Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 44 of 208
Found at i:12180277 original size:7 final size:7
Alignment explanation
Indices: 12180267--12180310 Score: 70
Period size: 7 Copynumber: 6.1 Consensus size: 7
12180257 ATATTTGAAA
*
12180267 TTTAATC
1 TTTAATT
12180274 TTTAATT
1 TTTAATT
12180281 TTTAAGTT
1 TTTAA-TT
12180289 TTTAATT
1 TTTAATT
12180296 TTTAATT
1 TTTAATT
12180303 TTTAATT
1 TTTAATT
12180310 T
1 T
12180311 AATAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (7 bp):
TTTAATT
Found at i:12180316 original size:22 final size:22
Alignment explanation
Indices: 12180269--12180317 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
12180259 ATTTGAAATT
* *
12180269 TAATCTTTAATTTTTAAGTTTT
1 TAATTTTTAATTTTTAAGTTTA
12180291 TAATTTTTAATTTTTAA-TTTAA
1 TAATTTTTAATTTTTAAGTTT-A
12180313 TAATT
1 TAATT
12180318 AAAATCTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TAATTTTTAATTTTTAAGTTTA
Found at i:12184700 original size:5 final size:6
Alignment explanation
Indices: 12184684--12184708 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12184674 ATTGATAATA
12184684 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
12184709 AAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:12184815 original size:9 final size:9
Alignment explanation
Indices: 12184801--12184825 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
12184791 TAATAATTTA
12184801 TTAATATAT
1 TTAATATAT
12184810 TTAATATAT
1 TTAATATAT
12184819 TTAATAT
1 TTAATAT
12184826 TTCAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATATAT
Found at i:12184909 original size:15 final size:16
Alignment explanation
Indices: 12184891--12184944 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 16
12184881 AAAGAATATT
12184891 AATAT-TTAAATAATA
1 AATATATTAAATAATA
*
12184906 AATATTTATTACAATTATA
1 AATA--TATTA-AATAATA
12184925 AATATATT-AATAATA
1 AATATATTAAATAATA
12184940 AATAT
1 AATAT
12184945 TTTTAGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 15 0.45
17 5 0.15
18 3 0.09
19 10 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATTAAATAATA
Found at i:12185071 original size:14 final size:14
Alignment explanation
Indices: 12185049--12185091 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
12185039 ATTGTTGACC
*
12185049 TTGTTAATTTTTTT
1 TTGTCAATTTTTTT
12185063 TTGTCAATTTTGTTT
1 TTGTCAATTTT-TTT
*
12185078 ATGTCACATTTTTT
1 TTGTCA-ATTTTTT
12185092 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.40
15 10 0.40
16 5 0.20
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.67
Consensus pattern (14 bp):
TTGTCAATTTTTTT
Found at i:12196069 original size:22 final size:22
Alignment explanation
Indices: 12196043--12196088 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12196033 GGTTCCGTTT
*
12196043 TTCTTTTCTT-TTTACTGTTTTG
1 TTCTTTT-TTGTTTACTGTCTTG
*
12196065 TTCTTTTTTGTTTTCTGTCTTG
1 TTCTTTTTTGTTTACTGTCTTG
12196087 TT
1 TT
12196089 TTTAAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.74
Consensus pattern (22 bp):
TTCTTTTTTGTTTACTGTCTTG
Found at i:12196675 original size:3 final size:3
Alignment explanation
Indices: 12196667--12196705 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12196657 TTTCAATAGA
12196667 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12196706 TCTATACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12196792 original size:2 final size:2
Alignment explanation
Indices: 12196785--12196815 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12196775 GTACATATTT
12196785 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 T
12196816 TATTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12200309 original size:17 final size:17
Alignment explanation
Indices: 12200287--12200321 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12200277 TTTGACTCGT
12200287 ATGCTTTGATGTAAGTG
1 ATGCTTTGATGTAAGTG
12200304 ATGCTTTGATGTAAGTG
1 ATGCTTTGATGTAAGTG
12200321 A
1 A
12200322 AAGCTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (17 bp):
ATGCTTTGATGTAAGTG
Found at i:12201158 original size:17 final size:17
Alignment explanation
Indices: 12201138--12201172 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12201128 AATTTGATTG
12201138 AGAAAATTATTTAATTA
1 AGAAAATTATTTAATTA
* *
12201155 AGAAATTTATTTAGTTA
1 AGAAAATTATTTAATTA
12201172 A
1 A
12201173 TTTAATTGAT
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:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
AGAAAATTATTTAATTA
Found at i:12202345 original size:4 final size:4
Alignment explanation
Indices: 12202336--12202365 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
12202326 TACCCAAAAT
12202336 ATTA ATTA ATTA ATTA ATTA ATTA ACTTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A-TTA A
12202366 CTAAATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:12221713 original size:16 final size:15
Alignment explanation
Indices: 12221674--12221714 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
12221664 AGAATGTGGA
12221674 CTATTAAT--TTTTT
1 CTATTAATCCTTTTT
12221687 CTATTAATCCTTTTT
1 CTATTAATCCTTTTT
12221702 CTATTAATTCCTT
1 CTATTAA-TCCTT
12221715 AATTATATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.32
15 12 0.48
16 5 0.20
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (15 bp):
CTATTAATCCTTTTT
Found at i:12223282 original size:117 final size:117
Alignment explanation
Indices: 12222902--12223304 Score: 429
Period size: 117 Copynumber: 3.4 Consensus size: 117
12222892 CTTGTTCTCT
* * ** * *
12222902 AATTTCATTTTCATCGGAACTAAGGCTTCTATACCTTCCACGATGCTCAAAGGGATTGCTTACAG
1 AATTTCATTTTCATCGGAACTATGGCTTCTACACCTTTGACGATGCTCAAGGGGATTACTTACAG
* * *
12222967 ATCCAGCTCCTAAGAAATGATGCCTGA-GAAGAGGCCAGCC-GAAAGGTTCTTG
66 ATTCAGCTCCCAAGAAATGACGCCTGAGGAA-AGGCCAGCCTG-AAGGTTCTTG
* * * * ** *
12223019 ATTTTCATTTTGACCGGAACTACGGAAGT-TACACCTTTGACGATGCTCAAGGGGATTATTTACA
1 AATTTCATTTTCATCGGAACTATGG-CTTCTACACCTTTGACGATGCTCAAGGGGATTACTTACA
* * * *
12223083 GATTCAGCTCCC-AGAAAATGACGCCTGAGGAAAGGCCGGCCTAAAGATTCGTG
65 GATTCAGCTCCCAAG-AAATGACGCCTGAGGAAAGGCCAGCCTGAAGGTTCTTG
* * * * * * *
12223136 AACTTCATTTCCATTGGAACCATGTCTTCTACACCTTTGACGATGCTCAGGGGGATTACTTATAG
1 AATTTCATTTTCATCGGAACTATGGCTTCTACACCTTTGACGATGCTCAAGGGGATTACTTACAG
* *
12223201 ATTCTGCTCCCAAGAAATGACGCCTGAGGAAAGGCCAACCTGAAGGTTCTTG
66 ATTCAGCTCCCAAGAAATGACGCCTGAGGAAAGGCCAGCCTGAAGGTTCTTG
** * *
12223253 AATTTCA-TTTCTATCATAACTATGGCTTCTACGCCTTTGACAATGCTCAAGG
1 AATTTCATTTTC-ATCGGAACTATGGCTTCTACACCTTTGACGATGCTCAAGG
12223305 AAATGAAGCC
Statistics
Matches: 230, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
116 6 0.03
117 218 0.95
118 6 0.03
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (117 bp):
AATTTCATTTTCATCGGAACTATGGCTTCTACACCTTTGACGATGCTCAAGGGGATTACTTACAG
ATTCAGCTCCCAAGAAATGACGCCTGAGGAAAGGCCAGCCTGAAGGTTCTTG
Found at i:12223586 original size:144 final size:146
Alignment explanation
Indices: 12223320--12223641 Score: 368
Period size: 144 Copynumber: 2.2 Consensus size: 146
12223310 AAGCCTAAAG
* *
12223320 AAAGGCCAACCTAAAGGTTCTTGATTATTAGAACGTTGTACATGTTCTTGTTCTCTAATTTCACT
1 AAAGGCCAACCTAAAGGTTCTTGATTATCAAAACGTTGTACATG----TGTTCTCTAATTTCACT
* * *
12223385 TCCATAGGAACTATGGCTTCTATACCTTCGACGATGCTCAAAGGGATTATTTACAGATTC-GGCT
62 TCCATAGAAACTATGGCTTCTACACCTTCGAAGATGCTCAAAGGGATTATTTACAGATTCAGG-T
* *
12223449 CCCAATAAACGACT-TCTGAGC
126 CCCAATAAACGA-TGCCCGAGC
* **
12223470 AAAGGCCAACCTAAAGGTTCTTGATTATCAAAACGTTGTGCA-G-GTTCTCTAATTTCGTTTCCA
1 AAAGGCCAACCTAAAGGTTCTTGATTATCAAAACGTTGTACATGTGTTCTCTAATTTCACTTCCA
* * * * *
12223533 TCA-AAACTATGGCTTCTACGCCTTTGAAGA-GACTCGAGGGGATTATTTACAGATTCAGGTCCT
66 T-AGAAACTATGGCTTCTACACCTTCGAAGATG-CTCAAAGGGATTATTTACAGATTCAGGTCCC
*
12223596 AGTAAACGATGCCCGAGC
129 AATAAACGATGCCCGAGC
* *
12223614 AAAGGCCAACTTACAGGTTCTTGATTAT
1 AAAGGCCAACCTAAAGGTTCTTGATTAT
12223642 TGGAACAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
143 2 0.01
144 105 0.70
145 3 0.02
149 1 0.01
150 39 0.26
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (146 bp):
AAAGGCCAACCTAAAGGTTCTTGATTATCAAAACGTTGTACATGTGTTCTCTAATTTCACTTCCA
TAGAAACTATGGCTTCTACACCTTCGAAGATGCTCAAAGGGATTATTTACAGATTCAGGTCCCAA
TAAACGATGCCCGAGC
Found at i:12230023 original size:44 final size:43
Alignment explanation
Indices: 12229960--12230357 Score: 411
Period size: 44 Copynumber: 9.7 Consensus size: 43
12229950 CACAAAGCTT
* *
12229960 TATCTCTCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAA-TCC
*
12230004 TATCTCTCTGGTCAGCAGTGGAATA----G--G--TG-AATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAATCC
* * *
12230038 TATCTCCTTGGTCCGCAGTGGAATAGGTTGAAGATTGTGAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AATCC
*
12230082 TATCTCCTTGGTCAGCAGTGGAATA----G--G--TG-AATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAATCC
*
12230116 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AATCC
*
12230160 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCA
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAA-TCC
*
12230204 TATCTCACTGGTCAGCAGTGGAATA----G--G--TG-AATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAATCC
* *
12230238 TATCTCCTTGGTCAGCAGTGGAATTGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AATCC
12230282 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AATCC
* *
12230326 TATCTCCCTGAGCCA-CAGTGGAGTAGGTTGAA
1 TATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
12230358 AATTACAGAT
Statistics
Matches: 302, Mismatches: 20, Indels: 64
0.78 0.05 0.17
Matches are distributed among these distances:
34 77 0.25
35 4 0.01
36 6 0.02
38 6 0.02
40 6 0.02
42 6 0.02
43 1 0.00
44 193 0.64
45 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAATCC
Found at i:12230070 original size:78 final size:77
Alignment explanation
Indices: 12229960--12230332 Score: 388
Period size: 78 Copynumber: 4.7 Consensus size: 77
12229950 CACAAAGCTT
* * *
12229960 TATCTCTCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCTCTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTC-CTGGTCAGCAGTGG
12230025 AATAGGTGAATCC
65 AATAGGTGAATCC
* *
12230038 TATCTCCTTGGTCCGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCTTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCC-TGGTCAGCAGTGG
12230103 AATAGGTGAATCC
65 AATAGGTGAATCC
12230116 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCT-CCTGGTCAGCAGTGG
*
12230181 AATAGGTTGAAGATTGTAAGTCA
65 AATA----G--G--TG-AA-TCC
*
12230204 TATCTCACTGGTCAGCAGTGGAATAGG-T---GA-----A-TCCTATCTCCTTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCC-TGGTCAGCAGTGG
12230259 AATTGGTTGAAGATTGTGAATCC
65 AA-----T--AG---GTGAATCC
*
12230282 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCC
12230333 CTGAGCCACA
Statistics
Matches: 251, Mismatches: 13, Indels: 52
0.79 0.04 0.16
Matches are distributed among these distances:
77 3 0.01
78 186 0.74
79 6 0.02
80 2 0.01
81 1 0.00
82 4 0.02
83 1 0.00
84 3 0.01
85 1 0.00
86 2 0.01
87 4 0.02
88 38 0.15
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (77 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCTGGTCAGCAGTGGA
ATAGGTGAATCC
Found at i:12230345 original size:122 final size:122
Alignment explanation
Indices: 12230030--12230353 Score: 517
Period size: 122 Copynumber: 2.7 Consensus size: 122
12230020 AGTGGAATAG
* * * *
12230030 GTGAATCCTATCTCCTTGGTCCGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCTTGGTC
1 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTC
12230095 AGCAGTGGAATAGGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 AGCAGTGGAATAGGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
* * *
12230152 GTGAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCATATCTCACTGGT
1 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGGT
* *
12230216 CAGCAGTGGAATAGGTGAATCCTATCTCCTTGGTCAGCAGTGGAATTGGTTGAAGATT
65 CAGCAGTGGAATAGGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
*
12230274 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGAGC
1 GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTG-GT
*
12230339 CA-CAGTGGAGTAGGT
65 CAGCAGTGGAATAGGT
12230354 TGAAAATTAC
Statistics
Matches: 185, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
121 1 0.01
122 179 0.97
123 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (122 bp):
GTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTC
AGCAGTGGAATAGGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
Found at i:12230374 original size:44 final size:44
Alignment explanation
Indices: 12230232--12230378 Score: 154
Period size: 44 Copynumber: 3.3 Consensus size: 44
12230222 TGGAATAGGT
* * * * **
12230232 GAATCCTATCTCCTTGGTCAGCAGTGGAATTGGTTGAAGATTGT
1 GAATCCTATCTCCCTGGCCAGCAGTGGAATAGGTTGAAAATTCA
* * **
12230276 GAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT
1 GAATCCTATCTCCCTGGCCAGCAGTGGAATAGGTTGAAAATTCA
*
12230320 GAATCCTATCTCCCTGAGCCA-CAGTGGAGTAGGTTGAAAATTACA
1 GAATCCTATCTCCCTG-GCCAGCAGTGGAATAGGTTGAAAATT-CA
*
12230365 G-ATCTTATCTCCCT
1 GAATCCTATCTCCCT
12230379 AAGCAGTAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
44 89 0.96
45 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (44 bp):
GAATCCTATCTCCCTGGCCAGCAGTGGAATAGGTTGAAAATTCA
Found at i:12231229 original size:22 final size:22
Alignment explanation
Indices: 12231169--12231226 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
12231159 AATCTTCAAG
12231169 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
12231188 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
12231210 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
12231227 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:12231472 original size:23 final size:23
Alignment explanation
Indices: 12231428--12231472 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12231418 TCTTATTTTG
* *
12231428 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
*
12231451 TTGATTTGTATATTATTGATTT
1 TTGATTTGTATATAATTGATTT
12231473 CAAATATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:12231965 original size:23 final size:22
Alignment explanation
Indices: 12231935--12231978 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
12231925 NNNNNNNACA
*
12231935 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
12231958 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
12231979 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:12236806 original size:24 final size:24
Alignment explanation
Indices: 12236774--12236822 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
12236764 ATTTTTATTC
*
12236774 TTCACAATTAACTTTATATTTTCA
1 TTCACAATTAACTCTATATTTTCA
12236798 TTCACAATTAACTCTATATTTTCA
1 TTCACAATTAACTCTATATTTTCA
12236822 T
1 T
12236823 ACTCATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (24 bp):
TTCACAATTAACTCTATATTTTCA
Found at i:12237320 original size:18 final size:18
Alignment explanation
Indices: 12237272--12237325 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
12237262 TTATTAATAT
12237272 TATAACATATATATATACA
1 TATAACATATATATATA-A
* *
12237291 T-T-TCTTAT-TATATAA
1 TATAACATATATATATAA
12237306 TATAACATATATATATAA
1 TATAACATATATATATAA
12237324 TA
1 TA
12237326 AGTTATCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
15 2 0.07
16 7 0.25
17 8 0.29
18 10 0.36
19 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAACATATATATATAA
Found at i:12237351 original size:18 final size:19
Alignment explanation
Indices: 12237314--12237352 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
12237304 AATATAACAT
*
12237314 ATATATATAATAAGTTATC
1 ATATATATAATAAGTAATC
*
12237333 ATATATA-AATATGTAATC
1 ATATATATAATAAGTAATC
12237351 AT
1 AT
12237353 CATTAATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
ATATATATAATAAGTAATC
Found at i:12240272 original size:25 final size:25
Alignment explanation
Indices: 12240235--12240317 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
12240225 ACACCATAGT
*
12240235 TCGTATGAGCTTC-CTGATTTACAGC
1 TCGTATGAGCTTCTC-GATTCACAGC
*
12240260 TCGTATGATCTTCTCGATTCACAGC
1 TCGTATGAGCTTCTCGATTCACAGC
* * *
12240285 TCATGA-GAGCATACT-GATTCATAGC
1 TCGT-ATGAGC-TTCTCGATTCACAGC
12240310 TCGTATGA
1 TCGTATGA
12240318 ACATACATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 1 0.02
25 41 0.87
26 5 0.11
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (25 bp):
TCGTATGAGCTTCTCGATTCACAGC
Found at i:12247670 original size:25 final size:25
Alignment explanation
Indices: 12247615--12247674 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
12247605 GCAGGCACAC
* **
12247615 CACAGCTCATATGAGCTTCCTGATT
1 CACAGCTCGTATGAGCTTCCCAATT
** *
12247640 TGCAGCTCGTATGAGTTTCCCAATT
1 CACAGCTCGTATGAGCTTCCCAATT
12247665 CACAGCTCGT
1 CACAGCTCGT
12247675 GAAAGCATAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTCCCAATT
Found at i:12253137 original size:30 final size:30
Alignment explanation
Indices: 12253103--12253160 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12253093 TTAACAAGCG
* *
12253103 AATGCTTCTAAAATAATAACAAACTTAACA
1 AATGCCTCTAAAATAATAACAAAATTAACA
*
12253133 AATGCCTCTAAAATAATAATAAAATTAA
1 AATGCCTCTAAAATAATAACAAAATTAA
12253161 TAATAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (30 bp):
AATGCCTCTAAAATAATAACAAAATTAACA
Found at i:12254154 original size:3 final size:3
Alignment explanation
Indices: 12254146--12254175 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12254136 ACATTACATG
*
12254146 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12254176 TATTCTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12256421 original size:19 final size:19
Alignment explanation
Indices: 12256394--12256432 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
12256384 CCCTGTTTTA
12256394 CCCTCTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
*
12256413 CCCTTTGCCTCTTCTGTTC
1 CCCTCTGCCTCTTCTGTTC
12256432 C
1 C
12256433 TTCCTTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.46, G:0.10, T:0.44
Consensus pattern (19 bp):
CCCTCTGCCTCTTCTGTTC
Found at i:12257553 original size:16 final size:16
Alignment explanation
Indices: 12257529--12257566 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12257519 TTTGGTTCGC
* *
12257529 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
12257545 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12257561 TGTAAT
1 TGTAAT
12257567 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:12257611 original size:45 final size:44
Alignment explanation
Indices: 12257545--12257635 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
12257535 GGATTAGAGG
*
12257545 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
12257590 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
12257634 TG
1 TG
12257636 GAATAGAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:12260353 original size:11 final size:11
Alignment explanation
Indices: 12260333--12260377 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
12260323 TTGTTGTTTC
12260333 GCTATTATTTT
1 GCTATTATTTT
*
12260344 GCTATCATTTT
1 GCTATTATTTT
* *
12260355 GTTATTATATT
1 GCTATTATTTT
*
12260366 GCTATTAATTT
1 GCTATTATTTT
12260377 G
1 G
12260378 TTGTTATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.58
Consensus pattern (11 bp):
GCTATTATTTT
Found at i:12260360 original size:22 final size:22
Alignment explanation
Indices: 12260335--12260385 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12260325 GTTGTTTCGC
*
12260335 TATTATTTTGCTATCATTTTGT
1 TATTATTTTGCTATCAATTTGT
* *
12260357 TATTATATTGCTATTAATTTGT
1 TATTATTTTGCTATCAATTTGT
*
12260379 TGTTATT
1 TATTATT
12260386 ATTTGAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.63
Consensus pattern (22 bp):
TATTATTTTGCTATCAATTTGT
Found at i:12265795 original size:28 final size:30
Alignment explanation
Indices: 12265764--12265831 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 30
12265754 GAATTCTTTG
12265764 AAAATAATAAAAATTG-TAAAAAATAAA-A
1 AAAATAATAAAAATTGTTAAAAAATAAATA
* **
12265792 AAAAT-ATTAAAATTGTTATGAAATAAATA
1 AAAATAATAAAAATTGTTAAAAAATAAATA
*
12265821 ATAATAATAAA
1 AAAATAATAAA
12265832 TAGGAGAGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.28
28 14 0.44
29 5 0.16
30 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (30 bp):
AAAATAATAAAAATTGTTAAAAAATAAATA
Found at i:12269447 original size:9 final size:9
Alignment explanation
Indices: 12269411--12269450 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12269401 TTTAATTGGG
12269411 AAATTAATT
1 AAATTAATT
* *
12269420 TAGTTAATT
1 AAATTAATT
*
12269429 TAATTAATT
1 AAATTAATT
12269438 AAATTAATT
1 AAATTAATT
12269447 AAAT
1 AAAT
12269451 AATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
AAATTAATT
Found at i:12271753 original size:20 final size:20
Alignment explanation
Indices: 12271725--12271765 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12271715 CTTGTACGGG
12271725 TTTGCACTTTGATGCCTCTA
1 TTTGCACTTTGATGCCTCTA
* * *
12271745 TTTGTACTTTGGTGTCTCTA
1 TTTGCACTTTGATGCCTCTA
12271765 T
1 T
12271766 ACAACACTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.51
Consensus pattern (20 bp):
TTTGCACTTTGATGCCTCTA
Found at i:12276026 original size:9 final size:9
Alignment explanation
Indices: 12276001--12276138 Score: 68
Period size: 10 Copynumber: 14.9 Consensus size: 9
12275991 CCAATTCAAG
*
12276001 TTTTTATTA
1 TTTTTATAA
12276010 TATTTTATAA
1 T-TTTTATAA
*
12276020 TTTTTATGA
1 TTTTTATAA
12276029 TTTTTATAGAA
1 TTTTTAT--AA
* * *
12276040 TTCTAATACG
1 TTTTTATA-A
12276050 TTTTTATAAA
1 TTTTTAT-AA
* *
12276060 ATTTTAAATA
1 TTTTTATA-A
12276070 TTTTTATTAA
1 TTTTTA-TAA
* *
12276080 CTTATAT-A
1 TTTTTATAA
*
12276088 TATTTATAA
1 TTTTTATAA
12276097 TTTTTTATAA
1 -TTTTTATAA
* *
12276107 TTTAT-TAG
1 TTTTTATAA
12276115 TTTTT-T-A
1 TTTTTATAA
12276122 TTTTTATAA
1 TTTTTATAA
12276131 TTTTTATA
1 TTTTTATA
12276139 TGTTTATTAT
Statistics
Matches: 95, Mismatches: 23, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
7 5 0.05
8 13 0.14
9 32 0.34
10 37 0.39
11 8 0.08
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12276111 original size:17 final size:17
Alignment explanation
Indices: 12276084--12276135 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
12276074 TATTAACTTA
12276084 TATATATTTATAATTTTT
1 TATA-ATTTATAATTTTT
*
12276102 TATAATTTATTAGTTTTT
1 TATAATTTA-TAATTTTT
*
12276120 TAT-TTTTATAATTTTT
1 TATAATTTATAATTTTT
12276136 ATATGTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
18 14 0.47
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TATAATTTATAATTTTT
Found at i:12276144 original size:17 final size:16
Alignment explanation
Indices: 12276086--12276145 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
12276076 TTAACTTATA
12276086 TATATTTATAATTTTT
1 TATATTTATAATTTTT
*
12276102 TATAATTTATTAGTTTTT
1 TAT-ATTTA-TAATTTTT
*
12276120 TATTTTTATAATTTTT
1 TATATTTATAATTTTT
*
12276136 ATATGTTTAT
1 -TATATTTAT
12276146 TATAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.27
17 17 0.46
18 10 0.27
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TATATTTATAATTTTT
Found at i:12279871 original size:16 final size:17
Alignment explanation
Indices: 12279847--12279885 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
12279837 TTTAATTCTT
12279847 TTTTAAAAATTTC-AAA
1 TTTTAAAAATTTCAAAA
*
12279863 TTTTCAAAATTTCAAAA
1 TTTTAAAAATTTCAAAA
12279880 TTTTAA
1 TTTTAA
12279886 GTTAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTAAAAATTTCAAAA
Found at i:12283205 original size:27 final size:28
Alignment explanation
Indices: 12283145--12283217 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
12283135 AAAAATAAAA
*
12283145 ATTTACCAAAATGT-TATAACTTTTTTTTT
1 ATTTACCAAAATATATATAA--TTTTTTTT
12283174 ATTTACCAAAATATATATAA-TTTTTTT
1 ATTTACCAAAATATATATAATTTTTTTT
*
12283201 ATTTACTAAAATATATA
1 ATTTACCAAAATATATA
12283218 AAAAAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 23 0.56
29 13 0.32
30 5 0.12
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTTACCAAAATATATATAATTTTTTTT
Found at i:12283314 original size:27 final size:27
Alignment explanation
Indices: 12283284--12283350 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
12283274 CGCCAATGGT
12283284 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* *
12283311 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
*
12283338 ATTGGTGGCACCA
1 ATTGGCGGCACCA
12283351 GTTAATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:12283403 original size:4 final size:4
Alignment explanation
Indices: 12283394--12283505 Score: 76
Period size: 4 Copynumber: 28.0 Consensus size: 4
12283384 GAAGGAGAGG
* * *
12283394 GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA GAAA AAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA
12283442 GAAA GAAA G-AA G-AA G-AA GAAAA GGAAAA GAGAA GAAA -AAA GAAA
1 GAAA GAAA GAAA GAAA GAAA G-AAA -G-AAA GA-AA GAAA GAAA GAAA
*
12283486 GAAA GAAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA
12283506 AGGAAAGGAG
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
3 18 0.20
4 48 0.54
5 17 0.19
6 6 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:12283468 original size:43 final size:43
Alignment explanation
Indices: 12283395--12283540 Score: 203
Period size: 43 Copynumber: 3.4 Consensus size: 43
12283385 AAGGAGAGGG
12283395 AAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGAAGAA-G-AAGAAAAGGAAAGGAGAAGAGAAAA
* *
12283439 AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAA
1 AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAA
*
12283482 GAAAGAAAGAAAGAAGGA-AAGAAAAGGAAAGGAGAAGAG-AAA
1 -AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAA
12283524 AAAG-AAG-AAGAAGAAGA
1 AAAGAAAGAAAGAAGAAGA
12283541 GGGAAGGAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
39 7 0.08
40 4 0.04
41 4 0.04
42 3 0.03
43 42 0.45
44 28 0.30
45 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (43 bp):
AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAGGAGAAGAGAAAA
Found at i:12283523 original size:34 final size:33
Alignment explanation
Indices: 12283481--12283563 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
12283471 AGAAGAAAAA
*
12283481 AGAAAGAAAGAAAGAAGGA-AAGAAAAGGAAAGG
1 AGAAAGAAA-AAAGAAGAAGAAGAAAAGGAAAGG
* *
12283514 AGAAGAGAAAAAAGAAGAAGAAGAAGAGGGAAGG
1 AGAA-AGAAAAAAGAAGAAGAAGAAAAGGAAAGG
12283548 AAGGAAA-AAAAAAGAA
1 -A-GAAAGAAAAAAGAA
12283564 AAAAAAGGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 12 0.28
34 26 0.60
35 2 0.05
36 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (33 bp):
AGAAAGAAAAAAGAAGAAGAAGAAAAGGAAAGG
Found at i:12283532 original size:48 final size:48
Alignment explanation
Indices: 12283394--12283532 Score: 142
Period size: 48 Copynumber: 2.9 Consensus size: 48
12283384 GAAGGAGAGG
* * * *
12283394 GAAAGAAAGAAAAAGAAGGAAA-GAAAAG-GAAAGGAGAAGAGAAAAAAA
1 GAAAGAAAGAAGAAGAAGAAAAGGAAAAGAG-AA-GAAAAAAGAAAAAAA
*
12283442 GAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAGAAA
1 GAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAAAAA
* * *
12283490 GAAAGAAGGAAAGAA-AAGGAAAGGAGAAGAGAA-AAAAGAAGAA
1 GAAAGAAAG-AAGAAGAAGAAAAGGAAAAGAGAAGAAAA-AAGAA
12283533 GAAGAAGAGG
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.05
48 61 0.77
49 13 0.16
50 1 0.01
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (48 bp):
GAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAAAAA
Found at i:12283538 original size:86 final size:84
Alignment explanation
Indices: 12283395--12283567 Score: 244
Period size: 86 Copynumber: 2.0 Consensus size: 84
12283385 AAGGAGAGGG
12283395 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGA-AGAA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAGAGAA
* *
12283459 GAAAAGGAAAAGAGAAGAAA
66 G-AAAGGAAAAAAAAAGAAA
12283479 AAAGAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG-AAAAAAG-AAGAAGAAGAAGAG
1 AAAGAAAG-AA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAG-A-AAGAAGAG
* *
12283542 GGAAGGAAGGAAAAAAAAAGAAA
62 AGAAGAAAGGAAAAAAAAAGAAA
12283565 AAA
1 AAA
12283568 AAGGTAATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
84 11 0.14
85 10 0.12
86 55 0.69
87 4 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (84 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAGAGAA
GAAAGGAAAAAAAAAGAAA
Found at i:12283552 original size:43 final size:42
Alignment explanation
Indices: 12283419--12283554 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 42
12283409 AAGGAAAGAA
*
12283419 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGA-AGAA-
1 AAGGAAAGGAGAAGAG-AAAAAAG-AAG-AAGAAGAAGAGGGAAG
* **
12283462 AAGGAAAAGAG-A-AGAAAAAAGAAAGAAAGAAAGAAGGAAAGAA-
1 AAGGAAAGGAGAAGAGAAAAAAG-AAG-AAG-AAGAA-GAGGGAAG
12283505 AAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAGAAGAGGGAAGG
1 AAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAGAAGAGGGAA-G
12283548 AAGGAAA
1 AAGGAAA
12283555 AAAAAAGAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
40 15 0.18
41 12 0.15
42 8 0.10
43 34 0.41
44 4 0.05
45 9 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (42 bp):
AAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAGAAGAGGGAAG
Found at i:12283878 original size:11 final size:12
Alignment explanation
Indices: 12283855--12283879 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12283845 CGAAAATAAT
12283855 AAAATGCGAAAA
1 AAAATGCGAAAA
12283867 AAAATGCGAAAA
1 AAAATGCGAAAA
12283879 A
1 A
12283880 TGTACATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAATGCGAAAA
Found at i:12284302 original size:27 final size:27
Alignment explanation
Indices: 12284272--12284327 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
12284262 AAAGAGGGTG
* *
12284272 ATGGAGGGGAATAAAAAAGCGGCATCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
*
12284299 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
12284326 AT
1 AT
12284328 ATGTGGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.32, T:0.11
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAAGCGGCACCA
Found at i:12285318 original size:14 final size:14
Alignment explanation
Indices: 12285299--12285329 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12285289 TGACGGGAGT
12285299 ATCTTCATTCACCG
1 ATCTTCATTCACCG
12285313 ATCTTCATTCACCG
1 ATCTTCATTCACCG
12285327 ATC
1 ATC
12285330 CGGCTGTAGT
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:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (14 bp):
ATCTTCATTCACCG
Found at i:12290098 original size:17 final size:18
Alignment explanation
Indices: 12290060--12290098 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
12290050 TTACTAAGTT
*
12290060 ACATCTTAATACACTAATA
1 ACATCTTAATA-ACTAACA
12290079 ACATCTTAAT-ACTAACA
1 ACATCTTAATAACTAACA
12290096 ACA
1 ACA
12290099 ACAACAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (18 bp):
ACATCTTAATAACTAACA
Found at i:12290206 original size:19 final size:21
Alignment explanation
Indices: 12290182--12290220 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12290172 CTAAAACAAA
*
12290182 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
12290201 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
12290221 ATCAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:12290427 original size:27 final size:26
Alignment explanation
Indices: 12290357--12290432 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
12290347 AATACGAATA
* *
12290357 GTGCCGCCAATCAATATGGCACCATTG
1 GTGCCGCCAATCCAT-TGGCATCATTG
* *
12290384 GTGCCGCCAATGGCATTAGCATCATTG
1 GTGCCGCCAAT-CCATTGGCATCATTG
12290411 GTGCCGCCAATCCCATTGGCAT
1 GTGCCGCCAAT-CCATTGGCAT
12290433 GACCAAGGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 39 0.95
28 2 0.05
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCCGCCAATCCATTGGCATCATTG
Found at i:12290512 original size:27 final size:28
Alignment explanation
Indices: 12290482--12290549 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
12290472 GTTTTTTTTT
12290482 TATATATTTTGGTAAATAAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
12290509 TATATATTTTGGTAAATAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAGTTA
12290537 TA-ATATTTTGGTA
1 TATATATTTTGGTA
12290550 TATTTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAGTTA
Found at i:12294817 original size:18 final size:19
Alignment explanation
Indices: 12294777--12294817 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
12294767 TGAATTAAAT
12294777 TATT-ACCAGATGAGATTA
1 TATTCACCAGATGAGATTA
*
12294795 -GTTCACCA-ATGAGATTA
1 TATTCACCAGATGAGATTA
12294812 TATTCA
1 TATTCA
12294818 ATGATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (19 bp):
TATTCACCAGATGAGATTA
Found at i:12299512 original size:37 final size:37
Alignment explanation
Indices: 12299466--12299587 Score: 106
Period size: 37 Copynumber: 3.3 Consensus size: 37
12299456 GTTTAGGTCG
*
12299466 GACGAGTAACCTGATGCCGTTTTATAGGTTTAGCCTA
1 GACGGGTAACCTGATGCCGTTTTATAGGTTTAGCCTA
* * * *** * *
12299503 TACGGGTAACCT--TACATGTGACATAGGTTTAG-GTCG
1 GACGGGTAACCTGATGC-CGTTTTATAGGTTTAGCCT-A
* *
12299539 GACGAGTAACCTGATGTCGTTTTATAGGTTTAGCCTA
1 GACGGGTAACCTGATGCCGTTTTATAGGTTTAGCCTA
12299576 GACGGGTAACCT
1 GACGGGTAACCT
12299588 TACATGTATA
Statistics
Matches: 60, Mismatches: 20, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
35 3 0.05
36 22 0.37
37 33 0.55
38 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (37 bp):
GACGGGTAACCTGATGCCGTTTTATAGGTTTAGCCTA
Found at i:12299548 original size:36 final size:37
Alignment explanation
Indices: 12299441--12299550 Score: 100
Period size: 36 Copynumber: 3.0 Consensus size: 37
12299431 TGGACTCAAC
12299441 ATACATGTGACATAGGTTTAGGTCGGACGAGTAACCT
1 ATACATGTGACATAGGTTTAGGTCGGACGAGTAACCT
* * *** * ** *
12299478 GATGC-CGTTTTATAGGTTTA-GCCTATACGGGTAACCT
1 -ATACATGTGACATAGGTTTAGGTC-GGACGAGTAACCT
12299515 -TACATGTGACATAGGTTTAGGTCGGACGAGTAACCT
1 ATACATGTGACATAGGTTTAGGTCGGACGAGTAACCT
12299551 GATGTCGTTT
Statistics
Matches: 51, Mismatches: 18, Indels: 8
0.66 0.23 0.10
Matches are distributed among these distances:
35 2 0.04
36 23 0.45
37 23 0.45
38 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (37 bp):
ATACATGTGACATAGGTTTAGGTCGGACGAGTAACCT
Found at i:12299561 original size:73 final size:73
Alignment explanation
Indices: 12299442--12299594 Score: 288
Period size: 73 Copynumber: 2.1 Consensus size: 73
12299432 GGACTCAACA
*
12299442 TACATGTGACATAGGTTTAGGTCGGACGAGTAACCTGATGCCGTTTTATAGGTTTAGCCTATACG
1 TACATGTGACATAGGTTTAGGTCGGACGAGTAACCTGATGCCGTTTTATAGGTTTAGCCTAGACG
12299507 GGTAACCT
66 GGTAACCT
*
12299515 TACATGTGACATAGGTTTAGGTCGGACGAGTAACCTGATGTCGTTTTATAGGTTTAGCCTAGACG
1 TACATGTGACATAGGTTTAGGTCGGACGAGTAACCTGATGCCGTTTTATAGGTTTAGCCTAGACG
12299580 GGTAACCT
66 GGTAACCT
12299588 TACATGT
1 TACATGT
12299595 ATATACAACT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (73 bp):
TACATGTGACATAGGTTTAGGTCGGACGAGTAACCTGATGCCGTTTTATAGGTTTAGCCTAGACG
GGTAACCT
Found at i:12306057 original size:42 final size:42
Alignment explanation
Indices: 12306010--12306099 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
12306000 AAGGCTGAAC
*
12306010 AGAAGCACATAACTGCTAAATAGAAACCCATAAGGGTTAAAA
1 AGAAGCACATAACAGCTAAATAGAAACCCATAAGGGTTAAAA
* * * * *
12306052 AGAAGCTCGTAAGAGCTGAATAGAAACCCATAAGGGTTAAAC
1 AGAAGCACATAACAGCTAAATAGAAACCCATAAGGGTTAAAA
12306094 AGAAGC
1 AGAAGC
12306100 TCAAAAGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (42 bp):
AGAAGCACATAACAGCTAAATAGAAACCCATAAGGGTTAAAA
Found at i:12306100 original size:42 final size:42
Alignment explanation
Indices: 12306028--12306144 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
12306018 ATAACTGCTA
* **
12306028 AATAGAAACCCATAAGGGTTAAAAAGAAGCTCGTAAGAGCTG
1 AATAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
*
12306070 AATAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGTTG
1 AATAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
** * * * *
12306112 AACGGAAACTCATTAGGGTTGAACAGAAACTCA
1 AATAGAAACCCATAAGGGTTAAACAGAAGCTCA
12306145 TATGAGTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.17
Consensus pattern (42 bp):
AATAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
Found at i:12306157 original size:21 final size:21
Alignment explanation
Indices: 12306026--12306182 Score: 107
Period size: 21 Copynumber: 7.5 Consensus size: 21
12306016 ACATAACTGC
* * *
12306026 TAAATAGAAACCCATAAGGGT
1 TAAACAGAAACTCATAAGAGT
* * * *
12306047 TAAAAAGAAGCTCGTAAGAGC
1 TAAACAGAAACTCATAAGAGT
* * * *
12306068 TGAATAGAAACCCATAAGGGT
1 TAAACAGAAACTCATAAGAGT
* *
12306089 TAAACAGAAGCTCAAAAGAGT
1 TAAACAGAAACTCATAAGAGT
* * * *
12306110 TGAACGGAAACTCATTAGGGT
1 TAAACAGAAACTCATAAGAGT
* *
12306131 TGAACAGAAACTCATATGAGT
1 TAAACAGAAACTCATAAGAGT
* * *
12306152 TAAACAGAAGCTCGTAAGAGC
1 TAAACAGAAACTCATAAGAGT
*
12306173 TAAACGGAAA
1 TAAACAGAAA
12306183 GTAAACACGA
Statistics
Matches: 100, Mismatches: 36, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 100 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (21 bp):
TAAACAGAAACTCATAAGAGT
Found at i:12307803 original size:57 final size:58
Alignment explanation
Indices: 12307714--12307835 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 58
12307704 ACAGAAATGG
* * *
12307714 TGAAAATGGAGAAATAAGAAACATTTTGAAATGATTATGGTTTTCTCTAAAATGAAAA
1 TGAAAATGGAGAAATAAGAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAA
* * *
12307772 TGAACATGGAGAAAT-AGAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATAAGAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAA
12307829 TGAAAAT
1 TGAAAAT
12307836 AACCTGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 43 0.75
58 14 0.25
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.30
Consensus pattern (58 bp):
TGAAAATGGAGAAATAAGAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAA
Found at i:12311404 original size:19 final size:19
Alignment explanation
Indices: 12311380--12311490 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
12311370 AATCTTCAGG
12311380 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12311399 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
12311418 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12311437 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
12311456 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12311475 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12311491 AGATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12311430 original size:38 final size:38
Alignment explanation
Indices: 12311387--12311490 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
12311377 AGGGATATGC
12311387 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
12311425 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
12311463 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
12311491 AGATATGATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:12311516 original size:22 final size:21
Alignment explanation
Indices: 12311380--12311516 Score: 114
Period size: 19 Copynumber: 6.9 Consensus size: 21
12311370 AATCTTCAGG
*
12311380 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12311399 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
12311418 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12311437 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12311456 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
12311475 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
12311497 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
12311517 TTAATTTGTA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
19 79 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:12312055 original size:30 final size:32
Alignment explanation
Indices: 12312002--12312079 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 32
12311992 TTACAGTTCA
12312002 AATTAGTCTTTTTTCATTTTCTTTATTTTT-TA-TT
1 AATTAGT-TTTTTT-A-TTTCTTT-TTTTTATATTT
12312036 AATTAGTTTTTTTA-TTCTTTTTTTTATATTT
1 AATTAGTTTTTTTATTTCTTTTTTTTATATTT
*
12312067 AGTTA-TTTTTTTA
1 AATTAGTTTTTTTA
12312080 AGAAAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
29 5 0.12
30 16 0.39
31 6 0.15
32 1 0.02
33 6 0.15
34 7 0.17
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (32 bp):
AATTAGTTTTTTTATTTCTTTTTTTTATATTT
Found at i:12312168 original size:21 final size:22
Alignment explanation
Indices: 12312135--12312192 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
12312125 TAGTATAATA
* *
12312135 TAATTATTTTTTTATTTATCTG
1 TAATTATTTTTTTATCTATATG
12312157 TAATTA-TTTTTTATCTATATG
1 TAATTATTTTTTTATCTATATG
12312178 T-ATATATTTATTTTA
1 TAAT-TATTT-TTTTA
12312193 GTATACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 16 0.52
22 8 0.26
23 5 0.16
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (22 bp):
TAATTATTTTTTTATCTATATG
Found at i:12315896 original size:28 final size:30
Alignment explanation
Indices: 12315865--12315928 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
12315855 ATAAAAAATG
*
12315865 AAAAATGTTAAATATAAAATATT-GTT-AA
1 AAAAATATTAAATATAAAATATTAGTTGAA
* *
12315893 AAAATTATTAAATATAAATTATTAGTTGAA
1 AAAAATATTAAATATAAAATATTAGTTGAA
12315923 AAAAAT
1 AAAAAT
12315929 TATAACCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 20 0.67
29 3 0.10
30 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (30 bp):
AAAAATATTAAATATAAAATATTAGTTGAA
Found at i:12323250 original size:24 final size:22
Alignment explanation
Indices: 12323204--12323252 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
12323194 TTATATTTGT
*
12323204 AAAAATTTAAAAATAAATTTTA
1 AAAAATTTAAAAATAAATATTA
*
12323226 AAAAAGTTCTAAAAATATATATTA
1 AAAAA-TT-TAAAAATAAATATTA
12323250 AAA
1 AAA
12323253 TTGAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 2 0.09
24 16 0.70
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATTTAAAAATAAATATTA
Found at i:12324361 original size:20 final size:20
Alignment explanation
Indices: 12324316--12324363 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
12324306 TTTTTTTCTT
** *
12324316 TTGAAAAATGATTTAGGTAA
1 TTGAAAAAACATTTAGATAA
*
12324336 TT-AAAAAACATTTAGATCA
1 TTGAAAAAACATTTAGATAA
12324355 TTGAAAAAA
1 TTGAAAAAA
12324364 AAAATTGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTGAAAAAACATTTAGATAA
Found at i:12329643 original size:12 final size:12
Alignment explanation
Indices: 12329624--12329657 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12329614 TGTTATATTG
12329624 CATTATTATTAT
1 CATTATTATTAT
**
12329636 TGTTATTATTAT
1 CATTATTATTAT
12329648 CATTATTATT
1 CATTATTATT
12329658 TCTATACATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (12 bp):
CATTATTATTAT
Found at i:12329711 original size:25 final size:23
Alignment explanation
Indices: 12329677--12329733 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
12329667 ATACACACGT
*
12329677 ATATTTTTTTATAACATATATATGC
1 ATATATTTTTATAA-A-ATATATGC
*
12329702 ATATA-TTTT-TAAAATATATGT
1 ATATATTTTTATAAAATATATGC
12329723 ATATATTTTTA
1 ATATATTTTTA
12329734 GACTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 12 0.43
22 5 0.18
23 3 0.11
24 4 0.14
25 4 0.14
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
ATATATTTTTATAAAATATATGC
Found at i:12329719 original size:21 final size:21
Alignment explanation
Indices: 12329694--12329733 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12329684 TTTATAACAT
12329694 ATATATGCATATATTTTTAAA
1 ATATATGCATATATTTTTAAA
*
12329715 ATATATGTATATATTTTTA
1 ATATATGCATATATTTTTA
12329734 GACTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
ATATATGCATATATTTTTAAA
Found at i:12329768 original size:18 final size:18
Alignment explanation
Indices: 12329745--12329783 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12329735 ACTTTTATAA
*
12329745 ATACATGTATATATTTTT
1 ATACATATATATATTTTT
12329763 ATACATATATATATTTTT
1 ATACATATATATATTTTT
12329781 ATA
1 ATA
12329784 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATACATATATATATTTTT
Found at i:12330818 original size:4 final size:4
Alignment explanation
Indices: 12330790--12330833 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
12330780 AATGGTATAG
* * *
12330790 AAAT AATAT AAAC AAAC AAAC AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
12330834 ATCAATGACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:12331199 original size:35 final size:36
Alignment explanation
Indices: 12331121--12331199 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 36
12331111 AAAAATATTT
* * *
12331121 ATTAAAAAATATATAAATATATTTACATGTACATAT
1 ATTAAAAAATATATAAATATATATACATATACATAG
* * *
12331157 A-TAAAAAAAATATATATATATATACATATATATAG
1 ATTAAAAAATATATAAATATATATACATATACATAG
12331192 ATTAAAAA
1 ATTAAAAA
12331200 TTACATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 29 0.81
36 7 0.19
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (36 bp):
ATTAAAAAATATATAAATATATATACATATACATAG
Found at i:12341982 original size:45 final size:46
Alignment explanation
Indices: 12341931--12342037 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 46
12341921 AACGGTAACA
* *
12341931 GTAACAGTAAAAGTAACAGTA-TTCAACACACAAAGTGCTGAATCT-
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAAT-TG
* *
12341976 GTAACAGTAACGGTAACAGTATTTCGACACACAAAGTGCCGAATTG
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
*
12342022 GTAAAAGTAACAGTAA
1 GTAACAGTAACAGTAA
12342038 TCGGCACATA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 20 0.37
46 34 0.63
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (46 bp):
GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
Found at i:12343170 original size:14 final size:14
Alignment explanation
Indices: 12343151--12343183 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
12343141 TAATTATTAT
12343151 ATATTTTATTCTAA
1 ATATTTTATTCTAA
12343165 ATA-TTTATTCTAA
1 ATATTTTATTCTAA
12343178 ATATTT
1 ATATTT
12343184 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTTATTCTAA
Found at i:12343173 original size:13 final size:13
Alignment explanation
Indices: 12343155--12343186 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
12343145 TATTATATAT
12343155 TTTATTCTAAATA
1 TTTATTCTAAATA
12343168 TTTATTCTAAATA
1 TTTATTCTAAATA
12343181 TTTATT
1 TTTATT
12343187 TTAATAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATTCTAAATA
Found at i:12343271 original size:4 final size:4
Alignment explanation
Indices: 12343257--12343289 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
12343247 AAAAATCTCA
12343257 TAAT ATAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT -TAAT TAAT TAAT TAAT TAAT TAAT TAAT
12343290 ATCTTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:12345460 original size:45 final size:45
Alignment explanation
Indices: 12345337--12345698 Score: 334
Period size: 45 Copynumber: 8.0 Consensus size: 45
12345327 AACAGATCGG
* * *
12345337 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGTAGTAGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
* * * ** ** *
12345382 TGAAGATATGCAAGTCTTATCTCTCTGAAGTTGCAACGGAGCAGAC
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
12345428 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
* * * * ** *
12345473 TGAAGATATGCAAGTCTTATCTCCCTGAAGTTACAGCGGAGCAGAC
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
* *
12345519 TGAAGATAGCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
* ** * *
12345564 TGAAGATAGCAAGTTTTATCCCCCTGAAGTTGCAGTGG-GATAGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAG-TGGAT
* ** ** **
12345609 TGAAGATGGTGAA-CCTTATCTCCCTGGGGTTGCAGTGGAGCAGAT
1 TGAAGATAGCAAATCC-TATCTCCCTGAAGTTGCAGTGGAGTGGAT
* * * * *
12345654 TGAAGTTAG-TAATCCTATCTCCCTAAATTTACAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
12345698 T
1 T
12345699 AAAACATCCA
Statistics
Matches: 249, Mismatches: 62, Indels: 13
0.77 0.19 0.04
Matches are distributed among these distances:
44 26 0.10
45 150 0.60
46 73 0.29
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
Found at i:12345492 original size:91 final size:91
Alignment explanation
Indices: 12345337--12345597 Score: 425
Period size: 91 Copynumber: 2.9 Consensus size: 91
12345327 AACAGATCGG
* * *
12345337 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGTAGTAGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
*
12345402 CTCTCTGAAGTTGCAACGGAGCAGAC
66 CTCCCTGAAGTTGCAACGGAGCAGAC
12345428 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
* *
12345493 CTCCCTGAAGTTACAGCGGAGCAGAC
66 CTCCCTGAAGTTGCAACGGAGCAGAC
* * *
12345519 TGAAGATAGCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGATTGAAGATA-GCAAGTTTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
*
12345583 CCCCCTGAAGTTGCA
66 CTCCCTGAAGTTGCA
12345598 GTGGGATAGA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 23 0.14
91 136 0.86
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (91 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
CTCCCTGAAGTTGCAACGGAGCAGAC
Found at i:12345589 original size:136 final size:135
Alignment explanation
Indices: 12345382--12345698 Score: 336
Period size: 136 Copynumber: 2.3 Consensus size: 135
12345372 TAGAGTGGAT
* * * ** ** *
12345382 TGAAGATATGCAAGTCTTATCTCTCTGAAGTTGCAACGGAGCAGACTGAAGATAGCAAATCCTAT
1 TGAAGATA-GCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGATTGAAGATAGCAAATCCTAT
* * *
12345447 CTCCCTGAAGTTGCAGT-GGAGTGGATTGAAGAT-ATGCAAGTCTTATCTCCCTGAAGTTACAGC
65 CCCCCTGAAGTTGCAGTGGGA-TAGATTGAAGATGATG-AA-CCTTATCTCCCTGAAGTTACAGC
12345510 GGAGCAGAC
127 GGAGCAGAC
* **
12345519 TGAAGATAGCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGATTGAAGATAGCAAGTTTTATC
1 TGAAGATAGCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGATTGAAGATAGCAAATCCTATC
* ** * *
12345584 CCCCTGAAGTTGCAGTGGGATAGATTGAAGATGGTGAACCTTATCTCCCTGGGGTTGCAGTGGAG
66 CCCCTGAAGTTGCAGTGGGATAGATTGAAGATGATGAACCTTATCTCCCTGAAGTTACAGCGGAG
*
12345649 CAGAT
131 CAGAC
* * * * *
12345654 TGAAGTTAG-TAATCCTATCTCCCTAAAT-TTACAGTGGAGTGGATT
1 TGAAGATAGCAAATCCTATCTCTCT-GATGTTGCAGTGGAGTGGATT
12345699 AAAACATCCA
Statistics
Matches: 152, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
134 29 0.19
135 36 0.24
136 74 0.49
137 13 0.09
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (135 bp):
TGAAGATAGCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGATTGAAGATAGCAAATCCTATC
CCCCTGAAGTTGCAGTGGGATAGATTGAAGATGATGAACCTTATCTCCCTGAAGTTACAGCGGAG
CAGAC
Found at i:12345717 original size:134 final size:136
Alignment explanation
Indices: 12345435--12345732 Score: 311
Period size: 134 Copynumber: 2.2 Consensus size: 136
12345425 GACTGAAGAT
* * * *
12345435 AGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTATCTCCCTG
1 AGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATATGCAAGCCTTATCTCCCTG
* * *
12345500 AAGTTACAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCTCTGATGTTGCAGTGGAGTGGATT
66 AAGTTACAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTAATGTTACAGTGGAGTGGATT
* *
12345565 GAAGAT
131 GAAAAC
* * *
12345571 AGCAAGTTTTATCCCCCTGAAGTTGCAGTGG-GATAGATTGAAGATGGTG-AA-CCTTATCTCCC
1 AGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAG-TAGATTGAAGAT-ATGCAAGCCTTATCTCCC
** * * * * *
12345633 TGGGGTTGCAGTGGAGCAGATTGAAGTTAG-TAATCCTATCTCCCTAAAT-TTACAGTGGAGTGG
64 TGAAGTTACAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCCCT-AATGTTACAGTGGAGTGG
12345696 ATT-AAAAC
128 ATTGAAAAC
* * **
12345704 ATCCAGATCTTATCTTTCTGAAGTTGCAG
1 AGCAAG-TCTTATCTCCCTGAAGTTGCAG
12345733 AAAGCAGATC
Statistics
Matches: 133, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
133 7 0.05
134 47 0.35
135 37 0.28
136 40 0.30
137 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (136 bp):
AGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATATGCAAGCCTTATCTCCCTG
AAGTTACAGCGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTAATGTTACAGTGGAGTGGATT
GAAAAC
Found at i:12345769 original size:40 final size:40
Alignment explanation
Indices: 12345711--12345941 Score: 176
Period size: 40 Copynumber: 5.5 Consensus size: 40
12345701 AACATCCAGA
* *
12345711 TCTTATCTTTCTGAAGTTGCAGAAAGCAGATCGCATCTAG
1 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * ** ** *
12345751 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAG
1 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCTAG
*
12345795 ATCTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * ** *
12345836 TCTTATCTCTCTGAAGTTGCAGTTGA-CTGGATTAAAACATCCAG
1 TCTTATCTCTCTGAAGTTGCAG-AGAGC-AGA-T--CGCATCTAG
* * *
12345880 ATCTTATCTTTCTGAAGTTGTAGAGAGTAGATCGCATCTAG
1 -TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
*
12345921 TCTTATCTCTCTAAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCA
12345942 ATGGAGTAGA
Statistics
Matches: 143, Mismatches: 36, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
40 59 0.41
41 20 0.14
42 2 0.01
43 2 0.01
44 21 0.15
45 39 0.27
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (40 bp):
TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:12345777 original size:85 final size:85
Alignment explanation
Indices: 12345666--12345948 Score: 440
Period size: 85 Copynumber: 3.3 Consensus size: 85
12345656 AAGTTAGTAA
* *
12345666 TCCTATCTCCCTAAATTTACAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGC
1 TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGC
*
12345731 AGAAAGCAGATCGCATCTAG
66 AGAGAGCAGATCGCATCTAG
*
12345751 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGC
1 TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGC
12345816 AGAGAGCAGATCGCATCTAG
66 AGAGAGCAGATCGCATCTAG
* * * * * *
12345836 TCTTATCTCTCTGAAGTTGCAGTTGACTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGT
1 TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGC
*
12345901 AGAGAGTAGATCGCATCTAG
66 AGAGAGCAGATCGCATCTAG
* * *
12345921 TCTTATCTCTCTAAAGTTGCAATGGAGT
1 TCCTATCTCCCTAAAGTTGCAGTGGAGT
12345949 AGACTGAATG
Statistics
Matches: 184, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 184 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (85 bp):
TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGAAGTTGC
AGAGAGCAGATCGCATCTAG
Found at i:12347421 original size:15 final size:16
Alignment explanation
Indices: 12347401--12347432 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12347391 TTATATTGCA
12347401 TTATTATTG-TATTAT
1 TTATTATTGTTATTAT
12347416 TTATTATTGTTATTAT
1 TTATTATTGTTATTAT
12347432 T
1 T
12347433 ATCATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTATTATTGTTATTAT
Found at i:12347434 original size:15 final size:15
Alignment explanation
Indices: 12347400--12347444 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
12347390 GTTATATTGC
12347400 ATTATTATTG-TATT
1 ATTATTATTGTTATT
12347414 ATTTATTATTGTTATT
1 A-TTATTATTGTTATT
* *
12347430 ATTATCATTATTATT
1 ATTATTATTGTTATT
12347445 TCTATACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 21 0.78
16 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (15 bp):
ATTATTATTGTTATT
Found at i:12347505 original size:20 final size:21
Alignment explanation
Indices: 12347482--12347520 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12347472 TTTATAACAT
12347482 ATATATGCATAT-TTTTTAAA
1 ATATATGCATATATTTTTAAA
*
12347502 ATATATGTATATATTTTTA
1 ATATATGCATATATTTTTA
12347521 GACTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (21 bp):
ATATATGCATATATTTTTAAA
Found at i:12347515 original size:22 final size:24
Alignment explanation
Indices: 12347462--12347519 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
12347452 ATATACACAC
12347462 GTATATATTTTTTATAACATATAT
1 GTATATATTTTTTATAACATATAT
* **
12347486 ATGCATATTTTTTA-AA-ATATAT
1 GTATATATTTTTTATAACATATAT
12347508 GTATATATTTTT
1 GTATATATTTTT
12347520 AGACTTTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 15 0.54
23 2 0.07
24 11 0.39
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (24 bp):
GTATATATTTTTTATAACATATAT
Found at i:12347548 original size:21 final size:18
Alignment explanation
Indices: 12347532--12347569 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
12347522 ACTTTTATAA
12347532 ATACATGTATATA-TTTT
1 ATACATGTATATATTTTT
12347549 ATACATGTATATATTTTT
1 ATACATGTATATATTTTT
12347567 ATA
1 ATA
12347570 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (18 bp):
ATACATGTATATATTTTT
Found at i:12348605 original size:30 final size:30
Alignment explanation
Indices: 12348544--12348605 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
12348534 TTACGGTCGG
* * * *
12348544 TAAAATTTTAATTTAATACTTTATAATTTA
1 TAAAATTTTAAATTAATAATGTATAAATTA
12348574 TAAAATTTTAAATTAATAATGGTA-AAATTA
1 TAAAATTTTAAATTAATAAT-GTATAAATTA
12348604 TA
1 TA
12348606 TTTTGACCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAATTTTAAATTAATAATGTATAAATTA
Found at i:12349911 original size:101 final size:102
Alignment explanation
Indices: 12349772--12349956 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
12349762 AAAATGATGG
* *
12349772 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTATCGG-ATGATAATGGTCACATGTGTAGT
12349835 ACTATGTGCAGGCTACTATGCGTACCAAATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCAAATAGTTTCGA
* * *
12349873 TCACGTGTGTAGTACTATGTGCAGTCTACCACGTGTATCGGATGGTAATGGTCATATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTATCGGATGATAATGGTCACATGTGTAGTA
12349938 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
12349957 TGAACCGAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.52
102 33 0.43
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTATCGGATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCAAATAGTTTCGA
Found at i:12349933 original size:51 final size:50
Alignment explanation
Indices: 12349768--12349954 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
12349758 AGAGAAAATG
* *
12349768 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGT
* * * * ** *
12349819 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAAATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
* * * * *
12349868 TTCGATCACGTGTGTAGTACTATGTGCAGTCTACCACGTGTATCGGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
*
12349919 AATGGTCATATGTGTAGTACTATGTGCAGGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
12349955 TGTGAACCGA
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
49 3 0.03
50 36 0.34
51 66 0.62
52 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGT
Found at i:12352307 original size:30 final size:30
Alignment explanation
Indices: 12352273--12352334 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
12352263 ACTTATTTTA
12352273 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
12352303 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
12352333 TT
1 TT
12352335 ACTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:12354945 original size:22 final size:25
Alignment explanation
Indices: 12354895--12354948 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 25
12354885 ATTAATATTT
12354895 TAAAATTCAAAATATATAAACTTTTAA
1 TAAAATTCAAAATATATAAA--TTTAA
12354922 TAAAATT-AAAATATAT-AA-TTAA
1 TAAAATTCAAAATATATAAATTTAA
12354944 TAAAA
1 TAAAA
12354949 ATATATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 9 0.33
25 2 0.07
26 9 0.33
27 7 0.26
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAATTCAAAATATATAAATTTAA
Found at i:12363202 original size:10 final size:10
Alignment explanation
Indices: 12363187--12363221 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
12363177 TTCGATTCGA
12363187 TTAAAAAAAT
1 TTAAAAAAAT
12363197 TTAAAAAAAT
1 TTAAAAAAAT
12363207 TTAAAAAAAT
1 TTAAAAAAAT
12363217 TTAAA
1 TTAAA
12363222 TTTTGAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:12363325 original size:9 final size:9
Alignment explanation
Indices: 12363313--12363343 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12363303 TTAAATTTTT
12363313 ATAATTCGA
1 ATAATTCGA
*
12363322 ATAACTCGA
1 ATAATTCGA
12363331 ATAATTCGA
1 ATAATTCGA
12363340 ATAA
1 ATAA
12363344 CAGATTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (9 bp):
ATAATTCGA
Found at i:12363477 original size:19 final size:19
Alignment explanation
Indices: 12363426--12363496 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
12363416 AATTACAAAA
* * *
12363426 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTT
*
12363445 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
12363465 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
12363483 AGAAATTCTAAAAT
1 A-AAATTC-AAAAT
12363497 TTATATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.14
19 17 0.40
20 20 0.47
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:12363498 original size:18 final size:19
Alignment explanation
Indices: 12363453--12363501 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
12363443 TCAAAATTTG
*
12363453 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
12363472 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
*
12363491 TAAA-ATTTATA
1 AAAATATTTATA
12363502 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:12363528 original size:18 final size:17
Alignment explanation
Indices: 12363492--12363537 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
12363482 TAGAAATTCT
*
12363492 AAAATTTATATTTTAAA
1 AAAATTTAAATTTTAAA
12363509 AAAATTATAAATTTTTAAA
1 AAAATT-TAAA-TTTTAAA
*
12363528 AAAATCTAAA
1 AAAATTTAAA
12363538 AAATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTTAAATTTTAAA
Found at i:12363541 original size:21 final size:19
Alignment explanation
Indices: 12363502--12363556 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
12363492 AAAATTTATA
*
12363502 TTTTAAAAAAATTATAAAT
1 TTTTAAAAAAATTAAAAAT
12363521 TTTTAAAAAAATCTAAAAAAT
1 TTTTAAAAAAAT-T-AAAAAT
*
12363542 TTATAAAAAAATTAA
1 TTTTAAAAAAATTAA
12363557 TACAATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.44
20 2 0.06
21 16 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTTAAAAAAATTAAAAAT
Found at i:12363898 original size:21 final size:22
Alignment explanation
Indices: 12363862--12363902 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12363852 ACATTTTCTA
*
12363862 AAGTTAAAAAGTCAAAACTATC
1 AAGTTAAAAAGGCAAAACTATC
12363884 AAGTT-AAAAGGCAAAACTA
1 AAGTTAAAAAGGCAAAACTA
12363903 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (22 bp):
AAGTTAAAAAGGCAAAACTATC
Found at i:12367065 original size:18 final size:19
Alignment explanation
Indices: 12367027--12367069 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
12367017 TCTAAATGAA
12367027 TTCATTTCTCATTTTTATT
1 TTCATTTCTCATTTTTATT
12367046 TTCATTTCT-ATTTTCT-TT
1 TTCATTTCTCATTTT-TATT
12367064 TTCATT
1 TTCATT
12367070 CTGAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCATTTCTCATTTTTATT
Found at i:12378401 original size:26 final size:26
Alignment explanation
Indices: 12378351--12378403 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
12378341 TAATATTTAA
*
12378351 AATTTTAAAATATATTATGTATAATT
1 AATTTTAAAATATATTATATATAATT
12378377 AATTTTACAAATA-ATT-TATACTAATT
1 AATTTTA-AAATATATTATATA-TAATT
12378403 A
1 A
12378404 CTCAAGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 16 0.67
27 5 0.21
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
AATTTTAAAATATATTATATATAATT
Found at i:12382787 original size:2 final size:2
Alignment explanation
Indices: 12382780--12382829 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
12382770 AATATAAAAG
12382780 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
12382822 TA TA TA TA
1 TA TA TA TA
12382830 AAAGTTAGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12383012 original size:3 final size:3
Alignment explanation
Indices: 12383004--12383054 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
12382994 GAATATAGAG
* * * *
12383004 ATA ATA ATA GTA ATA ATG ATA ATA TATA AT- ATA ATA ATA GTG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
12383049 ATA ATA
1 ATA ATA
12383055 GTAAAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12383021 original size:27 final size:28
Alignment explanation
Indices: 12382991--12383054 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 28
12382981 TATGCATGTG
*
12382991 AATGAATATA-GAGATAATAATAGTAAT
1 AATGAATATATAAGATAATAATAGTAAT
* *
12383018 AATGATAATATATAATATAATAATAGTGAT
1 AATG--AATATATAAGATAATAATAGTAAT
12383048 AAT-AATA
1 AATGAATA
12383055 GTAAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 8 0.26
29 6 0.19
30 17 0.55
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (28 bp):
AATGAATATATAAGATAATAATAGTAAT
Found at i:12383056 original size:12 final size:12
Alignment explanation
Indices: 12383004--12383054 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
12382994 GAATATAGAG
* *
12383004 ATAATAATAGTA
1 ATAATGATAATA
12383016 ATAATGATAATA
1 ATAATGATAATA
12383028 TATAAT-ATAATA
1 -ATAATGATAATA
*
12383040 ATAGTGATAATA
1 ATAATGATAATA
12383052 ATA
1 ATA
12383055 GTAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.12
12 25 0.74
13 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATGATAATA
Found at i:12383654 original size:2 final size:2
Alignment explanation
Indices: 12383649--12383673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12383639 GGAAAAAATA
12383649 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
12383674 CCCCCCAAAA
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:12388311 original size:20 final size:20
Alignment explanation
Indices: 12388286--12388325 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12388276 ATAATCAAGG
12388286 ATGCAATCAAGAAGGTTGAT
1 ATGCAATCAAGAAGGTTGAT
*
12388306 ATGCAATCAAGGAGGTTGAT
1 ATGCAATCAAGAAGGTTGAT
12388326 TGGATTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (20 bp):
ATGCAATCAAGAAGGTTGAT
Found at i:12393675 original size:2 final size:2
Alignment explanation
Indices: 12393668--12393695 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12393658 ACATATACAA
12393668 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
12393696 GATCAATTGT
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:12394028 original size:3 final size:3
Alignment explanation
Indices: 12394017--12394069 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
12394007 TGTTTTGCTT
* *
12394017 TTA TT- TTA TTA TTA -TA TTG CTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12394062 TTA TTA TT
1 TTA TTA TT
12394070 TGGATATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12394511 original size:21 final size:20
Alignment explanation
Indices: 12394470--12394509 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12394460 AATTTTGACT
*
12394470 TCAAAATTTTTAAATAAAAA
1 TCAAAATTTTTAAAAAAAAA
12394490 TCAAAATTTTTAAAAAAAAA
1 TCAAAATTTTTAAAAAAAAA
12394510 ATTGATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAAATTTTTAAAAAAAAA
Found at i:12396472 original size:32 final size:31
Alignment explanation
Indices: 12396434--12396505 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
12396424 TATAAAAATT
12396434 AAATCAAAACATTTAAAGTATAAAATTACATA-
1 AAATCAAAA-ATTT-AAGTATAAAATTACATAC
* *
12396466 AAATC-AAAATTTATGTATAATATTACATATC
1 AAATCAAAAATTTAAGTATAAAATTACATA-C
12396497 AAATCAAAA
1 AAATCAAAA
12396506 TTCATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 15 0.43
30 4 0.11
31 8 0.23
32 8 0.23
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATCAAAAATTTAAGTATAAAATTACATAC
Found at i:12396772 original size:6 final size:6
Alignment explanation
Indices: 12396763--12396790 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12396753 AAATGGAAGG
12396763 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
12396791 TGGTTTATGT
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:12398009 original size:17 final size:17
Alignment explanation
Indices: 12397983--12398016 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12397973 TATGGTCTAT
*
12397983 ATATAGTATACTAAAAA
1 ATATAGTATAATAAAAA
*
12398000 ATATATTATAATAAAAA
1 ATATAGTATAATAAAAA
12398017 TTTAAGTCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAGTATAATAAAAA
Found at i:12399273 original size:31 final size:30
Alignment explanation
Indices: 12399238--12399297 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
12399228 GGAGGTGGGA
*
12399238 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
12399269 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
12399298 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Done.