACTTGGCAATGAAACCAAACTGACTACGTACCTTCTAATATGAAGGATCAAGT
* * ** * ********** *
2668687 CGTCATGTAGTTCTTGTTTTTTTTTTCTTTACATTTTAACTTTTNNNNNNNNNNTCTTTTTAAGG
194 CATAACATAGTTCTTG-TTGTTTTTTCTTTACATTTTAACTTTTGCCCAACTCGTCATTTTAAGG
*
2668752 ATTTTCAACTTAATAGTCATTCCTTTTTATGGGACTTAATTTGCCTAAGCCATCGTATTAAGGAT
258 ATTCTCAACTTAATAGTCATTCCTTTTTATGGGACTTAATTTGCCTAAGCCATCGTATTAAGGAT
* * * *
2668817 TTTTGGTTGAACGGGCTATTTTTTATTGGCAGTTTAAGCTTTTACTGAGGAAGAATTAATATTCA
323 TTTTAGTTGAACGGGCTATTTTTTATTGGCAGTTTAAGCTTTTACCGAGGAAAAACTAATATTCA
* * *
2668882 TGCATTTCAACACTTCAAGAATTGGCAATTGATTGGGCCGAATGTGAGTCA-TAGACT
388 TGCATTTCAACACTTCAAGAATTGGCAATTGATTGGGCCGAATATAAG-CAGTAAACT
* ** *
2668939 CAAGCACTTAGTCTTTTTCACTTCATTGGCAATTGGCAGTATGAACTTTTTCAATTATCGACATC
1 CAAGCAATTAGTCTTTTTCACTTCATT-GCAATTGATAGTATGAACTTCTTCAATTATCGACATC
* * *
2669004 AACTTGGCAATTTCAAAATGGCAAAGATGTAAATAATCTTTAAGT-AAAGAGACTTTTTGTTTTT
65 AACTTGGCAATCTCAAAATGGCAAAGATTTAAATTATCTTTAA-TCAAAGAGACTTTTTGTTTTT
** * ** * *
2669068 TACGTTAACTGAACTTGGCAATGAAACCATGCT-ACTATGTACCTTCTAATATGAAGGATTAAGT
129 TGGGTTGACTGAACTTGGCAATGAAACCAAACTGACTACGTACCTTCTAATATGAAGGATCAAGT
* *
2669132 TATAACATAGTTCTTG-TGTTTTTT-TTTAGATTTTAACTTTTGCCCAACTCGTCATTTTAAGGA
194 CATAACATAGTTCTTGTTGTTTTTTCTTTACATTTTAACTTTTGCCCAACTCGTCATTTTAAGGA
** * * *
2669195 TTCTCAACTTAATAGTTTTTCCTTTTT-TGTAGGACTTAATTTTTTCCTAAGCCATTC-TGTTGA
259 TTCTCAACTTAATAGTCATTCCTTTTTATG--GGACTTAA--TTTGCCTAAGCCA-TCGTATTAA
* **
2669258 GGATTTTTAGTTGAAC-GGCTTTTTTTTTATTGGGTGTTTAAGCTTTTACCGAGGAAAAACTAAT
319 GGATTTTTAGTTGAACGGGC-TATTTTTTATTGGCAGTTTAAGCTTTTACCGAGGAAAAACTAAT
* * ** * * *
2669322 ATTCTTGTATTGT-AATGCTTCAAGAATTGGCAATTGATTGGGCTGACTATAAGGAGTAAACT
383 ATTCATGCATT-TCAACACTTCAAGAATTGGCAATTGATTGGGCCGAATATAAGCAGTAAACT
* * * * *
2669384 TAAGCAATTAGTCTTCTTCACTTCACTAGCAATTGATAGTATGAACTTCTTCAACTATCGACATT
1 CAAGCAATTAGTCTTTTTCACTTCA-TTGCAATTGATAGTATGAACTTCTTCAATTATCGACATC
* * * *
2669449 AACTTAGCAGTCTCAAAATGGCAAAGATTTGAATTATCTATAATCAAAGAGACTTTTT-TTTTTT
65 AACTTGGCAATCTCAAAATGGCAAAGATTTAAATTATCTTTAATCAAAGAGACTTTTTGTTTTTT
* ** ** * * * * *
2669513 GGGTTGATTGAACTTGGCTTTGAGGCCAAGCTGCCTACGTACCTTCTAATCTAAAGGATCTAGTC
130 GGGTTGACTGAACTTGGCAATGAAACCAAACTGACTACGTACCTTCTAATATGAAGGATCAAGTC
2669578 ATAA-AGTAGTTCTT
195 ATAACA-TAGTTCTT
2669592 ATATTACTGA
Statistics
Matches: 540, Mismatches: 98, Indels: 31
0.81 0.15 0.05
Matches are distributed among these distances:
441 2 0.00
442 51 0.09
443 15 0.03
444 35 0.06
445 301 0.56
446 135 0.25
447 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.39
Consensus pattern (444 bp):
CAAGCAATTAGTCTTTTTCACTTCATTGCAATTGATAGTATGAACTTCTTCAATTATCGACATCA
ACTTGGCAATCTCAAAATGGCAAAGATTTAAATTATCTTTAATCAAAGAGACTTTTTGTTTTTTG
GGTTGACTGAACTTGGCAATGAAACCAAACTGACTACGTACCTTCTAATATGAAGGATCAAGTCA
TAACATAGTTCTTGTTGTTTTTTCTTTACATTTTAACTTTTGCCCAACTCGTCATTTTAAGGATT
CTCAACTTAATAGTCATTCCTTTTTATGGGACTTAATTTGCCTAAGCCATCGTATTAAGGATTTT
TAGTTGAACGGGCTATTTTTTATTGGCAGTTTAAGCTTTTACCGAGGAAAAACTAATATTCATGC
ATTTCAACACTTCAAGAATTGGCAATTGATTGGGCCGAATATAAGCAGTAAACT
Found at i:2670682 original size:12 final size:12
Alignment explanation
Indices: 2670665--2670694 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2670655 ACCACTAGAA
2670665 GAAAATTGATTG
1 GAAAATTGATTG
2670677 GAAAATTGATTG
1 GAAAATTGATTG
2670689 GAAAAT
1 GAAAAT
2670695 CAAATTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (12 bp):
GAAAATTGATTG
Found at i:2686143 original size:20 final size:19
Alignment explanation
Indices: 2686118--2686162 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2686108 AGGCAGAAAG
*
2686118 AATATTTTTTAAAATAAAAT
1 AATATTTTAT-AAATAAAAT
*
2686138 AATATTTTATGAATAAAAT
1 AATATTTTATAAATAAAAT
2686157 AATATT
1 AATATT
2686163 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATATTTTATAAATAAAAT
Found at i:2687901 original size:21 final size:21
Alignment explanation
Indices: 2687867--2687907 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2687857 GCAATATATG
* *
2687867 ACAAAGACTAATGCGTTCATA
1 ACAAAGAATAATGCCTTCATA
*
2687888 ACAAAGAATGATGCCTTCAT
1 ACAAAGAATAATGCCTTCAT
2687908 GGAAAATACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (21 bp):
ACAAAGAATAATGCCTTCATA
Found at i:2689936 original size:22 final size:23
Alignment explanation
Indices: 2689895--2689942 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2689885 TATAATATAG
*
2689895 AGTTATTTGGTCTTAATTTTGAT
1 AGTTAATTGGTCTTAATTTTGAT
* *
2689918 AGTTAATTGG-CTTAGTTTTTAT
1 AGTTAATTGGTCTTAATTTTGAT
2689940 AGT
1 AGT
2689943 AATGCATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.04, G:0.19, T:0.54
Consensus pattern (23 bp):
AGTTAATTGGTCTTAATTTTGAT
Found at i:2694228 original size:8 final size:8
Alignment explanation
Indices: 2694193--2694267 Score: 75
Period size: 8 Copynumber: 9.5 Consensus size: 8
2694183 CAAGCCGAAC
2694193 CTTCTCTTT
1 CTTC-CTTT
*
2694202 C-TCTTTT
1 CTTCCTTT
2694209 CTT-CTTT
1 CTTCCTTT
*
2694216 C-TCCTCT
1 CTTCCTTT
2694223 CTTCCTTT
1 CTTCCTTT
2694231 CTTCCTTT
1 CTTCCTTT
*
2694239 GTTCCTTT
1 CTTCCTTT
*
2694247 CTTTCTTT
1 CTTCCTTT
2694255 CTTCCTTT
1 CTTCCTTT
2694263 GCTTC
1 -CTTC
2694268 GTAGCCGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
6 1 0.02
7 12 0.22
8 36 0.67
9 5 0.09
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.63
Consensus pattern (8 bp):
CTTCCTTT
Found at i:2695218 original size:22 final size:22
Alignment explanation
Indices: 2695179--2695223 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2695169 GCAGATAAAA
* *
2695179 TATTAATATTTTAATATTATTT
1 TATTAATAATATAATATTATTT
* *
2695201 TATTAATAATATATTATTGTTT
1 TATTAATAATATAATATTATTT
2695223 T
1 T
2695224 TCAAAATTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTAATAATATAATATTATTT
Found at i:2696134 original size:31 final size:32
Alignment explanation
Indices: 2696051--2696135 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
2696041 GGAAAAAAAT
* *
2696051 AAAATAAAACATATAATATAGAAAATTATATTAA
1 AAAATAAAACA-A-AATATATAAAATTATAATAA
* * *
2696085 GAAATGAAAATAAAATATATAAGATTATAATAA
1 AAAAT-AAAACAAAATATATAAAATTATAATAA
2696118 AAAATAAAA-AAAATATAT
1 AAAATAAAACAAAATATAT
2696136 GATATTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 9 0.20
32 4 0.09
33 21 0.48
34 5 0.11
35 5 0.11
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAATAAAACAAAATATATAAAATTATAATAA
Found at i:2698074 original size:23 final size:23
Alignment explanation
Indices: 2698048--2698094 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2698038 AGCAAATCTT
*
2698048 AAAA-CTAAAGACACCCACTAAAC
1 AAAATCTAAAAACACCC-CTAAAC
2698071 AAAATCTAAAAACACCCCTAAAC
1 AAAATCTAAAAACACCCCTAAAC
2698094 A
1 A
2698095 TGAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.57, C:0.30, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAATCTAAAAACACCCCTAAAC
Found at i:2700104 original size:21 final size:21
Alignment explanation
Indices: 2700075--2700122 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2700065 TGGAATGATG
* *
2700075 GCATCATTCTTTCCCATGTAT
1 GCATTATTCTTTACCATGTAT
2700096 GCATTATTCTTTACCATGTAT
1 GCATTATTCTTTACCATGTAT
*
2700117 TCATTA
1 GCATTA
2700123 CTCTGTGTCA
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (21 bp):
GCATTATTCTTTACCATGTAT
Found at i:2707175 original size:448 final size:446
Alignment explanation
Indices: 2706263--2707369 Score: 1206
Period size: 448 Copynumber: 2.5 Consensus size: 446
2706253 TTGTGAGGAG
* * * *** * * *
2706263 TAGACTCAAGCAATAAGTCTTCTTTACTTCACTTGTACTTGATAGTGTGAACTTCTTCAATTGTA
1 TAGACTCAAGCAATTAGTCTTGTTCACTTCACTAACAATTGATAGTATGAACTTCTTCAATTATA
* * *
2706328 GAG-ACCAACTTGGCAATTTCAAAATGGCAAAAATTTGAATTATCTTTAATCAAAGAGAGTTTTT
66 G-GCATCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTT
*
2706392 ATTTTTTAAGTTGACTGAACTTGGCAATGAGACCAAACTGCCTACATACCTTCTAATATGAAGGA
130 ATTTTTTAAGTTAACTGAACTTGGCAATGAGACCAAACTGCCTACATACCTTCTAATATGAAGGA
*
2706457 TCAAGTCATAACATAGTTCTTTTTTTTTTTCTTTACATTTTAACTTTTGCCTTAGTCGTCTTTTT
195 TCAAGTCATAACATAGTTCTTTTTTTTTTTCTTTACATTTTAACTTTTGCCTTAGTCGTCATTTT
* *
2706522 AAGGATTTTCAACTTAATAGTCATTCCTTTTTTGCAGGACTTAATTTTGCCTAAGCCATCCTATT
260 AAGGATTCTCAACTTAATAGTCATTCCTTTTTTGCAGGACCTAATTTTGCCTAAGCCATCCTATT
*
2706587 AAGGATTTTTGATTAAACGGGCTATTTTCTATTGGCAGTTTAAGCGTTCACTGAGGAGGAACTAA
325 AAGGATTTTTGATTAAACGGGCTATTTTCTATTGGCAGTTTAAGCGTTCACTGAGGAAGAACTAA
*
2706652 TATACATGCATTGCAACACTTCAAGAATTGACAATTGATTGGGCCGACTGTGAGTCA
390 TATACATGCATTGCAACACTTCAAGAATTGACAATTGATTGGGCCGACTATGAGTCA
* * * * *
2706709 TAGACTCAAGCAATTAGTCTTTTTCCCTTCATTAACAATTGATAGTATGAACTTTTTCAATTATT
1 TAGACTCAAGCAATTAGTCTTGTTCACTTCACTAACAATTGATAGTATGAACTTCTTCAATTATA
* * *
2706774 GGCATCAGCTTGGCAATTTCAAAATGGCAAAGATGTGAATAATCTTTAAGT-AAAGAGACTTTTT
66 GGCATCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAA-TCAAAGAGACTTTTT
* * ***********
2706838 GTTTTTTAGGTTAACTGAACTTGGCAATGAGACCAAGNNNNNNNNNNACCTTCTAATATGAAGGA
130 ATTTTTTAAGTTAACTGAACTTGGCAATGAGACCAAACTGCCTACATACCTTCTAATATGAAGGA
* * * * **********
2706903 TCAAGTTATAACGTAG-TCATTTTGTTTTTTTTTTTTAGATTTTAACTTTTNNNNNNNNNNTCAT
195 TCAAGTCATAACATAGTTC--TTT-TTTTTTTTCTTTACATTTTAACTTTTGCCTTAGTCGTCAT
* * *
2706967 TTTAAGGATTCTCAACTTAATAGTCTTTCCTTTTTTGTAGGACCTAATTTTTGCCTAAGCCATTC
257 TTTAAGGATTCTCAACTTAATAGTCATTCCTTTTTTGCAGGACCTAA-TTTTGCCTAAGCCATCC
* * * * * * *
2707032 TATTAAGGATTTTTGGTTGAAC-GGTTTTTTTTTATTGGCTA-TTTAAGTGTTTA-TCGAGGAAG
321 TATTAAGGATTTTTGATTAAACGGGCTATTTTCTATTGGC-AGTTTAAGCGTTCACT-GAGGAAG
* * * * * * *
2707094 AACTAATATTCATGCATTGTAACGCTTTAAGAATTGGCAATTGATTGGGCTGACTATGAG-GA
384 AACTAATATACATGCATTGCAACACTTCAAGAATTGACAATTGATTGGGCCGACTATGAGTCA
* * * *
2707156 GTGGACTCAAGCTATTAGTCTTGTTCACTTCACTAGCAATTGATAGTATGAACTCCTTCAATTAT
1 -TAGACTCAAGCAATTAGTCTTGTTCACTTCACTAACAATTGATAGTATGAACTTCTTCAATTAT
* * * * * * * * *
2707221 CGACATTAACTTAGCAGTTGCAAAATGGCAAAGATTTGAATTATCTATAATCAAAGAGAC-CTGT
65 AGGCATCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTT
** * * * *** * * * *
2707285 -TTTTTTGGGTTGACTAAAGTTGGGTTTGAGACCAATCTGCCTACCTACCTTCTAATATAAAGAA
130 ATTTTTTAAGTTAACTGAACTTGGCAATGAGACCAAACTGCCTACATACCTTCTAATATGAAGGA
*
2707349 TCAAGTCATAACGTAGTTCTT
195 TCAAGTCATAACATAGTTCTT
2707370 GTATTACTAG
Statistics
Matches: 540, Mismatches: 110, Indels: 23
0.80 0.16 0.03
Matches are distributed among these distances:
445 5 0.01
446 230 0.43
447 11 0.02
448 257 0.48
449 37 0.07
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.38
Consensus pattern (446 bp):
TAGACTCAAGCAATTAGTCTTGTTCACTTCACTAACAATTGATAGTATGAACTTCTTCAATTATA
GGCATCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTTA
TTTTTTAAGTTAACTGAACTTGGCAATGAGACCAAACTGCCTACATACCTTCTAATATGAAGGAT
CAAGTCATAACATAGTTCTTTTTTTTTTTCTTTACATTTTAACTTTTGCCTTAGTCGTCATTTTA
AGGATTCTCAACTTAATAGTCATTCCTTTTTTGCAGGACCTAATTTTGCCTAAGCCATCCTATTA
AGGATTTTTGATTAAACGGGCTATTTTCTATTGGCAGTTTAAGCGTTCACTGAGGAAGAACTAAT
ATACATGCATTGCAACACTTCAAGAATTGACAATTGATTGGGCCGACTATGAGTCA
Found at i:2707579 original size:21 final size:20
Alignment explanation
Indices: 2707553--2707593 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2707543 GTGAGATTAT
2707553 AATTGGAAGAAAAAAGAAGAG
1 AATTGGAAGAAAAAA-AAGAG
*
2707574 AATTGGAAGAAGAAAAAGAG
1 AATTGGAAGAAAAAAAAGAG
2707594 TTTAGTTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (20 bp):
AATTGGAAGAAAAAAAAGAG
Found at i:2712927 original size:106 final size:106
Alignment explanation
Indices: 2712796--2713009 Score: 419
Period size: 106 Copynumber: 2.0 Consensus size: 106
2712786 ACACTAGAGC
*
2712796 TTCTTAATGCACTAAGAAAAGTTTAAGATGAGGTCTAAAGAGACATCAATTTCAAGCAATAACAA
1 TTCTTAATGCACTAAGAAAAGTTTAAGATGAGATCTAAAGAGACATCAATTTCAAGCAATAACAA
2712861 ATAATATTGGAGTCATATTTTATGAAGACCTCCTAATTGAG
66 ATAATATTGGAGTCATATTTTATGAAGACCTCCTAATTGAG
2712902 TTCTTAATGCACTAAGAAAAGTTTAAGATGAGATCTAAAGAGACATCAATTTCAAGCAATAACAA
1 TTCTTAATGCACTAAGAAAAGTTTAAGATGAGATCTAAAGAGACATCAATTTCAAGCAATAACAA
2712967 ATAATATTGGAGTCATATTTTATGAAGACCTCCTAATTGAG
66 ATAATATTGGAGTCATATTTTATGAAGACCTCCTAATTGAG
2713008 TT
1 TT
2713010 AAGTAAATAT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (106 bp):
TTCTTAATGCACTAAGAAAAGTTTAAGATGAGATCTAAAGAGACATCAATTTCAAGCAATAACAA
ATAATATTGGAGTCATATTTTATGAAGACCTCCTAATTGAG
Found at i:2717481 original size:21 final size:21
Alignment explanation
Indices: 2717457--2717509 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2717447 GTTCATGCAA
*
2717457 TTCATGACAAAGACTAATGCC
1 TTCATGACAAAGAATAATGCC
* *
2717478 TTCATAACAAAGAATGATGCC
1 TTCATGACAAAGAATAATGCC
*
2717499 TTCATGGCAAA
1 TTCATGACAAA
2717510 TACAGATGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGAATAATGCC
Found at i:2720366 original size:18 final size:19
Alignment explanation
Indices: 2720339--2720382 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2720329 GGGCAGAAAG
*
2720339 AATATATTTA-AATAAAAT
1 AATATTTTTAGAATAAAAT
2720357 AATATTTTTATGAATAAAAT
1 AATATTTTTA-GAATAAAAT
2720377 AATATT
1 AATATT
2720383 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
20 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATTTTTAGAATAAAAT
Found at i:2725692 original size:31 final size:34
Alignment explanation
Indices: 2725633--2725695 Score: 87
Period size: 31 Copynumber: 1.9 Consensus size: 34
2725623 CAAAAGCATA
*
2725633 AAAAATAATAAATAATAATTAAACTAAAATAAAT
1 AAAAATAATAAATAATAATAAAACTAAAATAAAT
*
2725667 AAAAATAA-AAGT-ATAATAAAA-TAAAATAA
1 AAAAATAATAAATAATAATAAAACTAAAATAA
2725696 CCTAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 8 0.30
32 8 0.30
33 3 0.11
34 8 0.30
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (34 bp):
AAAAATAATAAATAATAATAAAACTAAAATAAAT
Found at i:2725693 original size:21 final size:20
Alignment explanation
Indices: 2725637--2725695 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
2725627 AGCATAAAAA
*
2725637 ATAATAAATAATAATTAAACT
1 ATAATAAATAA-AATAAAACT
* *
2725658 AAAATAAATAAAAATAAAAGT
1 ATAATAAAT-AAAATAAAACT
2725679 ATAATAAAATAAAATAA
1 ATAAT-AAATAAAATAA
2725696 CCTAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
ATAATAAATAAAATAAAACT
Found at i:2728776 original size:21 final size:20
Alignment explanation
Indices: 2728752--2728803 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
2728742 TAGAATGTTG
*
2728752 GCATCATTCTAAGCCATGTAT
1 GCATTATTCTAA-CCATGTAT
*
2728773 GCATTATTCTTTACCATGTAT
1 GCATTATTC-TAACCATGTAT
2728794 GCATTATTCT
1 GCATTATTCT
2728804 TGTCCATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (20 bp):
GCATTATTCTAACCATGTAT
Found at i:2728804 original size:21 final size:21
Alignment explanation
Indices: 2728765--2728814 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2728755 TCATTCTAAG
2728765 CCATGTATGCATTATTCTT-T
1 CCATGTATGCATTATTCTTGT
2728785 ACCATGTATGCATTATTCTTGT
1 -CCATGTATGCATTATTCTTGT
2728807 CCATGTAT
1 CCATGTAT
2728815 TCTTTACTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (21 bp):
CCATGTATGCATTATTCTTGT
Found at i:2740609 original size:21 final size:21
Alignment explanation
Indices: 2740584--2740637 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2740574 TGTTCATGTA
* * *
2740584 ATTCATGACAATGATTGATGC
1 ATTCATGACAAAGAATAATGC
*
2740605 CTTCAT-AGCAAAGAATAATGC
1 ATTCATGA-CAAAGAATAATGC
2740626 ATTCATGACAAA
1 ATTCATGACAAA
2740638 TACAGATGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
ATTCATGACAAAGAATAATGC
Found at i:2748981 original size:15 final size:15
Alignment explanation
Indices: 2748944--2749014 Score: 65
Period size: 16 Copynumber: 4.6 Consensus size: 15
2748934 CTCCTACTCT
*
2748944 TTTCTTCTATC-TCC
1 TTTCTTCTTTCTTCC
*
2748958 TCTCTTTCTTTCTTCC
1 TTTC-TTCTTTCTTCC
2748974 TTTCTTCTTT-TCTCC
1 TTTCTTCTTTCT-TCC
*
2748989 TTTCTTTCTTTCTTCT
1 TTTC-TTCTTTCTTCC
2749005 TTTGCTTCTT
1 TTT-CTTCTT
2749015 AGCTGAATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 4 0.09
15 19 0.40
16 22 0.47
17 2 0.04
ACGTcount: A:0.01, C:0.31, G:0.01, T:0.66
Consensus pattern (15 bp):
TTTCTTCTTTCTTCC
Found at i:2748988 original size:31 final size:31
Alignment explanation
Indices: 2748944--2749015 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
2748934 CTCCTACTCT
2748944 TTTCTTC-TATCTCCTCTCTTTCTTTCTTCC
1 TTTCTTCTTATCTCCTCTCTTTCTTTCTTCC
* * *
2748974 TTTCTTCTTTTCTCCTTTCTTTCTTTCTTCT
1 TTTCTTCTTATCTCCTCTCTTTCTTTCTTCC
2749005 TTTGCTTCTTA
1 TTT-CTTCTTA
2749016 GCTGAATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 7 0.19
31 23 0.64
32 6 0.17
ACGTcount: A:0.03, C:0.31, G:0.01, T:0.65
Consensus pattern (31 bp):
TTTCTTCTTATCTCCTCTCTTTCTTTCTTCC
Found at i:2748992 original size:7 final size:8
Alignment explanation
Indices: 2748955--2749003 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
2748945 TTCTTCTATC
*
2748955 TCCTCTCT
1 TCCTTTCT
*
2748963 TTCTTTCT
1 TCCTTTCT
2748971 TCCTTTCT
1 TCCTTTCT
*
2748979 TCTTTTC-
1 TCCTTTCT
2748986 TCCTTTCT
1 TCCTTTCT
*
2748994 TTCTTTCT
1 TCCTTTCT
2749002 TC
1 TC
2749004 TTTTGCTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
TCCTTTCT
Found at i:2751315 original size:25 final size:26
Alignment explanation
Indices: 2751277--2751325 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2751267 AAAAACTAGT
* *
2751277 AAATAATAATTATACTAAAATAAATG
1 AAATAATAAGTATAATAAAATAAATG
*
2751303 AAATAA-AAGTATAATAGAATAAA
1 AAATAATAAGTATAATAAAATAAA
2751326 ATAACTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (26 bp):
AAATAATAAGTATAATAAAATAAATG
Found at i:2762131 original size:446 final size:443
Alignment explanation
Indices: 2761357--2762739 Score: 1541
Period size: 446 Copynumber: 3.1 Consensus size: 443
2761347 NNNNNNNNNN
* * * * *
2761357 TTTGTTTTTTGGGTTGACTGAACTTTGCAATGAGACCAAA-CAGCCTATGTACCTTCTAATATGA
1 TTTGCTTTTTGGGTTAACTGAACTTGGCAATGAGA-CAAAGCTGCCTACGTACCTTCTAATATGA
* * * ** *
2761421 AGGATCAAGTCGTAACATAGTTCTCAATTATTTTTTTTTTACATTTTAACTTTTGCCTAAGTCG-
65 AAGATCAAGTCATAATATAGTTCT-TGTT-TTTTTTTTTTA-ATTCTAACTTTTGCCTAAGTCGT
* * * * * * *
2761485 CCTTTCTAAGGATT-TCCAACTTAATAGTCATTCCTTTTTTGCATGACTTAATTTTTCCTAAGTC
127 CATTT-TAAGGATTCT-CAACTTAATAGTCTTTCCTTTTTTGAAGGACCTAATTTTGCCTAAGCC
* * * * * *
2761549 GTCCTATTAAGGATTTTTGGTTGAACGGGCTATTTTCTATTGGCAATTTAAGCTTTTACTGAGGA
190 ATCCTATTAAGGATTTTTGGTTGAACGGGTTATTTTTTATTGTCAGTTTAAGCTTTTACCGAGGA
* * * * *
2761614 AGAACTAATATTCATGCATTGCAACGCT-TTAAGAATTGGCAATTGATTGGGCCGACTATGAGTC
255 AGAACTAATATTCATGCATTG-AAC-ATGTCAAGAATTGGCCATTGATTGGGCTGACTATGAG-G
*
2761678 A-TAGACTCAAGCAATTAGTCTTTTTCACTTCACTAGCAATTGGTAGTATGAACTTTTTCAATTA
317 AGTAGACTCAAGCAATTAGTCTTTTTCACTTCACTAGCAATTGATAGTATGAAC-TTTTCAATTA
*** ** *
2761742 TCGACATCAACTTGGCAATTTCAAAATGGCAATGACGTGAATAATCTTTAAGAAAAGAGACTT
381 TCGATGCCAACTTGGCAATTTCAAAATGGCAATGATTTGAATTATCTTTAAGAAAAGAGACTT
* *
2761805 TTTG-TTTTTGGGTTAACTGAACTTGGCAACGAGACAAAGCTGCCTACGTACCCTCTAATATGAA
1 TTTGCTTTTTGGGTTAACTGAACTTGGCAATGAGACAAAGCTGCCTACGTACCTTCTAATATGAA
* * * *
2761869 AGACCAAGTTATAATATAATTCTTGTGTTTTTTTTTTTAGATTCTAACTTTTGCCTAAGTTGTCA
66 AGATCAAGTCATAATATAGTTCTTGT-TTTTTTTTTTTA-ATTCTAACTTTTGCCTAAGTCGTCA
* * *
2761934 TTTTAAGGATTCTCAACTTAATAGTCTTTCCTTTTTTGAAGGACCTAATTTTGCTTGAGCCATTC
129 TTTTAAGGATTCTCAACTTAATAGTCTTTCCTTTTTTGAAGGACCTAATTTTGCCTAAGCCATCC
* *
2761999 TATTAAGGATTTTTGGTTGAACGGGTTTTTTTTTATTGTCTGTTTAAGCTTTTACCGAGGAAGAA
194 TATTAAGGATTTTTGGTTGAACGGGTTATTTTTTATTGTCAGTTTAAGCTTTTACCGAGGAAGAA
*
2762064 CTAATATTCATGCATTGTAACATGTCAAGAATTGGCCATTGATTGGGCTGACAATGAGGAGTAGA
259 CTAATATTCATGCATTG-AACATGTCAAGAATTGGCCATTGATTGGGCTGACTATGAGGAGTAGA
* * *
2762129 CTCAAGCAATTAGTCTTGTTCACTTCACTAGCAATTGATGGTATGAACTTCTTCAATTATTGATG
323 CTCAAGCAATTAGTCTTTTTCACTTCACTAGCAATTGATAGTATGAACTT-TTCAATTATCGATG
* * * *
2762194 CCAACTTAGCAGTTTCAAAATGGCAAAGATTTGAATTATCTATAATGAAAA-AGACTT
387 CCAACTTGGCAATTTCAAAATGGCAATGATTTGAATTATCTTTAA-GAAAAGAGACTT
* * ** * *
2762251 TTT--TTTTTAGGTTAACTGAGCTTGGCTTTGAGACCAAGCTGCCTACATACCTTCTAATAT-AA
1 TTTGCTTTTTGGGTTAACTGAACTTGGCAATGAGACAAAGCTGCCTACGTACCTTCTAATATGAA
* * * * *
2762313 AGGATCAAGTCATAATGTAGTTCTTGTATTTGTTTTTCT-ATTCTAACTTTTTCCTAGGTCGTCA
66 A-GATCAAGTCATAATATAGTTCTTGT-TTTTTTTTTTTAATTCTAACTTTTGCCTAAGTCGTCA
* * *
2762377 TTTTATGGATTCTCAACTTAATAGTCTTT-CTTTTTTCATAGGACCTAATTTTTGCCTAAGCTAT
129 TTTTAAGGATTCTCAACTTAATAGTCTTTCCTTTTTTGA-AGGACCTAA-TTTTGCCTAAGCCAT
* * * *
2762441 CCTATTAAGGATTTTTGGTTTAACGGGTTCTTTTTTATTAGT-AGTTTAAGCTCTTACCGAGGAG
192 CCTATTAAGGATTTTTGGTTGAACGGGTTATTTTTTATT-GTCAGTTTAAGCTTTTACCGAGGAA
* * * * * *
2762505 GAACTAATATTCATGCACTGGA-ATGCTTCAACAATTTGCCATTGATTGGGCTGAGTGTGAGGAG
256 GAACTAATATTCATGCATTGAACATG--TCAAGAATTGGCCATTGATTGGGCTGACTATGAGGAG
* * * *
2762569 TAAACTCAAGCAA-TACATC-TTTT--CTTCACTTGCAATTGATAGTTTGAAC--TTCAATTATC
319 TAGACTCAAGCAATTA-GTCTTTTTCACTTCACTAGCAATTGATAGTATGAACTTTTCAATTATC
* * **
2762628 GATGCCAACTTGTCAATTT-AAATATGGAAAAT-ATTTGAATTATCTTTAATCAAAGAGACTT
383 GATGCCAACTTGGCAATTTCAAA-ATGG-CAATGATTTGAATTATCTTTAAGAAAAGAGACTT
* * * * * * *
2762689 TTTGCGTTTTGGATTGATTGAACTTGACAATGAGACCAAGCTACCTACGTA
1 TTTGCTTTTTGGGTTAACTGAACTTGGCAATGAGACAAAGCTGCCTACGTA
2762740 TGTACCCCCT
Statistics
Matches: 797, Mismatches: 118, Indels: 48
0.83 0.12 0.05
Matches are distributed among these distances:
437 6 0.01
438 54 0.07
439 2 0.00
440 35 0.04
441 23 0.03
442 11 0.01
443 65 0.08
444 135 0.17
445 85 0.11
446 300 0.38
447 77 0.10
448 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (443 bp):
TTTGCTTTTTGGGTTAACTGAACTTGGCAATGAGACAAAGCTGCCTACGTACCTTCTAATATGAA
AGATCAAGTCATAATATAGTTCTTGTTTTTTTTTTTTAATTCTAACTTTTGCCTAAGTCGTCATT
TTAAGGATTCTCAACTTAATAGTCTTTCCTTTTTTGAAGGACCTAATTTTGCCTAAGCCATCCTA
TTAAGGATTTTTGGTTGAACGGGTTATTTTTTATTGTCAGTTTAAGCTTTTACCGAGGAAGAACT
AATATTCATGCATTGAACATGTCAAGAATTGGCCATTGATTGGGCTGACTATGAGGAGTAGACTC
AAGCAATTAGTCTTTTTCACTTCACTAGCAATTGATAGTATGAACTTTTCAATTATCGATGCCAA
CTTGGCAATTTCAAAATGGCAATGATTTGAATTATCTTTAAGAAAAGAGACTT
Found at i:2764628 original size:18 final size:19
Alignment explanation
Indices: 2764602--2764643 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2764592 GGGCGGAAAG
*
2764602 AATATTTTTA-AATAAAAT
1 AATAATTTTAGAATAAAAT
2764620 AATAATTTTATGAATAAAAT
1 AATAATTTTA-GAATAAAAT
2764640 AATA
1 AATA
2764644 TTAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAATTTTAGAATAAAAT
Found at i:2766642 original size:11 final size:11
Alignment explanation
Indices: 2766626--2766650 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2766616 CACTAGAAGA
2766626 AAATTGATTGG
1 AAATTGATTGG
2766637 AAATTGATTGG
1 AAATTGATTGG
2766648 AAA
1 AAA
2766651 AACAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (11 bp):
AAATTGATTGG
Found at i:2774762 original size:21 final size:21
Alignment explanation
Indices: 2774738--2774790 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2774728 GTTGATCCAA
* *
2774738 TTCATGACAATGACTAATGCC
1 TTCATGACAAAGAATAATGCC
* *
2774759 TTCATAACAAAGAATGATGCC
1 TTCATGACAAAGAATAATGCC
*
2774780 TTCATGGCAAA
1 TTCATGACAAA
2774791 TACGGATGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (21 bp):
TTCATGACAAAGAATAATGCC
Found at i:2779291 original size:21 final size:19
Alignment explanation
Indices: 2779266--2779331 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 19
2779256 TTACAAAACC
2779266 ATAAAAACTAATAAATAATAA
1 ATAAAAA-TAATAAATAA-AA
* *
2779287 TTAAAATAAAATAAATAAAA
1 ATAAAA-ATAATAAATAAAA
2779307 ATAAAAATAATATAATATAAA
1 ATAAAAATAATA-AATA-AAA
2779328 ATAA
1 ATAA
2779332 CTTAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 5 0.13
20 11 0.29
21 21 0.55
22 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAATAATAAATAAAA
Found at i:2779296 original size:16 final size:15
Alignment explanation
Indices: 2779275--2779328 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
2779265 CATAAAAACT
2779275 AATAAATAATAATTAA
1 AATAAA-AATAATTAA
*
2779291 AAT-AAAATAAATAAA
1 AATAAAAAT-AATTAA
2779306 AATAAAAATAATATAA
1 AATAAAAATAAT-TAA
*
2779322 TATAAAA
1 AATAAAA
2779329 TAACTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.09
15 13 0.41
16 16 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAAATAATTAA
Found at i:2779338 original size:15 final size:14
Alignment explanation
Indices: 2779282--2779336 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
2779272 ACTAATAAAT
2779282 AATAATTAAAATAA
1 AATAATTAAAATAA
*
2779296 AATAAATAAAAATAAA
1 AAT-AATTAAAAT-AA
*
2779312 AATAATATAATATAA
1 AATAAT-TAAAATAA
2779327 AATAACTTAA
1 AATAA-TTAA
2779337 TAAAAGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 21 0.62
16 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAATTAAAATAA
Found at i:2779341 original size:35 final size:33
Alignment explanation
Indices: 2779266--2779331 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
2779256 TTACAAAACC
2779266 ATAAAAACTAATAAATAATAATTAAAATAAAATAA
1 ATAAAAA-TAA-AAATAATAATTAAAATAAAATAA
*
2779301 ATAAAAATAAAAATAAT-A-TAATATAAAATAA
1 ATAAAAATAAAAATAATAATTAAAATAAAATAA
2779332 CTTAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 12 0.40
32 1 0.03
33 7 0.23
34 3 0.10
35 7 0.23
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (33 bp):
ATAAAAATAAAAATAATAATTAAAATAAAATAA
Found at i:2782794 original size:21 final size:21
Alignment explanation
Indices: 2782765--2782827 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2782755 TGGAATGATG
*
2782765 GCATCATTCGTTT-CCATGTAT
1 GCATTATTC-TTTACCATGTAT
*
2782786 GCATTATTCTTTATCATGTAT
1 GCATTATTCTTTACCATGTAT
*
2782807 GCATTATT-TTTGGCCATGTAT
1 GCATTATTCTTT-ACCATGTAT
2782828 TCTTGACTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (21 bp):
GCATTATTCTTTACCATGTAT
Found at i:2793408 original size:21 final size:21
Alignment explanation
Indices: 2793384--2793436 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2793374 GTTCATGCAA
* *
2793384 TTCATGACAATGATTGATGCC
1 TTCATGACAAAGAATGATGCC
* *
2793405 TTCATAACAAAGAATGATGCG
1 TTCATGACAAAGAATGATGCC
*
2793426 TTCATGGCAAA
1 TTCATGACAAA
2793437 TACGGGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (21 bp):
TTCATGACAAAGAATGATGCC
Found at i:2798095 original size:18 final size:18
Alignment explanation
Indices: 2798072--2798106 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2798062 TAATTTAACT
2798072 CCCCTTGGTTAGTAAATG
1 CCCCTTGGTTAGTAAATG
2798090 CCCCTTGGTTAGTAAAT
1 CCCCTTGGTTAGTAAAT
2798107 CCAACATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (18 bp):
CCCCTTGGTTAGTAAATG
Found at i:2799347 original size:33 final size:32
Alignment explanation
Indices: 2799310--2799371 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
2799300 AATATAAAAA
* *
2799310 ATTATATTAAGAAATGAAAATAAAATATATAGG
1 ATTATAATAAAAAATGAAAAT-AAATATATAGG
2799343 ATTATAATAAAAAATGAAAATAAATATAT
1 ATTATAATAAAAAATGAAAATAAATATAT
2799372 GATATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (32 bp):
ATTATAATAAAAAATGAAAATAAATATATAGG
Found at i:2799611 original size:15 final size:15
Alignment explanation
Indices: 2799591--2799627 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2799581 TCTTCCTTAT
*
2799591 AATCACATTACTTGC
1 AATCACATTACCTGC
*
2799606 AATCACATTACCTGT
1 AATCACATTACCTGC
2799621 AATCACA
1 AATCACA
2799628 CTGTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (15 bp):
AATCACATTACCTGC
Found at i:2807220 original size:21 final size:21
Alignment explanation
Indices: 2807194--2807241 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2807184 TGGAATGATG
*
2807194 GCATTATTCTTTGCCATGTAT
1 GCATTATTCTTGGCCATGTAT
*
2807215 GCATTATTCTTGGCTATGTAT
1 GCATTATTCTTGGCCATGTAT
*
2807236 TCATTA
1 GCATTA
2807242 CTCTGTGTCA
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:0.21, C:0.17, G:0.15, T:0.48
Consensus pattern (21 bp):
GCATTATTCTTGGCCATGTAT
Found at i:2813728 original size:445 final size:445
Alignment explanation
Indices: 2812838--2814792 Score: 1845
Period size: 445 Copynumber: 4.4 Consensus size: 445
2812828 ACCAAGTAGA
* ** * * * *
2812838 AATAAATCTTCTTGGCTTCACTTA-CAATTTGATAGTTTAAATTTCTTCAATTATCGACGTCC-A
1 AATAAGTCTTCTTTACTTCAC-TAGCAA-TTGATAGTATGAACTTCTTCAATTATCGAC-ACCAA
* * * * * *
2812901 CTTGGCAATTTCAACATCG-CAAATATTTAAATTATCTTTAATCAAAGAGACTTTTCATCCTTTT
63 CTTGGAAATTTCAAAAT-GACAAAGATTTGAATTATCTTTAATCAAAGAGACTTTT--T--GTTG
* * * * * *
2812965 TTTGGGTTGACTAAACTTGACAATGAGAACAAGCTACCTGCATACC-TCTTAATATGAAAGAACA
123 TTTGGGTTGACTGAACTTGGCAATGAGACCAAGCTACCTACATACCTTC-TAATATGAAGGATCA
* ** ** * *** * *
2813029 AGTCGTAACGTAGTTC---TTTTTTTTTTTTAGGTCCTAACTTTTATGTAAGCCATTATTTTAA-
187 AGTAGTAATATAGTTCTTGTTTTTTTTTTTTACATTCTAACTTTTGCCTAAGTCATCATTTTAAG
* * ** * * * * * *
2813090 GATTGTCAACTCAATCCTCTTTCTTTTTCTACAGAACCTAATTTTTGCCTAAGTTACCCTTTTAA
252 GATTTTCAACTTAATAGTCTTTCTTTTTTTA-GGGACCTAATTTTTGCCTAAGCTATCCTATTAA
* ** * * * * ** * *
2813155 GAATTTTTGGCTT-AATAGGCTCTGTTTTATTTGCAATGTAAG-TTCTTATTAAGGAGGAATTAA
316 GGATTTTTGG-TTGAACGGGCTAT-TTTTATTGGCAGTTTAAGCTT-TTATCGAGGAAGAACTAA
* * * * ** * *
2813218 TATCCAAGCACT-CTAATGCATCAAGAATTTTCCATTGATTGGGTC-AATTGTGAGGACGT-GAC
378 TATTCATGCATTGC-AATGCTTCAAGAATTGGCAATTGATTGGGCCGAA-TGTGAGGA-GTAGAC
*
2813280 TCAATC
440 TCAAGC
* * ** *
2813286 AATAAGTCTTCTTTACTTCACTGGCAATTGAAAGGGTGAACTTCTTCAATTGTCGACACCAACTT
1 AATAAGTCTTCTTTACTTCACTAGCAATTGATAGTATGAACTTCTTCAATTATCGACACCAACTT
* * * *
2813351 GGAAATTTCAAAATGGCAAAGATTTGAATTATTTTTAATGAAAGAGACTTTTTGTTGTTTAGGTT
66 GGAAATTTCAAAATGACAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTTGTTGTTTGGGTT
* * * * *
2813416 GATTGAACTTGGCAATGAGACCAAACTACCTACATACTTTCTAATATGATGGATCAAGTCGTAAT
131 GACTGAACTTGGCAATGAGACCAAGCTACCTACATACCTTCTAATATGAAGGATCAAGTAGTAAT
* * * *
2813481 GTAGTTATTGTTTTTTTTTCTTTACATTTTAACTTTTGCCTAAGTCATCTTTTTAAGGATTTTCA
196 ATAGTTCTTGTTTTTTTTT-TTTACATTCTAACTTTTGCCTAAGTCATCATTTTAAGGATTTTCA
* * *
2813546 ACTTAATACTCTTT-TTTTTTTAGGGACTTAA-TTTTGCCTAAGCTATCCCATTAAGGATTTTTG
260 ACTTAATAGTCTTTCTTTTTTTAGGGACCTAATTTTTGCCTAAGCTATCCTATTAAGGATTTTTG
* * * * * *
2813609 GTTGAACGGGCTGTTTTCTATTAGCAGTTTAAGCCTTTATTGAGGAAAAACTAATATTCATGCTT
325 GTTGAACGGGCTATTTT-TATTGGCAGTTTAAGCTTTTATCGAGGAAGAACTAATATTCATGCAT
* ** * **
2813674 TGCAATGCTTTAAGAATTGGCAATTGATTGGGTTGACTGTGAGTCGTAGACTCAAGC
389 TGCAATGCTTCAAGAATTGGCAATTGATTGGGCCGAATGTGAGGAGTAGACTCAAGC
* * * *
2813731 AATAAGTCTT-TTTCACTTCACTAGCAATTGGTAGTATGAACTTTTTCAATGATCGACATCAACT
1 AATAAGTCTTCTTT-ACTTCACTAGCAATTGATAGTATGAACTTCTTCAATTATCGACACCAACT
* * * * * * * *
2813795 TGGTAATTTCAAGATGGCAAAGATGTGAATAATCTTAAAGT-AAATAGACTTTTTGTTTTTTGGG
65 TGGAAATTTCAAAATGACAAAGATTTGAATTATCTTTAA-TCAAAGAGACTTTTTGTTGTTTGGG
* * * * *
2813859 TTAACTAAACTTGGCAATGAGACCAAGCTGCCTACGTACCTTCTAATATGAAGAATCAAGTTA-T
129 TTGACTGAACTTGGCAATGAGACCAAGCTACCTACATACCTTCTAATATGAAGGATCAAG-TAGT
* * * *
2813923 AACATAGTTCTTGTGGTTTTCTTTTTTTTAGATTCTAACTTTTACCTAAGTCGTCATTTTAAGGA
193 AATATAGTTC-T-T-GTTTT-TTTTTTTTACATTCTAACTTTTGCCTAAGTCATCATTTTAAGGA
* * * * *
2813988 TTCTCAACTTAATGGTCTTTCCTTTTTT-GCAGGACCTAATTTTTGCCTAAGCCATTCTATTAAG
254 TTTTCAACTTAATAGTCTTTCTTTTTTTAG--GGACCTAATTTTTGCCTAAGCTATCCTATTAAG
* *
2814052 GATTTTTGGTTGAACGGGGTTTATTTTTATTGGCTGTTTAAGCTTTTATCGAGGAAGAACTAATA
317 GATTTTTGGTTGAAC-GGG-CTATTTTTATTGGCAGTTTAAGCTTTTATCGAGGAAGAACTAATA
** * * * * *
2814117 TTCATGCATTATAACGCTTCAACAATTGGCAATTAATTGGGCTGAATGCGAGGAGTAGACTCAAG
380 TTCATGCATTGCAATGCTTCAAGAATTGGCAATTGATTGGGCCGAATGTGAGGAGTAGACTCAAG
*
2814182 A
445 C
** * * * *
2814183 AATTGGTCTTGTTCACTTAACTAGCAATTGATAGTATGAACTTCTTCAATTATCGACATCAACTT
1 AATAAGTCTTCTTTACTTCACTAGCAATTGATAGTATGAACTTCTTCAATTATCGACACCAACTT
* *
2814248 --AACAGTTTCAAAATTACAAAGATTTGAATTATCTATAATCAAAGAGACTTTTT-TT-TTTGGG
66 GGAA-A-TTTCAAAATGACAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTTGTTGTTTGGG
** * * * *
2814309 TTGACTGAACTTGGCTTTAAGACCAAGCTGCCTACGTACCTTCTAATATAAAGGATCAAGTAGTA
129 TTGACTGAACTTGGCAATGAGACCAAGCTACCTACATACCTTCTAATATGAAGGATCAAGTAGTA
* * * * * *
2814374 ATATGGTTCTTG-TATTTTTTTTTCCATTCTAACTTTTGCCTAAATCATCATTTTATGGATTTTT
194 ATATAGTTCTTGTTTTTTTTTTTTACATTCTAACTTTTGCCTAAGTCATCATTTTAAGGATTTTC
* *** * *
2814438 AACTTAATAGTCTTTCTTTTTTCACATAACCAAATTTTTGCCTAAGCTGTCCTATTAAGGATTTT
259 AACTTAATAGTCTTTCTTTTTTTA-GGGACCTAATTTTTGCCTAAGCTATCCTATTAAGGATTTT
* * * * *
2814503 TGGTTTAACGGGTTATTTGTTATTGGTAGTTTAAGCTTTTACCGAGGAGGAACTAATATTCATGC
323 TGGTTGAACGGGCTATTT-TTATTGGCAGTTTAAGCTTTTATCGAGGAAGAACTAATATTCATGC
* * * * *
2814568 ATTGGAATGCTCCAAGAATTTGCCATTGATTGGGCCGAGTGTGAGGAGTAGACTCAAGC
387 ATTGCAATGCTTCAAGAATTGGCAATTGATTGGGCCGAATGTGAGGAGTAGACTCAAGC
* * * * * *
2814627 AATAAGTCTTCTTTTCTTCACTTGCAATTGATAGTTTGAACTTCTTTAATTATTGACTCCAACTT
1 AATAAGTCTTCTTTACTTCACTAGCAATTGATAGTATGAACTTCTTCAATTATCGACACCAACTT
* * * *
2814692 GGCAATTTAAAAATGACAAAGATTTGAATTACCTTTAATCAAAGAGACTTTTTG-TGTTTTGGAT
66 GGAAATTTCAAAATGACAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTTGTTG-TTTGGGT
*
2814756 TGATTGAACTTGGCAATGAGACCAAGCTACCTACATA
130 TGACTGAACTTGGCAATGAGACCAAGCTACCTACATA
2814793 TGTACCCCCT
Statistics
Matches: 1238, Mismatches: 228, Indels: 84
0.80 0.15 0.05
Matches are distributed among these distances:
443 72 0.06
444 202 0.16
445 375 0.30
446 64 0.05
447 108 0.09
448 98 0.08
449 14 0.01
450 76 0.06
451 40 0.03
452 182 0.15
453 7 0.01
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (445 bp):
AATAAGTCTTCTTTACTTCACTAGCAATTGATAGTATGAACTTCTTCAATTATCGACACCAACTT
GGAAATTTCAAAATGACAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTTGTTGTTTGGGTT
GACTGAACTTGGCAATGAGACCAAGCTACCTACATACCTTCTAATATGAAGGATCAAGTAGTAAT
ATAGTTCTTGTTTTTTTTTTTTACATTCTAACTTTTGCCTAAGTCATCATTTTAAGGATTTTCAA
CTTAATAGTCTTTCTTTTTTTAGGGACCTAATTTTTGCCTAAGCTATCCTATTAAGGATTTTTGG
TTGAACGGGCTATTTTTATTGGCAGTTTAAGCTTTTATCGAGGAAGAACTAATATTCATGCATTG
CAATGCTTCAAGAATTGGCAATTGATTGGGCCGAATGTGAGGAGTAGACTCAAGC
Found at i:2824419 original size:32 final size:32
Alignment explanation
Indices: 2824383--2824509 Score: 209
Period size: 32 Copynumber: 4.0 Consensus size: 32
2824373 AGCCAAACCA
*
2824383 AAAAATAGCTTACGAATTATTTAGGTGATATG
1 AAAAATAGCTTATGAATTATTTAGGTGATATG
* *
2824415 AAAAATAACTTTTGAATTATTTAGGTGATATG
1 AAAAATAGCTTATGAATTATTTAGGTGATATG
2824447 AAAAATAGCTTATGAATTATTTAGGTGATATG
1 AAAAATAGCTTATGAATTATTTAGGTGATATG
* *
2824479 GAAAATAGTTTATGAATTATTTAGGTGATAT
1 AAAAATAGCTTATGAATTATTTAGGTGATAT
2824510 AAATTATTCC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 88 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (32 bp):
AAAAATAGCTTATGAATTATTTAGGTGATATG
Found at i:2827122 original size:443 final size:443
Alignment explanation
Indices: 2826278--2827397 Score: 1440
Period size: 443 Copynumber: 2.5 Consensus size: 443
2826268 GTTACAAAAG
* *
2826278 GAGGAACTAATATTCATGCATTGTAACACTTCAAGAATTTCCAATTGATTGGGCTGACTATGAGG
1 GAGGAACTAATATTCATGCATTGTAACACTTCAAGAATTTACAATTGATTGGGCTGACTGTGAGG
* * * **********
2826343 AGTAGACTCAAGCAATTAATCTTTTTTAGTTCACTAGCNNNNNNNNNNATGAATTTCTTCAATTA
66 AGTAGACTCAAGCAATTAGTCTTTTTCACTTCACTAGCAACTGAAAGTATGAATTTCTTCAATTA
* * *
2826408 TTAGTGTCAACTTGGCAATTTCAAAAGGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTT
131 TGA-CGTCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTT
** * * ** *
2826473 TGGTTTTTGGGTTGACTGAACTTGGCAACGAGACCAAATTGCCTACATACCTTCTAATATGAAGA
195 TCATTTTTGGGTTGACTGAACTTGGCAAAGAGACTAAGCTGCCTACATACCTTCTAATATAAAGA
* * * *
2826538 ATCAAGTTGTAACATAGTTCTCGTGTTTTTTTTTTTAGATTCTAACTTTTGCCTAAGTTGTCATT
260 ATCAAGTTGTAACATAATACTCGTGTTTTTTTTTTTAGATTCTAACTTTTGCCCAAGTCGTCATT
* * *
2826603 TTAAGGATTCTCAACAAATATTTTTTCTTTTTCTGCAGGATCTAATATTTGCCTAAGCCATCCTA
325 TTAAGGATTCTCAACAAATATTCTTTCTTTTTCTGCAGGACCTAATATTTGCCTAAGCCATCCGA
** **
2826668 TTAGGGATTTTTGGTTTAACGGGTTCATTTTTATTGGCAGTTTAAGCTTTTACC
390 TTAAAGATTTTTAATTTAACGGGTTCATTTTTATTGGCAGTTTAAGCTTTTACC
* * * *
2826722 GAGGAACGAACATTCATGCATTGTAACATTTCAAGAATTTGCAATTGATTGGGCTGACTGTGAGG
1 GAGGAACTAATATTCATGCATTGTAACACTTCAAGAATTTACAATTGATTGGGCTGACTGTGAGG
* * * * * *
2826787 AGTAGACTAAAGCAATTAGTCTTTTCCACTTCATTAGCAATTTAAAGTATGAACTTCTTCAATTA
66 AGTAGACTCAAGCAATTAGTCTTTTTCACTTCACTAGCAACTGAAAGTATGAATTTCTTCAATTA
** * *
2826852 TCGACACCAACTTGGCAATTTCAAAATGGCAAAGA-TTGAATTATCTTTAATTAAAGGGACTTTT
131 T-GACGTCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTT
*
2826916 TCATTTTTGGGTTGACTGAACTTGGCAAAGAGACTAAGCTGCCTACATACCTTCTAATATAAAGG
195 TCATTTTTGGGTTGACTGAACTTGGCAAAGAGACTAAGCTGCCTACATACCTTCTAATATAAAGA
* * *
2826981 ATCAAGTTGTAACGTAATACTCGTGTTTTTTTTTTTGGATGT-TCAC-TTTGCCCAAGTCGTCAT
260 ATCAAGTTGTAACATAATACTCGTGTTTTTTTTTTTAGAT-TCTAACTTTTGCCCAAGTCGTCAT
* * * * *
2827044 TTTAAGGATTCTCAACTTAATATTCTTTCTTTTTTTGCAGGACCTAATTTTTGCCTTAGCCGTCC
324 TTTAAGGATTCTCAAC-AAATATTCTTTCTTTTTCTGCAGGACCTAATATTTGCCTAAGCCATCC
**
2827109 GATTAAAGATTTTTAATTTAACGGGTTCATTTTTATTGGCAGTTTAAGCTTTTATG
388 GATTAAAGATTTTTAATTTAACGGGTTCATTTTTATTGGCAGTTTAAGCTTTTACC
* * * * *
2827165 GAGGAACTAATATTCGTGCATTGTAACGCTTCAAGAATTTACAATTGATTAGGCCGGCTGTGAGG
1 GAGGAACTAATATTCATGCATTGTAACACTTCAAGAATTTACAATTGATTGGGCTGACTGTGAGG
* * *
2827230 AGTAGACTCAAGCAATTAGTCTTTTTCACTTCACTAACAACTGATAGTATGAATTTCTTCAAATA
66 AGTAGACTCAAGCAATTAGTCTTTTTCACTTCACTAGCAACTGAAAGTATGAATTTCTTCAATTA
* ** * *
2827295 TTGACGTCAATTTCACAATTTCAAAATGGCAAAGATTTGAATGATCTTTAATGGAAA-AGACTTT
131 -TGACGTCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAAT-CAAAGAGACTTT
* * * *
2827359 TTGCA-TTTTGGATTGATTGAGCTTGGCAAGGAGACTAAG
194 TT-CATTTTTGGGTTGACTGAACTTGGCAAAGAGACTAAG
2827398 ATACCTATGT
Statistics
Matches: 581, Mismatches: 88, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
442 31 0.05
443 353 0.61
444 191 0.33
445 6 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.37
Consensus pattern (443 bp):
GAGGAACTAATATTCATGCATTGTAACACTTCAAGAATTTACAATTGATTGGGCTGACTGTGAGG
AGTAGACTCAAGCAATTAGTCTTTTTCACTTCACTAGCAACTGAAAGTATGAATTTCTTCAATTA
TGACGTCAACTTGGCAATTTCAAAATGGCAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTT
CATTTTTGGGTTGACTGAACTTGGCAAAGAGACTAAGCTGCCTACATACCTTCTAATATAAAGAA
TCAAGTTGTAACATAATACTCGTGTTTTTTTTTTTAGATTCTAACTTTTGCCCAAGTCGTCATTT
TAAGGATTCTCAACAAATATTCTTTCTTTTTCTGCAGGACCTAATATTTGCCTAAGCCATCCGAT
TAAAGATTTTTAATTTAACGGGTTCATTTTTATTGGCAGTTTAAGCTTTTACC
Done.