Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 62 of 172
Found at i:17149569 original size:17 final size:19
Alignment explanation
Indices: 17149536--17149572 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
17149526 TGCAAATGAA
17149536 TCATTTCTCATTTTCATTT
1 TCATTTCTCATTTTCATTT
17149555 TCATTTC-CA-TTTCATTT
1 TCATTTCTCATTTTCATTT
17149572 T
1 T
17149573 TGAGAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (19 bp):
TCATTTCTCATTTTCATTT
Found at i:17152935 original size:15 final size:15
Alignment explanation
Indices: 17152915--17152944 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17152905 GAGTATGGTA
17152915 AAATATTAAAAAAAT
1 AAATATTAAAAAAAT
*
17152930 AAATATTTAAAAAAT
1 AAATATTAAAAAAAT
17152945 TACTAATAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:17154469 original size:22 final size:23
Alignment explanation
Indices: 17154421--17154479 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
17154411 TTAAAAATTG
* *
17154421 AATATAAATATTAAAATATGAAA
1 AATAAAAAAATTAAAATATGAAA
*
17154444 AATAAAAAAATTAAAAT-TTAAA
1 AATAAAAAAATTAAAATATGAAA
*
17154466 AATACAAAAATTAA
1 AATAAAAAAATTAA
17154480 GTTCTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AATAAAAAAATTAAAATATGAAA
Found at i:17155064 original size:12 final size:12
Alignment explanation
Indices: 17155047--17155076 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
17155037 TTAGCAAGAT
17155047 ATATAAATTAAC
1 ATATAAATTAAC
17155059 ATATAAATTAAC
1 ATATAAATTAAC
17155071 ATATAA
1 ATATAA
17155077 GAAAGTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAAATTAAC
Found at i:17160299 original size:78 final size:77
Alignment explanation
Indices: 17160181--17160329 Score: 178
Period size: 78 Copynumber: 1.9 Consensus size: 77
17160171 AGTTTAAGTC
* * *
17160181 TTTAATTATGTCATAATTTGAACATCATTAATATGAGTTTTAATTATGGCATACTCTGA-ACATC
1 TTTAATTATGTCATAACTTAAACATCATTAATATGAGTTTTAAATATGGCATACT-TGAGACATC
17160245 TTTAATAAGGGTT
65 TTTAATAAGGGTT
* * * *
17160258 TTTAATTATGTCATAGCTTAAGACATC-TTAAATAT-ATGTTTTAAATATGTCATAGTTTAGACA
1 TTTAATTATGTCATAACTTAA-ACATCATT-AATATGA-GTTTTAAATATGGCATACTTGAGACA
17160321 TCTTTAATA
63 TCTTTAATA
17160330 CAAGTCTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
77 23 0.38
78 38 0.62
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (77 bp):
TTTAATTATGTCATAACTTAAACATCATTAATATGAGTTTTAAATATGGCATACTTGAGACATCT
TTAATAAGGGTT
Found at i:17160300 original size:39 final size:37
Alignment explanation
Indices: 17160181--17160329 Score: 133
Period size: 38 Copynumber: 3.9 Consensus size: 37
17160171 AGTTTAAGTC
** *
17160181 TTTAATTATGTCATAATTTGAACATCATTAATATGAGT
1 TTTAATTATGTCATAGCTTGAACATCTTTAATAT-AGT
*
17160219 TTTAATTATGGCATA-CTCTGAACATCTTTAATA-AGGGTT
1 TTTAATTATGTCATAGCT-TGAACATCTTTAATATA--G-T
* *
17160258 TTTAATTATGTCATAGCTTAAGACATCTTAAATATATGT
1 TTTAATTATGTCATAGCTTGA-ACATCTTTAATATA-GT
* *
17160297 TTTAAATATGTCATAG-TTTAGACATCTTTAATA
1 TTTAATTATGTCATAGCTTGA-ACATCTTTAATA
17160330 CAAGTCTTTA
Statistics
Matches: 94, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 44 0.47
39 33 0.35
40 14 0.15
41 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTAATTATGTCATAGCTTGAACATCTTTAATATAGT
Found at i:17166605 original size:39 final size:38
Alignment explanation
Indices: 17166486--17166642 Score: 149
Period size: 38 Copynumber: 4.1 Consensus size: 38
17166476 AGTTTAAGTC
*
17166486 TTTAATTATGTCATAATTTGAACAT-TATTAATATGA-GT
1 TTTAATTATGTCATAATTTAAACATCT-TTAATAT-ATGT
* ***
17166524 TTTAATTATGTCATAATCTAAACATCTTTAATAGGGGTT
1 TTTAATTATGTCATAATTTAAACATCTTTAATATATG-T
* * *
17166563 TTTAATTATGTCATATTTTAGGACATCTTAAATATATGT
1 TTTAATTATGTCATAATTTA-AACATCTTTAATATATGT
* * *
17166602 TTT-ATATATGTCATAGTTTAGACATCTTTAATACATGT
1 TTTAAT-TATGTCATAATTTAAACATCTTTAATATATGT
17166640 TTT
1 TTT
17166643 TAGTTCAGAC
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
38 51 0.51
39 37 0.37
40 12 0.12
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (38 bp):
TTTAATTATGTCATAATTTAAACATCTTTAATATATGT
Found at i:17166612 original size:78 final size:77
Alignment explanation
Indices: 17166486--17166634 Score: 187
Period size: 78 Copynumber: 1.9 Consensus size: 77
17166476 AGTTTAAGTC
*
17166486 TTTAATTATGTCATAATTTGAACATTATTAATATGAGTTTTAATTATGTCATAATCTAAACATCT
1 TTTAATTATGTCATAATTTGAACATTATAAATATGAGTTTTAATTATGTCATAATCTAAACATCT
17166551 TTAATAGGGGTT
66 TTAATAGGGGTT
* * * * *
17166563 TTTAATTATGTCATATTTTAGGACATCT-TAAATAT-ATGTTTT-ATATATGTCATAGTTTAGAC
1 TTTAATTATGTCATAATTT-GAACAT-TATAAATATGA-GTTTTAAT-TATGTCATAATCTAAAC
17166625 ATCTTTAATA
62 ATCTTTAATA
17166635 CATGTTTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
77 21 0.34
78 40 0.65
79 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (77 bp):
TTTAATTATGTCATAATTTGAACATTATAAATATGAGTTTTAATTATGTCATAATCTAAACATCT
TTAATAGGGGTT
Found at i:17168941 original size:13 final size:13
Alignment explanation
Indices: 17168923--17168947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17168913 TGGTTGAAAA
17168923 TTTTAAAAATAAT
1 TTTTAAAAATAAT
17168936 TTTTAAAAATAA
1 TTTTAAAAATAA
17168948 AAATTAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTAAAAATAAT
Found at i:17169450 original size:19 final size:19
Alignment explanation
Indices: 17169417--17169489 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 19
17169407 ATATCTAACC
*
17169417 AAAAATAATTTAAAAACTAT
1 AAAAATAATTCAAAAA-TAT
17169437 AAAAAT-ATTC-AAAA-AT
1 AAAAATAATTCAAAAATAT
**
17169453 AATCATAATTCAAAAAAATAT
1 AAAAATAATTC--AAAAATAT
17169474 ATAAAAT-ATTCAAAAA
1 A-AAAATAATTCAAAAA
17169490 AAACATGAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
16 6 0.14
17 4 0.10
18 4 0.10
19 8 0.19
20 10 0.24
21 7 0.17
22 3 0.07
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAATTCAAAAATAT
Found at i:17177193 original size:15 final size:14
Alignment explanation
Indices: 17177173--17177210 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
17177163 AATTTTTGTT
17177173 TTCTCTTCTCATCT-A
1 TTCTCTTCTC-T-TAA
17177188 TTCTCTTCTCTTAA
1 TTCTCTTCTCTTAA
17177202 TTCTCTTCT
1 TTCTCTTCT
17177211 TCTCCTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 11 0.50
15 10 0.45
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.58
Consensus pattern (14 bp):
TTCTCTTCTCTTAA
Found at i:17193617 original size:20 final size:20
Alignment explanation
Indices: 17193594--17193634 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17193584 ATTCGACACA
*
17193594 AACAAA-AATAATTAAAAAAG
1 AACAAACAATAA-AAAAAAAG
17193614 AACAAACAATAAAAAAAAAG
1 AACAAACAATAAAAAAAAAG
17193634 A
1 A
17193635 TGGATAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (20 bp):
AACAAACAATAAAAAAAAAG
Found at i:17194660 original size:21 final size:21
Alignment explanation
Indices: 17194634--17194687 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
17194624 CAGCGGTGGC
*
17194634 GGTGAGATTAGTTACTATAGA
1 GGTGAGATTAGATACTATAGA
* * *
17194655 GGTGAGATTGGATACTGTAGC
1 GGTGAGATTAGATACTATAGA
17194676 GGTGAGATTAGA
1 GGTGAGATTAGA
17194688 AACAATGGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.35, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGATACTATAGA
Found at i:17197746 original size:25 final size:25
Alignment explanation
Indices: 17197687--17197747 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
17197677 AGAATATGCT
17197687 AAGAA-GAGAA-G-ATGAAGAACGG
1 AAGAAGGAGAAGGAATGAAGAACGG
* * *
17197709 AAGAAGAAAAAGGAATGAAGAATGG
1 AAGAAGGAGAAGGAATGAAGAACGG
17197734 AAGAAGGAGAAGGA
1 AAGAAGGAGAAGGA
17197748 GCCTTACTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 3 0.10
24 1 0.03
25 22 0.71
ACGTcount: A:0.57, C:0.02, G:0.36, T:0.05
Consensus pattern (25 bp):
AAGAAGGAGAAGGAATGAAGAACGG
Found at i:17198818 original size:27 final size:27
Alignment explanation
Indices: 17198758--17198819 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
17198748 AGTAAAAATT
17198758 GGGTAGTCCGTTCGGACAGTAAACAGA
1 GGGTAGTCCGTTCGGACAGTAAACAGA
** *
17198785 GAATAGTCCG-TCGGGACCGTAAACACG-
1 GGGTAGTCCGTTC-GGACAGTAAACA-GA
17198812 GGGTAGTC
1 GGGTAGTC
17198820 TGCCAAGACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 2 0.07
27 25 0.89
28 1 0.04
ACGTcount: A:0.27, C:0.21, G:0.34, T:0.18
Consensus pattern (27 bp):
GGGTAGTCCGTTCGGACAGTAAACAGA
Found at i:17198835 original size:27 final size:27
Alignment explanation
Indices: 17198805--17198874 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
17198795 TCGGGACCGT
17198805 AAACACGGGGTAGTCTGCCAAGACAAC
1 AAACACGGGGTAGTCTGCCAAGACAAC
* * * ** *
17198832 AAACATGGGTTAGTTTGCCGGGACAAT
1 AAACACGGGGTAGTCTGCCAAGACAAC
**
17198859 AAACACGATGTAGTCT
1 AAACACGGGGTAGTCT
17198875 ACCAGGATGG
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (27 bp):
AAACACGGGGTAGTCTGCCAAGACAAC
Found at i:17205087 original size:3 final size:3
Alignment explanation
Indices: 17205079--17205112 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17205069 TACAGTGGCT
17205079 TCA TCA TCA TCA TCA TCA TCA TCA TCA -CA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
17205113 TTCTTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:17213679 original size:16 final size:15
Alignment explanation
Indices: 17213640--17213670 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17213630 GGAGTACATG
*
17213640 AAAAAAGAAATTAAA
1 AAAAAAGAAAATAAA
17213655 AAAAAAGAAAATAAA
1 AAAAAAGAAAATAAA
17213670 A
1 A
17213671 GAAAGAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAAAGAAAATAAA
Found at i:17219037 original size:25 final size:26
Alignment explanation
Indices: 17218993--17219046 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
17218983 ATTAGAAATT
*
17218993 AAATAATGAAAATAAATAAACA-ATA
1 AAATAATCAAAATAAATAAACAGATA
* * *
17219018 AAATAATCAAAATGACTAAATAGATA
1 AAATAATCAAAATAAATAAACAGATA
17219044 AAA
1 AAA
17219047 CCAATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (26 bp):
AAATAATCAAAATAAATAAACAGATA
Found at i:17222480 original size:21 final size:21
Alignment explanation
Indices: 17222456--17222496 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17222446 ACATTTTAGG
*
17222456 TTGGAATATG-TATGTTTTGAA
1 TTGGAAT-TGCTAAGTTTTGAA
17222477 TTGGAATTGCTAAGTTTTGA
1 TTGGAATTGCTAAGTTTTGA
17222497 TTAAGGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.46
Consensus pattern (21 bp):
TTGGAATTGCTAAGTTTTGAA
Found at i:17228270 original size:19 final size:20
Alignment explanation
Indices: 17228242--17228280 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
17228232 GAAAGTTAAT
17228242 AAAAATTTTGATTACGGTGG
1 AAAAATTTTGATTACGGTGG
17228262 AAAAA-TTTGATTACGGTGG
1 AAAAATTTTGATTACGGTGG
17228281 GTGACAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (20 bp):
AAAAATTTTGATTACGGTGG
Found at i:17231600 original size:22 final size:21
Alignment explanation
Indices: 17231560--17231619 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
17231550 AAAATGTAAA
17231560 AATTAAATTAAAAACAAAATT
1 AATTAAATTAAAAACAAAATT
* *
17231581 AATTTAATTAAAAACAAAAAT
1 AATTAAATTAAAAACAAAATT
* *
17231602 -ATTAAAATAAAAATAAAA
1 AATTAAATTAAAAACAAAA
17231620 AATGGCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTAAATTAAAAACAAAATT
Found at i:17247239 original size:41 final size:40
Alignment explanation
Indices: 17247171--17247451 Score: 170
Period size: 41 Copynumber: 6.9 Consensus size: 40
17247161 CAAACTTTAG
* *
17247171 ATTAAATTATATATTTTTATTAAATTATAT-TTAATAATTATT
1 ATTAAATTATATATTTATAGT--ATTATATATTAATAATT-TT
*
17247213 ATTTTAAATTATAT-TTTATAGTATTATATATT-ATGATTTT
1 A--TTAAATTATATATTTATAGTATTATATATTAATAATTTT
* *** *
17247253 AGTAAATTCATATAAGAATA-TATT-TAATATTAAGAATTTT
1 ATTAAATT-ATATATTTATAGTATTAT-ATATTAATAATTTT
* *
17247293 ATTAAATTATATATTTTTATTAAATTATAT-TTAATAATAATTAT
1 ATTAAATTATATATTTATAGT--ATTATATATTAATAAT--TT-T
* *
17247337 TTTAAATTATAT-TTTATAGTATTATATATT-ATGATTTT
1 ATTAAATTATATATTTATAGTATTATATATTAATAATTTT
* * * * * *
17247375 AGTAATTTA-ATATTAAGAATATCTA-ATATTAAGAATTTT
1 ATTAAATTATATATTTATAGTAT-TATATATTAATAATTTT
* *
17247414 ATTAAATTATATATTTTTATTAAATTATAT-TTAATAAT
1 ATTAAATTATATATTTATAGT--ATTATATATTAATAAT
17247452 AATTATGTTA
Statistics
Matches: 183, Mismatches: 34, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
37 2 0.01
38 26 0.14
39 37 0.20
40 27 0.15
41 39 0.21
42 14 0.08
43 15 0.08
44 23 0.13
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (40 bp):
ATTAAATTATATATTTATAGTATTATATATTAATAATTTT
Found at i:17247297 original size:18 final size:18
Alignment explanation
Indices: 17247276--17247321 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
17247266 AAGAATATAT
17247276 TTAATATTA-AGAATTTTA
1 TTAA-ATTATAGAATTTTA
* *
17247294 TTAAATTATATATTTTTA
1 TTAAATTATAGAATTTTA
17247312 TTAAATTATA
1 TTAAATTATA
17247322 TTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAAATTATAGAATTTTA
Found at i:17247387 original size:22 final size:20
Alignment explanation
Indices: 17247337--17247389 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
17247327 TAATAATTAT
*
17247337 TTTAA-ATTATATTTTATAG
1 TTTAATATTATATTTTATAA
17247356 TATTATATATTATGATTTTAGTAA
1 T-TTA-ATATTAT-ATTTTA-TAA
17247380 TTTAATATTA
1 TTTAATATTA
17247390 AGAATATCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 1 0.04
22 11 0.39
23 9 0.32
24 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTAATATTATATTTTATAA
Found at i:17247452 original size:121 final size:122
Alignment explanation
Indices: 17247171--17247463 Score: 518
Period size: 122 Copynumber: 2.4 Consensus size: 122
17247161 CAAACTTTAG
*
17247171 ATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
* *
17247236 TTATATATTATGATTTTAGTAAATTCATATAAGAATATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATATAAGAATATATCTAATATTAAGAATTTT
17247293 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
*
17247358 TTATATATTATGATTTTAGTAATTTAATATTAAG-A-ATATCTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTAATA-TAAGAATATATCTAATATTAAGAATTTT
*
17247414 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
17247464 ATATGATTAA
Statistics
Matches: 165, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
121 69 0.42
122 92 0.56
123 4 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (122 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATTAATATAAGAATATATCTAATATTAAGAATTTT
Found at i:17247691 original size:16 final size:16
Alignment explanation
Indices: 17247670--17247715 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
17247660 TTGATTTGCT
17247670 ATTATGCCTCTATTCC
1 ATTATGCCTCTATTCC
17247686 ATTATGCCTCTATTCC
1 ATTATGCCTCTATTCC
17247702 ATTA-GCCTCTATTC
1 ATTATGCCTCTATTC
17247716 TAATACAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTATGCCTCTATTCC
Found at i:17258778 original size:23 final size:23
Alignment explanation
Indices: 17258752--17258807 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
17258742 ATTGTTGTGG
*
17258752 CCAATGAGAAGAACGAGTTGATT
1 CCAACGAGAAGAACGAGTTGATT
17258775 CCAACGAGAAGAACGAGTTGATT
1 CCAACGAGAAGAACGAGTTGATT
*
17258798 CCAACAAGAA
1 CCAACGAGAA
17258808 CAACCACAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (23 bp):
CCAACGAGAAGAACGAGTTGATT
Found at i:17262088 original size:19 final size:19
Alignment explanation
Indices: 17262064--17262101 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17262054 GCTATGGTTA
17262064 GTCGAATCTTGGATTGAAC
1 GTCGAATCTTGGATTGAAC
17262083 GTCGAATCTTGGATTGAAC
1 GTCGAATCTTGGATTGAAC
17262102 ATAGTGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
GTCGAATCTTGGATTGAAC
Found at i:17268117 original size:25 final size:25
Alignment explanation
Indices: 17268089--17268167 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
17268079 TAGATCATGA
17268089 GAGCTTATCGATTCTCAGCTTGTAT
1 GAGCTTATCGATTCTCAGCTTGTAT
17268114 GAGCTTATCGATT-TACAGCTTGTGA-
1 GAGCTTATCGATTCT-CAGCTTGT-AT
* * *
17268139 GAGCATACCGATTCAT-AGCTCGTAT
1 GAGCTTATCGATTC-TCAGCTTGTAT
17268164 GAGC
1 GAGC
17268168 ATACATGTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 2 0.04
25 42 0.91
26 1 0.02
27 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (25 bp):
GAGCTTATCGATTCTCAGCTTGTAT
Found at i:17268140 original size:50 final size:51
Alignment explanation
Indices: 17268054--17268167 Score: 133
Period size: 50 Copynumber: 2.3 Consensus size: 51
17268044 AGACACACCA
** * *
17268054 CAGCTTGTATGAGCTTACCGATTTGTAGATCATGAGAGCTTATCGATTC-T
1 CAGCTTGTATGAGCTTACCGATTTACAGATCATGAGAGCATACCGATTCAT
* * **
17268104 CAGCTTGTATGAGCTTATCGATTTACAGCTTGTGAGAGCATACCGATTCAT
1 CAGCTTGTATGAGCTTACCGATTTACAGATCATGAGAGCATACCGATTCAT
*
17268155 -AGCTCGTATGAGC
1 CAGCTTGTATGAGC
17268168 ATACATGTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 53 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (51 bp):
CAGCTTGTATGAGCTTACCGATTTACAGATCATGAGAGCATACCGATTCAT
Found at i:17270375 original size:8 final size:8
Alignment explanation
Indices: 17270362--17270388 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17270352 CCCCTTCCTC
17270362 TTTAATTA
1 TTTAATTA
17270370 TTTAATTA
1 TTTAATTA
17270378 TTTAATTA
1 TTTAATTA
17270386 TTT
1 TTT
17270389 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATTA
Found at i:17272090 original size:6 final size:6
Alignment explanation
Indices: 17272081--17272133 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
17272071 TTTTATTTTT
* * *
17272081 TTTATG TTTATG TTTATA TTTATA TTTATA TTTATA TTTATA CTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
17272129 TTTAT
1 TTTAT
17272134 TTTTTTATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:17279990 original size:21 final size:21
Alignment explanation
Indices: 17279960--17280002 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17279950 GTATTATGCA
*
17279960 TTATACATATGTGCCCATAAT
1 TTATACATATGTGCCCACAAT
*
17279981 TTATATATATGTGCCCACAAT
1 TTATACATATGTGCCCACAAT
17280002 T
1 T
17280003 ATCCAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TTATACATATGTGCCCACAAT
Found at i:17281455 original size:127 final size:128
Alignment explanation
Indices: 17281228--17281483 Score: 469
Period size: 127 Copynumber: 2.0 Consensus size: 128
17281218 TATATATAAG
*
17281228 TAAATGAGGAAACATAAAACCTAGTTTTAAAACTCCATGTTTCCTCTTTTTTTTAACTTGATGTT
1 TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTTAACTTGATGTT
17281293 TAACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
66 TAACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
* *
17281356 TAAATGAGTAAACATAAAACCTGGTTCTAAAACTCCATGTTTCCTC-TTTTTTTAACTTGATGTT
1 TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTTAACTTGATGTT
*
17281420 TAACTCCTCAGCCAAGTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
66 TAACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
17281483 T
1 T
17281484 CTCCACTATA
Statistics
Matches: 124, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
127 81 0.65
128 43 0.35
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (128 bp):
TAAATGAGGAAACATAAAACCTAGTTCTAAAACTCCATGTTTCCTCTTTTTTTTAACTTGATGTT
TAACTCCTCAGCCAACTTTTTCAAATGTTGTAAGGTTCCACTGTCGGTATTATACCATCTTGA
Found at i:17304910 original size:30 final size:30
Alignment explanation
Indices: 17304872--17304936 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
17304862 TTCAACTAAG
17304872 AAAT-TTCGCTGCAAACTTAAGTGTTTTAT
1 AAATATTCGCTGCAAACTTAAGTGTTTTAT
17304901 AAATATTCGCTGCAAACTTAAGTGTTTTAT
1 AAATATTCGCTGCAAACTTAAGTGTTTTAT
17304931 AAATAT
1 AAATAT
17304937 ATAACAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (30 bp):
AAATATTCGCTGCAAACTTAAGTGTTTTAT
Found at i:17307930 original size:38 final size:38
Alignment explanation
Indices: 17307879--17307956 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
17307869 TTTATACCTA
17307879 GGTTAACTAGGCTTGGATGGCCCACACATTAAAACAAG
1 GGTTAACTAGGCTTGGATGGCCCACACATTAAAACAAG
17307917 GGTTAACTAGGCTTGGATGGCCCACACATTAAAACAAG
1 GGTTAACTAGGCTTGGATGGCCCACACATTAAAACAAG
17307955 GG
1 GG
17307957 GTTTTTCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (38 bp):
GGTTAACTAGGCTTGGATGGCCCACACATTAAAACAAG
Found at i:17310599 original size:40 final size:40
Alignment explanation
Indices: 17310544--17310891 Score: 588
Period size: 40 Copynumber: 8.7 Consensus size: 40
17310534 GAGCATTGGA
17310544 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17310584 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
17310624 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17310664 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
17310704 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17310744 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
17310784 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17310824 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17310864 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
17310892 AGGTGTTTGC
Statistics
Matches: 287, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 287 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:17319516 original size:40 final size:40
Alignment explanation
Indices: 17319461--17319808 Score: 588
Period size: 40 Copynumber: 8.7 Consensus size: 40
17319451 GAGCATTGGA
17319461 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17319501 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
17319541 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17319581 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
17319621 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17319661 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
17319701 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
17319741 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
17319781 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
17319809 AGGTGTTTGC
Statistics
Matches: 287, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 287 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:17322747 original size:26 final size:26
Alignment explanation
Indices: 17322718--17322778 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
17322708 TAGGTTAATT
* *
17322718 TTAAAATAAGTAATATGCAAAATAAC
1 TTAAAATAAATAATATACAAAATAAC
* *
17322744 TTAAAATAAATAATATATAAAGTAAC
1 TTAAAATAAATAATATACAAAATAAC
17322770 TTAAAATAA
1 TTAAAATAA
17322779 TTAGTCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
TTAAAATAAATAATATACAAAATAAC
Found at i:17322826 original size:21 final size:21
Alignment explanation
Indices: 17322797--17322836 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17322787 ATAAGTTAGG
17322797 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
17322818 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
17322837 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:17324291 original size:14 final size:15
Alignment explanation
Indices: 17324267--17324301 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
17324257 TTTTGGTTTG
17324267 TTATATGGACTGTTA
1 TTATATGGACTGTTA
*
17324282 TTAT-TGGACTTTTA
1 TTATATGGACTGTTA
17324296 TTATAT
1 TTATAT
17324302 ATATGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (15 bp):
TTATATGGACTGTTA
Found at i:17325323 original size:88 final size:88
Alignment explanation
Indices: 17325092--17325364 Score: 305
Period size: 88 Copynumber: 3.1 Consensus size: 88
17325082 ACTCAAGAAA
* * * ** *
17325092 ACAAGGTTGGTGTTTTCGATCTTCTTTACTGTCAGTACAGGGAAG-CGAGATCTGCTATCTTCAA
1 ACAAGGCTGGTGTATTCGATCTGCTTTACTACCAGTACA-GGAAGACAAGATCTGCTATCTTCAA
*
17325156 TCTACTCCACTGCTGCTCAAGGAG
65 TCTACTCCACTGCTGCTCAGGGAG
* * * * * * ** * *
17325180 ATAAGACTTGCTATCTTTGATCTGCTTCGCTACCAGTATAGGAAGACAAGATCTGCTATTTTCAA
1 ACAAGGC-TGGTGTATTCGATCTGCTTTACTACCAGTACAGGAAGACAAGATCTGCTATCTTCAA
* *
17325245 CCTACTCCACTGCTACTCAGGGAG
65 TCTACTCCACTGCTGCTCAGGGAG
* *
17325269 ACAAGGCTGGTGTATTCGATCTGCTTTAATACCAGTACAGGAAGACAAGATCTGCTATCTTCAGT
1 ACAAGGCTGGTGTATTCGATCTGCTTTACTACCAGTACAGGAAGACAAGATCTGCTATCTTCAAT
* *
17325334 CTACTCCACTACTGCTCAGTGAG
66 CTACTCCACTGCTGCTCAGGGAG
*
17325357 ATAAGGCT
1 ACAAGGCT
17325365 AGTGGCTTAA
Statistics
Matches: 148, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
88 83 0.56
89 65 0.44
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (88 bp):
ACAAGGCTGGTGTATTCGATCTGCTTTACTACCAGTACAGGAAGACAAGATCTGCTATCTTCAAT
CTACTCCACTGCTGCTCAGGGAG
Found at i:17325462 original size:44 final size:44
Alignment explanation
Indices: 17325414--17325813 Score: 126
Period size: 44 Copynumber: 9.1 Consensus size: 44
17325404 AGATTCATCG
*
17325414 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
* * ** * * * **
17325458 TCTTCCACCTATTCCACTGCTG-TCCAGGGAGATAGGATCTACAA
1 TCTTCAATCTGCTCCACTACTGCT-TAGGGAGATAAGATCTGTAA
* * * * * * * * *
17325502 TCTTCGACCTACTCCACTGCTACTCAAGGAGATAAG-GCTAGT-G
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTAA
* * * * **
17325545 GCTTAAATCTGCTTCC-CTAACT-ATATTGGGAAGATAAGAT-TCGCCA
1 TCTTCAATCTGC-TCCACT-ACTGCT-TAGGG-AGATAAGATCT-GTAA
** *
17325591 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
* * * * **
17325635 TCTTCAACCTACTCCACTA-T-TTTCAGGGAGATAAGGTCTAAAA
1 TCTTCAATCTGCTCCACTACTGCTT-AGGGAGATAAGATCTGTAA
* * * * * * * * *
17325678 TCTTAAACCTACTCCACTGCTGCTCAAGAAGATAAG-GCTAGT-G
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-GTAA
* * * *
17325721 GCTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCGCT-G
1 TCTTCAATCTGC-TCCACTACT-GCTTAGGG-AGATAAGATCT-G-TAA
* * *
17325766 TCTTCGATTTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAA
1 TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
17325810 TCTT
1 TCTT
17325814 TAACCTATTC
Statistics
Matches: 258, Mismatches: 73, Indels: 50
0.68 0.19 0.13
Matches are distributed among these distances:
42 2 0.01
43 65 0.25
44 139 0.54
45 40 0.16
46 12 0.05
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
Found at i:17325563 original size:176 final size:175
Alignment explanation
Indices: 17325325--17325887 Score: 792
Period size: 176 Copynumber: 3.2 Consensus size: 175
17325315 AAGATCTGCT
** * * **
17325325 ATCTTCAGTCTACTCCACTACTGCTC-AGTGAGATAAGGCTAGTGGCTTAAATTTAATTCCCTAC
1 ATCTTCAACCTACTCCACTGCTGCTCAAG-GAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTAC
*
17325389 TACCTTGGGAAGATAAGATTCATCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
65 TACCTTGGGAAGATAAGATTC-CCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
*
17325454 GTAATCTTCCACCTATTCCACTGCTGTCCAGGGAGATAGGATCTACA
129 GTAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATCTACA
* *
17325501 ATCTTCGACCTACTCCACTGCTACTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTAAC
1 ATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCT-AC
** * *
17325566 TATATTGGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
65 TACCTTGGGAAGATAAGATTC-CCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
* * * * * *
17325631 GAAATCTTCAACCTACTCCACT-ATTTTCAGGGAGATAAGG-TCTAAA
129 GTAATCTTCAACCTATTCCACTGCTGTCCAGGGAGAT-AGGATCTACA
* *
17325677 ATCTTAAACCTACTCCACTGCTGCTCAAGAAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACT
1 ATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACT
* * *
17325742 ACCTTGGGAAGATAAGATTCGCTGTCTTCGATTTGCTCCACTACTGCTTAGAGAGATAAGATCTG
66 ACCTTGGGAAGATAAGATTC-CCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
* *
17325807 TAATCTTTAACCTATTCCACTGCTGTCTAGGGAGATAGGA-CTCACA
130 TAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATCT-ACA
17325853 ATCTTCAACCTACTCCACTGCTGCTCAAGGAGATA
1 ATCTTCAACCTACTCCACTGCTGCTCAAGGAGATA
17325888 GGACTTACAA
Statistics
Matches: 339, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
175 84 0.25
176 170 0.50
177 85 0.25
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (175 bp):
ATCTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACT
ACCTTGGGAAGATAAGATTCCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
AATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATCTACA
Found at i:17325842 original size:44 final size:44
Alignment explanation
Indices: 17325808--17325989 Score: 249
Period size: 44 Copynumber: 4.1 Consensus size: 44
17325798 TAAGATCTGT
* * * *
17325808 AATCTTTAACCTATTCCACTGCTGTCTAGGGAGATAGGACTCAC
1 AATCTTCAACCTATTCCACTACTGTCCAAGGAGATAGGACTCAC
* * *
17325852 AATCTTCAACCTACTCCACTGCTG-CTCAAGGAGATAGGACTTAC
1 AATCTTCAACCTATTCCACTACTGTC-CAAGGAGATAGGACTCAC
* * *
17325896 AATCTTCAACCTATTCCACTATTGTCCAGGGAGATAGGATTCAC
1 AATCTTCAACCTATTCCACTACTGTCCAAGGAGATAGGACTCAC
*
17325940 AATCTTCAACCTATTCCACTACTGTCCAAGGAGATAGGATTCAC
1 AATCTTCAACCTATTCCACTACTGTCCAAGGAGATAGGACTCAC
17325984 AATCTT
1 AATCTT
17325990 AAATCCGCTT
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
43 1 0.01
44 121 0.98
45 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTACTGTCCAAGGAGATAGGACTCAC
Found at i:17325858 original size:88 final size:87
Alignment explanation
Indices: 17325414--17325963 Score: 305
Period size: 88 Copynumber: 6.3 Consensus size: 87
17325404 AGATTCATCG
* * * * * *
17325414 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCCACCTATTCCACTGCT
1 TCTTCGACCTACTCCACTACTGCTCA-AGAGATAAGATCTGTAATCTTCAACCTATTCCACTACT
*
17325479 GTCCAGGGAGATAGGA-TCTACAA
65 GTCTAGGGAGATAGGATTC-ACAA
* * * ** * * *
17325502 TCTTCGACCTACTCCACTGCTACTCAAGGAGATAAG-GCTAGT-GGCTTAAATCTGCTTCC-CTA
1 TCTTCGACCTACTCCACTACTGCTCAA-GAGATAAGATCT-GTAATCTTCAACCT-ATTCCACT-
* * * * * *
17325564 ACTATATTGGGAAGATAAGATTCGCCA
62 ACTGTCTAGGG-AGATAGGATTCACAA
* * * * * * * *
17325591 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAACCTACTCCACTATT
1 TCTTCGACCTACTCCACTACTGCTCA-AGAGATAAGATCTGTAATCTTCAACCTATTCCACTACT
* *
17325656 TTC-AGGGAGATAAGG--TCTAAAA
65 GTCTAGGGAGAT-AGGATTC-ACAA
** * * ** * * *
17325678 TCTTAAACCTACTCCACTGCTGCTCAAGAAGATAAG-GCTAGT-GGCTTAAATCTGCTTCC-CTA
1 TCTTCGACCTACTCCACTACTGCTCAAG-AGATAAGATCT-GTAATCTTCAACCT-ATTCCACTA
** * * * **
17325740 CTACCTTGGGAAGATAAGATTCGCTG
63 CTGTCTAGGG-AGATAGGATTCACAA
** * * * *
17325766 TCTTCGATTTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATCTTTAACCTATTCCACTGCT
1 TCTTCGACCTACTCCACTACTGCTCA-AGAGATAAGATCTGTAATCTTCAACCTATTCCACTACT
*
17325831 GTCTAGGGAGATAGGACTCACAA
65 GTCTAGGGAGATAGGATTCACAA
* * *
17325854 TCTTCAACCTACTCCACTGCTGCTCAAGGAGATAGGA-CT-TACAATCTTCAACCTATTCCACTA
1 TCTTCGACCTACTCCACTACTGCTCAA-GAGATAAGATCTGT--AATCTTCAACCTATTCCACTA
* *
17325917 TTGTCCAGGGAGATAGGATTCACAA
63 CTGTCTAGGGAGATAGGATTCACAA
* *
17325942 TCTTCAACCTATTCCACTACTG
1 TCTTCGACCTACTCCACTACTG
17325964 TCCAAGGAGA
Statistics
Matches: 332, Mismatches: 104, Indels: 52
0.68 0.21 0.11
Matches are distributed among these distances:
86 18 0.05
87 54 0.16
88 181 0.55
89 66 0.20
90 13 0.04
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (87 bp):
TCTTCGACCTACTCCACTACTGCTCAAGAGATAAGATCTGTAATCTTCAACCTATTCCACTACTG
TCTAGGGAGATAGGATTCACAA
Found at i:17328328 original size:21 final size:22
Alignment explanation
Indices: 17328302--17328359 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
17328292 ATCATTTTCA
17328302 TTTTTTATTTTGA-TTTTGA-CC
1 TTTTTTATTTT-ATTTTTGATCC
*
17328323 TTTTTT-TTATTATTTTTGATCT
1 TTTTTTATT-TTATTTTTGATCC
17328345 TTTTTTATTTT-TTTT
1 TTTTTTATTTTATTTT
17328360 GAATCTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 9 0.28
23 2 0.06
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTTTTATTTTATTTTTGATCC
Found at i:17328365 original size:21 final size:20
Alignment explanation
Indices: 17328302--17328361 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
17328292 ATCATTTTCA
*
17328302 TTTTTTATTTTGATTTTGACCTT
1 TTTTTTATTTT--TTTTGATC-T
*
17328325 TTTTTTATTATTTTTGATCT
1 TTTTTTATTTTTTTTGATCT
17328345 TTTTTTATTTTTTTTGA
1 TTTTTTATTTTTTTTGA
17328362 ATCTGAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.50
21 7 0.21
23 10 0.29
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTTTTTTGATCT
Found at i:17332857 original size:26 final size:26
Alignment explanation
Indices: 17332828--17332888 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
17332818 TAGGTTAATT
* *
17332828 TTAAAATAAGTAATATGTAAAATAAC
1 TTAAAATAAATAATATATAAAATAAC
*
17332854 TTAAAATAAATAATATATAAAGTAAC
1 TTAAAATAAATAATATATAAAATAAC
17332880 TTAAAATAA
1 TTAAAATAA
17332889 TTAGTCTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:17332931 original size:21 final size:21
Alignment explanation
Indices: 17332907--17332946 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17332897 ATAAGTTATG
17332907 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
17332928 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
17332947 AGAAAATTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:17334137 original size:14 final size:15
Alignment explanation
Indices: 17334113--17334147 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
17334103 TTTTGGTTTG
17334113 TTATATGGACTGTTA
1 TTATATGGACTGTTA
*
17334128 TTAT-TGGACTTTTA
1 TTATATGGACTGTTA
17334142 TTATAT
1 TTATAT
17334148 ATATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (15 bp):
TTATATGGACTGTTA
Found at i:17337968 original size:251 final size:251
Alignment explanation
Indices: 17337519--17338024 Score: 904
Period size: 251 Copynumber: 2.0 Consensus size: 251
17337509 AAATTTTAGA
*
17337519 TTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTGAGTTTCTTTAGAAGT
1 TTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTAAGTTTCTTTAGAAGT
*
17337584 AGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGCTCTTCATT
66 AGTTTTAACAATATTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGCTCTTCATT
* **
17337649 GGAGGGGAGATTAGAGTTGTTTGAAGGAAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGG
131 GGAGGGAAGATTAGAGCCGTTTGAAGGAAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGG
17337714 ACTTTATCTTTATTTTCTTGCTGTTCAATCTATTTTAAATTTCTACTTGTGTCGAT
196 ACTTTATCTTTATTTTCTTGCTGTTCAATCTATTTTAAATTTCTACTTGTGTCGAT
*
17337770 TTTTGTTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTAAGTTTCTTTAGAAGT
1 TTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTAAGTTTCTTTAGAAGT
*
17337835 AGTTTTAACAATATTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGTTCTTCATT
66 AGTTTTAACAATATTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGCTCTTCATT
* *
17337900 GGAGGGAAGGTTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGG
131 GGAGGGAAGATTAGAGCCGTTTGAAGGAAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGG
* * *
17337965 ACTTTATCTTTATTTTCTTGTTGTTCAATCTCTTTTAAATTTCTGCTTGTGTCGAT
196 ACTTTATCTTTATTTTCTTGCTGTTCAATCTATTTTAAATTTCTACTTGTGTCGAT
17338021 TTTT
1 TTTT
17338025 ATTAGCTAAT
Statistics
Matches: 243, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
251 243 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (251 bp):
TTTTGCTGAGTAAAAATTCTCTTAGAGTTTTCTCCAAGAATTCTCTCTTAAGTTTCTTTAGAAGT
AGTTTTAACAATATTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGCTCTTCATT
GGAGGGAAGATTAGAGCCGTTTGAAGGAAGTTGTGAAATCTTTCTCGATTTCAAGGCTTCTTAGG
ACTTTATCTTTATTTTCTTGCTGTTCAATCTATTTTAAATTTCTACTTGTGTCGAT
Found at i:17340139 original size:36 final size:33
Alignment explanation
Indices: 17340074--17340140 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
17340064 GTGAATGAAG
* *
17340074 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGGGAAAAAGAGAGAGAGCTAAAACAAGGAA
*
17340107 TGAGGGAAAAAGAAGAGAGTGCTCAAACACAAGG
1 TGAGGGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
17340141 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.49, C:0.09, G:0.31, T:0.10
Consensus pattern (33 bp):
TGAGGGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:17345198 original size:37 final size:38
Alignment explanation
Indices: 17345124--17345213 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 38
17345114 ACCACTCCGA
* **
17345124 CCACCCTGCACACCACAATAGGGCCATGTTAGACCCAT
1 CCACCCTGCACACCACAATAGGACCATAATAGACCCAT
* *
17345162 CCACCCTGCACACCAC-ATAGGACCTTAATAGGCCCAT
1 CCACCCTGCACACCACAATAGGACCATAATAGACCCAT
* *
17345199 CCGCCCTACACACCA
1 CCACCCTGCACACCA
17345214 AAAATGTGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 29 0.64
38 16 0.36
ACGTcount: A:0.29, C:0.43, G:0.13, T:0.14
Consensus pattern (38 bp):
CCACCCTGCACACCACAATAGGACCATAATAGACCCAT
Found at i:17351573 original size:29 final size:29
Alignment explanation
Indices: 17351531--17351619 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
17351521 GTGCTAAACA
* *
17351531 ATGGTTGTAACCATCCCTTTTCATAGTCG
1 ATGGTCGTCACCATCCCTTTTCATAGTCG
*
17351560 ATGGTCGTCACCATCCCTTTTCATAGTTG
1 ATGGTCGTCACCATCCCTTTTCATAGTCG
* * *
17351589 ACGGTCGTCCCCATCCCTTTTCATAATCG
1 ATGGTCGTCACCATCCCTTTTCATAGTCG
17351618 AT
1 AT
17351620 AGCTGAAGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36
Consensus pattern (29 bp):
ATGGTCGTCACCATCCCTTTTCATAGTCG
Found at i:17356965 original size:27 final size:27
Alignment explanation
Indices: 17356925--17357174 Score: 276
Period size: 27 Copynumber: 9.3 Consensus size: 27
17356915 AAAGGTTGTT
17356925 AAATTA-TGAAATACCCTCGAAGGGTA
1 AAATTACTGAAATACCCTCGAAGGGTA
* *
17356951 AAATTACTAAAATACCCTCAAAGGGTA
1 AAATTACTGAAATACCCTCGAAGGGTA
*
17356978 AAATTACTAAAATACCCTCGAAGGGTA
1 AAATTACTGAAATACCCTCGAAGGGTA
* * *
17357005 AAATTACTAAAATACCCTCGAAAGCTA
1 AAATTACTGAAATACCCTCGAAGGGTA
* **
17357032 AAATTA-TCGAAATACCCTCAAATCGTA
1 AAATTACT-GAAATACCCTCGAAGGGTA
* * *
17357059 AAATTACTGAAATGCCCTCGAA-AGTT
1 AAATTACTGAAATACCCTCGAAGGGTA
* *
17357085 AAATTATTGAAATACCCTCAAAGGGTA
1 AAATTACTGAAATACCCTCGAAGGGTA
17357112 AAATTA-TCGAAATACCCTCGAAGGGTA
1 AAATTACT-GAAATACCCTCGAAGGGTA
* * *
17357139 AAATTACCGAAAGACCC-CTATAGGGTA
1 AAATTACTGAAATACCCTCGA-AGGGTA
*
17357166 AAATGACTG
1 AAATTACTG
17357175 TTATGCCCCT
Statistics
Matches: 192, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
26 31 0.16
27 160 0.83
28 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGAAGGGTA
Found at i:17357167 original size:107 final size:107
Alignment explanation
Indices: 17356932--17357174 Score: 276
Period size: 107 Copynumber: 2.3 Consensus size: 107
17356922 GTTAAATTAT
* * *
17356932 GAAATACCCTCGAAGGGTAAAATTACTAAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTC
1 GAAAGACCCTCAAAGGGTAAAATTACTGAAATACCCTCAAA-GGTAAAATTACTAAAATACCCTC
* *
17356997 GAAGGGTAAAATTACTAAAATACCCTCGAAAGCTAAAATTATC
65 AAAGGGTAAAATTACTAAAATACCCTCGAAAGCTAAAATTACC
* ** * * * *
17357040 GAAATACCCTCAAATCGTAAAATTACTGAAATGCCCTCGAAA-GTTAAATTATTGAAATACCCTC
1 GAAAGACCCTCAAAGGGTAAAATTACTGAAATACCCTC-AAAGGTAAAATTACTAAAATACCCTC
* * *
17357104 AAAGGGTAAAATTA-TCGAAATACCCTCGAAGGGTAAAATTACC
65 AAAGGGTAAAATTACT-AAAATACCCTCGAAAGCTAAAATTACC
* *
17357147 GAAAGACCC-CTATAGGGTAAAATGACTG
1 GAAAGACCCTC-AAAGGGTAAAATTACTG
17357175 TTATGCCCCT
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
106 2 0.02
107 76 0.67
108 33 0.29
109 3 0.03
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (107 bp):
GAAAGACCCTCAAAGGGTAAAATTACTGAAATACCCTCAAAGGTAAAATTACTAAAATACCCTCA
AAGGGTAAAATTACTAAAATACCCTCGAAAGCTAAAATTACC
Found at i:17359604 original size:12 final size:12
Alignment explanation
Indices: 17359587--17359611 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17359577 TATGTTACAA
17359587 AAAATAATTTAT
1 AAAATAATTTAT
17359599 AAAATAATTTAT
1 AAAATAATTTAT
17359611 A
1 A
17359612 TTTTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATAATTTAT
Found at i:17361710 original size:22 final size:22
Alignment explanation
Indices: 17361667--17361731 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
17361657 TGCTAGTAAC
* *
17361667 CAGAATGGCTA-AGAGCCGTAAA
1 CAGAATAGCTACA-AGCCATAAA
* * *
17361689 CAGGATAGCTATAAGCTATAAA
1 CAGAATAGCTACAAGCCATAAA
*
17361711 CAGAATGGCTACAAGCCATAA
1 CAGAATAGCTACAAGCCATAA
17361732 GTACAGTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (22 bp):
CAGAATAGCTACAAGCCATAAA
Found at i:17361791 original size:32 final size:32
Alignment explanation
Indices: 17361721--17361928 Score: 233
Period size: 32 Copynumber: 6.5 Consensus size: 32
17361711 CAGAATGGCT
* * *
17361721 ACAAGCCATAAGTA-CAGTAATATGATTGGAAC
1 ACAA-CCATCAGTAGCAGTAATATGATCGGCAC
* *
17361753 AAAACCATCAGTAGCAGTGATATGATCGGCAC
1 ACAACCATCAGTAGCAGTAATATGATCGGCAC
* *
17361785 ACAACCATCAGTAAC-GATAATATGACCGGCAC
1 ACAACCATCAGTAGCAG-TAATATGATCGGCAC
* *
17361817 A-AAGCCATCAGTAGCAGTGATATGATTGGCAC
1 ACAA-CCATCAGTAGCAGTAATATGATCGGCAC
* *
17361849 ACAACCATCAGTAGCGGTAATATGATCGACAC
1 ACAACCATCAGTAGCAGTAATATGATCGGCAC
* * * *
17361881 AAAACCATCAGTAGTAGTGATATGATCGACAC
1 ACAACCATCAGTAGCAGTAATATGATCGGCAC
17361913 ACAACCATCAGTAGCA
1 ACAACCATCAGTAGCA
17361929 TCGCAGCAAA
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
31 11 0.07
32 134 0.91
33 3 0.02
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (32 bp):
ACAACCATCAGTAGCAGTAATATGATCGGCAC
Found at i:17361904 original size:96 final size:97
Alignment explanation
Indices: 17361721--17361928 Score: 264
Period size: 96 Copynumber: 2.2 Consensus size: 97
17361711 CAGAATGGCT
* * *
17361721 ACAAGCCATAAGTA-CAGTAATATGATTGGAACAAAACCATCAGTAGCAGTGATATGATCGGCAC
1 ACAAGCCATCAGTAGCAGTAATATGATTGGAACAAAACCATCAGTAGCAGTAATATGATCGACAC
* *
17361785 ACAACCATCAGTAACGATAATATGACCGGCAC
66 AAAACCATCAGTAACGATAATATGACCGACAC
* * * *
17361817 A-AAGCCATCAGTAGCAGTGATATGATTGGCACACAACCATCAGTAGCGGTAATATGATCGACAC
1 ACAAGCCATCAGTAGCAGTAATATGATTGGAACAAAACCATCAGTAGCAGTAATATGATCGACAC
* *
17361881 AAAACCATCAGT-A-GTAGTGATATGATCGACAC
66 AAAACCATCAGTAACG-A-TAATATGACCGACAC
17361913 ACAA-CCATCAGTAGCA
1 ACAAGCCATCAGTAGCA
17361929 TCGCAGCAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
94 1 0.01
95 13 0.13
96 81 0.84
97 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (97 bp):
ACAAGCCATCAGTAGCAGTAATATGATTGGAACAAAACCATCAGTAGCAGTAATATGATCGACAC
AAAACCATCAGTAACGATAATATGACCGACAC
Found at i:17361926 original size:64 final size:64
Alignment explanation
Indices: 17361737--17361927 Score: 285
Period size: 64 Copynumber: 3.0 Consensus size: 64
17361727 CATAAGTACA
* *
17361737 GTAATATGATTGGA-ACAAAACCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAACG
1 GTAATATGA-TCGACACAAAACCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAGCG
* * * * *
17361801 ATAATATGACCGGCACAAAGCCATCAGTAGCAGTGATATGATTGGCACACAACCATCAGTAGCG
1 GTAATATGATCGACACAAAACCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAGCG
* *
17361865 GTAATATGATCGACACAAAACCATCAGTAGTAGTGATATGATCGACACACAACCATCAGTAGC
1 GTAATATGATCGACACAAAACCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAGC
17361928 ATCGCAGCAA
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
63 1 0.01
64 111 0.99
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (64 bp):
GTAATATGATCGACACAAAACCATCAGTAGCAGTGATATGATCGGCACACAACCATCAGTAGCG
Found at i:17362013 original size:27 final size:27
Alignment explanation
Indices: 17361969--17362027 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
17361959 AGCAAAGCTG
* *
17361969 CCAGTAACGGTATATGTGGCCA-AGCCA
1 CCAGTAACAGTATATGTGG-AAGAGCCA
17361996 CCAGTAACAGTGAT-TGTGGAAGAGCCA
1 CCAGTAACAGT-ATATGTGGAAGAGCCA
17362023 CCAGT
1 CCAGT
17362028 GTTGTACTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 25 0.89
28 2 0.07
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGAAGAGCCA
Found at i:17362129 original size:24 final size:24
Alignment explanation
Indices: 17362097--17362154 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
17362087 CCATGCTCAG
17362097 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATACAAATCACAAACA
* *
17362121 AATCAGTCATACTAATCACAGACA
1 AATCAGTCATACAAATCACAAACA
17362145 AA-CTAGTCAT
1 AATC-AGTCAT
17362155 TTACATCACG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAAACA
Found at i:17362162 original size:24 final size:24
Alignment explanation
Indices: 17362111--17362183 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
17362101 AGTCATACAA
* * *
17362111 ATCACAAACAAATCAGTCATACTA-
1 ATCACAGACAAATCAATCAT-TTAC
*
17362135 ATCACAGACAAA-CTAGTCATTTAC
1 ATCACAGACAAATC-AATCATTTAC
*
17362159 ATCACGGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
17362183 A
1 A
17362184 CTCGAGGGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
23 3 0.07
24 38 0.90
25 1 0.02
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:17362280 original size:27 final size:26
Alignment explanation
Indices: 17362216--17362423 Score: 233
Period size: 27 Copynumber: 7.8 Consensus size: 26
17362206 TACCCTCTAG
* *
17362216 GGGCATTACAATCATTTTACCCTAGA
1 GGGCATTACAGTCATTTTACCCTACA
** *
17362242 -GGCATTATGGTCATTTTACCTTACA
1 GGGCATTACAGTCATTTTACCCTACA
* *
17362267 TGGGCATTACGGTCATTTTACCCTATAA
1 -GGGCATTACAGTCATTTTACCCTA-CA
*
17362295 GGGCATTACAATCATTTTACCCTACA
1 GGGCATTACAGTCATTTTACCCTACA
* *
17362321 GGGGCATTA-AGGTTATTTTACCCTATA
1 -GGGCATTACA-GTCATTTTACCCTACA
*
17362348 GGGGCATTACAGTTATTTTACCCTACAA
1 -GGGCATTACAGTCATTTTACCCTAC-A
17362376 GGGCATTACAGTCATTTTACCCTACA
1 GGGCATTACAGTCATTTTACCCTACA
17362402 GGGCATTAC-GATCATTTTACCC
1 GGGCATTACAG-TCATTTTACCC
17362424 ATAGGGGTAT
Statistics
Matches: 158, Mismatches: 16, Indels: 16
0.83 0.08 0.08
Matches are distributed among these distances:
25 21 0.13
26 23 0.15
27 111 0.70
28 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (26 bp):
GGGCATTACAGTCATTTTACCCTACA
Found at i:17362326 original size:54 final size:53
Alignment explanation
Indices: 17362204--17362448 Score: 253
Period size: 54 Copynumber: 4.6 Consensus size: 53
17362194 AAAATAGTTA
** * ***
17362204 TTTACCCT-CTAGGGGCATTACAATCATTTTACCCTAGA-GGCATTATGGTCAT
1 TTTACCCTAC-AGGGGCATTACGGTCATTTTACCCTAAAGGGCATTACAATCAT
* *
17362256 TTTACCTTACATGGGCATTACGGTCATTTTACCCTATAAGGGCATTACAATCAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTA-AAGGGCATTACAATCAT
* * * * *
17362310 TTTACCCTACAGGGGCATTAAGGTTATTTTACCCTATAGGGGCATTACAGTTAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTA-AAGGGCATTACAATCAT
* * * *
17362364 TTTACCCTACAAGGGCATTACAGTCATTTTACCCTACAGGGCATTACGATCAT
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTAAAGGGCATTACAATCAT
* * * *
17362417 TTTACCC-ATAGGGGTATTTCGGTAATTTTACC
1 TTTACCCTACAGGGGCATTACGGTCATTTTACC
17362449 TTTCAAGGGT
Statistics
Matches: 160, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
52 49 0.31
53 21 0.13
54 90 0.56
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (53 bp):
TTTACCCTACAGGGGCATTACGGTCATTTTACCCTAAAGGGCATTACAATCAT
Found at i:17362369 original size:81 final size:81
Alignment explanation
Indices: 17362199--17362448 Score: 303
Period size: 81 Copynumber: 3.1 Consensus size: 81
17362189 GGGGCAAAAT
* * * *
17362199 AGTTA-TTTACCCTCTAGGGGCATTACAATCATTTTACCCT--AGAGGCATTATGGTCATTTTAC
1 AGTTATTTTACCCTATAAGGGCATTACAATCATTTTACCCTACAGGGGCATTAAGGTCATTTTAC
* * *
17362261 CTTACATGGGCATTAC
66 CCTATAGGGGCATTAC
* * *
17362277 GGTCATTTTACCCTATAAGGGCATTACAATCATTTTACCCTACAGGGGCATTAAGGTTATTTTAC
1 AGTTATTTTACCCTATAAGGGCATTACAATCATTTTACCCTACAGGGGCATTAAGGTCATTTTAC
17362342 CCTATAGGGGCATTAC
66 CCTATAGGGGCATTAC
* * * *
17362358 AGTTATTTTACCCTACAAGGGCATTACAGTCATTTTACCCTACA-GGGCATTACGATCATTTTAC
1 AGTTATTTTACCCTATAAGGGCATTACAATCATTTTACCCTACAGGGGCATTAAGGTCATTTTAC
* *
17362422 CC-ATAGGGGTATTTC
66 CCTATAGGGGCATTAC
* *
17362437 GGTAATTTTACC
1 AGTTATTTTACC
17362449 TTTCAAGGGT
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
78 3 0.02
79 54 0.36
80 19 0.13
81 72 0.49
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (81 bp):
AGTTATTTTACCCTATAAGGGCATTACAATCATTTTACCCTACAGGGGCATTAAGGTCATTTTAC
CCTATAGGGGCATTAC
Found at i:17362462 original size:27 final size:27
Alignment explanation
Indices: 17362389--17362712 Score: 327
Period size: 27 Copynumber: 12.1 Consensus size: 27
17362379 CATTACAGTC
* * *
17362389 ATTTTACCC-TAC-AGGGCATTACGATC
1 ATTTTACCCAT-CGAGGGTATTTCGATA
* *
17362415 ATTTTACCCATAG-GGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
** *
17362441 ATTTTACCTTTCAAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
17362468 ATTTTATCCATCGAGGGTATCTTAG-TA
1 ATTTTACCCATCGAGGGTAT-TTCGATA
** *
17362495 ATTTTA-CCATTTAGGGGTATTT-TAGTA
1 ATTTTACCCATCGA-GGGTATTTCGA-TA
* * *
17362522 ATTTTACCCTTCGGGGGTATTTTGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
*
17362549 ATTTTACCCATCGAGGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
17362576 ATTTTACCCTTCGAGAGTATTTTGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
17362603 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
17362630 ATTTTACCCCTTGGGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* * **
17362657 ATTTCACCCATCGAAGGTATTTCGGCA
1 ATTTTACCCATCGAGGGTATTTCGATA
17362684 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
17362711 AT
1 AT
17362713 AACAGTGTAA
Statistics
Matches: 241, Mismatches: 48, Indels: 17
0.79 0.16 0.06
Matches are distributed among these distances:
26 34 0.14
27 200 0.83
28 7 0.03
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGATA
Found at i:17365597 original size:17 final size:17
Alignment explanation
Indices: 17365564--17365601 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
17365554 CAAGTCCACA
*
17365564 ACCAATTTACTTAGCAT
1 ACCAATTTACATAGCAT
17365581 ACCAATTTACCAT-GCAT
1 ACCAATTTA-CATAGCAT
17365598 ACCA
1 ACCA
17365602 TCCATTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (17 bp):
ACCAATTTACATAGCAT
Found at i:17367403 original size:15 final size:15
Alignment explanation
Indices: 17367360--17367407 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
17367350 TAGGGTTGTA
*
17367360 GTAAATAAAATATAT
1 GTAAGTAAAATATAT
*
17367375 ATAAGTAAATAATATAT
1 GTAAGT-AA-AATATAT
*
17367392 GTATGTAAAATATAT
1 GTAAGTAAAATATAT
17367407 G
1 G
17367408 CGATGTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
GTAAGTAAAATATAT
Found at i:17368161 original size:16 final size:17
Alignment explanation
Indices: 17368129--17368167 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
17368119 GCTTGGGAAT
17368129 TTATTTTGGACTTTGGA
1 TTATTTTGGACTTTGGA
*
17368146 TTATTTT-GATTTTGGA
1 TTATTTTGGACTTTGGA
17368162 TT-TTTT
1 TTATTTT
17368168 ACATGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.15, C:0.03, G:0.18, T:0.64
Consensus pattern (17 bp):
TTATTTTGGACTTTGGA
Found at i:17372495 original size:22 final size:22
Alignment explanation
Indices: 17372467--17372511 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
17372457 ATTATGATGA
17372467 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
17372489 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
17372511 T
1 T
17372512 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:17373667 original size:15 final size:15
Alignment explanation
Indices: 17373647--17373675 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17373637 TATGCATACA
17373647 AAATATAAAAGACAG
1 AAATATAAAAGACAG
17373662 AAATATAAAAGACA
1 AAATATAAAAGACA
17373676 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (15 bp):
AAATATAAAAGACAG
Found at i:17375744 original size:18 final size:18
Alignment explanation
Indices: 17375723--17375759 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17375713 AAGACTAAAA
17375723 ATTAATGATAATCAAACT
1 ATTAATGATAATCAAACT
**
17375741 ATTAATGATGTTCAAACT
1 ATTAATGATAATCAAACT
17375759 A
1 A
17375760 AATAACTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (18 bp):
ATTAATGATAATCAAACT
Found at i:17383121 original size:19 final size:19
Alignment explanation
Indices: 17383097--17383134 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17383087 CTCTTTGGCA
17383097 GTATTAAGCAAATATTTTT
1 GTATTAAGCAAATATTTTT
17383116 GTATTAAGCAAATATTTTT
1 GTATTAAGCAAATATTTTT
17383135 CATTTCAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (19 bp):
GTATTAAGCAAATATTTTT
Found at i:17389646 original size:31 final size:31
Alignment explanation
Indices: 17389608--17389700 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
17389598 TGCACATAGT
17389608 ACCACCCATGTAACTATTACCATTCGATACA
1 ACCACCCATGTAACTATTACCATTCGATACA
17389639 ACCACCCATGTAACTATTACCATTCGATACA
1 ACCACCCATGTAACTATTACCATTCGATACA
17389670 ACCACCCATGTAACTATTACCATTCGATACA
1 ACCACCCATGTAACTATTACCATTCGATACA
17389701 CGTAGTAGCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.26
Consensus pattern (31 bp):
ACCACCCATGTAACTATTACCATTCGATACA
Found at i:17389774 original size:50 final size:51
Alignment explanation
Indices: 17389697--17389884 Score: 213
Period size: 51 Copynumber: 3.7 Consensus size: 51
17389687 TACCATTCGA
* * **
17389697 TACACGTAGTAGCCTTCACATAGTACTATACACGTGATCAAA-CTTTCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAATCCCTCCAG
* * *
17389747 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAATCCCTCTAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAATCCCTCCAG
* * *
17389798 TACACATAGTAGCCTGCACATAGTACTACACATGTGATCATTAT--CTACC-G
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCA-AATCCCT-CCAG
* *
17389848 ATACATGTAGTAGCCTGCACTTAGTACTACACACGTG
1 -TACACGTAGTAGCCTGCACATAGTACTACACACGTG
17389885 TCCGCAAACA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 41 0.35
51 74 0.63
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAATCCCTCCAG
Found at i:17398903 original size:20 final size:20
Alignment explanation
Indices: 17398878--17398922 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
17398868 TAAATTCACA
17398878 TAATTAAAAC-AAGACAC-AAT
1 TAATT-AAACTAAGAC-CTAAT
17398898 TAATTAAACTAAGACCTAAT
1 TAATTAAACTAAGACCTAAT
17398918 TAATT
1 TAATT
17398923 CTGTTAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATTAAACTAAGACCTAAT
Found at i:17400925 original size:12 final size:12
Alignment explanation
Indices: 17400908--17400964 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
17400898 TCACTCTCAT
17400908 TTTCTTTTTCAA
1 TTTCTTTTTCAA
17400920 TTTCTTGTTTTC--
1 TTTC-T-TTTTCAA
* * *
17400932 TTTCATGTTCAT
1 TTTCTTTTTCAA
17400944 TTTCTTTTTCAA
1 TTTCTTTTTCAA
17400956 TTTCTTTTT
1 TTTCTTTTT
17400965 GTTTTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 4 0.11
12 26 0.72
13 1 0.03
14 5 0.14
ACGTcount: A:0.11, C:0.16, G:0.04, T:0.70
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:17402009 original size:14 final size:13
Alignment explanation
Indices: 17401990--17402024 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17401980 AATACAACCA
17401990 TTTTTTTTTTGAAC
1 TTTTTTTTTT-AAC
*
17402004 TTTTTTTTTTTAC
1 TTTTTTTTTTAAC
17402017 TTTTTTTT
1 TTTTTTTT
17402025 CAATTCACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTAAC
Found at i:17403249 original size:20 final size:20
Alignment explanation
Indices: 17403220--17403261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17403210 ATTTACATAT
17403220 TTAAAATAAAACAC-AATTAA
1 TTAAAATAAAAC-CTAATTAA
*
17403240 TTAAACTAAAACCTAATTAA
1 TTAAAATAAAACCTAATTAA
17403260 TT
1 TT
17403262 TTGTTAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAAATAAAACCTAATTAA
Found at i:17404464 original size:18 final size:16
Alignment explanation
Indices: 17404425--17404467 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
17404415 ACATGATTTG
*
17404425 TTTTCAAAAGTTATTC
1 TTTTCAAAAGTTATTA
17404441 TCTTTCAAAACGTTATTAA
1 T-TTTCAAAA-GTTATT-A
17404460 TTTTCAAA
1 TTTTCAAA
17404468 GCGTCACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 8 0.35
18 13 0.57
19 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (16 bp):
TTTTCAAAAGTTATTA
Found at i:17404954 original size:18 final size:19
Alignment explanation
Indices: 17404931--17404969 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17404921 CTTGGCCCAT
* *
17404931 TACAGTATC-GATATTCAG
1 TACAGTAACTGATATACAG
17404949 TACAGTAACTGATATACAG
1 TACAGTAACTGATATACAG
17404968 TA
1 TA
17404970 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TACAGTAACTGATATACAG
Found at i:17407121 original size:15 final size:15
Alignment explanation
Indices: 17407101--17407130 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17407091 CTATGCATGT
*
17407101 AAAATATAAAAGACA
1 AAAATACAAAAGACA
17407116 AAAATACAAAAGACA
1 AAAATACAAAAGACA
17407131 TAATACTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:17410780 original size:173 final size:173
Alignment explanation
Indices: 17410486--17410831 Score: 640
Period size: 173 Copynumber: 2.0 Consensus size: 173
17410476 TATAAACTCA
*
17410486 TCAGTATTAGCAAGATGAATTGTCTTAATTGCATGATCTGAAATTAATTATTTAAACAAATAATC
1 TCAGTATTAGCAAGATGAATTGTCTTAATTCCATGATCTGAAATTAATTATTTAAACAAATAATC
* *
17410551 TTGCAAACTACAGATTGCAAGTTGGTAACACATATGTGATTATTTTGTAGATGTATCTACCAAAA
66 TTGCAAACGACAGATTGCAAGTTGGTAACACATATGTGATTATTTTGTAAATGTATCTACCAAAA
17410616 TCATATAATATCAAAATCATCCACATTTTGGATGAATGAGCCC
131 TCATATAATATCAAAATCATCCACATTTTGGATGAATGAGCCC
*
17410659 TCAGTATTAGCAAGATGAATTGTCTTAATTCCATGATCTGAAATTAATTATTTAAATAAATAATC
1 TCAGTATTAGCAAGATGAATTGTCTTAATTCCATGATCTGAAATTAATTATTTAAACAAATAATC
17410724 TTGCAAACGACA-AGTTGCAAGTTGGTAACACATATGTGATTATTTTGTAAATGTATCTACCAAA
66 TTGCAAACGACAGA-TTGCAAGTTGGTAACACATATGTGATTATTTTGTAAATGTATCTACCAAA
17410788 ATCATATAATATCAAAATCATCCACATTTTGGATGAATGAGCCC
130 ATCATATAATATCAAAATCATCCACATTTTGGATGAATGAGCCC
17410832 ATATTCATTT
Statistics
Matches: 168, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
172 1 0.01
173 167 0.99
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (173 bp):
TCAGTATTAGCAAGATGAATTGTCTTAATTCCATGATCTGAAATTAATTATTTAAACAAATAATC
TTGCAAACGACAGATTGCAAGTTGGTAACACATATGTGATTATTTTGTAAATGTATCTACCAAAA
TCATATAATATCAAAATCATCCACATTTTGGATGAATGAGCCC
Found at i:17412316 original size:15 final size:16
Alignment explanation
Indices: 17412286--17412319 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
17412276 AGCATATTTA
17412286 ATAAAAATAATTTAATC
1 ATAAAAAT-ATTTAATC
17412303 ATAAAAAT-TTTAATC
1 ATAAAAATATTTAATC
17412318 AT
1 AT
17412320 CCAAATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAATATTTAATC
Found at i:17413332 original size:17 final size:18
Alignment explanation
Indices: 17413304--17413345 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17413294 TGCCAAGTCA
17413304 ATAAATAATTT-AAATTTT
1 ATAAA-AATTTAAAATTTT
17413322 ATAAAAATTTAAAATTTT
1 ATAAAAATTTAAAATTTT
17413340 -TAAAAA
1 ATAAAAA
17413346 AAATTAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAAAATTTAAAATTTT
Found at i:17419323 original size:31 final size:31
Alignment explanation
Indices: 17419288--17419355 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
17419278 GTATATGTTT
*
17419288 TATACATTGTCAAATTTGATTTGTTTATAGA
1 TATACATTGCCAAATTTGATTTGTTTATAGA
*
17419319 TATACATTGCCGAATTTGATTTGTTTATAGA
1 TATACATTGCCAAATTTGATTTGTTTATAGA
17419350 TATACA
1 TATACA
17419356 CTACCGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (31 bp):
TATACATTGCCAAATTTGATTTGTTTATAGA
Found at i:17419363 original size:31 final size:31
Alignment explanation
Indices: 17419300--17419368 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
17419290 TACATTGTCA
* *
17419300 AATTTGATTTGTTTATAGATATACATTGCCG
1 AATTTGATTTGTTTATAGATATACACTACCG
17419331 AATTTGATTTGTTTATAGATATACACTACCG
1 AATTTGATTTGTTTATAGATATACACTACCG
17419362 AATTTGA
1 AATTTGA
17419369 ATTGCCGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.43
Consensus pattern (31 bp):
AATTTGATTTGTTTATAGATATACACTACCG
Found at i:17419378 original size:14 final size:14
Alignment explanation
Indices: 17419359--17419386 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17419349 ATATACACTA
17419359 CCGAATTTGAATTG
1 CCGAATTTGAATTG
17419373 CCGAATTTGAATTG
1 CCGAATTTGAATTG
17419387 TTTATAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
CCGAATTTGAATTG
Found at i:17419388 original size:45 final size:45
Alignment explanation
Indices: 17419324--17419417 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
17419314 ATAGATATAC
*
17419324 ATTGCCGAATTTGATTTGTTTATAGATATACACTACCGAATTTGA
1 ATTGCCGAATTTGAATTGTTTATAGATATACACTACCGAATTTGA
* *
17419369 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGA
1 ATTGCCGAATTTGAATTGTTTATAGATATACACTACCGAATTTGA
17419414 ATTG
1 ATTG
17419418 TTTATAGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (45 bp):
ATTGCCGAATTTGAATTGTTTATAGATATACACTACCGAATTTGA
Found at i:17419407 original size:31 final size:31
Alignment explanation
Indices: 17419369--17419723 Score: 457
Period size: 31 Copynumber: 11.6 Consensus size: 31
17419359 CCGAATTTGA
* *
17419369 ATTGCCGAATTTGAATTGTTTATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
17419400 ATTGCCGAATTTGAATTGTTTATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
*
17419431 ATTGCCGAA-TTGATTTGTATATAGATATAT
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * * *
17419461 ACTGTCGAATTTGATTTGTATATGGTTATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
17419492 ATTGCCGAATTTGATTTGCATATGGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
17419523 ATTGCCGAA-TTGATTTGTATATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
*
17419553 ATTGCCGAATTTGATTTGTATATAGATAAAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * *
17419584 ATTGCCGAATTTTATTTGTATATGGTTATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * * * *
17419615 ATTGCCAAATTTGGTTTTTATATGGATATTC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* *
17419646 ATTGCCG-AGTTGATTTTTATATAGATATAC
1 ATTGCCGAATTTGATTTGTATATAGATATAC
* * *
17419676 ATTGTCGAATTTGATTTGTATATGGATATAT
1 ATTGCCGAATTTGATTTGTATATAGATATAC
17419707 ATTGCCGAA-TTGATTTG
1 ATTGCCGAATTTGATTTG
17419724 AGCATTAGAT
Statistics
Matches: 285, Mismatches: 36, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
30 86 0.30
31 199 0.70
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (31 bp):
ATTGCCGAATTTGATTTGTATATAGATATAC
Found at i:17419426 original size:76 final size:76
Alignment explanation
Indices: 17419300--17419441 Score: 248
Period size: 76 Copynumber: 1.9 Consensus size: 76
17419290 TACATTGTCA
* *
17419300 AATTTGATTTGTTTATAGATATACATTGCCGAATTTGATTTGTTTATAGATATACACTACCGAAT
1 AATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACACTACCGAAT
17419365 TTGAATTGCCG
66 TTGAATTGCCG
* *
17419376 AATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAAT
1 AATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACACTACCGAAT
17419441 T
66 T
17419442 GATTTGTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (76 bp):
AATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACACTACCGAAT
TTGAATTGCCG
Found at i:17419531 original size:92 final size:92
Alignment explanation
Indices: 17419369--17419723 Score: 480
Period size: 92 Copynumber: 3.9 Consensus size: 92
17419359 CCGAATTTGA
* * * * *
17419369 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
17419434 GCCGAATTGATTTGTATATAGATATAT
66 GCCGAATTGATTTGTATATAGATATAT
* * * * *
17419461 ACTGTCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGCATATGGATATACATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
*
17419526 GCCGAATTGATTTGTATATAGATATAC
66 GCCGAATTGATTTGTATATAGATATAT
* * *
17419553 ATTGCCGAATTTGATTTGTATATAGATAAACATTGCCGAATTTTATTTGTATATGGTTATACATT
1 ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
* * * *
17419618 GCCAAATTTGGTTTTTATATGGATAT-T
66 GCCGAA-TTGATTTGTATATAGATATAT
* * * *
17419645 CATTGCCG-AGTTGATTTTTATATAGATATACATTGTCGAATTTGATTTGTATATGGATATATAT
1 -ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACAT
17419709 TGCCGAATTGATTTG
65 TGCCGAATTGATTTG
17419724 AGCATTAGAT
Statistics
Matches: 227, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
91 6 0.03
92 198 0.87
93 23 0.10
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (92 bp):
ATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATACATT
GCCGAATTGATTTGTATATAGATATAT
Found at i:17419593 original size:123 final size:123
Alignment explanation
Indices: 17419369--17419723 Score: 516
Period size: 123 Copynumber: 2.9 Consensus size: 123
17419359 CCGAATTTGA
* * * * *
17419369 ATTGCCGAATTTGAATTGTTTATAGATATACATTGCCGAATTTGAATTGTTTATAGATATACATT
1 ATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAA-TTGATTTGTATATAGATATACATT
* *
17419434 GCCGAA-TTGATTTGTATATAGATATATACTGTCGAATTTGATTTGTATATGGTTATAC
65 GCCGAATTTGATTTGTATATAGATATATATTGCCGAATTTGATTTGTATATGGTTATAC
*
17419492 ATTGCCGAATTTGATTTGCATATGGATATACATTGCCGAATTGATTTGTATATAGATATACATTG
1 ATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATACATTG
* * *
17419557 CCGAATTTGATTTGTATATAGATAAACATTGCCGAATTTTATTTGTATATGGTTATAC
66 CCGAATTTGATTTGTATATAGATATATATTGCCGAATTTGATTTGTATATGGTTATAC
* * * * * *
17419615 ATTGCCAAATTTGGTTTTTATATGGATATTCATTGCCGAGTTGATTTTTATATAGATATACATTG
1 ATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATACATTG
* *
17419680 TCGAATTTGATTTGTATATGGATATATATTGCCGAA-TTGATTTG
66 CCGAATTTGATTTGTATATAGATATATATTGCCGAATTTGATTTG
17419724 AGCATTAGAT
Statistics
Matches: 208, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
122 35 0.17
123 173 0.83
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (123 bp):
ATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATACATTG
CCGAATTTGATTTGTATATAGATATATATTGCCGAATTTGATTTGTATATGGTTATAC
Found at i:17424024 original size:20 final size:20
Alignment explanation
Indices: 17423972--17424016 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
17423962 CTAAAATAAA
*
17423972 CTAAAAACGAGCTCATTGAG
1 CTAAGAACGAGCTCATTGAG
17423992 CTAAGAACGAGCTCATTGAG
1 CTAAGAACGAGCTCATTGAG
17424012 CTAAG
1 CTAAG
17424017 GTTGAGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
CTAAGAACGAGCTCATTGAG
Found at i:17424976 original size:13 final size:12
Alignment explanation
Indices: 17424956--17425002 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
17424946 TAAAACATCT
17424956 TTTCTTTTTCTC
1 TTTCTTTTTCTC
*
17424968 TTTCATTTT-TC
1 TTTCTTTTTCTC
** *
17424979 TTTCACTTTCTT
1 TTTCTTTTTCTC
17424991 TTTCTTTTTCTC
1 TTTCTTTTTCTC
17425003 CACTCTTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTTCTC
Found at i:17424987 original size:17 final size:16
Alignment explanation
Indices: 17424962--17424997 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17424952 ATCTTTTCTT
*
17424962 TTTCTCTTTCATTTTTC
1 TTTCACTTTC-TTTTTC
17424979 TTTCACTTTCTTTTTC
1 TTTCACTTTCTTTTTC
17424995 TTT
1 TTT
17424998 TTCTCCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCACTTTCTTTTTC
Found at i:17428629 original size:20 final size:20
Alignment explanation
Indices: 17428577--17428621 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
17428567 CTAAAATAAA
*
17428577 CTAAAAACGAGCTCATTGAG
1 CTAAGAACGAGCTCATTGAG
17428597 CTAAGAACGAGCTCATTGAG
1 CTAAGAACGAGCTCATTGAG
17428617 CTAAG
1 CTAAG
17428622 GTTGAGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
CTAAGAACGAGCTCATTGAG
Found at i:17429073 original size:27 final size:27
Alignment explanation
Indices: 17429029--17429147 Score: 168
Period size: 27 Copynumber: 4.4 Consensus size: 27
17429019 CTCTAAAATA
*
17429029 TTATAAAATGACTGTTATG-CCCTCATG
1 TTATAAAATGACTATTATGCCCCT-ATG
** *
17429056 TGGTAAAAGGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
**
17429083 TTATAAAATGACGGTTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
17429110 TTATAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
17429137 TTATAAAATGA
1 TTATAAAATGA
17429148 ATGTATACTT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 76 0.95
28 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (27 bp):
TTATAAAATGACTATTATGCCCCTATG
Found at i:17429088 original size:54 final size:54
Alignment explanation
Indices: 17429029--17429147 Score: 186
Period size: 54 Copynumber: 2.2 Consensus size: 54
17429019 CTCTAAAATA
* *
17429029 TTATAAAATGACTGTTATG-CCCTCATGTGGTAAAAGGACTATTATGCCCCTATG
1 TTATAAAATGACGGTTATGCCCCT-ATGTGATAAAAGGACTATTATGCCCCTATG
* *
17429083 TTATAAAATGACGGTTATGCCCCTATGTTATAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACGGTTATGCCCCTATGTGATAAAAGGACTATTATGCCCCTATG
17429137 TTATAAAATGA
1 TTATAAAATGA
17429148 ATGTATACTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 56 0.93
55 4 0.07
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (54 bp):
TTATAAAATGACGGTTATGCCCCTATGTGATAAAAGGACTATTATGCCCCTATG
Found at i:17433378 original size:20 final size:20
Alignment explanation
Indices: 17433353--17433391 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17433343 CATTAAATTT
17433353 AATTTAATATTAAAATAATC
1 AATTTAATATTAAAATAATC
*
17433373 AATTTAATATTAAATTAAT
1 AATTTAATATTAAAATAAT
17433392 AAAATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAATATTAAAATAATC
Found at i:17433385 original size:37 final size:35
Alignment explanation
Indices: 17433344--17433450 Score: 92
Period size: 37 Copynumber: 2.9 Consensus size: 35
17433334 GTAGATAAAC
17433344 ATTAAATTTAATTTAATATTAAAATAATCAATTTAAT
1 ATTAAATTTAATTTAATATTAAAATAAT--ATTTAAT
** * *
17433381 ATTAAATTAATAAAATACTATTAAGATAAGTATTTAAT
1 ATTAAATT--TAATTTAATATTAAAATAA-TATTTAAT
17433419 -TT-AATTTAATATTAAACTATTAAAATAATATT
1 ATTAAATTTAAT-TT-AA-TATTAAAATAATATT
17433451 ATTTTTGGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
34 3 0.05
35 1 0.02
36 9 0.16
37 20 0.36
38 7 0.12
39 15 0.27
40 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (35 bp):
ATTAAATTTAATTTAATATTAAAATAATATTTAAT
Found at i:17435748 original size:15 final size:15
Alignment explanation
Indices: 17435724--17435753 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17435714 TATGCATGTA
*
17435724 AAATATAAAAGACAT
1 AAATACAAAAGACAT
17435739 AAATACAAAAGACAT
1 AAATACAAAAGACAT
17435754 GATAGCGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:17447828 original size:9 final size:9
Alignment explanation
Indices: 17447810--17447849 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
17447800 GTTTCCCACG
17447810 TTAGGATTT
1 TTAGGATTT
*
17447819 TTAGGGTTT
1 TTAGGATTT
17447828 TTAGGATTT
1 TTAGGATTT
*
17447837 TTAGGGTTT
1 TTAGGATTT
17447846 TTAG
1 TTAG
17447850 AGAAAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (9 bp):
TTAGGATTT
Found at i:17447833 original size:18 final size:18
Alignment explanation
Indices: 17447810--17447849 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
17447800 GTTTCCCACG
17447810 TTAGGATTTTTAGGGTTT
1 TTAGGATTTTTAGGGTTT
17447828 TTAGGATTTTTAGGGTTT
1 TTAGGATTTTTAGGGTTT
17447846 TTAG
1 TTAG
17447850 AGAAAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (18 bp):
TTAGGATTTTTAGGGTTT
Found at i:17448246 original size:127 final size:125
Alignment explanation
Indices: 17447963--17448404 Score: 604
Period size: 124 Copynumber: 3.5 Consensus size: 125
17447953 GATAAAATCA
* * * * * * *
17447963 AAGCAGGATGATTTATCAGAAGGATTTTTTAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
17448028 AGGTCCTGGAAAGTAATTCTGAGTTGACGTTTCTGAGAAAATAGTTTAAAA-AACGCTTC
66 AGGTCCTGGAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATAACGCTTC
* * *
17448087 AAGCAGGATTCTTTATGAGAAGAATTTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
17448152 TGGTCCTGGAGGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATAACGCTGC
66 AGGTCCTGGA--AAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATAACGCTTC
*
17448214 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
17448278 TAGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCTAACAGTATAAAAT--CGCTTC
65 TAGGTCCTGG-AAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATAACGCTTC
* * * *
17448338 TAGCAGAATGCTTTATGAGAGGAATTTGTGAAATCGCGCCCACGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
17448403 AG
66 AG
17448405 CCTGTTTGGG
Statistics
Matches: 286, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
123 2 0.01
124 130 0.45
126 76 0.27
127 75 0.26
128 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATAACGCTTC
Found at i:17451627 original size:43 final size:42
Alignment explanation
Indices: 17451556--17452194 Score: 366
Period size: 43 Copynumber: 14.0 Consensus size: 42
17451546 TCAAATTATA
* * **
17451556 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAATTGTTAGGGTTT
1 TTTAAGTTAAGGGTTAGAGTTTTAAAGTTAAGGGTTAGGG-TT
* * * *
17451599 TTTTATTTAAGGGTTATAGTTTTAAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGAGTTTTAAAGTTAAGGG-TTAGGGTT
* * * *
17451642 TTTAATTTAAGGGTTATAATTTTAAAGTAAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGAGTTTTAAAGTTAAGGG-TTAGGGTT
17451685 TTTAAGTTAAGGGTTACGA-TTTTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTA-GAGTTTTAAAGTTAAGGGTTAGGGTT
* * *
17451727 TTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGAGTTTTAAAGTTAAGGGTTAGGGTT
* * * * *
17451770 TTTAGGTTAAGGGGTTAGGGTTTTTAGGTTAAGGGGTTATGG-T
1 TTTAAGTTAA-GGGTTAGAGTTTTAAAGTTAA-GGGTTAGGGTT
* * *
17451813 TTTAGGTTAAAGGGTTATG-GTTTTTAAGTTAACAGTTAAGGTTGGGGTT
1 TTTAAGTT-AAGGGTTA-GAGTTTTAAAGTT-A-AG----GGTTAGGGTT
* * *
17451862 TTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTAAGGTT
1 TTTAAGTTAAGG-GTTAGAGTTTTAAAGTTAAGGGTT-A-G----GGTT
* * * *
17451911 TTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTT
1 TTTAAGTTAAG-GGTTAGAGTTTTAAAGTT-A-----AGGGTTAGGGTT
* * * *
17451960 TTTAGGTTAAGGTGTTGGGGTTTTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGG-GTTAGAGTTTTAAAGTTAAGGGTTAGGGTT
* *
17452003 TTTAAGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAGTGTT
1 TTTAAGTTAAGG-GTTAGAGTTTTAAAGTTAAGGGTTA--G---G-GTT
* * *
17452052 TTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAGGGTTGGGGTT
1 TTTAAGTTAA-GGGTTAGAGTTTTAAAGTT-A-----AGGGTTAGGGTT
* * * *
17452101 TTTAGGTTAAGCTGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAAGGTT
1 TTTAAGTTAAG-GGTTAGAGTTTTAAAGTTAAGGGTTA--G----GGTT
* * *
17452150 TTTAGGTTAAGGGTTTAGGGTTTTTAAGTTAAGAGGTTAGGGTT
1 TTTAAGTTAAGGG-TTAGAGTTTTAAAGTTAAG-GGTTAGGGTT
17452194 T
1 T
17452195 GTCAATTAAA
Statistics
Matches: 508, Mismatches: 36, Indels: 103
0.79 0.06 0.16
Matches are distributed among these distances:
42 18 0.04
43 238 0.47
44 24 0.05
45 4 0.01
47 2 0.00
48 19 0.04
49 178 0.35
50 11 0.02
53 2 0.00
55 12 0.02
ACGTcount: A:0.23, C:0.01, G:0.33, T:0.44
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGAGTTTTAAAGTTAAGGGTTAGGGTT
Found at i:17451727 original size:49 final size:47
Alignment explanation
Indices: 17451672--17452193 Score: 553
Period size: 49 Copynumber: 11.1 Consensus size: 47
17451662 TTTAAAGTAA
* * * *
17451672 AGGGTTTAGGGTTTTTAAGTTAAGGGTTACGATTTTAAAGTT-A----
1 AGGG-TTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAAGTTAAGGTT
17451715 AGGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTT-A----
1 AGGGTTAGGGTTTTTAGGTTAA-GGGTTAGGGTTTTTAAGTTAAGGTT
*
17451758 AGGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAGGTTAA-G--
1 AGGGTTAGGGTTTTTAGGTTAA-GGGTTAGGGTTTTTAAGTTAAGGTT
* * *
17451803 -GGGTTATGG-TTTTAGGTTAAAGGGTTATGGTTTTTAAGTTAACAGTT
1 AGGGTTAGGGTTTTTAGGTT-AAGGGTTAGGGTTTTTAAGTTAA-GGTT
* *
17451850 AAGGTTGGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTT
1 AGGGTTAGGGTTTTTAGGTTAAGG-GTTAGGGTTTTTAAGTTAA-GGTT
* *
17451899 AAGGTTAAGGTTTTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAACGGTT
1 AGGGTTAGGGTTTTTAGGTTAAG-GGTTAGGGTTTTTAAGTTAA-GGTT
* *
17451948 AGGGTTGGGGTTTTTAGGTTAAGGTGTTGGGGTTTTTAAGTT-A----
1 AGGGTTAGGGTTTTTAGGTTAAGG-GTTAGGGTTTTTAAGTTAAGGTT
*
17451991 AGGGTTAGGGTTTTTAAGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTT
1 AGGGTTAGGGTTTTTAGGTTAAGG-GTTAGGGTTTTTAAGTTAA-GGTT
* *
17452040 AGGGTTAGTGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTT
1 AGGGTTAGGGTTTTTAGGTTAA-GGGTTAGGGTTTTTAAGTTAA-GGTT
* *
17452089 AGGGTTGGGGTTTTTAGGTTAAGCTGTTAGGGTTTTTAAGTTAAGGGTT
1 AGGGTTAGGGTTTTTAGGTTAAG-GGTTAGGGTTTTTAAGTTAA-GGTT
*
17452138 AGGGTTAAGGTTTTTAGGTTAAGGGTTTAGGGTTTTTAAGTTAAGAGGTT
1 AGGGTTAGGGTTTTTAGGTTAAGGG-TTAGGGTTTTTAAGTT-A-AGGTT
17452188 AGGGTT
1 AGGGTT
17452194 TGTCAATTAA
Statistics
Matches: 419, Mismatches: 36, Indels: 41
0.84 0.07 0.08
Matches are distributed among these distances:
42 17 0.04
43 129 0.31
44 12 0.03
45 1 0.00
48 14 0.03
49 231 0.55
50 14 0.03
51 1 0.00
ACGTcount: A:0.22, C:0.01, G:0.35, T:0.42
Consensus pattern (47 bp):
AGGGTTAGGGTTTTTAGGTTAAGGGTTAGGGTTTTTAAGTTAAGGTT
Found at i:17451919 original size:14 final size:14
Alignment explanation
Indices: 17451875--17451921 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
17451865 AGGTTAAGGT
* *
17451875 GTTAGGGTTTTTAA
1 GTTAAGGTTTTTAG
* *
17451889 GTTAAGG-GTTAAG
1 GTTAAGGTTTTTAG
17451902 GTTAAGGTTTTTAG
1 GTTAAGGTTTTTAG
17451916 GTTAAG
1 GTTAAG
17451922 TGGTTAGGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.43
Consensus pattern (14 bp):
GTTAAGGTTTTTAG
Found at i:17451942 original size:141 final size:141
Alignment explanation
Indices: 17451706--17452193 Score: 590
Period size: 141 Copynumber: 3.4 Consensus size: 141
17451696 GGTTACGATT
*
17451706 TTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAGGGTT-A-G---
1 TTAAAGTTAA-GGTTAGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTA
* **
17451766 GGTTTTTAGGTTAAGGGGTTAGGGTTTTTAGGTTAA-G-GGGTTATGG-TTTTAGGTTAAAGGGT
65 GGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAACGTGGGTTGGGGTTTTTAGGTT-AAGGGT
*
17451828 TATGGTTTTTAAG
129 TAGGGTTTTTAAG
*
17451841 TTAACAGTTAAGGTTGGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTA
1 TTAA-AGTTAAGGTTAGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTT-
*
17451906 AGGTTTTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAAG
64 AGGTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAC-G-T-GGGTTGGGGTTTTTAGGTTAAG
*
17451971 GTGTTGGGGTTTTTAAG
126 G-GTTAGGGTTTTTAAG
* *
17451988 TT-AAG----GGTTAGGGTTTTTAAGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAG
1 TTAAAGTTAAGGTTAGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTAG
*
17452048 TGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAAGC
66 -GTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAAC-G-T-GGGTTGGGGTTTTTAGGTTAAG-
*
17452113 TGTTAGGGTTTTTAAG
126 GGTTAGGGTTTTTAAG
* * * *
17452129 TTAAGGGTTAGGGTTAAGGTTTTTAGGTTAAGG-GTTTAGGGTTTTTAAGTTAAGAGGTTAGGGT
1 TTAA-AGTTAAGGTTAGGGTTTTTAGGTTAAGGTG-TTAGGGTTTTTAAGTTAAG-GGTTAAGGT
17452193 T
63 T
17452194 TGTCAATTAA
Statistics
Matches: 311, Mismatches: 18, Indels: 35
0.85 0.05 0.10
Matches are distributed among these distances:
135 49 0.16
136 7 0.02
137 1 0.00
140 2 0.01
141 161 0.52
142 1 0.00
143 2 0.01
145 2 0.01
146 13 0.04
147 63 0.20
148 10 0.03
ACGTcount: A:0.22, C:0.01, G:0.35, T:0.42
Consensus pattern (141 bp):
TTAAAGTTAAGGTTAGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTAG
GTTTTTAGGTTAAGGGGTTAGGGTTTTTAAGTTAACGTGGGTTGGGGTTTTTAGGTTAAGGGTTA
GGGTTTTTAAG
Found at i:17452031 original size:190 final size:188
Alignment explanation
Indices: 17451556--17452194 Score: 668
Period size: 190 Copynumber: 3.5 Consensus size: 188
17451546 TCAAATTATA
* * *
17451556 TTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAATTGTTAGGGTT----TTTTTA-TTTAAGGGTTA
1 TTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAA-GGTTAGGGTTAGGGTTTTTAGGTTAAGGGTTA
** * * * *** *
17451615 TAGTTTTAAAGTTAAGGGTTTATGGTTTTTAA-TTTAAGGGTTATAATTTTAAAG-TAA-AG---
65 GGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGGGTTAGGGTTTTTAAGTTAACAGTTA
* * *
17451674 -GGTTTAGGGTTTTTAAGTTAA-GGGTTACGATTTTAAAGTTAA--G----GGTTAGGGTT
129 AGG-TTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAAGGTTAGGGTT
*
17451727 TTTAGGTTAAGGGGTTAGGGTTTTTAAGTT-A----AGGGTTAGGGTTTTTAGGTTAAGGGGTTA
1 TTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAAGGTTAGGGTTAGGGTTTTTAGGTTAA-GGGTTA
* * * *
17451787 GGGTTTTTAGGTTAAGGGGTTATGG-TTTTAGGTTAAAGGGTTATGGTTTTTAAGTTAACAGTTA
65 GGGTTTTTAAGTTAA-GGGTTAGGGTTTTTAAGTTAAAGGGTTAGGGTTTTTAAGTTAACAGTTA
* * * * *
17451851 AGGTTGGGGTTTTTAGGTTAAGGTGTTAGGGTTTTTAAGTTAAGGGTTAAGGTTAAGGTT
129 AGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAAGGTTAGGGTT
*
17451911 TTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAACGGTTAGGGTTGGGGTTTTTAGGTTAAGGTGTT
1 TTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAA-GGTTAGGGTTAGGGTTTTTAGGTTAAGG-GTT
* **
17451976 GGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTT-AAGGTGTTAGGGTTTTTAAGTTAAGGGTT
64 AGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGG-GTTAGGGTTTTTAAGTTAACAGTT
* * * *
17452040 AGGGTTAGTGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAGGGTTGGGGTT
128 AAGGTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAAGGTTAGGGTT
*
17452101 TTTAGGTTAAGCT-GTTAGGGTTTTTAAGTTAAGGGTTAGGGTTAAGGTTTTTAGGTTAAGGGTT
1 TTTAGGTTAAG-TGGTTAGGGTTTTTAAGTTAA-GGTTAGGGTTAGGGTTTTTAGGTTAAGGG-T
17452165 TAGGGTTTTTAAGTTAAGAGGTTAGGGTTT
63 TAGGGTTTTTAAGTTAAG-GGTTAGGGTTT
17452195 GTCAATTAAA
Statistics
Matches: 394, Mismatches: 40, Indels: 48
0.82 0.08 0.10
Matches are distributed among these distances:
166 6 0.02
170 6 0.02
171 20 0.05
172 59 0.15
173 6 0.02
174 2 0.01
177 16 0.04
178 19 0.05
180 1 0.00
184 38 0.10
185 1 0.00
189 15 0.04
190 193 0.49
191 12 0.03
ACGTcount: A:0.23, C:0.01, G:0.33, T:0.44
Consensus pattern (188 bp):
TTTAGGTTAAGTGGTTAGGGTTTTTAAGTTAAGGTTAGGGTTAGGGTTTTTAGGTTAAGGGTTAG
GGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGGTTAGGGTTTTTAAGTTAACAGTTAAG
GTTAGGGTTTTTAGGTTAAGGGGTTAGGGTTTTAAAGTTAACGGTTAAGGTTAGGGTT
Found at i:17452067 original size:22 final size:22
Alignment explanation
Indices: 17451556--17452194 Score: 495
Period size: 22 Copynumber: 28.0 Consensus size: 22
17451546 TCAAATTATA
17451556 TTTAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
**
17451577 TTTAAGTTAA-TTGTTAGGGTTT
1 TTTAAGTTAAGGGGTTAGGG-TT
* * **
17451599 TTTTATTTAA-GGGTTATAGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
17451620 TTAAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* ***
17451642 TTTAATTTAA-GGGTTATAATT
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
17451663 TTAAAGTAAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
17451685 TTTAAGTTAA-GGGTTACGATT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17451706 TTAAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17451727 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
17451749 TTTAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17451770 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
17451792 TTTAGGTTAAGGGGTTATGG-T
1 TTTAAGTTAAGGGGTTAGGGTT
* * *
17451813 TTTAGGTTAAAGGGTTATGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
17451835 TTTAAGTTAACAGTTAAGGTTGGGGTT
1 TTTAAGTT-A-AG---GGGTTAGGGTT
* *
17451862 TTTAGGTTAAGGTGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17451884 TTTAAGTTAAGGGTTAAGGTTAAGGTT
1 TTTAAGTTAA-GG----GGTTAGGGTT
* *
17451911 TTTAGGTTAAGTGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17451933 TTTAAGTTAACGGTTAGGGTTGGGGTT
1 TTTAAGTTAA--G---GGGTTAGGGTT
* * *
17451960 TTTAGGTTAAGGTGTTGGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
17451982 TTTAAGTTAA-GGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17452003 TTTAAGTTAAGGTGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17452025 TTTAAGTTAAGGGTTAGGGTTAGTGTT
1 TTTAAGTTAA--G---GGGTTAGGGTT
*
17452052 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
* *
17452074 TTAAAGTTAACGGTTAGGGTTGGGGTT
1 TTTAAGTTAA--G---GGGTTAGGGTT
* **
17452101 TTTAGGTTAAGCTGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17452123 TTTAAGTTAAGGGTTAGGGTTAAGGTT
1 TTTAAGTTAA--G---GGGTTAGGGTT
* *
17452150 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
*
17452172 TTTAAGTTAAGAGGTTAGGGTT
1 TTTAAGTTAAGGGGTTAGGGTT
17452194 T
1 T
17452195 GTCAATTAAA
Statistics
Matches: 496, Mismatches: 85, Indels: 73
0.76 0.13 0.11
Matches are distributed among these distances:
21 134 0.27
22 243 0.49
23 3 0.01
24 5 0.01
25 6 0.01
26 2 0.00
27 103 0.21
ACGTcount: A:0.23, C:0.01, G:0.33, T:0.44
Consensus pattern (22 bp):
TTTAAGTTAAGGGGTTAGGGTT
Found at i:17452137 original size:15 final size:15
Alignment explanation
Indices: 17452117--17452165 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
17452107 TTAAGCTGTT
*
17452117 AGGGTTTTTAAGTTA
1 AGGGTTTTTAGGTTA
17452132 AGGG---TTAGGGTTA
1 AGGGTTTTTA-GGTTA
17452145 A-GGTTTTTAGGTTA
1 AGGGTTTTTAGGTTA
17452159 AGGGTTT
1 AGGGTTT
17452166 AGGGTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 6 0.21
15 12 0.43
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (15 bp):
AGGGTTTTTAGGTTA
Found at i:17452160 original size:27 final size:28
Alignment explanation
Indices: 17452016--17452171 Score: 92
Period size: 27 Copynumber: 6.1 Consensus size: 28
17452006 AAGTTAAGGT
*
17452016 GTTAGGGTTTTTAAGTTAAGGG-TTAGG
1 GTTAAGGTTTTTAAGTTAAGGGTTTAGG
*
17452043 GTT-AGTGTTTTTAGGTTAA--G----GG
1 GTTAAG-GTTTTTAAGTTAAGGGTTTAGG
* * *
17452065 GTTAGGGTTTTAAAGTTAACGG-TTAGG
1 GTTAAGGTTTTTAAGTTAAGGGTTTAGG
** * *
17452092 GTTGGGGTTTTTAGGTTAA--G-CT---
1 GTTAAGGTTTTTAAGTTAAGGGTTTAGG
*
17452114 GTTAGGGTTTTTAAGTTAAGGG-TTAGG
1 GTTAAGGTTTTTAAGTTAAGGGTTTAGG
*
17452141 GTTAAGGTTTTTAGGTTAAGGGTTTAGG
1 GTTAAGGTTTTTAAGTTAAGGGTTTAGG
17452169 GTT
1 GTT
17452172 TTTAAGTTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
22 33 0.32
23 1 0.01
24 3 0.03
25 3 0.03
26 1 0.01
27 53 0.52
28 8 0.08
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.42
Consensus pattern (28 bp):
GTTAAGGTTTTTAAGTTAAGGGTTTAGG
Found at i:17452171 original size:14 final size:14
Alignment explanation
Indices: 17452128--17452171 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
17452118 GGGTTTTTAA
17452128 GTTAAGGG-TTAGG
1 GTTAAGGGTTTAGG
*
17452141 GTTAAGGTTTTTA-G
1 GTTAAGG-GTTTAGG
17452155 GTTAAGGGTTTAGG
1 GTTAAGGGTTTAGG
17452169 GTT
1 GTT
17452172 TTTAAGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 11 0.42
14 12 0.46
15 3 0.12
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (14 bp):
GTTAAGGGTTTAGG
Found at i:17452291 original size:8 final size:8
Alignment explanation
Indices: 17452261--17452292 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
17452251 TAGTTTAGGG
*
17452261 TTTAGGGT
1 TTTAGGTT
17452269 TTTAGGTT
1 TTTAGGTT
17452277 TTTAGGTT
1 TTTAGGTT
17452285 TTTAGGTT
1 TTTAGGTT
17452293 AAGGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.59
Consensus pattern (8 bp):
TTTAGGTT
Found at i:17452306 original size:22 final size:22
Alignment explanation
Indices: 17452281--17452419 Score: 131
Period size: 22 Copynumber: 6.2 Consensus size: 22
17452271 TAGGTTTTTA
17452281 GGTTTTTAGGTTAAGGGGTTAG
1 GGTTTTTAGGTTAAGGGGTTAG
*
17452303 GGTTTTTAAGTTAAGGGTTAGGGTTAG
1 GGTTTTTAGGTTAA--G---GGGTTAG
*
17452330 GGTTTTTAGGTTAAGGTGTTAG
1 GGTTTTTAGGTTAAGGGGTTAG
** *
17452352 GG-TTAAAGGTT-A-GGGTTAA
1 GGTTTTTAGGTTAAGGGGTTAG
* * *
17452371 GGTTTTTAGGTTTAGGGTTTAT
1 GGTTTTTAGGTTAAGGGGTTAG
*
17452393 GGTTTTTAGGTTAAGAGGTTAG
1 GGTTTTTAGGTTAAGGGGTTAG
17452415 GGTTT
1 GGTTT
17452420 GTTAATTAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
19 7 0.07
20 8 0.09
21 8 0.09
22 49 0.52
24 1 0.01
25 1 0.01
27 20 0.21
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (22 bp):
GGTTTTTAGGTTAAGGGGTTAG
Done.