Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008358.1 Hibiscus syriacus cultivar Beakdansim tig00111097_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: 729890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:426922 original size:24 final size:24
Alignment explanation
Indices: 426894--426949 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
426884 GAATGTTTTA
*
426894 TCTGATTTCCAATTTGAATTCTGT
1 TCTGATTTCCAATCTGAATTCTGT
** *
426918 TCTGATTTCTTATCTGAATTTTGT
1 TCTGATTTCCAATCTGAATTCTGT
*
426942 TCTAATTT
1 TCTGATTT
426950 TTGTTCTGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (24 bp):
TCTGATTTCCAATCTGAATTCTGT
Found at i:426980 original size:24 final size:24
Alignment explanation
Indices: 426953--427014 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
426943 CTAATTTTTG
*
426953 TTCTGATTTCTGATCTGGATTCTA
1 TTCTGATTTCTGATCTGAATTCTA
* * *
426977 TTCTGATATATAATCTGAATTCTA
1 TTCTGATTTCTGATCTGAATTCTA
*
427001 TTTTGATTTCTGAT
1 TTCTGATTTCTGAT
427015 ATCTTCGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.52
Consensus pattern (24 bp):
TTCTGATTTCTGATCTGAATTCTA
Found at i:427203 original size:14 final size:14
Alignment explanation
Indices: 427184--427210 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
427174 TAGTGTTATG
427184 TTTTTAAAAATATA
1 TTTTTAAAAATATA
427198 TTTTTAAAAATAT
1 TTTTTAAAAATAT
427211 GTATGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTTAAAAATATA
Found at i:430525 original size:123 final size:124
Alignment explanation
Indices: 430305--430548 Score: 445
Period size: 123 Copynumber: 2.0 Consensus size: 124
430295 ACTAATAAAG
430305 CTCATTTTAACATTTGAAAATCTATAAAATAAAATCGATAACTAAATCGATATCAACCAAACTCA
1 CTCATTTTAACATTTGAAAATCTATAAAATAAAATCGATAACTAAATCGATATCAACCAAACTCA
*
430370 TAAATCCATTATAACTTCAAACTTATCGAAACACTTATGCAATTCCATAAATAATTGTT
66 TAAATCCATTATAACTTCAAACTTATCGAAACACTTATGCAATTCAATAAATAATTGTT
430429 CTCATTTTAACATTTGAAAATCTATAAAATAAAATCGAT-ACTAAATCGATATCAACCAAACTCA
1 CTCATTTTAACATTTGAAAATCTATAAAATAAAATCGATAACTAAATCGATATCAACCAAACTCA
* **
430493 TAAATCCATTATAACTTCAAACTTATCGAAACACTTGTGTGATTCAATAAATAATT
66 TAAATCCATTATAACTTCAAACTTATCGAAACACTTATGCAATTCAATAAATAATT
430549 ATTCCCAACA
Statistics
Matches: 116, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
123 77 0.66
124 39 0.34
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.32
Consensus pattern (124 bp):
CTCATTTTAACATTTGAAAATCTATAAAATAAAATCGATAACTAAATCGATATCAACCAAACTCA
TAAATCCATTATAACTTCAAACTTATCGAAACACTTATGCAATTCAATAAATAATTGTT
Found at i:434687 original size:31 final size:31
Alignment explanation
Indices: 434649--434791 Score: 110
Period size: 31 Copynumber: 4.6 Consensus size: 31
434639 GCCTATGGGT
* *
434649 CTACCCAAGAAAGTTCTCAAGGCCACGGGGC
1 CTACCCAAGAAAGATCTCAAGGCCACAGGGC
* * *
434680 CTACCCAAGAAAGATCTCAGGGACGCAGGGC
1 CTACCCAAGAAAGATCTCAAGGCCACAGGGC
* * *
434711 CTACCCATGAATGATCTCAAGGCTAC-GAGGC
1 CTACCCAAGAAAGATCTCAAGGCCACAG-GGC
* ** * * *
434742 ATACTTAAGAAAAAATC-CCAGGACCACAAGGC
1 CTACCCAAG-AAAGATCTCAAGG-CCACAGGGC
*
434774 CTACCCAAGAATGATCTC
1 CTACCCAAGAAAGATCTC
434792 GGGGACGCAG
Statistics
Matches: 82, Mismatches: 25, Indels: 9
0.71 0.22 0.08
Matches are distributed among these distances:
30 1 0.01
31 63 0.77
32 18 0.22
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (31 bp):
CTACCCAAGAAAGATCTCAAGGCCACAGGGC
Found at i:434752 original size:62 final size:63
Alignment explanation
Indices: 434649--434791 Score: 155
Period size: 62 Copynumber: 2.3 Consensus size: 63
434639 GCCTATGGGT
* * * * * * * *
434649 CTACCCAAGAAAGTTCTCAAGGCCACGGGGCCTACCCAAG-AAAGATCTCAGGGA-CGCAGGGC
1 CTACCCAAGAATGATCTCAAGGCCACGAGGCATACCCAAGAAAAAATCCCA-GGACCACAAGGC
* * **
434711 CTACCCATGAATGATCTCAAGGCTACGAGGCATACTTAAGAAAAAATCCCAGGACCACAAGGC
1 CTACCCAAGAATGATCTCAAGGCCACGAGGCATACCCAAGAAAAAATCCCAGGACCACAAGGC
434774 CTACCCAAGAATGATCTC
1 CTACCCAAGAATGATCTC
434792 GGGGACGCAG
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
62 35 0.53
63 31 0.47
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (63 bp):
CTACCCAAGAATGATCTCAAGGCCACGAGGCATACCCAAGAAAAAATCCCAGGACCACAAGGC
Found at i:440237 original size:30 final size:30
Alignment explanation
Indices: 440203--440277 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
440193 AAATGGATTT
* * *
440203 AGTTTAGTGATCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAAA
* *
440233 AGTTTGGTTACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
*
440263 AGTTTAGGGACCAAA
1 AGTTTAGTGACCAAA
440278 ATGTAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:441366 original size:476 final size:475
Alignment explanation
Indices: 440469--441418 Score: 1729
Period size: 476 Copynumber: 2.0 Consensus size: 475
440459 AATATTTTGT
440469 TCATATTTGACTATTGAAATATGATAAGGTTGTTGTGACTTGATATTAATATAAATATCATGTTC
1 TCATATTTGACTATTGAAATATGATAAGGTTGTTGTGACTTGATATTAATATAAATATCATGTTC
* *
440534 ATTAAGGGTAAATTAGTATGGATATTTTTATTTTAAGGGTAAAGTGGTAATTTGACATTTAATGA
66 ATTAAGGGTAAATTAGTATGGATATTTTGATTTTAAGGGTAAAGTGGTAATTTAACATTTAATGA
* *
440599 ATTTTAATTCATTATTAATTAGAAAATATGAAGAAATATCATGCCAAGATGTTCATCTTCTCCAG
131 ATTTTAATTCATTATTAATTAGAAAAGATAAAGAAATATCATGCCAAGATGTTCATCTTCTCCAG
440664 CAAAGGACGTGAGATAGCTTGGAGGTAAGGAAAAATATTTGTTTTCCATTTTTGAGCAATTTTCT
196 CAAAGGACGTGAGATAGCTTGGAGGTAAGGAAAAATATTTGTTTTCCATTTTTGAGCAATTTTCT
*
440729 TTGGATTTTGGGTTATGCCATAAAATAGAAATTTGTTCTACGTGAAAAACACTATCATTTGATAC
261 TTGGATTTTGGGTTATGCCATAAAATAGAAAATTGTTCTACGTGAAAAACACTATCATTTGATAC
* *
440794 CAATATTTCTTTCTAATCTTGTTGGATTTCAAATATCCCAAATCTAAGGGTTTATGTTTATGATA
326 CAATATTTCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAATCTAAGGGTTTATGTTCATGATA
440859 TGATCCATGAAATTGATAAATCTTGATGATTTAGAAGCTGTATATTCATTTTTCAAGCTTGATTT
391 TGATCCATGAAATTGATAAATCTTGATGATTTAGAAGCTGTATATTCA-TTTTCAAGCTTGATTT
440924 ATGGTTAAAACATGTTCAATA
455 ATGGTTAAAACATGTTCAATA
* * *
440945 TCATCTTTGACTATTGAAATATGATAAGGTTTTTGTGACTTGGTATTAATATAAATATCATGTTC
1 TCATATTTGACTATTGAAATATGATAAGGTTGTTGTGACTTGATATTAATATAAATATCATGTTC
*
441010 ATTTAGGGTAAATTAGTATGGATATTTTGATTTTAAGGGTAAAGTGGTAATTTAACATTTAATGA
66 ATTAAGGGTAAATTAGTATGGATATTTTGATTTTAAGGGTAAAGTGGTAATTTAACATTTAATGA
*
441075 ATTTTAATTCATTATTAATTAGAAAAGATAAAGAAATATCATGCCAAGATGTTCATCTTCTCTAG
131 ATTTTAATTCATTATTAATTAGAAAAGATAAAGAAATATCATGCCAAGATGTTCATCTTCTCCAG
*
441140 CAAAGGACGTGAGATAGCTTGGAGGTAAGGAAAAATATTTGTTTTCGATTTTTGAGCAATTTTCT
196 CAAAGGACGTGAGATAGCTTGGAGGTAAGGAAAAATATTTGTTTTCCATTTTTGAGCAATTTTCT
* * *
441205 TTGGATTTTGGGTTATGCCGTAAAATAGAAAATTGTTGTACGTGACAAACACTATCATTTGATAC
261 TTGGATTTTGGGTTATGCCATAAAATAGAAAATTGTTCTACGTGAAAAACACTATCATTTGATAC
441270 CAATATTTCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAATCTAAGGGTTTATGTTCATGATA
326 CAATATTTCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAATCTAAGGGTTTATGTTCATGATA
* *
441335 TGATTCATGAAATTGATAAATCTTGATGATTTAGAGGCTGTATATTCATTTTCAAGCTTGATTTA
391 TGATCCATGAAATTGATAAATCTTGATGATTTAGAAGCTGTATATTCATTTTCAAGCTTGATTTA
441400 TGGTTAAAACATGTTCAAT
456 TGGTTAAAACATGTTCAAT
441419 CTTTCTAGAA
Statistics
Matches: 456, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
475 36 0.08
476 420 0.92
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (475 bp):
TCATATTTGACTATTGAAATATGATAAGGTTGTTGTGACTTGATATTAATATAAATATCATGTTC
ATTAAGGGTAAATTAGTATGGATATTTTGATTTTAAGGGTAAAGTGGTAATTTAACATTTAATGA
ATTTTAATTCATTATTAATTAGAAAAGATAAAGAAATATCATGCCAAGATGTTCATCTTCTCCAG
CAAAGGACGTGAGATAGCTTGGAGGTAAGGAAAAATATTTGTTTTCCATTTTTGAGCAATTTTCT
TTGGATTTTGGGTTATGCCATAAAATAGAAAATTGTTCTACGTGAAAAACACTATCATTTGATAC
CAATATTTCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAATCTAAGGGTTTATGTTCATGATA
TGATCCATGAAATTGATAAATCTTGATGATTTAGAAGCTGTATATTCATTTTCAAGCTTGATTTA
TGGTTAAAACATGTTCAATA
Found at i:441946 original size:9 final size:9
Alignment explanation
Indices: 441929--442009 Score: 81
Period size: 9 Copynumber: 9.0 Consensus size: 9
441919 AATTCCAGCA
441929 CTGGAATTT
1 CTGGAATTT
*
441938 CTTGAATTT
1 CTGGAATTT
*
441947 ATGGAATTT
1 CTGGAATTT
*
441956 CTTGAATTT
1 CTGGAATTT
* *
441965 ATGGAATAT
1 CTGGAATTT
*
441974 ATGGAATTT
1 CTGGAATTT
441983 CTGGAATTT
1 CTGGAATTT
* *
441992 CTTGAACTT
1 CTGGAATTT
*
442001 ATGGAATTT
1 CTGGAATTT
442010 TTGGTATTTA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (9 bp):
CTGGAATTT
Found at i:441962 original size:27 final size:27
Alignment explanation
Indices: 441929--442018 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
441919 AATTCCAGCA
441929 CTGGAATTTCTTGAATTTATGGAATTT
1 CTGGAATTTCTTGAATTTATGGAATTT
* * * *
441956 CTTGAATTTATGGAATATATGGAATTT
1 CTGGAATTTCTTGAATTTATGGAATTT
*
441983 CTGGAATTTCTTGAACTTATGGAATTT
1 CTGGAATTTCTTGAATTTATGGAATTT
* *
442010 TTGGTATTT
1 CTGGAATTT
442019 ATAATTTAAG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.07, G:0.19, T:0.48
Consensus pattern (27 bp):
CTGGAATTTCTTGAATTTATGGAATTT
Found at i:442020 original size:18 final size:18
Alignment explanation
Indices: 441930--442009 Score: 115
Period size: 18 Copynumber: 4.4 Consensus size: 18
441920 ATTCCAGCAC
441930 TGGAATTTCTTGAATTTA
1 TGGAATTTCTTGAATTTA
441948 TGGAATTTCTTGAATTTA
1 TGGAATTTCTTGAATTTA
* * * *
441966 TGGAATATATGGAATTTC
1 TGGAATTTCTTGAATTTA
*
441984 TGGAATTTCTTGAACTTA
1 TGGAATTTCTTGAATTTA
442002 TGGAATTT
1 TGGAATTT
442010 TTGGTATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (18 bp):
TGGAATTTCTTGAATTTA
Found at i:443089 original size:31 final size:31
Alignment explanation
Indices: 443051--443298 Score: 369
Period size: 31 Copynumber: 8.1 Consensus size: 31
443041 GAGTCGAGGG
443051 TTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
443082 TTACCTATGTTCTTCGGGAGATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
443113 CTACCTATGTTCTTC--G-CATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
443141 TTACCTATTTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
443172 TTACCTATGTTCTTCGGGACATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
443203 TTACCTATGTTATTCGGGACATATGGACA-A
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* * * *
443233 TTTATCTATGTTATTCGCGACATATGGATAGA
1 -TTACCTATGTTCTTCGGGACATATGGACAGA
*
443265 TTACCTATGTTCTTCAGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
443296 TTA
1 TTA
443299 TTATACGAGT
Statistics
Matches: 195, Mismatches: 17, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
28 24 0.12
29 1 0.01
30 2 0.01
31 167 0.86
32 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:443285 original size:93 final size:90
Alignment explanation
Indices: 443051--443298 Score: 363
Period size: 90 Copynumber: 2.7 Consensus size: 90
443041 GAGTCGAGGG
* *
443051 TTACCTATGTTCTTCGGGACATATGGACAGATTACCTATGTTCTTCGGGAGATATGGACAGACTA
1 TTACCTATGTTCTTCGGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGATTA
*
443116 CCTATGTTCTTCGCATATGGACAGA
66 CCTATGTTATTCGCATATGGACAGA
* *
443141 TTACCTATTTTCTTCGGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGATAGATTA
1 TTACCTATGTTCTTCGGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGATTA
443206 CCTATGTTATTCGGGACATATGGACA-A
66 CCTATGTTATTC--G-CATATGGACAGA
* * * * *
443233 TTTATCTATGTTATTCGCGACATATGGATAGATTACCTATGTTCTTCAGGACATATGGACAGATT
1 -TTACCTATGTTCTTCGGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGATT
443298 A
65 A
443299 TTATACGAGT
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
90 72 0.51
92 2 0.01
93 68 0.48
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (90 bp):
TTACCTATGTTCTTCGGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGATTA
CCTATGTTATTCGCATATGGACAGA
Found at i:443556 original size:18 final size:18
Alignment explanation
Indices: 443533--443596 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
443523 AATGTATTAC
*
443533 TTGATATTGATATTGATG
1 TTGATAATGATATTGATG
** *
443551 TTGATAATGATAGAGATC
1 TTGATAATGATATTGATG
* *
443569 ATGATAACGATATTGATG
1 TTGATAATGATATTGATG
443587 TTGATAATGA
1 TTGATAATGA
443597 CGGTATTTAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (18 bp):
TTGATAATGATATTGATG
Found at i:448228 original size:30 final size:31
Alignment explanation
Indices: 448194--448268 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
448184 TAAATTACAT
* *
448194 TTTGGTCCCTAAACTTTTCAAAGT-TTATAC
1 TTTGGTCCCTAAACTTTTCAAAATCTTATAA
448224 TTTGGTCACC-AAAC-TTTCAAAATCTTATAA
1 TTTGGTC-CCTAAACTTTTCAAAATCTTATAA
* *
448254 TTTGATCACTAAACT
1 TTTGGTCCCTAAACT
448269 AAATCTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
29 9 0.24
30 26 0.70
31 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (31 bp):
TTTGGTCCCTAAACTTTTCAAAATCTTATAA
Found at i:448522 original size:31 final size:31
Alignment explanation
Indices: 448484--448634 Score: 232
Period size: 31 Copynumber: 4.9 Consensus size: 31
448474 GAGTCGAGGG
448484 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACATA
448515 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACATA
* *
448546 TTACCTATGTTCTTAGGGATATATGGACAGT-
1 TTACCTATGTTCTTCGGGACATATGGACA-TA
* *
448577 TTACCTATGTTCTTCGGGATATATGGACAAA
1 TTACCTATGTTCTTCGGGACATATGGACATA
**
448608 TTACCTATGTTCTTCAAGACATATGGA
1 TTACCTATGTTCTTCGGGACATATGGA
448635 TAGATTATTA
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
31 110 0.99
32 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACATA
Found at i:449665 original size:21 final size:24
Alignment explanation
Indices: 449632--449676 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
449622 TGTTTTGGTC
449632 TTATCTCACTTAAA-T-GAATATA
1 TTATCTCACTTAAAGTGGAATATA
*
449654 TTAT-TCATTTAAAGTGGAATATA
1 TTATCTCACTTAAAGTGGAATATA
449677 ATGTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (24 bp):
TTATCTCACTTAAAGTGGAATATA
Found at i:451312 original size:40 final size:40
Alignment explanation
Indices: 451255--451333 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
451245 TGCAGGGTTA
451255 TAATACACTTCGTTGTATATGGTAGGCACGACCTTATGTG
1 TAATACACTTCGTTGTATATGGTAGGCACGACCTTATGTG
*
451295 TAATACACTTCAG-TGTATATGGTGGGCACGACCTTATGT
1 TAATACACTTC-GTTGTATATGGTAGGCACGACCTTATGT
451334 TTAGCACTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGTTGTATATGGTAGGCACGACCTTATGTG
Found at i:451504 original size:44 final size:44
Alignment explanation
Indices: 451454--451595 Score: 162
Period size: 44 Copynumber: 3.2 Consensus size: 44
451444 TAAGCTTCCG
* *
451454 AGCTTATGGAACAATGGCAAGTATATTGGTAAAATAAACTTACG
1 AGCTTATGGAACAATGGTAAGTATATTGGTAAAATAAACTTACA
* * *
451498 AGCTTATGGAACAAATGATAAGTATATTGTTAATAT-AACTTACA
1 AGCTTATGGAAC-AATGGTAAGTATATTGGTAAAATAAACTTACA
* * * *
451542 AGTTTATGGGTTA-AATGGTAAGTATTTTGGTAAAATAAGCTTACA
1 AGCTTAT-GG-AACAATGGTAAGTATATTGGTAAAATAAACTTACA
451587 AGCTTATGG
1 AGCTTATGG
451596 CATAATTAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
44 46 0.57
45 34 0.42
46 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (44 bp):
AGCTTATGGAACAATGGTAAGTATATTGGTAAAATAAACTTACA
Found at i:453674 original size:329 final size:329
Alignment explanation
Indices: 453073--454729 Score: 3030
Period size: 329 Copynumber: 5.0 Consensus size: 329
453063 GAACTTGAAA
*
453073 AGTGTCAAGTTCGTAATGATAAGAAAAATAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
* *
453138 TACAATGAAGTTATTGCTACAATTATCAA-ATTTCTTATTGAACGATGTGAACATTGAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
*
453202 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATTTTTGGAATTGGAAAACGTTATACA
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
*
453267 GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
196 GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
*
453332 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGAAAAATAATAAA
261 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
453397 TGTC
326 TGTC
* *
453401 AGTATCAAGTTCATAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
*
453466 TACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
*
453531 ATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
453596 GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
196 GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
453661 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
261 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
453726 TGTC
326 TGTC
453730 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
*
453795 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTAAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
453860 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAAATTGGAAATGTGAACGT
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGG-AATTGG-AA----AACG-
453925 TTCATACAATTGAAATTTACCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCT
189 TT-ATAC-A--G--ATTT-CCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCT
453990 ACTTGATATCGAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATAT-AGTGTTAGTC
247 ACTTGATATCGAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTC
454054 GGACAAATAATAAATGTC
312 GGACAAATAATAAATGTC
* *
454072 AGTGTCAAGTTCGTAATGATAAGAATAATAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
*
454137 TACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
*
454202 ATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
454267 GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
196 GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
454332 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
261 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
454397 TGTC
326 TGTC
454401 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
454466 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
454531 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
*
454596 GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
196 GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
454661 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
261 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
454726 TGTC
326 TGTC
454730 CAAAAAAGAT
Statistics
Matches: 1288, Mismatches: 25, Indels: 31
0.96 0.02 0.02
Matches are distributed among these distances:
328 189 0.15
329 756 0.59
330 6 0.00
331 3 0.00
333 1 0.00
334 4 0.00
335 6 0.00
336 6 0.00
337 4 0.00
338 1 0.00
340 3 0.00
341 6 0.00
342 203 0.16
343 100 0.08
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (329 bp):
AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
GATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
TGTC
Found at i:454340 original size:671 final size:658
Alignment explanation
Indices: 453073--454729 Score: 3075
Period size: 671 Copynumber: 2.5 Consensus size: 658
453063 GAACTTGAAA
*
453073 AGTGTCAAGTTCGTAATGATAAGAAAAATAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
* *
453138 TACAATGAAGTTATTGCTACAATTATCAA-ATTTCTTATTGAACGATGTGAACATTGAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
*
453202 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATTTTTGGAATTGGAAAACGTTATACA
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
453267 GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
196 GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
*
453332 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGAAAAATAATAAA
261 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
453397 TGTCAGTATCAAGTTCATAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCAT
326 TGTCAGTATCAAGTTCATAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCAT
453462 TAACTACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGATGTGAACATTGAGAC
391 TAACTACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGATGTGAACATTGAGAC
453527 TTTCATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTA
456 TTTCATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTA
453592 TACAGATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATC
521 TACAGATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATC
453657 GAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAA
586 GAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAA
453722 TAAATGTC
651 TAAATGTC
453730 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
*
453795 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTAAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
453860 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAAATTGGAAATGTGAACGT
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGG-AATTGG-AA----AACG-
*
453925 TTCATACAATTGAAATTTACCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCT
189 TT-ATAC-A--G--ATTT-CCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCT
453990 ACTTGATATCGAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATAT-AGTGTTAGTC
247 ACTTGATATCGAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTC
* * * *
454054 GGACAAATAATAAATGTCAGTGTCAAGTTCGTAATGATAAGAATAATAGTAAATTTGTTTACTAG
312 GGACAAATAATAAATGTCAGTATCAAGTTCATAATGATAAGAAAAACAGTAAATTTGTTTACTAG
454119 TGTGAATTTAGCATTAACTACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGAT
377 TGTGAATTTAGCATTAACTACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGAT
454184 GTGAACATTGAGACTTTCATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGA
442 GTGAACATTGAGACTTTCATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGA
454249 ATTGGAAAACGTTATACAGATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAA
507 ATTGGAAAACGTTATACAGATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAA
454314 TTCTACTTGATATCGAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTT
572 TTCTACTTGATATCGAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTT
454379 AGTCGGACAAATAATAAATGTC
637 AGTCGGACAAATAATAAATGTC
454401 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
1 AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
454466 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
66 TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
454531 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
131 ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
454596 GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
196 GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
454661 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
261 GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
454726 TGTC
326 TGTC
454730 CAAAAAAGAT
Statistics
Matches: 971, Mismatches: 13, Indels: 31
0.96 0.01 0.03
Matches are distributed among these distances:
657 191 0.20
658 110 0.11
659 6 0.01
660 3 0.00
662 1 0.00
663 4 0.00
664 6 0.01
665 6 0.01
666 4 0.00
667 1 0.00
669 3 0.00
670 6 0.01
671 531 0.55
672 99 0.10
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (658 bp):
AGTGTCAAGTTCGTAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCATTAAC
TACTATGAAGTTATTGCTACAATTATCAAGTTTTCTTATTGAACGATGTGAACATTGAGACTTTC
ATTTGAGATTGAAAACATTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTATACA
GATTTCCTTAAGAATGAAATAAAGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATCGAGT
GATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAATAAA
TGTCAGTATCAAGTTCATAATGATAAGAAAAACAGTAAATTTGTTTACTAGTGTGAATTTAGCAT
TAACTACTATGAAGTTATTGCTACAATTTTCAAGTTTTCTTATTGAACGATGTGAACATTGAGAC
TTTCATTTGAGATTGAAAACGTTTCAATTGTTCCAAAATATTATCTTTGGAATTGGAAAACGTTA
TACAGATTTCCTTAAGAATGAAATAAGGAATTCTAAAGTAGAGATATTCAATTCTACTTGATATC
GAGTGATATTATAGCGGAAGACCCATAGGTCACGGTCATGATATAAGTGTTAGTCGGACAAATAA
TAAATGTC
Found at i:455788 original size:9 final size:9
Alignment explanation
Indices: 455756--455827 Score: 65
Period size: 9 Copynumber: 7.9 Consensus size: 9
455746 CATAAGAGTT
455756 GAAAACAAAA
1 GAAAA-AAAA
* *
455766 TAAAAAATAG
1 GAAAAAA-AA
455776 GAAAAAAAA
1 GAAAAAAAA
455785 GAAAAAAAA
1 GAAAAAAAA
* *
455794 GAAATAGAA
1 GAAAAAAAA
455803 GAAAAAAAA
1 GAAAAAAAA
* *
455812 -TAGAAAAA
1 GAAAAAAAA
455820 GAAAAAAA
1 GAAAAAAA
455828 TGAGATGCTT
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
8 6 0.12
9 31 0.65
10 11 0.23
ACGTcount: A:0.81, C:0.01, G:0.12, T:0.06
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:455812 original size:14 final size:13
Alignment explanation
Indices: 455762--455825 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
455752 AGTTGAAAAC
455762 AAAATAAAAAATAGG
1 AAAA-AAAAAATA-G
*
455777 AAAAAAAAGA-A-
1 AAAAAAAAAATAG
*
455788 AAAAAAGAAATAG
1 AAAAAAAAAATAG
455801 AAGAAAAAAAATAG
1 AA-AAAAAAAATAG
455815 AAAAAGAAAAA
1 AAAAA-AAAAA
455826 AATGAGATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.20
12 1 0.02
13 6 0.15
14 22 0.54
15 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (13 bp):
AAAAAAAAAATAG
Found at i:459753 original size:40 final size:40
Alignment explanation
Indices: 459698--459858 Score: 259
Period size: 40 Copynumber: 4.0 Consensus size: 40
459688 GCAGGGTTAA
459698 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
1 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
459738 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
1 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
* ** *
459778 AATACACTTCGGTGTATATGGTGGCCATTACCTTATGTAT
1 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
* * *
459818 AATACACTTCAGTGTATATGGTGGGAACAACCTTATGTGT
1 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
459858 A
1 A
459859 GAACTACAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 111 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
Found at i:460604 original size:21 final size:24
Alignment explanation
Indices: 460570--460614 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
460560 TAACGTACAT
460570 TATATTCCACTTTAAATGA-ATAA
1 TATATTCCACTTTAAATGAGATAA
*
460593 TATATT-CA-TTTAAGTGAGATAA
1 TATATTCCACTTTAAATGAGATAA
460615 GACCAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (24 bp):
TATATTCCACTTTAAATGAGATAA
Found at i:461561 original size:22 final size:22
Alignment explanation
Indices: 461536--461588 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
461526 TAATATTAGT
*
461536 ATTAAATATAATTAATTGTATG
1 ATTAAATATAATTAATAGTATG
461558 ATTAAATATAATTAATAGTATG
1 ATTAAATATAATTAATAGTATG
461580 ATTAAATAT
1 ATTAAATAT
461589 TATGATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (22 bp):
ATTAAATATAATTAATAGTATG
Found at i:469113 original size:14 final size:14
Alignment explanation
Indices: 469094--469140 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
469084 TATATATTCG
469094 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
469108 TTTA---T-GTTCA
1 TTTATGTTCGTTCA
469118 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
469132 TTTATGTTC
1 TTTATGTTC
469141 AAACAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:469126 original size:24 final size:24
Alignment explanation
Indices: 469076--469141 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
469066 CGTTTGTGAA
* *
469076 CGTTCGATTATATATTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTT
469102 CGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
469126 CGTTCATTTATGTTCA
1 CGTTCATTTATGTTCA
469142 AACAAAGGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 30 0.79
25 3 0.08
26 5 0.13
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:472959 original size:12 final size:13
Alignment explanation
Indices: 472942--472970 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
472932 CTTAATTGTG
472942 AAAATTAAAA-TT
1 AAAATTAAAATTT
472954 AAAATTAAAATTT
1 AAAATTAAAATTT
472967 AAAA
1 AAAA
472971 AACTCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:474391 original size:38 final size:38
Alignment explanation
Indices: 474349--474561 Score: 215
Period size: 36 Copynumber: 5.6 Consensus size: 38
474339 TTTCAAAAAC
474349 TATATAATATATATTTTCAAAAATATTTTTAAAAAA-A
1 TATATAATATATATTTTCAAAAATATTTTTAAAAAATA
* * *
474386 TTATATACTATATATTTT-AAAAAT-GTTTTAAAAACTA
1 -TATATAATATATATTTTCAAAAATATTTTTAAAAAATA
* * *
474423 TATATTATATTTAAGTTTTCAAAAATATTTTTAAAAACTA
1 TATATAATATAT-A-TTTTCAAAAATATTTTTAAAAAATA
* *
474463 TATAATATATATATTTTTTCAAAAATA-TTTTAAAAACTA
1 TAT-ATA-ATATATATTTTCAAAAATATTTTTAAAAAATA
* *
474502 TATAT--TATATATTTTCAAAAA-ATGTTTTTAAAAATC
1 TATATAATATATATTTTCAAAAATAT-TTTTAAAAAATA
*
474538 TATATAATATATATATTTAAAAAA
1 TATATAATATATAT-TTTCAAAAA
474562 CTATATATTA
Statistics
Matches: 148, Mismatches: 15, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
34 1 0.01
35 15 0.10
36 32 0.22
37 8 0.05
38 29 0.20
39 29 0.20
40 27 0.18
41 2 0.01
42 5 0.03
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (38 bp):
TATATAATATATATTTTCAAAAATATTTTTAAAAAATA
Found at i:474552 original size:40 final size:38
Alignment explanation
Indices: 474343--474793 Score: 306
Period size: 39 Copynumber: 11.8 Consensus size: 38
474333 AAAATATTTC
*
474343 AAAAACTATAT-A-ATATATATTTTCAAAAATATTTTT
1 AAAAACTATATAATATATATATTTTCAAAAATGTTTTT
*
474379 AAAAA-AAT-TATATACTATATATTTT-AAAAATG-TTTT
1 AAAAACTATATA-ATA-TATATATTTTCAAAAATGTTTTT
* * *
474415 AAAAACTATATATTATATTTAAGTTTTCAAAAATATTTTT
1 AAAAACTATATAATATATAT-A-TTTTCAAAAATGTTTTT
*
474455 AAAAACTATATAATATATATATTTTTTCAAAAAT-ATTTT
1 AAAAACTATATAATATATATA--TTTTCAAAAATGTTTTT
474494 AAAAACTATAT-AT-TATATATTTTCAAAAAATGTTTTT
1 AAAAACTATATAATATATATATTTTC-AAAAATGTTTTT
474531 AAAAATCTATATAATATATATA-TTT----AA-------
1 AAAAA-CTATATAATATATATATTTTCAAAAATGTTTTT
* *
474558 AAAA-CTATATATTATATATAAGTTATCAAAAATGTTTTT
1 AAAAACTATATAATATATAT-A-TTTTCAAAAATGTTTTT
474597 AAAAACTATATAATATATATATTTTCAAAAATG-TTTT
1 AAAAACTATATAATATATATATTTTCAAAAATGTTTTT
* * * *
474634 AAAAAATATTATATATATATATATATATATATATATTCAAAATGTTTTAA
1 AAAAACTA-TATA-ATATATATAT-T-T-T-CA-A---AAAT-GTTTT-T
*
474684 AAAAACTATATAATATATATATTTT-TAAAATGTTTTTTT
1 AAAAACTATATAATATATATATTTTCAAAAATG--TTTTT
* * *
474723 AAAAACTATATAACATATATATATTCGAAAAACCGTTTTCT
1 AAAAACTATATAATATATATATTTTC-AAAAA-TGTTTT-T
* *
474764 GAAAAATTATAT-AT-TATATTTTTTCAAAAA
1 -AAAAACTATATAATATATATATTTTCAAAAA
474794 CACTTTAAAA
Statistics
Matches: 333, Mismatches: 31, Indels: 99
0.72 0.07 0.21
Matches are distributed among these distances:
25 14 0.04
26 1 0.00
27 4 0.01
28 2 0.01
32 2 0.01
34 3 0.01
35 7 0.02
36 25 0.08
37 38 0.11
38 40 0.12
39 73 0.22
40 71 0.21
41 7 0.02
42 13 0.04
43 1 0.00
44 1 0.00
45 1 0.00
46 1 0.00
47 4 0.01
48 11 0.03
49 7 0.02
50 7 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (38 bp):
AAAAACTATATAATATATATATTTTCAAAAATGTTTTT
Found at i:474565 original size:25 final size:25
Alignment explanation
Indices: 474528--474577 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
474518 AAAAAATGTT
*
474528 TTTAAAAATCTATATAATATATATA
1 TTTAAAAAACTATATAATATATATA
*
474553 TTTAAAAAACTATATATTATATATA
1 TTTAAAAAACTATATAATATATATA
474578 AGTTATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTAAAAAACTATATAATATATATA
Found at i:474568 original size:102 final size:106
Alignment explanation
Indices: 474447--474659 Score: 303
Period size: 102 Copynumber: 2.1 Consensus size: 106
474437 GTTTTCAAAA
* ** *
474447 ATAT-TTTTAAAAACTATATAATATATATATTTTTTCAAAAAT-ATTTTAAAAACTATAT-AT-T
1 ATATATTTAAAAAACTATATAATATATATAAGTTATCAAAAATGATTTTAAAAACTATATAATAT
*
474508 ATATATTTTCAAAAAATGTTTTTAAAAAT-CTATATA-ATAT
66 ATATATTTTC-AAAAATGTTTTAAAAAATACTATATATATAT
* *
474548 ATATATTTAAAAAACTATATATTATATATAAGTTATCAAAAATGTTTTTAAAAACTATATAATAT
1 ATATATTTAAAAAACTATATAATATATATAAGTTATCAAAAATGATTTTAAAAACTATATAATAT
*
474613 ATATATTTTCAAAAATGTTTTAAAAAATATTATATATATAT
66 ATATATTTTCAAAAATGTTTTAAAAAATACTATATATATAT
474654 ATATAT
1 ATATAT
474660 ATATATATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
101 4 0.04
102 33 0.34
103 15 0.15
104 19 0.19
105 17 0.17
106 10 0.10
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (106 bp):
ATATATTTAAAAAACTATATAATATATATAAGTTATCAAAAATGATTTTAAAAACTATATAATAT
ATATATTTTCAAAAATGTTTTAAAAAATACTATATATATAT
Found at i:474612 original size:65 final size:63
Alignment explanation
Indices: 474487--474620 Score: 209
Period size: 63 Copynumber: 2.1 Consensus size: 63
474477 TTTTTCAAAA
*
474487 ATATTTTAAAAACTATATATTATATATTTTCAAAAAATGTTTTTAAAAATCTATATAATATAT
1 ATATTTAAAAAACTATATATTATATATTTTCAAAAAATGTTTTTAAAAATCTATATAATATAT
474550 ATATTTAAAAAACTATATATTATATATAAGTTATC-AAAAATGTTTTTAAAAA-CTATATAATAT
1 ATATTTAAAAAACTATATATTATATAT---TT-TCAAAAAATGTTTTTAAAAATCTATATAATAT
474613 AT
62 AT
474615 ATATTT
1 ATATTT
474621 TCAAAAATGT
Statistics
Matches: 66, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
63 26 0.39
65 19 0.29
66 19 0.29
67 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (63 bp):
ATATTTAAAAAACTATATATTATATATTTTCAAAAAATGTTTTTAAAAATCTATATAATATAT
Found at i:474613 original size:38 final size:38
Alignment explanation
Indices: 474557--474657 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 38
474547 TATATATTTA
474557 AAAAACTATATAT-TATATATAAGTTATCAAAAATGTTTTT
1 AAAAACTATATATATATATAT-A-TTATCAAAAATG-TTTT
*
474597 AAAAACTATATA-ATATATATATTTTCAAAAATGTTTT
1 AAAAACTATATATATATATATATTATCAAAAATGTTTT
*
474634 AAAAAATATTATATATATATATAT
1 AAAAACTA-TATATATATATATAT
474658 ATATATATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
37 11 0.20
38 15 0.27
39 11 0.20
40 19 0.34
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (38 bp):
AAAAACTATATATATATATATATTATCAAAAATGTTTT
Found at i:474648 original size:2 final size:2
Alignment explanation
Indices: 474639--474669 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
474629 GTTTTAAAAA
474639 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474670 TCAAAATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:474679 original size:48 final size:47
Alignment explanation
Indices: 474603--474705 Score: 156
Period size: 48 Copynumber: 2.2 Consensus size: 47
474593 TTTTAAAAAC
* *
474603 TATATA-ATATATATATTTTCAAAAATGTTTTAAAAAATATTATATATA
1 TATATATATATATATATATTCAAAAATGTTTTAAAAAA-ACTATATA-A
474651 TATATATATATATATATATTC-AAAATGTTTTAAAAAAACTATATAA
1 TATATATATATATATATATTCAAAAATGTTTTAAAAAAACTATATAA
474697 TATATATAT
1 TATATATAT
474706 TTTTAAAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
46 10 0.19
47 7 0.13
48 22 0.42
49 13 0.25
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (47 bp):
TATATATATATATATATATTCAAAAATGTTTTAAAAAAACTATATAA
Found at i:474741 original size:87 final size:86
Alignment explanation
Indices: 474586--474746 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 86
474576 TAAGTTATCA
* *
474586 AAAATGTTTTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAAATATTATATATA
1 AAAATGTTTTAAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAAATATTATATACA
474651 TATATATATATATATATATTC
66 TATATATATATATATATATTC
* *
474672 AAAATGTTTTAAAAAAACTATATAATATATATATTTT-TAAAATGTTTTTTTAAAAACTA-TATA
1 AAAATGTTTT-AAAAAACTATATAATATATATATTTTCAAAAATG---TTTTAAAAAATATTATA
474735 -ACATATATATAT
62 TACATATATATAT
474747 TCGAAAAACC
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
86 16 0.24
87 36 0.54
88 4 0.06
89 11 0.16
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (86 bp):
AAAATGTTTTAAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAAATATTATATACA
TATATATATATATATATATTC
Found at i:475520 original size:85 final size:85
Alignment explanation
Indices: 475371--476121 Score: 991
Period size: 85 Copynumber: 8.8 Consensus size: 85
475361 ATGTGTCATC
* * * ** * * *
475371 GAGCTGAATGAAATCGAACTCGACA-GTTTTTGTTGACAGATAGCTTTTCTCGACTTAAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* **
475435 CTGTAAATTTGACATGCCCCT
65 CTGTAAATTTGATATGCCTTT
* * * * *
475456 GAGCTTAATGGAATCAAACTCGAAGGTATTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
475521 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * ** *
475541 GAGTTGAATGTAATCGAACTCGAAGGTTTTTTGTTGACAGATAGTCCTTCACGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGG-TCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
475606 CTGTAAATTTAATATGCCTAT
65 CTGTAAATTTGATATGCCTTT
* *
475627 GAGATGAATGTAATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
475692 TATAAATTGGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * *
475712 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
475777 CTGTAAATTTGATATGCCTCT
65 CTGTAAATTTGATATGCCTTT
* * * * * *
475798 GAGCTGAGTGTAATCAAACTCGAAGGTATTGGTTGATATATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
475863 TGTAAATTTGATGTGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
475883 AAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
475948 TGTAAATTTGATGTGCCTGT
66 TGTAAATTTGATATGCCTTT
* * * *
475968 GAGCTGAGTGTAATCGAACTCGAAGGTCCTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
476033 TATAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * *
476053 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
476118 TGTA
66 TGTA
476122 CTGATCCGTT
Statistics
Matches: 589, Mismatches: 74, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
84 1 0.00
85 436 0.74
86 152 0.26
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCTTT
Found at i:475990 original size:170 final size:170
Alignment explanation
Indices: 475371--476121 Score: 1045
Period size: 171 Copynumber: 4.4 Consensus size: 170
475361 ATGTGTCATC
* * ** * *
475371 GAGCTGAATGAAATCGAACTCGACA-GTTTTTGTTGACAGATAGCTTTTCTCGACTTAAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* * * * **
475435 CTGTAAATTTGACATGCCCCTGAGCTTAATGGAATCAAACTCGAAGGTATTTATTGACAGATAAC
65 CTGTAAATTTGATATGCCTCTGAGCTGAATGTAATCAAACTCGAAGGTATTGGTTGACAGATAAC
*
475500 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTT
130 CCTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTT
* * * * *
475541 GAGTTGAATGTAATCGAACTCGAAGGTTTTTTGTTGACAGATAGTCCTTCACGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGG-TCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* * * * * * *
475606 CTGTAAATTTAATATGCCTATGAGATGAATGTAATCGAACTCGAAGGTCTTTGATGACAGATAAC
65 CTGTAAATTTGATATGCCTCTGAGCTGAATGTAATCAAACTCGAAGGTATTGGTTGACAGATAAC
*
475671 CCTTCTCGCCTTGAGTTATGCTATAAATTGGATATGCCTTT
130 CCTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTT
*
475712 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* * *
475777 CTGTAAATTTGATATGCCTCTGAGCTGAGTGTAATCAAACTCGAAGGTATTGGTTGATATATAAC
65 CTGTAAATTTGATATGCCTCTGAGCTGAATGTAATCAAACTCGAAGGTATTGGTTGACAGATAAC
* *
475842 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATGTGCCTTT
130 CCTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTT
* * *
475883 AAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * * * ** *
475948 TGTAAATTTGATGTGCCTGTGAGCTGAGTGTAATCGAACTCGAAGGTCCTGGTTGATAGATAACC
66 TGTAAATTTGATATGCCTCTGAGCTGAATGTAATCAAACTCGAAGGTATTGGTTGACAGATAACC
476013 CTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTT
131 CTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTT
* * * * *
476053 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
476118 TGTA
66 TGTA
476122 CTGATCCGTT
Statistics
Matches: 521, Mismatches: 57, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
169 1 0.00
170 220 0.42
171 300 0.58
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (170 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTCTGAGCTGAATGTAATCAAACTCGAAGGTATTGGTTGACAGATAACC
CTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTT
Found at i:482562 original size:26 final size:26
Alignment explanation
Indices: 482511--482562 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
482501 TGTAAGAAGC
* * *
482511 CCTTAGACCAACTAACCGCACTTGCT
1 CCTTAGACCAACTAAACACACATGCT
482537 CCTTAGACCAACTAAACACACATGCT
1 CCTTAGACCAACTAAACACACATGCT
482563 ATCATCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.10, T:0.21
Consensus pattern (26 bp):
CCTTAGACCAACTAAACACACATGCT
Found at i:487350 original size:20 final size:20
Alignment explanation
Indices: 487325--487424 Score: 139
Period size: 20 Copynumber: 4.9 Consensus size: 20
487315 TAGTTGGAAA
487325 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
487345 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
487365 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* *
487385 TCGCGTTGCGATAGTTTACAGT
1 TCGCGTTGCGAT--TTTCCATT
487407 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
487425 AATTCGTTGC
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
20 55 0.76
21 1 0.01
22 16 0.22
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:487541 original size:6 final size:6
Alignment explanation
Indices: 487530--487566 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
487520 GACATGTATT
487530 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
487567 GATGGCGGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:490574 original size:26 final size:27
Alignment explanation
Indices: 490545--490596 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
490535 AGGTGTTAGA
*
490545 CTGTTAAAG-AATATGCACGTGTATTG
1 CTGTTAAAGAAATATGCACATGTATTG
490571 CTGTTAAAGAAATATGCACATGTATT
1 CTGTTAAAGAAATATGCACATGTATT
490597 AAGCAGTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (27 bp):
CTGTTAAAGAAATATGCACATGTATTG
Found at i:492239 original size:36 final size:36
Alignment explanation
Indices: 492192--492404 Score: 313
Period size: 36 Copynumber: 5.9 Consensus size: 36
492182 TGAATAAGAA
**
492192 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
* *
492228 GAACGAAAGGAAGCATCGTCACTTTCGATTC-AAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAG-T
492264 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
* * *
492300 GAACGGAAGGAAGCATCCGCACTTTCGATTC-AAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAG-T
492336 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
* *
492372 GAACGGAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
492405 TTGTTCATCT
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
35 6 0.04
36 148 0.93
37 6 0.04
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
Found at i:492304 original size:72 final size:72
Alignment explanation
Indices: 492187--492404 Score: 393
Period size: 72 Copynumber: 3.0 Consensus size: 72
492177 GAAGGTGAAT
** *
492187 AAGAAGAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGAAAGGAAGCAT-CGTCACT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCG-CACT
492251 TTCGATTC
65 TTCGATTC
492259 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
492324 TCGATTC
66 TCGATTC
492331 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
492396 TCGATTC
66 TCGATTC
492403 AA
1 AA
492405 TTGTTCATCT
Statistics
Matches: 142, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
72 140 0.99
73 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.18
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
TCGATTC
Found at i:492483 original size:26 final size:27
Alignment explanation
Indices: 492454--492505 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
492444 GAATGTTAGA
*
492454 CTGTTAAAG-AACATGCACGTGTATTG
1 CTGTTAAAGAAACATGCACATGTATTG
*
492480 CTGTTAAAGAAATATGCACATGTATT
1 CTGTTAAAGAAACATGCACATGTATT
492506 AAGCAGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (27 bp):
CTGTTAAAGAAACATGCACATGTATTG
Found at i:496383 original size:18 final size:19
Alignment explanation
Indices: 496355--496396 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
496345 AATATTATTT
496355 TAATAGATTTATAATTT-AA
1 TAATAGATTTAT-ATTTAAA
496374 TAAT-GATTTATATTTAAA
1 TAATAGATTTATATTTAAA
496392 TAATA
1 TAATA
496397 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
TAATAGATTTATATTTAAA
Found at i:496431 original size:29 final size:31
Alignment explanation
Indices: 496377--496434 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
496367 AATTTAATAA
496377 TGATTTATATTTAAATAATAATTAATTTTAG
1 TGATTTATATTTAAATAATAATTAATTTTAG
**
496408 TGATTTA-ATTTATTTAA-AATTAATTTT
1 TGATTTATATTTAAATAATAATTAATTTT
496435 TTTAAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 8 0.32
31 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (31 bp):
TGATTTATATTTAAATAATAATTAATTTTAG
Found at i:496899 original size:35 final size:35
Alignment explanation
Indices: 496860--496927 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
496850 TGTTATTTAC
496860 AATAAGTCATGTCACTTGGTGAATAGACTTATTAT
1 AATAAGTCATGTCACTTGGTGAATAGACTTATTAT
* * *
496895 AATAAGTTATGTCATTTGGTGAATGGACTTATT
1 AATAAGTCATGTCACTTGGTGAATAGACTTATT
496928 TTTTAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (35 bp):
AATAAGTCATGTCACTTGGTGAATAGACTTATTAT
Found at i:498174 original size:64 final size:66
Alignment explanation
Indices: 498010--498170 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 66
498000 AATAAATTAT
*
498010 TTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAA
1 TTTTCTTTAA-CATTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAA
498075 AA
65 AA
* * * * * ** ** *
498077 TTAT-TTGATCA-TAATTGAACCAAAATTTATTTGAAAATTATTAACTGAA-CAAATTAACTGAT
1 TTTTCTTTAACATTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAA
*
498139 T
66 A
498140 TTGTTCTTTAACATTAATCGAACCGAAATTT
1 TT-TTCTTTAACATTAATCGAACCGAAATTT
498171 TTGACCGTTA
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
63 12 0.16
64 35 0.47
65 6 0.08
66 18 0.24
67 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (66 bp):
TTTTCTTTAACATTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAA
A
Found at i:498266 original size:26 final size:28
Alignment explanation
Indices: 498222--498278 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
498212 CGATTTTTTT
498222 TTTTAACCATTAATCGAA-CCAAAATTA
1 TTTTAACCATTAATCGAACCCAAAATTA
* * *
498249 TTTT-ACCGTTAATTGAACCCAAATTTA
1 TTTTAACCATTAATCGAACCCAAAATTA
498276 TTT
1 TTT
498279 GAAAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (28 bp):
TTTTAACCATTAATCGAACCCAAAATTA
Found at i:498277 original size:79 final size:78
Alignment explanation
Indices: 498129--498294 Score: 235
Period size: 79 Copynumber: 2.1 Consensus size: 78
498119 AACTGAACAA
* * *
498129 ATTAACTGATTTTGTTCTTTAACATTAATCGAACCGAAATTTTTGACCGTTAATCAAACCGAAAT
1 ATTAACCGATTTTGTTCTTTAACATTAATCGAACCAAAATTTTTGACCGTTAATCAAACCCAAAT
498194 TTATTTG-AAATT
66 TTATTTGAAAATT
* * * **
498206 ATTAACCGATTTTTTTTTTTAACCATTAATCGAACCAAAATTATTTTACCGTTAATTGAACCCAA
1 ATTAACCGATTTTGTTCTTTAA-CATTAATCGAACCAAAATT-TTTGACCGTTAATCAAACCCAA
498271 ATTTATTTGAAAATT
64 ATTTATTTGAAAATT
498286 ATTAACCGA
1 ATTAACCGA
498295 ATTAACCGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
77 19 0.24
78 18 0.23
79 27 0.35
80 14 0.18
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (78 bp):
ATTAACCGATTTTGTTCTTTAACATTAATCGAACCAAAATTTTTGACCGTTAATCAAACCCAAAT
TTATTTGAAAATT
Found at i:498422 original size:163 final size:158
Alignment explanation
Indices: 498209--498612 Score: 539
Period size: 158 Copynumber: 2.5 Consensus size: 158
498199 TGAAATTATT
* *
498209 AACCGATTTTTTTTTTTAACCATTAATCGAACCAAAATTATTTTACCGTTAATTGAACCCAAATT
1 AACCGA-TTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATTGAA-CCAAATT
*
498274 TATTTGAAAATTATTAACCGAATTAACCGAATAAATAAATTATTTT-TTTAACCGTTAATCGAAC
64 TATTTGAAAATTATTAACCGAA-TAA---AATAAAT-AATT-TTTTCCTTAACCGTTAATCGAAC
498338 C-AAATTTATTTCAAAATTATTAACCGAAA-CAAATC
123 CGAAATTTATTTCAAAATTATTAA-CGAAATCAAATC
** * *
498373 AACCGATTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAATTT
1 AACCGATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATTGAA-CCAAATTT
*
498438 ATTTGAAAA-TATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCGAAATT
65 ATTTGAAAATTATTAACCGAATAAAATAAATAATTTTTTCCTTAACCGTTAATCGAACCGAAATT
* ** *
498502 TATTTGAAAATTATTAACGAAATTGAATT
130 TATTTCAAAATTATTAACGAAATCAAATC
* * *
498531 AACCGAATTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCT-AACCGAATGT
1 AACCGATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAAT-TGAACCAAATTT
498595 ATTTGAAAATTATTAACC
65 ATTTGAAAATTATTAACC
498613 AAACCAAATT
Statistics
Matches: 215, Mismatches: 20, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
156 4 0.02
157 40 0.19
158 90 0.42
161 3 0.01
162 11 0.05
163 61 0.28
164 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (158 bp):
AACCGATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATTGAACCAAATTTA
TTTGAAAATTATTAACCGAATAAAATAAATAATTTTTTCCTTAACCGTTAATCGAACCGAAATTT
ATTTCAAAATTATTAACGAAATCAAATC
Found at i:498500 original size:91 final size:93
Alignment explanation
Indices: 498315--498508 Score: 252
Period size: 92 Copynumber: 2.1 Consensus size: 93
498305 TAAATAAATT
* * *
498315 ATTTTTTTAACCGTTAATCGAACCAAATTTATTTCAAAATTATTAACCGAAACAAATCAACCGAT
1 ATTTATTTGACCGTTAATCGAACCAAATTTATTTCAAAATTATTAACCGAAACAAATCAAACGAT
* *
498380 TTTTTCTTTAACCATTAATCGAACTGAA
66 TTTTTCCTTAACCATTAATCGAACCGAA
* * **
498408 A-TTATTTGACCGTTAATCGAATCGAAATTTATTTGAAAA-TATTAACCGAATA-AAAT-AAATT
1 ATTTATTTGACCGTTAATCGAA-CCAAATTTATTTCAAAATTATTAACCGAA-ACAAATCAAACG
*
498469 ATTTTTTCCTTAACCGTTAATCGAACCGAA
64 ATTTTTTCCTTAACCATTAATCGAACCGAA
498499 ATTTATTTGA
1 ATTTATTTGA
498509 AAATTATTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
91 30 0.34
92 41 0.47
93 17 0.19
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (93 bp):
ATTTATTTGACCGTTAATCGAACCAAATTTATTTCAAAATTATTAACCGAAACAAATCAAACGAT
TTTTTCCTTAACCATTAATCGAACCGAA
Found at i:498558 original size:67 final size:65
Alignment explanation
Indices: 498420--498574 Score: 179
Period size: 67 Copynumber: 2.4 Consensus size: 65
498410 TATTTGACCG
* ** * *
498420 TTAATCGAATCGAAATTTATTTGAAAATATTAACCGAATAAAATAAATTATTTTTTCCTTAACCG
1 TTAATCGAACCGAAATTTATTTGAAAATATTAACCGAATAAAATAAACGAATTTTTCCTTAACCA
* * * *
498485 TTAATCGAACCGAAATTTATTTGAAAATTATTAA-CGAAATTGAATTAACCGAATTTTTCTTTAA
1 TTAATCGAACCGAAATTTATTTGAAAA-TATTAACCG-AA-TAAAATAAACGAATTTTTCCTTAA
498549 CCA
63 CCA
*
498552 TTAATCGAACC-AAAATTATTTGA
1 TTAATCGAACCGAAATTTATTTGA
498575 CCGTTAATCT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 28 0.36
66 19 0.25
67 30 0.39
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (65 bp):
TTAATCGAACCGAAATTTATTTGAAAATATTAACCGAATAAAATAAACGAATTTTTCCTTAACCA
Found at i:498610 original size:92 final size:92
Alignment explanation
Indices: 498481--498702 Score: 340
Period size: 92 Copynumber: 2.4 Consensus size: 92
498471 TTTTTCCTTA
* ***
498481 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACGAAATTGAATTAACCGAA-TTTTTCT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
*
498545 TTAACCATTAATCGAACCAAAATTATTTG
66 TTAA-CATTAATC-AAACAAAATTATTTG
* *
498574 ACCGTTAATCTAACCG-AATGTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
*
498638 TTAACATTAATCAAACGAAATTATTTG
66 TTAACATTAATCAAACAAAATTATTTG
498665 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAA
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAA
498703 TCGATTAATG
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
91 28 0.24
92 63 0.54
93 26 0.22
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (92 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
TTAACATTAATCAAACAAAATTATTTG
Found at i:498657 original size:158 final size:157
Alignment explanation
Indices: 498206--498665 Score: 518
Period size: 158 Copynumber: 2.9 Consensus size: 157
498196 ATTTGAAATT
* * *
498206 ATTAACCGATTTTTTTTTTTAACCATTAATCGAACCAAAATTATTTTACCGTTAAT-TGAACCCA
1 ATTAACCGA-TTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCT-AA-CCG
*
498270 AATTTATTTGAAAATTATTAACCGAATTAACCGAATAAATAAATTATTTT-TTTAACCGTTAATC
63 AATTTATTTGAAAATTATTAACC--A--AACCAAATAAA-AAATT-TTTTCTTTAACCGTTAATC
* * *
498334 GAACCAAATTTATTTCAAAATTATTAACCGAAACAA
122 AAACGAAATTTATTTGAAAATTATTAACCGAAACAA
* ** * *
498370 ATCAACCGATTTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACCGTTAATCGAATCGAAA
1 ATTAACCGATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCG-AA
* ** ** * *
498435 TTTATTTGAAAA-TATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCGAA
65 TTTATTTGAAAATTATTAACCAAACCAAATAAAAAATTTTTTCTTTAACCGTTAATC-AAACGAA
**
498499 ATTTATTTGAAAATTATTAA-CGAAATTGA
129 ATTTATTTGAAAATTATTAACCGAAA-CAA
*
498528 ATTAACCGAATTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCGAAT
1 ATTAACCGATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCGAAT
* ** *
498593 GTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCTTTAA-CATTAATCAAACGAA
66 TTATTTGAAAATTATTAACCAAACCAAA-TAA-AAAATTTTTTCTTTAACCGTTAATCAAACGAA
498657 A-TTATTTGA
129 ATTTATTTGA
498666 CCGTTAATCG
Statistics
Matches: 251, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
156 4 0.02
157 42 0.17
158 108 0.43
159 10 0.04
160 12 0.05
162 9 0.04
163 58 0.23
164 8 0.03
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (157 bp):
ATTAACCGATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCGAAT
TTATTTGAAAATTATTAACCAAACCAAATAAAAAATTTTTTCTTTAACCGTTAATCAAACGAAAT
TTATTTGAAAATTATTAACCGAAACAA
Found at i:502894 original size:21 final size:21
Alignment explanation
Indices: 502858--502915 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
502848 TGAGGTATCT
* *
502858 AATATTTAAAAATATTAAAA-
1 AATATTTAATATTATTAAAAG
502878 ATATATTTAATATTATTTAAAAG
1 A-ATATTTAATATTA-TTAAAAG
*
502901 AAT-TTTATTATTATT
1 AATATTTAATATTATT
502916 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.09
21 20 0.62
22 8 0.25
23 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATATTTAATATTATTAAAAG
Found at i:502934 original size:12 final size:12
Alignment explanation
Indices: 502919--502944 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
502909 TATTATTTTT
502919 TAAAATAATTGA
1 TAAAATAATTGA
502931 TAAAATAATTGA
1 TAAAATAATTGA
502943 TA
1 TA
502945 CGTAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
TAAAATAATTGA
Found at i:504618 original size:18 final size:18
Alignment explanation
Indices: 504595--504630 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
504585 ATTTGGCATT
* *
504595 GACATTTTCATTTGCCAC
1 GACATTTCCATCTGCCAC
504613 GACATTTCCATCTGCCAC
1 GACATTTCCATCTGCCAC
504631 ATTGAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (18 bp):
GACATTTCCATCTGCCAC
Found at i:514539 original size:20 final size:20
Alignment explanation
Indices: 514514--514565 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
514504 ATATTCAAGC
514514 GATGATTGCAGTAAAAAAAG
1 GATGATTGCAGTAAAAAAAG
*
514534 GATGATTGCAGTAAAAAATG
1 GATGATTGCAGTAAAAAAAG
*
514554 AATGATTGCAGT
1 GATGATTGCAGT
514566 GGTGTGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (20 bp):
GATGATTGCAGTAAAAAAAG
Found at i:522737 original size:30 final size:30
Alignment explanation
Indices: 522701--522776 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
522691 TCTTTCAACA
* * *
522701 TAAAAATTGAATCAATTAAGTATTCAAATT
1 TAAAAATTGAATCAATTAAATATGCAAATC
* *
522731 TAAAAATTAAATCAATTAAATATGCGAATC
1 TAAAAATTGAATCAATTAAATATGCAAATC
522761 TAAAAATTGAATCAAT
1 TAAAAATTGAATCAAT
522777 CAAGCTCTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAAAATTGAATCAATTAAATATGCAAATC
Found at i:523514 original size:29 final size:29
Alignment explanation
Indices: 523433--523514 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 29
523423 TGGTTCTTTT
*
523433 AACAGTAGACACCTAAAAATGTAACGGAAAA
1 AACATTAGACACC-AAAAAT-TAACGGAAAA
* * ***
523464 AACTTTAGACACCTACTTTTAAC-GAAAA
1 AACATTAGACACCAAAAATTAACGGAAAA
*
523492 ATTCATTAGACACCAAAAATTAA
1 A-ACATTAGACACCAAAAATTAA
523515 TTTTAAGTGT
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
28 6 0.16
29 19 0.50
30 2 0.05
31 11 0.29
ACGTcount: A:0.50, C:0.18, G:0.10, T:0.22
Consensus pattern (29 bp):
AACATTAGACACCAAAAATTAACGGAAAA
Found at i:527003 original size:31 final size:31
Alignment explanation
Indices: 526952--527012 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
526942 GGAATGGTCC
*
526952 CTAATATTATCAATCCATTCAATTTTAGTCT
1 CTAACATTATCAATCCATTCAATTTTAGTCT
* *
526983 CTAACATTATCGATCTATTCAATTTTAGTC
1 CTAACATTATCAATCCATTCAATTTTAGTC
527013 CCTCGGCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (31 bp):
CTAACATTATCAATCCATTCAATTTTAGTCT
Found at i:536426 original size:27 final size:27
Alignment explanation
Indices: 536371--536435 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
536361 TAAAATAAGA
*
536371 AAAAAACTAAAATTTAAATATAATTAT
1 AAAAAACTAAAATTTAAATATAATAAT
536398 AAAAAA-TAAATATTTAAATAT--TAA-
1 AAAAAACTAAA-ATTTAAATATAATAAT
*
536422 AATAAACTAAAATT
1 AAAAAACTAAAATT
536436 AATAGTTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 8 0.24
25 6 0.18
26 4 0.12
27 16 0.47
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (27 bp):
AAAAAACTAAAATTTAAATATAATAAT
Found at i:542406 original size:21 final size:21
Alignment explanation
Indices: 542380--542449 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
542370 AACTATTGTT
542380 GTTGTTTATGGGTGGTTTAGG
1 GTTGTTTATGGGTGGTTTAGG
* * * ** *
542401 GTTGTTTCTTGTTTATTT-GTT
1 GTTGTTTATGGGTGGTTTAG-G
542422 GTTGTTTATGGGTGGTTTAGG
1 GTTGTTTATGGGTGGTTTAGG
542443 GTTGTTT
1 GTTGTTT
542450 CTTGTTTATT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.07, C:0.01, G:0.34, T:0.57
Consensus pattern (21 bp):
GTTGTTTATGGGTGGTTTAGG
Found at i:542434 original size:42 final size:42
Alignment explanation
Indices: 542375--542469 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
542365 GGTTGAACTA
542375 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
542417 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
*
542459 TTGTTTTTGTT
1 TTGTTGTTGTT
542470 CAGGGTGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.06, C:0.02, G:0.29, T:0.62
Consensus pattern (42 bp):
TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
Found at i:542488 original size:42 final size:42
Alignment explanation
Indices: 542375--542494 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
542365 GGTTGAACTA
* *
542375 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTCATGGGTGGTTTAAGGTTGTTTCTTGTTTAT
* *
542417 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTCATGGGTGGTTTAAGGTTGTTTCTTGTTTAT
* *
542459 TTGTTTTTGTTCA-GGGT-GTTTACCAGGTTGTATCTT
1 TTGTTGTTGTTCATGGGTGGTTTA--AGGTTGTTTCTT
542495 ATGTAATTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
40 5 0.07
41 4 0.06
42 63 0.88
ACGTcount: A:0.08, C:0.05, G:0.29, T:0.57
Consensus pattern (42 bp):
TTGTTGTTGTTCATGGGTGGTTTAAGGTTGTTTCTTGTTTAT
Found at i:546978 original size:70 final size:70
Alignment explanation
Indices: 546865--547007 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 70
546855 ATATAGCGGC
* *
546865 GTTTGTTGAACAAATGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAATACGCCGCAA
1 GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAAAACGCCGCAA
546930 TAGGT
66 TAGGT
* *
546935 GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTGTCAGAAAAATGCCGCAA
1 GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAAAACGCCGCAA
547000 TAGGT
66 TAGGT
547005 GTT
1 GTT
547008 GATGTTTAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (70 bp):
GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAAAACGCCGCAA
TAGGT
Found at i:546983 original size:43 final size:43
Alignment explanation
Indices: 546946--547110 Score: 116
Period size: 43 Copynumber: 3.8 Consensus size: 43
546936 TTTGTTGAAC
* * *
546946 AAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTGTCAGAA
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
* * * ** *
546989 AAATGCCGCAATAGGTGTTGATGTTTAGTGGCGTTT-TACTTAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-CAGAA
* * * * * ** *
547032 GAACGCCGCAGTAGGTGTTGATATTTTGCGGTGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
* * * * *
547075 AAACGCCGCAGTATGTGATGATTTTTAGCGACGTTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
547111 CTAGTATACA
Statistics
Matches: 95, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 1 0.01
43 93 0.98
44 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
Found at i:547156 original size:44 final size:44
Alignment explanation
Indices: 547102--547262 Score: 222
Period size: 44 Copynumber: 3.7 Consensus size: 44
547092 ATGATTTTTA
547102 GCGACGTTTCTAGTATACAAACGCCGCTAAATGT-TCGGTATATT
1 GCGACGTTTCTAGTATACAAACGCCGCTAAATGTAT-GGTATATT
*
547146 GCGACGTTTCTAGTATACAAACGCCGCTAAATATATGGTATATT
1 GCGACGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
* * *
547190 GTGACGTTTCTAGTATACAAACGCTGTTAAATGTATGGTATATT
1 GCGACGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
* * *
547234 GCGGCATTT-T--TTTACAAACGCCGCTAAAT
1 GCGACGTTTCTAGTATACAAACGCCGCTAAAT
547263 AACACATAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
41 16 0.15
43 1 0.01
44 87 0.83
45 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (44 bp):
GCGACGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
Found at i:547622 original size:21 final size:21
Alignment explanation
Indices: 547578--547648 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
547568 TTGTTGATAT
* *
547578 GCTGCTTCTCTCTGTACTGT-C
1 GCTGCTTCTCTCTATGCT-TCC
* *
547599 GCTGCTTCTTTCTCTGCTTCC
1 GCTGCTTCTCTCTATGCTTCC
* *
547620 GCTACTGCTCTCTATGCTTCC
1 GCTGCTTCTCTCTATGCTTCC
547641 -CTTGCTTC
1 GC-TGCTTC
547649 ATTTTCCGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.95
ACGTcount: A:0.04, C:0.37, G:0.15, T:0.44
Consensus pattern (21 bp):
GCTGCTTCTCTCTATGCTTCC
Found at i:558322 original size:28 final size:29
Alignment explanation
Indices: 558278--558341 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
558268 CTAAAATAAA
*
558278 ACAAAAACTAAAGCTTTTAAC-ACATGGT
1 ACAAAAACTAAAACTTTTAACGACATGGT
*
558306 ACAAAAACTAAAACTTTTAACGATATGGT
1 ACAAAAACTAAAACTTTTAACGACATGGT
*
558335 ACTAAAA
1 ACAAAAA
558342 TGAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (29 bp):
ACAAAAACTAAAACTTTTAACGACATGGT
Found at i:563426 original size:29 final size:27
Alignment explanation
Indices: 563368--563443 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 27
563358 AATTTCATTA
* *
563368 CTTTAATTTTCTATTTTATATTTTTTC
1 CTTTAATTTTCTACTTTATATTTTGTC
563395 CTTTAATTTTCATAACTTTA-ATTTTAGTC
1 CTTTAATTTTC-T-ACTTTATATTTT-GTC
*
563424 CTTTAATTATCGTACTTTAT
1 CTTTAATTTTC-TACTTTAT
563444 TTCATGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 11 0.27
28 12 0.29
29 18 0.44
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (27 bp):
CTTTAATTTTCTACTTTATATTTTGTC
Found at i:566512 original size:32 final size:31
Alignment explanation
Indices: 566468--566527 Score: 111
Period size: 32 Copynumber: 1.9 Consensus size: 31
566458 ATTATTATTA
566468 TTGATAAATTTAATGATTATTTTATAATTGT
1 TTGATAAATTTAATGATTATTTTATAATTGT
566499 TTGATAAAATTTAATGATTATTTTATAAT
1 TTGAT-AAATTTAATGATTATTTTATAAT
566528 AAATAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.53
Consensus pattern (31 bp):
TTGATAAATTTAATGATTATTTTATAATTGT
Found at i:566537 original size:32 final size:32
Alignment explanation
Indices: 566473--566543 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
566463 TATTATTGAT
*** *
566473 AAATTTAATGATTATTTTATAATTGTTTGATA
1 AAATTTAATGATTATTTTATAATAAATAGATA
566505 AAATTTAATGATTATTTTATAATAAATAGATA
1 AAATTTAATGATTATTTTATAATAAATAGATA
566537 AAATTTA
1 AAATTTA
566544 GGGTAAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (32 bp):
AAATTTAATGATTATTTTATAATAAATAGATA
Found at i:568257 original size:31 final size:31
Alignment explanation
Indices: 568221--568295 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
568211 AATATCGCAC
* *
568221 TATTAATATAATATAACATATCATATTAAAA
1 TATTAATATAATATAACACATCATATAAAAA
*
568252 TATTAATATAATATATCACATCATATAAAAA
1 TATTAATATAATATAACACATCATATAAAAA
* *
568283 TAATAATAAAATA
1 TATTAATATAATA
568296 ATTTGTCATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (31 bp):
TATTAATATAATATAACACATCATATAAAAA
Found at i:569525 original size:23 final size:23
Alignment explanation
Indices: 569494--569538 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
569484 CACCACAGCT
* *
569494 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
569517 CGTAGAATTGCACCGGAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
569539 GTAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:569792 original size:23 final size:27
Alignment explanation
Indices: 569764--569822 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
569754 CTTTCACAAT
569764 TCACATAAT-T-T-GTAT-AATTCATG
1 TCACATAATATATAGTATGAATTCATG
569787 TCACATAATGCATATAGTATGAATTCATG
1 TCACATAAT--ATATAGTATGAATTCATG
569816 TCACATA
1 TCACATA
569823 TCATAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.30
26 1 0.03
27 1 0.03
28 4 0.13
29 15 0.50
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (27 bp):
TCACATAATATATAGTATGAATTCATG
Found at i:575565 original size:23 final size:23
Alignment explanation
Indices: 575539--575583 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
575529 CACCACAGCT
*
575539 CATATAATTGCACCGAAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
*
575562 CATAGAATTGCACCGGAGTGCC
1 CATAGAATTGCACCGAAGTGCC
575584 GTAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:579052 original size:19 final size:19
Alignment explanation
Indices: 579028--579073 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
579018 AAATAGGTAC
579028 CGATACCACTCAAGAGTAT
1 CGATACCACTCAAGAGTAT
579047 CGATACCACTCAAGAGTAT
1 CGATACCACTCAAGAGTAT
579066 CGATACCA
1 CGATACCA
579074 TAGTGCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (19 bp):
CGATACCACTCAAGAGTAT
Found at i:580565 original size:17 final size:17
Alignment explanation
Indices: 580532--580566 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
580522 TGTTGAAGGA
* *
580532 AGAAGAAAAAGATGAAG
1 AGAAGAAAAACAAGAAG
580549 AGAAGAAAAACAAGAAG
1 AGAAGAAAAACAAGAAG
580566 A
1 A
580567 AAAAGGAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (17 bp):
AGAAGAAAAACAAGAAG
Found at i:584127 original size:17 final size:17
Alignment explanation
Indices: 584094--584128 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
584084 TGTTAAAAGA
*
584094 AGAAGAAAAAGATGAAG
1 AGAAGAAAAAGAAGAAG
*
584111 AGAAGAAAAATAAGAAG
1 AGAAGAAAAAGAAGAAG
584128 A
1 A
584129 AAAAGGAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.06
Consensus pattern (17 bp):
AGAAGAAAAAGAAGAAG
Found at i:585289 original size:18 final size:18
Alignment explanation
Indices: 585266--585304 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
585256 TGCAAATGAC
585266 ATCTCTCTAACAATTGAT
1 ATCTCTCTAACAATTGAT
*
585284 ATCTCTCTAATAATTGAT
1 ATCTCTCTAACAATTGAT
585302 ATC
1 ATC
585305 AACTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (18 bp):
ATCTCTCTAACAATTGAT
Found at i:585816 original size:52 final size:53
Alignment explanation
Indices: 585738--585845 Score: 200
Period size: 52 Copynumber: 2.1 Consensus size: 53
585728 AGAAGTATGG
585738 TTTGAAAAATTCAATTTCTTAATGAAAAAGG-GGAGCTGAACATTTTCATATA
1 TTTGAAAAATTCAATTTCTTAATGAAAAAGGTGGAGCTGAACATTTTCATATA
*
585790 TTTGAAAAATTCAATTTCTTAATGAAAAAGGTGGAGCTGAACATTTTCGTATA
1 TTTGAAAAATTCAATTTCTTAATGAAAAAGGTGGAGCTGAACATTTTCATATA
585843 TTT
1 TTT
585846 TCCAACAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 31 0.57
53 23 0.43
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (53 bp):
TTTGAAAAATTCAATTTCTTAATGAAAAAGGTGGAGCTGAACATTTTCATATA
Found at i:586205 original size:21 final size:21
Alignment explanation
Indices: 586175--586269 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
586165 AATTACAAGT
* *
586175 AGTATCGATATTGTTATTTGC
1 AGTATCGATACTGTTCTTTGC
*
586196 AGTATTGATACTGTTCTTTGC
1 AGTATCGATACTGTTCTTTGC
586217 AGTATCGATACTGTTCTTTGC
1 AGTATCGATACTGTTCTTTGC
*
586238 AGTATCGATATTGTTCTTTGC
1 AGTATCGATACTGTTCTTTGC
*
586259 AGTATCAATAC
1 AGTATCGATAC
586270 CACATGAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (21 bp):
AGTATCGATACTGTTCTTTGC
Found at i:587179 original size:2 final size:2
Alignment explanation
Indices: 587172--587200 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
587162 CATGTAGAAG
587172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
587201 TAATTAGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:587361 original size:4 final size:4
Alignment explanation
Indices: 587352--587376 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
587342 TGAAATAAGA
587352 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
587377 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:591582 original size:20 final size:21
Alignment explanation
Indices: 591546--591584 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
591536 AAACAAGTTG
591546 AATTATCTTCTATATATTTTA
1 AATTATCTTCTATATATTTTA
591567 AATTAT-TTCT-TAATATTT
1 AATTATCTTCTAT-ATATTT
591585 ACTTGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 10 0.59
21 6 0.35
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTATCTTCTATATATTTTA
Found at i:593766 original size:147 final size:149
Alignment explanation
Indices: 593417--593865 Score: 877
Period size: 147 Copynumber: 3.0 Consensus size: 149
593407 AAGTGCCACA
593417 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATT-CTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
593481 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
593546 TATATCCCGAAGGACCGCG
131 TATATCCCGAAGGACCGCG
593565 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
593630 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATATA
66 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
593693 TATATCCCGAAGGACCGCG
131 TATATCCCGAAGGACCGCG
593712 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
593777 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
593842 TATATCCCGAAGGACCGCG
131 TATATCCCGAAGGACCGCG
593861 TAGAA
1 TAGAA
593866 CCCTCGACTC
Statistics
Matches: 298, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
147 146 0.49
148 55 0.18
149 97 0.33
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
TATATCCCGAAGGACCGCG
Found at i:601380 original size:85 final size:87
Alignment explanation
Indices: 601265--601425 Score: 272
Period size: 85 Copynumber: 1.9 Consensus size: 87
601255 AAATATGTCA
*
601265 ATATAAGCGCTACCTATTTCATTATATAAGCGCTACTTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTTCATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
601330 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
* *
601352 ATATAAGCGCTATCTA-TT-ATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTTCATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
601415 CCGGTTAAATA
66 CCCGTTAAATA
601426 ATATAACATA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
85 53 0.76
86 2 0.03
87 15 0.21
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTTCATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:601397 original size:23 final size:21
Alignment explanation
Indices: 601347--601388 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
601337 AATACCTATT
*
601347 TTATTATATAAGCGCTATCTA
1 TTATTATATAAGCGCTACCTA
*
601368 TTATTATATAAGCGTTACCTA
1 TTATTATATAAGCGCTACCTA
601389 ATATGTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
TTATTATATAAGCGCTACCTA
Found at i:603954 original size:20 final size:21
Alignment explanation
Indices: 603929--603980 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
603919 TTTTCCCAAT
*
603929 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
603949 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
603970 TCGCAATGCGA
1 TCGCAATGCGA
603981 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:603994 original size:20 final size:20
Alignment explanation
Indices: 603969--604083 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
603959 AATTGGGAAA
*
603969 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
603989 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
604009 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
604030 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
604050 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
604070 TTCGCAACGCGATA
1 ATCGCAACGCGATA
604084 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:604013 original size:61 final size:61
Alignment explanation
Indices: 603966--604094 Score: 177
Period size: 61 Copynumber: 2.1 Consensus size: 61
603956 GCGAATTGGG
* * * * *
603966 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
604027 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
604088 ATAATCG
1 AAAATCG
604095 TAATGCGATT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:604299 original size:22 final size:22
Alignment explanation
Indices: 604271--604314 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
604261 CACTCTCTCA
604271 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
604293 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
604315 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:604568 original size:20 final size:20
Alignment explanation
Indices: 604539--604582 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
604529 GCGATTTTAG
604539 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
604559 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
604579 TTTC
1 TTTC
604583 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:605931 original size:18 final size:18
Alignment explanation
Indices: 605906--605947 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
605896 ACTTCGGGAT
*
605906 CCATCACCTCGCCCAGAG
1 CCATCACCTCACCCAGAG
*
605924 CTATCACCTCACCCAGAG
1 CCATCACCTCACCCAGAG
605942 CCATCA
1 CCATCA
605948 TCTGATCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.48, G:0.12, T:0.14
Consensus pattern (18 bp):
CCATCACCTCACCCAGAG
Found at i:606483 original size:19 final size:20
Alignment explanation
Indices: 606429--606495 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
606419 TAGTTTACTT
* *
606429 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
606449 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
606469 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
606488 TCGCAACG
1 TCGCAACG
606496 AAAATCGCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:606500 original size:12 final size:12
Alignment explanation
Indices: 606483--606507 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
606473 AATGCGAAAT
606483 GAAAATCGCAAC
1 GAAAATCGCAAC
606495 GAAAATCGCAAC
1 GAAAATCGCAAC
606507 G
1 G
606508 CGAAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (12 bp):
GAAAATCGCAAC
Found at i:606519 original size:19 final size:19
Alignment explanation
Indices: 606429--606520 Score: 54
Period size: 20 Copynumber: 5.1 Consensus size: 19
606419 TAGTTTACTT
* **
606429 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
606449 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
606469 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
606488 TCGCAA--C-----GAAAA
1 TCGCAACGCGAAATGAAAA
606500 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
606519 TC
1 TC
606521 ACAATGCGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
12 11 0.19
14 1 0.02
17 1 0.02
19 20 0.34
20 24 0.41
21 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:606560 original size:14 final size:14
Alignment explanation
Indices: 606541--606630 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
606531 TTGTGTTTCG
606541 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
606555 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
606571 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
606587 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
606604 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
606620 CGTTGCGATTT
1 CGTTGCGATTT
606631 GTATTTCGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 26 0.41
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:606605 original size:33 final size:33
Alignment explanation
Indices: 606536--606644 Score: 186
Period size: 33 Copynumber: 3.3 Consensus size: 33
606526 GCGATTTGTG
*
606536 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
606568 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
606601 TTTCGCATTGCGATTTTGTCGTTGCGATTTGT-A
1 TTTCGCATTGCGATTTTGTCGTTGCGATTT-TCA
606634 TTTCGCATTGC
1 TTTCGCATTGC
606645 AATAGCCATT
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
32 26 0.35
33 47 0.64
34 1 0.01
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:606613 original size:19 final size:18
Alignment explanation
Indices: 606557--606644 Score: 75
Period size: 14 Copynumber: 5.2 Consensus size: 18
606547 GATTTTGTCG
606557 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
606575 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
606589 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
*
606608 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
*
606622 TTGCGATTTGTATTTCGCA
1 TTGCGATTT-CATTTCGCA
606641 TTGC
1 TTGC
606645 AATAGCCATT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
14 15 0.27
15 3 0.05
16 8 0.14
17 8 0.14
18 12 0.21
19 10 0.18
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:606655 original size:19 final size:20
Alignment explanation
Indices: 606633--606675 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
606623 TGCGATTTGT
606633 ATTT-CGCATTGCAATAGCC
1 ATTTCCGCATTGCAATAGCC
* * *
606652 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCAATAGCC
606672 ATTT
1 ATTT
606676 TCGCGTTGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCAATAGCC
Found at i:606669 original size:20 final size:20
Alignment explanation
Indices: 606641--606687 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
606631 GTATTTCGCA
*
606641 TTGCAATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
606661 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
606681 TTGCGAT
1 TTGCGAT
606688 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:607148 original size:40 final size:40
Alignment explanation
Indices: 607053--607139 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
607043 GACTCACCTG
*
607053 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAAAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ATCGTTCAAAAGGCCACTA
* * *
607095 TCTTCCCTCAAGAGTCCCCCCATCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCATCGTTCAAAAGGCCACTA
607135 TCATC
1 TCATC
607140 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 20 0.50
41 2 0.05
42 18 0.45
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCATCGTTCAAAAGGCCACTA
Found at i:608588 original size:14 final size:14
Alignment explanation
Indices: 608554--608592 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
608544 TTGATTGTTT
608554 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
608568 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
608582 TGTTGATTTGT
1 AATTGATTTGT
608593 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:608753 original size:19 final size:17
Alignment explanation
Indices: 608728--608777 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 17
608718 TATCGTAACG
608728 AGAAAATCGCAATGCGAA
1 AGAAAATCGCAATGCG-A
608746 ATGAAAATCGCAA--CG-
1 A-GAAAATCGCAATGCGA
608761 AGAAAATCGCAATGCGA
1 AGAAAATCGCAATGCGA
608778 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (17 bp):
AGAAAATCGCAATGCGA
Found at i:608765 original size:14 final size:14
Alignment explanation
Indices: 608719--608772 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
608709 GAAACTGACT
*
608719 ATCGTAACGAGAAA
1 ATCGCAACGAGAAA
608733 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
608752 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
608766 ATCGCAA
1 ATCGCAA
608773 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:608821 original size:20 final size:20
Alignment explanation
Indices: 608804--608891 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
608794 TGATTTTCTA
608804 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** **
608824 GTTGCGATTTTTCA-TTTCAA
1 GTTGCGA-TAGCCATTTTCGC
* *
608844 ATTGCGGTAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
608864 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
608884 GTTGCGAT
1 GTTGCGAT
608892 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 3 0.06
20 46 0.88
21 3 0.06
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:609428 original size:12 final size:12
Alignment explanation
Indices: 609409--609442 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
609399 CTCTCCGGCG
609409 ACATCCGTTCCT
1 ACATCCGTTCCT
*
609421 ATATCCGTTCCT
1 ACATCCGTTCCT
609433 ACATCC-TTCC
1 ACATCCGTTCC
609443 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:610024 original size:24 final size:24
Alignment explanation
Indices: 609997--610050 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
609987 GTATTCAAAA
*
609997 TTTGATCTTAGTCAATACCCGGAC
1 TTTGATATTAGTCAATACCCGGAC
* * *
610021 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTAGTCAATACCCGGAC
610045 TTTGAT
1 TTTGAT
610051 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTAGTCAATACCCGGAC
Found at i:610261 original size:12 final size:12
Alignment explanation
Indices: 610225--610261 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
610215 ATATAATCCT
610225 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
610237 AAAGAAGAAAAA
1 GAAGAAGAAAAA
610249 GAAGAAGAAAAA
1 GAAGAAGAAAAA
610261 G
1 G
610262 TCCCCGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:612232 original size:19 final size:19
Alignment explanation
Indices: 612208--612255 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
612198 GACTGCGAAC
612208 ATGTGTGTATTTTGTATGT
1 ATGTGTGTATTTTGTATGT
612227 ATGTGTGTATTTTGTATGT
1 ATGTGTGTATTTTGTATGT
612246 ATGTGTGTAT
1 ATGTGTGTAT
612256 ATATAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (19 bp):
ATGTGTGTATTTTGTATGT
Found at i:614305 original size:10 final size:9
Alignment explanation
Indices: 614279--614407 Score: 50
Period size: 9 Copynumber: 13.6 Consensus size: 9
614269 CCCTTTTGAA
614279 ATTATTTTT
1 ATTATTTTT
614288 ATTATTTTT
1 ATTATTTTT
*
614297 ATTCCTTTTGT
1 ATT-ATTTT-T
*
614308 ATAACTATTATT
1 AT---TATTTTT
614320 ATT-TTTTT
1 ATTATTTTT
*
614328 ATTATGTTT
1 ATTATTTTT
*
614337 CTTATTTTAT
1 ATTATTTT-T
* *
614347 ATATATATTC
1 AT-TATTTTT
614357 ATT-TTGGTTT
1 ATTATT--TTT
*
614367 -TCTATTTAT
1 AT-TATTTTT
614376 -TTATATTTT
1 ATTAT-TTTT
*
614385 ATTATTATT
1 ATTATTTTT
*
614394 ATTATTATT
1 ATTATTTTT
614403 ATTAT
1 ATTAT
614408 ATTGTATATA
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
8 11 0.12
9 48 0.53
10 15 0.16
11 10 0.11
12 3 0.03
13 3 0.03
14 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (9 bp):
ATTATTTTT
Found at i:614391 original size:3 final size:3
Alignment explanation
Indices: 614379--614407 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
614369 TATTTATTTA
614379 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
614408 ATTGTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:618617 original size:94 final size:95
Alignment explanation
Indices: 618454--618634 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 95
618444 ATATTATTTA
* * * * *
618454 TATACAATAAAGGTTAAGTTGTACCTCTAAAGCAATTGGTTAAATGCTCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTAAGTTGTACCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
* *
618519 ATTCAGCTAGCC-GATAAAGGTGATTATAC
66 ATTCAACTAACCTGATAAAGGTGATTATAC
*
618548 TATACAATAAAGCTTAAGTTGTCCCTCT-AAGACAATTGGTTAAACGCCCCGACTTTATGGATAA
1 TATACAATAAAGCTTAAGTTGTACCTCTAAAG-CAATTGGTTAAACGCCCCGACTTTATGGATAA
618612 GATTCAACTAACCTGATAAAGGT
65 GATTCAACTAACCTGATAAAGGT
618635 ATTTACATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 3 0.04
94 65 0.84
95 9 0.12
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTAAGTTGTACCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATTCAACTAACCTGATAAAGGTGATTATAC
Found at i:620002 original size:36 final size:36
Alignment explanation
Indices: 619950--620066 Score: 198
Period size: 36 Copynumber: 3.2 Consensus size: 36
619940 TAATTTACTC
619950 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
619987 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
620023 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
620059 GAAACAAA
1 AAAACAAA
620067 ATCTTTGAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 68 0.89
37 8 0.11
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Done.