Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 46 of 82
Found at i:16992214 original size:19 final size:19
Alignment explanation
Indices: 16992190--16992226 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16992180 TAACAAGAGA
16992190 AAGGAAAGGAAAA-GAAAAT
1 AAGGAAA-GAAAATGAAAAT
16992209 AAGGAAAGAAAATGAAAA
1 AAGGAAAGAAAATGAAAA
16992227 AAATTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (19 bp):
AAGGAAAGAAAATGAAAAT
Found at i:16995986 original size:35 final size:35
Alignment explanation
Indices: 16995929--16995996 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
16995919 GTAACATTTG
16995929 TCTTGAGGTAAGATGCAACATGCCTTTAAACCCGA
1 TCTTGAGGTAAGATGCAACATGCCTTTAAACCCGA
* * *
16995964 TCTTGAGGTGAGGTGCATCATGCCTTTAAACCC
1 TCTTGAGGTAAGATGCAACATGCCTTTAAACCC
16995997 TGTTGAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (35 bp):
TCTTGAGGTAAGATGCAACATGCCTTTAAACCCGA
Found at i:17004926 original size:15 final size:15
Alignment explanation
Indices: 17004869--17004934 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
17004859 TTTTTTTTAA
17004869 TATTTATAAAATTTTT
1 TATTTAT-AAATTTTT
* * *
17004885 AATGTATACATTAATTT
1 TATTTATAAATT--TTT
*
17004902 TAATTGATAAATTTTT
1 T-ATTTATAAATTTTT
*
17004918 TATTTATAAATTATT
1 TATTTATAAATTTTT
17004933 TA
1 TA
17004935 AAAATAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
15 18 0.47
16 9 0.24
17 3 0.08
18 8 0.21
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (15 bp):
TATTTATAAATTTTT
Found at i:17017350 original size:20 final size:20
Alignment explanation
Indices: 17017333--17017370 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17017323 CCTCAAATCT
17017333 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
17017353 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
17017371 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:17018140 original size:30 final size:30
Alignment explanation
Indices: 17018104--17018160 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
17018094 ATCAAGTTCA
17018104 TATATTTTTATTTTGAG-CTAAATAAACCCT
1 TATATTTTTATTTTGAGTC-AAATAAACCCT
17018134 TATATTTTTATTTTGAGTCAAATAAAC
1 TATATTTTTATTTTGAGTCAAATAAAC
17018161 ATTTATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (30 bp):
TATATTTTTATTTTGAGTCAAATAAACCCT
Found at i:17018167 original size:30 final size:30
Alignment explanation
Indices: 17018104--17018167 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
17018094 ATCAAGTTCA
*
17018104 TATATTTTTATTTTGAGCTAAATAAACCCT
1 TATATTTTTATTTTGAGCTAAATAAACACT
*
17018134 TATATTTTTATTTTGAG-TCAAATAAACATT
1 TATATTTTTATTTTGAGCT-AAATAAACACT
17018164 TATA
1 TATA
17018168 ACTAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (30 bp):
TATATTTTTATTTTGAGCTAAATAAACACT
Found at i:17022980 original size:20 final size:20
Alignment explanation
Indices: 17022957--17022995 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
17022947 ACCTCAAACC
17022957 ATACTCCAATAAGTCAAATT
1 ATACTCCAATAAGTCAAATT
17022977 ATACTCCAATAAGTCAAAT
1 ATACTCCAATAAGTCAAAT
17022996 GGGGTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (20 bp):
ATACTCCAATAAGTCAAATT
Found at i:17023945 original size:30 final size:29
Alignment explanation
Indices: 17023905--17023964 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
17023895 ATTATTAGTC
* *
17023905 ATAAAGACTTATTTGATTCAAAATAAAAAT
1 ATAAAAACTTATTTGACTC-AAATAAAAAT
*
17023935 ATAAAAACTTATTTGGCTCAAATAAAAAT
1 ATAAAAACTTATTTGACTCAAATAAAAAT
17023964 A
1 A
17023965 CAAGAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (29 bp):
ATAAAAACTTATTTGACTCAAATAAAAAT
Found at i:17025377 original size:27 final size:27
Alignment explanation
Indices: 17025346--17025397 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
17025336 CATAAGCCAA
17025346 TTTCATTATTCCAACCGTACCAAGCTT
1 TTTCATTATTCCAACCGTACCAAGCTT
* *
17025373 TTTCATTGTTCCAACTGTACCAAGC
1 TTTCATTATTCCAACCGTACCAAGC
17025398 AACCTAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.37
Consensus pattern (27 bp):
TTTCATTATTCCAACCGTACCAAGCTT
Found at i:17035174 original size:40 final size:41
Alignment explanation
Indices: 17035128--17035213 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 41
17035118 TTCTCATCTT
*
17035128 TTATCTCTCTCCAAGTCCATCA-TCTTCTCCTCTTCTGCCA
1 TTATCTCTCTCCAACTCCATCATTCTTCTCCTCTTCTGCCA
*
17035168 TTATCTCTCTCCAACTCCATCATTTTCTTCTCCTCTTCTTCCA
1 TTATCTCTCTCCAACTCCATCA--TTCTTCTCCTCTTCTGCCA
17035211 TTA
1 TTA
17035214 AAATTAAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 21 0.51
43 20 0.49
ACGTcount: A:0.15, C:0.38, G:0.02, T:0.44
Consensus pattern (41 bp):
TTATCTCTCTCCAACTCCATCATTCTTCTCCTCTTCTGCCA
Found at i:17036349 original size:17 final size:17
Alignment explanation
Indices: 17036327--17036381 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
17036317 TGGTAATGCT
17036327 TATGTATAAATTAAATA
1 TATGTATAAATTAAATA
*
17036344 TATGTATATA-TATAATA
1 TATGTATAAATTA-AATA
* *
17036361 TATTTATACAATTATATA
1 TATGTATA-AATTAAATA
17036379 TAT
1 TAT
17036382 ATTCATAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 2 0.06
17 20 0.65
18 7 0.23
19 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
TATGTATAAATTAAATA
Found at i:17037252 original size:30 final size:28
Alignment explanation
Indices: 17037200--17037259 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17037190 GTCTATGGGC
* *
17037200 AATTTTTCAGTTTTATGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGCAAAAATGT
*
17037228 AATTTTTCACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA--GGGGCAAAAATGT
17037258 AA
1 AA
17037260 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 14 0.52
30 13 0.48
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (28 bp):
AATTTTTCACTTTTAGGGGCAAAAATGT
Found at i:17039572 original size:2 final size:2
Alignment explanation
Indices: 17039565--17039599 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17039555 GGTCGTGACA
*
17039565 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17039600 AAAAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17041801 original size:13 final size:13
Alignment explanation
Indices: 17041783--17041807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17041773 TTCCAGAAAA
17041783 TTTATAAAATCAT
1 TTTATAAAATCAT
17041796 TTTATAAAATCA
1 TTTATAAAATCA
17041808 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:17043080 original size:19 final size:19
Alignment explanation
Indices: 17043056--17043092 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17043046 CTTCTAAACT
17043056 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
17043075 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
17043093 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:17052506 original size:32 final size:33
Alignment explanation
Indices: 17052441--17052507 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
17052431 GTAATAGAAA
*
17052441 ATCCATCAGCATTCCTACTCCATAATGATCCAT
1 ATCCATCAGCATTCCAACTCCATAATGATCCAT
* **
17052474 ATCCGTCAGCATTCCAACTTTAT-ATGATCCAT
1 ATCCATCAGCATTCCAACTCCATAATGATCCAT
17052506 AT
1 AT
17052508 TAGTCAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 11 0.37
33 19 0.63
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (33 bp):
ATCCATCAGCATTCCAACTCCATAATGATCCAT
Found at i:17056963 original size:10 final size:10
Alignment explanation
Indices: 17056935--17056973 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
17056925 CCTCACCAAA
17056935 CATCAAATAT
1 CATCAAATAT
*
17056945 CACCAAAATAT
1 CATC-AAATAT
*
17056956 CATGAAATAT
1 CATCAAATAT
17056966 CATCAAAT
1 CATCAAAT
17056974 TCAGCCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (10 bp):
CATCAAATAT
Found at i:17064405 original size:19 final size:18
Alignment explanation
Indices: 17064367--17064405 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17064357 GTACTCTATT
* *
17064367 TTTCAAAATCATTATTAA
1 TTTCAAAATAATTATAAA
17064385 TTTCAAAATAATTTATAAA
1 TTTCAAAATAA-TTATAAA
17064404 TT
1 TT
17064406 AATTTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTCAAAATAATTATAAA
Found at i:17071887 original size:12 final size:12
Alignment explanation
Indices: 17071870--17071902 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17071860 CAAACCAACC
17071870 TCATAAATTGCA
1 TCATAAATTGCA
*
17071882 TCATAAA-TACA
1 TCATAAATTGCA
17071893 TCATAAATTG
1 TCATAAATTG
17071903 TGGGACAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATAAATTGCA
Found at i:17080505 original size:27 final size:28
Alignment explanation
Indices: 17080442--17080512 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
17080432 TTAAAATTTT
* * * *
17080442 AATA-TAATTATTTTTATTTTATTCTTA
1 AATATTAATAATTTATATTTCATTCTAA
*
17080469 AATGTTAATAATTTATATTTCATT-TAA
1 AATATTAATAATTTATATTTCATTCTAA
17080496 AATATTAATAATTTATA
1 AATATTAATAATTTATA
17080513 ATTAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (28 bp):
AATATTAATAATTTATATTTCATTCTAA
Found at i:17080648 original size:21 final size:19
Alignment explanation
Indices: 17080609--17080657 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 19
17080599 ATAGTATGCA
17080609 TTAAAATTTAAATTTAATT
1 TTAAAATTTAAATTTAATT
17080628 TTAAAATTTAAGATATTAATT
1 TTAAAATTTAA-AT-TTAATT
17080649 TTATAAATT
1 TTA-AAATT
17080658 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.41
20 2 0.07
21 9 0.33
22 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAAATTTAAATTTAATT
Found at i:17085644 original size:81 final size:79
Alignment explanation
Indices: 17085507--17085724 Score: 222
Period size: 81 Copynumber: 2.7 Consensus size: 79
17085497 AGTAAGCCAT
* * * * * * ** *
17085507 ATGTGACACGACTGTGGCACGATAGGGTTTAGAGTTTGTGAAAAGGCATGTTGGGAATGTGCGAC
1 ATGTGACACGGCTGTGACACGACAGGGTTTAGAGTTTGTGACACGCCATGAAGGGAATATGCGAC
* *
17085572 ACGACATGGTGGGAA
66 ACGACAGGGTGAG-A
* * * *
17085587 TATGTGACATGGCTGTGACATGGCAGGGTTTAGAGTTTGTGACACGCCAT-AGAGGGAATATGTG
1 -ATGTGACACGGCTGTGACACGACAGGGTTTAGAGTTTGTGACACGCCATGA-AGGGAATATGCG
* *
17085651 ACATGATAGGGTGAGA
64 ACACGACAGGGTGAGA
* * *
17085667 ATGTGGCACGGTTGTGACACGACAGGGTTTAGAATTTGTGACACGCCATGAAGGGAAT
1 ATGTGACACGGCTGTGACACGACAGGGTTTAGAGTTTGTGACACGCCATGAAGGGAAT
17085725 CTATGATACG
Statistics
Matches: 112, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
79 50 0.45
80 2 0.02
81 60 0.54
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.25
Consensus pattern (79 bp):
ATGTGACACGGCTGTGACACGACAGGGTTTAGAGTTTGTGACACGCCATGAAGGGAATATGCGAC
ACGACAGGGTGAGA
Found at i:17085801 original size:47 final size:47
Alignment explanation
Indices: 17085689--17085803 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
17085679 TGTGACACGA
* * * *
17085689 CAGGGTTTAGAATTTGTGACACGCCATGAAGGGAATCTATGATACGG
1 CAGGGTTTAGAGTTTGTGACACGCCATGAAGGAAATATATGAGACGG
* * * * * *
17085736 CAAGATTTAAAGTTTGTGACACGCCATGGAGGAAATATGTGAGATGG
1 CAGGGTTTAGAGTTTGTGACACGCCATGAAGGAAATATATGAGACGG
*
17085783 CAGGGTTTAGAGTGTGTGACA
1 CAGGGTTTAGAGTTTGTGACA
17085804 TGGCATGACT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.30, C:0.12, G:0.31, T:0.26
Consensus pattern (47 bp):
CAGGGTTTAGAGTTTGTGACACGCCATGAAGGAAATATATGAGACGG
Found at i:17086493 original size:31 final size:31
Alignment explanation
Indices: 17086455--17086658 Score: 309
Period size: 31 Copynumber: 6.6 Consensus size: 31
17086445 ATGTTAGCGT
*
17086455 TGGCGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
17086486 TGGCGTGTAACAACAATTGACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* * *
17086517 TGGTGAGTAACAACATTTTACTTGATATGCG
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17086548 TGGCGTGTAACAACATTTTACTTGAAATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17086579 TGGCATGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
17086610 TGGCGTGTAACTACATTTTACTTGATATGCG
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
17086641 TGGCATGTAACAACATTT
1 TGGCGTGTAACAACATTT
17086659 ATTTCTTTCT
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 156 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTTACTTGATATGCA
Found at i:17092235 original size:163 final size:162
Alignment explanation
Indices: 17091965--17092289 Score: 641
Period size: 163 Copynumber: 2.0 Consensus size: 162
17091955 AAACAAATAT
17091965 GGAAAAGGAATTGAAAGACAACTATTGTGGAAATCAATGCTCAATAAGTAACATGACAAATGGAG
1 GGAAAAGGAATTGAAAGACAACTATTGTGGAAATCAATGCTCAATAAGTAACATGACAAATGGAG
17092030 ACAAGGAATCAAGTGAAGAAGTACCCTCAAATCGAATTGAATTATGCTTCATGGCTCTTGAAGAG
66 ACAAGGAATCAAGTGAAGAAGTACCCTCAAATCGAATTGAATTATGCTTCATGGCTCTTGAAGAG
17092095 TTAAAGGTAACTTCTTCATCATGTGAACTTAA
131 TTAAAGGTAACTTCTTCATCATGTGAACTTAA
17092127 NGGAAAAGGAATTGAAAGACAACTATTGTGGAAATCAATGCTCAATAAGTAACATGACAAATGGA
1 -GGAAAAGGAATTGAAAGACAACTATTGTGGAAATCAATGCTCAATAAGTAACATGACAAATGGA
17092192 GACAAGGAATCAAGTGAAGAAGTACCCTCAAATCGAATTGAATTATGCTTCATGGCTCTTGAAGA
65 GACAAGGAATCAAGTGAAGAAGTACCCTCAAATCGAATTGAATTATGCTTCATGGCTCTTGAAGA
17092257 GTTAAAGGTAACTTCTTCATCATGTGAACTTAA
130 GTTAAAGGTAACTTCTTCATCATGTGAACTTAA
17092290 TTCATGTGAA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (162 bp):
GGAAAAGGAATTGAAAGACAACTATTGTGGAAATCAATGCTCAATAAGTAACATGACAAATGGAG
ACAAGGAATCAAGTGAAGAAGTACCCTCAAATCGAATTGAATTATGCTTCATGGCTCTTGAAGAG
TTAAAGGTAACTTCTTCATCATGTGAACTTAA
Found at i:17092296 original size:15 final size:15
Alignment explanation
Indices: 17092276--17092312 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
17092266 AACTTCTTCA
17092276 TCATGTGAACTTAAT
1 TCATGTGAACTTAAT
17092291 TCATGTGAACTTAAT
1 TCATGTGAACTTAAT
17092306 TCATGTG
1 TCATGTG
17092313 CTTTTGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (15 bp):
TCATGTGAACTTAAT
Found at i:17100939 original size:31 final size:31
Alignment explanation
Indices: 17100904--17101287 Score: 394
Period size: 31 Copynumber: 12.4 Consensus size: 31
17100894 CTCCAACAAG
* *
17100904 TCAGCGTGTCATGCCATAAATCTGCAACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * * *
17100935 TCAGCATGTCATGCCATAAATCTACAAGCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * *
17100966 TCAGCGTGTGACGCCTTCAATCTGCTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * **
17100997 ACAGCGTGTCACGCCATATATCTGCTAGGAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
17101028 TCAGCGTGTCACGCCATAAATCTGCTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * * *
17101059 TCAGCATGTCACACCATAAATCTGCTACGAT
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* *
17101090 TCAGTGTGTCACGCCATAAATTTGCTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* **
17101121 TTAGCGTGTCACGTAATAAATCTGCTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
* * *
17101152 TCATCGTGTCATGCCATAAATATGCTACCAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
** *
17101183 TCATTGTAG-CATGCCATAAATCTGCTACCAC
1 TCAGCGT-GTCACGCCATAAATCTGCTACCAC
* * *
17101214 TCAACGTGTCATGCCATAAATCAGCTTA-CAC
1 TCAGCGTGTCACGCCATAAATCTGC-TACCAC
* * * * **
17101245 TCAGAGTGTGATGCCATAAATTTGCTAAGAC
1 TCAGCGTGTCACGCCATAAATCTGCTACCAC
17101276 TCAGCGTGTCAC
1 TCAGCGTGTCAC
17101288 CAAAAGGTGT
Statistics
Matches: 292, Mismatches: 57, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
30 3 0.01
31 286 0.98
32 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (31 bp):
TCAGCGTGTCACGCCATAAATCTGCTACCAC
Found at i:17102193 original size:24 final size:23
Alignment explanation
Indices: 17102134--17102212 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
17102124 CACCAGCAAT
* *
17102134 AGCTTCACTTGGTGCAGCAGCAGC
1 AGCTTCACTTGGTACAG-AGTAGC
* * *
17102158 AACTTTAGTTGGTACAGTAGTAGC
1 AGCTTCACTTGGTACAG-AGTAGC
*
17102182 AGCTTCACTTGGTTCACGAGTAGC
1 AGCTTCACTTGGTACA-GAGTAGC
*
17102206 ATCTTCA
1 AGCTTCA
17102213 GTCGATCCAC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
24 42 0.98
25 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (23 bp):
AGCTTCACTTGGTACAGAGTAGC
Found at i:17104685 original size:21 final size:21
Alignment explanation
Indices: 17104665--17104756 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
17104655 GGGTTGCCAG
17104665 CAACTTTAGATGAGCCACCAGA
1 CAACTTTAGATGAGCCACCA-A
* * *
17104687 -AGCTTTAAATTG-GCCTCCAA
1 CAACTTTAGA-TGAGCCACCAA
* * * *
17104707 CAAGTTCAGATGGGCCGCCAA
1 CAACTTTAGATGAGCCACCAA
17104728 CAACTTTAGATGAGCCACCAA
1 CAACTTTAGATGAGCCACCAA
*
17104749 CAGCTTTA
1 CAACTTTA
17104757 AATTGGAGTC
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
20 3 0.06
21 49 0.91
22 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (21 bp):
CAACTTTAGATGAGCCACCAA
Found at i:17104688 original size:63 final size:63
Alignment explanation
Indices: 17104615--17104762 Score: 244
Period size: 63 Copynumber: 2.3 Consensus size: 63
17104605 CTTCGAAAAG
* ** *
17104615 GCCACCAGAAGCTTTAAATTGGCCTTCAACAAGTTCAGATGGGTTGCCAGCAACTTTAGATGA
1 GCCACCAGAAGCTTTAAATTGGCCTCCAACAAGTTCAGATGGGCCGCCAACAACTTTAGATGA
17104678 GCCACCAGAAGCTTTAAATTGGCCTCCAACAAGTTCAGATGGGCCGCCAACAACTTTAGATGA
1 GCCACCAGAAGCTTTAAATTGGCCTCCAACAAGTTCAGATGGGCCGCCAACAACTTTAGATGA
17104741 GCCACCA-ACAGCTTTAAATTGG
1 GCCACCAGA-AGCTTTAAATTGG
17104763 AGTCTAATAC
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 1 0.01
63 79 0.99
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (63 bp):
GCCACCAGAAGCTTTAAATTGGCCTCCAACAAGTTCAGATGGGCCGCCAACAACTTTAGATGA
Found at i:17104965 original size:21 final size:21
Alignment explanation
Indices: 17104939--17104982 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17104929 TATCAAAATA
17104939 ATCTTCATTTAAACCTTCTTC
1 ATCTTCATTTAAACCTTCTTC
*
17104960 ATCTTCATTTAAACGTTCTTC
1 ATCTTCATTTAAACCTTCTTC
17104981 AT
1 AT
17104983 GTCGATCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.25, G:0.02, T:0.48
Consensus pattern (21 bp):
ATCTTCATTTAAACCTTCTTC
Found at i:17109524 original size:21 final size:21
Alignment explanation
Indices: 17109500--17109552 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
17109490 CCTACATCAA
17109500 CACCTTCAACAGCTTCTGTTT
1 CACCTTCAACAGCTTCTGTTT
17109521 CACCTTCAACAGCTTCTGTTT
1 CACCTTCAACAGCTTCTGTTT
17109542 CACCTTCAACA
1 CACCTTCAACA
17109553 TTATTACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.36, G:0.08, T:0.34
Consensus pattern (21 bp):
CACCTTCAACAGCTTCTGTTT
Found at i:17110473 original size:22 final size:22
Alignment explanation
Indices: 17110422--17110701 Score: 102
Period size: 22 Copynumber: 12.2 Consensus size: 22
17110412 TCAGTCATGT
**
17110422 TGTTACACGCCATGTTTGAAATG
1 TGTTACACGCCATGTTT-AAAAA
*
17110445 TGTTACACACCATGTTTAAAAA
1 TGTTACACGCCATGTTTAAAAA
* *
17110467 TGTTACACGCCATATTCAAAAA
1 TGTTACACGCCATGTTTAAAAA
* * * *
17110489 TGTTACATG-CAAGTTCAACAGTA
1 TGTTACACGCCATGTTTAA-A-AA
* * *
17110512 TGCTATCTATATG-CATTGTTCAAAAA
1 TG---T-TACACGCCA-TGTTTAAAAA
* * *
17110538 TTGTTACACACCTTG-TCAAAAA
1 -TGTTACACGCCATGTTTAAAAA
* * *
17110560 TGTTACACG-CAAGTTCAAAATT
1 TGTTACACGCCATGTTTAAAA-A
* * * * *
17110582 TGTTATACTCCTTGTTCAAAAT
1 TGTTACACGCCATGTTTAAAAA
* * * *
17110604 TGTTTCATG-CAAGTTCAAAAA
1 TGTTACACGCCATGTTTAAAAA
* *
17110625 TGTTACACGCCATGTTCACAACA
1 TGTTACACGCCATGTTTA-AAAA
*
17110648 TGTTACACACCATGTTAAATAAAAA
1 TGTTACACGCCATGTT---TAAAAA
*
17110673 TGTTACACGCCATGTGCTAAAACA
1 TGTTACACGCCATGT-TTAAAA-A
17110697 TGTTA
1 TGTTA
17110702 TTTCAATATA
Statistics
Matches: 197, Mismatches: 41, Indels: 37
0.72 0.15 0.13
Matches are distributed among these distances:
20 2 0.01
21 37 0.19
22 58 0.29
23 56 0.28
24 8 0.04
25 17 0.09
26 3 0.02
27 10 0.05
28 6 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (22 bp):
TGTTACACGCCATGTTTAAAAA
Found at i:17110595 original size:43 final size:44
Alignment explanation
Indices: 17110529--17110655 Score: 150
Period size: 43 Copynumber: 2.9 Consensus size: 44
17110519 TATATGCATT
17110529 GTTCAAAAATTGTTACACACCTTG-TCAAAAATGTTACACGCAA
1 GTTCAAAAATTGTTACACACCTTGTTCAAAAATGTTACACGCAA
* * * * * *
17110572 GTTCAAAATTTGTTATACTCCTTGTTCAAAATTGTTTCATGCAA
1 GTTCAAAAATTGTTACACACCTTGTTCAAAAATGTTACACGCAA
* * *
17110616 GTTCAAAAA-TGTTACACGCCATGTTCACAACATGTTACAC
1 GTTCAAAAATTGTTACACACCTTGTTCA-AAAATGTTACAC
17110656 ACCATGTTAA
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 36 0.53
44 32 0.47
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (44 bp):
GTTCAAAAATTGTTACACACCTTGTTCAAAAATGTTACACGCAA
Found at i:17110656 original size:12 final size:12
Alignment explanation
Indices: 17110624--17110664 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
17110614 AAGTTCAAAA
*
17110624 ATGTTACACGCC
1 ATGTTACACACC
*
17110636 ATGTT-CACAAC
1 ATGTTACACACC
17110647 ATGTTACACACC
1 ATGTTACACACC
17110659 ATGTTA
1 ATGTTA
17110665 AATAAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (12 bp):
ATGTTACACACC
Found at i:17110675 original size:25 final size:23
Alignment explanation
Indices: 17110620--17110687 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
17110610 ATGCAAGTTC
*
17110620 AAAAATGTTACACGCCATGTTCA
1 AAAAATGTTACACGCCATGTTAA
* * *
17110643 CAACATGTTACACACCATGTTAAA
1 AAAAATGTTACACGCCATGTT-AA
17110667 TAAAAATGTTACACGCCATGT
1 -AAAAATGTTACACGCCATGT
17110688 GCTAAAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 18 0.50
24 1 0.03
25 17 0.47
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (23 bp):
AAAAATGTTACACGCCATGTTAA
Found at i:17125003 original size:21 final size:22
Alignment explanation
Indices: 17124978--17125018 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17124968 CCTAGGTGGA
*
17124978 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
17124999 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
17125019 AAAAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:17125019 original size:20 final size:21
Alignment explanation
Indices: 17124978--17125022 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
17124968 CCTAGGTGGA
*
17124978 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
17124999 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
17125019 AAAA
1 AAAA
17125023 AAAGTTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:17125023 original size:21 final size:20
Alignment explanation
Indices: 17124976--17125023 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
17124966 ACCCTAGGTG
*
17124976 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
17124996 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
17125018 GAAAAA
1 GAAAAA
17125024 AAGTTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:17137891 original size:21 final size:21
Alignment explanation
Indices: 17137867--17137921 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
17137857 ATTTTGCCAT
* *
17137867 TCTTTGTCATGTAGGCATTAG
1 TCTTTGTCATGAAGGCATCAG
17137888 TCTTTGTCATGAAGGCATCAG
1 TCTTTGTCATGAAGGCATCAG
*
17137909 TTTTTGTCATGAA
1 TCTTTGTCATGAA
17137922 TTACATGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (21 bp):
TCTTTGTCATGAAGGCATCAG
Found at i:17140177 original size:25 final size:25
Alignment explanation
Indices: 17140143--17140198 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
17140133 AAAGAAGAAA
*
17140143 AAGCTCCTCACAGGAGCTTTTCTTG
1 AAGCTCCTCACAGGAGCTTTTCCTG
17140168 AAGCTCCTCACAGGAGCTTTTCCTG
1 AAGCTCCTCACAGGAGCTTTTCCTG
17140193 AAGCTC
1 AAGCTC
17140199 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (25 bp):
AAGCTCCTCACAGGAGCTTTTCCTG
Found at i:17142470 original size:359 final size:354
Alignment explanation
Indices: 17141729--17142490 Score: 1005
Period size: 359 Copynumber: 2.1 Consensus size: 354
17141719 ATAAATAATA
* * *
17141729 TTACATTCTACTAAATTTACTAATAGATTTGGAATTGATTAGTTACTAATACATAAGTCTTCATA
1 TTACATT-TACTAAATTTACTAATACATTTGGAATTGATTAATTACTAATACATAAGTCTACATA
* *
17141794 ATTAGGTAAAAAATGTAATTAATTTCCAAAACCACTTAATTAATGTAAATAAATAATATATTACA
65 ATTAAGTAAAAAATGTAATTAATTTCCAAAACCACTTAATTAATGTAAATAAATAAAATATTACA
*
17141859 TAATATTACAAATTTAAATAATTGCTCAATTACTTATAACACATTACATACCTTAATGAACTAAA
130 TAATATGACAAATTTAAATAATTGCTCAATTACTTATAACACATTACATACCTTAATGAACTAAA
* *
17141924 TTATTTAATTAACTAATTAAACACCTTAATTTATTTAAATATTTTTAAAATCAAATAATACTACT
195 TTATTTAATTAACTAACTAAACACCTTAATTTATTTAAATATTTTTAAAATCAAACAATACTACT
*
17141989 AACTTAGTTAATTGCTCAACTATTAAAACTTTTATTCATTTGATTAGTTAAATTATTTAATTATT
260 AACTTAGTTAATTGCTCAACTACTAAAACTTTTATTCATTTGATTAGTTAAATTATTTAATTATT
*
17142054 TTAATAAAACATTAAATAATTTAAATACTT
325 TTAATAAAACATTAAATAATTAAAATACTT
* * * * *
17142084 TTATATTTTACTAAATTTACCAATACATTTGGAATTGCTTAATTAGTAATACAT-GGTTCTACAT
1 TTACA-TTTACTAAATTTACTAATACATTTGGAATTGATTAATTACTAATACATAAG-TCTACAT
* ** * *
17142148 AGTTAAGTAAATTATGTAATTAATTTCCTAAATTAACC-CTTTAATTAATTTAAATAACTAAAAT
64 AATTAAGTAAAAAATGTAATTAATTTCC--AA--AACCAC-TTAATTAATGTAAATAAATAAAAT
* * * * *
17142212 ATTATATAATATGACTAATTTAATTAATTGCGT-AATTACTTATAACACATTGCATACCTTAATT
124 ATTACATAATATGACAAATTTAAATAATTGC-TCAATTACTTATAACACATTACATACCTTAATG
* * * *
17142276 AACTAAATTATTTAATTACCTCACTAAACACCTTAATTTATTTTAATATTATTTAAAATTAAACA
188 AACTAAATTATTTAATTAACTAACTAAACACCTTAATTTATTTAAATATT-TTTAAAATCAAACA
* * * * *
17142341 ATATTACTAATTTAGTTAATTGCTTAATTACTAAAA-TATTTTTTCATTTGATTAGTTAAATTAT
252 ATACTACTAACTTAGTTAATTGCTCAACTACTAAAACT-TTTATTCATTTGATTAGTTAAATTAT
* * *
17142405 TTAATTATTTTAATAAAACCTTAATTAATTAAAATAAGTT
316 TTAATTATTTTAATAAAACATTAAATAATTAAAAT-ACTT
* * *
17142445 CTT-CA-TTCCTCATTTTACTAATACATTTGGAATTGATTAATTACTA
1 -TTACATTTACTAAATTTACTAATACATTTGGAATTGATTAATTACTA
17142491 TCATTTGATT
Statistics
Matches: 351, Mismatches: 44, Indels: 20
0.85 0.11 0.05
Matches are distributed among these distances:
354 1 0.00
355 75 0.21
356 2 0.01
357 2 0.01
358 1 0.00
359 163 0.46
360 101 0.29
361 4 0.01
362 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (354 bp):
TTACATTTACTAAATTTACTAATACATTTGGAATTGATTAATTACTAATACATAAGTCTACATAA
TTAAGTAAAAAATGTAATTAATTTCCAAAACCACTTAATTAATGTAAATAAATAAAATATTACAT
AATATGACAAATTTAAATAATTGCTCAATTACTTATAACACATTACATACCTTAATGAACTAAAT
TATTTAATTAACTAACTAAACACCTTAATTTATTTAAATATTTTTAAAATCAAACAATACTACTA
ACTTAGTTAATTGCTCAACTACTAAAACTTTTATTCATTTGATTAGTTAAATTATTTAATTATTT
TAATAAAACATTAAATAATTAAAATACTT
Found at i:17145050 original size:28 final size:27
Alignment explanation
Indices: 17145014--17145066 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
17145004 ATATCCTGGT
*
17145014 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
17145041 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
17145067 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:17145134 original size:20 final size:20
Alignment explanation
Indices: 17145111--17145156 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
17145101 CTTCTAAACC
17145111 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
17145131 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
17145151 TCAAAT
1 TCAAAT
17145157 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:17153087 original size:28 final size:27
Alignment explanation
Indices: 17153051--17153103 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
17153041 ATATCCTGGT
*
17153051 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
17153078 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
17153104 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:17153173 original size:20 final size:20
Alignment explanation
Indices: 17153148--17153193 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
17153138 CTTATAAACC
17153148 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
17153168 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
17153188 TCAAAT
1 TCAAAT
17153194 GGGGCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:17154788 original size:19 final size:20
Alignment explanation
Indices: 17154744--17154789 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
17154734 AATTGTTTCA
17154744 AATTGATTACCATCATTTACT
1 AATTGATTACCAT-ATTTACT
17154765 AATTGATTACCAT-TTT-CTT
1 AATTGATTACCATATTTAC-T
17154784 AATTGA
1 AATTGA
17154790 AGCTATCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 10 0.42
21 13 0.54
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (20 bp):
AATTGATTACCATATTTACT
Found at i:17156694 original size:3 final size:3
Alignment explanation
Indices: 17156688--17156712 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17156678 TAACAACTTG
17156688 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
17156713 TAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17159280 original size:28 final size:30
Alignment explanation
Indices: 17159218--17159281 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
17159208 TAATTTTTTT
* * *
17159218 AAAATTACATTTTTGCCCCCGTAAAAGTCA
1 AAAATTACATTTTTGACCCCGAAAAACTCA
*
17159248 AAAATTACATTTTT-ACCCC-AAAAACTGA
1 AAAATTACATTTTTGACCCCGAAAAACTCA
17159276 AAAATT
1 AAAATT
17159282 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 12 0.40
29 4 0.13
30 14 0.47
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAATTACATTTTTGACCCCGAAAAACTCA
Found at i:17159471 original size:19 final size:19
Alignment explanation
Indices: 17159447--17159484 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17159437 CTGCCAAACC
*
17159447 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
17159466 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17159485 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17163586 original size:20 final size:20
Alignment explanation
Indices: 17163550--17163592 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
17163540 AATAATAACC
*
17163550 AAATTAACATGAATAACATA
1 AAATTAAAATGAATAACATA
*
17163570 AAATTAAAAT-AACTAACTTA
1 AAATTAAAATGAA-TAACATA
17163590 AAA
1 AAA
17163593 GTAACCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATTAAAATGAATAACATA
Found at i:17167186 original size:22 final size:20
Alignment explanation
Indices: 17167140--17167189 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
17167130 CTAGAGCCAC
* *
17167140 AATATATGAAAATGCTTTAT
1 AATATATGAAAATGATTCAT
17167160 AATATATGAAAATGATTCAT
1 AATATATGAAAATGATTCAT
17167180 AATATATGAA
1 AATATATGAA
17167190 GAATTGACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (20 bp):
AATATATGAAAATGATTCAT
Found at i:17168843 original size:2 final size:2
Alignment explanation
Indices: 17168836--17168870 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
17168826 GAATATAATC
* *
17168836 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17168871 ATTTCATGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:17170137 original size:11 final size:11
Alignment explanation
Indices: 17170121--17170145 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17170111 GTAACAGAAA
17170121 TAAATGATAAT
1 TAAATGATAAT
17170132 TAAATGATAAT
1 TAAATGATAAT
17170143 TAA
1 TAA
17170146 TTTTCGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TAAATGATAAT
Found at i:17178934 original size:36 final size:36
Alignment explanation
Indices: 17178893--17178977 Score: 152
Period size: 36 Copynumber: 2.4 Consensus size: 36
17178883 ACACTGTGAC
*
17178893 ACTCGAGGATGACATTATGACGAAAGACACGACGCT
1 ACTCGAGGATGACATTATGACAAAAGACACGACGCT
*
17178929 GCTCGAGGATGACATTATGACAAAAGACACGACGCT
1 ACTCGAGGATGACATTATGACAAAAGACACGACGCT
17178965 ACTCGAGGATGAC
1 ACTCGAGGATGAC
17178978 TATGCGTCTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.16
Consensus pattern (36 bp):
ACTCGAGGATGACATTATGACAAAAGACACGACGCT
Found at i:17190261 original size:24 final size:24
Alignment explanation
Indices: 17190234--17190304 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 24
17190224 TCTTACGGGC
17190234 AATCAATGTTCAAAACGTCCAAGT
1 AATCAATGTTCAAAACGTCCAAGT
* * * * *
17190258 AATC-CTTTTCAAATCCTCCGAGT
1 AATCAATGTTCAAAACGTCCAAGT
* * *
17190281 AAGCAATGTTCAAAATGTCTAAGT
1 AATCAATGTTCAAAACGTCCAAGT
17190305 TATCCTTTCC
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (24 bp):
AATCAATGTTCAAAACGTCCAAGT
Found at i:17190270 original size:47 final size:47
Alignment explanation
Indices: 17190216--17190321 Score: 131
Period size: 47 Copynumber: 2.3 Consensus size: 47
17190206 CAGGATACAT
* * *
17190216 TTTTCAAATCTTACGGGCAATCAATGTTCAAAACGTCCAAGTAATCC
1 TTTTCAAATCCTACGAGCAAGCAATGTTCAAAACGTCCAAGTAATCC
* * * * *
17190263 TTTTCAAATCCTCCGAGTAAGCAATGTTCAAAATGTCTAAGTTATCC
1 TTTTCAAATCCTACGAGCAAGCAATGTTCAAAACGTCCAAGTAATCC
*
17190310 TTTCCAAATCCT
1 TTTTCAAATCCT
17190322 CCGAAAATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (47 bp):
TTTTCAAATCCTACGAGCAAGCAATGTTCAAAACGTCCAAGTAATCC
Found at i:17190378 original size:43 final size:44
Alignment explanation
Indices: 17190309--17190430 Score: 126
Period size: 43 Copynumber: 2.8 Consensus size: 44
17190299 CTAAGTTATC
* *
17190309 CTTTCCAAATCCTCCGA-AAATTCTTTTCAAAACCTTC-GAGCACA
1 CTTTCC-AATGCTCCGATAAA-CCTTTTCAAAACCTTCTGAGCACA
17190353 CTTTCCAATGCTCCGATAAACCTTTTCAAAACC-TCTGAGCACA
1 CTTTCCAATGCTCCGATAAACCTTTTCAAAACCTTCTGAGCACA
* * * * *
17190396 C-TTCTATTGCTCCAAGTAATCCTTTTCAAACCCTT
1 CTTTCCAATGCTCCGA-TAAACCTTTTCAAAACCTT
17190431 TAGGTAATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
42 13 0.19
43 44 0.66
44 10 0.15
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (44 bp):
CTTTCCAATGCTCCGATAAACCTTTTCAAAACCTTCTGAGCACA
Found at i:17190460 original size:23 final size:23
Alignment explanation
Indices: 17190408--17190609 Score: 116
Period size: 23 Copynumber: 8.9 Consensus size: 23
17190398 TCTATTGCTC
* *
17190408 CAAGTAATCCTTTTCAAACCCTT
1 CAAGTAATCATTTTCAAATCCTT
* * *
17190431 TAGGTAATCATCTTCAAATCCTT
1 CAAGTAATCATTTTCAAATCCTT
*
17190454 CAAGTAA-CA-ATTCAAATCCTT
1 CAAGTAATCATTTTCAAATCCTT
** * *
17190475 CGGGT-A-CAATCTTCAAAACC-T
1 CAAGTAATC-ATTTTCAAATCCTT
*
17190496 CTAAGTAAGCAATTTTCAAATCCTCT
1 C-AAGTAATC-ATTTTCAAATCCT-T
* ** * *
17190522 GAA-TAGCCATTTCCAAAACC-T
1 CAAGTAATCATTTTCAAATCCTT
*
17190543 CTAGGTAATCATTTTCAAATCCTT
1 C-AAGTAATCATTTTCAAATCCTT
*
17190567 CAAGTAGA-CATTTTCAAAACC-T
1 CAAGTA-ATCATTTTCAAATCCTT
17190589 CTAAGTAATCATTTTCAAATC
1 C-AAGTAATCATTTTCAAATC
17190610 TTCCACGTAC
Statistics
Matches: 136, Mismatches: 30, Indels: 26
0.71 0.16 0.14
Matches are distributed among these distances:
20 2 0.01
21 18 0.13
22 16 0.12
23 79 0.58
24 18 0.13
25 2 0.01
26 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (23 bp):
CAAGTAATCATTTTCAAATCCTT
Found at i:17190557 original size:46 final size:46
Alignment explanation
Indices: 17190488--17190609 Score: 174
Period size: 46 Copynumber: 2.6 Consensus size: 46
17190478 GTACAATCTT
* * *
17190488 CAAAACCTCTAAGTAAGCAATTTTCAAATCCTCTGAA-TAGCCATTTC
1 CAAAACCTCTAAGTAATC-ATTTTCAAATCCT-TCAAGTAGACATTTC
* *
17190535 CAAAACCTCTAGGTAATCATTTTCAAATCCTTCAAGTAGACATTTT
1 CAAAACCTCTAAGTAATCATTTTCAAATCCTTCAAGTAGACATTTC
17190581 CAAAACCTCTAAGTAATCATTTTCAAATC
1 CAAAACCTCTAAGTAATCATTTTCAAATC
17190610 TTCCACGTAC
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
45 3 0.04
46 49 0.72
47 16 0.24
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (46 bp):
CAAAACCTCTAAGTAATCATTTTCAAATCCTTCAAGTAGACATTTC
Found at i:17190809 original size:42 final size:43
Alignment explanation
Indices: 17190759--17190839 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
17190749 TGAGGAGTCT
*
17190759 TTATTCA-TTTCAAAGTTATATAACCTCATTCTAGATGAAGAG
1 TTATTCATTTTCAAAGTTATATAACCTCATTCCAGATGAAGAG
* *
17190801 TTATTCATTTTTAAAGTTATGTAACCTCATTCCAGATGA
1 TTATTCATTTTCAAAGTTATATAACCTCATTCCAGATGA
17190840 GAAGCTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 7 0.20
43 28 0.80
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (43 bp):
TTATTCATTTTCAAAGTTATATAACCTCATTCCAGATGAAGAG
Found at i:17194593 original size:21 final size:20
Alignment explanation
Indices: 17194567--17194610 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
17194557 TTAAATTAAG
17194567 TTATTTTAG-TTTAATTTTACT
1 TTATTTT-GTTTTAA-TTTACT
17194588 TTATTTTGTTTTAATTTACT
1 TTATTTTGTTTTAATTTACT
17194608 TTA
1 TTA
17194611 AGAAAAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTATTTTGTTTTAATTTACT
Found at i:17197106 original size:39 final size:40
Alignment explanation
Indices: 17197006--17197108 Score: 147
Period size: 39 Copynumber: 2.6 Consensus size: 40
17196996 GGTGCCAGTA
* * *
17197006 ATGTGCGGTGTGGGAGAGCACACG-TCGATGATATATGCC
1 ATGTGCGGTGTGGGAGAGCACATGATCAATGATATATACC
17197045 ATGTGCGGTGTGGGAGAGCACATGAT-AATGATATATACC
1 ATGTGCGGTGTGGGAGAGCACATGATCAATGATATATACC
* *
17197084 GTGTGCGGTGTGGGAGTGCACATGA
1 ATGTGCGGTGTGGGAGAGCACATGA
17197109 CGGTGATGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 57 0.98
40 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (40 bp):
ATGTGCGGTGTGGGAGAGCACATGATCAATGATATATACC
Found at i:17197131 original size:114 final size:113
Alignment explanation
Indices: 17196970--17197182 Score: 286
Period size: 114 Copynumber: 1.9 Consensus size: 113
17196960 ATAACCGTGT
* * *
17196970 GTGTGCGGTGTGGGAGTGCACATGACGGTGCCAGTAATGTGCGGTGTGGGAGAGCACACG-TCGA
1 GTGTGCGGTGTGGGAGTGCACATGACGGTGACAGTAAGGTGCAGTGTGGGAGAGCACACGAT-GA
*
17197034 TGATATATGCCATGTGCGGTGTGGGAGA-GCACATGATAATGATATATACC
65 TGATAT-TGCAATGTGCGGTGTGGGA-ATGCACATGATAATGATATATACC
** * * **
17197084 GTGTGCGGTGTGGGAGTGCACATGACGGTGATGGTGAGGTGCAGTGTGGGAGTGCACTTGATGAT
1 GTGTGCGGTGTGGGAGTGCACATGACGGTGACAGTAAGGTGCAGTGTGGGAGAGCACACGATGAT
*
17197149 GATATTGTAATGTGCGGTGTGGGAATGCACATGA
66 GATATTGCAATGTGCGGTGTGGGAATGCACATGA
17197183 GCCGGAGGAG
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
112 1 0.01
113 25 0.29
114 59 0.69
115 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.25
Consensus pattern (113 bp):
GTGTGCGGTGTGGGAGTGCACATGACGGTGACAGTAAGGTGCAGTGTGGGAGAGCACACGATGAT
GATATTGCAATGTGCGGTGTGGGAATGCACATGATAATGATATATACC
Found at i:17206175 original size:2 final size:2
Alignment explanation
Indices: 17206168--17206208 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17206158 ATTTTGAATA
17206168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17206209 CTTACTTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17206289 original size:2 final size:2
Alignment explanation
Indices: 17206282--17206321 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
17206272 NTTTTGAATA
17206282 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
17206322 CTTTACCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17208063 original size:12 final size:12
Alignment explanation
Indices: 17208046--17208074 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
17208036 AAACCAACCC
17208046 CATAAAATACAT
1 CATAAAATACAT
17208058 CAT-AAATACAT
1 CATAAAATACAT
17208069 CATAAA
1 CATAAA
17208075 TTGTGGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (12 bp):
CATAAAATACAT
Found at i:17208066 original size:11 final size:11
Alignment explanation
Indices: 17208050--17208075 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17208040 CAACCCCATA
17208050 AAATACATCAT
1 AAATACATCAT
17208061 AAATACATCAT
1 AAATACATCAT
17208072 AAAT
1 AAAT
17208076 TGTGGGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATACATCAT
Found at i:17214097 original size:27 final size:26
Alignment explanation
Indices: 17214037--17214088 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
17214027 TATTTTATTC
* *
17214037 TTAAATGTTAATAATTTATATTTCAT
1 TTAAATATTAATAATTTATAATTCAT
17214063 TTAAAATATTAATAATTTATAATTCA
1 TT-AAATATTAATAATTTATAATTCA
17214089 GTATTAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
TTAAATATTAATAATTTATAATTCAT
Found at i:17215224 original size:34 final size:34
Alignment explanation
Indices: 17215198--17215358 Score: 91
Period size: 34 Copynumber: 4.9 Consensus size: 34
17215188 GTTACATGCT
* * *
17215198 AAGGTCAAAACCTCAGCACTAGATGTTATACGTC
1 AAGGCCAAAACCTCAGCACCAGATGTTACACGTC
* * *
17215232 AAGGCCAAAGCTTCAGCACCAGATGTTACACGCC
1 AAGGCCAAAACCTCAGCACCAGATGTTACACGTC
* * * *
17215266 AAAG-CTAAA-GT-AG-A--AGATGTTACACATC
1 AAGGCCAAAACCTCAGCACCAGATGTTACACGTC
* * ** * * *
17215294 AAGGTCAAAATCTTTGATACTAGATGTTACATGTC
1 AAGGCCAAAACCTCAG-CACCAGATGTTACACGTC
* * *
17215329 AAGGCCAAAGCTTCAGCATCAGATGTTACA
1 AAGGCCAAAACCTCAGCACCAGATGTTACA
17215359 GGCCAAAGCT
Statistics
Matches: 93, Mismatches: 27, Indels: 14
0.69 0.20 0.10
Matches are distributed among these distances:
28 15 0.16
29 4 0.04
30 2 0.02
31 3 0.03
32 1 0.01
33 4 0.04
34 42 0.45
35 22 0.24
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (34 bp):
AAGGCCAAAACCTCAGCACCAGATGTTACACGTC
Found at i:17216161 original size:16 final size:16
Alignment explanation
Indices: 17216136--17216172 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
17216126 CCCAAGTGTG
*
17216136 GAATAGCCTTTCTTCA
1 GAATAACCTTTCTTCA
*
17216152 TAATAACCTTTCTTCA
1 GAATAACCTTTCTTCA
17216168 GAATA
1 GAATA
17216173 TCCATTCCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (16 bp):
GAATAACCTTTCTTCA
Found at i:17226278 original size:29 final size:29
Alignment explanation
Indices: 17226217--17226280 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
17226207 GCAAATTTTT
** *
17226217 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
*
17226246 AAAAATTACATTTTTA-CCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
17226274 AAAAATT
1 AAAAATT
17226281 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:17241493 original size:2 final size:2
Alignment explanation
Indices: 17241482--17241529 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
17241472 TTTTAGTATT
*
17241482 TA TA TA -A TA TA TA TA TA TT TA T- TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17241521 TA T- TA TA TA
1 TA TA TA TA TA
17241530 ATGAGAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17241498 original size:11 final size:11
Alignment explanation
Indices: 17241482--17241529 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
17241472 TTTTAGTATT
17241482 TATATAATATA
1 TATATAATATA
*
17241493 TATATATTTATTA
1 TATATA-ATA-TA
17241506 TATATAATATA
1 TATATAATATA
*
17241517 TATATATTATA
1 TATATAATATA
17241528 TA
1 TA
17241530 ATGAGAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 20 0.62
12 4 0.12
13 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATAATATA
Found at i:17241511 original size:26 final size:24
Alignment explanation
Indices: 17241478--17241524 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17241468 AGAATTTTAG
17241478 TATT-TATATAATATATATATATT
1 TATTATATATAATATATATATATT
17241501 TATTATATATAATATATATATATT
1 TATTATATATAATATATATATATT
17241525 ATATAATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTATATATAATATATATATATT
Found at i:17252184 original size:5 final size:5
Alignment explanation
Indices: 17252176--17252235 Score: 68
Period size: 5 Copynumber: 11.4 Consensus size: 5
17252166 TTTAACCCAC
*
17252176 AATAA AATAA AATAA AAT-A AACAA AATAAA AATAA AATAACA AATAA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA AAT-A-A AATAA
17252223 AATGAA AATAA AA
1 AAT-AA AATAA AA
17252236 GCATATATGG
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
4 3 0.06
5 29 0.60
6 12 0.25
7 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:17252203 original size:19 final size:19
Alignment explanation
Indices: 17252179--17252234 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
17252169 AACCCACAAT
17252179 AAAATAAAATAAAATAAAC
1 AAAATAAAATAAAATAAAC
17252198 AAAATAAAAATAAAAT-AAC
1 AAAAT-AAAATAAAATAAAC
17252217 -AAATAAAATGAAAATAAA
1 AAAATAAAAT-AAAATAAA
17252235 AGCATATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.15
18 9 0.26
19 10 0.29
20 10 0.29
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAATAAAATAAAATAAAC
Found at i:17252222 original size:18 final size:18
Alignment explanation
Indices: 17252179--17252233 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
17252169 AACCCACAAT
17252179 AAAATAAAATAAAATAAAC
1 AAAATAAAATAAAAT-AAC
17252198 AAAATAAAAATAAAATAAC
1 AAAAT-AAAATAAAATAAC
17252217 -AAATAAAATGAAAATAA
1 AAAATAAAAT-AAAATAA
17252234 AAGCATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 8 0.24
20 10 0.29
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAAATAAC
Found at i:17260319 original size:86 final size:84
Alignment explanation
Indices: 17260191--17260497 Score: 368
Period size: 86 Copynumber: 3.6 Consensus size: 84
17260181 GTGAAAGCAA
* * *
17260191 ACTTATGGCGTGACACGATGACTTGTTGCACTCTTGTGGGGTGACACGGCACGGCCCAATTGTGC
1 ACTT-TGGCGTGACACGCTGACTTGTTGCAATCTTATGGGGTGACACGGCACGGCCCAATTGTG-
17260256 TGACACCCTGAGTGCATGGAG
64 TGACACCCTGAGTGCATGGAG
* * *
17260277 ACTTCTGGCATGACACGCTGACTTGTTGCAGTCTTATGGGGTGACACGGCACAGCCCAATTGTTG
1 ACTT-TGGCGTGACACGCTGACTTGTTGCAATCTTATGGGGTGACACGGCACGGCCCAATTG-TG
* *
17260342 TGACACGCTAAGTGCATGGAG
64 TGACACCCTGAGTGCATGGAG
* * *
17260363 ACTTTTGACGTGACACACTGACTTGTTGCAATCTTGTGGGGTGACACGGCACGGCCCAATTGTGG
1 AC-TTTGGCGTGACACGCTGACTTGTTGCAATCTTATGGGGTGACACGGCACGGCCCAATTGT-G
* *
17260428 TCACACACC-GAGTGCATGCAG
64 TGACAC-CCTGAGTGCATGGAG
* ** * *
17260449 AC-TTGGTGTGACACGCCAAATTGTTACAATCTTAT-GGGTGACACGGCAC
1 ACTTTGGCGTGACACGCTGACTTGTTGCAATCTTATGGGGTGACACGGCAC
17260498 AAAATTAATA
Statistics
Matches: 191, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
83 14 0.07
84 25 0.13
85 1 0.01
86 146 0.76
87 5 0.03
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (84 bp):
ACTTTGGCGTGACACGCTGACTTGTTGCAATCTTATGGGGTGACACGGCACGGCCCAATTGTGTG
ACACCCTGAGTGCATGGAG
Found at i:17260401 original size:172 final size:169
Alignment explanation
Indices: 17260169--17260498 Score: 448
Period size: 172 Copynumber: 1.9 Consensus size: 169
17260159 AACTTATGGC
* *
17260169 GTGACACGCTAAGTGAAAGCAAACTTATGGCGTGACACGATGACTTGTTGCACTCTTGTGGGGTG
1 GTGACACGCTAAGTGAAAGCAAACTTATGACGTGACACGATGACTTGTTGCAATCTTGTGGGGTG
* * **
17260234 ACACGGCACGGCCCAATTGTGCTGACAC-CCTGAGTGCATGGAGACTTCTGGCATGACACGCTGA
66 ACACGGCACGGCCCAATTGTGCTCACACACC-GAGTGCATGCAGAC-T-TGGCATGACACGCCAA
* * *
17260298 CTTGTTGCAGTCTTATGGGGTGACACGGCACAGCCCAATTGTT
128 ATTGTTACAATCTTAT-GGGTGACACGGCACAGCCCAATTGTT
* * * * *
17260341 GTGACACGCTAAGTGCATGGAGACTTTTGACGTGACAC-ACTGACTTGTTGCAATCTTGTGGGGT
1 GTGACACGCTAAGTGAAAGCAAACTTATGACGTGACACGA-TGACTTGTTGCAATCTTGTGGGGT
* **
17260405 GACACGGCACGGCCCAATTGTGGTCACACACCGAGTGCATGCAGACTTGGTGTGACACGCCAAAT
65 GACACGGCACGGCCCAATTGTGCTCACACACCGAGTGCATGCAGACTTGGCATGACACGCCAAAT
17260470 TGTTACAATCTTATGGGTGACACGGCACA
130 TGTTACAATCTTATGGGTGACACGGCACA
17260499 AAATTAATAG
Statistics
Matches: 139, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
169 15 0.11
170 25 0.18
171 2 0.01
172 95 0.68
173 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (169 bp):
GTGACACGCTAAGTGAAAGCAAACTTATGACGTGACACGATGACTTGTTGCAATCTTGTGGGGTG
ACACGGCACGGCCCAATTGTGCTCACACACCGAGTGCATGCAGACTTGGCATGACACGCCAAATT
GTTACAATCTTATGGGTGACACGGCACAGCCCAATTGTT
Found at i:17262915 original size:20 final size:19
Alignment explanation
Indices: 17262877--17262915 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
17262867 AAAAAAACCT
*
17262877 AAGTGAAAATTCAAAGAAA
1 AAGTGAAAAATCAAAGAAA
*
17262896 AAGTGAAGAAATCAAGGAAA
1 AAGTGAA-AAATCAAAGAAA
17262916 CAAGCTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.62, C:0.05, G:0.21, T:0.13
Consensus pattern (19 bp):
AAGTGAAAAATCAAAGAAA
Found at i:17264145 original size:64 final size:63
Alignment explanation
Indices: 17263935--17264137 Score: 316
Period size: 63 Copynumber: 3.2 Consensus size: 63
17263925 AATTGATACA
* *
17263935 ACCGTGCATGTGCCGAGTGGGAAGTGCAATGCTAGTTGAATGACAAAGGATGTGATAATTACG
1 ACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTACG
*
17263998 ACCGGGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTACG
1 ACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTACG
* * * * * *
17264061 ATCGTGCATGTGCGGAGTGGGAAGTGCAAATGCCGGTTTAATGATAAAGGTTGTGATAATTACT
1 ACCGTGCATGTGCGGAGTGGGAAGTGC-AATGCCAGTTGAATGACAAAGGATGTGATAATTACG
17264125 ACCGTGCATGTGC
1 ACCGTGCATGTGC
17264138 AAAGTGGGGA
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 85 0.66
64 43 0.34
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.25
Consensus pattern (63 bp):
ACCGTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAAGGATGTGATAATTACG
Found at i:17270181 original size:55 final size:54
Alignment explanation
Indices: 17270110--17270378 Score: 304
Period size: 55 Copynumber: 4.9 Consensus size: 54
17270100 TCCGTACACC
* * **
17270110 AACAACCGTGACACGCTAAAAACCCAATAAACCAATTAACCCACAACATGCCAAG
1 AACAGCCGTGACACGCTAAAAACCCAA-AAACCAGTTAACCCACAACACACCAAG
* * *
17270165 AATAGCCGTGACACGCTAAAAACCCAAAAAATCAGTTAACCCACAACACGCCAAG
1 AACAGCCGTGACACGCTAAAAACCC-AAAAACCAGTTAACCCACAACACACCAAG
* * * * * * *
17270220 AACAGTCGTGACACGCCAAAAACTCAAAAATCCAATTAACCCGCAACACACTAGG
1 AACAGCCGTGACACGCTAAAAACCCAAAAA-CCAGTTAACCCACAACACACCAAG
* ** * * *
17270275 AACAGTCGTGACACGCTAAAAATCGAAAAAACTAGTTAACCCACAACACACTAGG
1 AACAGCCGTGACACGCTAAAAA-CCCAAAAACCAGTTAACCCACAACACACCAAG
*
17270330 AACAGCCGTGATACGCTAAAAACCCAAAAGACCAGTTAACCCACAACAC
1 AACAGCCGTGACACGCTAAAAACCCAAAA-ACCAGTTAACCCACAACAC
17270379 GCTATATGCA
Statistics
Matches: 184, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
54 10 0.05
55 166 0.90
56 8 0.04
ACGTcount: A:0.45, C:0.30, G:0.12, T:0.12
Consensus pattern (54 bp):
AACAGCCGTGACACGCTAAAAACCCAAAAACCAGTTAACCCACAACACACCAAG
Found at i:17270841 original size:23 final size:22
Alignment explanation
Indices: 17270809--17270866 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 22
17270799 CCCGCCTTCT
17270809 TTCACACCATGGCATGTCACACG
1 TTCA-ACCATGGCATGTCACACG
*
17270832 TTCAAGCCATGCCATGTCACACG
1 TTCAA-CCATGGCATGTCACACG
*
17270855 TTTAACCATGGC
1 TTCAACCATGGC
17270867 GTGTTCCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (22 bp):
TTCAACCATGGCATGTCACACG
Found at i:17270986 original size:104 final size:104
Alignment explanation
Indices: 17270860--17271211 Score: 406
Period size: 104 Copynumber: 3.4 Consensus size: 104
17270850 ACACGTTTAA
* * * * *
17270860 CCATGGCGTGTTC-CACACTCTAAACGCTGCCATGTCACACCCATCCCACATATTCTCACTGTGC
1 CCATGGCATG-TCACACACTCTAAACGCTGTCGTGTCACACCCGTCTCACATATTCTCACTGTGC
* *
17270924 CGTCTCACACATTTTCACCCTAG-CGTGTCATAAATTCCCT
65 CGTCTCACACATTATCACCCT-GTCGTGTCACAAATTCCCT
* *
17270964 CCATGGCATGTCACACACTCTAAAC-CTTGTCGTGTCACACCCGTGTCACATATTATCACTGTGC
1 CCATGGCATGTCACACACTCTAAACGC-TGTCGTGTCACACCCGTCTCACATATTCTCACTGTGC
* * * * * ***
17271028 CATTTCACACATTATGACCTTGTCGTGTCACAAGTTCTGA
65 CGTCTCACACATTATCACCCTGTCGTGTCACAAATTCCCT
* * *
17271068 CCATGGCATGTCACACACTCCAAACGCTGTCGTGTCACACCCGTCTCTCATATTCTCACCGTGCC
1 CCATGGCATGTCACACACTCTAAACGCTGTCGTGTCACACCCGTCTCACATATTCTCACTGTGCC
* * *
17271133 GTCTCACACATTATCACCCTGTAGTATCACAGATTCCCT
66 GTCTCACACATTATCACCCTGTCGTGTCACAAATTCCCT
* * *
17271172 CCATGACGTGTCACACACTTTAAAC-CATGTCGTGTCACAC
1 CCATGGCATGTCACACACTCTAAACGC-TGTCGTGTCACAC
17271212 ACTTTAAACC
Statistics
Matches: 206, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
103 5 0.02
104 200 0.97
105 1 0.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (104 bp):
CCATGGCATGTCACACACTCTAAACGCTGTCGTGTCACACCCGTCTCACATATTCTCACTGTGCC
GTCTCACACATTATCACCCTGTCGTGTCACAAATTCCCT
Found at i:17271200 original size:24 final size:24
Alignment explanation
Indices: 17271172--17271235 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
17271162 CAGATTCCCT
*
17271172 CCATGACGTGTCACACACTTTAAA
1 CCATGTCGTGTCACACACTTTAAA
17271196 CCATGTCGTGTCACACACTTTAAA
1 CCATGTCGTGTCACACACTTTAAA
17271220 CCATGTCGTGTCACAC
1 CCATGTCGTGTCACAC
17271236 CCGTGTCACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (24 bp):
CCATGTCGTGTCACACACTTTAAA
Found at i:17271240 original size:232 final size:232
Alignment explanation
Indices: 17270972--17271443 Score: 739
Period size: 232 Copynumber: 2.0 Consensus size: 232
17270962 CTCCATGGCA
* *
17270972 TGTCACACACTCTAAACCTTGTCGTGTCACACCCGTGTCACATATTATCACTGTGCCATTTCACA
1 TGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCATTTCACA
* * * * *
17271037 CATTATGACCTTGTCGTGTCACAAGTTCTGACCATGGCATGTCACACACTCCAAACGCTGTCGTG
66 CATTATGACATTGCCATGTCACAACTTCTGACCATGGCATGTCACACACTCCAAACGCTGTCATG
* * *
17271102 TCACACCCGTCTCTCATATTCTCACCGTGCCGTCTCACACATTATCACCCT-GTAGTATCACAGA
131 TCACACCCGTCTCACATATTCTCACCGTGCCATCTCACACATTATCACCCTACT-GTATCACAGA
*
17271166 TTCCCTCCATGACGTGTCACACACTTTAAACCATGTCG
195 TTCCCTCCATGACGTGTCACACACTCTAAACCATGTCG
* *
17271204 TGTCACACACTTTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCGTTTCACA
1 TGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCATTTCACA
* * *
17271269 CATTATGACATTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTAAACGTTGTCATG
66 CATTATGACATTGCCATGTCACAACTTCTGACCATGGCATGTCACACACTCCAAACGCTGTCATG
* * *
17271334 TCACACCCGTCTCACATATTCTCACTGTGTCATCTCACACATTATCACCCTACTGTGTCACAGAT
131 TCACACCCGTCTCACATATTCTCACCGTGCCATCTCACACATTATCACCCTACTGTATCACAGAT
* *
17271399 TCCCTCCATGGCGTGTCACACACTCTAAACCCTGTCG
196 TCCCTCCATGACGTGTCACACACTCTAAACCATGTCG
17271436 TGTCACAC
1 TGTCACAC
17271444 CCGTGTCACA
Statistics
Matches: 218, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
232 217 1.00
233 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (232 bp):
TGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCATTTCACA
CATTATGACATTGCCATGTCACAACTTCTGACCATGGCATGTCACACACTCCAAACGCTGTCATG
TCACACCCGTCTCACATATTCTCACCGTGCCATCTCACACATTATCACCCTACTGTATCACAGAT
TCCCTCCATGACGTGTCACACACTCTAAACCATGTCG
Found at i:17271262 original size:23 final size:23
Alignment explanation
Indices: 17271236--17271292 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
17271226 CGTGTCACAC
17271236 CCGTGTCACACATTATCAC-TGTG
1 CCGTGTCACACATTATCACAT-TG
* *
17271259 CCGTTTCACACATTATGACATTG
1 CCGTGTCACACATTATCACATTG
*
17271282 CCATGTCACAC
1 CCGTGTCACAC
17271293 CTTCTGACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.30
Consensus pattern (23 bp):
CCGTGTCACACATTATCACATTG
Found at i:17271300 original size:23 final size:23
Alignment explanation
Indices: 17271239--17271316 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
17271229 GTCACACCCG
* ** *
17271239 TGTCACACATTATCACTGTGCCG
1 TGTCACACATTATGACCATGCCA
*
17271262 TTTCACACATTATGA-CATTGCCA
1 TGTCACACATTATGACCA-TGCCA
* * *
17271285 TGTCACACCTTCTGACCATGGCA
1 TGTCACACATTATGACCATGCCA
17271308 TGTCACACA
1 TGTCACACA
17271317 CTCTAAACGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 41 0.95
24 2 0.05
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (23 bp):
TGTCACACATTATGACCATGCCA
Found at i:17271314 original size:208 final size:206
Alignment explanation
Indices: 17271131--17271661 Score: 510
Period size: 208 Copynumber: 2.6 Consensus size: 206
17271121 TCTCACCGTG
* * * *
17271131 CCGTCTCACACATTATCACCCTGT-AGTATCACAGATTCCCTCCATGAC-GTGTCACACACTTTA
1 CCGTCTCACACATTATCACCCTGTCA-TATCACACATTACCACCAT-ACTGTGTCACACA-TTCA
* *
17271194 AACCATGTCGTGTCACACACTTTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTG
63 AACCATGGCGTGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTG
*
17271259 CCGTTTCACACATTATGACATTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTAAA
128 CCGTTTCACACATTATGACACTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCT--A
** *
17271324 CGTTGTCATGTCACAC
191 CGTCATCATCTCACAC
* * ** * * * * ***
17271340 CCGTCTCACATATTCTCACTGTGTCATCTCACACATTATCACCCTACTGTGTCACAGATTCCCTC
1 CCGTCTCACACATTATCACCCTGTCATATCACACATTACCACCATACTGTGTCACACATTCAAAC
* *
17271405 CATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCTG
66 CATGGCGTGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCG
* * * **
17271470 TTTCACACATTATGACCCTGCCATGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAATGC
131 TTTCACACATTATGACACTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTACGT-C
*
17271535 -TGCCATGTCACAC
195 AT--CATCTCACAC
* * * * * * * * * ** * ***
17271548 TCGTCTCACATATTCTCACCATGCCGTCTCACACATTATCACCCTACCATGTCACAGATTCCCTC
1 CCGTCTCACACATTATCACCCTGTCATATCACACATTACCACCATACTGTGTCACACATTCAAAC
* * * * * * *
17271613 CAAGGCGTGTCACAAACTCTATACCCTATCGTGTCACACCTGTCTCACA
66 CATGGCGTGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACA
17271662 TAGTTTCACC
Statistics
Matches: 278, Mismatches: 39, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
206 3 0.01
208 232 0.83
209 42 0.15
210 1 0.00
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.28
Consensus pattern (206 bp):
CCGTCTCACACATTATCACCCTGTCATATCACACATTACCACCATACTGTGTCACACATTCAAAC
CATGGCGTGTCACACACTCTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCG
TTTCACACATTATGACACTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTACGTCA
TCATCTCACAC
Found at i:17271336 original size:104 final size:104
Alignment explanation
Indices: 17271195--17271661 Score: 493
Period size: 104 Copynumber: 4.5 Consensus size: 104
17271185 CACACTTTAA
* * * * *
17271195 ACCATGTCGTGTCACACACTTTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGC
1 ACCATGGCGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTATCACTGTGC
* ** *
17271260 CGTTTCACACATTATGACATTGCCATGTCACACCTTCTG
66 CGTCTCACACATTATGACCCTGCCATGTCACACATTCTG
* ** * * *
17271299 ACCATGGCATGTCACACACTCTAAACGTTGTCATGTCACACCCGTCTCACATATTCTCACTGTGT
1 ACCATGGCGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTATCACTGTGC
* * * ** * **
17271364 CATCTCACACATTATCACCCTACTGTGTCACAGATTCCC
66 CGTCTCACACATTATGACCCTGCCATGTCACACATTCTG
* * *
17271403 TCCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGC
1 ACCATGGCGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTATCACTGTGC
* * *
17271468 TGTTTCACACATTATGACCCTGCCATGTCACACGTTCTG
66 CGTCTCACACATTATGACCCTGCCATGTCACACATTCTG
** * * * * **
17271507 ACCATGGCGTGTCACACACTCTAAATGCTGCCATGTCACACTCGTCTCACATATTCTCACCATGC
1 ACCATGGCGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTATCACTGTGC
* * * **
17271572 CGTCTCACACATTATCACCCTACCATGTCACAGATTCCC
66 CGTCTCACACATTATGACCCTGCCATGTCACACATTCTG
* * * * * * *
17271611 TCCAAGGCGTGTCACAAACTCTATACCCTATCGTGTCACACCTGTCTCACA
1 ACCATGGCGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACA
17271662 TAGTTTCACC
Statistics
Matches: 291, Mismatches: 72, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
104 291 1.00
ACGTcount: A:0.24, C:0.34, G:0.13, T:0.28
Consensus pattern (104 bp):
ACCATGGCGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTATCACTGTGC
CGTCTCACACATTATGACCCTGCCATGTCACACATTCTG
Found at i:17271498 original size:23 final size:23
Alignment explanation
Indices: 17271472--17271524 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
17271462 CTGTGCTGTT
*
17271472 TCACACATTATGACCCTGCCATG
1 TCACACATTATGACCATGCCATG
* * * *
17271495 TCACACGTTCTGACCATGGCGTG
1 TCACACATTATGACCATGCCATG
17271518 TCACACA
1 TCACACA
17271525 CTCTAAATGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.25
Consensus pattern (23 bp):
TCACACATTATGACCATGCCATG
Found at i:17271658 original size:81 final size:80
Alignment explanation
Indices: 17271572--17271795 Score: 227
Period size: 81 Copynumber: 2.8 Consensus size: 80
17271562 CTCACCATGC
* * * * *
17271572 CGTCTCACACATTATCACCCTACCATGTCACAGATTCCCTCCAAGGCGTGTCACAAACTCTATAC
1 CGTCTCACATATT-TCACCATACCATGTCACACATTCCCACCAAGCCGTGTCACAAACTCTATAC
*
17271637 CCTATCGTGTCACAC-
65 CCTACCGTGTCACACT
* * * * *
17271652 CTGTCTCACATAGTTTCACCATGA-CGTATCACACATTGCCACCATGCCGTGTTACAAACTCTAT
1 C-GTCTCACATA-TTTCACCAT-ACCATGTCACACATTCCCACCAAGCCGTGTCACAAACTCTAT
17271716 ACCCTACCGTGTCACACT
63 ACCCTACCGTGTCACACT
* * * ** * *
17271734 CATCTCACATATTCTCACCATGCTATGTCACACATTCCCACCATTCCATTTCACAAACTCTA
1 CGTCTCACATATT-TCACCATACCATGTCACACATTCCCACCAAGCCGTGTCACAAACTCTA
17271796 AAACCATGCC
Statistics
Matches: 117, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
80 3 0.03
81 110 0.94
82 4 0.03
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.28
Consensus pattern (80 bp):
CGTCTCACATATTTCACCATACCATGTCACACATTCCCACCAAGCCGTGTCACAAACTCTATACC
CTACCGTGTCACACT
Found at i:17271688 original size:208 final size:207
Alignment explanation
Indices: 17271202--17271661 Score: 704
Period size: 208 Copynumber: 2.2 Consensus size: 207
17271192 TAAACCATGT
* *
17271202 CGTGTCACACACTTTAAACCATGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCGTTTCA
1 CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTG-CGTTTCA
* * *
17271267 CACATTATGACATTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTAAACGTTGTCA
65 CACATTATGACACTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTAAACGCTGCCA
** * **
17271332 TGTCACACCCGTCTCACATATTCTCACTGTGTCATCTCACACATTATCACCCTACTGTGTCACAG
130 TGTCACACCCGTCTCACATATTCTCACCATGCCATCTCACACATTATCACCCTACCATGTCACAG
*
17271397 ATTCCCTCCATGG
195 ATTCCCTCCAAGG
17271410 CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCTGTTTCA
1 CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGC-GTTTCA
* * * *
17271475 CACATTATGACCCTGCCATGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAATGCTGCCA
65 CACATTATGACACTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTAAACGCTGCCA
* *
17271540 TGTCACACTCGTCTCACATATTCTCACCATGCCGTCTCACACATTATCACCCTACCATGTCACAG
130 TGTCACACCCGTCTCACATATTCTCACCATGCCATCTCACACATTATCACCCTACCATGTCACAG
17271605 ATTCCCTCCAAGG
195 ATTCCCTCCAAGG
* * * * *
17271618 CGTGTCACAAACTCTATACCCTATCGTGTCACACCTGTCTCACA
1 CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACA
17271662 TAGTTTCACC
Statistics
Matches: 229, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
207 1 0.00
208 228 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (207 bp):
CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCGTTTCAC
ACATTATGACACTGCCATGTCACACCTTCTGACCATGGCATGTCACACACTCTAAACGCTGCCAT
GTCACACCCGTCTCACATATTCTCACCATGCCATCTCACACATTATCACCCTACCATGTCACAGA
TTCCCTCCAAGG
Found at i:17271732 original size:440 final size:438
Alignment explanation
Indices: 17270843--17271651 Score: 1129
Period size: 440 Copynumber: 1.8 Consensus size: 438
17270833 TCAAGCCATG
* *
17270843 CCATGTCACACGTTTAACCATGGCGTGTTCCACACTCTAAACGCTGCCATGTCACACCCATCCCA
1 CCATGTCACACCTTTAACCATGGCATGTTCCACACTCTAAACGCTGCCATGTCACACCCATCCCA
* * *
17270908 CATATTCTCACTGTGCCGTCTCACACATTTTCACCCTAGCGTGTCATAAATTCCCTCCATGGCAT
66 CATATTCTCACTGTGCCATCTCACACATTATCACCCTAGCGTGTCACAAATTCCCTCCATGGCAT
* *
17270973 GTCACACACTCTAAACCTTGTCGTGTCACACCCGTGTCACATATTATCACTGTGCCATTTCACAC
131 GTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCATTTCACAC
* * * * *
17271038 ATTATGACCTTGTCGTGTCACAAGTTCTGACCATGGCATGTCACACACTCCAAACGCTGTCGTGT
196 ATTATGACCCTGCCATGTCACAAGTTCTGACCATGGCATGTCACACACTCCAAACGCTGCCATGT
* * **
17271103 CACACCCGTCTCTCATATTCTCACCGTGCCGTCTCACACATTATCACCCTGTAGTATCACAGATT
261 CACACCCGTCTCACATATTCTCACCATGCCGTCTCACACATTATCACCCTCCAGTATCACAGATT
* * * *
17271168 CCCTCCATGACGTGTCACACACTTTAAACCATGTCGTGTCACACACTTTAAACCATGTCGTGTCA
326 CCCTCCAAGACGTGTCACAAACTCTAAACCATATCGTGTCACACACTTTAAACCATGTC-TGTCA
* * * ** * * *
17271233 CACCCGTGTCACACATTATCACTGTGCCGTTTCACACATTATGACATTG
390 CACACGTATCACACATTACCACCATGCCGTTTCAAACATTATGACACTA
* * * * *
17271282 CCATGTCACACCTTCTGACCATGGCATG-TCACACACTCTAAACGTTGTCATGTCACACCCGTCT
1 CCATGTCACACCTT-TAACCATGGCATGTTC-CACACTCTAAACGCTGCCATGTCACACCCATCC
* *
17271346 CACATATTCTCACTGTGTCATCTCACACATTATCACCCTA-CTGTGTCACAGATTCCCTCCATGG
64 CACATATTCTCACTGTGCCATCTCACACATTATCACCCTAGC-GTGTCACAAATTCCCTCCATGG
* **
17271410 CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCTGTTTCA
128 CATGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCATTTCA
* * * *
17271475 CACATTATGACCCTGCCATGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAATGCTGCCA
193 CACATTATGACCCTGCCATGTCACAAGTTCTGACCATGGCATGTCACACACTCCAAACGCTGCCA
* *
17271540 TGTCACACTCGTCTCACATATTCTCACCATGCCGTCTCACACATTATCACCCTACCA-TGTCACA
258 TGTCACACCCGTCTCACATATTCTCACCATGCCGTCTCACACATTATCACCCT-CCAGTATCACA
* * *
17271604 GATTCCCTCCAAGGCGTGTCACAAACTCTATACCCTATCGTGTCACAC
322 GATTCCCTCCAAGACGTGTCACAAACTCTAAACCATATCGTGTCACAC
17271652 CTGTCTCACA
Statistics
Matches: 327, Mismatches: 39, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
439 16 0.05
440 310 0.95
441 1 0.00
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (438 bp):
CCATGTCACACCTTTAACCATGGCATGTTCCACACTCTAAACGCTGCCATGTCACACCCATCCCA
CATATTCTCACTGTGCCATCTCACACATTATCACCCTAGCGTGTCACAAATTCCCTCCATGGCAT
GTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACACATTATCACTGTGCCATTTCACAC
ATTATGACCCTGCCATGTCACAAGTTCTGACCATGGCATGTCACACACTCCAAACGCTGCCATGT
CACACCCGTCTCACATATTCTCACCATGCCGTCTCACACATTATCACCCTCCAGTATCACAGATT
CCCTCCAAGACGTGTCACAAACTCTAAACCATATCGTGTCACACACTTTAAACCATGTCTGTCAC
ACACGTATCACACATTACCACCATGCCGTTTCAAACATTATGACACTA
Found at i:17271787 original size:23 final size:23
Alignment explanation
Indices: 17271738--17271788 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
17271728 CACACTCATC
* * *
17271738 TCACATATTCTCACCATGCTATG
1 TCACACATTCCCACCATGCCATG
* *
17271761 TCACACATTCCCACCATTCCATT
1 TCACACATTCCCACCATGCCATG
17271784 TCACA
1 TCACA
17271789 AACTCTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.37, G:0.04, T:0.31
Consensus pattern (23 bp):
TCACACATTCCCACCATGCCATG
Found at i:17275976 original size:22 final size:22
Alignment explanation
Indices: 17275949--17275992 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17275939 TGTTTTTCAT
17275949 TTTTCCTTATAGA-GTAAACCCA
1 TTTTCCTTATA-ACGTAAACCCA
17275971 TTTTCCTTATAACGTAAACCCA
1 TTTTCCTTATAACGTAAACCCA
17275993 AATTTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (22 bp):
TTTTCCTTATAACGTAAACCCA
Found at i:17278637 original size:19 final size:19
Alignment explanation
Indices: 17278615--17278652 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17278605 ACTTCTAAAC
*
17278615 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
17278634 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
17278653 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:17280877 original size:23 final size:25
Alignment explanation
Indices: 17280847--17280907 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
17280837 GTTAAGAAAA
17280847 AAAAAGAAAAAAAGAA-A-AA-TGAG
1 AAAAAGAAAAAAAGAAGAGAAGT-AG
*
17280870 AAAAAGAAAAGAAGAAGAGAAGTAG
1 AAAAAGAAAAAAAGAAGAGAAGTAG
*
17280895 AAAGAGAAAAAAA
1 AAAAAGAAAAAAA
17280908 AACAACTGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 15 0.47
24 1 0.03
25 15 0.47
26 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.03
Consensus pattern (25 bp):
AAAAAGAAAAAAAGAAGAGAAGTAG
Found at i:17284782 original size:11 final size:11
Alignment explanation
Indices: 17284748--17284783 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
17284738 GTGTCAAATC
17284748 AAAAAAAATTTT
1 AAAAAAAA-TTT
17284760 AAAAAAAATTT
1 AAAAAAAATTT
*
17284771 AATAAAAATTT
1 AAAAAAAATTT
17284782 AA
1 AA
17284784 CACTATTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:17285655 original size:31 final size:31
Alignment explanation
Indices: 17285614--17285681 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
17285604 ATTTTATCTC
* *
17285614 AAATTAAATAAAATTATAAAGTACAAGGATT
1 AAATTGAATAAAACTATAAAGTACAAGGATT
** **
17285645 AAATTGAATAAAACTATATTGTACATTGATT
1 AAATTGAATAAAACTATAAAGTACAAGGATT
17285676 AAATTG
1 AAATTG
17285682 GATATTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.34
Consensus pattern (31 bp):
AAATTGAATAAAACTATAAAGTACAAGGATT
Found at i:17299400 original size:55 final size:55
Alignment explanation
Indices: 17299334--17299452 Score: 229
Period size: 55 Copynumber: 2.1 Consensus size: 55
17299324 AAGGATGAAG
17299334 AAATTGAAGTTAAGCACTGTGGAACAAATGAACAACTAGTAGATATATTTACTAA
1 AAATTGAAGTTAAGCACTGTGGAACAAATGAACAACTAGTAGATATATTTACTAA
17299389 AAATTGAAGTTAAGCACTGTGGAACAAATGAACAACTAGTAGATATATTTACTAA
1 AAATTGAAGTTAAGCACTGTGGAACAAATGAACAACTAGTAGATATATTTACTAA
17299444 AAATCTGAA
1 AAAT-TGAA
17299453 CAAGGAGAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 59 0.94
56 4 0.06
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (55 bp):
AAATTGAAGTTAAGCACTGTGGAACAAATGAACAACTAGTAGATATATTTACTAA
Found at i:17304326 original size:19 final size:19
Alignment explanation
Indices: 17304302--17304338 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17304292 CATTTATTTA
*
17304302 TTGTTTGTTTGTTTGTTTT
1 TTGTTTGTTTATTTGTTTT
*
17304321 TTGTTTTTTTATTTGTTT
1 TTGTTTGTTTATTTGTTT
17304339 ATTGCTTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (19 bp):
TTGTTTGTTTATTTGTTTT
Found at i:17306675 original size:26 final size:25
Alignment explanation
Indices: 17306624--17306676 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
17306614 AAATAATAAA
* * *
17306624 AAAATAAAATTTTTAATAATTAATT
1 AAAATAAAATTTATAAAAAGTAATT
*
17306649 AAAATTAAATTTATAAAAAGTATATT
1 AAAATAAAATTTATAAAAAGTA-ATT
17306675 AA
1 AA
17306677 CTATATTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
AAAATAAAATTTATAAAAAGTAATT
Found at i:17308763 original size:2 final size:2
Alignment explanation
Indices: 17308756--17308780 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17308746 GTGAATGTCT
17308756 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
17308781 TAATTTGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:17315785 original size:27 final size:24
Alignment explanation
Indices: 17315747--17315800 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
17315737 ACTATTACTA
*
17315747 TTTTAAATATTATATATAACAAAATAT
1 TTTTAAATATTAGA-AT-A-AAAATAT
*
17315774 TTTTTAATATTAGAATAAAAATAT
1 TTTTAAATATTAGAATAAAAATAT
17315798 TTT
1 TTT
17315801 CATAATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 1 0.04
26 2 0.08
27 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTAAATATTAGAATAAAAATAT
Found at i:17316311 original size:2 final size:2
Alignment explanation
Indices: 17316304--17316340 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17316294 TTACTTTAGG
17316304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17316341 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17316438 original size:2 final size:2
Alignment explanation
Indices: 17316395--17316429 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17316385 GTTTTATTAG
17316395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17316430 GCATATATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17318939 original size:34 final size:34
Alignment explanation
Indices: 17318895--17319074 Score: 129
Period size: 34 Copynumber: 5.4 Consensus size: 34
17318885 GAAAGAAGCT
17318895 TTGGCATGTAACATCTGGTGCTGAAGCTTTGGCC
1 TTGGCATGTAACATCTGGTGCTGAAGCTTTGGCC
* *** * *
17318929 TTGGCGTGTAACATCTGGAATTGAAACTTTGACC
1 TTGGCATGTAACATCTGGTGCTGAAGCTTTGGCC
* *
17318963 TTGGCATGTAGCATCT--T-CT---GCTTTGGCT
1 TTGGCATGTAACATCTGGTGCTGAAGCTTTGGCC
* * * * *
17318991 TTGGTGAGTGCAACATCTAGTGATGAAGCTTTAGCC
1 TTGG-CA-TGTAACATCTGGTGCTGAAGCTTTGGCC
* * * *
17319027 TTGGCATGTATCATCTGGTGTTGAACCTTTGACC
1 TTGGCATGTAACATCTGGTGCTGAAGCTTTGGCC
* *
17319061 TTGGCGTTTAACAT
1 TTGGCATGTAACAT
17319075 TTGTTATAGG
Statistics
Matches: 108, Mismatches: 30, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
28 10 0.09
29 1 0.01
30 8 0.07
31 1 0.01
32 1 0.01
33 1 0.01
34 74 0.69
35 1 0.01
36 11 0.10
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (34 bp):
TTGGCATGTAACATCTGGTGCTGAAGCTTTGGCC
Found at i:17336331 original size:12 final size:12
Alignment explanation
Indices: 17336314--17336365 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
17336304 ACCTTGACTG
17336314 CAAAATAAAAAA
1 CAAAATAAAAAA
* *
17336326 CAAAATAGAAAG
1 CAAAATAAAAAA
*
17336338 CAAAGATAAAAGA
1 CAAA-ATAAAAAA
*
17336351 CATTAATAAAAAA
1 CA-AAATAAAAAA
17336364 CA
1 CA
17336366 TTTAAAATAG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
12 14 0.45
13 16 0.52
14 1 0.03
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.12
Consensus pattern (12 bp):
CAAAATAAAAAA
Found at i:17353968 original size:2 final size:2
Alignment explanation
Indices: 17353963--17353987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17353953 TATGTGTGTG
17353963 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17353988 TCTAATGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17362189 original size:36 final size:36
Alignment explanation
Indices: 17362142--17362246 Score: 142
Period size: 36 Copynumber: 3.0 Consensus size: 36
17362132 GCTTTGAAAG
* *
17362142 CTCTAAAGAGGTAACATATTGTAACTCTATCTTTTA
1 CTCTAGAGAGGTAACATCTTGTAACTCTATCTTTTA
*
17362178 CTCTAGAGAGGTAACATCTTGTAACTCTATCTTTTG
1 CTCTAGAGAGGTAACATCTTGTAACTCTATCTTTTA
* **
17362214 CTCTAG-GTGG-AGTATCTTGTAACTCTATCTTTT
1 CTCTAGAGAGGTAACATCTTGTAACTCTATCTTTT
17362247 GCTTTAGGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 21 0.33
35 3 0.05
36 39 0.62
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
CTCTAGAGAGGTAACATCTTGTAACTCTATCTTTTA
Found at i:17362260 original size:14 final size:14
Alignment explanation
Indices: 17362241--17362269 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17362231 TGTAACTCTA
17362241 TCTTTTGCTTTAGG
1 TCTTTTGCTTTAGG
17362255 TCTTTTGCTTTAGG
1 TCTTTTGCTTTAGG
17362269 T
1 T
17362270 GGCTTTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.59
Consensus pattern (14 bp):
TCTTTTGCTTTAGG
Found at i:17367479 original size:14 final size:14
Alignment explanation
Indices: 17367457--17367486 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17367447 ATTTGGTAAA
*
17367457 TTTTTTTTTATAAG
1 TTTTGTTTTATAAG
17367471 TTTTGTTTTATAAG
1 TTTTGTTTTATAAG
17367485 TT
1 TT
17367487 ATAATTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (14 bp):
TTTTGTTTTATAAG
Found at i:17367682 original size:17 final size:16
Alignment explanation
Indices: 17367647--17367697 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
17367637 GCTTTTTCTG
17367647 AAACTT-TTTTTTATAA
1 AAACTTATTTTTTA-AA
*
17367663 AAATTTTATTCTTTTAAA
1 AAA-CTTATT-TTTTAAA
17367681 AAACTTATTTTTTAAA
1 AAACTTATTTTTTAAA
17367697 A
1 A
17367698 TTTATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 11 0.37
17 7 0.23
18 7 0.23
19 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
AAACTTATTTTTTAAA
Found at i:17367890 original size:17 final size:18
Alignment explanation
Indices: 17367859--17367902 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17367849 AACTCTTAAA
17367859 AAAAAAGTAA-CTTTTTTT
1 AAAAAA-TAATCTTTTTTT
*
17367877 AAAAAATAATTTTTTTTT
1 AAAAAATAATCTTTTTTT
17367895 AAAAAATA
1 AAAAAATA
17367903 GCTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAAAATAATCTTTTTTT
Found at i:17368285 original size:24 final size:24
Alignment explanation
Indices: 17368249--17368371 Score: 92
Period size: 24 Copynumber: 5.2 Consensus size: 24
17368239 CATGTTACAC
17368249 GTCATGTACAAAAATCTGTGACAT
1 GTCATGTACAAAAATCTGTGACAT
* *
17368273 GTCATGTATAAAAATCTGTGACAA
1 GTCATGTACAAAAATCTGTGACAT
* ** ** *
17368297 GCCATG-ATTAGCA--TGTGACAC
1 GTCATGTACAAAAATCTGTGACAT
* *
17368318 GCCATGTACAAAAA-CATGTGACAC
1 GTCATGTACAAAAATC-TGTGACAT
** *
17368342 ACCATGTACAAAAATCTGTGACAA
1 GTCATGTACAAAAATCTGTGACAT
17368366 GTCATG
1 GTCATG
17368372 GTTAACGTGT
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
21 13 0.16
22 3 0.04
23 4 0.05
24 59 0.74
25 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
GTCATGTACAAAAATCTGTGACAT
Found at i:17368324 original size:69 final size:69
Alignment explanation
Indices: 17368200--17368409 Score: 260
Period size: 69 Copynumber: 3.0 Consensus size: 69
17368190 CTATGATATT
* * * * *
17368200 ACACGTCACGTACAAAAATCTGTAACAAGTTATGGTTAGCATGTTACACGTCATGTACAAAAATC
1 ACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTAGCATGTGACACGCCATGTACAAAAA-C
17368265 -TGTG
65 ATGTG
* * * *
17368269 ACATGTCATGTATAAAAATCTGTGACAAGCCATGATTAGCATGTGACACGCCATGTACAAAAACA
1 ACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTAGCATGTGACACGCCATGTACAAAAACA
17368334 TGTG
66 TGTG
** * * ** *
17368338 ACACACCATGTACAAAAATCTGTGACAAGTCATGGTTAACGTGTGACATACCATGTACAAAAACT
1 ACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTAGCATGTGACACGCCATGTACAAAAACA
17368403 TGTG
66 TGTG
17368407 ACA
1 ACA
17368410 AGCCATGGTT
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
68 1 0.01
69 119 0.99
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (69 bp):
ACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTAGCATGTGACACGCCATGTACAAAAACA
TGTG
Found at i:17368383 original size:45 final size:45
Alignment explanation
Indices: 17368334--17368506 Score: 222
Period size: 45 Copynumber: 3.8 Consensus size: 45
17368324 TACAAAAACA
*
17368334 TGTGACACACCATGTACAAAAA-TCTGTGACAAGTCATGGTTAACG
1 TGTGACACACCATGTACAAAAACT-TGTGACAAGTCATGGTTAGCG
* * *
17368379 TGTGACATACCATGTACAAAAACTTGTGACAAGCCATGGTTAGTG
1 TGTGACACACCATGTACAAAAACTTGTGACAAGTCATGGTTAGCG
* * *
17368424 TGTTACACACCATGTACAAAAGCTTATGACAAGTCATGGTTAGCG
1 TGTGACACACCATGTACAAAAACTTGTGACAAGTCATGGTTAGCG
** * * *
17368469 TGTGACACGTCATATACAAAAACCTGTGATAAGTCATG
1 TGTGACACACCATGTACAAAAACTTGTGACAAGTCATG
17368507 TACAAAAACC
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 108 0.99
46 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
TGTGACACACCATGTACAAAAACTTGTGACAAGTCATGGTTAGCG
Found at i:17368415 original size:24 final size:24
Alignment explanation
Indices: 17368251--17368416 Score: 86
Period size: 24 Copynumber: 7.2 Consensus size: 24
17368241 TGTTACACGT
* *
17368251 CATGTACAAAAA-TCTGTGACATGT
1 CATGTACAAAAACT-TGTGACAAGC
*
17368275 CATGTATAAAAA-TCTGTGACAAGC
1 CATGTACAAAAACT-TGTGACAAGC
** * * *
17368299 CATG---ATTAGCATGTGACACGC
1 CATGTACAAAAACTTGTGACAAGC
*
17368320 CATGTACAAAAACATGTGACACA-C
1 CATGTACAAAAACTTGTGACA-AGC
*
17368344 CATGTACAAAAA-TCTGTGACAAGT
1 CATGTACAAAAACT-TGTGACAAGC
* *
17368368 CATGGT----TAACGTGTGACATA-C
1 CAT-GTACAAAAACTTGTGACA-AGC
17368389 CATGTACAAAAACTTGTGACAAGC
1 CATGTACAAAAACTTGTGACAAGC
17368413 CATG
1 CATG
17368417 GTTAGTGTGT
Statistics
Matches: 108, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
20 2 0.02
21 27 0.25
22 1 0.01
23 2 0.02
24 74 0.69
25 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
CATGTACAAAAACTTGTGACAAGC
Done.