Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006932.1 Hibiscus syriacus cultivar Beakdansim tig00017792_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: 664293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:601014 original size:21 final size:21
Alignment explanation
Indices: 600983--601085 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
600973 GATTACACCC
600983 TAAA-CCTAAACCCTAAA-CT
1 TAAACCCTAAACCCTAAATCT
** **
601002 ATAAACTTTAAACTATAAATCT
1 -TAAACCCTAAACCCTAAATCT
601024 TAAACCCTAAACCCTAAATC-
1 TAAACCCTAAACCCTAAATCT
* * **
601044 CAAACACTAAACCCTAAGCCT
1 TAAACCCTAAACCCTAAATCT
* *
601065 TAAATCCTAAACTCTAAATCT
1 TAAACCCTAAACCCTAAATCT
601086 GATTATATGA
Statistics
Matches: 62, Mismatches: 18, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 20 0.32
21 40 0.65
22 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAATCT
Found at i:601055 original size:41 final size:40
Alignment explanation
Indices: 600983--601084 Score: 96
Period size: 41 Copynumber: 2.5 Consensus size: 40
600973 GATTACACCC
** ** * *
600983 TAAACCTAAACCCTAAACTATAAACTTTAAACTATAAATCT
1 TAAACCTAAACCCTAAA-TCCAAACACTAAACCATAAACCT
* *
601024 TAAACCCTAAACCCTAAATCCAAACACTAAACCCTAAGCCT
1 TAAA-CCTAAACCCTAAATCCAAACACTAAACCATAAACCT
*
601065 TAAATCCTAAACTCTAAATC
1 TAAA-CCTAAACCCTAAATC
601085 TGATTATATG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 37 0.74
42 13 0.26
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (40 bp):
TAAACCTAAACCCTAAATCCAAACACTAAACCATAAACCT
Found at i:601059 original size:27 final size:28
Alignment explanation
Indices: 601024--601082 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
601014 CTATAAATCT
601024 TAAACCCTAAACCCTAAATCC-AAACAC
1 TAAACCCTAAACCCTAAATCCTAAACAC
* * *
601051 TAAACCCTAAGCCTTAAATCCTAAACTC
1 TAAACCCTAAACCCTAAATCCTAAACAC
601079 TAAA
1 TAAA
601083 TCTGATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (28 bp):
TAAACCCTAAACCCTAAATCCTAAACAC
Found at i:601164 original size:7 final size:7
Alignment explanation
Indices: 601152--601259 Score: 83
Period size: 7 Copynumber: 15.4 Consensus size: 7
601142 TAGATTGCAT
601152 CCTAAAC
1 CCTAAAC
601159 CCTAAAC
1 CCTAAAC
*
601166 CGTAAAC
1 CCTAAAC
*
601173 TCTAAAC
1 CCTAAAC
*
601180 TCTAAAC
1 CCTAAAC
*
601187 CATAAAC
1 CCTAAAC
601194 CCTAAATC
1 CCTAAA-C
601202 CC-AAAC
1 CCTAAAC
601208 CCTAAAC
1 CCTAAAC
** *
601215 TATAAGC
1 CCTAAAC
601222 CCTAAAC
1 CCTAAAC
*
601229 CATAAAC
1 CCTAAAC
* **
601236 TCTAAGT
1 CCTAAAC
**
601243 TTTAAAC
1 CCTAAAC
601250 CCTAAAC
1 CCTAAAC
601257 CCT
1 CCT
601260 TAATCCGATT
Statistics
Matches: 77, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
6 3 0.04
7 71 0.92
8 3 0.04
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:601250 original size:21 final size:21
Alignment explanation
Indices: 601153--601240 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
601143 AGATTGCATC
*
601153 CTAAACCCTAAACCGTAAACT
1 CTAAACCCTAAACCATAAACT
* *
601174 CTAAACTCTAAACCATAAACC
1 CTAAACCCTAAACCATAAACT
*
601195 CTAAATCCC-AAACCCTAAACT
1 CTAAA-CCCTAAACCATAAACT
* *
601216 ATAAGCCCTAAACCATAAACT
1 CTAAACCCTAAACCATAAACT
601237 CTAA
1 CTAA
601241 GTTTTAAACC
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 3 0.05
21 50 0.91
22 2 0.04
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.19
Consensus pattern (21 bp):
CTAAACCCTAAACCATAAACT
Found at i:602154 original size:22 final size:23
Alignment explanation
Indices: 602117--602170 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
602107 AGTGAATACG
602117 AACCAGAAAAAGGGGGGTTTAAA
1 AACCAGAAAAAGGGGGGTTTAAA
*
602140 AACCAGAAAAA-GGGGTTTTAAA
1 AACCAGAAAAAGGGGGGTTTAAA
602162 AACCA-AAAA
1 AACCAGAAAA
602171 CCCATATCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.13
22 15 0.50
23 11 0.37
ACGTcount: A:0.54, C:0.11, G:0.22, T:0.13
Consensus pattern (23 bp):
AACCAGAAAAAGGGGGGTTTAAA
Found at i:602312 original size:22 final size:22
Alignment explanation
Indices: 602295--602346 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
602285 CAAGCTTGAT
602295 TCGAGCTTGATTCGAGCTTCAA
1 TCGAGCTTGATTCGAGCTTCAA
* *
602317 TCGAGTTTGATTCGAGTTTCAA
1 TCGAGCTTGATTCGAGCTTCAA
*
602339 TTGAGCTT
1 TCGAGCTT
602347 TTAGTCTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (22 bp):
TCGAGCTTGATTCGAGCTTCAA
Found at i:602335 original size:11 final size:11
Alignment explanation
Indices: 602287--602332 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
602277 GCTTGAACCA
602287 AGCTTGATTCG
1 AGCTTGATTCG
602298 AGCTTGATTCG
1 AGCTTGATTCG
* *
602309 AGCTTCAATCG
1 AGCTTGATTCG
*
602320 AGTTTGATTCG
1 AGCTTGATTCG
602331 AG
1 AG
602333 TTTCAATTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (11 bp):
AGCTTGATTCG
Found at i:602405 original size:16 final size:16
Alignment explanation
Indices: 602380--602410 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
602370 TTGAGAATTT
*
602380 TTTTTTGAGTTCGAGC
1 TTTTTCGAGTTCGAGC
602396 TTTTTCGAGTTCGAG
1 TTTTTCGAGTTCGAG
602411 TTGAGTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCGAGC
Found at i:604589 original size:15 final size:16
Alignment explanation
Indices: 604569--604604 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
604559 AACGTCTTTT
604569 AAAAAT-AATTTTAAG
1 AAAAATCAATTTTAAG
*
604584 AAAAATCATTTTTAAG
1 AAAAATCAATTTTAAG
604600 AAAAA
1 AAAAA
604605 AAGTAGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAATCAATTTTAAG
Found at i:605271 original size:2 final size:2
Alignment explanation
Indices: 605266--605401 Score: 272
Period size: 2 Copynumber: 68.0 Consensus size: 2
605256 AACAAATTTA
605266 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
605308 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
605350 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
605392 AT AT AT AT AT
1 AT AT AT AT AT
605402 GGGTATATGA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 134 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:607024 original size:3 final size:3
Alignment explanation
Indices: 607009--607065 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
606999 GCATAATATG
* * *
607009 TAA TAA TAT TAA TAA TAA AAA TAA TAA TAG TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
607055 TGA TAA TAA TA
1 TAA TAA TAA TA
607066 TTTTGTTGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:607635 original size:126 final size:126
Alignment explanation
Indices: 607382--607829 Score: 513
Period size: 126 Copynumber: 3.5 Consensus size: 126
607372 GACGAAGAGT
* * * * ** *
607382 TCTGGTTATCAAAGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGC
1 TCTGGTTATCTAA-GTTGACACAGCTCCTACGTGATGAGGAGATCTGATCATGTGATGACACTGC
* * * *
607447 TCATACGTGATGAAGAGT-TCTGGCCATCTAAAGGTGATAACACGGTTCCACTCTGATAGGGACG
65 TCAT-C-TGTTCATGAGTCT-TGGCCATCTAAAGGTGATAACACGGTTCCACTCTGATGGGGACG
* * * *
607511 TCTGGTTATCTAAGTTGACATAACTCCTACATGATGATGAGATCTGATCATGTGATGACACTGCT
1 TCTGGTTATCTAAGTTGACACAGCTCCTACGTGATGAGGAGATCTGATCATGTGATGACACTGCT
607576 CATCTGTTCATGAGTCTTGGCCATCTAAAGGTGATAACACGGTTCCACTCTGATGGGGACG
66 CATCTGTTCATGAGTCTTGGCCATCTAAAGGTGATAACACGGTTCCACTCTGATGGGGACG
* * *
607637 GCTAGTTATCTAAGTTGACACAGCTCCTACGTGATGAGGAGATATGATCATGTGATGACACTGCT
1 TCTGGTTATCTAAGTTGACACAGCTCCTACGTGATGAGGAGATCTGATCATGTGATGACACTGCT
* * *
607702 CATCTGTTCATGAGTCTTGGCCATCTTTAAGGAATATGATAACACGGTTCCTACGC-GATGAGGA
66 CATCTGTTCATGAGTCTTGGCCATC-TAAAGG----TGATAACACGGTTCC-ACTCTGATGGGGA
607766 CG
125 CG
* * * * * * * * *
607768 ACTGGTTATCTAGGGGTGACACGGCTCCTACGTGATGACGAGGTCTGGTCAAGGGATGACAC
1 TCTGGTTATCTA-AGTTGACACAGCTCCTACGTGATGAGGAGATCTGATCATGTGATGACAC
607830 GGTTCCTACG
Statistics
Matches: 275, Mismatches: 36, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
126 134 0.49
127 7 0.03
128 45 0.16
129 12 0.04
131 34 0.12
132 43 0.16
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (126 bp):
TCTGGTTATCTAAGTTGACACAGCTCCTACGTGATGAGGAGATCTGATCATGTGATGACACTGCT
CATCTGTTCATGAGTCTTGGCCATCTAAAGGTGATAACACGGTTCCACTCTGATGGGGACG
Found at i:607805 original size:43 final size:40
Alignment explanation
Indices: 607743--607855 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
607733 GAATATGATA
* * *
607743 ACACGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGACTGG---TCAAGGGATG
* * * *
607786 ACACGGCTCCTACGTGATGACGAGGTCTGGTCAAGGGATG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTCAAGGGATG
607826 ACACGGTTCCTACGTGATGAGGACGACTGG
1 ACACGGTTCCTACGTGATGAGGACGACTGG
607856 CCATCTTTAG
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 34 0.58
43 25 0.42
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.21
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGACGACTGGTCAAGGGATG
Found at i:608500 original size:66 final size:64
Alignment explanation
Indices: 608299--608502 Score: 168
Period size: 66 Copynumber: 3.1 Consensus size: 64
608289 AAGTGAGATG
* *
608299 ACTTTGTTTCAAAGGAAATAGACTCAAAGA-TTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAA
1 ACTTTGTTTC-AAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGAAAAA
* * * * * * * * *
608363 AC-TCGTTTCAAAAGAAAC-GATCTTACATATGGGTGTTTCAAAAGAAACTT-ACTCAA-AGATT
1 ACTTTGTTTC-AAGGAAACAGA-CTCAAAGAT--TTTTTTCAAAAGAAA-TTGTCTCAAGAGA-G
*
608424 ATAAA
60 AAAAA
*
608429 A-TTTGTTTCAAGTGAAACAGACTCAAAGATTTTTTTTAAAAAGAAATTGTCTCAAGAGAGAAAA
1 ACTTTGTTTCAAG-GAAACAGACTCAAAGA-TTTTTTTCAAAAGAAATTGTCTCAAGAGAGAAAA
608493 A
64 A
608494 ACTTTGTTT
1 ACTTTGTTT
608503 TTAGAGAAAC
Statistics
Matches: 105, Mismatches: 22, Indels: 24
0.70 0.15 0.16
Matches are distributed among these distances:
62 2 0.02
63 18 0.17
64 4 0.04
65 27 0.26
66 49 0.47
67 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (64 bp):
ACTTTGTTTCAAGGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGAAAAA
Found at i:608574 original size:37 final size:38
Alignment explanation
Indices: 608533--608605 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
608523 ATTTTTTTTA
*
608533 TGTCTCAAATGAGACAA-AATTTGTTTTGAGAGAAAAT
1 TGTCTCAAATGAGACAACAATTTGTTTCGAGAGAAAAT
* *
608570 TGTCTCAAGTGAGACAACATTTTGTTTCGAGAGAAA
1 TGTCTCAAATGAGACAACAATTTGTTTCGAGAGAAA
608606 CAACATCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 16 0.50
38 16 0.50
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (38 bp):
TGTCTCAAATGAGACAACAATTTGTTTCGAGAGAAAAT
Found at i:608727 original size:32 final size:32
Alignment explanation
Indices: 608686--608773 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
608676 TTCGCATCAG
* *
608686 GATGTTGAATCCCCAAAGATGCCCCAATATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
* * *
608718 GATGTTGAATTTCCAATGATGCCCCAGCATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTT
*
608750 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTCCAAAGATGCCC
608774 TCATTGTTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTT
Found at i:610006 original size:9 final size:9
Alignment explanation
Indices: 609992--610017 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
609982 AGGGAGACCG
609992 TCTTCCTTC
1 TCTTCCTTC
610001 TCTTCCTTC
1 TCTTCCTTC
610010 TCTTCCTT
1 TCTTCCTT
610018 AATATTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (9 bp):
TCTTCCTTC
Found at i:612241 original size:20 final size:22
Alignment explanation
Indices: 612216--612255 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
612206 AGTCGTATAA
612216 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
612236 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
612256 TATACTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:612309 original size:21 final size:21
Alignment explanation
Indices: 612283--612325 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
612273 CCCAGAACAG
612283 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
612304 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
612325 A
1 A
612326 ATATTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:612524 original size:29 final size:31
Alignment explanation
Indices: 612492--612551 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
612482 AAATTTTGAA
612492 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
612521 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
612552 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:613364 original size:21 final size:21
Alignment explanation
Indices: 613338--613385 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
613328 AATATAAAAG
613338 ACAAAACAAAAACGTGTTCAA
1 ACAAAACAAAAACGTGTTCAA
613359 ACAAAACAAAAACGTGTTCAA
1 ACAAAACAAAAACGTGTTCAA
613380 ACAAAA
1 ACAAAA
613386 TAATGCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.60, C:0.19, G:0.08, T:0.12
Consensus pattern (21 bp):
ACAAAACAAAAACGTGTTCAA
Found at i:613770 original size:15 final size:14
Alignment explanation
Indices: 613750--613800 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
613740 AATGAAATGC
613750 AGATGCAAAATACAA
1 AGATGCAAAAT-CAA
**
613765 AGATGC-AAAT-GT
1 AGATGCAAAATCAA
613777 AGATGCAAAATGCAA
1 AGATGCAAAAT-CAA
613792 AGATGCAAA
1 AGATGCAAA
613801 TGCAGATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 4 0.14
15 15 0.52
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.16
Consensus pattern (14 bp):
AGATGCAAAATCAA
Found at i:613775 original size:27 final size:27
Alignment explanation
Indices: 613744--613813 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
613734 ATTAAAAATG
613744 AAATGCAGATGCAAAATACAAAGATGC
1 AAATGCAGATGCAAAATACAAAGATGC
* *
613771 AAATGTAGATGCAAAATGCAAAGATGC
1 AAATGCAGATGCAAAATACAAAGATGC
*
613798 AAATGCAGATGAAAAA
1 AAATGCAGATGCAAAA
613814 AATGTTGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.53, C:0.11, G:0.20, T:0.16
Consensus pattern (27 bp):
AAATGCAGATGCAAAATACAAAGATGC
Found at i:616238 original size:2 final size:2
Alignment explanation
Indices: 616231--616268 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
616221 AACATTAATA
616231 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
616269 GAACATACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:616303 original size:2 final size:2
Alignment explanation
Indices: 616298--616327 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
616288 AAAAAAAATA
616298 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
616328 GGGTATATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:617938 original size:3 final size:3
Alignment explanation
Indices: 617923--617979 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
617913 GCATAATATG
* * *
617923 TAA TAA TAT TAA TAA TAA AAA TAA TAA TAG TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
617969 TGA TAA TAA TA
1 TAA TAA TAA TA
617980 TTTTATTGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:625779 original size:26 final size:27
Alignment explanation
Indices: 625726--625792 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
625716 AGGAATGAAT
* * * *
625726 AATAAATACAAAAAGTTACAGGACCAA
1 AATAAAAACAAAAACTTACAAGAACAA
625753 AATAAAAACAAAAACTTA-AAGAACAA
1 AATAAAAACAAAAACTTACAAGAACAA
*
625779 AA-AAAAACTAAAAC
1 AATAAAAACAAAAAC
625793 AGAAAGTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 11 0.31
26 8 0.23
27 16 0.46
ACGTcount: A:0.69, C:0.13, G:0.06, T:0.12
Consensus pattern (27 bp):
AATAAAAACAAAAACTTACAAGAACAA
Found at i:625798 original size:25 final size:26
Alignment explanation
Indices: 625750--625798 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
625740 GTTACAGGAC
**
625750 CAAAATAAAAACAAAAACTTAAAGAA
1 CAAAATAAAAACAAAAACAGAAAGAA
*
625776 CAAAA-AAAAACTAAAACAGAAAG
1 CAAAATAAAAACAAAAACAGAAAG
625799 TTAAAGGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.73, C:0.12, G:0.06, T:0.08
Consensus pattern (26 bp):
CAAAATAAAAACAAAAACAGAAAGAA
Found at i:626116 original size:76 final size:75
Alignment explanation
Indices: 625979--626142 Score: 170
Period size: 76 Copynumber: 2.2 Consensus size: 75
625969 AAAATGTAAC
* ** * *
625979 ATTTACAAATATCATAGCCAAATTGGAATATTAACAAAAATACCCAACAACCTGGAATTAGTGGC
1 ATTTACAAATATCATAGCCAAATTCGAATAACAACAAAAATACACAACAACCT-GAATTAGTGAC
*
626044 TAAAATAAAAT
65 CAAAATAAAAT
** *
626055 ATTTACAAATATGGTCGCCAAATTCGAATAACAACAAAGAATACACAACATA-CT-AACTTAGTG
1 ATTTACAAATATCATAGCCAAATTCGAATAACAACAAA-AATACACAACA-ACCTGAA-TTAGTG
*
626118 ACCAAAATTAAAT
63 ACCAAAATAAAAT
* *
626131 AATAACAAATAT
1 ATTTACAAATAT
626143 TGCTACCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
75 2 0.03
76 58 0.79
77 12 0.16
78 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.24
Consensus pattern (75 bp):
ATTTACAAATATCATAGCCAAATTCGAATAACAACAAAAATACACAACAACCTGAATTAGTGACC
AAAATAAAAT
Found at i:627803 original size:46 final size:45
Alignment explanation
Indices: 627753--628046 Score: 174
Period size: 46 Copynumber: 6.8 Consensus size: 45
627743 AATTTTGGCC
* * *
627753 ATCTAAGGGTGATAACATGGTTCCTATGTGATGAGGACG-GCTGGTT
1 ATCTAA-GGTGATAACACGGCTCCTACGTGATGAGGA-GAGCTGGTT
* * * *
627799 ATCTATGGT--TGACACGGCTCCTACGTGATGAGGAGATCAGG--
1 ATCTAAGGTGATAACACGGCTCCTACGTGATGAGGAGAGCTGGTT
* * * ** *
627840 -TC---GGTGATGACACGGCTCATACGTGATGAAGAGTTCTGGTC
1 ATCTAAGGTGATAACACGGCTCCTACGTGATGAGGAGAGCTGGTT
* *
627881 ATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACG-GCTGGTT
1 ATCT-AAGGTGATAACACGGCTCCTACGTGATGAGGA-GAGCTGGTT
* * * **
627927 ATCTATGGT--TGACACGGCTCCTACGTGATGAAGAGTTCTGG--
1 ATCTAAGGTGATAACACGGCTCCTACGTGATGAGGAGAGCTGGTT
* * * *
627968 -TC--AGGTGATGACACGGTTCCTACGTGATGAGGACGA-CAGGTC
1 ATCTAAGGTGATAACACGGCTCCTACGTGATGAGGA-GAGCTGGTT
* *
628010 ATCTATAGGTAATAACACGGTTCCTACGTGATGAGGA
1 ATCTA-AGGTGATAACACGGCTCCTACGTGATGAGGA
628047 AATCAGGTCA
Statistics
Matches: 196, Mismatches: 31, Indels: 42
0.73 0.12 0.16
Matches are distributed among these distances:
37 3 0.02
38 3 0.02
39 28 0.14
40 30 0.15
41 1 0.01
42 4 0.02
43 51 0.26
45 7 0.04
46 68 0.35
47 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (45 bp):
ATCTAAGGTGATAACACGGCTCCTACGTGATGAGGAGAGCTGGTT
Found at i:627912 original size:128 final size:129
Alignment explanation
Indices: 627546--628046 Score: 605
Period size: 129 Copynumber: 3.9 Consensus size: 129
627536 CGTCTAAGGG
* * ** * *
627546 TGACTCGGTTCCTACGTGATAAGGAGATTTGGTC-GGGGATGACACGACTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
* *
627610 GTTCTTGGCCATCTTTAGGAAGGTGATAACATGGCTCCTTCGTGATGAGGACGGCTGGTTATCTA
66 GTTC-TGGCCATC--TA--AAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
*
627675 TTGT
126 TGGT
* * * * * * * *
627679 TGACGCGCCTCCTACGCGATAAGAAGATCAGGTCAGTTGATGACACGGTTCCTACGCGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
* * * *
627744 ATTTTGGCCATCTAAGGGTGATAACATGGTTCCTATGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
*
627808 TGACACGGCTCCTACGTGATGAGGAGATCAGGTC-GGTGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
*
627872 GTTCTGGTCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * * *
627936 TGACACGGCTCCTACGTGATGAA-GAGTTCTGGTCAGGTGATGACACGGTTCCTACGTGATGAGG
1 TGACACGGCTCCTACGTGAT-AAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAG
* * * * * *
628000 ACG-ACAGGTCATCTATAGGTAATAACACGGTTCCTACGTGATGAGGA
65 A-GTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGA
628047 AATCAGGTCA
Statistics
Matches: 319, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
128 114 0.36
129 141 0.44
130 1 0.00
131 2 0.01
133 35 0.11
134 26 0.08
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATAAGGAGATCAGGTCAGGTGATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:628034 original size:257 final size:260
Alignment explanation
Indices: 627546--628046 Score: 679
Period size: 257 Copynumber: 1.9 Consensus size: 260
627536 CGTCTAAGGG
* * **
627546 TGACTCGGTTCCTACGTGATAAGGAGATTTGGTCGGGGATGACACGACTCATACGTGATGAAGAG
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCGGGGATGACACGACTCATACGTGATGAAGAG
*
627611 TTCTTGGCCATCTTTAGGAAGGTGATAACATGGCTCCTTCGTGATGAGGACGGCTGGTTATCTAT
66 TTCTTGGCCATC-TTA-GAAGGTGATAACATGGCTCCTACGTGATGAGGACGGCTGGTTATCTAT
* * *
627676 TGTTGACGCGCCTCCTACGCGATAAGAAGATCAGGTCAGTTGATGACACGGTTCCTACGCGATGA
129 GGTTGACACGCCTCCTACGCGATAAGAAGATCAGGTCAGGTGATGACACGGTTCCTACGCGATGA
**** * * *
627741 AGAATTTTGGCCATCTAAGGGTGATAACATGGTTCCTATGTGATGAGGACGGCTGGTTATCTATG
194 AGAAGACAGGCCATCTAAGGGTAATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATG
627806 GT
259 GT
* * *
627808 TGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGTGATGACACGGCTCATACGTGATGAAGAG
1 TGACACGGCTCCTACGTGATAAGGAGATCAGGTCGGGGATGACACGACTCATACGTGATGAAGAG
* *
627873 TTC-TGGTCATC-TA-AAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
66 TTCTTGGCCATCTTAGAAGGTGATAACATGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGG
* * * * * *
627935 TTGACACGGCTCCTACGTGATGAAG-AGTTCTGGTCAGGTGATGACACGGTTCCTACGTGATGAG
131 TTGACACGCCTCCTACGCGAT-AAGAAGATCAGGTCAGGTGATGACACGGTTCCTACGCGATGAA
* *
627999 GACGACAGGTCATCTATA-GGTAATAACACGGTTCCTACGTGATGAGGA
195 GAAGACAGGCCATCTA-AGGGTAATAACACGGTTCCTACGTGATGAGGA
628047 AATCAGGTCA
Statistics
Matches: 209, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
257 135 0.65
258 4 0.02
259 2 0.01
261 7 0.03
262 61 0.29
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (260 bp):
TGACACGGCTCCTACGTGATAAGGAGATCAGGTCGGGGATGACACGACTCATACGTGATGAAGAG
TTCTTGGCCATCTTAGAAGGTGATAACATGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGG
TTGACACGCCTCCTACGCGATAAGAAGATCAGGTCAGGTGATGACACGGTTCCTACGCGATGAAG
AAGACAGGCCATCTAAGGGTAATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:628064 original size:86 final size:83
Alignment explanation
Indices: 627887--628088 Score: 235
Period size: 86 Copynumber: 2.4 Consensus size: 83
627877 GGTCATCTAA
* * * * * *
627887 AGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACG
1 AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATGGTTAACACGGCTCCTACG
** *
627952 TGATGAAGAGTTCTGGTC
66 TGATGAAGAAATCAGGTC
*
627970 AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATAGGTAATAACACGGTTCCT
1 AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTAT-GGT--TAACACGGCTCCT
*
628035 ACGTGATGAGGAAATCAGGTC
63 ACGTGATGAAGAAATCAGGTC
* * *
628056 AAGG-GATGACACAGCTCATACGTGATGAGGACG
1 -AGGTGATGACACGGTTCCTACGTGATGAGGACG
628089 TCTGGCCATC
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
83 41 0.41
84 3 0.03
86 54 0.53
87 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (83 bp):
AGGTGATGACACGGTTCCTACGTGATGAGGACGACAGGTCATCTATGGTTAACACGGCTCCTACG
TGATGAAGAAATCAGGTC
Found at i:628153 original size:28 final size:29
Alignment explanation
Indices: 628128--628193 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
628118 AGGGAAACCG
628128 ACTCAAAGATTTGTTTCAA-AAGAAACAA
1 ACTCAAAGATTTGTTTCAAGAAGAAACAA
* *
628156 ACCCAAATATTTGTTTCAAGAAG-AACAA
1 ACTCAAAGATTTGTTTCAAGAAGAAACAA
628184 ACTCAAAGAT
1 ACTCAAAGAT
628194 GATGTATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (29 bp):
ACTCAAAGATTTGTTTCAAGAAGAAACAA
Found at i:628395 original size:66 final size:63
Alignment explanation
Indices: 628185--628388 Score: 180
Period size: 66 Copynumber: 3.2 Consensus size: 63
628175 GAAGAACAAA
* * *
628185 CTCAAAGATGATGTATTTCAAAAGCAACTGTCTCGAAAGAGACAAAATTCATTTCATGGGAAACG
1 CTCAAAGATGATG--TTT-AAAGGAAACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACG
628250 A-
62 AT
* * * * * *
628251 CTCAAAGATGACGTTTAAAGGAAACTGTCTCAAGCGAGAC-AAATT-TTTTTAAGGGAAATGTT
1 CTCAAAGATGATGTTTAAAGGAAACTGTCTCAA-AGAGACAAAATTCATTTCAAGGGAAACGAT
* ** * * *
628313 CTCAAAGATCGGTGTTTCATGGGAAACTGTCTCAATTGAGACAAAATTCGTTTCAAGGGAAACAA
1 CTCAAAGAT-GATGTTT-AAAGGAAACTGTCTCAA-AGAGACAAAATTCATTTCAAGGGAAACGA
628378 T
63 T
628379 CTCAAAGATG
1 CTCAAAGATG
628389 TTTGTTTTGT
Statistics
Matches: 112, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
61 11 0.10
62 16 0.14
63 23 0.21
64 23 0.21
65 6 0.05
66 33 0.29
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (63 bp):
CTCAAAGATGATGTTTAAAGGAAACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGAT
Found at i:628799 original size:64 final size:65
Alignment explanation
Indices: 628689--628850 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 65
628679 TTTCAAAATG
* * * * *
628689 AACAGACTCAAAGATTTGTTTCAAGAGAAACTGTCTCAAGATAGACAAAA-TATGTTT-TAAGAG
1 AACAGACTCAAAGATTTTTTTCAAAAGAAACTGTATCAAGAGAGACAAAATTATGTTTCCAA-AG
628752 A
65 A
* * *
628753 AACAAACTCAAAGATTTTTTTCAAAAGAAATTGTATCAAGAGAGACAAAATTTTGTTTCCAAAGA
1 AACAGACTCAAAGATTTTTTTCAAAAGAAACTGTATCAAGAGAGACAAAATTATGTTTCCAAAGA
*
628818 AACAGACTCAAAGGTTTTTGTTTCAAAAGAAAC
1 AACAGACTCAAA-GATTTT-TTTCAAAAGAAAC
628851 AACTCAAGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 44 0.53
65 20 0.24
66 7 0.08
67 12 0.14
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (65 bp):
AACAGACTCAAAGATTTTTTTCAAAAGAAACTGTATCAAGAGAGACAAAATTATGTTTCCAAAGA
Found at i:628865 original size:92 final size:92
Alignment explanation
Indices: 628741--628957 Score: 265
Period size: 92 Copynumber: 2.3 Consensus size: 92
628731 AGACAAAATA
* * *
628741 TGTTTTAAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTATCAAGAGAGACAAAATTT
1 TGTTTCAAAAGAAAC-AACTCAAAGA--TTTTTCAAAAGAAATTGTATCAAGAGAGACAAAACTT
* *
628806 TGTTTCCAAAGAAACAGACTCAAAGGTTTT
63 TGTTTCAAAAGAAACAGACTCAAAGATTTT
* *** * *
628836 TGTTTCAAAAGAAACAACTCAAGGATTTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGT
1 TGTTTCAAAAGAAACAACTCAAAGATTTTTCAAAAGAAATTGTATCAAGAGAGACAAAACTTTGT
*
628901 TTCAAAAGAAACAGACTTAAAGATTTT
66 TTCAAAAGAAACAGACTCAAAGATTTT
* *
628928 T-TTCTCAAAATAAATAACTCAAAGATTTTT
1 TGTT-TCAAAAGAAACAACTCAAAGATTTTT
628958 ATTCAAAAGG
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
91 2 0.02
92 82 0.77
94 9 0.08
95 13 0.12
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (92 bp):
TGTTTCAAAAGAAACAACTCAAAGATTTTTCAAAAGAAATTGTATCAAGAGAGACAAAACTTTGT
TTCAAAAGAAACAGACTCAAAGATTTT
Found at i:628866 original size:30 final size:30
Alignment explanation
Indices: 628803--628869 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
628793 AGAGACAAAA
*
628803 TTTTGTTTCCAAAGAAACAGACTCAAAGGT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGGT
*
628833 TTTTGTTTCAAAAGAAACA-ACTC-AAGGA
1 TTTTGTTTCAAAAGAAACAGACTCAAAGGT
628861 TTTT-TTTCA
1 TTTTGTTTCA
628870 CGAAATTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 5 0.14
28 8 0.23
29 4 0.11
30 18 0.51
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGGT
Found at i:628978 original size:29 final size:29
Alignment explanation
Indices: 628901--628997 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
628891 AAAACTTTGT
*
628901 TTCAAAAGAAACAGACTT-AAAGATTTTTT
1 TTCAAAAGAAACAGA-TTCAAAGATTTTTA
* * *
628930 TCTCAAAATAAATA-ACTCAAAGATTTTTA
1 T-TCAAAAGAAACAGATTCAAAGATTTTTA
* *
628959 TTCAAAAGGAACAGATTCAAAGATTTGT-
1 TTCAAAAGAAACAGATTCAAAGATTTTTA
*
628987 TTCAAGAGAAA
1 TTCAAAAGAAA
628998 TTGTCTCAAG
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 19 0.35
29 25 0.46
30 10 0.19
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (29 bp):
TTCAAAAGAAACAGATTCAAAGATTTTTA
Found at i:628990 original size:28 final size:28
Alignment explanation
Indices: 628896--628997 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 28
628886 GAGACAAAAC
628896 TTTGTTTCAAAAGAAACAGACTT-AAAGA
1 TTTGTTTCAAAAGAAACAGA-TTCAAAGA
* * * *
628924 TTTTTTTCTCAAAATAAATA-ACTCAAAGA
1 -TTTGTT-TCAAAAGAAACAGATTCAAAGA
* *
628953 TTTTTATTCAAAAGGAACAGATTCAAAGA
1 TTTGT-TTCAAAAGAAACAGATTCAAAGA
*
628982 TTTGTTTCAAGAGAAA
1 TTTGTTTCAAAAGAAA
628998 TTGTCTCAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 24 0.41
29 24 0.41
30 10 0.17
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (28 bp):
TTTGTTTCAAAAGAAACAGATTCAAAGA
Found at i:629420 original size:35 final size:35
Alignment explanation
Indices: 629329--629441 Score: 127
Period size: 36 Copynumber: 3.2 Consensus size: 35
629319 TATCTCAAAG
**
629329 GAAAAATGTCTCAAGCGAGATGAAATTTGTTTTAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
* * * *
629364 GAGAAATTGTCTTAAGTGAGACAAAATTTGTTTTTA
1 GA-AAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
* * *
629400 TAAAACTGTCTCAAGCGAGACAAAATTTTGTTTCAA
1 GAAAAATGTCTCAAGCGAGACAAAA-TTTGTTTTAA
629436 GAAAAA
1 GAAAAA
629442 CACTCTCAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
35 22 0.35
36 40 0.65
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (35 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:629768 original size:12 final size:12
Alignment explanation
Indices: 629753--629793 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
629743 TGTTGATGCA
*
629753 TGTATGTATATT
1 TGTATGTATGTT
629765 TGTATGTATGTGT
1 TGTATGTATGT-T
629778 TG-ATGTATGTT
1 TGTATGTATGTT
629789 TGTAT
1 TGTAT
629794 TGATGTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (12 bp):
TGTATGTATGTT
Found at i:629770 original size:32 final size:32
Alignment explanation
Indices: 629733--629793 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
629723 TCATGTAGCA
629733 TGTATGTATGTGTTGATGCATGTATGTATATT
1 TGTATGTATGTGTTGATGCATGTATGTATATT
* *
629765 TGTATGTATGTGTTGATGTATGTTTGTAT
1 TGTATGTATGTGTTGATGCATGTATGTAT
629794 TGATGTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.20, C:0.02, G:0.26, T:0.52
Consensus pattern (32 bp):
TGTATGTATGTGTTGATGCATGTATGTATATT
Found at i:629801 original size:32 final size:32
Alignment explanation
Indices: 629732--629803 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
629722 CTCATGTAGC
629732 ATGTATGTATGTGTTGATGCATGTATGTATAT
1 ATGTATGTATGTGTTGATGCATGTATGTATAT
* * *
629764 TTGTATGTATGTGTTGATGTATGTTTGTAT-T
1 ATGTATGTATGTGTTGATGCATGTATGTATAT
629795 GATGTATGT
1 -ATGTATGT
629804 TTTCTCGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 34 0.97
ACGTcount: A:0.21, C:0.01, G:0.26, T:0.51
Consensus pattern (32 bp):
ATGTATGTATGTGTTGATGCATGTATGTATAT
Found at i:629805 original size:16 final size:16
Alignment explanation
Indices: 629732--629803 Score: 83
Period size: 16 Copynumber: 4.5 Consensus size: 16
629722 CTCATGTAGC
*
629732 ATGTATGTATGTGTTG
1 ATGTATGTATGTATTG
*
629748 ATGCATGTATGTATAT-
1 ATGTATGTATGTAT-TG
* *
629764 TTGTATGTATGTGTTG
1 ATGTATGTATGTATTG
*
629780 ATGTATGTTTGTATTG
1 ATGTATGTATGTATTG
629796 ATGTATGT
1 ATGTATGT
629804 TTTCTCGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 44 0.96
17 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.26, T:0.51
Consensus pattern (16 bp):
ATGTATGTATGTATTG
Found at i:629962 original size:15 final size:15
Alignment explanation
Indices: 629924--629965 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
629914 ATTTGTTTTC
**
629924 TTTGCCCCATCAAAT
1 TTTGCCCCAAAAAAT
629939 TTT-CCCCAAAAAAT
1 TTTGCCCCAAAAAAT
629953 TTTGCCCCAAAAA
1 TTTGCCCCAAAAA
629966 CTTGGCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.29
Consensus pattern (15 bp):
TTTGCCCCAAAAAAT
Found at i:633271 original size:20 final size:20
Alignment explanation
Indices: 633228--633271 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
633218 TGCTTAAATG
* *
633228 AATGCCATGCAGAATGTAAT
1 AATGCCATGCAGAATGCAAA
633248 AATGCCAATGCAG-ATGCAAA
1 AATGCC-ATGCAGAATGCAAA
633268 AATG
1 AATG
633272 TTGATCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGCCATGCAGAATGCAAA
Found at i:634011 original size:30 final size:30
Alignment explanation
Indices: 633977--634035 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
633967 AAAATGACAC
* *
633977 AAACAAGAGAGAAGAAATAAATTAGTACAA
1 AAACAAAAGAAAAGAAATAAATTAGTACAA
* *
634007 AAACAAAAGAAAAGAAATTAGTTAGTACA
1 AAACAAAAGAAAAGAAATAAATTAGTACA
634036 TGAAAGACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (30 bp):
AAACAAAAGAAAAGAAATAAATTAGTACAA
Found at i:636331 original size:76 final size:75
Alignment explanation
Indices: 636195--636357 Score: 168
Period size: 76 Copynumber: 2.1 Consensus size: 75
636185 AAATGTAACG
* ** * * *
636195 TTTACAAATATCATAGCCAAATTGGAATATTAACAAAAATACCCAACAACCTGGAATTAGTGGCT
1 TTTACAAATATCATAGCCAAATTCGAATAACAACAAAAATACACAACAACCT-GAATTAGTGACC
636260 AAAATAAAATA
65 AAAATAAAATA
** *
636271 TTTACAAATATGGTGGCCAAATTCGAATAACAACAAAGAATACACAACATA-CT-AACTTAGTGA
1 TTTACAAATATCATAGCCAAATTCGAATAACAACAAA-AATACACAACA-ACCTGAA-TTAGTGA
*
636334 CCAAAATTAAATA
63 CCAAAATAAAATA
* *
636347 ATAACAAATAT
1 TTTACAAATAT
636358 TGCTACCAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
75 2 0.03
76 57 0.79
77 12 0.17
78 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.25
Consensus pattern (75 bp):
TTTACAAATATCATAGCCAAATTCGAATAACAACAAAAATACACAACAACCTGAATTAGTGACCA
AAATAAAATA
Found at i:637520 original size:3 final size:3
Alignment explanation
Indices: 637501--637567 Score: 50
Period size: 3 Copynumber: 22.0 Consensus size: 3
637491 AAAATTGTAT
637501 TAA TATA TAA GTAA TAA TAA TAA TAA TAA -ATA TAAA TAA TAA -AA -AA
1 TAA TA-A TAA -TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TAA TAA TAA
** *
637547 CGA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
637568 ATTAAAATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
2 5 0.09
3 41 0.75
4 8 0.15
5 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:637615 original size:2 final size:2
Alignment explanation
Indices: 637608--637639 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
637598 GGTGTCTACA
637608 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
637640 TCTCCACAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:637858 original size:65 final size:64
Alignment explanation
Indices: 637764--638085 Score: 556
Period size: 64 Copynumber: 5.0 Consensus size: 64
637754 ACAAATTTTG
*
637764 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAATTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
* * *
637828 TATGATCATCATATAAATACTTAATTTCTATATGATTTACGTAAAAGAAAAAGTCTTAGTTACAT
1 TATGATCATCATAT-AATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
637893 TATGATCATCATATAATACTTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTT-CTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
637958 TATGATCATCATATAATACTTAATTTCTATATGA-CTTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATC-TAAGTAAAAGAAAAAGTCTTAGTTACAA
* *
638022 TATGATCATCATATAATAATTAATTTCTATATGATCTATGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
638086 GTCTAGACTC
Statistics
Matches: 245, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
63 1 0.00
64 122 0.50
65 122 0.50
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (64 bp):
TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
Found at i:638002 original size:129 final size:129
Alignment explanation
Indices: 637764--638085 Score: 574
Period size: 129 Copynumber: 2.5 Consensus size: 129
637754 ACAAATTTTG
*
637764 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAATTCTTAGTTACAAT
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAAT
* * *
637829 ATGATCATCATATAAATACTTAATTTCTATATGATTTACGTAAAAGAAAAAGTCTTAGTTACAT
66 ATGATCATCATATAAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
637893 TATGATCATCATATAATACTTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTT-CTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
637958 TATGATCATCATAT-AATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
65 TATGATCATCATATAAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
* *
638022 TATGATCATCATATAATAATTAATTTCTATATGATCTATGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
638086 GTCTAGACTC
Statistics
Matches: 186, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
128 37 0.20
129 98 0.53
130 51 0.27
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (129 bp):
TATGATCATCATATAATACTTAATTTCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAAT
ATGATCATCATATAAATACTTAATTTCTATATGACTTAAGTAAAAGAAAAAGTCTTAGTTACAA
Found at i:644806 original size:28 final size:28
Alignment explanation
Indices: 644753--644807 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
644743 CAAGAACAAA
* *
644753 AAAGAAAATGAGCAAAAAAGCAAAAAAC
1 AAAGAAAAAGAGCAAAAAAGAAAAAAAC
*
644781 AAAGAAAAAGAG-AAACAAGAACAAAAA
1 AAAGAAAAAGAGCAAAAAAGAA-AAAAA
644808 GAACAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.75, C:0.09, G:0.15, T:0.02
Consensus pattern (28 bp):
AAAGAAAAAGAGCAAAAAAGAAAAAAAC
Found at i:644810 original size:16 final size:16
Alignment explanation
Indices: 644777--644827 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
644767 AAAAAGCAAA
*
644777 AAACAAAGAA-AAAGAG
1 AAAC-AAGAACAAAAAG
644793 AAACAAGAACAAAAAG
1 AAACAAGAACAAAAAG
644809 -AACAAGAATCAAAAAG
1 AAACAAGAA-CAAAAAG
644825 AAA
1 AAA
644828 AAGGGACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 13 0.42
16 16 0.52
17 2 0.06
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.02
Consensus pattern (16 bp):
AAACAAGAACAAAAAG
Found at i:645466 original size:22 final size:22
Alignment explanation
Indices: 645438--645492 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
645428 GCTACCCCAT
*
645438 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGA
645460 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
645482 CAAACCTTTGA
1 CAAACCTTTGA
645493 CAAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:646352 original size:36 final size:36
Alignment explanation
Indices: 646239--646352 Score: 97
Period size: 36 Copynumber: 3.1 Consensus size: 36
646229 ACTTGATATT
*
646239 GTTTTTTTTAAAAC-AGACTTTGTCTCGCTTGAGACC
1 GTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACC
* * * * * ** **
646275 G-TTTTCACTAGAAAGAAGATTTATTTCACTCAAGATT
1 GTTTTTC-TTA-AAACAAGATTTGTCTCGCTTGAGACC
646312 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
646348 GTTTT
1 GTTTT
646353 CACTATAAGA
Statistics
Matches: 55, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
35 4 0.07
36 26 0.47
37 17 0.31
38 8 0.15
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (36 bp):
GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
Found at i:646494 original size:37 final size:37
Alignment explanation
Indices: 646452--646546 Score: 154
Period size: 37 Copynumber: 2.6 Consensus size: 37
646442 AACAAATTTC
*
646452 GTCTCCCTTGAGACAGTTTCTTTTGGAACTCAGTTTT
1 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
* *
646489 GTCTCCCTTAAGACCGTTTCTTTTGGAACTAAGTTTT
1 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
*
646526 GTCTCTCTTGAGACAGTTTCT
1 GTCTCCCTTGAGACAGTTTCT
646547 CTCGAAACGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (37 bp):
GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTT
Found at i:646994 original size:106 final size:106
Alignment explanation
Indices: 646837--647330 Score: 725
Period size: 106 Copynumber: 4.7 Consensus size: 106
646827 ATATCGTGCC
* *
646837 ACTCGAGACAACACAAGTTTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
646902 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
646943 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGTACGGCTGATCGTCAAC-AA-AATTT--C
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * *
647004 -A-TGCAGAGTCGATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
647043 ACT-AGAGACAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC
1 ACTCA-AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
647107 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
647149 ACTCGAGACAACACAAGTTAAATTTCACAACGAAGGGACGGC-GGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
647213 AATTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
647254 ACCCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAACTTCTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
647319 AGTTTCAGAGCC
66 AATTTCAGAGCC
647331 CGCGGTTTCA
Statistics
Matches: 346, Mismatches: 33, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
99 1 0.00
100 81 0.23
101 3 0.01
102 6 0.02
104 6 0.02
105 100 0.29
106 149 0.43
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:647161 original size:206 final size:212
Alignment explanation
Indices: 646841--647330 Score: 719
Period size: 206 Copynumber: 2.3 Consensus size: 212
646831 CGTGCCACTC
* *
646841 GAGACAACACAAGTTTAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAATT
*
646906 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTAAACTTCAC
* * * *
646971 AACGAAGGTACGGCTGATCGTCAAC-AA-AA-TT-TC-A-TGCAGAGTCGATTTCAACTTCACAG
131 AACGAAGGGACGGC-GATCGTCAACAAACAACTTCCCAATTGCAGAGCCAATTTCAACTTCACAG
*
647030 CAAAGGATATTGGA-CTA
195 CAAAGGATATTGGACCCA
*
647047 GAGACAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAATT
* *
647112 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTAAATTTCAC
66 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTAAACTTCAC
* * * *
647177 AACGAAGGGACGGCGGTTGTCAACAAACAACTTCCCAATTTCAGGGCCAATTTCAACTTCACAGC
131 AACGAAGGGACGGCGATCGTCAACAAACAACTTCCCAATTGCAGAGCCAATTTCAACTTCACAGC
*
647242 GAAGGATATTGGACCCA
196 AAAGGATATTGGACCCA
* * * *
647259 -AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAA-CTTCTCAGT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-CAAT
647322 TTCAGAGCC
65 TTCAGAGCC
647331 CGCGGTTTCA
Statistics
Matches: 255, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
205 8 0.03
206 139 0.55
207 2 0.01
208 2 0.01
209 1 0.00
210 4 0.02
211 97 0.38
212 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (212 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTAAACTTCAC
AACGAAGGGACGGCGATCGTCAACAAACAACTTCCCAATTGCAGAGCCAATTTCAACTTCACAGC
AAAGGATATTGGACCCA
Found at i:661092 original size:27 final size:28
Alignment explanation
Indices: 661054--661111 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
661044 GTCTTTTCAC
661054 TTAAGTTATTGAATGTCTAAGAGCCCAT
1 TTAAGTTATTGAATGTCTAAGAGCCCAT
*
661082 TTAAG-TATTGAATGTCTAAGAGCTCAT
1 TTAAGTTATTGAATGTCTAAGAGCCCAT
661109 TTA
1 TTA
661112 GGACTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (28 bp):
TTAAGTTATTGAATGTCTAAGAGCCCAT
Found at i:663300 original size:20 final size:21
Alignment explanation
Indices: 663275--663316 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
663265 TCCATATTGT
663275 CCCAA-GGGAACCGATTCCCC
1 CCCAAGGGGAACCGATTCCCC
*
663295 CCCAAGGGGTACCGATTCCCC
1 CCCAAGGGGAACCGATTCCCC
663316 C
1 C
663317 TGAATGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.12
Consensus pattern (21 bp):
CCCAAGGGGAACCGATTCCCC
Found at i:663421 original size:21 final size:21
Alignment explanation
Indices: 663397--663438 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
663387 ATTTGAATAT
663397 TATGAAGGGGTACCGAATCCC
1 TATGAAGGGGTACCGAATCCC
* *
663418 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGAATCCC
663439 CCTATTGGGG
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:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
TATGAAGGGGTACCGAATCCC
Found at i:663504 original size:20 final size:22
Alignment explanation
Indices: 663466--663505 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
663456 TTTTTGTAGA
663466 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
663488 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
663506 AGATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Done.