Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 12 of 438
Found at i:3336175 original size:21 final size:20
Alignment explanation
Indices: 3336142--3336181 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3336132 TAATTTTTCG
3336142 ATATTCGATAATAAATAAAA
1 ATATTCGATAATAAATAAAA
* *
3336162 ATATTTGATTAATAATTAAA
1 ATATTCGA-TAATAAATAAA
3336182 TTGGAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
ATATTCGATAATAAATAAAA
Found at i:3336360 original size:17 final size:17
Alignment explanation
Indices: 3336318--3336360 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3336308 CAATAATTTT
*
3336318 TATTAAAAAGTTAAAAA
1 TATTAAAAAATTAAAAA
*
3336335 T-TCATAAAAATTAAAAA
1 TATTA-AAAAATTAAAAA
3336352 TATTAAAAA
1 TATTAAAAA
3336361 GTTTTTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
TATTAAAAAATTAAAAA
Found at i:3337455 original size:25 final size:25
Alignment explanation
Indices: 3337421--3337475 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
3337411 AAAAAGCAAA
3337421 GTATACTAGTAAAATCAAATGGCAT
1 GTATACTAGTAAAATCAAATGGCAT
3337446 GTATACTAGTAAAATCAAATGGCAT
1 GTATACTAGTAAAATCAAATGGCAT
3337471 GTATA
1 GTATA
3337476 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (25 bp):
GTATACTAGTAAAATCAAATGGCAT
Found at i:3343219 original size:146 final size:146
Alignment explanation
Indices: 3342955--3343245 Score: 417
Period size: 146 Copynumber: 2.0 Consensus size: 146
3342945 GTCCAAATAT
* * * *
3342955 GCTATCAACCCCAAGACTGCTTTTGCCTATTTAAACACAATTCAATCATTCAACATTAGAATACT
1 GCTATCAACCCCAAGACTGCTGTTGCCTAATTAAACACAATTCAATCATTCAACATTACAACACT
** * * *
3343020 TGATTTCGACTTAAAATCCAGCAACAATACAAGCACAGAAGTAGATTATTCATCCCTCCACACTA
66 CAATTTCGACTTAAAATCCAGCAACAATACAAGCACAGAAGTAGATTATTCATCCCTACAAACCA
3343085 ACAAATTCAAACAAAA
131 ACAAATTCAAACAAAA
**
3343101 GCTATCAACCCCAAGACTGCTGTT-CC-AATTAAA-ACAATTTTCAATCATTCAGTATTACAACA
1 GCTATCAACCCCAAGACTGCTGTTGCCTAATTAAACACAA--TTCAATCATTCAACATTACAACA
* *
3343163 CTCAATTTCTACTTAAAAATCCAGCAACAATACAAGCACATAAGTAGATTATTCATCCCTACAAA
64 CTCAATTTCGACTT-AAAATCCAGCAACAATACAAGCACAGAAGTAGATTATTCATCCCTACAAA
3343228 CCAACAAATTCAAACAAA
128 CCAACAAATTCAAACAAA
3343246 TGAGAATAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
143 4 0.03
144 6 0.05
145 32 0.25
146 87 0.67
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (146 bp):
GCTATCAACCCCAAGACTGCTGTTGCCTAATTAAACACAATTCAATCATTCAACATTACAACACT
CAATTTCGACTTAAAATCCAGCAACAATACAAGCACAGAAGTAGATTATTCATCCCTACAAACCA
ACAAATTCAAACAAAA
Found at i:3344579 original size:23 final size:22
Alignment explanation
Indices: 3344553--3344596 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
3344543 TTTTTATTTT
* *
3344553 TTTTTCTTGAATTTTTTAGAAAA
1 TTTTGCTTAAATTTTTT-GAAAA
*
3344576 TTTTGGTTAAATTTTTTGAAA
1 TTTTGCTTAAATTTTTTGAAA
3344597 GTCCTCGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTTGCTTAAATTTTTTGAAAA
Found at i:3345418 original size:29 final size:29
Alignment explanation
Indices: 3345382--3345440 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3345372 TTTTGATAAA
3345382 TGTTTACTCATTAAGTTAAAAAGTAAAAC
1 TGTTTACTCATTAAGTTAAAAAGTAAAAC
3345411 TGTTTACTCATTAAGTTAAAAAGTAAAAC
1 TGTTTACTCATTAAGTTAAAAAGTAAAAC
3345440 T
1 T
3345441 ATCATATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (29 bp):
TGTTTACTCATTAAGTTAAAAAGTAAAAC
Found at i:3346410 original size:21 final size:21
Alignment explanation
Indices: 3346386--3346427 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3346376 TATCAAAAAA
3346386 TTATGAAAT-TTTAGAATTTTT
1 TTAT-AAATATTTAGAATTTTT
*
3346407 TTATAAATATTTTGAATTTTT
1 TTATAAATATTTAGAATTTTT
3346428 GAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTATAAATATTTAGAATTTTT
Found at i:3346426 original size:20 final size:20
Alignment explanation
Indices: 3346393--3346450 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
3346383 AAATTATGAA
3346393 ATTTTAGAATTTTTTTATAAA-T
1 ATTTT-GAA-TTTTTTA-AAATT
*
3346415 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTTAAAATT
3346435 ATTTTGAATTGTTTTA
1 ATTTTGAATT-TTTTA
3346451 GATTTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.09
20 17 0.53
21 7 0.22
22 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (20 bp):
ATTTTGAATTTTTTAAAATT
Found at i:3346674 original size:23 final size:25
Alignment explanation
Indices: 3346623--3346675 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
3346613 AGTTAACTCA
*
3346623 AAAAATTGAATAACTCGAATAATTC
1 AAAATTTGAATAACTCGAATAATTC
*
3346648 --AATTTGATTAACTCG-A-AATTC
1 AAAATTTGAATAACTCGAATAATTC
3346669 AAAATTT
1 AAAATTT
3346676 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 5 0.21
22 1 0.04
23 18 0.75
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (25 bp):
AAAATTTGAATAACTCGAATAATTC
Found at i:3347978 original size:17 final size:17
Alignment explanation
Indices: 3347958--3347991 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3347948 AGATTTAGGT
3347958 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
3347975 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
3347992 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:3349857 original size:22 final size:21
Alignment explanation
Indices: 3349824--3349872 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
3349814 TCATATATAC
3349824 ATTTT-TAGTTTTAT-ATTTAT
1 ATTTTATAGTTTTATAATTT-T
3349844 ATTTTATAGTTTTTATAATTTT
1 ATTTTATAG-TTTTATAATTTT
3349866 ATTTTAT
1 ATTTTAT
3349873 TTAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.19
21 3 0.12
22 14 0.54
23 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
ATTTTATAGTTTTATAATTTT
Found at i:3350327 original size:23 final size:25
Alignment explanation
Indices: 3350283--3350333 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
3350273 TCGTTATTTT
* *
3350283 AAATATTAACAAAATTATAATTATA
1 AAATATTAACAAAAATAAAATTATA
3350308 AAATA-TAA-AAAAATAAAATTATA
1 AAATATTAACAAAAATAAAATTATA
3350331 AAA
1 AAA
3350334 CCAAAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.67
24 3 0.12
25 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AAATATTAACAAAAATAAAATTATA
Found at i:3354295 original size:24 final size:24
Alignment explanation
Indices: 3354263--3354309 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3354253 TTAAACTATT
*
3354263 ATTATGAAGCATCTTACAGTTTTC
1 ATTATGAAGCATCTTAAAGTTTTC
**
3354287 ATTATGAAGTGTCTTAAAGTTTT
1 ATTATGAAGCATCTTAAAGTTTT
3354310 TCTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (24 bp):
ATTATGAAGCATCTTAAAGTTTTC
Found at i:3361053 original size:20 final size:21
Alignment explanation
Indices: 3361028--3361067 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3361018 TTGATATTGA
3361028 CCGAAA-TGAACCAAAACACT
1 CCGAAACTGAACCAAAACACT
*
3361048 CCGAAACTTTAACCAAAACA
1 CCGAAAC-TGAACCAAAACA
3361068 AAATATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.50, C:0.30, G:0.07, T:0.12
Consensus pattern (21 bp):
CCGAAACTGAACCAAAACACT
Found at i:3365557 original size:9 final size:9
Alignment explanation
Indices: 3365530--3365570 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
3365520 ATAAGTATAA
3365530 AATTAACCG
1 AATTAACCG
* *
3365539 AATGACCCG
1 AATTAACCG
3365548 AATTAACCG
1 AATTAACCG
3365557 AATTAACCG
1 AATTAACCG
3365566 AATTA
1 AATTA
3365571 TTTGTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:3365603 original size:5 final size:6
Alignment explanation
Indices: 3365588--3365628 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
3365578 AAAATTATAT
*
3365588 TTTTTA TTTTTA TTTTTA GTTTTAAA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
3365629 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:3365616 original size:20 final size:21
Alignment explanation
Indices: 3365593--3365636 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3365583 TATATTTTTT
3365593 ATTTTTATTTTTAGTT-TTAA
1 ATTTTTATTTTTAGTTATTAA
*
3365613 ATTTTTATTTTTATTTATTAA
1 ATTTTTATTTTTAGTTATTAA
3365634 ATT
1 ATT
3365637 ATTTGTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTTATTTTTAGTTATTAA
Found at i:3367795 original size:2 final size:2
Alignment explanation
Indices: 3367777--3367896 Score: 72
Period size: 2 Copynumber: 66.5 Consensus size: 2
3367767 TTACTATTTT
* *
3367777 TA TA TA T- TA T- TA T- TA TA TA T- TT TA GTA TT TA 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
*
3367816 TA TA TA TA TA TA TA TA TA TA TA GT- TA T- TA -A CA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
3367854 T- TA T- TG TA T- TA TA TA T- TA T- TA TA TA TA TA TA T- TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3367890 TA TA TA T
1 TA TA TA T
3367897 TTTAGTACTA
Statistics
Matches: 94, Mismatches: 7, Indels: 34
0.70 0.05 0.25
Matches are distributed among these distances:
1 15 0.16
2 76 0.81
3 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:3367808 original size:22 final size:24
Alignment explanation
Indices: 3367774--3367900 Score: 81
Period size: 22 Copynumber: 5.2 Consensus size: 24
3367764 GACTTACTAT
3367774 TTTTATATATTAT-TAT-TATATA
1 TTTTATATATTATATATATATATA
3367796 TTTTAGTAT-TTATATATATATATA
1 TTTTA-TATATTATATATATATATA
*
3367820 -TATATATA-TATATATATAGT-TA
1 TTTTATATATTATATATATA-TATA
*
3367842 TTAACATTAT-TATTAT-TGTATTATATA
1 TT----TTATATATTATATATA-TATATA
*
3367869 TTATTATATATATATATTATGTATATA
1 TT-TTATATAT-TATA-TATATATATA
3367896 TTTTA
1 TTTTA
3367901 GTACTACATT
Statistics
Matches: 83, Mismatches: 5, Indels: 30
0.70 0.04 0.25
Matches are distributed among these distances:
22 24 0.29
23 11 0.13
24 11 0.13
25 3 0.04
26 12 0.14
27 20 0.24
28 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTTATATATTATATATATATATA
Found at i:3367965 original size:23 final size:22
Alignment explanation
Indices: 3367935--3367977 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3367925 GTTACGTATA
*
3367935 TATTTCTAATATCATATATTAAG
1 TATTTCTAAGATCAT-TATTAAG
3367958 TATTTCTAAGATCATTATTA
1 TATTTCTAAGATCATTATTA
3367978 TATACGTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (22 bp):
TATTTCTAAGATCATTATTAAG
Found at i:3368921 original size:30 final size:30
Alignment explanation
Indices: 3368885--3368999 Score: 176
Period size: 30 Copynumber: 3.8 Consensus size: 30
3368875 ACTTTTCTCA
*
3368885 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
3368915 ACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* * *
3368945 ACTAGCCACTCTTTTTCCACCACCAACTCT
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
3368975 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
3369000 CTTGTACCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.25, C:0.49, G:0.04, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:3368950 original size:60 final size:60
Alignment explanation
Indices: 3368885--3368999 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
3368875 ACTTTTCTCA
*
3368885 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAACTCC
* *
3368945 ACTAGCCACTCTTTTTCCACCACCAACTCTACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
3369000 CTTGTACCTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.25, C:0.49, G:0.04, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAACTCC
Found at i:3369599 original size:25 final size:25
Alignment explanation
Indices: 3369571--3369629 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3369561 TACGTGTATA
* *
3369571 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATTATG
* * *
3369596 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATG
3369621 TATATATAT
1 TATATATAT
3369630 ATATATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATG
Found at i:3369677 original size:22 final size:24
Alignment explanation
Indices: 3369651--3369709 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
3369641 ACATGTTATC
3369651 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
3369673 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
3369698 TTATGTACATAT
1 TTATGTATATAT
3369710 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:3369699 original size:25 final size:25
Alignment explanation
Indices: 3369667--3369715 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3369657 ATATATCTTA
**
3369667 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
3369692 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
3369716 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:3369895 original size:16 final size:15
Alignment explanation
Indices: 3369871--3369918 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3369861 TAATTATTAT
*
3369871 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
3369887 TATTTTAATATTTTA
1 TATTTTAATATTTTA
3369902 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3369918 T
1 T
3369919 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3369906 original size:7 final size:8
Alignment explanation
Indices: 3369871--3369922 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3369861 TAATTATTAT
*
3369871 TATTCTAA
1 TATTTTAA
*
3369879 TATTTTGA
1 TATTTTAA
3369887 TATTTTAA
1 TATTTTAA
3369895 TATTTT-A
1 TATTTTAA
3369902 TATTTTATA
1 TATTTTA-A
*
3369911 TATTTTAT
1 TATTTTAA
3369919 TATT
1 TATT
3369923 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:3371506 original size:12 final size:12
Alignment explanation
Indices: 3371489--3371519 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3371479 AACATTTTGA
3371489 CATTCATGCATT
1 CATTCATGCATT
3371501 CATTCATGCATT
1 CATTCATGCATT
3371513 CATTCAT
1 CATTCAT
3371520 ACACTGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:3378938 original size:73 final size:73
Alignment explanation
Indices: 3378847--3379228 Score: 356
Period size: 73 Copynumber: 5.0 Consensus size: 73
3378837 ATTTCTGATT
* * ** *
3378847 TTCA-AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACAAGCTGAGGTGGTTTT
1 TTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
*
3378911 AATTTATG
66 AATTTCTG
* * * * * *
3378919 TTCATAAAAAATTAGCTCATATTACAAGAGGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATT
1 TTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAAT
*
3378983 TTTAATTTCTGG
63 TTCAATTTCT-G
**
3378995 TTTTCAATTTCTGTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 --TTC-A--------TAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
3379060 GAGGTAATTTCAATTTCTG
55 GAGGTAATTTCAATTTCTG
** * *
3379079 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC
1 TTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
3379144 AATTTCTG
66 AATTTCTG
** * * **
3379152 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTT
1 TTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAAT
3379216 TTCAATTTCTG
63 TTCAATTTCTG
3379227 TT
1 TT
3379229 TTTCAATTTC
Statistics
Matches: 262, Mismatches: 28, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
72 7 0.03
73 143 0.55
75 46 0.18
76 1 0.00
78 3 0.01
79 1 0.00
82 2 0.01
84 1 0.00
85 23 0.09
87 33 0.13
88 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (73 bp):
TTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATTTCTG
Found at i:3379012 original size:14 final size:13
Alignment explanation
Indices: 3378981--3379014 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3378971 CGCTGAGGTA
3378981 TTTTTAATTTCTGG
1 TTTTTAATTTCT-G
*
3378995 TTTTCAATTTCTG
1 TTTTTAATTTCTG
3379008 TTTTTAA
1 TTTTTAA
3379015 AATCAACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.65
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:3379233 original size:14 final size:14
Alignment explanation
Indices: 3379214--3379242 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3379204 TGCTGAGGTC
3379214 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
3379228 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
3379242 T
1 T
3379243 CGTAAAAAAA
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:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:3379272 original size:167 final size:166
Alignment explanation
Indices: 3379085--3379400 Score: 510
Period size: 167 Copynumber: 1.9 Consensus size: 166
3379075 TCTGTTTGTC
*
3379085 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTA-ATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATATTTAAATTT
*
3379149 CTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGT
66 CTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGT
** *
3379213 CTTTTCAATTTCTGTTTTTCAATTTCTGTTCGTAAAAAA
128 AATTTCAATTTCTGTTTGTCAATTTCTGTTCGTAAAAAA
* *
3379252 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATATTTAAATTT
* *
3379317 CTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
66 CTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
3379382 TTCAATTTCTGTTTGTCAA
131 TTCAATTTCTGTTTGTCAA
3379401 AAATTAACTC
Statistics
Matches: 138, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
166 30 0.22
167 53 0.38
168 53 0.38
169 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (166 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATATTTAAATTT
CTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
TTCAATTTCTGTTTGTCAATTTCTGTTCGTAAAAAA
Found at i:3379431 original size:73 final size:73
Alignment explanation
Indices: 3379252--3379696 Score: 597
Period size: 74 Copynumber: 5.9 Consensus size: 73
3379242 TCGTAAAAAA
*
3379252 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTTCAATTT
*
3379317 CTGTTTTTC
65 CTGTTTGTC
* *
3379326 AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
3379391 TGTTTGTC
66 TGTTTGTC
* * * *
3379399 AAAAATTAACTCATATTACGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAAT
* *
3379463 TTCTGTTCGTAAAAAA
63 TTCTGTTTGT-----C
*
3379479 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTTCAATTT
*
3379544 CTGTTTTTC
65 CTGTTTGTC
* *
3379553 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
3379618 TGTTTGTC
66 TGTTTGTC
* * * *
3379626 AAAAATTAACTCATCTTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTCTTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAAT
3379690 TTCTGTT
63 TTCTGTT
3379697 CTTCAATTTC
Statistics
Matches: 329, Mismatches: 29, Indels: 25
0.86 0.08 0.07
Matches are distributed among these distances:
72 4 0.01
73 103 0.31
74 106 0.32
75 52 0.16
78 11 0.03
79 15 0.05
80 36 0.11
81 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTGTC
Found at i:3379623 original size:227 final size:227
Alignment explanation
Indices: 3379228--3379828 Score: 970
Period size: 227 Copynumber: 2.6 Consensus size: 227
3379218 CAATTTCTGT
3379228 TTTTCAATTTCTGTTCGTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTTCAATTTCTGTTCGTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
3379293 ACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTG
66 ACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
3379358 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTACGAGAG
131 AGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTACGAGAG
3379423 GTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
196 GTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
3379455 TTTTCAATTTCTGTTCGTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTTCAATTTCTGTTCGTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
3379520 ACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
66 ACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* *
3379585 AGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATCTTGCGAGAG
131 AGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTACGAGAG
3379650 GTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
196 GTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
* ** * *
3379682 TTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAAAAATCAACTCATATTGCAAAAGGTGAGTT
1 TTTTCAATTTCTGTTCGT-AA---------AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * * *
3379747 GAGCCTCGGGACACGCTGAGGTA-ATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAG
56 GAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAG
*
3379811 AGGTGAGTTGAGTCTCGG
121 AGGTGAGTTGAGCCTCGG
3379829 CTCACATGCT
Statistics
Matches: 349, Mismatches: 15, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
227 240 0.69
228 2 0.01
236 54 0.15
237 53 0.15
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (227 bp):
TTTTCAATTTCTGTTCGTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
ACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTACGAGAG
GTGAGTTGAGCCTCGGCTCACATGCTGAGGTC
Found at i:3379703 original size:14 final size:14
Alignment explanation
Indices: 3379684--3379711 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3379674 CTGAGGTCTT
3379684 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
3379698 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
3379712 GTAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCAATTTCTGTTC
Found at i:3379744 original size:163 final size:163
Alignment explanation
Indices: 3379553--3380196 Score: 952
Period size: 163 Copynumber: 3.9 Consensus size: 163
3379543 TCTGTTTTTC
3379553 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
*
3379618 TGTTTGTCAAAAATTAACTCATCTTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCT
66 TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCT
3379683 TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAA
131 TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAA
* *
3379716 AAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
*
3379781 TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCT
66 TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCT
* * *
3379846 TTTTAATTTCT-TCTTTTCAATTTCTGTTTTTCAATTTATA
131 TTTCAATTTCTGT-TCTTCAATTTCTG---TTC---GTA-A
3379886 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
1 ------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
*
3379951 AATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGCTG
60 AATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTG
3380016 AGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAA
125 AGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAA
* * *
3380055 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-ATTTCAATTT
* * * * *
3380120 CTGTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGG--GACACGCTGAGG
65 CTGTTTGTC--AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGG
**
3380183 TAATTTCAATTTCT
128 TCTTTTCAATTTCT
3380197 CTTTGTCAAA
Statistics
Matches: 438, Mismatches: 25, Indels: 35
0.88 0.05 0.07
Matches are distributed among these distances:
162 1 0.00
163 201 0.46
164 38 0.09
166 40 0.09
169 3 0.01
170 3 0.01
173 3 0.01
176 148 0.34
177 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (163 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCT
TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAA
Found at i:3379862 original size:14 final size:14
Alignment explanation
Indices: 3379843--3379882 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3379833 CATGCTGAGG
*
3379843 TCTTTTTAATTTCT
1 TCTTTTCAATTTCT
3379857 TCTTTTCAATTTCT
1 TCTTTTCAATTTCT
3379871 GT-TTTTCAATTT
1 -TCTTTTCAATTT
3379883 ATATTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.68
Consensus pattern (14 bp):
TCTTTTCAATTTCT
Found at i:3379889 original size:14 final size:14
Alignment explanation
Indices: 3379859--3379893 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3379849 TAATTTCTTC
* *
3379859 TTTTCAATTTCTGT
1 TTTTCAATTTATAT
3379873 TTTTCAATTTATAT
1 TTTTCAATTTATAT
3379887 TTTTCAA
1 TTTTCAA
3379894 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATAT
Found at i:3379975 original size:176 final size:178
Alignment explanation
Indices: 3379679--3380168 Score: 654
Period size: 176 Copynumber: 2.8 Consensus size: 178
3379669 ACATGCTGAG
* *
3379679 GTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAAAAATCAACTCATATTGCAAAAGGTGA
1 GTCTTTTCAATTTCTGTTCTTCAATTTATATTCGTAAAAAAATCAACTCATATTGCAAAAGGTGA
3379744 GTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCG
66 GTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCG
* * *
3379809 AGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCT
131 AGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTCTTTTCAATTTCT
* * ** * *
3379857 -TCTTTTCAATTTCTGTTTTTCAATTTATATT-TTTCAAAAATCAACTCATATTGCGAGAGGTGA
1 GTCTTTTCAATTTCTGTTCTTCAATTTATATTCGTAAAAAAATCAACTCATATTGCAAAAGGTGA
3379920 GTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCG
66 GTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCG
3379985 AGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTCTTTTCAATTTCT
131 AGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTCTTTTCAATTTCT
* * *
3380033 GT-TCTTCAATTTCTG--------------TTCGTAAAAAAATCAACTCATATTGCGAGAGGTGA
1 GTCTTTTCAATTTCTGTTCTTCAATTTATATTCGTAAAAAAATCAACTCATATTGCAAAAGGTGA
* * * * *
3380083 GTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAAAATCAACTCATATT
66 GTTGAGCCTCGGGACACGCTGAGGTA-ATTTCAATTTCTGTTTGTC--AAAAATTAACTCATATT
*
3380148 GCGAAAGGTGAGTTGAGCCTC
128 GCGAGAGGTGAGTTGAGCCTC
3380169 GGGACACGCT
Statistics
Matches: 286, Mismatches: 21, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
162 2 0.01
163 54 0.19
164 16 0.06
166 36 0.13
176 149 0.52
177 29 0.10
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (178 bp):
GTCTTTTCAATTTCTGTTCTTCAATTTATATTCGTAAAAAAATCAACTCATATTGCAAAAGGTGA
GTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCG
AGAGGTGAGTTGAGCCTCAGCTCACATGCTGAGGTCTTTTCAATTTCT
Found at i:3379993 original size:73 final size:75
Alignment explanation
Indices: 3379874--3380035 Score: 229
Period size: 73 Copynumber: 2.2 Consensus size: 75
3379864 AATTTCTGTT
* * * *
3379874 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACAC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCGCACAC
3379937 GCTGAGGTAA
66 GCTGAGGTAA
* * *
3379947 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACAT
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCGCACAC
**
3380012 GCTGAGGTCT
66 GCTGAGGTAA
3380022 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
3380036 CTTCAATTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 52 0.67
74 1 0.01
75 25 0.32
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (75 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCGCACAC
GCTGAGGTAA
Found at i:3380042 original size:14 final size:14
Alignment explanation
Indices: 3380023--3380050 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3380013 CTGAGGTCTT
3380023 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
3380037 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
3380051 GTAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCAATTTCTGTTC
Found at i:3380130 original size:89 final size:88
Alignment explanation
Indices: 3379947--3380130 Score: 262
Period size: 90 Copynumber: 2.1 Consensus size: 88
3379937 GCTGAGGTAA
* * * *
3379947 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACAT
1 TTTCAATTTCTGTTCGTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGC-CACAC
*
3380012 GCTGAGGTCTTTTCAATTTCTGTT
65 GCTGAGGTCTTTTAAATTTCTGTT
* *
3380036 CTTCAATTTCTGTTCGTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACAC
1 TTTCAATTTCTGTTCGT-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCCACAC
*
3380100 GCTGAGGTATTTTTAAATTTCTGTT
65 GCTGAGGT-CTTTTAAATTTCTGTT
3380125 TTTCAA
1 TTTCAA
3380131 AAAAATCAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 11 0.13
89 34 0.40
90 39 0.46
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (88 bp):
TTTCAATTTCTGTTCGTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCCACACG
CTGAGGTCTTTTAAATTTCTGTT
Found at i:3380165 original size:76 final size:75
Alignment explanation
Indices: 3380040--3380237 Score: 294
Period size: 76 Copynumber: 2.7 Consensus size: 75
3380030 TCTGTTCTTC
*
3380040 AATTTCTGTTCGT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
1 AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
3380104 AGGTATTTTTA
66 AGGTA-ATTTA
* * *
3380115 AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGACACGCTG
1 AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
3380180 AGGTAATTTC
66 AGGTAATTTA
* *
3380190 AATTTCTCTTTGTC--AAAAATTAACTCATATTGCGAGAGGTGAGTTGAG
1 AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
3380238 TCTTGGCTCA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
73 32 0.29
75 26 0.23
76 54 0.48
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32
Consensus pattern (75 bp):
AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
AGGTAATTTA
Found at i:3380269 original size:75 final size:71
Alignment explanation
Indices: 3380055--3380280 Score: 263
Period size: 76 Copynumber: 3.0 Consensus size: 71
3380045 CTGTTCGTAA
3380055 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGACACGCTGAGGTATTTTT-AATTT
*
3380120 CTGTTTTTC
64 CT-CTTTTC
* * * *
3380129 AAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGACACGCTGAGGTATTTTTAATT
3380194 TCTCTTTGTC
63 TCTCTTT-TC
* * * * *
3380204 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTTGGCTCACATGCTGAGGTCTTTTTAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG---ACACGCTGAGGTATTTTTAATT
3380269 TCTACTTTTC
63 TCT-CTTTTC
3380279 AA
1 AA
3380281 TTTCTGTTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
72 2 0.02
73 34 0.26
74 3 0.02
75 34 0.26
76 59 0.45
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (71 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGACACGCTGAGGTATTTTTAATTTCT
CTTTTC
Found at i:3381092 original size:30 final size:30
Alignment explanation
Indices: 3381056--3381230 Score: 287
Period size: 30 Copynumber: 5.8 Consensus size: 30
3381046 ACTTTTCTCA
*
3381056 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
3381086 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
3381116 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
3381146 ACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
3381176 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
3381206 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
3381231 CTTGTACCTA
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 133 1.00
ACGTcount: A:0.25, C:0.49, G:0.04, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:3381121 original size:60 final size:60
Alignment explanation
Indices: 3381056--3381230 Score: 323
Period size: 60 Copynumber: 2.9 Consensus size: 60
3381046 ACTTTTCTCA
* *
3381056 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAACTCC
*
3381116 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTGTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAACTCC
3381176 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
3381231 CTTGTACCTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 112 1.00
ACGTcount: A:0.25, C:0.49, G:0.04, T:0.22
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAACTCC
Found at i:3381832 original size:27 final size:27
Alignment explanation
Indices: 3381792--3381942 Score: 82
Period size: 25 Copynumber: 5.6 Consensus size: 27
3381782 ATTTTAAATT
3381792 CTATATTACGTGTATATATATATATTATA
1 CTATATTA--TGTATATATATATATTATA
* * *
3381821 CTATTTTATGTATATATCT-T-TAATA
1 CTATATTATGTATATATATATATTATA
* * *
3381846 TTATATTATTTATATATATATATTTTTTA
1 CTATATTATGTATATATATATA--TTATA
* * * *
3381875 C-ATGTTATCTTATGTATATATCTTA-A
1 CTATATTAT-GTATATATATATATTATA
* *
3381901 CTATATTATGTATGTAT-T-T-TTAACA
1 CTATATTATGTATATATATATATT-ATA
*
3381926 CTATATTATGTACATAT
1 CTATATTATGTATATAT
3381943 TTTTAATATT
Statistics
Matches: 96, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
23 2 0.02
24 2 0.02
25 36 0.38
26 11 0.11
27 18 0.19
28 6 0.06
29 21 0.22
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (27 bp):
CTATATTATGTATATATATATATTATA
Found at i:3381854 original size:25 final size:25
Alignment explanation
Indices: 3381733--3381954 Score: 79
Period size: 25 Copynumber: 8.7 Consensus size: 25
3381723 TTGTTATTAT
3381733 TATATTTCTTAATATTATATTA--TA
1 TATATTT-TTAATATTATATTATGTA
* *
3381757 TATATTCTTT--TAATATATTA-G-G
1 TATATT-TTTAATATTATATTATGTA
* *
3381779 TACATTTTAAAT-TCTATATTACGTGTA
1 TATATTTTTAATAT-TATATTA--TGTA
* *
3381806 TATATATATATT-ATACTATTTTATGTA
1 TATAT-T-T-TTAATATTATATTATGTA
* *
3381833 TATATCTTTAATATTATATTATTTATATATA
1 TATAT-TTT--TA--ATATTATAT-TATGTA
* *
3381864 TATATTTTTTACATGTTATCTTATGTA
1 TATA-TTTTTA-ATATTATATTATGTA
* *
3381891 TATA-TCTT-A-ACTATATTATGTA
1 TATATTTTTAATATTATATTATGTA
* * *
3381913 TGTATTTTTAACACTATATTATGTA
1 TATATTTTTAATATTATATTATGTA
*
3381938 CATATTTTTAATATTAT
1 TATATTTTTAATATTAT
3381955 CACGTATTTA
Statistics
Matches: 148, Mismatches: 27, Indels: 45
0.67 0.12 0.20
Matches are distributed among these distances:
21 2 0.01
22 27 0.18
23 12 0.08
24 9 0.06
25 31 0.21
26 2 0.01
27 24 0.16
28 8 0.05
29 11 0.07
30 9 0.06
31 12 0.08
32 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (25 bp):
TATATTTTTAATATTATATTATGTA
Found at i:3381860 original size:14 final size:15
Alignment explanation
Indices: 3381804--3381870 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 15
3381794 ATATTACGTG
*
3381804 TATATATATATATTA
1 TATATATTTATATTA
*
3381819 TACTAT-TTTAT-GTA
1 TA-TATATTTATATTA
*
3381833 TATATCTTTAATATTA
1 TATATATTT-ATATTA
3381849 TAT-TATTTATA-TA
1 TATATATTTATATTA
3381862 TATATATTT
1 TATATATTT
3381871 TTTACATGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.19
14 15 0.35
15 12 0.28
16 8 0.19
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (15 bp):
TATATATTTATATTA
Found at i:3382126 original size:16 final size:15
Alignment explanation
Indices: 3382102--3382149 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3382092 TAATTATTAT
*
3382102 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
3382118 TATTTTAATATTTTA
1 TATTTTAATATTTTA
3382133 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
3382149 T
1 T
3382150 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:3382137 original size:7 final size:8
Alignment explanation
Indices: 3382102--3382153 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
3382092 TAATTATTAT
*
3382102 TATTCTAA
1 TATTTTAA
*
3382110 TATTTTGA
1 TATTTTAA
3382118 TATTTTAA
1 TATTTTAA
3382126 TATTTT-A
1 TATTTTAA
3382133 TATTTTATA
1 TATTTTA-A
*
3382142 TATTTTAT
1 TATTTTAA
3382150 TATT
1 TATT
3382154 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:3385929 original size:25 final size:27
Alignment explanation
Indices: 3385901--3385970 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
3385891 TAAAGTTGTC
* *
3385901 ATTTTTTTT-T-TAATTTGGTACTTAA
1 ATTTTTTTTGTCTAATTTAGTACTGAA
3385926 ATTTTTTTTTGTCTAATTTAGTACTGAA
1 A-TTTTTTTTGTCTAATTTAGTACTGAA
*
3385954 A-TTTTTTTGTCCAATTT
1 ATTTTTTTTGTCTAATTT
3385971 GGCATTTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 23 0.59
27 1 0.03
28 14 0.36
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (27 bp):
ATTTTTTTTGTCTAATTTAGTACTGAA
Found at i:3385942 original size:28 final size:26
Alignment explanation
Indices: 3385902--3385961 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
3385892 AAAGTTGTCA
* *
3385902 TTTTTTTTTTAATTTGGTACTTAAAT
1 TTTTTTTTTTAATTTAGTACTGAAAT
3385928 TTTTTTTTGTCTAATTTAGTACTGAAAT
1 TTTTTTTT-T-TAATTTAGTACTGAAAT
3385956 TTTTTT
1 TTTTTT
3385962 GTCCAATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.27
27 1 0.03
28 21 0.70
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (26 bp):
TTTTTTTTTTAATTTAGTACTGAAAT
Found at i:3400177 original size:31 final size:31
Alignment explanation
Indices: 3400102--3400179 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
3400092 CCCAAAAAAT
* *
3400102 TTTAAGTACCAACTTAAGAAAAAATGTCAAA
1 TTTAAGTACCAAATTAAGAAAAAATATCAAA
* * *
3400133 TTTAAATATCAAATTAAGAAAAAATATCAAG
1 TTTAAGTACCAAATTAAGAAAAAATATCAAA
*
3400164 TTTAGGTACCAAATTA
1 TTTAAGTACCAAATTA
3400180 GACCAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.29
Consensus pattern (31 bp):
TTTAAGTACCAAATTAAGAAAAAATATCAAA
Found at i:3405949 original size:36 final size:36
Alignment explanation
Indices: 3405900--3405972 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3405890 AATAATTGAG
3405900 AAAGGTTTATTTTTCAAGGATTTATGCATCATAGTA
1 AAAGGTTTATTTTTCAAGGATTTATGCATCATAGTA
*
3405936 AAAGGTTTGTTTTTCAAGGATTTATGCATCATAGTA
1 AAAGGTTTATTTTTCAAGGATTTATGCATCATAGTA
3405972 A
1 A
3405973 CAATTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (36 bp):
AAAGGTTTATTTTTCAAGGATTTATGCATCATAGTA
Found at i:3406291 original size:47 final size:47
Alignment explanation
Indices: 3406222--3406316 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
3406212 TGTAAGTAAG
3406222 AAATCTTTATGAAAAACGTACTTTCGCCTGTTGTATAGTGCTGTTGC
1 AAATCTTTATGAAAAACGTACTTTCGCCTGTTGTATAGTGCTGTTGC
*
3406269 AAATCTTTATGAAAAACTTACTTTCGCCTGTTGTATAGTGCTGTTGC
1 AAATCTTTATGAAAAACGTACTTTCGCCTGTTGTATAGTGCTGTTGC
3406316 A
1 A
3406317 TTAGTCATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (47 bp):
AAATCTTTATGAAAAACGTACTTTCGCCTGTTGTATAGTGCTGTTGC
Found at i:3412718 original size:19 final size:20
Alignment explanation
Indices: 3412681--3412719 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3412671 TCAAATACAT
3412681 TTAAAACACAAAAACAAATA
1 TTAAAACACAAAAACAAATA
*
3412701 TTAAAACA-AAAAATAAATA
1 TTAAAACACAAAAACAAATA
3412720 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
TTAAAACACAAAAACAAATA
Found at i:3412821 original size:12 final size:12
Alignment explanation
Indices: 3412799--3412827 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3412789 AAATTGAAAC
3412799 AAATT-AGAACT
1 AAATTAAGAACT
3412810 AAATTAAGAACT
1 AAATTAAGAACT
3412822 AAATTA
1 AAATTA
3412828 TATTAATAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (12 bp):
AAATTAAGAACT
Found at i:3420617 original size:17 final size:18
Alignment explanation
Indices: 3420597--3420634 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3420587 TTAAGAATGA
* *
3420597 TATAAATTTATTAAAA-T
1 TATAAAATTAATAAAACT
3420614 TATAAAATTAATAAAACT
1 TATAAAATTAATAAAACT
3420632 TAT
1 TAT
3420635 TTAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAAAATTAATAAAACT
Found at i:3421373 original size:15 final size:15
Alignment explanation
Indices: 3421330--3421373 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3421320 CAGTTCATTT
*
3421330 AAAT-AAAACATTAA
1 AAATAAAAAAATTAA
3421344 AAATAAAAAATATTAA
1 AAATAAAAAA-ATTAA
*
3421360 ACATAAAAAAATTA
1 AAATAAAAAAATTA
3421374 GTTCAACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 14 0.54
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAAATTAA
Found at i:3421493 original size:12 final size:12
Alignment explanation
Indices: 3421476--3421501 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3421466 CAATTCAAAA
3421476 TTTTTATAATTT
1 TTTTTATAATTT
3421488 TTTTTATAATTT
1 TTTTTATAATTT
3421500 TT
1 TT
3421502 CTATGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:3421700 original size:9 final size:9
Alignment explanation
Indices: 3421628--3421779 Score: 98
Period size: 9 Copynumber: 16.7 Consensus size: 9
3421618 AATTCTTATA
3421628 TTTTATAAT
1 TTTTATAAT
*
3421637 ATTTATAAAT
1 TTTTAT-AAT
* *
3421647 TTATATCTAT
1 TTTTAT-AAT
*
3421657 TTTGAT-A-
1 TTTTATAAT
3421664 TTTT-TAAT
1 TTTTATAAT
3421672 TTTT-TAAT
1 TTTTATAAT
*
3421680 ATTTAATAAT
1 -TTTTATAAT
*
3421690 TTTTCTAAT
1 TTTTATAAT
* *
3421699 TTTTTTGTAT
1 TTTTAT-AAT
*
3421709 TTTTGTAATTT
1 TTTTATAA--T
*
3421720 TTTTATATT
1 TTTTATAAT
3421729 TTTTATAAT
1 TTTTATAAT
3421738 TTTTAT-AT
1 TTTTATAAT
*
3421746 TTTTATAGT
1 TTTTATAAT
3421755 TTTTATAAT
1 TTTTATAAT
*
3421764 TTTTAAATAT
1 TTTTATA-AT
3421774 TTTTAT
1 TTTTAT
3421780 GGAAAAATAT
Statistics
Matches: 111, Mismatches: 22, Indels: 19
0.73 0.14 0.12
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 17 0.15
9 51 0.46
10 31 0.28
11 7 0.06
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:3421710 original size:19 final size:19
Alignment explanation
Indices: 3421688--3421779 Score: 93
Period size: 19 Copynumber: 5.0 Consensus size: 19
3421678 ATATTTAATA
* *
3421688 ATTTTTCTAATTTTTTTGT
1 ATTTTTATAATTTTTTTAT
*
3421707 ATTTTTGTAATTTTTTTAT
1 ATTTTTATAATTTTTTTAT
3421726 ATTTTTTATAA--TTTTTAT
1 A-TTTTTATAATTTTTTTAT
* *
3421744 ATTTTTATAGTTTTTATA-
1 ATTTTTATAATTTTTTTAT
*
3421762 ATTTTTA-AATATTTTTAT
1 ATTTTTATAATTTTTTTAT
3421780 GGAAAAATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
17 15 0.25
18 15 0.25
19 23 0.38
20 8 0.13
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (19 bp):
ATTTTTATAATTTTTTTAT
Found at i:3421748 original size:26 final size:27
Alignment explanation
Indices: 3421714--3421779 Score: 98
Period size: 26 Copynumber: 2.4 Consensus size: 27
3421704 TGTATTTTTG
* *
3421714 TAATTTTTTTATATTTTTTATAATTTT
1 TAATATTTTTATAGTTTTTATAATTTT
3421741 T-ATATTTTTATAGTTTTTATAATTTT
1 TAATATTTTTATAGTTTTTATAATTTT
3421767 TAAATATTTTTAT
1 T-AATATTTTTAT
3421780 GGAAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 24 0.69
27 1 0.03
28 10 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (27 bp):
TAATATTTTTATAGTTTTTATAATTTT
Found at i:3421749 original size:46 final size:45
Alignment explanation
Indices: 3421628--3421777 Score: 112
Period size: 46 Copynumber: 3.3 Consensus size: 45
3421618 AATTCTTATA
* * *
3421628 TTTTATAATATTTATAA-ATTTATATCTATTTTG-ATATTTTTAA-TT
1 TTTTATATTTTTTATAATTTTTATAT-T-TTTTGTAT-TTTTTAATTT
* * *
3421673 TTTTA-ATATTTAATAATTTTTCTAATTTTTTTGTATTTTTGTAATTT
1 TTTTATATTTTTTATAATTTTTAT-A-TTTTTTGTATTTTT-TAATTT
*
3421720 TTTTATATTTTTTATAATTTTTATATTTTTATAGT-TTTTATAATTT
1 TTTTATATTTTTTATAATTTTTATATTTTT-T-GTATTTTTTAATTT
**
3421766 TTAAATATTTTT
1 TTTTATATTTTT
3421778 ATGGAAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
44 7 0.08
45 18 0.21
46 28 0.33
47 14 0.17
48 17 0.20
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (45 bp):
TTTTATATTTTTTATAATTTTTATATTTTTTGTATTTTTTAATTT
Found at i:3423338 original size:16 final size:16
Alignment explanation
Indices: 3423319--3423357 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3423309 ATAAAGATAG
*
3423319 AATTTATTTATAAT-AA
1 AATTT-TTTAAAATGAA
3423335 AATTTTTTAAAATGAA
1 AATTTTTTAAAATGAA
3423351 AATTTTT
1 AATTTTT
3423358 GAAGAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTTTTTAAAATGAA
Found at i:3423577 original size:27 final size:27
Alignment explanation
Indices: 3423519--3423577 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3423509 TAAATATTCC
* * * *
3423519 TTATTTAAAACATATTTTTTGAATATA
1 TTATTTAAAACATAATATCTAAATATA
3423546 TTATTTAAAACATAATATCTAAAT-TA
1 TTATTTAAAACATAATATCTAAATATA
3423572 TGTATT
1 T-TATT
3423578 AAATTTTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (27 bp):
TTATTTAAAACATAATATCTAAATATA
Found at i:3427415 original size:17 final size:17
Alignment explanation
Indices: 3427380--3427413 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3427370 AAAGTTTTTT
*
3427380 ATTTTCATTGTATTAAA
1 ATTTTCATTATATTAAA
3427397 ATTTT-ATTATATTAAA
1 ATTTTCATTATATTAAA
3427413 A
1 A
3427414 ATAATGGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTTCATTATATTAAA
Found at i:3429159 original size:31 final size:31
Alignment explanation
Indices: 3429123--3429187 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
3429113 AGATTTATAA
3429123 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
1 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
3429154 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
1 TTTAATTATTTTTTCCTTGTTTTTATAGTGT
3429185 TTT
1 TTT
3429188 TATAGTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.69
Consensus pattern (31 bp):
TTTAATTATTTTTTCCTTGTTTTTATAGTGT
Found at i:3433357 original size:16 final size:16
Alignment explanation
Indices: 3433336--3433366 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3433326 TAACTAAGCT
*
3433336 CTGCTATTTTGTTTTG
1 CTGCTATGTTGTTTTG
3433352 CTGCTATGTTGTTTT
1 CTGCTATGTTGTTTT
3433367 AATGTGTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.19, T:0.61
Consensus pattern (16 bp):
CTGCTATGTTGTTTTG
Found at i:3436116 original size:27 final size:27
Alignment explanation
Indices: 3436078--3436133 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3436068 AAATTGAAAA
3436078 AATGAGAGAATTAGAGAGATGCAAGTT
1 AATGAGAGAATTAGAGAGATGCAAGTT
3436105 AATGAGAGAATTAGAGAGATGCAAGTT
1 AATGAGAGAATTAGAGAGATGCAAGTT
3436132 AA
1 AA
3436134 GGGTGCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (27 bp):
AATGAGAGAATTAGAGAGATGCAAGTT
Found at i:3442251 original size:27 final size:28
Alignment explanation
Indices: 3442190--3442259 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
3442180 ACATATGGCT
* * *
3442190 TACACAACTAATTATATTTATTTATTATG
1 TACAAAACTGATT-TATTTATTTATAATG
*
3442219 -AAAAAACTGATTTATTTATTTA-AATG
1 TACAAAACTGATTTATTTATTTATAATG
3442245 TACAAAA-TGATTTAT
1 TACAAAACTGATTTAT
3442260 AACAAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 11 0.31
27 15 0.43
28 9 0.26
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (28 bp):
TACAAAACTGATTTATTTATTTATAATG
Found at i:3443839 original size:14 final size:12
Alignment explanation
Indices: 3443804--3443830 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3443794 AAATTACATA
3443804 TAATAAAATTTT
1 TAATAAAATTTT
3443816 TAATAAAATTTT
1 TAATAAAATTTT
3443828 TAA
1 TAA
3443831 AATAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATAAAATTTT
Found at i:3444765 original size:36 final size:36
Alignment explanation
Indices: 3444718--3444789 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3444708 TAGTATTAAG
3444718 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
1 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
3444754 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
1 ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
3444790 TAAGATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (36 bp):
ACTGCTTGAAACTAAAACAAGCTAGGTTCTAAAAGT
Found at i:3449113 original size:21 final size:20
Alignment explanation
Indices: 3449063--3449113 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
3449053 TTTTTTAGTT
3449063 TAAAATATTAAATTTTATTAA
1 TAAAAT-TTAAATTTTATTAA
*
3449084 AAAATATTTAAATTTTGA-TATA
1 TAAA-ATTTAAATTTT-ATTA-A
3449106 TAAAATTT
1 TAAAATTT
3449114 TTTGTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TAAAATTTAAATTTTATTAA
Found at i:3452331 original size:25 final size:25
Alignment explanation
Indices: 3452303--3452353 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3452293 AAAAAAACAA
3452303 TTACTAAGATCAGTTATGTCTCTAC
1 TTACTAAGATCAGTTATGTCTCTAC
3452328 TTACTAAGATCAGTTATGTCTCTAC
1 TTACTAAGATCAGTTATGTCTCTAC
3452353 T
1 T
3452354 CCGACCCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (25 bp):
TTACTAAGATCAGTTATGTCTCTAC
Found at i:3454468 original size:21 final size:21
Alignment explanation
Indices: 3454442--3454485 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3454432 CCCTCTTTCA
3454442 ACTCCGACACAAACAAAAATG
1 ACTCCGACACAAACAAAAATG
*
3454463 ACTCCGACACTAACAAAAATG
1 ACTCCGACACAAACAAAAATG
3454484 AC
1 AC
3454486 AATAGCAAGT
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:0.50, C:0.30, G:0.09, T:0.11
Consensus pattern (21 bp):
ACTCCGACACAAACAAAAATG
Found at i:3457098 original size:136 final size:136
Alignment explanation
Indices: 3456854--3457138 Score: 552
Period size: 136 Copynumber: 2.1 Consensus size: 136
3456844 CATTGGGCCT
**
3456854 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
3456919 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
3456984 ATATGC
131 ATATGC
3456990 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
3457055 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
3457120 ATATGC
131 ATATGC
3457126 AAGCCCATTTGGG
1 AAGCCCATTTGGG
3457139 GAGACTACTC
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 147 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:3457174 original size:21 final size:21
Alignment explanation
Indices: 3457145--3457192 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3457135 TGGGGAGACT
*
3457145 ACTCAACCC-ACCAACCACTAC
1 ACTCCACCCTACCAACCA-TAC
*
3457166 ACTCCACCCTACCAGCCATAC
1 ACTCCACCCTACCAACCATAC
3457187 ACTCCA
1 ACTCCA
3457193 TGTGGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.33, C:0.52, G:0.02, T:0.12
Consensus pattern (21 bp):
ACTCCACCCTACCAACCATAC
Found at i:3458959 original size:24 final size:25
Alignment explanation
Indices: 3458918--3459047 Score: 196
Period size: 25 Copynumber: 5.2 Consensus size: 25
3458908 CATGAAATTC
3458918 TTATCATGAAACATTTACCTAACC-A
1 TTATCATG-AACATTTACCTAACCTA
3458943 TTATCATGAACATTTACCTAACC-A
1 TTATCATGAACATTTACCTAACCTA
3458967 TTATCATGGAACA-TTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
3458992 TTAT-ATGAAACATTTACCTAACCTA
1 TTATCATG-AACATTTACCTAACCTA
*
3459017 TTATTATGAACATTTACCTAACCTA
1 TTATCATGAACATTTACCTAACCTA
3459042 TTATCA
1 TTATCA
3459048 ATTTGTATCA
Statistics
Matches: 99, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
23 1 0.01
24 39 0.39
25 56 0.57
26 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCTA
Found at i:3458974 original size:49 final size:51
Alignment explanation
Indices: 3458918--3459047 Score: 198
Period size: 49 Copynumber: 2.6 Consensus size: 51
3458908 CATGAAATTC
3458918 TTATCATGAAACATTTACCTAACC-ATTATCATG-AACATTTACCTAACC-A
1 TTATCATG-AACATTTACCTAACCTATTATCATGAAACATTTACCTAACCTA
3458967 TTATCATGGAACA-TTACCTAACCTATTAT-ATGAAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCTA
*
3459017 TTATTATGAACATTTACCTAACCTATTATCA
1 TTATCATGAACATTTACCTAACCTATTATCA
3459048 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
48 13 0.18
49 36 0.49
50 24 0.32
51 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (51 bp):
TTATCATGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCTA
Found at i:3463935 original size:12 final size:12
Alignment explanation
Indices: 3463918--3463960 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
3463908 AGTACTACCT
3463918 CGGCCTCGACCA
1 CGGCCTCGACCA
3463930 CGGCCTCGACCA
1 CGGCCTCGACCA
3463942 CGGCCTCGACCA
1 CGGCCTCGACCA
3463954 CGGCCTC
1 CGGCCTC
3463961 TTCCCCGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.14, C:0.51, G:0.26, T:0.09
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:3465446 original size:136 final size:136
Alignment explanation
Indices: 3465202--3465486 Score: 552
Period size: 136 Copynumber: 2.1 Consensus size: 136
3465192 CATTGGGCCT
**
3465202 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
3465267 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
3465332 ATATGC
131 ATATGC
3465338 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
3465403 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
3465468 ATATGC
131 ATATGC
3465474 AAGCCCATTTGGG
1 AAGCCCATTTGGG
3465487 GAGACTACTC
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 147 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:3465522 original size:21 final size:21
Alignment explanation
Indices: 3465493--3465540 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3465483 TGGGGAGACT
*
3465493 ACTCAACCC-ACCAACCACTAC
1 ACTCCACCCTACCAACCA-TAC
*
3465514 ACTCCACCCTACCAGCCATAC
1 ACTCCACCCTACCAACCATAC
3465535 ACTCCA
1 ACTCCA
3465541 TGTGGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.33, C:0.52, G:0.02, T:0.12
Consensus pattern (21 bp):
ACTCCACCCTACCAACCATAC
Found at i:3467310 original size:26 final size:26
Alignment explanation
Indices: 3467272--3467407 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
3467262 CATGAAATTC
3467272 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3467298 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
3467324 TTATCATGGAACACTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3467350 TTATTATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
3467376 TTATTATGAAACATTTACCTATCCTA
1 TTATCATGAAACATTTACCTAACCTA
3467402 TTATCA
1 TTATCA
3467408 ATTTGTATCA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:3472320 original size:33 final size:33
Alignment explanation
Indices: 3472245--3472310 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3472235 ACAAAACGGA
*
3472245 AGCAAGAATGTCAGCTTGAGTAATACAAACATT
1 AGCAAGAATCTCAGCTTGAGTAATACAAACATT
*
3472278 AGCAAGAATCTCGGCTTGAGTAATACAAACATT
1 AGCAAGAATCTCAGCTTGAGTAATACAAACATT
3472311 GGTGAGAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (33 bp):
AGCAAGAATCTCAGCTTGAGTAATACAAACATT
Found at i:3475224 original size:27 final size:27
Alignment explanation
Indices: 3475186--3475240 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3475176 TGTGTTATAA
3475186 AATAAATAATAATGAAAATAAAGAACC
1 AATAAATAATAATGAAAATAAAGAACC
3475213 AATAAATAATAATGAAAATAAAGAACC
1 AATAAATAATAATGAAAATAAAGAACC
3475240 A
1 A
3475241 GAGAAATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.18
Consensus pattern (27 bp):
AATAAATAATAATGAAAATAAAGAACC
Found at i:3476352 original size:20 final size:21
Alignment explanation
Indices: 3476323--3476368 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3476313 GAAACAAAAA
3476323 TTATACATTTTT-TTCTTAAT
1 TTATACATTTTTATTCTTAAT
* *
3476343 TTATATATTTTTAATTTTTAAT
1 TTATACATTTTT-ATTCTTAAT
3476365 TTAT
1 TTAT
3476369 GTTCACCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATACATTTTTATTCTTAAT
Found at i:3504695 original size:18 final size:18
Alignment explanation
Indices: 3504645--3504700 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
3504635 TTATTTTTTA
*
3504645 ATATAAAAATTTTAAAAT
1 ATATAAAAATATTAAAAT
*
3504663 ATATATAATATATTAAAAT
1 ATATA-AAAATATTAAAAT
3504682 -TACTAAAAATATTAAAAT
1 ATA-TAAAAATATTAAAAT
3504700 A
1 A
3504701 AATATTTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAAAAATATTAAAAT
Found at i:3514404 original size:47 final size:47
Alignment explanation
Indices: 3514334--3514436 Score: 152
Period size: 47 Copynumber: 2.2 Consensus size: 47
3514324 GTCGGAGAGA
* * *
3514334 TGTGATTATATGCTTCCGTATAAGACTATATCTGGGATATGACATCGG
1 TGTGA-TATATGCTACCGTATAAGACCATATCTGGGATATGACATCAG
*
3514382 TGTGATATATGCTACTGTATAAGACCATATCTGGGATATGACATCAG
1 TGTGATATATGCTACCGTATAAGACCATATCTGGGATATGACATCAG
*
3514429 TGAGATAT
1 TGTGATAT
3514437 GCGATTTGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 45 0.90
48 5 0.10
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (47 bp):
TGTGATATATGCTACCGTATAAGACCATATCTGGGATATGACATCAG
Found at i:3514478 original size:41 final size:41
Alignment explanation
Indices: 3514432--3514577 Score: 166
Period size: 41 Copynumber: 3.4 Consensus size: 41
3514422 ACATCAGTGA
* *
3514432 GATATGCGATTTGTGTAAGACCATAGCTGGGCTATGACATC
1 GATATGTGATTTGTGTAAGACCATAGCTGGGCTATGGCATC
*
3514473 GATATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATT
1 GATATGTG--A--T--TT--GTGTAAGACCATAGCTGGGCTATGGCATC
**
3514522 GATATGTGATCCGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATTTGTGTAAGACCATAGCTGGGCTATGGCATC
*
3514563 GATATGTGATATGTG
1 GATATGTGATTTGTG
3514578 ATTCCGTGTA
Statistics
Matches: 89, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
41 48 0.54
43 1 0.01
45 2 0.02
47 3 0.03
49 35 0.39
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (41 bp):
GATATGTGATTTGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:3514506 original size:49 final size:48
Alignment explanation
Indices: 3514354--3514613 Score: 236
Period size: 49 Copynumber: 5.6 Consensus size: 48
3514344 TGCTTCCGTA
* * * * * * *
3514354 TAAGACTATATCTGGGATATGACATCG-GTGTGATATATG-CTACTGTA
1 TAAGACCATAGCTGGGCTATGACATCGAATGTGATATGTGATTAC-GTG
* * * * * *
3514401 TAAGACCATATCTGGGATATGACATC-AGTGAGATATGCGATT-TGTG
1 TAAGACCATAGCTGGGCTATGACATCGAATGTGATATGTGATTACGTG
3514447 TAAGACCATAGCTGGGCTATGACATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGACATCGA-ATGTGATATGTGATTACGTG
* *
3514496 TAAGACCATAGCTGGGCTATG-----GCAT-TGATATGTGA-TCCGTG
1 TAAGACCATAGCTGGGCTATGACATCGAATGTGATATGTGATTACGTG
* *
3514537 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTCCGTG
1 TAAGACCATAGCTGGGCTATGACATCGA-ATGTGATATGTGATTACGTG
* **
3514586 TAAGACCATAGTTGAACTATGACATCGA
1 TAAGACCATAGCTGGGCTATGACATCGA
3514614 GAAAACGAAG
Statistics
Matches: 180, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
41 26 0.14
42 10 0.06
43 2 0.01
44 1 0.01
46 27 0.15
47 37 0.21
48 23 0.13
49 54 0.30
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (48 bp):
TAAGACCATAGCTGGGCTATGACATCGAATGTGATATGTGATTACGTG
Found at i:3520606 original size:17 final size:18
Alignment explanation
Indices: 3520584--3520636 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
3520574 AATCATATCT
*
3520584 TCTAAGATTG-TATCATA
1 TCTAAGATTGATATCACA
*
3520601 TCTAAGATTGCATGTCACA
1 TCTAAGATTG-ATATCACA
3520620 TCTAAGATTGCATATCA
1 TCTAAGATTG-ATATCA
3520637 TTGAAGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 10 0.32
19 21 0.68
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (18 bp):
TCTAAGATTGATATCACA
Found at i:3520795 original size:21 final size:21
Alignment explanation
Indices: 3520756--3520796 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3520746 TTGGACTTCG
* **
3520756 TTTTTTTTTTTGGGTTTATTA
1 TTTTTGTTTTTGGACTTATTA
3520777 TTTTTGTTTTTGGACTTATT
1 TTTTTGTTTTTGGACTTATT
3520797 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.02, G:0.15, T:0.73
Consensus pattern (21 bp):
TTTTTGTTTTTGGACTTATTA
Found at i:3521294 original size:77 final size:78
Alignment explanation
Indices: 3521157--3521372 Score: 337
Period size: 77 Copynumber: 2.8 Consensus size: 78
3521147 ATGTAAACAC
* * * *
3521157 ATGAAGGTCAGATCTACTATGTCTTCGATCTACTCTCTGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATAT
3521222 TGGATCTGCTTCA
66 TGGATCTGCTTCA
*
3521235 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTC-CCGTCTAATACAGAGATGCCAAATCATA
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATA
3521298 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* **
3521312 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATC
3521373 TGTTTCTTCA
Statistics
Matches: 126, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
76 2 0.02
77 71 0.56
78 51 0.40
79 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCTAATACAGAGATGCCAAATCATAT
TGGATCTGCTTCA
Found at i:3521524 original size:44 final size:44
Alignment explanation
Indices: 3521450--3522290 Score: 759
Period size: 44 Copynumber: 19.2 Consensus size: 44
3521440 CACGTAAAAA
* *
3521450 CCAAATCTACTACGTCTTCGATTTGCTCTCTGACAATACAGAGATG
1 CCAAATCTGCTA--TCTTCGATCTGCTCTCTGACAATACAGAGATG
* * *
3521496 CCGAATCTGCTATCTTCGATCTGTTCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * * *
3521540 CCAAA--T-C-ATCTTAGATCTGCT-TCAG-CATAAACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACA-ATACA-GAG-ATG
*
3521581 CCAAATCTGCTATATCTTC-ATTTTGCTCTCTGACAATACAGAGATG
1 CCAAATCTGC--TATCTTCGA-TCTGCTCTCTGACAATACAGAGATG
* *
3521627 CCAAATCTGCTATCTTCGATCTGCTCTCTGATAATACAAAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * *
3521671 CCAAATCTG----CTTAGATCTGCT-TCAG-CGTAA-ACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ATG
* * * **
3521712 CCAAATCTACTATATCTTCAATTTTTTCTCTGACAATACAGAGATG
1 CCAAATCTGC--TATCTTCGATCTGCTCTCTGACAATACAGAGATG
* *
3521758 CCAAATCTGCTATCTTCGATCTACTCTCTGGCAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
3521802 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * * *
3521846 CCAAATCTG----CTTAGATCCGCT-TCAG-CGTAA-ACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ATG
* *
3521887 CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGATG
1 CCAAATCTGC--TATCTTCGATCTGCTCTCTGACAATACAGAGATG
* ** *
3521933 CCAAATCTGTTATCTTTAATCTGCTCTTTGACAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
*
3521977 CCAAATCTGCTATCTTCGATCTGCTCTTTGACAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * *
3522021 CCAAA--T-CT-TCTTAGATCTGCT-TCAG-CGTAA-ACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ATG
* * * *
3522062 CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATATAGATATG
1 CCAAATCTGC--TATCTTCGATCTGCTCTCTGACAATACAGAGATG
* *
3522108 TCAAATCTGCTATCTTCGATCTGCTTTCTGACAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * *
3522152 CCAAATCTGCTATCTTTGATCTGCTCTTTGACAATACAAAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* *
3522196 CCAAATCTGCTATCTTCGATCTGCCCTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* *
3522240 CCAAATCTACTATCTTCGATCTGCTC-CTTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTC-TGACAATACAGAGATG
3522284 CCAAATC
1 CCAAATC
3522291 ATCTTAGATC
Statistics
Matches: 648, Mismatches: 94, Indels: 108
0.76 0.11 0.13
Matches are distributed among these distances:
38 4 0.01
39 24 0.04
40 58 0.09
41 38 0.06
42 2 0.00
43 3 0.00
44 384 0.59
45 1 0.00
46 57 0.09
47 48 0.07
48 24 0.04
49 5 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
Found at i:3521571 original size:131 final size:131
Alignment explanation
Indices: 3521323--3521808 Score: 636
Period size: 131 Copynumber: 3.7 Consensus size: 131
3521313 TGAAGGTCAG
* * * * * ** * * *
3521323 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTG-TTTCTTCAATTT
1 ATCTACTATATCTTCGATTTGCTCTCTGAC-AATACAGAGATGCCAAATCTGCTATCTTCGATCT
* * * * * * * *
3521387 GTTCTCTAACAGTACAGAGATACCAAATCATCTTAGATCCGCTTCAGTGTAAACACGTAAAAACC
65 GCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCC
3521452 AA
130 AA
** *
3521454 ATCTACTACGTCTTCGATTTGCTCTCTGACAATACAGAGATGCCGAATCTGCTATCTTCGATCTG
1 ATCTACTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTG
* * *
3521519 TTCTCTGACAATACAGAGACGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCA
66 CTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
3521584 A
131 A
*
3521585 ATCTGCTATATCTTC-ATTTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCT
1 ATCTACTATATCTTCGA-TTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCT
* *
3521649 GCTCTCTGATAATACAAAGATGCCAAATC-TGCTTAGATCTGCTTCAGCGTAAACACGTGAAAGC
65 GCTCTCTGACAATACAGAGATGCCAAATCAT-CTTAGATCTGCTTCAGCGTAAACACGTGAAAGC
3521713 CAA
129 CAA
* ** *
3521716 ATCTACTATATCTTCAATTTTTTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTA
1 ATCTACTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTG
*
3521781 CTCTCTGGCAATACAGAGATGCCAAATC
66 CTCTCTGACAATACAGAGATGCCAAATC
3521809 TGCTATCTTC
Statistics
Matches: 315, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
130 20 0.06
131 294 0.93
132 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (131 bp):
ATCTACTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTG
CTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
A
Found at i:3521774 original size:175 final size:175
Alignment explanation
Indices: 3521580--3522206 Score: 1022
Period size: 175 Copynumber: 3.6 Consensus size: 175
3521570 ACACGTGAAA
*
3521580 GCCAAATCTGCTATATCTTC-ATTTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTC
1 GCCAAATCTGC--TATCTTCGA-TCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTC
*
3521644 GATCTGCTCTCTGATAATACAAAGATGCCAAATCTGCTTAGATCTGCTTCAGCGTAAACACGTGA
63 GATCTGCTCTCTGACAATACAAAGATGCCAAATCTGCTTAGATCTGCTTCAGCGTAAACACGTGA
* **
3521709 AAGCCAAATCTACTATATCTTCAATTTTTTCTCTGACAATACAGAGAT
128 AAGCCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGAT
* *
3521757 GCCAAATCTGCTATCTTCGATCTACTCTCTGGCAATACAGAGATGCCAAATCTGCTATCTTCGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGAT
* *
3521822 CTGCTCTCTGACAATACAGAGATGCCAAATCTGCTTAGATCCGCTTCAGCGTAAACACGTGAAAG
66 CTGCTCTCTGACAATACAAAGATGCCAAATCTGCTTAGATCTGCTTCAGCGTAAACACGTGAAAG
3521887 CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGAT
131 CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGAT
* ** *
3521932 GCCAAATCTGTTATCTTTAATCTGCTCTTTGACAATACAGAGATGCCAAATCTGCTATCTTCGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGAT
* * *
3521997 CTGCTCTTTGACAATACAGAGATGCCAAATCTTCTTAGATCTGCTTCAGCGTAAACACGTGAAAG
66 CTGCTCTCTGACAATACAAAGATGCCAAATCTGCTTAGATCTGCTTCAGCGTAAACACGTGAAAG
* *
3522062 CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATATAGATAT
131 CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGAT
* * *
3522107 GTCAAATCTGCTATCTTCGATCTGCTTTCTGACAATACAGAGATGCCAAATCTGCTATCTTTGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGAT
*
3522172 CTGCTCTTTGACAATACAAAGATGCCAAATCTGCT
66 CTGCTCTCTGACAATACAAAGATGCCAAATCTGCT
3522207 ATCTTCGATC
Statistics
Matches: 420, Mismatches: 29, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
175 408 0.97
176 1 0.00
177 11 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (175 bp):
GCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGAT
CTGCTCTCTGACAATACAAAGATGCCAAATCTGCTTAGATCTGCTTCAGCGTAAACACGTGAAAG
CCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGAT
Found at i:3522080 original size:306 final size:304
Alignment explanation
Indices: 3521323--3522290 Score: 978
Period size: 306 Copynumber: 3.2 Consensus size: 304
3521313 TGAAGGTCAG
* * * ** * *
3521323 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCTTCAATTTG
1 ATCTGCTA--TCTTCAATCTGCTCTCTGAC-AATACAGAGATGCCAAATCTG-TTCTTCGATCTG
* * * * * * * * *
3521388 TTCTCTAACAGTACAGAGATACCAAATCATCTTAGATCCGCTTCAGTGTAAACACGTAAAAACCA
62 CTCTCTGACAATACAGAGATGCCAAATCTTCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
* ** *
3521453 AATCTACTACGTCTTCGATTTGCTCTCTGACAATACAGAGATGCCGAATCTGCTATCTTCGATCT
127 AATCTGCTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCT
* * *
3521518 GTTCTCTGACAATACAGAGACGCCAAATCAT-CTTAGATCTGCTTCAGCATAAACACGTGAAAGC
192 GCTCTCTGACAATACAGAGATGCCAAATC-TGCTTAGATCCGCTTCAGCATAAACACGTGAAAGC
*
3521582 CAAATCTGCTATATCTTCATTTTGCTCTCTGACAATACAGAGATGCCAA
256 CAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGATGCCAA
* * * *
3521631 ATCTGCTATCTTCGATCTGCTCTCTGATAATACAAAGATGCCAAATCTG--CTTAGATCTGCT-T
1 ATCTGCTATCTTCAATCTGCTCTCTGACAATACAGAGATGCCAAATCTGTTCTTCGATCTGCTCT
* * * * * * *** * * *
3521693 CAG-CGTAA-ACACGTGAAAGCCAAATCTAC-TATATCTTCAATTTTTTCTCTGACAATAC-AGA
66 CTGAC--AATACA-GAG-ATGCCAAATCTTCTTAGATCTGC---TTCAGC-GT-A-AACACGTGA
* * * *
3521754 GATGCCAAATCTGC--TATCTTCGATCTACTCTCTGGCAATACAGAGATGCCAAATCTGCTATCT
121 -AAGCCAAATCTGCTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCT
*
3521817 TCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTTAGATCCGCTTCAGCGTAAACACGT
185 TCGATCTGCTCTCTGACAATACAGAGATGCCAAATCTGCTTAGATCCGCTTCAGCATAAACACGT
3521882 GAAAGCCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGATGCCAA
250 GAAAGCCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGATGCCAA
* * *
3521937 ATCTGTTATCTTTAATCTGCTCTTTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCT
1 ATCTGCTATCTTCAATCTGCTCTCTGACAATACAGAGATGCCAAATCTG-T-TCTTCGATCTGCT
*
3522002 CTTTGACAATACAGAGATGCCAAATCTTCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAA
64 CTCTGACAATACAGAGATGCCAAATCTTCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAA
* * * *
3522067 TCTGCTATATCTTCAATTTGCTCTCTGACAATATAGATATGTCAAATCTGCTATCTTCGATCTGC
129 TCTGCTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTGC
* * * ** * **
3522132 TTTCTGACAATACAGAGATGCCAAATCTGCTATCTTTGATCTGCTCTTTGACA-ATACA-AAG-A
194 TCTCTGACAATACAGAGATGCCAAATCTG----CTTAGATCCGCT-TCAG-CATAAACACGTGAA
* * * * *
3522194 TGCCAAATCTGC--TATCTTCGATCTGCCCTCTGACAATACAGAGACGCCAA
253 AGCCAAATCTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGATGCCAA
* * *
3522244 ATCTACTATCTTCGATCTGCTC-CTTGACAATACAGAGACGCCAAATC
1 ATCTGCTATCTTCAATCTGCTCTC-TGACAATACAGAGATGCCAAATC
3522291 ATCTTAGATC
Statistics
Matches: 539, Mismatches: 91, Indels: 61
0.78 0.13 0.09
Matches are distributed among these distances:
300 1 0.00
301 5 0.01
302 17 0.03
303 9 0.02
304 16 0.03
305 24 0.04
306 297 0.55
307 79 0.15
308 22 0.04
309 23 0.04
310 33 0.06
311 11 0.02
312 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (304 bp):
ATCTGCTATCTTCAATCTGCTCTCTGACAATACAGAGATGCCAAATCTGTTCTTCGATCTGCTCT
CTGACAATACAGAGATGCCAAATCTTCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCAAATC
TGCTATATCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTC
TCTGACAATACAGAGATGCCAAATCTGCTTAGATCCGCTTCAGCATAAACACGTGAAAGCCAAAT
CTGCTATATCTTCAATTTGCTCTCTGACAATACAGAGATGCCAA
Found at i:3531727 original size:22 final size:21
Alignment explanation
Indices: 3531692--3531767 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
3531682 AAAAGGTATC
* *
3531692 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
3531713 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
3531736 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
3531755 TGC-AATCATATCT
1 TACAAATCATATCT
3531768 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:3531784 original size:35 final size:37
Alignment explanation
Indices: 3531728--3531818 Score: 141
Period size: 35 Copynumber: 2.5 Consensus size: 37
3531718 AATCATATCT
*
3531728 TCTAAGATTGCATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCACA
3531765 TCTAAGATTG-TATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGATATCATATCTAAGATTGCATATCACA
3531801 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
3531819 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 19 0.38
36 15 0.30
37 10 0.20
38 6 0.12
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCACA
Found at i:3531797 original size:14 final size:15
Alignment explanation
Indices: 3531742--3531797 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
3531732 AGATTGCATA
3531742 TCATATCTAAGATTG
1 TCATATCTAAGATTG
3531757 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
3531775 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
3531792 -CATATC
1 TCATATC
3531798 ACATCTAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:3531826 original size:17 final size:19
Alignment explanation
Indices: 3531728--3531818 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
3531718 AATCATATCT
3531728 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
3531747 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
3531765 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
3531782 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
3531801 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
3531819 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 35 0.52
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3531977 original size:21 final size:21
Alignment explanation
Indices: 3531938--3531978 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3531928 TGGACTTTGT
* **
3531938 TTTTTTTTTTTGGGTTTATTA
1 TTTTTGTTTTTGGACTTATTA
3531959 TTTTTGTTTTTGGACTTATT
1 TTTTTGTTTTTGGACTTATT
3531979 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.02, G:0.15, T:0.73
Consensus pattern (21 bp):
TTTTTGTTTTTGGACTTATTA
Found at i:3534079 original size:36 final size:36
Alignment explanation
Indices: 3534030--3534124 Score: 181
Period size: 36 Copynumber: 2.6 Consensus size: 36
3534020 TTATGTCTTC
3534030 AATAGATATGCTTCTTCTTTATCATCCAATCAATTA
1 AATAGATATGCTTCTTCTTTATCATCCAATCAATTA
*
3534066 AGTAGATATGCTTCTTCTTTATCATCCAATCAATTA
1 AATAGATATGCTTCTTCTTTATCATCCAATCAATTA
3534102 AATAGATATGCTTCTTCTTTATC
1 AATAGATATGCTTCTTCTTTATC
3534125 TATTAGTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (36 bp):
AATAGATATGCTTCTTCTTTATCATCCAATCAATTA
Found at i:3537220 original size:24 final size:24
Alignment explanation
Indices: 3537193--3537244 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3537183 GATTGTAAGG
3537193 GAGAAGTAGGTGTAACATTG-GGCT
1 GAGAAGTAGGTGTAAC-TTGTGGCT
* *
3537217 GAGAGGTTGGTGTAACTTGTGGCT
1 GAGAAGTAGGTGTAACTTGTGGCT
3537241 GAGA
1 GAGA
3537245 TGGCAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.25, C:0.08, G:0.40, T:0.27
Consensus pattern (24 bp):
GAGAAGTAGGTGTAACTTGTGGCT
Found at i:3542109 original size:21 final size:21
Alignment explanation
Indices: 3542084--3542126 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3542074 ACAAATATAT
3542084 ATAGTAAAATT-TTAAACTTAA
1 ATAGT-AAATTGTTAAACTTAA
*
3542105 ATAGTAAATTGTTAAATTTAA
1 ATAGTAAATTGTTAAACTTAA
3542126 A
1 A
3542127 ATATATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
ATAGTAAATTGTTAAACTTAA
Found at i:3547191 original size:17 final size:17
Alignment explanation
Indices: 3547171--3547206 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3547161 AATTAATTGT
3547171 TTTTAAAAAATTAAAAA
1 TTTTAAAAAATTAAAAA
**
3547188 TTTTAAAATTTTAAAAA
1 TTTTAAAAAATTAAAAA
3547205 TT
1 TT
3547207 GACATCTATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAATTAAAAA
Found at i:3549534 original size:355 final size:358
Alignment explanation
Indices: 3548873--3549611 Score: 1012
Period size: 355 Copynumber: 2.1 Consensus size: 358
3548863 GAGTTTTATC
* * *
3548873 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCCAGATTCAGCATCCCTTCCACTCGAAACAC
1 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATCCCTTCCACCCCAAACAC
* * *
3548938 CCTCTCAGTCTTTTGCCAAAATCAACTTATTCCGGGGGCGCGGAATGTGCGATTTTTGTGGTAAG
66 CCTCTCACTCTTTTGCCAAAACCAACTTATT-C--GGGCGC---A-GTGCGATTTGTGTGGTAAG
* * *
3549003 GAATTAAGGGGATTTGTTTATAATTGTAATGATTGTAAGTTCGATCTGCACATCAATTGTGCTTT
124 GAAATAAGAGGATTTGTTTATAATTGTAATGATTGTAAGTTCAATCTGCACATCAATTGTGCTTT
*
3549068 GCTTCAATCTTCCATTGCTGCTAATTTTCCTAATTCTTTGCACCCCCATCCATTGTTCTTCATTC
189 GCTTCAATCATCCATTGCTGCTAATTTTCCTAATTCTTTGCACCCCCATCCATTGTTCTTCATTC
* * *
3549133 AAAATCATAACAATGAAGTCGAGCCTGATTGCCCCTTGTGTCAAAAACCAATATCTGGTCCATTT
254 AAAATAATAACAAGGAAGTCGAGCCTGATTGCCCCTGGTGTCAAAAACCAATATCTGGTCCATTT
* * * *
3549198 TACCACTGTTCAGATTGCACTTATCCTTCA-TTGTTTAACA
319 TACCACTGCTCAGATTGCACATATCATACAGTT-TTTAACA
*
3549238 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATCCTTTCCACCCCAAACA-
1 TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATCCCTTCCACCCCAAACAC
**
3549302 CCTGCTCACTCTTTTGCCAGCACCATA-TT-TT-GGG-GC-GTGCGATTTGTGTGGTAAGGCAAA
66 CCT-CTCACTCTTTTGCCAAAACCA-ACTTATTCGGGCGCAGTGCGATTTGTGTGGTAAGG-AAA
* * * *
3549362 T-CGAGTACTTTTTTTATAATTGTTATGATTGTAAGTTCAATCTGCACATCAATTGTGCTTTGCT
128 TAAGAGGA-TTTGTTTATAATTGTAATGATTGTAAGTTCAATCTGCACATCAATTGTGCTTTGCT
*
3549426 TCAATCATCCATTGCTGCTAATTTTCCTATTTCTTTGCACCCCCATCCATTGTTCTTCATTCAAA
192 TCAATCATCCATTGCTGCTAATTTTCCTAATTCTTTGCACCCCCATCCATTGTTCTTCATTCAAA
* *
3549491 ATAA-ATACAAGGAAGTCGAGCCTGATTGCTCC-GGATGTCAAAAACCAATATCTGGTTCATTTT
257 ATAATA-ACAAGGAAGTCGAGCCTGATTGCCCCTGG-TGTCAAAAACCAATATCTGGTCCATTTT
* *
3549554 ACCACTGCTCAGATTGCACATATCATAGAGTTTTTAACC
320 ACCACTGCTCAGATTGCACATATCATACAGTTTTTAACA
*
3549593 TGCATAAGGAATGTGCTGA
1 TTCATAAGGAATGTGCTGA
3549612 ACTACCCCTT
Statistics
Matches: 337, Mismatches: 30, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
354 24 0.07
355 221 0.66
356 2 0.01
359 2 0.01
360 3 0.01
364 5 0.01
365 79 0.23
366 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (358 bp):
TTCATAAGGAATGTGCTGAGTTAGAGTTAGCCCCCAAGATTCAGCATCCCTTCCACCCCAAACAC
CCTCTCACTCTTTTGCCAAAACCAACTTATTCGGGCGCAGTGCGATTTGTGTGGTAAGGAAATAA
GAGGATTTGTTTATAATTGTAATGATTGTAAGTTCAATCTGCACATCAATTGTGCTTTGCTTCAA
TCATCCATTGCTGCTAATTTTCCTAATTCTTTGCACCCCCATCCATTGTTCTTCATTCAAAATAA
TAACAAGGAAGTCGAGCCTGATTGCCCCTGGTGTCAAAAACCAATATCTGGTCCATTTTACCACT
GCTCAGATTGCACATATCATACAGTTTTTAACA
Found at i:3552646 original size:32 final size:31
Alignment explanation
Indices: 3552610--3552682 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
3552600 AGCAAATTTG
*
3552610 AAAATTTTATTTAAGTTCTCTCAAACTTTTTA
1 AAAATTTTATTTAA-TTCTCTCAAAATTTTTA
* * *
3552642 AAAATTCTCA-TTAATTTTTTCAAAATTTTTA
1 AAAATT-TTATTTAATTCTCTCAAAATTTTTA
*
3552673 AAAAATTTAT
1 AAAATTTTAT
3552683 AATTAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
30 2 0.06
31 19 0.58
32 10 0.30
33 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (31 bp):
AAAATTTTATTTAATTCTCTCAAAATTTTTA
Found at i:3552705 original size:24 final size:24
Alignment explanation
Indices: 3552663--3552710 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3552653 TAATTTTTTC
*
3552663 AAAATTTTTAAAAAATTTATAATT
1 AAAATTTTTAAAAAATTTAAAATT
**
3552687 AAAATTTTTAAAAGTTTTAAAATT
1 AAAATTTTTAAAAAATTTAAAATT
3552711 TCTGATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAAATTTTTAAAAAATTTAAAATT
Found at i:3552719 original size:31 final size:32
Alignment explanation
Indices: 3552637--3552720 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 32
3552627 CTCTCAAACT
* * * *
3552637 TTTTAAAAATTCTCATT-AATTTTTTCAAAAT
1 TTTTAAAATTTCTAATTAAAATTTTTCAAAAG
*
3552668 TTTTAAAAAATTTATAATTAAAATTTTT-AAAAG
1 TTTT--AAAATTTCTAATTAAAATTTTTCAAAAG
*
3552701 TTTTAAAATTTCTGATTAAA
1 TTTTAAAATTTCTAATTAAA
3552721 CCCCCAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
31 18 0.42
33 18 0.42
34 7 0.16
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
TTTTAAAATTTCTAATTAAAATTTTTCAAAAG
Found at i:3553254 original size:13 final size:13
Alignment explanation
Indices: 3553222--3553265 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3553212 TGATGTGGGT
3553222 AAAAAATATGTAA
1 AAAAAATATGTAA
*
3553235 AATAAAT-TGTATA
1 AAAAAATATGTA-A
*
3553248 AAAAAATATTTAA
1 AAAAAATATGTAA
3553261 AAAAA
1 AAAAA
3553266 CAAATGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 19 0.73
14 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (13 bp):
AAAAAATATGTAA
Found at i:3558438 original size:18 final size:18
Alignment explanation
Indices: 3558415--3558500 Score: 109
Period size: 18 Copynumber: 4.8 Consensus size: 18
3558405 CGTTTATGGT
*
3558415 ACTATTCACGTATACAGC
1 ACTATTCACGTATATAGC
*
3558433 ACTATTCACGTATATAGT
1 ACTATTCACGTATATAGC
* * *
3558451 ACTATTTATGTATATGGC
1 ACTATTCACGTATATAGC
* *
3558469 ACTATTCACGTATATGGT
1 ACTATTCACGTATATAGC
3558487 ACTATTCACGTATA
1 ACTATTCACGTATA
3558501 CAGTAGTTGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (18 bp):
ACTATTCACGTATATAGC
Found at i:3558464 original size:36 final size:36
Alignment explanation
Indices: 3558413--3558503 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
3558403 ATCGTTTATG
3558413 GTACTATTCACGTATACAGCACTATTCACGTATATA
1 GTACTATTCACGTATACAGCACTATTCACGTATATA
* * ** *
3558449 GTACTATTTATGTATATGGCACTATTCACGTATATG
1 GTACTATTCACGTATACAGCACTATTCACGTATATA
3558485 GTACTATTCACGTATACAG
1 GTACTATTCACGTATACAG
3558504 TAGTTGGGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (36 bp):
GTACTATTCACGTATACAGCACTATTCACGTATATA
Found at i:3562133 original size:93 final size:93
Alignment explanation
Indices: 3562021--3562191 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3562011 GCCCATAACC
* * *
3562021 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
3562086 CGAGTTCGGATGCCTAGTTACATCTCAT
66 CGAGTTCGGATGCCTAGTTACATCTCAT
*
3562114 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
3562179 TGAGTTCGGATGC
66 CGAGTTCGGATGC
3562192 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAT
Found at i:3562188 original size:46 final size:46
Alignment explanation
Indices: 3562021--3562188 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 46
3562011 GCCCATAACC
* * *
3562021 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
* *
3562067 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-T
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGT
3562114 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
* *
3562160 GAACTCAGACTCAACTCAATGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
3562189 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 55 0.53
47 30 0.29
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
Found at i:3566713 original size:32 final size:31
Alignment explanation
Indices: 3566666--3566756 Score: 87
Period size: 33 Copynumber: 2.9 Consensus size: 31
3566656 TTAAGTTCTC
* *
3566666 TCAAACTTTTT-AAAAATTCTCATTAATTTGT
1 TCAAAATTTTTAAAAAATTCTAATTAATTT-T
*
3566697 TCAAAATTTTTAAAAAATTGTAATCTAACATTTT
1 TCAAAATTTTTAAAAAATTCTAAT-T-A-ATTTT
* *
3566731 T-AAAAGTTTTAAAAAATTCTTATTAA
1 TCAAAATTTTTAAAAAATTCTAATTAA
3566757 GCGCCCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.02
31 11 0.22
32 11 0.22
33 20 0.40
34 3 0.06
35 4 0.08
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (31 bp):
TCAAAATTTTTAAAAAATTCTAATTAATTTT
Found at i:3575112 original size:13 final size:13
Alignment explanation
Indices: 3575094--3575120 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3575084 AAAAGACTAA
3575094 ATTCAATTTAGGC
1 ATTCAATTTAGGC
3575107 ATTCAATTTAGGC
1 ATTCAATTTAGGC
3575120 A
1 A
3575121 AAATGTCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTCAATTTAGGC
Found at i:3576002 original size:22 final size:22
Alignment explanation
Indices: 3575972--3576029 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3575962 AAGTTCTCTC
*
3575972 AAAACTTTTTAAAAATTCTCATT
1 AAAA-TTTTTAAAAATTCTAATT
* *
3575995 -AAATTTTTCAAAATTTGTAATT
1 AAAATTTTT-AAAAATTCTAATT
3576017 AAAATTTTTAAAA
1 AAAATTTTTAAAA
3576030 GTTTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 5 0.17
22 17 0.57
23 8 0.27
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATTTTTAAAAATTCTAATT
Done.