Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008429.1 Hibiscus syriacus cultivar Beakdansim tig00111215_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: 508731
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:416074 original size:112 final size:111
Alignment explanation
Indices: 415958--416379 Score: 366
Period size: 114 Copynumber: 3.8 Consensus size: 111
415948 GTTTTCGAAA
* * *
415958 ATATATATGTTATATAGTTTTGAATACATTTTGAAAATATATATAGTATATAGTTTTTGAAAACA
1 ATATATAT-ATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * * *
416023 TTTTTCAAAA-ATATATAATATATACTCTCCT-CAACA-TTTTAATAT
65 TTTTTGAAAACATATATAATATATACT-TCCTAAAACATTTTTAAAAC
* *
416068 ATATATATAATATATAGCTTTTGAAAACATTTTTGAAAACATATATATTATATAG-TTTTGAAAA
1 ATATATAT-ATATATAG-TTTTGAAAACA-TTTTGAAAATATATATAATATATAGTTTTTGAAAA
* * * **
416132 CATTTTTGAAAACAAATATATTATATAGTTTTTAAAACATTTTTTAAAAC
63 CATTTTTGAAAACATATATAATATATACTTCCTAAAACA-TTTTTAAAAC
* * *
416182 ATATATATAATATATAGTTTTTAAAATATTTTGAATATATATATATAATATATAGTTTTTTAAAA
1 ATATATAT-ATATATAGTTTTGAAAACATTTTGAA-A-ATATATATAATATATAGTTTTTGAAAA
* * * ** *
416247 TA-TTTTGAAAACTTATATAATATATAGTTATTTAAAAAAACA-TTTTGAAA-
63 CATTTTTGAAAACATATATAATATATACTT-CCT---AAAACATTTTTAAAAC
*** * *
416297 ATATATAT-TATATA-TTAAAAAAACATTTTGAAAA-CTATATAATATATA-ATTTTGAAAAC-T
1 ATATATATATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACAT
*
416357 TTTT-AAAATTATATATAATATAT
66 TTTTGAAAA-CATATATAATATAT
416380 CGTTTTAAAT
Statistics
Matches: 263, Mismatches: 34, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
107 4 0.02
108 24 0.09
109 13 0.05
110 16 0.06
111 33 0.13
112 61 0.23
113 16 0.06
114 63 0.24
115 20 0.08
116 7 0.03
118 6 0.02
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (111 bp):
ATATATATATATATAGTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACAT
TTTTGAAAACATATATAATATATACTTCCTAAAACATTTTTAAAAC
Found at i:416103 original size:12 final size:12
Alignment explanation
Indices: 416086--416145 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
416076 AATATATAGC
416086 TTTTGAAAACAT
1 TTTTGAAAACAT
416098 TTTTGAAAACAT
1 TTTTGAAAACAT
* * *
416110 ATATATT--ATATAG
1 -T-T-TTGAAAACAT
416123 TTTTGAAAACAT
1 TTTTGAAAACAT
416135 TTTTGAAAACA
1 TTTTGAAAACA
416146 AATATATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
10 2 0.05
11 1 0.03
12 27 0.73
13 4 0.11
14 1 0.03
15 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:416151 original size:75 final size:74
Alignment explanation
Indices: 415912--416385 Score: 425
Period size: 75 Copynumber: 6.4 Consensus size: 74
415902 TAAAAATGTT
* ** * * **
415912 TTTTGAAAA-A-ATATAATATATAATTTTTAGAAAATGGTTTTCGAAAATATATATGTTATATAG
1 TTTTGAAAATATATATAATATATAGTTTTT-GAAAA-CATTTTTGAAAACATATATAATATATAG
*
415975 TTTTGAATACA
64 TTTTGAAAACA
* * * *
415986 TTTTGAAAATATATATAGTATATAGTTTTTGAAAACATTTTTCAAAA-ATATATAATATATACTC
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATAATATATAGTT
****
416050 TCCTCAACA
66 TTGAAAACA
* *
416059 TTTT-AATATATATATATAATATATAGCTTTTGAAAACATTTTTGAAAACATATATATTATATAG
1 TTTTGAA-A-ATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATAATATATAG
416123 TTTTGAAAACA
64 TTTTGAAAACA
* * * *
416134 TTTTTGAAAACAAATATATTATATAGTTTTT-AAAACATTTTTTAAAACATATATATAATATATA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAAC--ATATATAATATATA
* *
416198 GTTTTTAAAATA
63 GTTTTGAAAACA
* * *
416210 TTTTGAATATATATATATAATATATAGTTTTTTAAAATA-TTTTGAAAACTTATATAATATATAG
1 TTTTGAA-A-ATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATAATATATAG
*
416274 TTATTTAAAAAAACA
64 -T-TTT--GAAAACA
*** *
416289 TTTTGAAAATATATAT--TATATA--TTAAAAAAACA-TTTTGAAAAC-TATATAATATATAATT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATAATATATAGTT
416348 TTGAAAAC-
66 TTGAAAACA
* *
416356 TTTTTAAAATTATATATAATATATCGTTTT
1 TTTTGAAAA-TATATATAATATATAGTTTT
416386 AAATCTTTTT
Statistics
Matches: 329, Mismatches: 50, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
67 8 0.02
68 12 0.04
70 8 0.02
71 1 0.00
72 17 0.05
73 39 0.12
74 69 0.21
75 70 0.21
76 46 0.14
77 41 0.12
78 6 0.02
79 12 0.04
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (74 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACATATATAATATATAGTT
TTGAAAACA
Found at i:416336 original size:34 final size:33
Alignment explanation
Indices: 416265--416379 Score: 119
Period size: 34 Copynumber: 3.5 Consensus size: 33
416255 AAACTTATAT
*
416265 AATATATAGT-TAT-TTAAAAAAACATTTTGAA
1 AATATATATTATATATTAAAAAAACATTTTGAA
416296 AATATATATTATATATTAAAAAAACATTTTGAA
1 AATATATATTATATATTAAAAAAACATTTTGAA
* *** *
416329 AACTATATAATATATAATTTTGAAAAC-TTTTTAA
1 AA-TATATATTATAT-ATTAAAAAAACATTTTGAA
*
416363 AATTATATATAATATAT
1 AA-TATATATTATATAT
416380 CGTTTTAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
31 9 0.13
32 3 0.04
33 22 0.31
34 29 0.41
35 8 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (33 bp):
AATATATATTATATATTAAAAAAACATTTTGAA
Found at i:416423 original size:5 final size:5
Alignment explanation
Indices: 416402--416439 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
416392 TTTTTTATTA
*
416402 TTTAT TTTGAC TTTAT TTTAT TTTA- TTTAT TTTAT TTT
1 TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
416440 TTTATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:416427 original size:25 final size:22
Alignment explanation
Indices: 416391--416445 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 22
416381 GTTTTAAATC
416391 TTTTTTTA--TTATTTATTTTGA
1 TTTTTTTATTTTATTTATTTT-A
416412 CTTTATTTTATTTTATTTATTTTA
1 -TTT-TTTTATTTTATTTATTTTA
416436 TTTTTTTATT
1 TTTTTTTATT
416446 AATTGTGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.33
23 8 0.27
24 1 0.03
25 11 0.37
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTTTATTTTATTTATTTTA
Found at i:416432 original size:9 final size:9
Alignment explanation
Indices: 416413--416445 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
416403 TTATTTTGAC
416413 TTTATTTTAT
1 TTTA-TTTAT
416423 TTTATTTAT
1 TTTATTTAT
416432 TTTATTT-T
1 TTTATTTAT
416440 TTTATT
1 TTTATT
416446 AATTGTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.30
9 12 0.52
10 4 0.17
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTATTTAT
Found at i:427347 original size:41 final size:41
Alignment explanation
Indices: 427290--427367 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
427280 TCGAGTTAGG
*
427290 AAATGCTCTTAATTGTGATAATAAATACAATTTGCAATAGA
1 AAATGCTCTTAATTGTGATAATAAAGACAATTTGCAATAGA
**
427331 AAATGCTCTTGCTTGTGATAATAAAGACAATTTGCAA
1 AAATGCTCTTAATTGTGATAATAAAGACAATTTGCAA
427368 ATATTTTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (41 bp):
AAATGCTCTTAATTGTGATAATAAAGACAATTTGCAATAGA
Found at i:437359 original size:495 final size:496
Alignment explanation
Indices: 435370--438353 Score: 5201
Period size: 495 Copynumber: 6.0 Consensus size: 496
435360 GCTGTTCATT
*
435370 TCTATGTTATAGCATGTTCCAACCT-AACAAAAGAAGTTTGTAAGATGATGGTTATGGTATAGAA
1 TCTATATT-TAGCATGTTCCAACCTGAA-AAAAGAAGTTTGTAAGATGATGGTTATGG--TAGAA
* *
435434 AGTCTTGCCAAATAGTTAGTCATTTAAATGGGGGTATTACTTTTTGGGGAGCTAAACCTTTTGTT
62 AGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCT
435499 GTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCA
127 GTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCA
* * *
435564 GTTTTGAGGAACTTAAATTTGAATCCTGTTGAACCCTATTGCATTTATCCCCTATAACTGGAACT
192 GTTTTGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACT
* * *
435629 AATCTTTCTATTTCTCATCAATTACAGTTGCTCCAACTATTGCTATTCCCTTTGCTTCAACCAAT
257 AATCTTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAAT
* ** *
435694 GCTGAAACAAACCTACTGGATGTTTGGTCTGATTCATTTGCCATTGTCCCAGGTACACCTGAAAA
322 GCTGAAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAA
435759 CCATGCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTG
387 CCATGCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTG
*
435824 ATCCTAGTGGACTTCAATATATATATTTTAGTTAATTCGTTGCCA
452 ATCCTAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
435869 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
1 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
435934 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
66 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
* *
435999 GTTTCGTACCAGTG--AGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
131 GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
436062 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACTAATC
196 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACTAATC
* * *
436127 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTAAACTAGTGCTG
261 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAATGCTG
* *
436192 AAACAAACTTACTTGATGTTCGGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
326 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
* * * * *
436257 GCTACTAAATTTGAAAATCAGTCGACATTTAAATTTTGAAATCAGGTAATATGGTTCTTTGATCC
391 GCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
*
436322 TAGTGGACTTCAATATTATATATTTTAGTTAATCAG-TGCCA
456 TAGTGGACTTCAATA-TATATATTTTAGTTAATCCGTTGCCA
*
436363 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGAC
1 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
* *
436428 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTTCTGTCA
66 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
*
436493 GTTTCATACTAGTGAAAGTTTTAAAATAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
131 GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
436558 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCCTATAACTGGAACTAAT
196 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTAT-CCCCTATAACTGGAACTAAT
*
436623 CTTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTTTGCTTCAACCAATGCT
260 CTTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAATGCT
** * *
436688 GAAACAAACTTACTGGATGTTTGGTCTGATTCATTTTCCATTGTCCCAGTTACACATGAAAACCA
325 GAAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCA
* * *
436753 TGCTACTGAATTTGGAAATCAGCCGACATTTAAATATGGAAATCAGGTCATATGATTCTTTGATA
390 TGCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATC
436818 CTAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
455 CTAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
* *
436860 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGTTGGTTATGGTAGAAATTC
1 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
436925 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
66 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
*
436990 GTTTCGTACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
131 GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
* * *
437055 TGAGGAACTTAAATTTGAATCCTGTTGAACCCTGTTGCATTTATCCTC-ATAACTGGAACTAATC
196 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACTAATC
* *
437119 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTATTCCCTTTGCTTCAACCAATGCTG
261 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAATGCTG
* *
437184 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTTCCATTGTCCCAGTTACACCTGAAAAACAT
326 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
* ** *
437249 GCTACTGAATTTGAAAATCAATCAACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
391 GCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
437314 TAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
456 TAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
*
437355 TCTATATTTAGCATGTTCCAACCTGAGAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
1 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
437420 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
66 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
*
437485 GTTTCGTACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
131 GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
*
437550 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTATTGCATTTATCCCCTATAACTGGAACTAATC
196 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACTAATC
* * *
437615 TTTCTATTTCTCATCAATTACTGTTGCTCC-ACTACTGTTGTTCCCTCTGCTTCAACCAGTGCTG
261 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAATGCTG
437679 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
326 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
437744 GCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
391 GCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
* *
437809 TAGTGGACTTCAATATATATATTTTAGTTAATCTGCTGCCA
456 TAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
* *
437850 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGGTGATTATGGTAGAAAGTC
1 TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
437915 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
66 TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
437980 GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGAC--ATTTCAGTTT
131 GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
* *
438043 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGTATTTATCCACTATAACTGGAACTAATC
196 TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACTAATC
*
438108 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAGTGCTG
261 TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAATGCTG
* * *
438173 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCTCAGTTAAACCTGAAAACTAT
326 AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
* *
438238 GCTACTAAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAAGTAATATGATTCTTTGATCC
391 GCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
* *
438303 TAGTGGACTTCAAAATACATATTTTAGTTAATCCGTTGCCA
456 TAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
438344 TCTATATTTA
1 TCTATATTTA
438354 TGTTATATTG
Statistics
Matches: 2369, Mismatches: 108, Indels: 21
0.95 0.04 0.01
Matches are distributed among these distances:
493 101 0.04
494 655 0.28
495 866 0.37
496 243 0.10
497 450 0.19
498 45 0.02
499 9 0.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (496 bp):
TCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGTAGAAAGTC
TTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTTTGCTGTTA
GTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGACTTATTTCAGTTT
TGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGAACTAATC
TTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCAATGCTG
AAACAAACTTACTGGATGTTCAGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
GCTACTGAATTTGGAAATCAGCCGACATTTAAATTTGGAAATCAGGTAATATGATTCTTTGATCC
TAGTGGACTTCAATATATATATTTTAGTTAATCCGTTGCCA
Found at i:441850 original size:15 final size:15
Alignment explanation
Indices: 441830--441859 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
441820 GATTAGTATC
441830 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
441845 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
441860 ATATAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:442657 original size:2 final size:2
Alignment explanation
Indices: 442650--442692 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
442640 GGGGACTTCA
442650 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
442692 A
1 A
442693 CTGAATTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:446281 original size:60 final size:61
Alignment explanation
Indices: 446180--446354 Score: 173
Period size: 60 Copynumber: 2.9 Consensus size: 61
446170 ATTAATATTA
* *
446180 AATTGGTCCCTAAA-TATTTTTAATATTTC-ATTTCATCCCTAAACTAT-A-ATTATCATTCT-
1 AATTAGTCCCTAAACT-TTTTAAATATTTCAATTTCATCCCTAAACTATGACA-T-TCATTCTG
* ** * *
446239 AAGTTAGTCCTTAAAC-TTTTGGATATTTCAATTTTATCCCTAAATTATGACATTCATTCTG
1 AA-TTAGTCCCTAAACTTTTTAAATATTTCAATTTCATCCCTAAACTATGACATTCATTCTG
* *
446300 AATTGGTCCCTAAACTTTTTAAATATTTCAATTTCATCCCAAAACGTATGTACAT
1 AATTAGTCCCTAAACTTTTTAAATATTTCAATTTCATCCCTAAAC-TATG-ACAT
446355 ACTAATCACA
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
59 13 0.14
60 44 0.47
61 28 0.30
62 5 0.05
63 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (61 bp):
AATTAGTCCCTAAACTTTTTAAATATTTCAATTTCATCCCTAAACTATGACATTCATTCTG
Found at i:448890 original size:21 final size:21
Alignment explanation
Indices: 448851--448891 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
448841 TAAAAAAAAT
* *
448851 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
448872 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
448892 TTCTAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:448945 original size:20 final size:21
Alignment explanation
Indices: 448920--448965 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
448910 AATATCCAAC
448920 AATAACAAAACTGGTA-AAAA
1 AATAACAAAACTGGTAGAAAA
* *
448940 AATAACAAAACTTGTAGAAAT
1 AATAACAAAACTGGTAGAAAA
448961 AATAA
1 AATAA
448966 TATTTCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (21 bp):
AATAACAAAACTGGTAGAAAA
Found at i:449782 original size:60 final size:61
Alignment explanation
Indices: 449699--449825 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 61
449689 AACTATTTCT
* * * *
449699 TAACTTTTAATAGTCGAGGGACTCAATAAAGCAGCTCCCTATAGTTGGAGGACCATTT-TA
1 TAACTTTTAATAGCCGAGGGACTCAATAAAACAACTCCCTATAATTGGAGGACCATTTGTA
* * *
449759 TAACTTTTAATAGCCGAGTGACTCAATAAAATAACTCCCTATAATTTGAGGACCATTTGTA
1 TAACTTTTAATAGCCGAGGGACTCAATAAAACAACTCCCTATAATTGGAGGACCATTTGTA
449820 T-ACTTT
1 TAACTTT
449826 ACCCTTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 56 0.95
61 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (61 bp):
TAACTTTTAATAGCCGAGGGACTCAATAAAACAACTCCCTATAATTGGAGGACCATTTGTA
Found at i:450902 original size:416 final size:416
Alignment explanation
Indices: 450130--452600 Score: 4358
Period size: 419 Copynumber: 5.9 Consensus size: 416
450120 AAGTTTAGGA
*
450130 TTTAGGGTTTAACTACTCAACTTTCATATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
1 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
*
450195 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATATGTAAAAAATAAAAAAAAA
66 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAAAT-AAAAAAAA
* *
450260 TTGAAAGTTAGAGTGATTAAATCAGGGGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAA
130 TTAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAA
450325 CTGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAA
195 CTGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAA
*
450390 ACGTGTCACGTGCAAATCACCCGTTAAGTTTGTAACGGTGAGGTACTAAAATGAAATAAAATCTA
260 ACGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATCTA
450455 AATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAA
325 AATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAA
450520 TTTGAATACCCTATTTTGGTACTAAAG
390 TTTGAATACCCTATTTTGGTACTAAAG
450547 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
1 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
*
450612 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATATGTAAAAAATAAAAAAAAT
66 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAAATAAAAAAAAT
* *
450677 TGAAAGTTAGAGTGATTAAATCAGGGGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAAC
131 TAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAAC
450742 TGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAAA
196 TGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAAA
*
450807 CGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATCTAG
261 CGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATCTAA
450872 ATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAAT
326 ATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAAT
450937 TTGAATACCCTATTTTGGTACTAAAG
391 TTGAATACCCTATTTTGGTACTAAAG
450963 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
1 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
* *
451028 TAAATTTTGTGACAGGACATTTTTATTATTATTTTATTAATATATATGTAAAAAAT-AAAAAAAT
66 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAAATAAAAAAAAT
* *
451092 TGAAAGTTAGAGTGATTAAATCAGGGGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAAC
131 TAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAAC
451157 TGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAAA
196 TGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAAA
* * *
451222 CGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGTTGAGGTATTAAAATGAAATAAAATCTAC
261 CGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATCTAA
451287 ATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAA-TGATAGTAAT
326 ATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAAT
451351 TTGAATACCCTATTTTGGTACTAAAG
391 TTGAATACCCTATTTTGGTACTAAAG
*
451377 GTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
1 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
* * *
451442 TAACTTTTATGACATGATATTTTTATTATTATTTTATTAATATATAAGT-AAAAATAAAAAAAAA
66 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAAAT-AAAAAAAA
*
451506 TTAAAAGTTAGAGTTATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATT-AAAAAATAAA
130 TTAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAA
* * *
451570 CTTTAGTGACAAGAGTAAGAGTGATAAGATAGTTGACTGACGATGATGCAATTTTCTCATAAAAA
195 CTGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAA
*
451635 ACGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACAGTGAGGTACTAAAATGAAATAAAATCTA
260 ACGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATCTA
*
451700 AATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAATAA
325 AATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAA
451765 TTTGAATACCCTATTTTGGTACTAAAG
390 TTTGAATACCCTATTTTGGTACTAAAG
*
451792 TTTAGGGTTTAATTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
1 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
* * *
451857 TAACTTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAACTAAAAATAAAAAAAATA
66 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGT-AAAA-AATAAAAA-A
* *
451922 AATTTAAAAGTTAGAGTTATTAAATCAGGAGTAGTTTGAAAGTTAAGTAATTAAATT-AAAAAAT
128 AA-TTAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAAT
* * *
451986 AAACTTTAGTGACTAGAGTAAGAGTGATAAGATAGTTGACTGACGATGATGCAATTTTCTCATAA
192 AAACTGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAA
* * * *
452051 AAAACGTGTCATGTGCAAATCACCCGTTAAATTTTTAACAGTGAGGTACTAAAATGAAGTAAAAT
257 AAAACGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAAT
* * *
452116 CTAAATATTAGGTATGATTTTAAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAAATGATAG
322 CTAAATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAG
452181 TAATTTGAATACCCTATTTTGGTACTAAAG
387 TAATTTGAATACCCTATTTTGGTACTAAAG
*
452211 TTTAGGGTTTAATTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
1 TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
* *
452276 TAACTTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAATAAAAAAATAA
66 TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAA-ATAAAAA-AA
* *
452341 ATTTAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAATTTGAGTAATTAAATTAAAAAAATA
129 A-TTAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATA
* *
452406 AACTTTAGTGACCAGAGTAAGAGTGATAAGATAGTTAACTGATGATGATGCAATTTTCTCATAAA
193 AACTGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAA
*
452471 AAACGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAAGC
258 AAACGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATC
* *
452536 TAAATGTTAGGTATGATTTTGAAAAATTGAAGGTTTAGGTACTAAAACGGATCAAAACTGATAGT
323 TAAATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGT
452601 TTATGTACTA
Statistics
Matches: 1987, Mismatches: 57, Indels: 18
0.96 0.03 0.01
Matches are distributed among these distances:
413 6 0.00
414 332 0.17
415 456 0.23
416 413 0.21
417 129 0.06
418 71 0.04
419 580 0.29
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (416 bp):
TTTAGGGTTTAACTACTCAACTTTCAAATTGCTCCTATTTTAATCACCCTAATTTATTTTATTAA
TAAATTTTGTGACATGACATTTTTATTATTATTTTATTAATATATAAGTAAAAAATAAAAAAAAT
TAAAAGTTAGAGTGATTAAATCAGGAGTAATTTGAAAGTTAAGTAATTAAATTAAAAAAATAAAC
TGTAGTGACCAGAGTAAGAGTGATAAGATAGTTGACTGATGATGATGCAATTTTCTCATAAAAAA
CGTGTCACGTGCAAATCACCCGTTAAGTTTTTAACGGTGAGGTACTAAAATGAAATAAAATCTAA
ATGTTAGGTATGATTTTGAAAAATTGAAGGTCTAGGTACTAAAACGGATAAAAACTGATAGTAAT
TTGAATACCCTATTTTGGTACTAAAG
Found at i:455326 original size:36 final size:36
Alignment explanation
Indices: 455268--455336 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
455258 TACCAAACCC
* *
455268 GTCCCCGTCTCCATTTAGCATAAACGGTTTTTCCCT
1 GTCCCCGTCACCATTTAACATAAACGGTTTTTCCCT
*
455304 GTCCCCGTCACCGTTTAACATAAACGGTTTTTC
1 GTCCCCGTCACCATTTAACATAAACGGTTTTTC
455337 TCCATCCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.19, C:0.32, G:0.14, T:0.35
Consensus pattern (36 bp):
GTCCCCGTCACCATTTAACATAAACGGTTTTTCCCT
Found at i:455345 original size:36 final size:36
Alignment explanation
Indices: 455269--455345 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
455259 ACCAAACCCG
* * *
455269 TCCCCGTCTCCATTTAGCATAAACGGTTTTTCCCTG
1 TCCCCGTCACCATTTAACATAAACGGTTTTTCCCTA
*
455305 TCCCCGTCACCGTTTAACATAAACGGTTTTTCTCC-A
1 TCCCCGTCACCATTTAACATAAACGGTTTTTC-CCTA
455341 TCCCC
1 TCCCC
455346 ATTTAATTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.18, C:0.36, G:0.12, T:0.34
Consensus pattern (36 bp):
TCCCCGTCACCATTTAACATAAACGGTTTTTCCCTA
Found at i:455579 original size:8 final size:8
Alignment explanation
Indices: 455563--455605 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
455553 AACAATTCTT
*
455563 TATGTATG
1 TATGCATG
455571 TATGCATG
1 TATGCATG
455579 TATGCATG
1 TATGCATG
455587 TATGCATG
1 TATGCATG
*
455595 CATGCATG
1 TATGCATG
455603 TAT
1 TAT
455606 CACATGCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (8 bp):
TATGCATG
Found at i:456221 original size:31 final size:29
Alignment explanation
Indices: 456186--456262 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
456176 ATTTTTCATT
*
456186 TAAGTACATAAAGATATCTTTTTGGTCAAAA
1 TAAGTAC-TAAAGATAT-TTTTTGATCAAAA
* *
456217 TAAGTACTTAAGGTATTTTTTGATCAAAA
1 TAAGTACTAAAGATATTTTTTGATCAAAA
*
456246 TATGTACCTAAAG-TATT
1 TAAGTA-CTAAAGATATT
456263 CATTTTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 21 0.52
30 12 0.30
31 7 0.17
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (29 bp):
TAAGTACTAAAGATATTTTTTGATCAAAA
Found at i:456404 original size:30 final size:30
Alignment explanation
Indices: 456338--456406 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
456328 CTTAGATGAA
*
456338 AAGTACCTATTTTGACATAAAAAATACTTT
1 AAGTACTTATTTTGACATAAAAAATACTTT
* *
456368 AAGTACTTATTTTGACCA-AAAATATATTTT
1 AAGTACTTATTTTGA-CATAAAAAATACTTT
456398 AAGTACTTA
1 AAGTACTTA
456407 AATAAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (30 bp):
AAGTACTTATTTTGACATAAAAAATACTTT
Found at i:458466 original size:29 final size:29
Alignment explanation
Indices: 458424--458484 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
458414 CAAATAGCTA
458424 CACTGAATTTTTTTTCTAAGTTAGACGGC
1 CACTGAATTTTTTTTCTAAGTTAGACGGC
458453 CACTGAATTTTTTTTCTAAGTTAGACGGC
1 CACTGAATTTTTTTTCTAAGTTAGACGGC
458482 CAC
1 CAC
458485 GTTGAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (29 bp):
CACTGAATTTTTTTTCTAAGTTAGACGGC
Found at i:463558 original size:18 final size:18
Alignment explanation
Indices: 463535--463569 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
463525 AACCAGAAAT
463535 GAACATACCTATATATAC
1 GAACATACCTATATATAC
463553 GAACATACCTATATATA
1 GAACATACCTATATATA
463570 TACATCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (18 bp):
GAACATACCTATATATAC
Found at i:465434 original size:60 final size:60
Alignment explanation
Indices: 465370--465482 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
465360 ATCCCTTAAT
* *
465370 TATAGG-ATATTGCTTTATTAAGTCTCTCAACTATTAAAAGATATAAAATGGTCCTCTAAC
1 TATAGGTA-ATTGCTTTATTAAGTCCCTCAACTATTAAAAGATACAAAATGGTCCTCTAAC
* * * * *
465430 TATAGGTAATTGCTTTGTTGAGTCCCTTAACTTTTAAAAGTTACAAAATGGTC
1 TATAGGTAATTGCTTTATTAAGTCCCTCAACTATTAAAAGATACAAAATGGTC
465483 ACACGGCTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 44 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (60 bp):
TATAGGTAATTGCTTTATTAAGTCCCTCAACTATTAAAAGATACAAAATGGTCCTCTAAC
Found at i:468762 original size:40 final size:40
Alignment explanation
Indices: 468718--468801 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
468708 AGAACAGCTT
*
468718 CCGTGAAAGACCTCTGGCAGTCAGAATTATGAATTGCCCA
1 CCGTGAAAGACCTCTGGCAGCCAGAATTATGAATTGCCCA
468758 CCGTGAAAGACCTCTGGCAGCCAGAATTATGAATTGCCCA
1 CCGTGAAAGACCTCTGGCAGCCAGAATTATGAATTGCCCA
468798 CCGT
1 CCGT
468802 AGGACTCGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (40 bp):
CCGTGAAAGACCTCTGGCAGCCAGAATTATGAATTGCCCA
Found at i:473208 original size:21 final size:21
Alignment explanation
Indices: 473166--473210 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
473156 ATGATCGGAG
*
473166 AAATCAAACAAATCCAACTGA
1 AAATCAAAAAAATCCAACTGA
*
473187 AAATCAAATAAAATTCAA-TGA
1 AAATCAAA-AAAATCCAACTGA
473208 AAA
1 AAA
473211 GAGGATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.62, C:0.16, G:0.04, T:0.18
Consensus pattern (21 bp):
AAATCAAAAAAATCCAACTGA
Found at i:478741 original size:26 final size:28
Alignment explanation
Indices: 478711--478774 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 28
478701 AAAACTTTTA
478711 AGCTC-GT-GAGTTTTCGAGTCGAGTCG
1 AGCTCAGTAGAGTTTTCGAGTCGAGTCG
*
478737 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-CA-GT-AGAGTTTTCGAGTCGAGTCG
478768 AGCTCAG
1 AGCTCAG
478775 CAATACTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
29 1 0.03
30 2 0.06
31 23 0.74
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (28 bp):
AGCTCAGTAGAGTTTTCGAGTCGAGTCG
Found at i:479563 original size:27 final size:27
Alignment explanation
Indices: 479532--479586 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
479522 AAGTAAAAAA
*
479532 ACAAAGAA-AAATAAGTAAAAAAATAAT
1 ACAAAAAATAAATAA-TAAAAAAATAAT
**
479559 ACAAAAAATAAATAATATTAAAATAAT
1 ACAAAAAATAAATAATAAAAAAATAAT
479586 A
1 A
479587 TATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (27 bp):
ACAAAAAATAAATAATAAAAAAATAAT
Found at i:479591 original size:18 final size:17
Alignment explanation
Indices: 479548--479606 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
479538 AAAAATAAGT
*
479548 AAAA-AAATAAT-ACAA
1 AAAATAAATAATAATAA
*
479563 AAAATAAATAATATTAA
1 AAAATAAATAATAATAA
*
479580 AATAATATATAATAATAA
1 AA-AATAAATAATAATAA
*
479598 AAGATAAAT
1 AAAATAAAT
479607 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 7 0.20
17 9 0.26
18 15 0.43
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAATAAATAATAATAA
Found at i:479687 original size:12 final size:11
Alignment explanation
Indices: 479672--479842 Score: 72
Period size: 11 Copynumber: 14.1 Consensus size: 11
479662 ATAATATGAT
479672 ATATTTTCAAAA
1 ATATTTT-AAAA
479684 ATATTTTAAAA
1 ATATTTTAAAA
* * *
479695 CTATATATTATAT
1 --ATATTTTAAAA
*
479708 ATATTTTCAAA
1 ATATTTTAAAA
*
479719 ATGTTTTAAAA
1 ATATTTTAAAA
*
479730 ACTATATATTATATAT
1 A-TAT-T-TTA-A-AA
*
479746 ATATTTTCAAA
1 ATATTTTAAAA
*
479757 ATGTTTTAAAA
1 ATATTTTAAAA
*
479768 ACTATATATTATACAT
1 A-TAT-T-TTA-A-AA
*
479784 ATATTTTCAAA
1 ATATTTTAAAA
479795 ATATTTTAAAA
1 ATATTTTAAAA
* *
479806 ACTATATATTATAT
1 A-TAT-T-TTAAAA
*
479820 ATATTTTTAAA
1 ATATTTTAAAA
*
479831 ATGTTTTAAAA
1 ATATTTTAAAA
479842 A
1 A
479843 CTATATATTA
Statistics
Matches: 117, Mismatches: 27, Indels: 31
0.67 0.15 0.18
Matches are distributed among these distances:
11 57 0.49
12 17 0.15
13 18 0.15
14 13 0.11
15 8 0.07
16 4 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:479715 original size:36 final size:36
Alignment explanation
Indices: 479649--480076 Score: 553
Period size: 36 Copynumber: 11.6 Consensus size: 36
479639 AAAATAATTA
* * * *
479649 TTTTCAAAACCATATAATATGATATATTTTCAAAAATA
1 TTTTAAAAACTATATATTAT-ATATATTTTC-AAAATG
479687 TTTT-AAAACTATATATTATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
479722 TTTTAAAAACTATATATTATATATATATTTTCAAAATG
1 TTTTAAAAACTATATA-T-TATATATATTTTCAAAATG
*
479760 TTTTAAAAACTATATATTATACATATATTTTCAAAATA
1 TTTTAAAAACTATATATTAT--ATATATTTTCAAAATG
*
479798 TTTTAAAAACTATATATTATATATATTTTTAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
479834 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTTCAAAATG
* *
479870 TTTTTTAAAAATTATATATTGTATA-AGTTTTCAAAATG
1 --TTTTAAAAACTATATATTATATATA-TTTTCAAAATG
*
479908 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATATT
1 TTTTAAAAACTATATATTATATATA-TTTTC-AAA-ATG
*
479946 TTTTAAAAACCTATATATTATATATAGTTTCAAAATG
1 TTTTAAAAA-CTATATATTATATATATTTTCAAAATG
*
479983 TGTTAAAAACTATATATTATATA-AGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTTCAAAATG
480019 TTTTTAAAAACTATATATTATATA-AGTTTTCAAAATG
1 -TTTTAAAAACTATATATTATATATA-TTTTCAAAATG
480056 TTTTTAAAAACTATATATTAT
1 -TTTTAAAAACTATATATTAT
480077 GTTTTAAAAA
Statistics
Matches: 359, Mismatches: 17, Indels: 29
0.89 0.04 0.07
Matches are distributed among these distances:
35 11 0.03
36 123 0.34
37 84 0.23
38 122 0.34
39 18 0.05
40 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATG
Found at i:479775 original size:74 final size:74
Alignment explanation
Indices: 479660--480076 Score: 550
Period size: 74 Copynumber: 5.6 Consensus size: 74
479650 TTTCAAAACC
* *
479660 ATATAATATGATATATTTTCAAAAATATTTT-AAAACTATATATTATATATA-TTTTCAAAATGT
1 ATATTATAT-ATATATTTTC-AAAATGTTTTAAAAACTATATATTATATA-AGTTTTCAAAATGT
479723 TTTAAAAACTAT
63 TTTAAAAACTAT
*
479735 ATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATACATATA-TTTTCAAAATAT
1 ATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTAT--ATA-AGTTTTCAAAATGT
479799 TTTAAAAACTAT
63 TTTAAAAACTAT
479811 ATATTATATATAT-TTTT-AAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTT
1 ATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG--TT
*
479874 TTAAAAATTAT
64 TTAAAAACTAT
* * *
479885 ATATTGTATA-A-GTTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTT
1 ATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTC-AAA-ATGTT
479948 TTAAAAACCTAT
64 TTAAAAA-CTAT
* *
479960 ATA-T-TATATATAGTTTCAAAATGTGTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTT
1 ATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG-TTT
480023 TAAAAACTAT
65 TAAAAACTAT
*
480033 ATATTATATA-A-GTTTTCAAAATGTTTTTAAAAACTATATATTAT
1 ATATTATATATATATTTTCAAAATG-TTTTAAAAACTATATATTAT
480077 GTTTTAAAAA
Statistics
Matches: 310, Mismatches: 15, Indels: 35
0.86 0.04 0.10
Matches are distributed among these distances:
71 1 0.00
72 13 0.04
73 37 0.12
74 152 0.49
75 64 0.21
76 43 0.14
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (74 bp):
ATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTT
AAAAACTAT
Found at i:480083 original size:21 final size:21
Alignment explanation
Indices: 480057--480097 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
480047 TTCAAAATGT
480057 TTTTAAAAACTATATATTATG
1 TTTTAAAAACTATATATTATG
480078 TTTTAAAAACTATATATTAT
1 TTTTAAAAACTATATATTAT
480098 ATATATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTAAAAACTATATATTATG
Found at i:480107 original size:58 final size:59
Alignment explanation
Indices: 480020--480130 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 59
480010 TTCAAAATGT
480020 TTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTT-AAAAACTATATATTATG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTTAAAAAACTATATATTATG
480078 TTTTAAAAACTATATATTATATATA-TTTTCAAAATGTTTTTAAAAAACTATAT
1 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATGTTTTTAAAAAACTATAT
480131 GTTTTATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
58 39 0.76
59 12 0.24
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (59 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTTAAAAAACTATATATTATG
Found at i:482531 original size:19 final size:19
Alignment explanation
Indices: 482480--482531 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
482470 CTCGATCAAA
* *
482480 AGTCAAAGACAACAGATCT
1 AGTCAAAGTCAACAGATCG
482499 AGTCAACGAGTCAACA-ATCG
1 AGTCAA--AGTCAACAGATCG
482519 AGTCAATAGTCAA
1 AGTCAA-AGTCAA
482532 TTCAATGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 9 0.32
21 7 0.25
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (19 bp):
AGTCAAAGTCAACAGATCG
Found at i:488636 original size:22 final size:22
Alignment explanation
Indices: 488613--488654 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
488603 TTTGATCCCA
488613 AAAATT-AATTAAATAAAAATC
1 AAAATTAAATTAAATAAAAATC
*
488634 AAATTTAAATTAAATAAAAAT
1 AAAATTAAATTAAATAAAAAT
488655 TGGGGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTAAATTAAATAAAAATC
Found at i:489585 original size:21 final size:22
Alignment explanation
Indices: 489528--489586 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
489518 ATTAACTATT
*
489528 ATTTAGGATTTTAAG-TTAGGG
1 ATTTAGGGTTTTAAGTTTAGGG
* **
489549 ATTAAGGGTTAGAAGTTTA-GG
1 ATTTAGGGTTTTAAGTTTAGGG
489570 ATTTAGGGTTTTAAGTT
1 ATTTAGGGTTTTAAGTT
489587 GAGTTTAGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (22 bp):
ATTTAGGGTTTTAAGTTTAGGG
Found at i:493654 original size:2 final size:2
Alignment explanation
Indices: 493647--493685 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
493637 AATCTAAGTT
493647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
493686 TGTATTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:495569 original size:23 final size:23
Alignment explanation
Indices: 495551--495611 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
495541 CTCGTATAAA
495551 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
495574 TACACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
495597 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
495612 TATAAGATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:496295 original size:65 final size:66
Alignment explanation
Indices: 496224--496367 Score: 175
Period size: 65 Copynumber: 2.2 Consensus size: 66
496214 TTCCTTTAGG
* * * *
496224 GGGTATCGATACCCTACTTAAGGTATCGGTACCCTCATGACATTCTGTAATT-TT-TCGTTCAAG
1 GGGTATCGGTACCCAACTGAAGGTATCAGTACCCTCATGACATTCTGTAATTCTTCTCGTTCAAG
496287 A
66 A
** * * **
496288 GAGGTATCGGTACCCAACTGGGGGTATCAGTACCCTTATGGCATTCTGTAATTCTTCTCGTTTGA
1 G-GGTATCGGTACCCAACTGAAGGTATCAGTACCCTCATGACATTCTGTAATTCTTCTCGTTCAA
496353 GA
65 GA
496355 GGGTATCGGTACC
1 GGGTATCGGTACC
496368 TGTTGAATGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 1 0.01
65 43 0.64
66 14 0.21
67 9 0.13
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (66 bp):
GGGTATCGGTACCCAACTGAAGGTATCAGTACCCTCATGACATTCTGTAATTCTTCTCGTTCAAG
A
Done.