Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 6 of 438
Found at i:1693162 original size:2 final size:2
Alignment explanation
Indices: 1693157--1693337 Score: 104
Period size: 2 Copynumber: 95.5 Consensus size: 2
1693147 TAAATACTAT
1693157 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
* * * * * *
1693199 AA TA CCA TA T- TG TG TA TA TA T- TA T- TA T- TA CA AA T- TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1693236 TA CTA T- TGC TA GTA T- TA T- TA TA -A CTA T- TA T- TA TA T- TA
1 TA -TA TA T-A TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
1693273 -A TG TA TA T- TT TA TG TA TA TA TG TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1693313 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1693338 TTGTACATAT
Statistics
Matches: 141, Mismatches: 18, Indels: 40
0.71 0.09 0.20
Matches are distributed among these distances:
1 15 0.11
2 119 0.84
3 7 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1693165 original size:39 final size:39
Alignment explanation
Indices: 1693093--1693167 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1693083 TTTATATATA
* * *
1693093 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
1693132 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
1693168 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Found at i:1693389 original size:15 final size:15
Alignment explanation
Indices: 1693369--1693398 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1693359 ATTATTGTTG
1693369 TATATTTTTTATGTA
1 TATATTTTTTATGTA
1693384 TATATTTTTTATGTA
1 TATATTTTTTATGTA
1693399 CGTTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TATATTTTTTATGTA
Found at i:1694665 original size:127 final size:127
Alignment explanation
Indices: 1694439--1694671 Score: 396
Period size: 127 Copynumber: 1.8 Consensus size: 127
1694429 CTCAAAATTT
* * *
1694439 TTCAAAATAAAGGTAATGTTCGGTATTTAAAGAATTCGAAGAATCGTTCCCTAACGTACTGGGTT
1 TTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGAGTT
1694504 TCACTTTCTTTGTTTGTCTTGAATAGTCGAATATCCTCTTACCAGTTCACTCTAAAAAAAAA
66 TCACTTTCTTTGTTTGTCTTGAATAGTCGAATATCCTCTTACCAGTTCACTCTAAAAAAAAA
1694566 TTCAAAAT-AAGAGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGAGT
1 TTCAAAATAAAG-GCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGAGT
** *
1694630 TTTGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
65 TTCACTTTCTTTGTTTGTCTTGAATAGTCGAATATCCTCTTA
1694672 AGGCTAAAAC
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
126 3 0.03
127 96 0.97
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (127 bp):
TTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGAGTT
TCACTTTCTTTGTTTGTCTTGAATAGTCGAATATCCTCTTACCAGTTCACTCTAAAAAAAAA
Found at i:1697173 original size:33 final size:33
Alignment explanation
Indices: 1697131--1697200 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1697121 GTAAAAAGTA
1697131 TATGCATGCATTCGTCCATTCGTCAATTAGGGT
1 TATGCATGCATTCGTCCATTCGTCAATTAGGGT
1697164 TATGCATGCATTCGTCCATTCGTCAATTAGGGT
1 TATGCATGCATTCGTCCATTCGTCAATTAGGGT
1697197 TATG
1 TATG
1697201 ATGAAACCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (33 bp):
TATGCATGCATTCGTCCATTCGTCAATTAGGGT
Found at i:1700476 original size:56 final size:58
Alignment explanation
Indices: 1700405--1700514 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 58
1700395 CATGCACATG
* * *
1700405 ATCAAACTGGGAATCACTTTAATTTAGTGGCAATTA-GTTTATA-TATATTATCTTAT
1 ATCAAACTAGCAATCACTTTAATTTAGTGGCAATTACCTTTATATTATATTATCTTAT
* *
1700461 ATCAAACTAGCAATCACTTTCATTTAGTTGCAATTACCCTTTATATTATATTAT
1 ATCAAACTAGCAATCACTTTAATTTAGTGGCAATTA-CCTTTATATTATATTAT
1700515 AAGTGTTTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 32 0.70
58 6 0.13
59 8 0.17
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (58 bp):
ATCAAACTAGCAATCACTTTAATTTAGTGGCAATTACCTTTATATTATATTATCTTAT
Found at i:1704395 original size:32 final size:33
Alignment explanation
Indices: 1704348--1704410 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
1704338 TGATCCTTGA
* *
1704348 GTTCGAGGTTTAGGTTC-AAGCTTCAAGGTTTGG
1 GTTCGAGGTTAAGGTTCTAA-ATTCAAGGTTTGG
1704381 GTTCG-GGTTAAGGTTCTAAATTCAAGGTTT
1 GTTCGAGGTTAAGGTTCTAAATTCAAGGTTT
1704411 TGGATTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (33 bp):
GTTCGAGGTTAAGGTTCTAAATTCAAGGTTTGG
Found at i:1714110 original size:95 final size:95
Alignment explanation
Indices: 1714004--1714194 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
1713994 TAATCTATTT
* *
1714004 TTTTTTTATCAATTGCTTAATTACATTATTTCAATCAAGTCCTCCACTCACACATTTAGCCCTTT
1 TTTTTTTATCAATTGCCTAATTACATTATTTCAATCAAGTCCTCCACTCACAAATTTAGCCCTTT
1714069 CTAAGTCAAAGGAGTTGATAATTTAAATCA
66 CTAAGTCAAAGGAGTTGATAATTTAAATCA
1714099 TTTTTTTATCAATTGCCTAATTACATTATTTCAATCAAGTCCTCCACTCACAAATTTAGCCCTTT
1 TTTTTTTATCAATTGCCTAATTACATTATTTCAATCAAGTCCTCCACTCACAAATTTAGCCCTTT
1714164 CTAAGTCAAAGGAGTTGATAATTTAAATCA
66 CTAAGTCAAAGGAGTTGATAATTTAAATCA
1714194 T
1 T
1714195 AAAAGTAAAC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (95 bp):
TTTTTTTATCAATTGCCTAATTACATTATTTCAATCAAGTCCTCCACTCACAAATTTAGCCCTTT
CTAAGTCAAAGGAGTTGATAATTTAAATCA
Found at i:1715909 original size:20 final size:21
Alignment explanation
Indices: 1715879--1715920 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1715869 AAAACAAAAA
*
1715879 ATAATGTTCTAAAAATATTAT
1 ATAATGTTCTAAAAAAATTAT
1715900 ATAATG-TCTAAAAAAATTAT
1 ATAATGTTCTAAAAAAATTAT
1715920 A
1 A
1715921 GGTAGTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATAATGTTCTAAAAAAATTAT
Found at i:1718463 original size:101 final size:104
Alignment explanation
Indices: 1718292--1718493 Score: 365
Period size: 101 Copynumber: 2.0 Consensus size: 104
1718282 ATGGCTAGGC
*
1718292 TTTTCTCTTCTTTTTTTCTTTTTCTTTTTTGGTTATAGATGATGATAATAGATGATATTTGTTTA
1 TTTTCTCTTC-TTTTTTCTTTTTCTTTTTTGGTGATAGATGATGATAATAGATGATATTTGTTTA
1718357 TTTTATTAATTTATTATAACTTTAATCATTAATTTCTAAT
65 TTTTATTAATTTATTATAACTTTAATCATTAATTTCTAAT
1718397 TTTTCTCTTC-TTTTT-TTTTT-TTTTTTGGTGATAGATGATGATAATAGATGATATTTGTTTAT
1 TTTTCTCTTCTTTTTTCTTTTTCTTTTTTGGTGATAGATGATGATAATAGATGATATTTGTTTAT
1718459 TTTATTAATTTATTATAACTTTAATCATTAATTTC
66 TTTATTAATTTATTATAACTTTAATCATTAATTTC
1718494 CAAAATTGAC
Statistics
Matches: 96, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
101 76 0.79
102 5 0.05
103 5 0.05
105 10 0.10
ACGTcount: A:0.25, C:0.07, G:0.08, T:0.60
Consensus pattern (104 bp):
TTTTCTCTTCTTTTTTCTTTTTCTTTTTTGGTGATAGATGATGATAATAGATGATATTTGTTTAT
TTTATTAATTTATTATAACTTTAATCATTAATTTCTAAT
Found at i:1718753 original size:3 final size:3
Alignment explanation
Indices: 1718745--1718778 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1718735 TGTAGACCAT
1718745 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1718779 AATTTTTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1719432 original size:19 final size:18
Alignment explanation
Indices: 1719405--1719441 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1719395 ATAGATTTTT
1719405 TAAATTATAATAAAATTA
1 TAAATTATAATAAAATTA
*
1719423 TAAATGTATAATTAAATTA
1 TAAAT-TATAATAAAATTA
1719442 ATACAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAATTATAATAAAATTA
Found at i:1722158 original size:3 final size:3
Alignment explanation
Indices: 1722150--1722229 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
1722140 TACGGTTCCT
1722150 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1722198 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1722230 TATATATCTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1725984 original size:20 final size:21
Alignment explanation
Indices: 1725958--1726019 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 21
1725948 ATTAGACCAC
1725958 AAAAAAATTAGATACCAAATT
1 AAAAAAATTAGATACCAAATT
1725979 -AAAAAA-TAGATATCCAATGATT
1 AAAAAAATTAGATA-CCAA--ATT
1726001 AAAAAAATTATG-TACCAAA
1 AAAAAAATTA-GATACCAAA
1726020 AAGAAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
19 6 0.17
20 10 0.29
21 1 0.03
22 3 0.09
23 10 0.29
24 4 0.11
25 1 0.03
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (21 bp):
AAAAAAATTAGATACCAAATT
Found at i:1727514 original size:29 final size:31
Alignment explanation
Indices: 1727463--1727524 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
1727453 AATTTATATC
* *
1727463 TTTATAATTTTTAAAAAATTAAATTA-AATT
1 TTTATAATTTTTAAAAAACTAAAATATAATT
*
1727493 TTTATAA-TTTTAAAGAACTAAAATATAATT
1 TTTATAATTTTTAAAAAACTAAAATATAATT
1727523 TT
1 TT
1727525 ATCTTTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAAAACTAAAATATAATT
Found at i:1734261 original size:21 final size:21
Alignment explanation
Indices: 1734237--1734316 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
1734227 TCCTGTTCTT
*
1734237 CTTCACCCTCTTCATCATCAC
1 CTTCATCCTCTTCATCATCAC
* * * **
1734258 CTTCATCTTCTTCGTCTTCTT
1 CTTCATCCTCTTCATCATCAC
* * *
1734279 CTTCTTCTTCTTCATCTTCAC
1 CTTCATCCTCTTCATCATCAC
* *
1734300 CCTCAGCCTCTTCATCA
1 CTTCATCCTCTTCATCA
1734317 CCCTCATCTT
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.12, C:0.41, G:0.03, T:0.44
Consensus pattern (21 bp):
CTTCATCCTCTTCATCATCAC
Found at i:1734269 original size:3 final size:3
Alignment explanation
Indices: 1734258--1734297 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1734248 TCATCATCAC
* * *
1734258 CTT CAT CTT CTT CGT CTT CTT CTT CTT CTT CTT CAT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1734298 ACCCTCAGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.35, G:0.03, T:0.57
Consensus pattern (3 bp):
CTT
Found at i:1739601 original size:29 final size:29
Alignment explanation
Indices: 1739530--1739587 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1739520 TAAACATCAT
1739530 CCTAAATATGCATGAATTTCAGTTTAAAA
1 CCTAAATATGCATGAATTTCAGTTTAAAA
1739559 CCTAAATATGCATGAATTTCAGTTTAAAA
1 CCTAAATATGCATGAATTTCAGTTTAAAA
1739588 TCTGTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (29 bp):
CCTAAATATGCATGAATTTCAGTTTAAAA
Found at i:1742021 original size:15 final size:15
Alignment explanation
Indices: 1742001--1742035 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1741991 ATTCTCAAAT
1742001 CCATCATCATAATCA
1 CCATCATCATAATCA
*
1742016 CCATCATCATAGTCA
1 CCATCATCATAATCA
1742031 CCATC
1 CCATC
1742036 TTCAACTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (15 bp):
CCATCATCATAATCA
Found at i:1750290 original size:6 final size:6
Alignment explanation
Indices: 1750273--1750304 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1750263 ACCGCACGAA
1750273 TTAAATT TTAAAT TTAAAT TTAAAT TTAAAT T
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT T
1750305 AAAAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:1750561 original size:2 final size:2
Alignment explanation
Indices: 1750554--1750586 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1750544 TGGTTTTGTT
1750554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1750587 TATTATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1750593 original size:8 final size:9
Alignment explanation
Indices: 1750553--1750593 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
1750543 ATGGTTTTGT
1750553 TTATATATA
1 TTATATATA
1750562 -TATATATA
1 TTATATATA
1750570 -TATATATA
1 TTATATATA
1750578 -TATATATA
1 TTATATATA
1750586 TTAT-TATA
1 TTATATATA
1750594 ATTTTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 28 0.90
9 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATATATA
Found at i:1754671 original size:2 final size:2
Alignment explanation
Indices: 1754666--1754691 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1754656 AAAATAAAGA
1754666 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
1754692 GAGATTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1760778 original size:2 final size:2
Alignment explanation
Indices: 1760771--1760797 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1760761 ATGAAATCAA
1760771 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1760798 TTTTACTTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1766104 original size:19 final size:20
Alignment explanation
Indices: 1766058--1766130 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 20
1766048 TAACTCAATA
* *
1766058 AAAACATTAAATAA-TACTT
1 AAAATATTAAATAATTTCTT
*
1766077 AAAACATTAAATAATTTC-T
1 AAAATATTAAATAATTTCTT
* *
1766096 AAGATATTACATAA-TTCTT
1 AAAATATTAAATAATTTCTT
*
1766115 AAAATATTAAAGAATT
1 AAAATATTAAATAATT
1766131 ATTATCCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.07
19 38 0.86
20 3 0.07
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATATTAAATAATTTCTT
Found at i:1768464 original size:22 final size:22
Alignment explanation
Indices: 1768438--1768482 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1768428 TTTTAGGGAT
*
1768438 AAAAGAGACGAAATACAATCTA
1 AAAAGAGACAAAATACAATCTA
1768460 AAAAGAGACAAAATACAATCTA
1 AAAAGAGACAAAATACAATCTA
1768482 A
1 A
1768483 CTCCTAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAGAGACAAAATACAATCTA
Found at i:1773291 original size:18 final size:18
Alignment explanation
Indices: 1773270--1773305 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1773260 TAAAAATAAA
1773270 TATTAATTTTTAAATTAT
1 TATTAATTTTTAAATTAT
* *
1773288 TATTTATTTTTAATTTAT
1 TATTAATTTTTAAATTAT
1773306 CTTATTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTAATTTTTAAATTAT
Found at i:1782472 original size:22 final size:22
Alignment explanation
Indices: 1782447--1782494 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1782437 GGCCCTCAAC
*
1782447 ATTTACA-TCTTTTATCAATTTA
1 ATTTACATTCTTTT-TCAATTAA
*
1782469 ATTTTCATTCTTTTTCAATTAA
1 ATTTACATTCTTTTTCAATTAA
1782491 ATTT
1 ATTT
1782495 GTCATTAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTACATTCTTTTTCAATTAA
Found at i:1782480 original size:23 final size:23
Alignment explanation
Indices: 1782454--1782500 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
1782444 AACATTTACA
*
1782454 TCTTTTATCAATTTAATTT-TCAT
1 TCTTTT-TCAATTAAATTTGTCAT
1782477 TCTTTTTCAATTAAATTTGTCAT
1 TCTTTTTCAATTAAATTTGTCAT
1782500 T
1 T
1782501 AACCTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.60
Consensus pattern (23 bp):
TCTTTTTCAATTAAATTTGTCAT
Found at i:1787089 original size:20 final size:20
Alignment explanation
Indices: 1787051--1787089 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1787041 GCCTTAAATA
* *
1787051 CTAAACCCTAAACCTCAAAC
1 CTAAACCATAAACCCCAAAC
*
1787071 CTAAACCATAGACCCCAAA
1 CTAAACCATAAACCCCAAA
1787090 TTTGAACCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.38, G:0.03, T:0.13
Consensus pattern (20 bp):
CTAAACCATAAACCCCAAAC
Found at i:1793688 original size:15 final size:14
Alignment explanation
Indices: 1793668--1793703 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
1793658 ACATTAACCA
1793668 AAAAATTAAAATATT
1 AAAAATTAAAATA-T
1793683 AAAAATTTAAAATAT
1 AAAAA-TTAAAATAT
1793698 AAAAAT
1 AAAAAT
1793704 AATTACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 11 0.55
16 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATTAAAATAT
Found at i:1793692 original size:16 final size:15
Alignment explanation
Indices: 1793667--1793703 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1793657 CACATTAACC
*
1793667 AAAAAATTAAAATATT
1 AAAAATTTAAAATA-T
1793683 AAAAATTTAAAATAT
1 AAAAATTTAAAATAT
1793698 AAAAAT
1 AAAAAT
1793704 AATTACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATTTAAAATAT
Found at i:1793802 original size:18 final size:18
Alignment explanation
Indices: 1793769--1793804 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1793759 TTTAAAAATT
* *
1793769 TATTAAAAATTGAATAAA
1 TATTAAAAAATAAATAAA
1793787 TATTAAAAAATAAATAAA
1 TATTAAAAAATAAATAAA
1793805 ATCATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TATTAAAAAATAAATAAA
Found at i:1793888 original size:37 final size:37
Alignment explanation
Indices: 1793809--1793910 Score: 116
Period size: 37 Copynumber: 2.7 Consensus size: 37
1793799 AATAAAATCA
* * * * *
1793809 TTTAAAAACTTAAAAATTGTAAAAAATTCAAAAAAGT
1 TTTAAAAATTTTAAAAGTATAAAAAATTCAAAAAAAT
*
1793846 ATTAAAAATTTTAAAAGTATAAAAAA-TCAAAACAAAT
1 TTTAAAAATTTTAAAAGTATAAAAAATTCAAAA-AAAT
1793883 TTTAAAAATTATTAAAAGTAGTAAAAAA
1 TTTAAAAATT-TTAAAAGTA-TAAAAAA
1793911 CACTTATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 6 0.11
37 33 0.60
38 9 0.16
39 7 0.13
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (37 bp):
TTTAAAAATTTTAAAAGTATAAAAAATTCAAAAAAAT
Found at i:1794509 original size:30 final size:30
Alignment explanation
Indices: 1794473--1794537 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
1794463 GTAAAGAAAT
1794473 TTATAATACCTTAACTATTATTAGATTAGG
1 TTATAATACCTTAACTATTATTAGATTAGG
* *
1794503 TTATAATACTTTAACTATTATTAGATTATG
1 TTATAATACCTTAACTATTATTAGATTAGG
1794533 TTATA
1 TTATA
1794538 CCCATGACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (30 bp):
TTATAATACCTTAACTATTATTAGATTAGG
Found at i:1796380 original size:9 final size:9
Alignment explanation
Indices: 1796365--1796402 Score: 62
Period size: 8 Copynumber: 4.4 Consensus size: 9
1796355 ACCGAGAAAG
1796365 GAAAAAAAA
1 GAAAAAAAA
1796374 -AAAAAAAA
1 GAAAAAAAA
1796382 GAAAAAAAA
1 GAAAAAAAA
1796391 G-AAAAAAA
1 GAAAAAAAA
1796399 GAAA
1 GAAA
1796403 GGAAACCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.59
9 11 0.41
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:1796387 original size:17 final size:17
Alignment explanation
Indices: 1796365--1796402 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1796355 ACCGAGAAAG
1796365 GAAAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAAAA
*
1796382 GAAAAAAAAGAAAAAAA
1 GAAAAAAAAAAAAAAAA
1796399 GAAA
1 GAAA
1796403 GGAAACCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAAAAAAAA
Found at i:1809853 original size:11 final size:12
Alignment explanation
Indices: 1809837--1809865 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1809827 CGCCACGTTC
1809837 TATCTTTCCA-T
1 TATCTTTCCATT
1809848 TATCTTTCCATT
1 TATCTTTCCATT
1809860 TATCTT
1 TATCTT
1809866 CTTTATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTTTCCATT
Found at i:1813029 original size:17 final size:17
Alignment explanation
Indices: 1812991--1813028 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1812981 TATATAGTGC
*
1812991 AAAAATATAAAACATAT
1 AAAAATATAAAAAATAT
1813008 AAAAATATAAAAAA-AT
1 AAAAATATAAAAAATAT
1813024 AAAAA
1 AAAAA
1813029 AAAATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATATAAAAAATAT
Found at i:1813030 original size:8 final size:8
Alignment explanation
Indices: 1812991--1813028 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
1812981 TATATAGTGC
1812991 AAAAATAT
1 AAAAATAT
1812999 AAAACATAT
1 AAAA-ATAT
1813008 AAAAATAT
1 AAAAATAT
*
1813016 AAAAAAAT
1 AAAAATAT
1813024 AAAAA
1 AAAAA
1813029 AAAATCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAAATAT
Found at i:1813647 original size:3 final size:3
Alignment explanation
Indices: 1813623--1813693 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
1813613 AATATCCTTG
* * * * *
1813623 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA TTA TTA TTA CTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1813670 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
1813694 GTACGTATAA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1814043 original size:8 final size:8
Alignment explanation
Indices: 1814030--1814073 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
1814020 TTTTTTAATG
1814030 TTATATTA
1 TTATATTA
1814038 TTATATTA
1 TTATATTA
1814046 TTATATTATA
1 TTATA-T-TA
*
1814056 TTACATATA
1 TTATAT-TA
1814065 TTATATTA
1 TTATATTA
1814073 T
1 T
1814074 ATTCATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 16 0.50
9 10 0.31
10 6 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATATTA
Found at i:1814044 original size:5 final size:5
Alignment explanation
Indices: 1814030--1814096 Score: 61
Period size: 5 Copynumber: 13.6 Consensus size: 5
1814020 TTTTTTAATG
*
1814030 TTATA TTAT- TATATTA TTATA TTATA TTACA -TATA TTATA TTATA TTCATA
1 TTATA TTATA T-TA-TA TTATA TTATA TTATA TTATA TTATA TTATA TT-ATA
*
1814081 TT-TT TTATA -TATA TTA
1 TTATA TTATA TTATA TTA
1814097 CAATGTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
4 11 0.22
5 31 0.61
6 8 0.16
7 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:1814066 original size:14 final size:13
Alignment explanation
Indices: 1814036--1814072 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1814026 AATGTTATAT
*
1814036 TATTATATTATTA
1 TATTATATTAATA
1814049 TATTATATTACATA
1 TATTATATTA-ATA
1814063 TATTATATTA
1 TATTATATTA
1814073 TATTCATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATATTAATA
Found at i:1814068 original size:19 final size:19
Alignment explanation
Indices: 1814030--1814098 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
1814020 TTTTTTAATG
*
1814030 TTATATTATTATATTATTATA
1 TTATATTA-CATA-TATTATA
1814051 TTATATTACATATATTATA
1 TTATATTACATATATTATA
* *
1814070 TTATATT-CATATTTTTTA
1 TTATATTACATATATTATA
1814088 TATATATTACA
1 T-TATATTACA
1814099 ATGTATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 10 0.23
19 20 0.47
20 5 0.12
21 8 0.19
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATTACATATATTATA
Found at i:1816318 original size:27 final size:27
Alignment explanation
Indices: 1816280--1816333 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1816270 GTTCAGGTAA
1816280 CAAAGTTATTTCAGATGTGCTCTTTGT
1 CAAAGTTATTTCAGATGTGCTCTTTGT
1816307 CAAAGTTATTTCAGATGTGCTCTTTGT
1 CAAAGTTATTTCAGATGTGCTCTTTGT
1816334 ACCTGACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (27 bp):
CAAAGTTATTTCAGATGTGCTCTTTGT
Found at i:1821960 original size:18 final size:18
Alignment explanation
Indices: 1821914--1821950 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1821904 GATTTGAACG
1821914 AAGTAAAATATACATGTA
1 AAGTAAAATATACATGTA
1821932 AAGTAAAATATACATGTA
1 AAGTAAAATATACATGTA
1821950 A
1 A
1821951 TATATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27
Consensus pattern (18 bp):
AAGTAAAATATACATGTA
Found at i:1822356 original size:23 final size:25
Alignment explanation
Indices: 1822312--1822357 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
1822302 TGAAACAACT
*
1822312 TAAAATAAAATAGGATACATAAAAG
1 TAAAATAAAATAGGATAAATAAAAG
*
1822337 TAAAA-AAAA-AGGGTAAATAAA
1 TAAAATAAAATAGGATAAATAAA
1822358 CAATATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 4 0.21
25 5 0.26
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.17
Consensus pattern (25 bp):
TAAAATAAAATAGGATAAATAAAAG
Found at i:1822605 original size:26 final size:27
Alignment explanation
Indices: 1822544--1822610 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
1822534 TAAGTATAAG
*
1822544 ATAAATAATATGAAAGAAAAATTTTTAA
1 ATAAATAATA-GAAAGAAAAATTTTAAA
** * *
1822572 ATGGATAATA-AATGAAATATTTTAAA
1 ATAAATAATAGAAAGAAAAATTTTAAA
1822598 ATAAATAAATAGA
1 ATAAAT-AATAGA
1822611 GTTTTTAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
26 17 0.57
27 4 0.13
28 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (27 bp):
ATAAATAATAGAAAGAAAAATTTTAAA
Found at i:1822654 original size:14 final size:14
Alignment explanation
Indices: 1822637--1822670 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1822627 ATATATATAT
1822637 AATAATTTAAAATA
1 AATAATTTAAAATA
*
1822651 AATAGTTTAAAATA
1 AATAATTTAAAATA
*
1822665 CATAAT
1 AATAAT
1822671 ATATATAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (14 bp):
AATAATTTAAAATA
Found at i:1822833 original size:2 final size:2
Alignment explanation
Indices: 1822820--1822861 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1822810 CAAAGAATTA
*
1822820 AT AT AA AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1822860 AT
1 AT
1822862 TTAAAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1822842 original size:19 final size:19
Alignment explanation
Indices: 1822818--1822861 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1822808 AGCAAAGAAT
1822818 TAATATAAATATATATATA
1 TAATATAAATATATATATA
*
1822837 TAATATATATATATATATA
1 TAATATAAATATATATATA
1822856 TAATAT
1 TAATAT
1822862 TTAAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATATAAATATATATATA
Found at i:1825032 original size:16 final size:15
Alignment explanation
Indices: 1825013--1825179 Score: 130
Period size: 15 Copynumber: 10.7 Consensus size: 15
1825003 AAGGGGGGGA
1825013 AGCAAAAAAATTTTCC
1 AGCAAAAAAA-TTTCC
*
1825029 AGC-AAAAAATTCCAGC
1 AGCAAAAAAATTTC--C
1825045 AGCAAAAAAATTTTCC
1 AGCAAAAAAA-TTTCC
*
1825061 AGC-AAAAAATTCCAGC
1 AGCAAAAAAATTTC--C
1825077 AGCAAAAAAATTTTCC
1 AGCAAAAAAA-TTTCC
1825093 AGC-AAAAAA-TTCC
1 AGCAAAAAAATTTCC
*
1825106 AGCAGCAAAAAAATTCC
1 AGCA--AAAAAATTTCC
*
1825123 AGCCAAAAAAAAAATTCC
1 AG-C--AAAAAAATTTCC
1825141 AGCAAAGAAAA-TTCC
1 AGCAAA-AAAATTTCC
*
1825156 AGC-AAAACATTTCC
1 AGCAAAAAAATTTCC
1825170 AGCAAAAAAA
1 AGCAAAAAAA
1825180 AAAGCCAAAA
Statistics
Matches: 127, Mismatches: 6, Indels: 37
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.08
14 15 0.12
15 33 0.26
16 29 0.23
17 19 0.15
18 20 0.16
20 1 0.01
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.16
Consensus pattern (15 bp):
AGCAAAAAAATTTCC
Found at i:1825036 original size:32 final size:32
Alignment explanation
Indices: 1825013--1825132 Score: 217
Period size: 32 Copynumber: 3.8 Consensus size: 32
1825003 AAGGGGGGGA
1825013 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1825045 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1825077 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1825109 AGCAAAAAAA--TTCCAGCCAAAAAA
1 AGCAAAAAAATTTTCCAG-CAAAAAA
1825133 AAAATTCCAG
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.07
31 7 0.08
32 74 0.85
ACGTcount: A:0.53, C:0.22, G:0.09, T:0.17
Consensus pattern (32 bp):
AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
Found at i:1825170 original size:64 final size:61
Alignment explanation
Indices: 1825015--1825182 Score: 189
Period size: 64 Copynumber: 2.6 Consensus size: 61
1825005 GGGGGGGAAG
1825015 CAAAAAAATTTTCCAGCAAAAAATTCCAGCAGCAAAAAAATTTTCCAGCAAAAAATTCCAGCA
1 CAAAAAAA-TTTCCAGCAAAAAATTCCAGCAGCAAAAAAA-TTTCCAGCAAAAAATTCCAGCA
1825078 GCAAAAAAATTTTCCAGCAAAAAATTCCAGCAGCAAAAAAA-TTCCAGCCAAAAAAAAAATTCCA
1 -CAAAAAAA-TTTCCAGCAAAAAATTCCAGCAGCAAAAAAATTTCCAG-C----AAAAAATTCCA
1825142 GCA
59 GCA
* * **
1825145 -AAGAAAA-TTCCAGCAAAACATTTCCAGCAAAAAAAAAA
1 CAAAAAAATTTCCAGCAAAA-AATTCCAGCAGCAAAAAAA
1825183 GCCAAAATCT
Statistics
Matches: 94, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
62 6 0.06
63 12 0.13
64 56 0.60
65 6 0.06
67 14 0.15
ACGTcount: A:0.54, C:0.21, G:0.08, T:0.16
Consensus pattern (61 bp):
CAAAAAAATTTCCAGCAAAAAATTCCAGCAGCAAAAAAATTTCCAGCAAAAAATTCCAGCA
Found at i:1826576 original size:17 final size:17
Alignment explanation
Indices: 1826556--1826598 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1826546 AAAAATTCAG
*
1826556 GTTTCAAAAATTTTCGT
1 GTTTTAAAAATTTTCGT
*
1826573 GTTTTTAAAATTTTCGT
1 GTTTTAAAAATTTTCGT
1826590 GTTTTAAAA
1 GTTTTAAAA
1826599 TTTCTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (17 bp):
GTTTTAAAAATTTTCGT
Found at i:1826596 original size:16 final size:17
Alignment explanation
Indices: 1826562--1826601 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1826552 TCAGGTTTCA
1826562 AAAATTTTCGTGTTTTT
1 AAAATTTTCGTGTTTTT
1826579 AAAATTTTCGTG-TTTT
1 AAAATTTTCGTGTTTTT
1826595 AAAATTT
1 AAAATTT
1826602 CTCATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (17 bp):
AAAATTTTCGTGTTTTT
Found at i:1838380 original size:72 final size:72
Alignment explanation
Indices: 1838263--1838750 Score: 753
Period size: 72 Copynumber: 6.7 Consensus size: 72
1838253 TGATGCTTTT
*
1838263 ATTTCTG-TTTCAAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1838327 TAATTTCA
65 TAATTTCA
1838335 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
*
1838400 ATTTTCA
66 AATTTCA
*
1838407 ATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1838472 AATTTCA
66 AATTTCA
1838479 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1838544 AATTTCA
66 AATTTCA
* * *
1838551 ATTTCTATTTTCAAAATTGAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGT
1 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
1838616 AATTTCA
66 AATTTCA
* * * ** * *
1838623 ATTTCTGTTGTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1838688 GTAATTTCA
64 GTAATTTCA
* * **
1838697 ATTTCTGTTCATCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTCTGTT-TTC---AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC
1838751 GGGTCACATG
Statistics
Matches: 393, Mismatches: 18, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
72 285 0.73
73 4 0.01
74 63 0.16
75 2 0.01
76 39 0.10
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (72 bp):
ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
AATTTCA
Found at i:1839362 original size:22 final size:22
Alignment explanation
Indices: 1839331--1839375 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1839321 AAAAGTCTTT
1839331 ACTCTATTCTCGTTACACGACA
1 ACTCTATTCTCGTTACACGACA
*
1839353 ACTCTGTTCTCGTTACACGACA
1 ACTCTATTCTCGTTACACGACA
1839375 A
1 A
1839376 TGAGTAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (22 bp):
ACTCTATTCTCGTTACACGACA
Found at i:1839457 original size:15 final size:14
Alignment explanation
Indices: 1839437--1839644 Score: 130
Period size: 14 Copynumber: 13.4 Consensus size: 14
1839427 GGGGGAAGCA
1839437 AAAAAATTTTCCAGC
1 AAAAAA-TTTCCAGC
*
1839452 AAAAAATTCCAGCAGC
1 AAAAAATTTC--CAGC
1839468 AAAAAAATTTTCCAGC
1 -AAAAAA-TTTCCAGC
*
1839484 AAAAAATTCCAGCAGC
1 AAAAAATTTC--CAGC
*
1839500 AAAAAAAATTTTCCAAC
1 --AAAAAA-TTTCCAGC
*
1839517 AAAAAATTCCAGCAGC
1 AAAAAATTTC--CAGC
1839533 AAAAAAAATTTTCCAGC
1 --AAAAAA-TTTCCAGC
1839550 AAAAAA-TTCCAGCC
1 AAAAAATTTCCAG-C
*
1839564 AAAAAAATTCCAGCC
1 AAAAAATTTCCAG-C
*
1839579 AAAAAAAAAATTCCAGC
1 ---AAAAAATTTCCAGC
* *
1839596 AAAGAAAATTCCAAC
1 AAA-AAATTTCCAGC
*
1839611 AAAACATTTCCAGC
1 AAAAAATTTCCAGC
*
1839625 AAAACATTTCCAGC
1 AAAAAATTTCCAGC
1839639 AAAAAA
1 AAAAAA
1839645 AAAAGCCAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 41
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.04
14 46 0.29
15 45 0.28
16 15 0.09
17 14 0.09
18 28 0.17
19 6 0.04
ACGTcount: A:0.53, C:0.22, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAAATTTCCAGC
Found at i:1839470 original size:32 final size:32
Alignment explanation
Indices: 1839433--1839584 Score: 240
Period size: 33 Copynumber: 4.8 Consensus size: 32
1839423 AGGGGGGGGA
1839433 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1839465 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
*
1839497 AGCAAAAAAAATTTTCCAACAAAAAATTCCAGC
1 AGC-AAAAAAATTTTCCAGCAAAAAATTCCAGC
1839530 AGCAAAAAAAATTTTCCAGCAAAAAATTCCAGC
1 AGC-AAAAAAATTTTCCAGCAAAAAATTCCAGC
1839563 --CAAAAAAA--TTCCAGCCAAAAAA
1 AGCAAAAAAATTTTCCAG-CAAAAAA
1839585 AAAATTCCAG
Statistics
Matches: 116, Mismatches: 2, Indels: 7
0.93 0.02 0.06
Matches are distributed among these distances:
28 6 0.05
29 7 0.06
30 7 0.06
31 1 0.01
32 35 0.30
33 60 0.52
ACGTcount: A:0.53, C:0.22, G:0.08, T:0.17
Consensus pattern (32 bp):
AGCAAAAAAATTTTCCAGCAAAAAATTCCAGC
Found at i:1839523 original size:65 final size:64
Alignment explanation
Indices: 1839436--1839570 Score: 236
Period size: 65 Copynumber: 2.1 Consensus size: 64
1839426 GGGGGGAAGC
*
1839436 AAAAAAATTTTCCAGCAAAAAATTCCAGCAGC-AAAAAAATTTTCCAGCAAAAAATTCCAGCAGC
1 AAAAAAATTTTCCAACAAAAAATTCCAGCAGCAAAAAAAATTTTCCAGCAAAAAATTCCAGC--C
1839500 A
64 A
1839501 AAAAAAATTTTCCAACAAAAAATTCCAGCAGCAAAAAAAATTTTCCAGCAAAAAATTCCAGCCA
1 AAAAAAATTTTCCAACAAAAAATTCCAGCAGCAAAAAAAATTTTCCAGCAAAAAATTCCAGCCA
1839565 AAAAAA
1 AAAAAA
1839571 TTCCAGCCAA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
64 8 0.12
65 31 0.46
66 29 0.43
ACGTcount: A:0.54, C:0.21, G:0.07, T:0.18
Consensus pattern (64 bp):
AAAAAAATTTTCCAACAAAAAATTCCAGCAGCAAAAAAAATTTTCCAGCAAAAAATTCCAGCCA
Found at i:1839554 original size:48 final size:45
Alignment explanation
Indices: 1839510--1839625 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 45
1839500 AAAAAAAATT
**
1839510 TTCCAACAAAAAATTCCAGCAGCAAAAAAAATTTTCCAGCAAAAAA
1 TTCCAACAAAAAATTCCAGCA-CAAAAAAAAAATTCCAGCAAAAAA
*
1839556 TTCCAGCCAAAAAAATTCCAGC-CAAAAAAAAAATTCCAGCAAAGAAAA
1 TTCCA-AC-AAAAAATTCCAGCACAAAAAAAAAATTCCAGC-AA-AAAA
*
1839604 TTCCAACAAAACATTTCCAGCA
1 TTCCAACAAAA-AATTCCAGCA
1839626 AAACATTTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
46 25 0.42
47 12 0.20
48 22 0.37
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (45 bp):
TTCCAACAAAAAATTCCAGCACAAAAAAAAAATTCCAGCAAAAAA
Found at i:1839560 original size:46 final size:47
Alignment explanation
Indices: 1839496--1839625 Score: 140
Period size: 48 Copynumber: 2.7 Consensus size: 47
1839486 AAAATTCCAG
* **
1839496 CAGCAAAAAAAATTTTCCAACAAAAAATTCCAGCAGCAAAAAAAATTTTC
1 CAGCAAAGAAAA--TTCCAACAAAAAATTCCAGCA-CAAAAAAAAAATTC
*
1839546 CAGC-AA-AAAATTCCAGCCAAAAAAATTCCAGC-CAAAAAAAAAATTC
1 CAGCAAAGAAAATTCCA-AC-AAAAAATTCCAGCACAAAAAAAAAATTC
*
1839592 CAGCAAAGAAAATTCCAACAAAACATTTCCAGCA
1 CAGCAAAGAAAATTCCAACAAAA-AATTCCAGCA
1839626 AAACATTTCC
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
46 25 0.36
47 12 0.17
48 26 0.38
49 2 0.03
50 4 0.06
ACGTcount: A:0.54, C:0.23, G:0.07, T:0.16
Consensus pattern (47 bp):
CAGCAAAGAAAATTCCAACAAAAAATTCCAGCACAAAAAAAAAATTC
Found at i:1839587 original size:18 final size:15
Alignment explanation
Indices: 1839435--1839645 Score: 104
Period size: 15 Copynumber: 13.5 Consensus size: 15
1839425 GGGGGGGAAG
1839435 CAAAAAAATTTTCCAG-
1 CAAAAAAA--TTCCAGC
1839451 C-AAAAAATTCCAGC
1 CAAAAAAATTCCAGC
1839465 AGCAAAAAAATTTTCCAG-
1 --CAAAAAAA--TTCCAGC
1839483 C-AAAAAATTCCAGC
1 CAAAAAAATTCCAGC
*
1839497 AGCAAAAAAAATTTTCCA-A
1 --C-AAAAAAA--TTCCAGC
1839516 C-AAAAAATTCCAGC
1 CAAAAAAATTCCAGC
1839530 AGCAAAAAAAATTTTCCAG-
1 --C-AAAAAAA--TTCCAGC
1839549 C-AAAAAATTCCAGC
1 CAAAAAAATTCCAGC
1839563 CAAAAAAATTCCAGC
1 CAAAAAAATTCCAGC
1839578 CAAAAAAAAAATTCCAG-
1 C---AAAAAAATTCCAGC
*
1839595 CAAAGAAAATTCCA-A
1 CAAA-AAAATTCCAGC
* *
1839610 CAAAACATTTCCAG-
1 CAAAAAAATTCCAGC
* *
1839624 CAAAACATTTCCAG-
1 CAAAAAAATTCCAGC
1839638 CAAAAAAA
1 CAAAAAAA
1839646 AAAGCCAAAA
Statistics
Matches: 161, Mismatches: 6, Indels: 58
0.72 0.03 0.26
Matches are distributed among these distances:
13 23 0.14
14 31 0.19
15 51 0.32
16 5 0.03
17 9 0.06
18 25 0.16
19 6 0.04
20 11 0.07
ACGTcount: A:0.54, C:0.22, G:0.07, T:0.17
Consensus pattern (15 bp):
CAAAAAAATTCCAGC
Found at i:1841048 original size:17 final size:17
Alignment explanation
Indices: 1841028--1841070 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1841018 AAAAATTCAG
*
1841028 GTTTCAAAAATTTTCGT
1 GTTTTAAAAATTTTCGT
*
1841045 GTTTTTAAAATTTTCGT
1 GTTTTAAAAATTTTCGT
1841062 GTTTTAAAA
1 GTTTTAAAA
1841071 TTTCTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (17 bp):
GTTTTAAAAATTTTCGT
Found at i:1841068 original size:16 final size:17
Alignment explanation
Indices: 1841034--1841073 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1841024 TCAGGTTTCA
1841034 AAAATTTTCGTGTTTTT
1 AAAATTTTCGTGTTTTT
1841051 AAAATTTTCGTG-TTTT
1 AAAATTTTCGTGTTTTT
1841067 AAAATTT
1 AAAATTT
1841074 CTCATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (17 bp):
AAAATTTTCGTGTTTTT
Found at i:1847013 original size:17 final size:17
Alignment explanation
Indices: 1846991--1847026 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1846981 GAAAATTAAA
1846991 AATAATGAATTAAATGT
1 AATAATGAATTAAATGT
* *
1847008 AATAATGAGTTAGATGT
1 AATAATGAATTAAATGT
1847025 AA
1 AA
1847027 AAATTGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
AATAATGAATTAAATGT
Found at i:1849022 original size:11 final size:11
Alignment explanation
Indices: 1848997--1849030 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1848987 TTGTGTGTTC
1848997 TTTATTTTA--
1 TTTATTTTATT
1849006 TTTATTTTATT
1 TTTATTTTATT
1849017 TTTATTTTATT
1 TTTATTTTATT
1849028 TTT
1 TTT
1849031 CACAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1849030 original size:6 final size:5
Alignment explanation
Indices: 1848997--1849029 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1848987 TTGTGTGTTC
1848997 TTTAT TTTA- TTTAT TTTATT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
1849030 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1853476 original size:11 final size:11
Alignment explanation
Indices: 1853451--1853484 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1853441 TTGTGTGTTC
1853451 TTTATTTTA--
1 TTTATTTTATT
1853460 TTTATTTTATT
1 TTTATTTTATT
1853471 TTTATTTTATT
1 TTTATTTTATT
1853482 TTT
1 TTT
1853485 CACAACAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1853484 original size:6 final size:5
Alignment explanation
Indices: 1853451--1853483 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1853441 TTGTGTGTTC
1853451 TTTAT TTTA- TTTAT TTTATT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
1853484 TCACAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:1860554 original size:14 final size:13
Alignment explanation
Indices: 1860530--1860563 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1860520 ATCATTTCAC
1860530 TATTATGTTGTTAT
1 TATT-TGTTGTTAT
1860544 TAATTTGTTGTTAT
1 T-ATTTGTTGTTAT
1860558 TATTTG
1 TATTTG
1860564 AATATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (13 bp):
TATTTGTTGTTAT
Found at i:1867895 original size:2 final size:2
Alignment explanation
Indices: 1867890--1867928 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1867880 ATAAAAAAGA
1867890 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1867929 GTAAAGTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1867909 original size:15 final size:15
Alignment explanation
Indices: 1867889--1867928 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1867879 CATAAAAAAG
1867889 AATATATATATATAT
1 AATATATATATATAT
1867904 AATATATATATATAT
1 AATATATATATATAT
1867919 -ATA-ATATATA
1 AATATATATATA
1867929 GTAAAGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 7 0.28
14 3 0.12
15 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:1867912 original size:17 final size:17
Alignment explanation
Indices: 1867890--1867928 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1867880 ATAAAAAAGA
1867890 ATATATATATATATAAT
1 ATATATATATATATAAT
1867907 ATATATATATATATAAT
1 ATATATATATATATAAT
1867924 ATATA
1 ATATA
1867929 GTAAAGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATATATATATAAT
Found at i:1869110 original size:34 final size:34
Alignment explanation
Indices: 1869067--1869137 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
1869057 ATAACCTGGA
1869067 TTTGCTGTTAGCGTGGACTTTGCAGGCAGTCCAT
1 TTTGCTGTTAGCGTGGACTTTGCAGGCAGTCCAT
1869101 TTTGCTGTTAGCGTGGACTTTGCAGGCAGTCCAT
1 TTTGCTGTTAGCGTGGACTTTGCAGGCAGTCCAT
1869135 TTT
1 TTT
1869138 TCTTGTCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.14, C:0.20, G:0.28, T:0.38
Consensus pattern (34 bp):
TTTGCTGTTAGCGTGGACTTTGCAGGCAGTCCAT
Found at i:1869620 original size:49 final size:49
Alignment explanation
Indices: 1869548--1869642 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
1869538 AAAATGACAT
1869548 AGCGCCAATATTTCATAGAATCCTTTCTCTATCTCAATAATCAAGCAGC
1 AGCGCCAATATTTCATAGAATCCTTTCTCTATCTCAATAATCAAGCAGC
1869597 AGCGCCAATATTTCATAGAATCCTTTCTCTATCTCAATAATCAAGC
1 AGCGCCAATATTTCATAGAATCCTTTCTCTATCTCAATAATCAAGC
1869643 GGCTGATGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (49 bp):
AGCGCCAATATTTCATAGAATCCTTTCTCTATCTCAATAATCAAGCAGC
Found at i:1882019 original size:6 final size:6
Alignment explanation
Indices: 1882010--1882035 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1882000 AAACACACCC
1882010 GTGCTG GTGCTG GTGCTG GTGCTG GT
1 GTGCTG GTGCTG GTGCTG GTGCTG GT
1882036 TTAATCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTGCTG
Found at i:1882998 original size:18 final size:17
Alignment explanation
Indices: 1882977--1883010 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1882967 TTATAATATA
1882977 ATATATTATATTAATTTT
1 ATATATTATA-TAATTTT
1882995 ATATATTATATAATTT
1 ATATATTATATAATTT
1883011 ATAAGTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTATATAATTTT
Found at i:1887332 original size:25 final size:24
Alignment explanation
Indices: 1887285--1887332 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1887275 TGAATACATA
* *
1887285 CATTTATTTTTATATTATTGTATG
1 CATTTATTTTTATAATATAGTATG
1887309 CATTTATTTTTATACATATAGTAT
1 CATTTATTTTTATA-ATATAGTAT
1887333 ATTAACGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (24 bp):
CATTTATTTTTATAATATAGTATG
Found at i:1887436 original size:24 final size:24
Alignment explanation
Indices: 1887380--1887428 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1887370 GTGATTTGTG
1887380 AATATTAAATCCAATTAAAATTCT
1 AATATTAAATCCAATTAAAATTCT
*
1887404 AATATTAAATTCAATTAAAATTCT
1 AATATTAAATCCAATTAAAATTCT
1887428 A
1 A
1887429 TGTATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATTAAATCCAATTAAAATTCT
Found at i:1889981 original size:5 final size:5
Alignment explanation
Indices: 1889967--1889996 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1889957 TATATATGAA
1889967 TTAA- TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
1889997 CTATTATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:1889989 original size:15 final size:14
Alignment explanation
Indices: 1889967--1890013 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1889957 TATATATGAA
1889967 TTAATTAATTTAAT
1 TTAATTAATTTAAT
1889981 TTAATTTAATTTAAT
1 TTAA-TTAATTTAAT
*
1889996 TCT-ATT-ATTCAAT
1 T-TAATTAATTTAAT
1890009 TTAAT
1 TTAAT
1890014 GCTTATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.31
14 6 0.21
15 12 0.41
16 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATTAATTTAAT
Found at i:1894117 original size:38 final size:38
Alignment explanation
Indices: 1894065--1894138 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
1894055 GAATATATCT
1894065 TTAATGTGGATGCATGAATTCTAACCCTTTAATTGTCC
1 TTAATGTGGATGCATGAATTCTAACCCTTTAATTGTCC
*
1894103 TTAATGTGGGTGCATGAATTCTAACCCTTTAATTGT
1 TTAATGTGGATGCATGAATTCTAACCCTTTAATTGT
1894139 ACATTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (38 bp):
TTAATGTGGATGCATGAATTCTAACCCTTTAATTGTCC
Found at i:1894862 original size:12 final size:11
Alignment explanation
Indices: 1894831--1894856 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1894821 TAGTATGACC
1894831 ATTAATTAAAA
1 ATTAATTAAAA
1894842 ATTAATTAAAA
1 ATTAATTAAAA
1894853 ATTA
1 ATTA
1894857 TTTTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAATTAAAA
Found at i:1897271 original size:21 final size:22
Alignment explanation
Indices: 1897247--1897289 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1897237 TTTATCTTAG
*
1897247 ACTTCAAATCCTAAAT-TTGAA
1 ACTTCAAATCCCAAATATTGAA
**
1897268 ACTTTGAATCCCAAATATTGAA
1 ACTTCAAATCCCAAATATTGAA
1897290 TCCTAAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (22 bp):
ACTTCAAATCCCAAATATTGAA
Found at i:1897316 original size:14 final size:14
Alignment explanation
Indices: 1897271--1897317 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1897261 ATTTGAAACT
* *
1897271 TTGAATCCCAAATA
1 TTGAATCCTAAATC
1897285 TTGAATCCTAAA-C
1 TTGAATCCTAAATC
1897298 TTGAA-CCTAAAATC
1 TTGAATCCT-AAATC
1897312 TTGAAT
1 TTGAAT
1897318 AGAATTAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 17 0.61
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (14 bp):
TTGAATCCTAAATC
Found at i:1898821 original size:19 final size:19
Alignment explanation
Indices: 1898799--1898836 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1898789 AAAATACAAA
1898799 AAAAAAT-CAAAATATTTAT
1 AAAAAATCCAAAAT-TTTAT
*
1898818 AAAAATTCCAAAATTTTAT
1 AAAAAATCCAAAATTTTAT
1898837 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATCCAAAATTTTAT
Found at i:1899454 original size:75 final size:75
Alignment explanation
Indices: 1899329--1899468 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 75
1899319 AGAAGGATCG
** * * ** *
1899329 CACATATCTGCTATAGTTTGCCTAATGGAGTTCGCATATATAACAATTTATGTAAGCATTCGCAC
1 CACATATCAACTACAGTTCGCCTAACAGAGTTCGCATATATAACAATTTATATAAGCATTCGCAC
1899394 CTAGGGCTCT
66 CTAGGGCTCT
* ** **
1899404 CACATATCAACTACAGTTCGCCTAACAGAGTTCGCATGTATAACCGTTTATATAAGGGTTCGCAC
1 CACATATCAACTACAGTTCGCCTAACAGAGTTCGCATATATAACAATTTATATAAGCATTCGCAC
1899469 TTATGGGGGT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 53 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (75 bp):
CACATATCAACTACAGTTCGCCTAACAGAGTTCGCATATATAACAATTTATATAAGCATTCGCAC
CTAGGGCTCT
Found at i:1901440 original size:29 final size:28
Alignment explanation
Indices: 1901374--1901440 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 28
1901364 ATTTAAGGTT
* * **
1901374 ATAAATATTAAAAATTTTACTTTAATTT
1 ATAAATAATAAAAATTTTACATTAATAA
*
1901402 ATCAAA-AATAAAAATATTTTCATTAATAA
1 AT-AAATAATAAAAAT-TTTACATTAATAA
1901431 ATAAATAATA
1 ATAAATAATA
1901441 CACCCGTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAAATAATAAAAATTTTACATTAATAA
Found at i:1903218 original size:20 final size:21
Alignment explanation
Indices: 1903193--1903236 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1903183 TTCGAATCGG
*
1903193 TTTTCTTT-TTTTTTTTTTCT
1 TTTTCTTTATTTTTTTCTTCT
1903213 TTTTCTTTACTTTTTTTCTTCT
1 TTTTCTTTA-TTTTTTTCTTCT
1903235 TT
1 TT
1903237 GTTTACATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTCTTTATTTTTTTCTTCT
Found at i:1903226 original size:19 final size:20
Alignment explanation
Indices: 1903204--1903242 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1903194 TTTCTTTTTT
1903204 TTTTTTTCTT-TTTCTTTAC
1 TTTTTTTCTTCTTTCTTTAC
*
1903223 TTTTTTTCTTCTTTGTTTAC
1 TTTTTTTCTTCTTTCTTTAC
1903243 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (20 bp):
TTTTTTTCTTCTTTCTTTAC
Found at i:1916382 original size:2 final size:2
Alignment explanation
Indices: 1916338--1916364 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1916328 AATATATGCC
1916338 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1916365 GTTAAAGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1916557 original size:24 final size:22
Alignment explanation
Indices: 1916516--1916566 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
1916506 ACAGTAAGAA
1916516 ATATACAATACATAACATTAAAAT
1 ATATACAATACATAACA-T-AAAT
*
1916540 ATATATAATA-ATATACATAAAT
1 ATATACAATACATA-ACATAAAT
1916562 ATATA
1 ATATA
1916567 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 9 0.36
23 4 0.16
24 12 0.48
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATACAATACATAACATAAAT
Found at i:1916587 original size:20 final size:19
Alignment explanation
Indices: 1916538--1916590 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
1916528 TAACATTAAA
1916538 ATATAT-ATAATAATATAC
1 ATATATAATAATAATATAC
* *
1916556 ATAAAT-AT-ATAATATAT
1 ATATATAATAATAATATAC
1916573 ATATTATAATAATAATAT
1 ATA-TATAATAATAATAT
1916591 GAAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.38
18 9 0.31
19 2 0.07
20 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATAATAATAATATAC
Found at i:1917373 original size:27 final size:29
Alignment explanation
Indices: 1917343--1917401 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
1917333 TCATTTGAGA
1917343 AGGGGA-AGAAAAAAAAGAAGAGA-GGAG
1 AGGGGAGAGAAAAAAAAGAAGAGAGGGAG
* **
1917370 A-GGGAGAGAAAAGAAAGGGGAGAGGGAG
1 AGGGGAGAGAAAAAAAAGAAGAGAGGGAG
1917398 AGGG
1 AGGG
1917402 AGCTCCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 4 0.15
27 15 0.58
28 5 0.19
29 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (29 bp):
AGGGGAGAGAAAAAAAAGAAGAGAGGGAG
Found at i:1917398 original size:20 final size:23
Alignment explanation
Indices: 1917355--1917399 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1917345 GGGAAGAAAA
1917355 AAAAGAAGAGAGGAGAGGGAGAG
1 AAAAGAAGAGAGGAGAGGGAGAG
*
1917378 AAAAGAA-AGGGGAGAGGGAGAG
1 AAAAGAAGAGAGGAGAGGGAGAG
1917400 GGAGCTCCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (23 bp):
AAAAGAAGAGAGGAGAGGGAGAG
Found at i:1917531 original size:16 final size:17
Alignment explanation
Indices: 1917510--1917545 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1917500 TAAAAATCTG
*
1917510 ATTTTTTTTATTTTT-T
1 ATTTTTATTATTTTTAT
1917526 ATTTTTATTATTTTTAT
1 ATTTTTATTATTTTTAT
1917543 ATT
1 ATT
1917546 CTAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
ATTTTTATTATTTTTAT
Found at i:1918372 original size:20 final size:20
Alignment explanation
Indices: 1918340--1918394 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1918330 TATTCTTAAT
*
1918340 TTAAATACCAAAAATATAAA
1 TTAAATACTAAAAATATAAA
1918360 -TATAATACTAAAACAT-TAAA
1 TTA-AATACTAAAA-ATATAAA
1918380 TTAAATA-TAAAAATA
1 TTAAATACTAAAAATA
1918395 AATTTATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 7 0.23
20 17 0.57
21 4 0.13
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAATACTAAAAATATAAA
Found at i:1921525 original size:114 final size:114
Alignment explanation
Indices: 1921325--1921549 Score: 450
Period size: 114 Copynumber: 2.0 Consensus size: 114
1921315 AGCCTTATTC
1921325 TTATTCAGTGGGCTTATATTAAATTATGTGTGAGCCCATTCTCACTGAATTGATAGCTAAGGTTA
1 TTATTCAGTGGGCTTATATTAAATTATGTGTGAGCCCATTCTCACTGAATTGATAGCTAAGGTTA
1921390 CACGGGTAGCCCAAGTTGACTGTGAACCTACTGTAGGATCAGTAAGTTT
66 CACGGGTAGCCCAAGTTGACTGTGAACCTACTGTAGGATCAGTAAGTTT
1921439 TTATTCAGTGGGCTTATATTAAATTATGTGTGAGCCCATTCTCACTGAATTGATAGCTAAGGTTA
1 TTATTCAGTGGGCTTATATTAAATTATGTGTGAGCCCATTCTCACTGAATTGATAGCTAAGGTTA
1921504 CACGGGTAGCCCAAGTTGACTGTGAACCTACTGTAGGATCAGTAAG
66 CACGGGTAGCCCAAGTTGACTGTGAACCTACTGTAGGATCAGTAAG
1921550 CATTATTTAG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (114 bp):
TTATTCAGTGGGCTTATATTAAATTATGTGTGAGCCCATTCTCACTGAATTGATAGCTAAGGTTA
CACGGGTAGCCCAAGTTGACTGTGAACCTACTGTAGGATCAGTAAGTTT
Found at i:1926077 original size:8 final size:8
Alignment explanation
Indices: 1926064--1926089 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1926054 AGTTAGGCTC
1926064 ATCTATAT
1 ATCTATAT
1926072 ATCTATAT
1 ATCTATAT
1926080 ATCTATAT
1 ATCTATAT
1926088 AT
1 AT
1926090 ATTGTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATCTATAT
Found at i:1932691 original size:22 final size:21
Alignment explanation
Indices: 1932656--1932731 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
1932646 AAAAGGTATC
* *
1932656 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
1932677 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1932700 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
1932719 TGC-AATCATATCT
1 TACAAATCATATCT
1932732 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1932745 original size:17 final size:18
Alignment explanation
Indices: 1932692--1932754 Score: 101
Period size: 18 Copynumber: 3.5 Consensus size: 18
1932682 AATCATATCT
1932692 TCTAAGATTGCATATCATA
1 TCTAAGATTGC-TATCATA
*
1932711 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
1932729 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
1932746 TCTAAGATT
1 TCTAAGATT
1932755 AGATTGCATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.36
18 16 0.38
19 11 0.26
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:1935202 original size:59 final size:59
Alignment explanation
Indices: 1935127--1935266 Score: 246
Period size: 59 Copynumber: 2.4 Consensus size: 59
1935117 ATTAGGGTCT
1935127 GAATTTAGCCTGGACTGGTAATTCAAATCAAAGCTCATTAGAGTAATTGTCGTTGCAGGG
1 GAATTTAGCCTGGACTGGTAATTCAAATCAAAGCTCATTAGAGTAATTGTCGTTGC-GGG
* *
1935187 G-ATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCGGG
1 GAATTTAGCCTGGACTGGTAATTCAAATCAAAGCTCATTAGAGTAATTGTCGTTGCGGG
1935245 GAATTTAGCCTGGACTGGTAAT
1 GAATTTAGCCTGGACTGGTAAT
1935267 CCCGAAAATA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
58 4 0.05
59 72 0.94
60 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (59 bp):
GAATTTAGCCTGGACTGGTAATTCAAATCAAAGCTCATTAGAGTAATTGTCGTTGCGGG
Found at i:1935409 original size:46 final size:46
Alignment explanation
Indices: 1935357--1935624 Score: 367
Period size: 46 Copynumber: 5.8 Consensus size: 46
1935347 AGTATGCTCT
* *
1935357 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1935403 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
1935449 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1935495 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *
1935541 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
1935588 TTGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
1935625 TATGACATCA
Statistics
Matches: 204, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 163 0.80
47 41 0.20
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1936639 original size:45 final size:45
Alignment explanation
Indices: 1936575--1936842 Score: 283
Period size: 45 Copynumber: 5.9 Consensus size: 45
1936565 CGATATCTAC
* * *
1936575 TATCTTTGATCTGTTCCCCGTCTAATACAGAGACGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * *
1936620 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATTTGC
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* *
1936665 T-TCTTCAATCTGCTCCCCGTCTAATAAAGAGATGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * *
1936709 TATCTTCGATTTGTTCCCTGTCTAATACAGAGATGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * * * * * * *
1936754 CATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAGATCTGCT
1 TATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAAATCTG-T
*
1936800 ATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1 -TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1936843 ATCTTGGATC
Statistics
Matches: 180, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
43 5 0.03
44 44 0.24
45 100 0.56
46 1 0.01
47 19 0.11
48 5 0.03
49 6 0.03
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
Found at i:1936702 original size:89 final size:89
Alignment explanation
Indices: 1936583--1936749 Score: 271
Period size: 89 Copynumber: 1.9 Consensus size: 89
1936573 ACTATCTTTG
* *
1936583 ATCTGTTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
1 ATCTGCTCCCCGTCTAATAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
1936648 AGAGACGCCAAATTTGCTTCTTCA
66 AGAGACGCCAAATTTGCTTCTTCA
* * * *
1936672 ATCTGCTCCCCGTCTAATAAAGAGATGCCAAATCTGTTATCTTCGATTTGTTCCCTGTCTAATAC
1 ATCTGCTCCCCGTCTAATAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
*
1936737 AGAGATGCCAAAT
66 AGAGACGCCAAAT
1936750 CTGTCATCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (89 bp):
ATCTGCTCCCCGTCTAATAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
AGAGACGCCAAATTTGCTTCTTCA
Found at i:1936911 original size:78 final size:78
Alignment explanation
Indices: 1936782--1937154 Score: 613
Period size: 78 Copynumber: 4.8 Consensus size: 78
1936772 ATGTAAACAC
1936782 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1936847 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * * *
1936860 ATGAAAGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTACC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1936924 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
*
1936938 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1937003 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * *
1937016 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATAT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1937081 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * **
1937094 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1937155 CGTTTCTTCA
Statistics
Matches: 274, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
77 2 0.01
78 270 0.99
79 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:1939619 original size:24 final size:24
Alignment explanation
Indices: 1939588--1939638 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1939578 AACCAAAACC
1939588 AAAAAATAAAA-CAAAAAAATATA
1 AAAAAATAAAACCAAAAAAATATA
* *
1939611 AAAATAATAAAACCAAAATAATTTA
1 AAAA-AATAAAACCAAAAAAATATA
1939636 AAA
1 AAA
1939639 GTCCATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 7 0.29
25 13 0.54
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (24 bp):
AAAAAATAAAACCAAAAAAATATA
Found at i:1950276 original size:42 final size:43
Alignment explanation
Indices: 1950221--1950306 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
1950211 TAATAAAATC
* * * *
1950221 AATTATAATTTGAATATTTATTTTTAAAA-ATATCAAGAGTAT
1 AATTACAACTTGAATAATTATTTTTAAAATATATCAAAAGTAT
*
1950263 AATTACAACTTGAATAATTATTTTTAAAATTTATCAAAAGTAT
1 AATTACAACTTGAATAATTATTTTTAAAATATATCAAAAGTAT
1950306 A
1 A
1950307 TATATCGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 26 0.68
43 12 0.32
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (43 bp):
AATTACAACTTGAATAATTATTTTTAAAATATATCAAAAGTAT
Found at i:1950819 original size:30 final size:30
Alignment explanation
Indices: 1950785--1950877 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 30
1950775 TAAATTTAAA
*
1950785 TTTAAAATTTAAAATATTATTTTTATAATT
1 TTTAAAAATTAAAATATTATTTTTATAATT
* * *
1950815 TTTAAAAAATTAAATTAAT-TTTTTATTATT
1 TTT-AAAAATTAAAATATTATTTTTATAATT
* * *
1950845 TTAAAAAAATAAAAATATAATTTTATCATAATT
1 TT-TAAAAATTAAAATATTATTTT-T-ATAATT
1950878 AATTTAAGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
30 26 0.54
31 16 0.33
32 1 0.02
33 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAAAAATTAAAATATTATTTTTATAATT
Found at i:1954573 original size:29 final size:27
Alignment explanation
Indices: 1954487--1954576 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 27
1954477 TTTACAAGAA
*
1954487 TTACATCAAATTAAAACTTTATGTATGAAAT
1 TTACAT-AAATTAAAA-TTAATGTAT--AAT
*
1954518 TTACA-AAATTAAAATTCATATATATAAT
1 TTACATAAATTAAAATT-A-ATGTATAAT
1954546 TATACATTAAATTAAAATTAATGTATAAT
1 T-TACA-TAAATTAAAATTAATGTATAAT
1954575 TT
1 TT
1954577 TGAAAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 7 0.14
29 22 0.43
30 6 0.12
31 16 0.31
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (27 bp):
TTACATAAATTAAAATTAATGTATAAT
Found at i:1964856 original size:18 final size:18
Alignment explanation
Indices: 1964830--1964868 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1964820 TCCAATATAG
*
1964830 TCAAGCTTAAAGAAACCA
1 TCAAACTTAAAGAAACCA
1964848 TCAAACTTAAAGAAACCA
1 TCAAACTTAAAGAAACCA
1964866 TCA
1 TCA
1964869 GCTCCCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (18 bp):
TCAAACTTAAAGAAACCA
Found at i:1974492 original size:21 final size:21
Alignment explanation
Indices: 1974466--1974506 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1974456 AGACGAGCGA
* *
1974466 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1974487 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1974507 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1982006 original size:21 final size:21
Alignment explanation
Indices: 1981980--1982020 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1981970 ATCTGCTCAA
* *
1981980 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1982001 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1982021 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1985561 original size:16 final size:16
Alignment explanation
Indices: 1985540--1985570 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1985530 AACATTATGA
*
1985540 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
1985556 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
1985571 CCAAGTGGTG
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:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:1988361 original size:21 final size:21
Alignment explanation
Indices: 1988335--1988375 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1988325 AGACGAGCGA
* *
1988335 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1988356 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1988376 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1990308 original size:16 final size:16
Alignment explanation
Indices: 1990287--1990317 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1990277 AATATTATGA
*
1990287 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
1990303 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
1990318 CCAAGTGGTG
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:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:1999730 original size:31 final size:31
Alignment explanation
Indices: 1999669--1999750 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1999659 TTAGAATTAA
* *
1999669 TGTTTTTGGTTGTATTTTTATGTTAAATTTGC
1 TGTTTTTGGTTGCA-TTTTATATTAAATTTGC
* * *
1999701 TGTTTTTGGCTGCATTTTATATTATATTTGT
1 TGTTTTTGGTTGCATTTTATATTAAATTTGC
* *
1999732 TGTATTTGGTTGGATTTTA
1 TGTTTTTGGTTGCATTTTA
1999751 ATGCAAGAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 30 0.71
32 12 0.29
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.61
Consensus pattern (31 bp):
TGTTTTTGGTTGCATTTTATATTAAATTTGC
Done.