Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009234.1 Hibiscus syriacus cultivar Beakdansim tig00112856_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: 912649
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:490287 original size:60 final size:60
Alignment explanation
Indices: 490186--490301 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
490176 ATAGTCGGGT
* * *
490186 GATCATTTTGTAGTTTTTAATAGTCAGTGGACTCAACAAAACAACACTCTATAATCGAAA
1 GATCATTTTATAATTTTTAATAGTCAGTGGACTCAACAAAACAACACCCTATAATCGAAA
* * * * *
490246 GATCATTTTATAATTTTTAATAGTTGAG-GGATTTAATAAAACAATACCCTATAATC
1 GATCATTTTATAATTTTTAATAG-TCAGTGGACTCAACAAAACAACACCCTATAATC
490302 AAAATCCTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (60 bp):
GATCATTTTATAATTTTTAATAGTCAGTGGACTCAACAAAACAACACCCTATAATCGAAA
Found at i:490917 original size:31 final size:32
Alignment explanation
Indices: 490842--490927 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 32
490832 ACCAAAAGGT
* *
490842 AAATAATCGTTAAAATT-TCTAAACTTTTATA
1 AAATAATCATTAAAATTATCTAAACTATTATA
* * *
490873 CAATATTTATTAAAATTATC-AAACTATTATA
1 AAATAATCATTAAAATTATCTAAACTATTATA
*
490904 AAATAATCCTTAAAACTTAT-TAAA
1 AAATAATCATTAAAA-TTATCTAAA
490928 ATATATTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
31 34 0.79
32 9 0.21
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (32 bp):
AAATAATCATTAAAATTATCTAAACTATTATA
Found at i:492983 original size:30 final size:30
Alignment explanation
Indices: 492942--493016 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
492932 AAAACCGAAT
492942 TAAAC-GGGACGGGGAAAAACAGTTTATGC
1 TAAACGGGGACGGGGAAAAACAGTTTATGC
* *
492971 TAAACGGGGACGGAGAAAAACCGTTTATGC
1 TAAACGGGGACGGGGAAAAACAGTTTATGC
493001 TAAACGGGGACGGGGA
1 TAAACGGGGACGGGGA
493017 CGAGTTTAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 5 0.12
30 37 0.88
ACGTcount: A:0.36, C:0.15, G:0.35, T:0.15
Consensus pattern (30 bp):
TAAACGGGGACGGGGAAAAACAGTTTATGC
Found at i:493142 original size:42 final size:40
Alignment explanation
Indices: 493086--493175 Score: 135
Period size: 42 Copynumber: 2.2 Consensus size: 40
493076 AAATAATAAT
493086 TATATATATATATATAATATTAATAAATTCAATTTAAATTAA
1 TATATATATATATATAATATTAATAAATTCAATTTAAA-T-A
* * *
493128 TATATATATATATATAATATTTATATATTTAATTTAAATA
1 TATATATATATATATAATATTAATAAATTCAATTTAAATA
493168 TATATATA
1 TATATATA
493176 CCTGACCCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 9 0.20
41 1 0.02
42 35 0.78
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (40 bp):
TATATATATATATATAATATTAATAAATTCAATTTAAATA
Found at i:493147 original size:17 final size:17
Alignment explanation
Indices: 493125--493175 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
493115 CAATTTAAAT
493125 TAATATATATATATATA
1 TAATATATATATATATA
*
493142 TAATAT-T-TATATATT
1 TAATATATATATATATA
* *
493157 TAATTTAAATATATATA
1 TAATATATATATATATA
493174 TA
1 TA
493176 CCTGACCCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 1 0.04
17 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:494775 original size:60 final size:60
Alignment explanation
Indices: 494702--494863 Score: 179
Period size: 60 Copynumber: 2.7 Consensus size: 60
494692 TGCATCATAT
* * * *
494702 ATCCCCAAACTATA-ATCCTCATTTTAAATTAGTCCTTAAACTTTAAAATATTCCAATTTC
1 ATCCCCAAACTATAGATCC-CATTCTAAATTACTCCTTAAACTTTAAAACATTCCAATTTA
* *
494762 ATCCCCAAACTATAGCTCCCATTCTAAATTACTCCTTAAACTTTTAAACATTCCAATTTA
1 ATCCCCAAACTATAGATCCCATTCTAAATTACTCCTTAAACTTTAAAACATTCCAATTTA
** * * *
494822 ATCCTTAAACTATCGAT--AATTCTAAATTGAC-CCCTAAACTTT
1 ATCCCCAAACTATAGATCCCATTCTAAATT-ACTCCTTAAACTTT
494864 TGAATCTTCT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 20 0.23
59 2 0.02
60 63 0.72
61 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (60 bp):
ATCCCCAAACTATAGATCCCATTCTAAATTACTCCTTAAACTTTAAAACATTCCAATTTA
Found at i:497525 original size:31 final size:31
Alignment explanation
Indices: 497488--497555 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
497478 TCAAAAAACA
* * *
497488 TAAGATATAGTCACTTTCGTTTTTATTTAAT
1 TAAGATATAGCCACTTTCATTTTTATTTAAC
*
497519 TAAGATATGGCCACTTTCATTTTTATTTAAC
1 TAAGATATAGCCACTTTCATTTTTATTTAAC
497550 TAAGAT
1 TAAGAT
497556 GTGGTCATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (31 bp):
TAAGATATAGCCACTTTCATTTTTATTTAAC
Found at i:498089 original size:31 final size:31
Alignment explanation
Indices: 498050--498116 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
498040 TTATTAAAAG
*
498050 TATG-ACTAAATTGAGAGAATATATAAATAA
1 TATGAACTAAATTGAAAGAATATATAAATAA
498080 TATGAACTAAATTGAAAGAATATATAAATAA
1 TATGAACTAAATTGAAAGAATATATAAATAA
498111 TATGAA
1 TATGAA
498117 GCAAATGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (31 bp):
TATGAACTAAATTGAAAGAATATATAAATAA
Found at i:503776 original size:4 final size:4
Alignment explanation
Indices: 503769--503848 Score: 123
Period size: 4 Copynumber: 21.0 Consensus size: 4
503759 GAAAGTATGT
503769 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG --GG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
*
503815 ATGC ATGG --GG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
503849 GTAGATAGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
2 4 0.06
4 66 0.94
ACGTcount: A:0.24, C:0.01, G:0.51, T:0.24
Consensus pattern (4 bp):
ATGG
Found at i:508850 original size:60 final size:58
Alignment explanation
Indices: 508786--508944 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 58
508776 TAAATTTTTT
508786 CTTAAACTTTTAAACATTTCAATTTCATCCCTAAATTATGA-CTCTCATTCTATA-TTAGTC
1 CTTAAACTTTTAAA-ATTTCAATTTCATCCC-AAATTATGATCT-TCATTCTA-AGTTAGTC
* *
508846 CTTAAACTTTTTAAAATTTC-ATTTCCATCACCAAACTATGATCTTCATTCTAAGTTGGTCC
1 CTTAAAC-TTTTAAAATTTCAATTT-CATC-CCAAATTATGATCTTCATTCTAAGTTAGT-C
** * *
508907 CCAAAATTTTGTAATATTTCAATTTCATCCCAAATTAT
1 CTTAAACTTT-TAAAATTTCAATTTCATCCCAAATTAT
508945 ACGTATACAC
Statistics
Matches: 84, Mismatches: 7, Indels: 16
0.79 0.07 0.15
Matches are distributed among these distances:
59 5 0.06
60 47 0.56
61 28 0.33
62 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.42
Consensus pattern (58 bp):
CTTAAACTTTTAAAATTTCAATTTCATCCCAAATTATGATCTTCATTCTAAGTTAGTC
Found at i:509219 original size:60 final size:59
Alignment explanation
Indices: 509065--509238 Score: 188
Period size: 59 Copynumber: 2.9 Consensus size: 59
509055 TATTTAGATG
* *
509065 AATTTAGGGATGAAATTGGAATATTCAAAAGTTTAGGGATCAATTTAGAATGAAATCAT
1 AATTTAGGGATGAAATTGAAATATTCAAAAGTTTAAGGATCAATTTAGAATGAAATCAT
* * * * * *
509124 AGTTTGGGGATGAAATTGAAATGTACAAAAATTTAAGGA-CTAATTTAGAATGAGAGTCAT
1 AATTTAGGGATGAAATTGAAATATTCAAAAGTTTAAGGATC-AATTTAGAATGA-AATCAT
* * ** ** *
509184 AATTTAGAGATGAAATTAAAATATTTTAAAGTTTAATAATCAATTTAAAATGAAA
1 AATTTAGGGATGAAATTGAAATATTCAAAAGTTTAAGGATCAATTTAGAATGAAA
509239 GTCGTAGTTT
Statistics
Matches: 91, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
58 1 0.01
59 45 0.49
60 44 0.48
61 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (59 bp):
AATTTAGGGATGAAATTGAAATATTCAAAAGTTTAAGGATCAATTTAGAATGAAATCAT
Found at i:511050 original size:11 final size:11
Alignment explanation
Indices: 511030--511058 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
511020 AAATTGGCGG
511030 TTTTTT-CCGA
1 TTTTTTCCCGA
511040 TTTTTTCCCGA
1 TTTTTTCCCGA
511051 TTTTTTCC
1 TTTTTTCC
511059 AGTTTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.62
Consensus pattern (11 bp):
TTTTTTCCCGA
Found at i:516973 original size:15 final size:15
Alignment explanation
Indices: 516953--516985 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
516943 AGTATAGTTC
516953 TGAGAATACAATATT
1 TGAGAATACAATATT
516968 TGAGAATACAATATT
1 TGAGAATACAATATT
516983 TGA
1 TGA
516986 TCATCATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (15 bp):
TGAGAATACAATATT
Found at i:523305 original size:4 final size:4
Alignment explanation
Indices: 523298--523322 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
523288 GAAGGGGACA
523298 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
523323 CATAAATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:524281 original size:17 final size:18
Alignment explanation
Indices: 524259--524296 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
524249 TATTTTTTAA
524259 TATTTTTGAT-AAAATAT
1 TATTTTTGATAAAAATAT
*
524276 TATTTTTTATCAAAAATAT
1 TATTTTTGAT-AAAAATAT
524295 TA
1 TA
524297 ATTTCGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTTTTGATAAAAATAT
Found at i:530897 original size:17 final size:16
Alignment explanation
Indices: 530875--530908 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
530865 TAAAAACAGT
530875 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
530892 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
530908 A
1 A
530909 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:541126 original size:16 final size:15
Alignment explanation
Indices: 541105--541138 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
541095 GGTAAAACAG
541105 TAAATAAAAAGATAAA
1 TAAATAAAAAGA-AAA
*
541121 TAAATAAGAAGAAAA
1 TAAATAAAAAGAAAA
541136 TAA
1 TAA
541139 TCCTCAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
TAAATAAAAAGAAAA
Found at i:544156 original size:2 final size:2
Alignment explanation
Indices: 544105--544137 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
544095 TCTAAAAGAG
544105 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
544138 GAATAGTTGA
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:544447 original size:31 final size:31
Alignment explanation
Indices: 544409--544488 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
544399 AGTTGGGTAG
544409 TGTTCGACTCATGCTCGTTAA-AAAACTTTGT
1 TGTTCGACTCATGCTCGTTAAGAAAAC-TTGT
** * *
544440 T-TCTCGACTTGTGTTTGTTAAGAAAACTTGT
1 TGT-TCGACTCATGCTCGTTAAGAAAACTTGT
544471 TGTTCGACTCGATGCTCG
1 TGTTCGACTC-ATGCTCG
544489 CCTCTCTATT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
30 1 0.03
31 26 0.70
32 10 0.27
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
TGTTCGACTCATGCTCGTTAAGAAAACTTGT
Found at i:544739 original size:13 final size:13
Alignment explanation
Indices: 544723--544748 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
544713 TTAAGATAAC
544723 TATTAAAAAATTA
1 TATTAAAAAATTA
544736 TATTAAAAAATTA
1 TATTAAAAAATTA
544749 ACGAGTTGCT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAAAAAATTA
Found at i:548436 original size:2 final size:2
Alignment explanation
Indices: 548429--548479 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
548419 TGAAACTATC
548429 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
548471 AT AT AT AT A
1 AT AT AT AT A
548480 AAGAAGATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:566033 original size:18 final size:19
Alignment explanation
Indices: 565986--566034 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
565976 TTAGTTTTTT
565986 TAAAATATTTTTTAAAAAA
1 TAAAATATTTTTTAAAAAA
* ***
566005 TTAAGGCTTTTTT-AAAAA
1 TAAAATATTTTTTAAAAAA
566023 TAAAATATTTTT
1 TAAAATATTTTT
566035 AATTTTCTTT
Statistics
Matches: 22, Mismatches: 8, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (19 bp):
TAAAATATTTTTTAAAAAA
Found at i:566626 original size:16 final size:17
Alignment explanation
Indices: 566605--566656 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
566595 TTTTTAATTT
566605 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
566621 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
566636 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
566653 AATT
1 AATT
566657 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:566957 original size:29 final size:30
Alignment explanation
Indices: 566913--566991 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
566903 TAGATTTTTG
*
566913 AAAAAATGACCGGAAATATTATTAGACGCT
1 AAAAAATGACCGAAAATATTATTAGACGCT
*
566943 AAAAAATGACCGAAAATATTATTAGATGCT
1 AAAAAATGACCGAAAATATTATTAGACGCT
*
566973 -AAAAATGATCGAAAATATT
1 AAAAAATGACCGAAAATATT
566992 TTTTAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 18 0.39
30 28 0.61
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (30 bp):
AAAAAATGACCGAAAATATTATTAGACGCT
Found at i:572025 original size:16 final size:17
Alignment explanation
Indices: 571992--572025 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
571982 CATTCTGTTT
*
571992 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
572009 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
572025 T
1 T
572026 AATAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:573796 original size:14 final size:14
Alignment explanation
Indices: 573777--573811 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
573767 AACTTAATAT
573777 TATTATTTTTAAAA
1 TATTATTTTTAAAA
*
573791 TATTATTTTTATAA
1 TATTATTTTTAAAA
*
573805 TTTTATT
1 TATTATT
573812 AATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTTTTAAAA
Found at i:573944 original size:23 final size:23
Alignment explanation
Indices: 573895--573945 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
573885 GTGTTATATT
**
573895 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
573918 ATATTTTAAATATTTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
573941 ATATT
1 ATATT
573946 ATTATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:573984 original size:54 final size:51
Alignment explanation
Indices: 573926--574069 Score: 123
Period size: 54 Copynumber: 2.6 Consensus size: 51
573916 GTATATTTTA
*
573926 AATATTTTTATTAAAATATTATTATATTATTATATTAATATTAAA-TATATAAAT
1 AATATTTTTATTAAAATATTATTATA-TATTAT-TT-ATATGAAATTA-ATAAAT
* * *
573980 AATATTATTCATTATTAATATT-TTAATAATATTATTTCTATGAAATTAATAAAT
1 AATATT-TTTATTA-AAATATTATT-AT-ATATTATTTATATGAAATTAATAAAT
574034 AATATAAATTTTATTAATAAT-TTATTATATATTATT
1 AATAT---TTTTATTAA-AATATTATTATATATTATT
574070 AAAATAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
54 31 0.42
55 16 0.22
56 25 0.34
57 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (51 bp):
AATATTTTTATTAAAATATTATTATATATTATTTATATGAAATTAATAAAT
Found at i:574143 original size:22 final size:23
Alignment explanation
Indices: 574117--574161 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
574107 ATCGATTATT
574117 TTATAATATTAAAAATA-TAATA
1 TTATAATATTAAAAATATTAATA
* *
574139 TTATATTATTATAAATATTAATA
1 TTATAATATTAAAAATATTAATA
574162 AATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATAATATTAAAAATATTAATA
Found at i:574167 original size:24 final size:22
Alignment explanation
Indices: 574118--574169 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
574108 TCGATTATTT
* *
574118 TATAATATTAAAAATATAATAT
1 TATATTATTAAAAATATAATAA
*
574140 TATATTATTATAAATATTAATAAA
1 TATATTATTAAAAATA-TAAT-AA
574164 TATATT
1 TATATT
574170 TTACATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.56
23 4 0.16
24 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTATTAAAAATATAATAA
Found at i:574178 original size:52 final size:51
Alignment explanation
Indices: 574074--574232 Score: 130
Period size: 52 Copynumber: 3.1 Consensus size: 51
574064 ATTATTAAAA
* **
574074 TAAAAATATAATATCTTATATTATTATTATATAATCGATTATTTTATAATAT
1 TAAAAATATAATA-CTTATATTATTATAATATAATAAATTATTTTATAATAT
* *
574126 TAAAAATATAATA-TTATATTATTATAAATATTAATAAATATATTTTACATATTT
1 TAAAAATATAATACTTATATTATTAT-AATA-TAATAAAT-TATTTTATA-ATAT
* * ** *
574180 TAATAAT-TAATA-TTTTGATTAAAATAATATCA-AAA-TATTTTATTAATAT
1 TAAAAATATAATACTTAT-ATTATTATAATATAATAAATTATTTTA-TAATAT
574229 TAAA
1 TAAA
574233 TTTATAAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
49 13 0.15
50 13 0.15
51 6 0.07
52 21 0.24
53 20 0.23
54 15 0.17
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (51 bp):
TAAAAATATAATACTTATATTATTATAATATAATAAATTATTTTATAATAT
Found at i:575792 original size:36 final size:37
Alignment explanation
Indices: 575719--575792 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
575709 TACTATAATT
**
575719 AATTTATATATTTTCATTAAAAAAATTAAATTCATAA
1 AATTTATATATTTTCATTAAAAAAATTAAAAACATAA
* * * *
575756 AATTTATATATTTT-TTTTACAAAATTAAAAAGATAA
1 AATTTATATATTTTCATTAAAAAAATTAAAAACATAA
575792 A
1 A
575793 TAGGTTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
AATTTATATATTTTCATTAAAAAAATTAAAAACATAA
Found at i:579850 original size:12 final size:12
Alignment explanation
Indices: 579833--579857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
579823 CAAGCAAAGA
579833 ATGTGAAGAGAG
1 ATGTGAAGAGAG
579845 ATGTGAAGAGAG
1 ATGTGAAGAGAG
579857 A
1 A
579858 AGAAGAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.40, T:0.16
Consensus pattern (12 bp):
ATGTGAAGAGAG
Found at i:583316 original size:18 final size:17
Alignment explanation
Indices: 583283--583316 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
583273 TTATTCGGGC
583283 TACGAGACGAGAACGAG
1 TACGAGACGAGAACGAG
*
583300 TACGAGCACGAGCACGA
1 TACGAG-ACGAGAACGA
583317 ACACGAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.24, G:0.32, T:0.06
Consensus pattern (17 bp):
TACGAGACGAGAACGAG
Found at i:587011 original size:32 final size:32
Alignment explanation
Indices: 586970--587050 Score: 80
Period size: 32 Copynumber: 2.6 Consensus size: 32
586960 TAATGTATTT
*
586970 ATAAT-TATTTATTATATTTCAAACTGTT-AAA
1 ATAATATATTTATTATATTT-AAAATGTTAAAA
* *
587001 ATAATATATTT-TAATAATTTAAAATTTTAAAA
1 ATAATATATTTATTAT-ATTTAAAATGTTAAAA
*
587033 ATAATATATATA-TATATT
1 ATAATATATTTATTATATT
587051 AACCGAGTCG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
31 17 0.41
32 24 0.59
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (32 bp):
ATAATATATTTATTATATTTAAAATGTTAAAA
Found at i:587115 original size:2 final size:2
Alignment explanation
Indices: 587108--587149 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
587098 GCCCCGAAAT
587108 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
587150 ATTAACCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:592812 original size:2 final size:2
Alignment explanation
Indices: 592805--592839 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
592795 AATTTATAAC
592805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
592840 CTGTTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:599493 original size:11 final size:12
Alignment explanation
Indices: 599484--599540 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
599474 AGATAAAATT
599484 AATTTTAAATAA
1 AATTTTAAATAA
599496 AATTTTAAATATTAA
1 AATTTT-AA-A-TAA
*
599511 AATTATAATATAA
1 AATTTTAA-ATAA
*
599524 AATTTTATGATAA
1 AATTTTA-AATAA
599537 AATT
1 AATT
599541 AAATATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.16
13 19 0.50
14 5 0.13
15 8 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
AATTTTAAATAA
Found at i:599513 original size:15 final size:14
Alignment explanation
Indices: 599484--599530 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
599474 AGATAAAATT
599484 AATTTT-AA-ATAA
1 AATTTTAAATATAA
599496 AATTTTAAATATTAA
1 AATTTTAAATA-TAA
*
599511 AATTAT-AATATAA
1 AATTTTAAATATAA
599524 AATTTTA
1 AATTTTA
599531 TGATAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 6 0.21
13 10 0.34
14 5 0.17
15 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTTAAATATAA
Found at i:599526 original size:13 final size:13
Alignment explanation
Indices: 599492--599546 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
599482 TTAATTTTAA
*
599492 ATAAAATTTTAAAT
1 ATAAAATTAT-AAT
599506 ATTAAAATTATAAT
1 A-TAAAATTATAAT
*
599520 ATAAAATT-TTAT
1 ATAAAATTATAAT
599532 GATAAAATTA-AAT
1 -ATAAAATTATAAT
599545 AT
1 AT
599547 TTTATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 5 0.14
13 17 0.49
14 5 0.14
15 8 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATAAAATTATAAT
Found at i:599531 original size:15 final size:15
Alignment explanation
Indices: 599492--599531 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
599482 TTAATTTTAA
599492 ATAAAATTTTA-AAT
1 ATAAAATTTTATAAT
599506 ATTAAAA--TTATAAT
1 A-TAAAATTTTATAAT
599520 ATAAAATTTTAT
1 ATAAAATTTTAT
599532 GATAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAAATTTTATAAT
Found at i:601580 original size:21 final size:21
Alignment explanation
Indices: 601556--601602 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
601546 AGTACCCAAC
601556 AATAACAAAACCGATAGAAAA
1 AATAACAAAACCGATAGAAAA
* *
601577 AATAACAAAATCGGTAGAAAA
1 AATAACAAAACCGATAGAAAA
601598 AATAA
1 AATAA
601603 TGTTTTCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:602161 original size:23 final size:23
Alignment explanation
Indices: 602118--602162 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
602108 TTACCCATAA
**
602118 TTTTAAATAATTTATCTTTAAAT
1 TTTTAAATAATTTATAATTAAAT
*
602141 TTTTAATTAATTTATAATTAAA
1 TTTTAAATAATTTATAATTAAA
602163 CGTTGAGTCC
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:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTAAATAATTTATAATTAAAT
Found at i:602196 original size:15 final size:15
Alignment explanation
Indices: 602173--602202 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
602163 CGTTGAGTCC
602173 TTTAAAATTTAAATT
1 TTTAAAATTTAAATT
*
602188 TTTATAATTTAAATT
1 TTTAAAATTTAAATT
602203 ATCATTACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAAATTTAAATT
Found at i:608355 original size:21 final size:22
Alignment explanation
Indices: 608325--608370 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
608315 GTTTTATGTT
* * *
608325 TTTTTAAAATATATATTTTTAA
1 TTTTTAAAATAAAAATTTTAAA
608347 TTTTT-AAATAAAAATTTTAAA
1 TTTTTAAAATAAAAATTTTAAA
608368 TTT
1 TTT
608371 ATCAGGTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAAAATAAAAATTTTAAA
Found at i:610867 original size:6 final size:6
Alignment explanation
Indices: 610856--610887 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
610846 GAATGGACTT
610856 GAGCTC GAGCTC GAGCTC GAGCTC GA-CTC GAG
1 GAGCTC GAGCTC GAGCTC GAGCTC GAGCTC GAG
610888 TTCTTAACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.19, C:0.31, G:0.34, T:0.16
Consensus pattern (6 bp):
GAGCTC
Found at i:611020 original size:40 final size:36
Alignment explanation
Indices: 610947--611029 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 36
610937 TGAGCAGCTC
*
610947 AAAAATATAATATATTAAGATTTTATTTTATTTTTT
1 AAAAATATAATATATTAACATTTTATTTTATTTTTT
610983 AAAAATATTAATAATATTAACA-TTTATGTATTGATTTTTT
1 AAAAATA-TAAT-ATATTAACATTTTAT-T-TT-ATTTTTT
*
611023 TAAAATA
1 AAAAATA
611030 CAGTACGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 7 0.17
37 9 0.22
38 9 0.22
39 2 0.05
40 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
AAAAATATAATATATTAACATTTTATTTTATTTTTT
Found at i:613054 original size:32 final size:33
Alignment explanation
Indices: 613016--613105 Score: 123
Period size: 32 Copynumber: 2.8 Consensus size: 33
613006 GGGTACAATA
* *
613016 ATTATAAAATTAATTATT-AATTTTATCTAATT
1 ATTATAAAATTAATTATTAAATTTTATCAAAAT
613048 ATTAT-AAATTAATTATTAAATTTTATCAAAAT
1 ATTATAAAATTAATTATTAAATTTTATCAAAAT
* *
613080 GTTATAAAA-TAATCATTAAATTTTAT
1 ATTATAAAATTAATTATTAAATTTTAT
613106 TAAATCGATA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
31 12 0.23
32 37 0.71
33 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (33 bp):
ATTATAAAATTAATTATTAAATTTTATCAAAAT
Found at i:613118 original size:32 final size:32
Alignment explanation
Indices: 613018--613141 Score: 112
Period size: 32 Copynumber: 3.9 Consensus size: 32
613008 GTACAATAAT
* * *
613018 TATAAAATTAATTATT-AATTTTATC-TAATTA
1 TATAAAA-TAATCATTAAATTTTATCAAAATGA
* * *
613049 TTATAAATTAATTATTAAATTTTATCAAAATGT
1 -TATAAAATAATCATTAAATTTTATCAAAATGA
*
613082 TATAAAATAATCATTAAATTTTAT-TAAATCGA
1 TATAAAATAATCATTAAATTTTATCAAAAT-GA
* *
613114 TATAAACTAATCATTCAA-TTTATCAAAA
1 TATAAAATAATCATTAAATTTTATCAAAA
613142 CTTTTATACT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
31 17 0.22
32 57 0.74
33 3 0.04
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
TATAAAATAATCATTAAATTTTATCAAAATGA
Found at i:613149 original size:64 final size:64
Alignment explanation
Indices: 613017--613141 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 64
613007 GGTACAATAA
* * * *
613017 TTATAAAATTAATTATTAATTTTATCTAATTATTATAAATTAATTATTAAATTTTATCAAAATG
1 TTATAAAATTAATCATTAATTTTATCTAATGATTATAAACTAATCATTAAATTTTATCAAAATG
*
613081 TTATAAAA-TAATCATTAAATTTTAT-TAAATCGA-TATAAACTAATCATTCAA-TTTATCAAAA
1 TTATAAAATTAATCATT-AATTTTATCT-AAT-GATTATAAACTAATCATTAAATTTTATCAAAA
613142 CTTTTATACT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
63 18 0.34
64 34 0.64
65 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (64 bp):
TTATAAAATTAATCATTAATTTTATCTAATGATTATAAACTAATCATTAAATTTTATCAAAATG
Found at i:622225 original size:15 final size:15
Alignment explanation
Indices: 622207--622236 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
622197 AAAACCATGT
*
622207 TAGATAAAAAGGTAA
1 TAGATAAAAAAGTAA
622222 TAGATAAAAAAGTAA
1 TAGATAAAAAAGTAA
622237 GAAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAAGTAA
Found at i:622311 original size:15 final size:15
Alignment explanation
Indices: 622263--622313 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
622253 TTAAATTAAA
622263 ATAAAGAGAAACAAA-
1 ATAAAGA-AAACAAAG
* * *
622278 TTAAATAAAAGATAAG
1 ATAAAGAAAACA-AAG
622294 ATAAAGAAAACAAAG
1 ATAAAGAAAACAAAG
622309 ATAAA
1 ATAAA
622314 ATAGTAAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 4 0.14
15 15 0.54
16 9 0.32
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.14
Consensus pattern (15 bp):
ATAAAGAAAACAAAG
Found at i:622341 original size:13 final size:13
Alignment explanation
Indices: 622323--622443 Score: 52
Period size: 13 Copynumber: 8.9 Consensus size: 13
622313 AATAGTAAGT
622323 AAAATAAATATAA
1 AAAATAAATATAA
*
622336 AAAATAAAGA-AA
1 AAAATAAATATAA
*
622348 AAGAAGAAATA-AA
1 AA-AATAAATATAA
* * *
622361 TATAGAAATA-AA
1 AAAATAAATATAA
*
622373 ACAAATAAATAAAA
1 A-AAATAAATATAA
*
622387 TAATAATAAAAAGT-A
1 -AA-AATAAATA-TAA
*
622402 AAAATAATATATAT
1 AAAATAA-ATATAA
*
622416 AAAATAAAAAATAAA
1 AAAAT-AAATAT-AA
622431 AAAAGTAAATATA
1 AAAA-TAAATATA
622444 TATATATAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
12 13 0.16
13 31 0.38
14 16 0.20
15 21 0.26
16 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (13 bp):
AAAATAAATATAA
Found at i:622362 original size:21 final size:21
Alignment explanation
Indices: 622324--622385 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
622314 ATAGTAAGTA
*
622324 AAATAAATATAAA-AAATAAAG
1 AAATAAA-ACAAATAAATAAAG
* *
622345 AAA-AAGAAGAAATAAATATAG
1 AAATAA-AACAAATAAATAAAG
622366 AAATAAAACAAATAAATAAA
1 AAATAAAACAAATAAATAAA
622386 ATAATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.18
21 26 0.76
22 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (21 bp):
AAATAAAACAAATAAATAAAG
Found at i:622373 original size:24 final size:22
Alignment explanation
Indices: 622346--622424 Score: 52
Period size: 25 Copynumber: 3.2 Consensus size: 22
622336 AAAATAAAGA
622346 AAAAGAAGAAATAAATATAGAAAT
1 AAAAGAA-AAATAAATATA-AAAT
*
622370 AAAACAAATAAATAAA-ATAATAAT
1 AAAA-GAA-AAATAAATATAA-AAT
622394 AAAAAGTAAAAATAATATATATAAAAT
1 -AAAAG-AAAAAT-A-A-ATATAAAAT
622421 AAAA
1 AAAA
622425 AATAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
23 1 0.02
24 14 0.32
25 16 0.36
26 5 0.11
27 4 0.09
28 4 0.09
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAGAAAAATAAATATAAAAT
Found at i:622391 original size:21 final size:21
Alignment explanation
Indices: 622354--622481 Score: 55
Period size: 21 Copynumber: 5.8 Consensus size: 21
622344 GAAAAAGAAG
*
622354 AAATAAATATAGA-AATAAAAC
1 AAATAAATA-AAATAATAAAAC
622375 AAATAAATAAAATAATAATAA-
1 AAATAAATAAAATAATAA-AAC
* *
622396 AAAGTAAAAATAATATATATAAAAT
1 AAA-T--AAATAAAATA-ATAAAAC
* *
622421 AAA-AAATAAAAAAAGTAAATAT
1 AAATAAATAAAATAA-TAAA-AC
* * *
622443 ATATATATAAATTAATAAAAC
1 AAATAAATAAAATAATAAAAC
** *
622464 TGATAATAAAAAATAATA
1 AAATAA-ATAAAATAATA
622482 TATTATATAT
Statistics
Matches: 82, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
20 3 0.04
21 33 0.40
22 20 0.24
23 8 0.10
24 11 0.13
25 7 0.09
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (21 bp):
AAATAAATAAAATAATAAAAC
Found at i:622418 original size:33 final size:33
Alignment explanation
Indices: 622381--622460 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 33
622371 AAACAAATAA
622381 ATAAAATAATAAT-AAAAAGTAAAAATAATATAT
1 ATAAAATAATAATAAAAAAGTAAAAAT-ATATAT
* *
622414 ATAAAATAAAAAATAAAAAAAGTAAATATATATAT
1 ATAAAAT-AATAAT-AAAAAAGTAAAAATATATAT
*
622449 ATAAATTAATAA
1 ATAAAATAATAA
622461 AACTGATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 7 0.17
34 9 0.22
35 12 0.30
36 12 0.30
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (33 bp):
ATAAAATAATAATAAAAAAGTAAAAATATATAT
Found at i:622418 original size:37 final size:34
Alignment explanation
Indices: 622377--622454 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 34
622367 AATAAAACAA
622377 ATAAATAAAATAATAATAAAAAGTAAAAATAATATAT
1 ATAAATAAAA-AATAA-AAAAAGTAAAAAT-ATATAT
*
622414 ATAAAATAAAAAATAAAAAAAGTAAATATATATAT
1 AT-AAATAAAAAATAAAAAAAGTAAAAATATATAT
622449 ATAAAT
1 ATAAAT
622455 TAATAAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
34 4 0.10
35 8 0.21
36 12 0.31
37 7 0.18
38 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.27
Consensus pattern (34 bp):
ATAAATAAAAAATAAAAAAAGTAAAAATATATAT
Found at i:622426 original size:22 final size:20
Alignment explanation
Indices: 622375--622426 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 20
622365 GAAATAAAAC
622375 AAATAAATAAAATAATAATAA
1 AAATAAA-AAAATAATAATAA
622396 AAAGT--AAAAATAATATATATA
1 AAA-TAAAAAAATAATA-ATA-A
622417 AAATAAAAAA
1 AAATAAAAAA
622427 TAAAAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
19 9 0.35
20 5 0.19
21 7 0.27
22 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATAAAAAAATAATAATAA
Found at i:622445 original size:31 final size:31
Alignment explanation
Indices: 622366--622452 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 31
622356 ATAAATATAG
*
622366 AAATAAAACAAATAAATA-AAATAATAATAAA
1 AAATAAAA-AAATAAATATATATAATAATAAA
*
622397 AAGT--AAAAAT-AATATATATAA-AATAAA
1 AAATAAAAAAATAAATATATATAATAATAAA
622424 AAATAAAAAAAGTAAATATATATATATAA
1 AAATAAAAAAA-TAAATATATATA-ATAA
622453 ATTAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 13 0.28
28 9 0.20
29 7 0.15
30 1 0.02
31 13 0.28
32 1 0.02
33 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (31 bp):
AAATAAAAAAATAAATATATATAATAATAAA
Found at i:622560 original size:22 final size:21
Alignment explanation
Indices: 622506--622566 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
622496 TAAAAAAAAT
622506 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
* *
622526 AAAAGAAAATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
622549 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
622567 AAAAGAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 10 0.31
23 12 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:622911 original size:37 final size:36
Alignment explanation
Indices: 622868--622969 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
622858 ATAGTAGAAC
622868 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
622905 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
622939 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
622970 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:623730 original size:105 final size:105
Alignment explanation
Indices: 623516--623970 Score: 597
Period size: 105 Copynumber: 4.3 Consensus size: 105
623506 CATTGTTCCA
* ** * *
623516 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCT-AGAACCGGAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
623580 CCAGCCGTCCCTTCGTTGTGAAGTCGAACTTGTGTTGTCTCG
64 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
623622 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
623687 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
623727 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGA
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
623792 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
623832 AGTCCAATATCCTTTGTTGTGAAGTTGAAATAGGCTCTGAAATTGAGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* * * *
623897 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
66 AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
623937 AGTGCCACGATATCCTCCTTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTCGTGAAGTTGAAAT
623971 CGCAGATGGC
Statistics
Matches: 312, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
105 242 0.78
106 48 0.15
107 2 0.01
108 20 0.06
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:624707 original size:67 final size:67
Alignment explanation
Indices: 624529--624729 Score: 219
Period size: 68 Copynumber: 3.0 Consensus size: 67
624519 TGTCTTGAAA
* * * * * *
624529 GAGATAGAATTTGTTTCAAGGGAAA-CAATCTCAAAGATATCTGTTGTTTCATGAGAAACGGTCT
1 GAGATAAAATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCT
624593 CAAGG
63 CAAGG
* * ** *
624598 GAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCA
1 GAGATAAAATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCA
624663 AGG
65 AGG
* * *
624666 GAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAA
1 GAGATAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
624729 G
66 G
624730 ATAGACGAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
65 22 0.20
66 3 0.03
67 22 0.20
68 31 0.28
69 11 0.10
70 19 0.17
71 3 0.03
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.32
Consensus pattern (67 bp):
GAGATAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
GG
Found at i:624745 original size:65 final size:67
Alignment explanation
Indices: 624536--624755 Score: 189
Period size: 65 Copynumber: 3.3 Consensus size: 67
624526 AAAGAGATAG
* * * * *
624536 AATTTGTTTCAAGGGAAA-CAATCTCAAAGA-TATCTGTTGTTTCATGAGAAACGGTCTCAAGGG
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAGT-T-TG-TGTTTCAAGAGAAACTGTCTCAAGAG
* *
624599 AAACAA
62 AGAGAA
** * * *
624605 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGA
*
624670 TAA
65 GAA
* * *
624673 AATTTGTTTTAGGGGAAATAAATTCAAAG-GTTT-TGTTTCAAGGGAAACTGTCTCAAGATAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGA-
624736 GAA
65 GAA
* *
624739 AA-TTGTTTCAAGAGAAA
1 AATTTGTTTTAAGGGAAA
624756 CTGTCTCAAG
Statistics
Matches: 126, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
65 37 0.29
66 7 0.06
67 22 0.17
68 31 0.25
69 6 0.05
70 19 0.15
71 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGAGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAG
AA
Found at i:624756 original size:36 final size:35
Alignment explanation
Indices: 624705--624985 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
624695 TTCAAAGGTT
* *
624705 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
624741 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
624776 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
624814 TTGTTTCAA-AGAAAACATAT-T--A-A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
624843 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
624878 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
624915 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
624950 TTATTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
624986 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 1 0.00
31 2 0.01
32 2 0.01
33 1 0.00
34 2 0.01
35 12 0.06
36 130 0.64
37 33 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:624814 original size:138 final size:137
Alignment explanation
Indices: 624653--624959 Score: 393
Period size: 138 Copynumber: 2.2 Consensus size: 137
624643 TTTCAAGAGT
* * ** * * * *
624653 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTAAAAGATTTTGTTTCAAGGGA
* *
624718 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
624782 TCCAAAAGA
129 TCCAAAAGA
* * *
624791 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTAAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTAAAAGATTTTGTTTCAAGGGA
* * * * *
624856 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
624921 CAAGAGA
131 CAAAAGA
*
624928 AACTGTCTCAAGAGAGACAAAATTAT-TTTCAA
1 AACTGTCTCAAGGGAGACAAAATT-TGTTTCAA
624960 GGGAAACTGT
Statistics
Matches: 146, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
137 43 0.29
138 103 0.71
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTAAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:624929 original size:102 final size:102
Alignment explanation
Indices: 624741--624929 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
624731 TAGACGAAAA
*
624741 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
624806 GACGAAATTTGTTTCAAAGAAAACATATTAAAATATT
66 GACGAAATTTGTTTCAAAGAAAACATATTAAAATATT
* * * ** *
624843 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
624907 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAA-AGAAA
624930 CTGTCTCAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 37 0.47
102 42 0.53
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAAGAAAACATATTAAAATATT
Found at i:625007 original size:35 final size:35
Alignment explanation
Indices: 624847--625019 Score: 163
Period size: 36 Copynumber: 4.9 Consensus size: 35
624837 AATATTTTGT
*
624847 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT-
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAA--TATC
* * * * *
624883 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATAT-C
*
624919 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTATT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAA-TATC
* *
624955 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CTC
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATATC
* * *
624989 TTCTAGTGAAAACGGTCTCAAGTGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
625020 TCTTGTTTTA
Statistics
Matches: 117, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
34 8 0.07
35 22 0.19
36 84 0.72
37 3 0.03
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (35 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATATC
Found at i:625049 original size:36 final size:36
Alignment explanation
Indices: 625007--625122 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
624997 AAAACGGTCT
625007 CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
1 CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
** * * * ** * * *
625043 TGAGTGAAATAAATCTTCTTTCGAGTAAAACAGTCC
1 CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
* *
625079 CAAGTGAGACAAAGTC-TGTTTTAA-AAAAGCAATCT
1 CAAGTGAGACAAA-TCTTGTTTTAAGAAAAACAATCA
625114 CAAGTGAGA
1 CAAGTGAGA
625123 TAATCATCTG
Statistics
Matches: 58, Mismatches: 21, Indels: 3
0.71 0.26 0.04
Matches are distributed among these distances:
35 16 0.28
36 40 0.69
37 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
Found at i:625907 original size:22 final size:22
Alignment explanation
Indices: 625882--625930 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
625872 TTGTGTTTGG
625882 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
625904 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
625926 TCAAA
1 TCAAA
625931 AGATTGATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:626587 original size:22 final size:23
Alignment explanation
Indices: 626561--626626 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
626551 TTTGTTCTTT
626561 CTTTTTTG-TTCTTGT-TTTTTC
1 CTTTTTTGCTTCTTGTCTTTTTC
* *
626582 CTTTTTTGCTTCTTTTCTTTTTT
1 CTTTTTTGCTTCTTGTCTTTTTC
* * *
626605 CTTTTTTTCTTTTTGCCTTTTT
1 CTTTTTTGCTTCTTGTCTTTTT
626627 TGTTCTGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 8 0.22
22 6 0.16
23 23 0.62
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (23 bp):
CTTTTTTGCTTCTTGTCTTTTTC
Found at i:626588 original size:8 final size:7
Alignment explanation
Indices: 626575--626618 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 7
626565 TTTGTTCTTG
626575 TTTTTTCC
1 TTTTTT-C
626583 TTTTTTGC
1 TTTTTT-C
626591 TTCTTTTC
1 TT-TTTTC
626599 TTTTTTC
1 TTTTTTC
626606 TTTTTTTC
1 -TTTTTTC
626614 TTTTT
1 TTTTT
626619 GCCTTTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 10 0.30
8 19 0.58
9 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:626604 original size:7 final size:7
Alignment explanation
Indices: 626558--626618 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
626548 AATTTTGTTC
626558 TTTCTTT
1 TTTCTTT
*
626565 TTTGTTCT
1 TTTCTT-T
*
626573 TGT-TTT
1 TTTCTTT
*
626579 TTCCTTT
1 TTTCTTT
626586 TTTGCTTCT
1 TTT-CTT-T
626595 TTTCTTT
1 TTTCTTT
626602 TTTCTTTT
1 TTTC-TTT
626610 TTTCTTT
1 TTTCTTT
626617 TT
1 TT
626619 GCCTTTTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.05
7 22 0.50
8 16 0.36
9 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (7 bp):
TTTCTTT
Found at i:626612 original size:15 final size:16
Alignment explanation
Indices: 626575--626627 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
626565 TTTGTTCTTG
*
626575 TTTTTTCCTTTTTTGC
1 TTTTTTTCTTTTTTGC
*
626591 TTCTTTTCTTTTTT-C
1 TTTTTTTCTTTTTTGC
626606 TTTTTTTC-TTTTTGCC
1 TTTTTTTCTTTTTTG-C
626622 TTTTTT
1 TTTTTT
626628 GTTCTGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 19 0.59
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTTTTTGC
Found at i:626624 original size:16 final size:15
Alignment explanation
Indices: 626562--626627 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
626552 TTGTTCTTTC
* *
626562 TTTTTTGTTCTTG-T
1 TTTTTTCTTTTTGCT
*
626576 TTTTTCCTTTTTTGCT
1 TTTTTTC-TTTTTGCT
* *
626592 TCTTTTCTTTTTTCT
1 TTTTTTCTTTTTGCT
626607 TTTTTTCTTTTTGCCT
1 TTTTTTCTTTTTG-CT
626623 TTTTT
1 TTTTT
626628 GTTCTGATTG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 5 0.12
15 23 0.56
16 13 0.32
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTTTTGCT
Found at i:627813 original size:15 final size:15
Alignment explanation
Indices: 627793--627823 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
627783 AATGTAGATG
627793 AAAATGCAAAAATGC
1 AAAATGCAAAAATGC
*
627808 AAAATGCAAGAATGC
1 AAAATGCAAAAATGC
627823 A
1 A
627824 CGAAATGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (15 bp):
AAAATGCAAAAATGC
Found at i:630309 original size:15 final size:15
Alignment explanation
Indices: 630291--630320 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
630281 AAAACCATGT
*
630291 TAGATAAAAAGGTAA
1 TAGATAAAAAAGTAA
630306 TAGATAAAAAAGTAA
1 TAGATAAAAAAGTAA
630321 GAAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAAGTAA
Found at i:630464 original size:47 final size:47
Alignment explanation
Indices: 630407--630505 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 47
630397 AAATAGTAAG
*
630407 TAAAATAAATATAA-AAAATAA-AGA-AAAAGAAGAAAAAAATATAGAAA
1 TAAAACAAATA-AATAAAATAATA-ATAAAA-AAGAAAAAAATATAGAAA
* * *
630454 TAAAACAAATAAATAAAATAATAATAAAAAAGTAAAAAATATATATA
1 TAAAACAAATAAATAAAATAATAATAAAAAAGAAAAAAATATAGAAA
630501 TAAAA
1 TAAAA
630506 ATAAAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
46 2 0.04
47 38 0.84
48 5 0.11
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (47 bp):
TAAAACAAATAAATAAAATAATAATAAAAAAGAAAAAAATATAGAAA
Found at i:630465 original size:51 final size:53
Alignment explanation
Indices: 630408--630521 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 53
630398 AATAGTAAGT
*
630408 AAAATAAATATAAAAAATAA-AGAAAAAG-AAGAAAA-A-A-ATATAGAAATAAA
1 AAAATAAATATAAAAAATAATA-AAAAAGTAA-AAAATATATATATAAAAATAAA
*
630458 ACAAATAAATA-AAATAATAATAAAAAAGTAAAAAATATATATATAAAAATAAA
1 A-AAATAAATATAAAAAATAATAAAAAAGTAAAAAATATATATATAAAAATAAA
630511 AAAA-AAATATA
1 AAAATAAATATA
630522 TATATATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
50 19 0.35
51 18 0.33
52 5 0.09
53 13 0.24
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (53 bp):
AAAATAAATATAAAAAATAATAAAAAAGTAAAAAATATATATATAAAAATAAA
Found at i:630476 original size:21 final size:19
Alignment explanation
Indices: 630408--630519 Score: 71
Period size: 21 Copynumber: 5.5 Consensus size: 19
630398 AATAGTAAGT
630408 AAAATAAATATAAAAAATAAAGA
1 AAAAT-AATA-AAAAAAT-AA-A
* * *
630431 AAAAGAAGAAAAAAATATA
1 AAAATAATAAAAAAATAAA
* *
630450 GAAATAAAACAAATAAATAAA
1 AAAATAATA-AAA-AAATAAA
* *
630471 ATAATAATAAAAAAGTAAA
1 AAAATAATAAAAAAATAAA
*
630490 AAATATATATATAAAAATAAA
1 AAA-ATA-ATAAAAAAATAAA
*
630511 AAAAAAATA
1 AAAATAATA
630520 TATATATATA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
19 18 0.26
20 12 0.17
21 33 0.47
22 3 0.04
23 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (19 bp):
AAAATAATAAAAAAATAAA
Found at i:630552 original size:68 final size:68
Alignment explanation
Indices: 630465--630593 Score: 154
Period size: 68 Copynumber: 1.9 Consensus size: 68
630455 AAAACAAATA
* *
630465 AATAAAATAATAATAAAAAAGTAAAAAATATATATATAAAAATAAAAAAA-AAATATATATATAT
1 AATAAAATAATAATAAAAAAATAAAAAATATATATAT-AAAATAAAAAAATAAAAATATATATAT
630529 AATT
65 AATT
* * * * **
630533 AATAAAACTGATAAT-AAAAAATAATATATTTATATATAATCTAAAAAAATAAAAATATATA
1 AATAAAA-TAATAATAAAAAAATAAAAAATATATATATAAAATAAAAAAATAAAAATATATA
630594 CTAAAGTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
67 10 0.20
68 35 0.69
69 6 0.12
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (68 bp):
AATAAAATAATAATAAAAAAATAAAAAATATATATATAAAATAAAAAAATAAAAATATATATATA
ATT
Found at i:630637 original size:22 final size:21
Alignment explanation
Indices: 630583--630643 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
630573 CTAAAAAAAT
630583 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
* *
630603 AAAAGAAAATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
630626 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
630644 AAAAGAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 7 0.22
21 3 0.09
22 10 0.31
23 12 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:630989 original size:37 final size:36
Alignment explanation
Indices: 630946--631047 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
630936 ATAGTAGAAC
630946 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
630983 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
631017 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
631048 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:632153 original size:35 final size:35
Alignment explanation
Indices: 632114--632193 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
632104 GGGGTTGGGT
*
632114 ATGTAATTGAAATATTTTGGAATTTGAGGTTAAGA
1 ATGTAATTGAAATATTTTAGAATTTGAGGTTAAGA
* * *
632149 ATGTAATTGAAGTATTTTAGAATTTGGGGTTTAGA
1 ATGTAATTGAAATATTTTAGAATTTGAGGTTAAGA
632184 ATGTAATTGA
1 ATGTAATTGA
632194 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAATATTTTAGAATTTGAGGTTAAGA
Found at i:632770 original size:29 final size:29
Alignment explanation
Indices: 632738--632800 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
632728 GTATTTTCAA
* * * *
632738 AAAAATGATTGGAAACATTATTAGGTGCT
1 AAAAATGATCGGAAAAATTACTAGGCGCT
632767 AAAAATGATCGGAAAAATTACTAGGCGCT
1 AAAAATGATCGGAAAAATTACTAGGCGCT
632796 AAAAA
1 AAAAA
632801 ATTACCGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAAATGATCGGAAAAATTACTAGGCGCT
Found at i:633875 original size:20 final size:20
Alignment explanation
Indices: 633850--633888 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
633840 TCTGGGTTTA
*
633850 AGTATCAATACTGGATGAAC
1 AGTATCAATACTAGATGAAC
633870 AGTATCAATACTAGATGAA
1 AGTATCAATACTAGATGAA
633889 TCATGACACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
AGTATCAATACTAGATGAAC
Found at i:636242 original size:23 final size:22
Alignment explanation
Indices: 636218--636262 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
636208 CTTCGATATT
636218 AATAAATATTAATATAATAATTTA
1 AATAAA-ATTAA-ATAATAATTTA
*
636242 AATAAAATTAAATTATAATTT
1 AATAAAATTAAATAATAATTT
636263 TTTATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAATTAAATAATAATTTA
Found at i:637745 original size:3 final size:3
Alignment explanation
Indices: 637739--637789 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
637729 TAATATTTAT
637739 TAA TAA TAA -AA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
637785 TAA TA
1 TAA TA
637790 TTTAAATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.14
3 36 0.82
4 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:637796 original size:11 final size:11
Alignment explanation
Indices: 637739--637789 Score: 84
Period size: 11 Copynumber: 4.5 Consensus size: 11
637729 TAATATTTAT
637739 TAATAATAAAA
1 TAATAATAAAA
637750 TAATAATAAAA
1 TAATAATAAAA
637761 TAATAATAATAA
1 TAATAATAA-AA
637773 TAATAATATAAA
1 TAATAATA-AAA
637785 TAATA
1 TAATA
637790 TTTAAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
11 20 0.53
12 17 0.45
13 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:638621 original size:224 final size:225
Alignment explanation
Indices: 638027--638733 Score: 1000
Period size: 224 Copynumber: 3.2 Consensus size: 225
638017 TTGAATAAGC
* * * *
638027 TCTTC-TCC-TCTTTAGATGAGTTCTTCTTATTAT-GAACTCTTTCTAGCAATACTGATCCATCG
1 TCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATAG-ACTCTTTCT-GCAATATTAATCCATCA
* * * ** *
638089 AATGATGAAATCGAGCAAAAATTTGAACAAATTCTTCTCATTATGAA-TTCCTTCTTTCTTCTTC
64 AATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT-CTTCTTCCTTCTTC
** *
638153 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATCCATCAAGTGATGGATTTGAGC
128 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
*
638218 AAAAGGTTGACCAAATTCTTCTCATTATGAATT
193 AAAAGGTTGAACAAATTCTTCTCATTATGAATT
* * ** * *
638251 TCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCA-T-GA-ACTCTACCTGAAATTTTAATCCATC
1 TCTTCTTCCTTCTT--TA-GATGAGTTCTTCTCATTATAGACTCTTTCTGCAATATTAATCCATC
*
638313 AAATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
63 AAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* **
638378 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAGC
128 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
*
638443 AAAAAGTTGAACAAATTCTTCTCATTATGAATT
193 AAAAGGTTGAACAAATTCTTCTCATTATGAATT
* *
638476 TCTTCTT-C-TCTTTAGATGAGTTCTTCTTATTATAGACTCTTTCTGGCAATGTTAATCCATCAA
1 TCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATAGACTCTTTCT-GCAATATTAATCCATCAA
* *
638539 ATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
65 ATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
638604 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAA
130 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAA
*
638669 AAGGTTGAACAAATTCTTCTTATTATGAATT
195 AAGGTTGAACAAATTCTTCTCATTATGAATT
* *
638700 TCTTCTTCCTTCTTCAGATGAATTCTTCTCATTA
1 TCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTA
638734 CGAACTTCCT
Statistics
Matches: 427, Mismatches: 43, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
220 14 0.03
221 2 0.00
222 1 0.00
223 11 0.03
224 182 0.43
225 167 0.39
226 34 0.08
228 2 0.00
229 14 0.03
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (225 bp):
TCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATAGACTCTTTCTGCAATATTAATCCATCAAA
TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAA
AGGTTGAACAAATTCTTCTCATTATGAATT
Found at i:638777 original size:113 final size:113
Alignment explanation
Indices: 638027--638770 Score: 881
Period size: 113 Copynumber: 6.6 Consensus size: 113
638017 TTGAATAAGC
* * * * *
638027 TCTTC-TCC-TCTTTAGATGAGTTCTTCTTATTATGAACTCTT-TCTAGCAA-TACTGATCCATC
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAGT-TTGATCCATC
* * * **
638088 GAATGATGAAATCGAGCAAAAATTTGAACAAATTCTTCTCATTATGAATT
64 AAATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
* * **
638138 CCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATCCATCAA
* * *
638203 GTGATGGATTTGAGCAAAAGGTTGACCAAATTCTTCTCATTATGAATT
66 ATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
* * *
638251 TCTTCTTCCTTCTTCAGATGATGAGTTCTTCTC---ATGAACTCTAC-CT-GAAATTTTAATCCA
1 TCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAGTTTGATCCA
** * * *
638311 TCAAATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGAACT
62 TCAAATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
*
638363 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-CTGATCCATCA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGTTTGATCCATCA
** *
638427 AATGATGAATTCAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATT
65 AATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
* * * *
638476 TCTTCTT-C-TCTTTAGATGAGTTCTTCTTATTAT-AGACTCTT-TCTGGCAA-TGTTAATCCAT
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA-ACT-TTCTCTGGAAAGT-TTGATCCAT
* * * *
638536 CAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
63 CAAATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
*
638587 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG-CTGATCCATCA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGTTTGATCCATCA
* *
638651 AATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTTATTATGAATT
65 AATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
* * *
638700 TCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAAAGTTTGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATCCATCAA
*
638765 GTGATG
66 ATGATG
638771 GTTTTGAACA
Statistics
Matches: 544, Mismatches: 64, Indels: 48
0.83 0.10 0.07
Matches are distributed among these distances:
109 14 0.03
110 4 0.01
111 97 0.18
112 93 0.17
113 313 0.58
114 8 0.01
115 1 0.00
116 14 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATCCATCAA
ATGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
Found at i:638826 original size:34 final size:34
Alignment explanation
Indices: 638783--638873 Score: 157
Period size: 35 Copynumber: 2.6 Consensus size: 34
638773 TTTGAACAAA
638783 TTCTTCTCATTATGAA-TTTCTTCTTTCAGATGAG
1 TTCTTCTCATTATGAACTTTCTTC-TTCAGATGAG
638817 TTCTTCTCATTATGAACTTCTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTT-TCTTCTTCAGATGAG
638852 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAACTTTCT
638874 CTGGAAAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
34 19 0.35
35 31 0.56
36 5 0.09
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.49
Consensus pattern (34 bp):
TTCTTCTCATTATGAACTTTCTTCTTCAGATGAG
Found at i:638842 original size:19 final size:19
Alignment explanation
Indices: 638818--638875 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
638808 TCAGATGAGT
638818 TCTTCTCATTATGAACTTC
1 TCTTCTCATTATGAACTTC
* *
638837 TCTTCTTCA-GATG-A-GT-
1 TCTTC-TCATTATGAACTTC
638853 TCTTCTCATTATGAACTTTC
1 TCTTCTCATTATGAAC-TTC
638873 TCT
1 TCT
638876 GGAAAAGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 11
0.66 0.09 0.25
Matches are distributed among these distances:
15 3 0.10
16 8 0.28
17 2 0.07
18 1 0.03
19 9 0.31
20 6 0.21
ACGTcount: A:0.19, C:0.24, G:0.09, T:0.48
Consensus pattern (19 bp):
TCTTCTCATTATGAACTTC
Found at i:638902 original size:243 final size:245
Alignment explanation
Indices: 638569--639020 Score: 750
Period size: 243 Copynumber: 1.8 Consensus size: 245
638559 GTTGAACAAA
638569 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
638634 GAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTTATTATGAAT
64 GAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTTATTATGAAC
*
638699 TTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGG-AAAGTTTGATCCATC
129 TTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTT-CTCTGGAAAAG-CTGATCCATC
* *
638763 AAGTGATGGTTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCAGATGAG
192 AAATGATGGATTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCAGATGAG
638817 TTCTTCTCATTATGAA-CTTC-T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
1 TTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* *
638879 AAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
66 AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTTATTATGAACTT
* *
638944 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGCTGATCCATCAAAT
131 CTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCTCTGGAAAAGCTGATCCATCAAAT
639009 GATGGATTTGAA
196 GATGGATTTGAA
639021 TCTTTTCTAA
Statistics
Matches: 193, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
242 29 0.15
243 143 0.74
244 1 0.01
245 4 0.02
248 16 0.08
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (245 bp):
TTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTTATTATGAACTT
CTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCTCTGGAAAAGCTGATCCATCAAAT
GATGGATTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCAGATGAG
Found at i:639015 original size:112 final size:108
Alignment explanation
Indices: 638815--639020 Score: 342
Period size: 112 Copynumber: 1.9 Consensus size: 108
638805 CTTTCAGATG
638815 AGTTCTTCTCATTATGAACTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 AGTTCTTCTCATTATGAACTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
*
638880 AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
66 AAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
*
638923 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTC
1 AGTTCTTCTCATTATGAA---CTTC-T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
638987 TGGAAAAGCTGATCCATCAAATGATGGATTTGAA
61 TGGAAAAGCTGATCCATCAAATGATGGATTTGAA
639021 TCTTTTCTAA
Statistics
Matches: 91, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
108 17 0.19
111 4 0.04
112 39 0.43
113 31 0.34
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (108 bp):
AGTTCTTCTCATTATGAACTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
AAGCTGATCCATCAAATGATGGATTTGAACAAAAAGTTGAACA
Found at i:639967 original size:93 final size:93
Alignment explanation
Indices: 639808--639997 Score: 344
Period size: 93 Copynumber: 2.0 Consensus size: 93
639798 CTTATTTCTA
* * *
639808 CTATGATCACATTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
639873 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
639901 CTATGAGCACATTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
639966 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
639994 CTAT
1 CTAT
639998 TGGGTCTTCT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (93 bp):
CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:640075 original size:208 final size:208
Alignment explanation
Indices: 639705--640205 Score: 923
Period size: 208 Copynumber: 2.4 Consensus size: 208
639695 GATCATGCAG
* * *
639705 TTCATCTTTTAATTCCAATGATTGGTTCTGTGG-TTCCTACCAAACCAGATCAGATAACTCAAAG
1 TTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
639769 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACATTCATCTTTCAAATT
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACATTCATCTTTCAAATT
*
639834 CAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
131 CAATGATTGGTTATGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
639899 TGCTATGAGCACA
196 TGCTATGAGCACA
639912 TTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
639977 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACATTCATCTTTCAAATT
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACATTCATCTTTCAAATT
*
640042 CAATGATTGGTTATGTGTTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
131 CAATGATTGGTTATGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
640107 TGCTATGAGCACA
196 TGCTATGAGCACA
* * *
640120 TTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAATCAGATCAGATCACTCAAAG
1 TTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
640185 AACACTTCCAGAAGATGCTAT
66 AACACTTCCAGAAGATGCTAT
640206 GAGCACATTC
Statistics
Matches: 285, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
207 31 0.11
208 254 0.89
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (208 bp):
TTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGATCACATTCATCTTTCAAATT
CAATGATTGGTTATGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
TGCTATGAGCACA
Found at i:640103 original size:115 final size:115
Alignment explanation
Indices: 639901--640112 Score: 370
Period size: 115 Copynumber: 1.8 Consensus size: 115
639891 CCAGAAGATG
* *
639901 CTATGAGCACATTCATATTTTAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTATGTGGTTTCATACCAAACCAGATCAG
639966 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
66 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
* * * *
640016 CTATGATCACATTCATCTTTCAAATTCAATGATTGGTTATGTGTTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTATGTGGTTTCATACCAAACCAGATCAG
640081 ATAACTCAAAGAACACTTCCAGAAGATGCTAT
66 ATAACTCAAAGAACACTTCCAGAAGATGCTAT
640113 GAGCACATTC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 91 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (115 bp):
CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTATGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTA
Found at i:640175 original size:93 final size:93
Alignment explanation
Indices: 640016--640585 Score: 989
Period size: 93 Copynumber: 6.1 Consensus size: 93
640006 CTTATTTCTA
* * * * *
640016 CTATGATCACATTCATCTTTCAAATTCAATGATTGGTTATGTGTTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
640081 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
640109 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAATCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
*
640174 ATCACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
640202 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTTATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
640267 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
640295 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATTCCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
*
640360 ATAACTCAAAGAACACTTCCAAAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
640388 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
640453 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* * * *
640481 CTATGAGCACATTCATATTTCAAATTCAATGATTGGTTTTCGAGG-TTCATATCAAACCAGATCA
1 CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCT-GTGGTTTCATACCAAACCAGATCA
*
640545 GATAACTCAAAGAACACTTCCAAAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
640574 CTATGAGCACAT
1 CTATGAGCACAT
640586 GGCACTTGTT
Statistics
Matches: 456, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
93 453 0.99
94 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (93 bp):
CTATGAGCACATTCATATTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:641595 original size:6 final size:6
Alignment explanation
Indices: 641584--641677 Score: 88
Period size: 6 Copynumber: 15.5 Consensus size: 6
641574 TCTTGACCCC
* *
641584 CTTTTT CTTTTTT CTTTTTT CTTTTT -TTCTTT C-TTTT -TTCTC CTTTTCT
1 CTTTTT C-TTTTT C-TTTTT CTTTTT CTT-TTT CTTTTT CTTTTT CTTTT-T
*
641633 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTT CTTGTTT TTTTTT CTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT CTT
641678 CAAGCATAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
5 12 0.16
6 39 0.53
7 23 0.31
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:641602 original size:8 final size:8
Alignment explanation
Indices: 641585--641677 Score: 66
Period size: 8 Copynumber: 11.0 Consensus size: 8
641575 CTTGACCCCC
641585 TTTTTC-T
1 TTTTTCTT
641592 TTTTTC-T
1 TTTTTCTT
641599 TTTTTCTT
1 TTTTTCTT
641607 TTTTTCTT
1 TTTTTCTT
641615 TCTTTT-TT
1 T-TTTTCTT
*
641623 CTCCTTTTCTC
1 -T--TTTTCTT
641634 TTTTTCTT
1 TTTTTCTT
*
641642 TTTCTTTTT
1 TTT-TTCTT
641651 CTTTTTCTT
1 -TTTTTCTT
*
641660 TTCTTGTTTT
1 TT-TT-TCTT
641670 TTTTTCTT
1 TTTTTCTT
641678 CAAGCATAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
7 13 0.18
8 26 0.37
9 17 0.24
10 14 0.20
11 1 0.01
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:641630 original size:29 final size:28
Alignment explanation
Indices: 641585--641673 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
641575 CTTGACCCCC
641585 TTTTTCTTTTTTCT--TTTTTCT-TTTTT
1 TTTTTCTTTTTTCTCCTTTTT-TCTTTTT
* *
641611 TCTTTCTTTTTTCTCCTTTTCTCTTTTT
1 TTTTTCTTTTTTCTCCTTTTTTCTTTTT
**
641639 CTTTTTC-TTTTTCTTTTTCTTTTCTTGTTT
1 -TTTTTCTTTTTTCTCCTT-TTTTCTT-TTT
641669 TTTTT
1 TTTTT
641674 TCTTCAAGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 13 0.25
27 1 0.02
28 18 0.35
29 16 0.31
30 3 0.06
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (28 bp):
TTTTTCTTTTTTCTCCTTTTTTCTTTTT
Found at i:652845 original size:21 final size:22
Alignment explanation
Indices: 652807--652848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
652797 TCTTCGATAT
*
652807 AATAATATTATATAATAATTTA
1 AATAATATTAAATAATAATTTA
*
652829 AATAA-ATTAAATTATAATTT
1 AATAATATTAAATAATAATTT
652849 TTTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATATTAAATAATAATTTA
Found at i:654313 original size:3 final size:3
Alignment explanation
Indices: 654307--654367 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
654297 TAATATTTAT
* * *
654307 TAA TAA TAA -AA TAA TAA TAA TTA TTA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
654354 TAA T-A TAAA TAA TA
1 TAA TAA T-AA TAA TA
654368 TTTAAATGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:654333 original size:27 final size:26
Alignment explanation
Indices: 654294--654367 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 26
654284 TTTGGGCCTG
654294 TAATAATATTTATTAATAATAAAATAA
1 TAATAATA-TTATTAATAATAAAATAA
654321 TAATAATTATTA-TAATAATAAAAATAA
1 TAATAA-TATTATTAATAAT-AAAATAA
* *
654348 TAATAATAATATAAATAATA
1 TAATAATATTATTAATAATA
654368 TTTAAATGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 12 0.29
27 28 0.67
28 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAATATTATTAATAATAAAATAA
Found at i:654363 original size:18 final size:18
Alignment explanation
Indices: 654294--654367 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
654284 TTTGGGCCTG
* *
654294 TAATAATATTTATTAATAA
1 TAATAATA-ATATAAATAA
*
654313 TAA-AATAATA-ATAATTA
1 TAATAATAATATA-AATAA
* *
654330 TTATAATAATAAAAATAA
1 TAATAATAATATAAATAA
654348 TAATAATAATATAAATAA
1 TAATAATAATATAAATAA
654366 TA
1 TA
654368 TTTAAATGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 8 0.18
18 33 0.73
19 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATAATATAAATAA
Found at i:658989 original size:12 final size:12
Alignment explanation
Indices: 658974--659000 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
658964 TTAAATTAAT
658974 ACATAGGGATGG
1 ACATAGGGATGG
658986 ACATAGGGATGG
1 ACATAGGGATGG
658998 ACA
1 ACA
659001 CTCAACCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.37, T:0.15
Consensus pattern (12 bp):
ACATAGGGATGG
Found at i:660338 original size:20 final size:20
Alignment explanation
Indices: 660310--660356 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
660300 AAACAGTACT
660310 ATCGCAACGCGAATAGGAAA
1 ATCGCAACGCGAATAGGAAA
* *
660330 ATCGGAACGCGAATAGTAAA
1 ATCGCAACGCGAATAGGAAA
660350 ATCGCAA
1 ATCGCAA
660357 TGCTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAATAGGAAA
Found at i:660428 original size:56 final size:56
Alignment explanation
Indices: 660335--660451 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 56
660325 GGAAAATCGG
** ** *
660335 AACGCGAATAGTAAAATCGCAATGCTAATTATTGATATAGGTAAACAGTACTATCAC
1 AACGCGAATAGTAAAATCGCAACACTAATTACCGATATAGGTAAAC-GTACAATCAC
*
660392 AACGCGAATA-TAAAATCGCAACACTAATTACCGATATAGGTAAACGTACAATCGC
1 AACGCGAATAGTAAAATCGCAACACTAATTACCGATATAGGTAAACGTACAATCAC
660447 AACGC
1 AACGC
660452 TAATTACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 13 0.24
56 31 0.57
57 10 0.19
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (56 bp):
AACGCGAATAGTAAAATCGCAACACTAATTACCGATATAGGTAAACGTACAATCAC
Found at i:660455 original size:36 final size:37
Alignment explanation
Indices: 660402--660488 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 37
660392 AACGCGAATA
* *
660402 TAAAATCGCAACACTAATTACCGATATAGGTAAAC-G
1 TAAAATCGCAACGCTAATTACCAATATAGGTAAACAG
*
660438 TACAATCGCAACGCTAATTACCAATATAGGTAAACAG
1 TAAAATCGCAACGCTAATTACCAATATAGGTAAACAG
660475 TAAAATCGCAACGC
1 TAAAATCGCAACGC
660489 GATTTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 32 0.70
37 14 0.30
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.21
Consensus pattern (37 bp):
TAAAATCGCAACGCTAATTACCAATATAGGTAAACAG
Found at i:660791 original size:20 final size:20
Alignment explanation
Indices: 660766--660812 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
660756 GTGATTAGCG
*
660766 TTGCGATTTTGCTATTCGCA
1 TTGCGATTTTCCTATTCGCA
*
660786 TTGCGATTTTCCTATTCGCG
1 TTGCGATTTTCCTATTCGCA
660806 TTGCGAT
1 TTGCGAT
660813 AATACTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCCTATTCGCA
Found at i:660851 original size:77 final size:77
Alignment explanation
Indices: 660724--660869 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 77
660714 TATTTAAAAA
* * * *
660724 TCGCGTTGCGATAGTACTGTTTACCTATGTCAGTGATTAGCGTTGCGATTTTGCTATTCGCATTG
1 TCGCGTTGCGATAATACTGTTTACCTATATCAGTAATTAGCGTTGCGATTTTCCTATTCGCATTG
660789 CGATTTTCCTAT
66 CGATTTTCCTAT
* *
660801 TCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCGTTGCGATTTTCCTATTCGCGTTG
1 TCGCGTTGCGATAATACTGTTTACCTATATCAGTAATTAGCGTTGCGATTTTCCTATTCGCATTG
660866 CGAT
66 CGAT
660870 AGTACTGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (77 bp):
TCGCGTTGCGATAATACTGTTTACCTATATCAGTAATTAGCGTTGCGATTTTCCTATTCGCATTG
CGATTTTCCTAT
Found at i:660876 original size:57 final size:57
Alignment explanation
Indices: 660786--660926 Score: 264
Period size: 57 Copynumber: 2.5 Consensus size: 57
660776 GCTATTCGCA
660786 TTGCGATTTTCCTATTCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCG
1 TTGCGATTTTCCTATTCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCG
*
660843 TTGCGATTTTCCTATTCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
1 TTGCGATTTTCCTATTCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCG
*
660900 TTGCGATTTTACTATTCGCGTTGCGAT
1 TTGCGATTTTCCTATTCGCGTTGCGAT
660927 TTTAGAACCT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 82 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (57 bp):
TTGCGATTTTCCTATTCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCG
Found at i:662090 original size:20 final size:20
Alignment explanation
Indices: 662065--662258 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
662055 GATTTTCAAT
* *
662065 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
662085 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
662105 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
662125 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
662145 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
662165 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
662185 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
662205 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
662226 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
662246 AATCGCAACGCGA
1 AATCGCAACGCGA
662259 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:662110 original size:40 final size:39
Alignment explanation
Indices: 662065--662258 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
662055 GATTTTCAAT
* ** *
662065 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
662105 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
662145 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
662185 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
662226 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
662259 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:662148 original size:60 final size:60
Alignment explanation
Indices: 662065--662257 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
662055 GATTTTCAAT
* ** * *
662065 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
662125 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
662185 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
662246 AATCGCAACGCG
1 AATCGCAACGCG
662258 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:662677 original size:33 final size:33
Alignment explanation
Indices: 662638--662708 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
662628 TTCACTTAGA
*
662638 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
662671 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
662704 TTTCA
1 TTTCA
662709 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:662848 original size:14 final size:14
Alignment explanation
Indices: 662829--662883 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
662819 AGAATGACTG
662829 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
662843 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
662862 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
662876 TCGCAACG
1 TCGCAACG
662884 CGAACCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:662921 original size:19 final size:18
Alignment explanation
Indices: 662894--663011 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
662884 CGAACCAAAA
*
662894 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
662913 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
662927 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
662946 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
662960 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
662978 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
662993 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
663011 T
1 T
663012 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Done.