Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008322.1 Hibiscus syriacus cultivar Beakdansim tig00111025_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: 456513
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:365144 original size:17 final size:17
Alignment explanation
Indices: 365122--365155 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
365112 ATTTTAATCC
*
365122 TATATGTATTAATATTT
1 TATATGTATAAATATTT
*
365139 TATATGTCTAAATATTT
1 TATATGTATAAATATTT
365156 AGATTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TATATGTATAAATATTT
Found at i:365627 original size:58 final size:57
Alignment explanation
Indices: 365518--365628 Score: 127
Period size: 58 Copynumber: 1.9 Consensus size: 57
365508 TGTTTTTTGC
* * *
365518 TATTTTAGACCCTTAATTTTCTATTTTTAATGTTTTAGTTTTTAATTATTTATTTTAT
1 TATTTTAGAACCTTAATTTTCTATTTGTAATATTTTAGTTTTTAA-TATTTATTTTAT
* *
365576 TATTTTAGAACCTTAAATTTT-TGTTTGTAATATTTTGGTATTTTTAA-ATTTAT
1 TATTTTAGAACCTT-AATTTTCTATTTGTAATATTTTAG--TTTTTAATATTTAT
365629 ATTTTTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
58 32 0.71
59 6 0.13
60 7 0.16
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.61
Consensus pattern (57 bp):
TATTTTAGAACCTTAATTTTCTATTTGTAATATTTTAGTTTTTAATATTTATTTTAT
Found at i:377035 original size:8 final size:8
Alignment explanation
Indices: 377019--377056 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
377009 AGGAACAAAT
377019 AAAAA-GA
1 AAAAATGA
377026 AAAAATGAA
1 AAAAATG-A
377035 AAAAATGA
1 AAAAATGA
377043 AAAAATGA
1 AAAAATGA
377051 AAAAAT
1 AAAAAT
377057 AAATGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 5 0.17
8 16 0.55
9 8 0.28
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:377039 original size:9 final size:9
Alignment explanation
Indices: 377025--377055 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
377015 AAATAAAAAG
377025 AAAAAATGA
1 AAAAAATGA
377034 AAAAAATG-
1 AAAAAATGA
377042 AAAAAATGA
1 AAAAAATGA
377051 AAAAA
1 AAAAA
377056 TAAATGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:377067 original size:19 final size:19
Alignment explanation
Indices: 377003--377070 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 19
376993 TATGCTTGAA
* *
377003 GAAAAAAGGAACAAATAAAAA
1 GAAAAAATGAA-AAA-AAAAT
377024 GAAAAAATG--AAAAAAAT
1 GAAAAAATGAAAAAAAAAT
377041 GAAAAAATGAAAAAATAAAT
1 GAAAAAATGAAAAAA-AAAT
377061 G-AAAAATGAA
1 GAAAAAATGAA
377071 GAGAGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 13 0.31
18 3 0.07
19 13 0.31
20 5 0.12
21 8 0.19
ACGTcount: A:0.75, C:0.01, G:0.13, T:0.10
Consensus pattern (19 bp):
GAAAAAATGAAAAAAAAAT
Found at i:378206 original size:136 final size:136
Alignment explanation
Indices: 377909--378487 Score: 891
Period size: 136 Copynumber: 4.3 Consensus size: 136
377899 GGAGGGGAAC
* * *
377909 CAACATTTCCAATGGATAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATA
377974 ATGAGAAGAGCTTGTTCGA-CTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTG
**
378038 AGGGAT
131 AGCAAT
* * * *
378044 CAAAATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGATCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATA
* *
378109 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCAAATCAGTGATACCTCGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTG
*
378174 AGCAAC
131 AGCAAT
*
378180 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATA
378245 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTG
378310 AGGC-AT
131 A-GCAAT
* * *
378316 CAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAA-AGAGAGAGAATAAGTTCAT
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACAGAGGGAGAAGAAGTTCAT
*
378380 AATGAGAAGAGCTTGTTCGATCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCG-TT
65 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTT
**
378444 AGAGGGAT
130 -GAGCAAT
** *
378452 TGACATTTCCAA--AAGAGTTCATAATGAGAAGAACTC
1 CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
378488 GTCTTAAAGG
Statistics
Matches: 409, Mismatches: 30, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
134 23 0.06
135 80 0.20
136 303 0.74
137 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (136 bp):
CAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTG
AGCAAT
Found at i:380090 original size:17 final size:17
Alignment explanation
Indices: 380068--380101 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
380058 ATTTTAATCC
*
380068 TATATGTATTAATATTT
1 TATATGTATAAATATTT
*
380085 TATATGTCTAAATATTT
1 TATATGTATAAATATTT
380102 AGATTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TATATGTATAAATATTT
Found at i:380861 original size:16 final size:17
Alignment explanation
Indices: 380823--380861 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
380813 ATGCATACCA
380823 GTTTTTGTCTTAAAAAT
1 GTTTTTGTCTTAAAAAT
* *
380840 GATTTT-TCTTAAAATT
1 GTTTTTGTCTTAAAAAT
380856 GTTTTT
1 GTTTTT
380862 AAAAGACGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (17 bp):
GTTTTTGTCTTAAAAAT
Found at i:381581 original size:41 final size:41
Alignment explanation
Indices: 381507--381621 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
381497 CGAATATGTA
* *
381507 AATCGTAACGCAATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
* * * * *
381548 AATTGCAACGTGATTCTGACTATCACAATGCGATAATACGT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
381589 AATCGCAACGCGATTCTGACTATCGCAACGCGA
1 AATCGCAACGCGATTCTGACTATCGCAACGCGA
381622 CGCGTTGCGA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
Found at i:381615 original size:20 final size:20
Alignment explanation
Indices: 381508--381621 Score: 88
Period size: 20 Copynumber: 5.6 Consensus size: 20
381498 GAATATGTAA
* *
381508 ATCGTAACGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
381528 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
381548 AATTGCAACGTGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
* * **
381569 ATCACAATGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
381589 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
381610 ATCGCAACGCGA
1 ATCGCAACGCGA
381622 CGCGTTGCGA
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
19 4 0.06
20 36 0.51
21 26 0.37
22 4 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:381824 original size:22 final size:21
Alignment explanation
Indices: 381799--381858 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
381789 CTACGGCGAC
381799 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGA-GAA
* *
381821 ATCCGTCCCCATTTCTGGAGAA
1 ATCCGTCCCCATCTC-CGAGAA
* *
381843 ATTCATCCCCATCTCC
1 ATCCGTCCCCATCTCC
381859 AGCAAAATCT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.22, C:0.42, G:0.12, T:0.25
Consensus pattern (21 bp):
ATCCGTCCCCATCTCCGAGAA
Found at i:382293 original size:33 final size:33
Alignment explanation
Indices: 382248--382312 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
382238 ATCGCAACGT
*
382248 GATTTTAGTTTCGCGTTGAGATTTTCTCGTTGC
1 GATTTTAGTTTCGCGTTGAGATTATCTCGTTGC
*
382281 GATTTTCA-TTTCGCGTTGCGATTATCTCGTTG
1 GATTTT-AGTTTCGCGTTGAGATTATCTCGTTG
382313 TGATAGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (33 bp):
GATTTTAGTTTCGCGTTGAGATTATCTCGTTGC
Found at i:382337 original size:20 final size:20
Alignment explanation
Indices: 382308--382356 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
382298 GCGATTATCT
*
382308 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
382328 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
382348 TGTTGCGAT
1 CGTTGCGAT
382357 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:382362 original size:20 final size:20
Alignment explanation
Indices: 382324--382379 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
382314 GATAGTCAAA
* **
382324 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
382344 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
382364 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
382380 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:382386 original size:20 final size:20
Alignment explanation
Indices: 382343--382386 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
382333 CGATAGTCAT
* *
382343 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
382363 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
382383 TTTC
1 TTTC
382387 AGAAGCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:383453 original size:20 final size:20
Alignment explanation
Indices: 383428--383726 Score: 294
Period size: 20 Copynumber: 15.8 Consensus size: 20
383418 GCGATTTTCT
*
383428 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
383448 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
383468 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
383488 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
383508 CGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
383522 CATTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
383542 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
383562 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
383582 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
383602 CGTTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
383616 CGTTGCGATAGTCAAATT-G
1 CGTTGCGATAGTCAAATTCG
* *
383635 ACGTTGCGATAGTCATATTTG
1 -CGTTGCGATAGTCAAATTCG
383656 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
383676 AGTTACGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
383690 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
383710 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
383727 GAATGTGTAA
Statistics
Matches: 230, Mismatches: 29, Indels: 40
0.77 0.10 0.13
Matches are distributed among these distances:
14 29 0.13
15 1 0.00
16 3 0.01
17 2 0.01
18 3 0.01
19 2 0.01
20 189 0.82
21 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:383454 original size:34 final size:37
Alignment explanation
Indices: 383394--383720 Score: 131
Period size: 40 Copynumber: 8.8 Consensus size: 37
383384 ATCATATTCA
* * *
383394 CGTTGCGATAGTCTAATACACTTTGCGAT-T-TTC-T
1 CGTTGCGATAGTCAAATTCACGTTGCGATATATTCGT
*
383428 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGT
1 CGTTGCGATAGTCAAATTCACGTTGCGAT-AT---ATTCGT
*
383469 -GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCG-
1 CGTTGCGATAGTCAAATTCACGTTGCGATA-T---ATTCGT
* * *
383508 CGTTGTGAT--T---TTTGCA--TTGCGATAGTCAAATTC-A
1 CGTTGCGATAGTCAAATT-CACGTTGCGATA-T---ATTCGT
* *
383542 CGTTGCGATAGTCATATTCGCGTTGCGATAGTTAAATTCG-
1 CGTTGCGATAGTCAAATTCACGTTGCGATA--T--ATTCGT
* * * *
383582 CGTTGCGATAGTTAAATTCGCGTTGC-A-ATTTTTG-
1 CGTTGCGATAGTCAAATTCACGTTGCGATATATTCGT
* *
383616 CGTTGCGATAGTCAAATTGACGTTGCGATAGTCATAT-TT
1 CGTTGCGATAGTCAAATTCACGTTGCGATA-T-AT-TCGT
* *
383655 GCGTTGCGATAGTCAAATTCGA-GTTACGAT-T-TTTG-
1 -CGTTGCGATAGTCAAATTC-ACGTTGCGATATATTCGT
*
383690 CGTTGCGATAGTCAAATTCGCGTTGCGATAT
1 CGTTGCGATAGTCAAATTCACGTTGCGATAT
383721 TCAAATGAAT
Statistics
Matches: 236, Mismatches: 26, Indels: 61
0.73 0.08 0.19
Matches are distributed among these distances:
34 102 0.43
35 5 0.02
36 6 0.03
37 1 0.00
38 5 0.02
39 5 0.02
40 109 0.46
41 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (37 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATATATTCGT
Found at i:383561 original size:94 final size:94
Alignment explanation
Indices: 383389--383684 Score: 414
Period size: 94 Copynumber: 3.1 Consensus size: 94
383379 TCTGCATCAT
* * * * * *
383389 ATTCACGTTGCGATAGTCTAATACACTTTGCGATTTTCT-CGTTGCGATAGTCAAATTCCCGTTG
1 ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTGCGATAGTCAAATTCACGTTG
* * *
383453 CGATAATCAAATTCGTGTTGCGATAGTCAA
65 CGATAGTCATATTCGCGTTGCGATAGTCAA
* *
383483 ATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCATTGCGATAGTCAAATTCACGTTGC
1 ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAAATTCACGTTGC
*
383548 GATAGTCATATTCGCGTTGCGATAGTTAA
66 GATAGTCATATTCGCGTTGCGATAGTCAA
* * *
383577 ATTCGCGTTGCGATAGTTAAATTCGCGTTGCAATTTTTGCGTTGCGATAGTCAAATTGACGTTGC
1 ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAAATTCACGTTGC
*
383642 GATAGTCATATTTGCGTTGCGATAGTCAA
66 GATAGTCATATTCGCGTTGCGATAGTCAA
* *
383671 ATTCGAGTTACGAT
1 ATTCGCGTTGCGAT
383685 TTTTGCGTTG
Statistics
Matches: 180, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
93 1 0.01
94 179 0.99
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (94 bp):
ATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAGTCAAATTCACGTTGC
GATAGTCATATTCGCGTTGCGATAGTCAA
Found at i:383620 original size:74 final size:74
Alignment explanation
Indices: 383469--383726 Score: 306
Period size: 74 Copynumber: 3.5 Consensus size: 74
383459 TCAAATTCGT
* ** ** *
383469 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCATT-GCGATAG
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCG-TTG
* **
383533 TCAA-ATTCAC
65 -CAATTTTTGC
* *
383543 GTTGCGATAGTCATATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATAGTTAAATTCGCGTTGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGC
383608 AATTTTTGC
66 AATTTTTGC
* * * * *
383617 GTTGCGATAGTCAAATT-GACGTTGCGATAGTCATATTTGCGTTGCGATAGTCAAATTCGAGTTA
1 GTTGCGATAGTCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTG
*
383681 CGATTTTTGC
65 CAATTTTTGC
*
383691 GTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
383727 GAATGTGTAA
Statistics
Matches: 159, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
73 4 0.03
74 151 0.95
75 4 0.03
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (74 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGC
AATTTTTGC
Found at i:386263 original size:24 final size:24
Alignment explanation
Indices: 386212--386263 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
386202 ATCTGAGTAT
** *
386212 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
386236 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
386260 TGAC
1 TGAC
386264 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:387812 original size:60 final size:60
Alignment explanation
Indices: 387757--387871 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
387747 CAGTCCATTG
* * *
387757 ACTATAGAATGATGTTTTGTTGAGCCTCTCGATTATTAAAAGTTACAAAATAGTCCTTCA
1 ACTATAGAATGATATTTTGTTGAGCCTCCCGACTATTAAAAGTTACAAAATAGTCCTTCA
* * *
387817 ACTATAGGATGTTATTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATAGTC
1 ACTATAGAATGATATTTTGTTGAGCCTCCCGACTATTAAAAGTTACAAAATAGTC
387872 ACCCAACTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (60 bp):
ACTATAGAATGATATTTTGTTGAGCCTCCCGACTATTAAAAGTTACAAAATAGTCCTTCA
Found at i:388470 original size:25 final size:25
Alignment explanation
Indices: 388423--388473 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
388413 TTTAACACGT
* *
388423 TAGTAATTCAATACGTAAGGAAATG
1 TAGTAATTCAATACATAAAGAAATG
*
388448 TAGTAATTCAATATATAAAGAAATG
1 TAGTAATTCAATACATAAAGAAATG
388473 T
1 T
388474 CACATCTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (25 bp):
TAGTAATTCAATACATAAAGAAATG
Found at i:389260 original size:5 final size:5
Alignment explanation
Indices: 389252--389276 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
389242 ATTATATTAA
389252 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
389277 AATCTACGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:390856 original size:174 final size:174
Alignment explanation
Indices: 390637--392687 Score: 3403
Period size: 174 Copynumber: 11.8 Consensus size: 174
390627 CTAATTTTTG
* * * *
390637 ATCTTTTTACAAGAAATAAAATAAAAGAATTATAGACCAATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* *
390702 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGACAAGAGGAACT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
** * *
390767 TGGTTTATAACAGATTCTTTTATTGCATTGTCCATTTGCTGGCC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
* * *
390811 ATCTTTTTATAAGAGATAAAATAGAATAATTATAGACCGATCAAAATTTAAATTTGTAATAAAAA
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* *
390876 ATTTATTCATTTTTACATGTTACTGCAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* * * * *
390941 TGGTTTATAACTGATTCTTTTCCTACTTTTTCCATTTTCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
390985 ATCTTTTTATAAGAGAT-AAA-A-AAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
391047 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* *
391112 TGATTTATATCAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
* * * *
391156 ATCTTTTTATAGGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTATAATAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* *
391221 ATTTATCCATTTTTACATGTTCCTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* * *
391286 TGATTTATATCAGATTCTTTTCCTGCATTGTCCATTTTCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
*
391330 ATCTTTTTATAAGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
*
391395 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
*
391460 TGGTTTATAACAGATTCTTTTCTTGCATTGTCCATTTCCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
*
391504 ATCTTTTTATAAGAGATAAAATAGAACAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* *
391569 ATTTATTCAATTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* * *
391634 TGGTTTATAACTGATTCTTTTCCTGCTTTGTCCATTTTCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
*
391678 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAGTTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
*
391743 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTTTTTGGATAGTAGAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* *
391808 TGGTTTATAACAAATTCTTTTCCCGCATTGTCCATTTCCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
* *
391852 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACTGATCAAAATTTAAATTTGTAAGAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* *
391917 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGGTAGTAAAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
*
391982 TGGTTTATAACAGATTCTCTTCCTGCATTGTCCATTTCCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
*
392026 ATCTTTTTATAAGAGATAAAATA-AA-AATTATAGACTGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
392089 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* *
392154 TGATTTATATCAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
* *
392198 ATCTTTTTATAGGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
*
392263 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* * *
392328 TGGTTTATAACTGATTCTTTTCTTGCTTTGTCCATTTCCTGACC
131 TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
* *
392372 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACAGATCAAAGTTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* * *
392437 ATTTATTCATTTTTACATGCTACTGAAACTTACCATCTTTCTTTGGATAGTATAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
*
392502 TGGTTTATAGCA-AGTTCTTTTCCTGCATTGTCCATTTCCTGACC
131 TGGTTTATAACAGA-TTCTTTTCCTGCATTGTCCATTTCCTGACC
* *
392546 ATCTTTTTATAAGAGAGAAAATAGAAGAATTATAGACCGATCGAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
** * * *
392611 ATTTATTCATTTTTAGTTGTTACTAAAACTTACCAACATTCTTTGGATAATAGAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
*
392676 TGATTTATAACA
131 TGGTTTATAACA
392688 TATTGTTGTT
Statistics
Matches: 1759, Mismatches: 112, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
171 154 0.09
172 167 0.09
173 9 0.01
174 1429 0.81
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (174 bp):
ATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
TGGTTTATAACAGATTCTTTTCCTGCATTGTCCATTTCCTGACC
Found at i:392378 original size:694 final size:696
Alignment explanation
Indices: 390637--392687 Score: 3545
Period size: 694 Copynumber: 3.0 Consensus size: 696
390627 CTAATTTTTG
* * *
390637 ATCTTTTTACAAGAAATAAAATAAAAGAATTATAGACCAATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
* *
390702 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGACAAGAGGAACT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* * *
390767 TGGTTTATAACAGATTCTTTTATTGCATTGTCCATTTGCTGGCCATCTTTTTATAAGAGATAAAA
131 TGGTTTATAACAGATTCTTTTCTTGCATTGTCCATTTCCTGACCATCTTTTTATAAGAGATAAAA
* * *
390832 TAGAATAATTATAGACCGATCAAAATTTAAATTTGTAATAAAAAATTTATTCATTTTTACATGTT
196 TAGAACAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTT
*
390897 ACTGCAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
261 ACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
* *
390962 CCTACTTTTTCCATTTTCTGACCATCTTTTTATAAGAGAT-AAA-A-AAGAATTATAGACCGATC
326 CCTGCTTTGTCCATTTTCTGACCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATC
*
391024 AAAATTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCT
391 AAAGTTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCT
* * *
391089 TTGGATAGTAGAAAAGAGGAATTTGATTTATATCAGATTCTTTTCCTGCATTGTCCATTTCCTGA
456 TTGGATAGTAGAAAAGAGGAATTTGGTTTATAACAAATTCTTTTCCTGCATTGTCCATTTCCTGA
* * * *
391154 CCATCTTTTTATAGGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTATAATAAA
521 CCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAA
* *
391219 AGATTTATCCATTTTTACATGTTCCTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAA
586 AGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAA
* * *
391284 TTTGATTTATATCAGATTCTTTTCCTGCATTGTCCATTTTCTGACC
651 TTTGATTTATAACAGATTCTCTTCCTGCATTGTCCATTTCCTGACC
391330 ATCTTTTTATAAGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
*
391395 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
391460 TGGTTTATAACAGATTCTTTTCTTGCATTGTCCATTTCCTGACCATCTTTTTATAAGAGATAAAA
131 TGGTTTATAACAGATTCTTTTCTTGCATTGTCCATTTCCTGACCATCTTTTTATAAGAGATAAAA
*
391525 TAGAACAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCAATTTTACATGTT
196 TAGAACAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTT
391590 ACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
261 ACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
391655 CCTGCTTTGTCCATTTTCTGACCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATC
326 CCTGCTTTGTCCATTTTCTGACCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATC
*
391720 AAAGTTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTTT
391 AAAGTTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCT
*
391785 TTGGATAGTAGAAAAGAGGAATTTGGTTTATAACAAATTCTTTTCCCGCATTGTCCATTTCCTGA
456 TTGGATAGTAGAAAAGAGGAATTTGGTTTATAACAAATTCTTTTCCTGCATTGTCCATTTCCTGA
* *
391850 CCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACTGATCAAAATTTAAATTTGTAAGAAA
521 CCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAA
* *
391915 AGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGGTAGTAAAAAAGAGGAA
586 AGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAA
*
391980 TTTGGTTTATAACAGATTCTCTTCCTGCATTGTCCATTTCCTGACC
651 TTTGATTTATAACAGATTCTCTTCCTGCATTGTCCATTTCCTGACC
*
392026 ATCTTTTTATAAGAGATAAAAT-AAA-AATTATAGACTGATCAAAATTTAAATTTGTAACAAAAG
1 ATCTTTTTATAAGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
392089 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
66 ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
* * * *
392154 TGATTTATATCAGATTCTTTTCCTGCATTGTCCATTTCCTGACCATCTTTTTATAGGAGATAAAA
131 TGGTTTATAACAGATTCTTTTCTTGCATTGTCCATTTCCTGACCATCTTTTTATAAGAGATAAAA
* *
392219 TAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTT
196 TAGAACAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTT
392284 ACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
261 ACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
* * *
392349 CTTGCTTTGTCCATTTCCTGACCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACAGATC
326 CCTGCTTTGTCCATTTTCTGACCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATC
* *
392414 AAAGTTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGCTACTGAAACTTACCATCTTTCT
391 AAAGTTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCT
* * *
392479 TTGGATAGTATAAAAGAGGAATTTGGTTTATAGCAAGTTCTTTTCCTGCATTGTCCATTTCCTGA
456 TTGGATAGTAGAAAAGAGGAATTTGGTTTATAACAAATTCTTTTCCTGCATTGTCCATTTCCTGA
* *
392544 CCATCTTTTTATAAGAGAGAAAATAGAAGAATTATAGACCGATCGAAATTTAAATTTGTAACAAA
521 CCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAA
** * * *
392609 AGATTTATTCATTTTTAGTTGTTACTAAAACTTACCAACATTCTTTGGATAATAGAAAAGAGGAA
586 AGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAA
392674 TTTGATTTATAACA
651 TTTGATTTATAACA
392688 TATTGTTGTT
Statistics
Matches: 1289, Mismatches: 66, Indels: 5
0.95 0.05 0.00
Matches are distributed among these distances:
693 349 0.27
694 609 0.47
695 4 0.00
696 327 0.25
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (696 bp):
ATCTTTTTATAAGAGATAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAG
ATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAATT
TGGTTTATAACAGATTCTTTTCTTGCATTGTCCATTTCCTGACCATCTTTTTATAAGAGATAAAA
TAGAACAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTT
ACTGAAACTTACCAACTTTCTTTGGATAGTACAAAAGAGGAATTTGGTTTATAACTGATTCTTTT
CCTGCTTTGTCCATTTTCTGACCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATC
AAAGTTTAAATTTGTAACAAAAGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCT
TTGGATAGTAGAAAAGAGGAATTTGGTTTATAACAAATTCTTTTCCTGCATTGTCCATTTCCTGA
CCATCTTTTTATAAGAGATAAAATAGAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAA
AGATTTATTCATTTTTACATGTTACTGAAACTTACCAACTTTCTTTGGATAGTAGAAAAGAGGAA
TTTGATTTATAACAGATTCTCTTCCTGCATTGTCCATTTCCTGACC
Found at i:393985 original size:26 final size:26
Alignment explanation
Indices: 393946--394004 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
393936 TGAATATTTC
393946 TATGATG-TTTATAATTTTAATTGCT
1 TATGATGATTTATAATTTTAATTGCT
393971 TATGATGATTTATAATTTTAATTGCT
1 TATGATGATTTATAATTTTAATTGCT
393997 TATGATGA
1 TATGATGA
394005 CTCCTCTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 7 0.21
26 26 0.79
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (26 bp):
TATGATGATTTATAATTTTAATTGCT
Found at i:398187 original size:20 final size:20
Alignment explanation
Indices: 398138--398178 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
398128 AAGCCTTAAT
398138 GGATCACATCCCTCCTTCCG
1 GGATCACATCCCTCCTTCCG
398158 GGATCACATCCCTCCTTCCG
1 GGATCACATCCCTCCTTCCG
398178 G
1 G
398179 TATCTCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24
Consensus pattern (20 bp):
GGATCACATCCCTCCTTCCG
Found at i:401677 original size:19 final size:20
Alignment explanation
Indices: 401639--401680 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
401629 TTCTTCTCTA
401639 AGACCCAAAAATCTTGGTTT
1 AGACCCAAAAATCTTGGTTT
*
401659 AGACCCAAAAATCTTGTTTT
1 AGACCCAAAAATCTTGGTTT
401679 AG
1 AG
401681 CACATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
AGACCCAAAAATCTTGGTTT
Found at i:407134 original size:20 final size:21
Alignment explanation
Indices: 407102--407152 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
407092 ACTTGATTAG
*
407102 GGAGTATATATACT-AAACAAA
1 GGAGTATAAATACTCAAAC-AA
407123 GG-GTATAAATACTCAAACAA
1 GGAGTATAAATACTCAAACAA
407143 GGAGTATAAA
1 GGAGTATAAA
407153 AACCATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (21 bp):
GGAGTATAAATACTCAAACAA
Found at i:417578 original size:12 final size:12
Alignment explanation
Indices: 417561--417585 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
417551 CGCATTAATT
417561 GTTCAAGCTCAG
1 GTTCAAGCTCAG
417573 GTTCAAGCTCAG
1 GTTCAAGCTCAG
417585 G
1 G
417586 ATCGTTGTCA
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:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (12 bp):
GTTCAAGCTCAG
Found at i:423874 original size:20 final size:20
Alignment explanation
Indices: 423823--423877 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
423813 GGAGCGTGGG
*
423823 GGGGAATCGGTACCCCTCAT
1 GGGGAATCGGTTCCCCTCAT
423843 GGGGAATCGGTTCCCCTCAT
1 GGGGAATCGGTTCCCCTCAT
423863 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
423878 TAAGTGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (20 bp):
GGGGAATCGGTTCCCCTCAT
Found at i:426607 original size:18 final size:18
Alignment explanation
Indices: 426586--426622 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
426576 ATCTTTATTT
*
426586 ATTTAATCTCTTTTTACC
1 ATTTAATCTCATTTTACC
*
426604 ATTTAATTTCATTTTACC
1 ATTTAATCTCATTTTACC
426622 A
1 A
426623 AAACCCCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATCTCATTTTACC
Found at i:434360 original size:18 final size:18
Alignment explanation
Indices: 434339--434375 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
434329 ATCATTATTT
*
434339 ATTTAATCTCTTTTTACC
1 ATTTAATCTCATTTTACC
*
434357 ATTTAATTTCATTTTACC
1 ATTTAATCTCATTTTACC
434375 A
1 A
434376 AAACCCCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATCTCATTTTACC
Found at i:436675 original size:35 final size:35
Alignment explanation
Indices: 436636--436702 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
436626 ATTTTTTTCA
*
436636 CTTTTTTTCTTT-TTGGTTATTCCTAAACTAAAGAC
1 CTTTTTTTCTTTACTGGTTATTCC-AAACTAAAGAC
* *
436671 CTTTTTTTGTTTACTGGTTATTCCAAATTAAA
1 CTTTTTTTCTTTACTGGTTATTCCAAACTAAA
436703 TGAAAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 18 0.64
36 10 0.36
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (35 bp):
CTTTTTTTCTTTACTGGTTATTCCAAACTAAAGAC
Found at i:437158 original size:24 final size:23
Alignment explanation
Indices: 437087--437146 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
437077 TAGGTTAGGG
437087 TAGGCTCCGGGTCGAGTTTAGTT
1 TAGGCTCCGGGTCGAGTTTAGTT
*
437110 T-GTGTTCCGGGTCGAGTTCTAGTT
1 TAG-GCTCCGGGTCGAGTT-TAGTT
437134 TAGGCTCCGGGTC
1 TAGGCTCCGGGTC
437147 TGGGTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 15 0.47
24 15 0.47
25 1 0.03
ACGTcount: A:0.10, C:0.20, G:0.35, T:0.35
Consensus pattern (23 bp):
TAGGCTCCGGGTCGAGTTTAGTT
Found at i:437223 original size:13 final size:12
Alignment explanation
Indices: 437181--437214 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
437171 TTAGGACCTG
437181 TTTGGGTTTAAA
1 TTTGGGTTTAAA
437193 TTTGGGGTTTAAA
1 TTT-GGGTTTAAA
437206 TTTGGGTTT
1 TTTGGGTTT
437215 TATGTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (12 bp):
TTTGGGTTTAAA
Found at i:438172 original size:20 final size:20
Alignment explanation
Indices: 438143--438186 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
438133 TCAAATTCAA
* *
438143 GGGTCGGGTTGACTCGGTTT
1 GGGTCAGGTTGACTCAGTTT
438163 GGGTCAGGTTGACTCAGTTT
1 GGGTCAGGTTGACTCAGTTT
438183 GGGT
1 GGGT
438187 TAATAGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.43, T:0.34
Consensus pattern (20 bp):
GGGTCAGGTTGACTCAGTTT
Found at i:439525 original size:25 final size:27
Alignment explanation
Indices: 439470--439522 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
439460 CATTAAATGC
*
439470 AATATTATCTAAGAAAATAATAGGTTGT
1 AATATTATCTAAGAAAATAAGAGG-TGT
439498 AATATTATCTAAGAAAATAAGAGGT
1 AATATTATCTAAGAAAATAAGAGGT
439523 AATGAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (27 bp):
AATATTATCTAAGAAAATAAGAGGTGT
Found at i:439532 original size:28 final size:28
Alignment explanation
Indices: 439473--439532 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
439463 TAAATGCAAT
* ** *
439473 ATTATCTAAGAAAATAATAGGTTGTAAT
1 ATTATCTAAGAAAATAAGAGGTAATAAG
*
439501 ATTATCTAAGAAAATAAGAGGTAATGAG
1 ATTATCTAAGAAAATAAGAGGTAATAAG
439529 ATTA
1 ATTA
439533 CTATTGTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (28 bp):
ATTATCTAAGAAAATAAGAGGTAATAAG
Found at i:442438 original size:35 final size:35
Alignment explanation
Indices: 442360--442471 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
442350 TCTAAAACTT
* * * *
442360 AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATTG
1 AAATTGAATTATTTTGGAATTTAGGGTTTAGAA-TG
442396 -AATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
* * *
442430 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
442465 AAATTGA
1 AAATTGA
442472 GGACTGTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 2 0.03
35 66 0.97
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
Found at i:444479 original size:20 final size:21
Alignment explanation
Indices: 444448--444495 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
444438 TCATTTAAGG
*
444448 GAGTATAGATACTC-AACAAA
1 GAGTATAAATACTCAAACAAA
*
444468 GGGTATAAATACTCAAACAAA
1 GAGTATAAATACTCAAACAAA
444489 GAGTATA
1 GAGTATA
444496 GAAACCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (21 bp):
GAGTATAAATACTCAAACAAA
Found at i:445352 original size:23 final size:23
Alignment explanation
Indices: 445262--445350 Score: 115
Period size: 23 Copynumber: 3.9 Consensus size: 23
445252 TAACATTCAC
*
445262 GAACATATTCGTCTAATGTTAGT
1 GAACATGTTCGTCTAATGTTAGT
*
445285 GAACATATTCGTCTAATGTTAGT
1 GAACATGTTCGTCTAATGTTAGT
* * *
445308 GAACATGTTCGTGTAATATTTGT
1 GAACATGTTCGTCTAATGTTAGT
* *
445331 GAACGTGTTCGTTTAATGTT
1 GAACATGTTCGTCTAATGTT
445351 TGACAACCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (23 bp):
GAACATGTTCGTCTAATGTTAGT
Found at i:448321 original size:3 final size:3
Alignment explanation
Indices: 448315--448351 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
448305 TATGTAACAT
448315 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
448352 TTTATAATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:448684 original size:55 final size:55
Alignment explanation
Indices: 448589--449359 Score: 604
Period size: 55 Copynumber: 14.3 Consensus size: 55
448579 TCGCTCCTGA
* * *** *
448589 AGTATGGAACTCGAACAGTCTTTGCCAAT-GGGTTCGTTCCCTCTTTCTTTCAGGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTC-TTCAGGG
* * * * * * * *
448644 AGTATAGAACTCAAAC-ATCTTCAACACTCGTGTTTGTTCCCTATTCCTTCAGAG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* ** ** * * * *
448698 AGTATA-AGACTTGAACAATCTTCAACAATCATG-TCTTTTCCCTATTCCTTTAGAG
1 AGTATAGA-ACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCTTTCTTCAGGG
* ** * * *
448753 AGTATA-AGACTCGAACAATCTTCAACTATC-ATTTCTGCTCCCTATTCCTTCAGAG
1 AGTATAGA-ACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCTTTCTTCAGGG
** * *
448808 AGTAT-GAGACTCGAACAATCTTCTTC-TTACGGGTTCGCTCCCTCTTTCTTCAGAG
1 AGTATAGA-ACTCGAACAATCTTCAACAAT-CGGGTTCGCTCCCTCTTTCTTCAGGG
* *** * *
448863 AGTATAGAACTCGAA-TATCTTTTTCAAACGGGTTTGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTC-AGGG
* * *
448917 AGTATAAAACTCGAACAATCTTC-A-AA-CGGGTTCGCT--CTCTCTCTTTAGGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* ** * *
448967 AGTATGGAACTCGAAC-ATCTTCTTC-TTACGAGTTCGCTCCCTCTTTC-TCTAGGG
1 AGTATAGAACTCGAACAATCTTCAACAAT-CGGGTTCGCTCCCTCTTTCTTC-AGGG
* *
449021 AGTATAGAACTCGGACATCTTCTTCAA-AA-CGGGTTCGCTCCCTCTTTCTTCAGGG
1 AGTATAGAACTCGAACA--ATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* *
449076 AGTATAGAACTCGAA-AATCTTC-A-AA-CGGGTTCGCTCCTTC-TTCTTCAAGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* *
449126 AGTATAAAACTCGAACAATCTTCTGAA-AAT-GGGTTCACTCCCTCTTTCTTCAGGG
1 AGTATAGAACTCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* * *
449181 AGTATAGAACTCGAACAATCTTCTAA-AAACGGGTTCACTCCCTTTTTCTTCAGGG
1 AGTATAGAACTCGAACAATCTTC-AACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
449236 AGTATAGAACTCGAACAATCTTCTGAA-AAT-GGGTTCGCTCCCTCTTTCTTCAGGG
1 AGTATAGAACTCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* * * *
449291 AGTATAGAACTCAAAAAATCTTC-A-AA-CGGGTTTGCTCCCTC--TCTTTAGGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
449341 AGTATAGAACTCGAACAAT
1 AGTATAGAACTCGAACAAT
449360 AATCTTCCTA
Statistics
Matches: 600, Mismatches: 82, Indels: 73
0.79 0.11 0.10
Matches are distributed among these distances:
49 6 0.01
50 72 0.12
51 25 0.04
52 39 0.06
53 6 0.01
54 114 0.19
55 322 0.54
56 11 0.02
57 5 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (55 bp):
AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
Found at i:449231 original size:160 final size:158
Alignment explanation
Indices: 448800--449359 Score: 638
Period size: 160 Copynumber: 3.5 Consensus size: 158
448790 CTCCCTATTC
* ** *
448800 CTTCAGAGAGTAT-GAGACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGAGA
1 CTTCAGGGAGTATAGA-ACTCGAACAATCTTC-T-AAACGGGTTCGCTCCCTCTTTCTTCAGGGA
* * ** * *
448864 GTATAGAACTCGAA-TATCTTTTTCAAACGGGTTTGCTCCCTCTTTC-TCTAGGGAGTATAAAAC
63 GTATAGAACTCGAACAATCTTCTAAAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAAC
448927 TCGAACAATCTTCAAACGGGTTCGCT-CTCTCT
127 TCGAACAATCTTCAAACGGGTTCGCTCCTCT-T
* * ** *
448959 CTTTAGGGAGTATGGAACTCGAAC-ATCTTCTTCTTACGAGTTCGCTCCCTCTTTC-TCTAGGGA
1 CTTCAGGGAGTATAGAACTCGAACAATCTTC-T-AAACGGGTTCGCTCCCTCTTTCTTC-AGGGA
* *
449022 GTATAGAACTCGGAC-ATCTTCTTCAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAAC
63 GTATAGAACTCGAACAATCTTC-TAAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAAC
449086 TCGAA-AATCTTCAAACGGGTTCGCTCCTTCTT
127 TCGAACAATCTTCAAACGGGTTCGCTCC-TCTT
* * * *
449118 CTTCAAGGAGTATAAAACTCGAACAATCTTCTGAAAATGGGTTCACTCCCTCTTTCTTCAGGGAG
1 CTTCAGGGAGTATAGAACTCGAACAATCTTCT--AAACGGGTTCGCTCCCTCTTTCTTCAGGGAG
* *
449183 TATAGAACTCGAACAATCTTCTAAAAACGGGTTCACTCCCTTTTTCTTCAGGGAGTATAGAACTC
64 TATAGAACTCGAACAATCTTCTAAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC
*
449248 GAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTT
129 GAACAATCTTC---AAACGGGTTCGCT-CCTC-TT
* * * *
449283 CTTCAGGGAGTATAGAACTCAAAAAATCTTC-AAACGGGTTTGCTCCCTC--TCTTTAGGGAGTA
1 CTTCAGGGAGTATAGAACTCGAACAATCTTCTAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA
449345 TAGAACTCGAACAAT
66 TAGAACTCGAACAAT
449360 AATCTTCCTA
Statistics
Matches: 351, Mismatches: 33, Indels: 33
0.84 0.08 0.08
Matches are distributed among these distances:
157 2 0.01
158 72 0.21
159 82 0.23
160 120 0.34
161 15 0.04
162 15 0.04
164 14 0.04
165 31 0.09
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (158 bp):
CTTCAGGGAGTATAGAACTCGAACAATCTTCTAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA
TAGAACTCGAACAATCTTCTAAAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA
ACAATCTTCAAACGGGTTCGCTCCTCTT
Found at i:449282 original size:215 final size:209
Alignment explanation
Indices: 448790--449359 Score: 702
Period size: 215 Copynumber: 2.7 Consensus size: 209
448780 ATCATTTCTG
* * **
448790 CTCCCTATTCCTTCAGAGAGTAT-GAGACTCGAACAATCTTCTTC-TTACGGGTTCGCTCCCTCT
1 CTCCCTATTTCTTCAGGGAGTATAGA-ACTCGAACAATCTTC-TCAAAACGGGTTCGCTCCCTCT
* *
448853 TTCTTCAGAGAGTATAGAACTCGAATATCTTTTTCAAACGGGTTTGCTCCCTCTT-TCTCTAGGG
64 TTCTTCAGGGAGTATAGAACTCGAAAATC---TTCAAACGGGTTTGCTCCCTCTTCT-TC-AGGG
* * *
448917 AGTATAAAACTCGAACAATCTTCAAACGGGTTCGCTCTCTCTCTTTAGGGAGTATGGAACTCGAA
124 AGTATAAAACTCGAACAATCTTCAAACGGGTTCACTCTCTCTCTTCAGGGAGTATAGAACTCGAA
**** *
448982 CATCTTCTTCTTACGAGTTCG
189 CATCTTCTAAAAACGAGTTCA
* *
449003 CTCCCTCTTTC-TCTAGGGAGTATAGAACTCGGAC-ATCTTCTTCAAAACGGGTTCGCTCCCTCT
1 CTCCCTATTTCTTC-AGGGAGTATAGAACTCGAACAATCTTC-TCAAAACGGGTTCGCTCCCTCT
* * *
449066 TTCTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTCGCTCCTTCTTCTTCAAGGAGTAT
64 TTCTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTTGCTCCCTCTTCTTCAGGGAGTAT
* *
449131 AAAACTCGAACAATCTTCTGAAAATGGGTTCACTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA
129 AAAACTCGAACAATCTTC---AAACGGGTTCACT--CTCTCTCTTCAGGGAGTATAGAACTCGAA
*
449196 CAATCTTCTAAAAACGGGTTCA
189 C-ATCTTCTAAAAACGAGTTCA
* * *
449218 CTCCCTTTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTT
1 CTCCCTATTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTCAAAACGGGTTCGCTCCCTCTTT
* *
449283 CTTCAGGGAGTATAGAACTCAAAAAATCTTCAAACGGGTTTGCTCCCTC-TCTTTAGGGAGTATA
66 CTTCAGGGAGTATAGAACTC-GAAAATCTTCAAACGGGTTTGCTCCCTCTTCTTCAGGGAGTATA
*
449347 GAACTCGAACAAT
130 AAACTCGAACAAT
449360 AATCTTCCTA
Statistics
Matches: 312, Mismatches: 32, Indels: 24
0.85 0.09 0.07
Matches are distributed among these distances:
209 26 0.08
210 23 0.07
211 1 0.00
212 22 0.07
213 68 0.22
214 29 0.09
215 110 0.35
216 33 0.11
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (209 bp):
CTCCCTATTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTCAAAACGGGTTCGCTCCCTCTTT
CTTCAGGGAGTATAGAACTCGAAAATCTTCAAACGGGTTTGCTCCCTCTTCTTCAGGGAGTATAA
AACTCGAACAATCTTCAAACGGGTTCACTCTCTCTCTTCAGGGAGTATAGAACTCGAACATCTTC
TAAAAACGAGTTCA
Found at i:449512 original size:153 final size:156
Alignment explanation
Indices: 449345--449672 Score: 565
Period size: 153 Copynumber: 2.1 Consensus size: 156
449335 TTAGGGAGTA
449345 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAA-TTTCTTCAGGGACTAGAACTCGAACA
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGACTAGAACTCGAACA
* ** *
449409 ATAATCTTCCTACGGGTCTGCCCAATTTTCTTTAGGGACTAGAACTCGAA-AATAATCTTCCTAC
66 ATAATCTTCCTACGAGAATGCCCAATTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTAC
449473 GGG-CTGCCCAATTTTCTTCAAGGAC
131 GGGTCTGCCCAATTTTCTTCAAGGAC
* *
449498 TAGAACTCGAACAAT-ATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGACTAGAACTCGAACA
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGACTAGAACTCGAACA
449562 ATAATCTTCCTACGAGAATGCCCAATTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTAC
66 ATAATCTTCCTACGAGAATGCCCAATTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTAC
*
449627 GGGTCTGCCCAATTTTCTTCAGGGAC
131 GGGTCTGCCCAATTTTCTTCAAGGAC
449653 TAGAACTCGAACAATAATCT
1 TAGAACTCGAACAATAATCT
449673 CCAACGATCG
Statistics
Matches: 164, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
152 20 0.12
153 87 0.53
154 17 0.10
155 36 0.22
156 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (156 bp):
TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGACTAGAACTCGAACA
ATAATCTTCCTACGAGAATGCCCAATTTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTAC
GGGTCTGCCCAATTTTCTTCAAGGAC
Found at i:449591 original size:52 final size:52
Alignment explanation
Indices: 449345--449672 Score: 565
Period size: 52 Copynumber: 6.4 Consensus size: 52
449335 TTAGGGAGTA
* *
449345 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAA-TTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
*
449396 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTTAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
*
449448 TAGAACTCGAA-AATAATCTTCCTACGGG-CTGCCCAATTTTCTTCAAGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
449498 TAGAACTCGAACAAT-ATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
* **
449549 TAGAACTCGAACAATAATCTTCCTACGAGAATGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
449601 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
449653 TAGAACTCGAACAATAATCT
1 TAGAACTCGAACAATAATCT
449673 CCAACGATCG
Statistics
Matches: 261, Mismatches: 12, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
50 44 0.17
51 92 0.35
52 125 0.48
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (52 bp):
TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
Found at i:449621 original size:28 final size:28
Alignment explanation
Indices: 449538--449622 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
449528 TGCCCAATTT
449538 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACTCGAACAATAA
** * ** **
449566 TCTTC--CTACGAGAA-T-GCCCAATTT
1 TCTTCAGGGACTAGAACTCGAACAATAA
449590 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACTCGAACAATAA
449618 TCTTC
1 TCTTC
449623 CTACGGGTCT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 12 0.31
27 1 0.03
28 15 0.38
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (28 bp):
TCTTCAGGGACTAGAACTCGAACAATAA
Found at i:449727 original size:55 final size:55
Alignment explanation
Indices: 449668--450055 Score: 608
Period size: 55 Copynumber: 7.1 Consensus size: 55
449658 CTCGAACAAT
*
449668 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
449723 AATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTAT-AGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
449777 AATCTTCAACGATCGCGTCTGCCCCCTA-TTCTTTAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
449829 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
449884 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
449938 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
449993 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
450049 AATCTTC
1 AATCTTC
450056 TTTTGCATCA
Statistics
Matches: 302, Mismatches: 23, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
52 28 0.09
53 60 0.20
54 64 0.21
55 83 0.27
56 67 0.22
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:449796 original size:109 final size:109
Alignment explanation
Indices: 449665--450055 Score: 655
Period size: 109 Copynumber: 3.6 Consensus size: 109
449655 GAACTCGAAC
*
449665 AATAATCTCCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGA-TC-AACAATCTT
* *
449729 CAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTAT-AGACTCG
64 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
* * *
449774 AACAATCTTCAACGATCGCGTCTG-CCCCCTA-TTCTTTAGAGAGTATAAGATCCACAATCTTCA
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGATCAACAATCTTCA
449837 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
66 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
*
449881 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATCTTCA
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGATCAACAATCTTCA
449946 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
66 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
449990 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGA-TC-AACAATCTT
450055 C
64 C
450056 TTTTGCATCA
Statistics
Matches: 268, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
106 44 0.16
107 32 0.12
108 25 0.09
109 156 0.58
110 2 0.01
111 9 0.03
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (109 bp):
AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGATCAACAATCTTCA
TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
Found at i:449851 original size:161 final size:164
Alignment explanation
Indices: 449668--450055 Score: 597
Period size: 161 Copynumber: 2.4 Consensus size: 164
449658 CTCGAACAAT
* *
449668 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
449733 AATCGCGTCTG-CCCCCTATTTATTCAGAGAGTAT-AGACTCGAACAATCTTCAACGATCGCGTC
66 AATCGCGTCTGCCCCCCTATTTATTCAGAGAGTATAAGA-TC-AACAATCTTCAACAATCGCGTC
* *
449796 TGCCCCCTA-TTCTTTAGAGAGTATAAGA-TC-CAC
129 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
449829 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * * *
449894 GATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATCTTCATCAATCGCGTCTG
66 AATCGCGTCTGCCCCCCTATTTATTCAGAGAGTATAAGATCAACAATCTTCAACAATCGCGTCTG
*
449959 CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
131 CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
449993 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACAATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
450056 TTTTGCATCA
Statistics
Matches: 206, Mismatches: 15, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
161 99 0.48
162 42 0.20
163 5 0.02
164 20 0.10
165 40 0.19
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (164 bp):
AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTCTGCCCCCCTATTTATTCAGAGAGTATAAGATCAACAATCTTCAACAATCGCGTCTG
CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:451363 original size:14 final size:14
Alignment explanation
Indices: 451328--451363 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
451318 TTATTTTTTG
451328 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
* *
451342 CTTGTTTTCTTCTT
1 TTTTTTTTCTTCTT
451356 TTTTTTTT
1 TTTTTTTT
451364 TTTTTCCATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Done.