Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 46 of 55
Found at i:9239140 original size:65 final size:66
Alignment explanation
Indices: 9239021--9239143 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
9239011 GAAAATGGCT
* * * *
9239021 ATCGTAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
9239086 A
66 A
9239087 ATCGCAATGCGAAATG-AAATCACAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
9239144 TTCCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.69
66 15 0.29
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:9239161 original size:19 final size:19
Alignment explanation
Indices: 9239139--9239188 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
9239129 GAAACACAAA
*
9239139 TCGCATTCCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
9239158 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
9239177 TCGCATTGCGAT
1 TCGCATTGCGAT
9239189 AGCCATTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:9239207 original size:20 final size:19
Alignment explanation
Indices: 9239153--9239227 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
9239143 ATTCCGATTT
**
9239153 TCATTTCGCGTTGCGATTT
1 TCATTTCGCGTTGCGATAG
*
9239172 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
9239191 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
*
9239211 TCATTTTCGTGTTGCGA
1 TCA-TTTCGCGTTGCGA
9239228 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 21 0.45
20 23 0.49
21 3 0.06
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:9241108 original size:20 final size:20
Alignment explanation
Indices: 9241085--9241124 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9241075 AACCGTAACA
9241085 CGAAAATGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
**
9241105 CGAATTTGACTATCGCAACG
1 CGAAAATGACTATCGCAACG
9241125 AGAGAATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
CGAAAATGACTATCGCAACG
Found at i:9241644 original size:20 final size:20
Alignment explanation
Indices: 9241619--9241670 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
9241609 ATTATGTATT
9241619 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
9241639 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
9241659 ATCTCGTTGCGA
1 ATCGCGTTGCGA
9241671 TTTGTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:9241701 original size:20 final size:19
Alignment explanation
Indices: 9241598--9241711 Score: 84
Period size: 20 Copynumber: 5.7 Consensus size: 19
9241588 CGCTTTGAAA
*
9241598 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
9241619 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
9241639 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
9241659 ATCTCGTTGCGATTTGTATT
1 ATCGCATTGCGA-TAGTAGT
9241679 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
9241699 ATCGCATTGCGAT
1 ATCGCATTGCGAT
9241712 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
19 5 0.06
20 59 0.77
21 13 0.17
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:9241785 original size:21 final size:21
Alignment explanation
Indices: 9241761--9241811 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
9241751 AATTGGGAAA
9241761 ATCGCAACGATACTGTAGACC
1 ATCGCAACGATACTGTAGACC
*
9241782 ATCGCAACGATACTGTAGACT
1 ATCGCAACGATACTGTAGACC
9241803 ATCGCAACG
1 ATCGCAACG
9241812 CGATTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGATACTGTAGACC
Found at i:9241843 original size:21 final size:21
Alignment explanation
Indices: 9241800--9241843 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9241790 GATACTGTAG
** *
9241800 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
9241821 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
9241842 AC
1 AC
9241844 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:9258231 original size:20 final size:20
Alignment explanation
Indices: 9258208--9258375 Score: 176
Period size: 20 Copynumber: 8.3 Consensus size: 20
9258198 GTTTCCAGAT
9258208 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
9258228 TCGCATTGCGATTTTCCGACTA
1 TCGCAACGCGA--TTCTGACTA
* * * *
9258250 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
* * *
9258270 TCGCAATGCGAGTATGACTA
1 TCGCAACGCGATTCTGACTA
*
9258290 TCGCAACACGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
9258310 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
9258330 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
*
9258350 TCGCAACGCGATGCTGACTA
1 TCGCAACGCGATTCTGACTA
9258370 TCGCAA
1 TCGCAA
9258376 TGTGATTTTC
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 104 0.84
21 1 0.01
22 18 0.15
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:9259058 original size:20 final size:20
Alignment explanation
Indices: 9258973--9259060 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
9258963 AGAATCGCAA
9258973 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
9258992 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
*** *
9259012 TGCGATAGCCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
9259032 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
9259052 TGCGATTTT
1 TGCGATTTT
9259061 AAGTTTCAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 9 0.16
20 49 0.84
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:9259067 original size:20 final size:20
Alignment explanation
Indices: 9259024--9259067 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9259014 CGATAGCCAT
* *
9259024 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
9259044 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
9259064 TTTC
1 TTTC
9259068 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:9260797 original size:18 final size:18
Alignment explanation
Indices: 9260774--9260823 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
9260764 TTTACTCGTA
9260774 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
9260792 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
9260810 ATTTCACTTAGATT
1 ATTTCACTTAGATT
9260824 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:9261085 original size:18 final size:19
Alignment explanation
Indices: 9261036--9261087 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
9261026 GCATTGCGAT
*
9261036 TCTCTCGTTGCGATAGTCA
1 TCTCGCGTTGCGATAGTCA
*
9261055 TTTTCGCGTTGCGATAGTCA
1 -TCTCGCGTTGCGATAGTCA
*
9261075 -CTCGTGTTGCGAT
1 TCTCGCGTTGCGAT
9261088 TTTAAGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 11 0.39
20 17 0.61
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.38
Consensus pattern (19 bp):
TCTCGCGTTGCGATAGTCA
Found at i:9261655 original size:42 final size:41
Alignment explanation
Indices: 9261556--9261665 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 41
9261546 CCCGACTCAC
* * * *
9261556 CTGTCATCGTTCAAGAG-GCCTCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCCCTCCC-ACCGTTCAAAAGGCCA
* **
9261597 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAAAGGCCA
1 CTGTCATCGTTCAAGAGT-CCCTCCCACCGTTCAAAAGGCCA
*
9261639 CTGTCATCGTTGAAGAGGTCCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCTCCCA
9261666 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
41 14 0.25
42 33 0.60
43 8 0.15
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCTCCCACCGTTCAAAAGGCCA
Found at i:9263092 original size:14 final size:14
Alignment explanation
Indices: 9263055--9263116 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
9263045 TTGCTTGTTT
*
9263055 AATTGATTTATAAA
1 AATTGATTTGTAAA
9263069 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
9263083 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
9263098 TATTGATGTGTAAA
1 AATTGATTTGTAAA
9263112 TAATT
1 -AATT
9263117 CTTATTTATG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:9263240 original size:20 final size:20
Alignment explanation
Indices: 9263215--9263308 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
9263205 AGGTACACTT
* **
9263215 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
9263235 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
*
9263255 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
* *
9263275 CCGCAACGCGAAAGACATAA
1 TCGCAACGCGAAAGACAAAA
*
9263295 CCGCAACGCGAAAG
1 TCGCAACGCGAAAG
9263309 TCAATTCGCG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.09
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:9263406 original size:40 final size:40
Alignment explanation
Indices: 9263351--9263521 Score: 156
Period size: 40 Copynumber: 4.4 Consensus size: 40
9263341 GCGATTTTCT
*
9263351 CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACCCATTGCGATAGTCAAATTCG
* * *
9263391 CGTTGCGATAGTCAAATAGCCGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATACCCATTGCGATAGTCAAATTCG
* * * ** *
9263431 CGTTACGATAGACAAATTCGTATTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATACCCATTGCGATAGTCAAATTCG
* * ***
9263465 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATACCCATTGCGATAGTCAAATTCG
*
9263505 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
9263522 GAATGTGTAA
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
34 27 0.26
36 1 0.01
38 1 0.01
40 76 0.72
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATACCCATTGCGATAGTCAAATTCG
Found at i:9263448 original size:20 final size:19
Alignment explanation
Indices: 9263351--9263521 Score: 129
Period size: 20 Copynumber: 8.9 Consensus size: 19
9263341 GCGATTTTCT
*
9263351 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAAT-TC
* *
9263371 CATTGCGATAATCAAATTC
1 CGTTGCGATAGTCAAATTC
*
9263390 GCGTTGCGATAGTCAAATAGC
1 -CGTTGCGATAGTCAAAT-TC
9263411 CGTTGCGATAGTCAAATTC
1 CGTTGCGATAGTCAAATTC
* *
9263430 ACGTTACGATAGACAAATT-
1 -CGTTGCGATAGTCAAATTC
* *
9263449 CGTATTGCGAT--T---TTTG
1 CG--TTGCGATAGTCAAATTC
*
9263465 CGTTGCGATAGTCATATTC
1 CGTTGCGATAGTCAAATTC
*
9263484 GTGTTGCGATAGTCAAATTC
1 -CGTTGCGATAGTCAAATTC
*
9263504 GCGTTGCGATATTCAAAT
1 -CGTTGCGATAGTCAAAT
9263522 GAATGTGTAA
Statistics
Matches: 121, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
14 7 0.06
15 2 0.02
16 3 0.02
18 2 0.02
19 4 0.03
20 102 0.84
21 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (19 bp):
CGTTGCGATAGTCAAATTC
Found at i:9263469 original size:114 final size:113
Alignment explanation
Indices: 9263302--9263521 Score: 289
Period size: 114 Copynumber: 1.9 Consensus size: 113
9263292 TAACCGCAAC
* * * * *
9263302 GCGAAAGTCAATTCGCGTTGCGATAGTCTAATACGTTTTGCGATTTTCTCGTTGCGATAGTCAAA
1 GCGAAAGTCAATTCACGTTACGATAGACAAATACGTATTGCGATTTTCTCGTTGCGATAGTCAAA
9263367 TACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATAGCCGTT
66 TACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATAGCCGTT
* *
9263415 GCGATAGTCAAATTCACGTTACGATAGACAAATTCGTATTGCGATTTT-TGCGTTGCGATAGTCA
1 GCGAAAGTC-AATTCACGTTACGATAGACAAATACGTATTGCGATTTTCT-CGTTGCGATAGTCA
* * *** * *
9263479 TATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
64 AATACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAAT
9263522 GAATGTGTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
113 9 0.10
114 82 0.90
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (113 bp):
GCGAAAGTCAATTCACGTTACGATAGACAAATACGTATTGCGATTTTCTCGTTGCGATAGTCAAA
TACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATAGCCGTT
Found at i:9263744 original size:140 final size:140
Alignment explanation
Indices: 9263492--9263761 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
9263482 TCGTGTTGCG
* *
9263492 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTTATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
9263557 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
9263622 AATACACATA
131 AATACACATA
9263632 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
9263697 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
9263762 TACAACATTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:9263836 original size:12 final size:12
Alignment explanation
Indices: 9263821--9263851 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
9263811 AAGCCGGTTG
*
9263821 TGATTGGGATTT
1 TGATTGCGATTT
9263833 TGATTGCGATTT
1 TGATTGCGATTT
9263845 TGATTGC
1 TGATTGC
9263852 CTTTTTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.48
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:9265903 original size:14 final size:14
Alignment explanation
Indices: 9265884--9265920 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9265874 TCCCATGGCA
9265884 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
9265898 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
9265912 TTCTTCTTC
1 TT-TTCTTC
9265921 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:9267038 original size:20 final size:20
Alignment explanation
Indices: 9267015--9267131 Score: 164
Period size: 20 Copynumber: 5.8 Consensus size: 20
9267005 TTGCAATAGT
*
9267015 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
9267035 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
* *
9267055 CATATTCGCGTTGCGATAGT-
1 CATATTCGCATTGCGAT-TTA
* *
9267075 CATAATCGCATTGCAATTTA
1 CATATTCGCATTGCGATTTA
*
9267095 CATATTTGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
9267115 CATATTCGCATTGCGAT
1 CATATTCGCATTGCGAT
9267132 AGTCGGAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 82 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:9267064 original size:60 final size:60
Alignment explanation
Indices: 9267000--9267135 Score: 236
Period size: 60 Copynumber: 2.3 Consensus size: 60
9266990 ACAGTCAGAA
* *
9267000 TCGCGTTGCAATAGTCATAATCGCATTGCGATTTACATATTCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCAATTTACATATTCGCATTGCGATTTACATAT
*
9267060 TCGCGTTGCGATAGTCATAATCGCATTGCAATTTACATATTTGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCATAATCGCATTGCAATTTACATATTCGCATTGCGATTTACATAT
*
9267120 TCGCATTGCGATAGTC
1 TCGCGTTGCGATAGTC
9267136 GGAAAATCGT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGATAGTCATAATCGCATTGCAATTTACATATTCGCATTGCGATTTACATAT
Found at i:9268275 original size:2 final size:2
Alignment explanation
Indices: 9268268--9268293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9268258 TTATCTAACC
9268268 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
9268294 TATTCTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9277014 original size:53 final size:53
Alignment explanation
Indices: 9276941--9277053 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 53
9276931 TAATTTTACC
* *
9276941 CTTAGTAATGTATGGACTCCAATCAATTATGTATTTACATTTTATTTTAATAA
1 CTTAATAATGCATGGACTCCAATCAATTATGTATTTACATTTTATTTTAATAA
* * *
9276994 CTTAATAATGCATGGGCTCCAATCAATTATGTATTTATATTTTATTTTAGTAA
1 CTTAATAATGCATGGACTCCAATCAATTATGTATTTACATTTTATTTTAATAA
*
9277047 TTTAATA
1 CTTAATA
9277054 CTTACATTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.46
Consensus pattern (53 bp):
CTTAATAATGCATGGACTCCAATCAATTATGTATTTACATTTTATTTTAATAA
Found at i:9277563 original size:21 final size:21
Alignment explanation
Indices: 9277538--9277579 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9277528 GTTTTGATAC
*
9277538 TATGTTTGATATTTATAAATT
1 TATGTTTGATATATATAAATT
*
9277559 TATGTTTGATATATATTAATT
1 TATGTTTGATATATATAAATT
9277580 AATTCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATGTTTGATATATATAAATT
Found at i:9280559 original size:23 final size:24
Alignment explanation
Indices: 9280509--9280559 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
9280499 ATATGTCGTA
* *
9280509 TATTATTTACGTTATAATCTTATT
1 TATTATTTACATTATAATCTTATG
9280533 TATTATTATACATTA-AAT-TTATG
1 TATTATT-TACATTATAATCTTATG
9280556 TATT
1 TATT
9280560 GAGTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTATTTACATTATAATCTTATG
Found at i:9289899 original size:33 final size:33
Alignment explanation
Indices: 9289857--9289922 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
9289847 AATGGCAAGT
9289857 GTCAGTAAACATCAAGCCTAACCTCAATTCCTA
1 GTCAGTAAACATCAAGCCTAACCTCAATTCCTA
9289890 GTCAGTAAACATCAAGCCTAACCTCAATTCCTA
1 GTCAGTAAACATCAAGCCTAACCTCAATTCCTA
9289923 ATTAGAGCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.24
Consensus pattern (33 bp):
GTCAGTAAACATCAAGCCTAACCTCAATTCCTA
Found at i:9292966 original size:3 final size:3
Alignment explanation
Indices: 9292958--9293007 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
9292948 TGGCCTGCAA
*
9292958 AAT AAT AAT AAT AAT AAT AA- ACAT AAT AAT AAT -AC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
9293002 AAT AAT
1 AAT AAT
9293008 TAAAATTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 39 0.93
4 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9293481 original size:130 final size:134
Alignment explanation
Indices: 9293200--9293523 Score: 530
Period size: 131 Copynumber: 2.4 Consensus size: 134
9293190 TGAGAGTTCG
* * * * *
9293200 GGTTGTCTAAGGGTGACACGGTTCCTACGTGATGAGGAGATTTGGTCGGTGGATGACACGGCTCA
1 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
9293265 TACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGAC
66 TACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGAC
9293330 GGCT
131 GGCT
9293334 GGTTATCTAGGGGTGACACGGCT-CTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTC-
1 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
**
9293397 TACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGTGAT-ACACGGTTCCTACGTGATGAGGAC
66 TACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGAC
9293460 GGCT
131 GGCT
* * *
9293464 GGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACG
1 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACG
9293524 ATTCCTACAT
Statistics
Matches: 179, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
130 49 0.27
131 55 0.31
132 17 0.09
133 38 0.21
134 20 0.11
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (134 bp):
GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
TACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGAC
GGCT
Found at i:9293497 original size:43 final size:43
Alignment explanation
Indices: 9293306--9293541 Score: 163
Period size: 39 Copynumber: 5.5 Consensus size: 43
9293296 GAAGGCAATA
*
9293306 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGGGTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAGGGGTG
* *
9293349 ACACGGCT-CTACGTGATGAGGAGATCTGG---TC-GGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAGGGG-TG
* ** **
9293388 ACACGGCT-CTACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGTG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATC--TAGG--GGTG
* * *
9293434 ATACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 --ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAGGGGTG
*
9293479 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCT-GGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAGGGG-TG
** *
9293519 ACACGATTCCTACATGATGAGGA
1 ACACGGCTCCTACGTGATGAGGA
9293542 CGGCCCATCT
Statistics
Matches: 157, Mismatches: 20, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
38 4 0.03
39 33 0.21
40 25 0.16
41 1 0.01
42 21 0.13
43 33 0.21
45 5 0.03
46 2 0.01
47 5 0.03
48 7 0.04
49 20 0.13
50 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAGGGGTG
Found at i:9293621 original size:28 final size:28
Alignment explanation
Indices: 9293582--9293643 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
9293572 GAACCAAATT
*
9293582 AAAGATTTGTTTCAA-AAGAAACAAACCC
1 AAAGATTCGTTTCAAGAA-AAACAAACCC
*
9293610 AAAGATTCGTTTCAAGAAAAACAAACTC
1 AAAGATTCGTTTCAAGAAAAACAAACCC
9293638 AAAGAT
1 AAAGAT
9293644 GATGTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (28 bp):
AAAGATTCGTTTCAAGAAAAACAAACCC
Found at i:9293749 original size:31 final size:31
Alignment explanation
Indices: 9293708--9293818 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
9293698 CTCAAGATGA
*
9293708 TTTAAAGGAAACTG-TCTCAAGAAAATTTGTT
1 TTTAAGGGAAA-TGTTCTCAAGAAAATTTGTT
* ** **
9293739 TTTAAGGGAAATGTTCTC-A-AAGATCGGGG
1 TTTAAGGGAAATGTTCTCAAGAAAATTTGTT
* ** *
9293768 TTCATTGAAAACTG-TCTCAAGAAAATTTGTT
1 TTTAAGGGAAA-TGTTCTCAAGAAAATTTGTT
9293799 TTTAAGGGAAATGTTCTCAA
1 TTTAAGGGAAATGTTCTCAA
9293819 AGATCGGGGT
Statistics
Matches: 56, Mismatches: 19, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
29 16 0.29
30 8 0.14
31 32 0.57
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (31 bp):
TTTAAGGGAAATGTTCTCAAGAAAATTTGTT
Found at i:9293780 original size:60 final size:61
Alignment explanation
Indices: 9293716--9293848 Score: 259
Period size: 60 Copynumber: 2.2 Consensus size: 61
9293706 GATTTAAAGG
9293716 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGG-TTCATTGA
1 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
9293776 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
1 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
9293837 AAACTGTCTCAA
1 AAACTGTCTCAA
9293849 AATGAGACAA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
60 52 0.72
61 20 0.28
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (61 bp):
AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
Found at i:9294097 original size:65 final size:66
Alignment explanation
Indices: 9293971--9294104 Score: 148
Period size: 65 Copynumber: 2.0 Consensus size: 66
9293961 TTTCCAAAAG
* * *
9293971 AAATGTATCAAGAGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGA
1 AAATGTATCAAGAGACAAAA-CTTGTTTCAAGAGAAACAAACTCAAAGATGATCTTATTTTAAGA
9294036 GA
65 GA
* * * *
9294038 AAATGTTTCAAGAGACAAAA-TTCGTTTCAAGGGAAAC-GACTCAAAGAT-AGTTTTATTTTAAG
1 AAATGTATCAAGAGACAAAACTT-GTTTCAAGAGAAACAAACTCAAAGATGA-TCTTATTTTAAG
*
9294100 CGA
64 AGA
9294103 AA
1 AA
9294105 CAAACTTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
64 1 0.02
65 26 0.46
66 12 0.21
67 18 0.32
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (66 bp):
AAATGTATCAAGAGACAAAACTTGTTTCAAGAGAAACAAACTCAAAGATGATCTTATTTTAAGAG
A
Found at i:9294368 original size:29 final size:28
Alignment explanation
Indices: 9294309--9294388 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
9294299 AATTTATTTC
* * *
9294309 AAAGAAATAGACTCAAAGATGATTTTGTT
1 AAAGAAACAAACTCAAAGAT-TTTTTGTT
* * *
9294338 AAGATAAACAAACTGAAAGATTTTTTTTT
1 AA-AGAAACAAACTCAAAGATTTTTTGTT
*
9294367 AAAGGAACAAACTCAAAGATTT
1 AAAGAAACAAACTCAAAGATTT
9294389 GTTTCAAGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 17 0.41
29 10 0.24
30 14 0.34
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (28 bp):
AAAGAAACAAACTCAAAGATTTTTTGTT
Found at i:9294519 original size:28 final size:29
Alignment explanation
Indices: 9294464--9294575 Score: 86
Period size: 27 Copynumber: 3.7 Consensus size: 29
9294454 AGAGACAAAA
*
9294464 TTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTGTTTCAAAAGAAACAAACTCAAAGAT
* * *
9294493 TTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAAT
1 TTTGTTTCAAAAGAAACAAAC-TCA-A-AG-----AT
*
9294530 TTT-TTTCCAAAGAAACAAACTCAAAGA-
1 TTTGTTTCAAAAGAAACAAACTCAAAGAT
9294557 TTT-TTTCAAAAGAAACAAA
1 TTTGTTTCAAAAGAAACAAA
9294576 GATTTTTTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
27 18 0.27
28 1 0.02
29 18 0.27
30 2 0.03
31 1 0.02
32 2 0.03
33 2 0.03
34 1 0.02
35 2 0.03
36 14 0.21
37 5 0.08
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:9294527 original size:65 final size:63
Alignment explanation
Indices: 9294447--9294572 Score: 225
Period size: 65 Copynumber: 2.0 Consensus size: 63
9294437 TCAAAAATTG
9294447 TCTTAAGAGAGACAAAATTTGTTTCCAAAGAAACAAACTCAAAGATTTTGTTTCAAAAGAAACTA
1 TCTTAAGAGAGACAAAATTTGTTTCCAAAGAAACAAACTCAAAGA-TTT-TTTCAAAAGAAACTA
*
9294512 TCTTAAGAGAGACAAAATTTTTTTCCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAAC
1 TCTTAAGAGAGACAAAATTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAAC
9294573 AAAGATTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 13 0.22
64 3 0.05
65 44 0.73
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (63 bp):
TCTTAAGAGAGACAAAATTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTA
Found at i:9294575 original size:21 final size:21
Alignment explanation
Indices: 9294551--9294593 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9294541 GAAACAAACT
9294551 CAAAGATTTTTTCAAAAGAAA
1 CAAAGATTTTTTCAAAAGAAA
*
9294572 CAAAGATTTTTTCAAGAGAAA
1 CAAAGATTTTTTCAAAAGAAA
9294593 C
1 C
9294594 TCAAGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (21 bp):
CAAAGATTTTTTCAAAAGAAA
Found at i:9294673 original size:28 final size:27
Alignment explanation
Indices: 9294530--9294735 Score: 135
Period size: 29 Copynumber: 7.6 Consensus size: 27
9294520 GAGACAAAAT
*
9294530 TTTTTTCCAAAGAAACAAACTCAAAGA
1 TTTTTTCAAAAGAAACAAACTCAAAGA
9294557 TTTTTTCAAAAG----AAA--CAAAGA
1 TTTTTTCAAAAGAAACAAACTCAAAGA
* ** *
9294578 TTTTTTCAAGAGAAACTCAAGAGAGACAAAAA
1 TTTTTTCAAAAGAAA--C-A-A-ACTCAAAGA
* * * *
9294610 CTTGTTTC-AAA-ATATAGACTCAAAGA
1 -TTTTTTCAAAAGAAACAAACTCAAAGA
9294636 TTTTTTCAAAAGAAAC-AACTCAAAGA
1 TTTTTTCAAAAGAAACAAACTCAAAGA
* *
9294662 TATTTATTCAAAAGGAACAAACTCCAAGA
1 T-TTT-TTCAAAAGAAACAAACTCAAAGA
9294691 TTTTTATTCAAAATG-AACAAACTCAAAGA
1 -TTTT-TTCAAAA-GAAACAAACTCAAAGA
*
9294720 TTTTTTCAAGAGAAAC
1 TTTTTTCAAAAGAAAC
9294736 TGTCTCAAGA
Statistics
Matches: 140, Mismatches: 19, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
21 17 0.12
23 3 0.02
25 6 0.04
26 20 0.14
27 25 0.18
28 17 0.12
29 34 0.24
30 3 0.02
31 2 0.01
32 7 0.05
33 6 0.04
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (27 bp):
TTTTTTCAAAAGAAACAAACTCAAAGA
Found at i:9294696 original size:29 final size:29
Alignment explanation
Indices: 9294627--9294724 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
9294617 CAAAATATAG
*
9294627 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
9294653 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
9294682 ACTCCAAGATTTTTATTCAAAATGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
9294711 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
9294725 TCAAGAGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.14
27 3 0.05
28 11 0.17
29 40 0.63
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:9295057 original size:33 final size:33
Alignment explanation
Indices: 9294975--9295102 Score: 159
Period size: 35 Copynumber: 3.8 Consensus size: 33
9294965 GGAAAAAAAA
* * * *
9294975 TGTCCCAAGCGAGACGAAATTTGTTTCAGATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTCA-A-GAAC
* *
9295010 TGTCTTAAGTGAGACAAAATTTGTTTCAAGAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTCAAGAAC
9295043 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAC
1 TGTCTCAAGCGAGACAAAATTTG--TTTCAAGAAC
9295078 TGTCTCAAGCGAGACAAAA-TTGTTT
1 TGTCTCAAGCGAGACAAAATTTGTTT
9295103 TCGAAGGAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
32 3 0.04
33 23 0.28
34 4 0.05
35 53 0.64
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (33 bp):
TGTCTCAAGCGAGACAAAATTTGTTTCAAGAAC
Found at i:9295092 original size:68 final size:67
Alignment explanation
Indices: 9294975--9295102 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 67
9294965 GGAAAAAAAA
* * * *
9294975 TGTCCCAAGCGAGACGAAATTTGTTTCAGATAAATTGTCTTAAGTGAGACAAAATTTGTTTCAAG
1 TGTCCCAAGCGAGACAAAATTTGTTTCAGATAAACTGTCTCAAGCGAGACAAAA-TTGTTTCAAG
9295040 AAC
65 AAC
* *
9295043 TGTCTCAAGCGAGACAAAATTTGTTTTTCA-A-GAACTGTCTCAAGCGAGACAAAATTGTTT
1 TGTCCCAAGCGAGACAAAATTTG--TTTCAGATAAACTGTCTCAAGCGAGACAAAATTGTTT
9295103 TCGAAGGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
67 6 0.12
68 40 0.77
69 1 0.02
70 5 0.10
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (67 bp):
TGTCCCAAGCGAGACAAAATTTGTTTCAGATAAACTGTCTCAAGCGAGACAAAATTGTTTCAAGA
AC
Found at i:9303625 original size:3 final size:3
Alignment explanation
Indices: 9303617--9303656 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
9303607 GGCCTGCAAA
9303617 AAT AAT AAT AAT AAT AATT AAT AA- ACAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT AAT AAT
9303657 TAAAATTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 29 0.85
4 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9308840 original size:4 final size:4
Alignment explanation
Indices: 9308822--9308868 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
9308812 AAAATGTTAG
9308822 ATAA A-AA AT-A ATAA ATAA ATAA ATAA ATAAA ATAA AGTAAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA A-T-AA ATAA AT
9308869 CAAAAGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 6 0.16
4 23 0.61
5 6 0.16
6 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:9308908 original size:43 final size:43
Alignment explanation
Indices: 9308860--9309045 Score: 109
Period size: 43 Copynumber: 4.2 Consensus size: 43
9308850 AAAATAAAGT
*
9308860 AAAATAAATCAAA-AGAAAAAA-ATGAAAATGAAAATAGATAAAA
1 AAAATAAA-AAAATAGAAAAAATATGAAAATGAAAATA-ATAAAA
* * *
9308903 AAAATAAAAAAATATAAAAAATATTAAAATGACAATAATAAAA
1 AAAATAAAAAAATAGAAAAAATATGAAAATGAAAATAATAAAA
*
9308946 AATAA-AGATAAGTGAAATTAAGTAAAAAAAAT-AAAAT-AAAATAATAAAA
1 AA-AATA-A-AA---AAA-T-AG-AAAAAATATGAAAATGAAAATAATAAAA
* * * * *
9308995 ATAATAAAATAATA-AAAAAACAAG-ATA-GAAAATAATAAAA
1 AAAATAAAAAAATAGAAAAAATATGAAAATGAAAATAATAAAA
9309035 TAATAATAAAA
1 -AA-AATAAAA
9309046 GGGTTAAATT
Statistics
Matches: 114, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
40 21 0.18
41 1 0.01
42 11 0.10
43 25 0.22
44 18 0.16
45 2 0.02
47 2 0.02
48 6 0.05
49 14 0.12
50 6 0.05
51 8 0.07
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (43 bp):
AAAATAAAAAAATAGAAAAAATATGAAAATGAAAATAATAAAA
Found at i:9308912 original size:10 final size:10
Alignment explanation
Indices: 9308822--9309014 Score: 63
Period size: 10 Copynumber: 18.9 Consensus size: 10
9308812 AAAATGTTAG
*
9308822 ATAAAAAATA
1 ATAAAAAAAA
9308832 ATAAATAAATAA
1 ATAAA-AAA-AA
*
9308844 AT-AAATAAA
1 ATAAAAAAAA
**
9308853 ATAAAGTAAA
1 ATAAAAAAAA
9308863 ATAAATCAAAAGA
1 ATAAA--AAAA-A
9308876 A-AAAAATGAAA
1 ATAAAAA--AAA
* * *
9308887 ATGAAAATAG
1 ATAAAAAAAA
9308897 AT-AAAAAAA
1 ATAAAAAAAA
*
9308906 ATAAAAAAAT
1 ATAAAAAAAA
*
9308916 ATAAAAAATA
1 ATAAAAAAAA
* * *
9308926 TTAAAATGACA
1 ATAAAA-AAAA
*
9308937 ATAATAAAAA
1 ATAAAAAAAA
* *
9308947 ATAAAGATAA
1 ATAAAAAAAA
* * **
9308957 GTGAAATTAA
1 ATAAAAAAAA
*
9308967 GT-AAAAAAA
1 ATAAAAAAAA
*
9308976 ATAAAATAAA
1 ATAAAAAAAA
*
9308986 AT-AATAAAA
1 ATAAAAAAAA
*
9308995 ATAATAAAATA
1 ATAA-AAAAAA
9309006 ATAAAAAAA
1 ATAAAAAAA
9309015 CAAGATAGAA
Statistics
Matches: 133, Mismatches: 36, Indels: 28
0.68 0.18 0.14
Matches are distributed among these distances:
9 24 0.18
10 72 0.54
11 21 0.16
12 14 0.11
13 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:9309011 original size:39 final size:41
Alignment explanation
Indices: 9308939--9309040 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 41
9308929 AAATGACAAT
* *
9308939 AATAAAA-AATAAAGATAAGTGAAATTAAGTAAAAAAA-ATA-A
1 AATAAAATAATAAAAATAA-T-AAAATAAGTAAAAAAACA-AGA
9308980 AATAAAATAATAAAAATAATAAAATAA-TAAAAAAACAAGA
1 AATAAAATAATAAAAATAATAAAATAAGTAAAAAAACAAGA
* *
9309020 TAGAAAATAAT-AAAATAATAA
1 AATAAAATAATAAAAATAATAA
9309041 TAAAAGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 19 0.35
40 17 0.31
41 8 0.15
42 10 0.19
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.20
Consensus pattern (41 bp):
AATAAAATAATAAAAATAATAAAATAAGTAAAAAAACAAGA
Found at i:9309036 original size:8 final size:8
Alignment explanation
Indices: 9308822--9309040 Score: 78
Period size: 8 Copynumber: 25.9 Consensus size: 8
9308812 AAAATGTTAG
9308822 ATAA-AAA
1 ATAATAAA
9308829 ATAAT-AA
1 ATAATAAA
9308836 ATAA-ATAA
1 ATAATA-AA
9308844 ATAAATAAA
1 AT-AATAAA
9308853 ATAAAGTAAA
1 AT-AA-TAAA
9308863 ATAAATCAAA
1 AT-AAT-AAA
* *
9308873 AGAAAAAA
1 ATAATAAA
9308881 ATGAAAATGAAA
1 AT---AAT-AAA
9308893 ATAGATAAAA
1 ATA-AT-AAA
*
9308903 AAAATAAA
1 ATAATAAA
*
9308911 AAAATATAA
1 ATAATA-AA
* *
9308920 AAAATATTA
1 ATAATA-AA
*
9308929 A-AATGACA
1 ATAAT-AAA
9308937 ATAATAAA
1 ATAATAAA
9308945 A-AATAAA
1 ATAATAAA
9308952 GATAAGTGAAA
1 -ATAA-T-AAA
*
9308963 TTAAGTAAA
1 ATAA-TAAA
9308972 A-AA-AATA
1 ATAATAA-A
9308979 A-AATAAA
1 ATAATAAA
9308986 ATAATAAAA
1 ATAAT-AAA
9308995 ATAATAAA
1 ATAATAAA
9309003 ATAATAAA
1 ATAATAAA
* * *
9309011 AAAACAAG
1 ATAATAAA
*
9309019 AT-AGAAA
1 ATAATAAA
9309026 ATAATAAA
1 ATAATAAA
9309034 ATAATAA
1 ATAATAA
9309041 TAAAAGGGTT
Statistics
Matches: 170, Mismatches: 18, Indels: 47
0.72 0.08 0.20
Matches are distributed among these distances:
6 2 0.01
7 27 0.16
8 61 0.36
9 43 0.25
10 27 0.16
11 5 0.03
12 5 0.03
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (8 bp):
ATAATAAA
Found at i:9320070 original size:2 final size:2
Alignment explanation
Indices: 9320063--9320126 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
9320053 TTTATAGAAG
9320063 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
9320105 TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
9320127 TCATGGAGAC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9324910 original size:2 final size:2
Alignment explanation
Indices: 9324903--9324958 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
9324893 TGTTTTTATC
9324903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9324945 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
9324959 TTACACAACC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9341418 original size:18 final size:18
Alignment explanation
Indices: 9341395--9341430 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9341385 TTTTGGTGCA
*
9341395 GAGGGAATCGATCCCCCT
1 GAGGGAACCGATCCCCCT
*
9341413 GAGGGAACCGATTCCCCT
1 GAGGGAACCGATCCCCCT
9341431 TTGAAGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (18 bp):
GAGGGAACCGATCCCCCT
Found at i:9341479 original size:20 final size:21
Alignment explanation
Indices: 9341435--9341474 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9341425 TCCCCTTTGA
*
9341435 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
9341456 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
9341475 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:9349099 original size:25 final size:24
Alignment explanation
Indices: 9349071--9349139 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 24
9349061 TTTATAAGAC
9349071 TAATATAATAAAATAATAATTAAA
1 TAATATAATAAAATAATAATTAAA
*
9349095 GTAATGAT-TTAAAAT-AT-ATTAAA
1 -TAAT-ATAATAAAATAATAATTAAA
*
9349118 -AA-ATAATAATAATAAAAATTAA
1 TAATATAATAA-AATAATAATTAA
9349140 GTTAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
19 2 0.06
20 3 0.08
21 5 0.14
22 1 0.03
23 11 0.31
24 2 0.06
25 10 0.28
26 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (24 bp):
TAATATAATAAAATAATAATTAAA
Found at i:9350088 original size:3 final size:3
Alignment explanation
Indices: 9350080--9350112 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
9350070 GTATTTTATT
*
9350080 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9350113 AATTGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:9350716 original size:73 final size:73
Alignment explanation
Indices: 9350268--9350702 Score: 791
Period size: 73 Copynumber: 6.0 Consensus size: 73
9350258 ATGAATAACT
* *
9350268 CTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTA-AGTCTTA
1 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGA-TCTTA
9350332 CAGATGACC
65 CAGATGACC
*
9350341 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTAC
1 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
9350406 AGATGACC
66 AGATGACC
*
9350414 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTAC
1 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
9350479 AGATGACC
66 AGATGACC
*
9350487 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTAC
1 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
9350552 AGATGACC
66 AGATGACC
*
9350560 CTGAGGGTTTAAGATCAAAAAGCTCCGGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
1 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
9350625 AGATGACC
66 AGATGACC
*
9350633 CTGAGGGTTTAAGATCAAAAAGCTCCGGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
1 CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
9350698 AGATG
66 AGATG
9350703 TTGGAAATAG
Statistics
Matches: 356, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
73 356 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (73 bp):
CTGAGGGTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGATCTTAC
AGATGACC
Found at i:9350973 original size:166 final size:164
Alignment explanation
Indices: 9350701--9351027 Score: 582
Period size: 166 Copynumber: 2.0 Consensus size: 164
9350691 ATCTTACAGA
* *
9350701 TGTTGGAAATAGTTTACTAAGTAAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTCAT
1 TGTTGGAAATAGTATACTAAATAAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTCAT
9350766 TTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTT
66 TTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTT
9350831 GATTGGGTAACATGCCCCAATCTCAAGATAAGGT
131 GATTGGGTAACATGCCCCAATCTCAAGATAAGGT
*
9350865 TGTTGGAAATAGTATACTAAATAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTC
1 TGTTGGAAATAGTATACTAAAT--AAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTC
**
9350930 ATTTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTGAAATAACATG
64 ATTTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATG
*
9350995 TTGATTGGGTAACATTCCCCAATCTCAAGATAA
129 TTGATTGGGTAACATGCCCCAATCTCAAGATAA
9351028 TGCTCATTTT
Statistics
Matches: 155, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
164 20 0.13
166 135 0.87
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (164 bp):
TGTTGGAAATAGTATACTAAATAAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTCAT
TTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACATGTT
GATTGGGTAACATGCCCCAATCTCAAGATAAGGT
Found at i:9351569 original size:22 final size:22
Alignment explanation
Indices: 9351544--9351624 Score: 144
Period size: 22 Copynumber: 3.7 Consensus size: 22
9351534 AATAAAGCTT
9351544 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
9351566 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
9351588 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
9351610 TCATCTTTGAAAAGA
1 TCATCTTTGAAAAGA
9351625 ATGTAGATGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:9355575 original size:6 final size:6
Alignment explanation
Indices: 9355559--9355626 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
9355549 ATTTTTTCCC
** *
9355559 TTTTC- TTTTCT TTTTCT TTTT-T CTCAT-T TTTTCT TTTTCAT CTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTTTCT TTTTC-T TTTTCT
*
9355606 TTTTCT TTTTACT TATTCT TT
1 TTTTCT TTTT-CT TTTTCT TT
9355627 CTTTGCTGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
5 8 0.16
6 32 0.64
7 10 0.20
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:9355580 original size:13 final size:13
Alignment explanation
Indices: 9355559--9355626 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
9355549 ATTTTTTCCC
9355559 TTTTC-TTTTCTT
1 TTTTCTTTTTCTT
*
9355571 TTTCTTTTTTCTCATT
1 TTT-TCTTTT-TC-TT
*
9355587 TTTTCTTTTTCAT
1 TTTTCTTTTTCTT
*
9355600 CTTTCTTTTTCTT
1 TTTTCTTTTTCTT
* *
9355613 TTTACTTATTCTT
1 TTTTCTTTTTCTT
9355626 T
1 T
9355627 CTTTGCTGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
12 3 0.07
13 24 0.55
14 5 0.11
15 7 0.16
16 5 0.11
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:9355590 original size:36 final size:37
Alignment explanation
Indices: 9355542--9355615 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
9355532 CTTGATTCAA
9355542 TTTCTCCATTTTTTCCCTTTTC-T-TTTCTTTTTCTTT
1 TTTCTCCATTTTTT-CCTTTTCATCTTTCTTTTTCTTT
*
9355578 TTTCT-CATTTTTTCTTTTTCATCTTTCTTTTTCTTT
1 TTTCTCCATTTTTTCCTTTTCATCTTTCTTTTTCTTT
9355614 TT
1 TT
9355616 ACTTATTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 6 0.17
35 9 0.26
36 20 0.57
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (37 bp):
TTTCTCCATTTTTTCCTTTTCATCTTTCTTTTTCTTT
Found at i:9355624 original size:19 final size:18
Alignment explanation
Indices: 9355559--9355626 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
9355549 ATTTTTTCCC
9355559 TTTTCTT-TTCTTTTTCTT
1 TTTTCTTATTCTTTTTC-T
*
9355577 TTTTCTCA-T-TTTTTCT
1 TTTTCTTATTCTTTTTCT
9355593 TTTTCATCT-TTCTTTTTCT
1 TTTTC-T-TATTCTTTTTCT
9355612 TTTTACTTATTCTTT
1 TTTT-CTTATTCTTT
9355627 CTTTGCTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
16 6 0.15
17 7 0.17
18 9 0.22
19 18 0.44
20 1 0.02
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTTATTCTTTTTCT
Found at i:9355629 original size:17 final size:17
Alignment explanation
Indices: 9355569--9355630 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
9355559 TTTTCTTTTC
* *
9355569 TTTTTCTTTTTTCTCAT
1 TTTTTCTTTTTACTTAT
9355586 TTTTTCTTTTTCATCTT-T
1 TTTTTCTTTTT-A-CTTAT
9355604 CTTTTTCTTTTTACTTAT
1 -TTTTTCTTTTTACTTAT
*
9355622 TCTTTCTTT
1 TTTTTCTTT
9355631 GCTGGATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 22 0.58
18 3 0.08
19 13 0.34
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTTACTTAT
Found at i:9360404 original size:46 final size:49
Alignment explanation
Indices: 9360337--9360427 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
9360327 TATAATGTAT
* *
9360337 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCTCATGATTTCTAGTTCACATGCGTTTATTTAGGAAAAATTAA
9360383 CCTAA-CTGCATGATTTCTAGTTCACATGCGTTTATTTAGGAAAAA
1 CCTAACCT-CATGATTTCTAGTTCACATGCGTTTATTTAGGAAAAA
9360428 GAAAGGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 2 0.05
46 19 0.49
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (49 bp):
CCTAACCTCATGATTTCTAGTTCACATGCGTTTATTTAGGAAAAATTAA
Found at i:9361832 original size:25 final size:25
Alignment explanation
Indices: 9361771--9361847 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
9361761 TTTATAAGAC
*
9361771 TAATATAATAAAATAATAATTAAAG
1 TAATATAATAAAATAATAATTAAAA
*
9361796 TAATGAT-TTAAAAT-AT-ATTAAAAA
1 TAAT-ATAATAAAATAATAATT-AAAA
*
9361820 TAATAATAATAAAA-ATTAAGTTAAAA
1 TAAT-ATAATAAAATAATAA-TTAAAA
9361846 TA
1 TA
9361848 TAACTAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
23 3 0.07
24 11 0.27
25 16 0.39
26 9 0.22
27 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (25 bp):
TAATATAATAAAATAATAATTAAAA
Found at i:9362814 original size:28 final size:27
Alignment explanation
Indices: 9362747--9362814 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
9362737 CTTGCTTTTT
*
9362747 CTCTCTTTGCTTGTGTCGATCTGTGTTC
1 CTCTCTTT-CTTGTGTCGATCTCTGTTC
*
9362775 CTCTTCTTTCTTGCTGTCGATCTCTGTTG
1 CTC-TCTTTCTTG-TGTCGATCTCTGTTC
*
9362804 CTCTCCTTCTT
1 CTCTCTTTCTT
9362815 TTCTGTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.40
29 21 0.60
ACGTcount: A:0.03, C:0.29, G:0.16, T:0.51
Consensus pattern (27 bp):
CTCTCTTTCTTGTGTCGATCTCTGTTC
Found at i:9363309 original size:3 final size:3
Alignment explanation
Indices: 9363301--9363327 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9363291 GTATTTTATT
9363301 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
9363328 AATTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9364253 original size:34 final size:34
Alignment explanation
Indices: 9364210--9364278 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
9364200 CAGTCTTGCA
*
9364210 ATACTGTTCATGATGCATTTATTGTCAATATCAT
1 ATACTGTTCATGATGCATGTATTGTCAATATCAT
9364244 ATACTGTTCATGATGCATGTATTGTCAATATCAT
1 ATACTGTTCATGATGCATGTATTGTCAATATCAT
9364278 A
1 A
9364279 ATGGTGGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (34 bp):
ATACTGTTCATGATGCATGTATTGTCAATATCAT
Found at i:9366654 original size:3 final size:3
Alignment explanation
Indices: 9366646--9366686 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9366636 GAGCAGCTGC
9366646 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9366687 TTTTTGCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9374686 original size:35 final size:35
Alignment explanation
Indices: 9374645--9374712 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
9374635 CAGAGTTATA
*
9374645 AAATTTTAAAAAAT-TCAAAATTATACAATTAATTG
1 AAATTTTAAAAAATAT-AAAATTAAACAATTAATTG
*
9374680 AAATTTTAAAAAATATAAAATTAAATAATTAAT
1 AAATTTTAAAAAATATAAAATTAAACAATTAAT
9374713 AAAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (35 bp):
AAATTTTAAAAAATATAAAATTAAACAATTAATTG
Found at i:9374740 original size:25 final size:25
Alignment explanation
Indices: 9374687--9374759 Score: 67
Period size: 28 Copynumber: 2.8 Consensus size: 25
9374677 TTGAAATTTT
* *
9374687 AAAAAATATAAAATTAAATAATTAATAA
1 AAAAAATTTAAAATTTAA-AATT-AT-A
9374715 AAAAAATTTAAAATTTAAAATT-TA
1 AAAAAATTTAAAATTTAAAATTATA
* *
9374739 AAAGAATATGAAAATTTAAAA
1 AAAAAAT-TTAAAATTTAAAA
9374760 AAAGACGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 7 0.17
25 13 0.32
27 4 0.10
28 16 0.40
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAAAATTTAAAATTTAAAATTATA
Found at i:9374759 original size:7 final size:7
Alignment explanation
Indices: 9374717--9374741 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9374707 ATTAATAAAA
9374717 AAAATTT
1 AAAATTT
9374724 AAAATTT
1 AAAATTT
9374731 AAAATTT
1 AAAATTT
9374738 AAAA
1 AAAA
9374742 GAATATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:9376599 original size:31 final size:31
Alignment explanation
Indices: 9376561--9376654 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
9376551 CCCGAAGGAC
* * *
9376561 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
9376592 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
9376623 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
9376654 C
1 C
9376655 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:9380907 original size:31 final size:31
Alignment explanation
Indices: 9380883--9380962 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
9380873 CCATAGATTT
* *
9380883 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
9380914 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
9380945 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
9380963 CCTCGACCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:9381376 original size:42 final size:42
Alignment explanation
Indices: 9381304--9381501 Score: 136
Period size: 42 Copynumber: 4.8 Consensus size: 42
9381294 AATTGATACT
** * * * *
9381304 TTAGCGGCGTTT-TAGTACAAACGCTGCAATAGAGTTG-ACA
1 TTAGCGGCGTTTATACAAAAAACGCCGCAATAGAGTGGTAAA
* * *
9381344 TATAGCGGCGTTTTTACAAAAAATGCCGCAATAGGGTGGTAAA
1 T-TAGCGGCGTTTATACAAAAAACGCCGCAATAGAGTGGTAAA
* * * *
9381387 TTAGCGGCGTTTATACCACAAACGCCACAATAGAGT-ATAAA
1 TTAGCGGCGTTTATACAAAAAACGCCGCAATAGAGTGGTAAA
* * * *
9381428 TTTTGCGGCGATTGA-GC-CAAAACGCCGCAATAGAGTGGTAAA
1 -TTAGCGGCG-TTTATACAAAAAACGCCGCAATAGAGTGGTAAA
* * * * *
9381470 TTCGTGGCGTTTATACCACAAATGCCGCAATA
1 TTAGCGGCGTTTATACAAAAAACGCCGCAATA
9381502 TATTACACAT
Statistics
Matches: 121, Mismatches: 29, Indels: 14
0.74 0.18 0.09
Matches are distributed among these distances:
40 4 0.03
41 39 0.32
42 72 0.60
43 6 0.05
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (42 bp):
TTAGCGGCGTTTATACAAAAAACGCCGCAATAGAGTGGTAAA
Found at i:9381626 original size:82 final size:81
Alignment explanation
Indices: 9381531--9381704 Score: 269
Period size: 82 Copynumber: 2.1 Consensus size: 81
9381521 TTTATTCCTC
* *
9381531 AAACGCCGCAATAGTGATAATCAATAGTGGTG-TTTTTAGACAAACGCCATAATAGTGTTAATCA
1 AAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTTA-ACAAACGCCAGAATAGTG-TAATCA
9381595 ATAATGGCGTTTTTAGAA
64 ATAATGGCGTTTTTAGAA
9381613 AAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTTAACAAACGCCAGAATAGTGTAATCAAT
1 AAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTTAACAAACGCCAGAATAGTGTAATCAAT
* ** *
9381678 AGTGGCGTTTTTTTAT
66 AATGGCGTTTTTAGAA
9381694 AAACGCCGCAA
1 AAACGCCGCAA
9381705 AATGTTAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
81 31 0.36
82 48 0.56
83 6 0.07
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (81 bp):
AAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTTAACAAACGCCAGAATAGTGTAATCAAT
AATGGCGTTTTTAGAA
Found at i:9381685 original size:40 final size:41
Alignment explanation
Indices: 9381530--9381704 Score: 230
Period size: 41 Copynumber: 4.3 Consensus size: 41
9381520 GTTTATTCCT
*
9381530 CAAACGCCGCAATAGTGATAATCAATAGTGGTGTTTTTAGA
1 CAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGA
** * *
9381571 CAAACGCCATAATAGTGTTAATCAATAATGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGA
*
9381612 AAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTTA-A
1 CAAACGCCGCAATAGTGATAATCAATAGTGGCG-TTTTTAGA
**
9381653 CAAACGCCAG-AATAGTG-TAATCAATAGTGGCGTTTTTTTA
1 CAAACGCC-GCAATAGTGATAATCAATAGTGGCGTTTTTAGA
*
9381693 TAAACGCCGCAA
1 CAAACGCCGCAA
9381705 AATGTTAAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
39 6 0.05
40 25 0.21
41 79 0.68
42 7 0.06
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGA
Found at i:9384856 original size:28 final size:28
Alignment explanation
Indices: 9384825--9384878 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
9384815 TTATGAGTGC
9384825 ATATAATAT-TTGTCATAGAAGTTTATCA
1 ATAT-ATATCTTGTCATAGAAGTTTATCA
* * *
9384853 ATATTTCTCTTGTCATGGAAGTTTAT
1 ATATATATCTTGTCATAGAAGTTTAT
9384879 ATTTTCTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (28 bp):
ATATATATCTTGTCATAGAAGTTTATCA
Found at i:9387286 original size:21 final size:21
Alignment explanation
Indices: 9387268--9387373 Score: 124
Period size: 21 Copynumber: 5.0 Consensus size: 21
9387258 ATGAAGCAAG
*
9387268 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
9387289 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
9387310 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
9387331 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
9387352 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
9387373 G
1 G
9387374 ACAGAACAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
20 1 0.01
21 75 0.99
ACGTcount: A:0.37, C:0.21, G:0.41, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:9387366 original size:23 final size:21
Alignment explanation
Indices: 9387272--9387387 Score: 78
Period size: 21 Copynumber: 5.4 Consensus size: 21
9387262 AGCAAGGGAA
*
9387272 ACAGAGAGAGCAGCAGCGGAAG
1 ACAGAGAGAG-AGCAGCGGCAG
** *
9387294 -CAGCTAGAGCAGCAGCGGAAG
1 ACAGAGAGAG-AGCAGCGGCAG
** *
9387315 -CAGCTAGAGCAGCAGCGGAAG
1 ACAGAGAGAG-AGCAGCGGCAG
9387336 -CAGAGAGAGAAGCAGCGGCAG
1 ACAGAGAGAG-AGCAGCGGCAG
*
9387357 CACAGAGAGAG-GCAGCGACAG
1 -ACAGAGAGAGAGCAGCGGCAG
9387378 AACAGAGAGA
1 -ACAGAGAGA
9387388 AGTAATATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
21 75 0.89
23 9 0.11
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.02
Consensus pattern (21 bp):
ACAGAGAGAGAGCAGCGGCAG
Found at i:9387922 original size:43 final size:42
Alignment explanation
Indices: 9387764--9387988 Score: 118
Period size: 43 Copynumber: 5.3 Consensus size: 42
9387754 ATACATATTC
* * * * * * ** *
9387764 TGCGGCGTTTTTAGGAAAATGCCGGTAAAAATAAAAATTTAC
1 TGCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAACCTAT
* * *
9387806 TGCGGCGTTTTTGAA-GAAAACGCCGCTAAACATCAACGA-CTAA
1 TGCGGCG-TTTT-AATGAAAACGCCGCTAAATATCAA-AACCTAT
* * * *
9387849 TGCGGCGTTTGT-CTGCCAAATGCCGTTAAATATCAAAACCTAT
1 TGCGGCGTTT-TAATG-AAAACGCCGCTAAATATCAAAACCTAT
* * *
9387892 TGCGGCGTTTTAATGATAAACGCCGCTAAATATTAATACCTTT
1 TGCGGCGTTTTAATGA-AAACGCCGCTAAATATCAAAACCTAT
* * ***
9387935 TGCGGCGTTTGT--TGAACAATCGCCGCTATATGTTGTAACCTAT
1 TGCGGCGTTT-TAATGAA-AA-CGCCGCTAAATATCAAAACCTAT
9387978 TGCGGCGTTTT
1 TGCGGCGTTTT
9387989 TTTGTTGAAA
Statistics
Matches: 143, Mismatches: 28, Indels: 24
0.73 0.14 0.12
Matches are distributed among these distances:
41 1 0.01
42 19 0.13
43 120 0.84
44 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
TGCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAACCTAT
Found at i:9388042 original size:15 final size:15
Alignment explanation
Indices: 9388011--9388071 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
9388001 CGTCGCAAAC
* *
9388011 TTTAGCGGCGCTATT
1 TTTAGCGGCGTTTTT
9388026 TTTAGCGGCGTTTTTT
1 TTTAGCGGCG-TTTTT
*
9388042 TTTA-CGCCGTATGTGTT
1 TTTAGCGGCGT-T-T-TT
9388059 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
9388072 AAAAACGCCG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 15 0.41
16 9 0.24
17 7 0.19
18 5 0.14
ACGTcount: A:0.10, C:0.16, G:0.26, T:0.48
Consensus pattern (15 bp):
TTTAGCGGCGTTTTT
Found at i:9388502 original size:70 final size:70
Alignment explanation
Indices: 9388426--9388576 Score: 302
Period size: 70 Copynumber: 2.2 Consensus size: 70
9388416 CTACCTATTC
9388426 ATAATCACATAACATATACAAAGCATATAATTATCTTTAGTCATGCATACATACAATCAATGTAA
1 ATAATCACATAACATATACAAAGCATATAATTATCTTTAGTCATGCATACATACAATCAATGTAA
9388491 TACAG
66 TACAG
9388496 ATAATCACATAACATATACAAAGCATATAATTATCTTTAGTCATGCATACATACAATCAATGTAA
1 ATAATCACATAACATATACAAAGCATATAATTATCTTTAGTCATGCATACATACAATCAATGTAA
9388561 TACAG
66 TACAG
9388566 ATAATCACATA
1 ATAATCACATA
9388577 TAATTATAAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 81 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (70 bp):
ATAATCACATAACATATACAAAGCATATAATTATCTTTAGTCATGCATACATACAATCAATGTAA
TACAG
Found at i:9388550 original size:35 final size:35
Alignment explanation
Indices: 9388441--9388551 Score: 97
Period size: 35 Copynumber: 3.2 Consensus size: 35
9388431 CACATAACAT
9388441 ATACAAAGCATATAATTATCTTTAGTCATGCATAC
1 ATACAAAGCATATAATTATCTTTAGTCATGCATAC
* * ** *
9388476 ATAC-AATCAATGTAA-TA-CAGATAATCA--CATAAC
1 ATACAAAGC-ATATAATTATC-TTTAGTCATGCAT-AC
9388509 ATATACAAAGCATATAATTATCTTTAGTCATGCATAC
1 --ATACAAAGCATATAATTATCTTTAGTCATGCATAC
9388546 ATACAA
1 ATACAA
9388552 TCAATGTAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
32 3 0.05
33 3 0.05
34 10 0.18
35 24 0.43
36 10 0.18
37 3 0.05
38 3 0.05
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (35 bp):
ATACAAAGCATATAATTATCTTTAGTCATGCATAC
Found at i:9389773 original size:16 final size:16
Alignment explanation
Indices: 9389752--9389785 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9389742 AGTAACACAT
9389752 ATAATCATTCAATTAG
1 ATAATCATTCAATTAG
9389768 ATAATCATTCAATTAG
1 ATAATCATTCAATTAG
9389784 AT
1 AT
9389786 GATTAAATTT
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:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
ATAATCATTCAATTAG
Found at i:9389852 original size:66 final size:66
Alignment explanation
Indices: 9389776--9389899 Score: 221
Period size: 66 Copynumber: 1.9 Consensus size: 66
9389766 AGATAATCAT
* *
9389776 TCAATTAGATGATTAAATTTATTTAAATTTATTTTTAATTTAAAGATTTACTTTCCTCCAAAACA
1 TCAATTAGATGATTAAATTCATTTAAATTTATTTTTAATTTAAAGATTTACTTACCTCCAAAACA
9389841 A
66 A
*
9389842 TCAATTAGATGATTAAATTCATTTTAATTTATTTTTAATTTAAAGATTTACTTACCTC
1 TCAATTAGATGATTAAATTCATTTAAATTTATTTTTAATTTAAAGATTTACTTACCTC
9389900 TAATTTATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (66 bp):
TCAATTAGATGATTAAATTCATTTAAATTTATTTTTAATTTAAAGATTTACTTACCTCCAAAACA
A
Found at i:9389909 original size:34 final size:34
Alignment explanation
Indices: 9389866--9389936 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
9389856 AAATTCATTT
9389866 TAATTTATTTTTAATTTAAAGATTTACTTACCTC
1 TAATTTATTTTTAATTTAAAGATTTACTTACCTC
9389900 TAATTTATTTTTAATTTAAAGATTTACTTACCTC
1 TAATTTATTTTTAATTTAAAGATTTACTTACCTC
9389934 TAA
1 TAA
9389937 AACTTATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.52
Consensus pattern (34 bp):
TAATTTATTTTTAATTTAAAGATTTACTTACCTC
Found at i:9390194 original size:61 final size:60
Alignment explanation
Indices: 9390129--9390271 Score: 144
Period size: 61 Copynumber: 2.3 Consensus size: 60
9390119 TTTACATTAA
* ** *
9390129 AAAAAATATGAATATA-TAAAATATATTAAAATTATATGAATATAATATTAATATATATTTT
1 AAAAAATAT-AATA-ACTAAAATATATTAAAATTATACGAATATAATACAAATACATATTTT
* * **
9390190 AAAAAATATATTAACTTAAAATATTTTATTATTATACGAATATAATACAAATACATATTTT
1 AAAAAATATAATAAC-TAAAATATATTAAAATTATACGAATATAATACAAATACATATTTT
** *
9390251 TTAAAATATATTAACTTAAAA
1 AAAAAATATAATAAC-TAAAA
9390272 AAACAAATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 3 0.04
61 66 0.94
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (60 bp):
AAAAAATATAATAACTAAAATATATTAAAATTATACGAATATAATACAAATACATATTTT
Found at i:9390282 original size:61 final size:61
Alignment explanation
Indices: 9390167--9390477 Score: 197
Period size: 61 Copynumber: 5.1 Consensus size: 61
9390157 AAATTATATG
* ** * **** *
9390167 AATATAATATTAATATATATTTTAAAAAATATATTAACTTAAAATATTTTATTATTATACG
1 AATATAATATGAATATATATTTTTTAAAATATATTAACTTAAAAAAACAAATTATTATACA
** *
9390228 AATATAATACAAATACATATTTTTTAAAATATATTAACTTAAAAAAACAAATTA-TA-A-A
1 AATATAATATGAATATATATTTTTTAAAATATATTAACTTAAAAAAACAAATTATTATACA
* * * * * * * * *
9390286 AATATATTTTTAATACAAATATATATTT-AAATATATTAAATTACAAATACAAATTA-TATAAA
1 AATATAATATGAAT--ATATAT-TTTTTAAAATATATTAACTTAAAAAAACAAATTATTATACA
* * * ****
9390348 ATATATTTTTAATACGAATATATATTTTTT-AAATATATTGACTTAAAATATTTTATTATTATAC
1 A-ATA----TAATATGAATATATATTTTTTAAAATATATTAACTTAAAAAAACAAATTATTATAC
*
9390412 T
61 A
* * * *
9390413 AATATAATATGAATATATATATTTGAAAATATATTAACATAAAAATACAAATTA-TATA-A
1 AATATAATATGAATATATATTTTTTAAAATATATTAACTTAAAAAAACAAATTATTATACA
9390472 AATATA
1 AATATA
9390478 TTAACTTAAA
Statistics
Matches: 189, Mismatches: 49, Indels: 26
0.72 0.19 0.10
Matches are distributed among these distances:
58 10 0.05
59 7 0.04
60 56 0.30
61 69 0.37
62 2 0.01
63 3 0.02
64 26 0.14
65 10 0.05
67 6 0.03
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATAATATGAATATATATTTTTTAAAATATATTAACTTAAAAAAACAAATTATTATACA
Found at i:9390288 original size:31 final size:31
Alignment explanation
Indices: 9390253--9390354 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 31
9390243 CATATTTTTT
*
9390253 AAAATATATTAACTTAAAAAAACAAATTATA
1 AAAATATATTAAATTAAAAAAACAAATTATA
* * * * *
9390284 AAAATATATT--TTTAATACAA-ATATATATT
1 AAAATATATTAAATTAAAAAAACAAAT-TATA
* * *
9390313 TAAATATATTAAATTACAAATACAAATTATA
1 AAAATATATTAAATTAAAAAAACAAATTATA
9390344 TAAAATATATT
1 -AAAATATATT
9390355 TTTAATACGA
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
28 3 0.06
29 19 0.37
31 18 0.35
32 12 0.23
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATATATTAAATTAAAAAAACAAATTATA
Found at i:9390340 original size:60 final size:61
Alignment explanation
Indices: 9390254--9390374 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 61
9390244 ATATTTTTTA
*
9390254 AAATATATTAACTTAAAAAAACAAATTATA-AAAATATATTTTTAATACAAATATATATTT
1 AAATATATTAAATTAAAAAAACAAATTATATAAAATATATTTTTAATACAAATATATATTT
* * *
9390314 AAATATATTAAATTACAAATACAAATTATATAAAATATATTTTTAATACGAATATATATTT
1 AAATATATTAAATTAAAAAAACAAATTATATAAAATATATTTTTAATACAAATATATATTT
9390375 TTTAAATATA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
60 27 0.48
61 29 0.52
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (61 bp):
AAATATATTAAATTAAAAAAACAAATTATATAAAATATATTTTTAATACAAATATATATTT
Found at i:9390563 original size:44 final size:44
Alignment explanation
Indices: 9390427--9390570 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 44
9390417 TAATATGAAT
* * **
9390427 ATATATATTTGAAAATATATTAACATAAAAATACAAATTATATAAA
1 ATATATTTTTTAAAA-ATATTATTATAAAAATACAAA-TATATAAA
** * * * *
9390473 ATATATTAACTTAAAAATTTTATTATTATAAGA-AAATA-ATACAA
1 ATATATT-TTTTAAAAATATTATTATAAAAATACAAATATATA-AA
*
9390517 ATATATTTTTTAAATATATTATT-TAAAAATACAAATGATATAAA
1 ATATATTTTTTAAAAATATTATTATAAAAATACAAAT-ATATAAA
9390561 ATATATTTTT
1 ATATATTTTT
9390571 AATACAAATA
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
42 5 0.07
43 19 0.25
44 24 0.32
45 6 0.08
46 17 0.22
47 5 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (44 bp):
ATATATTTTTTAAAAATATTATTATAAAAATACAAATATATAAA
Found at i:9390601 original size:27 final size:28
Alignment explanation
Indices: 9390527--9390601 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 28
9390517 ATATATTTTT
*
9390527 TAAATATATTATTTAAAAATACAAATGATA
1 TAAA-ATA-TATTTTAAAATACAAATGATA
*
9390557 TAAAATATATTTT-TAATACAAAT-ATAA
1 TAAAATATATTTTAAAATACAAATGAT-A
9390584 TACAAAT-T-TTTTAAAATA
1 TA-AAATATATTTTAAAATA
9390602 TATTAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 6 0.15
27 17 0.44
28 9 0.23
29 3 0.08
30 4 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (28 bp):
TAAAATATATTTTAAAATACAAATGATA
Found at i:9390631 original size:20 final size:22
Alignment explanation
Indices: 9390599--9390647 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
9390589 ATTTTTTAAA
9390599 ATATATTAATTTAA-ATATTTT
1 ATATATTAATTTAATATATTTT
* *
9390620 AT-TATTATTTTAATATGTTTT
1 ATATATTAATTTAATATATTTT
9390641 ATATATT
1 ATATATT
9390648 CGTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATATTAATTTAATATATTTT
Found at i:9402877 original size:19 final size:19
Alignment explanation
Indices: 9402853--9402923 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 19
9402843 TATGTCACAT
9402853 ATGAACAATTTGATTTTAC
1 ATGAACAATTTGATTTTAC
* *
9402872 ATGAACAAATGTGTATTTAATATAT
1 ATGAAC-AATTTG-A-TT--T-TAC
9402897 ATGAACAATTTGATTTTAC
1 ATGAACAATTTGATTTTAC
9402916 ATGAACAA
1 ATGAACAA
9402924 ATGTGTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 16 0.38
20 6 0.14
21 1 0.02
22 4 0.10
23 1 0.02
24 6 0.14
25 8 0.19
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGAACAATTTGATTTTAC
Found at i:9402900 original size:25 final size:25
Alignment explanation
Indices: 9402872--9402944 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 25
9402862 TTGATTTTAC
9402872 ATGAACAAATGTGTATTTAATATAT
1 ATGAACAAATGTGTATTTAATATAT
* *
9402897 ATGAAC-AATTTG-A-TT--T-TAC
1 ATGAACAAATGTGTATTTAATATAT
9402916 ATGAACAAATGTGTATTTAATATAT
1 ATGAACAAATGTGTATTTAATATAT
9402941 ATGA
1 ATGA
9402945 GTAATTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
19 8 0.21
20 6 0.16
21 1 0.03
22 4 0.11
23 1 0.03
24 6 0.16
25 12 0.32
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (25 bp):
ATGAACAAATGTGTATTTAATATAT
Found at i:9402951 original size:44 final size:44
Alignment explanation
Indices: 9402851--9402944 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
9402841 AATATGTCAC
9402851 ATATGAACAATTTGATTTTACATGAACAAATGTGTATTTAATAT
1 ATATGAACAATTTGATTTTACATGAACAAATGTGTATTTAATAT
9402895 ATATGAACAATTTGATTTTACATGAACAAATGTGTATTTAATAT
1 ATATGAACAATTTGATTTTACATGAACAAATGTGTATTTAATAT
9402939 ATATGA
1 ATATGA
9402945 GTAATTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.40
Consensus pattern (44 bp):
ATATGAACAATTTGATTTTACATGAACAAATGTGTATTTAATAT
Found at i:9403797 original size:30 final size:30
Alignment explanation
Indices: 9403732--9403797 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
9403722 TCGGAGATAG
* *
9403732 ACTAGCAAGGTGGAAAATGAGAACTCTTTG
1 ACTAGCAAGGTGGAAAACGAGAACTCTTTC
* *
9403762 ACTAGCAAGGTGGAAAACGAGGACTTTTTC
1 ACTAGCAAGGTGGAAAACGAGAACTCTTTC
*
9403792 TCTAGC
1 ACTAGC
9403798 CGGAAGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (30 bp):
ACTAGCAAGGTGGAAAACGAGAACTCTTTC
Found at i:9420524 original size:23 final size:23
Alignment explanation
Indices: 9420456--9420516 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
9420446 ACATTTTATA
*
9420456 TGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
9420479 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
9420502 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
9420517 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:9425891 original size:23 final size:23
Alignment explanation
Indices: 9425823--9425883 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
9425813 ATATTTTATA
*
9425823 TGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
9425846 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
9425869 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
9425884 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:9425942 original size:16 final size:17
Alignment explanation
Indices: 9425921--9425954 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9425911 GTGCACAACC
9425921 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
9425937 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
9425954 T
1 T
9425955 GTACGTGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:9427413 original size:22 final size:23
Alignment explanation
Indices: 9427386--9427446 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
9427376 TTAAGGAAAG
9427386 AGAGTATCGATACTAC-ATCAAA
1 AGAGTATCGATACTACTATCAAA
* * * *
9427408 AGAGTATCGGTACTACTGTTATA
1 AGAGTATCGATACTACTATCAAA
9427431 AGTAGTATCGATACTA
1 AG-AGTATCGATACTA
9427447 GATAAGTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 15 0.47
23 5 0.16
24 12 0.38
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (23 bp):
AGAGTATCGATACTACTATCAAA
Found at i:9428500 original size:84 final size:85
Alignment explanation
Indices: 9428354--9428529 Score: 300
Period size: 84 Copynumber: 2.1 Consensus size: 85
9428344 AAATATCAAG
*
9428354 GGCCTCAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAATAAAGTATTATGGATCA
1 GGCCTCAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAACAAAGTATTATGGATCA
9428419 ATGGTAAAATTAAGATTTAA
66 ATGGTAAAATTAAGATTTAA
*
9428439 GGCC-CAAAAAATTAGATTTATTACTATTGTTACAATAAAAAAACAAACAAAGTATTATGGATCA
1 GGCCTCAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAACAAAGTATTATGGATCA
* *
9428503 GTGGTAAAATTGAGATTTAA
66 ATGGTAAAATTAAGATTTAA
9428523 GGACCTC
1 GG-CCTC
9428530 TTTTTAATAA
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
84 78 0.92
85 6 0.07
86 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (85 bp):
GGCCTCAAAAAATTAGATTTATTACTATTATTACAATAAAAAAACAAACAAAGTATTATGGATCA
ATGGTAAAATTAAGATTTAA
Found at i:9429667 original size:170 final size:171
Alignment explanation
Indices: 9429375--9429734 Score: 408
Period size: 170 Copynumber: 2.1 Consensus size: 171
9429365 AAGAAACGGT
* * * * *
9429375 AAATGATACAAATGGTTGCACGAATCAACTTATCTCAGTGATTAAGGGAATCATTATTGTTTTTA
1 AAATGATACAAATGGTTGCACGAACCAACTTACCTCAGTGATTAAAGAAATCATTATTGTTCTTA
* * ** *
9429440 GAGGTAACGGGTTCGAGCAACAGCTACTGCAGTATGGTGATTGAATGTTTATTGTCAAA-TGATT
66 GAGCTAACGGGTTCGAGCAACAGCTACTGCAGCATGGTGATTGAACATTCATTGTCAAATTG-TT
9429504 GAGATTATTTAGAACATATACTAATCACCTTAGCTTAATAAA
130 GAGATTATTTAGAACATATACTAATCACCTTAGCTTAATAAA
* * * * *
9429546 AAATTATATAAATGGTTGCACGAACCAACTTACCTCAGTGGTTAAAGAAATCGTTGTTG-TCTTA
1 AAATGATACAAATGGTTGCACGAACCAACTTACCTCAGTGATTAAAGAAATCATTATTGTTCTTA
* * * *
9429610 TAGCTTATGGGTTCGAGC-ACTAG-TGCCTGCAGCATGGTGATTGAACATTCATTGTCAAATTGT
66 GAGCTAACGGGTTCGAGCAAC-AGCT-ACTGCAGCATGGTGATTGAACATTCATTGTCAAATTGT
** *
9429673 TGAGATTATTTAGAACAAATATTACTTTGTTACCTTAGCTTAA-AAA
129 TGAGATTATTTAGAAC--ATA-TAC-TAATCACCTTAGCTTAATAAA
*
9429719 AAGT-ATACAAATGGTT
1 AAATGATACAAATGGTT
9429735 CTTCGACTAT
Statistics
Matches: 158, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
169 3 0.02
170 66 0.42
171 52 0.33
172 14 0.09
173 9 0.06
174 14 0.09
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (171 bp):
AAATGATACAAATGGTTGCACGAACCAACTTACCTCAGTGATTAAAGAAATCATTATTGTTCTTA
GAGCTAACGGGTTCGAGCAACAGCTACTGCAGCATGGTGATTGAACATTCATTGTCAAATTGTTG
AGATTATTTAGAACATATACTAATCACCTTAGCTTAATAAA
Found at i:9445568 original size:20 final size:21
Alignment explanation
Indices: 9445526--9445569 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
9445516 TCGAAAATGT
9445526 TAAAAAAATTAATATTTTAAG
1 TAAAAAAATTAATATTTTAAG
9445547 TAAAAATAA-TAATATTTT-AG
1 TAAAAA-AATTAATATTTTAAG
9445567 TAA
1 TAA
9445570 TTTTTATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAAAAAATTAATATTTTAAG
Found at i:9446039 original size:32 final size:34
Alignment explanation
Indices: 9446003--9446080 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
9445993 TTAAGTAACG
9446003 TTTAATATTAACA-TTT-TTAATAAA-AAT-AATAT
1 TTTAATA-TAACACTTTATTAA-AAATAATAAATAT
*
9446035 TTTAA-ATAACACTTTATTAAAAATATTAAATAT
1 TTTAATATAACACTTTATTAAAAATAATAAATAT
9446068 TTTAAT-TAACACT
1 TTTAATATAACACT
9446081 CAAATTAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 5 0.12
31 7 0.17
32 11 0.28
33 17 0.43
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (34 bp):
TTTAATATAACACTTTATTAAAAATAATAAATAT
Found at i:9446126 original size:32 final size:32
Alignment explanation
Indices: 9446092--9446154 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
9446082 AAATTAATAT
9446092 TTTTAATAAAAAATAAT-AT-TTTTAAATAACA
1 TTTT-ATAAAAAATAATAATATTTTAAATAACA
* *
9446123 TTTTATCAAAAATAATAATATTTTCAATAACA
1 TTTTATAAAAAATAATAATATTTTAAATAACA
9446155 CTTTCCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.39
31 6 0.21
32 11 0.39
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTTATAAAAAATAATAATATTTTAAATAACA
Found at i:9446144 original size:76 final size:75
Alignment explanation
Indices: 9446009--9446156 Score: 219
Period size: 77 Copynumber: 2.0 Consensus size: 75
9445999 AACGTTTAAT
* *
9446009 ATTAACATTTTTAATAAAAATAATATTTTAAATAACACTTTATTAAAAATATTAAATATTTT-AA
1 ATTAACATTTTTAATAAAAATAATATTTTAAATAACACTTTATCAAAAATAATAAATATTTTCAA
9446073 TTAACACTCAA
66 -TAACACTCAA
* *
9446084 ATTAATATTTTTAATAAAAAATAATATTTTTAAATAACATTTTATCAAAAATAAT-AATATTTTC
1 ATTAACATTTTTAAT-AAAAATAATA-TTTTAAATAACACTTTATCAAAAATAATAAATATTTTC
9446148 AATAACACT
64 AATAACACT
9446157 TTCCCATAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
75 14 0.21
76 25 0.38
77 27 0.41
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (75 bp):
ATTAACATTTTTAATAAAAATAATATTTTAAATAACACTTTATCAAAAATAATAAATATTTTCAA
TAACACTCAA
Found at i:9446567 original size:3 final size:3
Alignment explanation
Indices: 9446556--9446627 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
9446546 TTAAATAATA
*
9446556 TAT TA- TAT TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * * *
9446601 TA- TAT TTT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9446628 TTTTGCAGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
2 4 0.07
3 50 0.88
4 3 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:9446594 original size:22 final size:21
Alignment explanation
Indices: 9446556--9446604 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
9446546 TTAAATAATA
9446556 TATTAT-ATTATTATTATTAT
1 TATTATAATTATTATTATTAT
9446576 TATTATAATTACTTATTATTAT
1 TATTATAATTA-TTATTATTAT
9446598 TATTATA
1 TATTATA
9446605 TTTTTAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.22
21 4 0.15
22 17 0.63
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATAATTATTATTATTAT
Found at i:9448999 original size:16 final size:16
Alignment explanation
Indices: 9448980--9449010 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9448970 GATATCATGT
9448980 GGGGTTATAATACAAA
1 GGGGTTATAATACAAA
9448996 GGGGTTATAATACAA
1 GGGGTTATAATACAA
9449011 CGAGATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
GGGGTTATAATACAAA
Found at i:9451631 original size:106 final size:106
Alignment explanation
Indices: 9451501--9452663 Score: 1914
Period size: 106 Copynumber: 11.0 Consensus size: 106
9451491 TTGCTCGAGT
9451501 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
9451566 AGGGACCGCTGGTTATCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
9451607 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
9451672 AGAGACCGCTGGTTCTCAACAAACAACTTTTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
9451713 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
9451778 AGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* * *
9451819 GCCAATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACGCATGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
9451884 AGGGACCGCTGATTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
9451925 GCCAATTTCAGCTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
9451990 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
9452031 GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
9452096 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
9452137 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGGCAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
9452202 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
9452243 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
9452308 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
9452349 GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
9452414 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
9452455 GCCAAGTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * * *
9452520 AGGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* * * * *
9452561 GTCAATTTCAACTTCATAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
9452626 AGGGACCGCTGGTTGTCAATAAACAACTT-TCAACTTCA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCA
9452664 CGACGAAGGA
Statistics
Matches: 983, Mismatches: 74, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
105 7 0.01
106 976 0.99
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
Found at i:9452852 original size:84 final size:84
Alignment explanation
Indices: 9452698--9452970 Score: 377
Period size: 84 Copynumber: 3.2 Consensus size: 84
9452688 AGGCTATCTG
** * * *
9452698 CCAAAGACCCCCGAGTTCGATTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
*
9452763 GAGAAGGGTTATCTTCCAA
66 GAGAAGGGCTATCTTCCAA
* * * * *
9452782 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAGGC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
*
9452847 AAGAAGGGCTAT-TTGCCAA
66 GAGAAGGGCTATCTT-CCAA
* *
9452866 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
*
9452931 GAGAAGGGCTATCTGCCAA
66 GAGAAGGGCTATCTTCCAA
*
9452950 CCAAAGACCTGACGAGTTCGA
1 CCAAAGACCT-TCGAGTTCGA
9452971 TTTCATTCAG
Statistics
Matches: 163, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.01
84 152 0.93
85 9 0.06
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGCTATCTTCCAA
Found at i:9453213 original size:3 final size:3
Alignment explanation
Indices: 9453207--9453267 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
9453197 TATATTATAA
* *
9453207 TAT TAT TAT TAT TAT TAT TACT TAG TAT TAT TAT TA- TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* *
9453252 TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT T
9453268 TTTTGCAGGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:9455619 original size:26 final size:27
Alignment explanation
Indices: 9455590--9455644 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
9455580 TATTATAATC
*
9455590 ATTTAATAGTTTACT-ATTTTATTATT
1 ATTTAATAATTTACTAATTTTATTATT
** *
9455616 ATTTTTTAATTTACTAATTTTCTTATT
1 ATTTAATAATTTACTAATTTTATTATT
9455643 AT
1 AT
9455645 ATTTTGCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (27 bp):
ATTTAATAATTTACTAATTTTATTATT
Found at i:9455643 original size:27 final size:26
Alignment explanation
Indices: 9455599--9455649 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
9455589 CATTTAATAG
*
9455599 TTTACTATTTTATTATTATTTTTTAA
1 TTTACTATTTTATTATTATATTTTAA
*
9455625 TTTACTAATTTTCTTATTATATTTT
1 TTTACT-ATTTTATTATTATATTTT
9455650 GCAGATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTACTATTTTATTATTATATTTTAA
Found at i:9457380 original size:21 final size:21
Alignment explanation
Indices: 9457354--9457405 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
9457344 GGTACATCGT
9457354 CATTTCAAATAGCACCGCAGC
1 CATTTCAAATAGCACCGCAGC
* * *
9457375 CATTTCAAATGGTACCGTAGC
1 CATTTCAAATAGCACCGCAGC
*
9457396 CAGTTCAAAT
1 CATTTCAAAT
9457406 GCCACCACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (21 bp):
CATTTCAAATAGCACCGCAGC
Found at i:9457406 original size:21 final size:21
Alignment explanation
Indices: 9457357--9457411 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
9457347 ACATCGTCAT
* *
9457357 TTCAAATAGCACCGCAGCCAT
1 TTCAAATGGCACCGCAGCCAG
* *
9457378 TTCAAATGGTACCGTAGCCAG
1 TTCAAATGGCACCGCAGCCAG
*
9457399 TTCAAATGCCACC
1 TTCAAATGGCACC
9457412 ACCGTAGGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (21 bp):
TTCAAATGGCACCGCAGCCAG
Found at i:9458145 original size:13 final size:13
Alignment explanation
Indices: 9458127--9458152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9458117 GAATTGTAAC
9458127 GTTTATATTTAAT
1 GTTTATATTTAAT
9458140 GTTTATATTTAAT
1 GTTTATATTTAAT
9458153 TATTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
GTTTATATTTAAT
Done.