Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 29
Found at i:4592162 original size:16 final size:17
Alignment explanation
Indices: 4592130--4592162 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4592120 GCCTGCCTAC
*
4592130 AAGGGTACAATTATATA
1 AAGGGTACAACTATATA
4592147 AAGGGTA-AACTATATA
1 AAGGGTACAACTATATA
4592163 TTTAGTATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (17 bp):
AAGGGTACAACTATATA
Found at i:4592712 original size:14 final size:14
Alignment explanation
Indices: 4592693--4592719 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4592683 TTTTTAAAAA
4592693 AAAAATTATTATTT
1 AAAAATTATTATTT
4592707 AAAAATTATTATT
1 AAAAATTATTATT
4592720 AATAATCGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAAATTATTATTT
Found at i:4594687 original size:21 final size:21
Alignment explanation
Indices: 4594661--4594710 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
4594651 TCCAGATTCA
4594661 CAATGCGAACTTCGACTATCG
1 CAATGCGAACTTCGACTATCG
4594682 CAATGCGAACTTCGACTATCG
1 CAATGCGAACTTCGACTATCG
*
4594703 CATTGCGA
1 CAATGCGA
4594711 TTTACATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (21 bp):
CAATGCGAACTTCGACTATCG
Found at i:4594838 original size:42 final size:42
Alignment explanation
Indices: 4594744--4595064 Score: 489
Period size: 42 Copynumber: 7.8 Consensus size: 42
4594734 TCCAAGTTCA
* *
4594744 CGTTGCGATAGTCCAAGTTCGCGTTGTGA-TT-TTCTAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
4594784 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
4594826 TGTTGCGATAGTCCAAGTTCGTGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
4594868 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
4594908 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
4594950 AC---GCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 -CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
4594988 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
4595030 TGTTGCGATAGTCCAAGTTCGTGTTGCGATTTATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATT
4595065 ACGCGTTGCG
Statistics
Matches: 257, Mismatches: 14, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
37 1 0.00
38 9 0.04
39 2 0.01
40 112 0.44
41 8 0.03
42 124 0.48
43 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:4596026 original size:19 final size:19
Alignment explanation
Indices: 4595960--4596088 Score: 114
Period size: 19 Copynumber: 6.4 Consensus size: 19
4595950 GATTTTCGAC
*
4595960 TATCGCAACAAATTTGGAA
1 TATCGCAACGAATTTGGAA
* * *
4595979 TAAATCGCAACGTGAACTTCGAC
1 T--ATCGCAAC--GAATTTGGAA
4596002 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
4596021 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
* *
4596040 TAAATCGCAACGCGAACTTGGAC
1 T--ATCGCAA--CGAATTTGGAA
*
4596063 TATCGCAACGAATTTGAAA
1 TATCGCAACGAATTTGGAA
*
4596082 AATCGCA
1 TATCGCA
4596089 TTGCGATAGT
Statistics
Matches: 89, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
19 42 0.47
21 30 0.34
23 17 0.19
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (19 bp):
TATCGCAACGAATTTGGAA
Found at i:4596057 original size:61 final size:61
Alignment explanation
Indices: 4595960--4596088 Score: 213
Period size: 61 Copynumber: 2.1 Consensus size: 61
4595950 GATTTTCGAC
* *
4595960 TATCGCAACAAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGGAA
1 TATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAA
* *
4596021 TATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAA
1 TATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAA
*
4596082 AATCGCA
1 TATCGCA
4596089 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (61 bp):
TATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAA
Found at i:4596061 original size:42 final size:38
Alignment explanation
Indices: 4596003--4596088 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 38
4595993 AACTTCGACT
*
4596003 ATCGCAACGAATTTGGAATATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATATCGCAACGAATTT-GAA-AA
*
4596043 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAAA
1 ATCGCAA--CGAACTTGGAATATCGCAACGAATTTGAAAA
4596083 ATCGCA
1 ATCGCA
4596089 TTGCGATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 15 0.36
41 3 0.07
42 24 0.57
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (38 bp):
ATCGCAACGAACTTGGAATATCGCAACGAATTTGAAAA
Found at i:4596213 original size:77 final size:78
Alignment explanation
Indices: 4596083--4596251 Score: 250
Period size: 77 Copynumber: 2.2 Consensus size: 78
4596073 AATTTGAAAA
*
4596083 ATCGCATTGCGATAGTCGATGTTCGCGTTACGAATCTAGAAACTAATTTGCGATACCGGAGATCG
1 ATCGCATTGCG--AGTCGATGTTCGCATTACGAATCTAGAAACTAATTTGCGATACCGGAGATCG
* * *
4596148 TGTTGCGAATTATCG
64 CGTTACGAATTACCG
* * *
4596163 ATCGCATTGCG-GTCGATGTTCGCATTGCGAATCTGGAAACTGATTTGCGATACCGGAGATCGCG
1 ATCGCATTGCGAGTCGATGTTCGCATTACGAATCTAGAAACTAATTTGCGATACCGGAGATCGCG
4596227 TTACGAATTACCG
66 TTACGAATTACCG
4596240 ATCGCATTGCGA
1 ATCGCATTGCGA
4596252 TTTAGTTGGT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
77 70 0.86
80 11 0.14
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (78 bp):
ATCGCATTGCGAGTCGATGTTCGCATTACGAATCTAGAAACTAATTTGCGATACCGGAGATCGCG
TTACGAATTACCG
Found at i:4596234 original size:40 final size:40
Alignment explanation
Indices: 4596105--4596234 Score: 94
Period size: 40 Copynumber: 3.3 Consensus size: 40
4596095 TAGTCGATGT
*
4596105 TCGCGTTACGAATCTAGAAACTAATTTGCGATACCGGAGA
1 TCGCGTTACGAATCTAGAAACTGATTTGCGATACCGGAGA
* * * * *
4596145 TCGTGTTGCGAAT-TATCG-ATC-GCA-TTGCGGT--C-GATGT
1 TCGCGTTACGAATCTA--GAAACTG-ATTTGCGATACCGGA-GA
* * *
4596182 TCGCATTGCGAATCTGGAAACTGATTTGCGATACCGGAGA
1 TCGCGTTACGAATCTAGAAACTGATTTGCGATACCGGAGA
4596222 TCGCGTTACGAAT
1 TCGCGTTACGAAT
4596235 TACCGATCGC
Statistics
Matches: 65, Mismatches: 14, Indels: 22
0.64 0.14 0.22
Matches are distributed among these distances:
36 3 0.05
37 16 0.25
38 8 0.12
39 8 0.12
40 27 0.42
41 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (40 bp):
TCGCGTTACGAATCTAGAAACTGATTTGCGATACCGGAGA
Found at i:4599861 original size:137 final size:137
Alignment explanation
Indices: 4599690--4600049 Score: 372
Period size: 137 Copynumber: 2.6 Consensus size: 137
4599680 TCACGTCGAG
* * * *
4599690 CGCTTTAACA-TGAGGAGTAGGTAGGTGAAACAAAGTTCATGTCGAGCGCTTCAAGAAGGGAGTA
1 CGCTTCAACATTGA-GAGTAGGCAGGGGAGACAAAGTTCATGTCGAGCGCTTCAAGAAGGGAGTA
* * *
4599754 GGCAGGATGACCTGATCTTCCACTGAGCGTTCTAACGGGTGGAATAGGCAGGGTGCT-TTAATAT
65 GGCAGGATGACCTGATCTTACACTGAGCGCTCTAACGGGTGGAATAAGCAGGGTGCTCTTAAT-T
4599818 CAC-GCGAA
129 CACAGCGAA
* * *
4599826 GTGCTTCAACATTGAGAGTAGGCAGGGGAGACAAAGTTCATGTTGAGCGCTTCCAG-AGGGATGT
1 -CGCTTCAACATTGAGAGTAGGCAGGGGAGACAAAGTTCATGTCGAGCGCTTCAAGAAGGGA-GT
* * * * ** * *
4599890 AGGTAGGATGACCTAATCTTACACTGAGCGCTCTAACGTGTGGAGTAAGCATTGTGTTCTTGATT
64 AGGCAGGATGACCTGATCTTACACTGAGCGCTCTAACGGGTGGAATAAGCAGGGTGCTCTTAATT
*
4599955 CACATCGAA
129 CACAGCGAA
* * * * * *
4599964 CGCTTCAACTTATG-GTGTAGGCAGGGTAGACAGAGTTCATG-CTGAGTGCTTCCATGAAGGGAG
1 CGCTTCAACAT-TGAGAGTAGGCAGGGGAGACAAAGTTCATGTC-GAGCGCTT-CAAGAAGGGAG
* *
4600027 TATGCAGGATGACTTGATCTTAC
63 TAGGCAGGATGACCTGATCTTAC
4600050 GCCGAGCAAT
Statistics
Matches: 183, Mismatches: 32, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
136 5 0.03
137 138 0.75
138 35 0.19
139 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (137 bp):
CGCTTCAACATTGAGAGTAGGCAGGGGAGACAAAGTTCATGTCGAGCGCTTCAAGAAGGGAGTAG
GCAGGATGACCTGATCTTACACTGAGCGCTCTAACGGGTGGAATAAGCAGGGTGCTCTTAATTCA
CAGCGAA
Found at i:4603362 original size:2 final size:2
Alignment explanation
Indices: 4603355--4603440 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
4603345 TTGTATTTAA
4603355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4603397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4603439 AT
1 AT
4603441 GCGCGAGCGC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4614321 original size:2 final size:2
Alignment explanation
Indices: 4614314--4614340 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4614304 AGAAATTAAC
4614314 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4614341 GAATCACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4614752 original size:13 final size:13
Alignment explanation
Indices: 4614734--4614770 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4614724 TAGAAAATAT
4614734 TTTTTATTTTCTA
1 TTTTTATTTTCTA
*
4614747 TTTTTATTTTCTG
1 TTTTTATTTTCTA
4614760 TTTTTGATTTT
1 TTTTT-ATTTT
4614771 AGAAAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.78
Consensus pattern (13 bp):
TTTTTATTTTCTA
Found at i:4631854 original size:17 final size:17
Alignment explanation
Indices: 4631811--4631862 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
4631801 TATACAGTAG
*
4631811 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
4631828 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
4631843 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
4631860 AAA
1 AAA
4631863 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:4632210 original size:16 final size:17
Alignment explanation
Indices: 4632189--4632226 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
4632179 ATTAATAATT
*
4632189 ATTAATTTA-TCTCTAA
1 ATTAATTAACTCTCTAA
4632205 ATTAA-TAACTCTCTAA
1 ATTAATTAACTCTCTAA
4632221 ATTAAT
1 ATTAAT
4632227 AAATTTCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAATTAACTCTCTAA
Found at i:4632227 original size:16 final size:16
Alignment explanation
Indices: 4632198--4632228 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4632188 TATTAATTTA
4632198 TCTCTAAATTAATAAC
1 TCTCTAAATTAATAAC
4632214 TCTCTAAATTAATAA
1 TCTCTAAATTAATAA
4632229 ATTTCTCCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (16 bp):
TCTCTAAATTAATAAC
Found at i:4639448 original size:17 final size:16
Alignment explanation
Indices: 4639409--4639441 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4639399 TTAAAACTCG
*
4639409 ACTCAAACTCGAAAAA
1 ACTCAAACTCAAAAAA
4639425 ACTCAAACTCAAAAAA
1 ACTCAAACTCAAAAAA
4639441 A
1 A
4639442 ATTCAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.03, T:0.12
Consensus pattern (16 bp):
ACTCAAACTCAAAAAA
Found at i:4639499 original size:22 final size:24
Alignment explanation
Indices: 4639452--4639501 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4639442 ATTCAAAAAT
4639452 TCGACTGAAACTCAATACTCAAGC
1 TCGACTGAAACTCAATACTCAAGC
*
4639476 TCGATTGAAACTCAAT-C-CAAGC
1 TCGACTGAAACTCAATACTCAAGC
4639498 TCGA
1 TCGA
4639502 ATTAAGCTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 1 0.04
24 15 0.60
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (24 bp):
TCGACTGAAACTCAATACTCAAGC
Found at i:4639534 original size:34 final size:33
Alignment explanation
Indices: 4639472--4639537 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
4639462 CTCAATACTC
*
4639472 AAGCTCGATTGAAACTCAATCCAAGCTCGAATT
1 AAGCTCGATTGAAACTCAATACAAGCTCGAATT
* * *
4639505 AAGCTCGATTTTAAGCTCAATACATGCTCGAAT
1 AAGCTCGA-TTGAAACTCAATACAAGCTCGAAT
4639538 ATTAGACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (33 bp):
AAGCTCGATTGAAACTCAATACAAGCTCGAATT
Found at i:4641388 original size:7 final size:7
Alignment explanation
Indices: 4641376--4641538 Score: 105
Period size: 7 Copynumber: 23.4 Consensus size: 7
4641366 AATTGAAATA
4641376 AGGGTTT
1 AGGGTTT
4641383 AGGGTTT
1 AGGGTTT
*
4641390 AAGGTTT
1 AGGGTTT
***
4641397 ATAATTT
1 AGGGTTT
4641404 AGGGTTT
1 AGGGTTT
* *
4641411 ATGGCTT
1 AGGGTTT
* *
4641418 AAGGATT
1 AGGGTTT
4641425 AGGGTTT
1 AGGGTTT
*
4641432 AGGATTT
1 AGGGTTT
**
4641439 A-TATCTT
1 AGGGT-TT
* *
4641446 AAGGATT
1 AGGGTTT
4641453 AGGGTTT
1 AGGGTTT
4641460 AGGGTTT
1 AGGGTTT
4641467 AGGGTTT
1 AGGGTTT
*
4641474 AAGGTTT
1 AGGGTTT
*
4641481 AGGATTT
1 AGGGTTT
*
4641488 AAGGTTT
1 AGGGTTT
***
4641495 ATACTTT
1 AGGGTTT
*
4641502 AGAGTTT
1 AGGGTTT
4641509 AGGGTTT
1 AGGGTTT
*
4641516 AGGGTGT
1 AGGGTTT
4641523 A-GGTTT
1 AGGGTTT
*
4641529 AGGATTT
1 AGGGTTT
4641536 AGG
1 AGG
4641539 ATGTAATCTA
Statistics
Matches: 119, Mismatches: 34, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
6 7 0.06
7 112 0.94
ACGTcount: A:0.24, C:0.02, G:0.32, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:4641419 original size:28 final size:28
Alignment explanation
Indices: 4641376--4641496 Score: 116
Period size: 28 Copynumber: 4.3 Consensus size: 28
4641366 AATTGAAATA
* * * **
4641376 AGGGTTTAGGGTTTAAGGTTTATAATTT
1 AGGGTTTATGGCTTAAGGATTAGGATTT
*
4641404 AGGGTTTATGGCTTAAGGATTAGGGTTT
1 AGGGTTTATGGCTTAAGGATTAGGATTT
* ** *
4641432 AGGATTTATATCTTAAGGATTAGGGTTT
1 AGGGTTTATGGCTTAAGGATTAGGATTT
* * *
4641460 AGGGTTTAGGGTTTAAGGTTTAGGATTT
1 AGGGTTTATGGCTTAAGGATTAGGATTT
*
4641488 AAGGTTTAT
1 AGGGTTTAT
4641497 ACTTTAGAGT
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.25, C:0.02, G:0.31, T:0.43
Consensus pattern (28 bp):
AGGGTTTATGGCTTAAGGATTAGGATTT
Found at i:4645516 original size:20 final size:20
Alignment explanation
Indices: 4645437--4645518 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
4645427 CCAGAACCCC
* *
4645437 ATGGGGGTATCGATTCCCCT
1 ATGGGGGAATCGATTCCCTT
** *
4645457 ACAGGGGAATCGGTTCCCATT
1 ATGGGGGAATCGATTCCC-TT
*
4645478 CAAAGGGGGAATC-AGTTCCCTT
1 --ATGGGGGAATCGA-TTCCCTT
*
4645500 ATGGGGGTATCGATTCCCT
1 ATGGGGGAATCGATTCCCT
4645519 CTGTCAAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
20 29 0.62
21 2 0.04
22 2 0.04
23 14 0.30
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (20 bp):
ATGGGGGAATCGATTCCCTT
Found at i:4655123 original size:23 final size:24
Alignment explanation
Indices: 4655078--4655124 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
4655068 GATGAGTTTT
4655078 TAAAAATAAAATAACACGCACGCAA
1 TAAAAAT-AAATAACACGCACGCAA
* *
4655103 TAAAAAT-AATAATACGTACGCA
1 TAAAAATAAATAACACGCACGCA
4655125 CATTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
25 7 0.35
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (24 bp):
TAAAAATAAATAACACGCACGCAA
Found at i:4655609 original size:16 final size:17
Alignment explanation
Indices: 4655588--4655636 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 17
4655578 TTTTTAATTT
4655588 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
4655604 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
4655619 AATTACTCTAACTTTCA
1 AATTACTCTAACTTTCA
4655636 A
1 A
4655637 TTTTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.11
15 11 0.39
16 7 0.25
17 4 0.14
18 3 0.11
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:4655624 original size:15 final size:14
Alignment explanation
Indices: 4655582--4655629 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
4655572 TTAATTTTTT
4655582 TAATTTAATTACT-
1 TAATTTAATTACTC
4655595 TAACTTTCAAATTACTC
1 TAA-TTT--AATTACTC
4655612 ATAATTTAATTACTC
1 -TAATTTAATTACTC
4655627 TAA
1 TAA
4655630 CTTTCAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTTAATTACTC
Found at i:4656520 original size:23 final size:23
Alignment explanation
Indices: 4656489--4656540 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
4656479 CTGAATGATT
*
4656489 CAGTACTGACTAATTCAGCAAAA
1 CAGTACTGAATAATTCAGCAAAA
* *
4656512 CAGTGCTGAATGATTCAGCAAAA
1 CAGTACTGAATAATTCAGCAAAA
4656535 CAGTAC
1 CAGTAC
4656541 ATTCTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (23 bp):
CAGTACTGAATAATTCAGCAAAA
Found at i:4658043 original size:2 final size:2
Alignment explanation
Indices: 4658036--4658060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4658026 ATGCAAATAG
4658036 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4658061 GTGCATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4662067 original size:2 final size:2
Alignment explanation
Indices: 4662060--4662141 Score: 92
Period size: 2 Copynumber: 40.0 Consensus size: 2
4662050 TTATTTTGTT
* * * *
4662060 TA TA TA TA TA TA TA GA TT TCA GTA TA TA TA CA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA
* *
4662104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4662142 GTAATATAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 64 0.97
3 1 0.02
4 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4662285 original size:27 final size:27
Alignment explanation
Indices: 4662246--4662329 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
4662236 TTTTTTTAAA
*
4662246 TATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATT
* *
4662273 TATATATTGTATAGTTTTTAAAACATTT
1 TATATAATATATAGTTTTTAAAACA-TT
* *
4662301 TGAAATAGTATATAGTTTTTAAAACATT
1 T-ATATAATATATAGTTTTTAAAACATT
4662329 T
1 T
4662330 TTGAAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
27 22 0.45
28 6 0.12
29 21 0.43
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (27 bp):
TATATAATATATAGTTTTTAAAACATT
Found at i:4662285 original size:29 final size:29
Alignment explanation
Indices: 4662253--4662344 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
4662243 AAATATATAA
* * *
4662253 TATATAGTTTTGAAAACA-TTT-ATATAT
1 TATATAGTTTTTAAAACATTTTGAAATAG
*
4662280 TGTATAGTTTTTAAAACATTTTGAAATAG
1 TATATAGTTTTTAAAACATTTTGAAATAG
* *
4662309 TATATAGTTTTTAAAACATTTTTGAAAAAT
1 TATATAGTTTTTAAAACA-TTTTGAAATAG
4662339 TATATA
1 TATATA
4662345 ATATATAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
27 16 0.29
28 3 0.05
29 21 0.38
30 15 0.27
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (29 bp):
TATATAGTTTTTAAAACATTTTGAAATAG
Found at i:4662378 original size:38 final size:37
Alignment explanation
Indices: 4662309--4662541 Score: 273
Period size: 37 Copynumber: 6.3 Consensus size: 37
4662299 TTTGAAATAG
*
4662309 TATATAGTTTTTAAAACATTTTTGAAAAATTATATAA
1 TATATAGTTTTAAAAACATTTTTGAAAAATTATATAA
4662346 TATATAGTTTTAAAAACATTTTTTGAAAAATTATATAA
1 TATATAGTTTTAAAAACA-TTTTTGAAAAATTATATAA
* *
4662384 TATATAGTTTTAAAAAAACCTTTTTGGTAAAATTATATAA
1 TATATAGTTTT--AAAAACATTTTT-GAAAAATTATATAA
* *
4662424 TATATAATTTCAAAAACATTTTTGAAAAATTATATAA
1 TATATAGTTTTAAAAACATTTTTGAAAAATTATATAA
* * *
4662461 TTTATAATTTTAAAAACATTTTTTTG-AAAACT-TAT-A
1 TATATAGTTTTAAAAACA--TTTTTGAAAAATTATATAA
*
4662497 TA-ATA-TTTTAAAATA-ATTTTTG-AAAACTATATAA
1 TATATAGTTTTAAAA-ACATTTTTGAAAAATTATATAA
4662531 TATATAGTTTT
1 TATATAGTTTT
4662542 GGAAATTTTT
Statistics
Matches: 174, Mismatches: 11, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
32 12 0.07
33 3 0.02
34 12 0.07
35 7 0.04
36 6 0.03
37 49 0.28
38 46 0.26
39 11 0.06
40 28 0.16
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATAGTTTTAAAAACATTTTTGAAAAATTATATAA
Found at i:4662621 original size:3 final size:3
Alignment explanation
Indices: 4662613--4662672 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
4662603 TTTTAGGATA
*
4662613 TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT CAT TATT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* *
4662660 TTT TAT TTT TAT T
1 TAT TAT TAT TAT T
4662673 TTTTTTCCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:4662641 original size:25 final size:25
Alignment explanation
Indices: 4662613--4662672 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
4662603 TTTTAGGATA
*
4662613 TATTATTATTATTATTATTTATTAT
1 TATTATTATTATCATTATTTATTAT
*
4662638 TATTATTATTATCATTATTTATTTT
1 TATTATTATTATCATTATTTATTAT
*
4662663 TATTTTTATT
1 TATTATTATT
4662673 TTTTTTCCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TATTATTATTATCATTATTTATTAT
Found at i:4662673 original size:16 final size:15
Alignment explanation
Indices: 4662615--4662677 Score: 74
Period size: 16 Copynumber: 4.1 Consensus size: 15
4662605 TTAGGATATA
4662615 TTATTATTATTATTAT
1 TTATTATTATTATT-T
*
4662631 TTATTATTATTATTA
1 TTATTATTATTATTT
*
4662646 TTATCATTATTTATTT
1 TTATTATTA-TTATTT
*
4662662 TTATTTTTATT-TTT
1 TTATTATTATTATTT
4662676 TT
1 TT
4662678 TCCGTTTCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
14 5 0.12
15 10 0.24
16 26 0.63
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:4663989 original size:23 final size:24
Alignment explanation
Indices: 4663958--4664002 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4663948 ATCATTTTTG
4663958 ATTTATTTATTTTATCCTTATTAA
1 ATTTATTTATTTTATCCTTATTAA
* *
4663982 ATTT-TTTATTTTTTCTTTATT
1 ATTTATTTATTTTATCCTTATT
4664003 TTGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTATTTATTTTATCCTTATTAA
Found at i:4664034 original size:3 final size:3
Alignment explanation
Indices: 4664028--4664054 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4664018 TTAAATAATA
4664028 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
4664055 CTCTAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4666742 original size:287 final size:287
Alignment explanation
Indices: 4666224--4666798 Score: 1042
Period size: 287 Copynumber: 2.0 Consensus size: 287
4666214 AGAGATATGA
4666224 TCAACATTTCAAAATCGTTTACAGCTGTACCCTTTTCTAGGAAAGAACCAAGGAGAGAAAATGAG
1 TCAACATTTCAAAATCGTTTACAGCTGTACCCTTTTCTAGGAAAGAACCAAGGAGAGAAAATGAG
*
4666289 TGTTTCGATCCCATTCCCATGACATACAAGGTGCTCTACCAACAACTGTTTGACGCACATGTGGT
66 TATTTCGATCCCATTCCCATGACATACAAGGTGCTCTACCAACAACTGTTTGACGCACATGTGGT
*
4666354 GTCACCCTATCCCGAGATACCTCTAAAGCCCACATACCCCAGGTGGTATGACAAAAATGCACTCT
131 GTCACCCTATCCCGAGATACCTCTAAAGCCCACATACCCCAAGTGGTATGACAAAAATGCACTCT
* * *
4666419 GTGAATATCATGGCGGTGTTTTGGGGCATGCTATTGAAAATTACCTCCCCTTTAAGAGGGTTATC
196 GTGAATATCATGGCGGTGTTTCGGGGAATACTATTGAAAATTACCTCCCCTTTAAGAGGGTTATC
* *
4666484 CAAAGGATGTACAACAGGGGTTGTATT
261 CAAAGGATGCACAACAGGGGTTGGATT
*
4666511 TCAACATTTCAAAATCGTTTACAGCTGTACCCTTTTCTAGGCAAGAACCAAGGAGAGAAAATGAG
1 TCAACATTTCAAAATCGTTTACAGCTGTACCCTTTTCTAGGAAAGAACCAAGGAGAGAAAATGAG
*
4666576 TATTTCGATCCCATTCCCATGACATACAAGGTGTTCTACCAACAACTGTTTGACGCACATGTGGT
66 TATTTCGATCCCATTCCCATGACATACAAGGTGCTCTACCAACAACTGTTTGACGCACATGTGGT
* * *
4666641 GTCACCCTATCCTGAGATACCTCTAAAGCCCCCATACCCCAAGTGGTATGACAAAAATGCACTTT
131 GTCACCCTATCCCGAGATACCTCTAAAGCCCACATACCCCAAGTGGTATGACAAAAATGCACTCT
4666706 GTGAATATCATGGCGGTGTTTCGGGGAATACTATTGAAAATTACCTCCCCTTTAAGAGGGTTATC
196 GTGAATATCATGGCGGTGTTTCGGGGAATACTATTGAAAATTACCTCCCCTTTAAGAGGGTTATC
4666771 CAAAGGATGCACAACAGGGGTTGGATT
261 CAAAGGATGCACAACAGGGGTTGGATT
4666798 T
1 T
4666799 ATTTTAACAA
Statistics
Matches: 276, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
287 276 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (287 bp):
TCAACATTTCAAAATCGTTTACAGCTGTACCCTTTTCTAGGAAAGAACCAAGGAGAGAAAATGAG
TATTTCGATCCCATTCCCATGACATACAAGGTGCTCTACCAACAACTGTTTGACGCACATGTGGT
GTCACCCTATCCCGAGATACCTCTAAAGCCCACATACCCCAAGTGGTATGACAAAAATGCACTCT
GTGAATATCATGGCGGTGTTTCGGGGAATACTATTGAAAATTACCTCCCCTTTAAGAGGGTTATC
CAAAGGATGCACAACAGGGGTTGGATT
Found at i:4667884 original size:95 final size:95
Alignment explanation
Indices: 4667720--4667959 Score: 326
Period size: 95 Copynumber: 2.7 Consensus size: 95
4667710 TAATATTATA
* *
4667720 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
*
4667785 ATTCAGCTAGCCTGATAAAGGTAATTATGC
66 ATTCAGCTAACCTGATAAAGGTAATTATGC
4667815 TATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTATGGATAA
*
4667879 GATTCAGCTAACCTGATAAAGGT--GT-T--
65 GATTCAGCTAACCTGATAAAGGTAATTATGC
* *
4667905 TAT---AT--A--TTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGAT
4667960 CCAACCATCC
Statistics
Matches: 137, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
83 45 0.33
84 1 0.01
85 1 0.01
87 2 0.01
90 3 0.02
92 1 0.01
93 1 0.01
94 1 0.01
95 82 0.60
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTAATTATGC
Found at i:4669356 original size:84 final size:84
Alignment explanation
Indices: 4669077--4669882 Score: 917
Period size: 84 Copynumber: 9.7 Consensus size: 84
4669067 TTAAAGACAA
* *
4669077 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* * *
4669142 GCTCAGCTCTAATGCACAG
66 GCTCAGCTCCAAGGCACAT
* * * *
4669161 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* * *
4669222 ACTCAGCTTCGAGGGCACAT
66 GCTCAGC-TCCAAGGCACAT
* * * * * * * *
4669242 CATTTACATCATAACTCAAGGCTAGGAGGGTTATCTGTC-ACCAAAAGACATTCGAGTTTGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACC-AAAGACCTTCGAGTTCGACTA
*
4669306 CGCTCAGCTCCAAGGCATAT
65 CGCTCAGCTCCAAGGCACAT
*
4669326 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
*
4669391 GCTCAGCTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * * *
4669410 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCCTCAAGTTTGATTA-
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* * *
4669470 ACTCAGCTTCGAGGGCACAT
66 GCTCAGC-TCCAAGGCACAT
* * * * * * * * *
4669490 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATATGTC-ACTAAAAGACCTTCGATTTTGACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAAC-CAAAGACCTTCGAGTTCGACTA
*
4669554 CGCTCAGCTCCAAGGCATAT
65 CGCTCAGCTCCAAGGCACAT
* * * **
4669574 TATTTGCAACATAACTTAAGTCGATAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGTTTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGT-CAACCAAAGACCTTCGAGTTCGACTA
4669638 CGCTCAGCTCCAAGGCACAT
65 CGCTCAGCTCCAAGGCACAT
* * * *
4669658 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCAACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
4669719 GTTCAGCTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* **
4669738 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
4669803 GCTCAGCTCTAAGACACAT
66 GCTCAGCTCCAAGGCACAT
*
4669822 CATTTGCAGCATAGA-TTAAGTCGAGAAGGGTTATCTGTCAACCGAAGACCTTCGAGTTCGA
1 CATTTGCAGCATA-ACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGA
4669883 TTACATTCAG
Statistics
Matches: 601, Mismatches: 101, Indels: 40
0.81 0.14 0.05
Matches are distributed among these distances:
79 6 0.01
80 155 0.26
81 37 0.06
83 2 0.00
84 365 0.61
85 36 0.06
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (84 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACAT
Found at i:4669539 original size:164 final size:162
Alignment explanation
Indices: 4669077--4669882 Score: 697
Period size: 164 Copynumber: 4.9 Consensus size: 162
4669067 TTAAAGACAA
* * * * *
4669077 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTAC
1 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCT----ACCAAAGACCCTCAAGTTCGATTAC
* * * * * * * * *
4669142 GCTCAGCTCTAATGCACAGCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGA
62 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACAAAGA
* * * * * *
4669205 CCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
127 CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATAT
* * * * * * ** * * *
4669242 CATTTACATCATAACTCAAGGCTAGGAGGGTTATCTGTCACCAAAAGACATTCGAGTTTGACTAC
1 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATC--T-ACC-AAAGACCCTCAAGTTCGATTAC
* * ** * *
4669307 GCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAA
62 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-A-CAAA
4669372 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
125 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * *
4669410 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCAAGTTTGATTA-ACTC
1 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACCCTCAAGTTCGATTACACTC
* * * * *
4669474 AGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATATGTCACTAAAAGAC
66 AGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAC--AAAGAC
* *
4669539 CTTCGATTTTGACTACGCTCAGCTCCAAGGCATAT
128 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * *
4669574 TATTTGCAACATAACTTAAGTCGATAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGTTTAC
1 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATC-T---ACCAAAGACCCTCAAGTTCGATTAC
* * * * * *
4669639 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGA
62 ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACAAAGA
* * *
4669702 CCCTCGAGTTCAACTACGTTCAGCTCCAAGGCATAT
127 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * *
4669738 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCT----ACCAAAGACCCTCAAGTTCGATTAC
* * * * * * *
4669803 GCTCAGCTCTAAGACACATCATTTGCAGCATAGA-TTAAGTCGAGAAGGGTTATCTGTCAACCGA
62 ACTCAGCTCCAAGGCACATCATTTACAGCATA-ACTCAAGGCGAGAAGGGTTATCTGTC-A-CAA
4669867 AGACCTTCGAGTTCGA
124 AGACCTTCGAGTTCGA
4669883 TTACATTCAG
Statistics
Matches: 536, Mismatches: 84, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
162 1 0.00
163 8 0.01
164 277 0.52
165 101 0.19
166 3 0.01
167 2 0.00
168 111 0.21
169 33 0.06
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (162 bp):
CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACCCTCAAGTTCGATTACACTC
AGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGGCATAT
Found at i:4669618 original size:248 final size:246
Alignment explanation
Indices: 4669077--4669882 Score: 1152
Period size: 248 Copynumber: 3.2 Consensus size: 246
4669067 TTAAAGACAA
* *
4669077 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* * *
4669142 GCTCAGCTCTAATGCACAGCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
4669207 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACATCATAACTCAAGGCTAGGAGGG
131 CTCGAGTTCGATTA-ACTCAGCTTCGAGGGCACATCATTTACAT-ATAACTCAAGGCTAGAAGGG
*
4669272 TTATCTGTCACCAAAAGACATTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
194 TTATCTGTCA-CAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
*
4669326 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
4669391 GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* *
4669456 CTCAAGTTTGATTAACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGT
131 CTCGAGTTCGATTAACTCAGCTTCGAGGGCACATCATTTACA-TATAACTCAAGGCTAGAAGGGT
* *
4669521 TATATGTCACTAAAAGACCTTCGATTTTGACTACGCTCAGCTCCAAGGCATAT
195 TATCTGTCAC-AAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
* * * **
4669574 TATTTGCAACATAACTTAAGTCGATAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGTTTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGT-CAACCAAAGACCTTCGAGTTCGACTA
4669638 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * * * * * * * *
4669703 CCTCGAGTTCAACT-ACGTTCAGC-TCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAG
130 CCTCGAGTTCGATTAAC--TCAGCTTCGAGGGCACATCATTTAC-ATATAACTCAAGGCTAGAAG
** * * * * *
4669766 GGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGACACAT
192 GGTTATCTGTC-ACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
*
4669822 CATTTGCAGCATAGA-TTAAGTCGAGAAGGGTTATCTGTCAACCGAAGACCTTCGAGTTCGA
1 CATTTGCAGCATA-ACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGA
4669883 TTACATTCAG
Statistics
Matches: 500, Mismatches: 48, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
247 4 0.01
248 351 0.70
249 145 0.29
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (246 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGATTAACTCAGCTTCGAGGGCACATCATTTACATATAACTCAAGGCTAGAAGGGTT
ATCTGTCACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
Found at i:4670512 original size:2 final size:2
Alignment explanation
Indices: 4670505--4670569 Score: 96
Period size: 2 Copynumber: 32.5 Consensus size: 2
4670495 TTATTTTGTT
4670505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
* *
4670547 TA TA CA TG TA TA TA GTA -A TA TA T
1 TA TA TA TA TA TA TA -TA TA TA TA T
4670570 TTTGTGAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 54 0.95
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4670686 original size:98 final size:98
Alignment explanation
Indices: 4670583--4670793 Score: 222
Period size: 98 Copynumber: 2.1 Consensus size: 98
4670573 GTGAAAATGT
*
4670583 TTTTGACAAAATATA-A-TATATAATTTTCAGAAAACGATTTTCGAAAATTTATATAT-TATATA
1 TTTTGA-AAAATATATATTATATAATTTT--GAAAAC-ATTTT-GAAAACTTATAT-TGTATATA
*
4670645 GTTTTTGAAAATATTTTT-AAAA-T-T-TATAATATATAG
60 GTTTTT-AAAACATTTTTAAAAATTATATATAATATATAG
* * *
4670681 TTTTGAAAACATTTATATATTGTATAGTTTTTAAAACATTTTGAAAACTTATATTGTATATAGTT
1 TTTTGAAAA-A--TATATATTATATAATTTTGAAAACATTTTGAAAACTTATATTGTATATAGTT
4670746 TTTAAAACATTTTTGAAAAATTATATATAATATATAG
63 TTTAAAACATTTTT-AAAAATTATATATAATATATAG
4670783 TTTT-AAAAATA
1 TTTTGAAAAATA
4670794 GTTTTTGAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 22
0.78 0.04 0.18
Matches are distributed among these distances:
97 14 0.14
98 32 0.33
99 9 0.09
100 11 0.11
101 6 0.06
102 25 0.26
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (98 bp):
TTTTGAAAAATATATATTATATAATTTTGAAAACATTTTGAAAACTTATATTGTATATAGTTTTT
AAAACATTTTTAAAAATTATATATAATATATAG
Found at i:4670695 original size:62 final size:63
Alignment explanation
Indices: 4670629--4670757 Score: 181
Period size: 62 Copynumber: 2.1 Consensus size: 63
4670619 ATTTTCGAAA
* *
4670629 ATTTATATATTATATAGTTTTTGAAAATATTTTTAAAA-TT-TATAATATATAGTTTTGAAAAC
1 ATTTATATATTATATAGTTTTT-AAAACATTTTGAAAACTTATATAATATATAGTTTTGAAAAC
* ** *
4670691 ATTTATATATTGTATAGTTTTTAAAACATTTTGAAAACTTATATTGTATATAGTTTTTAAAAC
1 ATTTATATATTATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTGAAAAC
4670754 ATTT
1 ATTT
4670758 TTGAAAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 13 0.22
62 23 0.39
63 23 0.39
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (63 bp):
ATTTATATATTATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTGAAAAC
Found at i:4670723 original size:38 final size:37
Alignment explanation
Indices: 4670681--4670974 Score: 255
Period size: 38 Copynumber: 7.8 Consensus size: 37
4670671 TAATATATAG
* *
4670681 TTTTGAAAACATTTATATATTGTATAGTTTTTAAAACA-
1 TTTTGAAAA-A-TTATATAATATATAGTTTTTAAAACAT
* **
4670719 TTTTGAAAACTTATATTGTATATAGTTTTTAAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
* *
4670756 TTTTGAAAAATTATATATAATATATAGTTTTAAAAATAGT
1 TTTTGAAAAA-T-TATATAATATATAGTTTTTAAAACA-T
4670796 TTTTGAAAAATTATATAATATATA-TTTTTGAAAAAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTT----AAAACAT
* * *
4670836 TTTTGGTAAAATTATATAATATATAATTTTAAAAACATT
1 TTTT-GAAAAATTATATAATATATAGTTTTTAAAACA-T
* *
4670875 TTTTGAAAAATTATATAATATATAATTTTAAAAACATTTT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAACA---T
* *
4670915 TTTTG-AAAACT-TAT-ATA-ATA--TTTTAAAATAAT
1 TTTTGAAAAATTATATAATATATAGTTTTTAAAA-CAT
*
4670947 TTTTG-AAAACTATATAATATATAGTTTT
1 TTTTGAAAAATTATATAATATATAGTTTT
4670975 GGAAATTTTT
Statistics
Matches: 220, Mismatches: 17, Indels: 39
0.80 0.06 0.14
Matches are distributed among these distances:
32 12 0.05
33 3 0.01
34 10 0.05
35 4 0.02
36 26 0.12
37 19 0.09
38 63 0.29
39 32 0.15
40 23 0.10
41 24 0.11
42 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTTAAAACAT
Found at i:4671054 original size:3 final size:3
Alignment explanation
Indices: 4671046--4671099 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
4671036 TTTTAGGATA
* *
4671046 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT CAT TATT TAT TTT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
4671093 TTT TAT T
1 TAT TAT T
4671100 TTTTTCCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:4671055 original size:25 final size:25
Alignment explanation
Indices: 4671020--4671089 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
4671010 TGTTTTTGAA
*
4671020 ATATA-TA-TATTATATATTTTAGG
1 ATATATTATTATTATTTATTTTAGG
**
4671043 ATATATTATTATTATTTATTATTATT
1 ATATATTATTATTATTTATT-TTAGG
*
4671069 AT-TATTATCATTATTTATTTT
1 ATATATTATTATTATTTATTTT
4671090 TATTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 5 0.12
24 4 0.10
25 26 0.65
26 5 0.12
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (25 bp):
ATATATTATTATTATTTATTTTAGG
Found at i:4671092 original size:25 final size:25
Alignment explanation
Indices: 4671046--4671099 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
4671036 TTTTAGGATA
*
4671046 TATTATTATTATTTATTATTATTAT
1 TATTATCATTATTTATTATTATTAT
* *
4671071 TATTATCATTATTTATTTTTATTTT
1 TATTATCATTATTTATTATTATTAT
4671096 TATT
1 TATT
4671100 TTTTTCCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TATTATCATTATTTATTATTATTAT
Found at i:4671100 original size:16 final size:16
Alignment explanation
Indices: 4671046--4671104 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
4671036 TTTTAGGATA
4671046 TATTA-TTATTATTTAT
1 TATTATTTATT-TTTAT
*
4671062 TATTA-TTATTATTAT
1 TATTATTTATTTTTAT
*
4671077 CATTATTTATTTTTAT
1 TATTATTTATTTTTAT
*
4671093 TTTTATTT-TTTT
1 TATTATTTATTTT
4671105 CCGTTTCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.32
16 25 0.68
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTTATTTTTAT
Found at i:4672384 original size:15 final size:15
Alignment explanation
Indices: 4672354--4672418 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
4672344 CTTTTTTCTA
*
4672354 TTTTTATTTA-TCAT
1 TTTTTATTTATTTAT
4672368 TTTTTATTTATTTAT
1 TTTTTATTTATTTAT
* ** *
4672383 TTTATCCTTATTAAAT
1 TTTTTATTTATT-TAT
*
4672399 TTTTTATTTTTTTAT
1 TTTTTATTTATTTAT
4672414 TTTTT
1 TTTTT
4672419 TCTTTATTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
14 10 0.26
15 19 0.49
16 10 0.26
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTATTTATTTAT
Found at i:4673244 original size:110 final size:110
Alignment explanation
Indices: 4673051--4673342 Score: 449
Period size: 110 Copynumber: 2.7 Consensus size: 110
4673041 AGAAAAGTTT
* ** *
4673051 ACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGTCAATTTCAACTTCACATTGAAGAATATTG
1 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
* **
4673116 GACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGTGACTG
66 GACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGACTG
* * *
4673161 ACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAATTTTAACTTCACAGCGAAGGATACTG
1 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
4673226 GACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGACTG
66 GACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGACTG
* * * *
4673271 ACTGTCAACAAACAACCTTTCAGTTTCACTCTGTGTCAATTTCAACTTCACAGCGAAGGATATTG
1 ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
*
4673336 AACTCGA
66 GACTCGA
4673343 AGCAAAACAA
Statistics
Matches: 164, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 164 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (110 bp):
ACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
GACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACGACTG
Found at i:4673983 original size:252 final size:251
Alignment explanation
Indices: 4673665--4674294 Score: 902
Period size: 252 Copynumber: 2.5 Consensus size: 251
4673655 GGCTTCCCAC
* * *
4673665 TTTCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGGACTCGAAACAATATAACTTACTTGGA
1 TTTCAGAGTCAATTTTAACTTCAC-GCGGAGGATATTGGACTCGAAACAATACAACTTAATTGGA
* * *
4673730 TTTCAACTTCACAACGAAGGATATCCAATTCCAGGCTCAACTTCATGACAAAGGGGCTACCCGCG
65 TTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACGACAAAGGGGCCACCCGCG
4673795 GTTTCAACTTCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCTAGACTGGATTTCAA
130 GTTTCAACTTCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCTAGACTGGATTTCAA
* * * *
4673860 ATTCACGACGAAGGATATCCAACTCAAAGAATGAGTGTCTGTTAATAAACATTCCAG
195 ATTCACAACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACATGCCAG
* * * *
4673917 TTTCAGAGTCAATTTTAACCTCACAGCGGAGGATGTTGGACTTGAAACAATACAACTTATTTGGA
1 TTTCAGAGTCAATTTTAACTTCAC-GCGGAGGATATTGGACTCGAAACAATACAACTTAATTGGA
* * * * ** *
4673982 TTTCAACTTCACGACAAAGAATATCCAATTCCAGGCTCAGCTTCACGACTAATAGGCCACCTGCG
65 TTTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACGACAAAGGGGCCACCCGCG
* *
4674047 GTTTCAACTTCACGACGAAGGGAATCGTGCACACAAGCATCATCCATCTCTATACTGGATTTCAA
130 GTTTCAACTTCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCTAGACTGGATTTCAA
* *
4674112 CTTCACAACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACGTGCCAG
195 ATTCACAACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACATGCCAG
* * * * *
4674169 TTTCAGAGTCAATTTCAACTTCACGACGAAGGATATTGGCCTCAAAATAA-AGCAACTTACATTG
1 TTTCAGAGTCAATTTTAACTTCACG-CGGAGGATATTGGACTCGAAACAATA-CAACTTA-ATTG
* * *
4674233 GATTTCAATTTCACGATGAAGGATATCCAATTCCAAGGCTCAACTTCACGACGAAGGGGCCA
63 GATTTCAACTTCACGACGAAGGATATCCAATTCC-AGGCTCAACTTCACGACAAAGGGGCCA
4674295 TATATGATTC
Statistics
Matches: 332, Mismatches: 42, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
251 2 0.01
252 274 0.83
253 33 0.10
254 23 0.07
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (251 bp):
TTTCAGAGTCAATTTTAACTTCACGCGGAGGATATTGGACTCGAAACAATACAACTTAATTGGAT
TTCAACTTCACGACGAAGGATATCCAATTCCAGGCTCAACTTCACGACAAAGGGGCCACCCGCGG
TTTCAACTTCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCTAGACTGGATTTCAAA
TTCACAACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACATGCCAG
Found at i:4675276 original size:12 final size:13
Alignment explanation
Indices: 4675250--4675277 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4675240 CGGATTCGGG
4675250 TTCGGGGATTTTT
1 TTCGGGGATTTTT
4675263 TTCGGGGATTTTT
1 TTCGGGGATTTTT
4675276 TT
1 TT
4675278 GGGTCGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.29, T:0.57
Consensus pattern (13 bp):
TTCGGGGATTTTT
Found at i:4675331 original size:2 final size:2
Alignment explanation
Indices: 4675324--4675396 Score: 77
Period size: 2 Copynumber: 39.5 Consensus size: 2
4675314 CCGCCCTGAT
4675324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
4675364 TT TA TA TT TT TA TA T- TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4675397 TTTATATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
1 6 0.10
2 56 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:4675378 original size:34 final size:35
Alignment explanation
Indices: 4675338--4675433 Score: 137
Period size: 33 Copynumber: 2.8 Consensus size: 35
4675328 TATATATATA
4675338 TATATATATATATATATATATAATATTTTATATTTT
1 TATATATATAT-TATATATATAATATTTTATATTTT
4675374 TATAT-TA-ATTATATATATAATATTTTATATTTT
1 TATATATATATTATATATATAATATTTTATATTTT
*
4675407 T-TATAT-TAATTATATATAAAATATTTT
1 TATATATAT-ATTATATATATAATATTTT
4675434 CGGGTTCGGG
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
32 3 0.05
33 26 0.46
34 20 0.36
35 2 0.04
36 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
TATATATATATTATATATATAATATTTTATATTTT
Found at i:4675392 original size:33 final size:34
Alignment explanation
Indices: 4675350--4675433 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
4675340 TATATATATA
4675350 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
4675383 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
*
4675417 TATATATAAAATATTTT
1 TATATATATAATATTTT
4675434 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 20 0.41
34 29 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:4675421 original size:25 final size:24
Alignment explanation
Indices: 4675322--4675428 Score: 52
Period size: 23 Copynumber: 4.6 Consensus size: 24
4675312 CCCCGCCCTG
* *
4675322 ATTATATATATATA-TATATATATA
1 ATTATATATATAAATTTTATAT-TA
4675346 TATATATATATATAATATTTTATATT-
1 -AT-TATATATATAA-ATTTTATATTA
*
4675372 -TT-TATAT-T-AATTATATATATA
1 ATTATATATATAAATTTTATAT-TA
* **
4675393 A-TAT-TTTATATTTTTTATATTA
1 ATTATATATATAAATTTTATATTA
4675415 ATTATATATA-AAAT
1 ATTATATATATAAAT
4675429 ATTTTCGGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 24
0.64 0.11 0.25
Matches are distributed among these distances:
19 8 0.13
20 2 0.03
21 4 0.07
22 10 0.16
23 13 0.21
24 4 0.07
25 2 0.03
26 10 0.16
27 2 0.03
28 6 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTATATATATAAATTTTATATTA
Found at i:4676459 original size:20 final size:20
Alignment explanation
Indices: 4676436--4676480 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4676426 ATTTATAAAT
*
4676436 TTATTATTATTTTACGTTT-A
1 TTATTATTATCTT-CGTTTGA
*
4676456 TTATGATTATCTTCGTTTGA
1 TTATTATTATCTTCGTTTGA
4676476 TTATT
1 TTATT
4676481 TTTCAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (20 bp):
TTATTATTATCTTCGTTTGA
Found at i:4679892 original size:50 final size:50
Alignment explanation
Indices: 4679818--4679930 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
4679808 GTAGCAGTAA
* *
4679818 AACGC-CCCCCTGAACCGCGCTATACGCTAATTTGGCGCCACGTGGGTAT
1 AACGCGCCCCCTGAACCGCGATATACGCTAATCTGGCGCCACGTGGGTAT
** * * * *
4679867 AACGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCGTCACTTGGGTAT
1 AACGCGCCCCCTGAACCGCGATATACGCTAATCTGGCGCCACGTGGGTAT
*
4679917 AGCGCGCCCCCTGA
1 AACGCGCCCCCTGA
4679931 TCCACGCTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
49 5 0.09
50 48 0.91
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.19
Consensus pattern (50 bp):
AACGCGCCCCCTGAACCGCGATATACGCTAATCTGGCGCCACGTGGGTAT
Found at i:4680069 original size:10 final size:10
Alignment explanation
Indices: 4680054--4680088 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
4680044 TTTATAACAC
4680054 CAAATTCTCT
1 CAAATTCTCT
4680064 CAAATTCTCT
1 CAAATTCTCT
4680074 -AAATTTCTCT
1 CAAA-TTCTCT
4680084 CAAAT
1 CAAAT
4680089 AATCTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:4680496 original size:111 final size:111
Alignment explanation
Indices: 4680220--4680546 Score: 540
Period size: 105 Copynumber: 3.0 Consensus size: 111
4680210 TGGAAATCAT
*
4680220 ATATCTCTACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
4680285 TATTTAGTTGATTTATTTAATTCATGATTATTAGATTAAGAATT--
66 TAATTAGTTGATTTATTTAATTCATGATTATTAGATTAAGAATTAA
*
4680329 A-A--T-GACACTTTACTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
4680390 TAATTAGTTGATTTATTTAATTCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATTCATGATTATTAGATTAAGAATTAA
* * *
4680436 ATATCTCGACACTTTGCTGATACGGTAACATTTTAATGATTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
4680501 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATTCATGATTATTAGATTAAGAATTAA
4680547 TTTTTGTAAT
Statistics
Matches: 203, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
105 99 0.49
106 1 0.00
107 1 0.00
108 2 0.01
109 1 0.00
110 1 0.00
111 98 0.48
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATTCATGATTATTAGATTAAGAATTAA
Found at i:4682442 original size:9 final size:9
Alignment explanation
Indices: 4682430--4682459 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4682420 CGACGACGAC
*
4682430 GACGATGGT
1 GACGATGAT
4682439 GACGATGAT
1 GACGATGAT
4682448 GACGATGAT
1 GACGATGAT
4682457 GAC
1 GAC
4682460 AGCAAGGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (9 bp):
GACGATGAT
Found at i:4682712 original size:35 final size:32
Alignment explanation
Indices: 4682673--4682756 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 32
4682663 ATATTTCAGT
4682673 TAATTTTGTTTATTACCATTTAATATTAGTTATTG
1 TAATTTTGTTTATTACCATTTAAT-TT--TTATTG
*
4682708 TAATTTGGTTATCATTTACCATTTAATTTTTATTG
1 TAATTTTGTT-T-A-TTACCATTTAATTTTTATTG
* *
4682743 TAAGTTTGTGTATT
1 TAATTTTGTTTATT
4682757 TAAATACCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
32 2 0.05
33 1 0.02
34 1 0.02
35 22 0.52
36 1 0.02
37 3 0.07
38 12 0.29
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (32 bp):
TAATTTTGTTTATTACCATTTAATTTTTATTG
Found at i:4702368 original size:18 final size:19
Alignment explanation
Indices: 4702333--4702369 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4702323 CACGAAATGT
4702333 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
4702353 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
4702370 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:4702558 original size:36 final size:37
Alignment explanation
Indices: 4702518--4702592 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
4702508 CAAATTGTAA
4702518 AATATTTATAT-ATTTTCTTTA-AAAAATTAAATTCAT
1 AATATTTATATAATTTTCTTTACAAAAATTAAATT-AT
* *
4702554 AATATTTATATAATTTTTTTTACAAAATTTAAATTAT
1 AATATTTATATAATTTTCTTTACAAAAATTAAATTAT
4702591 AA
1 AA
4702593 AAAAGGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 11 0.31
37 13 0.37
38 11 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (37 bp):
AATATTTATATAATTTTCTTTACAAAAATTAAATTAT
Found at i:4703611 original size:72 final size:72
Alignment explanation
Indices: 4703473--4703682 Score: 343
Period size: 72 Copynumber: 2.9 Consensus size: 72
4703463 GGCCTCTACA
*
4703473 CATGCTTCCGGCCTTGAGCTTTTGGATT-TCTTT-TAACCAAAAAAGCTAAAAGAGGGATTAAAG
1 CATGCTT-CGGCCTTGAGCTTTTGGATTCTTTTTGTAACCAAAAAAGCTAAAAGAGGGATT--AG
4703536 AGACTCTCCC
63 AGACTCTCCC
*
4703546 CATGCTTAGGCCTTGAGCTTTTGGATTCTTTTTGTAACCAAAAAAGCTAAAAGAGGGATTAGAGA
1 CATGCTTCGGCCTTGAGCTTTTGGATTCTTTTTGTAACCAAAAAAGCTAAAAGAGGGATTAGAGA
4703611 CTCTCCC
66 CTCTCCC
* *
4703618 CATGCTTCGGCGTTGAGCTTTTGGATTCTTTTTGTAACTAAAAAAGCTAAAAGAGGGATTAGAGA
1 CATGCTTCGGCCTTGAGCTTTTGGATTCTTTTTGTAACCAAAAAAGCTAAAAGAGGGATTAGAGA
4703683 TTAGGGATCT
Statistics
Matches: 130, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
72 93 0.72
73 11 0.08
74 26 0.20
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (72 bp):
CATGCTTCGGCCTTGAGCTTTTGGATTCTTTTTGTAACCAAAAAAGCTAAAAGAGGGATTAGAGA
CTCTCCC
Found at i:4706020 original size:43 final size:43
Alignment explanation
Indices: 4705972--4706060 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
4705962 ATTAACGACA
*
4705972 TTTGTTTTTAAAATGATGCTATAGAACTTGACCTTTTGCGGCG
1 TTTGTTTTTAAAATGATGCTATAGAACTTGACCTATTGCGGCG
* ** *
4706015 TTTGTTTTTAAAATGTTTTTATAGATCTTGACCTATTGCGGCG
1 TTTGTTTTTAAAATGATGCTATAGAACTTGACCTATTGCGGCG
4706058 TTT
1 TTT
4706061 TTTGTTCACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (43 bp):
TTTGTTTTTAAAATGATGCTATAGAACTTGACCTATTGCGGCG
Found at i:4708144 original size:15 final size:14
Alignment explanation
Indices: 4708107--4708152 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
4708097 AATATTTTTT
*
4708107 TAAAATTACAAAAA
1 TAAAATTAAAAAAA
4708121 TAAAA-TAAAAAAA
1 TAAAATTAAAAAAA
*
4708134 TATAAATTAAAAAAT
1 TA-AAATTAAAAAAA
4708149 TAAA
1 TAAA
4708153 TGGAACTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.32
14 10 0.36
15 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATTAAAAAAA
Found at i:4720150 original size:27 final size:27
Alignment explanation
Indices: 4720120--4720176 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
4720110 GTGGATTCAA
4720120 CACCAACCAACTGAGGTAGAATGTTGG
1 CACCAACCAACTGAGGTAGAATGTTGG
4720147 CACCAACCAACTGAGGTAGAATGTTGG
1 CACCAACCAACTGAGGTAGAATGTTGG
4720174 CAC
1 CAC
4720177 TGACAGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (27 bp):
CACCAACCAACTGAGGTAGAATGTTGG
Found at i:4721588 original size:59 final size:59
Alignment explanation
Indices: 4721471--4721589 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 59
4721461 AGATATATGT
* * **
4721471 TTACACATACATGTGGTATGTGACAGAAGAGAAGAAACATGTGATTATAAGATCAATGA
1 TTACACATACATGTGATATGTGACAGAAAAGAAGAAACATGTGATTATAAGAGAAATGA
* * *
4721530 TTACACATACATGTGATATGTGACTGAAAAGAA-AAGATATGTGTTTATAAGAGAAATGA
1 TTACACATACATGTGATATGTGACAGAAAAGAAGAA-ACATGTGATTATAAGAGAAATGA
4721589 T
1 T
4721590 ATGATTAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
58 2 0.04
59 50 0.96
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (59 bp):
TTACACATACATGTGATATGTGACAGAAAAGAAGAAACATGTGATTATAAGAGAAATGA
Found at i:4721719 original size:31 final size:31
Alignment explanation
Indices: 4721681--4721782 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
4721671 AGGGTCGAGG
* *
4721681 GTTTACCTATATTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4721712 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4721743 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4721774 GATTACCTA
1 GTTTACCTA
4721783 GGTTTTTCAG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4722574 original size:21 final size:22
Alignment explanation
Indices: 4722548--4722588 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4722538 AGCAGTACTA
*
4722548 TAGCA-GGGTATCGGTTCCCTG
1 TAGCAGGGGAATCGGTTCCCTG
4722569 TAGCAGGGGAATCGGTTCCC
1 TAGCAGGGGAATCGGTTCCC
4722589 CTCTGACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.24
Consensus pattern (22 bp):
TAGCAGGGGAATCGGTTCCCTG
Found at i:4722636 original size:12 final size:12
Alignment explanation
Indices: 4722619--4722677 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
4722609 TTAACATTTG
*
4722619 GGTACTGTTCAT
1 GGTACTGTTCAC
4722631 GGTACTGTTCAC
1 GGTACTGTTCAC
*
4722643 AGTACTGTTCAC
1 GGTACTGTTCAC
*
4722655 --TACTGCTCATAC
1 GGTACTGTTC--AC
4722667 GGTACTGTTCA
1 GGTACTGTTCA
4722678 TACCATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.18
12 25 0.64
14 7 0.18
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (12 bp):
GGTACTGTTCAC
Found at i:4727202 original size:10 final size:10
Alignment explanation
Indices: 4727187--4727215 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
4727177 AAATTAGTAC
4727187 AATAAAATAT
1 AATAAAATAT
4727197 AATAAAATAT
1 AATAAAATAT
4727207 AATAAAATA
1 AATAAAATA
4727216 ATAAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAAATAT
Found at i:4737724 original size:4 final size:4
Alignment explanation
Indices: 4737707--4737741 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
4737697 CAAGAAAATA
*
4737707 ATTT ATTT CCTTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT AT
4737742 AATCATACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.89
5 3 0.11
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:4737805 original size:39 final size:38
Alignment explanation
Indices: 4737758--4737879 Score: 156
Period size: 39 Copynumber: 3.2 Consensus size: 38
4737748 ACGTAATTTC
* *
4737758 TAAGAAAATAAATTCAACAATTTATTTTCTTTTACAAA
1 TAAGAAAATAAATCCAACGATTTATTTTCTTTTACAAA
** *
4737796 TCCGGAAAATAAATCCAACGATTTATTTTATTTTACAAAA
1 T-AAGAAAATAAATCCAACGATTTATTTTCTTTTAC-AAA
*
4737836 TAAGAAAATAAATCCAACGATTTA-TTTCTTTTTACAAC
1 TAAGAAAATAAATCCAACGATTTATTTTC-TTTTACAAA
4737874 TAAGAA
1 TAAGAA
4737880 TCATATAAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
38 12 0.17
39 56 0.78
40 4 0.06
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (38 bp):
TAAGAAAATAAATCCAACGATTTATTTTCTTTTACAAA
Found at i:4737958 original size:39 final size:40
Alignment explanation
Indices: 4737895--4737970 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 40
4737885 TAAGATGATC
* *
4737895 AGAAAATAAAATTTAACAAGTTATTTCCTTTTTCAAAACA
1 AGAAAATAAAATTAAACAAGTTATTTCCTTTTACAAAACA
* * *
4737935 AGAAAAT-AAATTAAACGATTTATTTTCTTTTACAAA
1 AGAAAATAAAATTAAACAAGTTATTTCCTTTTACAAA
4737971 CCATAATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 24 0.77
40 7 0.23
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (40 bp):
AGAAAATAAAATTAAACAAGTTATTTCCTTTTACAAAACA
Found at i:4738030 original size:98 final size:98
Alignment explanation
Indices: 4737799--4738053 Score: 293
Period size: 97 Copynumber: 2.6 Consensus size: 98
4737789 TTACAAATCC
* * * *
4737799 GGAAAA-TAAATCCAACGATTTATTTTATTTTACAAAATAAGAAAATAAATCCAACGATTTATTT
1 GGAAAATTAAATTCAACAATTTATTTTCTTTTACAAAATAAGAAAATAAATCAAACGATTTATTT
4737863 CTTTTTACAACTAAGAATCATATAAGATGATCA
66 CTTTTTACAACTAAGAATCATATAAGATGATCA
* * * * * * *
4737896 -GAAAATAAAATTTAACAAGTTATTTCCTTTTTCAAAACAAGAAAATAAATTAAACGATTTATTT
1 GGAAAATTAAATTCAACAATTTATTTTCTTTTACAAAATAAGAAAATAAATCAAACGATTTATTT
* * * **
4737960 -TCTTTTACAAAC-CATAATCATTTAAGATTCTCA
66 CT-TTTTAC-AACTAAGAATCATATAAGATGATCA
* * *
4737993 GGAAAATTAAATTCAACAATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAATGATTT
1 GGAAAATTAAATTCAACAATTTATTTTCTTTTACAAAATAAGAAAATAAATCAAACGATTT
4738054 TAATTTTCCT
Statistics
Matches: 128, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
96 6 0.05
97 69 0.54
98 53 0.41
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (98 bp):
GGAAAATTAAATTCAACAATTTATTTTCTTTTACAAAATAAGAAAATAAATCAAACGATTTATTT
CTTTTTACAACTAAGAATCATATAAGATGATCA
Found at i:4738175 original size:40 final size:40
Alignment explanation
Indices: 4738131--4738290 Score: 128
Period size: 39 Copynumber: 3.8 Consensus size: 40
4738121 GATTCTTAGA
* *
4738131 AAAATAAATTC-AATAATTTATTTCCTTTCACAAAAACAGG
1 AAAATAAATTCAAATAATTTATTTCCTTTTAC-AAAATAGG
4738171 AAAATAAATCTAACAATTTATTTCAATTTATTTCCTTTTACAAAATAGG
1 AAAATAAAT-T--CAA---A--T-AATTTATTTCCTTTTACAAAATAGG
* * * *
4738220 AAACT-AATTCGAATGATTTATTTTCTTTTACAAAATAGG
1 AAAATAAATTCAAATAATTTATTTCCTTTTACAAAATAGG
* * *
4738259 AAAATAAATTC-TACAATTTATTTCTTTTTACA
1 AAAATAAATTCAAATAATTTATTTCCTTTTACA
4738291 TATCATAATC
Statistics
Matches: 97, Mismatches: 12, Indels: 23
0.73 0.09 0.17
Matches are distributed among these distances:
39 43 0.44
40 15 0.15
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
45 2 0.02
47 2 0.02
48 3 0.03
49 12 0.12
50 16 0.16
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (40 bp):
AAAATAAATTCAAATAATTTATTTCCTTTTACAAAATAGG
Found at i:4738242 original size:49 final size:50
Alignment explanation
Indices: 4738145--4738242 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 50
4738135 TAAATTCAAT
*
4738145 AATTTATTTCCTTTCACAAAAACAGGAAAATAAATCTAACAATTTATTTC
1 AATTTATTTCCTTTCACAAAAACAGGAAAATAAATCGAACAATTTATTTC
* * * * **
4738195 AATTTATTTCCTTTTAC-AAAATAGGAAACTAATTCGAATGATTTATTT
1 AATTTATTTCCTTTCACAAAAACAGGAAAATAAATCGAACAATTTATTT
4738243 TCTTTTACAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 25 0.61
50 16 0.39
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (50 bp):
AATTTATTTCCTTTCACAAAAACAGGAAAATAAATCGAACAATTTATTTC
Found at i:4738375 original size:39 final size:39
Alignment explanation
Indices: 4738317--4738434 Score: 148
Period size: 39 Copynumber: 3.0 Consensus size: 39
4738307 GATTCTTAGG
* * *
4738317 AAAATAAATTCAACAATTTATTTTCTTTTACAAAATAGA
1 AAAATAAATCCAACGATTTATTTACTTTTACAAAATAGA
* * *
4738356 AAAATAAATCCAACGATTTATTTCCTTTTACAAACTAGG
1 AAAATAAATCCAACGATTTATTTACTTTTACAAAATAGA
* *
4738395 AAAATAAATCCGACGATTTAATTACTTTTA-AAAGATAGA
1 AAAATAAATCCAACGATTTATTTACTTTTACAAA-ATAGA
4738434 A
1 A
4738435 TCATAAAAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 3 0.04
39 65 0.96
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.34
Consensus pattern (39 bp):
AAAATAAATCCAACGATTTATTTACTTTTACAAAATAGA
Found at i:4738438 original size:136 final size:136
Alignment explanation
Indices: 4738194--4738485 Score: 347
Period size: 136 Copynumber: 2.2 Consensus size: 136
4738184 CAATTTATTT
* * * * * * *
4738194 CAATTTATTTCCTTTTACAAAATAGGAAACTAATTCGAATGATTTATTTTCTTTTACAAAATAGG
1 CAATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* * * * * * * * *
4738259 AAAATAAATTCTACAATTTATTTCTTTTTACATATCATAATCATATAAGATTCT-TAGGAAAATA
66 AAAATAAATCCGACAATTTATTACTTTTAAAAGATCAGAATCATAAAAGATT-TATAAGAAAATA
4738323 AATTCAA
130 AATTCAA
*
4738330 CAATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAACTAGG
1 CAATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
*
4738395 AAAATAAATCCGACGATTTAATTACTTTTAAAAGAT-AGAATCATAAAAGATTTATAAGAAAATA
66 AAAATAAATCCGACAATTT-ATTACTTTTAAAAGATCAGAATCATAAAAGATTTATAAGAAAATA
*
4738459 AATTTAA
130 AATTCAA
* * *
4738466 TAATTTGTTTTC-CTTACAAA
1 CAATTTATTTTCTTTTACAAA
4738486 GTTAGAATCA
Statistics
Matches: 132, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
135 8 0.06
136 112 0.85
137 12 0.09
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (136 bp):
CAATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
AAAATAAATCCGACAATTTATTACTTTTAAAAGATCAGAATCATAAAAGATTTATAAGAAAATAA
ATTCAA
Found at i:4738492 original size:58 final size:57
Alignment explanation
Indices: 4738425--4738668 Score: 231
Period size: 58 Copynumber: 4.2 Consensus size: 57
4738415 ATTACTTTTA
* ** * * * *
4738425 AAAGATAGAATCATAAAAGATTTATAAGAAAATAAATTTAATAATTTGTTTTCCTTAC
1 AAAGTTAGAATCATTTAAGATTT-CAAGGAAATAAATTTAACAATTTATTTTCCTTAC
** * * *
4738483 AAAGTTAGAATCATTCCAGATTCTCAAGGAAATAAATTCAACATTTTATTTTTCTTAC
1 AAAGTTAGAATCATTTAAGATT-TCAAGGAAATAAATTTAACAATTTATTTTCCTTAC
* * *
4738541 AGAGTTAGAATCATTTAAGATTTTCAAGGAAAT-AATTTCAACGATTTATTTTCTTTAC
1 AAAGTTAGAATCATTTAAGA-TTTCAAGGAAATAAATTT-AACAATTTATTTTCCTTAC
* **** *
4738599 AATGTTAGAATCATTTAAGATTTCCAAGGAAATAAATTT-TTTTTTTATTTTTCTTAC
1 AAAGTTAGAATCATTTAAGATTT-CAAGGAAATAAATTTAACAATTTATTTTCCTTAC
*
4738656 AAGGTTAGAATCA
1 AAAGTTAGAATCA
4738669 ACAGAAGATT
Statistics
Matches: 153, Mismatches: 28, Indels: 11
0.80 0.15 0.06
Matches are distributed among these distances:
57 31 0.20
58 114 0.75
59 8 0.05
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (57 bp):
AAAGTTAGAATCATTTAAGATTTCAAGGAAATAAATTTAACAATTTATTTTCCTTAC
Found at i:4738677 original size:116 final size:116
Alignment explanation
Indices: 4738468--4738678 Score: 266
Period size: 116 Copynumber: 1.8 Consensus size: 116
4738458 AAATTTAATA
* *
4738468 ATTTGTTTTCCTTACAAAGTTAGAATCATTCCAGATTCTCAAGGAAATAAATTCAACATTTTATT
1 ATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACATTTTATT
***
4738533 TTTCTTACAGAGTTAGAATCATTTAAGATTTTCAAGGAAATAATTTCAACG
66 TTTCTTACAGAGTTAGAATCACAGAAGATTTTCAAGGAAATAATTTCAACG
* * * ****
4738584 ATTTATTTTCTTTACAATGTTAGAATCATTTAAGATT-TCCAAGGAAATAAATT-TTTTTTTTAT
1 ATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCT-CAAGGAAATAAATTCAACATTTTAT
4738647 TTTTCTTACA-AGGTTAGAATCAACAGAAGATT
65 TTTTCTTACAGA-GTTAGAATC-ACAGAAGATT
4738679 CTAATGATGA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
114 1 0.01
115 26 0.32
116 53 0.66
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (116 bp):
ATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACATTTTATT
TTTCTTACAGAGTTAGAATCACAGAAGATTTTCAAGGAAATAATTTCAACG
Found at i:4739068 original size:45 final size:45
Alignment explanation
Indices: 4738818--4739068 Score: 176
Period size: 45 Copynumber: 5.6 Consensus size: 45
4738808 GAATTAATCC
* * * * **
4738818 TTTAATTTTAACAACCCAATAATCACAAGGAACTAAT-CCTTGAT
1 TTTAATTTTGACAACACAATAATTAAAAGGAACTAATAATTTGAT
* * * ** * *
4738862 TTT-ATTTTCG-TAATACAACAATCGAAAGAAACTAATACTTTGAT
1 TTTAATTTT-GACAACACAATAATTAAAAGGAACTAATAATTTGAT
*
4738906 TTTAATTTT--C-ACACAATAA-TATAAAGGAGCTAATAATTTGAT
1 TTTAATTTTGACAACACAATAATTA-AAAGGAACTAATAATTTGAT
* * * * * * *
4738948 CTTAATTTTGGCAACTCAATAATCAAGACGAACTAATACTTTGATT
1 TTTAATTTTGACAACACAATAATTAAAAGGAACTAATAATTTGA-T
**
4738994 CTTTTTTTTTGGA-AACACAATAATTAAAAGGAACTAATAATTTGAT
1 -TTTAATTTT-GACAACACAATAATTAAAAGGAACTAATAATTTGAT
* *
4739040 TTTACTTTTGACAACTCAATAATTAAAAG
1 TTTAATTTTGACAACACAATAATTAAAAG
4739069 CCTTTGATTA
Statistics
Matches: 159, Mismatches: 36, Indels: 23
0.73 0.17 0.11
Matches are distributed among these distances:
42 32 0.20
43 24 0.15
44 15 0.09
45 51 0.32
46 3 0.02
47 33 0.21
48 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (45 bp):
TTTAATTTTGACAACACAATAATTAAAAGGAACTAATAATTTGAT
Found at i:4739266 original size:23 final size:23
Alignment explanation
Indices: 4739238--4739284 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4739228 AAGTTATATG
* *
4739238 TTAATAGTACTATAACAATTATA
1 TTAATAATACTATAACAATAATA
4739261 TTAATAATACTATAACAATAATA
1 TTAATAATACTATAACAATAATA
4739284 T
1 T
4739285 CATGAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (23 bp):
TTAATAATACTATAACAATAATA
Found at i:4740816 original size:35 final size:34
Alignment explanation
Indices: 4740777--4740890 Score: 111
Period size: 35 Copynumber: 3.1 Consensus size: 34
4740767 AATGATTATG
4740777 TTCAAAATAATAATATGAGCATATTAATTTTTTC
1 TTCAAAATAATAATATGAGCATATTAATTTTTTC
* * * * * *
4740811 ATTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATG
1 -TTCAAAATAATAA---T-AT-GAGCATATTAAT-TTTTTC
4740852 TTCAAAATAATAATATGAGCATATTAATTTTTTC
1 TTCAAAATAATAATATGAGCATATTAATTTTTTC
4740886 TTCAA
1 TTCAA
4740891 TCATTTAATG
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
34 8 0.13
35 22 0.36
36 2 0.03
37 1 0.02
38 1 0.02
39 2 0.03
40 22 0.36
41 3 0.05
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (34 bp):
TTCAAAATAATAATATGAGCATATTAATTTTTTC
Found at i:4740856 original size:40 final size:40
Alignment explanation
Indices: 4740737--4740864 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
4740727 ATAAATTTTA
*
4740737 TTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATG
1 TTCAAAATAATAACTCTAATGGTGCATGTTAATGATTATG
* * * * *
4740777 TTCAAAATAATAA---T-AT-GAGCATATTAAT-TTTTTCA
1 TTCAAAATAATAACTCTAATGGTGCATGTTAATGATTAT-G
*
4740812 TTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATG
1 TTCAAAATAATAACTCTAATGGTGCATGTTAATGATTATG
4740852 TTCAAAATAATAA
1 TTCAAAATAATAA
4740865 TATGAGCATA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
34 3 0.04
35 22 0.32
36 2 0.03
37 1 0.01
38 1 0.01
39 2 0.03
40 34 0.50
41 3 0.04
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (40 bp):
TTCAAAATAATAACTCTAATGGTGCATGTTAATGATTATG
Found at i:4740859 original size:75 final size:75
Alignment explanation
Indices: 4740732--4740890 Score: 304
Period size: 75 Copynumber: 2.1 Consensus size: 75
4740722 ATTATATAAA
4740732 TTTT-ATTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATGTTCAAAATAATAATATGAG
1 TTTTCATTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATGTTCAAAATAATAATATGAG
4740796 CATATTAATT
66 CATATTAATT
4740806 TTTTCATTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATGTTCAAAATAATAATATGAG
1 TTTTCATTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATGTTCAAAATAATAATATGAG
4740871 CATATTAATT
66 CATATTAATT
4740881 TTTTC-TTCAA
1 TTTTCATTCAA
4740891 TCATTTAATG
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
74 9 0.11
75 75 0.89
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (75 bp):
TTTTCATTCAAAATTATAACTCTAATGGTGCATGTTAATGATTATGTTCAAAATAATAATATGAG
CATATTAATT
Found at i:4741053 original size:41 final size:41
Alignment explanation
Indices: 4741008--4741094 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
4740998 CTATCAAAGA
4741008 TTTATTATGAATTATGCTAGTGCGACAATTAAAAGATAATT
1 TTTATTATGAATTATGCTAGTGCGACAATTAAAAGATAATT
4741049 TTTATTATGAATTATGCTAGTGCGACAATTAAAAGATAATT
1 TTTATTATGAATTATGCTAGTGCGACAATTAAAAGATAATT
4741090 TTTAT
1 TTTAT
4741095 ACTAACATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (41 bp):
TTTATTATGAATTATGCTAGTGCGACAATTAAAAGATAATT
Found at i:4741524 original size:14 final size:14
Alignment explanation
Indices: 4741505--4741532 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4741495 TGTCTTAATT
4741505 ATTAAAATAATAAA
1 ATTAAAATAATAAA
4741519 ATTAAAATAATAAA
1 ATTAAAATAATAAA
4741533 TTTTTAATTT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAAATAATAAA
Found at i:4743797 original size:9 final size:10
Alignment explanation
Indices: 4743770--4743796 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
4743760 GCAAACGAAA
4743770 TTTTTTTTCT
1 TTTTTTTTCT
4743780 TTTTTTTTCT
1 TTTTTTTTCT
4743790 TTTTTTT
1 TTTTTTT
4743797 CAAAACCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:4746376 original size:161 final size:163
Alignment explanation
Indices: 4746099--4746423 Score: 636
Period size: 161 Copynumber: 2.0 Consensus size: 163
4746089 ATCTTAAGGA
4746099 TGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGAGCTCTGTCACTGAAGTAGCTTCTGGTA
1 TGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGAGCTCTGTCACTGAAGTAGCTTCTGGTA
4746164 TACGAAGAGTGTACAATTTTCTCTTAAGAAAAATTTTATTGTGCAAAGATATGACCTCGTACAGT
66 TACGAAGAGTGTACAATTTTCTCTTAAGAAAAATTTTATTGTGCAAAGATATGACCTCGTACAGT
4746229 TTGGTGAGATGAT-CCATATCTCCTTAGCTATC
131 TTGGTGAGATGATCCCATATCTCCTTAGCTATC
4746261 TGTAAGCTGAG-AAATAAAGTGTTCAGTGTGTTTAAGAGCTCTGTCACTGAAGTAGCTTCTGGTA
1 TGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGAGCTCTGTCACTGAAGTAGCTTCTGGTA
4746325 TACGAAGAGTGTACAATTTTCTCTTAAGAAAAATTTTATTGTGCAAAGATATGACCTCGTACAGT
66 TACGAAGAGTGTACAATTTTCTCTTAAGAAAAATTTTATTGTGCAAAGATATGACCTCGTACAGT
4746390 TTGGTGAGATGATCCCATATCTCCTTAGCTATC
131 TTGGTGAGATGATCCCATATCTCCTTAGCTATC
4746423 T
1 T
4746424 TCTTCTCCTC
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 131 0.81
162 31 0.19
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (163 bp):
TGTAAGCTGAGAAAATAAAGTGTTCAGTGTGTTTAAGAGCTCTGTCACTGAAGTAGCTTCTGGTA
TACGAAGAGTGTACAATTTTCTCTTAAGAAAAATTTTATTGTGCAAAGATATGACCTCGTACAGT
TTGGTGAGATGATCCCATATCTCCTTAGCTATC
Found at i:4750771 original size:45 final size:45
Alignment explanation
Indices: 4750707--4750797 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
4750697 AGTCATGCAT
4750707 ATGTATTTTCAATATGTTTAATTTAATCCGTTACTTAGAAAATTG
1 ATGTATTTTCAATATGTTTAATTTAATCCGTTACTTAGAAAATTG
*
4750752 ATGTATTTTCACTATGTTTAATTTAATCCGTTACTTAGAAAATTG
1 ATGTATTTTCAATATGTTTAATTTAATCCGTTACTTAGAAAATTG
4750797 A
1 A
4750798 AAAACACCCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (45 bp):
ATGTATTTTCAATATGTTTAATTTAATCCGTTACTTAGAAAATTG
Found at i:4751984 original size:20 final size:20
Alignment explanation
Indices: 4751945--4751984 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4751935 ACGATTTATT
* *
4751945 TTCTTTTACAAACCAGGAAA
1 TTCTTTTACAAAACAAGAAA
*
4751965 TTCTTTTACAAAATAAGAAA
1 TTCTTTTACAAAACAAGAAA
4751985 ATAAATTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (20 bp):
TTCTTTTACAAAACAAGAAA
Found at i:4752141 original size:39 final size:39
Alignment explanation
Indices: 4752056--4752149 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
4752046 ATTCAACAAG
* *
4752056 TTATTTCCTTTTTCAAAACAAGAAAATAAACCCAACGAT
1 TTATTTCCTTTTACAAAACAAGAAAATAAACCAAACGAT
* *
4752095 TTATTTCCTTTTACAAAATAAGAAAATAAATCAAACTG-T
1 TTATTTCCTTTTACAAAACAAGAAAATAAACCAAAC-GAT
*
4752134 TTTTTTCCTTTTACAA
1 TTATTTCCTTTTACAA
4752150 CCCAGAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 48 0.98
40 1 0.02
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.38
Consensus pattern (39 bp):
TTATTTCCTTTTACAAAACAAGAAAATAAACCAAACGAT
Found at i:4752203 original size:96 final size:97
Alignment explanation
Indices: 4752074--4752332 Score: 310
Period size: 96 Copynumber: 2.7 Consensus size: 97
4752064 TTTTTCAAAA
** * * *
4752074 CAAGAAAATAAACCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATCAAACTG-TTT-T
1 CAAGAAAATAAATTCAACAATTTATTTACTTTTACAAAATAGGAAAATAAATCAAA-TGATTTAT
* * *
4752137 TTTCCTTTTACAACCCAGAATCATTTAAGTTTCT
65 TTT-CTTTTACAAACCAGAATAATTTAAGATTCT
* * *
4752171 CAAGAAAATAAATTCAACAATTTATTT-TTTTTATAAAATAGGAAAATAAATCCAATGATTTATT
1 CAAGAAAATAAATTCAACAATTTATTTACTTTTACAAAATAGGAAAATAAATCAAATGATTTATT
*
4752235 TTCTTTTACAAACTAGAATAATTTAAGATTCT
66 TTCTTTTACAAACCAGAATAATTTAAGATTCT
* * * * **
4752267 TAA-AAAATAAATTCAATAATTTATTTACTTTTACAAAACAGGAAAATAAATCTAACAATTTATT
1 CAAGAAAATAAATTCAACAATTTATTTACTTTTACAAAATAGGAAAATAAATCAAATGATTTATT
4752331 TT
66 TT
4752333 GATTTATTTC
Statistics
Matches: 140, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
95 24 0.17
96 88 0.63
97 28 0.20
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.37
Consensus pattern (97 bp):
CAAGAAAATAAATTCAACAATTTATTTACTTTTACAAAATAGGAAAATAAATCAAATGATTTATT
TTCTTTTACAAACCAGAATAATTTAAGATTCT
Found at i:4752216 original size:135 final size:134
Alignment explanation
Indices: 4751967--4752246 Score: 368
Period size: 135 Copynumber: 2.1 Consensus size: 134
4751957 CCAGGAAATT
*
4751967 CTTTTACAAAATAAGAAAATAAATTCAACGATTTATTTCCTTTTACAACTCAGAATCATGTAAAA
1 CTTTTACAAAATAAGAAAATAAATTCAACGATTTATTTCCTTTTACAACCCAGAATCATGTAAAA
*
4752032 TTATCAGGAAATAAATTCAACAAGTTATTTCCTTTTTCAAAACAAGAAAATAAACCCAACGATTT
66 TTATCAGAAAATAAATTCAACAAGTTATTT-CTTTTTCAAAACAAGAAAATAAACCCAACGATTT
4752097 ATTTC
130 ATTTC
* *
4752102 CTTTTACAAAATAAGAAAATAAA-TCAAACTG-TTTTTTTCCTTTTACAACCCAGAATCATTTAA
1 CTTTTACAAAATAAGAAAATAAATTC-AAC-GATTTATTTCCTTTTACAACCCAGAATCATGTAA
** * * * * * * *
4752165 GTTTCTCAAGAAAATAAATTCAACAATTTATTT-TTTTTATAAAATAGGAAAATAAATCCAATGA
64 AATTATC-AGAAAATAAATTCAACAAGTTATTTCTTTTT-CAAAACAAGAAAATAAACCCAACGA
*
4752229 TTTATTTT
127 TTTATTTC
4752237 CTTTTACAAA
1 CTTTTACAAA
4752247 CTAGAATAAT
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
134 7 0.06
135 96 0.76
136 24 0.19
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (134 bp):
CTTTTACAAAATAAGAAAATAAATTCAACGATTTATTTCCTTTTACAACCCAGAATCATGTAAAA
TTATCAGAAAATAAATTCAACAAGTTATTTCTTTTTCAAAACAAGAAAATAAACCCAACGATTTA
TTTC
Found at i:4752327 original size:39 final size:39
Alignment explanation
Indices: 4752270--4752428 Score: 108
Period size: 39 Copynumber: 3.8 Consensus size: 39
4752260 AGATTCTTAA
* *
4752270 AAAATAAAT-TCAATAATTTATTTACTTTTACAAAACAGG
1 AAAATAAATCT-AACAATTTATTTACTTTTACAAAATAGG
4752309 AAAATAAATCTAACAATTTATTTTGATTTATTTCCTTTTACAAAATAGG
1 AAAATAAATCTAAC-A---A-TTT-ATTTA----CTTTTACAAAATAGG
* * * *
4752358 AAATTAAATCCAACGATTTATTT-CTTTTTACAAAATAGA
1 AAAATAAATCTAACAATTTATTTAC-TTTTACAAAATAGG
* *
4752397 AAAATAAATTCT-ACGATTTATTTTCTTTTACA
1 AAAATAAA-TCTAACAATTTATTTACTTTTACA
4752429 TATTAGAATC
Statistics
Matches: 98, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
38 1 0.01
39 49 0.50
40 5 0.05
43 5 0.05
44 6 0.06
45 6 0.06
49 26 0.27
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (39 bp):
AAAATAAATCTAACAATTTATTTACTTTTACAAAATAGG
Found at i:4752359 original size:49 final size:49
Alignment explanation
Indices: 4752285--4752380 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
4752275 AAATTCAATA
*
4752285 ATTTATTTACTTTTACAAAACAGGAAAATAAATCTAACAATTTATTTTG
1 ATTTATTTACTTTTACAAAACAGGAAAATAAATCCAACAATTTATTTTG
* * * *
4752334 ATTTATTTCCTTTTACAAAATAGGAAATTAAATCCAACGATTTATTT
1 ATTTATTTACTTTTACAAAACAGGAAAATAAATCCAACAATTTATTT
4752381 CTTTTTACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (49 bp):
ATTTATTTACTTTTACAAAACAGGAAAATAAATCCAACAATTTATTTTG
Found at i:4752436 original size:39 final size:39
Alignment explanation
Indices: 4752333--4752428 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
4752323 AATTTATTTT
* * *
4752333 GATTTATTTCCTTTTACAAAATAGGAAATTAAATCCAAC
1 GATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAAC
* *
4752372 GATTTA-TTTCTTTTTACAAAATAGAAAAATAAATTCTAC
1 GATTTATTTTC-TTTTACAAAATAGAAAAATAAATCCAAC
4752411 GATTTATTTTCTTTTACA
1 GATTTATTTTCTTTTACA
4752429 TATTAGAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
38 3 0.06
39 43 0.86
40 4 0.08
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (39 bp):
GATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAAC
Found at i:4752548 original size:34 final size:35
Alignment explanation
Indices: 4752476--4752548 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
4752466 AAAACAATTT
* *
4752476 ATTTTCTTTTACAAAATAGTAAAATAAATCCAATG
1 ATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
* *
4752511 ATTTT-TTTTACAAACTAGGAAAATAAATCCGACG
1 ATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
4752545 ATTT
1 ATTT
4752549 AATTCCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 29 0.85
35 5 0.15
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (35 bp):
ATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
Found at i:4752579 original size:133 final size:137
Alignment explanation
Indices: 4752334--4752599 Score: 326
Period size: 133 Copynumber: 2.0 Consensus size: 137
4752324 ATTTATTTTG
* *
4752334 ATTTATTTCCTTTTACAAAATAGGAAATTAAATCCAACGATTTATTTCTTTTTACAAAATAGAAA
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAAC-ATTGATTTCTTTTTACAAAATAGAAA
* * * * * * * * *
4752399 AATAAATTCTACGATTTATTTTCTTTTACATATTAGAATCATATAAGATTCTTAATAAAATAAAT
65 AATAAATCCGACGATTTAATTCCTTTTACAAAATAAAATCATATAAGATTCTCAAGAAAATAAAT
4752464 TTAAAACA
130 TTAAAACA
* * * *
4752472 ATTTATTTTCTTTTACAAAATAGTAAAATAAATCC-A-A-TGATTT-TTTTTACAAACTAGGAAA
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACATTGATTTCTTTTTACAAAATAGAAAA
* *
4752533 ATAAATCCGACGATTTAATTCCTTTTA-AAAGATAAAATCATTTAAGATTCTCAAGGAAATAAAT
66 ATAAATCCGACGATTTAATTCCTTTTACAAA-ATAAAATCATATAAGATTCTCAAGAAAATAAAT
4752597 TTA
130 TTA
4752600 TTTTTTTATT
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
132 2 0.02
133 69 0.63
134 5 0.05
135 1 0.01
137 1 0.01
138 32 0.29
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (137 bp):
ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACATTGATTTCTTTTTACAAAATAGAAAA
ATAAATCCGACGATTTAATTCCTTTTACAAAATAAAATCATATAAGATTCTCAAGAAAATAAATT
TAAAACA
Found at i:4752923 original size:45 final size:44
Alignment explanation
Indices: 4752792--4752942 Score: 167
Period size: 45 Copynumber: 3.4 Consensus size: 44
4752782 AATTTTATCA
* * * *
4752792 ACCCAATAATCACAAGGAACTAATTATTTGATTTTAATTTTTGC
1 ACCCAATAATTAAAAGGAACTAATCATTTGATTTTAATTTTGGC
* **
4752836 ACCTCAATAATTAAAAGGAACTAATCATTTGATTATGTTTTTGGC
1 ACC-CAATAATTAAAAGGAACTAATCATTTGATTTTAATTTTGGC
* * * *
4752881 AGCACAATAATTAAAATGAACTAATCCTTTGATTTTACTTTTGGC
1 A-CCCAATAATTAAAAGGAACTAATCATTTGATTTTAATTTTGGC
*
4752926 AATCCAATAATTAAAAG
1 -ACCCAATAATTAAAAG
4752943 CCTTTGATTA
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
44 3 0.03
45 83 0.94
46 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (44 bp):
ACCCAATAATTAAAAGGAACTAATCATTTGATTTTAATTTTGGC
Found at i:4759748 original size:31 final size:31
Alignment explanation
Indices: 4759710--4759771 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
4759700 TTTGGTTAAA
4759710 TTTTTTATTTTATACTATATATGGTAACATT
1 TTTTTTATTTTATACTATATATGGTAACATT
4759741 TTTTTTATTTTATACTATATATGGTAACATT
1 TTTTTTATTTTATACTATATATGGTAACATT
4759772 GTTGATCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (31 bp):
TTTTTTATTTTATACTATATATGGTAACATT
Found at i:4760007 original size:21 final size:21
Alignment explanation
Indices: 4759974--4760017 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4759964 TCGTCGTGAG
* *
4759974 TTGTGCCGATAATGTGTTAAC
1 TTGTGCCGATAATGAGATAAC
4759995 TTGTGCC-ATTAATGAGATAAC
1 TTGTGCCGA-TAATGAGATAAC
4760016 TT
1 TT
4760018 ATGAAACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGTGCCGATAATGAGATAAC
Found at i:4760632 original size:45 final size:45
Alignment explanation
Indices: 4760568--4760658 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
4760558 AGGCATGCAT
4760568 ATGTATTTTCACTATGTTTAATTTAATCCGTTACTTAGAAAATTG
1 ATGTATTTTCACTATGTTTAATTTAATCCGTTACTTAGAAAATTG
*
4760613 ATGTATTTTCACTATGTTTAATTTAATCTGTTACTTAGAAAATTG
1 ATGTATTTTCACTATGTTTAATTTAATCCGTTACTTAGAAAATTG
4760658 A
1 A
4760659 AAAATACCCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (45 bp):
ATGTATTTTCACTATGTTTAATTTAATCCGTTACTTAGAAAATTG
Found at i:4761018 original size:2 final size:2
Alignment explanation
Indices: 4761011--4761064 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
4761001 GATAAGTACA
4761011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4761051 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
4761065 TAACTAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4769080 original size:9 final size:9
Alignment explanation
Indices: 4769066--4769099 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
4769056 TTTGTCATAA
4769066 TTATATGTG
1 TTATATGTG
4769075 TTATATGTG
1 TTATATGTG
*
4769084 ATTATATGTA
1 -TTATATGTG
4769094 TTATAT
1 TTATAT
4769100 TAATTGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (9 bp):
TTATATGTG
Found at i:4769271 original size:2 final size:2
Alignment explanation
Indices: 4769264--4769367 Score: 208
Period size: 2 Copynumber: 52.0 Consensus size: 2
4769254 TGAATCATTG
4769264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4769306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4769348 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
4769368 GTGAACATAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4770457 original size:23 final size:23
Alignment explanation
Indices: 4770404--4770460 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
4770394 CTTATATAGA
* * *
4770404 ACTTCGGTGCATTTCTACGCGGT
1 ACTTCGGTGCAATTCTACACGGC
* *
4770427 ACTACGGTGCAATTCTACATGGC
1 ACTTCGGTGCAATTCTACACGGC
4770450 ACTTCGGTGCA
1 ACTTCGGTGCA
4770461 CTTATACGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACACGGC
Found at i:4770519 original size:16 final size:17
Alignment explanation
Indices: 4770498--4770531 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4770488 GTGCACAACC
4770498 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
4770514 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
4770531 T
1 T
4770532 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:4771642 original size:26 final size:26
Alignment explanation
Indices: 4771606--4771668 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
4771596 TGAGGCCATT
4771606 TCCTCTCACCTGAACTATCTCGCTCG
1 TCCTCTCACCTGAACTATCTCGCTCG
4771632 TCCTCTCACCTGAACTATCTCGCTCG
1 TCCTCTCACCTGAACTATCTCGCTCG
4771658 TCCTCTCACCT
1 TCCTCTCACCT
4771669 AGGACGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.14, C:0.44, G:0.10, T:0.32
Consensus pattern (26 bp):
TCCTCTCACCTGAACTATCTCGCTCG
Found at i:4772286 original size:21 final size:21
Alignment explanation
Indices: 4772256--4772311 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
4772246 AATAAAGAGA
*
4772256 GGATCGATCA-TTTCTTTCAAG
1 GGATCGATCATTTTC-TCCAAG
*
4772277 GGATCTATCATTTTCTCCAAG
1 GGATCGATCATTTTCTCCAAG
*
4772298 GGATCGATCCTTTT
1 GGATCGATCATTTT
4772312 GAAAAGAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (21 bp):
GGATCGATCATTTTCTCCAAG
Found at i:4778649 original size:19 final size:18
Alignment explanation
Indices: 4778625--4778662 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4778615 TATTTCTTTA
4778625 TCTTC-TTATTCTCTTCATT
1 TCTTCTTTATT-TC-TCATT
4778644 TCTTCTTTATTTCTCATT
1 TCTTCTTTATTTCTCATT
4778662 T
1 T
4778663 TTCCCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTCTTTATTTCTCATT
Found at i:4779371 original size:20 final size:19
Alignment explanation
Indices: 4779324--4779378 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
4779314 TACTCATTCA
*
4779324 AGTATCGATACTTGACCATAG
1 AGTATCGATAC-T-ACAATAG
*
4779345 GGTATCGATACTACAAGTAG
1 AGTATCGATACTACAA-TAG
4779365 AGTATCGATACTAC
1 AGTATCGATACTAC
4779379 TCACTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 17 0.57
21 10 0.33
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (19 bp):
AGTATCGATACTACAATAG
Found at i:4794140 original size:14 final size:14
Alignment explanation
Indices: 4794123--4794153 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4794113 AATTTGAACG
4794123 ATAATATTTAGATA
1 ATAATATTTAGATA
4794137 ATAATATTTAGATA
1 ATAATATTTAGATA
4794151 ATA
1 ATA
4794154 TTATCTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATAATATTTAGATA
Found at i:4796052 original size:19 final size:19
Alignment explanation
Indices: 4796028--4796078 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
4796018 ACCAACTAAA
*
4796028 TCGCAATGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
4796047 TCGCAACGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
4796066 TCGCAACGCGATC
1 TCGCAACGCGATC
4796079 TCCGGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGATAAT
Found at i:4796159 original size:21 final size:21
Alignment explanation
Indices: 4796126--4796425 Score: 89
Period size: 20 Copynumber: 14.7 Consensus size: 21
4796116 ATTCTGACTA
*
4796126 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
4796147 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* * * * *
4796168 TCGCAATGCGA-ATACGAAAA
1 TCGCATTGCGATTTCCCAAAT
* * **
4796188 TCGCAATGCGATTTACGTAA-
1 TCGCATTGCGATTTCCCAAAT
* **
4796208 TCGCATTGCGATTTTCTTAAT
1 TCGCATTGCGATTTCCCAAAT
** *
4796229 TCGCATTGCGATTTTTCTAAT
1 TCGCATTGCGATTTCCCAAAT
* * **
4796250 TCACATTGCGATTTACGTAA-
1 TCGCATTGCGATTTCCCAAAT
* * **
4796270 CCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTCCCAAAT
* * **
4796290 CCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTCCCAAAT
* * **
4796310 CCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTCCCAAAT
** *
4796330 TCGCATTGCGATTTTACTAAT
1 TCGCATTGCGATTTCCCAAAT
* **
4796351 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTCCCAAAT
** *
4796371 TCGCATTGCGATTTTACTAAT
1 TCGCATTGCGATTTCCCAAAT
* **
4796392 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTCCCAAAT
4796412 TCGCATTGCGATTT
1 TCGCATTGCGATTT
4796426 AGTAAATCGC
Statistics
Matches: 234, Mismatches: 37, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.02
20 131 0.56
21 95 0.41
22 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:4796209 original size:20 final size:20
Alignment explanation
Indices: 4796186--4796436 Score: 298
Period size: 20 Copynumber: 12.3 Consensus size: 20
4796176 CGAATACGAA
*
4796186 AATCGCAATGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* *
4796206 AATCGCATTGCGATTTTCTT
1 AATCGCATTGCGATTTACGT
*
4796226 AATTCGCATTGCGATTTTTC-T
1 AA-TCGCATTGCGA-TTTACGT
*
4796247 AATTCACATTGCGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
4796268 AACCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
4796288 AACCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
4796308 AACCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
4796328 AATCGCATTGCGATTTTAC-T
1 AATCGCATTGCGA-TTTACGT
4796348 AATTCGCACTT-CGATTTACGT
1 AA-TCGCA-TTGCGATTTACGT
4796369 AATCGCATTGCGATTTTAC-T
1 AATCGCATTGCGA-TTTACGT
4796389 AATTCGCACTT-CGATTTACGT
1 AA-TCGCA-TTGCGATTTACGT
4796410 AATCGCATTGCGATTTA-GT
1 AATCGCATTGCGATTTACGT
4796429 AAATCGCA
1 -AATCGCA
4796437 ACGAGATTCT
Statistics
Matches: 209, Mismatches: 8, Indels: 28
0.85 0.03 0.11
Matches are distributed among these distances:
19 6 0.03
20 134 0.64
21 60 0.29
22 9 0.04
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Done.