Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 61 of 345
Found at i:16945046 original size:8 final size:9
Alignment explanation
Indices: 16945030--16945072 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
16945020 TCCTTTAATT
16945030 TTAAAAAAA
1 TTAAAAAAA
16945039 TTAAAAAAA
1 TTAAAAAAA
16945048 TTAAAAATAA
1 TTAAAAA-AA
*
16945058 GTAACAAAAA
1 TTAA-AAAAA
16945068 TTAAA
1 TTAAA
16945073 TTGAAGCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 17 0.57
10 10 0.33
11 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:16945066 original size:20 final size:18
Alignment explanation
Indices: 16945030--16945072 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
16945020 TCCTTTAATT
*
16945030 TTAAAAAAATTAAAAAAA
1 TTAAAAAAAGTAAAAAAA
16945048 TTAAAAATAAGTAACAAAAA
1 TTAAAAA-AAGTAA-AAAAA
16945068 TTAAA
1 TTAAA
16945073 TTGAAGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 5 0.23
20 10 0.45
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
TTAAAAAAAGTAAAAAAA
Found at i:16947303 original size:30 final size:30
Alignment explanation
Indices: 16947243--16947303 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16947233 GAGTTCTCAG
* * *
16947243 GATCCACACGGGCAGGCCACACGGCTATGT
1 GATCCACACGAGCAGGCCACACGCCCATGT
16947273 GATCCACACGAGCAGGCCACACGCCCATGT
1 GATCCACACGAGCAGGCCACACGCCCATGT
16947303 G
1 G
16947304 CCAGCCCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.36, G:0.28, T:0.11
Consensus pattern (30 bp):
GATCCACACGAGCAGGCCACACGCCCATGT
Found at i:16947705 original size:12 final size:13
Alignment explanation
Indices: 16947663--16947705 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
16947653 TTTAATCATA
16947663 AATACTTGTTCTT
1 AATACTTGTTCTT
16947676 AATTA-TGTGTTCTT
1 AA-TACT-TGTTCTT
16947690 AATACTTGTT-TT
1 AATACTTGTTCTT
16947702 AATA
1 AATA
16947706 TTTTCAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 12 0.44
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (13 bp):
AATACTTGTTCTT
Found at i:16954463 original size:27 final size:27
Alignment explanation
Indices: 16954433--16954562 Score: 102
Period size: 27 Copynumber: 4.8 Consensus size: 27
16954423 GGCTATTCCT
* *
16954433 TGTTTAATGT-CTCGTTAGACTATCTCG
1 TGTTTAACGTCCT-GTTAGACTACCTCG
*
16954460 TGTTTAACGTCCTGTTGGACTACCTCG
1 TGTTTAACGTCCTGTTAGACTACCTCG
* * * * *
16954487 TGTTTAACATCATATCAGACTACCTCA
1 TGTTTAACGTCCTGTTAGACTACCTCG
** * *
16954514 TGTTTAACGT-CTCGTCGGACTACTTCC
1 TGTTTAACGTCCT-GTTAGACTACCTCG
* *
16954541 TGTTTAACGTCCTATCAGACTA
1 TGTTTAACGTCCTGTTAGACTA
16954563 TCTATGATAA
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 78 0.94
28 4 0.05
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (27 bp):
TGTTTAACGTCCTGTTAGACTACCTCG
Found at i:16954507 original size:54 final size:54
Alignment explanation
Indices: 16954449--16954565 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
16954439 ATGTCTCGTT
* * *
16954449 AGACTATCTCGTGTTTAACGTC-CTGTTGGACTACCTCGTGTTTAACATCATATC
1 AGACTATCTCATGTTTAACGTCTC-GTCGGACTACCTCCTGTTTAACATCATATC
* * * *
16954503 AGACTACCTCATGTTTAACGTCTCGTCGGACTACTTCCTGTTTAACGTCCTATC
1 AGACTATCTCATGTTTAACGTCTCGTCGGACTACCTCCTGTTTAACATCATATC
16954557 AGACTATCT
1 AGACTATCT
16954566 ATGATAACAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 53 0.98
55 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (54 bp):
AGACTATCTCATGTTTAACGTCTCGTCGGACTACCTCCTGTTTAACATCATATC
Found at i:16954686 original size:45 final size:45
Alignment explanation
Indices: 16954635--16954764 Score: 170
Period size: 45 Copynumber: 2.9 Consensus size: 45
16954625 GGATTACTAG
* * * * * * *
16954635 GATGTCAAACCGTTTTTCAGCCATGATTTTACTCATTTTTATCAT
1 GATGTCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTAATCAT
* *
16954680 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCATCTTAATCAT
1 GATGTCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTAATCAT
*
16954725 GATGTCATAGCGCCTTTCAGCTATGGTCTTACTCATTTTA
1 GATGTCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTA
16954765 GGCGTATAGC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (45 bp):
GATGTCATAGCGTCTTTCAGCTATGGTCTTACTCATTTTAATCAT
Found at i:16956132 original size:15 final size:16
Alignment explanation
Indices: 16956106--16956135 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16956096 TTCAAGAAAA
16956106 AAAAATATAATTTATC
1 AAAAATATAATTTATC
16956122 AAAAATA-AATTTAT
1 AAAAATATAATTTAT
16956136 AAATATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATATAATTTATC
Found at i:16957416 original size:15 final size:15
Alignment explanation
Indices: 16957398--16957430 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
16957388 TGATTATGTG
16957398 TTAATTTTTTATTTA
1 TTAATTTTTTATTTA
16957413 TTAATTTTTTATTTA
1 TTAATTTTTTATTTA
16957428 TTA
1 TTA
16957431 TAATCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTAATTTTTTATTTA
Found at i:16957792 original size:5 final size:5
Alignment explanation
Indices: 16957782--16957807 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16957772 ATTTCTTTGA
16957782 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
16957808 TTGATTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:16961840 original size:24 final size:23
Alignment explanation
Indices: 16961801--16961857 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
16961791 ATAAAAAATA
* *
16961801 TTAAAAATATT-AAAATAAATGTT
1 TTAAAAAAATTGAAATTAAAT-TT
*
16961824 TTCAAACAAATTGAAATTAAATTT
1 TT-AAAAAAATTGAAATTAAATTT
16961848 TTAAAAAAAT
1 TTAAAAAAAT
16961858 ATTTACTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 9 0.32
24 11 0.39
25 8 0.29
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
TTAAAAAAATTGAAATTAAATTT
Found at i:16962367 original size:30 final size:30
Alignment explanation
Indices: 16962333--16962392 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16962323 ACTTAACAAG
*
16962333 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
16962363 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
16962393 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:16963558 original size:45 final size:45
Alignment explanation
Indices: 16963457--16963583 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 45
16963447 TTTTCTCAAA
* * *
16963457 TCACCAGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
*
16963499 TCACCGACATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
16963543 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
16963584 ATCAAGTCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
42 9 0.13
43 14 0.20
44 8 0.11
45 39 0.55
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:16963961 original size:43 final size:43
Alignment explanation
Indices: 16963913--16964088 Score: 284
Period size: 43 Copynumber: 4.1 Consensus size: 43
16963903 CCTGCATTAC
* *
16963913 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCGCGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
16963956 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
*
16963999 GCCTGCTAGGCACGAAGGCCTGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
* * *
16964042 GCCTGCTAGGCACGAAGGCCCGAATATA-AT-ACCAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
16964083 GCCTGC
1 GCCTGC
16964089 GGGATTTAAC
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
41 15 0.12
42 2 0.02
43 109 0.87
ACGTcount: A:0.29, C:0.34, G:0.25, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
Found at i:16965169 original size:2 final size:2
Alignment explanation
Indices: 16965151--16965197 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
16965141 CACTTTCAAA
*
16965151 AT AT A- AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16965192 AT AT AT
1 AT AT AT
16965198 TCGACTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16968662 original size:93 final size:93
Alignment explanation
Indices: 16968550--16968721 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
16968540 CGCCCATAAG
* *
16968550 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16968615 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
16968643 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16968708 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
16968722 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:16968718 original size:46 final size:46
Alignment explanation
Indices: 16968543--16968718 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
16968533 TGTAACCCGC
* * *
16968543 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
16968589 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
16968639 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
16968682 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
16968719 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:16976239 original size:93 final size:93
Alignment explanation
Indices: 16976127--16976298 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
16976117 CGCCCATAAG
* *
16976127 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16976192 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
16976220 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16976285 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
16976299 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:16976295 original size:46 final size:46
Alignment explanation
Indices: 16976120--16976295 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
16976110 TGTAACCCGC
* * *
16976120 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
16976166 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
16976216 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
16976259 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
16976296 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:16979355 original size:19 final size:20
Alignment explanation
Indices: 16979318--16979355 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
16979308 AAAAAGTATG
16979318 TAAAAGAATGTATAAAATAA
1 TAAAAGAATGTATAAAATAA
* *
16979338 TAAAATAAT-TATATAATA
1 TAAAAGAATGTATAAAATA
16979356 TATATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAAGAATGTATAAAATAA
Found at i:16979359 original size:28 final size:28
Alignment explanation
Indices: 16979291--16979370 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 28
16979281 GGTTTTTAAA
*
16979291 AAAATAATATATAAAATAAAAAGTATGT
1 AAAATAATATATAAAATAAAAAATATGT
* *
16979319 AAAAGAATGTATAAAATAATAAAATAAT-T
1 AAAATAATATATAAAATAA-AAAAT-ATGT
16979348 ATATAATATATATATAAATATAA
1 A-A-AATA-ATATATAAA-ATAA
16979371 GTTTAGAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
28 17 0.41
29 6 0.15
30 3 0.07
31 3 0.07
32 8 0.20
33 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAATAATATATAAAATAAAAAATATGT
Found at i:16979684 original size:3 final size:3
Alignment explanation
Indices: 16979676--16979797 Score: 56
Period size: 3 Copynumber: 39.3 Consensus size: 3
16979666 AAGTAAAAAC
* * *
16979676 ATA ATA ATA ATA TATA AGTA ATA AT- GTA A-A ATA ATA ATA ATTT GTGA
1 ATA ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA ATA A-TA AT-A
* * *
16979723 AAA ACA ATA TACA ATA GATA ATA ATA AT- ATAA ATA ATA TATA ATA A-A
1 ATA ATA ATA -ATA ATA -ATA ATA ATA ATA AT-A ATA ATA -ATA ATA ATA
* *
16979770 ATA ATT ATA ATAA ATA AT- ATA AAA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
16979798 GGTTAAAAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
2 9 0.10
3 61 0.68
4 20 0.22
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16981785 original size:205 final size:205
Alignment explanation
Indices: 16981427--16981802 Score: 628
Period size: 205 Copynumber: 1.8 Consensus size: 205
16981417 ATCTGCTTCC
*
16981427 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGT
1 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGT
*
16981492 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGG
66 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
* * **
16981557 ATCTACTTCAGTGAGATCATCTGAAGGTGAGATCTGCTATGTATCTGCTCTTCGTCAAAATGGAG
131 ATCTACTTCAGTGAAAGCATCTGAAGGCCAGATCTGCTATGTATCTGCTCTTCGTCAAAATGGAG
16981622 ATGCCAGACT
196 ATGCCAGACT
*
16981632 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAATACGT
1 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGT
* * *
16981697 GAAAGCCAAATCAGCTATGTCTTCGATTTTTTCCTTGTAAGTATAAGGATGCCAAACCATCTTGG
66 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
* *
16981762 ATCTGCTTCAGT-ACAAGCATCTGAAGGCCAGATCTGTTATG
131 ATCTACTTCAGTGA-AAGCATCTGAAGGCCAGATCTGCTATG
16981803 CTGCGGCCTA
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
204 1 0.01
205 157 0.99
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (205 bp):
TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGT
GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGG
ATCTACTTCAGTGAAAGCATCTGAAGGCCAGATCTGCTATGTATCTGCTCTTCGTCAAAATGGAG
ATGCCAGACT
Found at i:16992381 original size:23 final size:23
Alignment explanation
Indices: 16992310--16992396 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 23
16992300 ACCTGATCAG
*
16992310 AATACGACACATAA-GTGCCTG-
1 AATACGACACACAAGGTGCCTGA
*
16992331 AA-ACGACACACGAGGTGCC--A
1 AATACGACACACAAGGTGCCTGA
* *
16992351 ATTGCGACACACAAGGTGCCTGA
1 AATACGACACACAAGGTGCCTGA
* *
16992374 AATACGACACATAAAGTGCCTGA
1 AATACGACACACAAGGTGCCTGA
16992397 TCAGTAAAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 10 0.19
21 22 0.42
23 20 0.38
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
AATACGACACACAAGGTGCCTGA
Found at i:16992612 original size:23 final size:24
Alignment explanation
Indices: 16992586--16992680 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
16992576 AAATGTCCAA
16992586 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
16992609 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
16992637 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
16992666 CCAAAACACACCAGA
1 CCAAAACACACCAGA
16992681 ATAGCAAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:16992682 original size:29 final size:28
Alignment explanation
Indices: 16992600--16992683 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
16992590 AACACACCAG
* *
16992600 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
16992628 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
16992656 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
16992684 GCAAAAGTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:16995382 original size:2 final size:2
Alignment explanation
Indices: 16995375--16995409 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16995365 AATTATTTTA
16995375 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 A
16995410 GTGCATTTCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17001866 original size:17 final size:17
Alignment explanation
Indices: 17001846--17001881 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17001836 TGTGAAAAAC
17001846 AATATACAATAGATAAT
1 AATATACAATAGATAAT
* *
17001863 AATATATAATATATAAT
1 AATATACAATAGATAAT
17001880 AA
1 AA
17001882 AATAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AATATACAATAGATAAT
Found at i:17001871 original size:7 final size:7
Alignment explanation
Indices: 17001861--17001903 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
17001851 ACAATAGATA
17001861 ATAATAT
1 ATAATAT
17001868 ATAATAT
1 ATAATAT
*
17001875 ATAATAAA
1 ATAAT-AT
17001883 ATAAT-T
1 ATAATAT
17001889 ATAATAT
1 ATAATAT
17001896 ATAATAT
1 ATAATAT
17001903 A
1 A
17001904 AAAATAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 5 0.16
7 21 0.66
8 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:17001893 original size:21 final size:24
Alignment explanation
Indices: 17001846--17001901 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 24
17001836 TGTGAAAAAC
*
17001846 AATATACAATAGATAATAATATAT
1 AATATATAATAGATAATAATATAT
17001870 AATATATAATA-A-AATAAT-TAT
1 AATATATAATAGATAATAATATAT
17001891 AATATATAATA
1 AATATATAATA
17001902 TAAAAATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 14 0.45
22 6 0.19
23 1 0.03
24 10 0.32
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AATATATAATAGATAATAATATAT
Found at i:17012396 original size:81 final size:81
Alignment explanation
Indices: 17012289--17012544 Score: 404
Period size: 81 Copynumber: 3.1 Consensus size: 81
17012279 AATTATACAT
* * *
17012289 TAGCGGCGTTGTTGGCAAAGCGCCGCTAAAAATAGAACAATAGCGGCATTTTTGGCAAAGCGCCG
1 TAGCGACGTTTTTGGCAAAGCGCCGCTAAAAATAGAGCAATAGCGGCATTTTTGGCAAAGCGCCG
17012354 CTAAAAAACAGAGCAA
66 CTAAAAAACAGAGCAA
* *
17012370 TAGCGATGTTTTTGGCAAAGCTCCGCTAAAAATAGAGCAATAGCGGCATTTTTGGCAAAGCGCCG
1 TAGCGACGTTTTTGGCAAAGCGCCGCTAAAAATAGAGCAATAGCGGCATTTTTGGCAAAGCGCCG
17012435 CTAAAAAACAGAGCAA
66 CTAAAAAACAGAGCAA
* * * * *
17012451 TAGCGGCGTTTTTGTCAAAGCGCCGCTAAAAAACAGAGCAATAGCAGCGTTTTTGGCAAAGCGCC
1 TAGCGACGTTTTTGGCAAAGCGCCGCT-AAAAATAGAGCAATAGCGGCATTTTTGGCAAAGCGCC
17012516 GCTAAAAAACAGAGCAA
65 GCTAAAAAACAGAGCAA
*
17012533 TAGCGGCGTTTT
1 TAGCGACGTTTT
17012545 ACCAAAAACG
Statistics
Matches: 162, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
81 99 0.61
82 63 0.39
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (81 bp):
TAGCGACGTTTTTGGCAAAGCGCCGCTAAAAATAGAGCAATAGCGGCATTTTTGGCAAAGCGCCG
CTAAAAAACAGAGCAA
Found at i:17012563 original size:41 final size:41
Alignment explanation
Indices: 17012289--17012544 Score: 399
Period size: 41 Copynumber: 6.3 Consensus size: 41
17012279 AATTATACAT
* * *
17012289 TAGCGGCGTTGTTGGCAAAGCGCCGCT-AAAAATAGAACAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
17012329 TAGCGGCATTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
** * *
17012370 TAGCGATGTTTTTGGCAAAGCTCCGCT-AAAAATAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
17012410 TAGCGGCATTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
17012451 TAGCGGCGTTTTTGTCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
17012492 TAGCAGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
17012533 TAGCGGCGTTTT
1 TAGCGGCGTTTT
17012545 ACCAAAAACG
Statistics
Matches: 195, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
40 60 0.31
41 135 0.69
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (41 bp):
TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
Found at i:17012617 original size:44 final size:45
Alignment explanation
Indices: 17012567--17012702 Score: 148
Period size: 44 Copynumber: 2.8 Consensus size: 45
17012557 GCTAAAAGTC
*
17012567 ATATAACCCCTAAAACCTTAAACCCCAAAAAAATCATAGACACT-
1 ATATAACCCCTAAAACCTTAAACCCCAAAAAAATCATAAACACTA
*
17012611 ATATAACCCCTAAAACCTTAAACCCCTAACCCCCAAAAACCATAAACACTA
1 ATATAACCCCTAAAACCTTAAACCCC-AA-----AAAAATCATAAACACTA
* *
17012662 ATCTATAATCCCTAAAACCTTAAACCCTAAAAAACATCATA
1 A--TATAACCCCTAAAACCTTAAACCCCAAAAAA-ATCATA
17012703 TGGATGTTGA
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
44 26 0.34
45 2 0.03
47 4 0.05
48 5 0.06
50 14 0.18
51 1 0.01
52 2 0.03
53 23 0.30
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.19
Consensus pattern (45 bp):
ATATAACCCCTAAAACCTTAAACCCCAAAAAAATCATAAACACTA
Found at i:17013216 original size:7 final size:7
Alignment explanation
Indices: 17013202--17013230 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
17013192 GTTTTATGAC
17013202 TTAA-GG
1 TTAAGGG
17013208 TTAAGGG
1 TTAAGGG
17013215 TTAAGGG
1 TTAAGGG
17013222 TTAAGGG
1 TTAAGGG
17013229 TT
1 TT
17013231 TAGATTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (7 bp):
TTAAGGG
Found at i:17013336 original size:19 final size:20
Alignment explanation
Indices: 17013307--17013344 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
17013297 TAAAAAATAT
17013307 ATTGATAAATAAATAAAAAC
1 ATTGATAAATAAATAAAAAC
17013327 ATTGAT-AATAAATAAAAA
1 ATTGATAAATAAATAAAAA
17013345 TGAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
ATTGATAAATAAATAAAAAC
Found at i:17013557 original size:6 final size:6
Alignment explanation
Indices: 17013541--17013577 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
17013531 ACCCATATGA
*
17013541 TCCCTT CCCCTT TCCCTT TCCCTT TCCCTT TCCCTT T
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT T
17013578 GGTTTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCCTT
Found at i:17013742 original size:2 final size:2
Alignment explanation
Indices: 17013737--17013770 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17013727 TATTTTAAAA
17013737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17013771 CAAAATGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17014254 original size:7 final size:7
Alignment explanation
Indices: 17014242--17014273 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
17014232 AATATTTAAA
17014242 AAAATTG
1 AAAATTG
17014249 AAAATTG
1 AAAATTG
17014256 AAAATTG
1 AAAATTG
17014263 AAAATTG
1 AAAATTG
17014270 AAAA
1 AAAA
17014274 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (7 bp):
AAAATTG
Found at i:17014314 original size:16 final size:15
Alignment explanation
Indices: 17014241--17014308 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 15
17014231 AAATATTTAA
*
17014241 AAAAATTGAAAA-TT
1 AAAAATTAAAAACTT
* *
17014255 GAAAATTGAAAA-TT
1 AAAAATTAAAAACTT
17014269 GAAAAA-TAAAAA--T
1 -AAAAATTAAAAACTT
17014282 AAAAATTAAAAACTT
1 AAAAATTAAAAACTT
17014297 AAAAACTTAAAA
1 AAAAA-TTAAAA
17014309 TTTTAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 5 0.11
13 7 0.15
14 18 0.39
15 10 0.22
16 6 0.13
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAAACTT
Found at i:17014379 original size:16 final size:18
Alignment explanation
Indices: 17014360--17014395 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17014350 ATCAATATTC
17014360 AAAATT-TAAAAAAAATA
1 AAAATTCTAAAAAAAATA
*
17014377 AAAATTCTAAAAAATATA
1 AAAATTCTAAAAAAAATA
17014395 A
1 A
17014396 TCTCAGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTCTAAAAAAAATA
Found at i:17025926 original size:29 final size:29
Alignment explanation
Indices: 17025892--17025947 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
17025882 TTGATTTTCT
17025892 TTTAATAGTACAAG-GACTAAATTGATCTA
1 TTTAATAGTA-AAGAGACTAAATTGATCTA
* *
17025921 TTTAATAGTAGAGAGACTAATTTGATC
1 TTTAATAGTAAAGAGACTAAATTGATC
17025948 AAGTCCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTAATAGTAAAGAGACTAAATTGATCTA
Found at i:17028333 original size:31 final size:31
Alignment explanation
Indices: 17028298--17028396 Score: 74
Period size: 41 Copynumber: 2.9 Consensus size: 31
17028288 ACAACTCAGT
17028298 GACTTAAATAAAAGCTTTCAAATAGTTTAGC
1 GACTTAAATAAAAGCTTTCAAATAGTTTAGC
17028329 GACTTCAATGAAAACAAATAAAAGCTTTCAAATAGTTTAGC
1 GAC-T---T------AAATAAAAGCTTTCAAATAGTTTAGC
**
17028370 GACTTAAATGAAAA-CTTTTGAATAGTT
1 GACTTAAAT-AAAAGCTTTCAAATAGTT
17028397 CAATGATCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
31 18 0.33
32 5 0.09
35 1 0.02
37 1 0.02
40 1 0.02
41 29 0.53
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (31 bp):
GACTTAAATAAAAGCTTTCAAATAGTTTAGC
Found at i:17028360 original size:41 final size:41
Alignment explanation
Indices: 17028303--17028384 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
17028293 TCAGTGACTT
*
17028303 AAATAAAAGCTTTCAAATAGTTTAGCGACTTCAATGAAAAC
1 AAATAAAAGCTTTCAAATAGTTTAGCGACTTAAATGAAAAC
17028344 AAATAAAAGCTTTCAAATAGTTTAGCGACTTAAATGAAAAC
1 AAATAAAAGCTTTCAAATAGTTTAGCGACTTAAATGAAAAC
17028385 TTTTGAATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (41 bp):
AAATAAAAGCTTTCAAATAGTTTAGCGACTTAAATGAAAAC
Found at i:17035589 original size:13 final size:14
Alignment explanation
Indices: 17035571--17035599 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17035561 TCCTCCCTTC
17035571 AAAATAAAAA-AAA
1 AAAATAAAAATAAA
17035584 AAAATAAAAATAAA
1 AAAATAAAAATAAA
17035598 AA
1 AA
17035600 CATTCCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:17039605 original size:30 final size:28
Alignment explanation
Indices: 17039566--17039627 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 28
17039556 ATGGATTTAA
*
17039566 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTA-TTAAGTAAA-AGATACTT
*
17039596 ATTATTTATTATTAAGTAAAAGATACTT
1 ATTACTTATTATTAAGTAAAAGATACTT
17039624 ATTA
1 ATTA
17039628 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
29 9 0.30
30 10 0.33
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (28 bp):
ATTACTTATTATTAAGTAAAAGATACTT
Found at i:17040288 original size:17 final size:18
Alignment explanation
Indices: 17040266--17040301 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17040256 TAAATGAGTT
17040266 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
17040283 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
17040301 A
1 A
17040302 TGAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:17040320 original size:3 final size:3
Alignment explanation
Indices: 17040312--17040343 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
17040302 TGAAAATTCA
17040312 ATT ATT ATT ATT ATT ATT ATT ATT ATT GATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT A
17040344 GTGCCGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17040715 original size:21 final size:21
Alignment explanation
Indices: 17040691--17040767 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
17040681 AAGCACTTTA
* *
17040691 TGTGTCGTATCAGGTACCTCG
1 TGTGTCGTAACAGGAACCTCG
17040712 TGTGTCGTAACAGGAACCTCG
1 TGTGTCGTAACAGGAACCTCG
*
17040733 TGTGTCGTATCAGGAACCTCG
1 TGTGTCGTAACAGGAACCTCG
*
17040754 TGTGTTGTAACAGG
1 TGTGTCGTAACAGG
17040768 CACTTTATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTGTCGTAACAGGAACCTCG
Found at i:17040779 original size:42 final size:42
Alignment explanation
Indices: 17040683--17040784 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
17040673 TGCCGATCAA
*
17040683 GCACTTTATGTGTCGTATCAGGTACCTCGTGTGTCGTAACAG
1 GCACTTTATGTGTCGTATCAGGAACCTCGTGTGTCGTAACAG
* * ** *
17040725 GAACCTCGTGTGTCGTATCAGGAACCTCGTGTGTTGTAACAG
1 GCACTTTATGTGTCGTATCAGGAACCTCGTGTGTCGTAACAG
17040767 GCACTTTATGTGTCGTAT
1 GCACTTTATGTGTCGTAT
17040785 ACTGCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (42 bp):
GCACTTTATGTGTCGTATCAGGAACCTCGTGTGTCGTAACAG
Found at i:17041695 original size:3 final size:3
Alignment explanation
Indices: 17041687--17041722 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
17041677 ATTCGCACAA
*
17041687 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17041723 TTCTAGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17042643 original size:27 final size:27
Alignment explanation
Indices: 17042604--17042661 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
17042594 ATCCTAGCAA
17042604 ACTACCCTATGTTTAATGTCCCGACAG
1 ACTACCCTATGTTTAATGTCCCGACAG
*
17042631 ACTACTCCT-TGTTTAATGTCCCGGCAG
1 ACTAC-CCTATGTTTAATGTCCCGACAG
17042658 ACTA
1 ACTA
17042662 TGTATGATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (27 bp):
ACTACCCTATGTTTAATGTCCCGACAG
Found at i:17042876 original size:45 final size:45
Alignment explanation
Indices: 17042827--17042912 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
17042817 TCTTGTTTAC
* **
17042827 CATGATGCCATAGTGTCTTTCAACCATGGTCTTACACATTTCCAT
1 CATGATGACATAGCATCTTTCAACCATGGTCTTACACATTTCCAT
* * *
17042872 CATGATGACATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 CATGATGACATAGCATCTTTCAACCATGGTCTTACACATTT
17042913 TTGGTGTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (45 bp):
CATGATGACATAGCATCTTTCAACCATGGTCTTACACATTTCCAT
Found at i:17050273 original size:2 final size:2
Alignment explanation
Indices: 17050266--17050299 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17050256 AACCATTTAA
17050266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17050300 TCAAACATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17053418 original size:21 final size:21
Alignment explanation
Indices: 17053392--17053451 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
17053382 GGTAGATCAA
17053392 CTCTTATGAGCTTCTGTTCAC
1 CTCTTATGAGCTTCTGTTCAC
* *
17053413 CTCTTATGAGCTTCTGTTTAG
1 CTCTTATGAGCTTCTGTTCAC
17053434 CTCTTATGAGCTTCTGTT
1 CTCTTATGAGCTTCTGTT
17053452 GACAATGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAC
Found at i:17055573 original size:27 final size:27
Alignment explanation
Indices: 17055535--17055667 Score: 194
Period size: 27 Copynumber: 4.9 Consensus size: 27
17055525 AATACTTTAG
*
17055535 TTTACCAAATTACCGTTTTACCCTCAA
1 TTTACAAAATTACCGTTTTACCCTCAA
* * *
17055562 TTTATAGAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCGTTTTACCCTCAA
* *
17055589 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCGTTTTACCCTCAA
*
17055616 TTTACAAAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCGTTTTACCCTCAA
*
17055643 TTTACAAAATTATCGTTTTACCCTC
1 TTTACAAAATTACCGTTTTACCCTC
17055668 GATTGTGAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.39
Consensus pattern (27 bp):
TTTACAAAATTACCGTTTTACCCTCAA
Found at i:17055619 original size:54 final size:54
Alignment explanation
Indices: 17055535--17055671 Score: 220
Period size: 54 Copynumber: 2.5 Consensus size: 54
17055525 AATACTTTAG
* * * *
17055535 TTTACCAAATTACCGTTTTACCCTCAATTTATAGAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAA
*
17055589 TTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAA
*
17055643 TTTACAAAATTATCGTTTTACCCTCGATT
1 TTTACAAAATTACCGTTTTACCCTCGATT
17055672 GTGAAATTAC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (54 bp):
TTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAA
Found at i:17055841 original size:54 final size:55
Alignment explanation
Indices: 17055703--17055854 Score: 191
Period size: 54 Copynumber: 2.8 Consensus size: 55
17055693 TGTAGGATAG
* * * *
17055703 AATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAAAATTATCGAAATACCCTCTAATTTGTAA
* * *
17055757 AATTACCGAAATACCACTAGTTTGTGAAATTATCGAAATACCCTC-AATTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAAAATTATCGAAATACCCTCTAATTTGTAA
* ** *
17055811 AATTACCAAAATACCCCTAATTTACAAAATTATAGAAATACCCT
1 AATTACCAAAATACCCCTAGTTTGTAAAATTATCGAAATACCCT
17055855 TGACTTTCTA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 82 0.99
55 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (55 bp):
AATTACCAAAATACCCCTAGTTTGTAAAATTATCGAAATACCCTCTAATTTGTAA
Found at i:17055842 original size:27 final size:27
Alignment explanation
Indices: 17055670--17055829 Score: 180
Period size: 27 Copynumber: 5.9 Consensus size: 27
17055660 TTACCCTCGA
* *
17055670 TTGTGAAATTACTAAAATACCCCT-GT
1 TTGTAAAATTACCAAAATACCCCTAGT
** * *
17055696 AGGATAGAATTACCAAAATACCCTTAGT
1 TTG-TAAAATTACCAAAATACCCCTAGT
17055724 TTGTAAAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCCTAGT
* *
17055751 TTGTAAAATTACCGAAATACCACTAGT
1 TTGTAAAATTACCAAAATACCCCTAGT
* * * *
17055778 TTGTGAAATTATCGAAATA-CCCTCAAT
1 TTGTAAAATTACCAAAATACCCCT-AGT
17055805 TTGTAAAATTACCAAAATACCCCTA
1 TTGTAAAATTACCAAAATACCCCTA
17055830 ATTTACAAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.04
27 100 0.90
28 7 0.06
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCCTAGT
Found at i:17055849 original size:27 final size:27
Alignment explanation
Indices: 17055711--17055909 Score: 111
Period size: 27 Copynumber: 7.3 Consensus size: 27
17055701 AGAATTACCA
* * *
17055711 AAATACCCTTAGTTTGTAAAATTACCA-
1 AAATACCCCTAGTTTGCAAAATTA-TAG
* **
17055738 AAATACCCCTAGTTTGTAAAATTACCG
1 AAATACCCCTAGTTTGCAAAATTATAG
* ** *
17055765 AAATACCACTAGTTTGTGAAATTATCG
1 AAATACCCCTAGTTTGCAAAATTATAG
* * *
17055792 AAATA-CCCTCAATTTGTAAAATTACCA-
1 AAATACCCCT-AGTTTGCAAAATTA-TAG
* *
17055819 AAATACCCCTAATTTACAAAATTATAG
1 AAATACCCCTAGTTTGCAAAATTATAG
* *
17055846 AAATACCCTTGACTTT-CTAAAAATTATAG
1 AAATACCCCT-AGTTTGC--AAAATTATAG
** * *
17055875 AAATACCATTGGTTTACAAAATTACT-G
1 AAATACCCCTAGTTTGCAAAATTA-TAG
17055902 AAATACCC
1 AAATACCC
17055910 TTGGTTTGTA
Statistics
Matches: 143, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
26 5 0.03
27 106 0.74
28 12 0.08
29 20 0.14
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATACCCCTAGTTTGCAAAATTATAG
Found at i:17056011 original size:27 final size:27
Alignment explanation
Indices: 17055957--17056034 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
17055947 AAATAACTAA
* * *
17055957 AATACCCCTAATA-GGTAAAAAGATCGT
1 AATACCCCT-GTAGGGTAAAATGACCGT
*
17055984 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAATGACCGT
* *
17056011 AATACCCTTGTATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
17056035 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.07
27 37 0.90
28 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:17056879 original size:25 final size:25
Alignment explanation
Indices: 17056841--17056910 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
17056831 AAGAAGTGCT
* *
17056841 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
17056866 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
17056891 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
17056911 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:17056923 original size:24 final size:24
Alignment explanation
Indices: 17056840--17056935 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 24
17056830 GAAGAAGTGC
*
17056840 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAGTTTA-T
* *
17056865 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
17056889 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
17056913 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
17056936 ATATGATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 43 0.72
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:17056934 original size:50 final size:50
Alignment explanation
Indices: 17056841--17056935 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
17056831 AAGAAGTGCT
**
17056841 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
* **
17056891 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
17056936 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:17057174 original size:31 final size:31
Alignment explanation
Indices: 17057131--17057214 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
17057121 CGTTTACAGT
*
17057131 AAAGACTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
17057162 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
17057193 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
17057215 TCAAGACTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:17059079 original size:18 final size:18
Alignment explanation
Indices: 17059056--17059118 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
17059046 CAGTCATCAA
17059056 TAATAATCAGTTATTCAG
1 TAATAATCAGTTATTCAG
17059074 TAATAATCA-TCTATTCAG
1 TAATAATCAGT-TATTCAG
* *
17059092 TAACACTC-GTTTATTCAG
1 TAATAATCAG-TTATTCAG
*
17059110 TAATGATCA
1 TAATAATCA
17059119 TTTTTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (18 bp):
TAATAATCAGTTATTCAG
Found at i:17059301 original size:6 final size:6
Alignment explanation
Indices: 17059281--17059331 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
17059271 CATCGTATCG
* * * * *
17059281 GTAACA GTAAAA GTAGCA GTAACA GTAACA ATAGCA ATAACA GTAACA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA
17059329 GTA
1 GTA
17059332 GCGGTACACA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:17059304 original size:18 final size:18
Alignment explanation
Indices: 17059281--17059333 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
17059271 CATCGTATCG
17059281 GTAACAGTAAAAGTAGCA
1 GTAACAGTAAAAGTAGCA
17059299 GTAACAGTAACAA-TAGCA
1 GTAACAGTAA-AAGTAGCA
* *
17059317 ATAACAGTAACAGTAGC
1 GTAACAGTAAAAGTAGC
17059334 GGTACACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.90
19 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (18 bp):
GTAACAGTAAAAGTAGCA
Found at i:17063430 original size:26 final size:26
Alignment explanation
Indices: 17063401--17063508 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
17063391 TGGTACAAAT
17063401 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
17063427 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17063453 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17063479 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17063505 TGAT
1 TGAT
17063509 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:17065210 original size:27 final size:26
Alignment explanation
Indices: 17065106--17065217 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
17065096 AGGAAGCGTC
* *
17065106 CTGGTGGCTATGCCACAAATATCTGATT
1 CTGGTGGCTCTGCCAC-ATTATCTG-TT
*
17065134 -TGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
*
17065160 CTGGTGGCTTTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGT-T
* *
17065188 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
17065214 CTGG
1 CTGG
17065218 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.11
27 48 0.67
28 16 0.22
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:17065214 original size:54 final size:54
Alignment explanation
Indices: 17065106--17065217 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
17065096 AGGAAGCGTC
* * *
17065106 CTGGTGGCTATGCCACAAATATCTGATTTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
17065160 CTGGTGGCTTTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
17065214 CTGG
1 CTGG
17065218 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:17068172 original size:43 final size:42
Alignment explanation
Indices: 17068125--17068220 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
17068115 TCCTAGACGT
* *
17068125 GGTCTTACATGTAA-TCAAACATCGATGCCACTGTCCCAGACAG
1 GGTCTTACACG-AAGTCAAACAT-GATGCCAATGTCCCAGACAG
* * *
17068168 GGTCTTACACGAAGTCAGATATGATGCCAATGTCCCAGACAT
1 GGTCTTACACGAAGTCAAACATGATGCCAATGTCCCAGACAG
17068210 GGTCTTACACG
1 GGTCTTACACG
17068221 CAAAACAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
42 31 0.66
43 16 0.34
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGAAGTCAAACATGATGCCAATGTCCCAGACAG
Found at i:17069346 original size:20 final size:19
Alignment explanation
Indices: 17069298--17069344 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
17069288 AAATTCTAAA
17069298 AAAATAAATACAATTAATT
1 AAAATAAATACAATTAATT
17069317 AAAGATAAATA-AATATAATT
1 AAA-ATAAATACAAT-TAATT
17069337 AAAATAAA
1 AAAATAAA
17069345 ATCCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAATACAATTAATT
Found at i:17069369 original size:27 final size:26
Alignment explanation
Indices: 17069339--17069400 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
17069329 ATATAATTAA
17069339 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
17069366 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
17069393 AATAAAAT
1 AATAAAAT
17069401 AGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:17071310 original size:30 final size:30
Alignment explanation
Indices: 17071276--17071336 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
17071266 TTCCCAAGCC
17071276 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
17071306 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
17071336 T
1 T
17071337 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:17073027 original size:20 final size:20
Alignment explanation
Indices: 17072999--17073036 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17072989 TACATTAAGT
17072999 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
17073019 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
17073037 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:17074689 original size:12 final size:12
Alignment explanation
Indices: 17074672--17074703 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
17074662 CAGTCAGATA
17074672 CCAGAGCGCCGG
1 CCAGAGCGCCGG
17074684 CCAGAGCGCCGG
1 CCAGAGCGCCGG
17074696 CCAGAGCG
1 CCAGAGCG
17074704 TACGTAGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.41, G:0.41, T:0.00
Consensus pattern (12 bp):
CCAGAGCGCCGG
Found at i:17080494 original size:20 final size:20
Alignment explanation
Indices: 17080466--17080503 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17080456 TACATTAAGT
17080466 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
17080486 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
17080504 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:17081955 original size:15 final size:15
Alignment explanation
Indices: 17081932--17081987 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
17081922 TTAATATCTG
17081932 AAAATAATAAATAAT
1 AAAATAATAAATAAT
* *
17081947 AAAACAAT-AA-GAT
1 AAAATAATAAATAAT
17081960 AAAATAAATAAA-AAT
1 AAAAT-AATAAATAAT
17081975 AAAATAA-AAATAA
1 AAAATAATAAATAA
17081988 AAATTGGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 9 0.26
14 9 0.26
15 16 0.47
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:17081981 original size:11 final size:11
Alignment explanation
Indices: 17081932--17081989 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
17081922 TTAATATCTG
17081932 AAAATAATAAAT
1 AAAATAA-AAAT
*
17081944 AATAA-AACAAT
1 AA-AATAAAAAT
*
17081955 AAGAT-AAAAT
1 AAAATAAAAAT
17081965 -AAATAAAAAT
1 AAAATAAAAAT
17081975 AAAATAAAAAT
1 AAAATAAAAAT
17081986 AAAA
1 AAAA
17081990 ATTGGGTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
9 3 0.08
10 10 0.26
11 19 0.50
12 4 0.11
13 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:17085682 original size:10 final size:10
Alignment explanation
Indices: 17085650--17085697 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
17085640 TAAATTCTAA
17085650 AAAGATAAAT
1 AAAGATAAAT
*
17085660 AAA-ATTAATT
1 AAAGA-TAAAT
17085670 AAAGATAAAT
1 AAAGATAAAT
*
17085680 AAAGATAATT
1 AAAGATAAAT
17085690 AAA-ATAAA
1 AAAGATAAA
17085698 ATCCTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.16
10 26 0.81
11 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:17085699 original size:20 final size:20
Alignment explanation
Indices: 17085650--17085697 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
17085640 TAAATTCTAA
17085650 AAAGATAAATAAAATTAATT
1 AAAGATAAATAAAATTAATT
17085670 AAAGATAAATAAAGA-TAATT
1 AAAGATAAATAAA-ATTAATT
17085690 AAA-ATAAA
1 AAAGATAAA
17085698 ATCCTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.19
20 21 0.78
21 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAGATAAATAAAATTAATT
Found at i:17085741 original size:15 final size:15
Alignment explanation
Indices: 17085721--17085749 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17085711 ATAATCCTAA
17085721 TAATTATCTTAATAT
1 TAATTATCTTAATAT
17085736 TAATTATCTTAATA
1 TAATTATCTTAATA
17085750 AAATAGAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATCTTAATAT
Found at i:17092882 original size:40 final size:38
Alignment explanation
Indices: 17092807--17092902 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 38
17092797 CTATCTCCGT
* *
17092807 CCAACCCAACACACCATATGGGGATAGAATCAACCCAC
1 CCAACCCTACACACCATATAGGGATAGAATCAACCCAC
** *
17092845 CCAACCCTACACACCGAGTATAGGGATTTAATCAACCCAT
1 CCAACCCTACACACC-A-TATAGGGATAGAATCAACCCAC
*
17092885 CCAGCCCTACACACCATA
1 CCAACCCTACACACCATA
17092903 AGGTACCGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 16 0.32
39 2 0.04
40 32 0.64
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (38 bp):
CCAACCCTACACACCATATAGGGATAGAATCAACCCAC
Found at i:17094036 original size:33 final size:33
Alignment explanation
Indices: 17093995--17094061 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
17093985 AACGAAAGAG
17093995 AAGAAATTTTGCCAAAAAGAAGGAAATAAGAAA
1 AAGAAATTTTGCCAAAAAGAAGGAAATAAGAAA
*
17094028 AAGAAATTTTTCCAAAAAGAAGGAAATAAGAAA
1 AAGAAATTTTGCCAAAAAGAAGGAAATAAGAAA
17094061 A
1 A
17094062 CCCCTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.61, C:0.06, G:0.16, T:0.16
Consensus pattern (33 bp):
AAGAAATTTTGCCAAAAAGAAGGAAATAAGAAA
Found at i:17101722 original size:26 final size:26
Alignment explanation
Indices: 17101693--17101802 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
17101683 TGGTACAAAT
17101693 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17101719 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
17101745 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
17101771 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17101797 TGATAA
1 TGATAA
17101803 GAATATCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:17106831 original size:25 final size:25
Alignment explanation
Indices: 17106790--17106896 Score: 189
Period size: 25 Copynumber: 4.2 Consensus size: 25
17106780 TGGTACAAAT
17106790 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTT-CA
17106816 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTT-CA
17106841 TGATAATGGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCA
17106866 TGATAATGGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCA
17106891 TGATAA
1 TGATAA
17106897 GAATTCATGT
Statistics
Matches: 80, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
25 58 0.73
26 22 0.28
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.36
Consensus pattern (25 bp):
TGATAATGGGTTAGGTAAATGTTCA
Found at i:17106845 original size:51 final size:50
Alignment explanation
Indices: 17106790--17106896 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 50
17106780 TGGTACAAAT
17106790 TGATAATGGGTTAGGTAAATGTTCCATGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTT-CATGATAATGGGTTAGGTAAATGTT-CA
17106841 TGATAATGGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTCA
1 TGATAATGGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTCA
17106891 TGATAA
1 TGATAA
17106897 GAATTCATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
50 17 0.31
51 38 0.69
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.36
Consensus pattern (50 bp):
TGATAATGGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTCA
Found at i:17112628 original size:26 final size:26
Alignment explanation
Indices: 17112599--17112708 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
17112589 TGGTACAAAT
17112599 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17112625 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
17112651 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
17112677 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17112703 TGATAA
1 TGATAA
17112709 GAATTCATGT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:17135952 original size:28 final size:28
Alignment explanation
Indices: 17135920--17135979 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
17135910 CATATTAATA
17135920 GGGTATAGGAAAAGTCTCATAACTTATG
1 GGGTATAGGAAAAGTCTCATAACTTATG
* * *
17135948 GGGTATAGGAAGAGTTTTATAACTTATG
1 GGGTATAGGAAAAGTCTCATAACTTATG
17135976 GGGT
1 GGGT
17135980 TGATAATGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGTATAGGAAAAGTCTCATAACTTATG
Found at i:17141357 original size:28 final size:28
Alignment explanation
Indices: 17141326--17141388 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
17141316 TCCCATATTA
17141326 ATGGGGTATAGGAAAAGTCTCATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
* * *
17141354 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
17141382 ATGGGGT
1 ATGGGGT
17141389 TGACAATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCTCATAACTT
Found at i:17146309 original size:13 final size:15
Alignment explanation
Indices: 17146280--17146315 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
17146270 AAATTTAACT
17146280 ATATAT-TTTTAAAA
1 ATATATGTTTTAAAA
17146294 ATA-ATGTTTT-AAA
1 ATATATGTTTTAAAA
17146307 ATATATGTT
1 ATATATGTT
17146316 ACAAATTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
ATATATGTTTTAAAA
Found at i:17152945 original size:65 final size:64
Alignment explanation
Indices: 17152845--17152972 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 64
17152835 ACCACTTACG
*
17152845 CACCCTATTTTTCTTAAGCATCGAATGTAGGTTCCAACATTCTGTATTATAATGTTTGTATATA
1 CACCCTATTTTTCTTAAGCATCGAATGTAGATTCCAACATTCTGTATTATAATGTTTGTATATA
* *
17152909 CACCCTATTTTTCTTCAAGTATCGAATGTAGATTCCAACATTCTGTGTTATAATGTTTGTATAT
1 CACCCTATTTTTCTT-AAGCATCGAATGTAGATTCCAACATTCTGTATTATAATGTTTGTATAT
17152973 TGTTGATTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 15 0.25
65 45 0.75
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (64 bp):
CACCCTATTTTTCTTAAGCATCGAATGTAGATTCCAACATTCTGTATTATAATGTTTGTATATA
Found at i:17159305 original size:5 final size:5
Alignment explanation
Indices: 17159295--17159409 Score: 56
Period size: 5 Copynumber: 21.6 Consensus size: 5
17159285 ATCACCCTAT
* *
17159295 TTTTA TTTTA TTTTA -TTTA TTATTTA TTATA TTTT- TTTATT TTTTA
1 TTTTA TTTTA TTTTA TTTTA -T-TTTA TTTTA TTTTA TTT-TA TTTTA
* **
17159341 TTGTA TTAAA CTTTTTA TTTTA -TTTA TTATTA CTTATTA TTTTTA TTTTA
1 TTTTA TTTTA --TTTTA TTTTA TTTTA TT-TTA -TT-TTA -TTTTA TTTTA
**
17159391 TTAAA TTTTTA TTTTA TTT
1 TTTTA -TTTTA TTTTA TTT
17159410 ATTATTCTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
4 11 0.13
5 47 0.55
6 13 0.15
7 15 0.17
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:17159332 original size:24 final size:23
Alignment explanation
Indices: 17159292--17159414 Score: 89
Period size: 24 Copynumber: 5.4 Consensus size: 23
17159282 TTAATCACCC
* *
17159292 TATTT-TTATTTTATTTTATTTAT
1 TATTTATTATATTTTTTTATTT-T
17159315 TATTTATTATATTTTTTTATTTTT
1 TATTTATTATATTTTTTTA-TTTT
**
17159339 TATTGTATTA-AACTTTTTA-TTT
1 TATT-TATTATATTTTTTTATTTT
* *
17159361 TATTTATTAT-TACTTATTATTTT
1 TATTTATTATAT-TTTTTTATTTT
*
17159384 TATTTTATTA-A-ATTTTTA-TTT
1 TA-TTTATTATATTTTTTTATTTT
17159405 TATTTATTAT
1 TATTTATTAT
17159415 TCTTATACTT
Statistics
Matches: 83, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
20 7 0.08
21 10 0.12
22 18 0.22
23 10 0.12
24 30 0.36
25 8 0.10
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (23 bp):
TATTTATTATATTTTTTTATTTT
Found at i:17159364 original size:22 final size:21
Alignment explanation
Indices: 17159336--17159413 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 21
17159326 TTTTTTTATT
17159336 TTTTATTGTATTAAACTTTTTA
1 TTTTATT-TATTAAACTTTTTA
* *
17159358 TTTTATTTATTATTACTTATTA
1 TTTTATTTATTA-AACTTTTTA
17159380 TTTTTATTTTATTAAA-TTTTTA
1 -TTTTA-TTTATTAAACTTTTTA
17159402 TTTTATTTATTA
1 TTTTATTTATTA
17159414 TTCTTATACT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.14
21 10 0.20
22 19 0.39
23 6 0.12
24 7 0.14
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (21 bp):
TTTTATTTATTAAACTTTTTA
Found at i:17159414 original size:28 final size:28
Alignment explanation
Indices: 17159292--17159420 Score: 81
Period size: 28 Copynumber: 4.5 Consensus size: 28
17159282 TTAATCACCC
* *
17159292 TATTTTTATTTTATTTTATTTATTATTTAT
1 TATTTTTATTTTA--TTAATTATTACTTAT
* *
17159322 TATATTT-TTTTATT--TT-TTATTGTAT
1 TATTTTTATTTTATTAATTATTACT-TAT
*
17159347 TAAACTTTTTATTTTATTTATTATTACTTAT
1 T--A-TTTTTATTTTATTAATTATTACTTAT
*
17159378 TATTTTTATTTTATTAAATTTTTA-TT-T
1 TATTTTTATTTTATT-AATTATTACTTAT
17159405 TATTTATTATTCTTAT
1 TATTT-TTATT-TTAT
17159421 ACTTATATTC
Statistics
Matches: 83, Mismatches: 5, Indels: 23
0.75 0.05 0.21
Matches are distributed among these distances:
24 5 0.06
25 6 0.07
27 9 0.11
28 24 0.29
29 23 0.28
30 6 0.07
31 6 0.07
32 4 0.05
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (28 bp):
TATTTTTATTTTATTAATTATTACTTAT
Found at i:17159438 original size:44 final size:43
Alignment explanation
Indices: 17159345--17159459 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 43
17159335 TTTTTATTGT
* * *
17159345 ATTAAACTTTTTATTTTATTTATTATTACTTATTATTTTTATTTT
1 ATTAAA-TTTTTATTTTATTTATTATT-CTTATTACTTATATTTA
17159390 ATTAAATTTTTATTTTATTTATTATTCTTA-TACTTATATTCTAA
1 ATTAAATTTTTATTTTATTTATTATTCTTATTACTTATATT-T-A
* *
17159434 ATT-AATTTTAATTTT-TTTATTTTTCT
1 ATTAAATTTTTATTTTATTTATTATTCT
17159460 ATTTTTTAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 18 0.29
43 16 0.25
44 23 0.37
45 6 0.10
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (43 bp):
ATTAAATTTTTATTTTATTTATTATTCTTATTACTTATATTTA
Found at i:17159572 original size:22 final size:21
Alignment explanation
Indices: 17159528--17159582 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
17159518 ACTATTGTTG
*
17159528 TTTTATTTTTTTTATGTTTCT
1 TTTTATTTTTTTTATGTTGCT
17159549 TTTTAATTTTGTTTTA-GTTGC-
1 TTTT-ATTTT-TTTTATGTTGCT
17159570 -TTTATTTTTTTTA
1 TTTTATTTTTTTTA
17159583 ATTTTCTTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 3 0.10
21 4 0.13
22 9 0.29
23 5 0.16
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTATTTTTTTTATGTTGCT
Found at i:17165141 original size:11 final size:11
Alignment explanation
Indices: 17165097--17165179 Score: 87
Period size: 11 Copynumber: 7.5 Consensus size: 11
17165087 TTTTGCAGGT
17165097 TTTTGGTGTTG
1 TTTTGGTGTTG
* *
17165108 TTGGTGATGTTG
1 TT-TTGGTGTTG
*
17165120 TTTTTTGTGTTG
1 -TTTTGGTGTTG
*
17165132 TTTTGTTGTTG
1 TTTTGGTGTTG
17165143 -TTTGGTGTTG
1 TTTTGGTGTTG
*
17165153 TTTTGATGTTG
1 TTTTGGTGTTG
*
17165164 TTTTGGTGCTG
1 TTTTGGTGTTG
17165175 TTTTG
1 TTTTG
17165180 CTGCTACTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
10 9 0.16
11 34 0.59
12 13 0.22
13 2 0.03
ACGTcount: A:0.02, C:0.01, G:0.33, T:0.64
Consensus pattern (11 bp):
TTTTGGTGTTG
Found at i:17165150 original size:21 final size:21
Alignment explanation
Indices: 17165115--17165179 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
17165105 TTGTTGGTGA
*
17165115 TGTTGTT-TTTTGTGTTGTTT
1 TGTTGTTGTTTGGTGTTGTTT
17165135 TGTTGTTGTTTGGTGTTGTTT
1 TGTTGTTGTTTGGTGTTGTTT
* *
17165156 TGATGTTGTTTTGGTGCTGTTT
1 TGTTGTTG-TTTGGTGTTGTTT
17165178 TG
1 TG
17165180 CTGCTACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.17
21 19 0.47
22 14 0.35
ACGTcount: A:0.02, C:0.02, G:0.31, T:0.66
Consensus pattern (21 bp):
TGTTGTTGTTTGGTGTTGTTT
Found at i:17165163 original size:32 final size:30
Alignment explanation
Indices: 17165118--17165177 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
17165108 TTGGTGATGT
* *
17165118 TGTTTTTTGTGTTGTTTTGTTGTTGTTTGG
1 TGTTTTTTGTGTTGTTTTGGTGCTGTTTGG
17165148 TGTTGTTTTGATGTTGTTTTGGTGCTGTTT
1 TGTT-TTTTG-TGTTGTTTTGGTGCTGTTT
17165178 TGCTGCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.15
31 5 0.19
32 17 0.65
ACGTcount: A:0.02, C:0.02, G:0.30, T:0.67
Consensus pattern (30 bp):
TGTTTTTTGTGTTGTTTTGGTGCTGTTTGG
Found at i:17165445 original size:25 final size:25
Alignment explanation
Indices: 17165412--17165460 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
17165402 TTTATTTTAA
* *
17165412 TATTTATTT-TTATGTTTTTAAATG
1 TATTTATTTATTATATTTTAAAATG
17165436 TATTTGATTTATTATATTTTAAAAT
1 TATTT-ATTTATTATATTTTAAAAT
17165461 TTTCTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (25 bp):
TATTTATTTATTATATTTTAAAATG
Found at i:17169433 original size:20 final size:19
Alignment explanation
Indices: 17169385--17169455 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
17169375 AACTTTTCCT
*
17169385 TTATTTTATTT-TCATGTTCA
1 TTATTTTATTTCTTAT-TT-A
17169405 TTA-TTTATTTCTTATTTA
1 TTATTTTATTTCTTATTTA
*
17169423 CTT-TCTTTATTCCTTATTTA
1 -TTAT-TTTATTTCTTATTTA
17169443 TTATTTTATTTCT
1 TTATTTTATTTCT
17169456 AGCTTACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
18 1 0.02
19 21 0.49
20 21 0.49
ACGTcount: A:0.18, C:0.11, G:0.01, T:0.69
Consensus pattern (19 bp):
TTATTTTATTTCTTATTTA
Found at i:17171112 original size:12 final size:12
Alignment explanation
Indices: 17171026--17171127 Score: 80
Period size: 12 Copynumber: 8.3 Consensus size: 12
17171016 GTCTAATTTT
17171026 TTTTTATGTTTA
1 TTTTTATGTTTA
* *
17171038 TGTTTATCTTTA
1 TTTTTATGTTTA
* *
17171050 CTTTTATCTTTTA
1 TTTTTAT-GTTTA
*
17171063 TTTTTATCTTTTA
1 TTTTTAT-GTTTA
*
17171076 TCTTTTATTTTTA
1 T-TTTTATGTTTA
*
17171089 TTTTTATTTTTA
1 TTTTTATGTTTA
*
17171101 TTTTTCTGTTTA
1 TTTTTATGTTTA
* *
17171113 TGTTTGTG-TTA
1 TTTTTATGTTTA
17171124 TTTT
1 TTTT
17171128 CTTATTTTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
11 6 0.08
12 42 0.55
13 23 0.30
14 6 0.08
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.75
Consensus pattern (12 bp):
TTTTTATGTTTA
Found at i:17171117 original size:6 final size:6
Alignment explanation
Indices: 17171022--17171105 Score: 98
Period size: 6 Copynumber: 13.7 Consensus size: 6
17171012 TTTAGTCTAA
* * * *
17171022 TTTT-T TTTTAT GTTTAT GTTTAT CTTTAC TTTTAT CTTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT
17171070 CTTTTAT CTTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 -TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTT
17171106 CTGTTTATGT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.06
6 48 0.68
7 19 0.27
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:17177832 original size:17 final size:17
Alignment explanation
Indices: 17177810--17177843 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17177800 TGCTCAACTG
17177810 TGAGCATGGTAAGTGTT
1 TGAGCATGGTAAGTGTT
17177827 TGAGCATGGTAAGTGTT
1 TGAGCATGGTAAGTGTT
17177844 GTAATTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.35, T:0.35
Consensus pattern (17 bp):
TGAGCATGGTAAGTGTT
Found at i:17182324 original size:26 final size:24
Alignment explanation
Indices: 17182294--17182342 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
17182284 AATAAAAAAG
*
17182294 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
17182320 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
17182343 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:17182362 original size:21 final size:21
Alignment explanation
Indices: 17182313--17182371 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
17182303 ATAATAAATC
*
17182313 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
17182333 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
17182355 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
17182372 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:17182448 original size:15 final size:16
Alignment explanation
Indices: 17182418--17182450 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17182408 AAATAGTTCT
17182418 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
17182435 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
17182450 A
1 A
17182451 AAAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:17183430 original size:31 final size:32
Alignment explanation
Indices: 17183358--17183431 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
17183348 AAATTTGTTA
17183358 TTTAGTCACT-TCCGTTAGATAAATTGTCAAT
1 TTTAGTCACTCTCCGTTAGATAAATTGTCAAT
* * *
17183389 TTTAGTCACTCT-TGTTAGATAAGTTGTTAAT
1 TTTAGTCACTCTCCGTTAGATAAATTGTCAAT
17183420 TTTAGTCACTCT
1 TTTAGTCACTCT
17183432 ACCTTTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (32 bp):
TTTAGTCACTCTCCGTTAGATAAATTGTCAAT
Found at i:17184207 original size:6 final size:6
Alignment explanation
Indices: 17184196--17184224 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17184186 AACATAAGAA
17184196 TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
17184225 AAAAGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:17187059 original size:20 final size:20
Alignment explanation
Indices: 17187016--17187056 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
17187006 TTATAAAAAC
*
17187016 AATAAATTTAACTAATTATA
1 AATAAAATTAACTAATTATA
*
17187036 AATAAAATTAA-TTATTATA
1 AATAAAATTAACTAATTATA
17187055 AA
1 AA
17187057 ATATAAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAAAATTAACTAATTATA
Found at i:17188430 original size:3 final size:3
Alignment explanation
Indices: 17188422--17188471 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
17188412 CAATCAGATA
17188422 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17188470 AA
1 AA
17188472 AGAAATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17191454 original size:3 final size:3
Alignment explanation
Indices: 17191446--17191471 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17191436 TTTCCTCCCG
17191446 ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA AC
17191472 GCCGCAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:17192480 original size:6 final size:6
Alignment explanation
Indices: 17192469--17192507 Score: 51
Period size: 7 Copynumber: 6.0 Consensus size: 6
17192459 TGTCTCTTAG
17192469 TTTTTA TTTTTA TTTTTTA TTTTTA TTCTTTA TTCTTTA
1 TTTTTA TTTTTA -TTTTTA TTTTTA TT-TTTA TT-TTTA
17192508 AACATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 14 0.45
7 17 0.55
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:17192487 original size:13 final size:13
Alignment explanation
Indices: 17192469--17192507 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
17192459 TGTCTCTTAG
17192469 TTTTTATTTTTAT
1 TTTTTATTTTTAT
17192482 TTTTTATTTTTAT
1 TTTTTATTTTTAT
*
17192495 TCTTTATTCTTTA
1 TTTTTATT-TTTA
17192508 AACATAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:17193997 original size:5 final size:5
Alignment explanation
Indices: 17193987--17194018 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
17193977 TTGTTTCCTT
17193987 TTTTA TTTTA TTTTA TTTTA TTTTA TTATTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA T
17194019 AGTAAGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:17194553 original size:10 final size:9
Alignment explanation
Indices: 17194528--17194552 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17194518 TCAGATAAAC
17194528 AAAAAAATA
1 AAAAAAATA
17194537 AAAAAAATA
1 AAAAAAATA
17194546 AAAAAAA
1 AAAAAAA
17194553 AATTGCAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:17198268 original size:2 final size:2
Alignment explanation
Indices: 17198261--17198295 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
17198251 AATTGAACAA
*
17198261 AT AT AT AT AT AT AT AT AT AT AT AT GT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17198296 GAGAAGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17206940 original size:40 final size:41
Alignment explanation
Indices: 17206890--17206985 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
17206880 TATCTCGGTA
*
17206890 TCGCACACTTAGTGCC-TCATATAGCTAAAGCTA-TTCCAAC
1 TCGCACACTTAGTGCCAT-ATATAGCCAAAGCTATTTCCAAC
* * * *
17206930 TCGCACACTTAGTGCCATTTGTAGCCGAAGCTATTTCGAAC
1 TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTCCAAC
17206971 -CGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
17206986 GAACATAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 42 0.86
41 7 0.14
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTCCAAC
Done.