Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 62 of 230
Found at i:17064277 original size:6 final size:6
Alignment explanation
Indices: 17064266--17064313 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
17064256 AGTTAACATC
*
17064266 TAAATA TAAATA TAAATA TAAATA TTATAA-A TAAATT TAAA-A TAAATA
1 TAAATA TAAATA TAAATA TAAATA -TA-AATA TAAATA TAAATA TAAATA
17064314 AATAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 6 0.17
6 25 0.69
7 3 0.08
8 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:17064301 original size:19 final size:20
Alignment explanation
Indices: 17064266--17064333 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
17064256 AGTTAACATC
*
17064266 TAAATATAAAT--ATAAATA
1 TAAATATAAATAAATAAATT
*
17064284 TAAATAT-TATAAATAAATT
1 TAAATATAAATAAATAAATT
17064303 TAAA-ATAAATAAATAATATT
1 TAAATATAAATAAATAA-ATT
17064323 TAAATAATAAA
1 TAAAT-ATAAA
17064334 AAACTTTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.05
18 9 0.22
19 18 0.44
20 7 0.17
22 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATAAATAAATAAATT
Found at i:17068212 original size:27 final size:27
Alignment explanation
Indices: 17068190--17068550 Score: 275
Period size: 27 Copynumber: 13.4 Consensus size: 27
17068180 GGGTATAATA
17068190 GTCATTTTACCTTATGAGAGTATTTTG
1 GTCATTTTACCTTATGAGAGTATTTTG
* *
17068217 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCTTATGAGAGTATTTTG
* * * **
17068244 GTCATTTTATCTTATGGGGGTATTTCA
1 GTCATTTTACCTTATGAGAGTATTTTG
* * * * *
17068271 GTTATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCTTATGAGAGTATTTTG
* *
17068298 ATCATTTTACCCTATG-GAGGTATTTTG
1 GTCATTTTACCTTATGAGA-GTATTTTG
* * * *
17068325 GTCATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCTTATGAGAGTATTTTG
* * * **
17068352 GTTATTTTACCCTATCG-GGGTATTTCA
1 GTCATTTTACCTTAT-GAGAGTATTTTG
* *
17068379 GTCATTTTACCCTATG-G-GTATTTTA
1 GTCATTTTACCTTATGAGAGTATTTTG
* * * *
17068404 GTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCTTATGAGAGTATTTTG
* * *
17068431 GTCATTTTATCC-TATGGGGGTATTTTA
1 GTCATTTTA-CCTTATGAGAGTATTTTG
* * *
17068458 GTTATTTTACCCTATG-GGGTTATTTTG
1 GTCATTTTACCTTATGAGAG-TATTTTG
* * *
17068485 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCTTATGAGAGTATTTTG
* * *
17068512 ATCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCTTATGAGAGTATTTTG
17068539 GTCATTTTACCT
1 GTCATTTTACCT
17068551 ATTTTAGGGA
Statistics
Matches: 292, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
25 23 0.08
26 9 0.03
27 253 0.87
28 7 0.02
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (27 bp):
GTCATTTTACCTTATGAGAGTATTTTG
Found at i:17068248 original size:54 final size:53
Alignment explanation
Indices: 17068188--17068549 Score: 433
Period size: 54 Copynumber: 6.7 Consensus size: 53
17068178 AGGGGTATAA
* *
17068188 TAGTCATTTTACCTTATGAGAGTATTTTGGTCATTTTACCCTATGAGGGTATTT
1 TAGTCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCCTATGAGGGTATTT
* * * ** * *
17068242 TGGTCATTTTATCTTATGGGGGTATTTCAGTTATTTTACCCTATGGGGGTATTT
1 TAGTCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGAGGGTATTT
* *
17068296 TAATCATTTTACCCTATGGAGGTATTTTGGTCATTCTACCCTATGAGGGTATTT
1 TAGTCATTTTACCCTATGG-GGTATTTTGGTCATTTTACCCTATGAGGGTATTT
** * **
17068350 CGGTTATTTTACCCTATCGGGGTATTTCAGTCATTTTACCCTAT--GGGTATTT
1 TAGTCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGAGGGTATTT
* * *
17068402 TAGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTATCCTATGGGGGTATTT
1 TAGTCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGAGGGTATTT
*
17068456 TAGTTATTTTACCCTATGGGGTTATTTTGGTCATTTTACCCTATGAGGGTA-TT
1 TAGTCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCCTATGAGGGTATTT
* *
17068509 TCGATCATTTTACCTTATGGGGGTATTTTGGTCATTTTACC
1 TAG-TCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACC
17068550 TATTTTAGGG
Statistics
Matches: 264, Mismatches: 36, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
52 46 0.17
53 10 0.04
54 201 0.76
55 7 0.03
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (53 bp):
TAGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGAGGGTATTT
Found at i:17068303 original size:81 final size:80
Alignment explanation
Indices: 17068189--17068549 Score: 483
Period size: 81 Copynumber: 4.5 Consensus size: 80
17068179 GGGGTATAAT
* * * * *
17068189 AGTCATTTTACCTTATGAGAGTATTTTGGTCATTTTACCCTATGAGGGTATTTTGGTCATTTTAT
1 AGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATG-GGGTATTTTGGTCATTTTAC
* *
17068254 CTTATGGGGGTATTTC
65 CCTATGAGGGTATTTC
* * *
17068270 AGTTATTTTACCCTATGGGGGTATTTTAATCATTTTACCCTATGGAGGTATTTTGGTCATTCTAC
1 AGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGG-GGTATTTTGGTCATTTTAC
17068335 CCTATGAGGGTATTTC
65 CCTATGAGGGTATTTC
* * * * *
17068351 GGTTATTTTACCCTATCGGGGTATTTCAGTCATTTTACCCTAT-GGGTATTTTAGTCATTTTACC
1 AGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACC
* *
17068415 CTATGGGGGTATTTT
66 CTATGAGGGTATTTC
* *
17068430 AGTCATTTTATCCTATGGGGGTATTTTAGTTATTTTACCCTATGGGGTTATTTTGGTCATTTTAC
1 AGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGGGG-TATTTTGGTCATTTTAC
17068495 CCTATGAGGGTATTTC
65 CCTATGAGGGTATTTC
* *
17068511 -GATCATTTTACCTTATGGGGGTATTTTGGTCATTTTACC
1 AG-TCATTTTACCCTATGGGGGTATTTTAGTCATTTTACC
17068550 TATTTTAGGG
Statistics
Matches: 245, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
79 68 0.28
80 6 0.02
81 171 0.70
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (80 bp):
AGTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACC
CTATGAGGGTATTTC
Found at i:17071288 original size:18 final size:17
Alignment explanation
Indices: 17071254--17071360 Score: 97
Period size: 17 Copynumber: 6.2 Consensus size: 17
17071244 TTATCACAAC
17071254 TCACACAAAATAACAGT
1 TCACACAAAATAACAGT
*
17071271 TCACACAAATTAAACAGT
1 TCACACAAAAT-AACAGT
* * *
17071289 TCACATAGAATAGACAAT
1 TCACACAAAATA-ACAGT
*
17071307 TCACATAAAATAACAGT
1 TCACACAAAATAACAGT
** * *
17071324 TCATGCATAATAATAGT
1 TCACACAAAATAACAGT
* *
17071341 TCATACAATATAACAGT
1 TCACACAAAATAACAGT
17071358 TCA
1 TCA
17071361 TCTATACCAT
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
17 43 0.60
18 29 0.40
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.25
Consensus pattern (17 bp):
TCACACAAAATAACAGT
Found at i:17071962 original size:33 final size:33
Alignment explanation
Indices: 17071883--17071964 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
17071873 TTATCCACAC
* * **
17071883 ATATATATGTTATATATATAACAAGACCCTTTT
1 ATATATATATTATATATATAACAAGACCCATAA
* * *
17071916 ACACATATATTATATATATAACAAGACTCATAA
1 ATATATATATTATATATATAACAAGACCCATAA
*
17071949 ATATATATTTTATATA
1 ATATATATATTATATA
17071965 CATATCTATT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (33 bp):
ATATATATATTATATATATAACAAGACCCATAA
Found at i:17072146 original size:31 final size:31
Alignment explanation
Indices: 17072108--17072179 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 31
17072098 TAAGACCCTA
* *
17072108 CACGCATATATATTGTATATATAACAAAATC
1 CACGCATATATATTATATATATAACAAAACC
17072139 CACGC--ATATATTATATATATAACAAAACC
1 CACGCATATATATTATATATATAACAAAACC
*
17072168 CACACATATATA
1 CACGCATATATA
17072180 GGTTTAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 26 0.72
31 10 0.28
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.29
Consensus pattern (31 bp):
CACGCATATATATTATATATATAACAAAACC
Found at i:17073696 original size:32 final size:31
Alignment explanation
Indices: 17073653--17073719 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
17073643 ACCTAAAATT
* *
17073653 ATTAATTCTAATTATTTTAA-TATTTTATTTA
1 ATTAATTCTAATTA-TTTAATTATTTAATCTA
17073684 ATTAATTTCTAATTATTTAATTATTTAATCTA
1 ATTAA-TTCTAATTATTTAATTATTTAATCTA
17073716 ATTA
1 ATTA
17073720 CGGTTTCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 10 0.31
32 22 0.69
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTAATTCTAATTATTTAATTATTTAATCTA
Found at i:17075824 original size:5 final size:5
Alignment explanation
Indices: 17075809--17075839 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
17075799 CACTTTTTTA
17075809 GCCCGG GCCCG GCCCG GCCCG GCCCG GCCCG
1 GCCC-G GCCCG GCCCG GCCCG GCCCG GCCCG
17075840 ATATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.00, C:0.58, G:0.42, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:17075876 original size:8 final size:9
Alignment explanation
Indices: 17075857--17075941 Score: 50
Period size: 9 Copynumber: 9.1 Consensus size: 9
17075847 AAATATATTT
17075857 ATTTTTTAA
1 ATTTTTTAA
17075866 ATTTTTT-A
1 ATTTTTTAA
*
17075874 A-TTTTAAA
1 ATTTTTTAA
17075882 ATATTTTTAAA
1 AT-TTTTT-AA
17075893 ATACTTTTTAA
1 AT--TTTTTAA
* *
17075904 TTTTTTTTA
1 ATTTTTTAA
*
17075913 A-TTTTAAA
1 ATTTTTTAA
17075921 ATATTTTTAAA
1 AT-TTTTT-AA
*
17075932 ATATTTTAA
1 ATTTTTTAA
17075941 A
1 A
17075942 AATACTTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
7 4 0.07
8 10 0.17
9 16 0.28
10 12 0.21
11 11 0.19
12 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:17075878 original size:16 final size:17
Alignment explanation
Indices: 17075847--17075930 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 17
17075837 CCGATATAAT
* * *
17075847 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
17075864 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
17075880 AAATATTTTTAAAATACTTTTT
1 AAATATTTTT---A-A-TTTTA
* *
17075902 AATTTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
17075919 AAATATTTTTAA
1 AAATATTTTTAA
17075931 AATATTTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
16 13 0.25
17 23 0.44
18 1 0.02
19 1 0.02
20 1 0.02
21 1 0.02
22 12 0.23
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:17075889 original size:11 final size:11
Alignment explanation
Indices: 17075875--17075951 Score: 67
Period size: 11 Copynumber: 7.4 Consensus size: 11
17075865 AATTTTTTAA
17075875 TTTTAAAATAT
1 TTTTAAAATAT
17075886 TTTTAAAATACT
1 TTTTAAAATA-T
17075898 TTTT--AAT-T
1 TTTTAAAATAT
* *
17075906 TTTT---TTAA
1 TTTTAAAATAT
17075914 TTTTAAAATAT
1 TTTTAAAATAT
17075925 TTTTAAAATAT
1 TTTTAAAATAT
*
17075936 TTTAAAAATACT
1 TTTTAAAATA-T
17075948 TTTT
1 TTTT
17075952 TTAATTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 1 0.02
8 9 0.17
10 3 0.06
11 32 0.59
12 9 0.17
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:17075912 original size:39 final size:38
Alignment explanation
Indices: 17075859--17075966 Score: 137
Period size: 39 Copynumber: 2.7 Consensus size: 38
17075849 ATATATTTAT
*
17075859 TTTTTAA-ATTTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATA
17075896 CTTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATA
1 -TTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATA
*
17075935 TTTTAAAAATACTTTTTTTAATTTTTAAAATA
1 TTTT--TAAT--TTTTTTTAA-TTTTAAAATA
17075967 AATTTTTGGT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
38 11 0.18
39 29 0.47
40 3 0.05
42 9 0.15
43 10 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (38 bp):
TTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATA
Found at i:17075960 original size:22 final size:21
Alignment explanation
Indices: 17075905--17075973 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
17075895 ACTTTTTAAT
17075905 TTTTTTTAA-TTTT-AAAATA
1 TTTTTTTAATTTTTAAAAATA
**
17075924 TTTTTAAAATATTTTAAAAATA
1 TTTTTTTAAT-TTTTAAAAATA
*
17075946 CTTTTTTTAATTTTTAAAATAAA
1 -TTTTTTTAATTTTTAAAA-ATA
17075969 TTTTT
1 TTTTT
17075974 GGTATTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.17
21 4 0.10
22 19 0.47
23 10 0.25
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTTAATTTTTAAAAATA
Found at i:17075972 original size:21 final size:20
Alignment explanation
Indices: 17075906--17075973 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
17075896 CTTTTTAATT
17075906 TTTTTTAA-TTTTAAAAT-A
1 TTTTTTAATTTTTAAAATAA
* *
17075924 TTTTTAAAATATTTTAAAAATACT
1 TTTTT-TAAT-TTTT-AAAATA-A
17075948 TTTTTTAATTTTTAAAATAAA
1 TTTTTTAATTTTTAAAAT-AA
17075969 TTTTT
1 TTTTT
17075974 GGTATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
21 14 0.36
22 10 0.26
23 3 0.08
24 5 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTAATTTTTAAAATAA
Found at i:17079509 original size:25 final size:26
Alignment explanation
Indices: 17079474--17079523 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
17079464 ACAAGTTTTT
*
17079474 TATTCTAATTT-GATATTTGAATTTAA
1 TATTCTAATTTAG-TACTTGAATTTAA
17079500 TATT-TAATTTAGTACTTGAATTTA
1 TATTCTAATTTAGTACTTGAATTTA
17079524 TTTTCAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (26 bp):
TATTCTAATTTAGTACTTGAATTTAA
Found at i:17089380 original size:41 final size:41
Alignment explanation
Indices: 17089214--17089369 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
17089204 TTTATCGTTA
* * * *
17089214 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17089255 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17089296 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
17089337 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
17089370 AAGAGCCGGT
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 102 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:17089640 original size:33 final size:33
Alignment explanation
Indices: 17089584--17089681 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
17089574 ATAGATATGT
*
17089584 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
17089616 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
17089649 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
17089682 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:17097008 original size:40 final size:41
Alignment explanation
Indices: 17096844--17096997 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
17096834 TTTATCGTTA
* * * *
17096844 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17096885 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17096926 GTGACACATTTCAGACTATAAGTCTAGCA-GCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
17096966 GTGACACATTTC-GACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
17096998 AAGAGCCGGT
Statistics
Matches: 105, Mismatches: 3, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
39 17 0.16
40 27 0.26
41 58 0.55
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:17097257 original size:30 final size:32
Alignment explanation
Indices: 17097216--17097291 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
17097206 ATATGTATAT
*
17097216 ATATATATA-TGT-TGCATTCGGCATAGGTGA
1 ATATATATAGTGTATGCATTCAGCATAGGTGA
*
17097246 ATATATTTATGTGTATGCATTCAGCATAGGTGA
1 ATATATATA-GTGTATGCATTCAGCATAGGTGA
17097279 A-A-ATA-AGTGTATG
1 ATATATATAGTGTATG
17097292 TATCTATGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.17
30 9 0.22
31 2 0.05
32 4 0.10
33 18 0.45
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (32 bp):
ATATATATAGTGTATGCATTCAGCATAGGTGA
Found at i:17097273 original size:33 final size:32
Alignment explanation
Indices: 17097214--17097279 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
17097204 AGATATGTAT
*
17097214 ATATATATATATGTTGCATTCGGCATAGGTGA
1 ATATATATATATGTTGCATTCAGCATAGGTGA
* *
17097246 ATATATTTATGTGTATGCATTCAGCATAGGTGA
1 ATATATATATATGT-TGCATTCAGCATAGGTGA
17097279 A
1 A
17097280 AATAAGTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCAGCATAGGTGA
Found at i:17097310 original size:37 final size:33
Alignment explanation
Indices: 17097228--17097311 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 33
17097218 ATATATATGT
* * *
17097228 TGCATTCGGCATAGGTGAATATATTTATGTGTA
1 TGCATTCGGCATAGGTGAAAATATGTATGTCTA
*
17097261 TGCATTCAGCATAGGTGAAAATAAGTGTATGTATCTA
1 TGCATTCGGCATAGGTGAAAAT-A-TGTATG--TCTA
17097298 TGCATTCGGCATAG
1 TGCATTCGGCATAG
17097312 ATGGGTATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 20 0.48
34 1 0.02
35 5 0.12
37 16 0.38
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.35
Consensus pattern (33 bp):
TGCATTCGGCATAGGTGAAAATATGTATGTCTA
Found at i:17101334 original size:22 final size:22
Alignment explanation
Indices: 17101309--17101364 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
17101299 ACTGAACGCT
17101309 ATGTCGCAACATGGGGGATCCA
1 ATGTCGCAACATGGGGGATCCA
17101331 ATGTCGCAACATGGGGGATCCA
1 ATGTCGCAACATGGGGGATCCA
17101353 ATGTCGCAACAT
1 ATGTCGCAACAT
17101365 AGAAAGTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.20
Consensus pattern (22 bp):
ATGTCGCAACATGGGGGATCCA
Found at i:17109969 original size:6 final size:6
Alignment explanation
Indices: 17109958--17110022 Score: 130
Period size: 6 Copynumber: 10.8 Consensus size: 6
17109948 AATATAATAT
17109958 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
17110006 ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATA
17110023 TATGTTTACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:17111689 original size:28 final size:28
Alignment explanation
Indices: 17111649--17111823 Score: 160
Period size: 28 Copynumber: 6.3 Consensus size: 28
17111639 GATAACATTG
* * *
17111649 TAAAATTTGAAAAATAGGGGCAAAAATA
1 TAAAATTTTAAAAATAAGGGCAAAACTA
* * *
17111677 TAAAATTTTAAAAATAAGAGCAAAATTT
1 TAAAATTTTAAAAATAAGGGCAAAACTA
* * * **
17111705 TAAAA-TCTAAAAAT-AGGGTCGATACGG
1 TAAAATTTTAAAAATAAGGG-CAAAACTA
* **
17111732 TAAAATTTGAAAAATAAGGGCAAAAGGA
1 TAAAATTTTAAAAATAAGGGCAAAACTA
*
17111760 T-AAATTTTGAAAAATAGGGGCAAAACTA
1 TAAAATTTT-AAAAATAAGGGCAAAACTA
*
17111788 TAAAATTTAAAAAATAAGGGCAAAACTA
1 TAAAATTTTAAAAATAAGGGCAAAACTA
17111816 T-AAATTTT
1 TAAAATTTT
17111824 GAGTTACAAG
Statistics
Matches: 117, Mismatches: 25, Indels: 11
0.76 0.16 0.07
Matches are distributed among these distances:
26 3 0.03
27 28 0.24
28 76 0.65
29 10 0.09
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (28 bp):
TAAAATTTTAAAAATAAGGGCAAAACTA
Found at i:17111742 original size:83 final size:83
Alignment explanation
Indices: 17111648--17111800 Score: 218
Period size: 83 Copynumber: 1.8 Consensus size: 83
17111638 GGATAACATT
* * * *
17111648 GTAAAATTTGAAAAATAGGGGCAAAAATATAAAATTTT-AAAAATAAGAGCAAAATTTTAAAATC
1 GTAAAATTTGAAAAATAAGGGCAAAAAGAT-AAATTTTGAAAAATAAGAGCAAAACTATAAAATC
17111712 TAAAAATAGGGTCGATACG
65 TAAAAATAGGGTCGATACG
* * * *
17111731 GTAAAATTTGAAAAATAAGGGCAAAAGGATAAATTTTGAAAAATAGGGGCAAAACTATAAAATTT
1 GTAAAATTTGAAAAATAAGGGCAAAAAGATAAATTTTGAAAAATAAGAGCAAAACTATAAAATCT
17111796 AAAAA
66 AAAAA
17111801 ATAAGGGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 7 0.11
83 54 0.89
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.24
Consensus pattern (83 bp):
GTAAAATTTGAAAAATAAGGGCAAAAAGATAAATTTTGAAAAATAAGAGCAAAACTATAAAATCT
AAAAATAGGGTCGATACG
Found at i:17111794 original size:56 final size:56
Alignment explanation
Indices: 17111649--17111825 Score: 203
Period size: 56 Copynumber: 3.2 Consensus size: 56
17111639 GATAACATTG
* * * * *
17111649 TAAAATTTGAAAAATAGGGGCAAAAATATAAAATTTTAAAAATAAGAGCAAAATTT
1 TAAAATTTGAAAAATAGGGGCAAAACTATAAAATTTAAAAAATAAGGGCAAAACTA
* * * * ** * **
17111705 TAAAATCT-AAAAATAGGGTCGATACGGTAAAATTTGAAAAATAAGGGCAAAAGGA
1 TAAAATTTGAAAAATAGGGGCAAAACTATAAAATTTAAAAAATAAGGGCAAAACTA
*
17111760 TAAATTTTGAAAAATAGGGGCAAAACTATAAAATTTAAAAAATAAGGGCAAAACTA
1 TAAAATTTGAAAAATAGGGGCAAAACTATAAAATTTAAAAAATAAGGGCAAAACTA
*
17111816 TAAATTTTGA
1 TAAAATTTGA
17111826 GTTACAAGGG
Statistics
Matches: 98, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
55 42 0.43
56 56 0.57
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.25
Consensus pattern (56 bp):
TAAAATTTGAAAAATAGGGGCAAAACTATAAAATTTAAAAAATAAGGGCAAAACTA
Found at i:17111821 original size:83 final size:82
Alignment explanation
Indices: 17111648--17111822 Score: 194
Period size: 83 Copynumber: 2.1 Consensus size: 82
17111638 GGATAACATT
* * * *
17111648 GTAAAATTTGAAAAATAGGGGCAAAAATATAAAATTTTAAAAATAAGAGCAAAATTTTAAAATCT
1 GTAAAATTTGAAAAATAAGGGCAAAAAGATAAAATTTTAAAAATAAGAGCAAAACTATAAAATCT
* *
17111713 AAAAATAGGGTCGATAC
66 AAAAATAGGGTCAAAAC
* * *
17111730 GGTAAAATTTGAAAAATAAGGGCAAAAGGAT-AAATTTTGAAAAATAGGGGCAAAACTATAAAAT
1 -GTAAAATTTGAAAAATAAGGGCAAAAAGATAAAATTTT-AAAAATAAGAGCAAAACTATAAAAT
*
17111794 TTAAAAAATAAGGG-CAAAAC
64 CT-AAAAAT-AGGGTCAAAAC
17111814 -TATAAATTT
1 GTA-AAATTT
17111823 TGAGTTACAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
82 9 0.12
83 55 0.71
84 10 0.13
85 4 0.05
ACGTcount: A:0.54, C:0.06, G:0.16, T:0.25
Consensus pattern (82 bp):
GTAAAATTTGAAAAATAAGGGCAAAAAGATAAAATTTTAAAAATAAGAGCAAAACTATAAAATCT
AAAAATAGGGTCAAAAC
Found at i:17113829 original size:24 final size:25
Alignment explanation
Indices: 17113790--17113852 Score: 101
Period size: 25 Copynumber: 2.5 Consensus size: 25
17113780 TCGATTTCAT
17113790 TTTTTTGAAAACAA-TTTAAATTTTA
1 TTTTTTGAAAA-AATTTTAAATTTTA
*
17113815 TTTTTTGAAAAAATTTTATATTTTA
1 TTTTTTGAAAAAATTTTAAATTTTA
17113840 TTTTTTGAAAAAA
1 TTTTTTGAAAAAA
17113853 ATTGTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 2 0.06
25 34 0.94
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (25 bp):
TTTTTTGAAAAAATTTTAAATTTTA
Found at i:17119435 original size:85 final size:84
Alignment explanation
Indices: 17119340--17119499 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 84
17119330 GGATAAAATT
* * * * * *
17119340 GTAAAATTTGAAAAATAATGGCAAAACTATATAATCTTAAAAGTAGGGGCAAAATTGTAAAATTT
1 GTAAAATTTGAAAAATAATGGCAAAACGATAAAATATGAAAAATAGGGGCAAAATTGTAAAATCT
17119405 AGAAAAATAGGTTCAAATCA
66 A-AAAAATAGGTTCAAATCA
* * * *
17119425 GTAAAATTTGAAAAATAATTGCAAAAGGGTAAAATATGAAAAATAGGGGTAAAATTGTAAAATCT
1 GTAAAATTTGAAAAATAATGGCAAAACGATAAAATATGAAAAATAGGGGCAAAATTGTAAAATCT
17119490 AAAAAATAGG
66 AAAAAATAGG
17119500 GGAAAAATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
84 9 0.14
85 56 0.86
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.26
Consensus pattern (84 bp):
GTAAAATTTGAAAAATAATGGCAAAACGATAAAATATGAAAAATAGGGGCAAAATTGTAAAATCT
AAAAAATAGGTTCAAATCA
Found at i:17119507 original size:28 final size:28
Alignment explanation
Indices: 17119311--17119513 Score: 167
Period size: 28 Copynumber: 7.2 Consensus size: 28
17119301 GGTCAAGACA
* *
17119311 GTAAAATTTGTAAAATAGGGGATAAAATT
1 GTAAAATTTGAAAAATAGGGG-CAAAATT
** *
17119340 GTAAAATTTGAAAAATAATGGCAAAACT
1 GTAAAATTTGAAAAATAGGGGCAAAATT
* * *
17119368 ATATAATCTT-AAAAGTAGGGGCAAAATT
1 GTAAAAT-TTGAAAAATAGGGGCAAAATT
** *
17119396 GTAAAATTTAGAAAAATAGGTTC-AAATCA
1 GTAAAATTT-GAAAAATAGGGGCAAAAT-T
*** **
17119425 GTAAAATTTGAAAAATAATTGCAAAAGG
1 GTAAAATTTGAAAAATAGGGGCAAAATT
* *
17119453 GTAAAATATGAAAAATAGGGGTAAAATT
1 GTAAAATTTGAAAAATAGGGGCAAAATT
* * *
17119481 GTAAAATCTAAAAAATAGGGGAAAAATT
1 GTAAAATTTGAAAAATAGGGGCAAAATT
17119509 GTAAA
1 GTAAA
17119514 TTCTGAGTTA
Statistics
Matches: 137, Mismatches: 32, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
27 2 0.01
28 94 0.69
29 41 0.30
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.26
Consensus pattern (28 bp):
GTAAAATTTGAAAAATAGGGGCAAAATT
Found at i:17134321 original size:50 final size:50
Alignment explanation
Indices: 17134214--17134451 Score: 230
Period size: 50 Copynumber: 4.7 Consensus size: 50
17134204 ATTTGGGTAA
* *
17134214 AGAGATCCCATGTAAGACCATGTCTGGGACATAGCATTGGCATCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
*
17134270 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** ** *
17134320 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCACGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
17134370 AGA-ACTCCCATGTAAGACCATATTTGGGATATGGCATTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
17134419 AAACATCTCATGTAAGACCATGTCTGGGACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATG
17134452 ACTTTCGCAT
Statistics
Matches: 156, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 29 0.19
50 82 0.53
52 1 0.01
53 2 0.01
55 1 0.01
56 40 0.26
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:17143917 original size:26 final size:26
Alignment explanation
Indices: 17143883--17143933 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
17143873 TTTTGGATCA
* *
17143883 AAATAGTAAAATTTGAAAAATAGGGG
1 AAATAGTAAAATGTAAAAAATAGGGG
*
17143909 AAATTGTAAAATGTAAAAAATAGGG
1 AAATAGTAAAATGTAAAAAATAGGG
17143934 ACAAAATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.24
Consensus pattern (26 bp):
AAATAGTAAAATGTAAAAAATAGGGG
Found at i:17147118 original size:88 final size:89
Alignment explanation
Indices: 17146883--17147175 Score: 407
Period size: 88 Copynumber: 3.3 Consensus size: 89
17146873 AACTGGTGAA
** * *
17146883 ACTATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAA-ATTATAAATCCTAACTCCCT
1 ACTATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAAGATTGTAAATCCTAGCTCCCT
*
17146947 GACCAGCATTGGAATAGGTGGAAG
66 GACCAGCAGTGGAATAGGTGGAAG
* *
17146971 ACTGA-AAGTCCTAG-TCCCTGAACAGCAATAGAATAGGCAG-AAGATTGTAAATCCTAGCTCCC
1 ACT-ATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAAGATTGTAAATCCTAGCTCCC
*
17147033 TGAACAGCAGTGGAATAGGTGGAAG
65 TGACCAGCAGTGGAATAGGTGGAAG
*
17147058 ACTATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGG-AGAAAGATTGTAAATCCTAGCTCCTT
1 ACTATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAAGATTGTAAATCCTAGCTCCCT
**
17147122 GACCAGCAGTGGAATAGGCAGAAG
66 GACCAGCAGTGGAATAGGTGGAAG
* * * *
17147146 ATTGTAAGTCCCAGCTCCCTGACCAGCAGT
1 ACTATAAGTCCTAGCTCCCTGAACAGCAGT
17147176 AGAGCAGGTT
Statistics
Matches: 182, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
86 3 0.02
87 76 0.42
88 102 0.56
89 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (89 bp):
ACTATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCAGAAAGATTGTAAATCCTAGCTCCCT
GACCAGCAGTGGAATAGGTGGAAG
Found at i:17147191 original size:44 final size:44
Alignment explanation
Indices: 17146887--17147175 Score: 348
Period size: 44 Copynumber: 6.6 Consensus size: 44
17146877 GGTGAAACTA
* * *
17146887 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAAATTA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTG
* * * * * *
17146931 TAAATCCTAACTCCCTGACCAGCATTGGAATAGGTGGAAGACTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTG
* * * *
17146975 AAAGTCCTAG-TCCCTGAACAGCAATAGAATAGGCAGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTG
* * * *
17147018 TAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTA
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTG
17147062 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGG-AGAAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAG-AAGATTG
* * * *
17147106 TAAATCCTAGCTCCTTGACCAGCAGTGGAATAGGCAGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTG
* *
17147150 TAAGTCCCAGCTCCCTGACCAGCAGT
1 TAAGTCCTAGCTCCCTGAACAGCAGT
17147176 AGAGCAGGTT
Statistics
Matches: 208, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
43 36 0.17
44 170 0.82
45 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (44 bp):
TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTG
Found at i:17147920 original size:13 final size:13
Alignment explanation
Indices: 17147904--17147929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17147894 AACAACAGAG
17147904 AATAACAAGAAAA
1 AATAACAAGAAAA
17147917 AATAACAAGAAAA
1 AATAACAAGAAAA
17147930 TATAGGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAACAAGAAAA
Found at i:17151836 original size:21 final size:21
Alignment explanation
Indices: 17151812--17151859 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17151802 GGTTTCAAAT
* *
17151812 CGTGTGACAAAGGTACACGGC
1 CGTGTGACAAAGATACACGAC
* *
17151833 CGTGTGGCTAAGATACACGAC
1 CGTGTGACAAAGATACACGAC
17151854 CGTGTG
1 CGTGTG
17151860 GGTAGCCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (21 bp):
CGTGTGACAAAGATACACGAC
Found at i:17156192 original size:152 final size:152
Alignment explanation
Indices: 17155916--17156225 Score: 566
Period size: 152 Copynumber: 2.0 Consensus size: 152
17155906 ATATGTGTGA
*
17155916 GATTGATTGATTTTTCTATGAATGATGTTATGATTTAAATGTTTTGAATAGTTGATAGTTTTGAG
1 GATTGGTTGATTTTTCTATGAATGATGTTATGATTTAAATGTTTTGAATAGTTGATAGTTTTGAG
* *
17155981 TTGTAAACTTTTGATAATGCTCCGTAACCCTATTCCAACAATAGATACGGGATAAGGGTGTTACA
66 GTGTAAACTTTCGATAATGCTCCGTAACCCTATTCCAACAATAGATACGGGATAAGGGTGTTACA
17156046 CATGGCCGGTCATGGGAAAGGG
131 CATGGCCGGTCATGGGAAAGGG
*
17156068 GATTGGTTGATTTTTCTATGAATGATGTTATGATTTAAATGTTTTGAATATTTGATAGTTTTGAG
1 GATTGGTTGATTTTTCTATGAATGATGTTATGATTTAAATGTTTTGAATAGTTGATAGTTTTGAG
*
17156133 GTGTAAACTTTCGATAATGCTCCGTAACCCTATTCCAACAATGGATACGGGATAAGGGTGTTACA
66 GTGTAAACTTTCGATAATGCTCCGTAACCCTATTCCAACAATAGATACGGGATAAGGGTGTTACA
*
17156198 CATGGCCGGTCATGGGAAGGGG
131 CATGGCCGGTCATGGGAAAGGG
17156220 GATTGG
1 GATTGG
17156226 ATGCTATTTT
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (152 bp):
GATTGGTTGATTTTTCTATGAATGATGTTATGATTTAAATGTTTTGAATAGTTGATAGTTTTGAG
GTGTAAACTTTCGATAATGCTCCGTAACCCTATTCCAACAATAGATACGGGATAAGGGTGTTACA
CATGGCCGGTCATGGGAAAGGG
Found at i:17159062 original size:12 final size:12
Alignment explanation
Indices: 17159045--17159079 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
17159035 CAAAACTGGT
17159045 TTTTAGCGGCAC
1 TTTTAGCGGCAC
17159057 TTTTAGCGGCAC
1 TTTTAGCGGCAC
17159069 TTTTAGCGGCA
1 TTTTAGCGGCA
17159080 TTTGGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (12 bp):
TTTTAGCGGCAC
Found at i:17159168 original size:27 final size:26
Alignment explanation
Indices: 17159130--17159180 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
17159120 GCTTTATGGA
*
17159130 AAATGCCGCTAAAAAGAGCATTAGAG
1 AAATGCCACTAAAAAGAGCATTAGAG
17159156 AAATCGCCACTAAAAAGAGCATTAG
1 AAAT-GCCACTAAAAAGAGCATTAG
17159181 CGGCGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (26 bp):
AAATGCCACTAAAAAGAGCATTAGAG
Found at i:17159338 original size:40 final size:41
Alignment explanation
Indices: 17159226--17159500 Score: 306
Period size: 41 Copynumber: 6.8 Consensus size: 41
17159216 GTCACCTTTT
* * *
17159226 GGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTT
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
*
17159267 GGGGTTTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGCTA
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * *
17159308 GGGGTTTTAGC-GCGGTTTTGCAAATGCGCCGCTAATGCTA
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * *
17159348 GGGGTTTTAGCGGCGTTTTTG-GATAGCGCCGCTAGTGCTA
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * * * * * * *
17159388 GGAGCTTTAACAGCGTTTTTGGAAAAGTGCAGCTAATGCTC
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* *
17159429 GGGGTTTTAGCGGCGTTTGTGAAAAGGCGCCGCTAATGCT-
1 GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * *
17159469 -CGGTCTTTAGCTGCATTTTTGAAAAAGCGCCG
1 GGGGT-TTTAGCGGCGTTTTTGAAAAAGCGCCG
17159501 TAAAAAACAT
Statistics
Matches: 194, Mismatches: 37, Indels: 7
0.82 0.16 0.03
Matches are distributed among these distances:
39 3 0.02
40 91 0.47
41 100 0.52
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.30
Consensus pattern (41 bp):
GGGGTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
Found at i:17159344 original size:81 final size:81
Alignment explanation
Indices: 17159226--17159500 Score: 313
Period size: 81 Copynumber: 3.4 Consensus size: 81
17159216 GTCACCTTTT
* * *
17159226 GGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTTGGGGTTTTAGCGACGTTTTTGAAA
1 GGGGCTTTAGCAGCGTTTTTGA-AAAGCGCCGCTAATGCTAGGGGTTTTAGCGGCGTTTTTGAAA
17159291 AAGCGCCGCTAATGCTA
65 AAGCGCCGCTAATGCTA
* * * *
17159308 GGGGTTTTAGC-GCGGTTTTGCAAATGCGCCGCTAATGCTAGGGGTTTTAGCGGCGTTTTTG-GA
1 GGGGCTTTAGCAGCGTTTTTG-AAAAGCGCCGCTAATGCTAGGGGTTTTAGCGGCGTTTTTGAAA
* *
17159371 TAGCGCCGCTAGTGCTA
65 AAGCGCCGCTAATGCTA
* * * * * *
17159388 GGAGCTTTAACAGCGTTTTTGGAAAAGTGCAGCTAATGCTCGGGGTTTTAGCGGCGTTTGTGAAA
1 GGGGCTTTAGCAGCGTTTTT-GAAAAGCGCCGCTAATGCTAGGGGTTTTAGCGGCGTTTTTGAAA
*
17159453 AGGCGCCGCTAATGCT-
65 AAGCGCCGCTAATGCTA
* * * *
17159469 CGGTCTTTAGCTGCATTTTTGAAAAAGCGCCG
1 GGGGCTTTAGCAGCGTTTTTG-AAAAGCGCCG
17159501 TAAAAAACAT
Statistics
Matches: 159, Mismatches: 29, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
80 25 0.16
81 108 0.68
82 26 0.16
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.30
Consensus pattern (81 bp):
GGGGCTTTAGCAGCGTTTTTGAAAAGCGCCGCTAATGCTAGGGGTTTTAGCGGCGTTTTTGAAAA
AGCGCCGCTAATGCTA
Found at i:17159963 original size:15 final size:16
Alignment explanation
Indices: 17159943--17159973 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17159933 GGGTTAAGAG
17159943 TTAGGGATT-TAGGGT
1 TTAGGGATTCTAGGGT
17159958 TTAGGGATTCTAGGGT
1 TTAGGGATTCTAGGGT
17159974 CGGGTTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.03, G:0.39, T:0.39
Consensus pattern (16 bp):
TTAGGGATTCTAGGGT
Found at i:17160309 original size:291 final size:286
Alignment explanation
Indices: 17159777--17160331 Score: 753
Period size: 291 Copynumber: 1.9 Consensus size: 286
17159767 TATCACTATA
*
17159777 GTTTAGGGTTTTTGGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGGTTTAGGAGTTACTA
1 GTTTAGGATTTTTGGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGGTTTAGGAGTTACTA
* * * **
17159842 TTTTAAGGTTAATTTAGGGATTAGTATGGATTTAGGGATTATGGTTTAAGGGCTGAGATTTAAAG
66 TTTTAAGG---ATTTAGGGA-GAGTATAGATTTAGGGATTATGGATTAAGGAATGAGATTTAAAG
* * *
17159907 TTTAGGGGTTTAAGAGTTAAATGTTAGGGTTAAGAGTTAGGGATTTAGGGTTTAGGGATTCTAGG
127 TTTAGGGGTTTAAGAGTTAAATGTTAGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGATTCAAGA
17159972 GTCGGGTTAGGGTTTTGGGTTTAGATTAATTAGTTTTTTGAATTTATATATTAAATATGTTCTTA
192 GTCGGGTTAGGGTTTTGGGTTTAGATTAATTAGTTTTTTGAATTTATATATTAAATATGTTCTTA
17160037 TATAATTGTAAAAGAGATAATAATAAATTT
257 TATAATTGTAAAAGAGATAATAATAAATTT
* *
17160067 GTTTAGGATTTTTTGTTTAGGGTATATGATTAATTTAAGATTTAAGGCTGGTTTAGGAGTTACTA
1 GTTTAGGATTTTTGGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGGTTTAGGAGTTACTA
* *
17160132 TTTTAAGG-TTTAGGG-GAGTATAGATTTAGGGATTATGGATT-AGGAATTATGGTTTAAGGGTC
66 TTTTAAGGATTTAGGGAGAGTATAGATTTAGGGATTATGGATTAAGGAATGA-GATTTAA-----
* * * *
17160194 GGGATTTA-GGGTTTAAGGGTTAGACAT-TATA-GGTTCAGGGTTAGGGATTTAAGGTTTAGGGA
125 -AG-TTTAGGGGTTTAAGAGTTA-A-ATGT-TAGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGA
* * *
17160256 TTCAAGAGTCGGGTTAGGGTTTTGGGTTTAGATTAATTAGTTTTTTTAATTTATATTTTATATAT
185 TTCAAGAGTCGGGTTAGGGTTTTGGGTTTAGATTAATTAGTTTTTTGAATTTATATATTAAATAT
17160321 GTTCTTATATA
250 GTTCTTATATA
17160332 TTAATTAAAA
Statistics
Matches: 234, Mismatches: 20, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
283 5 0.02
284 29 0.12
286 7 0.03
290 84 0.36
291 105 0.45
292 4 0.02
ACGTcount: A:0.28, C:0.03, G:0.27, T:0.43
Consensus pattern (286 bp):
GTTTAGGATTTTTGGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGGTTTAGGAGTTACTA
TTTTAAGGATTTAGGGAGAGTATAGATTTAGGGATTATGGATTAAGGAATGAGATTTAAAGTTTA
GGGGTTTAAGAGTTAAATGTTAGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGATTCAAGAGTCG
GGTTAGGGTTTTGGGTTTAGATTAATTAGTTTTTTGAATTTATATATTAAATATGTTCTTATATA
ATTGTAAAAGAGATAATAATAAATTT
Found at i:17162399 original size:26 final size:27
Alignment explanation
Indices: 17162367--17162425 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
17162357 ATATTTTTTA
*
17162367 TTTTTA-TTTTTTAATTTTAAAATATT
1 TTTTTATTTTTTTAATTTTAAAATAAT
*
17162393 TTTTTATTTTTTTATTTTTAAAATAAT
1 TTTTTATTTTTTTAATTTTAAAATAAT
17162420 TTTTTA
1 TTTTTA
17162426 ATGTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTTATTTTTTTAATTTTAAAATAAT
Found at i:17162412 original size:33 final size:34
Alignment explanation
Indices: 17162350--17162413 Score: 96
Period size: 32 Copynumber: 1.9 Consensus size: 34
17162340 CCGAATATAA
17162350 TAAATATATATTTTTTATTTTTATTTTTTAATTT
1 TAAATATATATTTTTTATTTTTATTTTTTAATTT
*
17162384 TAAA-ATAT-TTTTTTATTTTTTTATTTTTAA
1 TAAATATATATTTTTTATTTTTAT-TTTTTAA
17162414 AATAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 11 0.39
34 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (34 bp):
TAAATATATATTTTTTATTTTTATTTTTTAATTT
Found at i:17162432 original size:26 final size:26
Alignment explanation
Indices: 17162367--17162434 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 26
17162357 ATATTTTTTA
* *
17162367 TTTTTATTTTTTAATTTTAAAATATT
1 TTTTTATTTTTTATTTTTAAAATAAT
17162393 TTTTTATTTTTTTATTTTTAAAATAAT
1 TTTTTA-TTTTTTATTTTTAAAATAAT
* *
17162420 TTTTTAATGTTTATT
1 TTTTTATTTTTTATT
17162435 AAAAATGGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 13 0.35
27 24 0.65
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (26 bp):
TTTTTATTTTTTATTTTTAAAATAAT
Found at i:17163914 original size:38 final size:38
Alignment explanation
Indices: 17163829--17163901 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
17163819 ATCTAATTAC
*
17163829 ATATACAAATATCACGTGTTGAAATTTACTTTGATCAT
1 ATATATAAATATCACGTGTTGAAATTTACTTTGATCAT
* *
17163867 ATATATAAATATCATGTGTCT-AAATTTATTTTGAT
1 ATATATAAATATCACGTGT-TGAAATTTACTTTGAT
17163902 TTTCTATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 30 0.97
39 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (38 bp):
ATATATAAATATCACGTGTTGAAATTTACTTTGATCAT
Found at i:17165699 original size:61 final size:57
Alignment explanation
Indices: 17165596--17165716 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 57
17165586 CAATTAAATA
*
17165596 ACTAAATTGTAATTTTTTTAATTAACCATAACAAAAATTGATTCTTATTCATAATTTAGTG
1 ACTAAATTGTAAGTTTTTTAATTAACCATAACAAAAATTGATTC----TCATAATTTAGTG
* **
17165657 ACTAAATTGTAAGTTTTTTAATTAATCATAAC-GGAATCTGATTCTCATAATTTAGTG
1 ACTAAATTGTAAGTTTTTTAATTAACCATAACAAAAAT-TGATTCTCATAATTTAGTG
17165714 ACT
1 ACT
17165717 TATGTGTAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
57 16 0.29
60 3 0.05
61 36 0.65
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (57 bp):
ACTAAATTGTAAGTTTTTTAATTAACCATAACAAAAATTGATTCTCATAATTTAGTG
Found at i:17165789 original size:26 final size:27
Alignment explanation
Indices: 17165753--17165816 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
17165743 AACTCAATTA
*
17165753 ATTTTCATATCAATTTTTTTCAA-ATAT
1 ATTTTCATATC-ATTTTTTTAAAGATAT
17165780 ATTTTC-TATCATTTTTTTAAAGATAT
1 ATTTTCATATCATTTTTTTAAAGATAT
17165806 ATTTGTCATAT
1 ATTT-TCATAT
17165817 TATTCTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 10 0.30
26 12 0.36
27 8 0.24
28 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.56
Consensus pattern (27 bp):
ATTTTCATATCATTTTTTTAAAGATAT
Found at i:17173437 original size:40 final size:40
Alignment explanation
Indices: 17173392--17173472 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
17173382 ATAAAGAGAC
17173392 ACCCATTAGATTAGAACTCATAACACATTCAGAGAATTTT
1 ACCCATTAGATTAGAACTCATAACACATTCAGAGAATTTT
17173432 ACCCATTAGATTAGAACTCATAACACATTCAGAGAATTTT
1 ACCCATTAGATTAGAACTCATAACACATTCAGAGAATTTT
17173472 A
1 A
17173473 TGTTTACGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (40 bp):
ACCCATTAGATTAGAACTCATAACACATTCAGAGAATTTT
Found at i:17173460 original size:22 final size:22
Alignment explanation
Indices: 17173395--17173460 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
17173385 AAGAGACACC
17173395 CATTAGATTAGAACTCATAACA
1 CATTAGATTAGAACTCATAACA
* * *
17173417 CATTCAG---AGAA-T-TTTACC
1 CATT-AGATTAGAACTCATAACA
17173435 CATTAGATTAGAACTCATAACA
1 CATTAGATTAGAACTCATAACA
17173457 CATT
1 CATT
17173461 CAGAGAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
17 2 0.06
18 7 0.22
19 1 0.03
20 8 0.25
21 1 0.03
22 11 0.34
23 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CATTAGATTAGAACTCATAACA
Found at i:17177231 original size:26 final size:26
Alignment explanation
Indices: 17177167--17177231 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
17177157 AATTAGAAAA
*
17177167 AAAATATAGAAAATATTATAAAAATAT
1 AAAAGATA-AAAATATTATAAAAATAT
* *
17177194 ATATAG-GAAAAATATTAT-AAAATAT
1 A-AAAGATAAAAATATTATAAAAATAT
17177219 AAAAGATATAAAA
1 AAAAGATA-AAAA
17177232 AAAAATAAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
24 3 0.10
25 9 0.30
26 14 0.47
27 2 0.07
28 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (26 bp):
AAAAGATAAAAATATTATAAAAATAT
Found at i:17177451 original size:23 final size:23
Alignment explanation
Indices: 17177423--17177466 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17177413 TGTTTTAAAA
*
17177423 TATAAAAAATATAGAAAAATTAT
1 TATAAAAAATATAAAAAAATTAT
**
17177446 TATAAAATGTATAAAAAAATT
1 TATAAAAAATATAAAAAAATT
17177467 CCCCCCTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TATAAAAAATATAAAAAAATTAT
Found at i:17177979 original size:17 final size:20
Alignment explanation
Indices: 17177946--17177996 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 20
17177936 TGATAATTAT
17177946 ATTT-TATATTTTATAAT-A
1 ATTTATATATTTTATAATAA
*
17177964 GTTTA-ATATTTT-TAATAA
1 ATTTATATATTTTATAATAA
17177982 ATTTATATATTTTAT
1 ATTTATATATTTTAT
17177997 TGTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.15
18 15 0.56
19 7 0.26
20 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTATATATTTTATAATAA
Found at i:17180215 original size:18 final size:17
Alignment explanation
Indices: 17180188--17180221 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17180178 ACAACATAAT
*
17180188 TTATTAAATTGTTTTTA
1 TTATTAAATTATTTTTA
17180205 TTATATAAATTATTTTT
1 TTAT-TAAATTATTTTT
17180222 TAATTTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATTAAATTATTTTTA
Found at i:17180574 original size:22 final size:22
Alignment explanation
Indices: 17180549--17180618 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
17180539 AAATTCAATA
17180549 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
17180571 TCAA-TTCCGTTCAAAAATTCTC
1 TCAATTTCC-TTCAAAAATTCTC
* *
17180593 TCAAATTACTTTC-AAAATTCTC
1 TC-AATTTCCTTCAAAAATTCTC
17180615 TCAA
1 TCAA
17180619 ACTCTCAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.14
22 30 0.70
23 5 0.12
24 2 0.05
ACGTcount: A:0.34, C:0.26, G:0.01, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:17180618 original size:11 final size:11
Alignment explanation
Indices: 17180584--17180648 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
17180574 ATTCCGTTCA
17180584 AAAATTCTCTC
1 AAAATTCTCTC
*
17180595 -AAATTACTTTC
1 AAAATT-CTCTC
17180606 AAAATTCTCTC
1 AAAATTCTCTC
17180617 -AAA--CTCTC
1 AAAATTCTCTC
*
17180625 AAATTTCT-TCC
1 AAAATTCTCT-C
17180636 AAAATTCTCTC
1 AAAATTCTCTC
17180647 AA
1 AA
17180649 TTTCCTTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 9 0.21
11 21 0.49
12 6 0.14
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAATTCTCTC
Found at i:17180619 original size:22 final size:23
Alignment explanation
Indices: 17180558--17180619 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
17180548 ATCAATTTCC
*
17180558 TTCAAAAATTCTCTC-AATTCCG
1 TTCAAAAATTCTCTCAAATTACG
*
17180580 TTCAAAAATTCTCTCAAATTACT
1 TTCAAAAATTCTCTCAAATTACG
17180603 TTC-AAAATTCTCTCAAA
1 TTCAAAAATTCTCTCAAA
17180620 CTCTCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 29 0.78
23 8 0.22
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (23 bp):
TTCAAAAATTCTCTCAAATTACG
Found at i:17180624 original size:30 final size:30
Alignment explanation
Indices: 17180590--17180648 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
17180580 TTCAAAAATT
*
17180590 CTCTCAAATTACTTTCAAAATTCTCTCAAA
1 CTCTCAAATTACTTCCAAAATTCTCTCAAA
*
17180620 CTCTCAAATTTCTTCCAAAATTCTCTCAA
1 CTCTCAAATTACTTCCAAAATTCTCTCAA
17180649 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAAATTACTTCCAAAATTCTCTCAAA
Found at i:17180652 original size:21 final size:23
Alignment explanation
Indices: 17180620--17180671 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
17180610 TTCTCTCAAA
* *
17180620 CTCTCAAATTT-CTTCCAAAATT
1 CTCTCAAATTTCCTTCAAAAAAT
17180642 CTCTC-AATTTCCTTCAAAAAAT
1 CTCTCAAATTTCCTTCAAAAAAT
17180664 CTC-CAAAT
1 CTCTCAAAT
17180672 CCATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (23 bp):
CTCTCAAATTTCCTTCAAAAAAT
Found at i:17180888 original size:14 final size:15
Alignment explanation
Indices: 17180859--17180892 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17180849 AAAATTTAAA
17180859 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
17180874 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
17180888 TTTTA
1 TTTTA
17180893 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:17183079 original size:28 final size:28
Alignment explanation
Indices: 17183039--17183889 Score: 884
Period size: 28 Copynumber: 30.4 Consensus size: 28
17183029 TTTTGACATT
* *
17183039 ATTTGATTAAAAACCCTAACTTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183067 ATTTAATTAAAAACCCTTACCCTAACCTA
1 ATTTAATTAAAAACCC-TAACCTAACTTA
*
17183096 ATTTAATTAAAAACCCTAACTTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
17183124 A-TT-A--AAAAA-CCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
17183147 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183175 AATTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
17183203 ATTTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183226 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* * *
17183255 TTTTACA-TGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAA-CCTAACTTA
* * *
17183284 ATTTAATTAAAAACCCTCACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* * *
17183312 ATTTAATTAAAAACACTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
17183340 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* * * *
17183369 TTTTAAATGAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
*
17183398 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183426 ATTTAATTAAAAACCCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183454 ATTTAATTAAAAACCCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183482 ATTTAATTAAAAATCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183510 ATTTAATTAAAAACCCTAACATAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
17183538 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* * *
17183567 TTTTACA-TGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAAACCCTAA-CCTAACTTA
*
17183596 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
17183624 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
17183652 A-TTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183674 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
17183703 ATTTAATTAAAAACCCTAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAA--CT----TA
*
17183738 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* * *
17183766 ATTTAATTTAATACCCTAACCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
17183794 ATTTAGTTAAAAACCCTAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAA-CCTAA-C----TTA
17183828 ATTTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
17183851 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
17183880 ATTTAATTAA
1 ATTTAATTAA
17183890 TGTAAAAAAA
Statistics
Matches: 712, Mismatches: 68, Indels: 85
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.00
23 69 0.10
24 8 0.01
25 5 0.01
26 2 0.00
27 28 0.04
28 343 0.48
29 202 0.28
30 3 0.00
31 1 0.00
32 2 0.00
34 25 0.04
35 21 0.03
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:17183473 original size:142 final size:142
Alignment explanation
Indices: 17183039--17183889 Score: 928
Period size: 142 Copynumber: 6.1 Consensus size: 142
17183029 TTTTGACATT
* * * * *
17183039 ATTTGATTAAAAACCCTAACTTAACTTAATTTAATTAAAAACCCTTACCCTAACCTAATTTAATT
1 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCC-TAACCTAACCTAATTTAAAT
* * **
17183104 AAAAACCCTAA--CT----TAACTTAATTAAAAAACCTAA-CCTAATTTAATTTAATTAAAAACC
65 AAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACC
*
17183162 CTAACCTAACCTA
130 CTAACATAACCTA
* **
17183175 AATTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA-C--A--TAATTTAGTTA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTAATTTAAATA
* *
17183235 AAAACCCTAACCCTAACCTATTTTACA-TGAAAACCCTAACCCTAACCTAATTTAATTAAAAACC
66 AAAACCCTAACCCTAACCTAATTTA-ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACC
* **
17183299 CTCACATAATTTA
130 CTAACATAACCTA
* * *
17183312 ATTTAATTAAAAACACTAACATAATTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTAAAT
1 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA-CCTAACCTAATTTAAAT
* **
17183377 GAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTTAATTAAAAACC
65 AAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACC
**
17183441 CTAACATAATTTA
130 CTAACATAACCTA
* * ** *
17183454 ATTTAATTAAAAACCCTAACATAATTTAATTTAATTAAAAATCCTAACCTAATTTAATTTAATTA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTAATTTAAATA
* ** * *
17183519 AAAACCCTAA-CATAATTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTACA-TGAAAACC
66 AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTA-ATTAAAAACC
*
17183582 CTAACCCTAACCTA
130 CTAA-CATAACCTA
** *
17183596 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAATTTAA-TTAATTA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTAATTTAAATA
*
17183660 AAAACCCTAA--C--A--TAATTTAGTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCC
66 AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCC
17183719 TAACCCTAACCCTAACCTA
131 TAA--C--A---TAACCTA
* * * **
17183738 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTTAATACCCTAACCTAACATAATTTAGTTA
1 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTAATTTAAATA
* *
17183803 AAAACCCTAACCCTAACCTAATTTAATTTAATTAAA----AACCCTAACATAATTTAGTTAAAAA
66 AAAACCCTAACCCTAACCTAATTTAA-TTAA--AAACCCTAACCCTAACCTAATTTAATTAAAAA
*
17183864 CCCTAACCCTAACCTA
128 CCCTAA-CATAACCTA
17183880 ATTTAATTAA
1 ATTTAATTAA
17183890 TGTAAAAAAA
Statistics
Matches: 619, Mismatches: 61, Indels: 64
0.83 0.08 0.09
Matches are distributed among these distances:
130 20 0.03
132 3 0.00
134 1 0.00
135 3 0.00
136 100 0.16
137 78 0.13
138 1 0.00
139 1 0.00
140 25 0.04
141 63 0.10
142 219 0.35
143 58 0.09
145 1 0.00
147 3 0.00
148 29 0.05
149 7 0.01
150 4 0.01
152 3 0.00
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (142 bp):
ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTAATTTAAATA
AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCC
TAACATAACCTA
Found at i:17183845 original size:23 final size:23
Alignment explanation
Indices: 17183826--17183870 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17183816 TAACCTAATT
17183826 TAATTTAATTAAAAACCCTAACA
1 TAATTTAATTAAAAACCCTAACA
*
17183849 TAATTTAGTTAAAAACCCTAAC
1 TAATTTAATTAAAAACCCTAAC
17183871 CCTAACCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACA
Found at i:17183875 original size:114 final size:114
Alignment explanation
Indices: 17183133--17183889 Score: 690
Period size: 114 Copynumber: 6.7 Consensus size: 114
17183123 AATTAAAAAA
*
17183133 CCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTAAATTAATTAAAAACCCTAACCTA
1 CCTAACCTAATTTAATTTAATTAAAAACCCTAA-C--A--TAATTTAATTAAAAACCCTAACCTA
17183198 ATTTAATTTAATT--AAA----AACCCTAACATAATTTAGTTAAAAACCCTAAC
61 ATTTAATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
* ** ***** * * *
17183246 CCTAACCTATTTTACATGAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTCACATAATTT
1 CCTAACCTAATTTA-ATTTAATTAAAAACCCTAACATAATTTAATTAAAAACCCTAACCTAATTT
* * ** *
17183311 AATTTAATTAAAAACACTAA-CATAATTTAATTTAATTAAAAACCCTAAC
65 AATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
* * * * *
17183360 CCTAACCTATTTTAAATGAA--AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAAT
1 CCTAACCTAATTTAATTTAATTAA---AAACCCTAACATAATTTAATTAAAAACCCTAACCTAAT
* ** *
17183423 TTAATTTAATTAAAAACCCTAA-CATAATTTAATTTAATTAAAAACCCTAA-
63 TTAATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
* *
17183473 -C--A--TAATTTAATTTAATTAAAAATCCTAACCTAATTTAATTTAATTAAAAACCCTAACATA
1 CCTAACCTAATTTAATTTAATTAAAAACCCTAA-C--A--TAATTTAATTAAAAACCCTAACCTA
* * ** *
17183533 ATTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAAC
61 ATTTAATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
17183587 CCTAACC-----TAATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTA
1 CCTAACCTAATTTAATTTAATTAAAAACCCTAA-C--A--TAATTTAATTAAAAACCCTAACCTA
17183647 ATTTAA-TTAATT--AAA----AACCCTAACATAATTTAGTTAAAAACCCTAAC
61 ATTTAATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
* * * *
17183694 CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
1 CCTAACCTAATTTAATT--TAA--TTAA---AAACCCTAACATAATTTAATTAAAAACCCTAACC
* *
17183759 TAATTTAATTTAATTTAATACCCTAA-CCTAACATAATTTAGTTAAAAACCCTAAC
59 TAATTTAATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
* **
17183814 CCTAACCTAATTTAATTTAATTAAAAACCCTAACATAATTTAGTTAAAAACCCTAACCCTAACCT
1 CCTAACCTAATTTAATTTAATTAAAAACCCTAACATAATTTAATTAAAAACCCTAA-CCTAATTT
17183879 AATTTAATTAA
65 AATTTAATTAA
17183890 TGTAAAAAAA
Statistics
Matches: 542, Mismatches: 58, Indels: 87
0.79 0.08 0.13
Matches are distributed among these distances:
107 41 0.08
108 11 0.02
109 35 0.06
110 3 0.01
111 6 0.01
112 54 0.10
113 73 0.13
114 242 0.45
115 9 0.02
116 6 0.01
117 3 0.01
118 3 0.01
119 8 0.01
120 46 0.08
121 2 0.00
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.32
Consensus pattern (114 bp):
CCTAACCTAATTTAATTTAATTAAAAACCCTAACATAATTTAATTAAAAACCCTAACCTAATTTA
ATTTAATTAAAAACCCTAACCCTAACATAATTTAGTTAAAAACCCTAAC
Found at i:17187220 original size:123 final size:124
Alignment explanation
Indices: 17186996--17187259 Score: 361
Period size: 123 Copynumber: 2.1 Consensus size: 124
17186986 CCACGAGGGC
* * *
17186996 GCGATTTGACACTATTTGCTTAGAAACGTCAAAAAAATTTATTTCCTACATGACCAATTGTAGCG
1 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAATTTATTTCCTACATGACCAACTGTAGCG
* * * * * * **
17187061 AAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATTA
66 AAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* * *
17187120 GCGATTTTATACTATTTACTCAGAAAACGTCAAAAAAA-TTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTGACACTATTTACTCAG-AAACGTCAAAAAAATTTATTTCCTACATGACCAACTGTAGC
17187183 GAAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
65 GAAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
**
17187243 GCGATTTCCCACTATTT
1 GCGATTTGACACTATTT
17187260 GACCAGATAC
Statistics
Matches: 122, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
123 73 0.60
124 35 0.29
125 14 0.11
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (124 bp):
GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAATTTATTTCCTACATGACCAACTGTAGCG
AAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:17190980 original size:43 final size:43
Alignment explanation
Indices: 17190888--17190982 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
17190878 CCTAAGACAC
* * * * *
17190888 GAGCATGTGTCTCAGCCGTGTGAGTCACACGGCCTGGCTACAC
1 GAGCGTGTGTCTCAGCCGTGTGAGTCACACGGCCCGACCACAA
* * *
17190931 TAGCGTGTGTCTCAGCCGTTTGAGTCATACGGCCCGACCACAA
1 GAGCGTGTGTCTCAGCCGTGTGAGTCACACGGCCCGACCACAA
*
17190974 GGGCGTGTG
1 GAGCGTGTG
17190983 ACCCCTGTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (43 bp):
GAGCGTGTGTCTCAGCCGTGTGAGTCACACGGCCCGACCACAA
Found at i:17193211 original size:114 final size:113
Alignment explanation
Indices: 17193072--17193482 Score: 475
Period size: 114 Copynumber: 3.6 Consensus size: 113
17193062 GATTTTGTTG
* * * *
17193072 AAGCGTCGCAAATAAACCGAAGCCCAACGATGCCGTTTTCTGAGCGTTCAGGGATTTAGTGGCTT
1 AAGCGCCGCAAATAAACCGAAGCCCAACGACGCCGTTTTCTGAGCATTCAGGGATTTAGCGGCTT
** *
17193137 TTTCGGCGAAGCGCAGCTAATGCTCAGAACTTTAGCGGCGTTTTTGAGT
66 TTTCGGTAAAGCGC-GCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGT
* * * * *
17193186 AAGCGTCGCAAATAAACCGAAGCCCAACGACGCTGTTTTCTGATCATTCGGGGATTTAGTGG-TA
1 AAGCGCCGCAAATAAACCGAAGCCCAACGACGCCGTTTTCTGAGCATTCAGGGATTTAGCGGCT-
* *
17193250 TTTTCGGTAAAGCGTCGCTAATGTTCAGGACTTTAGCGGTGTTTTTGAGT
65 TTTTCGGTAAAGCG-CGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGT
* * * * * *
17193300 AAGCGCCGCAAATAAACCAAAGCCCAACGACGCTGTTTTTTGAGCATTCGGGGATTTTGCGGCGT
1 AAGCGCCGCAAATAAACCGAAGCCCAACGACGCCGTTTTCTGAGCATTCAGGGATTTAGCGGCTT
* * * * *
17193365 TTTAGGTAAAGCGCTGCTAATGCTCAGGACTCTATCGGCGTTTTTTGTGG
66 TTTCGGTAAAGCGC-GCTAATGCTCAGGACTTTAGCGGCG-TTTTTGAGT
* * * * * *
17193415 AAGCGCCGCGAA-AAGCCTAAGCCCAACGATGCCATTTTCTGAGCATTCAGGAATTTAGCGGCGT
1 AAGCGCCGCAAATAAACCGAAGCCCAACGACGCCGTTTTCTGAGCATTCAGGGATTTAGCGGC-T
17193479 TTTT
65 TTTT
17193483 GATGAAGCGC
Statistics
Matches: 256, Mismatches: 35, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
113 2 0.01
114 231 0.90
115 23 0.09
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (113 bp):
AAGCGCCGCAAATAAACCGAAGCCCAACGACGCCGTTTTCTGAGCATTCAGGGATTTAGCGGCTT
TTTCGGTAAAGCGCGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGT
Found at i:17195552 original size:7 final size:7
Alignment explanation
Indices: 17195537--17195585 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
17195527 ATCGTATATA
*
17195537 GTTTGGG
1 GTTTAGG
17195544 GTTTAGG
1 GTTTAGG
17195551 GTTTAGG
1 GTTTAGG
*
17195558 AGTTTGGG
1 -GTTTAGG
*
17195566 GTTTAAG
1 GTTTAGG
*
17195573 GTTTGGG
1 GTTTAGG
17195580 GTTTAG
1 GTTTAG
17195586 TCTACTTTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:17195567 original size:15 final size:14
Alignment explanation
Indices: 17195537--17195585 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
17195527 ATCGTATATA
* *
17195537 GTTTGGGGTTTAGG
1 GTTTAGGGTTTGGG
17195551 GTTTAGGAGTTTGGG
1 GTTTAGG-GTTTGGG
*
17195566 GTTTAAGGTTTGGG
1 GTTTAGGGTTTGGG
17195580 GTTTAG
1 GTTTAG
17195586 TCTACTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.12, C:0.00, G:0.45, T:0.43
Consensus pattern (14 bp):
GTTTAGGGTTTGGG
Found at i:17198187 original size:15 final size:16
Alignment explanation
Indices: 17198150--17198193 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
17198140 TATAAATATT
*
17198150 TATATACATTTTTAATA
1 TATATA-ATTTTTAAAA
17198167 TATAT-ATTTTTAAAA
1 TATATAATTTTTAAAA
*
17198182 TCTATAATTTTT
1 TATATAATTTTT
17198194 TCAAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 6 0.25
17 5 0.21
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATTTTTAAAA
Found at i:17198254 original size:13 final size:13
Alignment explanation
Indices: 17198236--17198263 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17198226 AACTCAAATT
17198236 TATCAATAATATA
1 TATCAATAATATA
17198249 TATCAATAATATA
1 TATCAATAATATA
17198262 TA
1 TA
17198264 ATAACATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (13 bp):
TATCAATAATATA
Found at i:17198331 original size:33 final size:35
Alignment explanation
Indices: 17198263--17198335 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
17198253 AATAATATAT
17198263 AATAACATACAATATAATAACTTATACATAACTTA
1 AATAACATACAATATAATAACTTATACATAACTTA
*
17198298 AATAACATACAATAT-ATAAAC-T-TGCATAACTTA
1 AATAACATACAATATAAT-AACTTATACATAACTTA
17198331 AATAA
1 AATAA
17198336 TTATAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 15 0.42
34 3 0.08
35 18 0.50
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (35 bp):
AATAACATACAATATAATAACTTATACATAACTTA
Found at i:17198500 original size:23 final size:23
Alignment explanation
Indices: 17198472--17198515 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
17198462 CTTATATGTA
17198472 AACTTACATAATACATAACTTTT
1 AACTTACATAATACATAACTTTT
17198495 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
17198516 ACAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:17198629 original size:20 final size:19
Alignment explanation
Indices: 17198604--17198764 Score: 58
Period size: 19 Copynumber: 8.4 Consensus size: 19
17198594 AAACTGGCAT
*
17198604 AACTTACGTAATAACATAAC
1 AACTTACATAAT-ACATAAC
17198624 AACTTACATAATACATAGCATAC
1 AACTTACATAATACAT---A-AC
17198647 ATAACTTACATAATAC--AA-
1 --AACTTACATAATACATAAC
*
17198665 AACTTACATAACTTA-A-AAT
1 AACTTACATAA--TACATAAC
* *
17198684 ATCTTACACAACTTACATAAC
1 AACTTACATAA--TACATAAC
**
17198705 --C-TACATAATACAT-TT
1 AACTTACATAATACATAAC
17198720 AACTTACATAAATTACAT---
1 AACTTACAT-AA-TACATAAC
*
17198738 AACTTACATAATACATAAT
1 AACTTACATAATACATAAC
17198757 AACTTACA
1 AACTTACA
17198765 ACTTACATAA
Statistics
Matches: 114, Mismatches: 7, Indels: 41
0.70 0.04 0.25
Matches are distributed among these distances:
16 21 0.18
17 3 0.03
18 24 0.21
19 29 0.25
20 18 0.16
21 2 0.02
22 1 0.01
23 2 0.02
25 14 0.12
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.30
Consensus pattern (19 bp):
AACTTACATAATACATAAC
Found at i:17198656 original size:9 final size:9
Alignment explanation
Indices: 17198624--17198923 Score: 224
Period size: 9 Copynumber: 34.8 Consensus size: 9
17198614 ATAACATAAC
17198624 AACTTACAT
1 AACTTACAT
17198633 AA--TACAT
1 AACTTACAT
* *
17198640 AGCATACAT
1 AACTTACAT
17198649 AACTTACAT
1 AACTTACAT
*
17198658 AA--TACAA
1 AACTTACAT
17198665 AACTTACAT
1 AACTTACAT
*
17198674 AACTTAAAAT
1 AACTT-ACAT
* *
17198684 ATCTTACAC
1 AACTTACAT
17198693 AACTTACAT
1 AACTTACAT
*
17198702 AACCTACAT
1 AACTTACAT
17198711 AA--TACATTT
1 AACTTACA--T
17198720 AACTTACAT
1 AACTTACAT
*
17198729 AAATTACAT
1 AACTTACAT
17198738 AACTTACAT
1 AACTTACAT
*
17198747 AATACATA-AT
1 -A-ACTTACAT
17198757 AACTTAC--
1 AACTTACAT
17198764 AACTTACAT
1 AACTTACAT
*
17198773 AACATACAT
1 AACTTACAT
* **
17198782 TACTTTGAT
1 AACTTACAT
17198791 AACTTACAT
1 AACTTACAT
17198800 AACTTACAT
1 AACTTACAT
*
17198809 AA-TT-CAC
1 AACTTACAT
17198816 AACTTACAT
1 AACTTACAT
* *
17198825 AGCTTACTT
1 AACTTACAT
17198834 AA--TACAT
1 AACTTACAT
17198841 AACTTACAT
1 AACTTACAT
*
17198850 AA--TACAC
1 AACTTACAT
17198857 AACTTACAT
1 AACTTACAT
* *
17198866 AGCTTACTT
1 AACTTACAT
17198875 AA--TACAT
1 AACTTACAT
17198882 AACTTACAT
1 AACTTACAT
17198891 AA--TACAT
1 AACTTACAT
*
17198898 ACACGTACAT
1 A-ACTTACAT
17198908 AACTTACAT
1 AACTTACAT
*
17198917 AATTTAC
1 AACTTAC
17198924 TTAATACATA
Statistics
Matches: 228, Mismatches: 38, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
7 51 0.22
8 9 0.04
9 144 0.63
10 16 0.07
11 8 0.04
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:17198662 original size:16 final size:16
Alignment explanation
Indices: 17198643--17198934 Score: 145
Period size: 16 Copynumber: 17.5 Consensus size: 16
17198633 AATACATAGC
17198643 ATACATAACTTACATA
1 ATACATAACTTACATA
*
17198659 ATACAAAACTTACATA
1 ATACATAACTTACATA
* * *
17198675 ACTTAAAATATCTTACACA
1 A--T-ACATAACTTACATA
*
17198694 ACTTACATAACCTACATA
1 A--TACATAACTTACATA
17198712 ATACATTTAACTTACATAA
1 ATACA--TAACTTACAT-A
17198731 ATTACATAACTTACATA
1 A-TACATAACTTACATA
*
17198748 ATACATAA-TAAC-T-
1 ATACATAACTTACATA
17198761 -TAC--AACTTACATAA
1 ATACATAACTTACAT-A
* **
17198775 CATACATTACTTTGATA
1 -ATACATAACTTACATA
17198792 ACTTACATAACTTACATA
1 A--TACATAACTTACATA
* *
17198810 ATTCACAACTTACATA
1 ATACATAACTTACATA
* *
17198826 GCTTACTTAA--TACATA
1 --ATACATAACTTACATA
*
17198842 ACTTACATAA--TACACA
1 A--TACATAACTTACATA
* *
17198858 ACTTACATAGCTTACTTA
1 A--TACATAACTTACATA
17198876 ATACATAACTTACATA
1 ATACATAACTTACATA
*
17198892 ATACATACACGTACATA
1 ATACATA-ACTTACATA
* *
17198909 ACTTACATAATTTACTTA
1 A--TACATAACTTACATA
17198927 ATACATAA
1 ATACATAA
17198935 ATATATATCA
Statistics
Matches: 214, Mismatches: 36, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 4 0.02
14 1 0.00
15 3 0.01
16 97 0.45
17 12 0.06
18 66 0.31
19 22 0.10
20 4 0.02
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:17198766 original size:71 final size:70
Alignment explanation
Indices: 17198612--17198810 Score: 191
Period size: 71 Copynumber: 2.8 Consensus size: 70
17198602 ATAACTTACG
* *
17198612 TAATAACATAACAACTTACATAA-TACATAGCATACA--TAACTTACAT-AA-TACAAAACTTAC
1 TAATAAC-TTACAACTTACATAACTACATA--ATACATTTAACTTACATAAATTACATAACTTAC
17198672 ATAACTTAA
63 ATAAC-TAA
*
17198681 -AATATCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAAATTACATAACTTAC
1 TAATAACTT--ACAACTTACATAA-CTACATAATACATTTAACTTACATAAATTACATAACTTAC
17198745 ATAA-TACA
63 ATAACTA-A
* *
17198753 TAATAACTTACAACTTACATAACATACAT--TACTTTGATAACTTACATAACTTACATAA
1 TAATAACTTACAACTTACATAAC-TACATAATACATT--TAACTTACATAAATTACATAA
17198811 TTCACAACTT
Statistics
Matches: 111, Mismatches: 6, Indels: 24
0.79 0.04 0.17
Matches are distributed among these distances:
67 1 0.01
68 5 0.05
69 23 0.21
70 1 0.01
71 56 0.50
72 3 0.03
73 22 0.20
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (70 bp):
TAATAACTTACAACTTACATAACTACATAATACATTTAACTTACATAAATTACATAACTTACATA
ACTAA
Found at i:17198774 original size:19 final size:19
Alignment explanation
Indices: 17198602--17198764 Score: 85
Period size: 18 Copynumber: 8.5 Consensus size: 19
17198592 ATAAACTGGC
*
17198602 ATAACTTACGTAATAACATA
1 ATAACTTACATAAT-ACATA
*
17198622 ACAACTTACATAATACATAGCATA
1 ATAACTTAC---ATA-ATA-CATA
17198646 CATAACTTACATAATAC--A
1 -ATAACTTACATAATACATA
17198664 A-AACTTACATAACTTA-A-A
1 ATAACTTACATAA--TACATA
* * *
17198682 ATATCTTACA-CA-ACTTA
1 ATAACTTACATAATACATA
*
17198699 CATAACCTACATAATACAT-
1 -ATAACTTACATAATACATA
* *
17198718 TTAACTTACATAA-A-TTA
1 ATAACTTACATAATACATA
17198735 CATAACTTACATAATACATA
1 -ATAACTTACATAATACATA
17198755 ATAACTTACA
1 ATAACTTACA
17198765 ACTTACATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 39
0.67 0.09 0.24
Matches are distributed among these distances:
15 1 0.01
16 12 0.11
17 3 0.03
18 37 0.34
19 19 0.17
20 14 0.13
21 3 0.03
22 3 0.03
23 3 0.03
24 6 0.06
25 8 0.07
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.30
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:17198844 original size:25 final size:25
Alignment explanation
Indices: 17198624--17198851 Score: 170
Period size: 25 Copynumber: 9.1 Consensus size: 25
17198614 ATAACATAAC
* *
17198624 AACTTACATAATACATAGCATACAT
1 AACTTACATAATACATAACTTACAT
*
17198649 AACTTACATAATACAAAACTTACAT
1 AACTTACATAATACATAACTTACAT
*
17198674 AACTTA-A-AAT--AT--CTTACAC
1 AACTTACATAATACATAACTTACAT
17198693 AACTTACATAACCTACATAA--TACATTT
1 AACTTACATAA--TACATAACTTACA--T
17198720 AACTTACATAAATTACATAACTTACAT
1 AACTTACAT-AA-TACATAACTTACAT
*
17198747 AA--TACATAATAACTTACAACTTACAT
1 AACTTACATAAT-AC--ATAACTTACAT
* * **
17198773 AACATACATTACTTTGATAACTTACAT
1 AACTTACA-TA-ATACATAACTTACAT
* *
17198800 AACTTACATAATTCACAACTTACAT
1 AACTTACATAATACATAACTTACAT
* *
17198825 AGCTTACTTAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
17198850 AA
1 AA
17198852 TACACAACTT
Statistics
Matches: 162, Mismatches: 21, Indels: 40
0.73 0.09 0.18
Matches are distributed among these distances:
19 12 0.07
20 1 0.01
21 3 0.02
23 5 0.03
24 5 0.03
25 73 0.45
26 14 0.09
27 36 0.22
28 6 0.04
29 6 0.04
30 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:17198864 original size:25 final size:25
Alignment explanation
Indices: 17198601--17198919 Score: 86
Period size: 25 Copynumber: 12.6 Consensus size: 25
17198591 TATAAACTGG
*
17198601 CATAACTTACGTAATAACATAACAACTTA
1 CATAACTTACATAAT-ACAT---AACTTA
17198630 CATAA--TACATAGCATACATAACTTA
1 CATAACTTACATA--ATACATAACTTA
*
17198655 CATAA--TACAAAACTTACATAACTTAA
1 CATAACTTACATAA--TACATAACTT-A
* * * *
17198681 AATATCTTACACAACTTACATAACCTA
1 CATAACTTACATAA--TACATAACTTA
17198708 CATAA--TACAT--T---TAACTTA
1 CATAACTTACATAATACATAACTTA
* *
17198726 CATAAATTACATAACTTACATAATACATA
1 CATAACTTACATAA--TACAT-A-ACTTA
* *
17198755 -ATAACTTACA-ACTTACATAACATA
1 CATAACTTACATA-ATACATAACTTA
* **
17198779 CATTACTTTGATAACTTACATAACTTA
1 CATAACTTACATAA--TACATAACTTA
* *
17198806 CATAA-TTCACA-ACTTACATAGCTTA
1 CATAACTT-ACATA-ATACATAACTTA
*
17198831 CTTAA--TACATAACTTACATAA--TA
1 CATAACTTACATAA--TACATAACTTA
* * *
17198854 CACAACTTACATAGCTTACTTAA--TA
1 CATAACTTACATA--ATACATAACTTA
*
17198879 CATAACTTACATAATACATACACGTA
1 CATAACTTACATAATACATA-ACTTA
17198905 CATAACTTACATAAT
1 CATAACTTACATAAT
17198920 TTACTTAATA
Statistics
Matches: 222, Mismatches: 33, Indels: 73
0.68 0.10 0.22
Matches are distributed among these distances:
18 11 0.05
20 5 0.02
21 1 0.00
23 14 0.06
24 9 0.04
25 84 0.38
26 30 0.14
27 26 0.12
28 31 0.14
29 11 0.05
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
CATAACTTACATAATACATAACTTA
Found at i:17199525 original size:44 final size:44
Alignment explanation
Indices: 17199462--17199550 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
17199452 AACCCGGAAC
17199462 AAGTGTACATCATAAAGAGCCGAATGGAGAAGCGGAAAAGTTCT
1 AAGTGTACATCATAAAGAGCCGAATGGAGAAGCGGAAAAGTTCT
17199506 AAGTGTACATCATAAAGAGCCGAATGGAGAAGCGGAAAAGTTCT
1 AAGTGTACATCATAAAGAGCCGAATGGAGAAGCGGAAAAGTTCT
17199550 A
1 A
17199551 CGCGCTACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.18
Consensus pattern (44 bp):
AAGTGTACATCATAAAGAGCCGAATGGAGAAGCGGAAAAGTTCT
Found at i:17204454 original size:21 final size:21
Alignment explanation
Indices: 17204437--17204478 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17204427 AGGGAAGCGA
17204437 AGGCTGCAGCGA-GAGAAGCAG
1 AGGCTGCAGC-ATGAGAAGCAG
17204458 AGGCTGCAGCATGAGAAGCAG
1 AGGCTGCAGCATGAGAAGCAG
17204479 CAAGAGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.33, C:0.19, G:0.40, T:0.07
Consensus pattern (21 bp):
AGGCTGCAGCATGAGAAGCAG
Found at i:17204958 original size:43 final size:41
Alignment explanation
Indices: 17204862--17205090 Score: 228
Period size: 43 Copynumber: 5.4 Consensus size: 41
17204852 AATTCCAAAA
* * *
17204862 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATTA-CTT
1 TTAGCGGCG-TTTTT-TGAAAGCGCCGCTAAAGAACATGATC-T
* **
17204905 TTCGCGGCGTTCGTGATGAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTT--TTTTGAAAGCGCCGCTAAAGAACATGATCT
* * * *
17204948 ATAGCAGCGTTTTTTTACCAAGCGTCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTGA--AAGCGCCGCTAAAGAACATGATCT
*
17204991 TTAGCGGCATTTTTTTGAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGC-GTTTTTTGAAAGCGCCGCTAAAGAACATGATCT
* *
17205033 TTAACGGCGTCTTTTTTCG-AAGCGCCGCTAAAGAACATGATAT
1 TTAGCGGCG--TTTTTT-GAAAGCGCCGCTAAAGAACATGATCT
17205076 TTAGCGGCGTTTTTT
1 TTAGCGGCGTTTTTT
17205091 CTGTAAACGC
Statistics
Matches: 155, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
41 9 0.06
42 32 0.21
43 104 0.67
44 10 0.06
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTGAAAGCGCCGCTAAAGAACATGATCT
Found at i:17205031 original size:85 final size:85
Alignment explanation
Indices: 17204881--17205090 Score: 262
Period size: 85 Copynumber: 2.5 Consensus size: 85
17204871 TTTTTTATAA
* * * * **
17204881 AAGCGCCGCTAAAGAACATTACT-TTTCGCGGCGTTCGTGATGAAAGCGCCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGA-TATTTAGCGGCATT-TTTTTGAAAGCGCCGCTAAAGAACATGA
*
17204945 TCTATAGCAGCGT-TTTTTTACC
64 TCTATAACAGCGTCTTTTTT-CC
* *
17204967 AAGCGTCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTGAAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATATTTAGCGGCATTTTTTTGAAAGCGCCGCTAAAGAACATGATC
* * *
17205032 TTTAACGGCGTCTTTTTTCG
66 TATAACAGCGTCTTTTTTCC
*
17205052 AAGCGCCGCTAAAGAACATGATATTTAGCGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATATTTAGCGGCATTTTTT
17205091 CTGTAAACGC
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
85 73 0.68
86 35 0.32
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATATTTAGCGGCATTTTTTTGAAAGCGCCGCTAAAGAACATGATC
TATAACAGCGTCTTTTTTCC
Found at i:17207225 original size:61 final size:61
Alignment explanation
Indices: 17207131--17207257 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 61
17207121 AATTTTTTAA
* * * * * * **
17207131 TTTTTAGAGTTAGGACTAAATTGGCAGATTTTGTAAATGTTGAGGGCCAAATTTATTGAAT
1 TTTTTAGAATTAGAACTAAAATGACAAAATTTGTAAACATTGAGGGCCAAATTTATTGAAT
* * * *
17207192 TTTTTAGAATTAGAACTAAAATGACAAAATTTGTAAACATTTAGGGCTAAATTTGTTGATT
1 TTTTTAGAATTAGAACTAAAATGACAAAATTTGTAAACATTGAGGGCCAAATTTATTGAAT
17207253 TTTTT
1 TTTTT
17207258 TATATTTAGG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGACAAAATTTGTAAACATTGAGGGCCAAATTTATTGAAT
Found at i:17211164 original size:9 final size:9
Alignment explanation
Indices: 17211150--17211252 Score: 102
Period size: 9 Copynumber: 11.4 Consensus size: 9
17211140 GTAGTGATTC
17211150 AATTCGGTT
1 AATTCGGTT
17211159 AATTCGGTT
1 AATTCGGTT
*
17211168 AATTCGGGT
1 AATTCGGTT
*
17211177 AATTCGGGT
1 AATTCGGTT
*
17211186 AATTAGGTT
1 AATTCGGTT
*
17211195 AATTCGGGT
1 AATTCGGTT
17211204 AATTCGAG-T
1 AATTCG-GTT
17211213 AATTCGGTT
1 AATTCGGTT
* *
17211222 AATCCAAG-T
1 AATTC-GGTT
*
17211231 AATTAGGTT
1 AATTCGGTT
*
17211240 AATTCAGTT
1 AATTCGGTT
17211249 AATT
1 AATT
17211253 TTTAACCAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
8 2 0.03
9 74 0.95
10 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:17211182 original size:27 final size:27
Alignment explanation
Indices: 17211150--17211252 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
17211140 GTAGTGATTC
17211150 AATTCGGTTAATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
* *
17211177 AATTCGGGTAATTAGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
* **
17211204 AATTCGAG-TAATTCGGTTAATCCAAGT
1 AATTCG-GTTAATTCGGTTAATTCGGGT
* *
17211231 AATTAGGTTAATTCAGTTAATT
1 AATTCGGTTAATTCGGTTAATT
17211253 TTTAACCAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.02
27 63 0.97
28 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTCGGGT
Found at i:17214227 original size:24 final size:24
Alignment explanation
Indices: 17214184--17214229 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17214174 TAATCATAGT
**
17214184 TAAATATATTATGTTAATAAATGC
1 TAAATATATTATACTAATAAATGC
*
17214208 TAAATATATTATACTCATAAAT
1 TAAATATATTATACTAATAAAT
17214230 AATAAATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATGC
Found at i:17214235 original size:24 final size:24
Alignment explanation
Indices: 17214184--17214236 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
17214174 TAATCATAGT
** **
17214184 TAAATATATTATGTTAATAAATGC
1 TAAATATATTATACTAATAAATAA
*
17214208 TAAATATATTATACTCATAAATAA
1 TAAATATATTATACTAATAAATAA
17214232 TAAAT
1 TAAAT
17214237 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATAA
Found at i:17221114 original size:21 final size:21
Alignment explanation
Indices: 17221090--17221129 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17221080 CACCTAAAGT
* *
17221090 GGTATTGCAATATCCACTTTA
1 GGTATCGCAATACCCACTTTA
17221111 GGTATCGCAATACCCACTT
1 GGTATCGCAATACCCACTT
17221130 GCCAAGGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (21 bp):
GGTATCGCAATACCCACTTTA
Found at i:17222632 original size:22 final size:22
Alignment explanation
Indices: 17222600--17222661 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
17222590 TGCATTATGA
17222600 TGCCTACTGATTTACACTACAG
1 TGCCTACTGATTTACACTACAG
* * * *
17222622 TGCGTACTGATTCACATTTCAG
1 TGCCTACTGATTTACACTACAG
* *
17222644 TGCCTACTGCTCTACACT
1 TGCCTACTGATTTACACT
17222662 TTGGTGCCTA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.34
Consensus pattern (22 bp):
TGCCTACTGATTTACACTACAG
Found at i:17222668 original size:22 final size:22
Alignment explanation
Indices: 17222643--17222695 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17222633 TCACATTTCA
* *
17222643 GTGCCTACTGCTCTACACTTTG
1 GTGCCTACTGATCAACACTTTG
*
17222665 GTGCCTATTGATCAACACTTTG
1 GTGCCTACTGATCAACACTTTG
*
17222687 GTGACTACT
1 GTGCCTACT
17222696 ATTTAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (22 bp):
GTGCCTACTGATCAACACTTTG
Found at i:17248441 original size:6 final size:6
Alignment explanation
Indices: 17248430--17248466 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
17248420 ACGACCTGAA
*
17248430 AAAAAT AAAAAT AAAAGT AAAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT
17248467 CGTATCTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:17248452 original size:13 final size:13
Alignment explanation
Indices: 17248430--17248465 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
17248420 ACGACCTGAA
17248430 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
*
17248442 AAAAGTAAAAAAT
1 AAAAATAAAAAAT
17248455 AAAAATAAAAA
1 AAAAATAAAAA
17248466 TCGTATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:17254578 original size:20 final size:19
Alignment explanation
Indices: 17254551--17254595 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
17254541 TTTAGAATGT
*
17254551 AAAAATTAAATTAAAAACA
1 AAAAATTAAAATAAAAACA
*
17254570 AAAATATTAAAATAAAAATA
1 AAAA-ATTAAAATAAAAACA
17254590 AAAAAT
1 AAAAAT
17254596 GGCTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATTAAAATAAAAACA
Found at i:17259881 original size:17 final size:17
Alignment explanation
Indices: 17259831--17259893 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
17259821 CTTATCTTTG
*
17259831 GCGAATAAGAATTGCCTA
1 GCGAAT-AGTATTGCCTA
** * *
17259849 GTAAATAGAATAGCCTA
1 GCGAATAGTATTGCCTA
* *
17259866 GCGGATAGTATTGCCTG
1 GCGAATAGTATTGCCTA
17259883 GCGAATAGTAT
1 GCGAATAGTAT
17259894 CACTCGACGG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 31 0.89
18 4 0.11
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (17 bp):
GCGAATAGTATTGCCTA
Found at i:17273523 original size:14 final size:15
Alignment explanation
Indices: 17273501--17273577 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
17273491 CAATCAAACA
17273501 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
17273515 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
17273530 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
17273550 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
17273564 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
17273578 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:17273542 original size:20 final size:20
Alignment explanation
Indices: 17273517--17273556 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17273507 AATATTTTCC
*
17273517 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
17273537 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
17273557 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:17273562 original size:34 final size:35
Alignment explanation
Indices: 17273505--17273571 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
17273495 CAAACACCAG
*
17273505 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
17273540 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17273572 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:17273578 original size:14 final size:14
Alignment explanation
Indices: 17273540--17273579 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
17273530 ACAGAAAAGT
*
17273540 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
17273554 AAATCATTTTACGG
1 AAAACATTTTACAG
17273568 AAAACATTTTAC
1 AAAACATTTTAC
17273580 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:17273707 original size:20 final size:20
Alignment explanation
Indices: 17273682--17273750 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
17273672 TTATATGGAA
17273682 TTGCACTTCGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
** * *
17273702 TTGCACTTTTGTGCCTTTAT
1 TTGCACTTCGGTGCCTCTGT
** * *
17273722 TCACACTTTGGTGTCTCTGT
1 TTGCACTTCGGTGCCTCTGT
*
17273742 TAGCACTTC
1 TTGCACTTC
17273751 TATGCCTCTA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.10, C:0.26, G:0.19, T:0.45
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:17276476 original size:16 final size:17
Alignment explanation
Indices: 17276455--17276489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17276445 AGATGTGTAA
*
17276455 GTAATGAA-TTAATCAT
1 GTAATGAACTTAAACAT
17276471 GTAATGAACTTAAACAT
1 GTAATGAACTTAAACAT
17276488 GT
1 GT
17276490 TAAGTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (17 bp):
GTAATGAACTTAAACAT
Found at i:17286289 original size:82 final size:82
Alignment explanation
Indices: 17285993--17286344 Score: 406
Period size: 81 Copynumber: 4.3 Consensus size: 82
17285983 TAAAAACTAA
** * * * *
17285993 AATTGAATAA-TCTGTTCGGGGATTTATTCTCGCTGTTCAATAGATTTTATTCGATTTTGATTTT
1 AATTGAATAATTCTGTTTTGGGATTTATTCCCACTGTTTAACAGATTTTATTCGATTTTGATTTT
* ** *
17286057 GTTTCAAAATGAGAAAT
66 GTTTCCAAACAAGAATT
* * ** *
17286074 AATTGAATAA-ACTGTTTTGGGATTTATTCCCACAGTTTAACAGATTTTATTTTAGTTTGATTTT
1 AATTGAATAATTCTGTTTTGGGATTTATTCCCACTGTTTAACAGATTTTATTCGATTTTGATTTT
*
17286138 GTTTCCAAACGAGAATT
66 GTTTCCAAACAAGAATT
* * * * *
17286155 AATTGAATAATT-TGTTTTGGAATTTATTACCAATGTTTAATAGATTTTATTCGATTGTGATTTT
1 AATTGAATAATTCTGTTTTGGGATTTATTCCCACTGTTTAACAGATTTTATTCGATTTTGATTTT
*
17286219 GTTTCCAAACAAGATTT
66 GTTTCCAAACAAGAATT
* * * *
17286236 AATTAAATAATTCTGTTTCGGGATTTATTCCCTCCGTTTAACAGATTTTATTCGATTTTGATTTT
1 AATTGAATAATTCTGTTTTGGGATTTATTCCCACTGTTTAACAGATTTTATTCGATTTTGATTTT
*
17286301 GTTTCCAAACAAGATTT
66 GTTTCCAAACAAGAATT
* *
17286318 AATT-ATACAATTCTATTTTGGGATTTA
1 AATTGA-ATAATTCTGTTTTGGGATTTA
17286345 ATCCTATCGG
Statistics
Matches: 230, Mismatches: 38, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
81 147 0.64
82 83 0.36
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (82 bp):
AATTGAATAATTCTGTTTTGGGATTTATTCCCACTGTTTAACAGATTTTATTCGATTTTGATTTT
GTTTCCAAACAAGAATT
Found at i:17286309 original size:163 final size:162
Alignment explanation
Indices: 17286026--17286321 Score: 430
Period size: 163 Copynumber: 1.8 Consensus size: 162
17286016 TTATTCTCGC
* ** *
17286026 TGTTCAATAGATTTTATTCGATTTTGATTTTGTTTCAAAATGAGAAATAATTGAATAAACTGTTT
1 TGTTCAATAGATTTTATTCGATTGTGATTTTGTTTCAAAACAAGAAATAATTAAATAAACTGTTT
* ** *
17286091 TGGGATTTATTCCCACAGTTTAACAGATTTTATTTTAGTTTGATTTTGTTTCCAAACGAGAATTA
66 CGGGATTTATTCCCACAGTTTAACAGATTTTATTCGAGTTTGATTTTGTTTCCAAACAAGAATTA
17286156 ATTGAATAATTTGTTTTGGAATTTATTACCAA
131 ATTGAATAATTTGTTTTGGAATTTATTACCAA
* * ** *
17286188 TGTTTAATAGATTTTATTCGATTGTGATTTTGTTTCCAAACAAGATTTAATTAAATAATTCTGTT
1 TGTTCAATAGATTTTATTCGATTGTGATTTTGTTTCAAAACAAGAAATAATTAAATAA-ACTGTT
* * * *
17286253 TCGGGATTTATTCCCTCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAACAAGATTT
65 TCGGGATTTATTCCCACAGTTTAACAGATTTTATTCGAGTTTGATTTTGTTTCCAAACAAGAATT
17286318 AATT
130 AATT
17286322 ATACAATTCT
Statistics
Matches: 116, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
162 50 0.43
163 66 0.57
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (162 bp):
TGTTCAATAGATTTTATTCGATTGTGATTTTGTTTCAAAACAAGAAATAATTAAATAAACTGTTT
CGGGATTTATTCCCACAGTTTAACAGATTTTATTCGAGTTTGATTTTGTTTCCAAACAAGAATTA
ATTGAATAATTTGTTTTGGAATTTATTACCAA
Found at i:17290404 original size:22 final size:22
Alignment explanation
Indices: 17290378--17290427 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
17290368 ATAAATATAA
17290378 ATATTT-TTTATATTAACTTATTT
1 ATATTTGTTTATA-TAA-TTATTT
17290401 -TATTTGTTTATATAATTATTT
1 ATATTTGTTTATATAATTATTT
17290422 ATATTT
1 ATATTT
17290428 ATATTTGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATATTTGTTTATATAATTATTT
Found at i:17304781 original size:16 final size:18
Alignment explanation
Indices: 17304749--17304781 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
17304739 GCAAAATATG
17304749 TGTGACTTTGTAATTGGT
1 TGTGACTTTGTAATTGGT
17304767 TGTGA-TTTG-AATTGG
1 TGTGACTTTGTAATTGG
17304782 AATTTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.18, C:0.03, G:0.30, T:0.48
Consensus pattern (18 bp):
TGTGACTTTGTAATTGGT
Found at i:17310501 original size:19 final size:18
Alignment explanation
Indices: 17310471--17310518 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
17310461 GATTTACATC
*
17310471 TCATTTCATCATTTCGTATT
1 TCATTTC-TCATCTCGTA-T
17310491 TCATTTCTCATCTCGTAT
1 TCATTTCTCATCTCGTAT
17310509 TCATTTCTCA
1 TCATTTCTCA
17310519 ACTTTTCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.41
19 9 0.33
20 7 0.26
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (18 bp):
TCATTTCTCATCTCGTAT
Found at i:17325764 original size:16 final size:16
Alignment explanation
Indices: 17325743--17325791 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
17325733 ATATTTAGTC
17325743 ATATAATAAATTATTA
1 ATATAATAAATTATTA
17325759 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
17325772 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
17325789 ATA
1 ATA
17325792 ATTGAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
13 11 0.44
16 10 0.40
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:17325768 original size:29 final size:30
Alignment explanation
Indices: 17325735--17325791 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
17325725 AATTATTTAT
17325735 ATTTAGTCA-TATAATAAATTA-TTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* *
17325764 ATTTATTATTTTAATAAATTATTTAATA
1 ATTTATCATTATAATAAATTATTTAATA
17325792 ATTGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.67
30 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:17328038 original size:20 final size:20
Alignment explanation
Indices: 17328013--17328058 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
17328003 TAGTAAAGCT
*
17328013 TAACAACCTATTTAAATAAG
1 TAACAACCTATTTAAATAAA
*
17328033 TAACAACCTATTTGAATAAA
1 TAACAACCTATTTAAATAAA
17328053 TAACAA
1 TAACAA
17328059 AATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (20 bp):
TAACAACCTATTTAAATAAA
Found at i:17328064 original size:20 final size:20
Alignment explanation
Indices: 17328021--17328064 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17328011 CTTAACAACC
* **
17328021 TATTTAAATAAGTAACAACC
1 TATTTAAATAAATAACAAAA
*
17328041 TATTTGAATAAATAACAAAA
1 TATTTAAATAAATAACAAAA
17328061 TATT
1 TATT
17328065 AATAGATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (20 bp):
TATTTAAATAAATAACAAAA
Found at i:17332491 original size:20 final size:20
Alignment explanation
Indices: 17332466--17332504 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17332456 TAGTAAAGCT
17332466 TAACAACCTATTTAAATAAG
1 TAACAACCTATTTAAATAAG
*
17332486 TAACAACCTATTTGAATAA
1 TAACAACCTATTTAAATAA
17332505 AAAACAAAAT
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:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (20 bp):
TAACAACCTATTTAAATAAG
Found at i:17332510 original size:20 final size:20
Alignment explanation
Indices: 17332467--17332511 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17332457 AGTAAAGCTT
**
17332467 AACAACCTATTTAAATAAGT
1 AACAACCTATTTAAATAAAA
*
17332487 AACAACCTATTTGAATAAAA
1 AACAACCTATTTAAATAAAA
17332507 AACAA
1 AACAA
17332512 AATGTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (20 bp):
AACAACCTATTTAAATAAAA
Found at i:17344010 original size:16 final size:15
Alignment explanation
Indices: 17343990--17344036 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
17343980 TATAATAATT
*
17343990 TTAAATTATATAAAA
1 TTAAAATATATAAAA
*
17344005 TATAAAATATATATAA
1 T-TAAAATATATAAAA
17344021 TTAAAAATATATAAAA
1 TT-AAAATATATAAAA
17344037 AGGCTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 25 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAATATATAAAA
Found at i:17348865 original size:28 final size:28
Alignment explanation
Indices: 17348834--17348893 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
17348824 TCAACGGACT
17348834 TTCCGTTAAAGGTAGTCCTAGGCAGAAC
1 TTCCGTTAAAGGTAGTCCTAGGCAGAAC
17348862 TTCCGTTAAAGGTAGTCCTAGGCAGAAC
1 TTCCGTTAAAGGTAGTCCTAGGCAGAAC
17348890 TTCC
1 TTCC
17348894 TCTTCTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (28 bp):
TTCCGTTAAAGGTAGTCCTAGGCAGAAC
Found at i:17368703 original size:21 final size:21
Alignment explanation
Indices: 17368679--17368721 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17368669 TCATTCACAA
*
17368679 CTTCAAC-ACGAACGTCTTCCT
1 CTTCAACAAC-AACGTCCTCCT
*
17368700 CTTCCACAACAACGTCCTCCT
1 CTTCAACAACAACGTCCTCCT
17368721 C
1 C
17368722 AACAGCAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.23, C:0.44, G:0.07, T:0.26
Consensus pattern (21 bp):
CTTCAACAACAACGTCCTCCT
Found at i:17370484 original size:5 final size:5
Alignment explanation
Indices: 17370460--17370521 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
17370450 TTATTCTGCA
* * * *
17370460 AAAAT AAAA- ATAAAT AAAAAT AAAAC AAACTT GAAAC AAAAT AAAAT
1 AAAAT AAAAT A-AAAT -AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT
17370507 AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT
17370522 TACATAATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
4 1 0.02
5 37 0.82
6 6 0.13
7 1 0.02
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Done.