Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006936.1 Hibiscus syriacus cultivar Beakdansim tig00017808_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: 2176229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:234319 original size:3 final size:3
Alignment explanation
Indices: 234264--234290 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
234254 AAATATAAAT
234264 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
234291 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:236160 original size:111 final size:111
Alignment explanation
Indices: 235963--236186 Score: 358
Period size: 111 Copynumber: 2.0 Consensus size: 111
235953 TTAAAAGTAT
*
235963 ATTCCAAATAAAACTTTCGAAGGAATGAATAGATAAAATGATAGTGTAACATGAGCAATAATTAA
1 ATTCCAAATAAAACTTTCGAAGGAATGAATAGATAAAATGATAATGTAACATGAGCAATAATTAA
* * *
236028 TTATACATTGACAACGGATTTGATATTTCAATCAATCTCACGTAGC
66 TGACACATTGACAACGAATTTGATATTTCAATCAATCTCACGTAGC
* *
236074 ATTCCAAATAAAACTTTTGAATGAATGAATAGATAAAATGATAATGTAACATGAGCAATAATTAA
1 ATTCCAAATAAAACTTTCGAAGGAATGAATAGATAAAATGATAATGTAACATGAGCAATAATTAA
** * *
236139 TGACACATTGACAATTAATTTGTTATTTCAATCATTCTCACGTAGC
66 TGACACATTGACAACGAATTTGATATTTCAATCAATCTCACGTAGC
236185 AT
1 AT
236187 AAGGAAGAGA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (111 bp):
ATTCCAAATAAAACTTTCGAAGGAATGAATAGATAAAATGATAATGTAACATGAGCAATAATTAA
TGACACATTGACAACGAATTTGATATTTCAATCAATCTCACGTAGC
Found at i:240711 original size:14 final size:14
Alignment explanation
Indices: 240692--240723 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
240682 GTTGAATTCC
240692 AAATATTTAAATAA
1 AAATATTTAAATAA
*
240706 AAATATTTATATAA
1 AAATATTTAAATAA
240720 AAAT
1 AAAT
240724 TCATAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATTTAAATAA
Found at i:242386 original size:36 final size:35
Alignment explanation
Indices: 242318--242387 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
242308 CCTTAGGTCC
* ** *
242318 ATAAGGAATTACCAGTTGATCGGTGTTGAACCTAT
1 ATAAGGAATTACCAGTTGATCAGAATTAAACCTAT
242353 ATAAGGAATTACCAGCTTGATCAGAATTAAACCTA
1 ATAAGGAATTACCAG-TTGATCAGAATTAAACCTA
242388 CAGAGACTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTGATCAGAATTAAACCTAT
Found at i:249000 original size:16 final size:17
Alignment explanation
Indices: 248976--249010 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
248966 TGTTGAGCAA
248976 TATGAGAGGTT-TTGGT
1 TATGAGAGGTTGTTGGT
*
248992 TATGGGAGGTTGTTGGT
1 TATGAGAGGTTGTTGGT
249009 TA
1 TA
249011 CGCTGGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (17 bp):
TATGAGAGGTTGTTGGT
Found at i:250400 original size:41 final size:41
Alignment explanation
Indices: 250355--250496 Score: 221
Period size: 41 Copynumber: 3.5 Consensus size: 41
250345 ATTCACGTTG
* *
250355 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
250396 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
250437 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGTGGTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
250478 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
250497 CTACAGTTGT
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:250405 original size:20 final size:20
Alignment explanation
Indices: 250380--250491 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
250370 TAGTTGAAAA
250380 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGTTTTTCCATT
** ** **
250400 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCG-TTTTTCCATT
*
250421 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGTTTTTCCATT
** ** *
250441 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCG-TTTTTCCATT
* *
250462 TCGCGTTGTGGTTTTCCATT
1 TCGCGTTGCGTTTTTCCATT
250482 TCGCGTTGCG
1 TCGCGTTGCG
250492 ATAGTCTACA
Statistics
Matches: 63, Mismatches: 27, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 36 0.57
21 27 0.43
ACGTcount: A:0.12, C:0.21, G:0.28, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGTTTTTCCATT
Found at i:250466 original size:21 final size:21
Alignment explanation
Indices: 250358--250469 Score: 86
Period size: 21 Copynumber: 5.4 Consensus size: 21
250348 CACGTTGCAT
*
250358 TTCGCATTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* ** ** *
250379 ATCGCGTTGCG-TTTTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
*
250399 TTCGCGTTGCGATAGTTGGAGA
1 TTCGCGTTGCGATAGTT-GAAA
* ** *
250421 -TCGCGTTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
250440 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
250461 TTCGCGTTG
1 TTCGCGTTG
250470 TGGTTTTCCA
Statistics
Matches: 64, Mismatches: 23, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
20 28 0.44
21 36 0.56
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTTGAAA
Found at i:250530 original size:82 final size:81
Alignment explanation
Indices: 250364--250530 Score: 221
Period size: 82 Copynumber: 2.0 Consensus size: 81
250354 GCATTTCGCA
* **
250364 TTGCGATAGTTGAAAATCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGTTGGAGATCGCGTTG
1 TTGCGATAGTTGAAAATCGCGTTGCGGTTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTG
*
250429 CGATTTTCCATTTCGCG
66 CGATTTTCCAATTC-CG
* * *
250446 TTGCGATAGTTGAAATTCGCGTTGTGGTTTTCCATTTCGCGTTGCGATAGTCTACAG-TTGTCGT
1 TTGCGATAGTTGAAAATCGCGTTGCGGTTTTCCATTTCGCGTTGCGATAGT-TACAGATCG-CGT
250510 TGCGATTTTCCAAATT-CG
64 TGCGATTTTCC-AATTCCG
250528 TTG
1 TTG
250531 AAAAAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
82 55 0.73
83 17 0.23
84 3 0.04
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.40
Consensus pattern (81 bp):
TTGCGATAGTTGAAAATCGCGTTGCGGTTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTG
CGATTTTCCAATTCCG
Found at i:250621 original size:6 final size:6
Alignment explanation
Indices: 250606--250703 Score: 152
Period size: 6 Copynumber: 17.2 Consensus size: 6
250596 GACACGTATT
*
250606 ACCACA ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
250654 ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG A-CACG A-CACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
250698 A-CACG A
1 ACCACG A
250704 GACGGACGGA
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
5 25 0.27
6 66 0.73
ACGTcount: A:0.37, C:0.47, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:251192 original size:5 final size:5
Alignment explanation
Indices: 251178--251208 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
251168 CCGCCGCCGC
251178 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
251209 GGTCGGGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:251245 original size:6 final size:5
Alignment explanation
Indices: 251206--251261 Score: 76
Period size: 5 Copynumber: 10.4 Consensus size: 5
251196 TCGTCTCGTC
251206 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
251254 TCGTGG TC
1 TCG-GG TC
251262 ATACGTGTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 28 0.56
6 22 0.44
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:251368 original size:19 final size:19
Alignment explanation
Indices: 251344--251409 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
251334 TTAACTATCA
251344 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
251363 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
251385 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
251404 CAACGA
1 CAACGA
251410 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:251447 original size:20 final size:20
Alignment explanation
Indices: 251422--251494 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
251412 ACTGTAGACT
251422 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
251442 ATCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
251463 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
251483 ATCGCAACGCGA
1 ATCGCAACGCGA
251495 TTTTCAACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 25 0.57
21 13 0.30
22 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:251492 original size:41 final size:42
Alignment explanation
Indices: 251353--251516 Score: 230
Period size: 41 Copynumber: 4.0 Consensus size: 42
251343 ACAACGAATT
*
251353 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA-A
251394 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
*
251436 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
* * *
251477 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAA
1 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAA
251517 TTTGTGATAG
Statistics
Matches: 116, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
41 96 0.83
42 16 0.14
43 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (42 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
Found at i:260927 original size:648 final size:649
Alignment explanation
Indices: 259684--260988 Score: 2371
Period size: 648 Copynumber: 2.0 Consensus size: 649
259674 TCTCAGAGGG
*
259684 TATTTATAGCATTCTAAAACCCTAGATTAATCATAAGATAATTCTAAAAATAGTTTGAATAAATT
1 TATTTATAGCATTCTAAAACCCTAGATTAATCATAAGATAATTCTAAAAATAGTTTGAATAAAAT
*
259749 CCTAAGAATAATACAAAAATCTTGAATTTTGAATTGCTTGAAATTCTCAGCCGTCCATCCACCTT
66 CCTAAGAATAATACAAAAATCTTGAATTTTGAATTGCTTGAAATTCTCAACCGTCCATCCACCTT
*
259814 ATGGAAGCTGCTGACTAGACGTTACTGACTAGGTCTTCTAGAAGCTGTTGACTCACTGCCACATC
131 ATGGAAGCTGCTGACTAGACGTTACTGACTAGGTCTTCTAGAAGCTATTGACTCACTGCCACATC
* * *
259879 AGCATTTCATGCCTACTTTATTTCCCACTATTCTAACCTTGATTCTAGAACAAAAAATGTAGTTT
196 AACATTTCATGCCTACTTTATTTCCCACTATTCCAACCTTGATTCTAGAACAAAAAATATAGTTT
* *
259944 TTGGCCCATTTAAGCACATTTTCTAGAAGTCATTATCTGCGTAAAAATCACATAAAAAACGTCCA
261 TTGGCCCATTTAAGCACATTTTCTAGAAGTCATTATATGCATAAAAATCACATAAAAAACGTCCA
260009 ATTTAGTAGTAAACATGAACAATAAAAGAACATTTAAGAATAAAATGCAGCACAAAATAAACACA
326 ATTTAGTAGTAAACATGAACAATAAAAGAACATTTAAGAATAAAATGCAGCACAAAATAAACACA
260074 AGTAAAACATTTCATTCTTGAAAACATGTTAAATTTTTTTTGTTTCCTTAACATTTGTAAAATTT
391 AGTAAAACATTTCATTCTTGAAAACATGTTAAATTTTTTTTGTTTCCTTAACATTTGTAAAATTT
260139 AAACCTTCTTACTAAAATACTTAATCATATAAAATCAAAATATTATAAATTATCATATAAACCAA
456 AAACCTTCTTACTAAAATACTTAATCATATAAAATCAAAATATTATAAATTATCATATAAACCAA
*
260204 ACCTGATTTTAAGCAGAAGTTTGAATAGTTCATTACTAAACAATACTACTTAAAAATTGTCTACT
521 ACCTGATTTTAAGCAGAAGGTTGAATAGTTCATTACTAAACAATACTACTTAAAAATTGTCTACT
* *
260269 TTCTAATTATTTATTGATTCTAGGAAAATATTATTTTTTTATCTAAAACAAAAAACTTAAATTCA
586 TTCCAATTATTTATTGATTCTAGGAAAATA-TAATTTTTTATCTAAAACAAAAAACTTAAATTCA
260334 TATTTATAGCATTCTAAAACCCTAGATTAATCATAAGATAATTCTAAAAATAGTTTGAATAAAAT
1 TATTTATAGCATTCTAAAACCCTAGATTAATCATAAGATAATTCTAAAAATAGTTTGAATAAAAT
*
260399 CCTAAGAATAATACAAAAATCTTGAATTTTGAATTGCTTGAAATTGTCAACCGTCCATCCACCTT
66 CCTAAGAATAATACAAAAATCTTGAATTTTGAATTGCTTGAAATTCTCAACCGTCCATCCACCTT
*
260464 ATGGAAGCTGCTGACTAGACG-T-CTGACTGGGTCTTCTAGAAGCTATTGACTCACTGCCACATC
131 ATGGAAGCTGCTGACTAGACGTTACTGACTAGGTCTTCTAGAAGCTATTGACTCACTGCCACATC
* *
260527 AACATTTCATGCCTACTTTCTTTCTCACTATTCCAACCTTGATTCTAGAACAAAAAATATAGTTT
196 AACATTTCATGCCTACTTTATTTCCCACTATTCCAACCTTGATTCTAGAACAAAAAATATAGTTT
* *
260592 TTGGCCCATTTAAGCACATTTTCTATAAGTCATTATATGCATAAAAATCACATAAAAAACTTCCA
261 TTGGCCCATTTAAGCACATTTTCTAGAAGTCATTATATGCATAAAAATCACATAAAAAACGTCCA
* * *
260657 ATTTATTAGTAAACATGAACTATCAAAGAACATTTAAGAATAAAATGCAGCACAAAATAAACACA
326 ATTTAGTAGTAAACATGAACAATAAAAGAACATTTAAGAATAAAATGCAGCACAAAATAAACACA
*
260722 AGTCAAACATTTCATTCTTGAAAACATGTTAAATTTTTTTTGTTTCCTTAACATTTGTAAAATTT
391 AGTAAAACATTTCATTCTTGAAAACATGTTAAATTTTTTTTGTTTCCTTAACATTTGTAAAATTT
260787 AAACCTTCTTACTAAAATACTTAATCATATAAAATCAAAATATTATAAATTATCATATAAACCAA
456 AAACCTTCTTACTAAAATACTTAATCATATAAAATCAAAATATTATAAATTATCATATAAACCAA
*
260852 ACCTGATTTTAAGCAGCAGGTTGAATAGTTCATTACTAAACAATACTACTTAAAAATTGTCTACT
521 ACCTGATTTTAAGCAGAAGGTTGAATAGTTCATTACTAAACAATACTACTTAAAAATTGTCTACT
* *
260917 TTCCAATTATTTCTTGATTCTAGGAAAATATAATTTTTTATCTAAAACATAAAACTTAAATTCA
586 TTCCAATTATTTATTGATTCTAGGAAAATATAATTTTTTATCTAAAACAAAAAACTTAAATTCA
260981 TATTTATA
1 TATTTATA
260989 TCTATAATAC
Statistics
Matches: 631, Mismatches: 24, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
647 40 0.06
648 442 0.70
649 1 0.00
650 148 0.23
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (649 bp):
TATTTATAGCATTCTAAAACCCTAGATTAATCATAAGATAATTCTAAAAATAGTTTGAATAAAAT
CCTAAGAATAATACAAAAATCTTGAATTTTGAATTGCTTGAAATTCTCAACCGTCCATCCACCTT
ATGGAAGCTGCTGACTAGACGTTACTGACTAGGTCTTCTAGAAGCTATTGACTCACTGCCACATC
AACATTTCATGCCTACTTTATTTCCCACTATTCCAACCTTGATTCTAGAACAAAAAATATAGTTT
TTGGCCCATTTAAGCACATTTTCTAGAAGTCATTATATGCATAAAAATCACATAAAAAACGTCCA
ATTTAGTAGTAAACATGAACAATAAAAGAACATTTAAGAATAAAATGCAGCACAAAATAAACACA
AGTAAAACATTTCATTCTTGAAAACATGTTAAATTTTTTTTGTTTCCTTAACATTTGTAAAATTT
AAACCTTCTTACTAAAATACTTAATCATATAAAATCAAAATATTATAAATTATCATATAAACCAA
ACCTGATTTTAAGCAGAAGGTTGAATAGTTCATTACTAAACAATACTACTTAAAAATTGTCTACT
TTCCAATTATTTATTGATTCTAGGAAAATATAATTTTTTATCTAAAACAAAAAACTTAAATTCA
Found at i:263411 original size:29 final size:30
Alignment explanation
Indices: 263365--263426 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
263355 TTTTATTCAT
*
263365 TAAACTTTTTAAACTTTACACTTTGGCCCC
1 TAAACTTTTTAAACTTTACACTTTGGCCAC
* *
263395 TAAAC-TTTTAAATTTTACATTTTGGCCAC
1 TAAACTTTTTAAACTTTACACTTTGGCCAC
263424 TAA
1 TAA
263427 CCAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (30 bp):
TAAACTTTTTAAACTTTACACTTTGGCCAC
Found at i:269678 original size:15 final size:15
Alignment explanation
Indices: 269658--269688 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
269648 AATTTTAGTT
269658 ATAATTTTATTTATG
1 ATAATTTTATTTATG
269673 ATAATTTTATTTATG
1 ATAATTTTATTTATG
269688 A
1 A
269689 ATGAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATAATTTTATTTATG
Found at i:270874 original size:20 final size:19
Alignment explanation
Indices: 270812--270874 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
270802 TTCATTTTAT
* *
270812 GATTCAAAACTTATTTCCA
1 GATTCATAACTTATTTTCA
*
270831 GATTCATAACTTACTTTCA
1 GATTCATAACTTATTTTCA
270850 GATTCATAACTTAATTTTCA
1 GATTCATAACTT-ATTTTCA
*
270870 AATTC
1 GATTC
270875 CTAGCCCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 28 0.74
20 10 0.26
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (19 bp):
GATTCATAACTTATTTTCA
Found at i:292816 original size:41 final size:41
Alignment explanation
Indices: 292771--292866 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
292761 AAATTAATCT
* *
292771 ATCCCTTGAGAGAAAGAATCGAT-CTCTTTTCAAGAGGATCA
1 ATCCCTTGAGAGAAAGAATCGATAC-ATTTTCAAAAGGATCA
* * *
292812 ATCCCTCGAGAGAAAGGATCGATACATTTTCAAAAGGATCG
1 ATCCCTTGAGAGAAAGAATCGATACATTTTCAAAAGGATCA
292853 ATCCCTTG-GAGAAA
1 ATCCCTTGAGAGAAA
292867 AAGGGATTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.12
41 41 0.85
42 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (41 bp):
ATCCCTTGAGAGAAAGAATCGATACATTTTCAAAAGGATCA
Found at i:295072 original size:20 final size:20
Alignment explanation
Indices: 295049--295098 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
295039 GTTCATTAGG
*
295049 TATCGATATTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
* *
295069 TATCTATACTGTAAGAGCAA
1 TATCGATACTGTAAGAACAA
*
295089 TATCAATACT
1 TATCGATACT
295099 ACTTGTCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (20 bp):
TATCGATACTGTAAGAACAA
Found at i:298319 original size:21 final size:21
Alignment explanation
Indices: 298269--298321 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
298259 AGAGAAGAGG
*
298269 GTATCGATACTCCTAAAGGGA
1 GTATCGGTACTCCTAAAGGGA
298290 GTATCGGTACTCCTAAAGGGA
1 GTATCGGTACTCCTAAAGGGA
*
298311 GTATTGGTACT
1 GTATCGGTACT
298322 ACCTTTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (21 bp):
GTATCGGTACTCCTAAAGGGA
Found at i:302764 original size:45 final size:45
Alignment explanation
Indices: 302706--303021 Score: 384
Period size: 45 Copynumber: 7.1 Consensus size: 45
302696 GCAGTTTAAG
* * * *
302706 CTATAACAT-CTTTTCTGTTGATAATGCACCCATATGCATTACAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
* *
302750 CTATAGTATACTTTTCGGTTGATAATGTACCCATATACATTTCAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
* *
302795 CCATAGTATACTTTTCTGTTGATAATGTA-CCATATACATTTCAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
* * * * * *
302839 TTTTAGCATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
** * * * *
302884 CTCCAACATACTTTTCTGTTAATAATGTACCCATATGCATCTCAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
*
302929 CTCTAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
* ** **
302974 CTAAAATATGTTTTTCTGTTGATAATGTACCCATATACATTTCAA
1 CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
303019 CTA
1 CTA
303022 GGGCATCCTT
Statistics
Matches: 234, Mismatches: 36, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
44 44 0.19
45 190 0.81
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (45 bp):
CTATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAA
Found at i:302958 original size:134 final size:135
Alignment explanation
Indices: 302710--303021 Score: 414
Period size: 134 Copynumber: 2.3 Consensus size: 135
302700 TTTAAGCTAT
* * * ** *
302710 AACAT-CTTTTCTGTTGATAATGCACCCATATGCATTACAACTATAGTATACTTTTCGGTTGATA
1 AACATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTACAACATACTTTTCGGTTAATA
* *
302774 ATGTACCCATATACATTTCAACCATAGTATACTTTTCTGTTGATAATGTA-CCATATACATTTCA
66 ATGTACCCATATACATCTCAACCATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCA
* **
302838 ATTTT
131 ACTAA
* * *
302843 AGCATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTCCAACATACTTTTCTGTTAATA
1 AACATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTACAACATACTTTTCGGTTAATA
*
302908 ATGTACCCATATGCATCTCAACTC-TAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
66 ATGTACCCATATACATCTCAAC-CATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTC
302972 AACTAA
130 AACTAA
* * * * *
302978 AATATGTTTTTCTGTTGATAATGTACCCATATACATTTCAACTA
1 AACATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTA
303022 GGGCATCCTT
Statistics
Matches: 154, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
133 4 0.03
134 96 0.62
135 54 0.35
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (135 bp):
AACATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTACAACATACTTTTCGGTTAATA
ATGTACCCATATACATCTCAACCATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCA
ACTAA
Found at i:303055 original size:135 final size:134
Alignment explanation
Indices: 302710--303058 Score: 335
Period size: 134 Copynumber: 2.6 Consensus size: 134
302700 TTTAAGCTAT
* * * * ** * * *** *
302710 AACAT-CTTTTCTGTTGATAATGCACCCATATGCATTACAACTATAGTATACTTTTCGGTTGATA
1 AACATGCTCTTCTGTTGATAATGCACCCATATACATTTCAACTACAACATACCTTTCTGCCAACA
* * * *
302774 ATGTACCCATATACATTTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCATATACATTTCA
66 ATGCACCCATATGCATCTCAACTC-TAGCATACTTTTCTGTTGATAATGTACCATATACATTTCA
* **
302838 ATTTT
130 ACTAA
* * * * ** *
302843 AGCATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAACTCCAACATACTTTTCTGTTAATA
1 AACATGCTCTTCTGTTGATAATGCACCCATATACATTTCAACTACAACATACCTTTCTGCCAACA
*
302908 ATGTACCCATATGCATCTCAACTCTAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCA
66 ATGCACCCATATGCATCTCAACTCTAGCATACTTTTCTGTTGATAATGTA-CCATATACATTTCA
302973 ACTAA
130 ACTAA
* * * * ***
302978 AATATGTTTTTCTGTTGATAATGTACCCATATACATTTCAACTAGGGCAT-CCTTTCATGCCAAC
1 AACATGCTCTTCTGTTGATAATGCACCCATATACATTTCAACTACAACATACCTTTC-TGCCAAC
*
303042 AATGCACCTATATGCAT
65 AATGCACCCATATGCAT
303059 TAGTATTTTC
Statistics
Matches: 181, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
133 4 0.02
134 101 0.56
135 76 0.42
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (134 bp):
AACATGCTCTTCTGTTGATAATGCACCCATATACATTTCAACTACAACATACCTTTCTGCCAACA
ATGCACCCATATGCATCTCAACTCTAGCATACTTTTCTGTTGATAATGTACCATATACATTTCAA
CTAA
Found at i:308191 original size:2 final size:2
Alignment explanation
Indices: 308174--308211 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
308164 TCATAATTAC
* *
308174 TA TA GA TA TA -A TA TA TA TA TA TA TG 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
308212 GAAAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:316502 original size:118 final size:118
Alignment explanation
Indices: 316353--316588 Score: 472
Period size: 118 Copynumber: 2.0 Consensus size: 118
316343 TGTTTGAATA
316353 AGATATGATCCTGATAAATCATATTTTGAATAACTAATGATTCTTTTAGTTAATGAACTCTTCCA
1 AGATATGATCCTGATAAATCATATTTTGAATAACTAATGATTCTTTTAGTTAATGAACTCTTCCA
316418 AAAGTGATTCTAACTTCCGACATTCTATTGGTAAACTGACGATTCGTGTTTCT
66 AAAGTGATTCTAACTTCCGACATTCTATTGGTAAACTGACGATTCGTGTTTCT
316471 AGATATGATCCTGATAAATCATATTTTGAATAACTAATGATTCTTTTAGTTAATGAACTCTTCCA
1 AGATATGATCCTGATAAATCATATTTTGAATAACTAATGATTCTTTTAGTTAATGAACTCTTCCA
316536 AAAGTGATTCTAACTTCCGACATTCTATTGGTAAACTGACGATTCGTGTTTCT
66 AAAGTGATTCTAACTTCCGACATTCTATTGGTAAACTGACGATTCGTGTTTCT
316589 CCACCTGATA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (118 bp):
AGATATGATCCTGATAAATCATATTTTGAATAACTAATGATTCTTTTAGTTAATGAACTCTTCCA
AAAGTGATTCTAACTTCCGACATTCTATTGGTAAACTGACGATTCGTGTTTCT
Found at i:316695 original size:24 final size:24
Alignment explanation
Indices: 316667--316743 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
316657 GAATATTTTA
* *
316667 TCTGATTTCTGATTTGAATTATGT
1 TCTGATTTCTGATCTGAAATATGT
** *
316691 TCTGACATCTGATCTGAAATCTGT
1 TCTGATTTCTGATCTGAAATATGT
* * *
316715 TCTGATTCCTGACCTG-GATACTGT
1 TCTGATTTCTGATCTGAAATA-TGT
316739 TCTGA
1 TCTGA
316744 ATTATGTTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 2 0.05
24 39 0.95
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAAATATGT
Found at i:319518 original size:19 final size:19
Alignment explanation
Indices: 319444--319515 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
319434 ACATAACCAG
*
319444 TACTTTCACATTTAAGAATT
1 TACTTTCAGATTT-AGAATT
* * *
319464 CATTTTCTGATTTAGAATT
1 TACTTTCAGATTTAGAATT
* * *
319483 TA-TTTCAAAATTCATAATT
1 TACTTTC-AGATTTAGAATT
319502 TACTTTCAGATTTA
1 TACTTTCAGATTTA
319516 TAACTTAATT
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
18 4 0.10
19 22 0.56
20 13 0.33
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (19 bp):
TACTTTCAGATTTAGAATT
Found at i:320561 original size:18 final size:18
Alignment explanation
Indices: 320538--320663 Score: 225
Period size: 18 Copynumber: 7.0 Consensus size: 18
320528 AACCTTGCTT
320538 AGAAATTCACATTTCATC
1 AGAAATTCACATTTCATC
320556 AGAAATTCACATTTCATC
1 AGAAATTCACATTTCATC
*
320574 ATAAATTCACATTTCATC
1 AGAAATTCACATTTCATC
*
320592 AGAAATTCTCATTTCATC
1 AGAAATTCACATTTCATC
*
320610 ATAAATTCACATTTCATC
1 AGAAATTCACATTTCATC
320628 AGAAATTCACATTTCATC
1 AGAAATTCACATTTCATC
320646 AGAAATTCACATTTCATC
1 AGAAATTCACATTTCATC
320664 CTTAAGCTTC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 102 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (18 bp):
AGAAATTCACATTTCATC
Found at i:327850 original size:19 final size:20
Alignment explanation
Indices: 327828--327891 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 20
327818 TTCAGAATTC
327828 ATTTTCTGATTCATAACTT-
1 ATTTTCTGATTCATAACTTA
* *
327847 ATTTCCAT-ATTCATAACTTG
1 ATTTTC-TGATTCATAACTTA
* *
327867 CTTTT-AGATTCATAACTTA
1 ATTTTCTGATTCATAACTTA
327886 ATTTTC
1 ATTTTC
327892 AAATTGGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 31 0.89
20 4 0.11
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTTCTGATTCATAACTTA
Found at i:329409 original size:19 final size:20
Alignment explanation
Indices: 329385--329429 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
329375 CAAAATGGCC
*
329385 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
329404 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
329424 TAATTT
1 CAATTT
329430 GTATAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:333573 original size:16 final size:14
Alignment explanation
Indices: 333541--333576 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
333531 GCCCTGTCTT
333541 AATATTAAAAAATA
1 AATATTAAAAAATA
333555 AATATATAAAAAATA
1 AATAT-TAAAAAATA
333570 AA-ATTAA
1 AATATTAA
333577 GGTATAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 7 0.33
15 11 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AATATTAAAAAATA
Found at i:335278 original size:22 final size:23
Alignment explanation
Indices: 335250--335294 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
335240 AATAATAAAT
*
335250 ATAATAATAAT-ATTAAAACAAA
1 ATAATAATAATAAATAAAACAAA
335272 ATAATAATAATAAATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
335295 TGAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (23 bp):
ATAATAATAATAAATAAAACAAA
Found at i:335826 original size:113 final size:113
Alignment explanation
Indices: 335634--336492 Score: 1262
Period size: 113 Copynumber: 7.6 Consensus size: 113
335624 ATTGAACAAG
* * * * *
335634 TTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTC-TCTCTGGAAAAGTTGATCCATC-AA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-CTGGCAATGCTGATCCATCGAA
*
335697 GTGATGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
65 -TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
*
335747 TTCTTCCTTCTTCAGATGAGTTCTTCTCGTTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
335812 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * *
335860 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGACCTGGCAAAGCTGATTCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
** * *
335925 GATGAATTTGAG-AAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGAATTCAAGCAAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTC
* * ** * *
335973 TTCTTCCTTCTTTAGATGAGTTCTTTTCATTATGAACTCTTCCTTGCAATGTTGATCCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
* * *
336038 GATGAATTTAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAATTTC
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
336086 GTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGGAATGCTGATCCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
*
336151 GATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
336199 TTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTGACCTGGCAATGCTGAAT-CATCGAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTG-ATCCATCGAA
* * * *
336263 TGGTGAATTCGAG-AAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
65 TGATGAATTCAAGCAAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTC
* * **
336312 TTCTTCCTTCTTTAGATGAGTTCTTGTCATTATGAACTCTTCCTGGCAATGCTGATCCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
336377 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
** * * *
336425 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TTCTGGAAATGTTGATCCATTGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
336489 GATG
66 GATG
336493 GATTTAAATC
Statistics
Matches: 676, Mismatches: 62, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
112 36 0.05
113 626 0.93
114 14 0.02
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATCGAAT
GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:336261 original size:339 final size:339
Alignment explanation
Indices: 335634--336492 Score: 1445
Period size: 339 Copynumber: 2.5 Consensus size: 339
335624 ATTGAACAAG
* * * *
335634 TTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTC-TCTCTGGAAAAGTTGATCCATC-AA
1 TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTTC-CTGGCAATGTTGATCCATCGAA
*
335697 GTGATGAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
65 -TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
335762 ATGAGTTCTTCTCGTTATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAA
129 ATGAGTTCTTCTCATTATGAACTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAA
*
335827 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
194 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTA
* *
335892 TGAACTTGACCTGGCAAAGCTGATTCATCGAATGATGAATTTGAGAAAAAGGTTGAACAAATTCT
259 TGAACTTGACCTGGCAAAGCTGAATCATCGAATGATGAATTCGAGAAAAAGGTTGAACAAATTCT
335957 TCTCATTATGAATTTC
324 TCTCATTATGAATTTC
* *
335973 TTCTTCCTTCTTTAGATGAGTTCTTTTCATTATGAACTCTTCCTTGCAATGTTGATCCATCGAAT
1 TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCATCGAAT
* * * *
336038 GATGAATTTAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAATTTCGTCTTCCTTCTTCAGAT
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
* *
336103 GAGTTCTTCTCATTATGAACTCGACCTGGGAATGCTGATCCATCGAATGATGAATTCAAGCGAAA
131 GAGTTCTTCTCATTATGAACTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA
336168 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATG
196 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATG
* *
336233 AACTTGACCTGGCAATGCTGAATCATCGAATGGTGAATTCGAGAAAAAGGTTGAACAAATTCTTC
261 AACTTGACCTGGCAAAGCTGAATCATCGAATGATGAATTCGAGAAAAAGGTTGAACAAATTCTTC
336298 TCATTATGAATTTC
326 TCATTATGAATTTC
* *
336312 TTCTTCCTTCTTTAGATGAGTTCTTGTCATTATGAACTCTTCCTGGCAATGCTGATCCATCGAAT
1 TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCATCGAAT
336377 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
66 GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
** * *
336442 GAGTTCTTCTCATTATGAACTC-TTCTGGAAATGTTGATCCATTGAATGATG
131 GAGTTCTTCTCATTATGAACTCGACCTGGAAATGCTGATCCATCGAATGATG
336493 GATTTAAATC
Statistics
Matches: 487, Mismatches: 31, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
338 24 0.05
339 459 0.94
340 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (339 bp):
TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAATGTTGATCCATCGAAT
GATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTCGACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA
AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATG
AACTTGACCTGGCAAAGCTGAATCATCGAATGATGAATTCGAGAAAAAGGTTGAACAAATTCTTC
TCATTATGAATTTC
Found at i:339870 original size:114 final size:114
Alignment explanation
Indices: 339678--339905 Score: 402
Period size: 114 Copynumber: 2.0 Consensus size: 114
339668 AGACTATCAT
* * * *
339678 CAAATTCATCTTTTAAATCTAATGATTGGTTTTAGGGTTCATACCGAACCAGATTAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
*
339743 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCATATTTCTACTATGAG
66 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCATATTTATACTATGAG
339792 CAAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
*
339857 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAG
66 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCATATTTATACTATGAG
339906 AACGTGGCAC
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (114 bp):
CAAATTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAGAAGATGCTATTGGGTCTCCATATTTATACTATGAG
Found at i:345035 original size:43 final size:44
Alignment explanation
Indices: 344953--345037 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 44
344943 GTGCATCAAA
* *
344953 CAAAACTTTTACATATAGGGGACATCTTTCAGTCCTAACTTCAG
1 CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAG
* * *
344997 CAAAAC-TTTACATATAGGGGATAACTTTCCCTCTTAACTTC
1 CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
345038 TCTAAAGCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 30 0.83
44 6 0.17
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.33
Consensus pattern (44 bp):
CAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAG
Found at i:347189 original size:127 final size:129
Alignment explanation
Indices: 346970--347210 Score: 323
Period size: 127 Copynumber: 1.9 Consensus size: 129
346960 AGTTTATAAG
* * * *
346970 AAAATCTATTAATTTATATATAAATAAGATATTTATTTATTTAGAAATATCAGAAAATGGCTTCT
1 AAAATATATTAATTTATATATAAATAAGACATTTATTTATTTAGAAATATCAGAAAATGGCATCC
*
347035 AGGTGCTTTAAGACAGCTCTTTTCTTAATA-TAAAAAATAAATAAATATTAAAACATTTATTTA
66 AGGTGCTTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATTAAAACATTTATTTA
*
347098 AAAATATATATAATTTATA-A-AAGTAAGACATTTATTTATTTA-AGAATATCAGAAAATGGACA
1 AAAATATAT-TAATTTATATATAAATAAGACATTTATTTATTTAGA-AATATCAGAAAATGG-CA
* * *
347160 TCCAGTTGCTTTAAGA-ATGC-CCTTTCTTAATATTAAAAAATATATATATAT
63 TCCAGGTGCTTTAAGACA-GCTCCTTTCTTAATATTAAAAAATAAATAAATAT
347211 ATATAATTAA
Statistics
Matches: 99, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
126 1 0.01
127 47 0.47
128 42 0.42
129 9 0.09
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (129 bp):
AAAATATATTAATTTATATATAAATAAGACATTTATTTATTTAGAAATATCAGAAAATGGCATCC
AGGTGCTTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATTAAAACATTTATTTA
Found at i:349017 original size:3 final size:3
Alignment explanation
Indices: 349011--349063 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
349001 ATTATTTATT
* *
349011 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
349055 TAA TAA TAA
1 TAA TAA TAA
349064 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:349033 original size:19 final size:18
Alignment explanation
Indices: 349011--349066 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
349001 ATTATTTATT
349011 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
349030 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
349049 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
349067 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:349036 original size:22 final size:21
Alignment explanation
Indices: 348989--349067 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
348979 TGTAAAAGTG
* * *
348989 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
349011 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
349033 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
349052 TAATAATAATAAATAA
1 TAATAATAATAAATAA
349068 AACAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:349074 original size:22 final size:22
Alignment explanation
Indices: 349011--349074 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
349001 ATTATTTATT
* *
349011 TAATAAT-AATAATATAATATAA
1 TAATAATAAATAAAACAA-ATAA
*
349033 TAATAATA-TTAAAACAAAATAA
1 TAATAATAAATAAAAC-AAATAA
349055 TAATAATAAATAAAACAAAT
1 TAATAATAAATAAAACAAAT
349075 GAAATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAAATAAAACAAATAA
Found at i:350579 original size:16 final size:16
Alignment explanation
Indices: 350558--350591 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
350548 CACAATTTCC
350558 ATGCAAACTTCTTAGT
1 ATGCAAACTTCTTAGT
350574 ATGCAAACTTCTTAGT
1 ATGCAAACTTCTTAGT
350590 AT
1 AT
350592 ACTACACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGCAAACTTCTTAGT
Found at i:350843 original size:21 final size:20
Alignment explanation
Indices: 350781--350844 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
350771 TTTATCATTG
* *
350781 TTTAGGATTTTAAGTTAGGA
1 TTTAGGGTTTTAAGTTAGGT
350801 TTTAGGG-TTTAAGACTTAGGT
1 TTTAGGGTTTTAAG--TTAGGT
*
350822 TTTAGGGTTTTATGTTATGGT
1 TTTAGGGTTTTAAGTTA-GGT
350843 TT
1 TT
350845 AGACTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.16
20 9 0.24
21 17 0.46
22 5 0.14
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.50
Consensus pattern (20 bp):
TTTAGGGTTTTAAGTTAGGT
Found at i:358289 original size:35 final size:35
Alignment explanation
Indices: 358168--358292 Score: 162
Period size: 35 Copynumber: 3.6 Consensus size: 35
358158 TAAAGATGAA
** * *
358168 TACTTGAATTAAAAGTGTGATGTTTCCTTCCATTC
1 TACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTC
* * * * *
358203 GACTT-AATCGAAAGTGCGATACTTTCTTCCGCTC
1 TACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTC
358237 TACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTC
1 TACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTC
358272 TACTTGAATCGAAAGTGTGAT
1 TACTTGAATCGAAAGTGTGAT
358293 TGTAACCCCC
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
34 25 0.33
35 50 0.67
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (35 bp):
TACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTC
Found at i:366939 original size:18 final size:18
Alignment explanation
Indices: 366912--366947 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
366902 CAGGTTGGTT
*
366912 AACGGCTCGAGTTGGGTC
1 AACGGCTCGAGTAGGGTC
*
366930 AACGGGTCGAGTAGGGTC
1 AACGGCTCGAGTAGGGTC
366948 GGACTGGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (18 bp):
AACGGCTCGAGTAGGGTC
Found at i:367636 original size:34 final size:34
Alignment explanation
Indices: 367588--367715 Score: 114
Period size: 35 Copynumber: 3.7 Consensus size: 34
367578 GGTTGTTATA
*
367588 GTGATACTTCCTTCTGTCTACTTGAATCAAAAGT
1 GTGATACTTCCTTCCGTCTACTTGAATCAAAAGT
* * * * *
367622 GTGATGCTTACTTCTGTTTGACTTAAATCAAAAGT
1 GTGATACTTCCTTCCGTCT-ACTTGAATCAAAAGT
** * * *
367657 ACGATGCTTTCTTCCGT-TATGCTTGAATCGAAAGT
1 GTGATACTTCCTTCCGTCTA--CTTGAATCAAAAGT
367692 GTGATACTTCCTTCCGTTCTACTT
1 GTGATACTTCCTTCCG-TCTACTT
367716 TATTCACCTT
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
33 1 0.01
34 17 0.23
35 54 0.72
36 1 0.01
37 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (34 bp):
GTGATACTTCCTTCCGTCTACTTGAATCAAAAGT
Found at i:367691 original size:35 final size:35
Alignment explanation
Indices: 367607--367709 Score: 118
Period size: 35 Copynumber: 2.9 Consensus size: 35
367597 CCTTCTGTCT
*
367607 ACTTGAATCAAAAGTGTGATGCTTACTTCTGTTTG
1 ACTTGAATCAAAAGTGTGATGCTTACTTCCGTTTG
* ** *
367642 ACTTAAATCAAAAGTACGATGCTTTCTTCCGTTATG
1 ACTTGAATCAAAAGTGTGATGCTTACTTCCGTT-TG
* * *
367678 -CTTGAATCGAAAGTGTGATACTTCCTTCCGTT
1 ACTTGAATCAAAAGTGTGATGCTTACTTCCGTT
367710 CTACTTTATT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 54 0.96
36 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (35 bp):
ACTTGAATCAAAAGTGTGATGCTTACTTCCGTTTG
Found at i:372786 original size:54 final size:54
Alignment explanation
Indices: 372617--373167 Score: 732
Period size: 54 Copynumber: 10.3 Consensus size: 54
372607 ATAAGTTCTT
* * * * *
372617 TGGGGTGCACACGTAGTGCCGATACGGTCATTCAAAAACTCATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * *
372671 TGGGTTG-AAACTTAGTGCCGATACAGTCATTCAT-AACTTATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * **
372723 TGGGCTGCACACTTAGTGCCGATACAGTCGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
*
372777 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCAT-AACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
** * **
372830 TGGGTTGCACACTTAGTATCGAGACGGTCGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * *
372884 TGGGTTGCACACTTACTGCCAATTCGATCGTTCAT-AACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* *
372937 TGGGTTGCGCACTTAGTACCGATACGGTCGTTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* ** * *
372991 TGGGTTGCACAATTAGTGTTGATACGGTCGTTCATAAAATTATTATGAATTACG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * *
373045 TGGGTTGCACAATTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
* * * * *
373099 TGGGTTGCACACTTAGTGTCGATATGATCATTCATAAACTTATTATGAATTACG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
373153 TGGGTTGCACACTTA
1 TGGGTTGCACACTTA
373168 ACACATAGTA
Statistics
Matches: 441, Mismatches: 52, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
52 22 0.05
53 142 0.32
54 277 0.63
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
Found at i:372839 original size:107 final size:107
Alignment explanation
Indices: 372617--373167 Score: 753
Period size: 107 Copynumber: 5.1 Consensus size: 107
372607 ATAAGTTCTT
* * * * * * *
372617 TGGGGTGCACACGTAGTGCCGATACGGTCATTCAAAAACTCATTATGAATTCCGTGGGTTG-AAA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
* * * *
372681 CTTAGTGCCGATACAGTCATTCATAACTTATTATGAATTTCG
66 CTTAGTGTCGATACGGTCGTTCATAACTTATTATGAATTACG
* * *
372723 TGGGCTGCACACTTAGTGCCGATACAGTCGTTCATAAACTTATTATGAATTTTGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
*
372788 CTTAGTGTCGATACGGTCGTTCATAACTTATTATGAATTCCG
66 CTTAGTGTCGATACGGTCGTTCATAACTTATTATGAATTACG
** * *
372830 TGGGTTGCACACTTAGTATCGAGACGGTCGTTCATAAACTTATTATGAATTTTGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
* * * * * *
372895 CTTACTGCCAATTCGATCGTTCATAACTTATTATGAATTCCG
66 CTTAGTGTCGATACGGTCGTTCATAACTTATTATGAATTACG
* * *
372937 TGGGTTGCGCACTTAGTACCGATACGGTCGTTCATAAACTTATTATGAATTCCGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
* * *
373002 ATTAGTGTTGATACGGTCGTTCATAAAATTATTATGAATTACG
66 CTTAGTGTCGATACGGTCGTTCAT-AACTTATTATGAATTACG
* *
373045 TGGGTTGCACAATTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
* * *
373110 CTTAGTGTCGATATGATCATTCATAAACTTATTATGAATTACG
66 CTTAGTGTCGATACGGTCGTTCAT-AACTTATTATGAATTACG
373153 TGGGTTGCACACTTA
1 TGGGTTGCACACTTA
373168 ACACATAGTA
Statistics
Matches: 394, Mismatches: 49, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
106 53 0.13
107 214 0.54
108 127 0.32
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (107 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
CTTAGTGTCGATACGGTCGTTCATAACTTATTATGAATTACG
Found at i:378137 original size:54 final size:54
Alignment explanation
Indices: 378053--378733 Score: 822
Period size: 54 Copynumber: 12.7 Consensus size: 54
378043 TTTTCAAATC
* * * * * * *
378053 ATTAT-AAGTTCTTTGGGGTGCACACGTAGTGCCGATACGATTGTTCATTAACTC
1 ATTATGAA-TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * * *
378107 ATTATGAATTTTGTGGGTTGTACACTTAGTGTCGATACGGTCATTCAT-AACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
378160 ATTATGAATTCTGTGCGTTGCACTCTTAGTGCCAATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
378214 ATTATGAATTCTGTGGGTTACACACTTAGTGTCGATATGGTCGTTCAT-AACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
378267 ATTATGAATT-TCGTGGGTTGCACACTCAGTGCTGATACGAT-GTTCATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * * *
378320 ATTATGATTTCTGTGGGTTGCACACTTAGTGACGATACGGTCATTCAT-AGCTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* ** * *
378373 ATTATGAATT-TCGTGGGTTGCACACTTAGTTCCTCTATGGTCGTTGATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
*
378427 ATTATGAATTGCCT-T-GGTTGCACACTTAGTGCAGATACGGTCGTTCATAAACTT
1 ATTATGAATT--CTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
378481 ATTATGAATTCTGTGGGTTCCACACTTAGTGTCGATACAGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * ** * * *
378535 ATTATGAATTCCGTGGGTTGCACAATTAGTGTTGGTACGGTCATTCATAAACGT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * ** *
378589 ATTATGAATTCCGTGGGTTGTACACTTAGTGTTGATTCGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* *
378643 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCAATACGGTCATTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
*
378697 ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
378734 TTACACATAG
Statistics
Matches: 536, Mismatches: 78, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
52 10 0.02
53 165 0.31
54 357 0.67
55 3 0.01
57 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (54 bp):
ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
Found at i:384008 original size:24 final size:26
Alignment explanation
Indices: 383967--384042 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 26
383957 GAAAGCAAAG
* ** *
383967 ATAAAATAGTAAGTAAAATAAATATA
1 ATAAAAAAGTAAAAAAAATATATATA
*
383993 A-AAAAAAG-AAAAAAAACATATA-A
1 ATAAAAAAGTAAAAAAAATATATATA
384016 ATAAAAAAGTAAAAAATAATATATATA
1 ATAAAAAAGTAAAAAA-AATATATATA
384043 TATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
23 2 0.05
24 17 0.43
25 12 0.30
26 8 0.20
27 1 0.03
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.21
Consensus pattern (26 bp):
ATAAAAAAGTAAAAAAAATATATATA
Found at i:384013 original size:22 final size:25
Alignment explanation
Indices: 383967--384040 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
383957 GAAAGCAAAG
*
383967 ATAAAATAGTAAGTAAAATAA-ATATA
1 ATAAAAAAGTAA--AAAATAACATATA
383993 A-AAAAAAG-AAAAAA-AACATATAA
1 ATAAAAAAGTAAAAAATAACATAT-A
*
384016 ATAAAAAAGTAAAAAATAATATATA
1 ATAAAAAAGTAAAAAATAACATATA
384041 TATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 2 0.05
24 9 0.22
25 13 0.32
26 7 0.17
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.20
Consensus pattern (25 bp):
ATAAAAAAGTAAAAAATAACATATA
Found at i:384019 original size:4 final size:4
Alignment explanation
Indices: 384012--384095 Score: 57
Period size: 4 Copynumber: 20.8 Consensus size: 4
384002 AAAAAAACAT
* * * *
384012 ATAA ATAA A-AA AGTAA A-AA ATAA TATAT ATAT ATAT ATAT ATATA ATAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA -ATAA ATAA ATAA ATAA ATA-A ATAA
* *
384061 ATAAA ATAA ATAA AAAA ATAA AAAA ATAA A-AA ATA
1 AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
384096 GTGAATATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
3 9 0.13
4 45 0.67
5 13 0.19
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:384081 original size:62 final size:64
Alignment explanation
Indices: 384014--384170 Score: 193
Period size: 62 Copynumber: 2.5 Consensus size: 64
384004 AAAAACATAT
*
384014 AAATAAAAAAGTAAAAAATAATATATATATATATATATATATAATAAAT-AAAAT-A-AATAAAA
1 AAATAAAAAAATAAAAAATAATATATATATATATATATATA-AATAAATAAAAATGATAATAAAA
* * *
384076 AAATAAAAAAATAAAAAATAGT-GA-ATATATATATATATAAATTAATAAAAATGATAATAAAA
1 AAATAAAAAAATAAAAAATAATATATATATATATATATATAAATAAATAAAAATGATAATAAAA
*
384138 ATAATAATAAAAAT-AATAATAA-ATATATATATA
1 A-AATAA-AAAAATAAAAAATAATATATATATATA
384171 ATCTAAAGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
59 6 0.07
60 20 0.25
61 2 0.02
62 28 0.35
63 12 0.15
64 13 0.16
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (64 bp):
AAATAAAAAAATAAAAAATAATATATATATATATATATATAAATAAATAAAAATGATAATAAAA
Found at i:384135 original size:12 final size:12
Alignment explanation
Indices: 384118--384160 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
384108 ATATATAAAT
*
384118 TAATAAAAATGA
1 TAATAAAAATAA
384130 TAATAAAAATAA
1 TAATAAAAATAA
384142 TAATAAAAATAA
1 TAATAAAAATAA
384154 TAATAAA
1 TAATAAA
384161 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
TAATAAAAATAA
Found at i:384171 original size:12 final size:11
Alignment explanation
Indices: 384031--384171 Score: 66
Period size: 12 Copynumber: 12.8 Consensus size: 11
384021 AAAGTAAAAA
*
384031 ATAATATATAT
1 ATAATATAAAT
*
384042 ATATATATATAT
1 ATA-ATATAAAT
384054 ATAATAAATAAA-
1 ATAAT--ATAAAT
384066 ATAA-ATAAA-
1 ATAATATAAAT
* * *
384075 AAAATAAAAAA
1 ATAATATAAAT
384086 ATAA-A-AAAT
1 ATAATATAAAT
*
384095 AGTGAATATATAT
1 A-T-AATATAAAT
384108 AT-ATATAAAT
1 ATAATATAAAT
*
384118 -TAATAAAAAT
1 ATAATATAAAT
384128 GATAATA-AAA-
1 -ATAATATAAAT
*
384138 ATAATAATAAAA
1 ATAAT-ATAAAT
384150 ATAATAATAAAT
1 ATAAT-ATAAAT
384162 ATATATATAA
1 ATA-ATATAA
384172 TCTAAAGAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 31
0.72 0.06 0.21
Matches are distributed among these distances:
9 18 0.17
10 21 0.20
11 16 0.15
12 40 0.38
13 10 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:385362 original size:36 final size:36
Alignment explanation
Indices: 385311--385426 Score: 144
Period size: 36 Copynumber: 3.2 Consensus size: 36
385301 GAGGGTTTTT
* *
385311 TTTGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAA
1 TTTGTTTTAAAAGAAACTGTCTCAAGAGGGACAAAA
*
385347 TTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAAAGAAACTGTCTCAAGAGGGACAAAA
* * **
385383 CTTAGTTCTAAAAGAAACTGTCTCAAG-GGAGATGAAA
1 -TTTGTTTTAAAAGAAACTGTCTCAAGAGG-GACAAAA
385420 TTTGTTT
1 TTTGTTT
385427 CAAGGAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 39 0.57
37 29 0.43
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (36 bp):
TTTGTTTTAAAAGAAACTGTCTCAAGAGGGACAAAA
Found at i:385404 original size:37 final size:36
Alignment explanation
Indices: 385322--385414 Score: 141
Period size: 37 Copynumber: 2.6 Consensus size: 36
385312 TTGTTTCAAG
* * *
385322 AGAAACTGTCTCAAGAGGGACAAAATTTGTTTTAAA
1 AGAAACTGTCTCAAGAGAGACAAAATTAGTTCTAAA
385358 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAA
1 AGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCTAAA
*
385395 AGAAACTGTCTCAAGGGAGA
1 AGAAACTGTCTCAAGAGAGA
385415 TGAAATTTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 24 0.46
37 28 0.54
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (36 bp):
AGAAACTGTCTCAAGAGAGACAAAATTAGTTCTAAA
Found at i:385626 original size:37 final size:37
Alignment explanation
Indices: 385575--385647 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
385565 TCAAGGTTTA
* *
385575 TGTTTCAAGAGAAACTATCTTAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
385612 TGTTTCAAGGGAAACTCTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
385648 AATTTCAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:385676 original size:102 final size:100
Alignment explanation
Indices: 385548--385782 Score: 312
Period size: 102 Copynumber: 2.3 Consensus size: 100
385538 ATATTTTGTG
** * * *
385548 TTTCAAGGGAAACATTTTCAAGGTTTATGTTTCAAGAGAAACTATCTTAAGGGAG-ACAAAATTT
1 TTTCAA-GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAAATTT
385612 TGTTTCAAGGGAAACT-CTCTCAAGAGAGACAAAATTAA
65 T-TTTCAAGGGAAACTAC-C-CAAGAGAGACAAAATTAA
* * *
385650 TTTCAAAGGAATTGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCATGGGAGAAAAAAATTT
1 TTTC-AAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAAATTT
* * *
385715 TTTTCAAGGGAAACTACCCAAGCGAGATAAAATTTA
65 TTTTCAAGGGAAACTACCCAAGAGAGACAAAATTAA
385751 TTTCAAGGAAATGTTTTCAATGTTTATGTTTC
1 TTTCAAGGAAATGTTTTCAATGTTTATGTTTC
385783 GAGGGAGACA
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
100 27 0.23
101 19 0.16
102 60 0.51
103 12 0.10
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (100 bp):
TTTCAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGAAAAAAATTTT
TTTCAAGGGAAACTACCCAAGAGAGACAAAATTAA
Found at i:385840 original size:86 final size:84
Alignment explanation
Indices: 385709--385869 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 84
385699 TGGGAGAAAA
*
385709 AAATTTTTTTCAAGGGAAACTACCCAAGCGAGATAAAATTTATTTCAA-GGAAATGTTTTCAATG
1 AAATTTTTTTCAAGGGAAACTACCCAAGCGAGATAAAATTCATTTCAAGGGAAATGTTTTCAATG
385773 TTTATGTTTCGAGGGAGAC
66 TTTATGTTTCGAGGGAGAC
* * * *
385792 AAATTTTCGTTTCAATGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGGGAATGTTTTCA
1 AAATTTT--TTTCAAGGGAAACTA-CCCAAGCGAGATAAAATTCATTTCAAGGGAAATGTTTTCA
385857 ATGTTTATGTTTC
63 ATGTTTATGTTTC
385870 AAGAGAAACT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
83 7 0.10
85 14 0.20
86 23 0.33
87 25 0.36
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (84 bp):
AAATTTTTTTCAAGGGAAACTACCCAAGCGAGATAAAATTCATTTCAAGGGAAATGTTTTCAATG
TTTATGTTTCGAGGGAGAC
Found at i:385920 original size:37 final size:37
Alignment explanation
Indices: 385860--385940 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
385850 GTTTTCAATG
* * *
385860 TTTATGTTTCAAGAGAAACTGTCTAAAGGGATACAAAA
1 TTTA-GTTCCAAGAGAAAATGTCTAAAGGGAGACAAAA
* *
385898 TTTAGTTCCAAGAGAAAATGTCTCAAGGGAGACGAAA
1 TTTAGTTCCAAGAGAAAATGTCTAAAGGGAGACAAAA
385935 -TTAGTT
1 TTTAGTT
385941 TCAATGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
36 6 0.16
37 28 0.74
38 4 0.11
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (37 bp):
TTTAGTTCCAAGAGAAAATGTCTAAAGGGAGACAAAA
Found at i:386323 original size:106 final size:106
Alignment explanation
Indices: 386177--386451 Score: 309
Period size: 106 Copynumber: 2.6 Consensus size: 106
386167 CTGGAGCTAA
* * * * * * **
386177 GAAATTGTTTGTTGACAGCCAACCGCCCCTTTGCTATGAAGTTGAGCTTGTGCTATCTTTAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGCTATCTCGAGTCC
* * * *
386242 AATATCCTTTGTTGTGAAGTTGAAATTGGA-TCCGAAATTGG
66 AATATCCTTCGCTATGAAGTTGAAA-TCGACTCCGAAATTGG
* * * *
386283 GAAATTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGCTATCTCGAGTCC
*
386348 AATATCCTTCGCTATGAAGTTGAAATCGACTCTGAAATTGG
66 AATATCCTTCGCTATGAAGTTGAAATCGACTCCGAAATTGG
** * * * * * *
386389 GAAATTGTTTGTTGACAATAAGCCATCCATTCGTTTTGGAGTTGAACTTGTGTTGTCTCGAGT
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGCTATCTCGAGT
386452 GGCATGATAT
Statistics
Matches: 144, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
105 3 0.02
106 141 0.98
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (106 bp):
GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTATGAAGTTGAACTTGTGCTATCTCGAGTCC
AATATCCTTCGCTATGAAGTTGAAATCGACTCCGAAATTGG
Found at i:387083 original size:32 final size:32
Alignment explanation
Indices: 387047--387136 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
387037 ATTCCCAAAG
*
387047 ATGCCTCAACATTCGATGTTGAATCTAAAAAA
1 ATGCCTCAACATTTGATGTTGAATCTAAAAAA
* * *
387079 ATGCCCCAATATTTGATGTTAAATCTAAAAAA
1 ATGCCTCAACATTTGATGTTGAATCTAAAAAA
387111 ATG-CTCCAACATTTGATGTTGAATCT
1 ATGCCT-CAACATTTGATGTTGAATCT
387137 TCAAAGATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (32 bp):
ATGCCTCAACATTTGATGTTGAATCTAAAAAA
Found at i:388184 original size:69 final size:69
Alignment explanation
Indices: 388068--388205 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
388058 TCTCTCTCTC
**
388068 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTTGATCAAAC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAAAC
388133 TCAT
66 TCAT
*
388137 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAAAC
388202 TCAT
66 TCAT
388206 AGTTAGAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAAAC
TCAT
Found at i:391238 original size:31 final size:30
Alignment explanation
Indices: 391167--391252 Score: 75
Period size: 31 Copynumber: 2.7 Consensus size: 30
391157 TAAATTAAAT
* *
391167 TAAAATGAAGAAAAAACAAATTAAATAAAAGG
1 TAAAATAAAG-AAAAA-AAATAAAATAAAAGG
* *
391199 TAAGATAAAGAAAAAAAGATAAAATAGTAA-G
1 TAAAATAAAGAAAAAAA-ATAAAATA-AAAGG
*
391230 TAAAATAAATATAAAAAAATAAA
1 TAAAATAAAGA-AAAAAAATAAA
391253 GAAATAAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 2 0.04
31 27 0.60
32 16 0.36
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.17
Consensus pattern (30 bp):
TAAAATAAAGAAAAAAAATAAAATAAAAGG
Found at i:391254 original size:45 final size:44
Alignment explanation
Indices: 391203--391301 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
391193 AAAAGGTAAG
* * *
391203 ATAAAGAAAAAAAGATAAAATAGTAAGTAAAATA-AATATAAAA-AA
1 ATAAAGAAAAAAAGA-AAAAGAGGAA-AAAAATATAA-ATAAAACAA
*
391248 ATAAAGAAATAAAGAAAAAGAGGAAAAAAATATAAATAAAACAA
1 ATAAAGAAAAAAAGAAAAAGAGGAAAAAAATATAAATAAAACAA
*
391292 ATAAATAAAA
1 ATAAAGAAAA
391302 TAATAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
43 12 0.26
44 20 0.43
45 14 0.30
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (44 bp):
ATAAAGAAAAAAAGAAAAAGAGGAAAAAAATATAAATAAAACAA
Found at i:391314 original size:54 final size:53
Alignment explanation
Indices: 391203--391321 Score: 127
Period size: 54 Copynumber: 2.2 Consensus size: 53
391193 AAAAGGTAAG
* * *
391203 ATAAAGAAAAAAAGATAAAATAGTAAGTAAAATAAATATAAAAAAATAAAGAA
1 ATAAAGAAAAAAAGAAAAAATAGTAAATAAAACAAATATAAAAAAATAAAGAA
* *
391256 ATAAAGAAAAAGAGGAAAAAAATA-TAAATAAAACAAATA-AATAAAATAATA-ATA
1 ATAAAGAAAAA-AAG-AAAAAATAGTAAATAAAACAAATATAAAAAAATAA-AGA-A
*
391310 ATAAAGTAAAAA
1 ATAAAGAAAAAA
391322 TAATATATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
53 22 0.39
54 27 0.48
55 7 0.12
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (53 bp):
ATAAAGAAAAAAAGAAAAAATAGTAAATAAAACAAATATAAAAAAATAAAGAA
Found at i:391370 original size:33 final size:32
Alignment explanation
Indices: 391279--391374 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
391269 GGAAAAAAAT
391279 ATAAATAAAACAAATAAATAAA-ATA-ATA-ATA
1 ATAAATAAAA-AAATAAA-AAATATATATATATA
* *
391310 ATAAAGTAAAAATAAT-ATATATATATATATATA
1 ATAAA-TAAAAA-AATAAAAAATATATATATATA
391343 ATAAATAAAAAAATAAAAAATAGTATATATAT
1 ATAAATAAAAAAATAAAAAATA-TATATATAT
391375 GTATATAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
30 2 0.04
31 13 0.24
32 22 0.41
33 17 0.31
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (32 bp):
ATAAATAAAAAAATAAAAAATATATATATATA
Found at i:391374 original size:45 final size:46
Alignment explanation
Indices: 391291--391442 Score: 132
Period size: 45 Copynumber: 3.3 Consensus size: 46
391281 AAATAAAACA
* *
391291 AATAAATAAAATAATAATAATAAAGTAAAAATAATATATATATATATATAT
1 AATAAATAAAAAAATAA-AA-AAA-T-AATAT-ATATATATATATATATAT
* * *
391342 AATAAATAAAAAAAT-AAAAAATAGTATATATATGTATATAAAT-T
1 AATAAATAAAAAAATAAAAAAATAATATATATATATATATATATAT
** * *
391386 AATAAA-ACTGATAATAAAAAAATAATATATATATATATA-ATCTAT
1 AATAAATA-AAAAAATAAAAAAATAATATATATATATATATATATAT
*
391431 AAAAAATAAAAA
1 AATAAATAAAAA
391443 TATATACTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
43 1 0.01
44 13 0.16
45 42 0.52
46 4 0.05
47 1 0.01
48 3 0.04
49 2 0.02
50 1 0.01
51 14 0.17
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (46 bp):
AATAAATAAAAAAATAAAAAAATAATATATATATATATATATATAT
Found at i:391460 original size:26 final size:28
Alignment explanation
Indices: 391400--391461 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 28
391390 AAACTGATAA
*
391400 TAAAAAAATAATATATATATATATAATC
1 TAAAAAAATAATATATATATATATAAAC
*
391428 TATAAAAAATAA-A-A-ATATATACTAAAG
1 TA-AAAAAATAATATATATATATA-TAAAC
391455 TAAAAAA
1 TAAAAAA
391462 GAAAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 12 0.40
27 6 0.20
28 3 0.10
29 9 0.30
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAAAAAATAATATATATATATATAAAC
Found at i:396286 original size:20 final size:21
Alignment explanation
Indices: 396261--396304 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
396251 TCCCATACTT
396261 TTCCATAAGGTTCCACAC-TC
1 TTCCATAAGGTTCCACACATC
396281 TTCCATAAGGTTCCACACATC
1 TTCCATAAGGTTCCACACATC
396302 TTC
1 TTC
396305 ATATATCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.32
Consensus pattern (21 bp):
TTCCATAAGGTTCCACACATC
Found at i:396450 original size:20 final size:20
Alignment explanation
Indices: 396427--396484 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
396417 TTCCAAATTC
* *
396427 TTCCATACTTTTCCATAAGG
1 TTCCACACTCTTCCATAAGG
396447 TTCCACACTCTTCCATAAGG
1 TTCCACACTCTTCCATAAGG
396467 TTCCACACATCTT-CATAA
1 TTCCACAC-TCTTCCATAA
396485 TATTCCAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (20 bp):
TTCCACACTCTTCCATAAGG
Found at i:396490 original size:20 final size:20
Alignment explanation
Indices: 396427--396491 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
396417 TTCCAAATTC
* * *
396427 TTCCATACTTTTCCATAAGG
1 TTCCACACTCTTCCATAAGA
*
396447 TTCCACACTCTTCCATAAGG
1 TTCCACACTCTTCCATAAGA
*
396467 TTCCACACATCTT-CATAATA
1 TTCCACAC-TCTTCCATAAGA
396487 TTCCA
1 TTCCA
396492 GAGGATTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 36 0.90
21 4 0.10
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.35
Consensus pattern (20 bp):
TTCCACACTCTTCCATAAGA
Found at i:396491 original size:30 final size:29
Alignment explanation
Indices: 396457--396539 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
396447 TTCCACACTC
*
396457 TTCCATAAGGTTCCACACATCTTCATAATA
1 TTCCA-AAGGTTCCACACATCTTCAGAATA
* * *
396487 TTCCAGAGGATTCCACACATCTCCAGATTA
1 TTCCAAAGG-TTCCACACATCTTCAGAATA
*
396517 TTCCAGAAGATTCCACAC-TCTTC
1 TTCCA-AAGGTTCCACACATCTTC
396540 CACAAGCTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 7 0.16
30 35 0.80
31 2 0.05
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (29 bp):
TTCCAAAGGTTCCACACATCTTCAGAATA
Found at i:407473 original size:30 final size:30
Alignment explanation
Indices: 407425--407502 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
407415 TTCCATACTC
* * * *
407425 TTCCATAAGGTTCTACACATCTCTAGAATA
1 TTCCAGAAGATTCCACACATCTCCAGAATA
* *
407455 TTCCAGAGGATTCCACACATCTCCAGATTA
1 TTCCAGAAGATTCCACACATCTCCAGAATA
407485 TTCCAGAAGATTCCACAC
1 TTCCAGAAGATTCCACAC
407503 TCTTCCACAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (30 bp):
TTCCAGAAGATTCCACACATCTCCAGAATA
Found at i:408205 original size:31 final size:31
Alignment explanation
Indices: 408164--408223 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
408154 AGTAAACTAG
408164 CTTCCCTTAGTAAATCAATGACTCACATTAA
1 CTTCCCTTAGTAAATCAATGACTCACATTAA
*
408195 CTTCCTTTAGTAAATCAATGACTCACATT
1 CTTCCCTTAGTAAATCAATGACTCACATT
408224 TAACCTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (31 bp):
CTTCCCTTAGTAAATCAATGACTCACATTAA
Found at i:411198 original size:21 final size:21
Alignment explanation
Indices: 411151--411196 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
411141 GGATTTGGTA
* *
411151 AAAAGATATTTAAATAATAGT
1 AAAAGATATTTAAATAAAAAT
411172 AAAAGATATTTAAAGTAAAAAT
1 AAAAGATATTTAAA-TAAAAAT
411194 AAA
1 AAA
411197 GAAAAGCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAGATATTTAAATAAAAAT
Found at i:411922 original size:15 final size:17
Alignment explanation
Indices: 411902--411934 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
411892 AAAGATAAAC
411902 AAATAA-ACTAAA-ATA
1 AAATAATACTAAAGATA
411917 AAATAATACTAAAGATA
1 AAATAATACTAAAGATA
411934 A
1 A
411935 TTATTTCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAATACTAAAGATA
Found at i:415630 original size:23 final size:24
Alignment explanation
Indices: 415601--415653 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
415591 AAAATCAGAA
*
415601 AAGAAA-TTAAAGCACTCCAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
* *
415624 AAGAAATTTCAAGCATTCAAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
415648 AAGAAA
1 AAGAAA
415654 AGCAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.15
Consensus pattern (24 bp):
AAGAAATTTAAAGCACTCAAAAAG
Found at i:422920 original size:30 final size:30
Alignment explanation
Indices: 422880--423019 Score: 262
Period size: 30 Copynumber: 4.7 Consensus size: 30
422870 TCCGAAGGAC
* *
422880 CTATCTAGAGGTCATAAAGTTCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
422910 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
422940 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
422970 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
423000 CTATCCAGAGGTCATAAAGA
1 CTATCCAGAGGTCATAAAGA
423020 AACTATCCAG
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 108 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:423026 original size:22 final size:22
Alignment explanation
Indices: 422998--423041 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
422988 GATCCTCGGT
422998 AACTATCCAGAGGTCATAAAGA
1 AACTATCCAGAGGTCATAAAGA
423020 AACTATCCAGAGGTCATAAAGA
1 AACTATCCAGAGGTCATAAAGA
423042 TCCGTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (22 bp):
AACTATCCAGAGGTCATAAAGA
Found at i:427492 original size:30 final size:30
Alignment explanation
Indices: 427343--427475 Score: 257
Period size: 30 Copynumber: 4.4 Consensus size: 30
427333 TCCGAAGGAC
427343 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
427373 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
427403 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
427433 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
427463 CTATCCATAGGTC
1 CTATCCAGAGGTC
427476 CCGAAGAACC
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:427492 original size:60 final size:60
Alignment explanation
Indices: 427343--427500 Score: 244
Period size: 60 Copynumber: 2.6 Consensus size: 60
427333 TCCGAAGGAC
*
427343 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
*
427403 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
427463 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
427501 TATGTTCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 82 0.90
61 9 0.10
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:427515 original size:31 final size:31
Alignment explanation
Indices: 427461--427553 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
427451 GATCCTCGGT
* *
427461 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
427492 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
427523 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
427554 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:430009 original size:45 final size:45
Alignment explanation
Indices: 429925--430152 Score: 251
Period size: 45 Copynumber: 5.0 Consensus size: 45
429915 ATTATGCATT
* *
429925 TTTCAACAATAACATACTTTTTATGTTGATAATGCACCCATATTCA
1 TTTCAACTATAGCATAC-TTTTATGTTGATAATGCACCCATATTCA
* * * *
429971 TTTTAACTATAGCATACTTTTCTGTTGATAATGTACCCATATGCA
1 TTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATTCA
* * * *
430016 TTTCAACTCTAACATACTATTATGTTGATAATGCACACATATGT-A
1 TTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATAT-TCA
* **
430061 TTTCAACTATAGCATACTTTTTTGTTGATAATGCACCCATACGCA
1 TTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATTCA
* * * * * * *
430106 TTTCAACTGTGGCATCCTTTCATGCTGATAATACACCCATATACA
1 TTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATTCA
430151 TT
1 TT
430153 ATTATTTTTG
Statistics
Matches: 150, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
45 136 0.91
46 14 0.09
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.39
Consensus pattern (45 bp):
TTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATATTCA
Found at i:430069 original size:90 final size:91
Alignment explanation
Indices: 429925--430113 Score: 283
Period size: 90 Copynumber: 2.1 Consensus size: 91
429915 ATTATGCATT
* * * *
429925 TTTCAACAATAACATACTTTTTATGTTGATAATGCACCCATATTCATTTTAACTATAGCATACTT
1 TTTCAACTATAACATACTTATTATGTTGATAATGCACACATATTCATTTCAACTATAGCATACTT
* *
429990 TTCTGTTGATAATGTACCCATATGCA
66 TTCTGTTGATAATGCACCCATACGCA
*
430016 TTTCAACTCTAACATAC-TATTATGTTGATAATGCACACATATGT-ATTTCAACTATAGCATACT
1 TTTCAACTATAACATACTTATTATGTTGATAATGCACACATAT-TCATTTCAACTATAGCATACT
*
430079 TTTTTGTTGATAATGCACCCATACGCA
65 TTTCTGTTGATAATGCACCCATACGCA
430106 TTTCAACT
1 TTTCAACT
430114 GTGGCATCCT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 73 0.82
91 16 0.18
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.40
Consensus pattern (91 bp):
TTTCAACTATAACATACTTATTATGTTGATAATGCACACATATTCATTTCAACTATAGCATACTT
TTCTGTTGATAATGCACCCATACGCA
Found at i:433936 original size:29 final size:31
Alignment explanation
Indices: 433865--433937 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 31
433855 AGAATTACCA
433865 CTTTGGTC-CTTAAACTTTTCCAAATTTTACT
1 CTTTGGTCAC-TAAACTTTTCCAAATTTTACT
*
433896 CTTTAG-CTACTAAAC-TTT-CAAATTTTACAT
1 CTTTGGTC-ACTAAACTTTTCCAAATTTTAC-T
433926 -TTTGGTCACTAA
1 CTTTGGTCACTAA
433938 CCAAAATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
29 19 0.53
30 6 0.17
31 10 0.28
32 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (31 bp):
CTTTGGTCACTAAACTTTTCCAAATTTTACT
Found at i:434640 original size:15 final size:15
Alignment explanation
Indices: 434619--434657 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
434609 CACATAGAGG
434619 TACATTTAT-ATGTA
1 TACATTTATAATGTA
*
434633 TAACATTTTTAATGTA
1 T-ACATTTATAATGTA
434649 TACATTTAT
1 TACATTTAT
434658 GTGTTCAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 14 0.67
16 6 0.29
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (15 bp):
TACATTTATAATGTA
Found at i:437454 original size:64 final size:62
Alignment explanation
Indices: 437386--437564 Score: 173
Period size: 64 Copynumber: 2.8 Consensus size: 62
437376 TGTAACACTT
* * * **
437386 AGTGCATCGGTGCACCAAGTGTGCATCGATGCATAAAAGGTATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATAAAA-GCATTCGATGTTTGAATAA-AACCCA
* * * *
437450 AGTGCATCGGTGTAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCATAAG--TGTGCATCGATGCAT-AAAAGCATTCGATGTTTGAATAAAACCCA
* *
437514 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAAAGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCAT-AAAAGCATTCGATGTT
437565 CAATTCATTC
Statistics
Matches: 95, Mismatches: 14, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
64 88 0.93
65 5 0.05
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (62 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATAAAAGCATTCGATGTTTGAATAAAACCCA
Found at i:444166 original size:22 final size:21
Alignment explanation
Indices: 444124--444163 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
444114 AAGAATATTT
444124 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
444145 TCATTTTTTTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
444164 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:446182 original size:64 final size:64
Alignment explanation
Indices: 446092--446268 Score: 187
Period size: 64 Copynumber: 2.8 Consensus size: 64
446082 GAACACTTAG
* * * * **
446092 TGCATCGATGCACCA-AGTGTGAATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTGA
1 TGCATCGATGCA-TAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCAA
*
446155 G
64 A
* * ** * *
446156 TGCATCGGTGCATTGCTTGTGCATCGATGCATGAAATGCATTTGATGTTTTAATAAAACCCAAA
1 TGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAA
* *
446220 TGCATCGATGCATAGAGAGTGCATCGATGCATGAAATACATTCGATGTT
1 TGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
446269 CAATTCATTC
Statistics
Matches: 91, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
64 89 0.98
65 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAA
Found at i:474301 original size:141 final size:142
Alignment explanation
Indices: 474043--474330 Score: 562
Period size: 141 Copynumber: 2.0 Consensus size: 142
474033 TTATTTCATG
474043 ATTC-TACATTTGCTTTGAAGCATAAACCAAAACTTTTCTTCTTGTACAAACACACATCCCAAAC
1 ATTCTTACATTTGCTTTGAAGCATAAACCAAAACTTTTCTTCTTGTACAAACACACATCCCAAAC
474107 CATTATGAGATATTTTACTATAATTCGCATAATATTTTCCAGATTTTAATTATA-TGACCTTGGT
66 CATTATGAGATATTTTACTATAATTCGCATAATATTTTCCAGATTTTAATTATACTGACCTTGGT
474171 GCTTATGTCAAT
131 GCTTATGTCAAT
474183 ATTCTTACATTTGCTTTGAAGCATAAACCAAAACTTTTCTTCTTGTACAAACACACATCCCAAAC
1 ATTCTTACATTTGCTTTGAAGCATAAACCAAAACTTTTCTTCTTGTACAAACACACATCCCAAAC
474248 CATTATGAGATATTTTACTATAATTCGCATAATATTTTCCAGATTTTAATTATACTGACCTTGGT
66 CATTATGAGATATTTTACTATAATTCGCATAATATTTTCCAGATTTTAATTATACTGACCTTGGT
474313 GCTTATGTCAAT
131 GCTTATGTCAAT
474325 ATTCTT
1 ATTCTT
474331 TTTAATATCT
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
140 4 0.03
141 114 0.78
142 28 0.19
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.39
Consensus pattern (142 bp):
ATTCTTACATTTGCTTTGAAGCATAAACCAAAACTTTTCTTCTTGTACAAACACACATCCCAAAC
CATTATGAGATATTTTACTATAATTCGCATAATATTTTCCAGATTTTAATTATACTGACCTTGGT
GCTTATGTCAAT
Found at i:474829 original size:52 final size:52
Alignment explanation
Indices: 474747--474855 Score: 211
Period size: 52 Copynumber: 2.1 Consensus size: 52
474737 AGTATAACTA
474747 AAAT-ACTTGGTTTATCCAATCCATAAGTGTCGTAGGAAAATTCGTTAAATC
1 AAATGACTTGGTTTATCCAATCCATAAGTGTCGTAGGAAAATTCGTTAAATC
474798 AAATGACTTGGTTTATCCAATCCATAAGTGTCGTAGGAAAATTCGTTAAATC
1 AAATGACTTGGTTTATCCAATCCATAAGTGTCGTAGGAAAATTCGTTAAATC
474850 AAATGA
1 AAATGA
474856 GAGTATCGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 4 0.07
52 53 0.93
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (52 bp):
AAATGACTTGGTTTATCCAATCCATAAGTGTCGTAGGAAAATTCGTTAAATC
Found at i:482095 original size:256 final size:255
Alignment explanation
Indices: 481383--482186 Score: 712
Period size: 256 Copynumber: 3.1 Consensus size: 255
481373 ATACTTTCAA
* * * *
481383 AAAAATGAGAAAGTGATTTTTAAAGTTTCTCGTTTGATTTTCAGAAAATGAAATTTATGAAAAGT
1 AAAAATGAGAAAGTGAATTTTAAAGTTTCTCATTTGATTTTCAGAAAATGAATTTTTTGAAAAGT
* * * * * *
481448 GTGACATTGATTTCCAAAGATTCTTACCTAGTATAATATTTCCAAAACTAGTAAGTCATCAT-GC
66 GAGAAAGTGATTTCCAAAGTTTCTTACCTAGTATAATATTTCCAAAACTAGTAAGTCCT-TTGGC
* * * * * * * * *
481512 TCATTAGTAAGTGTTCTTAGC--CTGATGATTAAATCCT-CTAGGTCATATGTAAGTCTTTCGAG
130 -CATCAATAAATATT-TT-GCGGTTGATGATTAAATCCTCCGA-GTCATCTGTAAGTCTTTCAAT
* ** *
481574 CGAGATGATAAGTCCTTCAAGTCATCTATAAGACCTCTAGGAAGGATGTTTTCATATGATGTTTG
191 CAAGATGATAAGTCCTTCAAACCATCTATAAGACCTCTAGGAAGGATGTTTTCATATGATATTTG
* * * *
481639 -AAAATGAGAAAGT-TATTTCAAAGTTTCTCATTTGATTTTCAAAAAATGAAATTTCTT-AAAAG
1 AAAAATGAGAAAGTGAATTTTAAAGTTTCTCATTTGATTTTCAGAAAATG-AATTTTTTGAAAAG
* * *
481701 TGAGAAAGCGATTTCCAAAGTTTCTTA-TTAGTA-AACTATTTCCAAAACTAGTGAA-CCCTTCT
65 TGAGAAAGTGATTTCCAAAGTTTCTTACCTAGTATAA-TATTTCCAAAACTAGT-AAGTCCTT-T
* * * *
481763 GGCTATCACT--ATATCTTT-CGAGTCTGATGATTAAATCATCTG-GATCATCTGTAAGTCTTCT
127 GGCCATCAATAAATAT-TTTGCG-GT-TGATGATTAAATCCTCCGAG-TCATCTGTAAGTCTT-T
* * *
481824 GAAT-AAGATGATAAGTCC-TCAAAACCATGTATAAGACCT-TCCGGCAA-GATGTTTTCATATG
187 CAATCAAGATGATAAGTCCTTC-AAACCATCTATAAGACCTCT-AGG-AAGGATGTTTTCATATG
481885 ATATTTG
249 ATATTTG
* ** * * **
481892 AAAAATAAGAAAGTGAATTTTAAAGCCTCTAATTTTATTTTCAGAAAATGAATTTTTTGGCAAGT
1 AAAAATGAGAAAGTGAATTTTAAAGTTTCTCATTTGATTTTCAGAAAATGAATTTTTTGAAAAGT
* * *
481957 AAGAAAGTGATTTCCAAAGTTTCTTACCTAGTATAATATTTCCAAGACCAGTAAGTCCTTTGGGC
66 GAGAAAGTGATTTCCAAAGTTTCTTACCTAGTATAATATTTCCAAAACTAGTAAGTCCTTT-GGC
* * *
482022 CATCAATAAATATTTTGCGGTTGATGATTAAAGCCTCCGAGTCATCTATAAGTCTTTTAATCAAG
130 CATCAATAAATATTTTGCGGTTGATGATTAAATCCTCCGAGTCATCTGTAAGTCTTTCAATCAAG
* **** * * * *
482087 ATGATAAGTCATTTGGGCCATCTATTAGACCTAT-GAGCATGATGTTTTCATATGATATTTG
195 ATGATAAGTCCTTCAAACCATCTATAAGACCTCTAG-GAAGGATGTTTTCATATGATATTTG
* * *
482148 TAAAAAATGAGAAAGT-AATTTCCAAAATTTCTCAATTGA
1 --AAAAATGAGAAAGTGAATTT-TAAAGTTTCTCATTTGA
482187 AAAAAATCAA
Statistics
Matches: 437, Mismatches: 76, Indels: 68
0.75 0.13 0.12
Matches are distributed among these distances:
249 1 0.00
251 4 0.01
252 7 0.02
253 106 0.24
254 84 0.19
255 83 0.19
256 108 0.25
257 15 0.03
258 29 0.07
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (255 bp):
AAAAATGAGAAAGTGAATTTTAAAGTTTCTCATTTGATTTTCAGAAAATGAATTTTTTGAAAAGT
GAGAAAGTGATTTCCAAAGTTTCTTACCTAGTATAATATTTCCAAAACTAGTAAGTCCTTTGGCC
ATCAATAAATATTTTGCGGTTGATGATTAAATCCTCCGAGTCATCTGTAAGTCTTTCAATCAAGA
TGATAAGTCCTTCAAACCATCTATAAGACCTCTAGGAAGGATGTTTTCATATGATATTTG
Found at i:482204 original size:14 final size:14
Alignment explanation
Indices: 482187--482249 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
482177 TCTCAATTGA
482187 AAAAAATCAAAAAG
1 AAAAAATCAAAAAG
482201 --AAAATCAAAAA-
1 AAAAAATCAAAAAG
482212 AAGAAAATCAAAAAAG
1 AA-AAAATC-AAAAAG
*
482228 ATAAAGAT-AAACAAG
1 A-AAAAATCAAA-AAG
482243 AAAAAAT
1 AAAAAAT
482250 AAATACATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
12 11 0.28
14 14 0.35
15 9 0.22
16 5 0.12
17 1 0.03
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (14 bp):
AAAAAATCAAAAAG
Found at i:482211 original size:13 final size:13
Alignment explanation
Indices: 482189--482228 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 13
482179 TCAATTGAAA
482189 AAAATC-AAAAAG
1 AAAATCAAAAAAG
482201 AAAATCAAAAAAAG
1 AAAATC-AAAAAAG
482215 AAAATCAAAAAAG
1 AAAATCAAAAAAG
482228 A
1 A
482229 TAAAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 12 0.46
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAATCAAAAAAG
Found at i:483487 original size:96 final size:96
Alignment explanation
Indices: 483260--483465 Score: 283
Period size: 96 Copynumber: 2.1 Consensus size: 96
483250 ACTTAGGTGG
483260 GTATCGATACCATGAGGAAGGTATCGATACCATTGATTTACAGAATGCAAAAATGGTATCGATAC
1 GTATCGATACCATGAGGAAGGTATCGATACCATTGATTTACAGAATGCAAAAATGGTATCGATAC
*
483325 AGTAAGAGAGTATCGGTACCATAATACAGAA
66 AGAAAGAGAGTATCGGTACCATAATACAGAA
* * *
483356 GTATCGATA-CTTAGAGGAAGGTATCGATACCATTGATTTACAGAATGTC-GAAATGTTATCGAT
1 GTATCGATACCAT-GAGGAAGGTATCGATACCATTGATTTACAGAATG-CAAAAATGGTATCGAT
* * * * *
483419 ACTGAAAGGGAGTTTTC-GTACCATAGTATAGAA
64 ACAGAAAGAGAG-TATCGGTACCATAATACAGAA
483452 GTATCGATACCATG
1 GTATCGATACCATG
483466 GTATGGGTAC
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.02
96 88 0.92
97 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (96 bp):
GTATCGATACCATGAGGAAGGTATCGATACCATTGATTTACAGAATGCAAAAATGGTATCGATAC
AGAAAGAGAGTATCGGTACCATAATACAGAA
Found at i:483904 original size:45 final size:45
Alignment explanation
Indices: 483840--484320 Score: 514
Period size: 45 Copynumber: 10.7 Consensus size: 45
483830 AAATAAGACT
* * * *
483840 TTAAAGGCATGAAAAGATGCCATAAATGAAATACACAATGGTGCA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* * * * * ** *
483885 TTAAATGCATGAAATGATGCCATAATTGAAATACACAATAGTGTA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* ** ** *
483930 TTAAAGTCATGAAATAATGTTATAAA-GCAAATGCATAACGGTACA
1 TTAAAGGCATGAAAGGATGCCATAAATG-AAATGCATAACGGTGCA
* * * *
483975 ATAAAGGCATGAAAGGATGTCATAAATGAAATGCATAACGATTCA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* * * *
484020 TTAAAGGCATTAAAGGATGCAATAAATGAAATGCATAATGATGCA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* *
484065 TTAAAGGCATGAAAGGATGCCATAAATGAAATGTATAACGGTCCA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* *
484110 TTAAAGGCATGAAATGATGCCATAAATGAAATGCATAACAGTGCA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* * * * * *
484155 TTAATGGCATTAAATGATGCCATAAATAAAATTCATAATGGTGCA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* * * *
484200 TTAAAGGCATGAAAGGATGTCATAAATAAAATGCATAACAGTGCT
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* * * * * *
484245 TTAAAGGTATAAAAGGATGTCATAAATAAAATGCATAACTGTACA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
* *
484290 TTAAAGGCATGAAGGGATGCCATAACTGAAA
1 TTAAAGGCATGAAAGGATGCCATAAATGAAA
484321 ATAATGAATA
Statistics
Matches: 369, Mismatches: 65, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
44 1 0.00
45 367 0.99
46 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (45 bp):
TTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTGCA
Found at i:486799 original size:25 final size:26
Alignment explanation
Indices: 486754--486804 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
486744 CGACCCCATT
486754 ATATAATATGTTATCTATATTATATA
1 ATATAATATGTTATCTATATTATATA
*
486780 ATATAA-ATGTT-TTTATTATTATATA
1 ATATAATATGTTATCTA-TATTATATA
486805 TACATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 14 0.61
26 6 0.26
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
ATATAATATGTTATCTATATTATATA
Found at i:486846 original size:21 final size:20
Alignment explanation
Indices: 486792--486847 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 20
486782 ATAAATGTTT
486792 TTATTATTATATATACATATA
1 TTATTATTAT-TATACATATA
486813 TTA-TATTACATTATACATATTA
1 TTATTATT--ATTATACATA-TA
486835 TTATTATTATTAT
1 TTATTATTATTAT
486848 TATGTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.13
21 16 0.52
22 7 0.23
23 4 0.13
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTATTATTATACATATA
Found at i:496253 original size:37 final size:36
Alignment explanation
Indices: 496212--496302 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 36
496202 TTATAAAAAG
* *
496212 AAAGAAACAGAAAAGAAAATAATAAAAAATAGAAT-AA
1 AAAGAAA-AGAAAAGAAAAGAAT-AAAAAGAGAATAAA
* *
496249 AAAGAAAAAGAAAA-CAAAGAATAAAAAGGGAATAGAA
1 AAAG-AAAAGAAAAGAAAAGAATAAAAAGAGAATA-AA
496286 AAAGAAAAGAAAAGAAA
1 AAAGAAAAGAAAAGAAA
496303 TACATGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
35 9 0.20
36 15 0.33
37 18 0.40
38 3 0.07
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (36 bp):
AAAGAAAAGAAAAGAAAAGAATAAAAAGAGAATAAA
Found at i:500372 original size:43 final size:45
Alignment explanation
Indices: 500311--500432 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 45
500301 GGTAAGTATG
*
500311 AAAATAAGCTTACAAGCTTATGA-AT-AATGGCAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGAGATAAATGGCAAGTATATTGAT
* * * * *
500354 AAAATAAGCTTACGAGCTTATGGAGTTTAAATGGTAGGTATTTTGGT
1 AAAATAAGCTTACGAGCTTAT-GAG-ATAAATGGCAAGTATATTGAT
*
500401 AAAATAAGCTTACGAGCTTATGGGATAAATGG
1 AAAATAAGCTTACGAGCTTATGAGATAAATGG
500433 TAAGAGATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 20 0.30
44 2 0.03
45 7 0.10
46 3 0.04
47 35 0.52
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGAGATAAATGGCAAGTATATTGAT
Found at i:503173 original size:12 final size:11
Alignment explanation
Indices: 503156--503243 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 11
503146 TTATAAAAAG
503156 AAAGAAACATAA
1 AAAGAAA-ATAA
503168 AAAGAAAATAA
1 AAAGAAAATAA
*
503179 TAA-AAAATAGA
1 AAAGAAAATA-A
* *
503190 ATA-AAAAGAA
1 AAAGAAAATAA
*
503200 AAAGAAAACAA
1 AAAGAAAATAA
*
503211 AGAATAAAAATAA
1 A-AA-GAAAATAA
503224 AATAGAAAA-AGA
1 AA-AGAAAATA-A
503236 AAAGAAAA
1 AAAGAAAA
503244 GAAATAGATG
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
10 9 0.15
11 27 0.44
12 17 0.28
13 8 0.13
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.09
Consensus pattern (11 bp):
AAAGAAAATAA
Found at i:503214 original size:24 final size:26
Alignment explanation
Indices: 503164--503233 Score: 92
Period size: 24 Copynumber: 2.8 Consensus size: 26
503154 AGAAAGAAAC
503164 ATAAAAAGAAAATA-ATAAAAAATAGA
1 ATAAAAAGAAAATAGA-AAAAAATAGA
*
503190 ATAAAAAGAAAA-AGAAAACAA-AGA
1 ATAAAAAGAAAATAGAAAAAAATAGA
*
503214 ATAAAAATAAAATAGAAAAA
1 ATAAAAAGAAAATAGAAAAA
503234 GAAAAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 14 0.36
25 12 0.31
26 13 0.33
ACGTcount: A:0.79, C:0.01, G:0.09, T:0.11
Consensus pattern (26 bp):
ATAAAAAGAAAATAGAAAAAAATAGA
Found at i:507354 original size:47 final size:44
Alignment explanation
Indices: 507261--507375 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 44
507251 AAGTACGCAG
507261 ATAAGCTTACGAGCTTAT-GAATAATGGCAAGTATATTGATAAA
1 ATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGATAAA
* * * *
507304 ATAAGCTTACGAGCTTATGGAATTTAAATGGTAGGTATTTTGGTAAA
1 ATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATTGATAAA
* *
507351 ATAAGCTTATGAGCTTATGGGATAA
1 ATAAGCTTACGAGCTTATGGAATAA
507376 ATGGTAAGAG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
43 18 0.29
44 5 0.08
45 1 0.02
46 1 0.02
47 37 0.60
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (44 bp):
ATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGATAAA
Found at i:508647 original size:23 final size:22
Alignment explanation
Indices: 508591--508648 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
508581 AGAAATGTTT
508591 TTATTATTAT-ATATACATATA
1 TTATTATTATAATATACATATA
*
508612 TTA-TATTACAATATACATATTA
1 TTATTATTATAATATACATA-TA
*
508634 TTATTATAATAATAT
1 TTATTATTATAATAT
508649 TTTTATTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 5 0.16
21 12 0.39
22 5 0.16
23 9 0.29
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTATTATAATATACATATA
Found at i:509908 original size:18 final size:17
Alignment explanation
Indices: 509887--509970 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 17
509877 TTCACTTTTG
509887 TTTTATTTTGTTTTATTA
1 TTTTATTTT-TTTTATTA
**
509905 TTTT-TTTCTCTTTTAACA
1 TTTTATTT-T-TTTTATTA
*
509923 TTTTATTATTTTTTGTATTT
1 TTTTA-T-TTTTTT-TATTA
*
509943 TTATTATTTTTTTT-GTA
1 TT-TTATTTTTTTTATTA
509960 TTTTATTTTTT
1 TTTTATTTTTT
509971 CTTTTGAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
16 9 0.17
17 6 0.12
18 16 0.31
19 9 0.17
20 7 0.13
21 5 0.10
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTTTTATTA
Found at i:509935 original size:9 final size:9
Alignment explanation
Indices: 509887--509953 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
509877 TTCACTTTTG
*
509887 TTTTATTTT
1 TTTTATTAT
509896 GTTTTATTAT
1 -TTTTATTAT
*
509906 TTTT-TTCT
1 TTTTATTAT
**
509914 CTTTTAACA-
1 -TTTTATTAT
509923 TTTTATTAT
1 TTTTATTAT
509932 TTTT-TGTAT
1 TTTTAT-TAT
509941 TTTTATTAT
1 TTTTATTAT
509950 TTTT
1 TTTT
509954 TTTGTATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
8 10 0.22
9 26 0.58
10 9 0.20
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:509955 original size:19 final size:18
Alignment explanation
Indices: 509922--509976 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
509912 CTCTTTTAAC
509922 ATTTTATTA-TTTTTTGT
1 ATTTTATTATTTTTTTGT
509939 ATTTTTATTATTTTTTTTGT
1 A-TTTTATTA-TTTTTTTGT
*
509959 ATTTTATTTTTTCTTTTG
1 ATTTTATTATTT-TTTTG
509977 AAATTTAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.03
18 11 0.33
19 12 0.36
20 9 0.27
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (18 bp):
ATTTTATTATTTTTTTGT
Found at i:509956 original size:20 final size:19
Alignment explanation
Indices: 509922--509976 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 19
509912 CTCTTTTAAC
509922 ATTTTATTA--TTTTTTGT
1 ATTTTATTATTTTTTTTGT
509939 ATTTTTATTATTTTTTTTGT
1 A-TTTTATTATTTTTTTTGT
509959 ATTTTATT-TTTTCTTTTG
1 ATTTTATTATTTT-TTTTG
509977 AAATTTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.03
18 12 0.35
19 12 0.35
20 9 0.26
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (19 bp):
ATTTTATTATTTTTTTTGT
Found at i:509983 original size:19 final size:19
Alignment explanation
Indices: 509924--509983 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
509914 CTTTTAACAT
* **
509924 TTTATTATTTTTTGT-ATT
1 TTTATTATTTTTTTTGAAA
* *
509942 TTTATTATTTTTTTTGTAT
1 TTTATTATTTTTTTTGAAA
509961 TTTATT-TTTTCTTTTGAAA
1 TTTATTATTTT-TTTTGAAA
509980 TTTA
1 TTTA
509984 ACATTTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTATTATTTTTTTTGAAA
Found at i:510033 original size:16 final size:16
Alignment explanation
Indices: 510014--510044 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
510004 GTTTTTCTTT
510014 TAACATTTTTTATATA
1 TAACATTTTTTATATA
510030 TAACATTTTTTATAT
1 TAACATTTTTTATAT
510045 TTTTCTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TAACATTTTTTATATA
Found at i:510208 original size:6 final size:6
Alignment explanation
Indices: 510197--510223 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
510187 GAATCGGTTT
510197 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
510224 TTGCGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:512894 original size:10 final size:9
Alignment explanation
Indices: 512821--512913 Score: 53
Period size: 10 Copynumber: 9.4 Consensus size: 9
512811 AATTTAACAC
512821 TTTTTTATT
1 TTTTTTATT
*
512830 TCATTTTTGTT
1 T--TTTTTATT
*
512841 TTGTTTTTTT
1 TT-TTTTATT
512851 TGTTTTTATT
1 T-TTTTTATT
*
512861 ATTGTTTT-CT
1 -TT-TTTTATT
* *
512871 TTTTTAACAT
1 TTTTTTA-TT
512881 TTTTTTATT
1 TTTTTTATT
512890 ATTTTTTATT
1 -TTTTTTATT
512900 TTATTTTATT
1 TT-TTTTATT
512910 TTTT
1 TTTT
512914 CTCCTAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
8 3 0.05
9 9 0.14
10 40 0.61
11 14 0.21
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTTTATT
Found at i:512901 original size:17 final size:17
Alignment explanation
Indices: 512821--512913 Score: 57
Period size: 17 Copynumber: 5.4 Consensus size: 17
512811 AATTTAACAC
*
512821 TTTTTTATTTCATTTT-
1 TTTTTTATTTTATTTTA
* *
512837 TGTTTTGTTTT-TTTT-
1 TTTTTTATTTTATTTTA
* * *
512852 GTTTTTATTATTGTTTTC
1 TTTTTTATT-TTATTTTA
*
512870 TTTTTTAACATTTTTTTATTA
1 TTTTTT---ATTTTATT-TTA
512891 TTTTTTATTTTATTTTA
1 TTTTTTATTTTATTTTA
512908 TTTTTT
1 TTTTTT
512914 CTCCTAAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
15 10 0.17
16 10 0.17
17 13 0.22
18 12 0.20
20 4 0.07
21 11 0.18
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTTTATTTTATTTTA
Found at i:517307 original size:96 final size:95
Alignment explanation
Indices: 517133--517308 Score: 221
Period size: 96 Copynumber: 1.8 Consensus size: 95
517123 ACTTAGGTGT
* * *
517133 GTATCGATATCATTGATTTACAGAACGCAAAAATGGTATCGATACCGTAATAGAGTATCGATACC
1 GTATCGATACCATTGATTTACAGAACGCAAAAATGGTATCGATA-CATAAAAGAGTATCGATACC
517198 ATAATACAGAAGTATCGGTACTGAGAGGAAG
65 ATAATACAGAAGTATCGGTACTGAGAGGAAG
* * **
517229 GTATTGATACCATTGATTTACAGAATGCCGAAATGGTATCGATA-ATAAAAGGGAGTATC-AGTA
1 GTATCGATACCATTGATTTACAGAACGCAAAAATGGTATCGATACATAAAA--GAGTATCGA-TA
* *
517292 CCATAGTATAGAAGTAT
63 CCATAATACAGAAGTAT
517309 TGATACCATG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
94 4 0.06
95 1 0.01
96 63 0.93
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (95 bp):
GTATCGATACCATTGATTTACAGAACGCAAAAATGGTATCGATACATAAAAGAGTATCGATACCA
TAATACAGAAGTATCGGTACTGAGAGGAAG
Found at i:517742 original size:45 final size:45
Alignment explanation
Indices: 517690--518217 Score: 741
Period size: 45 Copynumber: 11.7 Consensus size: 45
517680 ATAAATAAGA
* **
517690 CATTAAAGGCATGAAAGGATGCTATAAATGAAATGCATAATAGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* *
517735 TATTAAAGGCATGAAAGGATTCCATAAATGAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * * * *
517780 CATTAAAGGCATGAAATGATGTCATAAAAGAAATGTATAACGATG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* *
517825 CATTAAAGGCATGAAAGGATGCCATGAATGAAATGTATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
*
517870 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGTTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * * ***
517915 TATTAAAGGCATGAAAGAATGCCATAAATGAAATGCATTATAATG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
517960 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * * * *
518005 TATTAAAGGCATGAAAAGATGCCATAAATAAAATGCATAATGGTT
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * *
518050 CATTAATGGCATGAAATGATGCCATAAATAAAATGCATAACGGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* **
518095 CATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAATAGTG
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* * *
518140 CATTAAAGGCATGAAAGAATGCCATAAATAAAATGCATAACGGTA
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
* *
518185 CATTAAAGGCATAAAAGGATGCCATAACTGAAA
1 CATTAAAGGCATGAAAGGATGCCATAAATGAAA
518218 ATAATGAATA
Statistics
Matches: 429, Mismatches: 54, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 429 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (45 bp):
CATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGTG
Done.