Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 21 of 33
Found at i:3273545 original size:23 final size:25
Alignment explanation
Indices: 3273492--3273557 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
3273482 CCTAACATAA
*
3273492 ATATATTATATTATTTATAATTTATT
1 ATATATT-TATTATATATAATTTATT
* *
3273518 TTATATTTATTATATAT-TTTTA-T
1 ATATATTTATTATATATAATTTATT
*
3273541 ATATATTTATTAAATAT
1 ATATATTTATTATATAT
3273558 GTAAAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 16 0.46
24 4 0.11
25 9 0.26
26 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATATTTATTATATATAATTTATT
Found at i:3282354 original size:50 final size:50
Alignment explanation
Indices: 3282291--3282550 Score: 317
Period size: 50 Copynumber: 5.2 Consensus size: 50
3282281 ATGTATTGTC
* * *
3282291 ATTGTTGACTATTCTTCATCAACATTTGACAATCGAAAGAGATGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTA
* * *
3282341 ATTGTTGATTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTA
* * * *
3282391 ATTGTTGACAATTCTTTACCAACCTTTGACAATCGAGAGAGGTGATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTA
* * ** * *
3282441 ATTGCTGACAATTCTTCACCAACCTTTGACAATTAAAAAAGGT-AGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGA-CCGTA
* * *
3282491 ATTATTAACTATTCTTCACCAACCTTTGACAAT-AAAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAA-AGAGGTGACCGTA
3282541 ATTGTTGACT
1 ATTGTTGACT
3282551 CTAAGCAACT
Statistics
Matches: 180, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
49 4 0.02
50 175 0.97
51 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACCGTA
Found at i:3286987 original size:50 final size:50
Alignment explanation
Indices: 3286928--3287133 Score: 306
Period size: 50 Copynumber: 4.1 Consensus size: 50
3286918 TGGTGTTACC
*
3286928 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* *
3286978 ATTGTTGACTATTCTTTACTAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* ***
3287028 ATTGTTGACTACTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTTGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* **
3287078 ATTGTTGA-TGATTCTTCACCAACCTTTGACAGTAAAGAGAGGTGACCGTA
1 ATTGTTGACT-ATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
3287128 ATTGTT
1 ATTGTT
3287134 AACTCTAAAC
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
49 1 0.01
50 138 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:3289875 original size:6 final size:6
Alignment explanation
Indices: 3289864--3289891 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3289854 AGCATCCCTG
3289864 CCTCTT CCTCTT CCTCTT CCTCTT CCTC
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTC
3289892 CACCACCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
CCTCTT
Found at i:3291041 original size:2 final size:2
Alignment explanation
Indices: 3290997--3291022 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3290987 TAGCAATAAA
3290997 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
3291023 GTGTATTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3296082 original size:3 final size:3
Alignment explanation
Indices: 3296074--3296099 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3296064 CAAGGAATAT
3296074 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
3296100 GAGGTACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3297231 original size:16 final size:15
Alignment explanation
Indices: 3297209--3297244 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
3297199 TATAAGTAAC
3297209 AAAATTAATTAATTA
1 AAAATTAATTAATTA
*
3297224 ATAAATTAATTATTTA
1 A-AAATTAATTAATTA
3297240 AAAAT
1 AAAAT
3297245 CATGAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTAATTAATTA
Found at i:3297719 original size:2 final size:2
Alignment explanation
Indices: 3297679--3297709 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3297669 AATAGCAATA
*
3297679 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3297710 GTTCATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3302289 original size:12 final size:12
Alignment explanation
Indices: 3302272--3302313 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
3302262 CATATAACAT
3302272 AATATTTATATA
1 AATATTTATATA
3302284 AATATTTA-ATTA
1 AATATTTATA-TA
3302296 TAATATTATATATA
1 -AATATT-TATATA
3302310 AATA
1 AATA
3302314 AAATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 10 0.38
13 10 0.38
14 4 0.15
15 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATTTATATA
Found at i:3302305 original size:8 final size:8
Alignment explanation
Indices: 3302292--3302351 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
3302282 TAAATATTTA
3302292 ATTATAAT
1 ATTATAAT
3302300 ATTATATAT
1 ATTATA-AT
* *
3302309 AAATAAAAT
1 -ATTATAAT
*
3302318 ATTTTAAT
1 ATTATAAT
3302326 ATTAT-AT
1 ATTATAAT
3302333 ATTATATAAT
1 A-T-TATAAT
3302343 ATTATAAT
1 ATTATAAT
3302351 A
1 A
3302352 CGAGAAAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
7 3 0.07
8 23 0.56
9 8 0.20
10 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTATAAT
Found at i:3302313 original size:13 final size:13
Alignment explanation
Indices: 3302272--3302334 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
3302262 CATATAACAT
3302272 AATATT-TATATA
1 AATATTATATATA
3302284 AATATT-TA-ATTA
1 AATATTATATA-TA
3302296 TAATATTATATATA
1 -AATATTATATATA
** * *
3302310 AATAAAATATTTT
1 AATATTATATATA
3302323 AATATTATATAT
1 AATATTATATAT
3302335 TATATAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
11 1 0.03
12 10 0.25
13 24 0.60
14 4 0.10
15 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATATTATATATA
Found at i:3302325 original size:26 final size:26
Alignment explanation
Indices: 3302270--3302351 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
3302260 ATCATATAAC
**
3302270 ATAATATT-TATATAAAT-ATTTAATT
1 ATAATATTATATATAAATAAAAT-ATT
3302295 ATAATATTATATATAAATAAAATATT
1 ATAATATTATATATAAATAAAATATT
* * *
3302321 TTAATATTATATAT-TATATAATATT
1 ATAATATTATATATAAATAAAATATT
3302346 ATAATA
1 ATAATA
3302352 CGAGAAAGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.45
26 25 0.51
27 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAATATTATATATAAATAAAATATT
Found at i:3310022 original size:24 final size:25
Alignment explanation
Indices: 3309993--3310052 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
3309983 TAACCATCAA
* *
3309993 TTTTGACAAGTAATA-AACTATAAT
1 TTTTGACAAATAAAAGAACTATAAT
*
3310017 TTTTGACAAATAAAAGGAACTATTAT
1 TTTTGACAAATAAAA-GAACTATAAT
3310043 TTTTGACAAA
1 TTTTGACAAA
3310053 CACGAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 13 0.42
26 18 0.58
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (25 bp):
TTTTGACAAATAAAAGAACTATAAT
Found at i:3310074 original size:28 final size:26
Alignment explanation
Indices: 3310008--3310063 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
3309998 ACAAGTAATA
* *
3310008 AACTATAATTTTTGACAAATAAAAGG
1 AACTATTATTTTTGACAAACAAAAGG
3310034 AACTATTATTTTTGACAAACACGAAAGG
1 AACTATTATTTTTGACAAACA--AAAGG
3310062 AA
1 AA
3310064 TCGTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
28 7 0.27
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (26 bp):
AACTATTATTTTTGACAAACAAAAGG
Found at i:3310334 original size:5 final size:5
Alignment explanation
Indices: 3310318--3310347 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
3310308 AAAAAAGTTT
3310318 TTAAA TTAAAA TTAAA TTAAA TTAAA TTAA
1 TTAAA TT-AAA TTAAA TTAAA TTAAA TTAA
3310348 TTTGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:3310416 original size:20 final size:22
Alignment explanation
Indices: 3310377--3310420 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
3310367 ATTTAAATAA
*
3310377 TATTAAAATATTATATTTATAT
1 TATTAAAATAATATATTTATAT
3310399 TATT-AAATAATA-ATTTATAT
1 TATTAAAATAATATATTTATAT
3310419 TA
1 TA
3310421 AATTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTAAAATAATATATTTATAT
Found at i:3312892 original size:22 final size:19
Alignment explanation
Indices: 3312843--3312894 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
3312833 AAATTAGAGT
3312843 TATTA-AATTATTTATTTA
1 TATTATAATTATTTATTTA
*
3312861 TAATATAATTATTTATTTTTA
1 TATTATAATTATTTA--TTTA
3312882 TCATTATAATTAT
1 T-ATTATAATTAT
3312895 ATTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
21 5 0.18
22 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATAATTATTTATTTA
Found at i:3312975 original size:16 final size:17
Alignment explanation
Indices: 3312927--3312978 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
3312917 TAATTTATAA
* *
3312927 TTTAAATTTA-AAATAT
1 TTTATATTTAGAATTAT
*
3312943 TTAATATTTAGAATTAT
1 TTTATATTTAGAATTAT
*
3312960 TTTATATTT-TAATTAT
1 TTTATATTTAGAATTAT
3312976 TTT
1 TTT
3312979 TTTATTCAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATATTTAGAATTAT
Found at i:3322145 original size:4 final size:4
Alignment explanation
Indices: 3322136--3322174 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
3322126 TTTGCGTATG
3322136 AATT AATT AATT AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AAT
3322175 CAATCAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:3322920 original size:2 final size:2
Alignment explanation
Indices: 3322907--3322969 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
3322897 GTTTCACCAA
* * *
3322907 AT AT AC AT AT AT AT AT AT AC AT AC AT AT AT AT A- AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3322947 AT CT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
3322970 GAGAGAGAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3323972 original size:18 final size:17
Alignment explanation
Indices: 3323949--3323983 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3323939 AATTAATAAA
3323949 AAATTAATATTTTATTTT
1 AAATT-ATATTTTATTTT
*
3323967 AAATTATTTTTTATTTT
1 AAATTATATTTTATTTT
3323984 TTATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AAATTATATTTTATTTT
Found at i:3324713 original size:18 final size:17
Alignment explanation
Indices: 3324690--3324731 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3324680 ATTTATTTTC
3324690 TTATTAATTCTAAATTCT
1 TTATTAATTCTAAATT-T
*
3324708 TTATTAA-TGTAAATTT
1 TTATTAATTCTAAATTT
3324724 TT-TTAATT
1 TTATTAATT
3324732 AATATAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 4 0.18
17 7 0.32
18 7 0.32
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATTAATTCTAAATTT
Found at i:3325022 original size:139 final size:139
Alignment explanation
Indices: 3324760--3325018 Score: 300
Period size: 139 Copynumber: 1.9 Consensus size: 139
3324750 AATTTTATCT
*
3324760 AATTTTAAACTAATTTTTTATTAAATGAATTTTTAATAAAATAAAATATCGGCTAATCTTTATTT
1 AATTTTAAACTAAATTTTTATTAAATGAATTTTTAATAAAATAAAATATCGGCTAATCTTTATTT
* * * *
3324825 ATTATTTTCTTATTAAATTTGAAATCCTAATTAATTTAAACTTTTCTTAATTGATATTTCTTCCT
66 ATTATTTTCTTACTAAATTTGAAATACTAATTAATCTAAACTTTTCTTAATGGATATTTCTTCCT
3324890 TATTAACTA
131 TATTAACTA
* * *
3324899 AATTTTAATCTAAATTTTTATT-AAT-AATTTTTTATTAAATTAAATATAT-GAAG-TAATCTTT
1 AATTTTAAACTAAATTTTTATTAAATGAA-TTTTTAATAAAATAAA-ATATCG--GCTAATCTTT
* * * *
3324960 ATTTATTA-TTT-TTACT-AATTTTAAAGTATTTATTAATCTAAA-TTTTCCTTCATGGATAT
62 ATTTATTATTTTCTTACTAAATTTGAAA-TACTAATTAATCTAAACTTTT-CTTAATGGATAT
3325019 ATTTTTGTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
136 12 0.12
137 28 0.27
138 21 0.21
139 40 0.39
140 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (139 bp):
AATTTTAAACTAAATTTTTATTAAATGAATTTTTAATAAAATAAAATATCGGCTAATCTTTATTT
ATTATTTTCTTACTAAATTTGAAATACTAATTAATCTAAACTTTTCTTAATGGATATTTCTTCCT
TATTAACTA
Found at i:3325961 original size:106 final size:106
Alignment explanation
Indices: 3325774--3325966 Score: 280
Period size: 106 Copynumber: 1.8 Consensus size: 106
3325764 AATAATCAGT
* * * *
3325774 TTTTATATTGAAAATCTTATTCGAGTTAATATTTTTATTGCATTAACCATAATTAATTTTAATAT
1 TTTTACATTGAAAATCTTATTCAAGTTAATATGTTTATTGCATTAACCATAATTAATTTTAATAC
3325839 GATGTTCTATAAGCCATAATTAAATGGTCAAGCAACCATGC
66 GATGTTCTATAAGCCATAATTAAATGGTCAAGCAACCATGC
* * * *
3325880 TTTTACATTGAAAATCTTTTTCAAGTTAATATGTTTATTTCATTAATCATAATTAATTTTAATGC
1 TTTTACATTGAAAATCTTATTCAAGTTAATATGTTTATTGCATTAACCATAATTAATTTTAATAC
* *
3325945 GA-GTTCTCTAAGGCCATGATTA
66 GATGTTCTATAA-GCCATAATTA
3325967 TCATGTTGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
105 8 0.11
106 68 0.89
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (106 bp):
TTTTACATTGAAAATCTTATTCAAGTTAATATGTTTATTGCATTAACCATAATTAATTTTAATAC
GATGTTCTATAAGCCATAATTAAATGGTCAAGCAACCATGC
Found at i:3327174 original size:20 final size:20
Alignment explanation
Indices: 3327146--3327184 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3327136 GGGAAGCATA
3327146 TTTCCTTTCTTTTCCTTTAC
1 TTTCCTTTCTTTTCCTTTAC
* *
3327166 TTTCTTTTCTTTTCTTTTA
1 TTTCCTTTCTTTTCCTTTA
3327185 TTATTTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCCTTTCTTTTCCTTTAC
Found at i:3328724 original size:18 final size:18
Alignment explanation
Indices: 3328701--3328735 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3328691 CATCTTTTAT
3328701 AAAAGAAAAGAAAAGAAA
1 AAAAGAAAAGAAAAGAAA
*
3328719 AAAAGAAAAGACAAGAA
1 AAAAGAAAAGAAAAGAA
3328736 GATCAGCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAGAAA
Found at i:3330489 original size:19 final size:20
Alignment explanation
Indices: 3330462--3330508 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
3330452 ATTTAAATAA
3330462 AAATATATTATTTTAATT-TT
1 AAAT-TATTATTTTAATTATT
*
3330482 AAATTATTATTTTTATTAATT
1 AAATTATTATTTTAATT-ATT
3330503 AAATTA
1 AAATTA
3330509 ATTTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTATTATTTTAATTATT
Found at i:3331828 original size:2 final size:2
Alignment explanation
Indices: 3331821--3331855 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3331811 CATCTTTATC
3331821 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3331856 CATATGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3333706 original size:2 final size:2
Alignment explanation
Indices: 3333699--3333731 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3333689 GAGGTTAGAC
3333699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3333732 TTTATACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3333930 original size:2 final size:2
Alignment explanation
Indices: 3333888--3333914 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3333878 AGTAAATGAA
3333888 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
3333915 CACACGCGTA
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:3337012 original size:2 final size:2
Alignment explanation
Indices: 3337005--3337050 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3336995 CATTTTGGGT
3337005 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
3337047 TA TA
1 TA TA
3337051 GAGAGAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3337055 original size:2 final size:2
Alignment explanation
Indices: 3337050--3337079 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3337040 ATATATATAT
3337050 AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3337080 AAGCTACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3337523 original size:20 final size:18
Alignment explanation
Indices: 3337493--3337558 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 18
3337483 TAAATTTGAT
*
3337493 TTAAATTAAATTTAATATA
1 TTAAATAAAATTTAAT-TA
*
3337512 TTTATATAAAATTTTTAATTA
1 -TTAAATAAAA--TTTAATTA
*
3337533 TTAAATAAAATTTAAAT-
1 TTAAATAAAATTTAATTA
3337550 TTAAATAAA
1 TTAAATAAA
3337559 TAATTTGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 9 0.22
18 6 0.15
20 17 0.43
21 2 0.05
22 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATAAAATTTAATTA
Found at i:3339513 original size:2 final size:2
Alignment explanation
Indices: 3339506--3339531 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3339496 AGATATGGAC
3339506 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3339532 AGCGGCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3339746 original size:26 final size:25
Alignment explanation
Indices: 3339709--3339764 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
3339699 TATTAAAACT
* *
3339709 AATTTATTTTAAA-ACATATTTTATA
1 AATTTATATTAAATA-ATATTTAATA
*
3339734 AATTTATAATTAAATAATATTTAATT
1 AATTTAT-ATTAAATAATATTTAATA
3339760 AATTT
1 AATTT
3339765 TTATAGACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 7 0.27
26 18 0.69
27 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTTATATTAAATAATATTTAATA
Found at i:3340795 original size:14 final size:14
Alignment explanation
Indices: 3340778--3340811 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
3340768 AAAAGAAAAT
3340778 AAATAAAATAATAA
1 AAATAAAATAATAA
3340792 AAAT-AAATAATAA
1 AAATAAAATAATAA
3340805 AGAATAA
1 A-AATAA
3340812 GATTAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.56
14 7 0.39
15 1 0.06
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAATAAAATAATAA
Found at i:3341428 original size:24 final size:23
Alignment explanation
Indices: 3341401--3341462 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
3341391 AGAGACATTC
*
3341401 AATTTTATAAAATTATTTAAATTT
1 AATTTTATAAAATTAATT-AATTT
*
3341425 AATTTTA-AAAA-AAATTAATTT
1 AATTTTATAAAATTAATTAATTT
*
3341446 AATTATTATCAAATTAA
1 AATT-TTATAAAATTAA
3341463 ATTTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 9 0.29
22 6 0.19
23 7 0.23
24 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTATAAAATTAATTAATTT
Found at i:3341499 original size:19 final size:18
Alignment explanation
Indices: 3341477--3341525 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
3341467 AAAATATATT
3341477 TTAATATTTTAATATTTAA
1 TTAATATTTTAAT-TTTAA
3341496 TTAATTATTTCATAATTTTAA
1 TTAA-TATTT--TAATTTTAA
3341517 TTAA-ATTTT
1 TTAATATTTT
3341526 TTAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
19 8 0.30
20 5 0.19
21 9 0.33
22 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTAATTTTAA
Found at i:3341596 original size:25 final size:25
Alignment explanation
Indices: 3341568--3341648 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
3341558 TAAAAAGATT
3341568 AATTTAAATTTAAATCAAATAATTA
1 AATTTAAATTTAAATCAAATAATTA
* *
3341593 AATTTAAAAGCTTATAT-AAA-AATTA
1 AATTT-AAA-TTTAAATCAAATAATTA
* * * *
3341618 AGTTTATATTTAATTC-AATAAATA
1 AATTTAAATTTAAATCAAATAATTA
3341642 AATTTAA
1 AATTTAA
3341649 TTAAACAAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
23 6 0.14
24 11 0.26
25 14 0.33
26 6 0.14
27 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AATTTAAATTTAAATCAAATAATTA
Found at i:3341672 original size:14 final size:14
Alignment explanation
Indices: 3341634--3341674 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3341624 TATTTAATTC
3341634 AATAAATAAATTTA
1 AATAAATAAATTTA
* *
3341648 ATTAAACAAATTTA
1 AATAAATAAATTTA
*
3341662 AATAATTAAATTT
1 AATAAATAAATTT
3341675 TTTTACCTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAATAAATTTA
Found at i:3342433 original size:31 final size:32
Alignment explanation
Indices: 3342376--3342448 Score: 112
Period size: 31 Copynumber: 2.3 Consensus size: 32
3342366 CAAACTTTTC
3342376 ATAAAACTTTGGGTAATAAGTTTTTACTCCTA
1 ATAAAACTTTGGGTAATAAGTTTTTACTCCTA
* *
3342408 GTAAAACTTTGGGTAAT-TGTTTTTACTCCTA
1 ATAAAACTTTGGGTAATAAGTTTTTACTCCTA
*
3342439 ATAGAACTTT
1 ATAAAACTTT
3342449 TTCATAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 21 0.57
32 16 0.43
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (32 bp):
ATAAAACTTTGGGTAATAAGTTTTTACTCCTA
Found at i:3342475 original size:76 final size:75
Alignment explanation
Indices: 3342336--3342534 Score: 247
Period size: 76 Copynumber: 2.6 Consensus size: 75
3342326 TTGTTGGGTG
* * *
3342336 AACTTTAGGTAATTGGTTTTTACTCCTAATCAAAC-TTTTCATAAAACTTTGGGTAATAAGTTTT
1 AACTTTGGGTAATT-GTTTTTACTCCTAAT-AAACTTTTTCATAAAACTTAGGCTAATAAGTTTT
*
3342400 TACTCCTAGTAA
64 TACTCCTAATAA
**
3342412 AACTTTGGGTAATTGTTTTTACTCCTAATAGAACTTTTTCATAAAACTTAGGCTAATTGGTTTTT
1 AACTTTGGGTAATTGTTTTTACTCCTAATA-AACTTTTTCATAAAACTTAGGCTAATAAGTTTTT
3342477 ACTCCTAATAA
65 ACTCCTAATAA
* *
3342488 AAATTTGGGTAATTGTTTTTTTTTACTCCTAATATTACTTTTTCATA
1 AACTTTGGGTAATTG----TTTTTACTCCTAATA-AACTTTTTCATA
3342535 GATGCTAAGC
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
74 1 0.01
75 18 0.17
76 63 0.58
80 26 0.24
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (75 bp):
AACTTTGGGTAATTGTTTTTACTCCTAATAAACTTTTTCATAAAACTTAGGCTAATAAGTTTTTA
CTCCTAATAA
Found at i:3348115 original size:2 final size:2
Alignment explanation
Indices: 3348110--3348136 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3348100 AAAAAAAAAC
3348110 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
3348137 AACAAAAAGG
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:3348800 original size:20 final size:22
Alignment explanation
Indices: 3348764--3348815 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
3348754 TTTTAAAAAA
*
3348764 TAAAAA-TAAAAATAATTAT-T
1 TAAAAATTTAAAATAATTATCT
*
3348784 TTAAAATTTAAAA-AATTATCT
1 TAAAAATTTAAAATAATTATCT
3348805 TAAAAATTTAA
1 TAAAAATTTAA
3348816 GGGATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATTTAAAATAATTATCT
Found at i:3350103 original size:29 final size:28
Alignment explanation
Indices: 3350035--3350102 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
3350025 GTTAAAAATT
*
3350035 AATAAATTAAAAGTTAAAATCTTATTTA
1 AATAAATTAAAAGATAAAATCTTATTTA
3350063 AATATAA-TAAAATGATAAAAT-TTATTTA
1 AATA-AATTAAAA-GATAAAATCTTATTTA
3350091 AATAAATTAAAA
1 AATAAATTAAAA
3350103 AAGTTCACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 2 0.06
28 25 0.69
29 9 0.25
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (28 bp):
AATAAATTAAAAGATAAAATCTTATTTA
Found at i:3353103 original size:3 final size:3
Alignment explanation
Indices: 3353095--3353120 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3353085 TCAGAGGAAA
3353095 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
3353121 AGCAGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3353764 original size:2 final size:2
Alignment explanation
Indices: 3353757--3353783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3353747 AATTATCAAT
3353757 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3353784 TTGAAAAGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3355126 original size:2 final size:2
Alignment explanation
Indices: 3355119--3355159 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3355109 GACGAGAATC
3355119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3355160 CTTTTTCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3355916 original size:2 final size:2
Alignment explanation
Indices: 3355909--3355933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3355899 TTAATTTCTC
3355909 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 A
3355934 CATACAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3356366 original size:37 final size:35
Alignment explanation
Indices: 3356321--3356426 Score: 90
Period size: 41 Copynumber: 2.8 Consensus size: 35
3356311 ATTTTGTTTG
*
3356321 ATTTAAATTATTATATAATAATAAAAATAATTATTAT
1 ATTTAAATTATTA-ATAATAATAAAAATAATTA-TAA
*
3356358 ATTTAAATTTAATTAAAATAATATATAAATATTAATTATAA
1 ATTTAAA-TT-ATT--AATAATA-ATAAA-AATAATTATAA
3356399 ATTTAATATT-TTAATAAT-ATAATAAATA
1 ATTTAA-ATTATTAATAATAATAA-AAATA
3356427 TTAAATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
35 7 0.12
36 1 0.02
37 13 0.22
38 2 0.03
39 5 0.09
40 6 0.10
41 16 0.28
42 8 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
ATTTAAATTATTAATAATAATAAAAATAATTATAA
Found at i:3356394 original size:42 final size:40
Alignment explanation
Indices: 3356335--3356423 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 40
3356325 AAATTATTAT
*
3356335 ATAATAATAAAAATAATTATTATATTTAA-A-TTTAATTAAA
1 ATAATAATAAAAATAATTA-TAAATTTAATATTTTAA-TAAA
* *
3356375 ATAATATATAAATATTAATTATAAATTTAATATTTTAATAAT
1 ATAATA-ATAAA-AATAATTATAAATTTAATATTTTAATAAA
3356417 ATAATAA
1 ATAATAA
3356424 ATATTAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
40 6 0.14
41 14 0.33
42 17 0.40
43 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
ATAATAATAAAAATAATTATAAATTTAATATTTTAATAAA
Found at i:3356400 original size:35 final size:38
Alignment explanation
Indices: 3356337--3356440 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 38
3356327 ATTATTATAT
* *
3356337 AATAATAAAAATAATTATTATATT-TAAATTT-A-ATTAA
1 AATAAT-ATAATAAATATTA-ATTATAAATTTAATATTAA
**
3356374 AATAATAT-ATAAATATTAATTATAAATTTAATATTTT
1 AATAATATAATAAATATTAATTATAAATTTAATATTAA
* *
3356411 AATAATATAATAAATATTAAATAAAAATTT
1 AATAATATAATAAATATTAATTATAAATTT
3356441 TAAATGATTC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
34 3 0.05
35 16 0.28
36 2 0.04
37 17 0.30
38 19 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (38 bp):
AATAATATAATAAATATTAATTATAAATTTAATATTAA
Found at i:3356414 original size:26 final size:23
Alignment explanation
Indices: 3356356--3356414 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 23
3356346 AATAATTATT
3356356 ATATTTAAAT-TTAATTAAAATA
1 ATATTTAAATATTAATTAAAATA
*
3356378 ATATATAAATATTAATTATAAATTTA
1 ATATTTAAATATTAATTA-AAA--TA
*
3356404 ATATTTTAATA
1 ATATTTAAATA
3356415 ATATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.30
23 7 0.23
24 3 0.10
26 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTAAATATTAATTAAAATA
Found at i:3356426 original size:20 final size:20
Alignment explanation
Indices: 3356374--3356428 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3356364 ATTTAATTAA
3356374 AATAATAT-ATAAATA--TT
1 AATAATATAATAAATATTTT
* *
3356391 AATTATA-AATTTAATATTTT
1 AATAATATAA-TAAATATTTT
3356411 AATAATATAATAAATATT
1 AATAATATAATAAATATT
3356429 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
20 15 0.52
21 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATAATAAATATTTT
Found at i:3361692 original size:2 final size:2
Alignment explanation
Indices: 3361685--3361714 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3361675 CAAGTCATTA
*
3361685 AT AT AT AT GT 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
3361715 GATCTTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3370286 original size:53 final size:53
Alignment explanation
Indices: 3370188--3370295 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 53
3370178 TCCGATCTTT
3370188 AGCCACTGATTTCCTTTCTTGTACCGGTCGACGTGGAGAGAAAAAATTGATAG
1 AGCCACTGATTTCCTTTCTTGTACCGGTCGACGTGGAGAGAAAAAATTGATAG
* *
3370241 AGCCACTGGTTTTCTTTCTTGTACCAGTGGTCGACGTGGAGA-AAAAAATTGATAG
1 AGCCACTGATTTCCTTTCTTGTACC---GGTCGACGTGGAGAGAAAAAATTGATAG
3370296 GCTGGTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
53 23 0.46
55 13 0.26
56 14 0.28
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (53 bp):
AGCCACTGATTTCCTTTCTTGTACCGGTCGACGTGGAGAGAAAAAATTGATAG
Found at i:3370796 original size:22 final size:22
Alignment explanation
Indices: 3370764--3370819 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
3370754 TTATTATTTA
*
3370764 ATTAATAAAAAAATTATATAAAT
1 ATTAATTAAAAAA-TATATAAAT
*
3370787 -TTAATT-AAAAATATTTAAAT
1 ATTAATTAAAAAATATATAAAT
3370807 ATTAATATAAAAA
1 ATTAAT-TAAAAA
3370820 TAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 8 0.29
21 10 0.36
22 6 0.21
23 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAATTAAAAAATATATAAAT
Found at i:3370820 original size:22 final size:22
Alignment explanation
Indices: 3370764--3370821 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
3370754 TTATTATTTA
*
3370764 ATTAATAAAAAAATTATATAAAT
1 ATTAATATAAAAA-TATATAAAT
*
3370787 -TTAAT-TAAAAATATTTAAAT
1 ATTAATATAAAAATATATAAAT
3370807 ATTAATATAAAAATA
1 ATTAATATAAAAATA
3370822 ATTATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 8 0.26
21 10 0.32
22 13 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAATATAAAAATATATAAAT
Found at i:3370887 original size:16 final size:16
Alignment explanation
Indices: 3370866--3370910 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3370856 CGGTGAGTTA
3370866 AATTAAAATTTTAAAT
1 AATTAAAATTTTAAAT
*
3370882 AATTAAAACTTTAAAT
1 AATTAAAATTTTAAAT
3370898 AA--AAAATTTTAAA
1 AATTAAAATTTTAAA
3370911 AAAATTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 10 0.37
16 17 0.63
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAAATTTTAAAT
Found at i:3371858 original size:2 final size:2
Alignment explanation
Indices: 3371851--3371895 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3371841 AAGATGGATC
3371851 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
3371893 TA T
1 TA T
3371896 TTTCGGTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3377862 original size:17 final size:17
Alignment explanation
Indices: 3377836--3377870 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3377826 GAAAAATAAA
*
3377836 TAAAATATATAAAAATT
1 TAAAAGATATAAAAATT
*
3377853 TAAAAGATATAAATATT
1 TAAAAGATATAAAAATT
3377870 T
1 T
3377871 TTATTTTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
TAAAAGATATAAAAATT
Found at i:3377885 original size:30 final size:30
Alignment explanation
Indices: 3377851--3377908 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3377841 TATATAAAAA
3377851 TTTAAAAGATATAAAT-ATTTTTATTTTACT
1 TTTAAAA-ATATAAATAATTTTTATTTTACT
* *
3377881 TTTAATAATATGAATAATTTTTATTTTA
1 TTTAAAAATATAAATAATTTTTATTTTA
3377909 TATTTTTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTAAAAATATAAATAATTTTTATTTTACT
Found at i:3378642 original size:18 final size:17
Alignment explanation
Indices: 3378603--3378652 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
3378593 GAAAGTGAAC
3378603 TTATTA-ATTTAATATT
1 TTATTATATTTAATATT
3378619 TATATTATATTTATATATT
1 T-TATTATATTTA-ATATT
3378638 TTATTATATTATAAT
1 TTATTATATT-TAAT
3378653 CATATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 5 0.17
18 16 0.53
19 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATATTTAATATT
Found at i:3378658 original size:40 final size:38
Alignment explanation
Indices: 3378612--3378709 Score: 97
Period size: 45 Copynumber: 2.4 Consensus size: 38
3378602 CTTATTAATT
* *
3378612 TAATATTTATATTATATTTATATATTTTATTATATTATAA
1 TAATATTTATATTATATGTATATATTTTA--ATATAATAA
*
3378652 TCATATTTAAAATATTTTATATGTATATATTTTAATATAATAA
1 TAATATTT---ATA--TTATATGTATATATTTTAATATAATAA
3378695 TAATAATTTATATTA
1 TAAT-ATTTATATTA
3378710 CATAAATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
39 3 0.06
40 7 0.15
41 3 0.06
43 14 0.29
44 4 0.08
45 17 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (38 bp):
TAATATTTATATTATATGTATATATTTTAATATAATAA
Found at i:3380812 original size:51 final size:52
Alignment explanation
Indices: 3380721--3380819 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 52
3380711 TGGTAGCATA
* * * *
3380721 GGTGTTGGAGGTGGTGTTGGCAGCGGGGGTGATGTAGGTGGTG-ACGTTGGT
1 GGTGTTGGAGGTGGTGGTGGCAGAGGGGGAGACGTAGGTGGTGCACGTTGGT
** * *
3380772 GGTGTTGGAGGTGGTGGTGGTGGAGTGGGAGACGTCGGTGGTGCACGT
1 GGTGTTGGAGGTGGTGGTGGCAGAGGGGGAGACGTAGGTGGTGCACGT
3380820 GGAGGTGCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
51 35 0.90
52 4 0.10
ACGTcount: A:0.10, C:0.07, G:0.56, T:0.27
Consensus pattern (52 bp):
GGTGTTGGAGGTGGTGGTGGCAGAGGGGGAGACGTAGGTGGTGCACGTTGGT
Found at i:3381209 original size:15 final size:15
Alignment explanation
Indices: 3381177--3381222 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3381167 TGCCCAAGCT
3381177 GGTGGTGGAGTA-GA
1 GGTGGTGGAGTAGGA
* *
3381191 --TGGTGGTGTTGGA
1 GGTGGTGGAGTAGGA
3381204 GGTGGTGGAGTAGGA
1 GGTGGTGGAGTAGGA
3381219 GGTG
1 GGTG
3381223 TGGGTGGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
12 8 0.32
13 2 0.08
15 15 0.60
ACGTcount: A:0.15, C:0.00, G:0.59, T:0.26
Consensus pattern (15 bp):
GGTGGTGGAGTAGGA
Found at i:3382046 original size:21 final size:20
Alignment explanation
Indices: 3382016--3382055 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3382006 CACATTCCAC
3382016 ACAAAAC-AAAAGACAAATTG
1 ACAAAACAAAAAG-CAAATTG
3382036 ACAAATACAAAAAGCAAATT
1 ACAAA-ACAAAAAGCAAATT
3382056 TTCAGCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.65, C:0.15, G:0.07, T:0.12
Consensus pattern (20 bp):
ACAAAACAAAAAGCAAATTG
Found at i:3384576 original size:39 final size:40
Alignment explanation
Indices: 3384533--3384612 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
3384523 CCATCATTAA
3384533 CTTTCAATAATGGCA-TTATAAGAAACATAGAAACATAAT
1 CTTTCAATAATGGCAGTTATAAGAAACATAGAAACATAAT
3384572 CTTTCAATAATGGCAGTTATAAGAAACATAGAAACATAAT
1 CTTTCAATAATGGCAGTTATAAGAAACATAGAAACATAAT
3384612 C
1 C
3384613 ACATTTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 15 0.38
40 25 0.62
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (40 bp):
CTTTCAATAATGGCAGTTATAAGAAACATAGAAACATAAT
Found at i:3386661 original size:2 final size:2
Alignment explanation
Indices: 3386623--3386650 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3386613 CATGAGTTGG
3386623 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
3386651 GCATGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3388905 original size:2 final size:2
Alignment explanation
Indices: 3388898--3388941 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3388888 GAGATTTAGT
*
3388898 TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3388940 TC
1 TC
3388942 ACACACACAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:3388946 original size:2 final size:2
Alignment explanation
Indices: 3388941--3388982 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3388931 CTCTCTCTCT
*
3388941 CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3388983 AACGCAAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:3395405 original size:54 final size:54
Alignment explanation
Indices: 3395343--3395450 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
3395333 TACACGTTAG
3395343 GCTTCCATCCTTCCCTAACCATTTCCTCCAATTTTCCAAAGGCTTGCTTTATGC
1 GCTTCCATCCTTCCCTAACCATTTCCTCCAATTTTCCAAAGGCTTGCTTTATGC
3395397 GCTTCCATCCTTCCCTAACCATTTCCTCCAATTTTCCAAAGGCTTGCTTTATGC
1 GCTTCCATCCTTCCCTAACCATTTCCTCCAATTTTCCAAAGGCTTGCTTTATGC
3395451 TACCATCTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (54 bp):
GCTTCCATCCTTCCCTAACCATTTCCTCCAATTTTCCAAAGGCTTGCTTTATGC
Found at i:3398094 original size:2 final size:2
Alignment explanation
Indices: 3398087--3398127 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3398077 TTTTCAAAAC
* *
3398087 TA TA TA TA TA TA TA TA TA -A TA TT TG 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
3398128 ATGTTAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3398149 original size:29 final size:31
Alignment explanation
Indices: 3398073--3398149 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
3398063 TAGTCAAGGG
3398073 TATCTTTTCAAAACTATATATATATATATATAA
1 TATCTTTTC-AAA-TATATATATATATATATAA
* * *
3398106 TAT-TTGT-ATATATATATATATA-ATGTTAA
1 TATCTTTTCAAATATATATATATATAT-ATAA
3398135 TATCTTTTCAAATAT
1 TATCTTTTCAAATAT
3398150 GTGAGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
28 2 0.06
29 18 0.50
30 5 0.14
31 5 0.14
32 3 0.08
33 3 0.08
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (31 bp):
TATCTTTTCAAATATATATATATATATATAA
Found at i:3405794 original size:21 final size:21
Alignment explanation
Indices: 3405770--3405812 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3405760 TTAGATGTAA
* *
3405770 ATTAA-AAATATAATATTCTTG
1 ATTAATAAA-ATAAAATTATTG
3405791 ATTAATAAAATAAAATTATTG
1 ATTAATAAAATAAAATTATTG
3405812 A
1 A
3405813 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTAATAAAATAAAATTATTG
Found at i:3413697 original size:29 final size:29
Alignment explanation
Indices: 3413655--3413712 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
3413645 CAATAAGTTA
3413655 GTAGTCCTCATGTTCTAGGTTTTGAAGAT
1 GTAGTCCTCATGTTCTAGGTTTTGAAGAT
*
3413684 GTAGTCCTGATGTTCTAGGTTTTGAAGAT
1 GTAGTCCTCATGTTCTAGGTTTTGAAGAT
3413713 TAACTTGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (29 bp):
GTAGTCCTCATGTTCTAGGTTTTGAAGAT
Found at i:3419402 original size:32 final size:35
Alignment explanation
Indices: 3419366--3419430 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
3419356 AAATAATATA
3419366 TATCAAAA-TTT-ATATAATATA-AAT-TATTAATT
1 TATCAAAATTTTAATA-AATATATAATATATTAATT
3419398 TATCAAAATTTTAATAAATATATAATATATTAA
1 TATCAAAATTTTAATAAATATATAATATATTAA
3419431 ATACAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 8 0.28
33 9 0.31
34 6 0.21
35 6 0.21
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (35 bp):
TATCAAAATTTTAATAAATATATAATATATTAATT
Found at i:3419471 original size:20 final size:18
Alignment explanation
Indices: 3419413--3419484 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 18
3419403 AAATTTTAAT
3419413 AAATATATAATATATTAAATA
1 AAATATATAAT-TA-TAAA-A
*
3419434 CAAT-TATAA-TATAAAA
1 AAATATATAATTATAAAA
*
3419450 AATTAATATAATTATAACAA
1 AAAT-ATATAATTATAA-AA
3419470 AAATATATGAATTAT
1 AAATATAT-AATTAT
3419485 TAAATTTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
16 3 0.07
17 4 0.10
18 7 0.17
19 9 0.21
20 16 0.38
21 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (18 bp):
AAATATATAATTATAAAA
Found at i:3420357 original size:17 final size:16
Alignment explanation
Indices: 3420335--3420372 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3420325 AAATAACTTA
*
3420335 ATATATTTTTAAATATT
1 ATATATTTAT-AATATT
3420352 ATATA-TTATAATATT
1 ATATATTTATAATATT
3420367 ATATAT
1 ATATAT
3420373 ATGTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTTATAATATT
Found at i:3423787 original size:15 final size:16
Alignment explanation
Indices: 3423757--3423831 Score: 52
Period size: 15 Copynumber: 5.0 Consensus size: 16
3423747 ACGTTAACAT
*
3423757 TTAAATTTTAAATTTA
1 TTAAATATTAAATTTA
3423773 TTAAATATT-AATTTA
1 TTAAATATTAAATTTA
* **
3423788 -AAAATAAAAAATTTA
1 TTAAATATTAAATTTA
* *
3423803 -TATATATT-AATAT-
1 TTAAATATTAAATTTA
*
3423816 TTAAATTTTAAATTTA
1 TTAAATATTAAATTTA
3423832 ATTATTGAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
14 15 0.35
15 20 0.47
16 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATATTAAATTTA
Found at i:3429071 original size:2 final size:2
Alignment explanation
Indices: 3429066--3429098 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3429056 CCAAAAAAAA
3429066 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3429099 GTTTTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3429731 original size:148 final size:149
Alignment explanation
Indices: 3429559--3429858 Score: 494
Period size: 152 Copynumber: 2.0 Consensus size: 149
3429549 TTTATGAAGA
*
3429559 TAAATATCTATGAATTCAATTTTTCCTGCTTATATTGTTTGGCCTTTTTAGGTGG-TTTTTTTTC
1 TAAATATCTATGAATTCAATTTTTCCTGCTTATATTGTTTGGCATTTTTAGGTGGTTTTTTTTTC
* *
3429623 CTTTACAAAAGATCCAAAAATTTTCAGCATATTATGATAAATACAAAATATAGAACAAATTAATA
66 CTTTACAAAAGATCCAAAAATTTTCACCATATTATGATAAATACAAAATATAAAACAAATTAATA
3429688 TATGAATAATTAATGAAAT
131 TATGAATAATTAATGAAAT
* *
3429707 TAAATATCTATGAATTTAATTTTTCCTGTTTATATTGTTTGGCATTTTTAGGTGGCTTTTTTTTT
1 TAAATATCTATGAATTCAATTTTTCCTGCTTATATTGTTTGGCATTTTTAGGTGG---TTTTTTT
* * *
3429772 TTCTTTTACAAAAGATCCAAAAATTTTCACCATATTATGATAAATATAAAATATAAAACTAATTA
63 TTCCTTTACAAAAGATCCAAAAATTTTCACCATATTATGATAAATACAAAATATAAAACAAATTA
3429837 ATATATGAATAATTAATGAAAT
128 ATATATGAATAATTAATGAAAT
3429859 GACATATGGA
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
148 52 0.37
152 88 0.63
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (149 bp):
TAAATATCTATGAATTCAATTTTTCCTGCTTATATTGTTTGGCATTTTTAGGTGGTTTTTTTTTC
CTTTACAAAAGATCCAAAAATTTTCACCATATTATGATAAATACAAAATATAAAACAAATTAATA
TATGAATAATTAATGAAAT
Found at i:3431253 original size:2 final size:2
Alignment explanation
Indices: 3431246--3431274 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3431236 TATGCTGCTT
3431246 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3431275 TTGCAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3431802 original size:2 final size:2
Alignment explanation
Indices: 3431795--3431834 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3431785 TTTCGAAAGG
3431795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3431835 CATTGAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3432093 original size:16 final size:16
Alignment explanation
Indices: 3432072--3432108 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3432062 TATGTATCAC
3432072 GAAATTTAACTTTTAA
1 GAAATTTAACTTTTAA
*
3432088 GAAATTTAATTTTTAA
1 GAAATTTAACTTTTAA
*
3432104 AAAAT
1 GAAAT
3432109 AAATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (16 bp):
GAAATTTAACTTTTAA
Found at i:3434329 original size:16 final size:17
Alignment explanation
Indices: 3434305--3434340 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3434295 TTTTTAATTT
*
3434305 TTTATTTAAA-TTTAAA
1 TTTAATTAAATTTTAAA
3434321 TTTAATTAAATTTTAAA
1 TTTAATTAAATTTTAAA
3434338 TTT
1 TTT
3434341 TAAATTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATTAAATTTTAAA
Found at i:3436499 original size:3 final size:3
Alignment explanation
Indices: 3436491--3436521 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
3436481 ACCTTTTGAA
3436491 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
3436522 TTAACATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3437277 original size:6 final size:6
Alignment explanation
Indices: 3437265--3437304 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
3437255 TTCAAAAAGA
* *
3437265 TTTATT ATTATT ATTATT TTTATT TTTATT TTTATCT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTAT-T TTT
3437305 TTAACATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:3437457 original size:19 final size:20
Alignment explanation
Indices: 3437421--3437458 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3437411 AGTTTAATTT
3437421 ATAAGTAAAAATAAAATAAA
1 ATAAGTAAAAATAAAATAAA
* *
3437441 ATAA-TAAAGATATAATAA
1 ATAAGTAAAAATAAAATAA
3437459 TCTTTCATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
ATAAGTAAAAATAAAATAAA
Found at i:3437756 original size:2 final size:2
Alignment explanation
Indices: 3437749--3437786 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3437739 CAGATTATTT
3437749 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
3437787 AAGATTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3439001 original size:2 final size:2
Alignment explanation
Indices: 3438994--3439027 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3438984 CTAATACACT
* *
3438994 TA TA TA TA TA TA TA TA TA TA TG TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3439028 ATTACTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3440639 original size:20 final size:20
Alignment explanation
Indices: 3440616--3440656 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3440606 CATTTGTTAG
*
3440616 AATAATAAAAATCAT-ATAAA
1 AATAAAAAAAAT-ATAATAAA
3440636 AATAAAAAAAATATAATAAA
1 AATAAAAAAAATATAATAAA
3440656 A
1 A
3440657 GTAGACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AATAAAAAAAATATAATAAA
Found at i:3441506 original size:20 final size:19
Alignment explanation
Indices: 3441470--3441514 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3441460 TTTACATATT
3441470 TTAAT-TTTAAAAAATTAA
1 TTAATATTTAAAAAATTAA
*
3441488 TTAATATTTAATAATATTAA
1 TTAATATTTAA-AAAATTAA
*
3441508 TTGATAT
1 TTAATAT
3441515 GTTATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATATTTAAAAAATTAA
Found at i:3441863 original size:3 final size:3
Alignment explanation
Indices: 3441855--3441887 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3441845 AATTCTAAAG
*
3441855 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3441888 GGTTCATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3443524 original size:23 final size:22
Alignment explanation
Indices: 3443481--3443526 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3443471 CTAAAAAAAT
*
3443481 AATTATAAATATTAAAATTTAA
1 AATTATAAATAATAAAATTTAA
* *
3443503 AATTATTAAATAATATATTTTAA
1 AATTA-TAAATAATAAAATTTAA
3443526 A
1 A
3443527 TATAATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATAAATAATAAAATTTAA
Found at i:3450843 original size:45 final size:45
Alignment explanation
Indices: 3450789--3450877 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
3450779 CCAGAATTCG
* *
3450789 TTTAATAACCAACAGCAACACCAGCAGCAGCCCCAGCATCCACTC
1 TTTAATAACCAACACCAACACCAACAGCAGCCCCAGCATCCACTC
3450834 TTTAATAACCAACACCAACACCAACAGCAGCCCCAGCATCCACT
1 TTTAATAACCAACACCAACACCAACAGCAGCCCCAGCATCCACT
3450878 GTCACAGCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.37, C:0.40, G:0.09, T:0.13
Consensus pattern (45 bp):
TTTAATAACCAACACCAACACCAACAGCAGCCCCAGCATCCACTC
Found at i:3460487 original size:3 final size:3
Alignment explanation
Indices: 3460479--3460511 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3460469 CTCTCCCATC
3460479 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3460512 TTGCAAGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3468174 original size:16 final size:16
Alignment explanation
Indices: 3468149--3468202 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 16
3468139 TTAAAAAAAT
*
3468149 AATATAAAAAATTATA
1 AATATTAAAAATTATA
3468165 AATATT-AAAATT-TA
1 AATATTAAAAATTATA
*
3468179 AAT-TTTAAAATTATTA
1 AATATTAAAAATTA-TA
3468195 AATATTAA
1 AATATTAA
3468203 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 2 0.06
14 11 0.34
15 6 0.19
16 10 0.31
17 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATTAAAAATTATA
Found at i:3468186 original size:14 final size:15
Alignment explanation
Indices: 3468156--3468202 Score: 69
Period size: 14 Copynumber: 3.1 Consensus size: 15
3468146 AATAATATAA
3468156 AAAATTATAAATATT
1 AAAATTATAAATATT
*
3468171 AAAATT-TAAATTTT
1 AAAATTATAAATATT
3468185 AAAATTATTAAATATT
1 AAAATTA-TAAATATT
3468201 AA
1 AA
3468203 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 13 0.46
15 6 0.21
16 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:3468202 original size:23 final size:23
Alignment explanation
Indices: 3468167--3468211 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3468157 AAATTATAAA
3468167 TATTAAAATTTAAATTTTAAAAT
1 TATTAAAATTTAAATTTTAAAAT
*
3468190 TATT-AAATATTAATTTTTAAAA
1 TATTAAAAT-TTAAATTTTAAAA
3468212 ATAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAAAATTTAAATTTTAAAAT
Found at i:3468773 original size:3 final size:3
Alignment explanation
Indices: 3468767--3468809 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3468757 AAAAAGAAAG
3468767 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3468810 AAGAGCTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3469845 original size:3 final size:3
Alignment explanation
Indices: 3469837--3469862 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3469827 TTTACAAAAA
3469837 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
3469863 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3473723 original size:104 final size:104
Alignment explanation
Indices: 3473524--3473729 Score: 396
Period size: 104 Copynumber: 2.0 Consensus size: 104
3473514 TGAAGCAAGC
3473524 TTAGGAACCTGGATGGCACGAACATGCAATTTTCATGACATTATAAAAAAAATTTTGCTCTCACA
1 TTAGGAACCTGGATGGCACGAACATGCAATTTTCATGACATTATAAAAAAAATTTTGCTCTCACA
3473589 TGGGGAAGTGCAATAAACTTCATTCAATAGA-ATGAAGT
66 TGGGGAAGTGCAATAAACTTCATTCAATAGACATGAAGT
3473627 TTAGGAACCTGGATGGCACGAACATGCAATTTTCATGACATTATAAAAAAAAATTTTGCTCTCAC
1 TTAGGAACCTGGATGGCACGAACATGCAATTTTCATGACATTAT-AAAAAAAATTTTGCTCTCAC
3473692 ATGGGGAAGTGCAATAAACTTCATTCAATAGACATGAA
65 ATGGGGAAGTGCAATAAACTTCATTCAATAGACATGAA
3473730 AATGAACAGT
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 44 0.44
104 52 0.51
105 5 0.05
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (104 bp):
TTAGGAACCTGGATGGCACGAACATGCAATTTTCATGACATTATAAAAAAAATTTTGCTCTCACA
TGGGGAAGTGCAATAAACTTCATTCAATAGACATGAAGT
Found at i:3493081 original size:82 final size:82
Alignment explanation
Indices: 3492974--3493141 Score: 336
Period size: 82 Copynumber: 2.0 Consensus size: 82
3492964 AAAATATGCA
3492974 GGAAAAGAATCATTATAAAGATAAAGATAACAAAAGCCATGGATAACAGAATAAATTTATGCATA
1 GGAAAAGAATCATTATAAAGATAAAGATAACAAAAGCCATGGATAACAGAATAAATTTATGCATA
3493039 CCTGAGCACCAAGGAGG
66 CCTGAGCACCAAGGAGG
3493056 GGAAAAGAATCATTATAAAGATAAAGATAACAAAAGCCATGGATAACAGAATAAATTTATGCATA
1 GGAAAAGAATCATTATAAAGATAAAGATAACAAAAGCCATGGATAACAGAATAAATTTATGCATA
3493121 CCTGAGCACCAAGGAGG
66 CCTGAGCACCAAGGAGG
3493138 GGAA
1 GGAA
3493142 TCATGTGTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.18
Consensus pattern (82 bp):
GGAAAAGAATCATTATAAAGATAAAGATAACAAAAGCCATGGATAACAGAATAAATTTATGCATA
CCTGAGCACCAAGGAGG
Found at i:3499290 original size:13 final size:13
Alignment explanation
Indices: 3499245--3499291 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3499235 TCACTGTTGC
3499245 AAATTGAATTTCA
1 AAATTGAATTTCA
* *
3499258 ACATTTACTATTTC-
1 AAATTGA--ATTTCA
3499272 AAATTGAATTTCA
1 AAATTGAATTTCA
3499285 AAATTGA
1 AAATTGA
3499292 CGGCACAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.19
13 12 0.44
14 5 0.19
15 5 0.19
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (13 bp):
AAATTGAATTTCA
Found at i:3499311 original size:12 final size:12
Alignment explanation
Indices: 3499294--3499319 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3499284 AAAATTGACG
3499294 GCACAGTTGGCA
1 GCACAGTTGGCA
3499306 GCACAGTTGGCA
1 GCACAGTTGGCA
3499318 GC
1 GC
3499320 CTTTGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.15
Consensus pattern (12 bp):
GCACAGTTGGCA
Found at i:3503981 original size:13 final size:13
Alignment explanation
Indices: 3503936--3503982 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3503926 TCACTGTTGC
3503936 AAATTGAATTTCA
1 AAATTGAATTTCA
* *
3503949 ACATTTACTATTTC-
1 AAATTGA--ATTTCA
3503963 AAATTGAATTTCA
1 AAATTGAATTTCA
3503976 AAATTGA
1 AAATTGA
3503983 CGGCAGACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.19
13 12 0.44
14 5 0.19
15 5 0.19
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (13 bp):
AAATTGAATTTCA
Found at i:3511349 original size:21 final size:21
Alignment explanation
Indices: 3511308--3511349 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3511298 TATTATTCTT
*
3511308 TTTTTATATTAAAATTTTGTA
1 TTTTTATATTAAAATTATGTA
*
3511329 TTTTTCTA-TAAAATTGATGTA
1 TTTTTATATTAAAATT-ATGTA
3511350 CCAAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTTATATTAAAATTATGTA
Found at i:3511693 original size:13 final size:13
Alignment explanation
Indices: 3511670--3511720 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
3511660 GTGTAAAAAT
3511670 TTATATAATATAAA
1 TTAT-TAATATAAA
**
3511684 TTATTAATATATT
1 TTATTAATATAAA
3511697 TTATTAATAT-AA
1 TTATTAATATAAA
3511709 TTATT-ATATAAA
1 TTATTAATATAAA
3511721 AATAATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 7 0.22
13 17 0.53
14 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATTAATATAAA
Found at i:3511697 original size:26 final size:24
Alignment explanation
Indices: 3511669--3511718 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
3511659 TGTGTAAAAA
3511669 TTTATATAATATAAATTATTAATATAT
1 TTTAT-TAATAT-AATTATT-ATATAT
3511696 TTTATTAATATAATTATTATATA
1 TTTATTAATATAATTATTATATA
3511719 AAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 7 0.30
26 6 0.26
27 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATTAATATAATTATTATATAT
Found at i:3511902 original size:13 final size:12
Alignment explanation
Indices: 3511876--3511912 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3511866 TATTAAAAAG
3511876 ATTAAT-TTTAA
1 ATTAATATTTAA
3511887 ATTAATATTTATA
1 ATTAATATTTA-A
3511900 ATTAA-ATTTAA
1 ATTAATATTTAA
3511911 AT
1 AT
3511913 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 9 0.38
13 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAATATTTAA
Found at i:3514215 original size:2 final size:2
Alignment explanation
Indices: 3514208--3514233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3514198 AATCCGTAAC
3514208 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
3514234 GATCAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3518449 original size:2 final size:2
Alignment explanation
Indices: 3518444--3518529 Score: 56
Period size: 2 Copynumber: 45.0 Consensus size: 2
3518434 AATATATGTT
* * *
3518444 TA TA TA TA TA TA TA TA TA TA TT TA TT TT TA TA TA TA TCA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * * *
3518486 T- TA TA TT TA -A AA TA T- TA TA TT TT TA TA TA CA -A 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
3518524 TA TA TA
1 TA TA TA
3518530 AAATTTTCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
1 5 0.07
2 61 0.90
3 2 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3518462 original size:22 final size:22
Alignment explanation
Indices: 3518435--3518529 Score: 79
Period size: 22 Copynumber: 4.3 Consensus size: 22
3518425 TTACATAATA
*
3518435 ATATATGTTTATATATATATAT
1 ATATATATTTATATATATATAT
*
3518457 ATATATATTTAT-T-TTTATAT
1 ATATATATTTATATATATATAT
* * *
3518477 ATATCATAATTATATTTA-AAAT
1 ATAT-ATATTTATATATATATAT
* *
3518499 ATTATATTTTTATATACAATATAT
1 A-TATATATTTATATA-TATATAT
3518523 ATATATA
1 ATATATA
3518530 AAATTTTCAT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
20 10 0.18
21 8 0.14
22 24 0.43
23 10 0.18
24 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (22 bp):
ATATATATTTATATATATATAT
Found at i:3518526 original size:35 final size:35
Alignment explanation
Indices: 3518445--3518553 Score: 105
Period size: 36 Copynumber: 3.0 Consensus size: 35
3518435 ATATATGTTT
* *
3518445 ATATATATATATATATATATT-TATTTTTATATA-T
1 ATATATATATATA-AAATATTATATTTTTATATACA
*
3518479 ATCATAATTATATTTAAAATATTATATTTTTATATACA
1 AT-AT-A-TATATATAAAATATTATATTTTTATATACA
* * *
3518517 ATATATATATATAAAATTTTCATAATTTAATATACA
1 ATATATATATATAAAATATT-ATATTTTTATATACA
3518553 A
1 A
3518554 AATTTACACA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
34 2 0.03
35 15 0.24
36 22 0.35
37 21 0.34
38 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (35 bp):
ATATATATATATAAAATATTATATTTTTATATACA
Found at i:3519341 original size:5 final size:5
Alignment explanation
Indices: 3519331--3519360 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3519321 CTTTCTCACG
3519331 TCATC TCATC TCATC TCATC TCATC TCATC
1 TCATC TCATC TCATC TCATC TCATC TCATC
3519361 CTTCCATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
TCATC
Found at i:3519457 original size:15 final size:15
Alignment explanation
Indices: 3519430--3519492 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 15
3519420 ATCAATCATA
3519430 ATTATATTTAAAATAT
1 ATTATA-TTAAAATAT
3519446 ATTATATTAAAATATTT
1 ATTATATTAAAATA--T
*
3519463 AATATATTAATAATTTAT
1 ATTATATTAA-AA--TAT
3519481 ATTA-ATTAAAAT
1 ATTATATTAAAAT
3519493 TTAAAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 8 0.20
16 8 0.20
17 15 0.38
18 6 0.15
20 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATATTAAAATAT
Found at i:3520251 original size:2 final size:2
Alignment explanation
Indices: 3520244--3520270 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3520234 CAAATCTCCT
3520244 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3520271 TATTGGAGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3520326 original size:3 final size:3
Alignment explanation
Indices: 3520314--3520349 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3520304 CCCAAAGTTT
3520314 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3520350 CTTACCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3520544 original size:19 final size:19
Alignment explanation
Indices: 3520509--3520558 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
3520499 GAGATACATT
*
3520509 TAATAAATACAAAAATAATA
1 TAATAAATA-TAAAATAATA
3520529 TAATAAATATAAAATAATA
1 TAATAAATATAAAATAATA
**
3520548 TTTTAAATATA
1 TAATAAATATA
3520559 TTTATCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAAATATAAAATAATA
Done.