Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 12 of 125
Found at i:1860226 original size:9 final size:9
Alignment explanation
Indices: 1860202--1860243 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
1860192 CAATTTGTCC
*
1860202 TGTATTATTT
1 TGTATT-TTA
1860212 TGTATTTTA
1 TGTATTTTA
1860221 TGTATTTTA
1 TGTATTTTA
1860230 TGTATTTTA
1 TGTATTTTA
1860239 T-TATT
1 TGTATT
1860244 ATGTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TGTATTTTA
Found at i:1860235 original size:18 final size:19
Alignment explanation
Indices: 1860202--1860255 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1860192 CAATTTGTCC
*
1860202 TGTATTATTTTGTATTTTA
1 TGTATTATTATGTATTTTA
1860221 TGTATT-TTATGTATTTTA
1 TGTATTATTATGTATTTTA
*
1860239 T-TATTATGTATATATTT
1 TGTATTAT-TATGTATTT
1860256 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (19 bp):
TGTATTATTATGTATTTTA
Found at i:1860726 original size:26 final size:24
Alignment explanation
Indices: 1860684--1860737 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
1860674 CTGGGAGTGA
*
1860684 GAAAAATTTTTTAGAAATTTTTGG
1 GAAAAATTTTTTAGAAATTTCTGG
* *
1860708 CGAAAATTTTTTCTGGAAATTTCTGG
1 -GAAAAATTTTT-TAGAAATTTCTGG
1860734 GAAA
1 GAAA
1860738 TTTCCAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (24 bp):
GAAAAATTTTTTAGAAATTTCTGG
Found at i:1860780 original size:19 final size:19
Alignment explanation
Indices: 1860758--1860817 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1860748 CCGACGAAAA
1860758 TTCCGGCGAAGTTTGAATT
1 TTCCGGCGAAGTTTGAATT
1860777 TTCCGGCGAA-----AA--
1 TTCCGGCGAAGTTTGAATT
*
1860789 TTCCGGCAAAGTTTGAATT
1 TTCCGGCGAAGTTTGAATT
1860808 TTCCGGCGAA
1 TTCCGGCGAA
1860818 AATTCCGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
12 9 0.28
14 2 0.06
17 2 0.06
19 19 0.59
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (19 bp):
TTCCGGCGAAGTTTGAATT
Found at i:1860781 original size:31 final size:31
Alignment explanation
Indices: 1860746--1860847 Score: 150
Period size: 31 Copynumber: 3.3 Consensus size: 31
1860736 AATTTCCAGA
* *
1860746 TTCCGACGAAAATTCCGGCGAAGTTTGAATT
1 TTCCGGCGAAAATTCCGGCAAAGTTTGAATT
1860777 TTCCGGCGAAAATTCCGGCAAAGTTTGAATT
1 TTCCGGCGAAAATTCCGGCAAAGTTTGAATT
* ** *
1860808 TTCCGGCGAAAATTCCGGCCAACATTGAAGT
1 TTCCGGCGAAAATTCCGGCAAAGTTTGAATT
1860839 TTCCGGCGA
1 TTCCGGCGA
1860848 CCTGCCCAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (31 bp):
TTCCGGCGAAAATTCCGGCAAAGTTTGAATT
Found at i:1860933 original size:20 final size:20
Alignment explanation
Indices: 1860908--1860945 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1860898 ACTTCCGGTG
*
1860908 AAATTTCCAGATTCCGGCGA
1 AAATTTCCAGAATCCGGCGA
1860928 AAATTTCCAGAATCCGGC
1 AAATTTCCAGAATCCGGC
1860946 ACCGGTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
AAATTTCCAGAATCCGGCGA
Found at i:1861433 original size:57 final size:57
Alignment explanation
Indices: 1861352--1861639 Score: 375
Period size: 57 Copynumber: 5.0 Consensus size: 57
1861342 AAATTCTAAA
* * *
1861352 AAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTTC
* *
1861410 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT-AAATTTAAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTT---C
* * *
1861469 AAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTTC
* *
1861526 AAAAACTATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCAAAATTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT-AAAATTTC
* *
1861584 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAA-AAAATT
1 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATT
1861640 CATTCTTTCC
Statistics
Matches: 202, Mismatches: 19, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
56 6 0.03
57 84 0.42
58 18 0.09
59 46 0.23
60 48 0.24
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTTC
Found at i:1861480 original size:116 final size:117
Alignment explanation
Indices: 1861341--1861640 Score: 437
Period size: 116 Copynumber: 2.6 Consensus size: 117
1861331 TAAAAATAAA
* * *
1861341 AAAATTCTAAAAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
1 AAAATT-TAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAA
* *
1861406 TTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT
65 TTCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCT-AGAAAAT
*
1861459 -AAATTTAAAAAAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAAT
1 AAAATTTAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAAT
* *
1861523 TCCAAAAACTATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
66 TCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
* * * *
1861575 CAAAATTT-CAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTACAAA-AAAA
1 -AAAATTTAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAA
1861638 TTC
65 TTC
1861641 ATTCTTTCCT
Statistics
Matches: 166, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
115 1 0.01
116 108 0.65
117 51 0.31
118 6 0.04
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (117 bp):
AAAATTTAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAAT
TCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTAGAAAAT
Found at i:1862337 original size:24 final size:22
Alignment explanation
Indices: 1862310--1862371 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 22
1862300 TTGAAAACAT
*
1862310 AAAAAAATATTTTTTAAATTCA
1 AAAAAAATATTTTTTAAATTAA
*
1862332 ACAAAAATGATGTTTTTAAAATTAA
1 AAAAAAAT-AT-TTTTT-AAATTAA
1862357 AAAACAAA-ATTTTTT
1 AAAA-AAATATTTTTT
1862372 GTTGAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 7 0.21
25 9 0.27
26 3 0.09
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (22 bp):
AAAAAAATATTTTTTAAATTAA
Found at i:1862371 original size:73 final size:74
Alignment explanation
Indices: 1862212--1862379 Score: 214
Period size: 72 Copynumber: 2.3 Consensus size: 74
1862202 TCTAAGATCT
* * * *
1862212 AAACATAATTTTTGTTGAAAACATAAAAAATATATTTTTTAAAATTTAATAAAGATGACGTTTTT
1 AAACAAAATTTTTGTTGAAAACATAAAAAATATATTTTTTAAAATTCAACAAAAATGACGTTTTT
* *
1862277 TAGATTAAA
66 AAAATTAAA
*** * *
1862286 AAATGCAATTTTTATTGAAAACATAAAAAA-ATATTTTTT-AAATTCAACAAAAATGATGTTTTT
1 AAACAAAATTTTTGTTGAAAACATAAAAAATATATTTTTTAAAATTCAACAAAAATGACGTTTTT
1862349 AAAATTAAA
66 AAAATTAAA
1862358 AAACAAAATTTTTTGTTGAAAA
1 AAACAAAA-TTTTTGTTGAAAA
1862380 TATGACATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
72 32 0.41
73 21 0.27
74 26 0.33
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (74 bp):
AAACAAAATTTTTGTTGAAAACATAAAAAATATATTTTTTAAAATTCAACAAAAATGACGTTTTT
AAAATTAAA
Found at i:1863501 original size:24 final size:25
Alignment explanation
Indices: 1863443--1863502 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
1863433 ATACAGATAT
1863443 AATTATTTA-TTTTGAATAGATAAA
1 AATTATTTATTTTTGAATAGATAAA
* * *
1863467 AATTATCTATTTTTTAATA-ATTAA
1 AATTATTTATTTTTGAATAGATAAA
*
1863491 AATTGTTTATTT
1 AATTATTTATTT
1863503 GAACCATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (25 bp):
AATTATTTATTTTTGAATAGATAAA
Found at i:1863995 original size:19 final size:19
Alignment explanation
Indices: 1863945--1863996 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1863935 CAAATATAAT
* *
1863945 ATTTATTAAATAATTTGTGA
1 ATTTATTAAAT-TTTTATGA
* * *
1863965 ATATATTTAATTTTTATGC
1 ATTTATTAAATTTTTATGA
1863984 ATTTATTAAATTT
1 ATTTATTAAATTT
1863997 AATAAATAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTATTAAATTTTTATGA
Found at i:1874639 original size:24 final size:24
Alignment explanation
Indices: 1874607--1874657 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1874597 TTTCCAACCT
1874607 TAATCTAGATAATTCTAAACACTA
1 TAATCTAGATAATTCTAAACACTA
*
1874631 TAATGTAGATAATTCTAAACACTA
1 TAATCTAGATAATTCTAAACACTA
1874655 TAA
1 TAA
1874658 AGTAACACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (24 bp):
TAATCTAGATAATTCTAAACACTA
Found at i:1874811 original size:11 final size:11
Alignment explanation
Indices: 1874797--1874821 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1874787 CATATATTTG
1874797 ATACAATACGA
1 ATACAATACGA
1874808 ATACAATACGA
1 ATACAATACGA
1874819 ATA
1 ATA
1874822 TACAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (11 bp):
ATACAATACGA
Found at i:1878307 original size:2 final size:2
Alignment explanation
Indices: 1878300--1878327 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1878290 ACTTAACAAA
1878300 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
1878328 GATCTCTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1881890 original size:22 final size:22
Alignment explanation
Indices: 1881864--1881907 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1881854 TGTATATTTA
*
1881864 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1881886 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1881908 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:1885551 original size:22 final size:22
Alignment explanation
Indices: 1885525--1885568 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1885515 TGTATATTTA
*
1885525 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1885547 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1885569 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:1896215 original size:20 final size:21
Alignment explanation
Indices: 1896179--1896218 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1896169 GTTCCGTAAT
1896179 AAATGTATTTTATTTATTTAA
1 AAATGTATTTTATTTATTTAA
1896200 AAAT-TATTATTA-TTATTTA
1 AAATGTATT-TTATTTATTTA
1896219 TAAGAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AAATGTATTTTATTTATTTAA
Found at i:1896358 original size:12 final size:12
Alignment explanation
Indices: 1896341--1896366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1896331 AATTATATAA
1896341 ATCTTATATCTT
1 ATCTTATATCTT
1896353 ATCTTATATCTT
1 ATCTTATATCTT
1896365 AT
1 AT
1896367 ATAAAAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (12 bp):
ATCTTATATCTT
Found at i:1896487 original size:7 final size:7
Alignment explanation
Indices: 1896475--1896501 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1896465 TCTATTAAGC
1896475 ATTTAAA
1 ATTTAAA
1896482 ATTTAAA
1 ATTTAAA
1896489 ATTTAAA
1 ATTTAAA
1896496 ATTTAA
1 ATTTAA
1896502 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:1896695 original size:166 final size:166
Alignment explanation
Indices: 1896415--1896744 Score: 597
Period size: 166 Copynumber: 2.0 Consensus size: 166
1896405 ATGTGAATAA
* *
1896415 TTTATCTTTTGCAACATGTGAACAATTTAAAAAATTGACATGTGTTAAAATCTATTAAGCATTTA
1 TTTATATTTTGCAACATGTGAACAATTTAAAAAATTGACATGTGTTAAAATCAATTAAGCATTTA
* *
1896480 AAATTTAAAATTTAAAATTTAATGATAAAATAAATTTAATTTCATATGCCATATTTCCATTATTA
66 AAATATAAAATATAAAATTTAATGATAAAATAAATTTAATTTCATATGCCATATTTCCATTATTA
1896545 TAAAACACGTTCAATGATTCTTATTAACATGTAAAT
131 TAAAACACGTTCAATGATTCTTATTAACATGTAAAT
* *
1896581 TTTATATTTTGCAACATGTGAACAATTTAAAAAATTGACATGTGTTAAAATCAATTATGCATTTC
1 TTTATATTTTGCAACATGTGAACAATTTAAAAAATTGACATGTGTTAAAATCAATTAAGCATTTA
*
1896646 AAATATAAAATATAAAATTTAATGATCAAATAAATTTAATTTCATATGCCATATTTCCATTATTA
66 AAATATAAAATATAAAATTTAATGATAAAATAAATTTAATTTCATATGCCATATTTCCATTATTA
1896711 TAAAACACGTTCAATGATTCTTATTAACATGTAA
131 TAAAACACGTTCAATGATTCTTATTAACATGTAA
1896745 GGAAAATATT
Statistics
Matches: 157, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 157 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (166 bp):
TTTATATTTTGCAACATGTGAACAATTTAAAAAATTGACATGTGTTAAAATCAATTAAGCATTTA
AAATATAAAATATAAAATTTAATGATAAAATAAATTTAATTTCATATGCCATATTTCCATTATTA
TAAAACACGTTCAATGATTCTTATTAACATGTAAAT
Found at i:1897907 original size:2 final size:2
Alignment explanation
Indices: 1897893--1897932 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1897883 TTTTAAAATC
* *
1897893 AT AT AT -T AA AT AT AT AT AT AT AT AT AT AT AC AT 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
1897933 GCTTAAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1898461 original size:16 final size:18
Alignment explanation
Indices: 1898425--1898461 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1898415 ATAATTTTTT
1898425 ATTAGTATTTTATATAAC
1 ATTAGTATTTTATATAAC
1898443 ATTA-TATTTTATA-AAC
1 ATTAGTATTTTATATAAC
1898459 ATT
1 ATT
1898462 TTATGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTAGTATTTTATATAAC
Found at i:1902820 original size:2 final size:2
Alignment explanation
Indices: 1902815--1902843 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1902805 TCTCTCTCTT
1902815 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 T
1902844 TTATTGAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1903527 original size:2 final size:2
Alignment explanation
Indices: 1903515--1903543 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1903505 TTCTTTTAGA
1903515 AT AT A- 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
1903544 TAATACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1907056 original size:18 final size:18
Alignment explanation
Indices: 1907033--1907068 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1907023 ATAAAAATAA
*
1907033 TGAGATCGAGGTTGAGGT
1 TGAGATCGAGATTGAGGT
*
1907051 TGAGATTGAGATTGAGGT
1 TGAGATCGAGATTGAGGT
1907069 CGCTAAGGTC
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:0.25, C:0.03, G:0.42, T:0.31
Consensus pattern (18 bp):
TGAGATCGAGATTGAGGT
Found at i:1920984 original size:19 final size:19
Alignment explanation
Indices: 1920952--1921003 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1920942 TCAGTATAAA
**
1920952 AAAAAATTAAAAAAAATCT
1 AAAAAATTTTAAAAAATCT
**
1920971 AAAAAATTTTAAAATTTCT
1 AAAAAATTTTAAAAAATCT
*
1920990 AAAAGTATTTTAAA
1 AAAA-AATTTTAAA
1921004 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAATTTTAAAAAATCT
Found at i:1921058 original size:9 final size:9
Alignment explanation
Indices: 1921016--1921298 Score: 76
Period size: 9 Copynumber: 29.2 Consensus size: 9
1921006 TTTTTTAAAA
*
1921016 ATAAAAAAT
1 ATAAAAATT
*
1921025 ATATAAAATA
1 ATA-AAAATT
* *
1921035 ATATATATT
1 ATAAAAATT
1921044 -TAAAAATT
1 ATAAAAATT
1921052 ATAAAAAACTTT
1 AT-AAAAA--TT
*
1921064 TTAAAAATT
1 ATAAAAATT
*
1921073 AAAAAAAATT
1 -ATAAAAATT
*
1921083 -TGAAAATTT
1 AT-AAAAATT
*
1921092 CTAAAAATT
1 ATAAAAATT
* *
1921101 TTAAAATTT
1 ATAAAAATT
*
1921110 CAACAAAAATT
1 --ATAAAAATT
1921121 CA-AATCAAATT
1 -ATAA--AAATT
*
1921132 TTAAAAATT
1 ATAAAAATT
1921141 ATAAAAACTT
1 ATAAAAA-TT
1921151 ATGAAAAATT
1 AT-AAAAATT
* *
1921161 TTCAAAAAAAT
1 AT--AAAAATT
1921172 ACTAAAAATT
1 A-TAAAAATT
*
1921182 ATTTTAAAATTT
1 A---TAAAAATT
*
1921194 CTAAAAAATT
1 AT-AAAAATT
1921204 ATAAAAATAT
1 ATAAAAAT-T
* *
1921214 TTGAAAATTTT
1 AT-AAAA-ATT
*
1921225 AAAAAAATT
1 ATAAAAATT
1921234 A-AGAAAATT
1 ATA-AAAATT
*
1921243 -TAAAATTT
1 ATAAAAATT
1921251 ATAAAAA-T
1 ATAAAAATT
1921259 ATTAAAAA-T
1 A-TAAAAATT
*
1921268 ATAAATTATTT
1 ATAAA--AATT
*
1921279 TTAAAAATT
1 ATAAAAATT
1921288 ATAAAAATT
1 ATAAAAATT
1921297 AT
1 AT
1921299 GATAATTTTT
Statistics
Matches: 202, Mismatches: 42, Indels: 60
0.66 0.14 0.20
Matches are distributed among these distances:
8 18 0.09
9 84 0.42
10 49 0.24
11 39 0.19
12 12 0.06
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1921088 original size:19 final size:20
Alignment explanation
Indices: 1921041--1921090 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1921031 AATAATATAT
1921041 ATTTAAAAATTATAAAAAAC
1 ATTTAAAAATTATAAAAAAC
*
1921061 TTTTTAAAAATTA-AAAAAA-
1 -ATTTAAAAATTATAAAAAAC
*
1921080 ATTTGAAAATT
1 ATTTAAAAATT
1921091 TCTAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.35
20 6 0.23
21 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTTAAAAATTATAAAAAAC
Found at i:1921266 original size:19 final size:18
Alignment explanation
Indices: 1921127--1921296 Score: 67
Period size: 19 Copynumber: 8.8 Consensus size: 18
1921117 AATTCAAATC
* *
1921127 AAATTTTAAAAATTATAA
1 AAATATTAAAAATTTTAA
*
1921145 AAACTTATGAAAAATTTTCAAAA
1 AAA--TATTAAAAATTTT---AA
* *
1921168 AAATACTAAAAATTATTTTA
1 AAATATTAAAAA-T-TTTAA
* *
1921188 AAATTTCTAAAAAATTATAA
1 AAATAT-T-AAAAATTTTAA
*
1921208 AAATATTTGAAAATTTTAA
1 AAATA-TTAAAAATTTTAA
* *
1921227 AAAAATTAAGAAAATTT-A
1 AAATATTAA-AAATTTTAA
* *
1921245 AAATTTATAAAAATATTAA
1 AAATAT-TAAAAATTTTAA
*
1921264 AAATA-TAAATTATTTTTAA
1 AAATATTAAA--AATTTTAA
1921283 AAAT-TATAAAAATT
1 AAATAT-TAAAAATT
1921297 ATGATAATTT
Statistics
Matches: 111, Mismatches: 24, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
17 4 0.04
18 19 0.17
19 37 0.33
20 27 0.24
21 10 0.09
22 6 0.05
23 8 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
AAATATTAAAAATTTTAA
Found at i:1921422 original size:34 final size:35
Alignment explanation
Indices: 1921384--1921450 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
1921374 TAAAGTTTAT
1921384 AAAATCTCAAAAA-CTTTAAAA-CTAAAAATAAAAA
1 AAAAT-TCAAAAATCTTTAAAATCTAAAAATAAAAA
* * *
1921418 AAAATTTAAAAATTTTTAAAATTTAAAAATAAA
1 AAAATTCAAAAATCTTTAAAATCTAAAAATAAA
1921451 TTCTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 6 0.21
34 12 0.43
35 10 0.36
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (35 bp):
AAAATTCAAAAATCTTTAAAATCTAAAAATAAAAA
Found at i:1921472 original size:60 final size:57
Alignment explanation
Indices: 1921408--1921530 Score: 131
Period size: 60 Copynumber: 2.1 Consensus size: 57
1921398 TTTAAAACTA
*
1921408 AAAATAAAAAAAAATTTAAA-AATTTTTAAAATTTAAAAATAAATTCTAAAAATTTTTTTT
1 AAAATAAAAAAAAA-TTAAATAA-TTTCAAAATTTAAAAA-AAATTCT-AAAATTTTTTTT
**** * *
1921468 AAAATTTTTGAAAAATTAAATAATTTCAAAATTTTAAAAACATTCTAAAATTTTTTTT
1 AAAA-TAAAAAAAAATTAAATAATTTCAAAATTTAAAAAAAATTCTAAAATTTTTTTT
1921526 AAAAT
1 AAAAT
1921531 CTAAAGAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
57 1 0.02
58 16 0.30
59 6 0.11
60 23 0.43
61 8 0.15
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (57 bp):
AAAATAAAAAAAAATTAAATAATTTCAAAATTTAAAAAAAATTCTAAAATTTTTTTT
Found at i:1931408 original size:2 final size:2
Alignment explanation
Indices: 1931403--1931436 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1931393 GCAAAAAAAA
*
1931403 AT AT AT AT AT AT AT GT 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
1931437 TATTTAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1937048 original size:20 final size:21
Alignment explanation
Indices: 1937010--1937048 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1937000 TTCAACTAAA
*
1937010 ACAATAAAAAAAACCAAAATT
1 ACAATAAAAAAAACAAAAATT
*
1937031 ACAA-AAAAAAAAGAAAAA
1 ACAATAAAAAAAACAAAAA
1937049 AAATCAAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.79, C:0.10, G:0.03, T:0.08
Consensus pattern (21 bp):
ACAATAAAAAAAACAAAAATT
Found at i:1937975 original size:19 final size:20
Alignment explanation
Indices: 1937941--1938003 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
1937931 TTTTAGGTTA
*
1937941 AATAAAAATTTAATTA-AAT
1 AATAAAAAATTAATTATAAT
* * *
1937960 ATTAAAAAATTGATTATTAT
1 AATAAAAAATTAATTATAAT
* *
1937980 AATAAAAAATAAAATTTTAAT
1 AATAAAAAAT-TAATTATAAT
1938001 AAT
1 AAT
1938004 TTTTAATTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 13 0.39
20 11 0.33
21 9 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATAAAAAATTAATTATAAT
Found at i:1938590 original size:2 final size:2
Alignment explanation
Indices: 1938583--1938608 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1938573 TGGTTACTAA
1938583 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
1938609 TATTTGTATA
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:1942031 original size:22 final size:23
Alignment explanation
Indices: 1942005--1942052 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1941995 AAATAAATAT
1942005 ATTATTTTTAAT-TATT-TAAAAA
1 ATTA-TTTTAATATATTGTAAAAA
*
1942027 ATTATTTTAATATATTGTAATAA
1 ATTATTTTAATATATTGTAAAAA
1942050 ATT
1 ATT
1942053 TTAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
23 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTATTTTAATATATTGTAAAAA
Found at i:1943004 original size:17 final size:18
Alignment explanation
Indices: 1942977--1943010 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1942967 TTCATTAAAA
*
1942977 TTTTGTTAAAAGATTTAC
1 TTTTGTTAAAAAATTTAC
1942995 TTTT-TTAAAAAATTTA
1 TTTTGTTAAAAAATTTA
1943011 TTTAGGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTTGTTAAAAAATTTAC
Found at i:1944794 original size:25 final size:25
Alignment explanation
Indices: 1944737--1944803 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 25
1944727 TAAAGGGATT
* * *
1944737 AAATGATTATGAAAGTCTGGCCAAA
1 AAATGATTATAAAAGTCCGACCAAA
1944762 AATATGATTATAAAAGTCCGACCAAA
1 AA-ATGATTATAAAAGTCCGACCAAA
1944788 AAATGATTATAAAAGT
1 AAATGATTATAAAAGT
1944804 GAATCAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 16 0.42
26 22 0.58
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (25 bp):
AAATGATTATAAAAGTCCGACCAAA
Found at i:1947144 original size:19 final size:18
Alignment explanation
Indices: 1947106--1947144 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1947096 TTATAATTTT
**
1947106 TTTATTTTAAAATTATGA
1 TTTATTTTAAAAAAATGA
1947124 TTTATTTTATAAAAAATGA
1 TTTATTTTA-AAAAAATGA
1947143 TT
1 TT
1947145 AATTATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTATTTTAAAAAAATGA
Found at i:1952766 original size:41 final size:41
Alignment explanation
Indices: 1952697--1952775 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
1952687 CCGGATTTTA
* *
1952697 ACAAATAAACTAAATCAAAGACTCTAACATCAGCAACCTCC
1 ACAAATAAACTAAATCAAACACTCTAACATCAACAACCTCC
* * *
1952738 ACAAATAAACTCAATCGAACACTTTAACATCAACAACC
1 ACAAATAAACTAAATCAAACACTCTAACATCAACAACC
1952776 AAGAAGAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.49, C:0.29, G:0.04, T:0.18
Consensus pattern (41 bp):
ACAAATAAACTAAATCAAACACTCTAACATCAACAACCTCC
Found at i:1953121 original size:2 final size:2
Alignment explanation
Indices: 1953114--1953154 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1953104 GTTATTCTAG
1953114 AT AT AT 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 AT AT AT A
1953155 GAAAGTGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1956972 original size:28 final size:25
Alignment explanation
Indices: 1956931--1957000 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
1956921 ACACAATACG
*
1956931 ATATTATAGTAGTATAATAGTATATT
1 ATATTATA-TAGTATAATAGTATATC
*
1956957 ATTATTACTATTAGTAT--TATTATATC
1 A-TATTA-TA-TAGTATAATAGTATATC
1956983 ATATTATATAGTATAATA
1 ATATTATATAGTATAATA
1957001 TATTACATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 6 0.16
24 2 0.05
25 7 0.19
26 9 0.24
27 5 0.14
28 8 0.22
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (25 bp):
ATATTATATAGTATAATAGTATATC
Found at i:1957943 original size:6 final size:6
Alignment explanation
Indices: 1957934--1958006 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
1957924 AGGTTTTCCT
* *
1957934 TTTTTA TTTTTA TTTTATT TTTTTA TTTTTA --TTTA TTTTCATA TTTTGA
1 TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA TTTT--TA TTTTTA
* *
1957983 --GTTA GTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
1958007 ATCTTTTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
4 6 0.11
6 36 0.68
7 5 0.09
8 6 0.11
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:1957955 original size:19 final size:18
Alignment explanation
Indices: 1957933--1957972 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
1957923 AAGGTTTTCC
1957933 TTTTTTATTTTTATTTTAT
1 TTTTTTATTTTTA-TTTAT
1957952 TTTTTTATTTTTATTTAT
1 TTTTTTATTTTTATTTAT
1957970 TTT
1 TTT
1957973 CATATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTATTTTTATTTAT
Found at i:1957956 original size:18 final size:17
Alignment explanation
Indices: 1957933--1958001 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
1957923 AAGGTTTTCC
1957933 TTTTTTATTTTTATTTTA
1 TTTTTTATTTTTA-TTTA
1957951 TTTTTTTATTTTTATTTA
1 -TTTTTTATTTTTATTTA
* * *
1957969 TTTTCATATTTTGAGTTA
1 TTTT-TTATTTTTATTTA
*
1957987 -GTTTTATTTTTATTT
1 TTTTTTATTTTTATTT
1958002 TTATTATCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 9 0.21
17 6 0.14
18 14 0.33
19 13 0.31
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTTATTTTTATTTA
Found at i:1958021 original size:15 final size:15
Alignment explanation
Indices: 1957933--1958016 Score: 68
Period size: 16 Copynumber: 5.5 Consensus size: 15
1957923 AAGGTTTTCC
1957933 TTTT-TTATTTTTA-
1 TTTTATTATTTTTAT
1957946 TTTTATT-TTTTTAT
1 TTTTATTATTTTTAT
1957960 TTTTATTTATTTTCATAT
1 TTTTA-TTATTTT--TAT
* *
1957978 TTTGAGTTAGTTTTAT
1 TTTTA-TTATTTTTAT
1957994 TTTTATT-TTTATTAT
1 TTTTATTATTT-TTAT
1958009 CTTTTATT
1 -TTTTATT
1958017 TTATTGGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
13 10 0.17
14 9 0.16
15 8 0.14
16 18 0.31
18 13 0.22
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:1967699 original size:17 final size:18
Alignment explanation
Indices: 1967664--1967709 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1967654 ATTCCAAAAA
*
1967664 TTTTA-TATTTTTATGTT
1 TTTTATTATTTTTATATT
1967681 TTTTATTATTTTTA-ATT
1 TTTTATTATTTTTATATT
*
1967698 TTTAATT-TTTTT
1 TTTTATTATTTTT
1967710 GGTTTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.19
17 13 0.50
18 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATTATTTTTATATT
Found at i:1969786 original size:31 final size:31
Alignment explanation
Indices: 1969748--1969810 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1969738 GTTTATCAAA
1969748 AAAGAGATAATCTATAGATATAAGCTCCTAG
1 AAAGAGATAATCTATAGATATAAGCTCCTAG
1969779 AAAGAGATAATCTATAGATATAAGCTCCTAG
1 AAAGAGATAATCTATAGATATAAGCTCCTAG
1969810 A
1 A
1969811 GAGGATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (31 bp):
AAAGAGATAATCTATAGATATAAGCTCCTAG
Found at i:1971304 original size:60 final size:60
Alignment explanation
Indices: 1971240--1971368 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
1971230 TCCAAATCAT
* * *
1971240 TTTCAGACTTACAACATCAT-TCTGATCATTCATTTATGACCTCGACTTGAGCTTGGTCGC
1 TTTCAGACTCACAACATCATCT-TGATCATTCATTTATGACCTCGACTCGAGCTTGGTCAC
* * * * *
1971300 TTTCAGACTCGCGATATCATCTTGGTCATTCATTTATGACCTCGACTCGATCTTGGTCAC
1 TTTCAGACTCACAACATCATCTTGATCATTCATTTATGACCTCGACTCGAGCTTGGTCAC
1971360 TTTCAGACT
1 TTTCAGACT
1971369 ATGAAATCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 59 0.98
61 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (60 bp):
TTTCAGACTCACAACATCATCTTGATCATTCATTTATGACCTCGACTCGAGCTTGGTCAC
Found at i:1972185 original size:3 final size:3
Alignment explanation
Indices: 1972171--1972210 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1972161 TACCATATCA
*
1972171 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1972211 TCTTCTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1972301 original size:17 final size:17
Alignment explanation
Indices: 1972271--1972303 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1972261 AAAATCAATT
1972271 GATCAGAAGATGTTTAC
1 GATCAGAAGATGTTTAC
1972288 GATCA-AAGAGTGTTTA
1 GATCAGAAGA-TGTTTA
1972304 ATGACACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (17 bp):
GATCAGAAGATGTTTAC
Found at i:1972722 original size:13 final size:13
Alignment explanation
Indices: 1972706--1972732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1972696 TTATGAGTTT
1972706 TTGAATTTTTCAA
1 TTGAATTTTTCAA
1972719 TTGAATTTTTCAA
1 TTGAATTTTTCAA
1972732 T
1 T
1972733 GAGGTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TTGAATTTTTCAA
Found at i:1973198 original size:25 final size:25
Alignment explanation
Indices: 1973166--1973214 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1973156 AAAAACGAAA
1973166 AAATAAGT-AAATAAAAAATCTTTTC
1 AAATAAGTCAAA-AAAAAATCTTTTC
*
1973191 AAATAAGTCTAAAAAAAATCTTTT
1 AAATAAGTCAAAAAAAAATCTTTT
1973215 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATAAGTCAAAAAAAAATCTTTTC
Found at i:1973316 original size:207 final size:210
Alignment explanation
Indices: 1973089--1973511 Score: 753
Period size: 211 Copynumber: 2.0 Consensus size: 210
1973079 ATTTTACTGG
* *
1973089 TTTATTTATTTACCTTATTTAGTAATACAATATTCATAAAAAAAGGGGTTTCTTCTTCCTGGAGA
1 TTTATTTATTTACCTTATTTAGTAATACAATATTCATAAAAAAAAGGGTTTCTTCTTCCTAGAGA
1973154 AT-AAAAACGAAAAAATAAGTAAATAAAAAATCTTTTCAAATAAGTCT-AAAA-AAAATCTTTTT
66 ATAAAAAACGAAAAAATAAGTAAATAAAAAATCTTTTCAAATAAGTCTAAAAAGAAAATCTTTTT
* *
1973216 TAAATAAATTTATAGAATCCACCAAACTATTGAAAAATTTTATAAATTAATTTTTTTAAAATAAT
131 TAAATAAATTTATAGAATCCACCAAACTATTGAAAAATTTCATAAATTAATTTTTTAAAAATAAT
1973281 AATAAATAAATATTT
196 AATAAATAAATATTT
1973296 TTTATTTATTTACCTTATTTAGTAATACAATATTCATAAAAAAAAGGGTTTCTTCTTCCTAGAGA
1 TTTATTTATTTACCTTATTTAGTAATACAATATTCATAAAAAAAAGGGTTTCTTCTTCCTAGAGA
1973361 ATAAAAAACGAAAAAATAAGTAAATAAAAAATCTTTTCAAATAAGTCTAAAAAAGAAAATCTTTT
66 ATAAAAAACGAAAAAATAAGTAAATAAAAAATCTTTTCAAATAAGTCT-AAAAAGAAAATCTTTT
* * *
1973426 TTAAATAAATTTATGGAATCCACCAAATTATTGAGAAATTTCATAAATTAATTTTTTAAAAATAA
130 TTAAATAAATTTATAGAATCCACCAAACTATTGAAAAATTTCATAAATTAATTTTTTAAAAATAA
1973491 TAATAAATAAATATTT
195 TAATAAATAAATATTT
1973507 TTTAT
1 TTTAT
1973512 CCTCTAAACT
Statistics
Matches: 205, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
207 65 0.32
208 45 0.22
210 4 0.02
211 91 0.44
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (210 bp):
TTTATTTATTTACCTTATTTAGTAATACAATATTCATAAAAAAAAGGGTTTCTTCTTCCTAGAGA
ATAAAAAACGAAAAAATAAGTAAATAAAAAATCTTTTCAAATAAGTCTAAAAAGAAAATCTTTTT
TAAATAAATTTATAGAATCCACCAAACTATTGAAAAATTTCATAAATTAATTTTTTAAAAATAAT
AATAAATAAATATTT
Found at i:1973402 original size:25 final size:27
Alignment explanation
Indices: 1973374--1973425 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1973364 AAAAACGAAA
*
1973374 AAATAAG-TAAATAA-AAAATCTTTTC
1 AAATAAGCTAAAAAAGAAAATCTTTTC
1973399 AAATAAGTCTAAAAAAGAAAATCTTTT
1 AAATAAG-CTAAAAAAGAAAATCTTTT
1973426 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
27 6 0.26
28 10 0.43
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (27 bp):
AAATAAGCTAAAAAAGAAAATCTTTTC
Found at i:1977520 original size:17 final size:17
Alignment explanation
Indices: 1977498--1977556 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1977488 ATATAAATAC
1977498 ATAATAAAATACATAAT
1 ATAATAAAATACATAAT
1977515 ATAATAAAATACATAA-
1 ATAATAAAATACATAAT
*
1977531 AT-A-AAAATACACAAT
1 ATAATAAAATACATAAT
1977546 -TCAATAAAATA
1 AT-AATAAAATA
1977557 TAATAATCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
16 3 0.08
17 22 0.59
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAATAAAATACATAAT
Found at i:1977530 original size:12 final size:12
Alignment explanation
Indices: 1977484--1977520 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1977474 TGAAAAAGAG
1977484 ATACAT-AT-AA
1 ATACATAATAAA
1977494 ATACATAATAAA
1 ATACATAATAAA
*
1977506 ATACATAATATA
1 ATACATAATAAA
1977518 ATA
1 ATA
1977521 AAATACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 6 0.25
11 2 0.08
12 16 0.67
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (12 bp):
ATACATAATAAA
Found at i:1977541 original size:31 final size:29
Alignment explanation
Indices: 1977492--1977556 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
1977482 AGATACATAT
*
1977492 AAATACATAATAAAATACATAATAT-AATA
1 AAATACATAATAAAATACACAAT-TCAATA
1977521 AAATACATAAATAAAAATACACAATTCAATA
1 AAATACAT-AAT-AAAATACACAATTCAATA
1977552 AAATA
1 AAATA
1977557 TAATAATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 8 0.25
30 4 0.12
31 20 0.62
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (29 bp):
AAATACATAATAAAATACACAATTCAATA
Found at i:1986792 original size:2 final size:2
Alignment explanation
Indices: 1986785--1986810 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1986775 AATCCCCTTC
1986785 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
1986811 TTTCTACAAA
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:1992770 original size:55 final size:56
Alignment explanation
Indices: 1992686--1992796 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 56
1992676 TATATTAATA
*
1992686 ATTAATGGAGAGTTGAATGATATTTATGTATT-AAAACAACATATCTAGCGTTTAT
1 ATTAATGGAGAGTTGAACGATATTTATGTATTAAAAACAACATATCTAGCGTTTAT
*
1992741 ATTAATGGAGAGTTGAACGATATTTATGTATTAAAAACCACATATCTAGCGTTTAT
1 ATTAATGGAGAGTTGAACGATATTTATGTATTAAAAACAACATATCTAGCGTTTAT
1992797 CAAATAAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
55 31 0.58
56 22 0.42
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (56 bp):
ATTAATGGAGAGTTGAACGATATTTATGTATTAAAAACAACATATCTAGCGTTTAT
Found at i:1993979 original size:20 final size:23
Alignment explanation
Indices: 1993954--1994000 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1993944 TGAGTAAATA
1993954 TTATTAAAAT-A-TTT-ATATTT
1 TTATTAAAATAATTTTAATATTT
*
1993974 TTATTAATATAATTTTAATATTT
1 TTATTAAAATAATTTTAATATTT
1993997 TTAT
1 TTAT
1994001 CTTTTCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 3 0.13
23 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTAAAATAATTTTAATATTT
Found at i:1994625 original size:135 final size:136
Alignment explanation
Indices: 1994366--1994634 Score: 328
Period size: 135 Copynumber: 2.0 Consensus size: 136
1994356 ACCCTAAATC
* * * **
1994366 CTAAACTCCTAAAAATTTTAGAAGATTATTCAAGGTATTTTTGCTCAGAAAATGTTTTAAATAAT
1 CTAAACTCATAAAAATTTAAGAAGATTATTCAAGGTATTTTTGCTCAAAAAACATTTTAAATAAT
* * * * * * *
1994431 CTCTTATAAAAAATTGAATGGGGTTATTGAAGACGTTTTTGACTAAAAAAGCTTTGAATAATTCT
66 CTCTTACAAAAAATTGAATGAGATCATTCAAGACGTTTTAGACTAAAAAAGCCTTGAATAATTCT
1994496 TAAACT
131 TAAACT
** * * *
1994502 CTAAACTCATAAAAATTTAAGGGGATTATTCAATGTGTTTTT-CTCAAAAAACATTTTCAATAAT
1 CTAAACTCATAAAAATTTAAGAAGATTATTCAAGGTATTTTTGCTCAAAAAACATTTTAAATAAT
*
1994566 CTCTTACAAAAAATTGAATGAGATCATTCAAGATGTTTCTAG-C-AAAAAATGCCTTGAATAATT
66 CTCTTACAAAAAATTGAATGAGATCATTCAAGACGTTT-TAGACTAAAAAA-GCCTTGAATAATT
*
1994629 TTTAAA
129 CTTAAA
1994635 AACTTTTATA
Statistics
Matches: 112, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
134 6 0.05
135 68 0.61
136 38 0.34
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (136 bp):
CTAAACTCATAAAAATTTAAGAAGATTATTCAAGGTATTTTTGCTCAAAAAACATTTTAAATAAT
CTCTTACAAAAAATTGAATGAGATCATTCAAGACGTTTTAGACTAAAAAAGCCTTGAATAATTCT
TAAACT
Found at i:1994683 original size:61 final size:60
Alignment explanation
Indices: 1994617--1994750 Score: 144
Period size: 62 Copynumber: 2.2 Consensus size: 60
1994607 GCAAAAAATG
* * *
1994617 CCTTGAATAATTT-TTAAAAACTTTTATAAAGGATTATTGAAGGCGTTTTTCGACAGAAACA
1 CCTTGAATAATTTATT-AAAACTTTTAT-AAGGATTATTCAAAGCGTTTTTCGACAAAAACA
** * * * *
1994678 CCTTGAATAACCTTTATTAAATTTTTTGTAAGGATTATTCAAAGCGTTTTTTGCCAAAAACG
1 CCTTGAATAA--TTTATTAAAACTTTTATAAGGATTATTCAAAGCGTTTTTCGACAAAAACA
1994740 CCTTGAATAAT
1 CCTTGAATAAT
1994751 CCCCTACTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
60 1 0.02
61 10 0.16
62 37 0.61
63 11 0.18
64 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (60 bp):
CCTTGAATAATTTATTAAAACTTTTATAAGGATTATTCAAAGCGTTTTTCGACAAAAACA
Found at i:1994765 original size:62 final size:61
Alignment explanation
Indices: 1994645--1994813 Score: 157
Period size: 62 Copynumber: 2.8 Consensus size: 61
1994635 AACTTTTATA
* * * ** *
1994645 AAGGATTATTGAAGGCGTTTTTCGACAGAAACACCTTGAATAA-CCTTTATTAAATTTTTTG
1 AAGGATTATT-AAAGCGTTTTTTGACAGAAACGCCTTGAATAATCCCCTACTAAATTTTTTG
* * *
1994706 TAAGGATTATTCAAAGCGTTTTTTGCCAAAAACGCCTTGAATAATCCCCTACT-ATTTTTTTG
1 -AAGGATTATT-AAAGCGTTTTTTGACAGAAACGCCTTGAATAATCCCCTACTAAATTTTTTG
* * *
1994768 AA-GATTATTTAAG-GTATTTTTAGGCAGAAACGCCTTGAATAGTCCC
1 AAGGATTATTAAAGCGT-TTTTT-GACAGAAACGCCTTGAATAATCCC
1994814 ATACAAAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 8 0.09
60 28 0.31
61 2 0.02
62 45 0.50
63 5 0.06
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (61 bp):
AAGGATTATTAAAGCGTTTTTTGACAGAAACGCCTTGAATAATCCCCTACTAAATTTTTTG
Found at i:2001523 original size:27 final size:26
Alignment explanation
Indices: 2001481--2001542 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
2001471 TTTTATCTTG
*
2001481 TATAT-TTAA-ATAATTTTTTATAAA
1 TATATATTAATATAATTTTTAATAAA
2001505 TATATATTAATATATATTTTTAATAAA
1 TATATATTAATATA-ATTTTTAATAAA
*
2001532 AATATATTAAT
1 TATATATTAAT
2001543 TCTAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 5 0.15
25 4 0.12
26 3 0.09
27 21 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TATATATTAATATAATTTTTAATAAA
Found at i:2011777 original size:11 final size:11
Alignment explanation
Indices: 2011761--2011792 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2011751 TTATTTTTAG
2011761 TTTTTTTCTTT
1 TTTTTTTCTTT
2011772 TTTTTTTCTTT
1 TTTTTTTCTTT
*
2011783 TCTTTTTCTT
1 TTTTTTTCTT
2011793 CCTGTTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2013519 original size:2 final size:2
Alignment explanation
Indices: 2013512--2013537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2013502 GCACAACATC
2013512 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
2013538 CTGTGTGTGT
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:2020531 original size:19 final size:19
Alignment explanation
Indices: 2020490--2020542 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2020480 TAAATTATAC
* *
2020490 TATTTTTATATTTTTTATG
1 TATTTTTATATTTATCATG
2020509 TATTTTTATATTGTATCAT-
1 TATTTTTATATT-TATCATG
2020528 TATTTTTTATATTTA
1 TA-TTTTTATATTTA
2020543 AAATTATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (19 bp):
TATTTTTATATTTATCATG
Found at i:2020548 original size:19 final size:20
Alignment explanation
Indices: 2020511--2020550 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2020501 TTTTTATGTA
**
2020511 TTTTTATATTGTATCATTAT
1 TTTTTATATTGTAAAATTAT
2020531 TTTTTATATT-TAAAATTAT
1 TTTTTATATTGTAAAATTAT
2020550 T
1 T
2020551 AGATTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTTTATATTGTAAAATTAT
Found at i:2024790 original size:35 final size:36
Alignment explanation
Indices: 2024751--2024828 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
2024741 TTTAAAAAAA
* *
2024751 AAATCTCATTTCT-TATTTTCACTTT-TTTTTTTTGG
1 AAATCTCATTT-TATAGTTTCACTTTAATTTTTTTGG
*
2024786 AAATCTTATTTTATAGTTTCACTTTAATTTTTTTGG
1 AAATCTCATTTTATAGTTTCACTTTAATTTTTTTGG
2024822 AAATCTC
1 AAATCTC
2024829 TCGACTCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 21 0.57
36 15 0.41
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (36 bp):
AAATCTCATTTTATAGTTTCACTTTAATTTTTTTGG
Found at i:2027979 original size:23 final size:23
Alignment explanation
Indices: 2027926--2028014 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
2027916 TCATCTTTCA
*
2027926 GGTATTCATTCATTACAAATTCT
1 GGTATTTATTCATTACAAATTCT
* * *
2027949 GGTTTTTATTTATTACAGATT-T
1 GGTATTTATTCATTACAAATTCT
2027971 AGGTATTTATTCATTACAAATTCT
1 -GGTATTTATTCATTACAAATTCT
* *
2027995 GGTTTTTATTTATTACAAAT
1 GGTATTTATTCATTACAAAT
2028015 GCTTTCTATG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.02
23 53 0.96
24 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (23 bp):
GGTATTTATTCATTACAAATTCT
Found at i:2029988 original size:22 final size:22
Alignment explanation
Indices: 2029962--2030005 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2029952 TGTATATTTA
**
2029962 TATTTGTATTTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2029984 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
2030006 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:2032684 original size:123 final size:123
Alignment explanation
Indices: 2032465--2032715 Score: 502
Period size: 123 Copynumber: 2.0 Consensus size: 123
2032455 CCTATGGAGT
2032465 GGATTACTAGGAAACCTTTGCTCCAGTTGTTAAGATGAATACAGTTAGGATTTTGTTATCATTGG
1 GGATTACTAGGAAACCTTTGCTCCAGTTGTTAAGATGAATACAGTTAGGATTTTGTTATCATTGG
2032530 CTGCAAATTACAATTGGCAGCTTCAACAATTTGATGTAAAGAATGCTTTTCTACATGG
66 CTGCAAATTACAATTGGCAGCTTCAACAATTTGATGTAAAGAATGCTTTTCTACATGG
2032588 GGATTACTAGGAAACCTTTGCTCCAGTTGTTAAGATGAATACAGTTAGGATTTTGTTATCATTGG
1 GGATTACTAGGAAACCTTTGCTCCAGTTGTTAAGATGAATACAGTTAGGATTTTGTTATCATTGG
2032653 CTGCAAATTACAATTGGCAGCTTCAACAATTTGATGTAAAGAATGCTTTTCTACATGG
66 CTGCAAATTACAATTGGCAGCTTCAACAATTTGATGTAAAGAATGCTTTTCTACATGG
2032711 GGATT
1 GGATT
2032716 TAGAAGAAGA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 128 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (123 bp):
GGATTACTAGGAAACCTTTGCTCCAGTTGTTAAGATGAATACAGTTAGGATTTTGTTATCATTGG
CTGCAAATTACAATTGGCAGCTTCAACAATTTGATGTAAAGAATGCTTTTCTACATGG
Found at i:2033945 original size:8 final size:8
Alignment explanation
Indices: 2033932--2033956 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2033922 TTACAGCTGG
2033932 TTGTAATC
1 TTGTAATC
2033940 TTGTAATC
1 TTGTAATC
2033948 TTGTAATC
1 TTGTAATC
2033956 T
1 T
2033957 ATATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TTGTAATC
Found at i:2033991 original size:22 final size:22
Alignment explanation
Indices: 2033966--2034009 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2033956 TATATATTTA
2033966 TATTTGTATCTCTAAAATTAAG
1 TATTTGTATCTCTAAAATTAAG
*
2033988 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAAAATTAAG
2034010 AAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (22 bp):
TATTTGTATCTCTAAAATTAAG
Found at i:2035393 original size:13 final size:13
Alignment explanation
Indices: 2035377--2035418 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2035367 CTAATTTTTT
*
2035377 TTTTGTATTTTAA
1 TTTTGTAGTTTAA
*
2035390 TTTTTTAGTTTAA
1 TTTTGTAGTTTAA
*
2035403 TTTT-TGGTTTAA
1 TTTTGTAGTTTAA
2035415 TTTT
1 TTTT
2035419 TTTAAGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (13 bp):
TTTTGTAGTTTAA
Found at i:2035419 original size:13 final size:13
Alignment explanation
Indices: 2035385--2035420 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
2035375 TTTTTTGTAT
2035385 TTTAATTTTTTAG
1 TTTAATTTTTTAG
*
2035398 TTTAA-TTTTTGG
1 TTTAATTTTTTAG
2035410 TTTAATTTTTT
1 TTTAATTTTTT
2035421 TAAGTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTAATTTTTTAG
Found at i:2036111 original size:12 final size:12
Alignment explanation
Indices: 2036094--2036119 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2036084 TGATGATGGT
2036094 ATATTTAATTGC
1 ATATTTAATTGC
2036106 ATATTTAATTGC
1 ATATTTAATTGC
2036118 AT
1 AT
2036120 GGGTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATTTAATTGC
Found at i:2036199 original size:24 final size:21
Alignment explanation
Indices: 2036162--2036219 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 21
2036152 TAATTGTATG
2036162 TTTATTTTGCATGATTATTAATAT
1 TTTA-TTTGCATGATTA-T-ATAT
2036186 TATTATTTGCATGATTATATAT
1 T-TTATTTGCATGATTATATAT
*
2036208 TTTAATTGCATG
1 TTTATTTGCATG
2036220 TGTAATTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.31
22 5 0.16
23 1 0.03
24 13 0.41
25 3 0.09
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTATTTGCATGATTATATAT
Found at i:2036216 original size:21 final size:24
Alignment explanation
Indices: 2036168--2036219 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2036158 TATGTTTATT
*
2036168 TTGCATGATTATTAATATTATTAT
1 TTGCATGATTATTAATATTATTAA
2036192 TTGCATGATTA-T-ATATT-TTAA
1 TTGCATGATTATTAATATTATTAA
2036213 TTGCATG
1 TTGCATG
2036220 TGTAATTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.37
22 5 0.19
23 1 0.04
24 11 0.41
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (24 bp):
TTGCATGATTATTAATATTATTAA
Found at i:2036274 original size:21 final size:20
Alignment explanation
Indices: 2036244--2036282 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2036234 TATTATTTTA
2036244 TTTATTTGTTAATTGCATAT
1 TTTATTTGTTAATTGCATAT
2036264 TTTACTTTGTTAATTGCAT
1 TTTA-TTTGTTAATTGCAT
2036283 GATTATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTATTTGTTAATTGCATAT
Found at i:2036352 original size:34 final size:34
Alignment explanation
Indices: 2036284--2036358 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
2036274 TAATTGCATG
*
2036284 ATTATTA-ATTTATTTATTGTGTGATTGTAGATT
1 ATTATTATATTTATTTATTGTGTGATTATAGATT
* **
2036317 ATTATTATATTTATTTATTG-GTTATATATTTATT
1 ATTATTATATTTATTTATTGTGTGAT-TATAGATT
2036351 ATTATTAT
1 ATTATTAT
2036359 TGCATGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 11 0.31
34 25 0.69
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.61
Consensus pattern (34 bp):
ATTATTATATTTATTTATTGTGTGATTATAGATT
Found at i:2036370 original size:22 final size:21
Alignment explanation
Indices: 2036345--2036411 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 21
2036335 TGGTTATATA
2036345 TTTATTATTATTATTGCATGAT
1 TTTATTATT-TTATTGCATGAT
*
2036367 TTTA-TA-TTTATTGCATTAT
1 TTTATTATTTTATTGCATGAT
*
2036386 GTGATATTATATGTTATTGCATGAT
1 -T-TTATTAT-T-TTATTGCATGAT
2036411 T
1 T
2036412 AATATTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 11 0.31
20 2 0.06
21 4 0.11
22 6 0.17
24 2 0.06
25 11 0.31
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTATTATTTTATTGCATGAT
Found at i:2036416 original size:24 final size:24
Alignment explanation
Indices: 2036368--2036423 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
2036358 TTGCATGATT
* *
2036368 TTATATTTATTGCATTATGTGATA
1 TTATATTTATTGCATGATGTAATA
2036392 TTATATGTTATTGCATGAT-TAATA
1 TTATAT-TTATTGCATGATGTAATA
2036416 TTATATTT
1 TTATATTT
2036424 GAATGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 16 0.55
25 11 0.38
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (24 bp):
TTATATTTATTGCATGATGTAATA
Found at i:2036519 original size:74 final size:74
Alignment explanation
Indices: 2036434--2036572 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
2036424 GAATGATATT
* * * *
2036434 TAATTGTATGATTATACACCAATACTAATATATTTTTGTGATTATTTTTGATTTCATAATTATAT
1 TAATTGCATGATTATACACCAATACTAATATATTTGTGTGATGATATTTGATTTCATAATTATAT
2036499 TTGTGTGCA
66 TTGTGTGCA
* *
2036508 TAATTGCATGATTATACACCAGTACTAATATATTTGTGTGATGATATTTGATTTCATGATTATAT
1 TAATTGCATGATTATACACCAATACTAATATATTTGTGTGATGATATTTGATTTCATAATTATAT
2036573 ATTTGCATGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (74 bp):
TAATTGCATGATTATACACCAATACTAATATATTTGTGTGATGATATTTGATTTCATAATTATAT
TTGTGTGCA
Found at i:2036606 original size:20 final size:18
Alignment explanation
Indices: 2036586--2036655 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
2036576 TGCATGAATG
2036586 GTTATTAATATATTTGCAT
1 GTTATT-ATATATTTGCAT
* *
2036605 GGTATTTTATATTATTGCA-
1 GTTATTATATA-T-TTGCAT
*
2036624 -TTATTAATATATTTGTAT
1 GTTATT-ATATATTTGCAT
*
2036642 GATATTATATATTT
1 GTTATTATATATTT
2036656 ATATAATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
17 4 0.10
18 17 0.43
19 14 0.35
20 5 0.12
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (18 bp):
GTTATTATATATTTGCAT
Found at i:2036664 original size:16 final size:18
Alignment explanation
Indices: 2036625--2036672 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2036615 ATTATTGCAT
*
2036625 TATTAATATATTTGTATGA
1 TATT-ATATATTTATATGA
*
2036644 TATTATATATTTATATAA
1 TATTATATATTTATATGA
2036662 TTATTAT-TATT
1 -TATTATATATT
2036673 GCATGACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TATTATATATTTATATGA
Found at i:2038486 original size:16 final size:16
Alignment explanation
Indices: 2038467--2038498 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2038457 TTTCGAGAAG
*
2038467 TAACTCTTTCACGGAA
1 TAACACTTTCACGGAA
2038483 TAACACTTTCACGGAA
1 TAACACTTTCACGGAA
2038499 CAGTGGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (16 bp):
TAACACTTTCACGGAA
Found at i:2042358 original size:74 final size:73
Alignment explanation
Indices: 2042278--2042421 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 73
2042268 TTTGTTTTTT
* * *
2042278 TATTTTTTTAGAGAAGTATTC-TCATGACTTATTCTTTTATTCTTTT-AGGAAACTATTTTCATT
1 TATTTTTTTAGAAAAGCATTCAT-ATGACTTATTCTTTT-TTCTTTTAAGGAAAC-ATTATCATT
2042341 ACTTGTTCTAG
63 ACTTGTTCTAG
* * * *
2042352 TATTTTTTTAGAAAAGCATTCATTTTACTTATTCTTTTTTTTTTTAAAGTAAACATTATCATTAC
1 TATTTTTTTAGAAAAGCATTCATATGACTTATTCTTTTTTCTTTT-AAGGAAACATTATCATTAC
2042417 TTGTT
65 TTGTT
2042422 TTCCTATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
73 6 0.10
74 47 0.78
75 7 0.12
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.54
Consensus pattern (73 bp):
TATTTTTTTAGAAAAGCATTCATATGACTTATTCTTTTTTCTTTTAAGGAAACATTATCATTACT
TGTTCTAG
Found at i:2042361 original size:37 final size:38
Alignment explanation
Indices: 2042278--2042362 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 38
2042268 TTTGTTTTTT
* **
2042278 TATTTTTTTA-GAGAAGTATTCTCATGACTTATTCTTT
1 TATTTTTTTAGGAGAACTATTCTCATGACTTATTCTAG
* * * *
2042315 TATTCTTTTAGGA-AACTATTTTCATTACTTGTTCTAG
1 TATTTTTTTAGGAGAACTATTCTCATGACTTATTCTAG
2042352 TATTTTTTTAG
1 TATTTTTTTAG
2042363 AAAAGCATTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 37 0.95
38 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (38 bp):
TATTTTTTTAGGAGAACTATTCTCATGACTTATTCTAG
Found at i:2042430 original size:74 final size:74
Alignment explanation
Indices: 2042269--2042432 Score: 172
Period size: 74 Copynumber: 2.2 Consensus size: 74
2042259 TTTATAATAT
** * *
2042269 TTGTTTTTTTATTTTTTTAGAGAAGTATTCTCATGACTTATTCTTTTATTCTTTTAGGAAACTAT
1 TTGTTTTACTATTTTTTTAGAAAAGCATTCTCATGACTTATTCTTTTATTCTTTTAGGAAACTAT
*
2042334 TTTCATTAC
66 TATCATTAC
* * * * * *
2042343 TTGTTCTAGTATTTTTTTAGAAAAGCATTCAT-TTTACTTATTCTTTT-TTTTTTTAAAGTAAAC
1 TTGTTTTACTATTTTTTTAGAAAAGCATTC-TCATGACTTATTCTTTTATTCTTTT--AGGAAAC
2042406 -ATTATCATTAC
63 TATTATCATTAC
*
2042417 TTGTTTTCCTATTTTT
1 TTGTTTTACTATTTTT
2042433 AGGGAAATAC
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
73 6 0.08
74 61 0.82
75 7 0.09
ACGTcount: A:0.24, C:0.11, G:0.08, T:0.57
Consensus pattern (74 bp):
TTGTTTTACTATTTTTTTAGAAAAGCATTCTCATGACTTATTCTTTTATTCTTTTAGGAAACTAT
TATCATTAC
Found at i:2042468 original size:36 final size:36
Alignment explanation
Indices: 2042410--2042631 Score: 175
Period size: 36 Copynumber: 6.2 Consensus size: 36
2042400 GTAAACATTA
* * *
2042410 TCATTACTTGTTTTCCTA-TTTTTAGGGAAATACTC
1 TCATTACTTGTTCTCCTATTTTTTAGGAAAACACTC
* * * *
2042445 ACATTACTTGTTCTCTTATTTTTTAGGAAAATATTC
1 TCATTACTTGTTCTCCTATTTTTTAGGAAAACACTC
* * *
2042481 -CTGTTACTTGTTTTCCTATTTTTTAGGGAAACACTC
1 TC-ATTACTTGTTCTCCTATTTTTTAGGAAAACACTC
* *
2042517 TCATTATTTGTTCTCCTTTTTTTTAGGAAAACACTC
1 TCATTACTTGTTCTCCTATTTTTTAGGAAAACACTC
* * * *
2042553 TTATTATTTGTTCTTCAATTTTTTTAAGG--AACACTC
1 TCATTACTTGTTCTCCTA-TTTTTT-AGGAAAACACTC
* * * *
2042589 CCATTATTTGTTCTTCGATTTTTTTAAGG-AAACACTC
1 TCATTACTTGTTCTCCTA-TTTTTT-AGGAAAACACTC
*
2042626 CCATTA
1 TCATTA
2042632 TTTTTTTTTA
Statistics
Matches: 158, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
35 16 0.10
36 119 0.75
37 20 0.13
38 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (36 bp):
TCATTACTTGTTCTCCTATTTTTTAGGAAAACACTC
Found at i:2042564 original size:72 final size:72
Alignment explanation
Indices: 2042412--2042631 Score: 234
Period size: 72 Copynumber: 3.1 Consensus size: 72
2042402 AAACATTATC
* *
2042412 ATTACTTGTTTTCCTA-TTTTTAGGGAAATACTCACATTACTTGTTCT-CTTATTTTTTAGGAAA
1 ATTACTTGTTTTCCTATTTTTTAGGGAAACACTCACATTATTTGTTCTCCTT-TTTTTTAGGAAA
* *
2042475 ATATTCCT
65 ACACTCCT
* *
2042483 GTTACTTGTTTTCCTATTTTTTAGGGAAACACTCTCATTATTTGTTCTCCTTTTTTTTAGGAAAA
1 ATTACTTGTTTTCCTATTTTTTAGGGAAACACTCACATTATTTGTTCTCCTTTTTTTTAGGAAAA
*
2042548 CACTCTT
66 CACTCCT
* * * * * *
2042555 ATTATTTGTTCTT-CAATTTTTTTAAGG-AACACTCCCATTATTTGTTCTTCGATTTTTTTAAGG
1 ATTACTTGTT-TTCCTA-TTTTTTAGGGAAACACTCACATTATTTGTTC-TC-CTTTTTTTTAGG
*
2042618 -AAACACTCCC
62 AAAACACTCCT
2042628 ATTA
1 ATTA
2042632 TTTTTTTTTA
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
71 15 0.12
72 74 0.58
73 28 0.22
74 10 0.08
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (72 bp):
ATTACTTGTTTTCCTATTTTTTAGGGAAACACTCACATTATTTGTTCTCCTTTTTTTTAGGAAAA
CACTCCT
Found at i:2042642 original size:27 final size:28
Alignment explanation
Indices: 2042607--2042662 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
2042597 TGTTCTTCGA
2042607 TTTTTTTAAGG-AAACACTCCCATTATT
1 TTTTTTTAAGGAAAACACTCCCATTATT
* *
2042634 TTTTTTTAAGGAAAACATTCCCTTTATT
1 TTTTTTTAAGGAAAACACTCCCATTATT
2042662 T
1 T
2042663 GTTGTCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTTTTTAAGGAAAACACTCCCATTATT
Found at i:2042682 original size:63 final size:62
Alignment explanation
Indices: 2042571--2042702 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 62
2042561 TGTTCTTCAA
2042571 TTTTTTTAAGGAACACTCCCATTATTTGTTCTTCGATTTTTTTAAGG-AAACACTCCCATTATT
1 TTTTTTTAAGGAACACTCCCATTATTTGTTCTTC-ATTTTTTTAAGGAAAACA-TCCCATTATT
* * *
2042634 TTTTTTTAAGGAAAACATTCCCTTTATTTGTTGTCTT-A-TTTTTT-AGGAAAACATTCCATTAT
1 TTTTTTTAAGG--AACACTCCCATTATTTG-T-TCTTCATTTTTTTAAGGAAAACATCCCATTAT
2042696 T
62 T
*
2042697 TATTTT
1 TTTTTT
2042703 ATTTGATAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
63 28 0.47
64 11 0.18
65 16 0.27
66 1 0.02
67 4 0.07
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (62 bp):
TTTTTTTAAGGAACACTCCCATTATTTGTTCTTCATTTTTTTAAGGAAAACATCCCATTATT
Found at i:2049924 original size:6 final size:6
Alignment explanation
Indices: 2049913--2049956 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
2049903 TTATTGAAGT
*
2049913 ATATAA ATATAA ATATAA ATATAA ATAT-- ATATAT ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
2049957 TAACTCCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
4 4 0.11
6 31 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:2049950 original size:16 final size:17
Alignment explanation
Indices: 2049912--2049956 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
2049902 TTTATTGAAG
2049912 TATATAAATATAAATATA
1 TATATAAATAT-AATATA
*
2049930 AATATAAATAT-ATATA
1 TATATAAATATAATATA
2049946 TATATAAATAT
1 TATATAAATAT
2049957 TAACTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.60
18 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAAATATAATATA
Found at i:2052619 original size:21 final size:21
Alignment explanation
Indices: 2052583--2052796 Score: 72
Period size: 21 Copynumber: 9.9 Consensus size: 21
2052573 GTAAGTCCAA
2052583 TTTT-TTTTATATTTTTATTAT
1 TTTTATTTTATA-TTTTATTAT
2052604 TTTTATTTTATATTTTATGTAT
1 TTTTATTTTATATTTTAT-TAT
**
2052626 ATATTT-TCCTTTATATCCTATGTATT
1 -T-TTTAT--TTTATATTTTAT-TA-T
*
2052652 TATTTATTTATTTATTTTTATTAT
1 T-TTTATTT-TATA-TTTTATTAT
* *
2052676 TTATTAATATATA-TTT-TTAT
1 TT-TTATTTTATATTTTATTAT
*
2052696 TTTTATTTT-TTTTATTATTATT
1 TTTTATTTTATATT-TTATTA-T
* * * *
2052718 TTTTCTCTTTCTCTTTT-TCA-
1 TTTTAT-TTTATATTTTATTAT
* *
2052738 TTTTATTTTATA-TGTATTTT
1 TTTTATTTTATATTTTATTAT
*
2052758 TATTTATCTTATA-TTTATCTA-
1 T-TTTATTTTATATTTTAT-TAT
*
2052779 TTTT-TTTTATTTTTTATT
1 TTTTATTTTATATTTTATT
2052797 TATCTTATAA
Statistics
Matches: 146, Mismatches: 25, Indels: 46
0.67 0.12 0.21
Matches are distributed among these distances:
18 3 0.02
19 17 0.12
20 22 0.15
21 31 0.21
22 19 0.13
23 11 0.08
24 14 0.10
25 23 0.16
26 6 0.04
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTATTTTATATTTTATTAT
Found at i:2052632 original size:25 final size:25
Alignment explanation
Indices: 2052582--2052669 Score: 69
Period size: 25 Copynumber: 3.7 Consensus size: 25
2052572 GGTAAGTCCA
*
2052582 ATTTT-TTTTATATTTT-TAT-TAT
1 ATTTTATTTTATATTTTATGTATAT
2052604 -TTTTATTTTATATTTTATGTATAT
1 ATTTTATTTTATATTTTATGTATAT
** ** *
2052628 ATTTTCCTTTATATCCTATGTATTT
1 ATTTTATTTTATATTTTATGTATAT
*
2052653 A-TTTATTTATTTATTTT
1 ATTTTATTT-TATATTTT
2052670 TATTATTTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
21 4 0.08
22 11 0.22
23 2 0.04
24 8 0.16
25 25 0.50
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (25 bp):
ATTTTATTTTATATTTTATGTATAT
Found at i:2052797 original size:41 final size:40
Alignment explanation
Indices: 2052648--2052797 Score: 98
Period size: 38 Copynumber: 3.7 Consensus size: 40
2052638 ATATCCTATG
* * * *
2052648 TATTTATTTA-TTTATTTA-TTTTTATTATTTATTAATATA
1 TATTTATCTATTTTTTTTATTTTTTATT-TTTATTTATTTA
* * *
2052687 TATTT-T-TATTTTTATT-TTTTTTATTATTATTT-TTTC
1 TATTTATCTATTTTTTTTATTTTTTATTTTTATTTATTTA
* *
2052723 TCTTTCTCT-TTTTCATTTTATTTTATATGTATTTTTATTTATCTTA
1 TATTTATCTATTTT--TTTTA-TTT-T-T-TATTTTTATTTAT-TTA
2052769 TATTTATCTATTTTTTTTATTTTTTATTT
1 TATTTATCTATTTTTTTTATTTTTTATTT
2052798 ATCTTATAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
36 6 0.07
37 12 0.14
38 15 0.18
39 8 0.09
41 8 0.09
42 2 0.02
43 2 0.02
44 13 0.15
45 6 0.07
46 9 0.11
47 4 0.05
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.74
Consensus pattern (40 bp):
TATTTATCTATTTTTTTTATTTTTTATTTTTATTTATTTA
Found at i:2052812 original size:24 final size:22
Alignment explanation
Indices: 2052648--2052862 Score: 93
Period size: 24 Copynumber: 9.5 Consensus size: 22
2052638 ATATCCTATG
*
2052648 TATTTATTTATTTAT-TTATTTT
1 TATTT-TTTATTTATCTTATTAT
* * * *
2052670 TATTATTTATTAATATATATTTT
1 TATTTTTTATTTATCT-TATTAT
* *
2052693 TA-TTTTTATTTTTTTTATTAT
1 TATTTTTTATTTATCTTATTAT
* * *
2052714 TATTTTTTCTCTTTCTCTTTTTCAT
1 TA-TTTTT-TATTTATCTTATT-AT
2052739 T-TTATTTTATATGTAT-TT-TTATT
1 TATT-TTTTAT-T-TATCTTATTA-T
* * * *
2052762 TATCTTATATTTATCTATTTTTTT
1 TATTTTTTATTTATC--TTATTAT
2052786 TATTTTTTATTTATCTTATAATAT
1 TATTTTTTATTTATCTTAT--TAT
* *
2052810 TATTGTTGATTTATCTTATTAT
1 TATTTTTTATTTATCTTATTAT
* *
2052832 TATTTTTTTAATTATC-TATTAA
1 TA-TTTTTTATTTATCTTATTAT
2052854 T-TTTTTTAT
1 TATTTTTTAT
2052863 CTGATTTTTA
Statistics
Matches: 148, Mismatches: 27, Indels: 38
0.69 0.13 0.18
Matches are distributed among these distances:
20 7 0.05
21 18 0.12
22 30 0.20
23 35 0.24
24 51 0.34
25 7 0.05
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (22 bp):
TATTTTTTATTTATCTTATTAT
Found at i:2052823 original size:35 final size:36
Alignment explanation
Indices: 2052754--2052832 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
2052744 TTTATATGTA
* *
2052754 TTTTTATTTATCTTATATTTATCTATTTTTTTTAT-
1 TTTTTATTTATCTTATATATATCTATTTTATTTATC
2052789 TTTTTATTTATCTTATA-ATAT-TATTGTTGATTTATC
1 TTTTTATTTATCTTATATATATCTATT-TT-ATTTATC
*
2052825 TTATTATT
1 TTTTTATT
2052833 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 4 0.11
34 5 0.13
35 22 0.58
36 7 0.18
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (36 bp):
TTTTTATTTATCTTATATATATCTATTTTATTTATC
Found at i:2052841 original size:19 final size:20
Alignment explanation
Indices: 2052658--2052876 Score: 85
Period size: 21 Copynumber: 11.2 Consensus size: 20
2052648 TATTTATTTA
2052658 TTTATTTAT-TT-TTATTA-
1 TTTATTTATCTTATTATTAT
* * *
2052675 TTTATTAATATATATTTTTATT
1 TTTATTTATCT-TATTATTA-T
* *
2052697 TTTATTTTTTTTATTATTA-
1 TTTATTTATCTTATTATTAT
* *
2052716 TTT-TTTCTCTT-TCTCTT-T
1 TTTATTTATCTTAT-TATTAT
* *
2052734 TTCATTTTATTTTA-TATGTATT
1 TTTA-TTTATCTTATTAT-TA-T
2052756 TTTATTTATCTTA-TATT-T
1 TTTATTTATCTTATTATTAT
*
2052774 ATCTATTT-T-TT-TTATT-T
1 -TTTATTTATCTTATTATTAT
2052791 TTTATTTATCTTATAATATTAT
1 TTTATTTATCTTAT--TATTAT
2052813 TGTTGATTTATCTTATTATTAT
1 T-TT-ATTTATCTTATTATTAT
*
2052835 TTT-TTTA-ATTATCTATTAAT
1 TTTATTTATCTTAT-TATT-AT
* *
2052855 TTT-TTTATCTGATTTTTAT
1 TTTATTTATCTTATTATTAT
2052874 TTT
1 TTT
2052877 GAAAGGTTGG
Statistics
Matches: 155, Mismatches: 21, Indels: 50
0.69 0.09 0.22
Matches are distributed among these distances:
16 6 0.04
17 17 0.11
18 20 0.13
19 26 0.17
20 25 0.16
21 27 0.17
22 21 0.14
23 2 0.01
24 11 0.07
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTATTTATCTTATTATTAT
Found at i:2053358 original size:19 final size:20
Alignment explanation
Indices: 2053333--2053378 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2053323 GATGAACTTT
*
2053333 CGGTGAAAAA-TTCAGATTC
1 CGGTGAAAAATTTCAGAATC
*
2053352 TGGTGAAAAATTTCAGAATC
1 CGGTGAAAAATTTCAGAATC
2053372 CGGTGAA
1 CGGTGAA
2053379 TATTCAACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (20 bp):
CGGTGAAAAATTTCAGAATC
Found at i:2053795 original size:6 final size:6
Alignment explanation
Indices: 2053784--2053853 Score: 67
Period size: 6 Copynumber: 11.8 Consensus size: 6
2053774 TTTATCTTTG
*
2053784 TTTTAT TTTTAT TTTTA- TTTTACT TTTT-T TTATTCT ATTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TT-TTAT -TTTTAT TTTTAT
*
2053832 TTTTAT TTTT-T TTTTAC TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTA
2053854 CTTTGTTACT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
5 18 0.33
6 28 0.51
7 7 0.13
8 2 0.04
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:2053798 original size:11 final size:11
Alignment explanation
Indices: 2053742--2053853 Score: 81
Period size: 11 Copynumber: 10.5 Consensus size: 11
2053732 AATTAATTTG
2053742 TTTT-TTTTTA
1 TTTTATTTTTA
**
2053752 TTTTAGGTTTA
1 TTTTATTTTTA
* * *
2053763 -TTTAATATTC
1 TTTTATTTTTA
* *
2053773 TTTTATCTTTG
1 TTTTATTTTTA
2053784 TTTTATTTTTA
1 TTTTATTTTTA
2053795 TTTT-TATTTTA
1 TTTTAT-TTTTA
*
2053806 CTTT-TTTTTA
1 TTTTATTTTTA
*
2053816 TTCTA-TTTTA
1 TTTTATTTTTA
2053826 TTTTATTTTTA
1 TTTTATTTTTA
*
2053837 TTTTTTTTTTA
1 TTTTATTTTTA
2053848 CTTTTA
1 -TTTTA
2053854 CTTTGTTACT
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
10 27 0.35
11 47 0.60
12 4 0.05
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:2053857 original size:6 final size:5
Alignment explanation
Indices: 2053742--2053844 Score: 75
Period size: 5 Copynumber: 19.8 Consensus size: 5
2053732 AATTAATTTG
* * * * * *
2053742 TTTTT TTTTA TTTTA GGTTTA TTTAA TATTC TTTTA TCTTTG TTTTA TTTTTA
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA -TTTTA
*
2053795 TTTTTA TTTTA CTTTT- TTTTA TTCTA TTTTA TTTTA TTTTTA TTTT-
1 -TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
2053841 TTTT
1 TTTT
2053845 TTACTTTTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
4 8 0.10
5 43 0.54
6 28 0.35
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:2053962 original size:58 final size:56
Alignment explanation
Indices: 2053883--2054215 Score: 350
Period size: 58 Copynumber: 5.7 Consensus size: 56
2053873 GAAAAATCAA
* * *
2053883 AAAAAATATTTTTGAGAAAAAGTCGAAAGTATCAATTTTTCTTAAACATAAAATTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAA-ATAAAGTTTC
** * *
2053940 AAAAAAGGGTTTTTGAGGAAAAGTTAAAAATATCAATTTTTCTTGAAAATCAAAGTTTC
1 AAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAAT-AAAGTTTC
*
2053999 CAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAA-TTTTCTTTAAAAATCAAAGTTCTC
1 AAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTC-TT-AAAAT-AAAGTT-TC
* * * *
2054058 AAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT-TAAAAT-AAAGTTTC
* * * *
2054116 TAAAAATATTTTTG-GCGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTC
1 AAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCT-TAAAATAAAGTTTC
2054173 AAAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTTC
1 --AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTC
2054216 CTGCACAAGA
Statistics
Matches: 235, Mismatches: 27, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
57 21 0.09
58 114 0.49
59 95 0.40
60 5 0.02
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (56 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAGTTTC
Found at i:2054113 original size:117 final size:114
Alignment explanation
Indices: 2053884--2054213 Score: 394
Period size: 117 Copynumber: 2.8 Consensus size: 114
2053874 AAAAATCAAA
* * * *
2053884 AAAAATATTTTT-GAGAAAAAGTCGAAAGTATCAATTTTTCTTAAACATAAAATTTCAAAAAAGG
1 AAAAATATTTTTGGAG-AAAAGTTGAAAGTATCAATTTTT-TTAAAAATAAAGTTTCAAAAAA-T
* * * * * * *
2053948 GTTTTTGAGGAAAAGTTAAAAATATCAATTTTTCTTGAAAATCAAAGTTTCC
63 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCC
2054000 AAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATCAAAGTTCTCAAAAAAT
1 AAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT-TTTAAAAAT-AAAGTT-TCAAAAAAT
* *
2054065 ATTTTTGAGAAAAAATTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCT
63 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCC
* * ** *
2054117 AAAAATATTTTTGGCGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAAAAAAAT
1 AAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTT-TTAAAAATAAAGTTTC--AAAAAAT
2054182 ATTTTT-AGGAAAAAGTTGAAAGTATCAATTTT
63 ATTTTTGA-GAAAAAGTTGAAAGTATCAATTTT
2054214 TCCTGCACAA
Statistics
Matches: 187, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
115 2 0.01
116 48 0.26
117 129 0.69
118 8 0.04
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (114 bp):
AAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTTTAAAAATAAAGTTTCAAAAAATATT
TTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAAGTTTCC
Found at i:2054248 original size:9 final size:9
Alignment explanation
Indices: 2054234--2054268 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2054224 GAACAATCAT
*
2054234 TTTTTTTTC
1 TTTTTTTTA
2054243 TTTTTTTTA
1 TTTTTTTTA
2054252 TTTTTTTTA
1 TTTTTTTTA
2054261 TTTTTTTT
1 TTTTTTTT
2054269 CTTTAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:2062623 original size:7 final size:8
Alignment explanation
Indices: 2062600--2062625 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2062590 GAAAAAAATG
2062600 AATGAAAA
1 AATGAAAA
2062608 AATGAAAA
1 AATGAAAA
2062616 AATGAAAA
1 AATGAAAA
2062624 AA
1 AA
2062626 AGTGAATGAA
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:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AATGAAAA
Found at i:2063663 original size:41 final size:41
Alignment explanation
Indices: 2063611--2063865 Score: 294
Period size: 41 Copynumber: 6.1 Consensus size: 41
2063601 ATGATTGTCA
* * *
2063611 AGGAGTAATTTACTTTCCAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* * *
2063652 ATGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
*
2063693 AGGAGCAATTTACTTTCTCAAAGTCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTC-CAAAGTCGTGGTGCCTCTGTTTAG
* *
2063735 AGGAGCAATTTATTTTCCAAAGTCGTGGTGTCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
2063776 AGGAGCAATTTATTTTCCAAAGTCGTTGAGCTTCTGATTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
* * * * ** *
2063817 AAGAGCCATTTATGTTTCTCAAAGTCGTTGAACCTCTGCTTAG
1 AGGAGCAATTTA-CTTTC-CAAAGTCGTGGTGCCTCTGTTTAG
2063860 AGGAGC
1 AGGAGC
2063866 TTTGGTAAAA
Statistics
Matches: 188, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 120 0.64
42 42 0.22
43 26 0.14
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:2063741 original size:83 final size:82
Alignment explanation
Indices: 2063611--2063865 Score: 291
Period size: 83 Copynumber: 3.1 Consensus size: 82
2063601 ATGATTGTCA
* * * *
2063611 AGGAGTAATTTACTTTCCAAAGTTGTGGTGCCTCTATTTAGATGAGCAATTTACTTTT-CAAAGT
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAAAGGAGCAATTTA-TTTTCCAAAGT
*
2063675 TGTGGTGCCTCTGTTTAG
65 CGTGGTGCCTCTGTTTAG
*
2063693 AGGAGCAATTTACTTTCTCAAAGTCGTGGTGCCTCTGTTTAAAGGAGCAATTTATTTTCCAAAGT
1 AGGAGCAATTTACTTTC-CAAAGTCGTGGTGCCTCTATTTAAAGGAGCAATTTATTTTCCAAAGT
*
2063758 CGTGGTGTCTCTGTTTAG
65 CGTGGTGCCTCTGTTTAG
* * * * *
2063776 AGGAGCAATTTATTTTCCAAAGTCGTTGAGCTTCTGA-TTAGAA-GAGCCATTTATGTTTCTCAA
1 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCT-ATTTA-AAGGAGCAATTTAT-TTTC-CAA
* ** *
2063839 AGTCGTTGAACCTCTGCTTAG
62 AGTCGTGGTGCCTCTGTTTAG
2063860 AGGAGC
1 AGGAGC
2063866 TTTGGTAAAA
Statistics
Matches: 149, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
82 48 0.32
83 76 0.51
84 25 0.17
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (82 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAAAGGAGCAATTTATTTTCCAAAGTC
GTGGTGCCTCTGTTTAG
Found at i:2063783 original size:124 final size:125
Alignment explanation
Indices: 2063610--2063844 Score: 321
Period size: 124 Copynumber: 1.9 Consensus size: 125
2063600 CATGATTGTC
* * *
2063610 AAGGAGTAATTTACTTTCCAAAGTTGTGGTGCCTCTATTTAGATGAGCAATTTACTTTT-CAAAG
1 AAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTA-TTTTCCAAAG
* * * *
2063674 TTGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTCTCAAAGTCGTGGTGCCTCTGTTTA
65 TCGTGGAGCCTCTGATTAGAAGAGCAATTTATCTTTCTCAAAGTCGTGGTGCCTCTGTTTA
* * *
2063734 AAGGAGCAATTTATTTTCCAAAGTCGTGGTGTCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGT
1 AAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCAAAGT
* * * *
2063799 CGTTGAGCTTCTGATTAGAAGAGCCATTTATGTTTCTCAAAGTCGT
66 CGTGGAGCCTCTGATTAGAAGAGCAATTTATCTTTCTCAAAGTCGT
2063845 TGAACCTCTG
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
123 4 0.04
124 77 0.81
125 14 0.15
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.38
Consensus pattern (125 bp):
AAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCAAAGT
CGTGGAGCCTCTGATTAGAAGAGCAATTTATCTTTCTCAAAGTCGTGGTGCCTCTGTTTA
Found at i:2063878 original size:1 final size:1
Alignment explanation
Indices: 2063872--2063914 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
2063862 GAGCTTTGGT
* * * *
2063872 AAAAAAAAAACAAAAAAAAAACAAAAAACAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2063915 TGTTGAGTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:2063888 original size:11 final size:11
Alignment explanation
Indices: 2063872--2063914 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
2063862 GAGCTTTGGT
2063872 AAAAAAAAAAC
1 AAAAAAAAAAC
2063883 AAAAAAAAAAC
1 AAAAAAAAAAC
2063894 AAAAAACAAAA-
1 AAAAAA-AAAAC
2063905 AAAATAAAAA
1 AAAA-AAAAA
2063915 TGTTGAGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 24 0.80
12 6 0.20
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:2063899 original size:18 final size:17
Alignment explanation
Indices: 2063872--2063914 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 17
2063862 GAGCTTTGGT
2063872 AAAAAAAAAACAAAAAA
1 AAAAAAAAAACAAAAAA
2063889 AAAACAAAAAACAAAAAA
1 AAAA-AAAAAACAAAAAA
2063907 AATAAAAA
1 AA-AAAAA
2063915 TGTTGAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAA
Found at i:2064207 original size:23 final size:23
Alignment explanation
Indices: 2064128--2064220 Score: 61
Period size: 23 Copynumber: 4.3 Consensus size: 23
2064118 TATGTATTCG
* *
2064128 TTATTTA-TT-TATTATTACTAT
1 TTATTTATTTCTATTATTAATTT
* * *
2064149 TTATTAATATATATT-TT-ATTT
1 TTATTTATTTCTATTATTAATTT
*
2064170 TTATTTATTTTTATTATTAATTT
1 TTATTTATTTCTATTATTAATTT
* * * *
2064193 TTCTTTCTTTCTATTTTTCA-TT
1 TTATTTATTTCTATTATTAATTT
2064215 TTATTT
1 TTATTT
2064221 TATATGTATT
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
21 20 0.36
22 12 0.22
23 23 0.42
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTTATTTCTATTATTAATTT
Found at i:2064244 original size:12 final size:12
Alignment explanation
Indices: 2064229--2064277 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
2064219 TTTATATGTA
2064229 TTTTTATTTATC
1 TTTTTATTTATC
2064241 -TTTTATTTATC
1 TTTTTATTTATC
* *
2064252 TATTTATTTATT
1 TTTTTATTTATC
2064264 TTTTTATTTATC
1 TTTTTATTTATC
2064276 TT
1 TT
2064278 ATAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATTTATC
Done.