Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 15 of 17
Found at i:2151029 original size:14 final size:14
Alignment explanation
Indices: 2151012--2151045 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2151002 AAATTTATAA
*
2151012 AAAAATATTTTTTT
1 AAAAATATTTTTTC
2151026 AAAAATATTTTTTC
1 AAAAATATTTTTTC
2151040 AAAAAT
1 AAAAAT
2151046 TTATTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAAATATTTTTTC
Found at i:2153264 original size:2 final size:2
Alignment explanation
Indices: 2153257--2153293 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2153247 ACTTCATCAT
*
2153257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2153294 GTATTGACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2153331 original size:3 final size:3
Alignment explanation
Indices: 2153323--2153350 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2153313 ACTAATAAAC
2153323 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2153351 CATCTTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2153502 original size:13 final size:13
Alignment explanation
Indices: 2153473--2153528 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
2153463 ATAATATTTT
*
2153473 TATTTTTTAATATA
1 TATTTTTT-ATAAA
2153487 TATTTTTTATAAA
1 TATTTTTTATAAA
* *
2153500 TATTTATCA-AAA
1 TATTTTTTATAAA
*
2153512 TATTTTTTATAAT
1 TATTTTTTATAAA
2153525 TATT
1 TATT
2153529 GAGAAATCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
12 10 0.29
13 17 0.49
14 8 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTTTATAAA
Found at i:2153621 original size:71 final size:70
Alignment explanation
Indices: 2153546--2153741 Score: 191
Period size: 71 Copynumber: 2.7 Consensus size: 70
2153536 CATCACTTAA
* *
2153546 TATTAATTATTAAAAAAAATTAAAAAAATAAAATTTAACTAAATTTTAAAAAATTCATGTT-AAA
1 TATTAATTATTAAATAAAA-TAAAAAAATAAAATTTAACTAAATTTTAAAAAATT-ATATTAAAA
*
2153610 ATTAATT
64 ATAAATT
* ** *
2153617 TATTAATTATTAATTTTTAATAAAATAAA-AAAATTTAACTAAATTTGAAAAAAATTATATTGAA
1 TATTAATTATTAA-ATAAAATAAAA-AAATAAAATTTAACTAAATTT-TAAAAAATTATATT-AA
2153681 AAATAAATT
62 AAATAAATT
* * * * * *
2153690 TGTTAATT-TTTAATAAAATAAAAAATTTTAAATTAAAATAAATTTTAAAAAA
1 TATTAATTATTAAATAAAATAAAAAA-ATAAAATTTAACTAAATTTTAAAAAA
2153742 GTGTGGACAT
Statistics
Matches: 101, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
70 2 0.02
71 53 0.52
72 30 0.30
73 16 0.16
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (70 bp):
TATTAATTATTAAATAAAATAAAAAAATAAAATTTAACTAAATTTTAAAAAATTATATTAAAAAT
AAATT
Found at i:2153716 original size:19 final size:20
Alignment explanation
Indices: 2153694--2153731 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2153684 TAAATTTGTT
*
2153694 AATTTTTAA-TAAAATAAAA
1 AATTTTAAATTAAAATAAAA
2153713 AATTTTAAATTAAAATAAA
1 AATTTTAAATTAAAATAAA
2153732 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTTAAATTAAAATAAAA
Found at i:2154152 original size:73 final size:73
Alignment explanation
Indices: 2154061--2154389 Score: 286
Period size: 73 Copynumber: 4.6 Consensus size: 73
2154051 TTTAATTAAG
* *
2154061 GTATTATTTATTTTTATTTATAGAAATTTAAATTTGTTTTTAGGGTATGATTATATAAGTTTAAA
1 GTATAATTTATTTTTATTTATAGAAATTTAAATTTGTTTTTA-GATATGATTATATAAGTTTAAA
2154126 -TTTTAAAA
65 TTTTTAAAA
* * * * *
2154134 GTATAATTTATTTTTATTTCTAGAAGTTCAAATTTGTTTTT---TAT--TT-TACAAATTTAAAT
1 GTATAATTTATTTTTATTTATAGAAATTTAAATTTGTTTTTAGATATGATTATATAAGTTTAAAT
*
2154193 TTTTAATAT
66 TTTTAA-AA
* * * ** *
2154202 GT-T-ATTTATTTTTATTTGTAGAAGTTTAAATTTGTATTTTAGAAATGATTATAGGAGCTTAAA
1 GTATAATTTATTTTTATTTATAGAAATTTAAATTTGT-TTTTAGATATGATTATATAAGTTTAAA
* **
2154265 GTTTTTTATG
65 -TTTTTAAAA
* * * * * *
2154275 GTATAATTTATTCTTATTTGTA-AAAGTTTTAAATTTATTTTTGGATATAATTATATAAGTTTTA
1 GTATAATTTATTTTTATTTATAGAAA--TTTAAATTTGTTTTTAGATATGATTATATAAGTTTAA
2154339 ATTTTT--AA
64 ATTTTTAAAA
* *
2154347 GTTATAATTTATTTTTATTTATAAAAATTTAAATTTATTTTTA
1 G-TATAATTTATTTTTATTTATAGAAATTTAAATTTGTTTTTA
2154390 TTTTTTTAGG
Statistics
Matches: 208, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
66 40 0.19
67 13 0.06
68 3 0.01
69 3 0.01
70 2 0.01
72 18 0.09
73 66 0.32
74 17 0.08
75 36 0.17
76 10 0.05
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (73 bp):
GTATAATTTATTTTTATTTATAGAAATTTAAATTTGTTTTTAGATATGATTATATAAGTTTAAAT
TTTTAAAA
Found at i:2154683 original size:23 final size:22
Alignment explanation
Indices: 2154608--2154683 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 22
2154598 TATAGATGTA
*
2154608 AATAAAAATTAAATTACAAT-AT
1 AATAAAAATTAAA-TAAAATAAT
*
2154630 AATCAAACATTATAATACAAA-AAT
1 AAT-AAAAATTA-AATA-AAATAAT
2154654 AAT--AAATTAAATAAAATAAT
1 AATAAAAATTAAATAAAATAAT
2154674 AAATAAAAAT
1 -AATAAAAAT
2154684 ATTCAGAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
19 3 0.07
20 7 0.16
21 8 0.19
22 3 0.07
23 13 0.30
24 9 0.21
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAAAATTAAATAAAATAAT
Found at i:2155112 original size:26 final size:26
Alignment explanation
Indices: 2155076--2155131 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
2155066 TTTTAAGAGT
2155076 TTTTTTATGTATTGATAATAAAATAA
1 TTTTTTATGTATTGATAATAAAATAA
2155102 TTTTTTATGTATTGATAATAAAATAA
1 TTTTTTATGTATTGATAATAAAATAA
2155128 TTTT
1 TTTT
2155132 AATTTCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (26 bp):
TTTTTTATGTATTGATAATAAAATAA
Found at i:2155197 original size:10 final size:11
Alignment explanation
Indices: 2155175--2155216 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
2155165 CTTAGTTTGT
*
2155175 TTTTTAATTAA
1 TTTTTAATAAA
2155186 TTTTTAA-AAA
1 TTTTTAATAAA
2155196 TTTTTAATAAA
1 TTTTTAATAAA
*
2155207 TTTTAAATAA
1 TTTTTAATAA
2155217 TATGTGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTTAATAAA
Found at i:2155828 original size:2 final size:2
Alignment explanation
Indices: 2155817--2155852 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2155807 CTTTTTCTTT
2155817 TA TA -A 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 T
2155853 TTGAGGGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2157263 original size:14 final size:15
Alignment explanation
Indices: 2157239--2157280 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2157229 ATAAATTTAT
*
2157239 AAAAAATATATATTTT
1 AAAAAATATAT-TTTC
2157255 AAAAAATAT-TTTTC
1 AAAAAATATATTTTC
*
2157269 AAAAAATTTATT
1 AAAAAATATATT
2157281 ATTATTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.48
15 3 0.13
16 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAAATATATTTTC
Found at i:2159022 original size:14 final size:15
Alignment explanation
Indices: 2158997--2159025 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2158987 AAAATATCTA
2158997 AATAACTAAAAAAAT
1 AATAACTAAAAAAAT
2159012 AATAA-TAAAAAAAT
1 AATAACTAAAAAAAT
2159026 TAAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAACTAAAAAAAT
Found at i:2159509 original size:15 final size:14
Alignment explanation
Indices: 2159481--2159515 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2159471 CCATCAATTT
*
2159481 AATTGAAAAATAAA
1 AATTTAAAAATAAA
2159495 AATTTAAAAATTAAA
1 AATTTAAAAA-TAAA
2159510 AATTTA
1 AATTTA
2159516 TTTAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AATTTAAAAATAAA
Found at i:2159819 original size:162 final size:165
Alignment explanation
Indices: 2159583--2159890 Score: 410
Period size: 164 Copynumber: 1.9 Consensus size: 165
2159573 AGTTAATTAA
* *
2159583 TTGATGTAATATGTCTTTGAATAGATAAAAATTATTTAAATCAATCAAATTTAAATGAAGTTGAT
1 TTGATGTAATATGTCTTTGAATAGATAAAAATTATTTAAATCAATCAAAATTAAATGAAATTGAT
* * * * *
2159648 GATTA-TTTTTTAATTTTTTTATAAGTAAAAAGCATATATATTTTAATTTTTTTAAAAAAAA-TC
66 GAATATTTTTTTAATTTTTTTATAAATAAAAAGCATAGATATTTTAA-TCTTTAAAAAAAAAGTC
* *
2159711 AAATTATTTCATCAATAAAAAAAATTAAAATTTTGT
130 AAACTATTCCATCAATAAAAAAAATTAAAATTTTGT
* * **
2159747 TTGATGTGATATGTCTTTGAATTGATAGAAAA-TA-TTAAATTGAT-AAAATTAAATGAAATTGA
1 TTGATGTAATATGTCTTTGAATAGATA-AAAATTATTTAAATCAATCAAAATTAAATGAAATTGA
* * *
2159809 TGAATATTTTTTTTAATTTTTTTATAAATAAAGAGCTTGGATATTTTAATCTTTAAAAAAAAAGT
65 TGAATA-TTTTTTTAATTTTTTTATAAATAAAAAGCATAGATATTTTAATCTTTAAAAAAAAAGT
2159874 CAAACTATTCCATCAAT
129 CAAACTATTCCATCAAT
2159891 GGAAAAATAA
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
162 21 0.17
163 20 0.16
164 79 0.64
165 4 0.03
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (165 bp):
TTGATGTAATATGTCTTTGAATAGATAAAAATTATTTAAATCAATCAAAATTAAATGAAATTGAT
GAATATTTTTTTAATTTTTTTATAAATAAAAAGCATAGATATTTTAATCTTTAAAAAAAAAGTCA
AACTATTCCATCAATAAAAAAAATTAAAATTTTGT
Found at i:2160079 original size:7 final size:7
Alignment explanation
Indices: 2160067--2160091 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2160057 ATATATATTT
2160067 TTATTAA
1 TTATTAA
2160074 TTATTAA
1 TTATTAA
2160081 TTATTAA
1 TTATTAA
2160088 TTAT
1 TTAT
2160092 ATTCATTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTAA
Found at i:2160121 original size:27 final size:27
Alignment explanation
Indices: 2160038--2160121 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
2160028 TTATATTAAA
2160038 CATTATATTATTAA-AATAAATATATATTTT
1 CATTA-ATTATTAATAATAAAT-TATA--TT
* * *
2160068 TATTAATTATTAATTATTAATTATATT
1 CATTAATTATTAATAATAAATTATATT
*
2160095 CATTACTTATATAATAATAAATT-TATT
1 CATTAATTAT-TAATAATAAATTATATT
2160122 TTTAAAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
27 14 0.31
28 10 0.22
29 12 0.27
30 9 0.20
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
CATTAATTATTAATAATAAATTATATT
Found at i:2160320 original size:12 final size:13
Alignment explanation
Indices: 2160296--2160325 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2160286 ACTTTTAAAA
2160296 CAAAATCAATTTT
1 CAAAATCAATTTT
2160309 CAAAAT-AATTTT
1 CAAAATCAATTTT
2160321 CAAAA
1 CAAAA
2160326 GTTATTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (13 bp):
CAAAATCAATTTT
Found at i:2160628 original size:3 final size:3
Alignment explanation
Indices: 2160620--2160682 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
2160610 ATTAAAAAGA
*
2160620 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2160668 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
2160683 GTAAGATTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2161641 original size:2 final size:2
Alignment explanation
Indices: 2161634--2161659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2161624 TAAGTCATGC
2161634 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
2161660 TTAAGTTTTG
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:2162241 original size:26 final size:24
Alignment explanation
Indices: 2162212--2162328 Score: 74
Period size: 26 Copynumber: 4.5 Consensus size: 24
2162202 TTAACATATT
2162212 ATTTATTTTTATTTGTAAGAGTTTAA
1 ATTTATTTTT-TTTGTAAGA-TTTAA
** *
2162238 ATTTATTTTTTAGGTATGATTATAAA
1 ATTTATTTTTTTTGTAAGATT-T-AA
*
2162264 AGTTTAATTTTTTTATAGTATA-ATTTAT
1 A-TTT-ATTTTTTT-T-GTA-AGATTTAA
* *
2162292 TTTTATTTTTATTTGTAAAAGTTTAA
1 ATTTATTTTT-TTTGTAAGA-TTTAA
2162318 ATTTATTTTTT
1 ATTTATTTTTT
2162329 GAATATAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
24 3 0.04
25 12 0.17
26 33 0.46
27 8 0.11
28 8 0.11
29 1 0.01
30 6 0.08
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.61
Consensus pattern (24 bp):
ATTTATTTTTTTTGTAAGATTTAA
Found at i:2162295 original size:74 final size:75
Alignment explanation
Indices: 2162191--2162400 Score: 209
Period size: 80 Copynumber: 2.8 Consensus size: 75
2162181 TTATTATACG
* * * *
2162191 AATTTAAATTTTTAACAT--ATTATTTATTTTTATTTGTAAGAGTTTAAATTTATTTTTT-AGGT
1 AATTTAAATTTTTAAGATACAATATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGA-AT
*
2162253 ATGATTATA-A
65 ATAATTATATA
* *
2162263 AAGTTTAATTTTTTTATAGTATA-ATTTATTTTTATTTTTATTTGTAAAAGTTTAAATTTATTTT
1 AA-TTTAA-ATTTTTA-AG-ATACA---ATATTTATTTTTATTTGTAAAAGTTTAAATTTATTTT
*
2162327 TTGAATATAATTATATG
59 TTGAATATAATTATATA
* *
2162344 AATTTAAATTTTTAAGATAC-A-ATTTATTTTTATTTATAAAAATTTAAATTTATTTTT
1 AATTTAAATTTTTAAGATACAATATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTT
2162401 ATTTTTATCA
Statistics
Matches: 115, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
72 2 0.02
73 38 0.33
74 7 0.06
75 1 0.01
76 2 0.02
77 4 0.03
78 2 0.02
79 6 0.05
80 50 0.43
81 3 0.03
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (75 bp):
AATTTAAATTTTTAAGATACAATATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGAATA
TAATTATATA
Found at i:2162315 original size:80 final size:79
Alignment explanation
Indices: 2162208--2162378 Score: 222
Period size: 80 Copynumber: 2.1 Consensus size: 79
2162198 ATTTTTAACA
* * *
2162208 TATTATTTATTTTTATTTGTAAGAGTTTAAATTTATTTTTT-AGGTATGATTATA-AAAGTTTAA
1 TATT-TTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGA-ATATAATTATATAAA-TTTAA
* *
2162271 TTTTTTTATAG-TATAATT
63 -ATTTTTA-AGATACAATT
*
2162289 TATTTTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGAATATAATTATATGAATTTAAATT
1 TATTTTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGAATATAATTATATAAATTTAAATT
2162354 TTTAAGATACAATT
66 TTTAAGATACAATT
2162368 TATTTTTATTT
1 TATTTTTATTT
2162379 ATAAAAATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
78 2 0.02
79 23 0.28
80 49 0.60
81 7 0.09
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (79 bp):
TATTTTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGAATATAATTATATAAATTTAAATT
TTTAAGATACAATT
Found at i:2163969 original size:24 final size:23
Alignment explanation
Indices: 2163933--2163977 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
2163923 ATATTTAAAA
2163933 TTAAAATAGTAAATACATTTTATT
1 TTAAAATAGTAAA-ACATTTTATT
** *
2163957 TTAAAATTTTAAAATATTTTA
1 TTAAAATAGTAAAACATTTTA
2163978 ATTAAACTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAATAGTAAAACATTTTATT
Found at i:2165670 original size:23 final size:23
Alignment explanation
Indices: 2165626--2165671 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2165616 AGTTTAAATT
* *
2165626 ATTTTAATTTTGAATCATTTTAA
1 ATTTTAAATTTGAATCAATTTAA
2165649 ATTTTAAATTT-AATCAGATTTAA
1 ATTTTAAATTTGAATCA-ATTTAA
2165672 GTTATTATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (23 bp):
ATTTTAAATTTGAATCAATTTAA
Found at i:2166402 original size:22 final size:22
Alignment explanation
Indices: 2166374--2166415 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2166364 ATATTGACAT
2166374 AAATA-TTAAATATTAATTATTA
1 AAATATTTAAA-ATTAATTATTA
*
2166396 AAATATTTAAAATTATTTAT
1 AAATATTTAAAATTAATTAT
2166416 CGTTAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATTTAAAATTAATTATTA
Found at i:2166447 original size:15 final size:13
Alignment explanation
Indices: 2166426--2166476 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
2166416 CGTTAAACTA
2166426 ATAAT-TTTTAAT
1 ATAATATTTTAAT
*
2166438 ATTAATATTTCAAGT
1 A-TAATATTTTAA-T
2166453 AGTAATATTTTAAT
1 A-TAATATTTTAAT
2166467 GATAATATTT
1 -ATAATATTT
2166477 CATGCTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.03
13 4 0.12
14 14 0.44
15 13 0.41
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (13 bp):
ATAATATTTTAAT
Found at i:2166488 original size:29 final size:29
Alignment explanation
Indices: 2166423--2166490 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
2166413 TATCGTTAAA
2166423 CTAATAAT-TTTTAATATTAATATTTCAAG
1 CTAA-AATATTTTAATATTAATATTTCAAG
* *
2166452 -TAGTAATATTTTAATGA-TAATATTTCATG
1 CTA-AAATATTTTAAT-ATTAATATTTCAAG
2166481 CTAAAATATT
1 CTAAAATATT
2166491 ATATTAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
28 5 0.16
29 24 0.75
30 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (29 bp):
CTAAAATATTTTAATATTAATATTTCAAG
Found at i:2167334 original size:3 final size:3
Alignment explanation
Indices: 2167326--2167355 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2167316 CATAAGAGAT
2167326 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2167356 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2167360 original size:3 final size:3
Alignment explanation
Indices: 2167354--2167386 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2167344 ATAATAATAA
2167354 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2167387 CATCATCTAG
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):
TAT
Found at i:2168093 original size:4 final size:4
Alignment explanation
Indices: 2168084--2168110 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2168074 TTATTCTGCT
2168084 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2168111 TGAACTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2172451 original size:2 final size:2
Alignment explanation
Indices: 2172438--2172482 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2172428 TTTCAGACAA
*
2172438 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2172478 AG AG A
1 AG AG A
2172483 AGAACAAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2172993 original size:12 final size:12
Alignment explanation
Indices: 2172978--2173024 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
2172968 TATTATATGG
*
2172978 AAAATGATATAA
1 AAAATAATATAA
2172990 AAAATTAAATATAA
1 AAAA-T-AATATAA
*
2173004 AAAATAAGAT-A
1 AAAATAATATAA
2173015 AAAATAATAT
1 AAAATAATAT
2173025 TAACATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 10 0.33
12 8 0.27
13 2 0.07
14 10 0.33
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:2173066 original size:18 final size:17
Alignment explanation
Indices: 2173041--2173087 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
2173031 TATATGAGTG
2173041 TATTATATAATATAAAT
1 TATTATATAATATAAAT
2173058 TATTA-AT-ATATTAAAT
1 TATTATATAATA-TAAAT
2173074 T-TTATATAAATATA
1 TATTATAT-AATATA
2173088 TAATGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 7 0.27
18 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATATAATATAAAT
Found at i:2173091 original size:27 final size:27
Alignment explanation
Indices: 2173050--2173104 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
2173040 GTATTATATA
*
2173050 ATATAAATTATTAAT-ATATTAAATTTT
1 ATATAAATTATTAATGAT-TTAAAATTT
2173077 ATATAAA-TATATAATGATTTAAAATTT
1 ATATAAATTAT-TAATGATTTAAAATTT
2173104 A
1 A
2173105 GACATGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 20 0.80
28 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATAAATTATTAATGATTTAAAATTT
Found at i:2174397 original size:21 final size:20
Alignment explanation
Indices: 2174365--2174406 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2174355 ATCTTTAACA
2174365 TTTATCATATATAATAATAAT
1 TTTATCATATATAATAA-AAT
*
2174386 TTTATC-TAATATATTAAAAT
1 TTTATCAT-ATATAATAAAAT
2174406 T
1 T
2174407 AATAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATCATATATAATAAAAT
Found at i:2175729 original size:22 final size:22
Alignment explanation
Indices: 2175704--2175756 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
2175694 AATAATTAAC
*
2175704 AAAATA-AAATTATTATTATTAT
1 AAAATATAAATAATTA-TATTAT
*
2175726 AAAATATATATAATTATATTAT
1 AAAATATAAATAATTATATTAT
2175748 AAAAATATA
1 -AAAATATA
2175757 TTTCATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATATAAATAATTATATTAT
Found at i:2175741 original size:23 final size:21
Alignment explanation
Indices: 2175715--2175757 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2175705 AAATAAAATT
2175715 ATTATTATTATAAAATATATATA
1 ATTA-TATTATAAAA-ATATATA
2175738 ATTATATTATAAAAATATAT
1 ATTATATTATAAAAATATAT
2175758 TTCATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATATTATAAAAATATATA
Found at i:2175846 original size:16 final size:16
Alignment explanation
Indices: 2175825--2175869 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
2175815 TAATGTCAGC
2175825 TTATTTTTTAATAAAT
1 TTATTTTTTAATAAAT
2175841 TTATTTTTTTATATAAAT
1 TTA-TTTTTTA-ATAAAT
*
2175859 ATATTTTTTAA
1 TTATTTTTTAA
2175870 ATATTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.15
17 14 0.54
18 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTTTTAATAAAT
Found at i:2175866 original size:19 final size:19
Alignment explanation
Indices: 2175828--2175886 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 19
2175818 TGTCAGCTTA
*
2175828 TTTTTTA-ATAAATTTA-T
1 TTTTTTATATAAATATATT
2175845 TTTTTTATATAAATATATT
1 TTTTTTATATAAATATATT
** *
2175864 TTTTAAATATTAAATAAATT
1 TTTTTTATA-TAAATATATT
2175884 TTT
1 TTT
2175887 GAATTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 7 0.20
18 8 0.23
19 8 0.23
20 12 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTATATAAATATATT
Found at i:2175877 original size:20 final size:18
Alignment explanation
Indices: 2175826--2175897 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
2175816 AATGTCAGCT
*
2175826 TATTTTTT-A-ATAAATT
1 TATTTTTTAATATAAATA
*
2175842 TATTTTTTTATATAAATA
1 TATTTTTTAATATAAATA
2175860 TATTTTTTAAATATTAAATA
1 TATTTTTT-AATA-TAAATA
* * *
2175880 AATTTTTGAATTTAAATA
1 TATTTTTTAATATAAATA
2175898 AATAATTCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
16 8 0.17
17 1 0.02
18 20 0.43
19 6 0.13
20 12 0.26
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
TATTTTTTAATATAAATA
Found at i:2178061 original size:5 final size:5
Alignment explanation
Indices: 2178051--2178076 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2178041 TAAATTTTTA
2178051 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
2178077 CTTTTAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:2185928 original size:22 final size:22
Alignment explanation
Indices: 2185903--2185944 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2185893 TATAACATTT
2185903 TAAAA-TTATAAATATTAATATC
1 TAAAATTTATAAATA-TAATATC
*
2185925 TAAAATTTTTAAATATAATA
1 TAAAATTTATAAATATAATA
2185945 AATTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATTTATAAATATAATATC
Found at i:2186366 original size:30 final size:31
Alignment explanation
Indices: 2186332--2186433 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 31
2186322 TGTACAGTTT
2186332 TTTAAAAATTTA-AATATTTT-TTATTAAAAA
1 TTTAAAAATTTATAATATTTTATT-TTAAAAA
* *
2186362 TTT-AAATTTTATAATATTTTATTTTATTAAA
1 TTTAAAAATTTATAATATTTTATTTTA-AAAA
* *
2186393 TTTAATTAATGTTATAATTATTTTATTTTAATAA
1 TTTAA-AAAT-TTATAA-TATTTTATTTTAAAAA
2186427 TTTAAAA
1 TTTAAAA
2186434 GAATCGTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
29 7 0.12
30 14 0.24
31 8 0.14
32 1 0.02
33 3 0.05
34 13 0.22
35 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
TTTAAAAATTTATAATATTTTATTTTAAAAA
Found at i:2186469 original size:20 final size:21
Alignment explanation
Indices: 2186446--2186485 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2186436 ATCGTTAAAA
2186446 ATTAAAAAT-ATATAAATTTG
1 ATTAAAAATCATATAAATTTG
* *
2186466 ATTAAATATCATATGAATTT
1 ATTAAAAATCATATAAATTT
2186486 TCTTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTAAAAATCATATAAATTTG
Found at i:2189997 original size:33 final size:34
Alignment explanation
Indices: 2189958--2190036 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 34
2189948 TTACTTCAAA
2189958 GTGTCTTCAACATAGTACTCTTA-TACTTCATTG
1 GTGTCTTCAACATAGTACTCTTATTACTTCATTG
2189991 GTGTCTTCAACATAGTACTCTTATTACTTCATTG
1 GTGTCTTCAACATAGTACTCTTATTACTTCATTG
2190025 GTGTCTTCAACA
1 GTGTCTTCAACA
2190037 CTTTCAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 23 0.51
34 22 0.49
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (34 bp):
GTGTCTTCAACATAGTACTCTTATTACTTCATTG
Found at i:2192595 original size:19 final size:19
Alignment explanation
Indices: 2192555--2192596 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2192545 AACCTTATGA
* *
2192555 TTTTATTTTATTTTTTATG
1 TTTTATTTTATTTATTAAG
2192574 TTTTATTTT-TTGTATTAAG
1 TTTTATTTTATT-TATTAAG
2192593 TTTT
1 TTTT
2192597 TATCATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTATTTTATTTATTAAG
Found at i:2195499 original size:106 final size:106
Alignment explanation
Indices: 2195314--2195526 Score: 417
Period size: 106 Copynumber: 2.0 Consensus size: 106
2195304 CATGAAAATT
2195314 TAAGAAAAGATATGCACGCTAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTT
1 TAAGAAAAGATATGCACGCTAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTT
*
2195379 TTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTGGGG
66 TTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGG
2195420 TAAGAAAAGATATGCACGCTAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTT
1 TAAGAAAAGATATGCACGCTAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTT
2195485 TTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGG
66 TTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGG
2195526 T
1 T
2195527 GGGTTTTGGT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.44
Consensus pattern (106 bp):
TAAGAAAAGATATGCACGCTAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTT
TTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGG
Found at i:2195562 original size:48 final size:47
Alignment explanation
Indices: 2195481--2195574 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 47
2195471 TTTCCGTTTT
2195481 GGTTTTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGGTG
1 GGTTTTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGGTG
*
2195528 GGTTTTGGTTTTGACTTTTTGAGTATCATCTTTCTCTTATGTGGGGT
1 GGTTTTGGTTTTGAC-TTTTGAGTATCATCTTTCTCTTATGTCGGGT
2195575 AAGAAAAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 15 0.33
48 30 0.67
ACGTcount: A:0.11, C:0.12, G:0.26, T:0.52
Consensus pattern (47 bp):
GGTTTTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTCGGGTG
Found at i:2195670 original size:154 final size:153
Alignment explanation
Indices: 2195375--2195683 Score: 600
Period size: 154 Copynumber: 2.0 Consensus size: 153
2195365 TTTCCGTTTT
2195375 GGTTTTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTGGGGTAAGAAAAGATATGCACGCT
1 GGTTTTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTGGGGTAAGAAAAGATATGCACGCT
2195440 AGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTTTTGGTTTTGACTTTTGAGTA
66 AGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTTTTGGTTTTGACTTTTGAGTA
2195505 TCATCTTTCTCTTATGTCGGGTG
131 TCATCTTTCTCTTATGTCGGGTG
2195528 GGTTTTGGTTTTGACTTTTTGAGTATCATCTTTCTCTTATGTGGGGTAAGAAAAGATATGCACGC
1 GGTTTTGGTTTTGAC-TTTTGAGTATCATCTTTCTCTTATGTGGGGTAAGAAAAGATATGCACGC
2195593 TAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTTTTGGTTTTGACTTTTGAGT
65 TAGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTTTTGGTTTTGACTTTTGAGT
*
2195658 ATCATCTTTCTCTTATGTGGGGTG
130 ATCATCTTTCTCTTATGTCGGGTG
2195682 GG
1 GG
2195684 AAGCATTTAA
Statistics
Matches: 154, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
153 15 0.10
154 139 0.90
ACGTcount: A:0.17, C:0.13, G:0.24, T:0.46
Consensus pattern (153 bp):
GGTTTTGGTTTTGACTTTTGAGTATCATCTTTCTCTTATGTGGGGTAAGAAAAGATATGCACGCT
AGTTGTTTGCAATCAGCAAAGTTGTTGTTCATTTCCGTTTTGGTTTTGGTTTTGACTTTTGAGTA
TCATCTTTCTCTTATGTCGGGTG
Found at i:2199728 original size:59 final size:59
Alignment explanation
Indices: 2199651--2199766 Score: 205
Period size: 59 Copynumber: 2.0 Consensus size: 59
2199641 CATGAGTCCT
* *
2199651 ACTGCATGAACCCTCTAGTGTTAGCAATCCATGTTCATTAATGTTTTATTGATACTCAG
1 ACTGCATGAACCCTCTAGTGTTAGCAATCCATGTTCATTAATATTCTATTGATACTCAG
*
2199710 ACTGGATGAACCCTCTAGTGTTAGCAATCCATGTTCATTAATATTCTATTGATACTC
1 ACTGCATGAACCCTCTAGTGTTAGCAATCCATGTTCATTAATATTCTATTGATACTC
2199767 TTTTAATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (59 bp):
ACTGCATGAACCCTCTAGTGTTAGCAATCCATGTTCATTAATATTCTATTGATACTCAG
Found at i:2214038 original size:27 final size:28
Alignment explanation
Indices: 2213989--2214048 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
2213979 AAGTTTATCG
*
2213989 ATATTTTTTTATTTTATATAT-AAATTT
1 ATATTTTTTTATTTTATATATAAAATAT
*
2214016 ATATTTTTTTAATTTTTTA-ATAAAATAT
1 ATATTTTTTT-ATTTTATATATAAAATAT
2214044 ATATT
1 ATATT
2214049 ATACACATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
ATATTTTTTTATTTTATATATAAAATAT
Found at i:2214098 original size:15 final size:14
Alignment explanation
Indices: 2214075--2214118 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
2214065 GTTTGTAGGT
2214075 AAATATAAATTTTA
1 AAATATAAATTTTA
2214089 AAATTATAAATATTTA
1 AAA-TATAAAT-TTTA
*
2214105 ATATATCAAATTTT
1 AAATAT-AAATTTT
2214119 TTATATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 13 0.50
16 10 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATATAAATTTTA
Found at i:2214115 original size:16 final size:16
Alignment explanation
Indices: 2214096--2214130 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2214086 TTAAAATTAT
2214096 AAATATTTAATATATC
1 AAATATTTAATATATC
* *
2214112 AAATTTTTTATATATC
1 AAATATTTAATATATC
2214128 AAA
1 AAA
2214131 CAAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATTTAATATATC
Found at i:2214949 original size:2 final size:2
Alignment explanation
Indices: 2214942--2214981 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2214932 TAGACAATTT
*
2214942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
2214982 AAATAGGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2215773 original size:2 final size:2
Alignment explanation
Indices: 2215766--2215793 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2215756 TTAATTTCTC
2215766 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
2215794 TGTACTGTCT
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:2216518 original size:21 final size:22
Alignment explanation
Indices: 2216492--2216543 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 22
2216482 ATAAAAAATA
2216492 ATATAAAATATTAAATT-TTAT-
1 ATATAAAATA-TAAATTATTATC
2216513 ATAT-AAATATAAATTATTATC
1 ATATAAAATATAAATTATTATC
2216534 ATATCAAAAT
1 ATAT-AAAAT
2216544 TTATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.22
20 9 0.33
21 8 0.30
23 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAAAATATAAATTATTATC
Found at i:2217746 original size:131 final size:131
Alignment explanation
Indices: 2217503--2217893 Score: 530
Period size: 130 Copynumber: 3.0 Consensus size: 131
2217493 TTATCAAAAA
* * ** *
2217503 AATTTAAACATATTTAATAATTTATATTATTTTTACACTTACACTATAAATGCACAAA-AAAAAT
1 AATTTAAACATGTTTAATAATTTATATTATTTTTACATTTACACTATAAACACAAAAATAAAAAT
* * * *
2217567 AAAAAGCACAAGATTTGACATTCATGCATTTATTGCTAATTCGACCTACCTTTCTTTATTGCTGT
66 AAAAAGCACAAAATTTGACATTCATACATTTATTGCTAATTCCACCTACCTTTCTTTATTGCTGC
2217632 T
131 T
2217633 AATTTAAACATGTTTAATAATTTATATTATTTTTACATTTACACTATAAACACAAAAATAAAAAT
1 AATTTAAACATGTTTAATAATTTATATTATTTTTACATTTACACTATAAACACAAAAATAAAAAT
* * *
2217698 AAAAAGCACAAAATTTGACATTTATACATTTATTGTTAATTCCACCTACCTTT-TTTATTGTTGC
66 AAAAAGCACAAAATTTGACATTCATACATTTATTGCTAATTCCACCTACCTTTCTTTATTGCTGC
2217762 T
131 T
* *
2217763 AATTTGAACATGTTTAATAATTTATATTATTTTTACATTTATACTATAAACACAAAAAATAAAAA
1 AATTTAAACATGTTTAATAATTTATATTATTTTTACATTTACACTATAAACAC-AAAAATAAAAA
* ** * *
2217828 -AAAAA-TA-AAAA---GCACATTCATACATTT-TTGCTAATTCCACAAACCTTTCTTTATGGTT
65 TAAAAAGCACAAAATTTG-ACATTCATACATTTATTGCTAATTCCACCTACCTTTCTTTATTGCT
2217886 GCT
129 GCT
2217889 AATTT
1 AATTT
2217894 TTTCTTGTAA
Statistics
Matches: 237, Mismatches: 20, Indels: 12
0.88 0.07 0.04
Matches are distributed among these distances:
125 19 0.08
126 29 0.12
128 4 0.02
129 1 0.00
130 119 0.50
131 65 0.27
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.40
Consensus pattern (131 bp):
AATTTAAACATGTTTAATAATTTATATTATTTTTACATTTACACTATAAACACAAAAATAAAAAT
AAAAAGCACAAAATTTGACATTCATACATTTATTGCTAATTCCACCTACCTTTCTTTATTGCTGC
T
Found at i:2218193 original size:2 final size:2
Alignment explanation
Indices: 2218186--2218226 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2218176 ATGCCCTTCA
2218186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2218227 AATTATAGAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2218769 original size:3 final size:3
Alignment explanation
Indices: 2218763--2218813 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
2218753 GCCGTCTATG
2218763 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2218811 TAT
1 TAT
2218814 GAAATAAGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2219433 original size:17 final size:16
Alignment explanation
Indices: 2219399--2219431 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2219389 TCAATAAAAC
*
2219399 TAGATTTTTTATTTTT
1 TAGAATTTTTATTTTT
2219415 TAGAATTTTTATTTTT
1 TAGAATTTTTATTTTT
2219431 T
1 T
2219432 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (16 bp):
TAGAATTTTTATTTTT
Found at i:2219465 original size:17 final size:17
Alignment explanation
Indices: 2219451--2219513 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
2219441 TAGATTTTGT
*
2219451 TTATTTATATTTTTTAT
1 TTATTTATATTTTTTAA
*
2219468 TTTTTTGA-ATTTTTTAAA
1 TTATTT-ATATTTTTT-AA
*
2219486 TTATTTTTATTTTTTAA
1 TTATTTATATTTTTTAA
2219503 TTATTTATATT
1 TTATTTATATT
2219514 AGGAGATGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TTATTTATATTTTTTAA
Found at i:2219466 original size:9 final size:9
Alignment explanation
Indices: 2219454--2219513 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
2219444 ATTTTGTTTA
2219454 TTTATATTT
1 TTTATATTT
2219463 TTTAT-TTT
1 TTTATATTT
2219471 TTTGA-ATTT
1 TTT-ATATTT
*
2219480 TTTAAATTAT
1 TTTATATT-T
2219490 TTT-TATTT
1 TTTATATTT
*
2219498 TTTA-ATTA
1 TTTATATTT
2219506 TTTATATT
1 TTTATATT
2219514 AGGAGATGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
8 18 0.42
9 21 0.49
10 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTATATTT
Found at i:2220073 original size:2 final size:2
Alignment explanation
Indices: 2220068--2220098 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2220058 AAATAAATAA
2220068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2220099 CTTTTACTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2235559 original size:91 final size:86
Alignment explanation
Indices: 2235395--2235559 Score: 183
Period size: 91 Copynumber: 1.9 Consensus size: 86
2235385 AAAAAATTAT
* **
2235395 TTAATTTTTATTTATATTTTTTATTATTTAAAATATTATAAATTTATATAATATTTATAATTTTT
1 TTAATTTTTATTTATATTTTTTATTATTTAAAATATTAGAAATTTATATAATATTTATAATCGTT
*
2235460 TATTTTTATATTTTATTTTAA
66 AATTTTTATATTTTATTTTAA
*
2235481 TTAATTTTTAATATTATATTTATGTT-TTATATATATAATATTAGAAATTTATATAA-ATTTTAT
1 TTAATTTTT-AT-TTATATTT-T-TTATTAT-T-TAAAATATTAGAAATTTATATAATA-TTTAT
*
2235544 CA-CGTTAATTATTTAT
59 AATCGTTAATT-TTTAT
2235560 TTATATACAT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
86 9 0.14
87 2 0.03
88 8 0.12
89 5 0.08
90 9 0.14
91 32 0.49
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (86 bp):
TTAATTTTTATTTATATTTTTTATTATTTAAAATATTAGAAATTTATATAATATTTATAATCGTT
AATTTTTATATTTTATTTTAA
Found at i:2236291 original size:18 final size:19
Alignment explanation
Indices: 2236259--2236296 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2236249 ATGTGTCGAG
*
2236259 TTATATTTTAATTAT-TTT
1 TTATATTATAATTATATTT
*
2236277 TTATATTATATTTATATTT
1 TTATATTATAATTATATTT
2236296 T
1 T
2236297 GTCTTAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATATTATAATTATATTT
Found at i:2237025 original size:21 final size:21
Alignment explanation
Indices: 2237000--2237077 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 21
2236990 TAATTTATTA
2237000 ATTTTTATAATTTTAAAAAAT
1 ATTTTTATAATTTTAAAAAAT
*
2237021 ATTTTTAATAATATTT-TAAAAT
1 ATTTTT-ATAAT-TTTAAAAAAT
*
2237043 A-TTTTATTAA-TTTAAAAATAA
1 ATTTTTA-TAATTTTAAAAA-AT
*
2237064 ATTATT-TAATTTTA
1 ATTTTTATAATTTTA
2237078 TGATAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
19 3 0.07
20 7 0.15
21 19 0.41
22 14 0.30
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTATAATTTTAAAAAAT
Found at i:2237031 original size:22 final size:22
Alignment explanation
Indices: 2237000--2237060 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
2236990 TAATTTATTA
2237000 ATTTTT-ATAATTTTAAAAAAT
1 ATTTTTAATAATTTTAAAAAAT
*
2237021 ATTTTTAATAATATTT-TAAAAT
1 ATTTTTAATAAT-TTTAAAAAAT
*
2237043 A-TTTTATTAA-TTTAAAAA
1 ATTTTTAATAATTTTAAAAA
2237061 TAAATTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 14 0.41
22 11 0.32
23 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTTAATAATTTTAAAAAAT
Found at i:2240626 original size:20 final size:21
Alignment explanation
Indices: 2240588--2240630 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2240578 AAATTTGATA
2240588 TATGTTGGTGTATTAAAAATT
1 TATGTTGGTGTATTAAAAATT
*
2240609 TATGTTAGGT-TATAAAAAATT
1 TATGTT-GGTGTATTAAAAATT
2240630 T
1 T
2240631 TGAAAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
TATGTTGGTGTATTAAAAATT
Found at i:2241257 original size:3 final size:3
Alignment explanation
Indices: 2241249--2241285 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2241239 AATTTACATC
*
2241249 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2241286 AGGTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2241746 original size:5 final size:5
Alignment explanation
Indices: 2241736--2241762 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2241726 TAACTTATCA
2241736 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
2241763 TAAACAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:2244572 original size:21 final size:21
Alignment explanation
Indices: 2244547--2244588 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2244537 CTCATCTTCA
*
2244547 TCCTCA-TCATCAGGCTTCTCC
1 TCCTCACTC-TCAGGATTCTCC
2244568 TCCTCACTCTCAGGATTCTCC
1 TCCTCACTCTCAGGATTCTCC
2244589 CTATACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.14, C:0.43, G:0.10, T:0.33
Consensus pattern (21 bp):
TCCTCACTCTCAGGATTCTCC
Found at i:2246251 original size:27 final size:27
Alignment explanation
Indices: 2246162--2246252 Score: 64
Period size: 27 Copynumber: 3.4 Consensus size: 27
2246152 TAATTATTTA
*
2246162 TAAATAATAAAAA-ATTTTAAAAATTAT
1 TAAATAATAAAAATATTTT-ATAATTAT
* ** *
2246189 ATTAAT-ATTTATATATTTTATAATTA-
1 -TAAATAATAAAAATATTTTATAATTAT
*
2246215 -AATTTAAATAAAAATATTTTATAATTAT
1 TAA-AT-AATAAAAATATTTTATAATTAT
2246243 TAAATAATAA
1 TAAATAATAA
2246253 TTTTGATCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 13
0.66 0.16 0.19
Matches are distributed among these distances:
24 1 0.02
25 1 0.02
27 32 0.70
28 10 0.22
29 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAATAATAAAAATATTTTATAATTAT
Found at i:2254832 original size:91 final size:91
Alignment explanation
Indices: 2254746--2254920 Score: 280
Period size: 91 Copynumber: 1.9 Consensus size: 91
2254736 TTATTAATTT
* * *
2254746 AAAATAAAATTATTTCAATTCGAACAATTATTAAAATTTT-AAATTTATAAATTTAAAATCAAAT
1 AAAATAAAATTATTTCAATTCAAACAATTATT-AAATTTTAAAACTTATAAATTAAAAATCAAAT
2254810 TAAATATATTTAATTTTATATTATATC
65 TAAATATATTTAATTTTATATTATATC
* *
2254837 AAAATAAAATTATTTCAGTTCAAACAATTATTAAGTTTTAAAACTTATAAATTAAAAATCAAATT
1 AAAATAAAATTATTTCAATTCAAACAATTATTAAATTTTAAAACTTATAAATTAAAAATCAAATT
2254902 AAATATATTTAATTATTAT
66 AAATATATTTAATT-TTAT
2254921 CCAATTAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
90 6 0.08
91 67 0.87
92 4 0.05
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (91 bp):
AAAATAAAATTATTTCAATTCAAACAATTATTAAATTTTAAAACTTATAAATTAAAAATCAAATT
AAATATATTTAATTTTATATTATATC
Found at i:2261787 original size:22 final size:22
Alignment explanation
Indices: 2261757--2261798 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2261747 AGACACTTAT
* *
2261757 GATTGAAAAATATTTAAATTAA
1 GATTAAAAAAGATTTAAATTAA
*
2261779 GATTAAAAAAGGTTTAAATT
1 GATTAAAAAAGATTTAAATT
2261799 CGGTTTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (22 bp):
GATTAAAAAAGATTTAAATTAA
Found at i:2262552 original size:16 final size:16
Alignment explanation
Indices: 2262533--2262574 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2262523 ATATTAAAAA
*
2262533 TAAAATTTTAATTTTT
1 TAAAATATTAATTTTT
*
2262549 T-AAATATTATTTTTT
1 TAAAATATTAATTTTT
2262564 TAAAAATATTA
1 T-AAAATATTA
2262575 TATAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAAAATATTAATTTTT
Found at i:2263495 original size:11 final size:11
Alignment explanation
Indices: 2263479--2263506 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2263469 AGGCTGAAGT
2263479 TTGACTCTGGC
1 TTGACTCTGGC
2263490 TTGACTCTGGC
1 TTGACTCTGGC
2263501 TTGACT
1 TTGACT
2263507 GGTAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (11 bp):
TTGACTCTGGC
Found at i:2266607 original size:21 final size:21
Alignment explanation
Indices: 2266564--2266607 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2266554 TTTTAATATA
* *
2266564 TATTAATTGTATGTATTATTT
1 TATTAATTGTATGTATAAATT
*
2266585 TATTAATTGTATTTATAAATT
1 TATTAATTGTATGTATAAATT
2266606 TA
1 TA
2266608 AAAATTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
TATTAATTGTATGTATAAATT
Found at i:2268995 original size:21 final size:21
Alignment explanation
Indices: 2268962--2269001 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2268952 TCCTGACAAG
2268962 TTTTTGTTATTTTTCACTTCC
1 TTTTTGTTATTTTTCACTTCC
* * *
2268983 TTTTTTTTTTTTTTTACTT
1 TTTTTGTTATTTTTCACTT
2269002 TTTATTGGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTTGTTATTTTTCACTTCC
Found at i:2270194 original size:41 final size:41
Alignment explanation
Indices: 2270137--2270218 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
2270127 TATATAAGAA
*
2270137 GGAATCATTCTAGTTTAGTAAATCTCGTATTAGATATGGCT
1 GGAATCATTCTAGTTTAGCAAATCTCGTATTAGATATGGCT
2270178 GGAATCATTCTAGTTTAGCAAATCTCGTATTAGATATGGCT
1 GGAATCATTCTAGTTTAGCAAATCTCGTATTAGATATGGCT
2270219 AAGTTTTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (41 bp):
GGAATCATTCTAGTTTAGCAAATCTCGTATTAGATATGGCT
Found at i:2271200 original size:13 final size:13
Alignment explanation
Indices: 2271182--2271209 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2271172 ATGCATTTGT
2271182 TGGAGTAAATGTC
1 TGGAGTAAATGTC
2271195 TGGAGTAAATGTC
1 TGGAGTAAATGTC
2271208 TG
1 TG
2271210 AGCATGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (13 bp):
TGGAGTAAATGTC
Found at i:2275177 original size:86 final size:86
Alignment explanation
Indices: 2275085--2275253 Score: 338
Period size: 86 Copynumber: 2.0 Consensus size: 86
2275075 TGTGTCATAA
2275085 AGTTAGATTGTCCATAATATATAAGAGAATTGTTTTTTTTAATTAAAAATTTTGATTATTATATA
1 AGTTAGATTGTCCATAATATATAAGAGAATTGTTTTTTTTAATTAAAAATTTTGATTATTATATA
2275150 TTTGTATTTTATGTTATATTT
66 TTTGTATTTTATGTTATATTT
2275171 AGTTAGATTGTCCATAATATATAAGAGAATTGTTTTTTTTAATTAAAAATTTTGATTATTATATA
1 AGTTAGATTGTCCATAATATATAAGAGAATTGTTTTTTTTAATTAAAAATTTTGATTATTATATA
2275236 TTTGTATTTTATGTTATA
66 TTTGTATTTTATGTTATA
2275254 ATCTACTATA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (86 bp):
AGTTAGATTGTCCATAATATATAAGAGAATTGTTTTTTTTAATTAAAAATTTTGATTATTATATA
TTTGTATTTTATGTTATATTT
Found at i:2275608 original size:3 final size:3
Alignment explanation
Indices: 2275600--2275647 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
2275590 TCAAAACCCA
* * *
2275600 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT CTT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2275648 TATAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2276478 original size:2 final size:2
Alignment explanation
Indices: 2276471--2276507 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2276461 TTTGCAATGG
2276471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2276508 AAGTTACGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2277078 original size:42 final size:41
Alignment explanation
Indices: 2277019--2277097 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
2277009 TCTTTTTTTC
*
2277019 TTTTTTTTTTTAATATTGAAGCAGATAAAGCAATGTTTCTT
1 TTTTTTTTTTTAATATTGAAGCAGATAAAACAATGTTTCTT
*
2277060 TTTTTATTTTTTAGTATTGAAGCAGATAAAACAATGTT
1 TTTTT-TTTTTTAATATTGAAGCAGATAAAACAATGTT
2277098 ATTTTATGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 5 0.14
42 30 0.86
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (41 bp):
TTTTTTTTTTTAATATTGAAGCAGATAAAACAATGTTTCTT
Found at i:2277302 original size:2 final size:2
Alignment explanation
Indices: 2277297--2277329 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2277287 CACAGCTTAG
2277297 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 T
2277330 GTATGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2278189 original size:2 final size:2
Alignment explanation
Indices: 2278182--2278212 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2278172 GTTTTCAAAT
2278182 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
2278213 GCATAATAAT
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:2285530 original size:2 final size:2
Alignment explanation
Indices: 2285523--2285550 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2285513 CTAACCTTAT
2285523 TC 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
2285551 CCCTGGTGTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2293703 original size:2 final size:2
Alignment explanation
Indices: 2293687--2293725 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2293677 AATCACTATG
*
2293687 TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TG 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
2293726 GCAACAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2296158 original size:3 final size:3
Alignment explanation
Indices: 2296152--2296205 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
2296142 TCCAAAGAAG
2296152 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2296200 ATA ATA
1 ATA ATA
2296206 GTAAAAGATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2302682 original size:14 final size:13
Alignment explanation
Indices: 2302663--2302701 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2302653 AAAATGAGAA
2302663 TTTCTTCACCTTTT
1 TTTCTTC-CCTTTT
2302677 TTTCTTCCC-TTT
1 TTTCTTCCCTTTT
2302689 TTT-TTCCCTTTT
1 TTTCTTCCCTTTT
2302701 T
1 T
2302702 GGTTTGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 10 0.42
13 2 0.08
14 7 0.29
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTTCCCTTTT
Found at i:2302700 original size:10 final size:12
Alignment explanation
Indices: 2302663--2302701 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
2302653 AAAATGAGAA
2302663 TTTCTTCACCTTTT
1 TTTCTTC-CC-TTT
2302677 TTTCTTCCCTTT
1 TTTCTTCCCTTT
2302689 TTT-TTCCCTTT
1 TTTCTTCCCTTT
2302700 TT
1 TT
2302702 GGTTTGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.40
12 6 0.24
13 2 0.08
14 7 0.28
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTCCCTTT
Found at i:2302832 original size:15 final size:15
Alignment explanation
Indices: 2302812--2302858 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2302802 TAATATAATA
*
2302812 AAAATAAAATAACAT
1 AAAATAAAATAAAAT
*
2302827 AAAATATAATAAAAT
1 AAAATAAAATAAAAT
*
2302842 -AAATAATATAAATAT
1 AAAATAAAATAAA-AT
2302857 AA
1 AA
2302859 TATGATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 10 0.38
15 15 0.58
16 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:2302852 original size:9 final size:9
Alignment explanation
Indices: 2302813--2302860 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
2302803 AATATAATAA
2302813 AAATAAAAT
1 AAATAAAAT
2302822 AACATAAAAT
1 AA-ATAAAAT
2302832 ATAATAAAAT
1 A-AATAAAAT
*
2302842 AAATAATAT
1 AAATAAAAT
*
2302851 AAATATAAT
1 AAATAAAAT
2302860 A
1 A
2302861 TGATTATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 17 0.50
10 16 0.47
11 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2303391 original size:29 final size:29
Alignment explanation
Indices: 2303334--2303404 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
2303324 CTCATGTACT
* *
2303334 TTATTATATTATA-GTAATATTTAAAATA
1 TTATAATATTATATATAATATTTAAAATA
* *
2303362 TTATAATATTATATATAATTTTTAATATA
1 TTATAATATTATATATAATATTTAAAATA
*
2303391 TAATTAAT-TTATAT
1 TTA-TAATATTATAT
2303405 TATATTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.33
29 20 0.56
30 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TTATAATATTATATATAATATTTAAAATA
Found at i:2303398 original size:18 final size:15
Alignment explanation
Indices: 2303368--2303416 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 15
2303358 AATATTATAA
2303368 TATTATATATAATTTT
1 TATTATAT-TAATTTT
*
2303384 TAATATATAATTAATTTA
1 T-AT-TAT-ATTAATTTT
2303402 TATTATATTAATTTT
1 TATTATATTAATTTT
2303417 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 4 0.14
18 10 0.36
19 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATATTAATTTT
Found at i:2303417 original size:16 final size:16
Alignment explanation
Indices: 2303367--2303417 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2303357 AAATATTATA
2303367 ATATTATATATAATTTT
1 ATATTATAT-TAATTTT
2303384 -TAATATATAATTAA-TTT
1 AT-AT-TAT-ATTAATTTT
2303401 ATATTATATTAATTTT
1 ATATTATATTAATTTT
2303417 A
1 A
2303418 AATTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
15 5 0.17
16 8 0.28
17 7 0.24
18 7 0.24
19 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTATATTAATTTT
Found at i:2304815 original size:4 final size:4
Alignment explanation
Indices: 2304806--2304830 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2304796 ATGATAGGAA
2304806 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2304831 TTTATTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2305235 original size:30 final size:29
Alignment explanation
Indices: 2305150--2305237 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
2305140 TTTAATAATA
* *
2305150 TTAAATATAATAAAAATATATAAAA-ATT
1 TTAAATATATTAATAATATATAAAATATT
*
2305178 TATATAATATAATTTATTAATAT-TAAAATATT
1 T-TA-AATAT-A-TTAATAATATATAAAATATT
2305210 TTAAATATATTAATAATATAATAAAATA
1 TTAAATATATTAATAATAT-ATAAAATA
2305238 CATAAATTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
28 10 0.20
29 3 0.06
30 17 0.35
31 8 0.16
32 11 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAATATATTAATAATATATAAAATATT
Found at i:2311825 original size:27 final size:27
Alignment explanation
Indices: 2311795--2311847 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2311785 GTTCAATTAA
*
2311795 TTTAATATTT-AATTTTTTAAATAAAAT
1 TTTAA-ATTTAAATTTTATAAATAAAAT
2311822 TTTAAATTTAAATTTTATAAATAAAA
1 TTTAAATTTAAATTTTATAAATAAAA
2311848 AAATAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTAAATTTAAATTTTATAAATAAAAT
Found at i:2313421 original size:16 final size:19
Alignment explanation
Indices: 2313390--2313428 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
2313380 TTTTTAAAAT
2313390 TTAAATATTAAATAAGT-A
1 TTAAATATTAAATAAGTAA
2313408 TTAAATA-T-AATAAGTAA
1 TTAAATATTAAATAAGTAA
2313425 TTAA
1 TTAA
2313429 TAAAAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 6 0.30
18 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAATATTAAATAAGTAA
Found at i:2314690 original size:21 final size:22
Alignment explanation
Indices: 2314664--2314706 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2314654 TGCTTAAATT
* *
2314664 TTATAT-TTTATATTATTTTTA
1 TTATATGTTAATATTAATTTTA
2314685 TTATATGTTAATATTAATTTTA
1 TTATATGTTAATATTAATTTTA
2314707 ATATTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTATATGTTAATATTAATTTTA
Found at i:2314951 original size:2 final size:2
Alignment explanation
Indices: 2314944--2314970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2314934 CAAGTCATTA
2314944 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
2314971 AACTTTTTCA
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:2315783 original size:13 final size:13
Alignment explanation
Indices: 2315765--2315789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2315755 ATTAAAAAAT
2315765 AAATAATTTTAAA
1 AAATAATTTTAAA
2315778 AAATAATTTTAA
1 AAATAATTTTAA
2315790 TTTTAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATAATTTTAAA
Found at i:2316629 original size:12 final size:13
Alignment explanation
Indices: 2316604--2316628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2316594 ATTTAAATAA
2316604 AAAAATTATTTTT
1 AAAAATTATTTTT
2316617 AAAAATTATTTT
1 AAAAATTATTTT
2316629 ATTATTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:2317050 original size:2 final size:2
Alignment explanation
Indices: 2317043--2317073 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2317033 GGATAATTTG
2317043 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
2317074 TGCCATTTAC
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:2320966 original size:28 final size:27
Alignment explanation
Indices: 2320908--2320970 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2320898 TAAACTAATT
*
2320908 TTTTTATTTAAAAATAAAATAAATAAT
1 TTTTTATTTAAAAATAAAATAAATAAA
* * *
2320935 TTTTTATTTAAAGATTAGACTAAATAAA
1 TTTTTATTTAAA-AATAAAATAAATAAA
2320963 -TTTTATTT
1 TTTTTATTT
2320971 TATTTAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
TTTTTATTTAAAAATAAAATAAATAAA
Found at i:2321839 original size:2 final size:2
Alignment explanation
Indices: 2321832--2321862 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2321822 CACATAAATT
2321832 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
2321863 TCATAAAATA
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:2324477 original size:3 final size:3
Alignment explanation
Indices: 2324469--2324512 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2324459 TTAATTACAC
2324469 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2324513 AAGAACAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2325931 original size:19 final size:19
Alignment explanation
Indices: 2325907--2325952 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2325897 AACTATTTTA
*
2325907 TTTTAAT-ATACTTTTATTT
1 TTTTAATAATA-TTTAATTT
2325926 TTTTAATTAATATTTAATTT
1 TTTTAA-TAATATTTAATTT
2325946 TTTTAAT
1 TTTTAAT
2325953 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTAATAATATTTAATTT
Found at i:2327661 original size:47 final size:46
Alignment explanation
Indices: 2327572--2327661 Score: 108
Period size: 47 Copynumber: 1.9 Consensus size: 46
2327562 ATATGTGTCG
* * *
2327572 GATACAAGTAATTCAAGAAAAATAAAAAGTCGGAACAACATAGTCT
1 GATACAAGTAATTAAAAAAAAATAAAAACTCGGAACAACATAGTCT
* * * *
2327618 GATACAAGTACTTGAAAAAAAAATGAAAACTCGGAGCACCATAG
1 GATACAAGTAATT-AAAAAAAAATAAAAACTCGGAACAACATAG
2327662 ATTCTGAAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 12 0.33
47 24 0.67
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.18
Consensus pattern (46 bp):
GATACAAGTAATTAAAAAAAAATAAAAACTCGGAACAACATAGTCT
Found at i:2331753 original size:2 final size:2
Alignment explanation
Indices: 2331746--2331784 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2331736 TCAGCATAAA
2331746 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2331785 CGGAAGGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2336958 original size:21 final size:21
Alignment explanation
Indices: 2336912--2336963 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2336902 TTTAGATAAA
2336912 ATTTAATAATTTTAAAAATTAT
1 ATTTAAT-ATTTTAAAAATTAT
*
2336934 -TTTAAT-TTTTAAATAATTTT
1 ATTTAATATTTTAAA-AATTAT
2336954 ATTTAA-ATTT
1 ATTTAATATTT
2336964 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 7 0.27
20 5 0.19
21 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTAATATTTTAAAAATTAT
Found at i:2337340 original size:17 final size:16
Alignment explanation
Indices: 2337320--2337368 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2337310 TATTTGAGTT
2337320 TTTTATATTTTGTGTAA
1 TTTTATATTTTGT-TAA
* * *
2337337 TTTTTTATTTTATTTA
1 TTTTATATTTTGTTAA
2337353 TTTATATATTTTGTTA
1 TTT-TATATTTTGTTA
2337369 TATCATATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTATATTTTGTTAA
Found at i:2337419 original size:32 final size:30
Alignment explanation
Indices: 2337376--2337441 Score: 71
Period size: 32 Copynumber: 2.1 Consensus size: 30
2337366 TTATATCATA
* *
2337376 TTTAAATTTAAT-GTATATATTTATTTAAAT
1 TTTAAATTTAATAATATAT-TTTATGTAAAT
*
2337406 TTTAATATATTAATAATTTATTTTATGTAAAT
1 TTTAA-AT-TTAATAATATATTTTATGTAAAT
2337438 TTTA
1 TTTA
2337442 TGTATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 5 0.17
31 2 0.07
32 19 0.63
33 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTAAATTTAATAATATATTTTATGTAAAT
Found at i:2337424 original size:23 final size:23
Alignment explanation
Indices: 2337367--2337425 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2337357 TATATTTTGT
* *
2337367 TATATCAT-ATTTAAATTTAATG
1 TATATAATAATTTAAATTTAATA
* *
2337389 TATATATTTATTTAAATTTTAATA
1 TATATAATAATTTAAA-TTTAATA
2337413 TAT-TAATAATTTA
1 TATATAATAATTTA
2337426 TTTTATGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 6 0.20
23 15 0.50
24 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TATATAATAATTTAAATTTAATA
Found at i:2337744 original size:32 final size:31
Alignment explanation
Indices: 2337694--2337755 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2337684 TAAAAGTGTT
2337694 ATATATTTATATAAATTTTAACATATTAATA
1 ATATATTTATATAAATTTTAACATATTAATA
* *
2337725 ATATATTT-TATACAGATTTTAATATGTTAAT
1 ATATATTTATATA-A-ATTTTAACATATTAAT
2337756 CTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 9 0.33
32 14 0.52
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (31 bp):
ATATATTTATATAAATTTTAACATATTAATA
Found at i:2346381 original size:17 final size:18
Alignment explanation
Indices: 2346359--2346409 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
2346349 TGAATCGTTG
*
2346359 TAAAAAAATTTAATT-AA
1 TAAAAAAATTAAATTAAA
2346376 TAAAAAAA-TAAATTAAA
1 TAAAAAAATTAAATTAAA
*
2346393 TTAAAAAATTAATATTA
1 TAAAAAAATTAA-ATTA
2346410 CTTAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 17 0.59
18 3 0.10
19 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAAAATTAAATTAAA
Found at i:2346382 original size:16 final size:18
Alignment explanation
Indices: 2346361--2346409 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
2346351 AATCGTTGTA
*
2346361 AAAAAATTTAATT-AA-T
1 AAAAAATTAAATTAAATT
*
2346377 AAAAAAATAAATTAAATT
1 AAAAAATTAAATTAAATT
2346395 AAAAAATTAATATTA
1 AAAAAATTAA-ATTA
2346410 CTTAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 10 0.37
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATTAAATTAAATT
Found at i:2346406 original size:21 final size:21
Alignment explanation
Indices: 2346360--2346400 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2346350 GAATCGTTGT
*
2346360 AAAA-AAATTTAATTAATAAA
1 AAAATAAATTAAATTAATAAA
2346380 AAAATAAATTAAATTAA-AAA
1 AAAATAAATTAAATTAATAAA
2346400 A
1 A
2346401 TTAATATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATAAATTAAATTAATAAA
Done.