Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 6 of 198
Found at i:2061623 original size:30 final size:30
Alignment explanation
Indices: 2061541--2061615 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
2061531 ACTTTTCTCT
2061541 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCTTCCCACTTTCCCCC
2061571 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCTTCCCACTTTCCCCC
2061601 CAAAACTTTTACTCC
1 CAAAACTTTTACTCC
2061616 CCTCCACTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (30 bp):
CAAAACTTTTACTCCTTCCCACTTTCCCCC
Found at i:2061760 original size:30 final size:31
Alignment explanation
Indices: 2061726--2061783 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
2061716 AAACCTTTTA
*
2061726 TTTTCCCCCAAAATTTTTACT-CCTTCCTAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCTAC
* *
2061756 TTTTCCCCTAAAACTTTTATTCCCTTCC
1 TTTTCCCCCAAAACTTTTACTCCCTTCC
2061784 CATCCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCTAC
Found at i:2062016 original size:27 final size:27
Alignment explanation
Indices: 2061978--2062039 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
2061968 TCTACTATTA
2061978 ATATTATTAAATTAAATTTCACATTTT
1 ATATTATTAAATTAAATTTCACATTTT
2062005 ATATTATTAAATTAAATTTCACATTTT
1 ATATTATTAAATTAAATTTCACATTTT
2062032 ATATTATT
1 ATATTATT
2062040 TATATTATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATTATTAAATTAAATTTCACATTTT
Found at i:2066518 original size:24 final size:23
Alignment explanation
Indices: 2066477--2066522 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2066467 TTTATAATAA
* *
2066477 AATTATTTTTTATCATTAATTAT
1 AATTATTTTTCATAATTAATTAT
2066500 AATTATTTTTCATAAATTAATTA
1 AATTATTTTTCAT-AATTAATTA
2066523 ATTTATTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTATTTTTCATAATTAATTAT
Found at i:2066594 original size:13 final size:13
Alignment explanation
Indices: 2066578--2066608 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2066568 TCTTATAACC
2066578 ATTTTAATATAAT
1 ATTTTAATATAAT
2066591 ATTTTAATATAAT
1 ATTTTAATATAAT
*
2066604 CTTTT
1 ATTTT
2066609 TCAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTTAATATAAT
Found at i:2067256 original size:11 final size:11
Alignment explanation
Indices: 2067240--2067264 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2067230 GAGCATTTAA
2067240 TATTAACCATG
1 TATTAACCATG
2067251 TATTAACCATG
1 TATTAACCATG
2067262 TAT
1 TAT
2067265 ATTAATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (11 bp):
TATTAACCATG
Found at i:2069629 original size:29 final size:28
Alignment explanation
Indices: 2069583--2069638 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
2069573 GACGCTTGTT
*
2069583 TAATTTGGTATCGTAGTTTTTTTTAATTA
1 TAATTTGGTACCGTAG-TTTTTTTAATTA
2069612 TAATTTGGTACC-TGAGTTTTTTTAATT
1 TAATTTGGTACCGT-AGTTTTTTTAATT
2069639 GGTTACTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.57
Consensus pattern (28 bp):
TAATTTGGTACCGTAGTTTTTTTAATTA
Found at i:2070939 original size:3 final size:3
Alignment explanation
Indices: 2070931--2070970 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2070921 GCTAAAATCT
2070931 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2070971 GGGTAAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2071848 original size:31 final size:29
Alignment explanation
Indices: 2071779--2071852 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
2071769 ACAAAATAAT
**
2071779 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGGCA
*
2071808 AACATAAGTGACTAAAATGTAACATGAGGCA
1 AACATAAGTGACTAAAACGTAACAT--GGCA
*
2071839 AACAAAAGTGACTA
1 AACATAAGTGACTA
2071853 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGGCA
Found at i:2077495 original size:28 final size:30
Alignment explanation
Indices: 2077455--2077529 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
2077445 AGTTAGTGAT
2077455 TTATTATAA-ATATA-AA-TATATATAATAA
1 TTATTATAACATATATAATTA-ATATAATAA
*
2077483 TTATT-TAACATATATAATTAATATAATAT
1 TTATTATAACATATATAATTAATATAATAA
*
2077512 TTTTTATAACATAATATA
1 TTATTATAACAT-ATATA
2077530 TTATGGCTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 3 0.08
28 10 0.25
29 14 0.35
30 8 0.20
31 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATTATAACATATATAATTAATATAATAA
Found at i:2077638 original size:18 final size:17
Alignment explanation
Indices: 2077594--2077648 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
2077584 TGGGTTTTAA
2077594 ATTTTATCCAAA-C-CT
1 ATTTTATCCAAACCTCT
2077609 ATTTT-T-CAAACCTCGT
1 ATTTTATCCAAACCTC-T
2077625 ATTTTATCCAAACCCTCCT
1 ATTTTATCCAAA-CCT-CT
2077644 ATTTT
1 ATTTT
2077649 TTCTACAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 6 0.18
16 6 0.18
17 1 0.03
18 4 0.12
19 9 0.27
20 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTTATCCAAACCTCT
Found at i:2082168 original size:21 final size:21
Alignment explanation
Indices: 2082123--2082183 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
2082113 CGAATACACC
*
2082123 AACAGAAGCTCA-AAG--TTG
1 AACAGAAGCTCATAAGAACTG
*
2082141 AACAGAAGTTCATAAGAACTG
1 AACAGAAGCTCATAAGAACTG
* * *
2082162 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAACTG
2082183 A
1 A
2082184 TTCACCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.32
19 3 0.09
21 20 0.59
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAACTG
Found at i:2084299 original size:20 final size:20
Alignment explanation
Indices: 2084270--2084316 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
2084260 ATATACTTGG
2084270 ATTAATTTATATTTTAGC-TTA
1 ATTAA-TTATATTTTA-CTTTA
*
2084291 ATTAATTATGTTTTACTTTA
1 ATTAATTATATTTTACTTTA
2084311 ATTAAT
1 ATTAAT
2084317 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTAATTATATTTTACTTTA
Found at i:2089944 original size:21 final size:20
Alignment explanation
Indices: 2089920--2089962 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2089910 TGTCTAAAGC
2089920 TTCCATTCCAATTCTA-TTTTT
1 TTCC-TTCCAA-TCTACTTTTT
*
2089941 TTCCTTTCAATCTACTTTTT
1 TTCCTTCCAATCTACTTTTT
2089961 TT
1 TT
2089963 GAGGGTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (20 bp):
TTCCTTCCAATCTACTTTTT
Found at i:2102914 original size:31 final size:29
Alignment explanation
Indices: 2102862--2102921 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 29
2102852 GGACAAATCT
2102862 AATATTAATTAATCTTTAATTATTTTACA
1 AATATTAATTAATCTTTAATTATTTTACA
*
2102891 AATATTTAATTAATTTTTTAATTATTTTACA
1 AATA-TTAATTAA-TCTTTAATTATTTTACA
2102922 TTGTTGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 4 0.14
30 8 0.29
31 16 0.57
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (29 bp):
AATATTAATTAATCTTTAATTATTTTACA
Found at i:2114254 original size:71 final size:72
Alignment explanation
Indices: 2114166--2114325 Score: 277
Period size: 71 Copynumber: 2.2 Consensus size: 72
2114156 AAAGTACAGA
* *
2114166 GATTATATCTCAAATTCGAGAGACTTACAAGGACTAATAACACATTTTAACCAAAA-CAAAAAGT
1 GATTATATCCCAAATTCGAGAGACTTACAAGGACTAATAACACATTTTAACCAAAATAAAAAAGT
2114230 ATATAGG
66 ATATAGG
2114237 GATTATATCCCAAATTCGAGAGACTTACAAGGACTAATAACACATTTTAACCAAAATAAAAAAGT
1 GATTATATCCCAAATTCGAGAGACTTACAAGGACTAATAACACATTTTAACCAAAATAAAAAAGT
*
2114302 CTATAGG
66 ATATAGG
*
2114309 GATTATATCCCATATTC
1 GATTATATCCCAAATTC
2114326 AGGTCTAACT
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 55 0.65
72 29 0.35
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (72 bp):
GATTATATCCCAAATTCGAGAGACTTACAAGGACTAATAACACATTTTAACCAAAATAAAAAAGT
ATATAGG
Found at i:2116137 original size:2 final size:2
Alignment explanation
Indices: 2116130--2116166 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2116120 AGACAATGAG
2116130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2116167 GTGTGTTTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2124477 original size:41 final size:41
Alignment explanation
Indices: 2124432--2124516 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
2124422 TAAATTTACA
*
2124432 TATCAATCGAATACTTAAAAGTTATTTTTAAAATTTTTTTT
1 TATCAATCGAATACTTAAAAGTTATTTTTAAAAATTTTTTT
2124473 TATCAATCGAATACTTAAAAGTTATTTTTAAAAATTTTTTT
1 TATCAATCGAATACTTAAAAGTTATTTTTAAAAATTTTTTT
2124514 TAT
1 TAT
2124517 AGAATCACTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (41 bp):
TATCAATCGAATACTTAAAAGTTATTTTTAAAAATTTTTTT
Found at i:2125465 original size:21 final size:22
Alignment explanation
Indices: 2125439--2125492 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
2125429 AATAGCGGTG
*
2125439 GCGGTGAGATTAG-TTACTATA
1 GCGGTGAGATTAGAATACTATA
*
2125460 GCGGTGAGATT-GAATACTGTA
1 GCGGTGAGATTAGAATACTATA
2125481 GCGGTGAGATTA
1 GCGGTGAGATTA
2125493 AAAATAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (22 bp):
GCGGTGAGATTAGAATACTATA
Found at i:2131057 original size:20 final size:20
Alignment explanation
Indices: 2131032--2131071 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2131022 CGTAAAATGA
*
2131032 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
2131052 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2131072 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2131061 original size:34 final size:35
Alignment explanation
Indices: 2131017--2131083 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2131007 CAGTAAAATA
*
2131017 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2131051 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2131084 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2131087 original size:14 final size:15
Alignment explanation
Indices: 2131011--2131087 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2131001 GATTGCCAGT
* *
2131011 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
2131025 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
2131039 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
2131059 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
2131074 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
2131088 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:2134205 original size:68 final size:69
Alignment explanation
Indices: 2134105--2134258 Score: 238
Period size: 68 Copynumber: 2.2 Consensus size: 69
2134095 TCACTTGTCT
*
2134105 TTTCTTGCAGGGAATATTTCATGTTCACGCATTATTTTGTTGCAGGGAATCTCCCCTGTTCACAC
1 TTTCTTGCAGGGAATCTTTCATGTTCACGCATTATTTTGTTGCAGGGAATCTCCCCTGTTCACAC
*
2134170 ATTA
66 ATCA
* * * *
2134174 TTTCTTG-TGGGAATCTTTCCTGTTCAGGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAC
1 TTTCTTGCAGGGAATCTTTCATGTTCACGCATTATTTTGTTGCAGGGAATCTCCCCTGTTCACAC
2134238 ATCA
66 ATCA
*
2134242 TTTATTGCAGGGAATCT
1 TTTCTTGCAGGGAATCT
2134259 CTCCAGGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
68 61 0.80
69 15 0.20
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (69 bp):
TTTCTTGCAGGGAATCTTTCATGTTCACGCATTATTTTGTTGCAGGGAATCTCCCCTGTTCACAC
ATCA
Found at i:2134255 original size:34 final size:35
Alignment explanation
Indices: 2134104--2134262 Score: 180
Period size: 35 Copynumber: 4.6 Consensus size: 35
2134094 TTCACTTGTC
* * * * *
2134104 TTTTCTTGCAGGGAATATTTCATGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
*
2134139 TTTTGTTGCAGGGAATCTCCCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
* * * **
2134174 -TTTCTTG-TGGGAATCTTTCCTGTTCAGGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
*
2134207 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
*
2134242 -TTTATTGCAGGGAATCTCTCC
1 TTTTGTTGCAGGGAATCTCTCC
2134263 AGGTATTTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
33 21 0.20
34 32 0.31
35 50 0.49
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
Found at i:2143156 original size:14 final size:13
Alignment explanation
Indices: 2143129--2143162 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2143119 ATTTTTTAAA
*
2143129 TAATTTTATTTAT
1 TAATTTTATATAT
2143142 TAATTTATATATAT
1 TAATTT-TATATAT
2143156 TAATTTT
1 TAATTTT
2143163 GATAAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TAATTTTATATAT
Found at i:2146167 original size:3 final size:3
Alignment explanation
Indices: 2146159--2146208 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2146149 ACATGGAAGC
2146159 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
2146207 AT
1 AT
2146209 TAGGATGCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2148285 original size:3 final size:3
Alignment explanation
Indices: 2148279--2148311 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2148269 TCTTTTGTTG
2148279 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2148312 AGGCATCAGA
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):
TTA
Found at i:2150751 original size:29 final size:30
Alignment explanation
Indices: 2150708--2150765 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2150698 TTAACGTTGT
* *
2150708 TTGATTCTTTTTAATAGTACAAGGATTAAA
1 TTGATTCTATTTAATAGTACAAAGATTAAA
*
2150738 TTGATT-TATTTAATAGTAGAAAGATTAA
1 TTGATTCTATTTAATAGTACAAAGATTAA
2150766 TTTAATCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (30 bp):
TTGATTCTATTTAATAGTACAAAGATTAAA
Found at i:2153137 original size:14 final size:14
Alignment explanation
Indices: 2153120--2153148 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2153110 CTTAATTTTT
2153120 AATTATATAGATGA
1 AATTATATAGATGA
2153134 AATTATATAGATGA
1 AATTATATAGATGA
2153148 A
1 A
2153149 GTTACCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
AATTATATAGATGA
Found at i:2156153 original size:11 final size:11
Alignment explanation
Indices: 2156137--2156163 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2156127 AGGGATCTGG
2156137 ATCTTGATTGA
1 ATCTTGATTGA
2156148 ATCTTGATTGA
1 ATCTTGATTGA
2156159 ATCTT
1 ATCTT
2156164 TCGTGTGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (11 bp):
ATCTTGATTGA
Found at i:2167059 original size:22 final size:22
Alignment explanation
Indices: 2167017--2167059 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2167007 TACTGAAGTG
*
2167017 AAAATAAAAATTAAAAAAATTA
1 AAAATAAAAACTAAAAAAATTA
* *
2167039 AAAATAAAAACTGAAACAATT
1 AAAATAAAAACTAAAAAAATT
2167060 TGACCAGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAAAACTAAAAAAATTA
Found at i:2168219 original size:31 final size:31
Alignment explanation
Indices: 2168181--2168242 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2168171 TCAAAAAGAG
2168181 AAAAAAAATCATTGTAAAAATATAACTTAAT
1 AAAAAAAATCATTGTAAAAATATAACTTAAT
*
2168212 AAAAAAAATCATTGTACAAATATAACTTAAT
1 AAAAAAAATCATTGTAAAAATATAACTTAAT
2168243 TTATATATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAAAAAATCATTGTAAAAATATAACTTAAT
Found at i:2172745 original size:44 final size:46
Alignment explanation
Indices: 2172697--2172785 Score: 103
Period size: 46 Copynumber: 2.0 Consensus size: 46
2172687 GTGTATTTCA
* * *
2172697 TTAATAATAT-AAA-TAAATTTTTT-TTTACAAAATACATTAAAATT
1 TTAATAAT-TGAAATTAAATTTTTTCATTAAAAAATAAATTAAAATT
* *
2172741 TTAATGATTGAAATTAAGTTTTTTCATTAAAAAATAAATTAAAAT
1 TTAATAATTGAAATTAAATTTTTTCATTAAAAAATAAATTAAAAT
2172786 ATCCTGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.03
44 10 0.27
45 9 0.24
46 17 0.46
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (46 bp):
TTAATAATTGAAATTAAATTTTTTCATTAAAAAATAAATTAAAATT
Found at i:2174982 original size:30 final size:31
Alignment explanation
Indices: 2174917--2174985 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
2174907 ACTACAAAAT
2174917 AGTCACTGAACTACTCGAAAGTTTTCATGTA
1 AGTCACTGAACTACTCGAAAGTTTTCATGTA
* * * *
2174948 AGTCATTGAACTATTTGAAAGTTTT-ATTTA
1 AGTCACTGAACTACTCGAAAGTTTTCATGTA
2174978 AGTCACTG
1 AGTCACTG
2174986 GACTGTTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (31 bp):
AGTCACTGAACTACTCGAAAGTTTTCATGTA
Found at i:2178123 original size:31 final size:31
Alignment explanation
Indices: 2178088--2178154 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2178078 AACAACCTAT
*
2178088 TGATTTAAATAAAAACTTTCGAAGAGTTCAA
1 TGATTTAAATAAAAACTTTCGAAGAATTCAA
* * * *
2178119 TGATTTAAATGAAAATTTTTGAATAATTCAA
1 TGATTTAAATAAAAACTTTCGAAGAATTCAA
2178150 TGATT
1 TGATT
2178155 AACTTTTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (31 bp):
TGATTTAAATAAAAACTTTCGAAGAATTCAA
Found at i:2178845 original size:16 final size:16
Alignment explanation
Indices: 2178824--2178854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2178814 TGAATAAATT
2178824 ATAAAAAATATTTTTC
1 ATAAAAAATATTTTTC
*
2178840 ATAAAATATATTTTT
1 ATAAAAAATATTTTT
2178855 TTCACATAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAAAAATATTTTTC
Found at i:2178945 original size:2 final size:2
Alignment explanation
Indices: 2178938--2178990 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
2178928 TTCATCTCTT
* * *
2178938 TA TA TA TA TA AA TA TA AA TA TA AA 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
2178980 TA TA TA TA TA T
1 TA TA TA TA TA T
2178991 TTCACATTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2196817 original size:2 final size:2
Alignment explanation
Indices: 2196810--2196834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2196800 CCAAATAGTA
2196810 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
2196835 ATAACATAAT
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:2198071 original size:31 final size:31
Alignment explanation
Indices: 2198033--2198097 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2198023 AACTCAAAAC
*
2198033 TCACTAAACTATTCGAAAATTTTCATTTAAG
1 TCACTAAACTATTCGAAAATTTTCATTAAAG
* *
2198064 TCACTAAATTATTCGAAAATTTTTATTAAAG
1 TCACTAAACTATTCGAAAATTTTCATTAAAG
2198095 TCA
1 TCA
2198098 TTAGGTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (31 bp):
TCACTAAACTATTCGAAAATTTTCATTAAAG
Found at i:2202454 original size:26 final size:25
Alignment explanation
Indices: 2202422--2202476 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
2202412 TCTTGTATAC
* *
2202422 TTAAATTTGAGTTTTAATTTATATTT
1 TTAAATTTGAATTTTAATTT-TAATT
*
2202448 TTAAATTTTAATTTTAATTTTAATT
1 TTAAATTTGAATTTTAATTTTAATT
2202473 TTAA
1 TTAA
2202477 TATATATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
TTAAATTTGAATTTTAATTTTAATT
Found at i:2202460 original size:6 final size:6
Alignment explanation
Indices: 2202433--2202477 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
2202423 TAAATTTGAG
*
2202433 TTTTAA TTTATAT TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTT-TAA TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA T
2202478 ATATATTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 25 0.71
7 10 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:2202854 original size:24 final size:24
Alignment explanation
Indices: 2202823--2202869 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2202813 TCTATTAATT
*
2202823 TATTATTTTTATTTTTTAAATTTG
1 TATTATTTTTATTTGTTAAATTTG
2202847 TATTATTTTTATTTGTTAAATTT
1 TATTATTTTTATTTGTTAAATTT
2202870 TTTTATGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (24 bp):
TATTATTTTTATTTGTTAAATTTG
Found at i:2202882 original size:24 final size:24
Alignment explanation
Indices: 2202823--2202884 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
2202813 TCTATTAATT
* *
2202823 TATTATTTTTATTTTTTAAATTTG
1 TATTATTGTTATTTGTTAAATTTG
*
2202847 TATTATTTTTATTTGTTAAATTT-
1 TATTATTGTTATTTGTTAAATTTG
*
2202870 TTTTATGTGTTATTT
1 TATTAT-TGTTATTT
2202885 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (24 bp):
TATTATTGTTATTTGTTAAATTTG
Found at i:2203942 original size:20 final size:21
Alignment explanation
Indices: 2203919--2203975 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
2203909 ACTATTTTTT
2203919 ATTTTTAT-ACTTTTAA-AGTA
1 ATTTTTATGACTTTTAATA-TA
* *
2203939 ATTTTAATGATTTTTAATATA
1 ATTTTTATGACTTTTAATATA
*
2203960 ATTTTT-TGAATTTTAA
1 ATTTTTATGACTTTTAA
2203976 AAAATCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 16 0.52
21 14 0.45
22 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (21 bp):
ATTTTTATGACTTTTAATATA
Found at i:2212050 original size:181 final size:179
Alignment explanation
Indices: 2211727--2212075 Score: 502
Period size: 181 Copynumber: 1.9 Consensus size: 179
2211717 TGCGATTAGG
* * * *
2211727 AAAACTAGACTAATTAATCGCAAATCGGGCTAATTTATATTAATCCAAATTGAGTTTTACTTTTT
1 AAAACTAGACTAATCAATCGCAAATCGGACCAATTTATATTAATCCAAATTGAGTTTTAATTTTT
* * * * *
2211792 TCGAATCATTTCATTTTGTTTAGCATCATATTTGGATCATTTTAAGTTCGAGTCATTTTTAGATT
66 CCGAATCATTTCATTTTGGTTAGCATCATATTTGGATCATTTCAAGTTCGAATCAATTTTAGATT
* * *
2211857 TAAATATTTTCGAGTTTAAGTTATTTTGAATTTAGTTTAAGTCATTTGA
131 CAAATATTTTCGAGTTCAAGTCATTTTGAATTTAGTTTAAGTCATTTGA
* *
2211906 AAAACTAGACTAATCAATTGGGCAAATCGGACCAATTTATATTAATCCAATTTGAGTTTTAATTT
1 AAAACTAGACTAATCAA-T-CGCAAATCGGACCAATTTATATTAATCCAAATTGAGTTTTAATTT
* *
2211971 TTCCGAATCATTTCATTTTGGTTAGTC-TCATATTTGGATCATTTCAAGTTTGAATGAATTTTAG
64 TTCCGAATCATTTCATTTTGGTTAG-CATCATATTTGGATCATTTCAAGTTCGAATCAATTTTAG
* *
2212035 ATTCAAATCTTTTCGAGTTCAAGTCGTTTTGAATTTAGTTT
128 ATTCAAATATTTTCGAGTTCAAGTCATTTTGAATTTAGTTT
2212076 TTTTTTTTTA
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
179 16 0.11
180 1 0.01
181 131 0.88
182 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (179 bp):
AAAACTAGACTAATCAATCGCAAATCGGACCAATTTATATTAATCCAAATTGAGTTTTAATTTTT
CCGAATCATTTCATTTTGGTTAGCATCATATTTGGATCATTTCAAGTTCGAATCAATTTTAGATT
CAAATATTTTCGAGTTCAAGTCATTTTGAATTTAGTTTAAGTCATTTGA
Found at i:2214803 original size:16 final size:16
Alignment explanation
Indices: 2214784--2214814 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2214774 AGAATGATAC
2214784 AAATTTAAAATAATCG
1 AAATTTAAAATAATCG
*
2214800 AAATTTGAAATAATC
1 AAATTTAAAATAATC
2214815 CGATCTCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
AAATTTAAAATAATCG
Found at i:2225413 original size:42 final size:42
Alignment explanation
Indices: 2225349--2225429 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
2225339 TGGTGCGGGA
* * *
2225349 GGTGGTGCAGGAGGACTGGCTCTAATTGGGGCAGGAGGTGGT
1 GGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGGAGGTGGT
*
2225391 GGTGGTGGAGGAGAACTAGCTCTAATCGGGGCAGGAGGT
1 GGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGGAGGT
2225430 TCTGGAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.48, T:0.20
Consensus pattern (42 bp):
GGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGGAGGTGGT
Found at i:2231750 original size:7 final size:7
Alignment explanation
Indices: 2231738--2231773 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
2231728 AACATTTTGT
2231738 AACTTAA
1 AACTTAA
2231745 AACTTAA
1 AACTTAA
2231752 AACTTAA
1 AACTTAA
2231759 AA--TAA
1 AACTTAA
2231764 AAC-TAA
1 AACTTAA
2231770 AACT
1 AACT
2231774 AGCATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 6 0.22
7 16 0.59
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (7 bp):
AACTTAA
Found at i:2233501 original size:2 final size:2
Alignment explanation
Indices: 2233494--2233523 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2233484 TCAACACTAA
2233494 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2233524 TCACTCACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2234497 original size:12 final size:12
Alignment explanation
Indices: 2234482--2234513 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2234472 TAATGAAAAT
2234482 ATAAATAAAGAA
1 ATAAATAAAGAA
2234494 ATAAATAAAGAA
1 ATAAATAAAGAA
*
2234506 ATGAATAA
1 ATAAATAA
2234514 GGCTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:2234571 original size:2 final size:2
Alignment explanation
Indices: 2234533--2234562 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2234523 AATATAAAAG
2234533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2234563 GTGTATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2235215 original size:3 final size:3
Alignment explanation
Indices: 2235198--2235269 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
2235188 TAAATAAAAC
*
2235198 TAA TAA TGA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2235244 TAA TAA AAA CTAA T-T TAA TAA TAA TA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TA
2235270 GAAATAACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 55 0.92
4 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2252982 original size:228 final size:227
Alignment explanation
Indices: 2252638--2253306 Score: 1048
Period size: 223 Copynumber: 3.0 Consensus size: 227
2252628 GTGATAAAAT
* **
2252638 ACATGCACAAAGATGCTTTG-AATATTGATAACTAAGAAAGGCACATCCATGAGGACTCAGATGA
1 ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCA-ACAA
2252702 GAC-TGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
65 GACTTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
*
2252766 TATGCCAATATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
130 TATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
2252831 TGCGAACCATCGAGGATCTCCATATCATTAAAC
195 TGCGAACCATCGAGGATCTCCATATCATTAAAC
* *
2252864 ACATGCACAAAGATGCTTTGAAATATTGGTAACTAAAAAAGGCACATGCATGAGGACTCAACAAG
1 ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCAACAAG
* *
2252929 ACTATGGACGGCCAAAACAAATGACATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
66 ACT-TGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
*
2252994 TATGCCAAAATGTAAACCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
130 TATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
*
2253059 TGCGAACCATTGAGGA--T-C---TCATTAAAC
195 TGCGAACCATCGAGGATCTCCATATCATTAAAC
* *
2253086 GCATGCACAAAGATGCTTTGAAATATTGATAACTATGAAAGGCACATGCATGAGGACTCGAACAA
1 ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTC-AACAA
*
2253151 TACTGTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTA
65 GACT-TGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTA
* * * * *
2253216 GTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGACAGTAATAAACACAA
129 CTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAA
** * *
2253281 TCACGAACCTTCAAGGATCTCCATAT
194 TTGCGAACCATCGAGGATCTCCATAT
2253307 ACTAAAAGTG
Statistics
Matches: 404, Mismatches: 29, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
222 64 0.16
223 137 0.34
225 2 0.00
226 27 0.07
227 36 0.09
228 137 0.34
229 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (227 bp):
ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCAACAAG
ACTTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTACT
ATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAATT
GCGAACCATCGAGGATCTCCATATCATTAAAC
Found at i:2253240 original size:223 final size:224
Alignment explanation
Indices: 2252638--2253265 Score: 1032
Period size: 228 Copynumber: 2.8 Consensus size: 224
2252628 GTGATAAAAT
* **
2252638 ACATGCACAAAGATGCTTTG-AATATTGATAACTAAGAAAGGCACATCCATGAGGACTCAGATGA
1 ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCA-ACAA
2252702 GAC-TGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
65 GACTTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
*
2252766 TATGCCAATATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
130 TATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
2252831 TGCGAACCATCGAGGATCTCCATATCATTAAAC
195 TGCGAACCATCGAGGA-CTCC--ATCATTAAAC
* *
2252864 ACATGCACAAAGATGCTTTGAAATATTGGTAACTAAAAAAGGCACATGCATGAGGACTCAACAAG
1 ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCAACAAG
* *
2252929 ACTATGGACGGCCAAAACAAATGACATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
66 ACT-TGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTAC
*
2252994 TATGCCAAAATGTAAACCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
130 TATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
*
2253059 TGCGAACCATTGAGGA-T-C-TCATTAAAC
195 TGCGAACCATCGAGGACTCCATCATTAAAC
* *
2253086 GCATGCACAAAGATGCTTTGAAATATTGATAACTATGAAAGGCACATGCATGAGGACTCGAACAA
1 ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTC-AACAA
*
2253151 TACTGTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTA
65 GACT-TGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTA
*
2253216 GTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGA
129 CTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGA
2253266 CAGTAATAAA
Statistics
Matches: 378, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
222 64 0.17
223 114 0.30
225 1 0.00
226 26 0.07
227 36 0.10
228 137 0.36
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (224 bp):
ACATGCACAAAGATGCTTTGAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCAACAAG
ACTTGGATGGCCAAAACAAATGATATAAAGCTAGAAGAGACATATAAGTTGTGAGCTTCACTACT
ATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAATT
GCGAACCATCGAGGACTCCATCATTAAAC
Found at i:2275616 original size:14 final size:14
Alignment explanation
Indices: 2275593--2275626 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2275583 TGTCATTTCG
*
2275593 TTATTATATTATTA
1 TTATTTTATTATTA
*
2275607 TTATTTTATTGTTA
1 TTATTTTATTATTA
2275621 TTATTT
1 TTATTT
2275627 AGAAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:2276140 original size:14 final size:14
Alignment explanation
Indices: 2276119--2276152 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2276109 TGGTATGGGT
2276119 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
2276132 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
2276146 TTATAGG
1 TTATAGG
2276153 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:2277135 original size:154 final size:151
Alignment explanation
Indices: 2276855--2277160 Score: 567
Period size: 154 Copynumber: 2.0 Consensus size: 151
2276845 TGAAAGTATA
2276855 TCGAAGTTGCGTTCACGTTTCAAAAGCTTTGACTGGTTTCAGGAGAACCCGACAACAGACGAACA
1 TCGAAGTTGCGTTCACGTTTCAAAAGCTTTGACTGGTTTCAGGAGAACCCGACAACAGACGAACA
*
2276920 AATCTTCGGCGAATCGCTTGGAGCTTTCATTTGGATGCCACGTGTTACCAATTTAATTTCTGTTT
66 AATCTTCGGCGAATCGCTTGGAGCTTTCATTTGGATGCCACGTGTTACCAATTTAACTTCTGTTT
2276985 CTCACGTGCTATTTATTGCCT
131 CTCACGTGCTATTTATTGCCT
2277006 TCGAAGTTGCGTTCACGTTTCAAAAGCTTTGACTGGTTTCAGCAGGAGAACCCGACAACAGACGA
1 TCGAAGTTGCGTTCACGTTTCAAAAGCTTTGACTGGTTT---CAGGAGAACCCGACAACAGACGA
*
2277071 ACAAATCTTCGGCGAATTGCTTGGAGCTTTCATTTGGATGCCACGTGTTACCAATTTAACTTCTG
63 ACAAATCTTCGGCGAATCGCTTGGAGCTTTCATTTGGATGCCACGTGTTACCAATTTAACTTCTG
2277136 TTTCTCACGTGCTATTTATTGCCT
128 TTTCTCACGTGCTATTTATTGCCT
2277160 T
1 T
2277161 TTGACTGTGT
Statistics
Matches: 150, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
151 39 0.26
154 111 0.74
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (151 bp):
TCGAAGTTGCGTTCACGTTTCAAAAGCTTTGACTGGTTTCAGGAGAACCCGACAACAGACGAACA
AATCTTCGGCGAATCGCTTGGAGCTTTCATTTGGATGCCACGTGTTACCAATTTAACTTCTGTTT
CTCACGTGCTATTTATTGCCT
Found at i:2278568 original size:3 final size:3
Alignment explanation
Indices: 2278560--2278584 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2278550 GTTAAAAGGT
2278560 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2278585 CAATGAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2280604 original size:57 final size:57
Alignment explanation
Indices: 2280540--2280654 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
2280530 ACATTAAACC
* *
2280540 AAAATTTATATATAATTTTAAAATATATACCATTAAAAAAGGACTATATATAGAGAG
1 AAAATTTATATATAATTTTAAAATATATACAATTAAAAAAGGACTATATAGAGAGAG
2280597 AAAATTTATATATAATTTTAAAATATATACAATTAAAAAAGGACTATATAGAGAGAG
1 AAAATTTATATATAATTTTAAAATATATACAATTAAAAAAGGACTATATAGAGAGAG
2280654 A
1 A
2280655 GAGAGAGACT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (57 bp):
AAAATTTATATATAATTTTAAAATATATACAATTAAAAAAGGACTATATAGAGAGAG
Found at i:2282788 original size:3 final size:3
Alignment explanation
Indices: 2282780--2282813 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2282770 GAGCTATTTC
2282780 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2282814 AAGATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2285494 original size:2 final size:2
Alignment explanation
Indices: 2285487--2285527 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2285477 CAAAGAAGTA
2285487 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
2285528 GATAGATAGA
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:2289102 original size:21 final size:20
Alignment explanation
Indices: 2289056--2289142 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 20
2289046 CCTGATCAGT
*
2289056 ATACGACACATAAGTGCCTG
1 ATACGACACAGAAGTGCCTG
* * *
2289076 AAACGACACACGAGGTGCTTG
1 ATACGACACA-GAAGTGCCTG
*
2289097 ATACGACACATAAAGTGCCTGAG
1 ATACGACACA-GAAGTGCCT--G
*
2289120 ATACGACACATAAAGTGCCTG
1 ATACGACACA-GAAGTGCCTG
2289141 AT
1 AT
2289143 CGGCAAAGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.16
21 25 0.45
23 21 0.38
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
ATACGACACAGAAGTGCCTG
Found at i:2289126 original size:23 final size:23
Alignment explanation
Indices: 2289056--2289141 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 23
2289046 CCTGATCAGT
2289056 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** * *
2289077 A-ACGACACACGAGGTG-CT-TG
1 ATACGACACATAAAGTGCCTGAG
2289097 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
2289120 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
2289142 TCGGCAAAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
20 11 0.21
21 17 0.32
22 2 0.04
23 23 0.43
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:2290360 original size:15 final size:16
Alignment explanation
Indices: 2290342--2290373 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2290332 TTAATTAATA
2290342 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
2290357 TAATTTAATAATATTT
1 TAATTTAATAATATTT
2290373 T
1 T
2290374 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:2290364 original size:25 final size:26
Alignment explanation
Indices: 2290329--2290381 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
2290319 TATTATCTTA
2290329 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
2290353 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
2290380 AT
1 AT
2290382 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:2293796 original size:4 final size:4
Alignment explanation
Indices: 2293787--2293815 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2293777 TGGTTTTTCG
2293787 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
2293816 AAGTTCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:2295223 original size:18 final size:19
Alignment explanation
Indices: 2295202--2295248 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
2295192 AACAAGAAAG
2295202 TTTAGTTTAAATT-AGAGT
1 TTTAGTTTAAATTAAGAGT
*
2295220 TTTAG--TATATTAAGAGT
1 TTTAGTTTAAATTAAGAGT
2295237 TTTA-TTTAAATT
1 TTTAGTTTAAATT
2295249 TAATTAGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TTTAGTTTAAATTAAGAGT
Found at i:2318980 original size:6 final size:6
Alignment explanation
Indices: 2318969--2318995 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2318959 AATATAATTT
2318969 AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
2318996 TCATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:2319748 original size:27 final size:26
Alignment explanation
Indices: 2319687--2319749 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
2319677 ATATAGACGT
2319687 GTTTAAATTAAGAAAAAAAACCTCAA
1 GTTTAAATTAAGAAAAAAAACCTCAA
* ** **
2319713 ATACCAAATTAAGAAAAAAACATGTCAA
1 GT-TTAAATTAAGAAAAAAA-ACCTCAA
2319741 GTTTAAATT
1 GTTTAAATT
2319750 TCAAATGTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
26 1 0.04
27 20 0.74
28 6 0.22
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (26 bp):
GTTTAAATTAAGAAAAAAAACCTCAA
Found at i:2320032 original size:24 final size:25
Alignment explanation
Indices: 2320004--2320061 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
2319994 CTAATAATAT
2320004 TACAAAAATAAAA-TA-AGCAAATTA
1 TACAAAAATAAAAGTAGAG-AAATTA
2320028 TACAAAAATAAAAGTAGAGAAATTA
1 TACAAAAATAAAAGTAGAGAAATTA
*
2320053 -AAAAAAATA
1 TACAAAAATA
2320062 GGGAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 21 0.68
25 8 0.26
26 2 0.06
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (25 bp):
TACAAAAATAAAAGTAGAGAAATTA
Found at i:2320067 original size:18 final size:20
Alignment explanation
Indices: 2320032--2320072 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
2320022 AAATTATACA
2320032 AAAATAAAAGTAGAGAAATT
1 AAAATAAAAGTAGAGAAATT
*
2320052 AAAA-AAAA-TAGGGAAATT
1 AAAATAAAAGTAGAGAAATT
2320070 AAA
1 AAA
2320073 TATTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 4 0.20
20 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (20 bp):
AAAATAAAAGTAGAGAAATT
Found at i:2327164 original size:25 final size:25
Alignment explanation
Indices: 2327111--2327161 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2327101 TAGAATGATA
*
2327111 TTAATTAGTCTGAATAGTTAACTTT
1 TTAATTAGTCCGAATAGTTAACTTT
* *
2327136 TTAATTATTCCGAA-AGTTAATTTT
1 TTAATTAGTCCGAATAGTTAACTTT
2327160 TT
1 TT
2327162 TAAAACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (25 bp):
TTAATTAGTCCGAATAGTTAACTTT
Found at i:2331750 original size:133 final size:132
Alignment explanation
Indices: 2331512--2332107 Score: 723
Period size: 133 Copynumber: 4.5 Consensus size: 132
2331502 CTATGTCAAG
* *
2331512 TTTAAGTCTTTTGTTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCCTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
* * ** *
2331577 GTTATAATTGTGCTTTGCTGTAATGTGTATCTTCAAGTCTATTGAATTTTTGAGCTTTTGTTGAA
66 GTTATAATTATACTTTGCTGTAATGTGTAGATTCAAGTCTATTAAATTTTTGAGCTTTTGTTGAA
2331642 AGT
131 A-T
2331645 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
* * * *
2331710 GTTATAATTATACTTTGCTGTAATATGTAGATTCAAGTCTACTAAAATTTTGAGCTTTTTTTGAA
66 GTTATAATTATACTTTGCTGTAATGTGTAGATTCAAGTCTATTAAATTTTTGAGCTTTTGTTGAA
2331775 AT
131 AT
* * * * *
2331777 TTCATGTCCTTTGCTCCAATAGGTTCTAAGTTTTTCTTCC-TTTTTGTTGGTTAGTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
* * * *
2331841 GTTGTAATTATACTTTGCCGTAATGTGTAGATTCAAGTCTATTGAGTTTTTGAGCTTTTTGTTGA
66 GTTATAATTATACTTTGCTGTAATGTGTAGATTCAAGTCTATTAAATTTTTGAGC-TTTTGTTGA
2331906 AAGT
130 AA-T
** * * ** *
2331910 TTTAAGTCTTTTGCTTTAATGGGTTCTAACTCTCACTTCCTTTTTTGTTGGTTGGTATGTTCTTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
* * * * * * * * * *
2331975 GTGTAATAATTGTAATCTCCAGAAATGGGTAGCTTC-TGTTCTTTTAAATTTTTGAGCTTTTGTT
66 GT-T-ATAATTATACTTTGCTGTAATGTGTAGATTCAAG-TCTATTAAATTTTTGAGCTTTTGTT
2332039 GAAAT
128 GAAAT
* * * * *
2332044 TTCATGTCTTTTGCTCCAATGGGTTCTAAGTTTTCCTT-ATCTTTTTG-TGGTTGGTATGTTCTT
1 TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCT-TTTTTGTTGGTTCGTATGTTCTT
2332107 T
65 T
2332108 ATAGGTTAGG
Statistics
Matches: 399, Mismatches: 57, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
131 71 0.18
132 47 0.12
133 169 0.42
134 62 0.16
135 13 0.03
136 37 0.09
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.52
Consensus pattern (132 bp):
TTTAAGTCTTTTGCTCCAATGGGTTCTAAGTTTTTCTTCCTTTTTTGTTGGTTCGTATGTTCTTT
GTTATAATTATACTTTGCTGTAATGTGTAGATTCAAGTCTATTAAATTTTTGAGCTTTTGTTGAA
AT
Found at i:2337962 original size:2 final size:2
Alignment explanation
Indices: 2337955--2337980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2337945 ATTAAAAATG
2337955 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
2337981 AATTAAAAGA
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):
TA
Found at i:2338043 original size:2 final size:2
Alignment explanation
Indices: 2338036--2338069 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2338026 GAATACGTAC
*
2338036 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2338070 GCATATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2338587 original size:3 final size:3
Alignment explanation
Indices: 2338579--2338675 Score: 61
Period size: 3 Copynumber: 31.3 Consensus size: 3
2338569 ATGAACAATA
* *
2338579 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AAAT AAA AAA AAGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AA-T AAT
* * * * * * * *
2338627 AGT AAT AAC AGT ATT AA- ACAT AAT AAT AGT AGT AAA AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
2338672 AAT A
1 AAT A
2338676 TTATTAAAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
2 1 0.01
3 65 0.88
4 7 0.09
5 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2338673 original size:21 final size:21
Alignment explanation
Indices: 2338649--2338689 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2338639 ATTAAACATA
2338649 ATAATAGTAGTAAAAATAATG
1 ATAATAGTAGTAAAAATAATG
* * *
2338670 ATAATATTATTAAAATTAAT
1 ATAATAGTAGTAAAAATAAT
2338690 TAATAGCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (21 bp):
ATAATAGTAGTAAAAATAATG
Found at i:2343365 original size:17 final size:17
Alignment explanation
Indices: 2343345--2343386 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2343335 TATGTATTAT
2343345 AAATTACATAATATAAA
1 AAATTACATAATATAAA
*
2343362 AAATAACATAATATAAA
1 AAATTACATAATATAAA
*
2343379 ACATTACA
1 AAATTACA
2343387 AACTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATTACATAATATAAA
Found at i:2346242 original size:23 final size:25
Alignment explanation
Indices: 2346215--2346275 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
2346205 TTATTTAAAC
2346215 AAATATTCATGTTTATA-TA-ATTA
1 AAATATTCATGTTTATACTAGATTA
* *
2346238 AAATAATCATATTTTTATACTAGATTA
1 AAATATTC--ATGTTTATACTAGATTA
2346265 AAATATGTCAT
1 AAATAT-TCAT
2346276 AATTTCTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 7 0.23
25 8 0.27
26 4 0.13
27 9 0.30
28 2 0.07
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (25 bp):
AAATATTCATGTTTATACTAGATTA
Found at i:2346720 original size:16 final size:16
Alignment explanation
Indices: 2346655--2346723 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
2346645 TAAATATTTA
*
2346655 TTATTAAATTAA-AAT
1 TTATTATATTAATAAT
2346670 TTA--AGTATTAAATAAT
1 TTATTA-TATT-AATAAT
2346686 TTATT-TA--AATAAT
1 TTATTATATTAATAAT
**
2346699 AAATTATATTAATAAT
1 TTATTATATTAATAAT
2346715 TTATTATAT
1 TTATTATAT
2346724 GTTTAATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 15
0.67 0.08 0.25
Matches are distributed among these distances:
13 10 0.24
14 5 0.12
15 5 0.12
16 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (16 bp):
TTATTATATTAATAAT
Found at i:2348358 original size:8 final size:7
Alignment explanation
Indices: 2348309--2348342 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2348299 CTTTCTTAAA
*
2348309 TTTAAAT
1 TTTAATT
*
2348316 TTAAATT
1 TTTAATT
2348323 TTTAATT
1 TTTAATT
2348330 TTTAATT
1 TTTAATT
2348337 TTTAAT
1 TTTAAT
2348343 ATAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTAATT
Found at i:2351288 original size:22 final size:22
Alignment explanation
Indices: 2351263--2351309 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2351253 TTTACTGTCA
**
2351263 TTTTACTTTATATTGTTATTGT
1 TTTTACTTTATATAATTATTGT
* *
2351285 TTTTATTTTGTATAATTATTGT
1 TTTTACTTTATATAATTATTGT
2351307 TTT
1 TTT
2351310 GTTGTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTACTTTATATAATTATTGT
Found at i:2351305 original size:28 final size:26
Alignment explanation
Indices: 2351273--2351330 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
2351263 TTTTACTTTA
*
2351273 TATTGTTATTGTT-TTTATTTTGTATAAT
1 TATTGTT-TTGTTGTTAATTTTGT-T-AT
2351301 TATTGTTTTGTTGTTAATTTTGTTAT
1 TATTGTTTTGTTGTTAATTTTGTTAT
2351327 TATT
1 TATT
2351331 TTAAAAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 6 0.21
28 16 0.57
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (26 bp):
TATTGTTTTGTTGTTAATTTTGTTAT
Found at i:2356895 original size:18 final size:19
Alignment explanation
Indices: 2356835--2356911 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 19
2356825 AAAATATTAT
*
2356835 AATATTAATGTATTAAATAA
1 AATATTAAT-TATTAAACAA
**
2356855 AA-A-TAATTAATT-AATTA
1 AATATTAATT-ATTAAACAA
*
2356872 ATTATTAATTATTAAA-AA
1 AATATTAATTATTAAACAA
* *
2356890 AATATTAAATATAAAACAA
1 AATATTAATTATTAAACAA
2356909 AAT
1 AAT
2356912 TTTCAAATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.13
18 25 0.54
19 13 0.28
20 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
AATATTAATTATTAAACAA
Found at i:2362089 original size:20 final size:22
Alignment explanation
Indices: 2362044--2362097 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
2362034 ATAATTGAAT
*
2362044 ATTATTAATTTTTTATAATGTAA
1 ATTATTAATTTTATATAA-GTAA
2362067 ATTATTAATTTTATATAA-T-A
1 ATTATTAATTTTATATAAGTAA
*
2362087 ATTATAAATTT
1 ATTATTAATTT
2362098 AATTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.38
21 1 0.03
23 17 0.59
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATTAATTTTATATAAGTAA
Found at i:2362105 original size:20 final size:20
Alignment explanation
Indices: 2362066--2362105 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2362056 TTATAATGTA
* *
2362066 AATTATTAATTTTATATAAT
1 AATTATAAATTTAATATAAT
*
2362086 AATTATAAATTTAATTTAAT
1 AATTATAAATTTAATATAAT
2362106 TTAACTCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTATAAATTTAATATAAT
Found at i:2363117 original size:30 final size:30
Alignment explanation
Indices: 2363071--2363149 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
2363061 GGACGAGGAG
*
2363071 GAGGGGGAGGAGGATGAAAATGATGATGAT
1 GAGGAGGAGGAGGATGAAAATGATGATGAT
*
2363101 GAGGAGGAGGATGATGAAAATGATGATGAT
1 GAGGAGGAGGAGGATGAAAATGATGATGAT
* *
2363131 GATGAGGAGGAGGACGAAA
1 GAGGAGGAGGAGGATGAAA
2363150 TGGAAGAGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.39, C:0.01, G:0.44, T:0.15
Consensus pattern (30 bp):
GAGGAGGAGGAGGATGAAAATGATGATGAT
Found at i:2364385 original size:182 final size:182
Alignment explanation
Indices: 2364078--2364443 Score: 732
Period size: 182 Copynumber: 2.0 Consensus size: 182
2364068 TTAATTGCCT
2364078 TTTCGTGATATTTTTGAGTATGCACATATATGCATTTACATATATTATGCTGATTTTATCAACTA
1 TTTCGTGATATTTTTGAGTATGCACATATATGCATTTACATATATTATGCTGATTTTATCAACTA
2364143 TTGTTTCCTCCTCAATAAGCTCTAGGATTTTATAGGTATTTTGGACGTCCACTATTGTTACTGTA
66 TTGTTTCCTCCTCAATAAGCTCTAGGATTTTATAGGTATTTTGGACGTCCACTATTGTTACTGTA
2364208 GTCTGTAGCTTCTTTGGGCTTTTGATACATCATGGTCTTGTACCATAGCTTG
131 GTCTGTAGCTTCTTTGGGCTTTTGATACATCATGGTCTTGTACCATAGCTTG
2364260 TTTCGTGATATTTTTGAGTATGCACATATATGCATTTACATATATTATGCTGATTTTATCAACTA
1 TTTCGTGATATTTTTGAGTATGCACATATATGCATTTACATATATTATGCTGATTTTATCAACTA
2364325 TTGTTTCCTCCTCAATAAGCTCTAGGATTTTATAGGTATTTTGGACGTCCACTATTGTTACTGTA
66 TTGTTTCCTCCTCAATAAGCTCTAGGATTTTATAGGTATTTTGGACGTCCACTATTGTTACTGTA
2364390 GTCTGTAGCTTCTTTGGGCTTTTGATACATCATGGTCTTGTACCATAGCTTG
131 GTCTGTAGCTTCTTTGGGCTTTTGATACATCATGGTCTTGTACCATAGCTTG
2364442 TT
1 TT
2364444 GTCCATTCCA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 184 1.00
ACGTcount: A:0.22, C:0.16, G:0.17, T:0.44
Consensus pattern (182 bp):
TTTCGTGATATTTTTGAGTATGCACATATATGCATTTACATATATTATGCTGATTTTATCAACTA
TTGTTTCCTCCTCAATAAGCTCTAGGATTTTATAGGTATTTTGGACGTCCACTATTGTTACTGTA
GTCTGTAGCTTCTTTGGGCTTTTGATACATCATGGTCTTGTACCATAGCTTG
Found at i:2385136 original size:15 final size:15
Alignment explanation
Indices: 2385097--2385138 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2385087 GGTGAAAGAA
* *
2385097 ATTATGTAATAAATAT
1 ATTATATAA-AAAAAT
2385113 ATT-TATAAAAAAAT
1 ATTATATAAAAAAAT
2385127 ATTATATAAAAA
1 ATTATATAAAAA
2385139 TTAAATGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 8 0.35
15 12 0.52
16 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
ATTATATAAAAAAAT
Found at i:2385428 original size:36 final size:37
Alignment explanation
Indices: 2385388--2385464 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
2385378 TTTAGAATAC
*
2385388 AAATGTGT-GTTTAAAAATAATATAA-AATAA-ATAATG
1 AAATGTATGGTTTAAAAATAAT-TAATAATAACAT-ATG
* *
2385424 AAATGTATGGTTTGAAACTAATTAATAATAACATATG
1 AAATGTATGGTTTAAAAATAATTAATAATAACATATG
2385461 AAAT
1 AAAT
2385465 ATGTACGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 10 0.29
37 23 0.66
38 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.34
Consensus pattern (37 bp):
AAATGTATGGTTTAAAAATAATTAATAATAACATATG
Found at i:2399039 original size:26 final size:25
Alignment explanation
Indices: 2399002--2399054 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
2398992 TCGCCCATAT
*
2399002 TATTTTAATATTTAATAATTTTATA
1 TATTTTAATATTAAATAATTTTATA
* **
2399027 TATTTTATTTATTAAATTTTTTTATA
1 TATTTTA-ATATTAAATAATTTTATA
2399053 TA
1 TA
2399055 GTCACTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTTTAATATTAAATAATTTTATA
Found at i:2400600 original size:121 final size:121
Alignment explanation
Indices: 2400386--2400623 Score: 377
Period size: 121 Copynumber: 2.0 Consensus size: 121
2400376 GTCCTTTGTC
* *
2400386 GGTCTTTGGTAGTGTCCAATTGGTTGATTGTAATTTGACGTCAAAATAATCTGACAATAGCAATG
1 GGTCTTTGGTAGTGTCCAATTGGTTGATCGGAATTTGACGTCAAAATAATCTGACAATAGCAATG
* **
2400451 CTAAGATGCCAGTATTGATGATTGATCTAGGTGATGCATCTTTGGTTAGTTCTTTG
66 CTAAGATGCCAGTATTGATGATTGATCTAAGTGATGCATCTTTAATTAGTTCTTTG
* * * *
2400507 GGTCTTTGGTAGTGTCCAATTGGTTGATCGGAATTTGTCGTTAAAATAATTTGGCAATAGCAATG
1 GGTCTTTGGTAGTGTCCAATTGGTTGATCGGAATTTGACGTCAAAATAATCTGACAATAGCAATG
* *
2400572 CTAAGATGTCATTATTGATGATTGATCTAAGTGATGCATCTTTAATTAGTTC
66 CTAAGATGCCAGTATTGATGATTGATCTAAGTGATGCATCTTTAATTAGTTC
2400624 ATTAAACTTG
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 106 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (121 bp):
GGTCTTTGGTAGTGTCCAATTGGTTGATCGGAATTTGACGTCAAAATAATCTGACAATAGCAATG
CTAAGATGCCAGTATTGATGATTGATCTAAGTGATGCATCTTTAATTAGTTCTTTG
Found at i:2409539 original size:27 final size:28
Alignment explanation
Indices: 2409495--2409553 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
2409485 TGCTCTTATT
* *
2409495 AAAA-ATAATAAATAATAAATTTTAATA
1 AAAATATAAAAAATAATAAAATTTAATA
*
2409522 AAAATATAAAAAAT-ATAAAATTTATTA
1 AAAATATAAAAAATAATAAAATTTAATA
2409549 AAAAT
1 AAAAT
2409554 TAGTACTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAATATAAAAAATAATAAAATTTAATA
Found at i:2409610 original size:20 final size:21
Alignment explanation
Indices: 2409582--2409626 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2409572 AAAAACTTTT
*
2409582 AAAATTTTATAATAAT-CAT-A
1 AAAACTTTATAA-AATGCATCA
2409602 AAAACTTTATAAAATGCATCA
1 AAAACTTTATAAAATGCATCA
2409623 AAAA
1 AAAA
2409627 GTCCCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAACTTTATAAAATGCATCA
Found at i:2409884 original size:10 final size:10
Alignment explanation
Indices: 2409871--2409940 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
2409861 CTTTATAAAA
2409871 TTTTATAATT
1 TTTTATAATT
2409881 TTTTAT-A-T
1 TTTTATAATT
* *
2409889 TTCTAT-ATG
1 TTTTATAATT
*
2409898 TTTTATAA-A
1 TTTTATAATT
*
2409907 TTTTATAAAT
1 TTTTATAATT
2409917 TTTTATATATT
1 TTTTATA-ATT
*
2409928 TTTTCTAATT
1 TTTTATAATT
2409938 TTT
1 TTT
2409941 AATATTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
8 7 0.14
9 14 0.29
10 20 0.41
11 8 0.16
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2409908 original size:28 final size:27
Alignment explanation
Indices: 2409870--2409947 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
2409860 ACTTTATAAA
2409870 ATTTTATAATTTTTTATATTTCTATAT
1 ATTTTATAATTTTTTATATTTCTATAT
* * * *
2409897 GTTTTATAAATTTTATAAATTTTTATAT
1 ATTTTAT-AATTTTTTATATTTCTATAT
* *
2409925 ATTTTTTCTAATTTTTAATATTT
1 A--TTTTATAATTTTTTATATTT
2409948 AATTTTTTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 6 0.15
28 17 0.44
29 11 0.28
30 5 0.13
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (27 bp):
ATTTTATAATTTTTTATATTTCTATAT
Found at i:2409931 original size:21 final size:19
Alignment explanation
Indices: 2409871--2409947 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 19
2409861 CTTTATAAAA
*
2409871 TTTTATAATTTTTTATA-T
1 TTTTATAATTTTTAATATT
* **
2409889 TTCTAT-ATGTTTT-ATAAA
1 TTTTATAAT-TTTTAATATT
2409907 TTTTATAAATTTTTATATATT
1 TTTTAT-AATTTTTA-ATATT
*
2409928 TTTTCTAATTTTTAATATT
1 TTTTATAATTTTTAATATT
2409947 T
1 T
2409948 AATTTTTTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
17 5 0.11
18 14 0.30
19 10 0.21
20 10 0.21
21 8 0.17
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTAATATT
Found at i:2410120 original size:89 final size:88
Alignment explanation
Indices: 2410004--2410195 Score: 262
Period size: 89 Copynumber: 2.1 Consensus size: 88
2409994 TGTTTTTTTT
* ** * *
2410004 AAGTTTGAGGGTCTTTTTTATGCATTTTGAAATTTCAAGTACCCAATTAAGTGC-AAAAAAAAGT
1 AAGTTTGAGGGTATTTGCTATGCATTTTGAAAGTTCAAGTACCCAAATAAGTGCAAAAAAAAAGT
*
2410068 AGGGGCTTAATTGCTTTTTTTGAA-
66 A-AGGCTTAATTGCTTTTTTT-AAG
2410092 AAGGTTTGAGGGTATTTGCTATGCATTTTGAAAGTTCAAGTACCCAAATAAGTGCAAAAAAAAAA
1 AA-GTTTGAGGGTATTTGCTATGCATTTTGAAAGTTCAAGTACCCAAATAAGTGC---AAAAAAA
2410157 AAGTAAGGCTTAATTGCTTTTTTTAAG
62 AAGTAAGGCTTAATTGCTTTTTTTAAG
2410184 AAGTTTGAGGGT
1 AAGTTTGAGGGT
2410196 TTTTTTTGTA
Statistics
Matches: 92, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
88 2 0.02
89 47 0.51
91 12 0.13
92 20 0.22
93 11 0.12
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.35
Consensus pattern (88 bp):
AAGTTTGAGGGTATTTGCTATGCATTTTGAAAGTTCAAGTACCCAAATAAGTGCAAAAAAAAAGT
AAGGCTTAATTGCTTTTTTTAAG
Found at i:2411571 original size:11 final size:11
Alignment explanation
Indices: 2411555--2411579 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2411545 ATAATGTGTC
2411555 AAAAAAATATT
1 AAAAAAATATT
2411566 AAAAAAATATT
1 AAAAAAATATT
2411577 AAA
1 AAA
2411580 TAATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAAATATT
Found at i:2418834 original size:26 final size:28
Alignment explanation
Indices: 2418790--2418852 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
2418780 ACCAAAATTT
* * * *
2418790 ATAACAAAACAATAGTTTAGGTATTAAA
1 ATAAGAAAACAATAGTTTACGCAATAAA
*
2418818 ATAGGAAAA-AATA-TTTACGCAATAAA
1 ATAAGAAAACAATAGTTTACGCAATAAA
2418844 ATAAGAAAA
1 ATAAGAAAA
2418853 GCAGAACGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 18 0.62
27 4 0.14
28 7 0.24
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.24
Consensus pattern (28 bp):
ATAAGAAAACAATAGTTTACGCAATAAA
Found at i:2428977 original size:42 final size:42
Alignment explanation
Indices: 2428918--2429022 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
2428908 TATCGAAGCA
* * *
2428918 ATCATCGGATGTACCGAAATAAATATACTAGAACGTAAGTGC
1 ATCATTGGATATACCGAAATAAATATACTAGAACGCAAGTGC
* * *
2428960 ATCATTGGATATACCGAAGA-AATTATACTGGTACGCAAGTGC
1 ATCATTGGATATACCGAA-ATAAATATACTAGAACGCAAGTGC
* *
2429002 ATCATTGGCTAAACCGAAATA
1 ATCATTGGATATACCGAAATA
2429023 TAACCTGTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 51 0.96
43 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (42 bp):
ATCATTGGATATACCGAAATAAATATACTAGAACGCAAGTGC
Found at i:2433480 original size:27 final size:27
Alignment explanation
Indices: 2433438--2433512 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
2433428 ACAATGTGCA
*
2433438 TCACATGGGCCGAATGTTCAACATTCC
1 TCACATGGGCCAAATGTTCAACATTCC
2433465 TCACATGGGCCAAATGTTCAACATTCC
1 TCACATGGGCCAAATGTTCAACATTCC
2433492 TCACATGGGCCAAATGTTCAA
1 TCACATGGGCCAAATGTTCAA
2433513 AATGTTCACC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (27 bp):
TCACATGGGCCAAATGTTCAACATTCC
Found at i:2437501 original size:23 final size:21
Alignment explanation
Indices: 2437448--2437501 Score: 54
Period size: 25 Copynumber: 2.4 Consensus size: 21
2437438 TATAATGCAA
*
2437448 TTTTTTAATGATTTTTACAAT
1 TTTTTTAACGATTTTTACAAT
*
2437469 TTTTAGTTAACGATTATTTTACAGT
1 TTTT--TTAACGA-T-TTTTACAAT
2437494 TTTTTTAA
1 TTTTTTAA
2437502 GAATTGAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.15
23 10 0.37
24 1 0.04
25 12 0.44
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTTTAACGATTTTTACAAT
Found at i:2440926 original size:24 final size:24
Alignment explanation
Indices: 2440891--2440958 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
2440881 CGGCCCGAAT
*
2440891 TATATATTAAATATATA-TTTTTA
1 TATATATCAAATATATATTTTTTA
* *
2440914 TTTTTAATCAAATATATATTTTTTA
1 TATAT-ATCAAATATATATTTTTTA
*
2440939 TATATATTAAATATATATTT
1 TATATATCAAATATATATTT
2440959 AATATGGGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 3 0.08
24 25 0.68
25 9 0.24
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATATCAAATATATATTTTTTA
Found at i:2442884 original size:11 final size:11
Alignment explanation
Indices: 2442868--2442893 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2442858 ATTTTTTTAA
2442868 TTTTAAAATAC
1 TTTTAAAATAC
2442879 TTTTAAAATAC
1 TTTTAAAATAC
2442890 TTTT
1 TTTT
2442894 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2442904 original size:39 final size:39
Alignment explanation
Indices: 2442861--2442982 Score: 160
Period size: 39 Copynumber: 3.1 Consensus size: 39
2442851 TATTTTTATT
*
2442861 TTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAAA
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
* * *
2442900 TTTTTTAAATTTTTAAATTTTTTTAAAATAC-TTTTTTAATT
1 -TTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTAA-A
2442941 TTTTTAATTTTAAAATATTTTTAAAATA-TTTTTTT-AA
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
2442978 TTTTT
1 TTTTT
2442983 GTTTTAATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
37 5 0.07
38 1 0.01
39 27 0.38
40 18 0.25
41 21 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAA
Found at i:2442912 original size:8 final size:8
Alignment explanation
Indices: 2442892--2442921 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2442882 TAAAATACTT
2442892 TTTTTAAA
1 TTTTTAAA
2442900 TTTTTTAAA
1 -TTTTTAAA
2442909 TTTTTAAA
1 TTTTTAAA
2442917 TTTTT
1 TTTTT
2442922 TTAAAATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTAAA
Found at i:2442944 original size:8 final size:9
Alignment explanation
Indices: 2442891--2442965 Score: 64
Period size: 9 Copynumber: 8.0 Consensus size: 9
2442881 TTAAAATACT
2442891 TTTTTTAAA
1 TTTTTTAAA
2442900 TTTTTTAAA
1 TTTTTTAAA
2442909 -TTTTTAAA
1 TTTTTTAAA
2442917 TTTTTTTAAAA
1 -TTTTTT-AAA
*
2442928 TACTTTTTTAA
1 T--TTTTTAAA
*
2442939 TTTTTTTAA
1 TTTTTTAAA
*
2442948 -TTTTAAAA
1 TTTTTTAAA
2442956 TATTTTTAAA
1 T-TTTTTAAA
2442966 ATATTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
8 14 0.25
9 17 0.31
10 13 0.24
11 6 0.11
12 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:2454657 original size:30 final size:30
Alignment explanation
Indices: 2454621--2454681 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2454611 GCAATAATAC
*
2454621 TTTATAAAATAATCTAATAATACTGACGAT
1 TTTATAAAATAATCTAATAATACTAACGAT
2454651 TTTATAAAATAATCTAATAATACTAACGAT
1 TTTATAAAATAATCTAATAATACTAACGAT
2454681 T
1 T
2454682 CAATCTGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTATAAAATAATCTAATAATACTAACGAT
Found at i:2456135 original size:14 final size:14
Alignment explanation
Indices: 2456116--2456146 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2456106 TTTATGATAG
*
2456116 AATATAAAGCTAGA
1 AATATAAAACTAGA
2456130 AATATAAAACTAGA
1 AATATAAAACTAGA
2456144 AAT
1 AAT
2456147 TATGTTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.23
Consensus pattern (14 bp):
AATATAAAACTAGA
Found at i:2456618 original size:13 final size:13
Alignment explanation
Indices: 2456600--2456630 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2456590 TTCCAGCAAC
2456600 TATGAATTTATTT
1 TATGAATTTATTT
2456613 TATGAATTTATTT
1 TATGAATTTATTT
*
2456626 GATGA
1 TATGA
2456631 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:2456800 original size:50 final size:50
Alignment explanation
Indices: 2456725--2456966 Score: 394
Period size: 50 Copynumber: 4.8 Consensus size: 50
2456715 ATTTGGGTAA
2456725 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
2456775 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGGGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
2456825 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
2456875 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
2456925 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC
2456967 GTGTTATTAT
Statistics
Matches: 177, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 144 0.81
51 33 0.19
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:2464257 original size:22 final size:23
Alignment explanation
Indices: 2464232--2464291 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
2464222 AAACTGTATA
*
2464232 TATATATTAAAAATATGCATAT-
1 TATATATGAAAAATATGCATATG
* *
2464254 TATATATGGAAAATATGCGTATG
1 TATATATGAAAAATATGCATATG
2464277 TACTATATGAAAAAT
1 TA-TATATGAAAAAT
2464292 GCATGTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.59
23 2 0.06
24 11 0.34
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (23 bp):
TATATATGAAAAATATGCATATG
Found at i:2464300 original size:22 final size:24
Alignment explanation
Indices: 2464241--2464300 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
2464231 ATATATATTA
2464241 AAAATATGCATAT-TA-TATATGG
1 AAAATATGCATATGTACTATATGG
*
2464263 AAAATATGCGTATGTACTATAT-G
1 AAAATATGCATATGTACTATATGG
*
2464286 AAAA-ATGCATGTGTA
1 AAAATATGCATATGTA
2464301 TAAATATGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 21 0.64
23 7 0.21
24 5 0.15
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (24 bp):
AAAATATGCATATGTACTATATGG
Found at i:2469534 original size:17 final size:17
Alignment explanation
Indices: 2469512--2469544 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2469502 ATGACATGTT
*
2469512 GCCCTTTTAAAATTTAG
1 GCCCTTTAAAAATTTAG
2469529 GCCCTTTAAAAATTTA
1 GCCCTTTAAAAATTTA
2469545 TAAAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (17 bp):
GCCCTTTAAAAATTTAG
Found at i:2474996 original size:31 final size:31
Alignment explanation
Indices: 2474939--2474997 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2474929 CTAAAATGGA
* *
2474939 AAAATTTTTATTTAGTTCTTTTAAAATTTTT
1 AAAATTTTAATTTAGTTCTTTAAAAATTTTT
2474970 AAAATTTTAATTTA-TTCCTTTAAAAATT
1 AAAATTTTAATTTAGTT-CTTTAAAAATT
2474998 ATAAAGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (31 bp):
AAAATTTTAATTTAGTTCTTTAAAAATTTTT
Found at i:2475252 original size:22 final size:22
Alignment explanation
Indices: 2475227--2475271 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2475217 GTTTTGATAT
*
2475227 TCTTTTTAATTTTAAAATTTAA
1 TCTTTATAATTTTAAAATTTAA
* **
2475249 TCTTTATATTTTTTTAATTTAA
1 TCTTTATAATTTTAAAATTTAA
2475271 T
1 T
2475272 TTCTTTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (22 bp):
TCTTTATAATTTTAAAATTTAA
Found at i:2479204 original size:31 final size:31
Alignment explanation
Indices: 2479169--2479231 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2479159 CAGCCTAGTA
2479169 ACTTAAATAAAAACTTTCAAATAATTCAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
* * *
2479200 ACTTAAATGAAAACTTTTAAATAATTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
2479231 A
1 A
2479232 TCATTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTCAATG
Found at i:2479514 original size:31 final size:31
Alignment explanation
Indices: 2479470--2479536 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2479460 AATTGAATAT
*
2479470 CAAATTAAACATTGGAA-CTAAACTCAAGTAC
1 CAAATTAAACATTGAAATC-AAACTCAAGTAC
* * *
2479501 CAAATTGAGCATTGAAATCAATCTCAAGTAC
1 CAAATTAAACATTGAAATCAAACTCAAGTAC
2479532 CAAAT
1 CAAAT
2479537 GATATATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.24
Consensus pattern (31 bp):
CAAATTAAACATTGAAATCAAACTCAAGTAC
Found at i:2485789 original size:23 final size:23
Alignment explanation
Indices: 2485759--2485805 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2485749 TTATAGCTAC
2485759 CAAGGACGCCTCGGACACCAACT
1 CAAGGACGCCTCGGACACCAACT
2485782 CAAGGACGCCTCGGACACCAACT
1 CAAGGACGCCTCGGACACCAACT
2485805 C
1 C
2485806 TTCCTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.40, G:0.21, T:0.09
Consensus pattern (23 bp):
CAAGGACGCCTCGGACACCAACT
Done.