Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:384290 original size:10 final size:10
Alignment explanation
Indices: 384275--384313 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
384265 TCATCATACA
384275 AAATTCTCTC
1 AAATTCTCTC
384285 AAATTCTCTC
1 AAATTCTCTC
*
384295 AACTTCTCTC
1 AAATTCTCTC
*
384305 AAATACTCT
1 AAATTCTCT
384314 TATAATATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:391357 original size:31 final size:32
Alignment explanation
Indices: 391259--391362 Score: 106
Period size: 31 Copynumber: 3.3 Consensus size: 32
391249 GTAAATTAAG
** *
391259 ATAAAATATATACTTTGAAAAGTTAAAATAATA
1 ATAAAATATATA-TTTTTAAAGTTAAAATAAAA
* * * *
391292 AT--AACATATATTTTTAATAGTTTAGATAAGA
1 ATAAAATATATATTTTTAA-AGTTAAAATAAAA
391323 ATAAAATATATATTTTTAAA-TTAAAATAAAA
1 ATAAAATATATATTTTTAAAGTTAAAATAAAA
391354 ATAAAATAT
1 ATAAAATAT
391363 TTTAATCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
30 5 0.09
31 36 0.62
32 1 0.02
33 16 0.28
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (32 bp):
ATAAAATATATATTTTTAAAGTTAAAATAAAA
Found at i:391365 original size:26 final size:26
Alignment explanation
Indices: 391336--391393 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
391326 AAATATATAT
*
391336 TTTTAAATTAAAATAAAAATAAAATA
1 TTTTAAATCAAAATAAAAATAAAATA
** *
391362 TTTT-AATCAAGTTAATAATAAAATA
1 TTTTAAATCAAAATAAAAATAAAATA
391387 TATTTAA
1 T-TTTAA
391394 TAAGTAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 18 0.69
26 7 0.27
27 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (26 bp):
TTTTAAATCAAAATAAAAATAAAATA
Found at i:391412 original size:25 final size:25
Alignment explanation
Indices: 391349--391402 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
391339 TAAATTAAAA
391349 TAAA-AATAAAATATTTTAATCAAG
1 TAAATAATAAAATATTTTAATCAAG
*
391373 TTAATAATAAAATATATTTAAT-AAG
1 TAAATAATAAAATAT-TTTAATCAAG
391398 TAAAT
1 TAAAT
391403 CTAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 3 0.12
25 17 0.65
26 6 0.23
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (25 bp):
TAAATAATAAAATATTTTAATCAAG
Found at i:400348 original size:216 final size:216
Alignment explanation
Indices: 399974--400398 Score: 769
Period size: 216 Copynumber: 2.0 Consensus size: 216
399964 GATCAAGCCT
* *
399974 ATGCCAACATCTATCGACAAGGTGTCCAAGCTTAATTTCCACAAAGCTGACACTTCTGCCTTGGC
1 ATGCCAACATCTATCGACAAGGTGTCCAAGCTTAATTTCCACAAAGCCGACACTACTGCCTTGGC
* *
400039 ATTTCTTTATACTTACCATCATTATTACCATTGGGTTTGGATCCCCTAAAATGTTTGTTTAACTG
66 ATTTCTTTATACTTACCACCATTATTACCATTGGGTTTAGATCCCCTAAAATGTTTGTTTAACTG
400104 ATTATTGTATTAACCACCAGATCCATGATCCGAATTGTATCGGGTGAAGTTTACTCCTACAAGAA
131 ATTATTGTATTAACCACCAGATCCATGATCCGAATTGTATCGGGTGAAGTTTACTCCTACAAGAA
400169 ATCACGAGGAATCTAAACCCA
196 ATCACGAGGAATCTAAACCCA
400190 ATGCCAACATCTATCGACAAGGTGTCCAAGCTTAATTTCCACAAAGCCGACACTACTGCCTTGGC
1 ATGCCAACATCTATCGACAAGGTGTCCAAGCTTAATTTCCACAAAGCCGACACTACTGCCTTGGC
*
400255 GTTTCTTTATACTTACCACCATTATTACCATTGGGTTTAGATCCCCTAAAATGTTTGTTTAACTG
66 ATTTCTTTATACTTACCACCATTATTACCATTGGGTTTAGATCCCCTAAAATGTTTGTTTAACTG
* * *
400320 ATTATTGTGTTAACCACCAGATCCATGATCCTAGTTGTATCGGGTGAAGTTTACTCCTACAAGAA
131 ATTATTGTATTAACCACCAGATCCATGATCCGAATTGTATCGGGTGAAGTTTACTCCTACAAGAA
*
400385 ATCGCGAGGAATCT
196 ATCACGAGGAATCT
400399 TCAAGTCAAG
Statistics
Matches: 200, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 200 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (216 bp):
ATGCCAACATCTATCGACAAGGTGTCCAAGCTTAATTTCCACAAAGCCGACACTACTGCCTTGGC
ATTTCTTTATACTTACCACCATTATTACCATTGGGTTTAGATCCCCTAAAATGTTTGTTTAACTG
ATTATTGTATTAACCACCAGATCCATGATCCGAATTGTATCGGGTGAAGTTTACTCCTACAAGAA
ATCACGAGGAATCTAAACCCA
Found at i:402329 original size:2 final size:2
Alignment explanation
Indices: 402317--402382 Score: 123
Period size: 2 Copynumber: 32.5 Consensus size: 2
402307 CCCAACAGTT
402317 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
402360 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
402383 TAAAAATGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 61 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:402866 original size:40 final size:40
Alignment explanation
Indices: 402763--402894 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
402753 TGCGAATTTG
* * * *
402763 GAAAATCACAATGCGATACTGACTATCGCAACGCGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
*
402803 ACAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
** * * *
402844 GAATTTCGCAACGCGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
402884 GAAAATCGCAA
1 GAAAATCGCAA
402895 TCATCTTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 43 0.55
41 35 0.45
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
Found at i:402885 original size:20 final size:20
Alignment explanation
Indices: 402775--402876 Score: 125
Period size: 20 Copynumber: 5.0 Consensus size: 20
402765 AAATCACAAT
*
402775 GCGATACTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
* **
402795 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TTTCGCAAC
402816 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
402836 GCGATACTGAATTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
402856 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
402876 G
1 G
402877 AGATTCTGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
19 2 0.03
20 52 0.73
21 15 0.21
22 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
GCGATACTGACTTTCGCAAC
Found at i:403133 original size:20 final size:20
Alignment explanation
Indices: 403108--403183 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
403098 CATCGGGGAA
*
403108 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
* *
403128 ATCGCAATGTGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
403148 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
403168 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
403184 CGCATTGCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:403230 original size:19 final size:19
Alignment explanation
Indices: 403183--403247 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
403173 AACGAGAAAA
403183 TCGCATTGCGA-TTT--TT
1 TCGCATTGCGATTTTCATT
*
403199 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
403216 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
403235 TCGCATTGCGATT
1 TCGCATTGCGATT
403248 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.15
15 3 0.07
16 3 0.07
17 5 0.12
19 24 0.59
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:404876 original size:41 final size:42
Alignment explanation
Indices: 404831--404922 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
404821 CCTCTTCAAC
* * *
404831 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGAACTCTTGAGG
* *
404872 GATGATAGGGGCCTCTTGAACGATTGGAGGGAACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGAACTCTTGAGG
404914 GATGACAGG
1 GATGACAGG
404923 TGAGTCAGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGAACTCTTGAGG
Found at i:405285 original size:20 final size:20
Alignment explanation
Indices: 405260--405298 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
405250 GAAGAATAGT
405260 TTACTTTCACAACACGAAAC
1 TTACTTTCACAACACGAAAC
* *
405280 TTACTTTCGCAACGCGAAA
1 TTACTTTCACAACACGAAA
405299 ATGACTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (20 bp):
TTACTTTCACAACACGAAAC
Found at i:405309 original size:20 final size:20
Alignment explanation
Indices: 405286--405372 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
405276 AAACTTACTT
*
405286 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
405306 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
405326 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* * **
405346 TCGTAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
405365 TCGCAACG
1 TCGCAACG
405373 ACAAAATCGC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 13 0.22
20 45 0.78
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:405424 original size:19 final size:19
Alignment explanation
Indices: 405397--405498 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
405387 CGAACACAAA
*
405397 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
405416 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
405435 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
405451 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
405468 TCGCATTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
405488 TCGTGTTGCGA
1 TCGCGTTGCGA
405499 AAGTAAACTA
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
14 8 0.12
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 40 0.58
20 11 0.16
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:406062 original size:18 final size:18
Alignment explanation
Indices: 406039--406086 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
406029 CGGGTCGATC
406039 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
406057 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
406075 AGGTGATGGCTC
1 AGGTGATGGCTC
406087 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:407428 original size:20 final size:20
Alignment explanation
Indices: 407403--407476 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
407393 AATAGTTTAT
407403 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* *
407423 GAAAATGACAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
** ** *
407443 GAATTTGACTATCGCAACAA
1 GAAAATGAAAATCGCAACAC
*
407463 GAGAAT-AAAATCGC
1 GAAAATGAAAATCGC
407477 GTTGCGATTT
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 6 0.14
20 36 0.86
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.15
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:407751 original size:22 final size:22
Alignment explanation
Indices: 407724--407767 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
407714 GATGGAGATA
407724 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
407746 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
407768 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:408068 original size:20 final size:20
Alignment explanation
Indices: 407954--408067 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
407944 GATTATGTAT
*
407954 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
407974 TATCACGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
407994 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
408014 TATCGCGTTACGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
408035 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
408055 TATCGCGTTGCGA
1 TATCGCGTTGCGA
408068 TTTTCCAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:408071 original size:41 final size:41
Alignment explanation
Indices: 407934--408069 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
407924 CGCTTTGAAA
* *
407934 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
407975 ATCACGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * *
408015 ATCGCGTTACGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
408056 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
408070 TTCCAAATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.39
41 44 0.55
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:408087 original size:41 final size:41
Alignment explanation
Indices: 407954--408089 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
407944 GATTATGTAT
* * * *** *
407954 TATCTCGTTGCGAAAGTCAGTATCACGTTGCGAAAGT-AAG
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTACGATTTTCAAA
** *
407994 TATCGCGTTGCGAAAGTCAGTATCGCGTTACGATTTTGTAT
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTACGATTTTCAAA
* *
408035 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAA
1 TATCGCGTTGCGAAAGTCAGTATCGCGTTACGATTTT-CAAA
*
408077 T-TCGCATTGCGAA
1 TATCGCGTTGCGAA
408090 TTGGGAAAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
40 31 0.39
41 46 0.58
42 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGTCAGTATCGCGTTACGATTTTCAAA
Found at i:408102 original size:21 final size:20
Alignment explanation
Indices: 408078--408130 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
408068 TTTTCCAAAT
408078 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
** *
408099 TCGCAACGCGAAATTGTAAAA
1 TCGCATTGCG-AATTGGAAAA
408120 TCGCATTGCGA
1 TCGCATTGCGA
408131 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:408151 original size:41 final size:41
Alignment explanation
Indices: 407961--408151 Score: 118
Period size: 41 Copynumber: 4.7 Consensus size: 41
407951 TATTATCTCG
* * * *
407961 TTGCGAAAGTCAGTATCACGTTGCGAAA--GTAAGTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGAAATTGTAA-AATCGCA
* * ** ** *
408001 TTGCGAAAGTCAGTATCGCGTTACGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGAAATTGTAAAATCGCA
** ** *
408042 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGAAATTGTAAAATCGCA
* ** ** ***
408083 TTGCGAATTGGGAAAATCGCAACGCGAAATTGTAAAATCGCA
1 TTGCG-ATAGTCAGTATCGCGTTGCGAAATTGTAAAATCGCA
408125 TTGCGATAGTCA-TAATCGCGTTGCGAA
1 TTGCGATAGTCAGT-ATCGCGTTGCGAA
408152 TCTGGAAACT
Statistics
Matches: 114, Mismatches: 33, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
40 24 0.21
41 59 0.52
42 31 0.27
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGAAATTGTAAAATCGCA
Found at i:413667 original size:31 final size:31
Alignment explanation
Indices: 413632--413702 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
413622 TAATAATATG
*
413632 TATATATTTC-AAAAAAATATGTTTTTAAAAC
1 TATATATTTCGAAAAAAATAT-TTTTAAAAAC
* *
413663 TATATGTTTTCGAAAAAACTATTTTTAAAAAC
1 TATAT-ATTTCGAAAAAAATATTTTTAAAAAC
413695 TATATATT
1 TATATATT
413703 ATATTTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 7 0.21
32 18 0.53
33 9 0.26
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (31 bp):
TATATATTTCGAAAAAAATATTTTTAAAAAC
Found at i:425926 original size:21 final size:21
Alignment explanation
Indices: 425896--425935 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
425886 TACGAAAGTT
*
425896 ACTGTTGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
425917 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
425936 ACACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:428854 original size:18 final size:19
Alignment explanation
Indices: 428821--428858 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
428811 AGAAACACAC
428821 TAAAATAATTTGATTCGAA
1 TAAAATAATTTGATTCGAA
*
428840 TAAATTAATTT-ATTCGAA
1 TAAAATAATTTGATTCGAA
428858 T
1 T
428859 CAAGTCGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (19 bp):
TAAAATAATTTGATTCGAA
Found at i:429199 original size:30 final size:31
Alignment explanation
Indices: 429147--429220 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
429137 TTACGGCAGT
*
429147 GACCATATTGCAAACGGACTAAATGTTGAGG
1 GACCATATTGCAAACAGACTAAATGTTGAGG
* *
429178 GACCATATTG-AAATAGACTAAATTTTGAGG
1 GACCATATTGCAAACAGACTAAATGTTGAGG
**
429208 GATTATATTGCAA
1 GACCATATTGCAA
429221 GTTTTAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATGTTGAGG
Found at i:432778 original size:29 final size:30
Alignment explanation
Indices: 432726--432805 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
432716 CTTTTAATAC
** * *
432726 TTACAATATAATCCCCAAATATTTAG-TCTT
1 TTACAATATGGTCCCC-AACATTTAGTTCAT
432756 TTACAATAT-GTCCCTCAACATTTAGTTCAT
1 TTACAATATGGTCCC-CAACATTTAGTTCAT
*
432786 TTGCAATATGGTCCCCAACA
1 TTACAATATGGTCCCCAACA
432806 ACTATTGGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 12 0.28
30 26 0.60
31 5 0.12
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (30 bp):
TTACAATATGGTCCCCAACATTTAGTTCAT
Found at i:450881 original size:19 final size:20
Alignment explanation
Indices: 450834--450870 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
450824 TCTAAATCTT
450834 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
450854 TTTTCAAAA-TTCATTTT
1 TTTTCAAAATTTCATTTT
450871 TGCTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGA
Found at i:455321 original size:26 final size:26
Alignment explanation
Indices: 455292--455344 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
455282 AAAATATTGA
455292 AGGTCGCCATGGCATCTGTGCGAGGT
1 AGGTCGCCATGGCATCTGTGCGAGGT
*
455318 AGGTCGCCATGGTATCTGTGCGAGGT
1 AGGTCGCCATGGCATCTGTGCGAGGT
455344 A
1 A
455345 TGCGAGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.38, T:0.25
Consensus pattern (26 bp):
AGGTCGCCATGGCATCTGTGCGAGGT
Found at i:455413 original size:16 final size:16
Alignment explanation
Indices: 455362--455413 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
455352 GAATTCGAGC
455362 GAGCTATGTAATGCAT
1 GAGCTATGTAATGCAT
* * * *
455378 GAGCCAAG-AACTGAAC
1 GAGCTATGTAA-TGCAT
455394 GAGCTATGTAATGCAT
1 GAGCTATGTAATGCAT
455410 GAGC
1 GAGC
455414 CATGAACGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (16 bp):
GAGCTATGTAATGCAT
Found at i:455945 original size:21 final size:21
Alignment explanation
Indices: 455920--455963 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
455910 AACTTAGTTA
455920 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
455941 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
455962 AT
1 AT
455964 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:456004 original size:32 final size:28
Alignment explanation
Indices: 455940--455999 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
455930 TAGTATAAAT
455940 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
455968 TATTAGTTTGTTAGTTTAAGTTATA-TA
1 TATTAGTTTGTTAGTTTAAGTTATATTA
455995 TATTA
1 TATTA
456000 TATTATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 7 0.22
28 25 0.78
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTTAAGTTATATTA
Found at i:456503 original size:37 final size:37
Alignment explanation
Indices: 456438--456511 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
456428 ATAATTATCG
456438 TTTAAGAAAATATTGTGTTTAAAAATATT-TAGTGTTT
1 TTTAAGAAAATATTGTGTTTAAAAATATTATA-TGTTT
* **
456475 TTTAA-AAAATATTTTGTTTAATTTATATTATATGTTT
1 TTTAAGAAAATATTGTGTTTAA-AAATATTATATGTTT
456512 AAATTAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 15 0.47
37 15 0.47
38 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.54
Consensus pattern (37 bp):
TTTAAGAAAATATTGTGTTTAAAAATATTATATGTTT
Found at i:456771 original size:26 final size:24
Alignment explanation
Indices: 456722--456785 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
456712 AAATCATATT
*
456722 ATTATTAAATCATAAATATCAAATC
1 ATTATT-AATAATAAATATCAAATC
* * *
456747 ATTAGATTAATAATAATTATTAAATT
1 ATT--ATTAATAATAAATATCAAATC
456773 ATTATTAATAATA
1 ATTATTAATAATA
456786 TTAGTAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 10 0.30
25 3 0.09
26 17 0.52
27 3 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTATTAATAATAAATATCAAATC
Found at i:459808 original size:21 final size:22
Alignment explanation
Indices: 459779--459835 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
459769 CATTATTTAA
*
459779 TAATGATTTTATATTTAA-ATT
1 TAATAATTTTATATTTAATATT
459800 TAATAA-TTTAT-TATTAATATT
1 TAATAATTTTATAT-TTAATATT
* *
459821 TTATAATTTGATATT
1 TAATAATTTTATATT
459836 AATGATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 9 0.31
21 13 0.45
22 5 0.17
23 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
TAATAATTTTATATTTAATATT
Found at i:459836 original size:21 final size:20
Alignment explanation
Indices: 459786--459838 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
459776 TAATAATGAT
459786 TTTATATTTAA-ATTTAATAA
1 TTTATA-TTAATATTTAATAA
*
459806 TTTATTATTAATATTTTATAA
1 TTTA-TATTAATATTTAATAA
459827 TTTGATATTAAT
1 TTT-ATATTAAT
459839 GATTAAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.28
21 20 0.69
22 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTATATTAATATTTAATAA
Found at i:460170 original size:52 final size:54
Alignment explanation
Indices: 460108--460216 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 54
460098 TAATAATTAT
*
460108 ATGATTTAGTAATGATTTGATAATAATAATTTAATAATAATTT-TAAT-ATTTG
1 ATGATTTAGTAATGATTTGATAATAATAATTTAACAATAATTTATAATGATTTG
* *
460160 ATGATTTAGTAATGATTTGATAATAATGATTTAACAATGATTTAGTAATGATTTG
1 ATGATTTAGTAATGATTTGATAATAATAATTTAACAATAATTTA-TAATGATTTG
460215 AT
1 AT
460217 AATAATAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
52 40 0.78
54 4 0.08
55 7 0.14
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (54 bp):
ATGATTTAGTAATGATTTGATAATAATAATTTAACAATAATTTATAATGATTTG
Found at i:460186 original size:14 final size:13
Alignment explanation
Indices: 460117--460280 Score: 105
Period size: 14 Copynumber: 12.8 Consensus size: 13
460107 TATGATTTAG
460117 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
460131 TAAT-AATT-TAA
1 TAATGATTTATAA
*
460142 TAATAATTT-TAA
1 TAATGATTTATAA
* *
460154 TATTTGATGATT-TAG
1 TA-ATGAT--TTATAA
460169 TAATGATTTGATAA
1 TAATGATTT-ATAA
460183 TAATGA-TT-TAA
1 TAATGATTTATAA
* *
460194 CAATGA-TT-TAG
1 TAATGATTTATAA
460205 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
460219 TAAT-AATTATAA
1 TAATGATTTATAA
460231 TAATGATTTAGTAA
1 TAATGATTTA-TAA
*
460245 TAATCA-TTATAA
1 TAATGATTTATAA
460257 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
460271 AAATGATTTA
1 TAATGATTTA
460281 CTAACGATTT
Statistics
Matches: 121, Mismatches: 16, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
11 24 0.20
12 28 0.23
13 21 0.17
14 42 0.35
15 6 0.05
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:460200 original size:88 final size:89
Alignment explanation
Indices: 460108--460342 Score: 277
Period size: 88 Copynumber: 2.7 Consensus size: 89
460098 TAATAATTAT
* *
460108 ATGATTTAGTAATGATTTGATAATAATAATTTAATAATAATTTTAATATTTGATGATT-TAGTAA
1 ATGATTTAGTAATGATTTGATAATAATAATTTAATAATAATTTTAATATTTGATCATTATAATAA
*
460172 TGATTTGATAATAATGATTTAAC-A
66 TGATTTGATAAAAATGATTT-ACTA
* * * *
460196 ATGATTTAGTAATGATTTGATAATAATAATTATAATAATGA-TTTAGTA-ATAATCATTATAATA
1 ATGATTTAGTAATGATTTGATAATAATAATT-TAATAATAATTTTAATATTTGATCATTATAATA
460259 ATGATTTGATAAAAATGATTTACTA
65 ATGATTTGATAAAAATGATTTACTA
* * * *
460284 ACGATTTAGTAATGA-TT-ATTAATAATTATTTATTATTAATATTTAATGATTTGAT-ATTA
1 ATGATTTAGTAATGATTTGA-TAATAATAATTTAATAATAAT-TTTAAT-ATTTGATCATTA
460343 ATGATTAAAT
Statistics
Matches: 124, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
86 7 0.06
87 20 0.16
88 81 0.65
89 13 0.10
90 3 0.02
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (89 bp):
ATGATTTAGTAATGATTTGATAATAATAATTTAATAATAATTTTAATATTTGATCATTATAATAA
TGATTTGATAAAAATGATTTACTA
Found at i:460208 original size:25 final size:25
Alignment explanation
Indices: 460108--460202 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
460098 TAATAATTAT
**
460108 ATGATTTAGTAATGATTTGATAATA
1 ATGATTTAACAATGATTTGATAATA
* * * * * *
460133 ATAATTTAATAATAATTTTAATATTTG
1 ATGATTTAACAATGA-TTTGATA-ATA
**
460160 ATGATTTAGTAATGATTTGATAATA
1 ATGATTTAACAATGATTTGATAATA
460185 ATGATTTAACAATGATTT
1 ATGATTTAACAATGATTT
460203 AGTAATGATT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
25 29 0.54
26 12 0.22
27 13 0.24
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (25 bp):
ATGATTTAACAATGATTTGATAATA
Found at i:460232 original size:12 final size:12
Alignment explanation
Indices: 460215--460260 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
460205 TAATGATTTG
460215 ATAATAATAATT
1 ATAATAATAATT
*
460227 ATAATAATGATTT
1 ATAATAAT-AATT
*
460240 AGTAATAATCATT
1 A-TAATAATAATT
460253 ATAATAAT
1 ATAATAAT
460261 GATTTGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 15 0.52
13 7 0.24
14 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:460234 original size:26 final size:26
Alignment explanation
Indices: 460205--460270 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
460195 AATGATTTAG
460205 TAATGATTTGATAATAATAATTATAA
1 TAATGATTTGATAATAATAATTATAA
*
460231 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATAATTATAA
460257 TAATGATTTGATAA
1 TAATGATTTGATAA
460271 AAATGATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.03
26 35 0.95
27 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (26 bp):
TAATGATTTGATAATAATAATTATAA
Found at i:460408 original size:11 final size:11
Alignment explanation
Indices: 460108--460390 Score: 84
Period size: 11 Copynumber: 22.9 Consensus size: 11
460098 TAATAATTAT
*
460108 ATGATTTAGTA
1 ATGATTTAATA
460119 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
460133 ATAATTTAATA
1 ATGATTTAATA
*
460144 ATAATTTTAATA
1 ATGA-TTTAATA
*
460156 TTTGATGATTTAGTA
1 ----ATGATTTAATA
460171 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
460185 ATGATTTAACA
1 ATGATTTAATA
*
460196 ATGATTTAGTA
1 ATGATTTAATA
460207 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
460221 ATAATTATAATA
1 ATGATT-TAATA
460233 ATGATTTAGTAATA
1 ATGA-TT--TAATA
*
460247 ATCATTATAATA
1 ATGATT-TAATA
*
460259 ATGATTTGATAAAA
1 ATGA-TT--TAATA
*
460273 ATGATTTACTA
1 ATGATTTAATA
* *
460284 ACGATTTAGTA
1 ATGATTTAATA
460295 ATGATTATTAATA
1 ATGA-T-TTAATA
* *
460308 ATTATTTATTA
1 ATGATTTAATA
* *
460319 TTAATATT--TA
1 ATGAT-TTAATA
460329 ATGATTTGATATTA
1 ATGATTT-A-A-TA
*
460343 ATGATTAAATA
1 ATGATTTAATA
*
460354 GTGATTAGTAATA
1 ATGATT--TAATA
460367 ATGAAATTGTAATA
1 ATG--ATT-TAATA
*
460381 ATAATTTAAT
1 ATGATTTAAT
460391 CATTAATAAT
Statistics
Matches: 209, Mismatches: 33, Indels: 60
0.69 0.11 0.20
Matches are distributed among these distances:
9 2 0.01
10 5 0.02
11 68 0.33
12 38 0.18
13 29 0.14
14 55 0.26
15 9 0.04
16 3 0.01
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:460632 original size:19 final size:19
Alignment explanation
Indices: 460599--460635 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
460589 ATCAAAACAC
**
460599 ATATGATTTTTTAATAATT
1 ATATGATTTAGTAATAATT
460618 ATATGATTTAGTAATAAT
1 ATATGATTTAGTAATAAT
460636 GATTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
ATATGATTTAGTAATAATT
Found at i:460639 original size:14 final size:14
Alignment explanation
Indices: 460608--460647 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
460598 CATATGATTT
460608 TTTAATAATTATATGA
1 TTTAATAA-TA-ATGA
*
460624 TTTAGTAATAATGA
1 TTTAATAATAATGA
460638 TTTAATAATA
1 TTTAATAATA
460648 TTTAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 2 0.09
16 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TTTAATAATAATGA
Found at i:460645 original size:11 final size:11
Alignment explanation
Indices: 460629--460792 Score: 88
Period size: 11 Copynumber: 14.6 Consensus size: 11
460619 TATGATTTAG
460629 TAATAATGATT
1 TAATAATGATT
460640 TAATAAT-ATT
1 TAATAATGATT
460650 TAATAATGATT
1 TAATAATGATT
*
460661 TAATAATGTTT
1 TAATAATGATT
* * *
460672 TAAATATTTAAT
1 T-AATAATGATT
* *
460684 GATTTAATGATT
1 TA-ATAATGATT
* *
460696 TAGTAAAGATT
1 TAATAATGATT
*
460707 TGAT-A--A--
1 TAATAATGATT
460713 TAATAATGATTT
1 TAATAATGA-TT
**
460725 AGTAATAACCATT
1 --TAATAATGATT
460738 ATAATAATGATTT
1 -TAATAATGA-TT
460751 GATAATAATGATT
1 --TAATAATGATT
460764 TAATAATGATT
1 TAATAATGATT
*
460775 TAGTAATGATT
1 TAATAATGATT
*
460786 TGATAAT
1 TAATAAT
460793 AATAATTTAT
Statistics
Matches: 116, Mismatches: 24, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
6 3 0.03
7 1 0.01
8 1 0.01
9 1 0.01
10 11 0.09
11 57 0.49
12 19 0.16
13 6 0.05
14 17 0.15
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:460655 original size:21 final size:21
Alignment explanation
Indices: 460629--460683 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
460619 TATGATTTAG
460629 TAATAATGATTTAATAATATT
1 TAATAATGATTTAATAATATT
*
460650 TAATAATGATTTAATAATGTT
1 TAATAATGATTTAATAATATT
*
460671 TTA-AAT-ATTTAAT
1 TAATAATGATTTAAT
460684 GATTTAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.22
20 3 0.09
21 22 0.69
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TAATAATGATTTAATAATATT
Found at i:460702 original size:27 final size:27
Alignment explanation
Indices: 460653--460729 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
460643 TAATATTTAA
* * *
460653 TAATGATTTAATAATGTT-TTAAATATT
1 TAATGATTTAATGAT-TTAGTAAAGATT
460680 TAATGATTTAATGATTTAGTAAAGATT
1 TAATGATTTAATGATTTAGTAAAGATT
* * *
460707 TGATAATAATAATGATTTAGTAA
1 TAATGAT-TTAATGATTTAGTAA
460730 TAACCATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.05
27 26 0.62
28 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (27 bp):
TAATGATTTAATGATTTAGTAAAGATT
Found at i:460758 original size:499 final size:480
Alignment explanation
Indices: 459800--460845 Score: 1235
Period size: 499 Copynumber: 2.1 Consensus size: 480
459790 TATTTAAATT
* *
459800 TAATAATTTATTATTAATATTTTATAATTTGATATTAATGATTAAGTAATGATTAGTAATAATGA
1 TAAT-ATTTATTATTAATATTTAATAATTTGATATTAATGATTAAATAATGATTAGTAATAATGA
*
459865 AATTGTAATAATGATTTAATCATTAATAATGATTTAATTTGTAACAAATAACAAATGAGTTTACA
65 AATTGTAATAATAATTTAATCATTAATAATGATTTAATTTG------ATAACAAATGAGTTTACA
*
459930 AGTGTAGACTACTCGAATTTAAATTTATAAATAGTCGAATTTATTAATGATTTCTAAATATTTAA
124 AGTATAGACTACTCGAATTTAAATTTATAAATAGTCGAATTTATTAATGATTTCTAAATATTTAA
* *
459995 TGATTTGATACTAATGATTTAGTAATGATTCGAACGTTAACCATTTAATTTTTAGCAAATAACAA
189 TGATTTGATACTAATGATTTAGTAATGATTCGAACGATAACCATTTAAGTTTTAGCAAATAACAA
* ** * *
460060 ATCTGTTCATATTTAAATCATTACAAATAATTATTTTCTAATAATTATATGATTTAGTAATGATT
254 ATATGTTCATATTTAAATCAAAACAAATAATGATTTTCTAATAATTATATGATTTAGTAATAATT
460125 TGATAATAATAATTTAATAATAATTTTAATATTTGATGATTTAGTAATGATTTGATAATAATGAT
319 T-ATAATAATAATTTAATAATAATTTTAATA--T-ATGATTTA-TAA-GA-TTGATAATAATGAT
* **
460190 TTAACAATGATTTAGTAATGATTTGATAATAATAATTATAATAATGATTTAGTAATAATCATTAT
377 TT-A-AATGATTTAGTAAAGATTTGATAATAATAATTATAATAACCATTTAGTAATAATCATTAT
460255 AATAATGATTTGATAAAAATGATTTACTAACGATTTAGTAATGATTATTAA
440 AATAATGA-TT--TAAAAATGATTTACTAACGATTT-G--AT-A--A-TAA
* *
460306 TAATTATTTATTATTAATATTTAATGATTTGATATTAATGATTAAATAGTGATTAGTAATAATGA
1 TAA-TATTTATTATTAATATTTAATAATTTGATATTAATGATTAAATAATGATTAGTAATAATGA
*
460371 AATTGTAATAATAATTTAATCATTAATAATGATTTAATTTG-TAACAAATGAGTTTACAAGTATG
65 AATTGTAATAATAATTTAATCATTAATAATGATTTAATTTGATAACAAATGAGTTTACAAGTATA
*
460435 GACTACTCGAATTTAAATTTATACATAGTCGAATTTATTAATGATTTCTAAATATTTAATGATTT
130 GACTACTCGAATTTAAATTTATAAATAGTCGAATTTATTAATGATTTCTAAATATTTAATGATTT
* *
460500 GATATTAATGATTTAGTAATCAAGTTTTTAAAGAGATTTGAACGATAACCATTTAAGTTTTAGCA
195 GATACTAATGATTTAG---T-AA-----T-----GATTCGAACGATAACCATTTAAGTTTTAGCA
* *
460565 AATAACAAATATGTTCATATTTAAATCAAAACACAT-ATGATTTTTTAATAATTATATGATTTAG
246 AATAACAAATATGTTCATATTTAAATCAAAACAAATAATGATTTTCTAATAATTATATGATTTAG
* *
460629 TAATAATGATT-TAATAAT-ATTTAATAATGA-TTTAATA-ATG-TTT-TAA-A-T-AT-TTAAT
311 TAATAAT--TTATAATAATAATTTAATAATAATTTTAATATATGATTTATAAGATTGATAATAAT
460684 GATTT-AATGATTTAGTAAAGATTTGATAATAATAATGATTTAGTAATAACCA-TTA-TAATAAT
374 GATTTAAATGATTTAGTAAAGATTTGATAATAAT-A--A-TTA-TAATAACCATTTAGTAATAAT
* * * *
460746 GATTTGATAATAATGATTTAATAATGATTTAGTAATGATTTGATAATAA
434 CA-TT-ATAATAATGATTTAAAAATGATTTACTAACGATTTGATAATAA
* *
460795 T-A-ATTTATTATTAATATTTAATTATTTGATACTAATGATTACTAATAATGA
1 TAATATTTATTATTAATATTTAATAATTTGATATTAATGATTA--AATAATGA
460846 AATTATAATA
Statistics
Matches: 483, Mismatches: 31, Indels: 70
0.83 0.05 0.12
Matches are distributed among these distances:
486 37 0.08
488 8 0.02
489 4 0.01
490 1 0.00
492 1 0.00
493 2 0.00
494 27 0.06
495 2 0.00
496 20 0.04
497 18 0.04
498 12 0.02
499 118 0.24
501 1 0.00
502 1 0.00
503 5 0.01
505 3 0.01
506 102 0.21
507 1 0.00
508 1 0.00
510 7 0.01
511 11 0.02
512 39 0.08
513 60 0.12
514 2 0.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (480 bp):
TAATATTTATTATTAATATTTAATAATTTGATATTAATGATTAAATAATGATTAGTAATAATGAA
ATTGTAATAATAATTTAATCATTAATAATGATTTAATTTGATAACAAATGAGTTTACAAGTATAG
ACTACTCGAATTTAAATTTATAAATAGTCGAATTTATTAATGATTTCTAAATATTTAATGATTTG
ATACTAATGATTTAGTAATGATTCGAACGATAACCATTTAAGTTTTAGCAAATAACAAATATGTT
CATATTTAAATCAAAACAAATAATGATTTTCTAATAATTATATGATTTAGTAATAATTTATAATA
ATAATTTAATAATAATTTTAATATATGATTTATAAGATTGATAATAATGATTTAAATGATTTAGT
AAAGATTTGATAATAATAATTATAATAACCATTTAGTAATAATCATTATAATAATGATTTAAAAA
TGATTTACTAACGATTTGATAATAA
Found at i:460795 original size:14 final size:13
Alignment explanation
Indices: 460712--460802 Score: 84
Period size: 14 Copynumber: 7.2 Consensus size: 13
460702 AGATTTGATA
460712 ATAATAATGATTT
1 ATAATAATGATTT
**
460725 AGTAATAACCA-TT
1 A-TAATAATGATTT
460738 ATAATAATGATTT
1 ATAATAATGATTT
460751 GATAATAATGA-TT
1 -ATAATAATGATTT
460764 -TAATAATGA-TT
1 ATAATAATGATTT
*
460775 -TAGTAATGATTT
1 ATAATAATGATTT
*
460787 GATAATAATAATTT
1 -ATAATAATGATTT
460801 AT
1 AT
460803 TATTAATATT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
11 19 0.29
12 9 0.14
13 10 0.15
14 27 0.42
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (13 bp):
ATAATAATGATTT
Found at i:463271 original size:30 final size:30
Alignment explanation
Indices: 463236--463340 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
463226 TTCCCTTAAA
463236 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
*
463266 CAACTAATACACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
463296 AAACTAATAAACGATT-TTTAATTATAATTT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
* *
463326 ACTACTAAAAAACTA
1 -CAACTAATAAACTA
463341 ATTAACTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 5 0.08
30 49 0.77
31 10 0.16
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:463452 original size:41 final size:37
Alignment explanation
Indices: 463397--463510 Score: 106
Period size: 41 Copynumber: 2.9 Consensus size: 37
463387 CTTAACTATT
463397 TAACTAAC--ACAAACTAATTACATATTTTTTTATATA
1 TAACTAACAAACAAACTAATTA-ATATTTTTTTATATA
*
463433 TAACTAACGACTAACAAACTAACTAATTATTTTTATTAATATA
1 TAACTAAC-A--AACAAACTAATTAA-TATTTTT-TT-ATATA
* * *
463476 TAACTATCAAACATACTAATTAAATAATTTTTTAT
1 TAACTAACAAACAAACTAATT-AATATTTTTTTAT
463511 TTCTATGTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
36 8 0.12
38 2 0.03
39 2 0.03
40 17 0.27
41 20 0.31
42 3 0.05
43 12 0.19
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (37 bp):
TAACTAACAAACAAACTAATTAATATTTTTTTATATA
Found at i:463721 original size:36 final size:35
Alignment explanation
Indices: 463654--463723 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
463644 TCTTTTATAT
463654 AACTTAAACTAATAAACTATTTTTTATTATAATAA
1 AACTTAAACTAATAAACTATTTTTTATTATAATAA
*
463689 AACTTAAACTAATTAACTAAATTTTTTA-TATAATA
1 AACTTAAACTAATAAACT--ATTTTTTATTATAATA
463724 TAAATTCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 17 0.53
36 7 0.22
37 8 0.25
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (35 bp):
AACTTAAACTAATAAACTATTTTTTATTATAATAA
Found at i:463849 original size:38 final size:43
Alignment explanation
Indices: 463765--463871 Score: 134
Period size: 44 Copynumber: 2.6 Consensus size: 43
463755 TTAACTAACT
*
463765 ACAAACTAATTAACTATTTTTTATATATAACTAATGACTAACAA
1 ACAAACTAATTAATTATTTTTTATATATAACTAA-GACTAACAA
*
463809 ACAAACTAATTAATTATTTTTTA-ATAT-A-T-A-ACTATCAA
1 ACAAACTAATTAATTATTTTTTATATATAACTAAGACTAACAA
*
463847 ACAAACTAATTAAATAATTTTTTAT
1 ACAAACTAATT-AATTATTTTTTAT
463872 TTGTGTATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
38 18 0.31
39 11 0.19
40 1 0.02
41 1 0.02
42 1 0.02
43 4 0.07
44 22 0.38
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (43 bp):
ACAAACTAATTAATTATTTTTTATATATAACTAAGACTAACAA
Found at i:464237 original size:22 final size:23
Alignment explanation
Indices: 464212--464264 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
464202 CAGCAATAAT
*
464212 TGCTGCATGAAGCA-GTAAATGA
1 TGCTGCATGAAGCACGAAAATGA
*
464234 TGCTACATGAAGCAGCGAAAATGA
1 TGCTGCATGAAGCA-CGAAAATGA
464258 TGCTGCA
1 TGCTGCA
464265 ATAATGCAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 13 0.50
24 13 0.50
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCTGCATGAAGCACGAAAATGA
Found at i:464394 original size:32 final size:32
Alignment explanation
Indices: 464353--464415 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
464343 CCTACCCCAC
*
464353 GTTCATGGCTCATTCATTACATAGCTCGCTCG
1 GTTCATGGCTCATGCATTACATAGCTCGCTCG
464385 GTTCATGGCTCATGCATTACATAGCTCGCTC
1 GTTCATGGCTCATGCATTACATAGCTCGCTC
464416 AGATGCCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (32 bp):
GTTCATGGCTCATGCATTACATAGCTCGCTCG
Found at i:467340 original size:54 final size:54
Alignment explanation
Indices: 467255--467358 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
467245 TTTCACAAGG
*
467255 ACTAGCCAACCTCCAAAAGACAGTTCGTTCACTTTCCAGCTAGCTAACCGAAGT
1 ACTAGCCAACCTCCAAAAGACAGTTCCTTCACTTTCCAGCTAGCTAACCGAAGT
*
467309 ACTAGCCGACCTCCAAAAGACAGTTCCTTCACTTTCCAGCTAGCTAACCG
1 ACTAGCCAACCTCCAAAAGACAGTTCCTTCACTTTCCAGCTAGCTAACCG
467359 GTTTATAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (54 bp):
ACTAGCCAACCTCCAAAAGACAGTTCCTTCACTTTCCAGCTAGCTAACCGAAGT
Found at i:476138 original size:21 final size:21
Alignment explanation
Indices: 476096--476138 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
476086 TTTTCGGGCT
* * *
476096 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
476117 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
476138 A
1 A
476139 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:476971 original size:144 final size:144
Alignment explanation
Indices: 476680--476974 Score: 456
Period size: 144 Copynumber: 2.0 Consensus size: 144
476670 GGGTAGAGGG
* *
476680 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
476745 GCTTGATCCTTAGTATTATATGATTCTTAAGGAATTCATGTGGTCCTTATGGACATCATTATATG
65 ACTTGATCCCTAGTATTATATGATTCTTAAGGAATTCATGTGGTCCTTATGGACATCATTATATG
476810 GCACTACGGTGCAAT
130 GCACTACGGTGCAAT
476825 TCTACGC-GTCCTTCGGG-ATATATATATTCTGT-GAACATGTGTGAAGTCTTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACACAT
*
476887 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCA-T-
65 ACTTGATCCCTAG--TAT-TATATGATTCTTAAGGAATT-CATGTGGTCCTTATGGACATCATTA
476950 TATGGCACTACGGTGCAAT
126 TATGGCACTACGGTGCAAT
476969 TCTACG
1 TCTACG
476975 GCACTTCGGT
Statistics
Matches: 140, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
141 18 0.13
142 35 0.25
144 38 0.27
145 28 0.20
146 21 0.15
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (144 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
CTTGATCCCTAGTATTATATGATTCTTAAGGAATTCATGTGGTCCTTATGGACATCATTATATGG
CACTACGGTGCAAT
Found at i:476995 original size:21 final size:21
Alignment explanation
Indices: 476953--476995 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
476943 ACATCATTAT
*
476953 GGCACTACGGTGCAATTCTAC
1 GGCACTACGGTGCAATTATAC
* *
476974 GGCACTTCGGTGCATTTATAC
1 GGCACTACGGTGCAATTATAC
476995 G
1 G
476996 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGCACTACGGTGCAATTATAC
Found at i:479310 original size:182 final size:182
Alignment explanation
Indices: 478978--479342 Score: 714
Period size: 182 Copynumber: 2.0 Consensus size: 182
478968 ATCCGGGTTC
478978 TAATTATTCTTATATTGCAAGTAAGTTAGTAAAGGAGTTGAGGATTCCTATAGAAGCTACGAGTA
1 TAATTATTCTTATATTGCAAGTAAGTTAGTAAAGGAGTTGAGGATTCCTATAGAAGCTACGAGTA
479043 ATGTGATGATAGTAACTAATCCGTTAGGCATAGTACTCAGGTGGACAAAGTCTGTAAGGGGTGCC
66 ATGTGATGATAGTAACTAATCCGTTAGGCATAGTACTCAGGTGGACAAAGTCTGTAAGGGGTGCC
479108 CCATAAAGGTTCAGGGAATTGAATTCCCTGCTAATCTGATGGAATTACCCTT
131 CCATAAAGGTTCAGGGAATTGAATTCCCTGCTAATCTGATGGAATTACCCTT
479160 TAATTATTCTTATATTGCAAGTAAGTTAGTAAAGGAGTTGAGGATTCCTATAGAAGCTACGAGTA
1 TAATTATTCTTATATTGCAAGTAAGTTAGTAAAGGAGTTGAGGATTCCTATAGAAGCTACGAGTA
479225 ATGTGATGATAGTAACTAATCCGTTAGGGCATAGTACTCAGGTGGACAAAGTCTGTAAGGGGTGC
66 ATGTGATGATAGTAACTAATCCGTTA-GGCATAGTACTCAGGTGGACAAAGTCTGTAAGGGGTGC
479290 CCCATAAAGGTTCA-GGAATTGAATTCCCTGCTAATCTGATGGAATTACCCTT
130 CCCATAAAGGTTCAGGGAATTGAATTCCCTGCTAATCTGATGGAATTACCCTT
479342 T
1 T
479343 GACGAGTTTA
Statistics
Matches: 182, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
182 130 0.71
183 52 0.29
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (182 bp):
TAATTATTCTTATATTGCAAGTAAGTTAGTAAAGGAGTTGAGGATTCCTATAGAAGCTACGAGTA
ATGTGATGATAGTAACTAATCCGTTAGGCATAGTACTCAGGTGGACAAAGTCTGTAAGGGGTGCC
CCATAAAGGTTCAGGGAATTGAATTCCCTGCTAATCTGATGGAATTACCCTT
Found at i:483980 original size:150 final size:149
Alignment explanation
Indices: 483710--484025 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
483700 GGGTAGAGGG
* *
483710 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* * *
483775 GCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
483840 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
483859 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACACA
483924 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
483989 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
484009 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
484026 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:484037 original size:23 final size:23
Alignment explanation
Indices: 483993--484037 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
483983 ATCATTATAT
*
483993 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
484016 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
484038 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:484946 original size:21 final size:21
Alignment explanation
Indices: 484920--484964 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
484910 AATCATATTG
*
484920 CCCAGGGGGAACATATTCCCC
1 CCCAGGGGGAACAGATTCCCC
**
484941 CCCAGGGGTTACAGATTCCCC
1 CCCAGGGGGAACAGATTCCCC
484962 CCC
1 CCC
484965 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.42, G:0.22, T:0.16
Consensus pattern (21 bp):
CCCAGGGGGAACAGATTCCCC
Found at i:485892 original size:54 final size:54
Alignment explanation
Indices: 485819--486206 Score: 481
Period size: 54 Copynumber: 7.4 Consensus size: 54
485809 GAATTATGGG
**
485819 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTTTGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* *
485873 GAAATGCACACTTAGTGCCGAAACAGTTATTCATCCCCATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * * * *
485927 GATATGAACACTTAGTGCCGAAATGATTATTCATCCACATATGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * * *
485981 AAAATGCACACTTAGTACCGAAACGGTTATTCATCCACATAGCATGAATTTCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
*
486035 GAAATGCACACTTAGTGCCAAAACGGTTATTCATCCACAT---ATG------GT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * ** * *
486080 GAATTGCACAATTAGTGGTGAAACGGATATTCATCCACATATGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* *
486134 GAAATGCACACTTAGTGCTGAAACGGTTATTCATCCACCTAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
**
486188 -ACTTTGCACACTTAGTGCC
1 GA-AATGCACACTTAGTGCC
486207 TATTTGGTAA
Statistics
Matches: 286, Mismatches: 38, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
45 36 0.13
48 3 0.01
51 3 0.01
53 1 0.00
54 243 0.85
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
Found at i:492759 original size:54 final size:54
Alignment explanation
Indices: 492684--493059 Score: 567
Period size: 54 Copynumber: 7.0 Consensus size: 54
492674 GAATTCTGGG
492684 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* *
492738 GAAATGCACACTAAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
*
492792 GAAATGCACACTTAGTGCCTAAACGGTTATTCATCCACATAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * ** * *
492846 GAAATGTACACTTAGTGTCGAAACAATTATTTATCCACATAGGATGAATTCCAT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* ** *
492900 GAAATGCACACTTAATTTCGAAACGGTTATTCATCCACATATGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* ** *
492954 GAAATG--CACTTAATTTCGAAACGGTTATTCATCCACATATGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* *
493006 GAAATGCACACTTAGTGCAGAAACGGTTATTCATCCACCTAGGATGAATTCCGT
1 GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
493060 ATTTTGCACA
Statistics
Matches: 294, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
52 52 0.18
54 242 0.82
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
GAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
Found at i:503486 original size:34 final size:36
Alignment explanation
Indices: 503439--503540 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
503429 TTTCGTCCTA
*
503439 CTAGGATTGAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
503474 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
503509 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
503541 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:503991 original size:2 final size:2
Alignment explanation
Indices: 503986--504048 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
503976 TTAGTGTTAT
503986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
504028 TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
504049 TTCCTATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:504158 original size:27 final size:27
Alignment explanation
Indices: 504128--504195 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
504118 TATATATGCT
*
504128 TTTA-CTTTTTATATATTTACTCATTTA
1 TTTATCTTTTTATATATTTA-TCATATA
*
504155 TTTATCTATTT-TATATTTATCATATA
1 TTTATCTTTTTATATATTTATCATATA
*
504181 TTTATGTTTTTATAT
1 TTTATCTTTTTATAT
504196 TCTTTTACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 15 0.43
27 15 0.43
28 5 0.14
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTATCTTTTTATATATTTATCATATA
Found at i:504173 original size:15 final size:17
Alignment explanation
Indices: 504153--504185 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
504143 TTTACTCATT
504153 TATTTATC-TAT-TTTA
1 TATTTATCATATATTTA
504168 TATTTATCATATATTTA
1 TATTTATCATATATTTA
504185 T
1 T
504186 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTATCATATATTTA
Found at i:507399 original size:16 final size:16
Alignment explanation
Indices: 507373--507406 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
507363 AGATCCAATC
507373 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
507388 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
507405 AA
1 AA
507407 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:508129 original size:22 final size:22
Alignment explanation
Indices: 508104--508152 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
508094 TCATCAATCT
* *
508104 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
508126 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
508148 TTTGA
1 TTTGA
508153 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:508590 original size:18 final size:18
Alignment explanation
Indices: 508567--508602 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
508557 TCAACATCAA
* *
508567 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
508585 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
508603 GGATTCAACA
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:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:509239 original size:36 final size:36
Alignment explanation
Indices: 509131--509253 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
509121 TTGAATATGT
* * *
509131 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
509166 TTTCTTTTGGAACTAAGTTTT-GTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
*
509203 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
*
509239 TTTCCCTTGAAACAA
1 TTTCTCTTGAAACAA
509254 AACCTTTGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
35 9 0.12
36 37 0.49
37 28 0.37
38 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:509316 original size:65 final size:67
Alignment explanation
Indices: 509212--509369 Score: 187
Period size: 67 Copynumber: 2.4 Consensus size: 67
509202 GTTTCTCTTG
** * **
509212 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCC
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTACCCTTGAAACACAAAACCTTCAAATTTATTTCCC
509274 CTA
65 CTA
* * * *
509277 AAACAAATTTTGTCTCCCTTGAGATAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAACCTTCAAATTTATTTCCCC
509342 TA
66 TA
*
509344 AAACATAATTTTGTTTCCCTTGAGAC
1 AAACA-AATTTTGTCTCCCTTGAGAC
509370 CATTTCTCAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 24 0.31
66 8 0.10
67 28 0.36
68 18 0.23
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAACCTTCAAATTTATTTCCCC
TA
Found at i:510211 original size:105 final size:105
Alignment explanation
Indices: 510028--510964 Score: 1452
Period size: 105 Copynumber: 9.0 Consensus size: 105
510018 GGCACTGAGG
* * * *
510028 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
510093 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
510134 CAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
510199 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
510239 CAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
510304 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
510344 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
510409 GCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
510449 CAATGCAAGTTTAACTTCACGACGAATGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
510514 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
510554 CAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
510619 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
510659 CAATGCAAGTTCAACTTCACGAGGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
510724 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
510764 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
510824 TTCAATTTCAACTTCACAACGAAGAATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * ** *
510864 CAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
510929 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
510965 TGGAACAATA
Statistics
Matches: 774, Mismatches: 51, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
100 80 0.10
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 607 0.78
106 74 0.10
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:511559 original size:34 final size:36
Alignment explanation
Indices: 511512--511613 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
511502 TTTCGTCCTA
*
511512 CTAGGATTGAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
511547 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
511582 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
511614 GTTCTACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:512065 original size:2 final size:2
Alignment explanation
Indices: 512060--512092 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
512050 TTAGTGTTAT
512060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
512093 TTCCTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:512175 original size:20 final size:20
Alignment explanation
Indices: 512150--512187 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
512140 TTTATTATTA
512150 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
512170 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
512188 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:512216 original size:16 final size:18
Alignment explanation
Indices: 512197--512231 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
512187 TTTTACTCAT
512197 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
512213 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
512231 T
1 T
512232 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:513022 original size:2 final size:2
Alignment explanation
Indices: 513015--513046 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
513005 TGATATCTGA
513015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
513047 TTGCAACAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:522703 original size:24 final size:24
Alignment explanation
Indices: 522672--522721 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
522662 TTATCGATGA
* *
522672 TATAATTTCACATTCTTTAAAATTT
1 TATATTTTCACA-CCTTTAAAATTT
*
522697 TATATTTTCACACCTTTTAAATTT
1 TATATTTTCACACCTTTAAAATTT
522721 T
1 T
522722 GAGTTAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATTTTCACACCTTTAAAATTT
Found at i:522873 original size:60 final size:61
Alignment explanation
Indices: 522789--522928 Score: 203
Period size: 60 Copynumber: 2.3 Consensus size: 61
522779 TTTGTAAATG
* *
522789 TTCCAATTTCATCCCTAAAATATGA-CTATCATTCTAAATTAGTACTTAAAC-TTTTGAATA
1 TTCCAATTTCATCCCCAAAATATGACCT-TCATTCTAAATTAGTACTCAAACTTTTTGAATA
* * * *
522849 TTTCAATTTCATCCCCAAACTATGACCTTCATTCTAAATTAGTCCTCAAACTTTTTGAGTA
1 TTCCAATTTCATCCCCAAAATATGACCTTCATTCTAAATTAGTACTCAAACTTTTTGAATA
522910 TTCCAATTTCATCCCCAAA
1 TTCCAATTTCATCCCCAAA
522929 TTCATCCAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
60 43 0.61
61 28 0.39
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (61 bp):
TTCCAATTTCATCCCCAAAATATGACCTTCATTCTAAATTAGTACTCAAACTTTTTGAATA
Found at i:523515 original size:29 final size:29
Alignment explanation
Indices: 523473--523531 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
523463 TTTTAAGTTA
523473 AGGGCGAACCTGAACTTATAAAATTTTAG
1 AGGGCGAACCTGAACTTATAAAATTTTAG
*
523502 AGGGCGAACTTGAACTTATAAAATTTTAG
1 AGGGCGAACCTGAACTTATAAAATTTTAG
523531 A
1 A
523532 ATGAGGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (29 bp):
AGGGCGAACCTGAACTTATAAAATTTTAG
Found at i:523768 original size:21 final size:20
Alignment explanation
Indices: 523709--523768 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
523699 AATTTAAATT
*
523709 ATAATATTAATTATCTTTAAA
1 ATAATATTAATT-TTTTTAAA
* *
523730 ATAAAAATTAATATTTTTAAA
1 AT-AATATTAATTTTTTTAAA
523751 ATAATATTAATGTTTTTT
1 ATAATATTAAT-TTTTTT
523769 CAATAGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAATATTAATTTTTTTAAA
Found at i:523773 original size:20 final size:20
Alignment explanation
Indices: 523709--523767 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
523699 AATTTAAATT
*
523709 ATAATATTAATTATCTTTAAA
1 ATAATATTAA-TATTTTTAAA
*
523730 ATAAAAATTAATATTTTTAAA
1 AT-AATATTAATATTTTTAAA
*
523751 ATAATATTAATGTTTTT
1 ATAATATTAATATTTTT
523768 TCAATAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.39
21 13 0.39
22 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
ATAATATTAATATTTTTAAA
Found at i:526544 original size:51 final size:51
Alignment explanation
Indices: 526436--526578 Score: 137
Period size: 51 Copynumber: 2.8 Consensus size: 51
526426 CAGCCGTAGC
* * * * * *
526436 AGTAAAGCGCGCCCCCTGCCCCGCGCTATATGCTGA-TTTGGCGCCACATG
1 AGTATAGCGCGACCCCTGCCCCGCGCTATACGCTGACATAGGCGACACATG
* ** *
526486 AGATATAGCGCGTCCCCTGCCCCGCGCTATACGCTGACATAGGTTACACGTG
1 AG-TATAGCGCGACCCCTGCCCCGCGCTATACGCTGACATAGGCGACACATG
** * *
526538 AGTATAGCGCGACCCCTGATCCACGCTATACGC-CACATAGG
1 AGTATAGCGCGACCCCTGCCCCGCGCTATACGCTGACATAGG
526579 GGTATAGCGT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
50 9 0.12
51 58 0.75
52 10 0.13
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (51 bp):
AGTATAGCGCGACCCCTGCCCCGCGCTATACGCTGACATAGGCGACACATG
Found at i:526763 original size:12 final size:10
Alignment explanation
Indices: 526731--526761 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
526721 TTCATCACAC
526731 CAAATTCTCT
1 CAAATTCTCT
526741 CAAATTCTCT
1 CAAATTCTCT
*
526751 CAAATACTCT
1 CAAATTCTCT
526761 C
1 C
526762 TCTGTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:526831 original size:17 final size:18
Alignment explanation
Indices: 526794--526834 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
526784 ATATTATGTA
*
526794 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
526812 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
526829 TTTACT
1 TTTACT
526835 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:528558 original size:18 final size:18
Alignment explanation
Indices: 528516--528565 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
528506 GCAGCCACCG
* * *
528516 CAGCCATTTATAATGTCG
1 CAGCCATTTATGATGCCA
*
528534 CAACCATTTATGATGCCA
1 CAGCCATTTATGATGCCA
*
528552 CAGCCATATATGAT
1 CAGCCATTTATGAT
528566 ACCGCCATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (18 bp):
CAGCCATTTATGATGCCA
Found at i:529189 original size:35 final size:33
Alignment explanation
Indices: 529150--529234 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
529140 ATATTTTAGT
529150 TAATTTTGTT-TATTACCATTTAATATCAATTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
529185 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
529220 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
529235 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:532379 original size:16 final size:15
Alignment explanation
Indices: 532357--532404 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
532347 ATATTTTTTC
*
532357 AAATAATGATAATAA
1 AAATAATTATAATAA
532372 ACAATAATTATAATTAA
1 A-AATAATTATAA-TAA
532389 AAAT-ATTATAATAA
1 AAATAATTATAATAA
532403 AA
1 AA
532405 TTACCTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.17
15 8 0.27
16 13 0.43
17 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATAATTATAATAA
Found at i:533658 original size:14 final size:15
Alignment explanation
Indices: 533634--533665 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
533624 AAAAACTTCA
533634 ATTAGTGATAATTCG
1 ATTAGTGATAATTCG
533649 ATTA-TGATAATTCG
1 ATTAGTGATAATTCG
533663 ATT
1 ATT
533666 CGGTCGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (15 bp):
ATTAGTGATAATTCG
Found at i:542241 original size:20 final size:20
Alignment explanation
Indices: 542212--542260 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
542202 AGTAAAGAAT
*
542212 TTGACTAAACC-GATTAAAAA
1 TTGACAAAACCAG-TTAAAAA
* *
542232 TTGACAAAACCAGTTGAAAT
1 TTGACAAAACCAGTTAAAAA
542252 TTGACAAAA
1 TTGACAAAA
542261 TCGGTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.24
Consensus pattern (20 bp):
TTGACAAAACCAGTTAAAAA
Found at i:542621 original size:170 final size:171
Alignment explanation
Indices: 542326--542644 Score: 432
Period size: 170 Copynumber: 1.9 Consensus size: 171
542316 TCGATACGTT
* * *
542326 TATATGTATCAAAGTATCGGTATTGTAGGAATTTAAAAGAAATGTAAAAAGGAAAACGTCTCGAA
1 TATATGCACCAAAGTATCGGTATTGTAGGAATTTAAAAGAAATGTAAAAA-GAAAACGTCTAGAA
* *
542391 AGTATCGATATTTTACACACATGTATCAATACATGAAAATATAACAAGTTGAAGTTTGACAAAAC
65 AGTATCGATATCTTACACACATGTATCAATACATGAAAATATAACAAGTTGAAATTTGAC-AAA-
542456 CG-GTTTCAATTTGACAAAACTGGTAAAGAGTTACTTTTATAAG
128 CGAGTTTCAATTTGACAAAACTGGTAAAGAGTTACTTTTATAAG
* * * * * *
542499 TATATGCACCAAAGTATCGGTACTT-TAGGAATTTAAAAGAATTG-CAATA-ATAGCGTCTATAA
1 TATATGCACCAAAGTATCGGTA-TTGTAGGAATTTAAAAGAAATGTAAAAAGAAAACGTCTAGAA
* * *
542561 AGTATTGATATCTTAGACACATGTATCAATACATGACAATATAAC-AGATTGAAATTTGACAAAC
65 AGTATCGATATCTTACACACATGTATCAATACATGAAAATATAACAAG-TTGAAATTTGACAAAC
542625 GAGTTTCAATTTGACAAAAC
129 GAGTTTCAATTTGACAAAAC
542645 CGATAAAGCA
Statistics
Matches: 129, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
168 2 0.02
169 23 0.18
170 61 0.47
172 3 0.02
173 38 0.29
174 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (171 bp):
TATATGCACCAAAGTATCGGTATTGTAGGAATTTAAAAGAAATGTAAAAAGAAAACGTCTAGAAA
GTATCGATATCTTACACACATGTATCAATACATGAAAATATAACAAGTTGAAATTTGACAAACGA
GTTTCAATTTGACAAAACTGGTAAAGAGTTACTTTTATAAG
Found at i:547004 original size:23 final size:23
Alignment explanation
Indices: 546978--547023 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
546968 AAAATGTATT
546978 GATATACGAAAAATGAAGGTTGA
1 GATATACGAAAAATGAAGGTTGA
547001 GATATACGAAAAATGAAGGTTGA
1 GATATACGAAAAATGAAGGTTGA
547024 AATGTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
GATATACGAAAAATGAAGGTTGA
Found at i:554770 original size:12 final size:12
Alignment explanation
Indices: 554744--554781 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
554734 ATTGGCAAGG
*
554744 AGGAAAAAAAG-
1 AGGAAAAAGAGA
554755 AGGAAAAAGAGA
1 AGGAAAAAGAGA
*
554767 AGGAAGAAGAGA
1 AGGAAAAAGAGA
554779 AGG
1 AGG
554782 TAGTAGGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (12 bp):
AGGAAAAAGAGA
Found at i:557757 original size:38 final size:38
Alignment explanation
Indices: 557714--557786 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
557704 TAATTCGCTA
557714 TCAACTAGTTGATATGCATTTTACTAATTCCTTCTCTT
1 TCAACTAGTTGATATGCATTTTACTAATTCCTTCTCTT
* *
557752 TCAACTCGTTGATATGTATTTTACTAATTCCTTCT
1 TCAACTAGTTGATATGCATTTTACTAATTCCTTCT
557787 TCTATTGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.48
Consensus pattern (38 bp):
TCAACTAGTTGATATGCATTTTACTAATTCCTTCTCTT
Found at i:559798 original size:20 final size:21
Alignment explanation
Indices: 559752--559790 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
559742 TGTAAACATA
559752 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTTATTATAT
559773 AAGTATCGATACTT-TTAT
1 AAGTATCGATACTTATTAT
559791 TCCAGTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
AAGTATCGATACTTATTATAT
Found at i:559906 original size:201 final size:201
Alignment explanation
Indices: 559551--559989 Score: 537
Period size: 201 Copynumber: 2.2 Consensus size: 201
559541 GAAATTGTCC
* ** * * *
559551 AAGTTTCGATACTTTTTATATCCGTATTGATACTTTTATTCTAGTATCGATCTCAAACAATTTGG
1 AAGTATCGATACTTTTTATATAAGTATCGATACTTTTATTCCAGTATCGATCTCAAACAATTTGA
* * ** * *
559616 CAGCAACAAAGTATCGATACCCATATATAAAGTATCGATACTTGGAATTTCGAAACCTATTACTT
66 CAGCAACAAAGTATCGATACACATATAAAAAGTATCGATACTTAAAATTCCGAAACCTACTACTT
* * * * * *
559681 TACATTAATACTTAAATATACAATGGAAA-CG-ATAACAATCTATCGATTTAATGATAATGGGTG
131 TAAAGTAATACATAAATATACAATGGAAATCGTA-AAC-ATCTACCAATTTAATGATAATGGGCG
559744 TAAACATA
194 TAAACATA
*
559752 AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTAT-GCATCTCAAACAATTT-
1 AAGTATCGATACTTTTTATATAAGTATCGATACTTTTATTCCAGTATCG-ATCTCAAACAATTTG
* * *
559815 ACACGCAA-ATAAGTATCGATACATATATAAAAAGTATTGATACTTAAAATTCCGAAACCTACTC
65 ACA-GCAACA-AAGTATCGATACACATATAAAAAGTATCGATACTTAAAATTCCGAAACCTACTA
* * * * *
559879 CTTTAAAGTAATAGATAAATTTACAATGTAAATTGTAAACGTCTACCAATTTAATGATAATGGGC
128 CTTTAAAGTAATACATAAATATACAATGGAAATCGTAAACATCTACCAATTTAATGATAATGGGC
559944 GTAAACATA
193 GTAAACATA
* *
559953 AAGTATCGATACTTTTTCTATAGGTATCGATACTTTT
1 AAGTATCGATACTTTTTATATAAGTATCGATACTTTT
559990 TATATAGGTA
Statistics
Matches: 203, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
200 4 0.02
201 194 0.96
202 4 0.02
203 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (201 bp):
AAGTATCGATACTTTTTATATAAGTATCGATACTTTTATTCCAGTATCGATCTCAAACAATTTGA
CAGCAACAAAGTATCGATACACATATAAAAAGTATCGATACTTAAAATTCCGAAACCTACTACTT
TAAAGTAATACATAAATATACAATGGAAATCGTAAACATCTACCAATTTAATGATAATGGGCGTA
AACATA
Found at i:560042 original size:21 final size:21
Alignment explanation
Indices: 559955--560032 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
559945 TAAACATAAA
*
559955 GTATCGATACTTTTTCTATAG
1 GTATCGATACTTTTTATATAG
559976 GTATCGATACTTTTTATATAG
1 GTATCGATACTTTTTATATAG
559997 GTATCGATACTTTTTATATAG
1 GTATCGATACTTTTTATATAG
560018 GTATCGATACTTTTT
1 GTATCGATACTTTTT
560033 TTTCCAGTAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.49
Consensus pattern (21 bp):
GTATCGATACTTTTTATATAG
Found at i:560269 original size:242 final size:238
Alignment explanation
Indices: 559773--560220 Score: 548
Period size: 233 Copynumber: 1.9 Consensus size: 238
559763 CTTATTATAT
*
559773 AAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTACACGCAAATAAGTATCGATACA
1 AAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTACACGCAAATAAATATCGATACA
* *
559838 TATATAAAAAGTATTGATACTTAAAATTCCGAAACCTACTCCTTTAAAGTAATAGATAAATTTAC
66 TATATAAAAAGTATCGATACTTAAAATTCCGAAACCTACTACTTTAAAGTAATAGATAAATTTAC
* * * *
559903 AATGTAAATTGTAAACGTCTACCAATTTAATGATAATGGGCGTAAACATAAAGTATCGATACTTT
131 AA-GT-AA-T-TAAACG-CGACCAATTTAATGATAATAGGCGTAAACAGAAAGTATCGATACTTA
* * * * * * * * *
559968 TTCTATAGGTATCGATACTTTTTATATAGGTATCGATACTTTTTATAT
191 TTATATAAGTATCAATACTTTTTATATAGGAATCCAAACTTTTCAAAA
* * *
560016 AGGTATCGATACTTTTTTTTCCAGTATGCATCTCAAACAATTTGCACGCAAA-AAATATCGATAC
1 AAGTATCGATAC-TTTTATTCCAGTATGCATCTCAAACAATTTACACGCAAATAAATATCGATAC
* ** ** * *
560080 ATATAT-AAAAGTATCGATACTTAGAATTTTGAAACCTTTTATTTTAAAGTAATAGGTAAATTTA
65 ATATATAAAAAGTATCGATACTTAAAATTCCGAAACCTACTACTTTAAAGTAATAGATAAATTTA
* *
560144 CAA-T-A-TAAACG-GACCAGTTTAATGATAATAGGTGTAAACAGAAAGTATCGATACTTATTAT
130 CAAGTAATTAAACGCGACCAATTTAATGATAATAGGCGTAAACAGAAAGTATCGATACTTATTAT
560205 ATAAGTATCAATACTT
195 ATAAGTATCAATACTT
560221 ATATTCCAAT
Statistics
Matches: 182, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
233 57 0.31
235 6 0.03
238 1 0.01
240 1 0.01
242 52 0.29
243 28 0.15
244 37 0.20
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (238 bp):
AAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTACACGCAAATAAATATCGATACA
TATATAAAAAGTATCGATACTTAAAATTCCGAAACCTACTACTTTAAAGTAATAGATAAATTTAC
AAGTAATTAAACGCGACCAATTTAATGATAATAGGCGTAAACAGAAAGTATCGATACTTATTATA
TAAGTATCAATACTTTTTATATAGGAATCCAAACTTTTCAAAA
Found at i:560431 original size:20 final size:20
Alignment explanation
Indices: 560386--560423 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
560376 GTAAACATAA
560386 AGTATCGATACTTATTATAT
1 AGTATCGATACTTATTATAT
560406 AGGTATCGATACTT-TTAT
1 A-GTATCGATACTTATTAT
560424 TCCAGTATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (20 bp):
AGTATCGATACTTATTATAT
Found at i:560601 original size:201 final size:199
Alignment explanation
Indices: 559997--560670 Score: 838
Period size: 201 Copynumber: 3.4 Consensus size: 199
559987 TTTTATATAG
* * *
559997 GTATCGATACTTTTTATATAGGTATCGATACTTTTTTTTCCAGTATGCATCTCAAACAATTTGCA
1 GTATCGATACTTATTATATAAGTATCGATAC-TTTTATTCCAGTATGCATCTCAAACAATTTGCA
* * * * *
560062 CGCAAAAAA-TATCGATACATATATAA-AAGTATCGATACTTAGAATTTTGAAACCTTTTATTTT
65 CGCAAAAAAGTATCGATACACATATAACAAGTATCGATACTTATAATTTCGAAACCATTT-CTTT
* * * *
560125 AAAGTAATAGGTAAATTTACAATATAAACGG-----A-C--CAGTTTAATGATAATAGGTGTAAA
129 AAAGTAATATGTAAATTTACAATGTAAACGGTAAAAATCTACGGTTTAATGATAATAGGCGTAAA
*
560182 CAGAAA
194 CATAAA
* * * * * *
560188 GTATCGATACTTATTATATAAGTATCAATACTTATATTCCAATATGAATCACAAACATTTTGCAC
1 GTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCAC
* * * * *
560253 GC-AAAAAGTATCGATACACATGT-ACAAAGTATCAATACTTGTAATTTCGAAACCTATTACTAT
66 GCAAAAAAGTATCGATACACATATAAC-AAGTATCGATACTTATAATTTCGAAACC-ATTTCTTT
* * * *
560316 AAAG-AATACT-TAAGTTTACAAAGTAAA-GTATAAAAATCTACCGGTTTAATTATAATAGGCGT
129 AAAGTAATA-TGTAAATTTACAATGTAAACG-GTAAAAATCTA-CGGTTTAATGATAATAGGCGT
560378 AAACATAAA
191 AAACATAAA
*
560387 GTATCGATACTTATTATATAGGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCAC
1 GTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCAC
*
560452 GCAAAAAAGTATCGATACACATATAACAAGTATCGATACTTATAATTTCAAAATCCATTTCTTTA
66 GCAAAAAAGTATCGATACACATATAACAAGTATCGATACTTATAATTTCGAAA-CCATTTCTTTA
*
560517 AAGTAATATGTAAATTTACAATGTAAACGGTAAAAATCTATCGGTTGAATGATAATAGGCGTAAA
130 AAGTAATATGTAAATTTACAATGTAAACGGTAAAAATCTA-CGGTTTAATGATAATAGGCGTAAA
560582 CATAAA
194 CATAAA
* * * *
560588 GTATCGGTACTTATTATATAAGTATTGATACTTTTATTCCAGTATGCATCTCAAACAATTTACAT
1 GTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCAC
*
560653 GCAAAAAAGTATTGATAC
66 GCAAAAAAGTATCGATAC
560671 TTATAATTTT
Statistics
Matches: 409, Mismatches: 53, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
189 7 0.02
190 61 0.15
191 58 0.14
192 2 0.00
195 1 0.00
196 1 0.00
199 86 0.21
200 54 0.13
201 138 0.34
202 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (199 bp):
GTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAATTTGCAC
GCAAAAAAGTATCGATACACATATAACAAGTATCGATACTTATAATTTCGAAACCATTTCTTTAA
AGTAATATGTAAATTTACAATGTAAACGGTAAAAATCTACGGTTTAATGATAATAGGCGTAAACA
TAAA
Found at i:560619 original size:21 final size:20
Alignment explanation
Indices: 560586--560624 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
560576 CGTAAACATA
*
560586 AAGTATCGGTACTTATTATAT
1 AAGTATCGATACTT-TTATAT
*
560607 AAGTATTGATACTTTTAT
1 AAGTATCGATACTTTTAT
560625 TCCAGTATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (20 bp):
AAGTATCGATACTTTTATAT
Found at i:565134 original size:19 final size:19
Alignment explanation
Indices: 565110--565149 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
565100 TATCAAAACA
565110 TTTTATCTCTGAAGCTTTG
1 TTTTATCTCTGAAGCTTTG
565129 TTTTATCTCTGAAGCTTTG
1 TTTTATCTCTGAAGCTTTG
565148 TT
1 TT
565150 GGTTGATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (19 bp):
TTTTATCTCTGAAGCTTTG
Found at i:565846 original size:200 final size:201
Alignment explanation
Indices: 565498--566771 Score: 907
Period size: 200 Copynumber: 6.5 Consensus size: 201
565488 ACAAAATTTT
* ** ** *
565498 GATACTTAGAATTTTGAAACATATTACTTTAAAGTAATACATAAATTTAAAATGTAAACGGTAAA
1 GATACTTAGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * * * * * * * *
565563 AATCTA-TCAATTGAATGATAATAGGAGAAAATATAAAGAATCGATACTTATTATATATGTATCG
66 AATCTACT-GATTTAATGATAATAGGCGTAAATATAAAGTATCAATATTTATTATATAAGTATTG
* *
565627 ATA-TTGTTATTCCAGTATGCATCTCAAACAATTTGGACGCAAAAAGTATTAATACACATATATA
130 ATACTTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCAATACACATATATA
565691 AAGTATC
195 AAGTATC
* * * * * *
565698 AATACTTATAAATTCGAAACCTA-TATCTTTAAAGTAATAGGTAAATTTATAATATAAACGGTAA
1 GATACTTAGAATTTCGAAACCGATTA-CTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAA
* * **
565762 AAATCTACCGATTTAATGATAATAGGAGTAAATATAAAGTATCGCTATTTATTATATAAGTATTG
65 AAATCTACTGATTTAATGATAATAGGCGTAAATATAAAGTATCAATATTTATTATATAAGTATTG
* * * *
565827 ATACTT-TTATTCTAGTATGCATCTCAAACAATTTACACGCAAAAAAATATCGATACACATATAT
130 ATACTTGTTATTCCAGTATGCATCTCAAACAATTTGCACGC-AAAAAGTATCAATACACATATAT
565891 AAAGTATC
194 AAAGTATC
* * * * * *
565899 GATACTTAGACTTTCGAAATCGATTACTTTAAAGTAATAAGTAAATTTACAATGCAGACGTTAAA
1 GATACTTAGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* ** * * * **
565964 AATCTACCGGGTTAATGATAATAGGCGTCAACATCAAGTATCAATACATTTA-T-TCCAA-TA-T
66 AATCTACTGATTTAATGATAATAGGCGTAAATATAAAGTATCAAT--ATTTATTATATAAGTATT
* * ** * * * * * *
566025 G---CTTCTCA-AACATTTTGCA-CGCAAA-AGGTATTGATACACATGTACAAAGTATCAAT--A
129 GATACTTGTTATTCCAGTATGCATCTCAAACA---ATT--TGCAC--GCAAAAAGTATCAATACA
* *
566082 C-T-TGT-AA-TCTC
187 CATATATAAAGTATC
* * * * * * * * * * *
566093 AAAACCT---ATTACTATAA-AG-TTA---TACA-TAA-A--T---TTATAGAGT-AAA-CGATA
1 GATACTTAGAATTTCGA-AACCGATTACTTTAAAGTAATAGGTAAATT-TACAATGTAAACGGTA
* * * * *
566141 AAAATCTACTTG-TTTAATTATAATAGGCGTAAAGACAAAGTATCAATACTTATTATATAGGTAT
64 AAAATCTAC-TGATTTAATGATAATAGGCGTAAATATAAAGTATCAATATTTATTATATAAGTAT
* * *
566205 TAATA-TTGTTATTCCAGTATGCATTTCAAACAATTTGCACGCAAAAAATAT-AGATACACATAT
128 TGATACTTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCA-ATACACATAT
566268 ATAAAGTATC
192 ATAAAGTATC
* *
566278 GATACTTGGACTTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
1 GATACTTAGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * * * * * *
566343 AATCTACTGGTTTAATGATAATAGGCGTAAACATTAAGTATCAATAGTTT-TTGTATAGGGATCG
66 AATCTACTGATTTAATGATAATAGGCGTAAATATAAAGTATCAATA-TTTATTATATAAGTATTG
* * * *
566407 ATACTT-TTAATCCAGTATGCTTCTC-AACAATTTGCACGCACAAAA-TATCGATACACATGTAT
130 ATACTTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCA-AAAAGTATCAATACACATATAT
*
566469 AAATTATC
194 AAAGTATC
*** * * * *
566477 GATACGCGGAATTTGGAAACCGATTTCTTTAAAGTTATATGTAAATTTACAATGTAAACGGT-AA
1 GATACTTAGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * * * * ** * * *
566541 AGTCTACTGGTATATTAATAATAGGCGTAAATACCAAGTATCGATACTGT-CTATATAAGTATTG
66 AATCTACTGATTTAATGATAATAGGCGTAAATATAAAGTATCAATA-TTTATTATATAAGTATTG
** * * *
566605 ATACTT-TTATTCCAGTATGTTTCTCATACAATTTGCACGCAAAATGTATCGATACACATATATA
130 ATACTTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCAATACACATATATA
566669 AAGTATTC
195 AAGTA-TC
* * * * * * ** **
566677 -ATACTTATAATTTCGAAACCTATTACTGTAAAATAATATGTTAATTTACAATAAAAACATTAAA
1 GATACTTAGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * *
566741 AGTCTACTGATATAATGATAATAGGCATAAA
66 AATCTACTGATTTAATGATAATAGGCGTAAA
566772 CATCTAGTAT
Statistics
Matches: 841, Mismatches: 172, Indels: 122
0.74 0.15 0.11
Matches are distributed among these distances:
177 4 0.00
178 2 0.00
179 54 0.06
180 6 0.01
181 11 0.01
182 1 0.00
183 10 0.01
184 9 0.01
185 12 0.01
186 4 0.00
187 5 0.01
188 5 0.01
189 3 0.00
190 3 0.00
191 5 0.01
192 5 0.01
193 3 0.00
194 9 0.01
195 7 0.01
196 12 0.01
197 6 0.01
198 83 0.10
199 187 0.22
200 262 0.31
201 125 0.15
202 3 0.00
203 5 0.01
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (201 bp):
GATACTTAGAATTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
AATCTACTGATTTAATGATAATAGGCGTAAATATAAAGTATCAATATTTATTATATAAGTATTGA
TACTTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCAATACACATATATAA
AGTATC
Found at i:566145 original size:179 final size:180
Alignment explanation
Indices: 565827--566189 Score: 394
Period size: 179 Copynumber: 2.0 Consensus size: 180
565817 ATAAGTATTG
* * * *
565827 ATACTTTTATTCTAGTATGCATCTCAAACAATTTACACGCAAAAAAATATCGATACACATATATA
1 ATACATTTATTCCAATATGCATCTCAAACAATTTACACGCAAAAAAATATCGATACACATATACA
* * * * * * *
565892 AAGTATCGATACTTAGACTTTCGAAATCGATTACTTTAAAGTAATAAGTAAATTTACAATGCAGA
66 AAGTATCAATACTTAGAATCTCAAAACCGATTACTATAAAGTAATAAGTAAATTTACAATGCAAA
* *
565957 CGTTAAAAATCTACCGGGTTAATGATAATAGGCGTCAACATC-AAGTATCA
131 CGATAAAAATCTACCGGGTTAATGATAATAGGCGTAAACA-CAAAGTATCA
* * * ** * *
566007 ATACATTTATTCCAATATGCTTCTCAAACATTTTGCACGC-AAAAGGTATTGATACACATGTACA
1 ATACATTTATTCCAATATGCATCTCAAACAATTTACACGCAAAAAAATATCGATACACATATACA
* * * *
566071 AAGTATCAATACTT-GTAATCTCAAAACCTATTACTATAAAGTTATACA-TAAATTTATAGA-GT
66 AAGTATCAATACTTAG-AATCTCAAAACCGATTACTATAAAGTAATA-AGTAAATTTACA-ATGC
** * * *
566133 AAACGATAAAAATCTACTTGTTTAATTATAATAGGCGTAAAGACAAAGTATCA
128 AAACGATAAAAATCTACCGGGTTAATGATAATAGGCGTAAACACAAAGTATCA
566186 ATAC
1 ATAC
566190 TTATTATATA
Statistics
Matches: 150, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
178 2 0.01
179 112 0.75
180 36 0.24
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (180 bp):
ATACATTTATTCCAATATGCATCTCAAACAATTTACACGCAAAAAAATATCGATACACATATACA
AAGTATCAATACTTAGAATCTCAAAACCGATTACTATAAAGTAATAAGTAAATTTACAATGCAAA
CGATAAAAATCTACCGGGTTAATGATAATAGGCGTAAACACAAAGTATCA
Found at i:566807 original size:398 final size:400
Alignment explanation
Indices: 565999--566810 Score: 926
Period size: 398 Copynumber: 2.0 Consensus size: 400
565989 CGTCAACATC
* * * * *
565999 AAGTATCAATACATTTATTCCAATATGCTTCTCAAACATTTTGCACGCAAAAGGTATTGATACAC
1 AAGTATCGATACATTTAATCCAATATGCTTCTCAAACAATTTGCACGCAAAAGATATCGATACAC
** * * *
566064 ATGTACAAAGTATCAATACTTGTAATCTCAAAACCTATTACTATAAAGTTATACATAAATTTATA
66 ATGTACAAAGTATCAATACGCGGAATCTCAAAACCGATTACTATAAAGTTATACATAAATTTACA
* * *
566129 GAGTAAACGATAAAAATCTACTTGTTTAATTATAATAGGCGTAAAGACAAAGTATCAATACTTAT
131 GAGTAAACGATAAAAATCTACTGGTATAATTATAATAGGCGTAAAGACAAAGTATCAATACTTAC
*
566194 TATATAGGTATTAATATTGTTATTCCAGTATGCATTTCAAACAATTTGCACGCAAAAAATATAGA
196 TATATAAGTATTAATATTGTTATTCCAGTATGCATTTCAAACAATTTGCACGCAAAAAATATAGA
* * * *
566259 TACACATATATAAAGTATCGATACTTGGACTTTCGAAACCGATTACTTTAAAGTAATAGGTAAAT
261 TACACATATATAAAGTATCGATACTTAGAATTTCGAAACCGATTACTGTAAAATAATAGGTAAAT
** * * * *
566324 TTACAATGTAAACGGTAAAAATCTACTGGTTTAATGATAATAGGCGTAAACATTAAGTATCAATA
326 TTACAATAAAAACAGTAAAAATCTACTGATATAATGATAATAGGCATAAACATTAAGTATCAATA
****
566389 GTTTTTGTAT
391 GCACATGTAT
* * * *
566399 AGGGATCGATACTTTTAATCCAGTATGCTTCTC-AACAATTTGCACGCACAAA-ATATCGATACA
1 AAGTATCGATACATTTAATCCAATATGCTTCTCAAACAATTTGCACGCA-AAAGATATCGATACA
* * * * ** * * **
566462 CATGTATAAATTATCGATACGCGGAATTTGGAAACCGATTTCTTTAAAGTTATATGTAAATTTAC
65 CATGTACAAAGTATCAATACGCGGAATCTCAAAACCGATTACTATAAAGTTATACATAAATTTAC
* * * * *
566527 A-ATGTAAACGGT-AAAGTCTACTGGTAT-ATTAATAATAGGCGTAAATACCAAGTATCGATACT
130 AGA-GTAAACGATAAAAATCTACTGGTATAATT-ATAATAGGCGTAAAGACAAAGTATCAATACT
* * * **
566589 GT-CTATATAAGTATTGATACTT-TTATTCCAGTATG-TTTCTCATACAATTTGCACGCAAAATG
193 -TACTATATAAGTATTAATA-TTGTTATTCCAGTATGCATT-TCAAACAATTTGCACGCAAAAAA
* * *
566651 TATCGATACACATATATAAAGTATTC-ATACTTATAATTTCGAAACCTATTACTGTAAAATAATA
255 TATAGATACACATATATAAAGTA-TCGATACTTAGAATTTCGAAACCGATTACTGTAAAATAATA
* * * *
566715 TGTTAATTTACAATAAAAACATTAAAAGTCTACTGATATAATGATAATAGGCATAAACATCT-AG
319 GGTAAATTTACAATAAAAACAGTAAAAATCTACTGATATAATGATAATAGGCATAAACAT-TAAG
*
566779 TATCGATA-CACATGTAT
383 TATCAATAGCACATGTAT
566796 AAAGTATCGATACAT
1 -AAGTATCGATACAT
566811 GCAATTTCGA
Statistics
Matches: 340, Mismatches: 63, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
397 10 0.03
398 212 0.62
399 88 0.26
400 30 0.09
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (400 bp):
AAGTATCGATACATTTAATCCAATATGCTTCTCAAACAATTTGCACGCAAAAGATATCGATACAC
ATGTACAAAGTATCAATACGCGGAATCTCAAAACCGATTACTATAAAGTTATACATAAATTTACA
GAGTAAACGATAAAAATCTACTGGTATAATTATAATAGGCGTAAAGACAAAGTATCAATACTTAC
TATATAAGTATTAATATTGTTATTCCAGTATGCATTTCAAACAATTTGCACGCAAAAAATATAGA
TACACATATATAAAGTATCGATACTTAGAATTTCGAAACCGATTACTGTAAAATAATAGGTAAAT
TTACAATAAAAACAGTAAAAATCTACTGATATAATGATAATAGGCATAAACATTAAGTATCAATA
GCACATGTAT
Found at i:566928 original size:20 final size:20
Alignment explanation
Indices: 566904--566996 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
566894 AACGTAAATG
* *
566904 TACAAGTATCGATGCTGTCG
1 TACAAGTATCGATACTGTCA
566924 TACAAGTATCGATACTGTCA
1 TACAAGTATCGATACTGTCA
566944 TACAAGTATCGATACTGTCA
1 TACAAGTATCGATACTGTCA
*
566964 TACAAGTATCGATACTATCA
1 TACAAGTATCGATACTGTCA
*
566984 TATAAGTATCGAT
1 TACAAGTATCGAT
566997 TCCTATAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
TACAAGTATCGATACTGTCA
Found at i:567007 original size:21 final size:20
Alignment explanation
Indices: 566927--567007 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
566917 GCTGTCGTAC
* * *
566927 AAGTATCGATACTGTCATAC
1 AAGTATCGATACTATAATAT
* * *
566947 AAGTATCGATACTGTCATAC
1 AAGTATCGATACTATAATAT
*
566967 AAGTATCGATACTATCATAT
1 AAGTATCGATACTATAATAT
*
566987 AAGTATCGATTCCTATAATAT
1 AAGTATCGA-TACTATAATAT
567008 CGAAATCTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 47 0.84
21 9 0.16
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
AAGTATCGATACTATAATAT
Found at i:568525 original size:201 final size:202
Alignment explanation
Indices: 568019--568508 Score: 704
Period size: 200 Copynumber: 2.5 Consensus size: 202
568009 CAAAATTTTG
* * *
568019 ATACTTAGAATTTTGAAACAT--ATTACTTTAAAGTAATACGTAAATTTAAAATGTAAACGGTAA
1 ATACTTAGAAATTCGAAACATAGATTACTTTAAAGTAATAAGTAAATTTAAAATGTAAACGGTAA
* *
568082 AAATCTACCGATTTAATGATAATAGGAGTAAATATAAAGAATCGATACTTATTATATATGTATTG
66 AAATCTACCGATTTAATGATAATAGGAGTAAATATAAAGTATCGATACTTATTATATAAGTATTG
* * *
568147 ATACTGTTATTCCAGTATGGATCTCAAACAATTTGGACGCAAAAAGTATCAATACACATATATAA
131 ATACTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAATATCAATACACATATATAA
568212 AGTATCA
196 AGTATCA
* * * * *
568219 ATACTTATAAATTCGAAACCTATA-T-CTTTAAAGTAATAGGTAAATTTATAATGTAAACGGTAA
1 ATACTTAGAAATTCGAAACATAGATTACTTTAAAGTAATAAGTAAATTTAAAATGTAAACGGTAA
* *
568282 AAATCTACCGATTTAATGATAATAGGAGTAAATATAAAGTATCGCTATTTATTATATAAGTATTG
66 AAATCTACCGATTTAATGATAATAGGAGTAAATATAAAGTATCGATACTTATTATATAAGTATTG
* *
568347 ATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACACATATATA
131 ATACTGTTATTCCAGTATGCATCTCAAACAATTTGCACGC-AAAAAATATCAATACACATATATA
*
568412 AAGTATCG
195 AAGTATCA
** ** * *
568420 ATACTTAGACTTTC-AAA-ATAGATTACTTTAAAGTAATAAGTAAATTTACCATGTAGACGTTAA
1 ATACTTAGAAATTCGAAACATAGATTACTTTAAAGTAATAAGTAAATTTAAAATGTAAACGGTAA
*
568483 AAATCTACCGGTTTAATGATAATAGG
66 AAATCTACCGATTTAATGATAATAGG
568509 CGTCAACATC
Statistics
Matches: 258, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
199 3 0.01
200 155 0.60
201 99 0.38
202 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (202 bp):
ATACTTAGAAATTCGAAACATAGATTACTTTAAAGTAATAAGTAAATTTAAAATGTAAACGGTAA
AAATCTACCGATTTAATGATAATAGGAGTAAATATAAAGTATCGATACTTATTATATAAGTATTG
ATACTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAATATCAATACACATATATAA
AGTATCA
Found at i:568665 original size:179 final size:180
Alignment explanation
Indices: 568347--568709 Score: 435
Period size: 179 Copynumber: 2.0 Consensus size: 180
568337 ATAAGTATTG
* * *
568347 ATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACACATATATA
1 ATACGTTTATTCCAATATGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACACATATACA
* * * * * * *
568412 AAGTATCGATACTTAGACTTTCAAAATAGATTACTTTAAAGTAATAAGTAAATTTACCATGTAGA
66 AAGTATCAATACTTAGAATCTCAAAACAGATTACTATAAAGTAATAAGTAAATTTACCAAGTAAA
* * * *
568477 CGTTAAAAATCTACCGGTTTAATGATAATAGGCGTCAACATCAAGTATCA
131 CGGTAAAAATCTACCAGTTTAATGATAATAGGCGTAAACATAAAGTATCA
* * * ** * *
568527 ATACGTTTATTCCAATTTGCTTCTCAAACATTTTGCACGC-AAAAGGTATTGATACACATGTACA
1 ATACGTTTATTCCAATATGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACACATATACA
** *
568591 AAGTATCAATACTT-GTAATCTCAAAACCTATTACTATAAAGTAATATGTAAATTTA-CAGAGTA
66 AAGTATCAATACTTAG-AATCTCAAAACAGATTACTATAAAGTAATAAGTAAATTTACCA-AGTA
* * * *
568654 AATGGTAAAAATCTACTAGTTTAATTATAATAGGCGTAAAGATAAAGTATCA
129 AACGGTAAAAATCTACCAGTTTAATGATAATAGGCGTAAACATAAAGTATCA
568706 ATAC
1 ATAC
568710 TTATTATATA
Statistics
Matches: 153, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
178 3 0.02
179 115 0.75
180 35 0.23
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (180 bp):
ATACGTTTATTCCAATATGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACACATATACA
AAGTATCAATACTTAGAATCTCAAAACAGATTACTATAAAGTAATAAGTAAATTTACCAAGTAAA
CGGTAAAAATCTACCAGTTTAATGATAATAGGCGTAAACATAAAGTATCA
Found at i:568886 original size:200 final size:200
Alignment explanation
Indices: 568533--568908 Score: 533
Period size: 200 Copynumber: 1.9 Consensus size: 200
568523 ATCAATACGT
* * ** * *
568533 TTATTCCAATTTGCTTCTCAAACATTTTGCACGCAAAAGGTATTGATACACATGTACAAAGTATC
1 TTATTCCAATATGCTTCTCAAACAATTTGCACGCAAAAAATATCGATACACATATACAAAGTATC
* * * *
568598 AATACTTGTAATCTCAAAACCTATTACTATAAAGTAATATGTAAATTTACAGAGTAAATGGTAAA
66 AATACTTGGAATCTCAAAACCGATTACTATAAAGTAATAGGTAAATTTACAGAGTAAACGGTAAA
* *
568663 AATCTACTAGTTTAATTATAATAGGCGTAAAGATAAAGTATCAATACTTATTATATATGTATTAA
131 AATCTACTAGTTTAATGATAATAGGCGTAAACATAAAGTATCAATACTTATTATATATGTATTAA
568728 TATTG
196 TATTG
* *
568733 TTATTCCAGTATGCATT-TCAAACAATTTGCACGCAAAAAATATCGATACACATATATAAAGTAT
1 TTATTCCAATATGC-TTCTCAAACAATTTGCACGCAAAAAATATCGATACACATATACAAAGTAT
* * * *
568797 CAATACTTGGACTTTCGAAACCGATTACTTTAAAGTAATAGGTAAATTTACA-ATGTAAACGGTA
65 CAATACTTGGAATCTCAAAACCGATTACTATAAAGTAATAGGTAAATTTACAGA-GTAAACGGTA
*
568861 AAAATCTACT-GATTTAATGATAATAGGCGTAAACATTAAGTATCAATA
129 AAAATCTACTAG-TTTAATGATAATAGGCGTAAACATAAAGTATCAATA
568909 GTTTTTGTAT
Statistics
Matches: 154, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
199 2 0.01
200 150 0.97
201 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (200 bp):
TTATTCCAATATGCTTCTCAAACAATTTGCACGCAAAAAATATCGATACACATATACAAAGTATC
AATACTTGGAATCTCAAAACCGATTACTATAAAGTAATAGGTAAATTTACAGAGTAAACGGTAAA
AATCTACTAGTTTAATGATAATAGGCGTAAACATAAAGTATCAATACTTATTATATATGTATTAA
TATTG
Found at i:568939 original size:16 final size:16
Alignment explanation
Indices: 568918--568951 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
568908 AGTTTTTGTA
568918 TAGGTGCATCACATTT
1 TAGGTGCATCACATTT
568934 TAGGTGCATCACATTT
1 TAGGTGCATCACATTT
568950 TA
1 TA
568952 TTATTAAAAA
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:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (16 bp):
TAGGTGCATCACATTT
Found at i:570062 original size:16 final size:15
Alignment explanation
Indices: 570025--570067 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
570015 GATTATTTTA
570025 AAATTTTAAAATAATT
1 AAATTTTAAAA-AATT
570041 AAATTTTAAAAAA-T
1 AAATTTTAAAAAATT
*
570055 ATATATTTAAAAA
1 AAAT-TTTAAAAA
570068 CTACTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTTTAAAAAATT
Found at i:572139 original size:58 final size:59
Alignment explanation
Indices: 572037--572157 Score: 217
Period size: 58 Copynumber: 2.1 Consensus size: 59
572027 AAAACATAAA
* *
572037 TCAAATAAAAGAAATCATAGTTCAAATACTTAAACACTAATAGTGTAAACAACCATAGT
1 TCAAATAAAAGAAAGCATAGTTCAAATACTAAAACACTAATAGTGTAAACAACCATAGT
572096 TCAAATAAAAGAAAGCATAGTT-AAATACTAAAACACTAATAGTGTAAACAACCATAGT
1 TCAAATAAAAGAAAGCATAGTTCAAATACTAAAACACTAATAGTGTAAACAACCATAGT
572154 TCAA
1 TCAA
572158 TATCATGACC
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 39 0.65
59 21 0.35
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (59 bp):
TCAAATAAAAGAAAGCATAGTTCAAATACTAAAACACTAATAGTGTAAACAACCATAGT
Found at i:572414 original size:23 final size:23
Alignment explanation
Indices: 572387--572434 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
572377 CCATATGAAT
* *
572387 TATTATTTAAA-ATTCATTAACAA
1 TATTATATAAATATTC-TCAACAA
572410 TATTATATAAATATTCTCAACAA
1 TATTATATAAATATTCTCAACAA
572433 TA
1 TA
572435 AATTACAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTATATAAATATTCTCAACAA
Found at i:573134 original size:2 final size:2
Alignment explanation
Indices: 573127--573170 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
573117 TTATTTTACC
573127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
573169 TA
1 TA
573171 GGGTTATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:577579 original size:35 final size:37
Alignment explanation
Indices: 577500--577581 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 37
577490 AGGGATGTAC
*
577500 CGATGCACTATTTGATGTATCGATGCACACCATAATT
1 CGATGCACTATTTGATGTACCGATGCACACCATAATT
*
577537 CGAATGCA-T-TTTG-TGTACCGATGCACAACCATGCA-T
1 CG-ATGCACTATTTGATGTACCGATGCAC-ACCAT-AATT
577573 CGATGCACT
1 CGATGCACT
577582 CCTGATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
35 17 0.44
36 13 0.33
37 4 0.10
38 5 0.13
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (37 bp):
CGATGCACTATTTGATGTACCGATGCACACCATAATT
Done.