Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397279.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.0, 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: 2022356
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6073 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:1465333 original size:110 final size:110
Alignment explanation
Indices: 1465119--1465367 Score: 246
Period size: 114 Copynumber: 2.3 Consensus size: 110
1465109 CTTTAAGAGT
* *
1465119 AAGATTGAGCATTGTTAAAGTAAAGGAAAATGTCATAGTCCCAAAGGGGGCTTTAAGAGTAAGAA
1 AAGATTAAGCATTGTTAAAGTAAAGGAAAATGTCATAGTCCCAAAGGGGGCTATAAGAGTAAG--
***
1465184 AAATTAAACATTGTTAAAGCGAGGGAAGATAAGGGCTCTAAGAGTAAAA
64 -AATTAAACATTGTTAAA-CGAGGGAAGATAAAAACTCTAAGAGTAAAA
* ** *
1465233 AAGATTAAGCATTGTTATAGTTGGAGGAAAATGTCAT-GATCTCAAA-GGGGCTATAAGAGTAAG
1 AAGATTAAGCATTGTTAAAG-TAAAGGAAAATGTCATAG-TCCCAAAGGGGGCTATAAGAGTAAG
* *
1465296 -ATTAAGCATTGTTAGAA-TAGGGAAAGATAAAAACTCTAAGAGT----
64 AATTAAACATTGTTA-AACGAGGG-AAGATAAAAACTCTAAGAGTAAAA
*
1465339 AAGATTGAGCATTGTTAGAA-TAAAGGAAA
1 AAGATTAAGCATTGTTA-AAGTAAAGGAAA
1465368 TTGGGGGTTC
Statistics
Matches: 115, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
105 7 0.06
106 16 0.14
107 1 0.01
109 4 0.03
110 30 0.26
111 2 0.02
114 35 0.30
115 20 0.17
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.24
Consensus pattern (110 bp):
AAGATTAAGCATTGTTAAAGTAAAGGAAAATGTCATAGTCCCAAAGGGGGCTATAAGAGTAAGAA
TTAAACATTGTTAAACGAGGGAAGATAAAAACTCTAAGAGTAAAA
Found at i:1476366 original size:32 final size:32
Alignment explanation
Indices: 1476325--1476390 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1476315 ATATATTTGA
1476325 TAAAATTTAACATTAAAAAAATTACAAGCTTG
1 TAAAATTTAACATTAAAAAAATTACAAGCTTG
1476357 TAAAATTTAACATTAAAAAAATTACAAGCTTG
1 TAAAATTTAACATTAAAAAAATTACAAGCTTG
1476389 TA
1 TA
1476391 GAAAAGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (32 bp):
TAAAATTTAACATTAAAAAAATTACAAGCTTG
Found at i:1478091 original size:2 final size:2
Alignment explanation
Indices: 1478086--1478119 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1478076 AAGCATTACC
*
1478086 TA TA TA TA TA TA AA TA T- 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 TA T
1478120 TGTCTTGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1478108 original size:15 final size:15
Alignment explanation
Indices: 1478088--1478117 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1478078 GCATTACCTA
1478088 TATATATATAAATAT
1 TATATATATAAATAT
*
1478103 TATATATATATATAT
1 TATATATATAAATAT
1478118 ATTGTCTTGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATATAAATAT
Found at i:1478108 original size:17 final size:17
Alignment explanation
Indices: 1478086--1478120 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1478076 AAGCATTACC
1478086 TATATATATATAAATAT
1 TATATATATATAAATAT
*
1478103 TATATATATATATATAT
1 TATATATATATAAATAT
1478120 T
1 T
1478121 GTCTTGAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATATATAAATAT
Found at i:1478470 original size:25 final size:25
Alignment explanation
Indices: 1478425--1478472 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1478415 TTTATTTTAA
*
1478425 ATTAAATAATTTTTGATAATTAATT
1 ATTAAATAATTATTGATAATTAATT
*
1478450 ATTAATTAATTATT-ATAAATTAA
1 ATTAAATAATTATTGAT-AATTAA
1478473 AATATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTAAATAATTATTGATAATTAATT
Found at i:1492799 original size:19 final size:19
Alignment explanation
Indices: 1492775--1492812 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1492765 AGAAAAAGAT
1492775 GGTGAGCCAACCAAATTCC
1 GGTGAGCCAACCAAATTCC
1492794 GGTGAGCCAACCAAATTCC
1 GGTGAGCCAACCAAATTCC
1492813 TCTTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (19 bp):
GGTGAGCCAACCAAATTCC
Found at i:1509044 original size:19 final size:19
Alignment explanation
Indices: 1509020--1509062 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1509010 CTATGACAAC
1509020 ATCAGACTTGTTAAAAAAT
1 ATCAGACTTGTTAAAAAAT
1509039 ATCAGACTTGTTAAAAAAT
1 ATCAGACTTGTTAAAAAAT
1509058 ATCAG
1 ATCAG
1509063 GCTTTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (19 bp):
ATCAGACTTGTTAAAAAAT
Found at i:1512494 original size:53 final size:53
Alignment explanation
Indices: 1512431--1512531 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
1512421 AAAAACCATA
* * **
1512431 AATGTCCATTCCTTGA-AGTGAATGTGACAAATGAGCTACTAATAAAAATTATG
1 AATGTCCATTCCCT-ATAGTGAATGTGACAAACGAAATACTAATAAAAATTATG
*
1512484 AATGTTCATTCCCTATAGTGAATGTGACAAACGAAATACTAATAAAAA
1 AATGTCCATTCCCTATAGTGAATGTGACAAACGAAATACTAATAAAAA
1512532 AATTATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.02
53 41 0.98
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.29
Consensus pattern (53 bp):
AATGTCCATTCCCTATAGTGAATGTGACAAACGAAATACTAATAAAAATTATG
Found at i:1512769 original size:26 final size:25
Alignment explanation
Indices: 1512726--1512774 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1512716 GAATTTAAGA
*
1512726 ATAATTTTACCATTAAAAGTGGATAG
1 ATAATTTTACCA-TAAAAATGGATAG
**
1512752 ATAATTTTATTATAAAAATGGAT
1 ATAATTTTACCATAAAAATGGAT
1512775 GGATGCCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (25 bp):
ATAATTTTACCATAAAAATGGATAG
Found at i:1512989 original size:64 final size:63
Alignment explanation
Indices: 1512866--1512989 Score: 167
Period size: 64 Copynumber: 2.0 Consensus size: 63
1512856 CACAAATAGA
* * ** *
1512866 TGAATAATTTTAACGCACCAAAGTAAATGGATACCTTAACTTACTAGCCCATTAGAAGTGAAT
1 TGAATAATTTTAACGCACAAAAGTAAATGGATACCTTAACCTACTAGCCCACAAAAAGTGAAT
* * *
1512929 TGAATAATTTTAACGCGTCAAAAGTAGATGGATACCTTAACCTACTGGCCCACAAAAAGTG
1 TGAATAATTTTAACGC-ACAAAAGTAAATGGATACCTTAACCTACTAGCCCACAAAAAGTG
1512990 GATATCCCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 16 0.31
64 36 0.69
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (63 bp):
TGAATAATTTTAACGCACAAAAGTAAATGGATACCTTAACCTACTAGCCCACAAAAAGTGAAT
Found at i:1517310 original size:15 final size:15
Alignment explanation
Indices: 1517290--1517326 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1517280 CCTAAATATT
1517290 TTCTTTCCCTTTAAA
1 TTCTTTCCCTTTAAA
1517305 TTCTTTCCCTTTAAA
1 TTCTTTCCCTTTAAA
1517320 TTCTTTC
1 TTCTTTC
1517327 TCTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCTTTCCCTTTAAA
Found at i:1531510 original size:27 final size:25
Alignment explanation
Indices: 1531444--1531528 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 25
1531434 AGATAATGTA
*
1531444 AATTTATTTATTAATTA-AAATATT
1 AATTTATATATTAATTATAAATATT
*
1531468 -ATTTA-ATTGATAAATTAATAAATTATT
1 AATTTATA-T-ATTAATT-ATAAA-TATT
*
1531495 AATTTATATATTAATTGATAAAAAATT
1 AATTTATATATTAATT-AT-AAATATT
1531522 AATTTAT
1 AATTTAT
1531529 CAAGATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 6 0.12
24 6 0.12
25 1 0.02
26 3 0.06
27 22 0.46
28 9 0.19
29 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AATTTATATATTAATTATAAATATT
Found at i:1536993 original size:2 final size:2
Alignment explanation
Indices: 1536986--1537015 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1536976 CATAGCTAAG
1536986 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
1537016 GTAGTTATGG
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:1540231 original size:21 final size:21
Alignment explanation
Indices: 1540205--1540244 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1540195 TCTCATGTGA
1540205 TACAAA-TCGTGTTAGACATTT
1 TACAAACT-GTGTTAGACATTT
1540226 TACAAACTGTGTTAGACAT
1 TACAAACTGTGTTAGACAT
1540245 CAACAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
TACAAACTGTGTTAGACATTT
Found at i:1540326 original size:18 final size:18
Alignment explanation
Indices: 1540303--1540337 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1540293 CATGAGTTAT
1540303 GTTTGTTCAAATAATTAA
1 GTTTGTTCAAATAATTAA
*
1540321 GTTTGTTCGAATAATTA
1 GTTTGTTCAAATAATTA
1540338 TGGTGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (18 bp):
GTTTGTTCAAATAATTAA
Found at i:1540399 original size:23 final size:23
Alignment explanation
Indices: 1540350--1540414 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1540340 GTGAAAAAGC
*
1540350 AACAATTA-GATTTGTTGGAAAATA
1 AACAATTATG-TTTGTT-GAAAACA
*
1540374 AACAATTATGTTTATTGAAAACA
1 AACAATTATGTTTGTTGAAAACA
* *
1540397 AACACTTGTGTTTGTTGA
1 AACAATTATGTTTGTTGA
1540415 GAAGAGGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 21 0.60
24 13 0.37
25 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (23 bp):
AACAATTATGTTTGTTGAAAACA
Found at i:1540938 original size:19 final size:18
Alignment explanation
Indices: 1540889--1540941 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
1540879 GATATTATTT
* *
1540889 TATTAGTATAATTTTTTA
1 TATTAATATAATTTTATA
1540907 T-TTAATATTTAATTTTAATA
1 TATTAATA--TAATTTT-ATA
1540927 TATTAATATAATTTT
1 TATTAATATAATTTT
1540942 TATTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 14 0.48
20 3 0.10
21 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTAATATAATTTTATA
Found at i:1540948 original size:20 final size:19
Alignment explanation
Indices: 1540883--1540950 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
1540873 ATCTAAGATA
* *
1540883 TTATTTTATTAGTATAATT
1 TTATTATATTAATATAATT
1540902 TT-TTAT-TTAATATTTAATT
1 TTATTATATTAATA--TAATT
*
1540921 TTAATATATTAATATAATTT
1 TTATTATATTAATATAA-TT
1540941 TTATTATATT
1 TTATTATATT
1540951 TTAATAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.12
18 3 0.08
19 12 0.30
20 14 0.35
21 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (19 bp):
TTATTATATTAATATAATT
Found at i:1551146 original size:26 final size:26
Alignment explanation
Indices: 1551117--1551177 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
1551107 TGAACTCACC
1551117 AACAATGAATCATTGCCAAACTTCGT
1 AACAATGAATCATTGCCAAACTTCGT
1551143 AACAATGAATCATTGCCAAACTTCGT
1 AACAATGAATCATTGCCAAACTTCGT
**
1551169 GTCAATGAA
1 AACAATGAA
1551178 CAAAAATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (26 bp):
AACAATGAATCATTGCCAAACTTCGT
Found at i:1552229 original size:2 final size:2
Alignment explanation
Indices: 1552222--1552256 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1552212 CTTAGCGAGA
1552222 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
1552257 CACACACACA
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:1567017 original size:21 final size:21
Alignment explanation
Indices: 1566990--1567048 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1566980 TGTTGCCCTC
1566990 AAGCATCGCAATGTCATCCTT
1 AAGCATCGCAATGTCATCCTT
* *
1567011 GAGCATCGCAGTGTCATCCTT
1 AAGCATCGCAATGTCATCCTT
* *
1567032 AAGCATCTCAATATCAT
1 AAGCATCGCAATGTCAT
1567049 TTAAAAATGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (21 bp):
AAGCATCGCAATGTCATCCTT
Found at i:1568135 original size:25 final size:25
Alignment explanation
Indices: 1568107--1568154 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1568097 GATCCAAAAC
*
1568107 ATTGCTACATGCCATGTTGAAAGAT
1 ATTGCTACATGCCATGTTCAAAGAT
* *
1568132 ATTGTTACATGCCTTGTTCAAAG
1 ATTGCTACATGCCATGTTCAAAG
1568155 TAAAAAGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (25 bp):
ATTGCTACATGCCATGTTCAAAGAT
Found at i:1573152 original size:27 final size:27
Alignment explanation
Indices: 1573130--1573186 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
1573120 ATTTTATATT
1573130 ATTT-TTTAAA-TATTAATAATTTATA
1 ATTTATTTAAAGTATTAATAATTTATA
* *
1573155 ATTTATTTAAAGTATTGATAATTGATA
1 ATTTATTTAAAGTATTAATAATTTATA
*
1573182 GTTTA
1 ATTTA
1573187 AATATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (27 bp):
ATTTATTTAAAGTATTAATAATTTATA
Found at i:1573242 original size:23 final size:24
Alignment explanation
Indices: 1573117--1573242 Score: 68
Period size: 26 Copynumber: 5.1 Consensus size: 24
1573107 ATTATTTATT
*
1573117 TTAAT-TTTATATTATTTTTTAAATA
1 TTAATATTT-TATTA-TATTTAAATA
1573142 TTAATAATTTATAATT-TATTTAAAGTA
1 TTAAT-ATTT-T-ATTATATTTAAA-TA
* * * *
1573169 TTGATAATTGA-TA-GTTTAAATA
1 TTAATATTTTATTATATTTAAATA
1573191 TTAATATTTTAGTTATATGTT-AATAA
1 TTAATATTTTA-TTATAT-TTAAAT-A
1573217 TTAAT-TTTT-TTATAATTTAAATA
1 TTAATATTTTATTAT-ATTTAAATA
1573240 TTA
1 TTA
1573243 TTATGATTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 26
0.70 0.08 0.23
Matches are distributed among these distances:
22 10 0.12
23 17 0.21
24 8 0.10
25 13 0.16
26 18 0.22
27 11 0.14
28 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (24 bp):
TTAATATTTTATTATATTTAAATA
Found at i:1573299 original size:27 final size:27
Alignment explanation
Indices: 1573269--1573322 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1573259 TTATTTTAGT
* *
1573269 TTTAAAAAATTTATATTTTATAATTTA
1 TTTAAAAAATTCATAATTTATAATTTA
**
1573296 TTTAAAATGTTCATAATTTATAATTTA
1 TTTAAAAAATTCATAATTTATAATTTA
1573323 AATATTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAAAAAATTCATAATTTATAATTTA
Found at i:1573301 original size:136 final size:139
Alignment explanation
Indices: 1573116--1573405 Score: 369
Period size: 136 Copynumber: 2.1 Consensus size: 139
1573106 GATTATTTAT
* * * * * * *
1573116 TTTAATTTTATATTATTTTTTAAATATTAATAATTTATAATTTATTTAAAGTATTGATAATTGAT
1 TTTATTTTTATTTTAGTTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGAT
*
1573181 AGTTTAAATATTAATATTTTAGTTAT-ATGTTAATAATT-A-ATTTT-T-TTATAATTTA-AATA
66 AATTTAAATATTAATATTTTAGTTATAAT-TTAATAATTAACATTTTATATTA-AATTTATAAT-
*
1573240 TTATTATG-ATTA
128 TTA-AATGTATTA
* * * *
1573252 TTTATTTTTATTTTAGTTTTAAAAAATTTATATTTTATAATTTATTTAAAATGTTCATAATTTAT
1 TTTATTTTTATTTTAGTTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGAT
1573317 AATTTAAATATTAATATTTTAGTTATAATTTAATAATTAACATTTTATATTAAATTTATAATTTA
66 AATTTAAATATTAATATTTTAGTTATAATTTAATAATTAACATTTTATATTAAATTTATAATTTA
1573382 AATGTTATTA
131 AATG-TATTA
1573392 TTTATTTTTATTTT
1 TTTATTTTTATTTT
1573406 TTAATATTAA
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
136 88 0.66
137 3 0.02
138 8 0.06
139 10 0.08
140 24 0.18
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (139 bp):
TTTATTTTTATTTTAGTTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGAT
AATTTAAATATTAATATTTTAGTTATAATTTAATAATTAACATTTTATATTAAATTTATAATTTA
AATGTATTA
Found at i:1573349 original size:26 final size:26
Alignment explanation
Indices: 1573313--1573379 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
1573303 TGTTCATAAT
*
1573313 TTATAATTTAA-ATATTAATATTTTAG
1 TTATAATTTAATA-ATTAACATTTTAG
*
1573339 TTATAATTTAATAATTAACATTTTATA
1 TTATAATTTAATAATTAACATTTTA-G
1573366 TTA-AATTT-ATAATT
1 TTATAATTTAATAATT
1573380 TAAATGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.16
26 27 0.73
27 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
TTATAATTTAATAATTAACATTTTAG
Found at i:1573367 original size:33 final size:34
Alignment explanation
Indices: 1573308--1573382 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
1573298 TAAAATGTTC
**
1573308 ATAATTT-ATAATTTAAATATTAATATTTTAGTT
1 ATAATTTAATAATTTAAATATTAATATTAAAGTT
* *
1573341 ATAATTTAATAA-TTAACAT-TTTATATTAAATTT
1 ATAATTTAATAATTTAA-ATATTAATATTAAAGTT
1573374 ATAATTTAA
1 ATAATTTAA
1573383 ATGTTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (34 bp):
ATAATTTAATAATTTAAATATTAATATTAAAGTT
Found at i:1573408 original size:136 final size:132
Alignment explanation
Indices: 1573128--1573468 Score: 349
Period size: 136 Copynumber: 2.6 Consensus size: 132
1573118 TAATTTTATA
* * * *
1573128 TTATTTTTT-AAATATTAATAATTTATAATTTATTTAAAGTATTGATAATTGATAGTTTAAATAT
1 TTATTTTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGATAATTTAAATAT
*
1573192 TAATATTTTAGTTATATGTTAATAATTAATTTTTTTATAATTTAAATATTATTATGATTATTTAT
66 TAATATTTTAGTTATATGTTAATAATTAATTTTTTTATAATTTAAATATTATAATGATTATTTAT
1573257 TT
131 TT
* * * *
1573259 TTATTTTAGTTTTAAAAAATTTATATTTTATAATTTATTTAAAATGTTCATAATTTATAATTTAA
1 TTA--TT--TTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGATAATTTAA
1573324 ATATTAATATTTTAGTTATAAT-TTAATAATTAACATTTTATATTA-AATTTATAAT-TTA-AAT
62 ATATTAATATTTTAGTTAT-ATGTTAATAATT-A-ATTTT-T-TTATAATTTA-AATATTATAAT
1573385 GTTATTATTTATTT
121 G--ATTATTTATTT
* * ** * * * *
1573399 TTATTTTTT--AATATTAATAATGTATAATAAACTTACAATATTAACAA-TGATCAA-TTAAATA
1 TTATTTTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGAT-AATTTAAATA
1573460 TTAATATTT
65 TTAATATTT
1573469 ATTTATAATT
Statistics
Matches: 175, Mismatches: 21, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
131 3 0.02
133 21 0.12
134 29 0.17
135 4 0.02
136 75 0.43
137 3 0.02
138 10 0.06
139 10 0.06
140 20 0.11
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (132 bp):
TTATTTTTTAAAAAATTAATAATTTATAATTTATTTAAAATATTCATAATTGATAATTTAAATAT
TAATATTTTAGTTATATGTTAATAATTAATTTTTTTATAATTTAAATATTATAATGATTATTTAT
TT
Found at i:1573642 original size:152 final size:151
Alignment explanation
Indices: 1573435--1573745 Score: 414
Period size: 153 Copynumber: 2.1 Consensus size: 151
1573425 ATAAACTTAC
* *
1573435 AATATTAACAATGATCAATTAAATATTAATATTTATTTATAATTTAAATGATATTATTATTAAAA
1 AATATTAACAATGATCAATTAAATATTAATATTTATTTATAATTGAAATGATATTATGATTAAAA
* * * * *
1573500 TATTAA-AGAGTTTAATCAATTTTTAAATTTAAAAT-ATA-TTTTTATAACATATTATTAAAAAT
66 TATGAATA-A-TTTAATCAAATTTTAAAATTAAAATGATATTTTTTATAACATATAATCAAAAAT
*
1573562 TTAAACTTTTTTCTTTTTACAAT
129 TTAAACTTTTTCCTTTTTACAAT
* *
1573585 AATATTAGCAATTGAT-AATTTAAATATTAATATTTTATTTATAATTGAAATGTTATTATGATTA
1 AATATTAACAA-TGATCAA-TTAAATATTAATA-TTTATTTATAATTGAAATGATATTATGATTA
* * * *
1573649 AAATATGAATAATTTAATTAAATTTTAAAATTAAAATGTTATTTTTTATAATATATAATCAAAAT
63 AAATATGAATAATTTAATCAAATTTTAAAATTAAAATGATATTTTTTATAACATATAATCAAAAA
*
1573714 TTTAAACTTTTTCCTTTTTATAAT
128 TTTAAACTTTTTCCTTTTTACAAT
1573738 AATATTAA
1 AATATTAA
1573746 TAATTATTAT
Statistics
Matches: 139, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
150 12 0.09
151 39 0.28
152 39 0.28
153 49 0.35
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (151 bp):
AATATTAACAATGATCAATTAAATATTAATATTTATTTATAATTGAAATGATATTATGATTAAAA
TATGAATAATTTAATCAAATTTTAAAATTAAAATGATATTTTTTATAACATATAATCAAAAATTT
AAACTTTTTCCTTTTTACAAT
Found at i:1573748 original size:9 final size:9
Alignment explanation
Indices: 1573734--1573779 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
1573724 TTCCTTTTTA
1573734 TAATAATAT
1 TAATAATAT
1573743 TAATAATTAT
1 TAATAA-TAT
*
1573753 TATATAAAAAT
1 TA-AT-AATAT
1573764 TAATAATAT
1 TAATAATAT
1573773 TAATAAT
1 TAATAAT
1573780 TGATTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 17 0.53
10 7 0.22
11 6 0.19
12 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATAATAT
Found at i:1573766 original size:152 final size:151
Alignment explanation
Indices: 1573435--1573782 Score: 420
Period size: 152 Copynumber: 2.3 Consensus size: 151
1573425 ATAAACTTAC
* *
1573435 AATATTAACAA-TGATCAAT-TAAATATTAATATTTATTTATAATTTAAATGATATTATTATTAA
1 AATATTAACAATTGAT-AATATAAATATTAATATTTATTTATAATTGAAATGATATTATGATTAA
* * * * *
1573498 AATATTAAAGAGTTTAATCAATTTTTAAATTTAAAATATATTTTTATAACATATTATTAAAAATT
65 AATATGAAAGAGTTTAATCAAATTTTAAAATTAAAATATATTTTTATAACATATAATCAAAAATT
*
1573563 TAAACTTTTTTCTTTTTACAAT
130 TAAACTTTTTCCTTTTTACAAT
* * *
1573585 AATATTAGCAATTGATAATTTAAATATTAATATTTTATTTATAATTGAAATGTTATTATGATTAA
1 AATATTAACAATTGATAATATAAATATTAATA-TTTATTTATAATTGAAATGATATTATGATTAA
* * *
1573650 AATATGAATA-A-TTTAATTAAATTTTAAAATTAAAATGTTATTTTTTATAATATATAATCAAAA
65 AATATGAA-AGAGTTTAATCAAATTTTAAAATTAAAAT-ATA-TTTTTATAACATATAATCAAAA
* *
1573713 TTTTAAACTTTTTCCTTTTTATAAT
127 ATTTAAACTTTTTCCTTTTTACAAT
* * * * *
1573738 AATATTAATAATT-ATTATATAAAAATTAATA-ATATTAATAATTGA
1 AATATTAACAATTGATAATATAAATATTAATATTTATTTATAATTGA
1573783 TTATTTAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
150 25 0.15
151 38 0.22
152 54 0.32
153 53 0.31
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (151 bp):
AATATTAACAATTGATAATATAAATATTAATATTTATTTATAATTGAAATGATATTATGATTAAA
ATATGAAAGAGTTTAATCAAATTTTAAAATTAAAATATATTTTTATAACATATAATCAAAAATTT
AAACTTTTTCCTTTTTACAAT
Found at i:1573770 original size:30 final size:31
Alignment explanation
Indices: 1573734--1573799 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
1573724 TTCCTTTTTA
1573734 TAATAATATTAATAATT-ATTATATAAAAAT
1 TAATAATATTAATAATTGATTATATAAAAAT
* *
1573764 TAATAATATTAATAATTGATTATTTAAATAT
1 TAATAATATTAATAATTGATTATATAAAAAT
1573795 TAATA
1 TAATA
1573800 TTTTATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (31 bp):
TAATAATATTAATAATTGATTATATAAAAAT
Found at i:1573805 original size:19 final size:21
Alignment explanation
Indices: 1573768--1573853 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 21
1573758 AAAAATTAAT
1573768 AATATTAATAATTGATTATTTA
1 AATATTAATAATT-ATTATTTA
1573790 AATATTAAT-ATT-TTATTTA
1 AATATTAATAATTATTATTTA
*
1573809 TAAT-TTAA-AGGTTATTATGATTCA
1 -AATATTAATA-ATTATTAT--TT-A
*
1573833 AATATTAATAATT-TTAATTA
1 AATATTAATAATTATTATTTA
1573853 A
1 A
1573854 TTTTAAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
19 11 0.21
20 7 0.13
21 9 0.17
22 9 0.17
23 8 0.15
24 7 0.13
25 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (21 bp):
AATATTAATAATTATTATTTA
Found at i:1573874 original size:20 final size:21
Alignment explanation
Indices: 1573849--1573900 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1573839 AATAATTTTA
*
1573849 ATTAATTTTA-AATTTAAAAT
1 ATTAATTTTATAATATAAAAT
*
1573869 ATTAATTTTTATAATATATAAT
1 ATTAA-TTTTATAATATAAAAT
1573891 ATGTAATTTT
1 AT-TAATTTT
1573901 TCAAACTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 5 0.19
22 14 0.52
23 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTAATTTTATAATATAAAAT
Found at i:1583524 original size:21 final size:21
Alignment explanation
Indices: 1583500--1583573 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1583490 AGATAGGATA
* *
1583500 TAAATTTAAATTGAATTTCTT
1 TAAATTTAAATTAAATTTATT
* *
1583521 TAAATTTAAA-TAAAGATTAAT
1 TAAATTTAAATTAAA-TTTATT
* *
1583542 TACATTTAAATTTAATTTATT
1 TAAATTTAAATTAAATTTATT
1583563 TAAATTTAAAT
1 TAAATTTAAAT
1583574 GTAATATCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
TAAATTTAAATTAAATTTATT
Found at i:1583531 original size:27 final size:28
Alignment explanation
Indices: 1583500--1583560 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
1583490 AGATAGGATA
*
1583500 TAAATTTAA-ATTGAATTTC-TTTAAATT
1 TAAATTTAAGATT-AATTACATTTAAATT
*
1583527 TAAA-TAAAGATTAATTACATTTAAATT
1 TAAATTTAAGATTAATTACATTTAAATT
1583554 T-AATTTA
1 TAAATTTA
1583561 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (28 bp):
TAAATTTAAGATTAATTACATTTAAATT
Found at i:1592962 original size:2 final size:2
Alignment explanation
Indices: 1592955--1592981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1592945 CAACAAGAAA
1592955 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1592982 ATCAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1603518 original size:17 final size:15
Alignment explanation
Indices: 1603492--1603537 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 15
1603482 AAAATTAATT
1603492 ATTAAT-TAAATATA
1 ATTAATATAAATATA
*
1603506 ATTTACATATAAACATA
1 A-TTA-ATATAAATATA
1603523 ATTAATAT-AATATA
1 ATTAATATAAATATA
1603537 A
1 A
1603538 AATATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
16 5 0.19
17 8 0.30
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAATATAAATATA
Found at i:1614604 original size:18 final size:18
Alignment explanation
Indices: 1614583--1614662 Score: 63
Period size: 18 Copynumber: 4.2 Consensus size: 18
1614573 CTCTTTGTAT
1614583 AAACACAACCT-TTTGAAC
1 AAACACAA-CTATTTGAAC
*
1614601 AAACATAACTATTTGAAC
1 AAACACAACTATTTGAAC
* * *
1614619 AAACATAATTAATTATTTAAAC
1 AAAC---A-CAACTATTTGAAC
*
1614641 AAACATAACTATTTGAAC
1 AAACACAACTATTTGAAC
1614659 AAAC
1 AAAC
1614663 TTAATTCTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.04
18 33 0.63
19 1 0.02
21 1 0.02
22 15 0.29
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (18 bp):
AAACACAACTATTTGAAC
Found at i:1614623 original size:22 final size:22
Alignment explanation
Indices: 1614598--1614662 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1614588 CAACCTTTTG
1614598 AACAAACATAACTATTTGAACA
1 AACAAACATAACTATTTGAACA
* *
1614620 AACATAA-TTAATTATTT----A
1 AACA-AACATAACTATTTGAACA
1614638 AACAAACATAACTATTTGAACA
1 AACAAACATAACTATTTGAACA
1614660 AAC
1 AAC
1614663 TTAATTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
17 2 0.06
18 13 0.39
22 16 0.48
23 2 0.06
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (22 bp):
AACAAACATAACTATTTGAACA
Found at i:1614667 original size:36 final size:37
Alignment explanation
Indices: 1614598--1614684 Score: 122
Period size: 40 Copynumber: 2.3 Consensus size: 37
1614588 CAACCTTTTG
1614598 AACAAACATAACTATTTGAACAAACATAATTAATTATTTA
1 AACAAACATAACTATTTGAACAAAC---ATTAATTATTTA
*
1614638 AACAAACATAACTATTTGAACAAAC-TTAATTCTTTA
1 AACAAACATAACTATTTGAACAAACATTAATTATTTA
*
1614674 AACAAATATAA
1 AACAAACATAA
1614685 TTGTTTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 20 0.44
40 25 0.56
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (37 bp):
AACAAACATAACTATTTGAACAAACATTAATTATTTA
Found at i:1614677 original size:18 final size:18
Alignment explanation
Indices: 1614627--1614693 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
1614617 ACAAACATAA
1614627 TTAATTATTTAAACAAAC
1 TTAATTATTTAAACAAAC
* * *
1614645 ATAACTATTTGAACAAAC
1 TTAATTATTTAAACAAAC
*
1614663 TTAATTCTTTAAACAAA-
1 TTAATTATTTAAACAAAC
*
1614680 TATAATTGTTTAAA
1 T-TAATTATTTAAA
1614694 AGATTTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 1 0.03
18 39 0.98
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (18 bp):
TTAATTATTTAAACAAAC
Found at i:1628698 original size:26 final size:26
Alignment explanation
Indices: 1628664--1628719 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1628654 ATGTTTTATA
1628664 ATCACAATAGTACCAGAAAATTGATT
1 ATCACAATAGTACCAGAAAATTGATT
1628690 ATCACAATAGTACCAGAAAATTGATT
1 ATCACAATAGTACCAGAAAATTGATT
1628716 ATCA
1 ATCA
1628720 GAGAGGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (26 bp):
ATCACAATAGTACCAGAAAATTGATT
Found at i:1630178 original size:13 final size:13
Alignment explanation
Indices: 1630160--1630185 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1630150 AGGTAATTGC
1630160 TGTTATTGTAGGT
1 TGTTATTGTAGGT
1630173 TGTTATTGTAGGT
1 TGTTATTGTAGGT
1630186 GCTTTCATGC
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:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
TGTTATTGTAGGT
Found at i:1652204 original size:12 final size:12
Alignment explanation
Indices: 1652187--1652224 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1652177 ACAAGGTGGA
1652187 TTCTTTTCTTCT
1 TTCTTTTCTTCT
*
1652199 TTCTTTTATTCCT
1 TTCTTTTCTT-CT
1652212 TTCTTTTC-TCT
1 TTCTTTTCTTCT
1652223 TT
1 TT
1652225 TAAATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 10 0.43
13 9 0.39
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:1652214 original size:20 final size:20
Alignment explanation
Indices: 1652186--1652226 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1652176 GACAAGGTGG
*
1652186 ATTCTTTTCTTCTT-TCTTTT
1 ATTCCTTTCTT-TTCTCTTTT
1652206 ATTCCTTTCTTTTCTCTTTT
1 ATTCCTTTCTTTTCTCTTTT
1652226 A
1 A
1652227 AATTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTCCTTTCTTTTCTCTTTT
Found at i:1662615 original size:15 final size:15
Alignment explanation
Indices: 1662595--1662635 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1662585 NNNNNNNNGT
1662595 AATCACATTGCTTGC
1 AATCACATTGCTTGC
*
1662610 AATCACATTACTTGC
1 AATCACATTGCTTGC
1662625 AATCACATTGC
1 AATCACATTGC
1662636 ATTATAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (15 bp):
AATCACATTGCTTGC
Found at i:1662878 original size:12 final size:13
Alignment explanation
Indices: 1662855--1662884 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1662845 AATTTAGGAT
1662855 TCAAATTATTTAG
1 TCAAATTATTTAG
1662868 TCAAA-TATTTAG
1 TCAAATTATTTAG
1662880 TCAAA
1 TCAAA
1662885 ATCCACCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (13 bp):
TCAAATTATTTAG
Found at i:1670227 original size:23 final size:24
Alignment explanation
Indices: 1670180--1670228 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1670170 CAGTCTGTTC
*
1670180 TGAAGATTTCAAACCCACTATTTT
1 TGAAGATTTCAAACCCACTAGTTT
* *
1670204 TGAATATTTCAAA-CTACTAGTTT
1 TGAAGATTTCAAACCCACTAGTTT
1670227 TG
1 TG
1670229 TTCCTCAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (24 bp):
TGAAGATTTCAAACCCACTAGTTT
Found at i:1673856 original size:30 final size:31
Alignment explanation
Indices: 1673820--1673905 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 31
1673810 TGCAAATAAG
*
1673820 TTTCATGGGCTTGATT-TACAAAAAGAAAAA
1 TTTCATGGGCTAGATTGTACAAAAAGAAAAA
*
1673850 TTTCATGGGCTAGATTAGTA-AAAAA-AGAAA
1 TTTCATGGGCTAGATT-GTACAAAAAGAAAAA
* *
1673880 CTTCATGGGCTGGATTGT-CAAAAAGA
1 TTTCATGGGCTAGATTGTACAAAAAGA
1673906 TTGGATCTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 7 0.15
30 34 0.71
31 5 0.10
32 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (31 bp):
TTTCATGGGCTAGATTGTACAAAAAGAAAAA
Found at i:1694257 original size:16 final size:16
Alignment explanation
Indices: 1694236--1694266 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1694226 ATGCCAAAAG
1694236 TAAGAGCAAGAGTTTC
1 TAAGAGCAAGAGTTTC
1694252 TAAGAGCAAGAGTTT
1 TAAGAGCAAGAGTTT
1694267 TTGTGGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.26
Consensus pattern (16 bp):
TAAGAGCAAGAGTTTC
Found at i:1698592 original size:19 final size:20
Alignment explanation
Indices: 1698554--1698593 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1698544 AAACATTTGA
1698554 TAGATTGAAAGAGTGAAATG
1 TAGATTGAAAGAGTGAAATG
* *
1698574 TAGATT-AAAGTGTGGAATG
1 TAGATTGAAAGAGTGAAATG
1698593 T
1 T
1698594 TGGTCTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (20 bp):
TAGATTGAAAGAGTGAAATG
Found at i:1714548 original size:3 final size:3
Alignment explanation
Indices: 1714540--1714564 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1714530 AAAATCATGA
1714540 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1714565 TAACTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1715500 original size:21 final size:21
Alignment explanation
Indices: 1715474--1715516 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1715464 CTTTTGATTG
*
1715474 AAAATGTCGATCCATGACAAT
1 AAAATGTCGATCCATAACAAT
* *
1715495 AAAATGTTGGTCCATAACAAT
1 AAAATGTCGATCCATAACAAT
1715516 A
1 A
1715517 GGGACTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AAAATGTCGATCCATAACAAT
Found at i:1719994 original size:15 final size:15
Alignment explanation
Indices: 1719966--1720032 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
1719956 CGTTTGGTAC
1719966 ATTACAATGTAATGTG
1 ATTACAA-GTAATGTG
*
1719982 ATTACAGGTAATGT-
1 ATTACAAGTAATGTG
*
1719996 ATTTGCAAGTAATGTG
1 A-TTACAAGTAATGTG
* *
1720012 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
1720027 ATTACA
1 ATTACA
1720033 GGAAAAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 1 0.02
15 36 0.82
16 7 0.16
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:1720217 original size:30 final size:28
Alignment explanation
Indices: 1720183--1720772 Score: 170
Period size: 28 Copynumber: 21.1 Consensus size: 28
1720173 TATAAGTTTA
1720183 ATATATTTATATTTTTTAGTATTAATTTTT
1 ATATA-TTATATTTTTTA-TATTAATTTTT
* * *
1720213 ATATAATATCATTTCTTA-AATATATTTTT
1 ATATATTAT-ATTTTTTATATTA-ATTTTT
* * * *
1720242 A-ATATCATATATTTTATTTTTATTTATT
1 ATATATTATATTTTTTATATTAATTT-TT
* * *
1720270 AT-TATAATATTTTATAT-TTTATTTTT
1 ATATATTATATTTTTTATATTAATTTTT
1720296 AATATATT-TATATTTTTATTATTAA-TTTT
1 -ATATATTATAT-TTTTTA-TATTAATTTTT
* * *
1720325 ATATAATATCATTTCTTA-AATATATTTTT
1 ATATATTAT-ATTTTTTATATTA-ATTTTT
* * * * *
1720354 A-ATGTCATA-TATTTATTTTTATTTATT
1 ATATATTATATTTTTTATATTAATTT-TT
* *
1720381 AGTATA-TATATTTATT-T-TT-ATTTTA
1 A-TATATTATATTTTTTATATTAATTTTT
*
1720406 ATATATT-TATATTTTATTATTAATTTTT
1 ATATATTATATTTTTTA-TATTAATTTTT
* * *
1720434 ATATAATATCATATTTTA-AATATATTTTT
1 ATATATTAT-ATTTTTTATATTA-ATTTTT
* *
1720463 A-ATATCA-ATATTTTAT-TT--TTATTT
1 ATATATTATATTTTTTATATTAATT-TTT
* *
1720487 AT-TATTATAATTTTATATATTTTATTTTT
1 ATATATTAT-ATTTTTTATA-TTAATTTTT
1720516 AATATATT-TATATTTTTATTATTAATTTTT
1 -ATATATTATAT-TTTTTA-TATTAATTTTT
* * *
1720546 ATATAATATCATTTCTTA-AATATATTTTT
1 ATATATTAT-ATTTTTTATATTA-ATTTTT
* * * * *
1720575 A-ATGTCATATATTTTAT-TTTATTTAT
1 ATATATTATATTTTTTATATTAATTTTT
* * *
1720601 AT-TATAATATTTTATAT-TTTATTTTT
1 ATATATTATATTTTTTATATTAATTTTT
*
1720627 AATATATT-TATATTTATATTATTAATTTTT
1 -ATATATTATAT-TTTTTA-TATTAATTTTT
* * *
1720657 ATATAATATCATATTTTA-AATATATTTTT
1 ATATATTAT-ATTTTTTATATTA-ATTTTT
* * * *
1720686 A-ATGTCATATATTTTTTTTTATTTATTATT
1 ATATAT--TATA-TTTTTTATATTAATTTTT
* * *
1720716 ATA-AGTTTATATATTTTATTTTTATTTTT
1 ATATA--TTATATTTTTTATATTAATTTTT
1720745 -T-TA--ATATTTTTTATATTATATATTTT
1 ATATATTATATTTTTTATATTA-AT-TTTT
1720771 AT
1 AT
1720773 TTTAATTTGT
Statistics
Matches: 414, Mismatches: 82, Indels: 131
0.66 0.13 0.21
Matches are distributed among these distances:
23 2 0.00
24 30 0.07
25 5 0.01
26 60 0.14
27 47 0.11
28 90 0.22
29 86 0.21
30 80 0.19
31 13 0.03
32 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (28 bp):
ATATATTATATTTTTTATATTAATTTTT
Found at i:1720264 original size:6 final size:6
Alignment explanation
Indices: 1720253--1720326 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
1720243 ATATCATATA
* * * *
1720253 TTTTAT TTTTAT TTATTAT TATAAT ATTTTAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* * *
1720303 TTATAT TTTTAT TATTAA TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT
1720327 ATAATATCAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
5 3 0.06
6 34 0.64
7 16 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAT
Found at i:1720284 original size:20 final size:20
Alignment explanation
Indices: 1720259--1720660 Score: 94
Period size: 21 Copynumber: 18.4 Consensus size: 20
1720249 TATATTTTAT
1720259 TTTTAT-TTATTATTATAATA
1 TTTTATATT-TTATTATAATA
*
1720279 TTTTATATTTTATTTTTAATA
1 TTTTATATTTTA-TTATAATA
*
1720300 TATTTATATTTTTATTATTAATT
1 T-TTTATA-TTTTATTA-TAATA
*
1720323 TTATATAATATCATTTCTTA-AATA
1 TT-T-T-ATAT--TTTATTATAATA
* * * *
1720347 TATTTTTAATGTCA-TATATTTA
1 T-TTTAT-ATTTTATTATA-ATA
1720369 TTTT-TA-TTTATTAGTATATA
1 TTTTATATTTTATTA-TA-ATA
*
1720389 TATTTAT-TTTTATTTTAATA
1 T-TTTATATTTTATTATAATA
1720409 TATTTATATTTTATTATTAAT-
1 T-TTTATATTTTATTA-TAATA
** *
1720430 TTTTATATAATATCAT-AT-
1 TTTTATATTTTATTATAATA
*
1720448 TTTAAATATATTTTTAATATCAATA
1 TTT---TATA-TTTTATTAT-AATA
1720473 TTTTAT-TTTTATTTATTATTATAA
1 TTTTATATTTTA-TTA-TA--AT-A
*
1720497 TTTTATATATTTTATTTTTAATA
1 -TTT-TATATTTTA-TTATAATA
1720520 TATTTATATTTTTATTATTAAT-
1 T-TTTATA-TTTTATTA-TAATA
** * * *
1720542 TTTTATATAATATCAT-TTC
1 TTTTATATTTTATTATAATA
*
1720561 TTAAATATATTTTTAATGTCAT-ATA
1 TT--TTATA-TTTT-AT-T-ATAATA
1720586 TTTTATTTTATTTATATTATAATA
1 TTTTA---TATTT-TATTATAATA
*
1720610 TTTTATATTTTATTTTTAATA
1 TTTTATATTTTA-TTATAATA
1720631 TATTTATATTTATATTATTAAT-
1 T-TTTATATTT-TATTA-TAATA
1720653 TTTTATAT
1 TTTTATAT
1720661 AATATCATAT
Statistics
Matches: 289, Mismatches: 38, Indels: 109
0.66 0.09 0.25
Matches are distributed among these distances:
18 8 0.03
19 7 0.02
20 51 0.18
21 65 0.22
22 55 0.19
23 40 0.14
24 21 0.07
25 20 0.07
26 14 0.05
27 8 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTATATTTTATTATAATA
Found at i:1720482 original size:6 final size:6
Alignment explanation
Indices: 1720473--1720547 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
1720463 AATATCAATA
* * * *
1720473 TTTTAT TTTTAT TTATTAT TATAAT TTTATAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTAT
* *
1720523 TTATAT TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
1720548 ATAATATCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
5 3 0.06
6 33 0.61
7 15 0.28
8 3 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:1720499 original size:24 final size:24
Alignment explanation
Indices: 1720470--1720660 Score: 101
Period size: 21 Copynumber: 8.4 Consensus size: 24
1720460 TTTAATATCA
*
1720470 ATATTT-TATTTTTATTTATTATT
1 ATATTTATATTTTTATTTATTAAT
1720493 ATAATTTTATATATTTTATTT-TTAAT
1 AT-A-TTTATAT-TTTTATTTATTAAT
1720519 ATATTTATATTTTTA-TTATTAAT
1 ATATTTATATTTTTATTTATTAAT
* * *
1720542 -T-TTTATATAATATCATTTCTTAAAT
1 ATATTTATAT--TTTTATTTATT-AAT
* * * * *
1720567 ATATTTTTAATGTCATATATT--T
1 ATATTTATATTTTTATTTATTAAT
*
1720589 -TATTT-TATTTATA-TTA-TAAT
1 ATATTTATATTTTTATTTATTAAT
*
1720609 ATT-TTATA-TTTTATTT-TTAAT
1 ATATTTATATTTTTATTTATTAAT
*
1720630 ATATTTATATTTATA-TTATTAAT
1 ATATTTATATTTTTATTTATTAAT
1720653 -T-TTTATAT
1 ATATTTATAT
1720661 AATATCATAT
Statistics
Matches: 130, Mismatches: 18, Indels: 42
0.68 0.09 0.22
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 11 0.08
21 30 0.23
22 12 0.09
23 24 0.18
24 12 0.09
25 15 0.12
26 10 0.08
27 13 0.10
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (24 bp):
ATATTTATATTTTTATTTATTAAT
Found at i:1720568 original size:221 final size:222
Alignment explanation
Indices: 1720179--1720739 Score: 949
Period size: 221 Copynumber: 2.5 Consensus size: 222
1720169 AAAATATAAG
*
1720179 TTTAATATATTTATATTTTTTAGTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTA
1 TTTAATATATTTATA--TTTTATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTA
1720243 ATATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATTTTTAATATATTTAT
63 ATATCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATTTTTAATATATTTAT
1720307 ATTTTTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATA-TTTATT
127 ATTTTTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTA-T
1720371 TTTATTTATTAGTAT-ATATATTTAT-TTTTA-T
191 TTTATTTA-TAGTATAATAT-TTTATATTTTATT
1720402 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATA
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATA
1720467 TCA-ATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAATATATTTATATTT
66 TCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAATATATTTATATTT
1720531 TTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTA
131 TTATTATTAA-TTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTA
*
1720596 TTTATATTATAATATTTTATATTTTATT
195 TTTATAGTATAATATTTTATATTTTATT
1720624 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
1 TTTAATATATTTATATTT-TATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
* *
1720689 GTCATATATTTT-TTTTTATTTATTATTATAAGTTTATATATTTTATTTTTA
65 ATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTA
1720740 TTTTTTTAAT
Statistics
Matches: 325, Mismatches: 4, Indels: 18
0.94 0.01 0.05
Matches are distributed among these distances:
219 3 0.01
220 77 0.24
221 111 0.34
222 25 0.08
223 102 0.31
224 7 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (222 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATA
TCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAATATATTTATATTT
TTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTTTAT
TTATAGTATAATATTTTATATTTTATT
Found at i:1720618 original size:31 final size:29
Alignment explanation
Indices: 1720582--1720775 Score: 132
Period size: 31 Copynumber: 6.4 Consensus size: 29
1720572 TTTAATGTCA
*
1720582 TATATTTTATTTTATTTATATTATAATATTT
1 TATATTTTATTTT-TATATATTAT-ATATTT
1720613 TATATTTTATTTTTAATATATT-TATA-TT
1 TATATTTTATTTTT-ATATATTATATATTT
*
1720641 TATATTATTAATTTTTATATAATATCATATTT
1 TATATT-TT-ATTTTTATATATTAT-ATATTT
* * * *
1720673 TA-AATATATTTTTA-ATGTCATATATTT
1 TATATTTTATTTTTATATATTATATATTT
1720700 T-T-TTTTATTTATTATTATAAGTTTATATATTT
1 TATATTTTATTT-TTA-TAT-A--TTATATATTT
* * *
1720732 TAT-TTTTATTTTTTTAATATTTTTTATATTA
1 TATATTTTA--TTTTT-ATATATTATATATTT
1720763 TATATTTTATTTT
1 TATATTTTATTTT
1720776 AATTTGTTTT
Statistics
Matches: 131, Mismatches: 14, Indels: 37
0.72 0.08 0.20
Matches are distributed among these distances:
26 6 0.05
27 10 0.08
28 12 0.09
29 20 0.15
30 14 0.11
31 35 0.27
32 19 0.15
33 6 0.05
34 5 0.04
35 4 0.03
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (29 bp):
TATATTTTATTTTTATATATTATATATTT
Found at i:1720627 original size:111 final size:113
Alignment explanation
Indices: 1720179--1720739 Score: 916
Period size: 111 Copynumber: 5.0 Consensus size: 113
1720169 AAAATATAAG
*
1720179 TTTAATATATTTATATTTTTTAGTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
1720244 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
65 TGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
1720293 TTTAATATATTTATATTTTTATTATTAA-TTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
1720357 GTCATATA-TTTATTTTTATTTATTAGTAT-ATATATTTAT-TTTTA-T
66 GTCATATATTTTATTTTTATTTATTATTATAATAT-TTTATATTTTATT
1720402 TTTAATATATTTATA-TTTTATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
1720465 TATCA-ATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATT
65 TGTCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
1720513 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1720578 GTCATATATTTTA-TTTTATTTA-TATTATAATATTTTATATTTTATT
66 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
*
1720624 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
1720688 TGTCATATATTTT-TTTTTATTTATTATTATAAGT-TTATATATTTTATT
65 TGTCATATATTTTATTTTTATTTATTATTATAA-TATTTTATATTTTATT
1720736 TTTA
1 TTTA
1720740 TTTTTTTAAT
Statistics
Matches: 423, Mismatches: 8, Indels: 34
0.91 0.02 0.07
Matches are distributed among these distances:
108 17 0.04
109 76 0.18
110 18 0.04
111 145 0.34
112 131 0.31
113 21 0.05
114 15 0.04
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (113 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:1720679 original size:48 final size:42
Alignment explanation
Indices: 1720589--1720684 Score: 113
Period size: 43 Copynumber: 2.1 Consensus size: 42
1720579 TCATATATTT
*
1720589 TATTTTATTTATATTATAATATTTTATATTTTATTTTTAATA
1 TATTTTATTTATATTATAATATTTTATATTTTATTTTAAATA
1720631 TATTTATATTTATATTATTAAT-TTTTATATAATATCATATTTTAAATA
1 TATTT-TATTTATATTA-TAATATTTTATAT--T-T--TATTTTAAATA
1720679 TATTTT
1 TATTTT
1720685 TAATGTCATA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
42 5 0.11
43 19 0.41
44 4 0.09
45 1 0.02
46 1 0.02
47 1 0.02
48 15 0.33
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (42 bp):
TATTTTATTTATATTATAATATTTTATATTTTATTTTAAATA
Found at i:1720798 original size:38 final size:37
Alignment explanation
Indices: 1720699--1720786 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 37
1720689 GTCATATATT
* *
1720699 TTTTTTTATTTATTATTATAAGTTTATATATTTTATTTTTA
1 TTTTTTTA-ATATTATTAT-A--TTATATATTTTATTTTAA
*
1720740 TTTTTTTAATATTTTTTATATTATATATTTTATTTTAA
1 TTTTTTTAATA-TTATTATATTATATATTTTATTTTAA
1720778 TTTGTTTTA
1 TTT-TTTTA
1720787 CCTATATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 20 0.48
39 5 0.12
40 3 0.07
41 14 0.33
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (37 bp):
TTTTTTTAATATTATTATATTATATATTTTATTTTAA
Found at i:1720849 original size:26 final size:27
Alignment explanation
Indices: 1720737--1720859 Score: 69
Period size: 29 Copynumber: 4.4 Consensus size: 27
1720727 TATTTTATTT
* *
1720737 TTATTT-TTTTAATATTTTTTATATTATA
1 TTATTTATTTTAAT-TTTTAT-TCTTATA
*
1720765 -TATTTTATTTTAATTTGTT-TTACCTATA
1 TTA-TTTATTTTAATTT-TTATT-CTTATA
* *
1720793 TTATATAAATGTTAATTTTTTATAT-TT-TA
1 TTAT-T-TATTTTAA-TTTTTAT-TCTTATA
1720822 TT-TTTATTTTAATTTTTATTCTTATA
1 TTATTTATTTTAATTTTTATTCTTATA
*
1720848 TTATATATTTTA
1 TTATTTATTTTA
1720860 TTTAATATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 27
0.68 0.07 0.25
Matches are distributed among these distances:
24 1 0.01
25 9 0.12
26 10 0.14
27 12 0.16
28 12 0.16
29 16 0.22
30 9 0.12
31 4 0.05
32 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTATTTATTTTAATTTTTATTCTTATA
Found at i:1738093 original size:80 final size:82
Alignment explanation
Indices: 1737960--1738119 Score: 245
Period size: 80 Copynumber: 2.0 Consensus size: 82
1737950 GGCTTTAGCT
* * * *
1737960 TTTGCATACTACTTCTCTATTAAAGCCGAAGCTTAGATTGTTAATCTATATTTTAATTTGAGAAA
1 TTTGCAGACCACTTCTCCATTAAAGCCGAAGCTTAGATTGTTAATCTAAATTTTAATTTGAGAAA
1738025 AA-AATT-ATTAATTCC
66 AAGAATTAATTAATTCC
*
1738040 TTTGCAGACCACTTCTCCATTAATGCC-AATGCTTAGATTGTTAATCTAAATTTTAATTTGAGAA
1 TTTGCAGACCACTTCTCCATTAAAGCCGAA-GCTTAGATTGTTAATCTAAATTTTAATTTGAGAA
1738104 AAAGAATTAATTAATT
65 AAAGAATTAATTAATT
1738120 ATTAATTGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
79 2 0.03
80 59 0.82
81 4 0.06
82 7 0.10
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (82 bp):
TTTGCAGACCACTTCTCCATTAAAGCCGAAGCTTAGATTGTTAATCTAAATTTTAATTTGAGAAA
AAGAATTAATTAATTCC
Found at i:1740609 original size:2 final size:2
Alignment explanation
Indices: 1740602--1740634 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1740592 AAGCTCTCAC
*
1740602 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1740635 TTCCATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1745239 original size:22 final size:22
Alignment explanation
Indices: 1745189--1745232 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1745179 AATTGTACTA
*
1745189 AATATATCAAGCTTTATGTATAT
1 AATA-ATCAAGCTTTATGCATAT
1745212 AATAATCAAGCTTTATGCATA
1 AATAATCAAGCTTTATGCATA
1745233 CTATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
AATAATCAAGCTTTATGCATAT
Found at i:1748482 original size:19 final size:19
Alignment explanation
Indices: 1748458--1748497 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1748448 ACAAACTTAG
*
1748458 CTCCCTGTTCCCCATAATC
1 CTCCCTATTCCCCATAATC
*
1748477 CTCCCTATTCCCCATGATC
1 CTCCCTATTCCCCATAATC
1748496 CT
1 CT
1748498 ATCGTCGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.47, G:0.05, T:0.33
Consensus pattern (19 bp):
CTCCCTATTCCCCATAATC
Found at i:1751046 original size:21 final size:22
Alignment explanation
Indices: 1751007--1751049 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1750997 AGTGTATGCA
1751007 TTATTTATAATTGACAAATTAT
1 TTATTTATAATTGACAAATTAT
* *
1751029 TTATTT-TAATTTATAAATTAT
1 TTATTTATAATTGACAAATTAT
1751050 CTAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATTTATAATTGACAAATTAT
Found at i:1752912 original size:26 final size:26
Alignment explanation
Indices: 1752831--1752912 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
1752821 GTTTATAAAA
* *
1752831 ATATCAATATTTATCAATTGTGTAAG
1 ATATCAATATTTATCAATTATTTAAG
** * * ** * *
1752857 ATATTTATCTGTATTTATTA-TAAAA
1 ATATCAATATTTATCAATTATTTAAG
1752882 ATATCAATATTTATCAATTATTTAAG
1 ATATCAATATTTATCAATTATTTAAG
1752908 ATATC
1 ATATC
1752913 CAAAATCTAT
Statistics
Matches: 37, Mismatches: 18, Indels: 2
0.65 0.32 0.04
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (26 bp):
ATATCAATATTTATCAATTATTTAAG
Found at i:1752928 original size:51 final size:51
Alignment explanation
Indices: 1752823--1752929 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
1752813 TAATGTAAGT
* ** ** * *
1752823 TTATAAAAATATCAATATTTATCAATTGTGTAAGATATTTATCTGTATTTA
1 TTATAAAAATATCAATATTTATCAATTATGTAAGATATCAAAATCTATTAA
*
1752874 TTATAAAAATATCAATATTTATCAATTATTTAAGATATCCAAAATCTA-TAA
1 TTATAAAAATATCAATATTTATCAATTATGTAAGATAT-CAAAATCTATTAA
1752925 TTATA
1 TTATA
1752930 TATATTCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 43 0.91
52 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (51 bp):
TTATAAAAATATCAATATTTATCAATTATGTAAGATATCAAAATCTATTAA
Found at i:1753088 original size:15 final size:18
Alignment explanation
Indices: 1753050--1753089 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
1753040 AGTATTTTTA
1753050 ATTTTAATAGTATTGAAT
1 ATTTTAATAGTATTGAAT
*
1753068 AATTTAA-A-TATT-AAT
1 ATTTTAATAGTATTGAAT
1753083 ATTTTAA
1 ATTTTAA
1753090 GTTAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTAATAGTATTGAAT
Found at i:1753122 original size:16 final size:17
Alignment explanation
Indices: 1753081--1753120 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
1753071 TTAAATATTA
1753081 ATATTTTAAGTTAAAAT
1 ATATTTTAAGTTAAAAT
*
1753098 AAATTTTAAGTTAAATAT
1 ATATTTTAAGTTAAA-AT
1753116 ATATT
1 ATATT
1753121 AATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATTTTAAGTTAAAAT
Found at i:1761729 original size:22 final size:22
Alignment explanation
Indices: 1761667--1761738 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1761657 GTCATTGTCC
* *
1761667 AAAAATTAGTCACATAATGCCT
1 AAAAATCAGTCTCATAATGCCT
* * *
1761689 ACAATTCAGT-TACACAATGCCT
1 AAAAATCAGTCT-CATAATGCCT
*
1761711 AAAAATCAGTCTCATAATGTCT
1 AAAAATCAGTCTCATAATGCCT
1761733 AAAAAT
1 AAAAAT
1761739 AAAAAACGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (22 bp):
AAAAATCAGTCTCATAATGCCT
Found at i:1764421 original size:34 final size:34
Alignment explanation
Indices: 1764354--1764423 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
1764344 GTACCAATTG
* *
1764354 ATTAAAATTATATCTTGGATTGGAAATGTTAATA
1 ATTAAAATTATATCTTGGATTAGAAATGCTAATA
1764388 ATTAAAATTATATCTTGGATTAGAACA-GCTAATA
1 ATTAAAATTATATCTTGGATTAGAA-ATGCTAATA
1764422 AT
1 AT
1764424 CAAGAAACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (34 bp):
ATTAAAATTATATCTTGGATTAGAAATGCTAATA
Found at i:1771938 original size:22 final size:22
Alignment explanation
Indices: 1771883--1771938 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1771873 TTTTAAATAT
1771883 ATATTTATAAATAAAAAATTTAA
1 ATATTT-TAAATAAAAAATTTAA
* * *
1771906 ATATATAAAATAAATAA-TTAA
1 ATATTTTAAATAAAAAATTTAA
1771927 ATAATTTTAAAT
1 AT-ATTTTAAAT
1771939 TTTAATTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTTTAAATAAAAAATTTAA
Found at i:1773752 original size:25 final size:25
Alignment explanation
Indices: 1773718--1773780 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
1773708 TGATATTGAT
1773718 ATCATAGTTATCAGAATAGAACTGG
1 ATCATAGTTATCAGAATAGAACTGG
1773743 ATCATAGTTATCAGAATAGAACTGG
1 ATCATAGTTATCAGAATAGAACTGG
1773768 ATCATAGTTATCA
1 ATCATAGTTATCA
1773781 AAATCGGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (25 bp):
ATCATAGTTATCAGAATAGAACTGG
Found at i:1781581 original size:26 final size:24
Alignment explanation
Indices: 1781552--1781599 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1781542 TAATTGATGA
*
1781552 AAAAGAAATGAATTTAAAATATTTGT
1 AAAAG-AATGAATCTAAAA-ATTTGT
*
1781578 AAAAGACTGAATCTAAAAATTT
1 AAAAGAATGAATCTAAAAATTT
1781600 ACCGACGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 11 0.55
26 5 0.25
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.31
Consensus pattern (24 bp):
AAAAGAATGAATCTAAAAATTTGT
Found at i:1788791 original size:2 final size:2
Alignment explanation
Indices: 1788784--1788833 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1788774 TTCATCATTT
1788784 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
1788826 TA TA TA TA
1 TA TA TA TA
1788834 ACATGTCTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1799420 original size:27 final size:29
Alignment explanation
Indices: 1799367--1799420 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
1799357 TGTGTTTTAA
*
1799367 AATTAAATTTTTACATTTTTATCATATTT
1 AATTAAATTTTTACATTTATATCATATTT
* *
1799396 AATT-AATTTTT-TATTTATATTATAT
1 AATTAAATTTTTACATTTATATCATAT
1799421 CGTATGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 7 0.32
29 4 0.18
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
AATTAAATTTTTACATTTATATCATATTT
Found at i:1817687 original size:20 final size:21
Alignment explanation
Indices: 1817631--1817687 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
1817621 ATAAATATTA
*
1817631 TCAATATTGTTAAAATACATT
1 TCAATATTTTTAAAATACATT
** * *
1817652 TCAA-AAATATATAATACATT
1 TCAATATTTTTAAAATACATT
1817672 T-AATATTTTTAAAATA
1 TCAATATTTTTAAAATA
1817688 TATGTTAAAG
Statistics
Matches: 26, Mismatches: 9, Indels: 3
0.68 0.24 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TCAATATTTTTAAAATACATT
Found at i:1820726 original size:16 final size:17
Alignment explanation
Indices: 1820693--1820730 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1820683 TTATGTATTC
1820693 TTTTTCCTTCACTCAGA
1 TTTTTCCTTCACTCAGA
* *
1820710 TTTTTCTTTCA-TGAGA
1 TTTTTCCTTCACTCAGA
1820726 TTTTT
1 TTTTT
1820731 TCTTAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (17 bp):
TTTTTCCTTCACTCAGA
Found at i:1821399 original size:20 final size:18
Alignment explanation
Indices: 1821374--1821414 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1821364 AATTTTAGTT
1821374 ATAAATTATTAATATTTTAA
1 ATAAATTA-TAA-ATTTTAA
1821394 ATAAATTATAAATTTTAA
1 ATAAATTATAAATTTTAA
1821412 ATA
1 ATA
1821415 TTTGAATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATTATAAATTTTAA
Found at i:1822445 original size:17 final size:17
Alignment explanation
Indices: 1822417--1822472 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1822407 CTTAAACAAA
*
1822417 AGAAAGAAAAAGAAAAG
1 AGAAAAAAAAAGAAAAG
*
1822434 AGATAAAAAAAG-AAAG
1 AGAAAAAAAAAGAAAAG
* *
1822450 CAAAAAAAAAAAGAAATG
1 -AGAAAAAAAAAGAAAAG
1822468 AGAAA
1 AGAAA
1822473 TATACTTGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 4 0.13
17 24 0.77
18 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAG
Found at i:1826710 original size:35 final size:35
Alignment explanation
Indices: 1826656--1826725 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1826646 TTTAAACAGA
* * *
1826656 TCTCATGAACCCAATAAATATTGAATGAGACCAAC
1 TCTCATGAACCCAAAAAATAGTGAATCAGACCAAC
* *
1826691 TCTCATGAACTCAAAAAATAGTGGATCAGACCAAC
1 TCTCATGAACCCAAAAAATAGTGAATCAGACCAAC
1826726 ACGACCCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (35 bp):
TCTCATGAACCCAAAAAATAGTGAATCAGACCAAC
Found at i:1831189 original size:2 final size:2
Alignment explanation
Indices: 1831182--1831212 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1831172 TACTTCACTG
1831182 TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1831213 CGCTACGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1835046 original size:29 final size:30
Alignment explanation
Indices: 1835013--1835069 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
1835003 TTCCCCACCC
*
1835013 ATTTCCCTCCAAAA-TTTTCCCTCCAAAGG
1 ATTTCCCTCCAAAAGATTTCCCTCCAAAGG
*
1835042 ATTTCCCTCCAAAAGATTTCCTTCCAAA
1 ATTTCCCTCCAAAAGATTTCCCTCCAAA
1835070 ACCATTTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.32
Consensus pattern (30 bp):
ATTTCCCTCCAAAAGATTTCCCTCCAAAGG
Found at i:1835070 original size:15 final size:15
Alignment explanation
Indices: 1835013--1835070 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
1835003 TTCCCCACCC
1835013 ATTTCCCTCCAAAA-
1 ATTTCCCTCCAAAAG
* *
1835027 TTTTCCCTCCAAAGG
1 ATTTCCCTCCAAAAG
1835042 ATTTCCCTCCAAAAG
1 ATTTCCCTCCAAAAG
*
1835057 ATTTCCTTCCAAAA
1 ATTTCCCTCCAAAA
1835071 CCATTTGGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (15 bp):
ATTTCCCTCCAAAAG
Found at i:1835151 original size:27 final size:27
Alignment explanation
Indices: 1835121--1835178 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1835111 GGAGGGAAAT
1835121 CCCTACATGGGTCTTGGTGGGCTGGCA
1 CCCTACATGGGTCTTGGTGGGCTGGCA
1835148 CCCTACATGGGTCTTGGTGGGCTGGCA
1 CCCTACATGGGTCTTGGTGGGCTGGCA
1835175 CCCT
1 CCCT
1835179 CTTGGGCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.10, C:0.29, G:0.34, T:0.26
Consensus pattern (27 bp):
CCCTACATGGGTCTTGGTGGGCTGGCA
Found at i:1835223 original size:14 final size:14
Alignment explanation
Indices: 1835204--1835231 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1835194 GGGTCTGGAC
1835204 TGTGGCCCGTGACA
1 TGTGGCCCGTGACA
1835218 TGTGGCCCGTGACA
1 TGTGGCCCGTGACA
1835232 AATGTACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (14 bp):
TGTGGCCCGTGACA
Found at i:1835923 original size:2 final size:2
Alignment explanation
Indices: 1835916--1835947 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1835906 GGGTTTGCAG
1835916 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
1835948 TAGTTTAAAG
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:1836673 original size:19 final size:19
Alignment explanation
Indices: 1836649--1836688 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1836639 GCAAGGTTTA
1836649 TTGACAAATCCATCTCACT
1 TTGACAAATCCATCTCACT
*
1836668 TTGACAAATCCATCTTACT
1 TTGACAAATCCATCTCACT
1836687 TT
1 TT
1836689 AAGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.38
Consensus pattern (19 bp):
TTGACAAATCCATCTCACT
Found at i:1844539 original size:16 final size:16
Alignment explanation
Indices: 1844504--1844545 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1844494 ATAAAAATTT
*
1844504 ATTAATTAATTGAGAC
1 ATTAATTAATTGAGAA
* *
1844520 ATTATTTAATTGATAA
1 ATTAATTAATTGAGAA
1844536 ATTAA-TAATT
1 ATTAATTAATT
1844546 TATTAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAATTAATTGAGAA
Found at i:1850883 original size:12 final size:13
Alignment explanation
Indices: 1850866--1850898 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1850856 TGAGTAATTT
1850866 TTATAT-TATACC
1 TTATATATATACC
1850878 TTATATGATATACC
1 TTATAT-ATATACC
1850892 TTATATA
1 TTATATA
1850899 GTAAAACCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 1 0.05
14 12 0.63
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (13 bp):
TTATATATATACC
Found at i:1852197 original size:21 final size:22
Alignment explanation
Indices: 1852152--1852203 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1852142 TTCAATGATC
1852152 TTTAAACTTGTTTGAATGAGTT
1 TTTAAACTTGTTTGAATGAGTT
* *
1852174 TTTAAACTTGTTTTAAT-TGTT
1 TTTAAACTTGTTTGAATGAGTT
1852195 TTTAAACTT
1 TTTAAACTT
1852204 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.56
Consensus pattern (22 bp):
TTTAAACTTGTTTGAATGAGTT
Found at i:1852307 original size:21 final size:21
Alignment explanation
Indices: 1852294--1852337 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1852284 ATAATATTTG
*
1852294 AACTTGTTTAAATAGCTTTTA
1 AACTTGTTTAAATAGATTTTA
1852315 AACTTGTTTAAATTA-ATTTTA
1 AACTTGTTTAAA-TAGATTTTA
1852336 AA
1 AA
1852338 TCTCCCTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
AACTTGTTTAAATAGATTTTA
Found at i:1856762 original size:16 final size:17
Alignment explanation
Indices: 1856733--1856765 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1856723 TTAAAAGAAG
1856733 GAAAAAAATGAAAATCAT
1 GAAAAAAA-GAAAATCAT
1856751 GAAAAAAA-AAAATCA
1 GAAAAAAAGAAAATCA
1856766 GACGAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.12
Consensus pattern (17 bp):
GAAAAAAAGAAAATCAT
Found at i:1863758 original size:6 final size:6
Alignment explanation
Indices: 1863747--1863773 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1863737 AGGTGATTTG
1863747 ATTGGA ATTGGA ATTGGA ATTGGA ATT
1 ATTGGA ATTGGA ATTGGA ATTGGA ATT
1863774 AGACTTCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (6 bp):
ATTGGA
Found at i:1869840 original size:13 final size:13
Alignment explanation
Indices: 1869824--1869848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1869814 AAAAAAAATA
1869824 CATTAAAAGCATC
1 CATTAAAAGCATC
1869837 CATTAAAAGCAT
1 CATTAAAAGCAT
1869849 TGGCTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
CATTAAAAGCATC
Found at i:1882470 original size:30 final size:30
Alignment explanation
Indices: 1882429--1882493 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1882419 CAATCAAACT
*
1882429 CTTATAGTTTTATTTTTAACCAATTAAGCC
1 CTTATAGTTTTATTTTTAACCAAATAAGCC
* *
1882459 CTTATATTTTTATTTTTGACCAAATAAGCC
1 CTTATAGTTTTATTTTTAACCAAATAAGCC
*
1882489 ATTAT
1 CTTAT
1882494 GACTAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (30 bp):
CTTATAGTTTTATTTTTAACCAAATAAGCC
Found at i:1891683 original size:26 final size:26
Alignment explanation
Indices: 1891651--1891745 Score: 113
Period size: 26 Copynumber: 3.7 Consensus size: 26
1891641 CCATCCACGC
*
1891651 TGATGGTAAAATTATCTATATACTTT
1 TGATGGCAAAATTATCTATATACTTT
* * *
1891677 TGGTGGTAAAATTATCTATACACTTT
1 TGATGGCAAAATTATCTATATACTTT
*
1891703 TGATGACAAAATTAT-TCAT-TCACTTT
1 TGATGGCAAAATTATCT-ATAT-ACTTT
1891729 TGATGGCAAAATTATCT
1 TGATGGCAAAATTATCT
1891746 TTAAAATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.02
26 57 0.97
27 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (26 bp):
TGATGGCAAAATTATCTATATACTTT
Found at i:1899245 original size:14 final size:15
Alignment explanation
Indices: 1899228--1899256 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1899218 TAATTTAGGG
1899228 TTAAAATTT-TAAAA
1 TTAAAATTTATAAAA
1899242 TTAAAATTTATAAAA
1 TTAAAATTTATAAAA
1899257 CGAGAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATTTATAAAA
Found at i:1900027 original size:2 final size:2
Alignment explanation
Indices: 1900014--1900062 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
1900004 CAAACTACTG
* ** *
1900014 AT AT AT AC AT AT AT GC AT AC 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
1900056 AT AT AT A
1 AT AT AT A
1900063 AAACCATTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1903476 original size:2 final size:2
Alignment explanation
Indices: 1903469--1903501 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1903459 CTCATCTTTC
1903469 CT CT CT CT -T CT CT CT CT C- CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1903502 ACACACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1903483 original size:11 final size:11
Alignment explanation
Indices: 1903469--1903498 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1903459 CTCATCTTTC
1903469 CTCTCTCTTCT
1 CTCTCTCTTCT
*
1903480 CTCTCTCCTCT
1 CTCTCTCTTCT
1903491 CTCTCTCT
1 CTCTCTCT
1903499 CTCACACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCTCTTCT
Found at i:1913917 original size:119 final size:120
Alignment explanation
Indices: 1913735--1913950 Score: 292
Period size: 119 Copynumber: 1.8 Consensus size: 120
1913725 TTTTTTATCT
* * * *
1913735 TTTTTTTTTCAAGATATCTCAAAATGAAAATTAAAATTTAAACTTAATCTCATGCAGTCTTAAAA
1 TTTTTTTTTCAAGATATCTCAAAATGAAAATTAAAATATAAACCTAACCTCATACAGTCTTAAAA
* *
1913800 TCTGAAAATATAACTTAAGTAAGTTTATAAATCATAGATCCACATTAACTCAAAA
66 TCTGAAAATAAAACTTAAGTAAGCTTATAAATCATAGATCCACATTAACTCAAAA
* * * ** *
1913855 TTTTTTTTTC-AGATATTTCAAAATGAAATTTAAAATATAAGCCTAACCTTGTACGGGT-TTAAA
1 TTTTTTTTTCAAGATATCTCAAAATGAAAATTAAAATATAAACCTAACCTCATAC-AGTCTTAAA
*
1913918 TTCTGAAAATAAAACTTAAGTAAGCTTATAAAT
65 ATCTGAAAATAAAACTTAAGTAAGCTTATAAAT
1913951 TACGGATCTA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
119 70 0.85
120 12 0.15
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (120 bp):
TTTTTTTTTCAAGATATCTCAAAATGAAAATTAAAATATAAACCTAACCTCATACAGTCTTAAAA
TCTGAAAATAAAACTTAAGTAAGCTTATAAATCATAGATCCACATTAACTCAAAA
Found at i:1914206 original size:112 final size:113
Alignment explanation
Indices: 1914009--1914215 Score: 292
Period size: 112 Copynumber: 1.8 Consensus size: 113
1913999 AGACCCATGT
* * * *
1914009 TTATATACTCAAGACCCATCTCATCTCTTACTGATGTAAGATTTGTGACATTTTATCCCACTTAA
1 TTATATACCCAAGACACATCCCATCTCTTACTGATGTAAGATTTGTGACATTTTATCCCACATAA
** *
1914074 TTATGCAATGCCTTTATGCACTAGC-CTTTTACTTGTAGAGGAGAGAA
66 TTATGCAACACCCTTATGCACTAGCTCTTTTACTTGTAGAGGAGAGAA
* * *
1914121 TTATATACCCAAGACACATCCCATTTCTTACTGATGTGAGATTTGTGATATTTTA-CCTCACATA
1 TTATATACCCAAGACACATCCCATCTCTTACTGATGTAAGATTTGTGACATTTTATCC-CACATA
*
1914185 ATTGTGCAACACCCTTATGCACTAGCTCTTT
65 ATTATGCAACACCCTTATGCACTAGCTCTTT
1914216 ACTCACAGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
111 2 0.02
112 76 0.93
113 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (113 bp):
TTATATACCCAAGACACATCCCATCTCTTACTGATGTAAGATTTGTGACATTTTATCCCACATAA
TTATGCAACACCCTTATGCACTAGCTCTTTTACTTGTAGAGGAGAGAA
Found at i:1927754 original size:39 final size:39
Alignment explanation
Indices: 1927711--1927786 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
1927701 TGGTGACGAA
* **
1927711 GCTGCTGCTGTCGCTGAAGTTCCAACTGTTGCTGCTGCT
1 GCTGCTGCTGCCGCTGAAGTTCCAACTGCCGCTGCTGCT
1927750 GCTGCTGCTGCCGCTGAAGTTCCAACTGCCGCTGCTG
1 GCTGCTGCTGCCGCTGAAGTTCCAACTGCCGCTGCTG
1927787 TTGATACTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.11, C:0.32, G:0.29, T:0.29
Consensus pattern (39 bp):
GCTGCTGCTGCCGCTGAAGTTCCAACTGCCGCTGCTGCT
Found at i:1927786 original size:30 final size:30
Alignment explanation
Indices: 1927745--1927804 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1927735 ACTGTTGCTG
* * *
1927745 CTGCTGCTGCTGCTGCCGCTGAAGTTCCAA
1 CTGCCGCTGCTGCTGACACTGAAGTTCCAA
* *
1927775 CTGCCGCTGCTGTTGATACTGAAGTTCCAA
1 CTGCCGCTGCTGCTGACACTGAAGTTCCAA
1927805 AAGATGTTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.30, G:0.25, T:0.28
Consensus pattern (30 bp):
CTGCCGCTGCTGCTGACACTGAAGTTCCAA
Found at i:1932229 original size:2 final size:2
Alignment explanation
Indices: 1932222--1932253 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1932212 ATGATTTTGC
*
1932222 AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1932254 GAATTGCTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1945766 original size:4 final size:4
Alignment explanation
Indices: 1945752--1945781 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1945742 TCAGTTTTTC
*
1945752 CTTT TTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1945782 CCAGACATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
CTTT
Found at i:1952806 original size:2 final size:2
Alignment explanation
Indices: 1952799--1952827 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1952789 TGAAAATGAA
1952799 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1952828 TGCCGCCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1960034 original size:14 final size:15
Alignment explanation
Indices: 1960017--1960052 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1960007 AACAAAAACA
1960017 AAATAAAAC-TAAAT
1 AAATAAAACATAAAT
1960031 AAAT-AAACATAAAT
1 AAATAAAACATAAAT
1960045 AAATAAAA
1 AAATAAAA
1960053 TGAGTAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 13 0.65
15 3 0.15
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAAACATAAAT
Found at i:1964380 original size:181 final size:182
Alignment explanation
Indices: 1964001--1964773 Score: 687
Period size: 181 Copynumber: 4.1 Consensus size: 182
1963991 TGTGTATATG
* * * * * * *
1964001 GTGACTTATTGTTATGTATTGCGTGACGTTGGGTCAG-TACATGACTAGTTATGTTGGCATAACG
1 GTGACTGATTTTTATGTATTGCGTGACATTGGATCAGTTACGTGACTGGTTATGTTGGCATAATG
* * * * * * * **
1964065 TGAGTAGATATTA-AGCGTCGAATGACTTATTATTAGGTATTGCAAGATTGGAGGTGTGTGACTT
66 TGAGTGGATATTACA-CATTGAATGACTTATTATTAGGTATTACGAGACTGGAGATGCATGACTT
* * * * * * *
1964129 GTGCAATTCATCTCTTATTTTAAGGCTTTTGTTCAGTAGTTTGTAAGTATTGC
130 GTGCAATTCATCTCTTGTTTTGAGGCTTTTGTTCAATAGTTTGTAGGCACTAC
* * * *
1964182 ATGACTTG-TTGTTATGTATTGTGTGACATTGGATC-GTTACGTGACTGGTTATGTTAGCATAAT
1 GTGAC-TGATTTTTATGTATTGCGTGACATTGGATCAGTTACGTGACTGGTTATGTTGGCATAAT
* * * * *
1964245 GTGAGTGGATATTACACATTGAGTGACTTATTAGTAAGTATTACGAGACTGAAGGTGCATGACTT
65 GTGAGTGGATATTACACATTGAATGACTTATTATTAGGTATTACGAGACTGGAGATGCATGACTT
**
1964310 GTGCAATTCATCTAC-TGTTTTGAGAATTTTGTTCAATAGTTTGTAGGCACTAC
130 GTGCAATTCATCT-CTTGTTTTGAGGCTTTTGTTCAATAGTTTGTAGGCACTAC
* ** *
1964363 GTGATTGATTTTTATGTATTACATGACCCGTTGTTATGTGTTGCGTGACATTTCGCTATTACGTG
1 GTGACTGATTTTTATGTA-T---TG---CG-TGACAT-TG--G-AT--CA----G---TTACGTG
** * * *
1964428 ACTTATTATGTTGGCACAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGGTATTGCG
45 ACTGGTTATGTTGGCATAATGTGAGTGGATATTACACATTGAATGACTTATTATTAGGTATTACG
* * * * * *
1964493 AGACTGGAGATGCGTGACTTGTGTAATTCATCTCTTGTTTTGAGGTTTTTGTTTACTAGTTTTTA
110 AGACTGGAGATGCATGACTTGTGCAATTCATCTCTTGTTTTGAGGCTTTTGTTCAATAGTTTGTA
*
1964558 GGCACTGC
175 GGCACTAC
* * *
1964566 GTGACT-ATTTTTTATGTATTACGTGACATTGG-GCTGTTACGTGACTGGTTATGTTGGCATAAT
1 GTGACTGA-TTTTTATGTATTGCGTGACATTGGATCAGTTACGTGACTGGTTATGTTGGCATAAT
** * * * **
1964629 GTGAGTGGATATTATGCATTGAGTGACTAATTATTAGGTATTATGAGACTGCTGATGCATGACTT
65 GTGAGTGGATATTACACATTGAATGACTTATTATTAGGTATTACGAGACTGGAGATGCATGACTT
* * *
1964694 GTGCAATTCATCTATTGTTTTGAGGCTTTTGTTCATTAGTTTTTAGGCACTAC
130 GTGCAATTCATCTCTTGTTTTGAGGCTTTTGTTCAATAGTTTGTAGGCACTAC
* *
1964747 GTGACTGGTTTTTATATATTGCGTGAC
1 GTGACTGATTTTTATGTATTGCGTGAC
1964774 TTGTTGTTAT
Statistics
Matches: 480, Mismatches: 82, Indels: 60
0.77 0.13 0.10
Matches are distributed among these distances:
180 3 0.01
181 306 0.64
182 4 0.01
184 1 0.00
185 2 0.00
188 2 0.00
189 4 0.01
190 2 0.00
192 2 0.00
193 1 0.00
194 2 0.00
195 5 0.01
196 2 0.00
199 1 0.00
200 1 0.00
202 3 0.01
203 139 0.29
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (182 bp):
GTGACTGATTTTTATGTATTGCGTGACATTGGATCAGTTACGTGACTGGTTATGTTGGCATAATG
TGAGTGGATATTACACATTGAATGACTTATTATTAGGTATTACGAGACTGGAGATGCATGACTTG
TGCAATTCATCTCTTGTTTTGAGGCTTTTGTTCAATAGTTTGTAGGCACTAC
Found at i:1964545 original size:203 final size:203
Alignment explanation
Indices: 1964218--1964592 Score: 529
Period size: 203 Copynumber: 1.8 Consensus size: 203
1964208 CATTGGATCG
* * *
1964218 TTACGTGACTGGTTATGTTAGCATAATGTGAGTGGATATTACACATTGAGTGACTTATTAGTAAG
1 TTACGTGACTGATTATGTTAGCACAATGTGAGTGGATATTACACATTGAATGACTTATTAGTAAG
*
1964283 TATTACGAGACTGAAGGTGCATGACTTGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATA
66 TATTACGAGACTGAAGATGCATGACTTGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATA
*
1964348 GTTTGTAGGCACTACGTGATTGA-TTTTTATGTATTACATGACCCGTTGTTATGTGTTGCGTGAC
131 GTTTGTAGGCACTACGTGACT-ATTTTTTATGTATTACATGACCCGTTGTTATGTGTTGCGTGAC
1964412 ATTTCGCTA
195 ATTTCGCTA
* * * * *
1964421 TTACGTGACTTATTATGTTGGCACAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGG
1 TTACGTGACTGATTATGTTAGCACAATGTGAGTGGATATTACACATTGAATGACTTATTAGTAAG
* * * * ** * *
1964486 TATTGCGAGACTGGAGATGCGTGACTTGTGTAATTCATCT-CTTGTTTTGAGGTTTTTGTTTACT
66 TATTACGAGACTGAAGATGCATGACTTGTGCAATTCATCTAC-TGTTTTGAGAATTTTGTTCAAT
* * *
1964550 AGTTTTTAGGCACTGCGTGACTATTTTTTATGTATTACGTGAC
130 AGTTTGTAGGCACTACGTGACTATTTTTTATGTATTACATGAC
1964593 ATTGGGCTGT
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
202 2 0.01
203 147 0.99
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.41
Consensus pattern (203 bp):
TTACGTGACTGATTATGTTAGCACAATGTGAGTGGATATTACACATTGAATGACTTATTAGTAAG
TATTACGAGACTGAAGATGCATGACTTGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATA
GTTTGTAGGCACTACGTGACTATTTTTTATGTATTACATGACCCGTTGTTATGTGTTGCGTGACA
TTTCGCTA
Found at i:1964726 original size:384 final size:384
Alignment explanation
Indices: 1964049--1964953 Score: 1215
Period size: 384 Copynumber: 2.4 Consensus size: 384
1964039 ACATGACTAG
* * * * * * *
1964049 TTATGTTGGCATAACGTGAGTAGATATTAAGCGTCGAATGACTTATTATTAGGTATTGCAAGATT
1 TTATGTTGGCATAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGGTATTGCGAGACT
* * * * * * * * * *
1964114 GGAGGTGTGTGACTTGTGCAATTCATCTCTTATTTTAAGGCTTTTGTTCAGTAGTTTGTAAGTAT
66 GGAGGTGAGTGACTTGTGTAATTCATCTCTTGTTTTAAGGTTTTTGTTTACTAGTTTTTAGGCAC
**
1964179 TGCATGACTTGTTGTTATGTATTGTGTGACATTGGATCGTTACGTGACTGGTTATGTTAGCATAA
131 TGCATGACTTGTTGTTATGTATTACGTGACATTGGATCGTTACGTGACTGGTTATGTTAGCATAA
* *
1964244 TGTGAGTGGATATTACACATTGAGTGACTTATTAGTAAGTATTACGAGACTGAAGGTGCATGACT
196 TGTGAGTGGATATTACACATTGAGTGACTAATTAGTAAGTATTACGAGACTGAAGATGCATGACT
*
1964309 TGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATAGTTTGTAGGCACTACGTGATTGATTT
261 TGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATAGTTTGTAGGCACTACGTGACTGATTT
* * *
1964374 TTATGTATTACATGACCCGTTGTTATGTGTTGCGTGACATTTCGCTATTACGTGACTT-A
326 TTATATATTACATGACCCGTTGTTATGTATTGCGTGACATTACGCTATTACGTGA-TTGA
*
1964433 TTATGTTGGCACAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGGTATTGCGAGACT
1 TTATGTTGGCATAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGGTATTGCGAGACT
* * *
1964498 GGAGATGCGTGACTTGTGTAATTCATCTCTTGTTTTGAGGTTTTTGTTTACTAGTTTTTAGGCAC
66 GGAGGTGAGTGACTTGTGTAATTCATCTCTTGTTTTAAGGTTTTTGTTTACTAGTTTTTAGGCAC
* * * *
1964563 TGCGTGACTAT-TTTTTATGTATTACGTGACATTGG-GCTGTTACGTGACTGGTTATGTTGGCAT
131 TGCATGACT-TGTTGTTATGTATTACGTGACATTGGATC-GTTACGTGACTGGTTATGTTAGCAT
** * * * **
1964626 AATGTGAGTGGATATTATGCATTGAGTGACTAATTATTAGGTATTATGAGACTGCTGATGCATGA
194 AATGTGAGTGGATATTACACATTGAGTGACTAATTAGTAAGTATTACGAGACTGAAGATGCATGA
* ** * * *
1964691 CTTGTGCAATTCATCTATTGTTTTGAGGCTTTTGTTCATTAGTTTTTAGGCACTACGTGACTGGT
259 CTTGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATAGTTTGTAGGCACTACGTGACTGAT
* * ** * * *
1964756 TTTTATATATTGCGTGACTTGTTGTTATGTATTGCGTGACATTAGGCTATTATGTGATTGG
324 TTTTATATATTACATGACCCGTTGTTATGTATTGCGTGACATTACGCTATTACGTGATTGA
* *
1964817 TTATGTTGGCATAATGTGAGTGGATATTACGCATTGAGTGACTTATTCTTAGGTATTGCGAGACT
1 TTATGTTGGCATAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGGTATTGCGAGACT
* * *
1964882 -GACGGTGAGTGACTTGTTTAATTCATCTCTTGTTTTAAGGTTTTAGTTTACTAATTTTTAGGCA
66 GGA-GGTGAGTGACTTGTGTAATTCATCTCTTGTTTTAAGGTTTTTGTTTACTAGTTTTTAGGCA
*
1964946 TTGCATGA
130 CTGCATGA
1964954 ATGTGTATTA
Statistics
Matches: 454, Mismatches: 63, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
383 5 0.01
384 448 0.99
385 1 0.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (384 bp):
TTATGTTGGCATAATGTGAGTGGATATTACGCATTGAATGACTTATTATTAGGTATTGCGAGACT
GGAGGTGAGTGACTTGTGTAATTCATCTCTTGTTTTAAGGTTTTTGTTTACTAGTTTTTAGGCAC
TGCATGACTTGTTGTTATGTATTACGTGACATTGGATCGTTACGTGACTGGTTATGTTAGCATAA
TGTGAGTGGATATTACACATTGAGTGACTAATTAGTAAGTATTACGAGACTGAAGATGCATGACT
TGTGCAATTCATCTACTGTTTTGAGAATTTTGTTCAATAGTTTGTAGGCACTACGTGACTGATTT
TTATATATTACATGACCCGTTGTTATGTATTGCGTGACATTACGCTATTACGTGATTGA
Done.